MYCOLOGY

NAME RESERVOIR MORPHOLOGY CLINICAL SYNDROME TREATMENT DIAGNOSIS NOTES ANATOMIC LOCATION
Malassezia furfur N aturally found on the skin surfaces of “Spaghetti and meat balls” Tinea/Pityriasis versicolor - a common, benign, Dandruff shampoo (containing Potassium hydroxide (KOH) prep: reveals short, SUPERFICIAL (SKIN)
AN-AN many animals, including humans. Dimorphic, lipophilic fungi superficial cutaneous fungal infection usually selenium sulfide) curved, unbranched hyphae with spherical yeast
AP-AP characterized by hypopigmented or hyperpigmented cells ( look like “spaghetti and meatballs”)
macules and patches on the chest and the back. In
Isolated in 18% of infants and 90-100% patients with a predisposition, tinea versicolor may Topical imidazole Malassezia is extremely difficult to propagate in
of adults. chronically recur. The fungal infection is localized to laboratory culture and is culturable only in
the stratum corneum. media enriched with C12- to C14-sized fatty
acids.
DERMATOPHYTES Depending on the particular species Dermatophytosis Topical imidazole KOH: branched hyphae Secretes the enzyme keratinase, CUTANEOUS
Tinea corporis (body): “ringworm” Oral griseofuivin is used for tinea Wood’s lamp: ceratin species of Microsporum which digests keratin
Tinea cruRis (groin): “jock itch” unguium and tinea capitis will fluoresce under ultraviolet light
Microsporum Soil (geophilic) Tinea pedis (feet): “athlete’s foot” Oral terbinafine A fungal culture, which is often used as an For atypical presentations of
Trichopyton Animals (zoophilic) Tinea capitis (scalp) adjunct to KOH for diagnosis, is more specific tinea corporis, further evaluation
Epidermophyton floccosum Human (anthropophilic) Tinea unguium (nail): Onychomycosis than KOH for detecting a dermatophyte for HIV infection and/or an
infection. Therefore, if the clinical suspicion is immunocompromised state
high yet the KOH result is negative, a fungal should be considered.
culture should be obtained.
Infections due to zoophilic or geophilic If the above clinical evaluations are inconclusive,
dermatophytes may produce a more a polymerase chain reaction (PCR) assay for
intense inflammatory response than fungal deoxyribonucleic acid (DNA)
those caused by anthropophilic identification can be used.
microbes
Sporothrix schenkii Found on rose thorns Suppurating subcutaneous nodules that progress Itraconazole Dimorphic Primary pulmonary infection SUBCUTANEOUS
proximally along lymphatic channels Fluconazole Culture at 25ºC will grow branching hyphae (pulmonary sporotrichosis) is
(lymphocutaneous sporotrichosis) Oral potassium iodide Culture at 37ºC will grow yeast cells rare, as is direct inoculation into
tendons, bursae, or joints.
Definitive diagnosis of sporotrichosis at any site Osteoarticular sporotrichosis is
requires the isolation of S schenckii in a caused by direct inoculation or
specimen culture from a normally sterile body hematogenous seeding.
site.
The organism can be recovered with fungal In rare cases, disseminated S
culture from sputum, pus, subcutaneous tissue schenckii infection
biopsy, synovial fluid, synovial biopsy, bone (disseminated sporotrichosis)
drainage or biopsy, and cerebrospinal fluid occurs, characterized by
(CSF). disseminated cutaneous lesions
and involvement of multiple
visceral organs; this occurs most
commonly in persons with AIDS.

Coccidioides immitis Desert areas of the southwestern Dimorphic: Coccidiodomycosis Amphotericin B Biopsy of affected tissue: lung biopsy, skin Common oppurtunisitc infection SYSTEMIC
United States and northern Mexico Mycelial forms with spores at Asymtomatic (in most persons) Itraconazole biopsy, etc. in AIDS patients from the
25ºC Pneumonia Fluconazole Silver stain or KOH prep southwest United States
Respiratory transmission Yeast forms at 37ºC Disseminated: can affect the lungs, skin , bones and Culture on Sabouraud’s agar SPHERULES WITH ENDOSPORES
meninges Serology
Skin test

Page 1 of 34
Histoplasma capsulatum Mississippi valley
Present in bird and bat droppings
Respiratory transmission
Blastomyces dermatitidis
Cryptococcus neoformans Pigeon droppings
Dimorphic :
Mycelial forms with spores at
o immunocompromised patients
25 C
o Pneumonia: lessions calcify, which can be seen on
Yeast forms at 37 C
Dimorphic:
Mycelial forms with spores at
25oC
Yeast forms at 37oC
Polysaccharide capsule
Yeast form only (Not dimorphic) Subacute or chronic meningitis
Histoplasmosis Itraconazole Lung biopsy Can survive intracellularly within SYSTEMIC
macrophages
Asymptomatic (in most persons) Amphotericin B (in Silver stain specimen
Culture on Sabouraud’s agar will reveal hyphae YEASTS WITHIN MACROPHAGES
chest X-ray (may look similar to PTB) at 25oC and yeast at 37oC
Disseminated: can occur in almost any organ, Serology
especially in lung, spleen, or liver
Skin test (test for exposure only)
Urine antigen test
Blastomycosis Itraconazole Biopsy of affected tissue: lung biopsy, skin BROAD-BASED BUD SYSTEMIC
biopsy, etc.
Asymptomatic (uncommon) Ketoconazole Silver stain specimen
Pneumonia: lesion rarely calcifies Amphotericin B Culture on Sabouraud’s agar
Dessiminated (most common): present with weight Serology
loss, night sweats, lung involvement and skin ulcers
Cutaneuos: skin ulcer Skin test (test for exposure only)
Blastomycosis is usually localized to the lungs and Sputum specimens processed with 10%
may present with: potassium hydroxide, cytology smears, or a
fungal stain
A self-limited flulike illness with fever, chills, myalgia, Enzyme immunoassay (EIA) techniques on
headache, and a nonproductive cough sputum, tissue, or bronchoscopic specimens
An acute illness resembling bacterial pneumonia,
with high fever, chills, a productive cough, and
pleuritic chest pain; mucopurulent or purulent
sputum
Chronic illness, with low-grade fever, a productive
cough, fatigue, night sweats, and weight loss
Rapidly progressive, and severe disease, eg,
multilobar pneumonia or ARDS, with fever, shortness
of breath, tachypnea, hypoxemia, and finally
hemodynamic collapse
Cryptococcus Amphotericin B and flucytosine India-ink stain of cerebrospinal fluid (CSF): Most cases occur in SYSTEMIC
(is superior to amphotericin B observe encapsulated yeast immunocompromised person
alone) Cryptococcal antigen test of CSF: detects
polysaccharide antigens
Pneumonia: usually self-limited and asymptomatic Fungal culture MCC of meningoencephalitis in
HIV
Skin lesions: look like acne
YEAST WITH A HALO
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Candida albicans Normal flora of the skin, mouth and
gastrointrointestinal tract
Aspergillius fumigatus Ubiquitous
Aspergillus may cause a broad
spectrum of disease in the human host,
ranging from hypersensitivity reactions
to direct angioinvasion. Aspergillus
primarily affects the lungs, causing the
Aspergillius flavus following four main syndromes:
• Allergic bronchopulmonary
aspergillosis (ABPA)
Aspergillius niger • Chronic necrotizing Aspergillus
pneumonia (or chronic necrotizing
pulmonary aspergillosis [CNPA])
• Aspergilloma
• Invasive aspergillosis
Rhizopus Saprophytic molds
Rhizomucor
Mucor
Pneumocystis jirovecii Unicellular fungi found in the
respiratory tracts of many mammals
and humans
Pseudohyphae and yeast Candidiasis in a normal host The choice of antifungal agent KOH stain of specimen YEAST WITH PSEUDOHYPHAE CUTANEOUS or SYSTEMIC
Oral thrush depends on the area involved Silver stain of specimen (normal host, or opportunistic)
Vulvovaginal candidiasis and its severity. Blood culture: growth must be respected
Cutaneous Blood assay for beta-D-glucan
Diaper rash
Rash in the skin folds of obese individuals
Candidiasis in an immunocompromised host
Thrush, vaginitis and/or cutaneous, plus:
Esophageal
Disseminated candidiasis: acquired by very sick
hospitalized patients, resulting in multi-organ system
failure
Chronic mucocutaneous candidiasis
Branching septated hyphae Aspergillosis Allergic bronchopulmonary Allergic brochopulmonary aspergillosis: Rarely found in individuals who OPPORTUNISTIC
O Allergic bronchopulmonary aspergillosis (IgE aspergillosis -> treat with High level of IgE (IgE level > 1000 IU/dL) are immunocompetent
(acute angles, 45 )
mediated): asthma type asthma type reaction with corticosteroids Sputum culture
shortness of breath and high fever Wheezing patient and chest X-ray with fleeting The FDA has approved an
infiltrates intravenous formulation of the
Increased level of eosinophils triazole antifungal posaconazole
Skin test: immediate hypersensitivity reaction (Noxafil), which is indicated for
Asperigilloma (Fungus ball): associated with Aspergilloma: removal via Aspergilloma: diagnose with chest X-ray or CT the prophylaxis of invasive
hemoptysis (blood cough) thoracic surgery scan Aspergillus and Candida
infections in severely
Invasive aspergillosis: necrotizing pneumonia. May Invasive aspergillosis: treat with Invasive aspergillosis: sputum examination and immunocompromised adults
disseminate to other organs in immunocompromised voriconazole, possibly culture who are at high risk of
patients caspofungin. (very high developing these infections.
mortality)
Aflatoxin consumption (produced by Aspergillus Aflatoxins contaminate peanuts,
flavus ) can cause liver damage and live cancer grains, and rice
Broad, non-septated, branching Mucormycosis Amphotericin B and surgery Biopsy The disease is rapidly fatal OPPORTUNISTIC
hyphae (right angles, 90o) Rhinocerebral (associated with diabetes): starts on Black nasal discharge
nasal mucosa and invades the sinus and orbit
Pulmonary mucormycosis
The organism is found in 3 PJP – Pneumocystis jirovecii pneumonia occurs when TMP-SMX A lactic dehydrogenase (LDH) study is performed The taxonomic classification of
distinct morphologic stages, as both cellular immunity and humoral immunity are as part of the initial workup.[24] LDH levels are the Pneumocystis genus was
follows: defective. usually elevated (>220 U/L) in patients with P debated for some time. It was
The trophozoite (trophic form), jiroveci pneumonia (PJP). They are elevated in initially mistaken for a
in which it often exists in clusters Once inhaled, the trophic form of Pneumocystis 90% of patients with PJP who are infected with trypanosome and then later for a
The sporozoite (precystic form) organisms attach to the alveoli. Multiple host HIV. The study has a high sensitivity (78%-100%); protozoan. In the 1980s,
The cyst, which contains several immune defects allow for uncontrolled replication of its specificity is much lower because other biochemical analysis of the
intracystic bodies (spores) Pneumocystis organisms and development of illness. disease processes can result in an elevated LDH nucleic acid composition of
Activated alveolar macrophages without CD4+ cells level. [Clin Invest Med. 1992 Aug. 15(4):309-17. Pneumocystis rRNA and
are unable to eradicate Pneumocystis organisms. mitochondrial DNA identified the
Increased alveolar-capillary permeability is visible on organism as a unicellular fungus
electron microscopy. rather than a protozoan.
Quantitative PCR for pneumocystis may become Subsequent genomic sequence
useful in distinguishing between colonization analysis of multiple genes
and active infection, but these assays are not yet including elongation factor 3, a
available for routine clinical use. component of fungi protein
synthesis not found in protozoa,
Page 3 of 34
Page 4 of 34
 DNA VIRUSES

VIRUS MORPHOLOGY VIRULENCE FACTORS CLINICAL SYNDROMES TREATMENT & PREVENTION DIAGNOSIS
Herpesviridae

HSV 1 and 2 Double-stranded DNA Direct contact of mucous membranes
Enveloped Viral shedding usually occurs in the presence of obvious herpetic
lesions, but viral shedding can also occur when there no visible
lesions
Icosahedral symmetry Sexually transmitted
HSV travels up sensory nerve fibers to the sensory nerve ganglia,
where it replicates then returns along the sensory nerve fibers to
produce skin lesions (NEUROTROPISM, LATENCY)
Varicella-Zoster Virus Aerosolized respiratory secretions
Contact with ruptured vesicles
Zoster: reactivation of VZV from dorsal root ganglion
Risk factors for severe varicella in neonates are as follows:
The first month of life: A neonate’s first month of life is a
susceptible period for severe varicella, especially if the mother is
seronegative.
Early delivery: Delivery before 28 weeks’ gestation also renders a
baby susceptible because transplacental transfer of immunoglobulin
G (IgG) antibodies occurs after this time
Gingivostomatitis Acyclovir Tzanck smear reveals multinucleated giant cells with intranuclear
inclusions
Reactivation of Gingivostomatitis occurs immunocompromised Valacyclovir Viral culture
individuals
Herpetic keratitis Famciclovir Polymerase chain reaction
TEMPORAL lobe encephalitis: infection (most cases are reactivation Trifluridine eye drops: for corneal infection Serology
of latent HSV-1) of the brain results in cell death and brain tissue
swelling , manifested as fever, headache and neurologic
abnormalities
Genital herpes: painful group local vesicles on the cervix, or on the Direct Fluorescent Antibodies (DFA) Ulcer base scrapings can be
external genitalia of men and women. Often associated with fever tested with antibodies will latch onto HSV if present, & will fluoresce
and viral symptoms. These vesicles usually do not scar.
Reactivation of genital herpes similar eruption of vesicles, but less
painful and vesicles last for few more days
Neonatal herpes: acquired during the passage of a fetus through an
infected birth canal. The risk of transmission is highest when a
primary genital infection is present during delivery (One of the
TORCHES Organism)
Herpetic whitlow
Disseminated herpes infection of organs
Varicella (chicken pox) Acyclovir Vesicles are described as few drops on the top of a rose petal: a red
base with fluid filled vesicle on top
2 week incubation period Valacyclovir Lesions appear in all stages of development (erupting papules,
active vesicles, crusting lesions) at a single time -> differentiates
varicella from other pediatric rashes
Fever and headache Famciclovir Tzanck smear reveals multinucleated giant cells
Rashes: vesicles first erupts on the trunk and face, and spread to Varicella vaccine
involve the entire body (including mucous membranes). Vesicles
erupt in crops, so one crop forms as another crop scabs over.
Patients are infectious until all their lesions scab over.
Pneumonia or encephalitis can occur in immunocompromised Zoster immune globulin
patients
Zoster (shingles): painful eruption of vesicles isolated to a single
dermatome distribution. The vesicles dry up and form crusts, which
disappear in about 3 weeks. Pain in the dermatomal distribution can
last for months in the elderly.
Herpes zoster ophthalmicus: vesicles on one side of the forehead
and on tip of the nose (the dermatomal distribution of the first
division of cranial nerve V) may be associated with severe corneal
involvement that (similar to HSV) can lead to blindness

Although most varicella infection confers life-long immunity,

varicella clinical reinfections among healthy children have been
described [Pediatrics . 2002 Jun. 109(6):1068-73.]

