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INTRODUCTION
Salmonella enterica serotype Enteritidis is one of the major
Salmonella serovars which may cause human salmonellosis and
animal infections in Tunisia and in many other countries (Medici
et al., 2003; Liebana et al., 2004; Ben Aissa et al., 2007). The
main sources of human infections are foods of animal origin, such
as poultry, eggs, eggs products, milk, beef and pork (Suzuky,
1994; Boonmar et al., 1998). Previous studies have reported that
poultry can become contaminated with S. enteritidis at the farm
level. These organisms can be transferred to the production facil-
ity and can become a source of contamination for the final prod-
ucts (Bryan and Doyle, 1995; Hoover et al., 1997). Accordingly,
it’s interesting to have available phenotypic and genotypic mark-
ers that can be used in epidemiological investigations for S.
enteritidis isolates from avian sources. Traditional methods for
identifying and typing S. enteritidis include biotyping, serotyping,
and phage typing and are not efficiently discriminative due to the
instability of phenotypic traits (Thong et al., 1995; Liebana et al.,
2001). However, DNA based methods such as plasmid analysis,
IS200 restriction fragment length polymorphism; ribotyping and
pulsed field gel electrophoresis (PFGE) have proven to be efficient
for genotypic characterization of many serovar Enteritidis strains
(Millemann et al., 1995; Lin et al., 1996; Liebana et al., 2001;
Pang et al., 2007). These methods have provided useful insight
into evolution and epidemiological relationships between strains
belonging to the same serotype and phage type (Thong et al.,
1995; Lin et al., 1996; Nauerby et al., 2000).
	 The aim of this study was to investigate the occurrence of
Salmonella spp. in the environments of poultry farms in Tunisia,
as well as to characterize strains of serovar Enteritidis by plasmid
analysis, PFGE and antibiotic sensitivity testing.
Materials and methods
Sample collection and bacterial isolates. Two hundred forty
five samples (faeces, water and environmental swabs), taken at
eight poultry farms localized in different geographical areas of
Tunisia (Tunis, Ben Arous and Nabeul), were examined in this
study. Samples were processed according to international norms
for Salmonella ISO 6579, 2002 and Annex D, 2006.
	 Each sample was pre-enriched in Buffered Peptone Water
at 37 °C for 18 h and then 0.1 ml of pre-enriched mixture was
inoculated onto modified semi solid Rappaport Vassiliadis agar
(MSRV) with 0.01% novobiocin and incubated at 41.5 °C for
24 h. Where opaque growth was seen on MSRV, a 1 µl loop
from the edge of the opaque zone was inoculated onto Xylose
Lysine Desoxycholate (XLD) agar. In addition, aliquots of 0.1 ml
* Corresponding Author. Phone: +216 71 562 602;
Fax: +216 71 569 692; E-mail: salahtoumi_mohamed@
yahoo.com.
Annals of Microbiology, 59 (2) 1-5 (2009)
Phenotypic and genotypic typing of Salmonella enterica serovar Enter-
itidis isolates from poultry farms environments in Tunisia
Intissar Guedda1, Mohamed Salah Abbassi1*, Leila Soufi1, Rafika Debya1, Assia Ben Hassen2, Salah
Hammami1
1Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdar, Bab Saadoun, 1006 Tunis; 2Services des Laboratoi-
res, Centre National de Greffe de Moelle Osseuse, Tunis, Tunisie
Received 11 November 2008 / Accepted 16 March 2009
Abstract - Salmonella enterica serovar Enteritidis is one of the major Salmonella serovars which may cause animal infec-
tions and human salmonellosis. In this study, two hundred forty five samples (faeces, water and environmental swabs)
were taken from eight poultry farms localized in different geographical areas of Tunisia. We found Salmonella serovar
Enteritidis (16 strains), Salmonella typhimirium (2), Salmonella scharzengrund (2), and Salmonella braenderup (1). Sal-
monella Enteritidis strains were characterized by pulsed field gel electrophoresis (PFGE) analysis, plasmid analysis and
antibiotic resistance profiles. XbaI PFGE analysis revealed two PFGE types and plasmid profiling identified four plasmid
types. The majority of isolates were susceptible to all antibiotic tested. The combined use of phenotypic and genotypic
methods indicates the spread of a particular Salmonella Enteritidis clone. This clone is highly related to a major world-wide
clone identified in many other countries.
Key words: Salmonella Enteritidis; poultry farms; clonally related.
2	 I. Guedda et al.
and 1 ml of the pre-enrichment were respectively transferred
in 10 ml of Rappaport Vassiliadis broth incubated and 10 ml of
Muller-Kauffmann broth, and incubated at 41.5 °C (Rappaport
Vassiliadis) and at 37 °C (Muller-Kauffmann) for 18-24 h.
