Parasitology International 60 (2011) 507511

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Parasitology International
journal homepage: www.elsevier.com/locate/parint

Identication of a novel Assemblage B subgenotype and a zoonotic Assemblage C in

human isolates of Giardia intestinalis in Egypt
R.H. Soliman a, b,, I. Fuentes b, J.M. Rubio b
a
b

Faculty of Medicine, Parasitology department. Suez Canal University, Ismaillia, Egypt

Microbiology National Center. Instituto de Salud Carlos III, Cra. Majadahonda- Pozuelo Km. 2, Majadahonda, 28220 Madrid, Spain

a r t i c l e

i n f o

Article history:
Received 30 March 2011
Received in revised form 21 September 2011
Accepted 24 September 2011
Available online 1 October 2011
Keywords:
Giardia intestinalis
Assemblage C
Zoonosis
-giardin

a b s t r a c t
Giardia intestinalis (G. intestinalis) is a agellate parasite which has been considered the most common protozoan infecting human. Molecular techniques are of great value in studying the taxonomy, the zoonotic potential of animal isolates and the correlation between the genetic variability of the parasite and the range of
clinical symptoms observed in humans. The present work aims at genotyping G. intestinalis isolates from
Egypt using molecular techniques. PCR targeting the -giardin locus, RFLP and sequencing were applied to
12 microscopically positive and 3 microscopically negative samples (which were positive by real time PCR
targeting SSUr DNA). Two other loci, triose phosphate isomerase (TPI) gene and glutamate dehydrogenase
(GDH) gene PCR and RFLP were also applied to all study isolates. The most frequent genotype was Assemblage B (13 out of 15), while Assemblage A and C were present in one sample each. This is the rst report
on zoonotic transmission of Assemblage C (dog genotype) to human in Egypt. Sequencing of the Assemblage
B isolates revealed new subgenotypes with consistent mutations at specic positions, some of which were
not characterized previously. The results shed light on the possibility that G. intestinalis can infect humans
through a zoonotic route and open the door to wider investigations using different genetic loci to genotype
Giardia isolates.
2011 Elsevier Ireland Ltd. All rights reserved.

1. Introduction
Giardia is a genus of intestinal agellates that infects a wide range
of vertebrate hosts. The genus currently comprises of six species.
Giardia intestinalis (syn. Giardia dudenalis, Giardia lamblia) [1] is the
only species found in humans [2]. It has a global distribution and is
the most common intestinal parasite of humans in developed countries, about 200 million people have symptomatic giardiasis with a
high variable infection rates between countries [3]. Giardia is one of
the most important emerging food-borne parasites [4] and is the
most common intestinal parasite of humans identied in the United
States to cause a nationally notiable gastrointestinal illness [5].
Giardia intestinalis (G. intestinalis) was the most common parasite
found in immunocompromised Egyptian patients in a study conducted by Baiomy et al. [6], while its prevalence was 10% in a rural
population [7] and 19.8% in Great Cairo, Egypt [8].
G. intestinalis is considered as a species complex, whose members
show little variation in their morphology. Due to its invariant morphology, investigation on aspects such as host specicity and transmission patterns requires a direct genetic characterization of

Corresponding author at: Parasitology department, Faculty of Medicine, Suez Canal

University, Ismaillia, Egypt. Tel.: + 20 2 012 3313394; fax: + 20 2 64 328543.
E-mail address: dr_rashasoliman@yahoo.com (R.H. Soliman).
1383-5769/$ see front matter 2011 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.parint.2011.09.006

cysts/trophozoites from host samples. A major limiting factor, in understanding and interpretation of the genetic heterogeneity within
the G. intestinalis group, has been the refractory growth in vitro of
many isolates of Giardia [9]. The recent advent of PCR-based procedures that can characterize isolates of Giardia directly from feces
has thus allowed a more comprehensive range of genotypes to be
characterized from humans and animals [1012]. A coherent picture
has emerged from those studies, indicating the existence of eight genetic groups (or assemblages). Two of this assemblages (A and B) are
found in both humans and animals, whereas the remaining six (CH)
are host-specic [1315]. Assemblages C and D contain isolates from
dogs and cats [16], Assemblage E contains isolates from cattle, sheep
and goats [17], Assemblage F contains isolates from cats, Assemblage
G contains isolates from rats [18] and Assemblage H in marine vertebrates [15]. Several sequence based surveys had identied subgenotypes of Assemblages A and B having zoonotic potential [13,14,3].
Different studies were conducted to identify genotypes related
risk factors with divergent conclusions. Assemblage B has been associated with non-symptomatic infections for example in a study in
children less than 5 years of age [19] or in a study carried out in Bangladesh [20]. On the other hand, it was related with persistent diarrhoeal complaints in the general Dutch population [21]. A study in
aboriginal community in Pahang, Malaysia, shows that Assemblage
B infection was signicantly correlated with clinical symptoms of
giardiasis [22]. The zoonotic risk associated with Giardia Assemblages

