Multilocus variable number tandem repeat analysis as a tool to discern genetic relationships among strains of<i>Yersinia enterocolitica</i>biovar 1A

Gulati, Pooja; Varshney, Rajeev K.; Virdi, Jugsharan Singh

doi:10.1111/j.1365-2672.2009.04267.x

Cited by 23 publications

(27 citation statements)

References 42 publications

(55 reference statements)

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“…MLVA also has proved successful with Y. enterocolitica serotype O:9 (7,8,21,22). A separate MLVA application has been developed for Y. enterocolitica biotype 1A (23).…”

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confidence: 99%

Multiple-Locus Variable-Number Tandem-Repeat Analysis in Genotyping Yersinia enterocolitica Strains from Human and Porcine Origins

et al. 2013

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c Sporadic and epidemiologically linked Yersinia enterocolitica strains (n ‫؍‬ 379) isolated from fecal samples from human patients, tonsil or fecal samples from pigs collected at slaughterhouses, and pork samples collected at meat stores were genotyped using multiple-locus variable-number tandem-repeat analysis (MLVA) with six loci, i.e., V2A, V4, V5, V6, V7, and V9. In total, 312 different MLVA types were found. Similar types were detected (i) in fecal samples collected from human patients over 2 to 3 consecutive years, (ii) in samples from humans and pigs, and (iii) in samples from pigs that originated from the same farms. Among porcine strains, we found farm-specific MLVA profiles. Variations in the numbers of tandem repeats from one to four for variable-number tandem-repeat (VNTR) loci V2A, V5, V6, and V7 were observed within a farm. MLVA was applicable for serotypes O:3, O:5,27, and O:9 and appeared to be a highly discriminating tool for distinguishing sporadic and outbreak-related strains. With long-term use, interpretation of the results became more challenging due to variations in more-discriminating loci, as was observed for strains originating from pig farms. Additionally, we encountered unexpectedly short V2A VNTR fragments and sequenced them. According to the sequencing results, updated guidelines for interpreting V2A VNTR results were prepared.

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“…MLVA also has proved successful with Y. enterocolitica serotype O:9 (7,8,21,22). A separate MLVA application has been developed for Y. enterocolitica biotype 1A (23).…”

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confidence: 99%

Multiple-Locus Variable-Number Tandem-Repeat Analysis in Genotyping Yersinia enterocolitica Strains from Human and Porcine Origins

et al. 2013

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“…In a few instances, the biovar 1A strains have also been reported to cause nosocomial (8) and foodborne outbreaks (9). Previous genotyping studies from our laboratory differentiated strains of Y. enterocolitica biovar 1A into two clonal groups (A & B) (10)(11)(12). These studies especially, multilocus variable number tandem repeat analysis or MLVA (11) and multilocus restriction typing or MLRT (12) unequivocally established that the clinical and non-clinical strains were distinctly different.…”

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confidence: 84%

“…Previous genotyping studies from our laboratory differentiated strains of Y. enterocolitica biovar 1A into two clonal groups (A & B) (10)(11)(12). These studies especially, multilocus variable number tandem repeat analysis or MLVA (11) and multilocus restriction typing or MLRT (12) unequivocally established that the clinical and non-clinical strains were distinctly different. In light of these observations, we also hypothesized that the waste water strains represent primordial strains from which the clinical strains originated by host adaption and genetic change (11).…”

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confidence: 96%

“…These studies especially, multilocus variable number tandem repeat analysis or MLVA (11) and multilocus restriction typing or MLRT (12) unequivocally established that the clinical and non-clinical strains were distinctly different. In light of these observations, we also hypothesized that the waste water strains represent primordial strains from which the clinical strains originated by host adaption and genetic change (11). The existence of two clonal groups has also been shown in studies conducted using European and American biovar 1A strains (13,14).…”

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confidence: 97%

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Analysis of iron acquisition and storage‐related genes in clinical and non‐clinical strains of Yersinia enterocolitica biovar 1A

Kanaujia

Bajaj

Virdi

2015

APMIS

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Possession of mechanisms for iron acquisition and its storage enhances the ability of the bacteria to survive in the iron-limiting environment of the host. In this study, 81 strains of Yersinia enterocolitica biovar 1A isolated from various clinical (n = 51) and non-clinical (n = 30) sources were investigated for the presence of the genes related to iron acquisition and storage. Important genes which were present in more than 85% of the strains included hasA, foxA, bfr, bfd, ftnA, and hmsT as well as the fhuCDB, fepBDGCfesfepA, feoAB, yfuABCD, hemPRSTUV, and hmsHFRS gene clusters. Majority of these genes is being reported for the first time in biovar 1A strains and showed significant homology with genes present in the known pathogenic biovars of Y. enterocolitica. However, no significant difference was observed in the distribution of iron acquisition and storage-related genes among clinical and non-clinical biovar 1A strains. Thus, it may be suggested that the presence of iron acquisition and storage-related genes per se might not be responsible for the supposedly better ability of clinical biovar 1A strains to cause infections in humans. However, in the backdrop of this data, the need to undertake functional studies are highly recommended.

