BMC Infectious Diseases
BioMed Central
Open Access
Research article
Genetic relatedness among isolates of Shigella sonnei carrying class
2 integrons in Tehran, Iran, 2002–2003
Reza Ranjbar†1, Aurora Aleo†2, Giovanni M Giammanco†2,
Anna Maria Dionisi†3, Nourkhoda Sadeghifard†4 and Caterina Mammina*2
Address: 1Research Center of Molecular Biology, Baqiyatallah University of Medical Sciences, Tehran, Iran, 2Dipartimento di Igiene e Microbiologia
"G. D'Alessandro", Università di Palermo, Via del Vespro 133, I-90127 Palermo, Italy, 3Dipartimento di Malattie Infettive, Parassitarie e
Immunomediate, Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161Rome, Italy and 4Department of Microbiology, Faculty of Medicine,
Ilam University of Medical Sciences, Ilam, Iran
Email: Reza Ranjbar - ranjbar@bmsu.ac.ir; Aurora Aleo - batteriologia@igiene.unipa.it; Giovanni M Giammanco - g.m.giammanco@unipa.it;
Anna Maria Dionisi - annamaria.dionisi@iss.it; Nourkhoda Sadeghifard - sadeghifard@gmail.com; Caterina Mammina* - diptigmi@unipa.it
* Corresponding author †Equal contributors
Published: 22 June 2007
BMC Infectious Diseases 2007, 7:62
doi:10.1186/1471-2334-7-62
Received: 20 February 2007
Accepted: 22 June 2007
This article is available from: http://www.biomedcentral.com/1471-2334/7/62
© 2007 Ranjbar et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Background: Shigella spp. are major cause of diarrhoeal disease in both developing and developed
countries. Shigella sonnei is the serogroup of Shigella most frequently responsible for sporadic and
epidemic enteritis in developed countries. In recent years the emergence and spread of S. sonnei
biotype g carrying class 2 integron have been frequently reported in many countries. Recently, S.
sonnei has been reported as the prevalent serogroup of Shigella in Iran.
The present study was carried out to investigate phenotypic and genetic characteristics of Shigella
sonnei isolates identified in the years 2002 and 2003 in Tehran, Iran.
Methods: Biotyping, drug susceptibility testing, pulsed field gel electrophoresis (PFGE) and analysis
of class 2 integrons have been carried out on 60 S. sonnei isolates, including 57 sporadic isolates
from paediatric cases of shigellosis occurring in 2002 and 2003, two sporadic isolates recovered in
1984 and the ATCC 9290 strain.
Results: Biotype g and resistance to streptomycin, sulfamethoxazole-trimethoprim and
tetracycline were exhibited by 54 of the 57 recent isolates. Of the 54 biotype g isolates, 28
exhibited a class 2 integron of 2161 bp, and 24 a class 2 integron of 1371 bp, respectively. Class 2
integrons were not detected in four isolates only, including the two endemic isolates recovered in
1984 and two strains from recent sporadic cases. PFGE divided the strains into eight pulsotypes
labeled A to H, three major pulsotypes – A to C – including the large majority of the recent
sporadic S. sonnei isolates. Pulsotypes A and C were the most prevalent groups, accounting for
41.6% and 35.0%, respectively, of the isolates under study.
Conclusion: The results suggest that biotype g, class 2 integron carrying S. sonnei are prevalent in
our geographic area. S. sonnei isolated in the years 2002 and 2003 could be attributed to a few
predominant clusters including, respectively, strains with pulsotypes B and C carrying a 2161 bp
class 2 integron, and those having pulsotype A and a 1371 bp class 2 integron. A few epidemic
clones are responsible for the apparently endemic occurrence of shigellosis in Tehran, Iran.
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Background
Methods
Infections caused by Shigella species are a major cause of
diarrhoeal disease in both developing and developed
countries. Globally, it is estimated that shigellosis causes
about 1,100,000 deaths per year, two-thirds of the
patients being children under 5 years of age [1,2].