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R.H. Soliman et al. / Parasitology International 60 (2011) 507511

can be better understood based on molecular data, and the use of

these data represents an objective means of determining the source
of infection in outbreaks and single cases [23,24].
The prevalence of each assemblage varies considerably from country to country [14]. The current study was conducted to characterize
the Giardia Assemblages in human cases of giardiasis in Egypt based
on the molecular amplication of three genes: TPI (triose phosphate
isomerase) gene, GDH (glutamate dehydrogenase) gene and the giardin gene amplication and sequencing.
2. Materials and methods
2.1. Source of isolates
Twelve fecal samples, positively diagnosed for G. intestinalis by
wet mount microscopic examination of 130 diarrheic stool samples,
were used in this study. The samples were collected from the pediatrics outpatient clinic, Suez Canal University, Egypt. The positive samples belonged to 8 boys and 4 girls, ranging from 2 to 11 years in age,
complaining of diarrhea, abdominal pain and/or atulence. Twenty
diarrheic fecal samples collected from the oncology department,
Suez Canal University hospital were included. The samples belonged
to 12 males and 8 females ranging from 41 to 70 years in age, complaining of diarrhea and abdominal cramps and were diagnosed negative for G. intestinalis by wet mount microscopy. Samples were
preserved in 70% ethanol until DNA extraction was performed. Verbal
and/or written consent were obtained from each participant or their
parent/guardian prior to participation. The study was approved by
the Suez Canal University Research Ethics Committee.
2.2. DNA isolation
DNA was extracted from ethanol preserved fecal samples using
QIAamp DNA stool mini kit (Qiagen) according to the manufacturer's
instructions with some minor modications. 300 l of the sample
was transferred into a centrifuge tube, centrifuged for 2 min at
13,000 rpm and the supernatant was discarded. The sediment was
re-suspended in distilled water and centrifuged at the same conditions. Repetition of this step was performed 3 times to ensure the removal of all ethanol. The extraction protocol was followed, with some
modications in heating step by increasing it to 95 C for 10 min to
increase total DNA yield. Elution of DNA was done in 200 l distilled
water, incubated for 5 min in room temperature before centrifuging
at full speed.
G. intestinalis diagnosis by PCR amplication Real-time PCR, targeting the small subunit ribosomal DNA (SSUr DNA) gene, was used
for diagnosis positive cases of G. intestinalis [25]. All samples were analyzed in duplicate.
2.3. Genotyping G. intestinalis:
1. G. intestinalis TPI (triose phosphate isomerase) gene: A nested PCR
assay was used to detect and distinguish between G. intestinalis
Assemblages A and B from human feces by analysis of the TPI gene.
The assay comprised an initial multiplexed amplication. This was
followed by two separate PCR assays specic for Assemblages A
and B to identify PCR products. The expected fragment size for
Assemblage A is 476 bp and 140 bp for Assemblage B [8]. Furthermore
RFLP analysis using Rsa I was applied to distinguish G. intestinalis
Assemblage A groups I and II. PCR products were puried using the
Qiaquick gel extraction kit (Qiagen) according to the manufacturer's
instructions. Puried PCR products were digested using 5 l Rsa I
(Promega, Madison). The aliquots were digested for 3 h at 37 C and
the digestion products were electrophoresed on ethidium bromide
stained 2.5% agarose gels. The predicted fragment size for Assemblage
A I: 39, 437 bp; Assemblage A II: 39, 202, 235 bp. [8].

