Molecular typing of Salmonella enterica serovar typhi

RAPD Fingerprinting and Genetic Diversity of Salmonella Spp. Isolated from Broiler and Layer Flocks in Karbala, Iraq

Salmonellosis in poultry is one of the most significant bacterial infections causing mortality, reduced production, and serious economic losses. This study aimed to study the molecular diversity among Salmonella isolates and investigate the epidemiological spread of these bacteria in broiler and layer chicken flocks in five different farms in Karbala, Iraq, using random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR). In total, 217 cloac a swabs were collected from the farms, out of which 129 and 88 swabs were taken from broiler and layer chickens. The samples were screened by PCR for S. enterica subsp. enterica using primers specific for the invA gene. Afterward, RAPD-PCR with uniplex or multiplex octamer primers was applied to genotype the isolates. The incidence rate of Salmonella infections in broilers and layers was estimated to be 27.9% and 12.5%. The uniplex primers P2 and P3, along with the multiplex primers yielded discriminatory patterns. Moreover, the RAPD typing showed a diverse range of banding patterns of Salmonella spp. Dendrograms created through GelJ software revealed various Salmonella genotypes in broilers and layers. The RAPD-PCR could be used as an accurate and fast tool to identify genetic relatedness among Salmonella spp. The obtained results would assist researchers in epidemiological studies and controlling salmonellosis in poultry fields.

Genotyping of Salmonella Typhi using 8-loci multi locus VNTR analysis

Background

Typhoid fever has caused severe epidemics in many Asian and African countries. The early detection of outbreaks and their sources may promote the prevention and control of typhoid fever, for which effective and timely molecular subtyping techniques are required. Pulsed field gel electrophoresis (PFGE) is routinely used as the molecular typing technique for foodborne and waterborne pathogens. However, maneuverable techniques remain necessary to expedite the experimental procedure and obtain more effective subtyping. The multilocus loci of a variable number of tandem repeats (VNTR) analysis (MLVA) is a polymerase chain reaction (PCR)-based subtyping method.

Methods

MLVA method and PFGE based on Xba I enzyme were applied to the 103 Salmonella Typhi (S. Typhi) isolated from different years and regions. Dendrograms were constructed and analyzed to help understand the data. The Simpson’s index of diversity (D value) was calculated to estimate the discriminatory power of MLVA and PFGE. In addition, a set of endogenous 3 bp DNA ladder markers were established to accurately determine the repeat copy number of the VNTR with only a 3 bp repetitive unit, using microfluidics chip-based electrophoresis to generate comparable VNTR data in the public health laboratory network.

Results

The established 8-loci MLVA for S. Typhi subtyping had higher discriminatory power than PFGE. In some cases, PFGE could not distinguish the strains isolated over long intervals and with different epidemic provinces. By contrast, 8-loci MLVA distinctly distinguished these strains, and the strains with the same MLVA patterns were from the same or contiguous years and the same province, showing its significance in epidemiological discrimination. The established set of endogenous 3 bp DNA ladder markers improved the accuracy and reproducibility of VNTR analysis using microfluidics chip-based electrophoresis to 100 %.

Conclusions

Eight VNTRs can be used for the MLVA analysis of the 103 S. Typhi isolates. MLVA based on the 8-loci had higher discriminatory power than PFGE for S. Typhi subtyping. The 8-loci MLVA is easier for the analysis and interpretation of relationships between strains compared to PFGE.

Electronic supplementary material

The online version of this article (doi:10.1186/s13099-016-0094-4) contains supplementary material, which is available to authorized users.

Molecular typing and resistance analysis of travel-associated Salmonella enterica serotype Typhi