Bacterial strains
In the years 2002 and 2003, a total of 178 isolates of S.
sonnei have been isolated from enteritis cases in children
at five hospitals in Tehran, Iran. A random sample of 57
isolates was selected for the investigation. Three further
strains were added: the S. sonnei strain ATCC 9290 and
two apparently sporadic strains isolated in Tehran, Iran, in
1984.
Development and spread of multidrug resistance is
becoming a serious threat to Public Health worldwide
since the early 1960s [3]. Mobile genetic elements, such as
plasmids, transposons, genomic islands and integrons,
disseminating via horizontal transfer are exponentially
amplifying the problem [4]. In particular, the role of integrons in the dissemination of multidrug resistance in
Gram-negative bacteria is well-established [5], and their
carriage by several members of the family Enterobacteriaceae has been reported [6].
Recently, several reports have shown the successful emergence and spread in different countries of S. sonnei biotype
g carrying a class 2 integron [4,7-12]. Pulsed Field Gel
Electrophoresis (PFGE) analysis has proved that related
groups of isolates may have circulating in recent years in
different European countries [8]. Emergence and selective
pressure by use of some antimicrobial agents or, alternatively, international trade are under debate as possible
epidemiological mechanisms of the successful dissemination of this organism [13].
Shigellosis is one of the major causes of morbidity in children with diarrhea in Iran, but reports about prevalence of
serogroups and molecular epidemiological features are
limited. In two previous studies, S. flexneri has been
reported as the most prevalent species in this country in
the years 1984–'85 and 2001–'02 [14,15]. Similar patterns of serogroup prevalence have been detected in some
neighboring countries. Indeed, S. flexneri, as the most frequent serogroup, accounted for 44.0%, 58.0%, and
65.0%, respectively, of shigellosis cases in Saudi Arabia
[16], Pakistan [17] and Jordan [18]. In a subsequent
investigation conducted in 2003, however, shifting of species distribution of Shigella appeared to occur in Tehran,
Iran, where the proportion of S. sonnei isolates was 58.9
%, while that of S. flexneri 36.4% [19]. More recently, Farshad et al. (2006) has identified S. sonnei as the most prevalent Shigella species in Shiraz, Iran [20].
The present study was therefore undertaken to describe
phenotypic and genetic characteristics of S. sonnei isolates
identified in the years 2002–2003 in Tehran, Iran. Prevalence of biotypes, drug susceptibility patterns, pulsotypes
and carriage of class 2 integrons was investigated with special attention to obtain an interpretative key of the apparently endemic occurrence of disease in this geographic
area.
All strains had been identified at a genus level by conventional methods by previously described procedures [21]
while agglutination with specific antiserum from MAST
Group LTD (Mast House, Derby Road, Bootle, Merseyside, L20 1EA, UK) was used to identify the species.
Biotyping was performed by the method of Nastasi et al.
[21]. Antimicrobial susceptibility test was performed by
the disk diffusion method according to the guidelines of
the National Committee for Clinical Laboratory Standards [22]. The following antimicrobial agents were tested:
ampicillin, AMP (10 μg); ceftriaxone, CRO (30 μg); kanamycin, K (30 μg); streptomycin, STR (10 μg); tetracycline, TET (30 μg); ciprofloxacin, CP (5 μg); nalidixic acid,
NA (30 μg); chloramphenicol, C (30 μg); and sulfamethoxazole-trimethoprim, SXT (1.25/23.75 μg). Escherichia
coli ATCC 25922 was used as a quality control strain.
Pulsed Field Gel Electrophoresis (PFGE) analysis
All S. sonnei isolates were analyzed by PFGE with the
restriction enzyme XbaI (Promega, Madison, WI, USA)
under standardized conditions [23]. The Salmonella serotype Braenderup strain H9812 restricted with XbaI was
used as molecular weight standard. Strain H9812 was
kindly provided by the National Reference Centre for
Enteric Pathogens at Istituto Superiore di Sanità, Rome,
Italy.
PFGE patterns were initially visually assessed and interpreted by using the criteria established by Tenover et al.
[24]. Computer-assisted analysis of the PFGE banding
patterns was then performed with the Taxotron software
(Taxolab, Institut Pasteur, Paris, France). Genetic distances were calculated using the Unweighted Pair Group
Method using arithmetic Averages (UPGMA). Only bands
whose molecular weight exceeded 90 Kbp were considered and the calculated error was set at 10% for low
molecular weight and progressively decreased to 5% for
the highest weights (1,000 Kbp).
