Analysis of Salmonella enteritidis strains isolated from food-poisoning cases in Taiwan by pulsed field gel electrophoresis, plasmid profile and phage typing

Molecular epidemiological analysis of five outbreaks associated with Salmonella enterica serovar Enteritidis between 2008 and 2010 on Jeju Island, Republic of Korea

With the increasing incidence of Salmonella enterica serovar Enteritidis (SE) infections, five SE foodborne outbreaks were identified between 2008 and 2010 on Jeju Island, Republic of Korea. In this study, the genetic relatedness of isolates recovered from the five outbreaks was investigated to identify the source of foodborne SE infections. In total, 57 SE isolates from five outbreaks (17 isolates, 5 isolates, 18 isolates, 8 isolates, and 9 isolates, respectively) were used for antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), and multiple-locus variable-number tandem repeat analysis (MLVA). SE isolates from 2008 and 2009 were resistant to nalidixic acid, whereas SE isolates from 2010 were resistant to five antibiotics. Of the five outbreaks, outbreaks A, B, and D had identical PFGE-XbaI and PFGE-BlnI patterns, SEGX01.003 and SEGA26.001, respectively. Outbreak C had patterns SEGX01.011 and SEGA26.005, and outbreak E had patterns SEGX01.007 and SEGA26.007. However, MLVA profiles further distinguished the SE isolates from each outbreak into patterns SEGM.014 (outbreak A), SEGM.012 (outbreak B), SEGM.008 (outbreak C), SEGM.016 (outbreak D), and SEGM.015 (outbreak E). Among these five outbreaks, three outbreaks were presumed to be caused by the clonal SE isolates depending on PFGE pattern, but the MLVA results elucidated that these were caused by different SE isolates from the different origins. Therefore, for the epidemiological investigation or surveillance of SE foodborne diseases, both PFGE and MLVA should be used together.

MLVA typing reveals higher genetic homogeneity among S. Enteritidis strains isolated from food, humans and chickens in Brazil in comparison to the North American strains

Salmonella Enteritidis (S. Enteritidis) is a major causative agent of food-borne gastroenteritis associated with the consumption of contaminated poultry products. In this study we used multilocus variable number of tandem repeats (VNTRs) analysis (MLVA) to discriminate a total of 188 S. Enteritidis strains recovered from human (n=67), food (n=61) and chickens (n=60) during a 24 year period (1986 through 2010) in Brazil. MLVA profiles of the 188 strains from Brazil were compared to the MLVA profiles of 100 human clinical (n=52) and poultry-associated (n=48) strains isolated in North America between 1986 and 2008. MLVA typing led to classification of the 288 strains from Brazil and North America into two major clusters named A and B with 35% of similarity. Cluster A consisted of a vast majority of strains isolated from North America (n=71) and only three strains isolated from Brazil which included two pre-pandemic strains (SE5 and SE4). In contrast, cluster B consisted of all of the post-pandemic strains isolated from Brazil (n=185) and fewer strains isolated from North America (n=29). In general, MLVA typing showed that the North American strains were more genetically diverse whereas Brazilian strains were more genetically clonal. The clustering of pre-pandemic strains from Brazil with the North American strains suggests the possibility that the pre-pandemic strains were more likely genetically diverse; however after 1993 a new and prevalent subtype of S. Enteritidis was introduced in this country. This is the first study describing MLVA genotyping of the S. Enteritidis strains isolated from Brazil.

Development of a sequence typing scheme for differentiation of Salmonella Enteritidis strains

A DNA sequence typing scheme based on the caiC and SEN0629 loci was developed for differentiation of Salmonella Enteritidis strains and validated using a diverse collection of 102 isolates representing 38 phage types from different sources, year of isolation, geographical locations and epidemiological backgrounds. caiC encodes a probable crotonobetaine/carnitine-CoA ligase, and SEN0629 is a pseudogene. Our system allowed for discrimination of 16 sequence types (STs) among the 102 isolates analysed and intraphage type differentiation. Our findings also suggested that the stability of phage typing may be adversely affected by the occurrence of phage type conversion events. During a confirmatory phage typing analysis performed by a reference laboratory, 13 of 31 S.  Enteritidis strains representing nine phage types were assigned phage types that differed from the ones originally determined by the same reference laboratory. It is possible that this phenomenon passes largely unrecognized in reference laboratories performing routine phage typing analyses. Our results demonstrate that phage typing is an unstable system displaying limited reproducibility and that the two-loci sequence typing scheme is highly discriminatory, stable, truly portable and has the potential to become the new gold standard for epidemiological typing of S . Enteritidis strains.