Salmonella enterica serotype Typhi is a human pathogen causing 12 to 30% mortality and requiring antibiotic therapy to control the severity of the infection. Typhoid fever in United States is often associated with foreign travel to areas of endemicity. Increasing resistance to multiple drugs, including quinolones, is associated with decreased susceptibility to ciprofloxacin (DCS). We investigated 31 clinical strains isolated in Florida from 2007 to 2010, associated with travel to six countries, to examine the clonal distribution of the organism and apparent nalidixic acid (NAL) resistance. The strains were isolated from blood or stool of patients aged 2 to 68 years. The isolates were subtyped by ribotyping and pulsed-field gel electrophoresis. Susceptibilities to 15 antimicrobials were determined, and the isolates were screened for integrons and gyrase A gene mutations. Both typing techniques effectively segregated the strains. Identical clones were associated with different countries, while diverse types coexisted in the same geographic location. Fifty-one percent of the strains were resistant to at least one antimicrobial, and five were resistant to three or more drugs (multidrug resistant [MDR]). All 12 isolates from the Indian subcontinent were resistant to at least one drug, and 83% of those were resistant to NAL. Three of the MDR strains harbored a 750-bp integron containing the dfr7 gene. Ninety-three percent of the resistant strains showed a DCS profile. All the NAL-resistant strains contained point mutations in the quinolone resistance-determining region of gyrA. This study affirms the global clonal distribution, concomitant genetic heterogeneity, and increased NAL resistance of S. enterica serovar Typhi.

Chromosomal rearrangements in Salmonella enterica serovar Typhi strains isolated from asymptomatic human carriers

Host-specific serovars of Salmonella enterica often have large-scale chromosomal rearrangements that occur by recombination between rrn operons. Two hypotheses have been proposed to explain these rearrangements: (i) replichore imbalance from horizontal gene transfer drives the rearrangements to restore balance, or (ii) the rearrangements are a consequence of the host-specific lifestyle. Although recent evidence has refuted the replichore balance hypothesis, there has been no direct evidence for the lifestyle hypothesis. To test this hypothesis, we determined the rrn arrangement type for 20 Salmonella enterica serovar Typhi strains obtained from human carriers at periodic intervals over multiple years. These strains were also phage typed and analyzed for rearrangements that occurred over long-term storage versus routine culturing. Strains isolated from the same carrier at different time points often exhibited different arrangement types. Furthermore, colonies isolated directly from the Dorset egg slants used to store the strains also had different arrangement types. In contrast, colonies that were repeatedly cultured always had the same arrangement type. Estimated replichore balance of isolated strains did not improve over time, and some of the rearrangements resulted in decreased replicore balance. Our results support the hypothesis that the restricted lifestyle of host-specific Salmonella is responsible for the frequent chromosomal rearrangements in these serovars.

Characterization of antimicrobial resistance, molecular and phage types ofSalmonella entericaserovar Typhi isolations

Isolation rates in Canada ofSalmonella entericaserovar Typhi increased from 0·29 to 0·55 isolations/100 000 population during 2000–2006. Although no ciprofloxacin resistance was detected, nalidixic acid resistance increased from 41% to 80%. Multidrug-resistantS. Typhi represented 18% of the strains tested. Pulsed-field gel electrophoresis (PFGE) analysis of 222 isolates resulted in 91 distinct patterns clustering into four major genetic similarity groups. The five most frequently occurring PFGE patterns accounted for 46% of the isolates. Drug-resistant isolates predominantly occurred in one PFGE similarity group. There were 39 phage types identified in 826 isolates analysed with 60% described by five phage types; 134 were untypable. The phage types associated with multidrug resistance were phage types 53, B1, D1, E1, E9, G3 and M1. Improved integration of epidemiological and laboratory case data will facilitate the protection of public health in Canada during an era of increasing travel and globalization.

Evaluation of genome-derived amplicon length polymorphism PCR primers for the genetic evaluation of related strains of Salmonella

AIMS

The intent of this study is to exploit both the genetic diversity and conservation demonstrated between the Salmonella enterica ssp. enterica serovar Typhi CT18 and Salm. enterica ssp. enterica serovar Typhimurium LT2 genomes by utilizing amplicon length polymorphism (ALP) to detect and differentiate various Salmonella strains.

METHODS AND RESULTS

Methods of ALP-PCR analysis were developed based on identifying DNA sequence deletions within highly homologous regions of the Salm. Typhi CT18 and Salm. Typhimurium LT2 genomes. This study describes the application of genome-based ALP-PCR using primer pairs designed to detect genomic differences present within both Salmonella genomes and evaluated against a reference set of Salmonella strains.

