Multilocus variable-number tandem repeat analysis for molecular typing and phylogenetic analysis of Shigella flexneri

Wang, You-Wun; Watanabe, Haruo; Phung, Dac Cam; Tung, Shu-Chu; Lee, Yeong-Sheng; Terajima, Jun; Liang, Shiu-Yun; Chiou, Chien-Shun

doi:10.1186/1471-2180-9-278

Cited by 32 publications

(35 citation statements)

References 24 publications

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“…The L-repeat loci are suitable for establishing phylogenetic relationships among strains evolving over a long period (40). Conversely, S-repeat loci, particularly those with high HGDI values, are characterized by more rapid evolution and provide more subtle diversification, which is crucial to discriminate between closely related isolates (20), as in the case of disease surveillance and/or investigations of outbreaks (29).…”

Section: Discussionmentioning

confidence: 99%

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme

et al. 2011

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Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and costeffective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR-and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from http://mlva.u-psud.fr/.The Gram-negative bacterium Acinetobacter baumannii has emerged worldwide as a major nosocomial pathogen and a serious threat to patients in intensive care units (ICUs) (18,27). Hallmarks of A. baumannii infection are resistance to a broad range of antimicrobial agents, the tendency for epidemic spread, and long-term persistence in the hospital setting (4,8,27).Most A. baumannii clinical strains from multiple hospital outbreaks throughout the world have been referred to a few epidemic lineages. Two of these, called international clonal lineages I and II, were first identified in northwestern Europe in the early 1980s and then worldwide (8, 17), while a third clone, called international clonal lineage III, was later detected in France, Netherlands, Italy, and Spain, probably persisting in European hospitals since the 1990s (17, 34).Several typing methods have been developed to trace A. baumannii epidemiology from the local to the global scale. Among them, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) (23) and multilocus sequence typing (MLST) (2, 7) are currently considered the methods of choice for epidemi...

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Section: Discussionmentioning

confidence: 99%

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme

et al. 2011

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“…MLVA was performed as previously described [ 10 ]. Eight VNTR loci (SF3, SF4, SF6, SF7, SF8, SF9, SF10 and SF25) were selected.…”

Section: Methodsmentioning

confidence: 99%

Genetic Characterization of Shigella flexneri Isolates in Guizhou Province, China

Sun

Wei

et al. 2015

PLoS ONE

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Shigella flexneri is one of the major etiologic causes of shigellosis in Guizhou Province, China. However, the genetic characteristics of circulating isolates are unknown. Phenotypic and molecular profiles of 60 S. flexneri isolates recovered in Guizhou between 1972 to 1982 and 2008 to 2010 were determined. Nine serotypes (1a, 2a, 3a, 1b, 2b, X, Y, 4av and Yv) were identified. Multi-locus sequence typing differentiated the isolates into 20 sequence types (STs); 18 were novel. Four STs, ST 129, ST 100, ST 126 and ST 18, were most abundant, accounting for 65% of the isolates. Thirty-nine NotI-pulsed field gel electrophoresis patterns (pulsotypes, PTs) were observed; eight PTs were represented by more than one isolate with six isolates sharing the PT 13 profile. Multi-locus variable-nucleotide tandem-repeat analysis recognized 44 different types (MTs); seven MTs were represented by more than one isolate and MT 1 was most commonly encountered. Correlation between genetic relationships and serotypes was observed among the isolates studied; the majority of isolates belonging to the same serotype from different years clustered together based on the molecular data. These clustered isolates were also from similar geographical origins. These results enhance our understanding of genetic relationships between S. flexneri in Guizhou Province and can be used to help understand the changing etiology of shigellosis in China.

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“…Recently, a variety of molecular methods have been developed for distinguishing among strains of Salmonella/Shigella/Yersina , including multi-locus sequence typing approaches, and PCR-based approaches. 35–42 Whole genome sequencing-based approaches have also been used, facilitated by published reference genomes. 13, 14, 43–45 …”

Section: Introductionmentioning

confidence: 99%

Salmonella, Shigella, and Yersinia

Dekker

Frank

2015

Clinics in Laboratory Medicine

119

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Synopsis Salmonella, Shigella, and Yersinia cause a well-characterized spectrum of disease in humans, ranging from asymptomatic carriage to hemorrhagic colitis and fatal typhoidal fever. These pathogens are responsible for millions of cases of food-borne illness in the U.S. each year, with substantial costs measured in hospitalizations and lost productivity. In the developing world, illness caused by these pathogens is not only more prevalent, but is also associated with a greater case-fatality rate. Classical methods for identification rely on selective media and serology, but newer methods based on mass spectrometry and PCR show great promise for routine clinical testing.

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Multilocus variable-number tandem repeat analysis for molecular typing and phylogenetic analysis of Shigella flexneri

Cited by 32 publications

References 24 publications

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme

Genetic Characterization of Shigella flexneri Isolates in Guizhou Province, China

Salmonella, Shigella, and Yersinia

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