Molecular typing of Salmonella enterica serovar Sofia in Australia by pulsed-field gel electrophoresis and repetitive element PCR typing

AIMS

In this study, we used two molecular fingerprinting methods to investigate the genetic and clonal relationship shared by Australian Salmonella Sofia isolates.

METHODS AND RESULTS

A total of 84 Australian Salm. Sofia isolates from various states in Australia were typed using pulsed-field gel electrophoresis (PFGE) (XbaI and SpeI) and repetitive element PCR (REP1R-I primer). The previous problem of DNA degradation of Salm. Sofia strains was solved by modifying the lysis solution used to treat the bacterial plugs, allowing Salm. Sofia to be subtyped using PFGE. Molecular typing of isolates resulted in the generation of eight XbaI, six SpeI and five REP1 pattern profiles. Individual typing methods showed low discrimination index values (<0·5), indicating the poor discriminatory ability of the methods. However, the combination of the typing methods was able to improve the discrimination of isolates, further dividing them into 16 subtypes and raising the index value to 0·721.

CONCLUSIONS

The combination of typing methods was shown to be the best approach to fingerprint Salm. Sofia. The Australian Salm. Sofia isolates only showed limited genetic diversity and probably share a clonal relationship. A majority of the Salm. Sofia isolates were not geographically restricted with the predominant pattern subtype observed amongst the isolates from various states.

SIGNIFICANCE AND IMPACT OF THE STUDY

We have successfully devised a PFGE protocol that counteracts DNase activity of Salm. Sofia, enabling typing of this serovar.

Limited genetic diversity and gene expression differences between egg- and non-egg-related Salmonella Enteritidis strains

Salmonella Enteritidis strains of egg- and non-egg-related origin were characterized molecularly to find markers correlated with the egg-contaminating property of Salmonella Enteritidis. Isolates were examined by random amplified polymorphic DNA (RAPD), plasmid profiling and phage typing. Furthermore, the presence of 30 virulence genes was tested by PCR. In genetic fingerprinting and gene content, only small differences between the strains were found and no correlation was observed with the origin (egg-related versus non-egg-related). A major RADP group was present in both egg- and non-egg-related strains, but other smaller RAPD groups were present as well in both categories of strains. Phage types PT4 and PT21 were predominant. Differential mRNA expression levels of fimA and agfA under conditions of growth simulating the conditions during egg formation were determined by real-time RT-PCR. Although differences in fimA and agfA expression levels were observed between the strains, these could not be correlated with the origin of the strains (egg-related versus non-egg-related). The highest expression levels of agfA and fimA were only found in two non-egg-related strains, which seemed to be correlated with the presence of a 93 kb plasmid instead of the 60 kb virulence plasmid. Our results seem to indicate only a limited role for at least type I fimbriae (encoded by fim operon) in egg contamination by Salmonella Enteritidis.

Molecular study of Salmonella enteritidis in poultry samples by PCR, plasmid curing, antibiotic resistance and protein pattern analysis

In this study two control isolates of Salmonella enteritidis, RTCC1623 and RTCC1624, were obtained from the institute ofRazi (Karaj-Iran) and 14 strains were isolated from poultry samples in Kermanshah province of Iran, according to a standard protocol. These isolates were confirmed by PCR amplification of SefA gene fragments. Results showed that, 6 isolates of 14 isolates of Salmonella which their biochemical tests were positive contain 511 bp amplified fragments of the SefA gene. In other purpose, to correlating the presence of plasmids with antibiotic resistance and protein pattern, plasmid DNA was isolated before and after plasmid curing by using the alkaline lysis method. Strains of S. enteritidis contain seven different plasmid profiles (P1-P7) which were characterized by antibiotic resistance and protein pattern. Our observed showed, there was a high molecular weight plasmid with Rf 0.17 in all strains and the frequency of other plasmids was low. The plasmid with Rf about 0.2 is responsible for resistance to Cephalothin and the isolates that lost it were susceptible to this antibiotic. All strains, 100%, were resistant to ampicillin before and after curing of strains. According to present findings, PCR is a rapid and sensitive method for typing of S. enteritidis and plasmid profiling; antibiotic resistance and protein pattern are suitable methods for subtyping of S. enteritidis isolates. No direct correlation was found between plasmid contents, antibiotic resistance patterns and protein profiles of local S. enteritidis isolates.