CONCLUSIONS

This study defines a collection of primer sequences broadly distributed along the Salmonella genome that can differentiate various Salmonella strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

Genome-based ALP-PCR provides a useful and powerful analytical method to evaluate variability within a group of Salmonella strains independent of serological, phenotypic or other molecular approaches.

Clonal diversity of Salmonella enterica serotype Typhi isolated from patients with typhoid fever in Tehran

In this study, antimicrobial susceptibility test and genetic typing were used to characterize 15 Salmonella enterica serotype Typhi (S. Typhi) isolates recovered from sporadic cases of typhoid fever in Tehran, Iran during 2004. Antimicrobial susceptibility test showed that all isolates were susceptible to 20 antimicrobials examined in this study. Analysis of insertion elements showed that 2 IS200 types with 10 and 11 copies were present. 11 of the 15 isolates were found to possess 10 IS200 elements residing on fragments from 23 to 2.3 kb. Comparison of the RiboPrinter (automated ribotyping) patterns of S. Typhi showed that 60% (9/15) of the isolates belonged to a single ribotype. PCR based random amplified polymorphic DNA analysis (RAPD) and enterobacterial repetitive intergenic consensus (ERIC) and pulsed-field gel electrophresis (PFGE) were also performed. ERIC and RAPD-PCR method showed 2 and 3 genotyping patterns amongst the isolates, respectively. The PFGE typing was carried out by using XbaI restriction enzyme, and 7 restriction patterns were observed. Overall, the molecular typing methods applied in this study showed that the isolated S. Typhi populations were highly polyclonal as shown by PFGE.

Clonal expansion and microevolution of quinolone-resistant Salmonella enterica serotype typhi in Vietnam from 1996 to 2004

Salmonella enterica serotype Typhi clinical isolates (n = 91) resistant to nalidixic acid (Nal(r)) were collected from sporadic cases and minor outbreaks throughout Vietnam between 1996 and 2004. These isolates were typed and compared by four methods: Vi phage typing, PstI ribotyping, XbaI and SpeI pulsed-field gel electrophoresis (PFGE), and single-nucleotide polymorphism (SNP) analysis. The results indicated that 65% of the isolates were not typeable by Vi phage typing. In contrast, the ribotyping and, with more accuracy, the SNP analysis methods indicated that all Nal(r) isolates belonged to a single clone (ribotype 3a, haplotype H58) that was found previously and that largely consisted of plasmid-encoded multidrug-resistant serotype Typhi isolates. PFGE demonstrated the occurrence of microevolution within this clone. We identified two major combined PFGE profiles: X1-S1 and X3-S6. X3-S6 predominated between 1996 and 2002 but was replaced by X1-S1 after 2002. Nevertheless, PFGE, with a Simpson's index of 0.78, was not considered an optimal discriminatory method for investigating typhoid fever outbreaks in Vietnam. The rate of quinolone resistance increased and the rate of multidrug resistance decreased during the study period. From 2002 to 2004, 80.6% of the isolates from South Vietnam were resistant only to Nal. The mechanism of Nal resistance in most of the isolates (94%) was a mutation in the quinolone resistance-determining chromosomal region of gyrA that led to the amino acid substitution Ser83Phe. No plasmid-located qnrA, qnrB, or qnrS was detected.

Genotypic analysis of Salmonella enterica serovar Typhi collected during two successive autumnal typhoid outbreaks in southeast Tunisia

OBJECTIVE

Investigation of two successive autumnal outbreaks of typhoid fever that occurred in southeast Tunisia.

PATIENTS AND METHODS

Salmonella typhi isolates collected from confirmed cases of typhoid fever during the two outbreaks occurred in autumn 2004 and 2005 and from healthy carriers were analyzed by antibiogram and pulsed-field gel electrophoresis (PFGE).

RESULTS

A total of 86 isolates of Salmonella enterica serovar Typhi (76 from blood culture or stool of patients involved in both outbreaks and 10 from stool of healthy carriers) were obtained. All isolates of S. typhi were fully sensitive to all antibiotics tested, particularly to co-trimoxazole and ciprofloxacin. All isolates of 2004 (39 from patients and 10 from healthy carriers) appeared to be genetically identical when digested with SpeI, AvrII and XbaI. XbaI digestion of 2005 outbreak isolates gave five different patterns with predominance of the 2004 outbreak pattern. Both outbreaks were concomitant with the season of "legmi", fermented juice traditionally extracted from palm-tree.