Class 2 integron analysis
To detect the class 2 integrons, primer pair hep74 (5'CGGGATCCCGGACGGCATGCAC GATTTGTA-3') and
hep51 (5'-GATGCCATCGCAAGTACGAG-3') was used
under conditions described previously [8]. Amplified
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DNA products of interest were cloned by use of the TA
cloning Kit (Invitrogen Life Technology, Italy) in invα F'
cells. The cloned products were sequenced by fluorescent
dye-labeled dideoxynucleotides and a 373 automatic
DNA sequencer (Perkin-Elmer, Foster City, CA), using the
universal primers M13fw and M13rev for the first 1400 bp
and the primer ss1, 5'-AAGTGGCAGCAACGGATTCG-3',
to complete the sequence. The resulting DNA sequence
was analyzed by use of the BLAST search program 2.0
within the QBLAST system at the National Center for Biotechnology Information site.
PFGE-CeuI and hybridization
To establish if the class 2 integrons were located on the
chromosome, the restriction enzyme CeuI was used to
generate a pulsed-field gel electrophoresis (PFGE) profile
to be hybridized with the int2 sequence. CeuI is a rare-cutting enzyme, which produces very large restriction fragments. The preparation of genomic DNA of S. sonnei
strains was performed according to the above protocol.
Then, DNA restriction was done with 10U CeuI enzyme
(New England Biolabs, Beverly, MA, US) at 37°C for 3 h
and DNA macrorestriction fragments were resolved on
0.7% agarose gel (Pulsed Field Certified, Bio-Rad, Hercules, CA, US) prepared in 0.5X TBE buffer (50 mM Tris,
50 mM boric acid, 0.5 mM EDTA). Lambda ladder concatamers (New England Biolabs) were used as molecular
marker. The gel was run on a CHEF-DRII system (Bio-Rad
Laboratories) under the conditions described by Liu et al.
[25]. The gel, after staining for 10 min in ethidium bromide solution (0.4 μg/ml) and destaining in distilled
water for 20 min, was visualised under UV light and photographed.
Restricted fragments were transferred onto positively
charged nylon membranes (Roche Diagnostics, Monza,
Italy) by standard methods [25]. Southern blot hybridization was carried out under high-stringency conditions
[26] using specific int2 and 16sRNA probes, obtained
amplifying the internal part of the respective genes with
the following primers: int2, ssfw 5'-TTTCAGGTGGTGGGGAGATA-3' and ssrv 5'-TTGGTACAAAAGGCGTGACA-3';
16sRNA,
S16fw
5'-CAGCCACACTGGAACTGAGA-3' and S16rev 5'-GTTAGCCGGTGCTTCTTCTG-3'. Probes were labelled by the "PCR DIG
labelling" kit (Roche Diagnostics).
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isolates obtained during the years 2002 and 2003 were
resistant to streptomycin, sulfamethoxazole-trimethoprim and tetracycline. Additional resistances to nalidixic
acid, ampicillin or kanamycin were carried by four, five
and two isolates, respectively. Two further isolates showed
ampicillin resistance associated to nalidixic acid or kanamycin, respectively. No isolates were resistant to ceftriaxone, ciprofloxacin, or chloramphenicol.
Three major clusters of S. sonnei were identified by XbaIPFGE among the sample of isolates recovered in Tehran,
Iran, in 2002 and 2003 (Figure 1): PFGE type A (n = 25
isolates), PFGE type B (n = 7 isolates) and PFGE type C (n
= 21 isolates). Three subtypes – a to c – were included into
PFGE type A, subtype a including 18 of the 25 strains. Two
subtypes, a and b, grouping five and two isolates, respectively, were observed among type B strains. Type C contained three subtypes, a to c, but subtype a included 15 of
21 isolates. The two isolates identified in 1984 were type
E.