Afterwards, broth cultures were streaked onto both XLD agar and
Brilliant Green agar, and plates were incubated at 37 °C for 18-24
h. Plates were then examined to identify Salmonella presence.
Colonies presumptively identified as Salmonella were confirmed
by API 20E (Bio-Mérieux, Marcy l’Etoile, France).
Salmonella serotyping. Salmonella isolates were serotyped
at the National Centre for Enteropathogenic Bacteria at Pasteur
Institute, Tunisia, according to the Kauffmann-White serotyping
scheme with the use of antiserum (BioRad, France, Marnes la
coquette). Serotyping was performed by the slide agglutina-
tion method to identify the somatic O antigen and flagellar H
antigen.
Antimicrobial susceptibility testing. Antibiotic susceptibility
was determined by the disk diffusion method on Mueller-Hinton
agar as described by the Comité de l’Antibiogramme de la Société
Française de Microbiologie (www.sfm.2007). The following anti-
microbial agents were tested: amoxicillin, ticarcillin, cefoxitin,
cefotaxime, ceftazidime, azetronam, gentamicin, kanamycin,
streptomycin, tetracycline, chloramphenicol, colistin, nalidixic
acid, ciprofloxacin, trimethoprim-sulfamethoxazol, and fosfomy-
cin. Escherichia coli ATCC 25922 was used as the control.
Isolation of plasmid DNA. Plasmid DNA was isolated by the
alkaline lysis method as described by Woodford et al. (1993)
with slight modification for application to Gram negative bac-
teria. Briefly, all strains were grown overnight in 5 ml of Brain
Heart Infusion broth at 37 °C, after which 2 ml of the cultures
was harvested and washed with TE1 (100 mM Tris-HCl, 100 mM
EDTA, pH 8) at 8000 x g at 4 °C for 10 min. Cells were suspended
in 200 µl of TEG buffer (10 mM Tris-HCl, 1 mM EDTA, 50 mM
of sucrose, pH 8.0) containing lysozyme (Sigma) 1 mg/ml and
RNase (Sigma) 10 µg/ml, then incubated at 37 °C for 30 min.
The cells were lysed by the addition of 300 µl of alkaline sodium
dodecyl sulfate (0.2 M NaOH, 1% sodium dodecyl sulfate), and
the samples were incubated at 56 °C for 1 h. After addition of
200 µl of 3 M potassium acetate (pH 4.8), the samples were left
on ice for 20 min. The samples were centrifuged at 12000 x g
for 5 min at 4 °C and the precipitated debris was removed by
decanting the supernatant into a fresh tube. An equal volume
(approximately 500 µl) of phenol-chloroform-isoamyl alcohol
(25:24:1) was added, and samples were again spun for 5 min.
The DNA from 400 µl of the supernatant was precipitated with
2 volumes of cold ethanol at -20 °C during overnight, and then
centrifuged at 12000 x g at 4 °C for 20 min. The DNA pellets
were dried at 37 °C for 1 h and suspended in 25 µl of TE (10 mM
Tris-HCl, 1 mM EDTA, pH 8.0). DNA samples were analyzed by
electrophoresis in 1X TBE buffer at 80 V for 2 h on 0.7% agarose
gels. The approximate molecular sizes of plasmids were deter-
mined by comparison with known-size plasmids from Escherichia
coli V 517 (53.7, 7.2, 5.4, 5, 4, 3, 2.6 and 2 kb).
Pulsed field gel electrophoresis (PFGE). Preparation and
digestion of genomic DNA using XbaI restriction endonuclease
(Amersham Bio-sciences, Orsay, France) were performed as
described previously (Liebana et al., 2001). Electrophoresis
was performed with CHEF DR III system (BioRad laboratories,
Richmond, CA) using the following conditions: pulse times
ranged from 12 s to 40 s during 20 h at 6.0 V/cm at 14 °C. DNA
banding patterns were compared visually using the criteria of
Tenover et al. (1995).