CONCLUSION

PFGE with XbaI was discriminatory and can be useful for epidemiological routine investigation of typhoid fever. Typing results suggests the monoclonality of 2004 outbreak and the multiclonality of the 2005 outbreak. The epidemic clone of S. typhi is able to persist for long period in a quiet state in the population and to give again a new outbreak, when the conditions become favorable.

Analysis of Salmonella enterica serotype Typhi pulsed-field gel electrophoresis patterns associated with international travel

Typhoid fever is a significant cause of morbidity and mortality worldwide, causing an estimated 16 million cases and 600,000 deaths annually. Although overall rates of the disease have dramatically decreased in the United States, the number of travel-related infections has increased in recent decades. Drug resistance among Salmonella enterica serotype Typhi strains has emerged worldwide, making antimicrobial susceptibility testing an important function in public health laboratories. Pulsed-field gel electrophoresis (PFGE) subtyping of food-borne and waterborne pathogens has proven to be a valuable tool for the detection of outbreaks and laboratory-based surveillance. This retrospective study examined the distribution of PFGE patterns of S. enterica serotype Typhi isolates from patients with a history of international travel. Isolates were collected as part of a passive laboratory-based antimicrobial susceptibility surveillance study. Isolates were PFGE subtyped by using the restriction enzyme XbaI to restrict the total genomic DNA. Isolates indistinguishable with XbaI were further characterized using the restriction enzyme BlnI. A total of 139 isolates were typed, representing travel to 31 countries. Restriction fragment patterns consisted of 14 to 18 fragments ranging in size from 580 to 40 kbp. Seventy-nine unique PFGE patterns were generated using XbaI. Isolates from the same geographic region did not necessarily have similar PFGE patterns. Of the 139 isolates, 46 (33%) were resistant to more than one antimicrobial agent (multidrug resistant [MDR]). Twenty-seven (59%) of 46 MDR isolates had indistinguishable PFGE patterns with both XbaI and BlnI. It appears that MDR S. enterica serotype Typhi has emerged as a predominant clone in Southeast Asia and the Indian subcontinent.

Endemic, epidemic clone of Salmonella enterica serovar typhi harboring a single multidrug-resistant plasmid in Vietnam between 1995 and 2002

Salmonella enterica serovar Typhi strains resistant to ampicillin, chloramphenicol, tetracyclines, streptomycin, and cotrimoxazole, isolated from sporadic cases and minor outbreaks in Vietnam between 1995 and 2002, were typed and compared. Plasmid fingerprinting, Vi bacteriophage typing, XbaI pulsed-field gel electrophoresis, and PstI ribotyping showed that endemic, epidemic multidrug-resistant typhoid fever was due, for at least 74.1% of the isolates, to one or two clones of serovar Typhi harboring a single resistance plasmid. PstI ribotyping was used as a basic technique to ensure that a serovar Typhi expansion was clonal.

Optimization of randomly amplified polymorphic DNA-polymerase chain reaction for molecular typing of Salmonella enterica serovar Typhi

Optimization of the RAPD reaction for characterizing Salmonella enterica serovar Typhi strains was studied in order to ensure the reproducibility and the discriminatory power of this technique. Eight Salmonella serovar Typhi strains isolated from various regions in Brazil were examined for the fragment patterns produced using different concentrations of DNA template, primer, MgCl2 and Taq DNA polymerase. Using two different low stringency thermal cycle profiles, the RAPD fingerprints obtained were compared. A set of sixteen primers was evaluated for their ability to produce a high number of distinct fragments. We found that variations associated to all of the tested parameters modified the fingerprinting patterns. For the strains of Salmonella enterica serovar Typhi used in this experiment, we have defined a set of conditions for RAPD-PCR reaction, which result in a simple, fast and reproducible typing method.

Molecular epidemiology of invasive Salmonella typhi in southeast Turkey

The objective of this study was to determine the molecular epidemiology of Salmonella typhi isolates from patients with typhoid fever in southeast Turkey and to determine the relationship between the clinical strains and environmental subtypes. Both demographic and clinical data were obtained by chart review and compared to the molecular subtyping results.