Page 5 of 34
Cytomegalovirus (CMV) Double-stranded linear DNA Virus present in milk, saliva, urine & tears Asymptomatic infection (latent phase) Ganciclovir CMV shell viral culture: Blood buffy coat (WBC) is cultured
Enveloped Foscarnet overnight. The cells are then centrifuged. This breaks up the white
Icoshedral symmetry Congenital disease (TORCHES) Cidofovir blood cells, releasing CMV antigens, which are detected with
CMV mononucleosis (heterophil-negative) Formivirsen monoclonal antibodies
Transmission occurs with prolonged exposure, such as between Reactivation in immunocompromised patients Healthy people who are infected with CMV but who have no MV has been detected via culture (human fibroblast), serologies,
children in households or day care center A. Pneumonia symptoms usually do not require medical treatment. antigen assays, polymerase chain reaction (PCR), and cytopathology.
B. Retinitis (MCC of blindness in HIV) In the transplant population, antigen assays or PCR is used
C. Esophagitis Antiviral treatment is used for immunocompromised individuals (sometimes in conjunction with cytopathology) for diagnosis and
D. Disseminated DIsease who have eye infections or life-threatening illnesses due to CMV. treatment determinations.

Sexual transmission DOC for prevention of CMV disease in solid-organ transplant Histology: reveals enlarged (Cytomegalic) cells with intranuclear and
patients is valganciclovir [Lancet . 2005 Jun 18-24. 365(9477):2105- cytoplasmic inclusion bodies. The pathologic hallmark of CMV
15] infection is an enlarged cell with viral inclusion bodies.
Currently, no vaccine available CMV early antigens can be detected in WBC’s. These antigens are an
early marker for infection in bone marrow transplant patients
PCR testing for CMV DNA
Epstein-Barr virus (EBV) Double-stranded linear DNA Intimate contact from asymptomatic shedders of EBV Infectious mononucleosis: fever, sore throat, severe lethargy, Supportive Elevated heterophileantibodies
enlarged lymph nodes and spleen (generalized)
Enveloped Infects human B-cells -> transforms them (Receptor: CD 21) Infectious mononucleosis was first described by Sprunt and Evans in Differential white blood cells count will show elevated “atypical
the Bulletin of the Johns Hopkins Hospital in 1920. lymphocytes” -> Downey cells
Icoshedral symmetry Immune response to EBV infection is fever -> occurs because of Associated with Burkitt’s B-cell lymphoma (MCC lymphoma in Serology: IgM against the viral capsids antigens (VCA)
cytokine release consequent to B-lymphocyte invasion by EBV. children)
Lymphocytosis observed in the RES is caused by a proliferation of
EBV-infected B lymphocytes.
Pharyngitis observed in EBV infectious mononucleosis is caused by
the proliferation of EBV-infected B lymphocytes in the lymphatic
tissue of the oropharynx.
Human Herpesvirus 6 (HHV-6) Double-stranded linear DNA Transmitted by saliva Roseola (exanthum subitum): Supportive Clinical diagnosis
Enveloped
Icoshedral High fever lasting 3-5 days, which resolves, and is followed by a …

Rash: located mostly on trunk, which lasts just a day or two

HHV-8 Double-stranded linear DNA Sexual transmission, especially with MSM practice Appears to be the cause of Kaposi’s sarcoma HAART is an integral part of successful Kaposi sarcoma therapy. CD4 lymphocyte counts and plasma HIV viral-load studies should be
HAART may be tried as the sole modality in nonvisceral disease. performed for patients with HIV infection.
For visceral disease, chemotherapy may be added.
Enveloped Kaposi’s sarcoma - a spindle-cell tumor thought to be derived from The following local therapies can be used for palliation of locally
endothelial cell lineage; carries a variable clinical course ranging advanced symptomatic disease or in individuals who have
from minimal mucocutaneous disease to extensive organ cosmetically unacceptable lesions:
involvement.
Icoshedral Categorized into 4 types: • Radiation therapy
• Epidemic of AIDS-related • Cryotherapy
• Immunocompromised • Laser therapy
• Classic, or sporadic • Surgical excision
• Endemic (African) • Intralesional vinca alkaloid therapy
AIDS-related Kaposi sarcoma, unlike other forms of the disease, • Topical retinoids
tends to have an aggressive clinical course. It is the most common
presentation of Kaposi sarcoma.
Immunomodulation with interferon-alfa has clinical activity in
Kaposi sarcoma that may be mediated by its antiangiogenic,
antiviral, and immunomodulatory properties.

Page 6 of 34
Poxviridae Complex coat: large, brick-shaped
virus (making it cytoplasmic in
location)
Double-stranded linear DNA
The only DNA virus to replicate in
cytoplasm
Papovaviridae Naked icosahedral
Double-stranded circular DNA
Replicates in nucleus
koilocytes
Smallpox is a high-priority (category A) agent for bioterrorism,
defined as follows by the CDC:
• Easily disseminated or transmitted from person to person
• High mortality rate and potential for significant public health
effect
• Probable instigator of panic and social disruption
Special actions required for public health preparedness
Smallpox: causes skin lesions and death. This disease has been
eradicated from the earth. Histopathology: Guarnieri bodies
Molluscum contagiosum: small white bumps with a central dimple
(like a wart). Often found in the genital region. Histopathology:
Henderson-Peterson bodies
Human papilloma virus (HPV) causes warts (over 50 viral strains)
A. Common warts (types 1, 2, 4 & 7)
B. Genital warts (types 6, 11, 16, 18 and others) – condylomata
acuminata
C. Laryngeal warts (6, 11)
D. Penile, vulvar, cervical, anal cancer (type 16, 18, 31, 33)
About 50% of men who are homosexual and have anal squamous
cell carcinoma (SCC) have a history of anorectal warts
BK Polyomavirus: causes kidney disease in renal transplant patients, Relapses are common after treatment, because HPV DNA is found in Laboratory studies that may be considered include the following:
hemorrhagic cystitis in bone marrow transplant patients, and mild normal appearing tissue around the wart
respiratory illness in children
JC polyomavirus: Progressive multifocal leukoencephalopathy,
characterized by degenerative central nervous system white matter
disease
Vaccine: an avirulent pox vaccine was developed that included No animal reservoirs: Virologists have speculated that it evolved
immunity to virulent pox virus from an African rodent poxvirus 10 millennia ago. Because of the
absence of an animal vector, communities had to reach a critical
population (estimated at 200,000 around 3000 B.C.) before endemic
smallpox could be established.
Codes for DNA and RNA polymerase
Methods of wart removal Second smallest DNA virus
Liquid nitrogen (freeze them off) - best method
Surgical HPV is oncogenic because of E6 and E7 genes that code for
suppressors of human tumor suppressor genes.
Electrosurgery (laser ablation)
Podophyllin: for genital warts Condylomata lata – syphilis
Many warts resolves spontaneously in 1-2 years Condylomata acuminate – genital warts, okay?
In genital intraepithelial neoplasia, it is essential to determine the
extent of disease through careful inspection and colposcopy.
Cervical cytologic testing with the Papanicolaou (Pap) test to screen
for cervical neoplasia (guidelines for cervical cancer screening now
include a delay in the initiation of screening and longer intervals
between subsequent screens
HPV DNA testing (eg, with Hybrid Capture II or polymerase chain
reaction [PCR] assay) for detection of HPV and posttreatment follow-
up of cervical intraepithelial neoplasia
The acetic acid test: This test can be used in conjunction with
colposcopy to examine cervical lesions; however, it is reserved for
suspicious lesions and should not be used for routine screening

Adenoviridae Naked icosahedral Childhood upper respiratory tract infections Illness is self-limited Pharyngo-conjunctival fevel
Double-stranded circular DNA A. Rhinitis
Replicates in nucleus B. Sore throat
C. Fever
D. Conjunctivitis
2. Epidemic keratoconjunctivitis (pink eye)
3. Epidemic diarrheal illness in infants and children
Parvoviridae Naked icosahedral Erythema infectiosum (fifth disease): affects children between the Illness is self-limited Smallest DNA virus
ages of 4 to 12
Parvovirus B-19 Double-stranded linear DNA virus Fever + “Slapped cheek” rash
(negative stranded)
Replicates in nucleus Transient aplastic anemia crisis: occurs when the Parvovirus stops I.V. immunoglobulin can be used with aplastic crisis
the production of red blood cells in the boone marrow

Page 7 of 34
 RNA VIRUSES

VIRUS MORPHOLOGY VIRULENCE FACTORS CLINICAL SYNDROMES TREATMENT & PREVENTION DIAGNOSIS
Orthomyxoviridae

Influenza A: human and animal strain
Influenza B: human only strain
Influenza C: human only strain
Paramyxoviridae
Negative (-) single-stranded RNA Hemagglutinin (HA) glycoprotein: binds to red blood cells. Also
Segmented (7-8) genome binds to cells of the upper respiratory tract. The HA is then cleaved
Lipid containing envelope into pieces (HA1 & HA2) by host cell proteases, which allows HA to
Helical symmetry activate fusion. The viral RNA in then dumped into these cells
Replicates in the nucleus (Retroviruses are the only other Neuraminidase (NA) glycoprotein: breaks down neuraminic acid, an
type of RNA viruses that replicate in the nucleus) important component of mucin
The hemagglutinin and neuraminidase variants are used to identify
influenza A virus subtypes. For example, influenza A subtype H3N2
expresses hemagglutinin 3 and neuraminidase 2. The most common
subtypes of human influenza virus identified to date contain only
hemagglutinins 1, 2, and 3 and neuraminidases 1 and 2. H3N2 and
H1N1 are the most common prevailing influenza A subtypes that
infect humans. Each year, the trivalent vaccine used worldwide
contains influenza A strains from H1N1 and H3N2, along with an
influenza B strain.
Because the viral RNA polymerase lacks error-checking
mechanisms, the year-to-year antigenic drift is sufficient to ensure
that there is a significant susceptible host population each year.
However, the segmented genome also has the potential to allow
reassortment of genome segments from different strains of
influenza in a coinfected host.
Influenza Vaccine contraindicated in egg allergies (vaccine grown in eggs) Antigenic drift, small mutations, resulting in minor changes in the antigenicity
• Fever of HA or NA. This results in epidemics of the common flu
• Sore throat
• Myalgias
• Frontal or retro-orbital headache Prevention of influenza is the most effective management strategy. Antigenic shift (occurs with Influenza A): genomic reassortment. Major
• Nasal discharge Influenza A and B vaccine is administered each year before flu changes of the HA or NA (including acquisition of animal HA or NA). This results
• Weakness and severe fatigue season. The CDC analyzes the vaccine subtypes each year and makes in devastating influenza pandemics
• Cough and other respiratory symptoms any necessary changes on the basis of worldwide trends.
• Tachycardia
• Watery eyes Traditionally, the vaccine is trivalent (ie, designed to provide New avian influenza H5N1 has infected hundreds of people and represents a
protection against 3 viral subtypes, generally an A-H1, an A-H3, and a great risk of starting a human pandemic.
B). The first quadrivalent vaccines, which also provide coverage
against a second influenza B subtype, were approved in 2012 and Mortality is highest in infants and the elderly. The 2012-2013 season was
were made available for the 2013-2014 flu season. notable for widespread disease and a higher death rate than was reported in
previous years. In addition, the predominant influenza virus subtype was an
Amantadine and Rimantidine (used in parkinsonism) prevent viral H3N2, in contrast to dominance by H1N1 subtypes in recent past years.
uncoating of influenza A
Complications Zanamivir (inhaled) & Oseltamivir (oral) are neuraminidase inhibitors. Year 1918 - the Spanish flu (though cases appeared earlier in the United States
Secondary bacterial pneumonias in the elderly Can shorten course of influenza A and B and elsewhere in Europe), this pandemic killed an estimated 20-50 million
Reye’s syndrome in children who use aspirin, get liver and persons [Emerg Infect Dis . 2006 Jan. 12(1):9-14.]
brain disease
Increased mortality in the elderly and in those underlying
pulmonary and cardiac disease

Negative (-) single stranded RNA HA, but no NA Measles - one of the most contagious infectious diseases,
Measles (Rubeola) Unsegmented with at least a 90% secondary infection rate in susceptible
Lipid containing envelope F-protein (fusion protein) – leads to formations of multinucleated domestic contacts. Despite being considered primarily a
Helical symmetry giant cells childhood illness, measles can affect people of all ages.
Replicates in cytoplasm Prodrome: high fever, hacking cough and conjunctivitis
Koplik’s spots: small red-based blue-white centered lesions
in the mouth
Rash: from head, then to neck and torso, then to feet. As
the rash spreads, it coaleces
Complications:
Pneumonia, eye damage, myocarditis and encephalitis
20% risk of fetal death if acquired by a pregnant women
early in her pregnancy
Subacute Sclerosing Panencephalitis: slow form of
encephalitis that occurs many years after a measles
infection (Damson disease)
Treatment of measles is essentially supportive care, as follows: Although the diagnosis of measles is usually determined from the classic clinical
• Maintenance of good hydration and replacement of fluids lost picture, laboratory identification and confirmation of the diagnosis are
through diarrhea or emesis necessary for public health and outbreak control. Laboratory confirmation is
• IV rehydration may be necessary if dehydration is severe achieved by means of the following:
• Vitamin A supplementation should be considered • Serologic testing for measles-specific IgM or IgG titers
• Isolation of the virus
Postexposure prophylaxis should be considered in unvaccinated Reverse-transcriptase polymerase chain reaction (RT-PCR) evaluation
contacts; timely tracing of contacts should be a priority. Patients Biopsy of rash or Koplik’s spots reveals multinucleated giant cells
should receive regular follow-up care with a primary care physician Warthin-Finkeldey bodies (multinucleated giant cells in measles)
for surveillance of complications arising from the infection.
WHO recommends vitamin A supplementation for all children
diagnosed with measles, regardless of their country of residence,
based on their age, as follows:
• Infants younger than 6 months: 50,000 IU/day PO for 2 doses
• Age 6-11 months: 100,000 IU/day PO for 2 doses
• Older than 1 year: 200,000 IU/day PO for 2 doses
Children with clinical signs of vitamin A deficiency : The first 2 doses
as appropriate for age, then a third age-specific dose given 2-4 weeks
later
Prevention: MMR vaccine:
1. Measles (live attenuated)
2. Mumps
3. Rubella