Results
Occurrence of Salmonella serovars
Twenty-one Salmonella isolates were collected from the eight
poultry farms; sixteen were identified as Salmonella enterica
serovar Enteritidis (Salmonella Enteritidis). These isolates were
detected from samples originated from four out of the eight
farms. The other non Salmonella Enteritidis isolates were:
TABLE 1 - Phenotypic and genotypic characteristics of S. Enteritidis isolates from poultry farms in Tunisia
Strain Source Farm/ Regiona Resistance profilesb PFGE type Plasmid profile (kb) Fingerprintc
S1 Environment A/BA Am, S, N, Cip X2 P2 (40) F1: X2-P2
S2 Environment A/BA Am, T, N, Cip, F X2 P4 (54) F2: X2-P4
S3 Faeces A/BA Am, S, N, Cip, Sxt, F X2 P1 (-) F3: X2-P1
S4 Faeces A/BA Am, T, N, Cip, F X2 P3 (2,3,4) F4: X2-P3
S5 Environment A/BA Susceptible X1 P4 (54) F5: X1-P4
S6 Environment B/BA Ch X1 P4 (54) F5: X1-P4
S7 Environment B/BA Ch, S X1 P4 (54) F5: X1-P4
S8 Faeces B/BA S, T, Sxt, N X1 P4 (54) F5: X1-P4
S9 Faeces B/BA Susceptible X1 P4 (54) F5: X1-P4
S10 Faeces B/BA G X1 P4 (54) F5: X1-P4
S11 Faeces C/Nab Susceptible X1 P4 (54) F5: X1-P4
S12 Faeces C/Nab Susceptible X1 P1 (-) F6: X1-P1
S13 Faeces C/Nab Susceptible X1 P4 (54) F5: X1-P4
S14 Faeces C/Nab Susceptible X1 P1 (-) F6: X1-P1
S15 Faeces C/Nab Am, S, Cip X1 P3 (2,3,4) F7: X1-P3
S16 Environment D/Nab Susceptible X1 P4 (54) F5: X1-P4
a	 BA: Ben Arous region, Nab: Nabeul region.
b	 Am:	 amoxicillin, S: streptomycin, N: nalidixic acid, Cip: ciprofloxacin, T: tetracycline, F: fosfomycin,
		 Sxt: trimethoprim-sulfamethoxazol, Ch: chlormaphenicol, G: gentamicin.
c	 Fingerprint is composed of PFGE type/plasmid profile.
Ann. Microbiol., 59 (2), 1-5 (2009)	 3
Salmonella typhimurium (2 strains), Salmonella scharzengrund
(2 strains) and Salmonella braenderup (1 strain).
Antibiotic susceptibility
Ten distinctive antimicrobial resistance profiles were identified
among the 16 Salmonella Enteritidis isolates (Table 1). Seven
strains were susceptible to all the antimicrobial agents tested.
Nine Salmonella Enteritidis isolates exhibited resistance to at
least one antimicrobial, from which six were resistant to three
or more of tested antibiotics. Salmonella Enteritidis isolates dis-
played resistance most often to amoxicillin and nalidixic acid and
were susceptible to third-generation cephalosporins (cefotaxime
and ceftazidime) and azetronam.
Plasmid profile analysis
Plasmid analysis showed that 13 strains carried one to three
plasmids with molecular sizes ranging from 2 to 54 kb (Table 1).
Ten strains possessed only the 54-kb plasmid. Three strains were
plasmid free. According to plasmid profiles, strains were classi-
fied into 4 clusters (P1 to P4).
PFGE patterns
XbaI-PFGE analysis of 16 isolates generated two pulsotypes con-
taining 9 to 12 DNA restriction fragments. The most prevalent
genotype was the pulsotype X1, encompassing 12 isolates, which
were isolated from four farms. The second pulsotype X2 was
detected in a unique farm (Farm A) and contained four isolates
(Table 1, Fig. 1).
Combination of fingerprinting profiles
The use of various typing methods identified different groups
of clones. Therefore, their results could be combined to obtain
a detailed overall fingerprint type. A combination of results
described above (plasmid profiles and PFGE patterns) allowed
clear differentiation of seven groups (F1-F7), among which the
combined type F5 (X1-P4) was the most frequent, found in nine
strains. Of the combined types, five were present as a single
isolate (Table 1).
Discussion
In bacteria, epidemiological studies are based on many pheno-
typic and genotypic methods. The phenotypic methods are based
on the comparison of phenotypic traits exhibited by different
strains of the same species or serotype. These traits are general-
ly showed as unstable and varied according to the environmental
conditions as well as to the stability degree of the genetic pool of
the strain. However, genotypic methods investigate strains at the
genomic level, therefore were considered more reliable.
	 In our study, phenotypic typing of Salmonella isolates from
the eight poultry farms showed that S. Enteritidis was the most
prevalent serovar (16 out of 21 Salmonella strains). The other
non S. Enteritidis isolates were: S. typhimurium (2), S. scharzen-
grund (2) and S. braenderup (1). This finding is concordant with
a recent study published by Ben Aissa et al. (2007) confirming
that S. Enteritidis is the most common serotype isolated from
animal origin (especially poultry) in Tunisia during the last dec-
ade.