Increasing genetic diversity of Salmonella enterica serovar typhi isolates from papua new guinea over the period from 1992 to 1999

Pulsed-field gel electrophoresis (PFGE) of XbaI-digested chromosomal DNA was performed on 133 strains of Salmonella enterica serovar Typhi obtained from Papua New Guinea, with the objective of assessing the temporal variation of these strains. Fifty-two strains that were isolated in 1992 and 1994 were of one phage type, D2, and only two predominant PFGE profiles, X1 and X2, were present. Another 81 strains isolated between 1997 and 1999 have shown divergence, with four new phage types, UVS I (n = 63), UVS (n = 5), VNS (n = 4), and D1 (n = 9), and more genetic variability as evidenced by the multiple and new PFGE XbaI profiles (21 profiles; Dice coefficient, F = 0.71 to 0.97). The two profiles X1 and X2 have remained the stable, dominant subtypes since 1992. Cluster analysis based on the unweighted pair group method using arithmetic averages algorithm identifies two main clusters (at 87% similarity), indicating that the divergence of the PFGE subtypes was probably derived from some genomic mutations of the X1 and X2 subtypes. The majority of isolates were from patients with mild and moderate typhoid fever and had various XbaI profiles. A single isolate from a patient with fatal typhoid fever had a unique X11 profile, while four of six isolates from patients with severe typhoid fever had the X1 pattern. In addition, 12 paired serovar Typhi isolates recovered from the blood and fecal swabs of individual patients exhibited similar PFGE patterns, while in another 11 individuals paired isolates exhibited different PFGE patterns. Three pairs of isolates recovered from three individuals had different phage types and PFGE patterns, indicating infection with multiple strains. The study reiterates the usefulness of PFGE in assessing the genetic diversity of S. enterica serovar Typhi for both long-term epidemiology and in vivo stability and instability within an individual patient.

Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old

A global collection of 26 isolates of Salmonella typhi was investigated by sequencing a total of 3336 bp in seven housekeeping genes. Only three polymorphic sites were found and the isolates fell into four sequence types. These results show that S. typhi is a recent clone whose last common ancestor existed so recently that multiple mutations have not yet accumulated. Based on molecular clock rates for the accumulation of synonymous polymorphisms, we estimate that the last common ancestor of S. typhi existed 15,000-150,000 years ago, during the human hunter-gatherer phase and prior to the development of agriculture and the domestication of animals.

Multidrug-resistant strains of Salmonella enterica serotype typhi are genetically homogenous and coexist with antibiotic-sensitive strains as distinct, independent clones

OBJECTIVE

The goal of this study was to report the molecular analysis of antibiotic-sensitive and multidrug-resistant (MDR) strains of Salmonella typhi, using pulsed-field gel electrophoresis (PFGE), with a particular emphasis on the coexistence of these strains in a typhoid-endemic region of Karachi, Pakistan.

METHODS

One hundred isolates of S. typhi in humans (50 MDR and 50 antibiotic-sensitive isolates) from sporadic cases of typhoid fever were analyzed by Vi-phage typing, antibiograms and PFGE.

RESULTS

The MDR S. typhi strains were resistant to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole. Analysis by PFGE showed that 50 MDR isolates of S. typhi had a single, homogenous PFGE profile, which was distinctly different from that of 50 antibiotic-sensitive isolates obtained in the same time frame from the same area. This latter group of isolates showed much greater diversity of PFGE profiles, as has been observed in other endemic regions.

CONCLUSIONS

Multidrug-resistant and antibiotic-susceptible strains of S. typhi can coexist in endemic areas as epidemiologically independent pathogens and are not in competition for continued persistence and transmission.