Two different class 2 integron structures were identified
within the isolates under study. Twenty-eight (49.1%) of
the 57 isolates shared a 2161 bp class 2 integron, identified by DNA sequencing as containing four open reading
frames, namely dhfrI, satI, aadA and orfX (99% of homology with respect to the class 2 integron described by Pan
JC et al, 2006). The second smaller integron of 1371 bp
containing only two genes within the cassettes, dhfrI and
satI, was detected in 24 strains (42.1%). Alignments of the
deduced amino acid sequences revealed two sequence
substitutions in both gene cassettes, dhfrI and satI. The
sequence of the class 2 integron of 1371 bp has been submitted to GenBank (accession number AM745943).
Class 2 integrons were not detected in two strains from
sporadic cases occurring in 2003 and in the two strains
isolated in 1984. Probing using specific int2 and 16sRNA
probes confirmed the chromosomal location of both
types of class 2 integrons (see additional file 2).
All isolates belonging to PFGE types B and C proved to
possess the 2161 bp class 2 integron. Moreover, a closest
association was found between pulsotype A and the 1371
bp class 2 integron: indeed, all, but one, PFGE type A isolates were found to carry the smaller class 2 integron
(Additional file 1 and Figure 1).
Results
Fifty-four of the 57 isolates of S. sonnei identified in the
period 2002–'03 and selected for the study were attributed to biotype g and three only to biotype a. Both strains
isolated in 1984 were biotype g (Additional file 1).
Discussion
Additional file 1 summarizes the antimicrobial resistance
phenotypes of the isolates under study. Fifty-four S. sonnei
Biotype g included all, but three, recent isolates of S. sonnei. Emergence of biotype g or rhamnose negative strains
Our study was undertaken to perform a baseline assessment of the epidemiologic features characterizing the
endemic circulation of S. sonnei in Iran.
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Figure
Phylogenetic
XbaI
restriction
1
dendrogram
endonuclease
showing
fromthe
59 genetic
Shigella distances
sonnei isolates
obtained
and from the
th comparison
type strain of the serogroup
PFGE patterns produced using
Phylogenetic dendrogram showing the genetic distances obtained from th comparison of the PFGE patterns produced using
XbaI restriction endonuclease from 59 Shigella sonnei isolates and from the type strain of the serogroup.
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has been repeatedly signaled in several countries from different continents in association with the characteristic
resistance pattern streptomycin-trimethoprim frequently
associated to tetracycline [4,8,11]. Moreover, antimicrobial susceptibility testing of the Iranian isolates showed a
highest prevalence of a consistent resistance profile,
accordingly to the reports from a number of countries
[3,6,28-31]. These antibacterial drugs are commonly used
worldwide in the treatment of dysentery. No resistance
was observed to ciprofloxacin, ceftriaxone, and chloramphenicol, probably because of their very infrequent use as
alternative therapeutic regimens in our geographic area.
Selective pressure by indiscriminate use of antibiotics and
mechanisms of horizontal gene transfer have undoubtedly contributed to the emergence and diffusion of multiresistance in Shigella [6].
Although other mechanisms are possible, resistance to
streptomycin and trimethoprim seems to be attributable
to expression of genes contained in class 2 integrons.
These structures have proved to be highly prevalent within
isolates of Shigella spp. from a number of countries
[4,6,8,10,11,14]. Their gene array, generally including the
open reading frames dhfrI, sat and aad, is rather stable,
because of the presence of a defective integrase, but some
different structures have been very infrequently found in
sporadic isolates of S. sonnei [3,8,32]. Our paper firstly
describes the simultaneous circulation at approximately
similar frequencies (49.1% vs. 42.1%) in an apparently
endemic context of two groups of strains carrying, respectively, a class 2 integron of 2161 bp and a shorter integron, not containing the aad gene cassette sequence. No
specific association was apparent with the resistance pattern.