	 Antibiotic resistance profiles were employed in many previ-
ous studies as a typing method for several Salmonella serotypes
(Moore et al., 2003). In this report, we found that antibiogram
typing is not a very useful tool for subtyping S. enteritidis strains,
because the majority of isolates were susceptible to all antibi-
otic tested. It is interesting to note that six of all isolates were
multi-drug resistant. The presence of these strains may be due
to therapeutic practices at the farm level (Olah et al., 2004).
However, an overview of our results supports in part the reported
findings that most of the S. enteritidis strains are susceptible to
a wide range of antimicrobial agents (Ling et al., 1998).
	 Analysis of plasmid profiles has proven to be efficient for
typing several Salmonella serovars (Baggessen et al., 2000;
Malorny et al., 2001; Michael et al., 2006). However, other work-
ers (Martinetti and Altwegg, 1990; Morris et al., 1992, Liebana
et al., 2001) have reported that this method presents serious
limitations. Indeed, it has been shown that the vast majority of
serovars Enteritidis strains carry just the serospecific virulence
plasmid of ca.54 kb (Poppe et al., 1993; Nauerby et al., 2000;
FIG. 1 -	 Pulsed field gel electrophoresis (PFGE) patterns of XbaI-digested genomic DNA of Salmonella Enteritidis strains obtained from
Tunisian poultry farms. Lane M: lambda ladder marker for PFGE; lanes 1 to 10: strains S5 to S14, respectively; lanes 11 to
14: strains S1 to S4, respectively.
4	 I. Guedda et al.
Rychlick and Hradecka, 2006). Similarly, a single 54 kb plasmid
was also common in our S. Enteritidis isolates and was detected
in 12 out of 16 strains. Furthermore, it is recognised that extra-
chromosomal DNA is an unstable genetic marker owing to its
ability to integrate in the chromosome or the spontaneous curing
under unselective conditions (Liebana et al., 2001, 2002). Thus,
analysis of plasmid profiles seems to be insufficient to identify
subtypes of S. Enteritidis.
	 PFGE has been successfully used for molecular character-
ization of S. enteritidis strains in comparison with other typing
techniques (Liebana et al., 2002, 2004; Moore et al., 2003;
Dionisi et al., 2006). Many restriction endonucleases were evalu-
ated for their usefulness in PFGE such as XbaI, SpeI, AvrII, and
NotI (Tsen et al., 1999; Malorney et al., 2001). Among these,
XbaI was the most discriminative for the PFGE analysis of S.
Enteritidis strains. In our study two XbaI-PFGE types (pulso-
types X1 and X2) were found within sixty S. Enteritidis isolates.
Those types differed by more than four DNA fragments. Thus,
they were considered unrelated strains based on the previously
published consensus guidelines for PFGE interpretation (Tenover
et al., 1995). The majority of S. Enteritidis isolates (12/16)
belonged to the XbaI-PFGE X1 genotype. Strains of this cluster
were isolated from four farms located in different geographical
areas far apart from each other. This finding is in agreement with
a study reported by Liebana et al. (2001) in which the major-
ity of S. enteritidis strains isolated from English poultry farms
belonged to a single XbaI-PFGE pattern. Similarly, other workers
(Thong et al., 1995; Pang et al., 2005, 2007) have reported that
the genome of S. Enteritidis strains isolated from human and
animal origins in areas geographically far apart from (Germany,
Malaysia, Switzerland, Thailand ) each other were found to be
highly similar by PFGE. Unfortunately, we have not included
some of the reported strains as control strains in our PFGE to
evaluate their genetic relatedness with our strains. However, a
meticulous comparison of PFGE pattern X1 with published PFGE
photo of reported Malaysian and Swiss strains (Thong et al.,
1995) showed a high genetic similarity of our PFGE pattern X1
and the predominant PFGE pattern B of those strains. We can
speculate that this international dissemination of major clone
could be indicative of movement of the strains between these
countries and may be a reflection of increased global travel
(Thong et al., 1995). Furthermore, this phenomenon may be
indicates limited genetic rearrangement or recombination in
the genome of S. Enteritidis during the evolution (Pang et al.,
2007). It is important to note that instability of plasmid added
to independent phenomenon of acquisition of exogenous genetic
elements such as integrons would have contributed to the occur-
rence of closely related strains with different phenotypic pat-
terns.
	 In conclusion, the combined uses of phenotypic and geno-
typic methods indicate the emergence of a particular S. enteri-
tidis clone in different poultry farms in Tunisia. Many strains
belonging to this clone were resistant to at least one antibiotic.