Genotypic characterisation by PFGE of Salmonella enterica serotype Enteritidis phage types 1, 4, 6, and 8 isolated from animal and human sources in three European countries

A total of 101 strains of Salmonella Enteritidis phage types (PT) 1, 4, 6, and 8 from Denmark, England and Spain were studied by PFGE to elucidate genetic relationships among strains isolated from animal, human and environmental sources between 1983 and 1997. Analysis with Xba I, Bln I and Spe I enzymes showed that the power of discrimination of this method was increased by the combination of the three enzymes (D=0.802), subdividing the strains into 28 genomic groups or genotypes. Many of the PT1, PT4, and PT6 strains from the three countries shared the same PFGE combination profile A1-A1-A1, confirming the close relationship among these phage types and the protracted spread of a single clone over a large geographical area. In general, strains from Denmark showed more variation in their PFGE profiles than those from England and Spain. PT4 strains exhibited genetic homogeneity in the three countries independently of their sources and period of isolation. Spe I gave the highest index of discrimination among PT6 strains as evidenced by a variety of PFGE profiles. The data clearly confirmed that PT8 strains isolated in the three countries were of a unique clonal origin, and the PFGE combination profile A10-A10-A1 was predominant and specific for this phage type. It is concluded that PFGE, in combination with phage typing, represents a suitable tool for the epidemiological typing of Salmonella Enteritidis strains which could be used for investigations or surveillance of the international spread of these clones.

Genotypic characterization of Salmonella typhi by amplified fragment length polymorphism fingerprinting provides increased discrimination as compared to pulsed-field gel electrophoresis and ribotyping

Amplified fragment length polymorphism (AFLP) is a recently developed, PCR-based high resolution fingerprinting method that is able to generate complex banding patterns which can be used to delineate intraspecific genetic relationships among bacteria. In the present study, AFLP was evaluated for its usefulness in the molecular typing of Salmonella typhi in comparison to ribotyping and pulsed-field gel electrophoresis (PFGE). Six S. typhi isolates from diverse geographic areas (Malaysia, Indonesia, India, Chile, Papua New Guinea and Switzerland) gave unique, heterogeneous profiles when typed by AFLP, a result which was consistent with ribotyping and PFGE analysis. In a further study of selected S. typhi isolates from Papua New Guinea which caused fatal and non-fatal disease previously shown to be clonally related by PFGE, AFLP discriminated between these isolates but did not indicate a linkage between genotype with virulence. We conclude that AFLP (discriminatory index=0.88) has a higher discriminatory power for strain differentiation among S. typhi than ribotyping (DI=0.63) and PFGE (DI=0.74).

Epidemic typhoid in vietnam: molecular typing of multiple-antibiotic-resistant Salmonella enterica serotype typhi from four outbreaks

Multidrug-resistant Salmonella enterica serotype Typhi isolates from four outbreaks of typhoid fever in southern Vietnam between 1993 and 1997 were compared. Pulsed-field gel electrophoresis, bacteriophage and plasmid typing, and antibiotic susceptibilities showed that independent outbreaks of multidrug-resistant typhoid fever in southern Vietnam are caused by single bacterial strains. However, different outbreaks do not derive from the clonal expansion of a single multidrug-resistant serotype Typhi strain.

Molecular methods for the epidemiological typing of Salmonella enterica serotype Typhi from Hong Kong and Vietnam

A total of 217 and 73 strains of Salmonella enterica serotype Typhi isolated from 1985 to 1997 in Hong Kong and in 2 months of 1989 and 1990 in Vietnam, respectively, were studied. These isolates were typed by plasmid profile analysis, plasmid fingerprinting, ribotyping with PstI, and total DNA fingerprinting with NarI. There appeared to be no major outbreak of typhoid fever in Hong Kong during the study period since there was considerable heterogeneity among the isolates. Isolates from Hong Kong were different from those from Vietnam. Thirty-seven percent of Vietnamese isolates belonged to two predominant clones, with the rest being heterogeneous in nature. Total DNA fingerprinting supplemented with ribotyping could be a reliable and rapid method for epidemiological typing of S. enterica serotype Typhi.