Page 8 of 34
Parainfluenza 1 and 2
Respiratory syncytial virus (RSV)
The leading cause of lower respiratory tract
infections (LRTIs) in infants and young children.
Mumps (Rubulavirus)
Negative (-) single stranded RNA
Unsegmented
Lipid containing envelope
Helical symmetry
Replicates in cytoplasm
Negative (-) single stranded RNA
Unsegmented
Lipid containing envelope
Helical symmetry
Replicates in cytoplasm
Negative (-) single stranded RNA
Unsegmented
Lipid containing envelope
Helical symmetry
Replicates in cytoplasm
Glycoproteins with combined HA and NA activity Upper respiratory tract infection in adults: bronchitis,
F-protein (Fusion protein): results in multinucleated giant cells pharyngitis, rhinitis
(called syncytial cells) Viral pneumonia in children elderly and
immunocompromised
Human PIVs are common community-acquired respiratory Croup. Children develop a barking cough due to infection
pathogens without ethnic, socioeconomic, gender, age, or and swelling (narrowing) of the larynx -> steeple sign
geographic boundaries. Many factors have been found that Human PIV-1 is most commonly associated with croup.
predispose individuals to these infections, including the following: Human PIV-2 is also associated with croup.
• Malnutrition Human PIV-3 is second only to RSV as a cause of pneumonia
• Overcrowding and bronchiolitis in infants and young children.
• Vitamin A deficiency Human PIV-4 is detected in patients less often, perhaps
• Lack of breastfeeding because HPIV-4 causes less severe disease.
• Environmental smoke or toxins Bronchiolitis in children
F-protein Most common cause of pneumonia in infants less 6 months
NO HA nor NA glycoproteins of age
Acute otitis media occurs in up to 33% of children with RSV
illness
Glycoproteins with combined HA and NA activity Mumps - acute, self-limited, systemic viral illness
characterized by the swelling of one or more of the salivary
glands, typically the parotid glands. The illness is caused by
the RNA virus, Rubulavirus
F-protein Parotid gland swelling (painful)
Testicular inflammation (very painful)
MeningitisEncephalitis
Page 9 of 34
Supportive: racemic epinephrine Isolation and identification of the virus in cell culture or direct detection of the
virus in respiratory secretions by means of immunofluorescent assay, enzyme-
Antiviral agents are of uncertain benefit; antibiotics are used only if linked immunosorbent assay (ELISA), or polymerase chain reaction (PCR) assay
bacterial complications (eg, otitis and sinusitis) develop.
Demonstration of a significant rise in specific immunoglobulin G (IgG)
antibodies between appropriately collected paired serum specimens or in
specific immunoglobulin M (IgM) antibodies in a single serum specimen
Palivizumab: a monoclonal antibody against RSV that is produced a Specific diagnostic tests for confirming RSV infection include the following:
recombinant DNA. It is given intramuscularly. • Culture
The American Academy of Pediatrics has released updated guidelines • Antigen-revealing techniques
addressing palivizumab prophylaxis for respiratory syncytial virus • Polymerase chain reaction (PCR) assay
(RSV). • Molecular probes
According to the updated recommendations, palivizumab
prophylaxis for RSV should be limited to infants born before 29
weeks' gestation and to infants with chronic illness such as
congenital heart disease or chronic lung disease. Other
recommendations include the following:
• Give infants who qualify for prophylaxis in the first year of life no
more than five monthly doses of palivizumab (15 mg/kg per dose)
during the RSV season
• In the second year of life, palivizumab prophylaxis is recommended
only for children who needed supplemental oxygen for 28 days or
more after birth and who continue to need medical intervention
(supplemental oxygen, chronic corticosteroid, or diuretic therapy).
• Clinicians may consider prophylaxis for children younger than 24
months if they will be profoundly immunocompromised during the
RSV season.
Ribavirin - primarily reserved for patients with significant underlying
risk factors and severe acute RSV disease (eg, transplant recipients)
Conservative, supportive medical care is indicated for patients with Mumps is a clinical diagnosis.
mumps. No antiviral agent is indicated for viral illness, as mumps is a
self-limited disease.
Current evidence suggests that patients diagnosed with mumps Only one antigenic type. Therefore, the vaccine is protective.
should be isolated for 5 days from the onset of symptoms.
Prevention: MMR vaccine:
1. Measles (live attenuated)
2. Mumps
3. Rubella
Togaviridae

Rubella
Derived from a Latin term meaning "little red."
Enveloped virus with an icosahedral nucleocapsid and one ss- The virus attaches to and invades the respiratory epithelium. It then
positive-RNA spreads hematogenously (primary viremia) to regional and distant
lymphatics and replicates in the reticuloendothelial system. This is
followed by a secondary viremia that occurs 6-20 days after
infection.
Rubella: ( Geman mesles/3 day measles)
Fever, lymphadenopathy and mild flu-like symptoms
Rash: from forehead to face to torso to extremities (lasts 3
days)
The major complication of rubella is its teratogenic effects
when pregnant women contract the disease, especially in
the early weeks of gestation.
Congenital defects: occurs when a women in her first
trimester of pregnancy gets exposed. The fetus may develop
defects of the heart, eyes, or central nervous system
Prevention: MMR vaccine: A clinical diagnosis of rubella may be difficult to make because many
1. Measles (live attenuated) exanthematic diseases may mimic rubella infection. In addition, as many as 50%
2. Mumps of rubella infections may be subclinical; therefore, laboratory studies are
3. Rubella important to confirm the diagnosis of acute rubella infection.
The laboratory diagnosis of rubella can be made either though serologic testing
or by viral culture. The serologic diagnosis consists of demonstrating the
presence of rubella-specific immunoglobulin M (IgM) antibody in a single
serum sample or observation of a significant (>4-fold) rise in rubella-specific
immunoglobulin G (IgG) antibody titer between the acute and convalescent
serum specimens drawn 2-3 weeks apart.

False-positive rubella IgM test results have been reported in persons with other
viral infections (eg, acute EBV, CMV, parvovirus B19 infection) and in the
presence of rheumatoid factor (RF).

The “R” in TORCHES

Flaviviridae

Yellow fever virus Positive (+) single-stranded RNA Yellow fever: hepatitis with(jaundice), Fever, Backache Prevention: mosquito control Viral culture
Dengue virus Nonsegmented RNA Serology
St. Louis encephalitis Icosahedral symmetry Dengue fever: “Break bone fever” Vaccination required when travelling to and from endemic countries With repeat infections, individuals are at higher risk of developing the
hemorrhagic form of dengue fever
Japanese B encephalitis Replicates the cytoplasm “Painful fever”: High fever along with West Nile: Serology is much more sensitive that PCR, although because of cross-
reactions with other flaviviruses, it is less specific
Hepatitis C virus Enveloped 1. Headaches
West Nile Virus Vector = mosquito 2. Muscle aches
Aedes : yellow fever and dengue fever 3. Joint aches
4. backache
Culex : St. Louis, Japanese, and West Nile Dengue hemorrhagic fever: hemorrhage, thrombocytopenia
encephalitis and septic shock
St. Louis, Japanese, West Nile encephalitis: encephalitis and
fever
Hepatitis C virus – see Hepatitides
West Nile: fever and encephalitis or myelitis that produces
flaccid paralysis
Picornaviridae

Poliovirus Positive (+) single-stranded RNA Inapparent, asymptomatic infection
Naked icosahedral symmetry Abortive poliomyelitis – most common clinical form; mild,
febrile illness with headache, sore throat, nausea, and
vomiting.
Replication occurs in the cytoplasm Nonparalytic poliomyelitis – aseptic meningitis
Paralytic poliomyelitis – virus destroys the anterior horn
cells in the spinal cord -> flaccid paralysis; permanent motor
nerve damage
Vaccine:
Salk vaccine formalinkilied polio virus that is injected subcutaneously
Oral polio vaccine (developed by Sabin): Attenuated (non-virulent)
polio virus is ingested
Transmission : Fecal-oral
The chance of developing paralytic poliomyelitis increase as one gets older.
Since the World Health Assembly in May 1988 resolved to eradicate
poliomyelitis, the estimated global incidence of polio has decreased by more
than 99%, and 3 World Health Organization (WHO) regions (the Americas, the
Western Pacific, and Europe) have been certified as polio-free.

Coxsackie A “Cold” rashes, viral meningitis

Coxsackie B Herpangina: Fever, sore throat and small red- based vesicle
over the back of the patient’s throat
Hand Foot and Mouth Disease: Occurs in children less than
5, Vesicles erupt on hands, foot and mouth, which are highly
contagious
Viral meningitis
Myocarditis/pericarditis: arrhythmia, cardiomyopathy, heart
failure
Pleurodynia: fever and sharp pleuritic chest pain

Page 10 of 34
 ECHOviruses (Enteric, Cytopathic, Human Orphan) “Cold”, rashes, viral meningitis

Pericarditis
Rhinovirus Common colds
113 serotypes Replicates better at 33°C than at 37°C -> they affect
primarily the nose and conjunctiva rather than the lower
respiratory tract.
Acid-labile -> killed by gastric acid when swallowed -> they
do not infect the gastrointestinal tract, unlike the
enteroviruses.
Host range is limited to humans and chimpanzees
Caliciviridae

Norwalk virus ; Positive (+) single stranded RNA Noroviruses are highly contagious, with infection requiring fever Viral gastroenteritis: (explosive, but self-limited): Supportive Immune electron microscopy: Immune serum is used to aggregate virus in stool
Naked icosahedral symmetry than 10 virions (ID50 = 10 virions), leading to disease in 50% of samples to aid detection
Replication occurs in the cytoplasm inoculated individuals.
New name: NOROVIRUS Fecal-oral transmission The virus is extremely stable in the environment and resists freezing Fever, Abdominal pain, Vomiting, Diarrhea Antigen detection immunoassay: Has high sensitivity but low specificity
temperatures, heat (up to 60°C), disinfection with chlorine, acidic because of reactivity with antigenic variants and homologous viruses
conditions, vinegar, alcohol, antiseptic hand solutions, and high
sugar concentrations.
The most common cause of epidemic nonbacterial The incubation period is approximately 1-2 days, and symptoms Nucleic acid amplification: Highly sensitive and specific
gastroenteritis in the world typically last 1-3 days (or longer in immunocompromised Serum antibody titers can be detected within 2 weeks of illness. During
individuals). Viral shedding occurs for up to 3 weeks following norovirus infection, immunoglobulin M (IgM) to norovirus has been found to
infection. be more specific than IgG.
Reoviridae

Rotavirus Double-stranded RNA Viral gastroenteritis: causes profound dehydaration Intravenous fluids Rotavirus may be identifies by the following means:
Hyperactive bowel sounds: Most common finding New oral rotavirus vaccine appears safe and effective in infants • enxyme immuno assay (most common)
Segmented (11 segments) genome Especially in infants. Fever, abdominal pain, vomiting and There are currently 2 FDA-approved rotavirus vaccines to protect • latex agglutination
diarrhea against rotavirus gastroenteritis (ie, RotaTeq and Rotarix). These • electron microscopy
Naked icosahedral symmetry No blood, No pus in diarrhea vaccines are indicated in infants aged 6-32 weeks (RotaTeq) and • culture
Fecal-oral tranmission A major cause of infant death in underdeveloped countries those aged 6-24 weeks (Rotarix)
and the most common cause of diarrhea in infants less than
3 years of age
Coronaviridae

Coronavirus Positive (+) single-stranded RNA Upper respiratory tract infection (“common cold”) Supportive
Nonsegmented
Helical symmetry
Enveloped
Replication in the cytoplasm

After establishment of infection, SARS-CoV causes tissue damage by Severe acute respiratory syndrome (SARS) is a serious, According to guidelines from the Centers for Disease Control and Prevention
(1) direct lytic effects on host cells and (2) indirect consequences potentially life-threatening viral infection caused by a (CDC), the laboratory diagnosis of SARS-CoV infection is established on the
resulting from the host immune response. Autopsies demonstrated previously unrecognized virus from the Coronaviridae basis of detection of any of the following with a validated test, with
changes that were confined mostly to pulmonary tissue, where family, the SARS-associated coronavirus (SARS-CoV) confirmation in a reference laboratory:
diffuse alveolar damage was the most prominent feature. • Serum antibodies to SARS-CoV in a single serum specimen
• A 4-fold or greater increase in SARS-CoV antibody titer between acute- and
The other mechanism was thought to be the induction of apoptosis. The clinical course of SARS generally follows a typical convalescent-phase serum specimens tested in parallel
The SARS-CoV–3a and –7a proteins have been demonstrated to be pattern. • Negative SARS-CoV antibody test result on acute-phase serum and positive
inducers of apoptosis in various cell lines Stage 1 is a flulike prodrome that begins 2-7 days after SARS-CoV antibody test result on convalescent-phase serum tested in parallel
incubation, lasts 3-7 days, and is characterized by the • Isolation in cell culture of SARS-CoV from a clinical specimen, with
following: confirmation using a test validated by the CDC
• Fever (>100.4°F [38°C]) • Detection of SARS-CoV RNA via reverse transcriptase polymerase chain
• Fatigue reaction (RT-PCR) assay validated by the CDC, with confirmation in a reference
• Headaches laboratory, from (1) two clinical specimens from different sources or (2) two
• Chills clinical specimens collected from the same source on 2 different days
• Myalgias
• Malaise
• Anorexia
Middle East respiratory syndrome (MERS) is a respiratory No vaccine currently exists for MERS, and no specific treatment has The recommended algorithm for detection of MERS-CoV includes testing using
disease caused by a newly recognized coronavirus (MERS- been recommended. Management is currently supportive. rRT-PCR.
CoV). It was first reported in 2012 in Saudi Arabia and is
thus far linked to countries in or near the Arabian Peninsula Serologic testing is available for the evaluation of MERS-CoV infection or
(United Arab Emirates [UAE], Qatar, Oman, Jordan, Kuwait, exposure
Yemen, and Lebanon). As of May 2014, two cases had been
reported in the United States, both in men who had recently
returned from Saudi Arabia. [MMWR Morb Mortal Wkly
Rep . 2015 Jan 30. 64 (3):61-2]

Page 11 of 34
Rhabdoviridae

Rabies virus Bullet shaped Rabies is a highly neurotropic virus that evades immune surveillance
Negative (-) single-stranded RNA by its sequestration in the nervous system. Upon inoculation, it
Nonsegmented enters the peripheral nerves. A prolonged incubation follows, the
Helical nucleocapsid is coiled into a bullet shape length of which depends on the size of the inoculum and its
Replication in the cytoplasm proximity to the CNS. Amplification occurs until bare nucleocapsids
Zoonotic (all warm blooded animals): dogs, cats, skunks, spill into the myoneural junction and enter motor and sensory
coyotes, foxes, raccoons, and bats are reservoirs in the U.S. axons. At this point, prophylactic therapy becomes futile, and rabies
Transmitted via an animal bite can be expected to follow its fatal course, with a mortality rate of
100%.
The rabies virus travels along these axons at a rate of 12-24 mm/d to
enter the spinal ganglion. Its multiplication in the ganglion is
heralded by the onset of pain or paresthesia at the site of the
inoculum, which is the first clinical symptom and a hallmark finding.
From here, the rabies virus spreads quickly, at a rate of 200-400
mm/d, into the CNS, and spread is marked by rapidly progressive
encephalitis. Thereafter, the virus spreads to the periphery and
salivary glands.
Retroviridae
Incubation period: asymptomatic
Prodromal period: The virus enters the CNS. The duration of
this period is 2-10 days. Nonspecific symptoms and signs
develop. Paresthesia, pain, or intense itching at the
inoculation site is pathognomonic for rabies and occurs in
50% of cases during this phase; this may be the individual’s
only presenting sign.
Acute neurologic period: associated with objective signs of
developing CNS disease.
Furious rabies may develop during this period: patients
develop agitation, hyperactivity, restlessness, thrashing,
biting, confusion, or hallucinations.
Paralytic rabies (dumb rabies or apathetic rabies) -> patient 3. Active immunization with killed rabies virus baccine
is relatively quiet compared with a person with the furious
form
NO TREATMENT Diagnosis: Microscopic examination of the central nervous system reveals Negri
bodies. These are collections of virions in the cytoplasm where replication
Vaccination of animals occurs
If bitten by possible rabid animal, there are three possibilities:
Capture animal: observe for 10 days
Destroy animal: examine for Negri bodies
Treat immediately (if you can not capture the animal, or the animal is Viral cultures and PCR
found to have a rabies): • Saliva - Results of saliva culture for rabies virus are positive in low yield within
1. Clean wound 2 weeks of illness onset
2. Passive immunization with rabies immune globulin • Cerebrospinal fluid - After the first week of illness, 80% monocytosis is
observed; protein and glucose test results are normal
• Brain tissue - Often postmortem; staining with immunohistochemical or
florescent antibody staining is definitive. Negri bodies are pathognomonic
(cytoplasmic inclusion bodies reflective of accumulated virions within rabies-
infected neurons). They are found in the horn of Ammon of the hippocampus
and cerebral cortex

HIV Enveloped virus with two copies (diploid ) of a single-
stranded, positive-polarity RNA genome
Most complex of the known retroviruses
Many serotypes
Transmembrane protein, TM (fusion protein, also called gp41), PHASE 0 – INFECTION: HIV acquired through sexual highly active antiretroviral therapy (HAART): two nucleoside Presumptive diagnosis -> detection of antibodies by ELISA. There are some false-
which is linked to a surface protein, and SU (attachment protein, intercourse, blood, or perinatally inhibitors (zidovudine and lamivudine) and protease inhibitor positive results with this test
gp120) PHASE 1 - WINDOW PERIOD: rapid viral replication but HIV (indinavir) Definitive diagnosis -> Western blot analysis
test is negative Grown in culture from clinical specimens
Cone-shaped, icosahedral core containing the major capsid protein PHASE 2 – SEROCONVERSION: peak of viral load, positive
(CA also called p24) HIV test, mild flu-like illness, lasting 1-2 weeks
MA (p17)-- directs entry of the double-stranded DNA provirus into PHASE 3 - LATENT PERIOD: asymptomatic, CD4 goes down, Polymerase chain reaction (PCR) -> very sensitive and specific: To detect HIV
the nucleus, and is later essential for the process of virus assembly. lasts 1-15 years DNA within infected cells. Some individuals who do not have detectable
There are two identical copies of the positive sense, single-stranded PHASE 4 - EARLY SYMPTOMATIC: CD4 500 to 200, lasts 5 antibodies have been shown by this test to be infected. Amount of viral RNA in
RNA genome in the capsid (that is, unlike other viruses, retroviruses years, mild mucocutaneous, dermatologic and hematologic the plasma (i.e., the viral load) can also be determined using PCR-based assays.
are diploid). illnesses
The RNA is tightly complexed with a basic protein, NC (p7), in a PHASE 5 – AIDS: CD4 <200, lasts 2 years, AIDS-defining
nucleocapsid structure that differs in morphology among the illnesses develop
different retrovirus genera.