These antimicrobial resistant strains can pose a significant
health risk for humans. It would be interesting to investigate
more strains from more regions to confirm the clonality of
Tunisian isolates and to determine the extent of antimicrobial
resistant strains.
Acknowledgments
We thank Dr. Chebbi Chokri and Dr. Mami Hela for providing
samples and for technicians in the laboratory of National Bone
Marrow Transplantation Centre for their excellent technical
assistance.
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Salmonella

  • 1. INTRODUCTION Salmonella enterica serotype Enteritidis is one of the major Salmonella serovars which may cause human salmonellosis and animal infections in Tunisia and in many other countries (Medici et al., 2003; Liebana et al., 2004; Ben Aissa et al., 2007). The main sources of human infections are foods of animal origin, such as poultry, eggs, eggs products, milk, beef and pork (Suzuky, 1994; Boonmar et al., 1998). Previous studies have reported that poultry can become contaminated with S. enteritidis at the farm level. These organisms can be transferred to the production facil- ity and can become a source of contamination for the final prod- ucts (Bryan and Doyle, 1995; Hoover et al., 1997). Accordingly, it’s interesting to have available phenotypic and genotypic mark- ers that can be used in epidemiological investigations for S. enteritidis isolates from avian sources. Traditional methods for identifying and typing S. enteritidis include biotyping, serotyping, and phage typing and are not efficiently discriminative due to the instability of phenotypic traits (Thong et al., 1995; Liebana et al., 2001). However, DNA based methods such as plasmid analysis, IS200 restriction fragment length polymorphism; ribotyping and pulsed field gel electrophoresis (PFGE) have proven to be efficient for genotypic characterization of many serovar Enteritidis strains (Millemann et al., 1995; Lin et al., 1996; Liebana et al., 2001; Pang et al., 2007). These methods have provided useful insight into evolution and epidemiological relationships between strains belonging to the same serotype and phage type (Thong et al., 1995; Lin et al., 1996; Nauerby et al., 2000). The aim of this study was to investigate the occurrence of Salmonella spp. in the environments of poultry farms in Tunisia, as well as to characterize strains of serovar Enteritidis by plasmid analysis, PFGE and antibiotic sensitivity testing. Materials and methods Sample collection and bacterial isolates. Two hundred forty five samples (faeces, water and environmental swabs), taken at eight poultry farms localized in different geographical areas of Tunisia (Tunis, Ben Arous and Nabeul), were examined in this study. Samples were processed according to international norms for Salmonella ISO 6579, 2002 and Annex D, 2006. Each sample was pre-enriched in Buffered Peptone Water at 37 °C for 18 h and then 0.1 ml of pre-enriched mixture was inoculated onto modified semi solid Rappaport Vassiliadis agar (MSRV) with 0.01% novobiocin and incubated at 41.5 °C for 24 h. Where opaque growth was seen on MSRV, a 1 µl loop from the edge of the opaque zone was inoculated onto Xylose Lysine Desoxycholate (XLD) agar. In addition, aliquots of 0.1 ml * Corresponding Author. Phone: +216 71 562 602; Fax: +216 71 569 692; E-mail: salahtoumi_mohamed@ yahoo.com. Annals of Microbiology, 59 (2) 1-5 (2009) Phenotypic and genotypic typing of Salmonella enterica serovar Enter- itidis isolates from poultry farms environments in Tunisia Intissar Guedda1, Mohamed Salah Abbassi1*, Leila Soufi1, Rafika Debya1, Assia Ben Hassen2, Salah Hammami1 1Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdar, Bab Saadoun, 1006 Tunis; 2Services des Laboratoi- res, Centre National de Greffe de Moelle Osseuse, Tunis, Tunisie Received 11 November 2008 / Accepted 16 March 2009 Abstract - Salmonella enterica serovar Enteritidis is one of the major Salmonella serovars which may cause animal infec- tions and human salmonellosis. In this study, two hundred forty five samples (faeces, water and environmental swabs) were taken from eight poultry farms localized in different geographical areas of Tunisia. We found Salmonella serovar Enteritidis (16 strains), Salmonella typhimirium (2), Salmonella scharzengrund (2), and Salmonella braenderup (1). Sal- monella Enteritidis strains were characterized by pulsed field gel electrophoresis (PFGE) analysis, plasmid analysis and antibiotic resistance profiles. XbaI PFGE analysis revealed two PFGE types and plasmid profiling identified four plasmid types. The majority of isolates were susceptible to all antibiotic tested. The combined use of phenotypic and genotypic methods indicates the spread of a particular Salmonella Enteritidis clone. This clone is highly related to a major world-wide clone identified in many other countries. Key words: Salmonella Enteritidis; poultry farms; clonally related.