Propagation of TEM- and PSE-type beta-lactamases among amoxicillin-resistant Salmonella spp. isolated in France

A survey conducted between 1987 and 1994 at the University Hospital of Besançon, France, demonstrated a dramatic increase (from 0 to 42. 5%) in the prevalence of amoxicillin resistance among Salmonella spp. Of the 96 resistant isolates collected during this period (including 77 Typhimurium), 54 were found to produce TEM-1 beta-lactamase, 40 produced PSE-1 (equivalent to CARB-2), one produced PSE-1 plus TEM-2, and one produced OXA-1 in isoelectric focusing and DNA hybridization experiments. Plasmids coding for these beta-lactamases were further characterized by (i) profile analysis, (ii) restriction fragmentation pattern analysis, (iii) hybridization with an spvCD-orfE virulence probe, and (iv) replicon typing. In addition, isolates of S. typhimurium were genotypically compared by pulsed-field gel electrophoresis of XbaI-macrorestricted chromosomal DNA. Altogether, these methods showed that 40 of the 41 PSE-1 producers were actually the progeny of a single epidemic S. typhimurium strain lysotype DT104. Isolates of that strain were found to harbor RepFIC virulence plasmids with somewhat different restriction profiles, but which all carried the bla(PSE-1) gene. Of these virulence/resistance plasmids, 15 were transmissible to Escherichia coli. TEM-1-producing S. typhimurium displayed much greater genotypic and plasmidic diversities, suggesting the acquisition of the bla(TEM-1) gene from multiple bacterial sources by individual strains. In agreement with this, 32 of the 35 S. typhimurium plasmids encoding TEM-1 were found to be conjugative. These data show that development of amoxicillin resistance among Salmonella, especially in serovar Typhimurium, results from both gene transfers and strain dissemination.

Molecular typing of multiple-antibiotic-resistant Salmonella enterica serovar Typhi from Vietnam: application to acute and relapse cases of typhoid fever

The rate of multiple-antibiotic resistance is increasing among Salmonella enterica serovar Typhi strains in Southeast Asia. Pulsed-field gel electrophoresis (PFGE) and other typing methods were used to analyze drug-resistant and -susceptible organisms isolated from patients with typhoid fever in several districts in southern Vietnam. Multiple PFGE and phage typing patterns were detected, although individual patients were infected with strains of a single type. The PFGE patterns were stable when the S. enterica serovar Typhi strains were passaged many times in vitro on laboratory medium. Paired S. enterica serovar Typhi isolates recovered from the blood and bone marrow of individual patients exhibited similar PFGE patterns. Typing of S. enterica serovar Typhi isolates from patients with relapses of typhoid indicated that the majority of relapses were caused by the same S. enterica serovar Typhi strain that was isolated during the initial infection. However, some individuals were infected with distinct and presumably newly acquired S. enterica serovar Typhi isolates.

Use of pulsed field gel electrophoresis as an epidemiological tool for analysis of sporadic associated strains of Salmonella typhi isolated in Taiwan

In order to characterize the subtypes of Salmonella typhi which cause sporadic disease in Taiwan, 55 isolates of Salm. typhi obtained from unrelated patients of sporadic cases during 1992-96 were subjected to chromosomal DNA digestion and pulsed field gel electrophoresis (PFGE). When DNAs of these 55 Salm. typhi strains were digested with XbaI, 41 PFGE patterns were observed. Strains sharing the same XbaI digestion pattern could not be further discriminated by PFGE analysis using SpeI and NotI as digestion enzymes. Thus, considerable genetic diversity exists among the Salm. typhi isolates. Although strains of the same patterns were mainly isolated during the same time, recirculation of certain infectious strains could be possible. When 12 antibiotics, i.e. ampicillin, trimethoprim/sulfamethoxazole, erythromycin, norfloxacin, tetracycline, sulphonamide, streptomycin, neomycin, chloramphenicol, kanamycin, cefoperazone and gentamycin were used to test the antibiotic susceptibility for these Salmonella isolates, only three antibiogram patterns were obtained and 49 of the 55 Salm. typhi isolates were found to belong to one pattern. Phage typing and plasmid profiles were also poor in discriminating these strains. Thus, PFGE alone may be used as a powerful tool for analysis of sporadic associated Salm. typhi strains.