Page 12 of 34
 HEPATITIDES
VIRUS TAXONOMY/MORPHOLOGY TRANSMISION CLINICAL TREATMENT SEROLOGY
Hepatitis A Picornaviridae Fecal-oral Acute viral hepatitis fever, jaundice and a painful Pooled immune serum globulin Anti-HAV IgM - Active disease
enlarged liver Supportive care Anti-HAV IgG – old: No active disease against repeated
infection
Positive (+) single-stranded RNA HAV vaccine
No envelope (naked)
Icosahedal capsid
Hepatitis B Hepadnaviridae Blood transfusion Acute viral hepatitis Prevention: Hepatitis B recombinant vaccine HBsAg – Disease (acute or chronic)
Double-stranded circular DNA Needlestick injury Fulminant haepatitis: severe acute hepatitis and rapid Screen blood to remove HBV contaminated blood to the Anti-HbsAg – immunity provides protection against
destruction of liver donor pool repeated infection
Enveloped Sexual Chronic hepatitis (10%) Treatment options: interferons (alfa and pegylated- IgM anti-HBcAg – New infection
Icosahedal capsid A. Asymptomatic carrier interfron alfa) or nucleoside analogs (Iamivudine, HBeAg – high infectivity
B. Chonic persistent hepatitis adefovir, entecavir and telbivudine Anti- HBeAg – Low infectivity
C. Chronic active hepatitis
Dane particle (intact virus) includes: envelope, capsid- Across the placenta Coinfection or superinfection with hepatitis Delta virus Lamivudine – antiretroviral drug; also used in HIV; a Hepatitis B antigen (HBeAg): soluble component of the
associated proteins, capsid, core (DNA+protein (HDV) reverse transcriptase inhibitor because HBV also core, which is marker for active disease
enzymes), hepatis B surface antigen (HBsAg), envelope, expresses reverse transcriptase
capsid-associated proteins, heptitis B core antigen
(HBcAg)
Double-stranded DNA Perinatally Complications: primary hepatocellular carcinoma,
cirrhosis
DNA polymerase enzyme
Capsid

Hepatitis C Flavivirus Blood transfusion Acute viral hepatitis Treatment: combination therapy with interferon and Screening anti-HCV antibodies
Single-stranded RNA Needlestick injury Up to 85% develop chronic hepatitis ribavirin
Enveloped icosachedral capsid Sexually 20% will develop cirrhosis
Across the placenta Increased risk of developing primary hepatocellular
carcinoma (especially with alcoholism)
Hepatitis D Incomplete RNA virus-only infective with the help of Blood transfusion Coinfection: HBV and HDV are acquired at the same Control of HBV infection is currently the only way to Serology is not very helpful, since detectable titers of IgM
hepatitis B virus time, and caused an acute hepatitis. protect against HDV and IgG anti-HDV are present only fleetingly
Complementation with HBV Helical nucleocapsid that requires the hepatitis B Needlestick injury Anti-HBV antibodies help cure infections
envelope (HBsAg) to be infectious
Sexual Superinfection: HDV infects a patient with chronic
hepatitis B who can not manufacture Anti-HBsAg
antibodies
Across the placenta Complications :
A. Fulminany hepatitis
B. Cirrhosis
Hepatitis E Hepeviridae Fecal-oral Hepatitis (like hepatitis A)
Single-stranded RNA
No envelope (naked) High mortality in pregnant women

Page 13 of 34
 GRAM POSITIVE SUMMARY

GRAM POSITIVE COCCI

GRAM POSITIVE BACILLI

Page 14 of 34

MICROORGANISM
Staphylococcus aureus
Staphylococcus epidermidis
Staphylococcus saphrophyticus
GRAM POSITIVE COCCI
RESERVOIR TRANSMISSION METABOLISM VIRULENCE FACTORS TOXINS CLINICAL SYNDROMES TREATMENT AND PREVENTION DIAGNOSIS NOTES
Humans (nasal) Direct contact, fomites, Catalase-positive Protein A: binds IgG, preventing Exofoliatin: Scaled SKIN and SOFT TISSUE INFECTIONS methicillin-sensitive SA (MSSA) - Gram-stain: reveals gram-positive 95% resistance to
contaminated food opsonization and phagocytosis skin syndrome; - bullous impetigo , folliculitis, furuncles, carbuncles, Penicillinase-resistant penicillins cocci in cluster penicillins
epidermal separation cellulitis, hidradenitis suppurativa , mastitis , surgical site (nafcillin, oxacillin, and dicloxacillin)
infections
Coagulase-positive Coagulase: Allows fibrin Enterotoxin: ACUTE ENDOCARDITIS methicillin-resistant SA (MRSA) - Culture: 60% MRSA in the
formation around organism superantigen causing - most common cause of acute endocarditis contain altered PBP; DOC is Beta-hemolytic Philippines
food poisoning - native/non-prosthetic/natural/normal valve (tricuspid valve) vancomycin Produces a golden yellow pigment.
in IV drug abusers
Facultative anaerobe Hemolysins: toxc to Toxic shock syndrome PNEUMONIA vancomycin-resistant SA (VRSA)- Polymerase chain reaction (PCR): Mode of resistance: mecA
hematopoietic cells toxin (TSST-1) - nosocomial, necrotizing, complicated by empyema , abscess DOC is linezolid mecA gene for MRSA gene
or pneumatocele
- post-viral
Penicillase : inactivate penicillin Alpha toxin: marked OSTEOMYELITIS and SEPTIC ARTHRITIS DDX strawberry tongue:
derivatives necrosis of skin and TSS, Kawasaki, Scarlet
hemolysis eg fever
Gangrene
Hyaluronidase: breaks down GASTROENTERITIS Vancomycin: rapid infusion
connective tissue - acute onset (4 hrs) of vomiting and diarrhea due to casues histamine release --
ingestion of preformed heat-stable enterotoxin > Red man/neck syndrome
- source: salad made with mayonnaise (potato or tuna
salad)
Staphylokinase: lyses formed SCALDED SKIN SYNDROME (Ritter Disease) Linezolid: inhibits initiation
- exfoliatin cleaves desmoglein in desmosomes; separation of translation
at Stratum granulosum
PV Leukocidin: white blood cell
secific
Lipase : spread in fat containing TOXIC SHOCK SYNDROME
areas of the body eg cellulitis - fever, hypotension, strawberry tongue , desquamating
rash and multi-organ involvement (>3)
- usually no site of pyogenic inflammation; blood CS
negative; TOXEMIA
-tampon- using menstruating women or in patients with
nasal packing for epistaxis
Humans Nosocomial Catalase-positive Polysaccharide capsule Prosthetic device infections (valves, joints, plates) Removal of prosthetic device Gram stain: gram-positive cocci in
(glycocalyx): adheres to a Vancomycin (50% methicillin clusters
variety of prosthetic devices. resistance)
Forms a biofilm.
Coagulase-negative Highly resistant to antibiotics Culture: white colonies on blood agar,
non-hemolytic
Facultative anaerobe Metabolism:
Catalase-positive
Coagulase-positive
NOVOBIOCIN
SENSITIVE
Humans Catalase-positive 2nd most common cause of UTI in sexually active women Fluoroquinolones Gram stain: gram-positive cocci in 2nd most common cause of
clusters UTI in sexually active
Coagulase-negative TMP-SMX Culture: gamma-hemolytic women
Facultative anaerobe Metabolism:
Catalase-positive
Coagulase-positive
NOVOBIOCIN
RESISTANT
NO STRES
Page 15 of 34
Streptococcus pyogenes Humans Respiratory droplets
GABHS
Streptococcus agalactiae/ Vagina Transvaginally
Group B streptococcus Transplacentally
Catalase-negative Erythrogenic toxin: produces
scarlet fever
Streptolysin O (oxygen-labile):
highly antigenic, causes AB
Streptolysin S (oxygen-stable)
Pyogenic exotoxin A:
superantigen similar to TSST
Exotoxin B: protease that
rapidly destroys tissue →
necrotizing fasciitis
Bacitracin-resistant
Hydrolyzes hippurtae
grows using LIM
broth
Catalase negative
Hyaluronidase: Impetigo contagiosa: accummulation of neutrophils beneath DOC is Penicillin G Gram-positive cocci in chains Disease of poverty
degrades hyaluronic stratum corneum
acid (spreading factor)
Streptokinase Erysipelas: infection that extends into dermal lymphatics Patients with a history of rheumatic Catalase-negative ASO titers: antecedent
(fibrinolysin) fever require long-term antibiotic pharyngitis
DNase Cellulitis Beta-hemolytic Anti-DNAase B: antecedent
(streptodornase): skin infection
degrades DNA in
exudates or necrotic
tissue
C5a peptidase: Necrotizing Bacitracin-sensitive Anti-streptokinase
inactivates antibodies: decrease
complement C5a efficacy of streptokinase in
managing MI
PHARYNGITIS: most common bacterial cause of sore throat Lancefield group A M protein: major virulence
foof Group A
streptococcus; inhibits the
activation of complement
and protects the organism
from phagocytosis; it is the
weakest point in the
organism's defense
SCARLET FEVER: "Second disease"; due to erythrogenic toxin; positive PYR test : non-specific; cannot
Dick Test for susceptibility differentiate pygenes from other
streptococci
STREPTOCOCCAL TOXIC SHOCK SYNDROME: clinically similar
but milder than S. aureus TSS, due to pyogenic exotoxin A,
recognizable site of pyogenic inflammation, blood cultures
are often positive
ACUTE RHEUMATIC FEVER
APSGN
UTI in pregnant women DOC: Penicillin G Gram-positive cocci in chains Most common cause of
Neonatal sepsis (meningitis, pneumonia) Penicillin G + Aminoglycoside for Beta-hemolytic neonatal sepsis in the
Endometritis → most commonly polymicrobial; foul-smelling serious infections CAMP test positive: CAMP factor world (the universe,
lochia enlarges the area of hemolysis formed rather)
All pregnant women should be by S. aureus
screened for GBS colonization at 35-
37wks AOG; if (+), chemoprophylaxis
with IV penicillin or ampicillin 4 hrs
prior to delivery
Page 16 of 34
Group D streptococci Human colon May enter bloodstream Catalase-negative UTIs due to indwelling urinary catheters and urinary tract Penicillin plus gentamicin Gram-positive cocci in chains There is aremarkable
during GIT or GUT instrumentation association between S.
Urethra and female genital tract can be surgery Bile and optochin Biliary tract infections Vancomycin for penicillin-resistance Catalase-negative bovis and colon CA
colonized resistant
Endocarditis in patients who underwent GIT surgery due to Linezolid for vancomycin-resistant Gamma hemolytic colonies
Hydrolyzes essculin in E. faecalis strains
Bile esculin agar
Marantic endocarditis in patients with abdominal
E. faecalis can grow in malignancy due to S. bovis
6.5% NaCl while S.
bovis cannot

Viridans streptococci Oral flora Enters blood stream Cata;ase-negative Glycocalyx enhances adhesion Dental caries: S. mutans Penicillin G +/- aminoglycoside Gram positive cocci in chains OVeRPaSs
during dental procedures to damaged heart valves (Gentamicin)
Bile and optochin Subacute bacterial endocarditis: S sanguis--> most common Alpha-hemolytic Optochin
resistant protected from host defenses cause of subacute and native valve endocarditis Vancomycin for penicilli resistance Viridans
within vegetations Resistant
Brain Abscess: S. intermedius Linezolid for vancomycin resistant Pneumoniae
strains Sensitive

Page 17 of 34
 GRAM POSITIVE BACILLI

MICROORGANISM RESERVOIR TRANSMISSION METABOLISM VIRULENCE FACTORS TOXINS CLINICAL SYNDROMES TREATMENT AND PREVENTION DIAGNOSIS NOTES
Bacillus anthracis Herbivores (zoonotic): Endopores Aerobic (but since it can Protein capsule (polymer of gamma-D- Exotoxin : 3 proteins Anthrax Cutaneous: Ciprofloxacin (DOC) Gram stain: box-car shaped bacteria Protein capsule
Sheep Goats Cattle grow without oxygen. It is glutamatic acid): antiphagocytic
classified as a facultative Non-motile Protective antigen (PA) Cutaneous (95%) painless black vesicles; can Inhalational/GI anthrax: Ciprifloxacin or Culture: Medusa head morphology Permamnent immunity
anaerobe be fatal if untreated Doxycycline with 1 or 2 additional - ground glass surface and irregular with of the patient survives
antibiotics (Rifampin, vancomycin, projectios along lines of inoculation
penicillin, imipinem, clindamycin, or
clarithromycin)
Edema factor (EF) Pulmonary (woolsorter’s disease) Vaccine: for high-risk individuals Serology MCC of death in
-prolonged latent period before rapid woolsorter’s disease is
deterioration pulmonary hemorrhage
- massively enlarged mediastinal lymph
nodes; pulmonary hemorrhage
- 100% mortality withput immediate
treatment
Lethal factor (LF) GI: abdominal pain, vomiting and bloody Vaccine is composed of the protective PCR of nasal swab MCC of death is
diarrhea antigen (PA) pulmonary hemorrhage
- rapidly progressive course in: Anthrax,
- mortality approaches 100% Leptospirosis (Weil’s
syndrome), Congenital
syphilis
Infections result to permanent immunity Animal vaccine is composed of a live
strain, attenuated by loss of its protein
capsule

Bacillus cereus Endospores Aerobic No capsule Enterotoxins ENTERAL Form: Vomiting, nausea and Food poisoning: Symptomatic treatment Culture specimen from suspected food source Chinese fried rice
abdominal cramps only; food poisoning is caused by the pre- syndrome
-duration: 8-10hrs formed enterotoxin
-heat-stable enterotoxin
Motile heat labile: similar to interotoxin of similar to staphylococcal food poisoning Ophthalmitis:
cholera and E. coli (diarrheal form) -Vancomycin
DIARRHEAL Form: Diarrhea, nausea, -Clindamycin
abdominal cramps -Ciprofloxacin
-duration: 20-36hrs -Gentamicin
-heat-labile enterotoxin
heat stable: produces syndrome -resembles clostridial gastroenteritis Resistant to beta-lactam antibiotics
similar to that of Staphylococcus
aureus food poisoning, but with OPHTHALMITIS: occur after penetrating eye
limited diarrhea (emetic form) injuries with soil contaminated object;
complete loss of light perception within 48hrs
of injury