2. G. intestinalis GDH (glutamate dehydrogenase) gene: A seminested PCR was performed to amplify the G. intestinalis GDH
gene according to the method described by Read et al. [26]. Diagnostic genotyping was performed by RFLP digestion with Nla IV
and Rsa I after PCR product purication. Using Nla IV, the predicted
digestion fragment sizes for Assemblage AI are 90, 120 and 150 bp;
for Assemblage AII are 70, 80, 90 and 120 bp; for Assemblages BIII
and BIV are 120 and 290 bp; for Assemblage C are 70, 120 and
190 bp; for Assemblage D are 120 and 250 bp and for Assemblage
E the predicted fragment sizes are 80, 100 and 220 bp. Digestion
with Rsa I is used to differentiate between Assemblage BIII,
which renders two fragments of 130 and 300 bp, and Assemblage
BIV, which renders a fragment of 430 bp.
3. G. intestinalis -giardin gene: Nested PCR targeting the -giardin
gene was performed according to Lalle et al. [27] with some
minor modications. PCR products were puried and digested
using Hae III (New England Biolabs, USA) as above. The expected
fragments were: Assemblage A: 201, 150, 110 and 50 bp; Assemblage B: 150, 117, 110, 84, 26, and 24 bp; Assemblage C: 194,
150, 102, 50 and 15 bp; Assemblage D: 200, 194, and 117 bp; Assemblage E: 186, 150, 110, 26, 24, and 15 bp; Assemblage F: 186,
150, 110, 50 and 15 bp [27].
Puried PCR products were sequenced (sense and antisense)
using the BigDye Terminator v3.1 Cycle Sequencing Kit (ABI prism,
Applied biosystems) in an ABI PRISM 3700 DNA Analyzer. The sequences were optimized and assembled using BioEdit version 7.0.0
software [28]. BLAST was used to search homologies in NCBIGenBank sequence data base. Sequence alignment was carried out
by ClustalW [29]. Phylogenetic relationships by neighbor-joining distance method were performed with Treecon software [30]. Giardia
Assemblage F (cat genotype) was introduced as outgroup to draw
the NJ-tree.
3. Results
3.1. Diagnosis and conrmation of infection by G. intestinalis
The results of the real time PCR amplication of the subunit ribosomal DNA (SSUr DNA) gene for the 12 ethanol preserved, microscopically positive fecal samples were all positive with mean Ct
value (25.14 5.11) while the 20 microscopically negative stool samples revealed 3 positive samples with mean Ct value (37.43 1.26).
All the samples were done in duplicate so the high Ct value of these
three samples indicated a true infection with low parasite burden.
3.2. TPI gene
The TPI gene amplication was successful in only 7 out of 15 samples. PCR and RFLP allowed the identication of an Assemblage AII
and 6 Assemblage B isolates (Table 1).
3.3. GDH gene
The GDH gene amplication was successful in 7 out of 15 samples.
Five samples could show mixed infections of Assemblages of the same
family. The other two samples were individual infection identied as
Assemblage BIII and BIV (Table 1).
3.4. -giardin gene
The -giardin gene amplication was successful in 15 out of 15
positive Giardia samples. The Hae III digestion pattern revealed that
11 out of 15 samples belonged to Assemblage B, one sample was Assemblage A and another sample showed Assemblage C pattern
(Fig. 1). This sample was negative by microscopy and belonged to

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Table 1
Genotyping of the study isolates using the three genetic loci: -giardin, TPI and GDH
genes.
Isolate

TPI

GDH

-giardin RFLP

-giardin seq.

796
797
821
822
798
823
799
800
810
802
812
824
818
819
820

B
A2
NEG
NEG
NEG
NEG
B
B
B
B
B
NEG
NEG
NEG
NEG

B/BIII
AI/AII
AI/AII
NEG
NEG
NEG
NEG
BIV
BIII
BIII/BIV
BIII/BIV
NEG
NEG
NEG
NEG

B
A
B
B
B
B
B/A?
B
B
B/A
B
B
B
C
B

B1 NEW
A9
B1 NEW
B1 NEW
B1 NEW
B1 NEW
B1 NEW
B3
B1 NEW
B5 OR B6
B3
B1 NEW
B1 NEW
C
B1 NEW

S1
S2
S3
S4
S5
S6
S7
S8
S9
S 10
S 11
S 12
S 1UN
S 6UN
S 7UN

NEG: negative amplication.