Bacterial population genetics, evolution and epidemiology

Asexual bacterial populations inevitably consist of an assemblage of distinct clonal lineages. However, bacterial populations are not entirely asexual since recombinational exchanges occur, mobilizing small genome segments among lineages and species. The relative contribution of recombination, as opposed to de novo mutation, in the generation of new bacterial genotypes varies among bacterial populations and, as this contribution increases, the clonality of a given population decreases. In consequence, a spectrum of possible population structures exists, with few bacterial species occupying the extremes of highly clonal and completely non-clonal, most containing both clonal and non-clonal elements. The analysis of collections of bacterial isolates, which accurately represent the natural population, by nucleotide sequence determination of multiple housekeeping loci provides data that can be used both to investigate the population structure of bacterial pathogens and for the molecular characterization of bacterial isolates. Understanding the population structure of a given pathogen is important since it impacts on the questions that can be addressed by, and the methods and samples required for, effective molecular epidemiological studies.

Application of random amplified polymorphic DNA analysis to differentiate strains of Salmonella typhi and other Salmonella species

A Random Amplified Polymorphic DNA (RAPD) fingerprinting method was developed to differentiate isolates of Salmonella serotype typhi (S. typhi) and other Salmonella isolates. A panel of five primers was used to examine 63 isolates of Salm. typhi, including 56 strains isolated in Taiwan and seven strains obtained abroad. Twenty-one RAPD types were revealed using the RAPD fingerprinting method. An RAPD with primer 6032 yielded a polymorphism in a 350 bp fragment that differentiated the attenuated vaccine strain Salm. typhi Ty21a from the rest of the Salm. typhi strains. Strains of Salm. typhi were divided into five types with primer D14307. Primer D14307 also proved capable of discrimination among 65 other Salmonella isolates representing 42 different serotypes. The bacterial DNA used in this RAPD protocol was obtained using a commercially available DNA extraction kit (GeneReleaser). The DNA of various strains of Salmonella from this simple extraction procedure could be discriminated within a few hours using the RAPD technique.

Chromosomal rearrangements in Salmonella enterica serotype typhi affecting molecular typing in outbreak investigations

Salmonella enterica serotype Typhi strains belonging to eight different outbreaks of typhoid fever that occurred in Spain between 1989 and 1994 were analyzed by ribotyping and pulsed-field gel electrophoresis. For three outbreaks, two different patterns were detected for each outbreak. The partial digestion analysis by the intron-encoded endonuclease I-CeuI of the two different strains from each outbreak provided an excellent tool for examining the organization of the genomes of epidemiologically related strains. S. enterica serotype Typhi seems to be more susceptible than other serotypes to genetic rearrangements produced by homologous recombinations between rrn operons; these rearrangements do not substantially alter the stability or survival of the bacterium. We conclude that genetic rearrangements can occur during the emergence of an outbreak.

Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms

Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms. To evaluate MLST, we determined the sequences of approximately 470-bp fragments from 11 housekeeping genes in a reference set of 107 isolates of Neisseria meningitidis from invasive disease and healthy carriers. For each locus, alleles were assigned arbitrary numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus enzyme electrophoresis. A subset of six gene fragments was chosen that retained the resolution and congruence achieved by using all 11 loci. Most isolates from hyper-virulent lineages of serogroups A, B, and C meningococci were identical for all loci or differed from the majority type at only a single locus. MLST using six loci therefore reliably identified the major meningococcal lineages associated with invasive disease. MLST can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate. The overwhelming advantage of MLST over other molecular typing methods is that sequence data are truly portable between laboratories, permitting one expanding global database per species to be placed on a World-Wide Web site, thus enabling exchange of molecular typing data for global epidemiology via the Internet.

Genetic typing methods applied to the differentiation of clonal lines among Salmonella enterica serogroup G strains causing human salmonellosis

In Spain, in November 1995, an epidemiological alert recommended the surveillance of Salmonella serogroup G. The nine clinical isolates collected after and the four collected before the alert in Asturias were differentiated into six clonal lines by the combination of results from HincII ribotyping, PCR ribotyping, and RAPD typing using primers named A and S. The seven Gumpensis isolates showed identical DNA fingerprinting with the four typing procedures falling into a line. Six of these were collected during May-August from people living in a single health area suggesting that they could be associated with a community outbreak. The four Worthington isolates fell into three other lines, one Poona isolate into another line and one Havana isolate into another. 100% typeability was shown with all methods. The reproducibility of HincII ribotyping was better than that of PCR-based methods, although these were less time-consuming. The highest discriminatory power was obtained with HincII ribotyping and RAPD typing using primer A.