Page 18 of 34
Clostridium Soil Endospores (heat Anaerobic Motile: flagella (so H-antigen positive) Neurotoxins inhibits release of Food-Borne botulism: cranial nerve palsies, Antitoxin (for food-borne and wound Gram stain TRIAD of BOTULISM:
botulinum resistant) acetylcholine from peripheral nerves muscle weakness, respiratory paralysis botulism) - Symmetric descending
flaccid paralysis (with
prominent bulbar
involvement)
- Absence of fever
- Intact sensorium

Stored vegetables: Anaerobes: ABC Toxin is not secreted, rather it is Infant botulism: constipation, flaccid Human botulism: immunoglobulin (for Culture: requires anaerobic condition Floppy baby syndrome
home-canned Actinomyces released upon the death of the paralysis (floppy baby syndrome) infant botulism) (thioglycollate-enriched agar)
zip-lock storage bags Bacteroides bacterium
Clostridium
Smoked fish Wound botulism: s imilar to food-borne Penicillin Patient’s serum injected into mice results in Botox neurotoxin
except absence of GI prodromal symptoms death
Wild, raw honey: Supportive therapy: including incubation
associated with infant and ventilator assistance
botulism
Clostridium tetani Soil Endospores: Anaerobic Motile flagella (so H-antigen-positive) Tetanospasmin: inhibits release of Tetanus Tetanus toxoid: vaccination with Gram stain: gram-positive rods, often with an Spastic paralysis
introduced through GABA and glycine (both inhibitory - muscle spasm formalin- inactivated toxin (toxoid), part endospore at one end, giving them the
wound neurotransmitters) from nerve cells, - lockjaw (trismus) of the DPT vaccine appearance of a drumstick
resulting in sustained muscle - risus sardonicus
contraction - respiratory muscle paralysis
Antitoxin: human tetanus immnue Requires anaerobic conditions Drumstick, tennis
globulin (pre-formed anti-tetanus racquet, lollipop
antibodies) appearance
Clean the wound
Penicillin (DOC)
Supportive therapy: may require
ventilator assistance

vaccine DPT:
diphtheria
pertussis
tetanus
Clostridium Ubiquitous: Endospores Anaerobic NON-motile Alpha toxin: lecithinase (splits lecithin Cellulitis/wound infection Radical surgery (may require Gram stain: spore-forming rods Double hemolysis on
perfringens into phosphocoline and diglyceride) amputation) blood agar

Soil 11 other tissue destructive enzymes Clostridial myonecrosis: fatal if untreated Penicillin Culture: requires anaerobic conditions Looks motile, but not
motile on blood agar ->
Growth on egg yolk agar: non-motile but with due to avidity for
rapidly spreading growth on culture media lecithin in the blood
membranes
G tract of humans and Watery diarrhea: associated with food-borne Hyperbaric oxygen
mammals ingestion
Clostridium difficile Intestinal tract Fecal-oral: ingestion Anaerobic Motile flagella (so H-antigen-positive) Toxin A: diarrhea Pseudomembranous enterocolitis: Metronidazole Immunoassay for C. difficile toxin PO vancomycin because
Endospores found in of endospores Toxin B: cytotoxic to colonic epithelial -antibiotic-associated diarrhea Oral vancomycin Examine colon with colonoscopy it has poor intestinal
hospitals and nursing cells -Clindamycin, 2nd and 3rd generation absorption, hence,
homes cephalosporins, ampicillin “coats” the lesions with
-non-bloody diarrhea associated with Terminate use of the responsilbe antibiotic
pseudomembranes (yellow-white plaques) on antibiotic
the colonic mucosa

Page 19 of 34
Corynebacterium Throat Respiratory droplets Facultative anaerobe Pseudomembrane forms in the pharynx, Exotoxin (coded by a bacteriophage) Diphtheria Antitoxins Gram stain: gram-positive pleomorphic rods Obtains exotoxin from a
diphtheriae from carrier Catalase-positve which serves as a base from where it Subunit A: blocks protein synthesis by - mild sore throat with fever initially Penicillin or Erythromycin (sometimes describe as looking like Chinese temperate
secretes its toxin inactivating EF2 - pseudomembrane forms on pharynx letters) bacteriophage by
Subunit B: provides entry into cardiac - myocarditis causing A-V condution block vaccine DPT: lysogenic conversion
and neural tissue and dysrhythmia diphtheria: formalin inactivated Culture:
- neural involvement: perpheral nerve exotoxin, as antibodies to the B-subunit Potassium tellurite: dark black colonies Schick test: injection of
Exotoxin is like a human antibiotic, as palsies, GBS, palatal paralysis, and are protective diphtheria exotoxin into
it inhibits eukaryotic protein neuropathies pertussis Loeffler’s medium: after 12 hours of growth, the skin, to determine
synthesis, just as tetracycline inhibits tetanus stain with methylene blue. Reddish (Babes- whether a person is
protein synthesis in bacteria Ernst) granules can be seen susceptible to infection
by diphtheriae

Modified Elek test: for

detection of toxigenicity

Listeria Ubiquitous Ingestion of Facultative anaerobe Motile (via flagella): so has H-antigen -> The Only gram positive bacteria that EARLYONSET NEONATAL LISTERIOSIS Ampicillin +/p Gentamicin Gram stain:gram-positive rods Facultative intracellular
monocytogenes contaminated raw tumbling motility produces LPS (Granulomatosis Infantiseptica) TMP-SMX: if allergic to penicillin parasite
milk or cheese from -transplacental transmission Narrow zone of beta-hemlysis
infected cows -characterized by late miscarriage; birth
complicated by sepsis, multiorgan abscess,
and disseminated granulomas

LATE-ONSET NEONATAL LISTERIOSIS

-transmission during childbirth
-manfests as meningitis or
meningoencephalitis

Plants (vegetables) Vaginally (during Catalase-positive Hemolysin: (like streptolysin O) Meningitis in immune-suppressed patients Culture: can grow at temperature as low as 0 C Cell-mediated immunity
birth) and the elderly (>50) so use cold enrichment technique to isolate is protective
Listeriolysin O: allows escape from the from mixed flora
phagolysosomes of macrophages; major Septicemia in pregnant women
virulence factor

Internalin: Interacts with E-cadherin on

the surface of cells

Actin rockets: propel the bacteria

through the membrane of one human
cell to another

Tranplacental Beta-hemolytic on blood NOT CEPHALOSPORINS:

infection of fetus agar NONE OF THE CEPHALOSPORINS ARE
from bacteremic ACTIVE AGAINST MRSA, LISTERIA , AND
mother ENTEROCOCCI

Page 20 of 34
GRAM NEGATIVE SUMMARY
GRAM NEGATIVE COCCI

GRAM NEGATIVE BACILLI

Page 21 of 34

MICROORGANISM RESERVOIR TRANSMISSION METABOLISM VIRULENCE FACTORS
Neisseria meningitidis Respiratory tract Respiratory droplets Ferments both Antiphagocytic polysaccharide capsule
maltose and
glucose
Oxidase-positive Endotoxin (LOS):
colonies on An LOS can be shed in large amounts by a process called
chocolate agar blebbing, causing fever, shock, and other pathophysiology.
This is considered the principal factor that produces the
high endotoxin levels in meningococcal sepsis.
Meningococcal LOS interacts with human cells, producing
proinflammatory cytokines and chemokines, including
interleukin 1 (IL-1), IL-6, and tumor necrosis factor (TNF). LOS
is one of the important structures that mediate
meningococcal attachment to and invasion into epithelial
cells.
LOS triggers the innate immune system by activating the Toll-
like receptor 4MD2 cell surface receptor complex and
myeloid in non-myeloid human sounds. The degree of
activation of complement then coagulation system is directly
related to the bacterial load.
IgA protease
At least 13 serogroups have been described: A, B, C, D, E, H, I,
K, L, W-135, X, Y, and Z. Serogroups B and C have caused
most cases of meningococcal meningitis in the United States
since the end of World War II; before that, group A was more
prevalent. More than 99% of meningococcal infections are
caused by serogroups A, B, C, 29E, or W-135.
GRAM NEGATIVE COCCI
TOXINS CLINICAL SYNDROMES
No exotoxins MENINGITIS: most common cause among aged 2-18 yrs
MENINGOCOCCEMIA: dissemination of meningococci into the bloodstream;
mmultiorgan disease, consumptive coagulopathy, petechial or purpuric rash
(purpura fulminans)
Meningococcemia is defined as dissemination of meningococci (Neisseria
meningitidis) into the bloodstream (see the image below). Patients with acute
meningococcemia may present with (1) meningitis (2) meningitis with
meningococcemia, or (3) meningococcemia without clinically apparent
meningitis.
WATERHOUSE-FRIDERICHSEN SYNDROME: most severe form of
meningococcemia; high fever, shock, widespread purpura, disseminated
intravascular coagulation, thrombocytopenia, and adrenal insufficiency ->
bilateral hemorrhagic destruction of the adrenal glands
TREATMENT AND PREVENTION
Penicillin
Ceftriaxone (or cefotaxime) - The drug of choice for
the treatment of meningococcal meningitis and
septicemia
Vaccine contains capsular polysaccharide of strains A,
C, Y, and W-135 coupled to a carrier protein
(diphtheria toxoid) to enhance immunogenicity
Currently, vaccinations against meningococcus A, C,
W, and Y are available. The first meningococcal
vaccine for serogroup B was approved in October
2014.
Rifampin chemoprophylaxis to close contacts
DIAGNOSIS
Culture on chocolate agar
Gram-negative, aerobic, encapsulated
diplococcus that grows best on enriched
media, such as Mueller-Hinton or chocolate
agar, at 37°C and in an atmosphere of 5-10%
carbon dioxide
NOTES
Complement deficiencies in the late-acting
complement components (C5–C9) predispose to
illness
Most patients with meningococcal meningitis, caused
by the gram-negative diplococcus Neisseria
meningitidis, recover completely if appropriate
antibiotic therapy is instituted promptly. Nonetheless,
the disease still is associated with a high mortality
rate and persistent neurologic defects, particularly
among infants and young children.

Neisseria gonorhoeae
Moraxella (Branhamella catarrhalis) Part of the normal flora
Humans only (no immunity to repeated Sexually Facultative- Pili: Endotoxin: lipooligosaccharide (LOS) Asymptomatic (but still infectious) Antibiotic of choice: third generation cephalosporin Gram-stain of urethral plus reveals the tiny Kidney bean shaped with concave sides facing each
infections) Birth anaerobe Adherence to epithelial cells such as ceftriaxone (Add doxycycline to cover gram-negative doughnut-shaped diplococci other forming the appearance of doughnut
Antigenic variation incubating Chlamydia trachomatis and syphilis) within white blood cells
Antiphagocytic, binds bacteria tightly to host cell protecting
it from phagocytosis
Grows best in IgA protease No exotoxins Men: urethritis The Centers for Disease Control (CDC) recommends Culture: Specimen on chocolate agar Gram-negative diplococci
high CO2 Women: cervical gonorrhea, which can progress to pelvic inflammatory disease that all patients with gonorrheal infection also be
environment (PID) complications of PID treated for presumed co-infection with Chlamydia
trachomatis (2015)
Lower abdominal pain: Most consistent symptom of PID
Ferments only Outer membrane proteins: Protein I: porin protein II (opacity Both men and women: Second line, but not effective against syphilis: Selective media: prevents growth of other Reinfection because there is no immunity to previous
glucose (not protein): presence associated with dark, opaque colonies Gonococcal bacteremia Flouroquinolones bacteria infections
maltose)- easy to Septic arthritis: gonococcal arthritis is the most common cause of septic arthritis Spectinomycin
remember, since in sexually active individuals
there is only a
“g” (no “m”) in
gonorrhoeae
For adherence: Neonates: Ophthalmia neonatorum conjunctivitis in newborns -> N. gonorrhoeae For opthalmia neonatorum: Thayer Martin with VCN Fitz-Hugh-Curtis syndrome
Has unique protein that can extract iron from transferrrin, is acquired during passage through an infected birth canal; conjunctivitis usually Erythromycin eye drops should be given immediately Cell wall contains cytochrome oxidase which Septic arthritis in sexually active patients
lactoferrin and hemoglobin erupts within the first 5 days following birth, for prophylaxis against both N. oxidizes dye tetramethylphenylene diamine Well-characterized plasmids commonly carry
gonorrhoeae and Chlamydia trachomatis from colorless to deep pink. Used to ID antibiotic-resistance genes, most notably
conjunctivitis colonies penicillinase. Plasmid and nonplasmid genes are
Infants with ophthalmia neonatorum require PCR in bacterial DNA in clinical specimens transmitted freely between different subtypes. The
systemic treatment with ceftriaxone. ensuing exchange of surface protein genes results in
Erythromycin syrup should also be provided to cover high host susceptibility to reinfection. The exchange
for possible concurrent chlamydial disease (this is of antibiotic resistance genes has led to extremely
important, as failure to treat neonatal Chlamydia high levels of resistance to beta-lactam antibiotics.
conjunctivitis can lead to chlamydial pneumonia)
Otitis media in children Azithromycin or clarithromycin Resistant to penicilins
Can cause other respiratory tract infections, such as sinusitis, bronchitis and Amoxicillin with clavulanate
pneumonia
COPD exacerbation Oral second or third generation cephalosporin
TMP-SMX

Page 22 of 34
 GRAM NEGATIVE BACILLI
TOXINS CLINICAL SYNDROMES TREATMENT AND PREVENTION DIAGNOSIS NOTES
Hib meningitis: Most serious manifestation of Hib infection; Second or third generation cephalosporins (since H. influenzae Gram stain NTHi strains form biofilm in vitro and ex vivo and have been
antecedent upper respiratory tract infections are common; Hib can acquire ampicillin resistance by plasmids) implicated in chronic infection such as otitis media, sinusitis, and
meningitis manifestations indistinguishable from other bacterial bronchitis. NTHi biofilm formation was found in patients with CF
meningitis causes on the apical surface of airway epithelia with decreased
antibiotic susceptibility.
Cellulitis: Most commonly involves the buccal and periorbital Hi b vaccine: H. influenza e polysaccharide capsule of type b Culture specimen on blood agar that has been heated to 80 oCApproximately 6% of individuals with Hib meningitis experience
regions; usually associated with fever strain (Hib) is conjugated to diphtheria toxoid for 15 minutes (now called chocolate agar). This high permanent sensorineural hearing loss.
Passive Immunization: mother is immunized during 8th month temperature lyses the red blood cells releasing both hematin
Epiglottitis: Fever, sore throat, dysphagia, drooling, and difficulty of pregnancy to increase passive antibody transfer in breast (called X factor) and NAD+ (called V factor). Like the Neisseria,
breathing milk H. influenzae grows best when the chocolate agar is placed in a
o
high CO2 environment at 37 C
Hib pneumonia: Clinically indistinguishable from other bacterial The Centers for Disease Control and Prevention (CDC) Advisory Fluorescently labeled antibodies (ELISA and latex particle
pneumonias—except for its insidious onset and a history of Committee on Immunization has released updated 2014 agglunation)
fever, cough, and purulent sputum production vaccination recommendations for adults aged 19 years and
older. Key changes in the recommendations include the Positive Quellung test: due to its capsule, similar to
following: Streptococcus pneumoniae
Hib pericarditis: Fever, respiratory distress, and tachycardia Hib vaccine: Vaccination is recommended for (1) certain adults
Septic arthritis: Joint pain, swelling, and decreased mobility at increased risk for Hib who have not previously received the
Occult bacteremia: Fever, anorexia, and lethargy vaccine—except for individuals with human immunodeficiency
NTHi infections: Commonly causes various mucosal infections, (HIV) infection, who have a low risk for Hib infection; and (2)
including otitis media and conjunctivitis adults who have undergone a successful hematopoietic stem
cell transplant (HSCT). (Administer a 3-dose series of Hib vaccine
Chancroid: painful genital ulcer, often associated with unilateral Azithromycin or erythromycin Gram stain and culture of ulcer exudate and pus released from A sexually transmitted disease
swollen lymph nodes that can rupture, releasing pus Ceftriaxone(IM) swollen lymph node Requires X factor (hematin) only.
Ciprofloxacin Chancroid is most commonly observed in nonwhite men who are
uncircumcised. Women represent only 10% of known cases
because they are more likely to be asymptomatic carriers.