Note. Genetic Diversity of Food Isolates of Salmonella enterica serovar Typhimurium in India

The study aimed to determine the genetic diversity of Salmonella enterica serovar Typhimurium isolates from sprouts and fish samples from India. Twenty-eight S. Typhimurium isolates were genotyped by pulsed-field gel electrophoresis and tested for antibiotic susceptibility, plasmid profile, and presence of virulence genes ( invA and spvC). Three distinct XbaI-pulsed-field profiles (PFPs) were observed. Out of 22 isolates from sprouts, 20 showed PFP-A and remaining two showed PFP-B. All six fish isolates showed PFP-C. All the strains were sensitive to the examined antibiotics except two strains of PFP-A. Two different plasmid profiles P1 and P2 were observed. P2 was observed only in the antibiotic resistant strains. All strains were positive for the invA, whereas spvC was detected only in sprout isolates. There was no specific pattern in occurrence of the genotypes with respect to seasons. However, PFP-A was dominant and was isolated throughout the year. This is the first report to assess the genotypic diversity of S. Typhimurium obtained in foods from India. As S. Typhimurium is the predominant serotype in India, the data generated in this study would be useful in epidemiological studies during outbreaks of Salmonellosis in India.

Trends in Salmonella enterica serotypes isolated from human, food, animal, and environment in Tunisia, 1994–2004

OBJECTIVE

The present study was conducted to investigate, for the first time in Tunisia, the current trends in Salmonella enterica serotypes in Tunisia (human, food, animal, and environment) which would help to improve the control and prevention of Salmonella infections.

METHODS

Data from 1994 to 2004 from the National Centre of Enteropathogenic Bacteria - Pasteur Institute - Tunis, were analysed a total of 16,214 Salmonella isolates that were reported from all over Tunisia and serotyped according to the Kauffman-White scheme. Statistical analysis was done by SPSS v.11.5 software.

RESULTS

The isolation rate was decreasing in the human and food categories only. The top three frequently isolated serotypes during the 11-years were: Enteritidis (25.5%), Anatum (14%), and Corvallis (13.2%), indicating Tunisia as an endemic area for these serotypes. Among human isolates, Enteritidis was the most common serotype, accounting for 24% of all isolates. Among nonhuman isolates, Anatum (28%), Enteritidis (69%), and Corvallis (17.3%) were reported as the first common serotypes for food, animal and environmental samples, respectively. Percentage of Salmonella isolates demonstrated a marked pattern of seasonality, increasing in the warm spring months for human, food and animal isolates. Except for environmental isolates which increased in the spring season. Human salmonellosis outbreak by serotypes Mbandaka, Livingstone, and Typhi Vi+ had been reported during the years: 1997, 1999, 2002 and 2004.

CONCLUSION

Importance of enhancing the Salmonella surveillance system not only in Tunisia but also in the neighboring countries, and the need to get a better monitoring of trends in serotypes over time which would provide information about emerging serotypes and about the efficacy of prevention and control measures.

Molecular typing of Salmonella enterica serovars Enteritidis, Corvallis, Anatum and Typhimurium from food and human stool samples in Tunisia, 2001-2004

During the period from 2001 to 2004, a total of 72 isolates of Salmonella enterica serovars: Anatum (n=40), Enteritidis (n=18), Corvallis (n=8), and Typhimurium (n=6), of various origins (mainly food and diarrhoeagenic stool samples), were collected and further characterized by antibiotic resistance, plasmid analysis, and pulsed-field gel electrophoresis (PFGE). Forty-five isolates presented multidrug resistance to antibiotics. Among which one S. enterica serovar Anatum isolate was resistant to 11 antibiotics, and one S. enterica serovar Typhimurium DT104 isolate was resistant to eight antibiotics. Plasmid profiling identified eight plasmid profiles (with 1-5 plasmids) among the isolates, of which one plasmid profile (P01) was predominant. XbaI PFGE analysis revealed the presence of a predominant clone of the four studied Salmonella serovars circulating in Tunisia throughout the years 2001-2004.

