Variable-number Tandem-repeat Analysis Profiles Research Articles

Characterization of quinolone resistance in Salmonella enterica serovar Typhimurium and its monophasic variants from food and patients in China

The study aimed to characterize the quinolone resistance of Salmonella enterica serovar Typhimurium and its monophasic variant (Salmonella enterica serovar 1,4,[5],12:i:-) isolated from food and patients in China. All of the isolates were assessed for quinolone susceptibility via the broth microdilution method. Then, the isolates were checked for mutations within quinolone resistance-determining regions of gyrA, gyrB, parC, and parE and were examined for plasmid-mediated quinolone resistance genes. High rates of resistance to nalidixic acid in the S. Typhimurium (70.7%) and S. 1,4,[5],12:i:- (41.9%) isolates were observed, and a considerable proportion of isolates with reduced susceptibility to ciprofloxacin and levofloxacin were also detected. The high frequency of mutations in GyrA (60.8%) and a variety of genes (aac[6']-Ib-cr [23.2%], oqxAB [19.2%], qnrS [13.6%], and qnrA [3.2%]) conferring quinolone resistance in these Salmonella isolates were noteworthy. Lastly, the isolates carrying qnrS for transferability and transmission of the quinolone resistance were analysed by conjugation. Multiple locus variable-number tandem repeat analysis profiles indicated that some qnrS-positive isolates were clonally related, whilst the other isolates were genetically divergent. This suggested that both clonal spread of resistant strains and horizontal transmission of the plasmid-mediated resistance genes contributed to the dissemination of qnrS-positive Salmonella isolates. This study highlights the prevalence of quinolone-resistant S. Typhimurium and S. 1,4,[5],12:i:- in China, posing a threat to public health.

Comparison of Multiple-Locus Variable-Number Tandem Repeat Analysis Profiles of Enteropathogenic Yersinia spp. Obtained from Humans, Domestic Pigs, Wild Boars, Rodents, Pork and Dog Food.

The enteropathogenic Yersinia genus is commonly detected in wildlife including wild boars. Difficulties in its cultivation may hamper subsequent epidemiological studies and outbreak investigations. Multiple-locus variable-number tandem repeat analysis (MLVA) of Yersinia (Y.) enterocolitica and Y. pseudotuberculosis has proven useful in source attribution and epidemiological studies but has hitherto relied on the analysis of isolates. In the present study, MLVA profiles generated from 254 isolates of Y. enterocolitica indicated similarities between human, pig and rodent isolates. Further, MLVA analyses of 13 Y. pseudotuberculosis pure-cultured isolates were compared to MLVA analyses performed directly on the 14 PCR-positive enrichment broths from which the isolates originated, which showed matching MLVA profiles. This indicates that MLVA analysis performed directly on enrichment broths could be a useful method for molecular epidemiological investigations. In addition, 10 out of 32 samples of wild boar minced meat obtained from private hunters and from approved wild-game-handling establishments were PCR-positive for the presence of Y. enterocolitica and may indicate a risk for public health.

Erratum for Cadel-Six et al., "Draft Genome Sequences of Salmonella enterica subsp. enterica Serovar Dublin Strains from Raw Milk Cheeses Characterized by Multilocus Variable-Number Tandem-Repeat Analysis Profiles Associated with Two Outbreaks in France".

Volume 8, no. 1, e01361-18, 2019, [https://doi.org/10.1128/MRA.01361-18][1]. Page 1: The article title should read as given above. Page 1, abstract, line 2: “St. Nectaire and Morbier cheeses” should read “two raw milk cheeses.” Page 1, abstract, lines 3 and 4: “fatal outbreaks” should

Draft Genome Sequences of Salmonella enterica subsp. enterica Serovar Dublin Strains from St. Nectaire and Morbier Cheeses Characterized by Multilocus Variable-Number Tandem-Repeat Analysis Profiles Associated with Two Fatal Outbreaks in France.

We report here the draft genome sequences of 2 Salmonella enterica subsp. enterica serovar Dublin strains from St. Nectaire and Morbier cheeses having multilocus variable-number tandem-repeat analysis (MLVA) profiles identified during the fatal outbreaks that occurred in France in 2012 and 2015 to 2016, respectively. These draft genome sequences will help uncover the virulence determinants in invasive S. Dublin strains.