  • 2. 2 I. Guedda et al. and 1 ml of the pre-enrichment were respectively transferred in 10 ml of Rappaport Vassiliadis broth incubated and 10 ml of Muller-Kauffmann broth, and incubated at 41.5 °C (Rappaport Vassiliadis) and at 37 °C (Muller-Kauffmann) for 18-24 h. Afterwards, broth cultures were streaked onto both XLD agar and Brilliant Green agar, and plates were incubated at 37 °C for 18-24 h. Plates were then examined to identify Salmonella presence. Colonies presumptively identified as Salmonella were confirmed by API 20E (Bio-Mérieux, Marcy l’Etoile, France). Salmonella serotyping. Salmonella isolates were serotyped at the National Centre for Enteropathogenic Bacteria at Pasteur Institute, Tunisia, according to the Kauffmann-White serotyping scheme with the use of antiserum (BioRad, France, Marnes la coquette). Serotyping was performed by the slide agglutina- tion method to identify the somatic O antigen and flagellar H antigen. Antimicrobial susceptibility testing. Antibiotic susceptibility was determined by the disk diffusion method on Mueller-Hinton agar as described by the Comité de l’Antibiogramme de la Société Française de Microbiologie (www.sfm.2007). The following anti- microbial agents were tested: amoxicillin, ticarcillin, cefoxitin, cefotaxime, ceftazidime, azetronam, gentamicin, kanamycin, streptomycin, tetracycline, chloramphenicol, colistin, nalidixic acid, ciprofloxacin, trimethoprim-sulfamethoxazol, and fosfomy- cin. Escherichia coli ATCC 25922 was used as the control. Isolation of plasmid DNA. Plasmid DNA was isolated by the alkaline lysis method as described by Woodford et al. (1993) with slight modification for application to Gram negative bac- teria. Briefly, all strains were grown overnight in 5 ml of Brain Heart Infusion broth at 37 °C, after which 2 ml of the cultures was harvested and washed with TE1 (100 mM Tris-HCl, 100 mM EDTA, pH 8) at 8000 x g at 4 °C for 10 min. Cells were suspended in 200 µl of TEG buffer (10 mM Tris-HCl, 1 mM EDTA, 50 mM of sucrose, pH 8.0) containing lysozyme (Sigma) 1 mg/ml and RNase (Sigma) 10 µg/ml, then incubated at 37 °C for 30 min. The cells were lysed by the addition of 300 µl of alkaline sodium dodecyl sulfate (0.2 M NaOH, 1% sodium dodecyl sulfate), and the samples were incubated at 56 °C for 1 h. After addition of 200 µl of 3 M potassium acetate (pH 4.8), the samples were left on ice for 20 min. The samples were centrifuged at 12000 x g for 5 min at 4 °C and the precipitated debris was removed by decanting the supernatant into a fresh tube. An equal volume (approximately 500 µl) of phenol-chloroform-isoamyl alcohol (25:24:1) was added, and samples were again spun for 5 min. The DNA from 400 µl of the supernatant was precipitated with 2 volumes of cold ethanol at -20 °C during overnight, and then centrifuged at 12000 x g at 4 °C for 20 min. The DNA pellets were dried at 37 °C for 1 h and suspended in 25 µl of TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). DNA samples were analyzed by electrophoresis in 1X TBE buffer at 80 V for 2 h on 0.7% agarose gels. The approximate molecular sizes of plasmids were deter- mined by comparison with known-size plasmids from Escherichia coli V 517 (53.7, 7.2, 5.4, 5, 4, 3, 2.6 and 2 kb). Pulsed field gel electrophoresis (PFGE). Preparation and digestion of genomic DNA using XbaI restriction endonuclease (Amersham Bio-sciences, Orsay, France) were performed as described previously (Liebana et al., 2001). Electrophoresis was performed with CHEF DR III system (BioRad laboratories, Richmond, CA) using the following conditions: pulse times ranged from 12 s to 40 s during 20 h at 6.0 V/cm at 14 °C. DNA banding patterns were compared visually using the criteria of Tenover et al. (1995). Results Occurrence of Salmonella serovars Twenty-one Salmonella isolates were collected from the eight poultry farms; sixteen were identified as Salmonella enterica serovar Enteritidis (Salmonella Enteritidis). These isolates were detected from samples originated from four out of the eight farms. The other non Salmonella Enteritidis isolates were: TABLE 1 - Phenotypic and genotypic characteristics of S. Enteritidis isolates from poultry farms in Tunisia Strain Source Farm/ Regiona Resistance profilesb PFGE type Plasmid profile (kb) Fingerprintc S1 Environment A/BA Am, S, N, Cip X2 P2 (40) F1: X2-P2 S2 Environment A/BA Am, T, N, Cip, F X2 P4 (54) F2: X2-P4 S3 Faeces A/BA Am, S, N, Cip, Sxt, F X2 P1 (-) F3: X2-P1 S4 Faeces A/BA Am, T, N, Cip, F X2 P3 (2,3,4) F4: X2-P3 S5 Environment A/BA Susceptible X1 P4 (54) F5: X1-P4 S6 Environment B/BA Ch X1 P4 (54) F5: X1-P4 S7 Environment B/BA Ch, S X1 P4 (54) F5: X1-P4 S8 Faeces B/BA S, T, Sxt, N X1 P4 (54) F5: X1-P4 S9 Faeces B/BA Susceptible X1 P4 (54) F5: X1-P4 S10 Faeces B/BA G X1 P4 (54) F5: X1-P4 S11 Faeces C/Nab Susceptible X1 P4 (54) F5: X1-P4 S12 Faeces C/Nab Susceptible X1 P1 (-) F6: X1-P1 S13 Faeces C/Nab Susceptible X1 P4 (54) F5: X1-P4 S14 Faeces C/Nab Susceptible X1 P1 (-) F6: X1-P1 S15 Faeces C/Nab Am, S, Cip X1 P3 (2,3,4) F7: X1-P3 S16 Environment D/Nab Susceptible X1 P4 (54) F5: X1-P4 a BA: Ben Arous region, Nab: Nabeul region. b Am: amoxicillin, S: streptomycin, N: nalidixic acid, Cip: ciprofloxacin, T: tetracycline, F: fosfomycin, Sxt: trimethoprim-sulfamethoxazol, Ch: chlormaphenicol, G: gentamicin. c Fingerprint is composed of PFGE type/plasmid profile.