A pulsed field gel electrophoresis (PFGE) study that suggests a major world-wide clone of Salmonella enterica serovar Enteritidis

Since human infections by Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) have been increasing world-wide over the past years and epidemiological studies have implicated the consumption of meat, poultry, eggs and egg products, elucidation of the predominant subtypes for this Salmonella spp. is important. In this study, 107 poultry and food isolates of Salmonella Enteritidis obtained from Germany were analyzed by pulsed field gel electrophoresis (PFGE), and the subtypes were compared with those of the 124 human isolates obtained in Taiwan. Results showed that for these 107 poultry and food isolates, when XbaI, SpeI and NotI were used for chromosomal DNA digestion followed by PFGE analysis, a total of 19, 20 and 19 PFGE patterns, respectively, were identified. Of them, 51 (47.7%), 52 (48.6%) and 42 (39.3%) strains belong to a single pattern of X3, S3 and N3, respectively, and 34 strains belong to a pattern combination of X3S3N3, which was the major subtype. When PFGE patterns of these 107 German isolates were compared with those of the 124 human isolates obtained in Taiwan, pattern combination of X3S3N3 was found as the most common pattern shared by isolates from both areas. PT4 is a major phage type for German and Taiwan isolates. Although most of the X3S3N3 strains are of this phage type, some strains of other PFGE patterns are also of this phage type. Since strains used in this study were unrelated, i.e., they were isolated from different origins in areas geographically far apart from each other, the PFGE study suggests a major world-wide clone of S. enterica serovar Enteritidis.

Molecular analysis of Salmonella enteritidis and Typhimurium clinical and food isolates by pulsed-field gel electrophoresis in Bogotá, Colombia

In 1997, the Microbiology Group of the Colombian Instituto Nacional de Salud set up a surveillance program with the National Public Health Laboratories to monitor the principal etiological agents responsible for acute diarrheal disease. The main goal of this study was to determine the XbaI DNA digestion patterns of clinical and food Salmonella spp. isolates recovered in Bogotá from 1997 to 2002, and related them to the susceptibility patterns to antimicrobial agents. Two hundred and twenty-four Salmonella spp. isolates were studied, 153 (63%) S. Enteritidis and 71 (37%) S. Typhimurium. Pulsed-field gel electrophoresis (PFGE) was done using the XbaI restriction enzyme and Salmonella Braenderup H9812 as the molecular weight marker. For S. Enteritidis, pattern S. En0001 was found to be prevalent in 127 (83%) isolates, 78 (61%) susceptible to the antimicrobial agents tested. For S. Typhimurium, pattern S. Typ0001 was predominant in 18 (25%) isolates with different antimicrobial resistance profiles. Patterns S. En0001 and S. Typ0001 prevailed monthly during the 6 years of the study. Data collected demonstrate that there was a dominant pattern of S. Enteritidis and S. Typhimurium circulating in clinical and food isolates in Bogotá, Colombia.

Pulsed-field gel electrophoresis, plasmid profiles and phage types for the human isolates of Salmonella enterica serovar Enteritidis obtained over 13 years in Taiwan

AIMS

Plasmid profile, phage typing, and pulsed-field gel electrophoresis (PFGE) patterns of 124 Salmonella Enteritidis strains isolated in 1998-2002 in Taiwan were analysed and the results were compared with those of the 63 strains obtained in 1991-1997, so that molecular subtypes and epidemic strains for Salmonella Enteritidis over a 13-year period (1991-2002) could be elucidated.