Prevalence, antimicrobial resistance and multiple-locus variable-number tandem-repeat analysis profiles of diarrheagenic Escherichia coli isolated from different retail foods

Diarrheagenic E. coli (DEC) isolates were recovered from local retail markets and the Osaka Municipal Central Wholesale Market in Japan. Retail food samples were collected for analysis in Osaka Japan from 2005 to 2008 and consisted of 32 beef, 28 pork, 20 poultry, 136 fish, 66 fruits and vegetables and 51 ready–to-eat (RTE) food samples. A total of 82 DEC strains were recovered from 64 (19%) food samples with the highest prevalence in poultry (100%, 20/20), followed by pork (54%, 15/28), beef (28%, 9/32), fruits and vegetables (12%, 8/66), fish (6.6%, 9/136) and RTE foods (5.9%, 3/51). Most of the strains belonged to E. coli possessing the enteroaggregative E. coli (EAEC) heat-stable enterotoxin 1 (EAST1) gene (EAST1EC; n=62, P<0.0001) and enteropathogenic E. coli (EPEC; n=16, P<0.01), whereas only 1 strain belonged to Shiga toxin-producing E. coli (STEC), 1 to EAEC and 2 to enterotoxigenic E. coli (ETEC) strains. Of the 82 DEC isolates, 22 O and 13H serogroups were detected, including some specific serogroups (O91, O103, O115, O119, O126, and O157) which have been associated with human diarrheal infections. Phylogenetic group A and B1 were predominant among the DEC isolates. Antimicrobial resistance to tetracycline was most common (49%), followed by nalidixic acid (28%), ampicillin (24%), sulfamethoxazole/trimethoprim (20%), and cephalothin (18%). All isolates were susceptible to aztreonam. Of the resistant strains, 44% (22/50) demonstrated resistance to >3 antimicrobial agents. Isolates resistant to >5 antimicrobials were only found in the meat samples, while isolates from the fruits and vegetables as well as RTE foods showed resistance to only 1 or 2 antimicrobial agents. Sixty one percent of EAST1EC, 56% of EPEC and all of the EAEC and ETEC were resistant to at least 1 antimicrobial agent. Multiple-locus variable-number tandem repeat analysis (MLVA) was used in this study for genotyping of DEC. The 82 isolates collected for this study showed 77 distinct MLVA profiles located among 3 branches. The Simpson's Index of Diversity (D) was 99.9% at its highest. The high diversity of these food strains would suggest their originating from a variety of sources and environments. In conclusion, retail food samples in Japan were contaminated with DEC; EAST1EC, a putative DEC, were detected at high rates in poultry, pork and beef. Isolates resistant to >3 antimicrobials were found only in raw meat and fish. Food animals may act as the reservoir for multi-resistant bacteria. Due to the finding that nearly 1/3 of EAST1EC strains were resistant to >3 antimicrobials, additional surveillance for EAST1EC should be initiated.

A case study on Salmonella enterica serovar Typhimurium at a dairy farm associated with massive sparrow death.

Background Salmonella enterica Typhimurium (S. Typhimurium) is the most common cause of bovine salmonellosis in Japan and where it is also cause of salmonellosis in wild birds. In 2008, a postpartum cow at a dairy farm developed diarrhea caused by S. Typhimurium. The herd was extensively surveilled for Salmonella sp. and we characterized bacterial isolates from this and other cows to determine the source of infection.ResultsEight isolates of S. Typhimurium from cattle were identified as phage type DT40 and showed a 100 % similarity by pulsed-field gel electrophoresis and the same or similar multiple-locus variable-number tandem-repeat analysis profiles as those of S. Typhimurium isolated from dead sparrows (Passer montanus) collected at Asahikawa in 2006. S. Typhimurium DT40 was considered to be a major cause of high sparrow mortality in Hokkaido in 2005–2006 and 2008–2009, suggesting that DT40 maintained in sparrows was transmitted to cattle.Conclusions S. Typhimurium DT40 may be transmitted from sparrows to dairy cattle.

Phenotypic and Genotypic Characterization of Salmonella enterica Serovar Enteritidis Isolates Associated with a Mousse Cake-Related Outbreak of Gastroenteritis in Ningbo, China.