  • 3. Ann. Microbiol., 59 (2), 1-5 (2009) 3 Salmonella typhimurium (2 strains), Salmonella scharzengrund (2 strains) and Salmonella braenderup (1 strain). Antibiotic susceptibility Ten distinctive antimicrobial resistance profiles were identified among the 16 Salmonella Enteritidis isolates (Table 1). Seven strains were susceptible to all the antimicrobial agents tested. Nine Salmonella Enteritidis isolates exhibited resistance to at least one antimicrobial, from which six were resistant to three or more of tested antibiotics. Salmonella Enteritidis isolates dis- played resistance most often to amoxicillin and nalidixic acid and were susceptible to third-generation cephalosporins (cefotaxime and ceftazidime) and azetronam. Plasmid profile analysis Plasmid analysis showed that 13 strains carried one to three plasmids with molecular sizes ranging from 2 to 54 kb (Table 1). Ten strains possessed only the 54-kb plasmid. Three strains were plasmid free. According to plasmid profiles, strains were classi- fied into 4 clusters (P1 to P4). PFGE patterns XbaI-PFGE analysis of 16 isolates generated two pulsotypes con- taining 9 to 12 DNA restriction fragments. The most prevalent genotype was the pulsotype X1, encompassing 12 isolates, which were isolated from four farms. The second pulsotype X2 was detected in a unique farm (Farm A) and contained four isolates (Table 1, Fig. 1). Combination of fingerprinting profiles The use of various typing methods identified different groups of clones. Therefore, their results could be combined to obtain a detailed overall fingerprint type. A combination of results described above (plasmid profiles and PFGE patterns) allowed clear differentiation of seven groups (F1-F7), among which the combined type F5 (X1-P4) was the most frequent, found in nine strains. Of the combined types, five were present as a single isolate (Table 1). Discussion In bacteria, epidemiological studies are based on many pheno- typic and genotypic methods. The phenotypic methods are based on the comparison of phenotypic traits exhibited by different strains of the same species or serotype. These traits are general- ly showed as unstable and varied according to the environmental conditions as well as to the stability degree of the genetic pool of the strain. However, genotypic methods investigate strains at the genomic level, therefore were considered more reliable. In our study, phenotypic typing of Salmonella isolates from the eight poultry farms showed that S. Enteritidis was the most prevalent serovar (16 out of 21 Salmonella strains). The other non S. Enteritidis isolates were: S. typhimurium (2), S. scharzen- grund (2) and S. braenderup (1). This finding is concordant with a recent study published by Ben Aissa et al. (2007) confirming that S. Enteritidis is the most common serotype isolated from animal origin (especially poultry) in Tunisia during the last dec- ade. Antibiotic resistance profiles were employed in many previ- ous studies as a typing method for several Salmonella serotypes (Moore et al., 2003). In this report, we found that antibiogram typing is not a very useful tool for subtyping S. enteritidis strains, because the majority of isolates were susceptible to all antibi- otic tested. It is interesting to note that six of all isolates were multi-drug resistant. The presence of these strains may be due to therapeutic practices at the farm level (Olah et al., 2004). However, an overview of our results supports in part the reported findings that most of the S. enteritidis strains are susceptible to a wide range of antimicrobial agents (Ling et al., 1998). Analysis of plasmid profiles has proven to be efficient for typing several Salmonella serovars (Baggessen et al., 2000; Malorny et al., 2001; Michael et al., 2006). However, other work- ers (Martinetti and Altwegg, 1990; Morris et al., 1992, Liebana et al., 2001) have reported that this method presents serious limitations. Indeed, it has been shown that the vast majority of serovars Enteritidis strains carry just the serospecific virulence plasmid of ca.54 kb (Poppe et al., 1993; Nauerby et al., 2000; FIG. 1 - Pulsed field gel electrophoresis (PFGE) patterns of XbaI-digested genomic DNA of Salmonella Enteritidis strains obtained from Tunisian poultry farms. Lane M: lambda ladder marker for PFGE; lanes 1 to 10: strains S5 to S14, respectively; lanes 11 to 14: strains S1 to S4, respectively.