Bacterial vaginosis: foul smelling vaginal discharge (with fishy Metronidazole Clue cells: vaginal epithelial cells Does not require X factor or V factor for growth
odor), vaginal pruritus, and often dysuria that contain tiny pleomorphic
Gray, thin, and homogeneous vaginal discharge, which adheres Therapy with metronidazole or clindamycin may alter the gram-negative bacilli Demonstration of clue cells on a saline smear (the most specific
to the vaginal mucosa (milk-splattered) vaginal flora and predispose the patient to development of within the cytoplasm diagnostic criterion)
vaginal candidiasis

Page 23 of 34
Pertussis toxins: activates G proteins that increases cAMP
resulting in:
Increased sensitivity to histamine
Increased insulin release
Increased number of lymphocytes in blood
2. Extracytoplasmic adenylate cyclase: ”weakens” neutrophils
lymphocytes and monocytes
3. Filamentous hemagglutinin: allows binding to ciliated
epithelial cells
4. Tracheal cytotoxin: kills ciliated epithelial cells
Cytotoxins: kill hamster ovary cells
Whooping Cough
1. Catarrhal phase: patient is highly contagious (1-2 weeks)
2. Paroxysmal phase (2-10 weeks)
Whoop (burst of non-productive coughs)
Increased number of lymphocytes in blood smear
Antibiotics ineffective during this stage
3. Convalescent stage
Pontiac fever: headache, fever, muscle aches and fatigue, self-
timing: recovery in a week is common
Legionnaires’ Disease: pneumonia: fever and non-productive
cough
Erythromycin (most effective when given in catarrhal stage) Bordet-Gengou agar: potatoes, blood and glycerol agar, with The diagnosis of pertussis is made by isolation of B pertussis in
Vaccine: DaPT penicillin added culture. A polymerase chain reaction (PCR) test can also be
Pertussis vaccination during pregnancy is safe performed.
Treat household contacts with erythromycin. The culture specimen should be obtained during the first 2
weeks of cough by using deep nasopharyngeal aspiration
For PCR testing, nasopharyngeal specimens should be taken at 0-
3 weeks following cough onset
Rapid serologic tests: (ELISA) The CDC recommends a combination of culture and PCR assay if
Collect specimen from posterior pharynx on a calcium alginate a patient has a cough lasting longer than 3 weeks
swab since B. pertussis will not grow on cotton Early serial monitoring of white blood cell (WBC) counts is
Direct fluorescein-labeled antibodies applied to nasopharyngeal warranted
specimens for rapid diagnosis
PCR detection of bacterial DNA in respiratory seceretions
Azithromycin Culture on buffered charcoal yeasts extract agar (L-cysteine is a Facultative intracellular parasite: inside alveolar macrophages
critical ingredient)
Levofloxacin Serology (IFA and ELISA) Persons with compromised immune systems are especially
susceptible
Doxycycline Urinary antigen can be detected by radioimmunoassay with Atypical pneumonia + diarrhea + hyponatremia
high sensitivity and specify and will remain positive for months
after infection. Urine antigen test only detects L. pneumophilia
serogroup 1, but this accounts for 90% of cases.
Legionnaires disease (LD) was recognized in 1976 after an
outbreak of pneumonia at an American Legion convention in
Philadelphia.
Page 24 of 34
 GRAM NEGATIVE BACILLI GI AND GU
MICROORGANISM RESERVOIR TRANSMISSION METABOLISM VIRULENCE FACTORS TOXINS CLINICAL SYNDROMES TREATMENT AND PREVENTION DIAGNOSIS NOTES
Escherichia coli Humans: Fecal-oral Indole-positive Fimbriae (pili): attachment/ colonization factor Enterotoxins Neonatal meningitis Penicillins Gram-negative

GI and urinary tract Ascending infection to the urethra Beta-hemolytic Siderophore: obtains iron fro human transferrin 1. LT (heat-labile): increases cAMP (same as cholera UTI Aminoglycosides Culture (specimen may be urine, sputum, CSF or
or lactoferrin toxin) blood); can grow at 45.5 C
Colonization of catheters in Ferments lactose Adhesins 2. ST (heat-stable) Increases cGMP Nosocomial sepsis 2nd and 3rd gen cephalosporins Pathogenic strains may be isolated from stool
hospitalized patients
Aspiration Capsule (K-antigen): causes pneumonia 3. Shiga-like toxin (verotoxin): inhibits protein Nosocomial pneumonia Fluoroquinolones E. coli ferments lactose, so colonies appear purple
synthesis by inactivating the 60S ribosomal subunit to black on EMB agar and pink to purple on
of eukaryotic cells (E. coli O157:H7, STEC, EHEC) MacConkey agar
Flagella (H-antigen): attachment/colonization Endotoxins: Diarrhea
factor; causes cystitis and pyelonephritis - Lipid A [porion of LPS
-causes septic shock
ETEC: releases LT and ST toxins, traveler’s
diarrhea
EHEC/STEC (Shiga-like toxic producing E. coli):
no fever, no pus in stool; secretes shiga-like
toxin (verotoxin): causes hemorrhagic colitis and
hemolytic uremic syndrome (E. coli strain
O157:H7)
EIEC: with pus in the stool and fever
Proteus mirabilis Urease: hydrolyzes ureas into NH3 and CO2 Swarming motility No toxins UTI: high urine pH due to urease production -> Ampicilin Culture: Colonies swarm over entire culture plate Weil-Felix reaction: a test that uses antibodies
struvite calculi formation; staghorn calculi (tx against certain strains of Proteus to diagnose
with surgery) rickettsial disease (as certain rickettsiae share
similar antigens)
Indole-negative Sepsis TMP-SMX Alkaline urine (high pH) See also: Rickettsia species
Does not ferment lactose
Shigella dysenteriae Humans Fecal-oral No H2S production Invades submucosa of intestinal trac, but not Shiga toxin MOA: inactivates the 60S ribosome, Bloody diarrhea with mucus and pus (similar to Floruoquinolones Stool culture: because Shigella is never a part of IgA is best for immunity
the lamina propria -> ulcers -> bleeding inhibiting protein synthesis and killing intestinal enteroinvasive E. coli ) the normal intestinal flora
epithelial cells
Does not ferment lactose NON-motile: No H-antigen (since they have no Shiga toxin, therefore, is a protein synthesis inhibitor Azithromycin Shigella is more toxic and invasive than
flagella) of EUKARYOTES Salmonella
TMP-SMX
Salmonella typhi S. typhi is found only in S. typhi is transmitted via fecal-oral Produces H2S Motile (H-antigen) Enteric fever Ciprofloxacin Culture: blood stool or urine may contain S. typhi A. Facultative intracellular parasite:
humans route
Non-typhoidal groups of Does not ferment lactose Capsule (called the Vi antigen): protects from Typhoid fever Ceftriaxone 1. Lives within macrophages in lymph nodes
Salmonella intracellular killing
Zoonotic: Siderophores Parathypoid - fever (similar to typhoid fever, but TMP-SMX Never part of the intestinal flora 2. Can live in gall bladder for years (carriers
1. Pet turtles caused by non-typhoidal Salmonella ) secrete S. typhi in stool)
2. Chickens
3. Uncooked eggs
Chronic carrier state in the gall bladder Azithromycin B. Persons who are asplenic or have non-
functioning spleens (sickle cell anemia) are at
increased risk of infection by this organism
Gastroentritis *Salmonella gastroenteritis: there is little Gastric acid is protetive against salmonellosis,
benefit from antibiotic treatment; it may hence, gastrectomy/antacids increase the risk
prolong carrier state
Sepsis In the Philippines, first line drug for
typhoid: Amoxicillin, TMP-SMX,
Chloramphenicol
Osteomyelitis: Especially in sickle cell patients
(Salmonella choleraesuis )

Page 25 of 34
Yersinia enterocolitica Zoonotic: can be found in Ingestion of contaminated food or Non-lactose fermenter V and W antigens Enterotoxin similar to the heat stable toxin of E. coli
Pseudoappendicitis (RLQ pain) -> mesenteric Antibiotics do not alter the course of the Stool or blood cultures mat be positive Survives refrigeration
pigs water increases cGMP levels lymphadenitis diarrhea. However, patients with positive
Unpasteurized milk Virulence factors are temperature sensitive Motile Acute enterocolitis, with fever, diarrhea and blood culture should be treated with Examination of the terminal ilium with Closely related to Yersinia pestis
o abdominal pain colonoscopy will reveal mucosal ulceration
expressed at 37 C antibiotics
Diarrhea - The most common clinical Mesenteric lymphadenitis in children ->
manifestation of this infection; diarrhea may be pseudoappendicitis
bloody in severe cases
Low-grade fever
Abdominal pain - May localize to the right lower
quadrant
Vomiting - Present in approximately 15-40% of cases
Vibrio cholerae Humans only Fecal-oral transmiision Oxidase-positive Motile (H-antigen) -> Shooting star motility Choleragen (enterotoxin): like LT of E. coli, increases Cholera: severe diarrhea with rice water stools. Fluid and electrolyte replacement Dark field microscopy of stool reveals motile Death by dehydration: children affected in
levels of cAMP, causing secretion of electrolytes No pus in stools organism that are immobilized with antiserum endemic areas 1991: Latin America epidemic
Morphology: Short, comma shaped, Ferments sugar (except lactose) Digest mucous layer so V. cholera can attach to from the intestinal epithelium. This results in -Washer woman's hands sign: wrinkled skin due Doxycycline Grows as flat yellow colonies on selective media: 1993: Epidemic in Bangladesh and India
with a single polar flagellum cells secretion of fluid into the intestinal tract. -> to loss of skin turgor due to dehydration thiosulfate-citrate-bile-salts-sucrose (TCBS) agar
secretory diarrhea -Complications: cardiac and renal failure,
3. Fimbrae: helps with attachment to cells hypokalemia Flouroquinolones
4. Non-invasive

Vibrio parahaemolyticus Fish, seafood Consumption of raw fish Halophilic (likes salt) Motile (H-antigen) Hemolytic cytotoxins Cause of 25% of food poisoning in Japan Doxycycline TCBS Diarrhea after ingestion of raw seafood; also
Morphology: short, comma shaped, Capsule (diarrhea for 3 days) -> because Japanese love Fluoroquinolone consider Norwalk virus; important to distinguish
with a single polar flagellum seafood J viral from bacterial
Unclear if antibiotics change clinical course
of the disease
Campylobacter jejuni Zoonotic: wild and Uncooked meat (especially poultry) Microaerophilic Motile (H-antigen) Enterotoxin: similar to cholera toxin and the LT of E. Gastroentritis Fluoroquinolone Microscopic exam of stool reveals motile, curved One of the three most common causes of
domestic animal and coli -most common cause of bacterial gram-negative rods diarrhea in the world:
poultry; undercooked gastroenteritis -Campylobacter jejuni
chicken ingestion of undercooked chicken -ETEC
-watery, foul-smelling diarrhea followed by -Rotavirus
bloody stools accompanied by fever and severe
abdominal pain
-may mimic ulcerative colitis

Unpasteurized milk Oxidase Positive Invasive Cytotoxins: destroy mucosal cells Associated with Guillain-Barre syndrome Erythromycin : for severe disease Selective media with antibiotic at 42oC
-antigenic cross-reactivity between
oligosaccharides in bacterial capsule and
glycosphingolipids on surface of neural tissue

Fecal-oral Optimum temperature is 42oC – to inhibit Reactive Arthritis (Reiter's Syndrome) Skirrow’s agar
the growth of other fecal species -Urethritis
-Uveitis
-Arthritis
Morphology: curved gram-negative Campy’s agar
rods with a single polar flagellum
Helicobacter pylori Habitat is the human Transmission by ingestion Microaerophilic Urease: produces ammonia; makes the No toxin Peptic ulcer disease Bismuth, ampicillin, metronidazole and Morphology: curved gram-negative rods with a Peptic ulcer disease
stomach Oxidase postive environment alkaline--> helpas H. pylori survive -most common cause of duodenal ulcers and tetracycline tuft of polar flagella
Cayalase-positive in acidic mucosa chronic gastritis
Urease positive -second leading cause of gastric ulcer EGD with biopsy showing H. pylori
Disease associations: Clarithromycin and omeprazole Gastric carcinoma
Urease breath test, h.pylori stool antigen:
-Gastric carcinoma
document cure
-MALT Lymphoma
Both regimens reduce duodenal ulcer MALT lymphoma
relapse

Page 26 of 34
Bacteriodes fragilis Colon Part of the normal flora of the
intestine
Most common colonic flora
Spreads to blood or peritoneum during
bowel trauma, perforation or surgery
Anaerobic (O2 inhibits its growth) Capsular polysaccharide: antiphagocytic and
anticomplement
Gram-negative rod
Succinate: inhibits PMN phagocytosis
Attachment factors: pili
Does not contain lipid A Abscesses in the gastrointestinal tract, pelvis Metronidazole – DOC for anaerobic Gram-stain Infection occurs when the organism enters the
and lungs infections peritoneal cavity
Brain abscesses (chloramphenicol is ideal Clindamycin Anaerobic culture Hence, if the anatomy of the GI tract is altered
because it is lipophilic) (surgery, trauma, perforation)

Non-spore former Chloramphenicol

Chloramphenicol is static, but cidal to the
following:
N eisseria meningitidis
B acteroides fragilis
S treptococcus pneumonia
H aemophilus influenza
NBSH – No Boyfriend Since Highschool
Pseudomonas Soil, Water, Plants, Medical devices 1. Obligate aerobe (does not ferment) Motile (polar flagella) Exotoxin A (similar to diphtheria toxin): inhibits Burn infections MDR, XDR strains Culture: greenish, metallic colonies on blood agar, Common etiology for infection in neutropenic
aeruginosa Animals, Intestinal Flora, protein synthesis by blocking EF2 with fruity odor (grape-like odor) patients.
Skin Hands of healthcare workers 2.Non-lactose fermenter Hemolysins Endocarditis in IV drug users SEE ANTIPSEUDOMONAL LIST GIVEN BY Cetrimide medium Produces pigments when cultured:
DR. CALDERON
3. Oxidase-positive Collagenase Necrotizing pneumonia – fleur de lys Antimicrobials are the mainstay of a. pyocyanin (blue pigment)
morphology on histopath therapy.
Elastase Sepsis (in the immunocompromised); ecthyma Meningitis: Ceftazidime is the antibiotic of b. pyoverdin (green pigment)
gangrenosum choice
Fibrinolysin Malignant otitis externa Eye infections: Treat small superficial Norocomial organisms similar to Pseudomonas:
ulcers with topical therapy (eg, ophthalmic Acinetobacter baumannii
aminoglycoside solution rather than an Elizabethkingia meningosepticum
ointment) every 30-60 minutes; when Burkholderia cepacia
perforation is imminent, subconjunctival
(or subtenon) administration is preferred;
management of endophthalmitis requires
aggressive antibiotic therapy (parenteral,
topical, subconjunctival [or subtenon],
and, often, intraocular)

Phopholipase C UTI (catheter-related)

DNAse Diabetic osteomyelitis
Antiphagocytic capsule Typhlitis, Shanghai fever
It is the most common pathogen isolated from
patients who have been hospitalized longer
than 1 week, and it is a frequent cause of
nosocomial infections.