When considering results obtained by PFGE, a first
impressive feature is the limited genetic heterogeneity of
the isolates under study, along with their clustering in a
few predominant PFGE types. These findings could suggest that what is apparent as an endemic circulation of S.
sonnei in Tehran, Iran, is more likely to be interpreted as
an oligo-clonal epidemic. The paucity of types for a pathogen which has only humans as a significant reservoir of
infection, might derive from few sources of infection in a
context of epidemiological transition that, along with the
recent switching of predominant serogroup from flexneri
to sonnei, could suggest increasingly effective sanitary conditions in Tehran, Iran. On the other hand, success of S.
sonnei is warranted also in developed countries by low
infectious minimal dose, high secondary attack rates and,
in comparison with the other serogroups, a better capability to survive to stressing environmental conditions and
exploit alternative and more complex infectious routes,
such as food vehicles [33-35].
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When considering the association of phenotypic and
genetic properties of multidrug resistance, our findings
reinforce the previous considerations and suggest the
involvement of our geographic area within an epidemiological global picture of emergence and/or dissemination
of a limited number of well defined multiresistant clones
of S. sonnei. The question whether a multicentric emergence under analogous selective factors of similar particularly "fit" organisms or, alternatively, a dissemination
driven by the international trade of human and food
related resources were the most scientifically sound mechanism, arises with special evidence, when considering the
geographic scale of the phenomenon.
Molecular epidemiology provides a crucial contribution
to accurately interpret epidemiological evolution of infectious diseases in communities, when screening by phenotypic methods, such as biotyping or drug resistance
pattern analysis, is seriously hindered by the homogeneity
of circulating strains.
Conclusion
The results suggest that biotype g, class 2 integron carrying
S. sonnei are prevalent in our geographic area. S. sonnei isolated in the years 2002 and 2003 could be attributed to a
few predominant clusters including, respectively, strains
with pulsotypes B and C carrying a 2161 bp class 2 integron, and those having pulsotype A and a 1371 bp class 2
integron. A few epidemic clones are responsible for the
apparently endemic occurrence of shigellosis in Tehran,
Iran.
Competing interests
The author(s) declare that they have no competing interests.
Authors' contributions
RR and NS conceived the study, carried out biotyping,
drug resistance analysis and drafted the manuscript. RR
and AA performed PFGE analysis and detection of class 2
integrons. GMG carried out analysis of genetic similarity.
AMD performed hybridization and sequencing experiments. CM participated in study design and coordination
and helped to draft the manuscript. All authors read and
approved the final manuscript.
Additional material
Additional file 1
Characteristics of S. sonnei isolates identified in Tehran, Iran, 2002–
2003
Click here for file
[http://www.biomedcentral.com/content/supplementary/14712334-7-62-S1.doc]
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Additional file 2
PFGE-CeuI and hybridization of representative isolates of S. sonnei.
DNA restriction was done with 10U CeuI enzyme (New Englad Biolabs,
Beverly, MA, US) at 37°C for 3 h and DNA macrorestriction fragments
were resolved on 0.7% agarose gel (Pulsed Field Certified, Bio-Rad, Hercules, CA, US) suspended in 0.5X TBE buffer (50 mM Tris, 50 mM boric
acid, 0.5 mM EDTA). Lambda ladder concatamers (New England
Biolabs) were used as molecular marker. The gel was run on a CHEFDRII system (Bio-Rad Laboratories) under the conditions described by Liu
et al. (1993). The gel was stained for 10 min in ethidium bromide solution (0,4 μg/ml), destained in distilled water for 20 min, then visualised
under UV light and photographed. Restricted fragments were transferred
onto positively charged nylon membranes (Roche Diagnostics, Monza,
Italy) by standard methods (Southern, 1975). Southern blot hybridization was carried out under high-stringency conditions, by using specific
int2 and 16sRNA probes obtained amplifying the internal portion of the
respective genes and labelling the probes by the "PCR DIG labelling" kit
(Roche Diagnostics).
Click here for file
[http://www.biomedcentral.com/content/supplementary/14712334-7-62-S2.ppt]
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10.
11.
12.
13.
14.
15.
16.
17.
Acknowledgements
18.
RR has been financially supported during his study period in Italy by the
Research Center of Molecular Biology, Baqiyatallah University of Medical
Sciences, Tehran, Iran
19.
20.
The authors would like to thank the staff of the Department of Hygiene and
Microbiology, University of Palermo, for their helpful assistance in this
study. The authors would also greatly appreciate the scientific contribute
of Dr. Alessandra Carattoli.
21.
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