  • 4. 4 I. Guedda et al. Rychlick and Hradecka, 2006). Similarly, a single 54 kb plasmid was also common in our S. Enteritidis isolates and was detected in 12 out of 16 strains. Furthermore, it is recognised that extra- chromosomal DNA is an unstable genetic marker owing to its ability to integrate in the chromosome or the spontaneous curing under unselective conditions (Liebana et al., 2001, 2002). Thus, analysis of plasmid profiles seems to be insufficient to identify subtypes of S. Enteritidis. PFGE has been successfully used for molecular character- ization of S. enteritidis strains in comparison with other typing techniques (Liebana et al., 2002, 2004; Moore et al., 2003; Dionisi et al., 2006). Many restriction endonucleases were evalu- ated for their usefulness in PFGE such as XbaI, SpeI, AvrII, and NotI (Tsen et al., 1999; Malorney et al., 2001). Among these, XbaI was the most discriminative for the PFGE analysis of S. Enteritidis strains. In our study two XbaI-PFGE types (pulso- types X1 and X2) were found within sixty S. Enteritidis isolates. Those types differed by more than four DNA fragments. Thus, they were considered unrelated strains based on the previously published consensus guidelines for PFGE interpretation (Tenover et al., 1995). The majority of S. Enteritidis isolates (12/16) belonged to the XbaI-PFGE X1 genotype. Strains of this cluster were isolated from four farms located in different geographical areas far apart from each other. This finding is in agreement with a study reported by Liebana et al. (2001) in which the major- ity of S. enteritidis strains isolated from English poultry farms belonged to a single XbaI-PFGE pattern. Similarly, other workers (Thong et al., 1995; Pang et al., 2005, 2007) have reported that the genome of S. Enteritidis strains isolated from human and animal origins in areas geographically far apart from (Germany, Malaysia, Switzerland, Thailand ) each other were found to be highly similar by PFGE. Unfortunately, we have not included some of the reported strains as control strains in our PFGE to evaluate their genetic relatedness with our strains. However, a meticulous comparison of PFGE pattern X1 with published PFGE photo of reported Malaysian and Swiss strains (Thong et al., 1995) showed a high genetic similarity of our PFGE pattern X1 and the predominant PFGE pattern B of those strains. We can speculate that this international dissemination of major clone could be indicative of movement of the strains between these countries and may be a reflection of increased global travel (Thong et al., 1995). Furthermore, this phenomenon may be indicates limited genetic rearrangement or recombination in the genome of S. Enteritidis during the evolution (Pang et al., 2007). It is important to note that instability of plasmid added to independent phenomenon of acquisition of exogenous genetic elements such as integrons would have contributed to the occur- rence of closely related strains with different phenotypic pat- terns. In conclusion, the combined uses of phenotypic and geno- typic methods indicate the emergence of a particular S. enteri- tidis clone in different poultry farms in Tunisia. Many strains belonging to this clone were resistant to at least one antibiotic. These antimicrobial resistant strains can pose a significant health risk for humans. It would be interesting to investigate more strains from more regions to confirm the clonality of Tunisian isolates and to determine the extent of antimicrobial resistant strains. Acknowledgments We thank Dr. Chebbi Chokri and Dr. Mami Hela for providing samples and for technicians in the laboratory of National Bone Marrow Transplantation Centre for their excellent technical assistance. 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