Salmonella enterica subsp. enterica serovar Enteritidis (Salmonella Enteritidis) is a major pathogen responsible for causing the largest number of sporadic cases and outbreaks of human salmonellosis worldwide. In this study, an outbreak of Salmonella Enteritidis involving 112 cases in Ningbo, China was investigated with a combination of genotypic subtyping methods and phenotypic analysis. The pulsed-field gel electrophoresis and multilocus variable-number tandem-repeat analysis profiles showed that most of the outbreak clinical isolates (22/23) were indistinguishable from each other and were identical to the isolates obtained from implicated mousse cakes, demonstrating that this outbreak of gastroenteritis was caused by Salmonella Enteritidis-contaminated mousse cakes. Moreover, all isolates, irrespective of source, had an identical antibiotic susceptibility pattern. Five virulence-associated genes in Salmonella pathogenicity islands and the plasmid-associated virulence genes spvB/C were present in both the food and clinical isolates. Importantly, all of these isolates can survive well under low-temperature treatment, indicating that manufacturers of foodstuffs with raw ingredients (not subjected to thermal processing) should use an effective approach to prevent or eliminate the microbial hazards to public health.

Clonal distribution of monophasic Salmonella enterica subsp. enterica serotype 4,[5],12:i:- in the Czech Republic.

Abstract Salmonella 4,[5],12:i:- has become the third most common serotype in Europe, including the Czech Republic. In this study, phenotypic and genotypic methods for a more detailed description of this serotype were used. Analysis of a limited number of isolates revealed that 76% of them belonged to phage type DT193. Also, rare phage types DT208 and U311 were identified. In total, 88.6% of the isolates were resistant to at least four antimicrobial agents. In this study, 24 multilocus variable-number tandem-repeat analysis profiles were detected, and some of them matched with the profiles recently described in Europe.

Bacterial Bronchitis Caused by Streptococcus pneumoniae and Nontypable Haemophilus influenzae in Children: The Impact of Vaccination

Protracted bacterial bronchitis is a major cause of persistent cough in childhood. The organisms most commonly isolated are nontypable Haemophilus influenzae and Streptococcus pneumoniae . There are no studies addressing typing of these organisms when recovered from the lower airways.Isolates of these two organisms (identified in BAL samples from children undergoing routine investigation of a chronic cough thought to be attributable to a protracted bacterial bronchitis) were subject to typing. Samples were collected in Sheffield, England, and Athens, Greece. The majority of the children from Sheffield had received pneumococcal-conjugate vaccines 7 or 13 (PCV-7 or PCV-13) conjugate vaccine but only a minority of Greek children had received PCV-7.All 18 S pneumoniae isolates from Greek BAL samples are serotypes contained in PCV-13 while 10 are contained in PCV-7. In contrast, 28 of the 39 samples from Sheffield contained serotypes that are not included in PCV-13. All 26 of the nontypable H influenzae samples obtained in Sheffield produced distinct multilocus variable-number tandem repeat analysis profiles. There was a significant difference between children from Athens and Sheffield in the distribution of serotypes contained or not contained in the pneumococcal vaccine ( P = .04). More specifically, immunization with pneumococcal vaccine was related with isolation of S pneumoniae serotypes not included in the vaccine (OR, 0.021; CI, 0.003-0.115; P < .001).The data suggest that both vaccine and nonvaccine S pneumoniae serotypes may play a role in protracted bacterial bronchitis and provide some hints that serotype replacement may occur in response to the introduction of conjugate vaccines.

An outbreak of Salmonella enterica serotype Litchfield infection in Australia linked to consumption of contaminated papaya.

An outbreak of 26 cases of Salmonella Litchfield infection occurred in the states of Western Australia and Queensland between October 2006 and January 2007. A case-control study was conducted with 12 cases and 24 controls, and a significant association was found between illness and consumption of papaya (odds ratio, 32.8; 95% confidence interval, 2.71 to 883.5). Papaya samples were collected from 26 stores in Western Australia, and 9 of 38 samples were contaminated with Salmonella Litchfield. These samples had pulsed-field gel electrophoresis patterns and multilocus variable-number tandem-repeat analysis profiles indistinguishable from the outbreak strain. Three farms in Western Australia supplied the contaminated papaya, and two of these farms were inspected. Salmonella Litchfield was not detected in papaya samples, fungal sprays, or water samples from the farms; however, at one farm other serotypes of Salmonella were detected in untreated river water that was used for washing papaya. Only treated potable water should be used for washing fresh produce that is to be eaten raw.