Page 27 of 34
 GRAM NEGATIVE BACILLI ZOONOTIC
MICROORGANISM RESERVOIR TRANSMISSION METABOLISM VIRULENCE FACTORS TOXINS CLINICAL SYNDROMES TREATMENT AND PREVENTION DIAGNOSIS NOTES

Yersinia pestis Wild rodents Vector: Flea bite Facultative anaerobe Fraction 1 (F1): this capsular antigen is Pesticins: kills other Bubonic plague: rRegional Streptomycin or gentamicin Gram strain will reveal gram- Facultative intracellular parasite
antiphagocytic bacteria (including E. coli) lymph nodes ( usually groin) negative rods with bipolar
swell, and become red, hot and staining: the ends of these rod
tender (called a bubo); high shaped bacteria take up stain
fever; conjunctivitis more than the center (closed
safety pin appearance)

City rats Contact with infected animal Virulence factors are temperature V and W proteins Intracellular murine toxin: Septicemic plague: bacteria Doxycycline Blood culture Yersinia can accept plasmids in E. coli , and shares many
tissue sensitive: only expressed at 37oC lethal to mice survive in macrophages, and antigens with enteric bacteria
(temperature inside spread to blood and organs.
macrophages) Death occurs in 75% in
untreated
Squirrels and prairie dogs in the Inhaled aerosolized Virulence is plasmid-mediated Non-motile Pneumonic plague: during Killed vaccine is effective only Culture bubo aspirate Subcutaneuos hemorrhage result in a blackish skin
U.S organisms: human to human epidemics, pneumonia occurs, for a few months (attenuated discoloration, giving the name “Black Death”
transmission occurs during as bacteria are spread from vaccine is more effective but
epidemics person to person by aerosolized also has more side effects)
respiratory secretion: 100% in
untreated

Francisella tularensis Rabbits and squirrels
Ticks can serve as a reservoir
Requires calcium at 37oC. If insufficient Serology Yersinia is named in honor of Alexander Yersin, who successfully
calcium, Y. pestis alters its metabolism and isolated the bacteria in 1894 during the pandemic that began in
protein production. This trait assists with its China in the 1860s.
intracellular state
The virulence of this bacterium results from Rapid diagnositic test: antibody Plague was first described in the Old Testament and has
the 32 Y pestis chromosomal genes and two against F1 (capsular antigen) persisted into the modern era. Plague has caused large-scale
Y pestis –specific plasmids, constituting the epidemics, thereby changing the course of history in many
only new genetic material acquired since its nations. The first pandemic was believed to have started in
evolution from its predecessor. These Africa and killed 100 million people over a span of 60 years. In
acquired genetic changes have allowed the the Middle Ages, plague killed approximately one fourth of
pathogen to colonize fleas and to use them Europe's population. The pandemic that began in China in the
as vectors for transmission. 1860s spread to Hong Kong in the 1890s and was subsequently
Bite of tick, deerfly or Obligate aerobe Capsule antiphagocytic Tularemia Gentamicin or streptomycin Culture (but very dangerous The diagnosis of tularemia is usually based on serology results.
infected animals (DOC) due to its high infectivity, Tests vary from antibody detection (using latex agglutination or
requires addition of cysteineto enzyme-linked immunosorbent assay [ELISA] testing) to the
blood agar media examination of a range of polymerase chain reaction (PCR) assay
products.
Direct contact with infected Requires cysteine Non-motile Ulceroglandular: at the site of Doxycycline Skin test An agglutination titer greater than 1:160 is considered
animal tissue (usually rabbit) tick bite or direct contact with presumptively positive, and treatment may be started if this
contaminated rabbit, an ulcer result is obtained. A second titer, demonstrating a 4-fold
devcelops, with swelling of focal increase after 2 weeks, confirms the diagnosis.
lymph nodes

Inhaled aerosolized The ability of F tularensis to impair phagocyte Pneumonic: inhalation, or Attenuated vaccine: onlfor high- Measure rise in IgG antibody
organisms function and survive in infected cells is through the blood risk individuals titer (IgM is not very good)
central to its virulence. This intracellular life
cycle has been shown to be related to the
tightly regulated expression of a series of
genes.

Ingestion of contaminated Oculoglandular: direct

meat or water inoculation into eyes

Easily transmitted to lab Typhoidal: ingestion results in

personnel gastrointestinal symptoms
(abdominal pain) and fever
Brucella Direct contact with
contaminated livestock or
aborted placentas
Brucella meltitensis Goats (meeee!) Ingestion of infected milk
(highest pathogenicity) products
Obligate aerobe
Brucellae are aerobic gram-
negative coccobacilli that possess
a unique ability to invade both
phagocytic and nonphagocytic
cells and to survive in the
intracellular environment by
finding ways to avoid the
immune system.
Capsule Brucellosis: Pasteurization of milk Culture blood, bone marrow Brucella ovis – nonpathogenic to man
(best yield), liver, or lymph
nodes
Non-motile Undulating fever (fever peaks in 2Treat with combination of Serologic tests Although Brucella infection is primarily controlled through cell-
the evening, and returns to doxyxycline and one other drug mediated immunity rather than antibody activity, some
normal by morning) (gentamicin, streptomycin, or immunity to reinfection is provided by serum immunoglobulin
rifampin). (Ig). Initially, IgM levels rise, followed by IgG titers. IgM may
remain in the serum in low levels for several months, whereas
IgG eventually declines. Persistently elevated IgG titers or
second rises in IgG usually indicate chronic or relapsed infection.
IgA antibodies are elaborated late and also may persist for very
long intervals.

Brucella abortus Cattle Aerozolization in laboratory Tropism for erythritol, a sugar found in Weakness All cattle are immunized with a Skin test: Indicates exposure
or possibly due to animal placentas living attenuated strain of only
bioterrorism Brucella abortus
Brucella suis Pigs Erythritol is a four-carbon sugar Loss of appetite
preferentially utilized by Brucella spp. The
presence of erythritol in the placentas of
goats, cows, and pigs has been used to
explain the localization of Brucella to these
sites and the subsequent accumulation of
large amounts of bacteria, eventually leading
to abortion. [Microbes Infect. 2013 Jun;15(6-
7):440-9]

Brucella canis: Dogs Includes abortions in animals

Pasteurella multocida Part of the normal flora of Bite from dog or cat Facultative anaerobe Capsule Wound infections (following Penicillin G Culture specimen on standard Not a faculatative intracellular organism
domestic and wild animals Non-motile dog or cat bites): may progress Doxycycline laboratory media Human bite infection- Eikenella corrodens
to infection of nearby bones Third generation cephalosporin
and joints
 MISC
MICROORGANISM RESERVOIR TRANSMISSION METABOLISM VIRULENCE FACTORS CLINICAL SYNDROMES TREATMENT DIAGNOSIS NOTES
Chlamydia trachomatis Humans Direct contact LIFE CYCLE Resistant to lysozyme (since their cell wall lacks Serotypes A, B, & C Trachoma: causes scarring of the Genital and eye infections: Can NOT be grown artificial media. Can Gram-negative, but lacks peptidoglycan layer and muramic acid
muramic acid) inside of the eyelid, resulting in redirection of the Doxycycline (use only for adults classically be grown in chick yolk sacs: More
eyelashes onto the corneal surface -> corneal scarring Erythromycin (especially for infants commonly chlamydia is cultured in certain cell
and blindness and pregnant women) lines (McCoy cells for example)
Azithromycin
A-C: trachoma Primarily affects the eyes, genitals, lungs Elementary body (EB): dense spherule Prevents phagosome – lysosome fusion Serotypes D through K Inclusion conjunctivitis For inclusion conjunctivitis (ophthalmia Trachoma is seen in underdeveloped countries, and transmission occurs
D-K: genital, neonatal that infects cells (opthalmia neonatorum) neonatorum): Scraping from the surface of the due to poor hygiene
L1-3: LGV Initial (reticulate) body: After EB enters conjunctiva will show intracytoplasmic inclusion
cell, it transforms into an initial body; bodies within conjunctival epithelial cells
larger, osmotically fragile; can produce (Halberstaedter-Prowazek inclusions). The
via binary fission; requires ATP from the inclusion bodies contain glycogen and thus, stain
host of iodine or Giemsa
The initial body transform back into EB,
which leaves the cell to infect the other
cells
Poor hygiene for trachoma Non-motile Infant pneumonia Gram-stain of genital secretions will not show Presence of chlamydial inclusions or elementary bodies on Giemsa-
gram-negative organisms stained smears of the conjunctivae or nasopharynx confirms the
diagnosis
No pili Urethritis, cervicitis and pelvic inflammatory disease Urethritis: most commonly diagnosed by Interesting risk factors:
(PID) in women polymerase chain reaction of urethral swab or Certain cytokine polymorphisms – These have been associated with
urine sample severe disease and risk of tubal factor infertility
Certain variants in Toll-like receptor 1 and 4 genes – These predispose to
infection
Having been a foster child (males only)
No exotoxins Nongonococcal urethritis, epididymitis and prostatitis in Immunofluorescent slide test place infected
men genital or ocular secretions on a slide and stain
with fluorescein-conjugated anti-chlamydial
antibody
Complications of chlamydial genital tract infection: Serologic: Examine blood for elevated titers of
Sterility, ectopic pregnancy and chronic pain may occur antichlamydial antibodies with compliment
after pelvic inflammatory disease fixation and immunofluorescence tests.
Reiter’s syndrome: triad of conjunctivitis, urethritis, and Lymphogranuloma venereum: Serologic test
arthritis
Fitz-Hugh-Curtis Syndrome: perihepatitis Frei test, which is rarely used, is similar to the
PPD skin test for tuberculosis
Serotypes L1, L2 & L3 Lymphogranuloma venereum
(LGV)
Chlamydophila psittaci Birds, poultry Bird feces dry out, fecal particles are inhaled, Life cycle is similar to Chlamydia Psittacosis: a viral-like atypical pneumonia, with fever Doxycycline Serologic: Examine blood for elevated titers of History of occupational exposure to birds
infecting the lungs trachomatis and dry, non-productive cough (similar to Mycoplasma antibodies compliment fixation and
pneumonia) immunofluorescence tests
An occupational disease of zoo and pet-shop Erythromycin According to case definitions from the CDC This bacterium can infect parrots, parakeets, canaries, and other avian
employees, poultry farmers, and ranchers. Human- (2000), a confirmed case involves one of the species (eg, turkeys, pigeons, ducks). Another term for this infection is
to-human transmission is rare. following criteria: ornithosis, which describes the infection caused by nonpsittacine birds.

Isolation of the organism by culture Psittacosis is found worldwide. The incidence seems to be increasing in
developed countries, which is correlated to the import of exotic birds.

Compatible clinical illness with a 4-fold rise (to a

reciprocal titer of 32 or greater by paired sera
collected at least 2 weeks apart) in CF or MIF
antibodies against C psittaci
Detection of an IgM titer of 16 or greater against
C psittaci by MIF

Page 30 of 34
Chlamydophila pneumoniae Humans (spread from human to Respiratory route Life cycle is similar to Chlamydia Atypical pneumonia: viral like atypical pneumonia ( Macrolides are the first-line Serologic: Examine blood for elevated titers of Accelerated atherosclerosis
human) trachomatis similar to Mycoplasma ) in young adults antibiotics for the treatment of C antibodies with compliment fixation and
pneumoniae pneumonia immunofluorescence test. Criteria for infection
include a single IgM titer ≥1:16 or a 4-fold
increase in IgG titer.
Doxycycline Intracytoplasmic inclusion bodies do not stain Culture for C. pneumoniae is technically complex and time consuming.
with iodine When compared to serology and PCR, it also has low sensitivity and is
mainly used in research labs
Erthromycin The Infectious Diseases Society of America and The FilmArray Respiratory Panel is a multiplex PCR which detects
American Society of Microbiology currently common respiratory pathogens in nasopharyngeal specimens. In 2012,
recommend serologic testing or polymerase the US Food and Drug Administration (FDA) approved the addition of 2
chain reaction (PCR) for the diagnosis of C corona viruses and 3 bacteria to the Panel, including C pneumoniae ,
pneumoniae. Despite evident drawbacks, Bordetella pertussis , and Mycoplasma pneumonia . The FilmArray Panel
serology is still considered the gold standard can now detect 17 viruses and 3 bacteria from a single sample. Reported
sensitivity and specificity were both 100% for C pneumoniae but the
sample size was small and fewer than 10 samples were positive in the
study.
Real-time PCR assays of pharyngeal swab,
bronchoalveolar lavage, sputum or tissue can be
used to detect C pneumoniae-specific DNA.
Because of the complexity of these tests,
widespread implementation had been limited
until recent years.
Rickettsia rickettsii Dogs, rabbits & wild rodents Wood tick: In western U.S Dermacentor Rocky mountain spotted fever : Doxycycline Clinical exam
andersoni
Dog tick: In Eastern U.S Dermacentor variabilis 1. Fever Chloramphenicol Direct immunofluorescent exam of skin biopsy
from rash site
2. Conjunctival injection (redness) Serology
3. Severe headache Well-Felix reaction
4. Rash on wrists, ankles, soles and palms initially, Positive OX-19
become generalized later
Positive OX-2
Rickettsia akari House mice Mites (which live on the house mice) Rickettsial Pox : Vesicular rash similar to chicken pox. It Doxycycline Well-Felix reaction negative
resolves over 2 weeks Chloramphenicol
Rickettsia prowazekii Humans Human body louse (Pediculus humanus var. 1, Epidemic Louse-borne typhus Doxycycline Well-Felix reaction: positive OX-19 Epidemic typhus is caused by Rickettsia prowazekii and transmitted by
corporis ) human body lice. For centuries, it has been associated with
overcrowding, cold weather, and poor hygiene.
Flying squirrels A. Abrupt onset of fever and headache Chloramphenicol Serology Brill-Zinsser disease is a recurrent form of epidemic typhus that is
unrelated to louse infestation and develops sporadically years after the
primary illness. Clinical features are similar to, but milder than, those of
epidemic typhus
B. Rash, which spares the palms, soles, and face Eradicate human lice
C. Delirium/stupor
D. Gangrene of hands or feet
2. Brill-Zinsser Disease:
A. Reactivation of Rickettsia prowazekii
B. Mild symptoms
C. NO rash
Rickettsia Rats Rat flea (Xenosylla cheopsis ) Endemic (or murine) typhus : fever, headache and rash Doxycycline Well-Felix reaction: positive OX-19
typhi Small Rodents Chloramphenicol

Orientia tsutsugamushi Rats Mite larvae (chiggers) Scrub typhus: Doxycycline Well-Felix reaction: positive OX-K
Shrew Fever and headache Chloramphenicol
Mongooses Eschar (scab) at bite site
Birds Followed by a rash
Bartonella quintana Humans Body louse Not an obligate intracellular parasite 1. Trench Fever : fever, headache and back pain. It last Doxycycline Serology
for 5days recurs at 5 day interval
2. Bacteremia, endocarditis, and baciliary angiomatosis Chloramphericol PCR

Azithromycin
Bartonella henselae Cats Cat bite or scratch Not an obligate intracellular parasite Cat-scratch disease Azithromycin Serology Bacillary angiomatosis is a differential diagnosis for Kaposi’s sarcoma
Baciliary angiomatosis Doxycycline PCR
Bacteremia
Endocarditis, “culture negative”
Coxiella burnetii Cattle,sheep, goats No anthropod vector required. Direct airborne Can grow at pH 4.5 within Q fever. Fever, headache & viral-like pneumonia. No Doxycycline Complement fixation test demonstrating a rise in This is the only rickettsial disease without a skin rash.
transmission of endospore from cow hide or dried phagolysosomes rash! antibody
placenta, or via consumption of endospore- Has an endospore form Complications: Erythromycin PCR
contaminated unpasteurized cowmilk 1. Hepatitis Pasteurize milk at 60oC
2. Endocarditis

Page 31 of 34
Ehrlichia chaffeensis
Anaplasma phogocytophilum
Ehrlichia ewingii
Deer, white-footed mouse
Deer, dogs, coyotes Ticks Clusters of Ehrlichia multiply in host monocyte Human ehrlichiosis: similar to rocky mountain spotted Doxycycline Rise in acute and convalescent antibody liters Ehrlichiosis is an infection of white blood cells that affects various
vacuoles (phagosomes) to form large, mulberry- fever, but rash is rare mammals, including mice, cattle, dogs, deer, horses, sheep, goats, and
shaped aggregates called morulae humans
Rifampin Characteristic ehrlichial inclusion bodies are The primary target cell for human monocytic erlochiosis (HME) is the
sometimes seen in leukocytes on blood smears macrophage, and the primary target for human granulocytic
anaplasmosis (HGA) is the granulocyte.
Resistant to chloramphericol PCR Intracellular infection is established within phagosomes, most often
found in macrophages in the liver, spleen, lymph nodes, bone marrow,
lung, kidney, and CNS.