METHODS AND RESULTS

A total of 124 strains of Salmonella Enteritidis isolated from human in Taiwan between 1998 and 2002 were analysed by PFGE, plasmid analysis and phage typing. The results obtained were compared with those of the 63 strains obtained in 1991-1997, so that the clonal relationships for a total of 187 strains obtained over 13 years could be elucidated. For PFGE, restriction enzymes XbaI, SpeI and NotI were used for chromosomal DNA digestion. Results showed 28 PFGE pattern combinations for the 187 Salmonella strains. Of them, pattern X3S3N3 was the major subtype as 130 strains isolated from different locations during 1991-2002 showed this PFGE pattern. For all these 187 strains, the genetic similarity was higher than 80%. Plasmid analysis showed 17 distinct types, which consist of one to four plasmids and the predominant phage type of those strains was PT4 (71.6%) and PT6a (13.4%). The three methods identified different degrees of polymorphism in the following order: plasmid profile (18 types, D = 0.659) > PFGE (28 types, D = 0.512) > phage typing (13 types, D = 0.438). As PFGE patterns, phage type and plasmid profile were combined for subtyping, the 187 strains could be grouped into 46 subtypes and the discriminatory index was raised to 0.795. For these 46 subtypes, the predominant one was X3S3N3/P1/PT4, which contained 77 (41%) isolates.

CONCLUSIONS

Most of the Salmonella Enteritidis strains from sporadic cases were with pattern X3S3N3. They were the prevalent and may be the epidemic strains found in Taiwan during 1991-2002. The present study suggested that the several variants were derived from a single clonal line and the genome for strains of Salmonella Enteritidis are highly conserved over a 13-year period (1991-2002).

SIGNIFICANCE AND IMPACT OF THE STUDY

The results obtained here are useful for epidemiolgical study of salmonellosis caused by Salmonella Enteritidis in Taiwan. Comparing the data of the present study with those obtained for strains from other countries, the major subtypes for Salmonella Enteritidis infection in the world can be elucidated.

Automated genotyping of Saccharomyces cerevisiae using the RiboPrinter®

This research note addresses the development of an automated molecular typing system for yeast. Specifically, our objectives were to generate specific probes for genotyping yeast with an automated fingerprinting system. We have adapted the RiboPrinter microbial characterization system for use with Saccharomyces cerevisiae yeast using alternative probes based on specific multi-copy gene families. Manual construction and labeling of probes proved successful in initial experiments. Results indicate that this method could be applied to food or clinical environments if the appropriate probes are developed.

Molecular and epidemiologic analysis of a county-wide outbreak caused by Salmonella enterica subsp. enterica serovar Enteritidis traced to a bakery

Background

An increase in the number of attendees due to acute gastroenteritis and fever was noted at one hospital emergency room in Taiwan over a seven-day period from July to August, 2001. Molecular and epidemiological surveys were performed to trace the possible source of infection.

Methods

An epidemiological investigation was undertaken to determine the cause of the outbreak. Stool and blood samples were collected according to standard protocols per Center for Disease Control, Taiwan. Typing of the Salmonella isolates from stool, blood, and food samples was performed with serotyping, antibiotypes, and pulsed field gel electrophoresis (PFGE) following XbaI restriction enzyme digestion.

Results

Comparison of the number of patients with and without acute gastroenteritis (506 and 4467, respectively) during the six weeks before the outbreak week revealed a significant increase in the number of patients during the outbreak week (162 and 942, respectively) (relative risk (RR): 1.44, 95% confidence interval (CI): 1.22–1.70, P value < 0.001). During the week of the outbreak, 34 of 162 patients with gastroenteritis were positive for Salmonella, and 28 of these 34 cases reported eating the same kind of bread. In total, 28 of 34 patients who ate this bread were positive for salmonella compared to only 6 of 128 people who did not eat this bread (RR: 17.6, 95%CI 7.9–39.0, P < 0.001). These breads were produced by the same bakery and were distributed to six different traditional Chinese markets., Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) was isolated from the stool samples of 28 of 32 individuals and from a recalled bread sample. All S. Enteritidis isolates were of the same antibiogram. PFGE typing revealed that all except two of the clinical isolates and the bread isolates were of the same DNA macrorestriction pattern.

Conclusions

The egg-covered bread contaminated with S. Enteritidis was confirmed as the vehicle of infection. Alertness in the emergency room, surveillance by the microbiology laboratory, prompt and thorough investigation to trace the source of outbreaks, and institution of appropriate control measures provide effective control of community outbreaks.