one of the oncology patients. Two samples did not show clear digestion pattern and may reect mixed infections of A and B genotype
(Table 1). The nucleotide sequences of the -giardin gene from the
positive samples were phylogenetically compared with those
reported in the GenBank for a number of Giardia assemblages. A phylogenetic tree was produced by using the neighbor-joining method
with Jukes and Cantor distance corrections (Fig. 2).The bootstrap consensus tree yielded separated clusters for each represented assemblage from A to F, the last being used as outgroup for the tree
construction. No samples were integrated in clusters corresponding
to Assemblages D, E and F. One sample belonged to the Assemblage
A cluster, as it was characterized by TPI, GDH and -giardin genes.
Another sample belonged to Assemblage C cluster, as it was typed
by -giardin gene. The monophyly of this node is supported by strong
bootstrap (100%). The 13 left samples, were included in the Assemblage B cluster. Of these samples, three were similar to Assemblage
B subgenotypes present in GenBank, the other ten samples were associated in a novel Assemblage B subcluster. These sequences have specic base substitutions (Table 2) which was not present in -giardin
sequences reported in the GenBank database until the date of its deposition (Accession numbers, see Fig. 2).
4. Discussion
Giardiasis is a common cause of diarrheal disease in almost all vertebrates, including humans. In industrialized countries, it is referred
to as re-emerging infectious disease because of its increasingly recognized role in outbreaks of diarrheal diseases in daycare centers and

Fig. 1. Agarose gel electrophoresis for the RFLP digestion of -giardin gene PCR. Lanes
1, 2, 3, 4, 5 and 7: Assemblage B. Lane 6: Assemblage C. Three DNA markers were used:
a 100 bp ladder, X174/Hinf I (Biotools, B&M labs, Spain) and a 50 bp ladder (Promega,
Madison).

509

water- and foodborne outbreaks [31]. In Egypt, Zaki et al. [32] found
G. intestinalis in 44% of the population studied in rural zones and
Shukry et al. [33] in 33% of people in Cairo residents. Curtale et al.
[34] and Fawzi et al. [35] detected G. intestinalis in 24.7% of the samples in Behera governerate and in 10.4% in El-Prince, Alexandria respectively. Recently, Foronda et al. [36] detected a prevalence of
G. intestinalis reaching 34.6% in Egypt.
In this study, we evaluated the different genotypes of G. intestinalis
in the study population using the TPI gene, GDH gene and -giardin
locus heterogenicity. The data obtained with TPI and GDH corresponded with that obtained by -giardin method, except for one discrepancy using the GDH gene compared to the rest of the methods
(Table 1). This observation was reported by other authors [26] and
could be due to the presence of mixed genotypes, with one genotype
being preferentially amplied over another at one locus. Interestingly,
while the -giardin method showed results in 15 out of 15 positive
Giardia samples, TPI and GDH only showed amplication and digestion pattern in 7 out of 15 samples. These negative samples corresponded with high Ct values for the Giardia real time PCR diagnosis
which indicated positive but low burden infection.
Giardins are dened as a family of structural proteins that are approximately 2938 kDa in size and have an alphacoiled-helix structure. The proteins are found at the edges of microribbons (or dorsal
ribbons), which are an integral part of the ventral disk of the trophozoite [37]. The advantage of using giardin genes as targets for the molecular detection of Giardia cysts is that they are considered to be
unique to this parasite [38]. Caccio et al. [39] stated that the giardin gene assay is highly discriminatory, even if the sequence is
relatively well conserved.
The most frequent genotype detected was Assemblage B accounting for 13 out of 15 of positive Giardia samples while Assemblage A
accounted for only 1 out of 15 of the positive cases. This comes in accordance with other studies carried out in Gharbia and Kafr El Sheik
governorates (a more rural area), Egypt, where Assemblage B was
the most prevalent (80%) genotype while Assemblage A had a prevalence of only 5% using PCR and DNA sequence analysis of TPI gene
[36]. On the other hand, Helmy et al. [40] reported 75.6% of their
study population in Cairo belonging to Assemblage A while only
19.5% belonged to Assemblage B using the TPI gene amplication.
The reasons behind the geographic variation in the predominance of
the Giardia assemblages are still unclear. It may be explained by the
difference in the dynamics of transmission. It has been known that
Assemblage A is most often responsible for zoonotic transmission
with wide range of animals acting as reservoir hosts. Although Assemblage B is most likely transmitted from human to human, it has
been reported in some animals and may represent a zoonotic potential as well [41,42].
One sample contained Assemblage C in our study, this result was
conrmed by -giardin typing and by sequencing followed by comparison to the GenBank database with Blast and by phylogenetic analysis. No possible cross contamination could have occurred in the
laboratory since no previous history of working with this Assemblage
in our laboratory exist. The sample belonged to an adult immunocompromised male suffering from cancer bladder and diarrhea. This sample was collected from the patient in the hospital using the hospital
collecting cup, without possibility of contamination with zoonotic assemblages. The level of parasites in the sample was very low as it was
not detected by microscopy and the Real time PCR diagnosis method
was capable to detect it with a very high Ct (37.43 1.26) which correspond with low parasitaemia [25].
Assemblage C is present in dogs. Although the potential for zoonotic transmission of Giardia from domestic dogs to humans remains
largely an unresolved issue, if zoonotic transmission is possible, then
both domestic as well as stray dogs may constitute a potential source
of infection for humans. Studies show that the dog isolates have an
important genetic similarity with human isolates [43]. Traub et al.