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“…Furthermore, the technique can be multiplexed and automated and is conducive to rapid and relatively high-throughput strain typing. MLVA assays are relatively robust (5,(15)(16)(17) and, while not perfect, they can provide phylogenetic information even with a limited number of loci (13,18). While access to a sequenced genome dramatically speeds the ability to establish new assays (3), it is not a requisite to assay development.…”

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confidence: 99%

Improved Identification of Epidemiologically Related Strains of Salmonella enterica by use of a Fusion Algorithm Based on Pulsed-Field Gel Electrophoresis and Multiple-Locus Variable-Number Tandem-Repeat Analysis

et al. 2010

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Pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem-repeat analysis (MLVA) are used to assess genetic similarity between bacterial strains. There are cases, however, when neither of these methods quantifies genetic variation at a level of resolution that is well suited for studying the molecular epidemiology of bacterial pathogens. To improve estimates based on these methods, we propose a fusion algorithm that combines the information obtained from both PFGE and MLVA assays to assess epidemiological relationships. This involves generating distance matrices for PFGE data (Dice coefficients) and MLVA data (single-step stepwise-mutation model) and modifying the relative distances using the two different data types. We applied the algorithm to a set of Salmonella enterica serovar Typhimurium isolates collected from a wide range of sampling dates, locations, and host species. All three classification methods (PFGE only, MLVA only, and fusion) produced a similar pattern of clustering relative to groupings of common phage types, with the fusion results being slightly better. We then examined a group of serovar Newport isolates collected over a limited geographic and temporal scale and showed that the fusion of PFGE and MLVA data produced the best discrimination of isolates relative to a collection site (farm). Our analysis shows that the fusion of PFGE and MLVA data provides an improved ability to discriminate epidemiologically related isolates but provides only minor improvement in the discrimination of less related isolates.Salmonellosis is one of the most common food-borne diseases in the United States (5). Consequently, it is important to understand how Salmonella strains disseminate within and between reservoirs and environments. Many molecular typing tools have been used for this purpose (11). Of these methods, pulsed-field gel electrophoresis (PFGE) is considered by many to be the gold standard for strain typing, and variable-number tandem-repeat (VNTR) assays are powerful alternative or complementary typing tools (3,22). Both methods offer a high degree of genetic resolution for strain typing, depending on several factors.PFGE involves separating chromosomal DNA macro-restriction fragments by size, and strains are discriminated based on the resulting band pattern observed after electrophoresis has been completed. It is one of the most reproducible and highly discriminatory typing techniques and has been widely and successfully used for a variety of Salmonella enterica serovars (12, 15); for many situations, PFGE is capable of discriminating between closely related strains. In addition, the use of the assay to analyze different serovars does not require a great deal of modification, as might be required with procedures that are dependent on PCR. Difficulties arise when strains are very closely related (i.e., poor discrimination [18,27]) or when bands comigrate in the gel or identically sized bands represent completely different fragments of chromosomal DNA and thereby produce spurio...

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Multilocus variable number tandem repeat analysis as a tool to discern genetic relationships among strains ofYersinia enterocoliticabiovar 1A

Cited by 23 publications

References 42 publications

Multiple-Locus Variable-Number Tandem-Repeat Analysis in Genotyping Yersinia enterocolitica Strains from Human and Porcine Origins

Multiple-Locus Variable-Number Tandem-Repeat Analysis in Genotyping Yersinia enterocolitica Strains from Human and Porcine Origins

Analysis of iron acquisition and storage‐related genes in clinical and non‐clinical strains of Yersinia enterocolitica biovar 1A

Improved Identification of Epidemiologically Related Strains of Salmonella enterica by use of a Fusion Algorithm Based on Pulsed-Field Gel Electrophoresis and Multiple-Locus Variable-Number Tandem-Repeat Analysis

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