Diversity of phage types among archived cultures of the Demerec collection of Salmonella enterica serovar Typhimurium strains

The existence of several thousand Salmonella enterica serovar Typhimurium LT2 and LT7 cultures originally collected by M. Demerec and sealed in agar stab vials for 33 to 46 years is a resource for evolutionary and mutational studies. Cultures from 74 of these vials, descendants of cells sealed and stored in nutrient agar stabs several decades ago, were phage typed by the Callow and Felix, Lilleengen, and Anderson systems. Among 53 LT2 archived strains, 16 had the same phage type as the nonarchival sequenced LT2 strain. The other 37 archived cultures differed in phage typing pattern from the sequenced strain. These 37 strains were divided into 10 different phage types. Among the 19 LT7 strains, only one was similar to the parent by phage typing, while 18 were different. These 18 strains fell into eight different phage types. The typing systems were developed to track epidemics from source to consumer, as well as geographic spread. The value of phage typing is dependent upon the stability of the phage type of any given strain throughout the course of the investigation. Thus, the variation over time observed in these archived cultures is particularly surprising. Possible mechanisms for such striking diversity may include loss of prophages, prophage mosaics as a result of recombination events, changes in phage receptor sites on the bacterial cell surface, or mutations in restriction-modification systems.

Genetic diversity of human isolates of Salmonella enterica serovar Enteritidis in Malaysia

AIMS

The study was undertaken to determine clonal relationship and genetic diversity of the human strains of Salmonella enterica serovar Enteritidis isolated from 1995 to 2002 from different parts of Malaysia.

METHODS AND RESULTS

Antimicrobial susceptibility test, plasmid profiling and pulsed-field gel electrophoresis were applied to analyse 65 human isolates of S. Enteritidis obtained over an eight year period from different parts of Malaysia. Four nonhuman isolates were included for comparison. A total of 14 distinct XbaI-pulsed-field profiles (PFPs) were observed, although a single PFP X1 was predominant and this particular clone was found to be endemic in Malaysia. The incidence of drug resistant S. Enteritidis remained relatively low with only 37% of the strains analysed being resistant to one or more antimicrobial agents. All except one resistant strain carried at least one plasmid ranging in size from 3.7 to 62 MDa giving nine plasmid profiles. The three isolates from raw milk and one from well-water had similar PFPs to that of the human isolates.

CONCLUSIONS

Salmonella Enteritidis strains were more diverse than was previously thought. Fourteen subtypes were noted although one predominant clone persisted in Malaysia. The combination of pulsed-field gel electrophoresis, plasmid profiling and antibiograms provided additional discrimination to the highly clonal strains of S. Enteritidis.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report to assess the genotypes of the predominant clinical S. Enteritidis in different parts of the country. As S. Enteritidis is highly endemic in Malaysia, the data generated would be useful for tracing the source during outbreaks of gastroenteritis in the study area.

Molecular subtyping methods for detection of Salmonella enterica serovar Oranienburg outbreaks

This study involved 82 Salmonella enterica serovar Oranienburg isolates from patients with gastroenteritis and/or focal infections, healthy carriers, and cuttlefish chips which were epidemiologically linked to a major outbreak that had affected 1,505 people in Japan between 1998 and 1999. We concurrently investigated four different molecular subtyping methods using human salmonellosis-associated Salmonella serovars and their applicability in detection of serovar Oranienburg in an outbreak. Pulsed-field gel electrophoresis (PFGE), enterobacterial repetitive intergenic sequence PCR (ERIC2-PCR), or 16S/23S rRNA ribotyping provided a high degree of interserovar discrimination for most of the serovars, with PFGE being the most discriminatory. For intraserovar typing of serovar Oranienburg, ERIC2-PCR was found to be the most sensitive. Native plasmid profiling, however, revealed nine different subgroups among epidemiologically and genetically related outbreak strains. Using these methods, a link was confirmed between food (cuttlefish chips) and patients in the serovar Oranienburg outbreak. This study underscores the limitations of chromosome-based and plasmid-based typing methods.