Treponema pallidum pallidum
Between 1905 and 1910, Schaudinn
and Hoffman identified T pallidum
as the cause of syphilis, and
Wasserman described a diagnostic
test for the long-recognized
infection. Pathogenic treponemes
are associated with the following 4
diseases:
Venereal syphilis, caused by T
pallidum pallidum
Yaws, caused by T pallidum
pertenue
Endemic syphilis (bejel), caused by
T pallidum endemicum Pinta,
caused by T carateum
Humans only Sexual Microaerophilic Motile Syphilis Penicillin G Cultaneuos lesions examined by dark field Jarisch-Herxheimer reaction: acute worsening of symptoms after
A. Primary: painless chancre microscopy, immunofluorescence. ELISA, or Penicillin is started
silverstain
Morphology: thick rigid spirals B. Second stage: Rash on palms and soles Erythromycin Non-specific treponemal tests: VDRL; RPR
Condylomata lata: painless, wart-like lesion which
occurs in warm, moist places (vulva or scrotum)
CNS, eyes, bones, kidneys and/or joints can be involved
Highly sensitive to elevated C. Latent: 25% may relapse back to the secondary stage Doxycycline Specific treponemal test : FTA-ABS, MHA-TP
temperatures
D. Tertiary (33%): VDRL and FTA-ABS are positive
Gummas of skin and bone
Cardiovascular syphilis (aortitis)
Neurosyphilis: Agryll-Robertson pupil
E. Congenital syphilis: contacted transplacentally (MCC
of death is pulmonary hemorrhage) -> According to a
Centers for Disease Control and Prevention report,
untreated syphilis, especially early syphilis, during
pregnancy can lead to deafness, neurologic impairment,
bone deformities, stillbirth, and neonatal death

Borrelia burgdorferi
White-footed mouse Vector = Ixodes ticks
White-tailed deer Ixodes scapularis : East & Midwest
Ixodes pacificus : West coast
Together with Babesia microti
Microaerophilic LYME DISEASE Doxycycline (DOC) Elevated levels of antibodies against Borellia Largest medically important bacterium (size)
A. Early localized stage (stage 1): Erythema chronicum burgdorferi ban be detected by ELISA
migrans (ECM)
B. Early disseminated stage (stage 2): Amoxicilin Western immunoblotting
Multiple smaller ECM Ceftriaxone for neurologic disease
Neurologic: aseptic meningitis, cranial nerve palsies
(Bell’s palsy), and peripheral neuropathy
Cardiac: transient heart block or myocarditis
Brief attacks of arthritis of large joints (knee)

C. Late stage (stage 3):

Leptospira interorgans
23 serogroups, 250 serovars
Chronic arthritis
Acrodermatitis chronica atrophicans
Encephalopathy
Zoonotic (dogs, cats, livestock, and Direct contact with infected urine or animal AEROBIC – the other spirochetes are Leptospiremic phase: organisms in blood and CSF Penicillin G First week: culture blood or cerebral spinal fluid The traditional system divided the genus into 2 species: the pathogenic
wild animals) tissue: Organism penetrate broken skin (i.e. on microaerophiles causes high spiking temperature, headache and severe (on lab media, or by inoculation into animals Leptospira interrogans and the nonpathogenic Leptospira biflexa .
feet) and mucous membranes (swallowing urine- muscle aches (thighs and lower back) These species were divided further into serogroups, serovars, and
History of wading in flood water (in contaminated water) Spiral shaped, with hooks on both ends Immune phase: correlates with emergence of IgM and Doxycycline for chemoprophylaxis Second week to months: culture urine strains based on shared antigens. L interrogans included more than 250
3rd world setting) (“ice tongs”) -> Shepherd’s crook involves recurrence of the above symptoms, often with serovars.
appearance meningismus (neck pain)
History of exposure to animals Two axial flagella wrap around and run WEIL’S DISEASE: most severe case of leptospirosis with Rarely, dark field microscopy is successful (not
(butcher) along the length of the organism under renal failure, hepatitis (and jaundice), mental status recommended)
the outer membrane (oeriplasmic changes, and hemorrhage in many organs. ECG Antibody based ELISA to detect Leptospira
flagella) abnormalities are common during the leptospiremic antigens in the urine
phase of Weil syndrome. In severe cases, congestive Polymerase Chain Reaction (PCR) to detect
heart failure and cardiogenic shock may occur. bacterial DNA in serum, CSF and urine
Microscopic agglutination testing (MAT; the
criterion standard for serologic identification of
leptospires, available only at reference
laboratories)

Page 32 of 34
Mycobactrium tuberculosis 40% of total cell dry weight is lipid
Composed of mycolic acids
Thin rods
Non-motile
Facultative intracellular growth: M.
tuberculosis can survive and
multiply in macrophages
Aerobic Mycosides No exotoxin nor endotoxin Tuberculosis First line drugs : Acid-fast stain of specimen (carbolfuchsin Mycolic acids are also found in Nocardia (which also is acid fast)
primary stain; methylene blue secondary stain)
Catalase-positive Cord factor: only found in virulent strain A. Primary tuberculosis: Isoniazid (INH) RAPID CULTURE:
Slow growth rate (May be responsible for release of Asymptomatic Rifampin Bactec radiometric culture: a liquid broth in a Purified Protein Derivative (PPD) Test
tumor necrosis factor Overt disease, involving the lungs or other organs bottle, with radioactive palmitate as a carbon 1. Measure zone of unduration:
source. Mycobacteria grow and use the carbon, Positive reaction:
B. Reactivation or secondary tuberculosis: allowing early detection (in 1-2 weeks) even > 5mm (immune-compromised host)
1. Pulmonary before colonies can be seen. > 10 mm (have chronic disease or risk factors for exposure to TB)
Sulfatides: inhibit phagosome-lysosome 2. Pleural or pericardial Pyrazinamide PPD skin test >15mm (all others)
fusion 3. Lymph node infection 2. A positive reaction does not mean active disease.
Wax D: acts as an adjuvant 4. Kidney Ethambutol Chest X-ray 3. Can get false negative in patients with AIDS or malnourished
5. Sketetal individuals
6. Joints
Iron siderophore (mycobactin) 7. Central Nervous System Streptomycin PCR and DNA probes
8. Miliary Tuberculosis Mycobacterium Tb Direct Test (MTDT): amplifies
ribosomal RNA in respiratory secretions, allowing
rapid identification of M. tuberculosis

QuantiFERON-TB - blood test that measures

Mycobacterium leprae Humans Catalase-positive Non-motile Leprosy - the most common cause of crippling of the
hand
Armadillos Grows best at low temperature Facultative intracellular growth A. Lepromatous leprosy (LL):
1. Low cell-mediated immunity
Phenolase-positve: converts DOPA into a 2. Organisms found everywhere (organs and blood)
pigmented product (used for diagnosis) 3. Skin, nerves, eyes and testes involved bilaterally:
multiple skin lumps and bumps, leonine facies, saddle
nose, peripheral neuropathy, digit absorption, blindness
and infertility in men (from testicular damage)
B. Tubercoloid leprosy (TL):
1. Intact-cell mediated immunity
2. Difficult to isolate M. leprae from skin or blood
3. Skin and nerves involved: 1 or 2 superficial unilateral
lesions
Damage in the following nerves is associated with
characteristic impairments in leprosy:
• Ulnar and median - clawed hand
• Posterior tibial - Plantar insensitivity and clawed toes
• Common peroneal - Foot drop
• Radial cutaneous, facial, and greater auricular nerves
(may also be involved)
interferon gamma levels produced in whole
blood in response to addition of specific
tuberculosis antigens has been approved by the
FDA. An advantage of this test is the relative
specificity for Mycobacterium tuberculosis ; it is
not positive in patient in previous BCG
vaccination, (MMWR, Recommendation and
Reports, 2005)
Luciferase Reporter Mycobacteriophage (LRP)
Assays - can detect Mycobacterium tuberculosis
and characterize mycobacterial drug
susceptibility patterns within 24 to 48 h in
positive cultures (luciferase is an enzyme
obtained from fireflies)
Rifampin Can NOT be grown on artificial lab media: can
only be cultured in certain animals, such as mice
foot pads, armadillos or monkeys
Dapsone Skin or nerve biopsy will reveal acid-fast bacilli
(lepromatous) or granulomas (tubercoloid)
Clofazimine
Lepromin skin test - Although not useful for diagnosis, it allows
positioning of patients on the immunologic spectrum
Also known as Hansen disease, named after G.A. Hansen, who is
credited with the 1873 discovery of M leprae .
Classification of leprosy: Leprosy has 2 classification schemas: the 5-
category Ridley-Jopling system and the simpler and more commonly
used WHO standard.
Ridley-Jopling: Depending on the host response to the organism, leprosy
can manifest clinically along a spectrum bounded by the tuberculoid and
lepromatous forms of the disease. Most patients fall into the
intermediate classifications, which include borderline tuberculoid
leprosy, midborderline leprosy, and borderline lepromatous leprosy.
The classification of the disease typically changes as it evolves during its
progression or management. The Ridley-Jopling system is used globally
and forms the basis of clinical studies of leprosy. It may also be more
useful in guiding treatment regimens and assessing risk of acute
complications. Physical findings in each subtype are presented in the
Clinical section.
WHO system: The WHO recommends classifying leprosy according to
the number of lesions and the presence of bacilli on a skin smear. This
method is useful in countries where biopsy analysis in unavailable.
Paucibacillary leprosy is characterized by 5 or fewer lesions with
absence of organisms on smear. Paucibacillary leprosy generally
includes the tuberculoid and borderline lepromatous categories from
the Ridley-Jopling system.
Multibacillary leprosy is marked by 6 or more lesions with possible
visualization of bacilli on smear. Lepromatous leprosy, borderline
lepromatous leprosy, and midborderline leprosy on the Ridley-Jopling
scale are included in the multibacillary leprosy category.

Page 33 of 34
Mycoplasma pneumoniae
The smallest free-living organisms.
Although scientists have isolated at oblong shaped
least 17 species of Mycoplasma
from humans, 4 types of organisms & reproduction outside a living cell
are responsible for most clinically (smaller that some viruses: 1-2
significant infections that may
come to the attention of practicing Motile (glides)
physicians. These species are
Mycoplasma pneumoniae,
Mycoplasma hominis, Mycoplasma
genitalium, and Ureaplasma
species.
Actinomyces israelii
Nocardia asteroides
No cell wall
Pleomorphic: can appear round to
Smallest bacteria capable of growth
microns)
Normal flora of the mouth and GI
tract
Never part of the normal flora
Respiratory transmission
Members of the genus Nocardia
are aerobic actinomycetes that are
ubiquitous saprophytes in soil,
decaying organic matter, and fresh
and salt water.
Requires STEROL for membrane formation ->
bacteria do not normally contain sterols
Aerobic (the other mycoplasmas are facultative
anaerobes)
Gram-positive rod; filamentous bacterium
Anaerobic bacteria (ABC!)
Grow as branching chains or beaded filaments
Gram-positive rods
Partially acid-fast: due to mycolic acids in the cell
wall
Aerobic
Grow as branching chains or beaded filaments
Protein P1 adhsesin: adheres to
epithelial cells of the respiratory tract;
mediates attachment, followed by
induction of ciliostasis, local
inflammation that consists primarily of
perivascular and peribronchial
infiltration of mononuclear leukocytes,
and tissue destruction that may be
mediated by liberation of hydrogen
peroxide
Recently, M pneumoniae has been shown to Tracheobronchitis
produce an exotoxin that is also believed to play
a major role in the damage to the respiratory Walking pneumonia (also called atypical pneumonia):
epithelium that occurs during acute infection. fever with a dry, non-productive hacking cough
This toxin, named the community-acquired
respiratory disease toxin (CARDS) is an ADP-
ribosylating and vacuolating cytotoxin similar to
pertussis toxin. [Infect Immun . 2005 May.
73(5):2828-34.; Am J Respir Crit Care Med . 2010
Sep 15. 182(6):797-804.]
Evidence from animal models of M pneumoniae
infection have proven that recombinant CARDS
toxin results in significant pulmonary
inflammation, release of proinflammatory
cytokines, and airway dysfunction. [PLoS One.
2009. 4(10):e7562]
Actinomycosis is a subacute, chronic, cellulitic invasion Penicillin G
of the soft tissues that causes the formation of external
sinus tracts that discharge sulfur granules. This process
spreads unimpeded by traditional anatomic barriers
after the endogenous oral commensal organisms
invade the tissues of the face and neck. Actinomycosis
may also spread to the pulmonary and GI systems.
Surgery
Eroding abscesses of the mouth, lung or gastrointestinal
tract, classified as:
1. Cervicofacial actinomycosis
2. Thoracic actinomycosis
3. Abdominal actinomycosis
Pneumonia Thrimethoprim/sulfamethozole
Formation of abscesses in the lung, kidney, and central
nervous system
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Macrolides (azithromycin,
clarithromycin)
Tetracyclines (doxycycline)
Quinolones (ciprofloxacin,
levofloxacin)
Penicillin and cephalosporins do Dome-shape colonies with “fried egg”
NOT work as mycoplasma does not appearance or “mulberry” appearance (in the
have a cell wall
SNAP=
Sulfa -> Nocardia
Actinomyces ß Penicillin
Cold agglutinins Chest X-ray will show patchy infiltrates that look worse than physical
examples and clinical symptoms suggest
Complement fixation test Disease usually occurs in children, adolescents and young adults
Culture: takes 2-3 weeks (Eaton’s agent) CHILD 5-15 YEARS OLD WITH PNEUMONIA? THINK MYCOPLASMA!
Requires cholesterol and nucleic acids Children with sickle cell disease and functional asplenia may be at
Add penicillin to inhibit growth of contaminating greater risk for severe respiratory tract disease
bacteria
case of Mycoplasma pneumoniae )
Rapid identification Test:
Sputum can be tested with DNA probes (nucleic
acid hybridization). PCR sputum samples.
Examine tissue or pus from infection site, and Yellow “sulfur granules”: microcolonies of Actinomyces and cellular
look for “sulfur granules” debris
All species of Actinomyces are normal commensal inhabitants of the oral
and buccal cavities in humans and certain other mammals. They cannot
be classified as symbiotic organisms because they do not have a
mutually beneficial relationship with their host. They are not true
parasites because they usually do not cause harm to the host; however,
Anaerobic culture they definitely assume a parasitic role when they result in an infection
with an inflammatory tissue response.
Does not appear to be an opportunistic infection because actinomycosis
is not common in patients who are immunosuppressed or in patients
Gram-stain Nocardia infection usually occurs in immunocompromised patients
Modified acid-fast stain: Decolorized with
1%sulfuric acid instead of acid alcohol. Nocardia
are typically weakly acid-fast after traditional
staining and positive on modified acid-fast
staining, but this is not invariable.
Aerobic culture