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R.H. Soliman et al. / Parasitology International 60 (2011) 507511

Fig. 2. Phylogenetic relationship of human isolates of G. intestinalis by neighbor joining analysis, based on the -giardin nucleotide sequences.

[44] conducted an epidemiological and molecular study on zoonotic

transmission of Giardia among humans and dogs living in the same
community. Phylogenetic analysis of the SSU-rDNA data of their
study placed 10 of the G. intestinalis isolates into Assemblage C. The
authors were skeptical with their ndings and explained it by introgression or retention of ancestral polymorphism and that in such
cases analysis of a single locus can result in incorrect species identication. They concluded the importance of using multiple loci when
genotyping Giardia isolates to provide denitive evidences. Recent reports in other localities gave more evidence on retrieving Assemblage
C from humans [45,3]. Our data using another variable -giardin
locus can provide support to their preliminary ndings. These ndings are very important as they shed the light on the possibility that
G. intestinalis may infect humans through a zoonotic route. Further investigations on wider scale are needed to give full support to our ndings using other different loci.
In our study, the sequencing of the -giardin gene in the positive
samples showed an elevated frequency (10 out of 13) of a subtype
Table 2
The position of nucleotide base substitution in the -giardin in the new assemblage B
subgenotype.
Subgenotypes

New subgenotype
B1
B2
B3
B4
B5
B6

Position
67

73

232

301

379

A
G
G
G
G
G
G

C/T
T
C
C
C
C
T

T
C
C
C
C
C
C

T
T
C
C
C
C
C

C
T
T
T
T
T
T

of Assemblage B not described previously in the sequence database

until the date of its submission to the GenBank. The importance of
this discovery and its rule in the disease transmission must be analyzed deeply in the future, especially into the geographical context
of transmission, as a clear example of local anthropomorphic transmission. Surprisingly, the same sequence was discovered in a later research conducted by Wielinga et al. [46], who interpreted their
ndings as intra-assemblage B substitution pattern rather than a
true subassemblage. Their study was conducted on cloned culture
isolates which increase the chance for genetic drift to occur. On the
other hand, our study was conducted on human isolates and there
is a cluster of cases carrying the same sequence which may require
further investigations using Multiple Loci Genotyping (MLG) in the
same, and in other localities to validate these results.
Surprisingly, mixture of genotypes in two individual isolates were
observed when -giardin typing was used, the other two typing
genes showed just a single Assemblage. The presence of more than
one Assemblage infecting one patient is possible and can be explained
by the possible uptake of genetically different Giardia cysts by a host,
or subsequent infection of an already infected host, likely without
overt symptoms, with a different Giardia species, which may cause
disease [12]. In conclusion: G. intestinalis is one of the prevalent protozoa in Egypt, with high incidence of Assemblage B rather than other
genotypes. The study represented the presence of high percentage of
a possible new Assemblage B subgenotype in this locality which may
reect focal transmission, which must be conrmed by further investigations. In the same time, the discovery of an Assemblage C in an
immunocompromised patient is very important and requires the extensive genetic analysis of Giardia isolates from this category of patients as they may play a major role in spreading new assemblages
to the immunocompetent population. The presence of few samples

R.H. Soliman et al. / Parasitology International 60 (2011) 507511

exhibiting mixed assemblages or subgenotypes requires its re-evaluation

using other genes to clarify their nature.
Acknowledgment
This work was supported by the granted project PET2007_0217
granted by the Spanish MICINN and by BIOTOOLS, S.A.
We thank Diana Dado and Begoa Bailo for their technical assistance. Marwa Tammam is acknowledged for organizing the work.
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