scholarly journals Host Range-Associated Clustering Based on Multilocus Variable-Number Tandem-Repeat Analysis, Phylotypes, and Virulence Genes of Atypical EnteropathogenicEscherichia coliStrains

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Md Shafiullah Parvej ◽  
Hiromi Nakamura ◽  
Md Ashraful Alam ◽  
Lili Wang ◽  
Shaobo Zhang ◽  
...  
Keyword(s):  
Spanning Tree ◽  
Virulence Genes ◽  
Minimum Spanning Tree ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Epidemiological Methods ◽  
Content Type ◽  
Repeat Analysis ◽  
Group I ◽  
Virulence Group

ABSTRACTAtypical enteropathogenicEscherichia coli(aEPEC) strains (36 Japanese and 50 Bangladeshi) obtained from 649 poultry fecal samples were analyzed by molecular epidemiological methods. Clermont’s phylogenetic typing showed that group A was more prevalent (58%, 50/86) than B1 (31%, 27/86). Intimin type β1, which is prevalent among human diarrheal patients, was predominant in both phylogroups B1 (81%, 22/27) and A (70%, 35/50). However, about 95% of B1-β1 strains belonged to virulence group I, and 77% of them were Japanese strains, while 17% (6/35) of A-β1 strains did. Multilocus variable-number tandem-repeat analysis (MLVA) distributed the strains into 52 distinct profiles, with Simpson’s index of diversity (D) at 73%. When the data were combined with those of 142 previous strains from different sources, the minimum spanning tree formed five zones for porcine strains, poultry strains (excluding B1-β1), strains from healthy humans, bovine and human patient strains, and the B1-β1 poultry strains. Antimicrobial resistance to nalidixic acid was most common (74%) among the isolates. Sixty-eight percent of them demonstrated resistance to ≥3 antimicrobial agents, and most of them (91%) were from Bangladesh. The strains were assigned into two groups by hierarchical clustering. Correlation matrix analysis revealed that the virulence genes were negatively associated with antimicrobial resistance. The present study suggested that poultry, particularly Japanese poultry, could be another reservoir of aEPEC (phylogroup B1, virulence group I, and intimin type β1); however, poultry strains seem to be apart from patient strains that were closer to bovine strains. Bangladeshi aEPEC may be less virulent for humans but more resistant to antibiotics.IMPORTANCEAtypical enteropathogenicEscherichia coli(aEPEC) is a diarrheagenic type ofE. coli, as it possesses the intimin gene (eae) for attachment and effacement on epithelium. Since aEPEC is ubiquitous even in developed countries, we previously used molecular epidemiological methods to discriminate aEPEC as a human pathogen. The present study assessed poultry as another source of human diarrheagenic aEPEC. Poultry could be the source of aEPEC (phylogroup B1, virulence group I, and intimin type β1) found among patient strains in Japan. However, the minimum spanning tree (MST) suggested that the strains from Japanese poultry were far from Japanese patient strains compared with the distance between bovine and patient strains. Bangladeshi avian strains seemed to be less diarrheagenic but are hazardous as a source of drug resistance genes.

scholarly journals Multilocus Variable-Number Tandem-Repeat Analysis ofYersinia ruckeriConfirms the Existence of Host Specificity, Geographic Endemism, and Anthropogenic Dissemination of Virulent Clones

2018 ◽  
Vol 84 (16) ◽  
Author(s):  
Snorre Gulla ◽  
Andrew C. Barnes ◽  
Timothy J. Welch ◽  
Jesús L. Romalde ◽  
David Ryder ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Tandem Repeat ◽  
Minimum Spanning Tree ◽  
Clonal Complex ◽  
Variable Number Tandem Repeat ◽  
Geographic Origin ◽  
Variable Number ◽  
Yersinia Ruckeri ◽  
Content Type ◽  
Repeat Analysis

ABSTRACTA multilocus variable-number tandem-repeat analysis (MLVA) assay was developed for epizootiological study of the internationally significant fish pathogenYersinia ruckeri, which causes yersiniosis in salmonids. The assay involves amplification of 10 variable-number tandem-repeat (VNTR) loci in two five-plex PCRs, followed by capillary electrophoresis. A collection of 484Y. ruckeriisolates, originating from various biological sources and collected from four continents over 7 decades, was analyzed. Minimum-spanning-tree cluster analysis of MLVA profiles separated the studied population into nine major clonal complexes and a number of minor clusters and singletons. The major clonal complexes could be associated with host species, geographic origin, and serotype. A single large clonal complex of serotype O1 isolates dominating the yersiniosis situation in international rainbow trout farming suggests anthropogenic spread of this clone, possibly related to transport of fish. Moreover, subclustering within this clonal complex indicates putative transmission routes and multiple biotype shift events. In contrast to the situation in rainbow trout,Y. ruckeristrains associated with disease in Atlantic salmon appear as more or less geographically isolated clonal complexes. A single complex of serotype O1 exclusive to Norway was found to be responsible for almost all major yersiniosis outbreaks in modern Norwegian salmon farming, and site-specific subclustering further indicates persistent colonization of freshwater farms in Norway. Identification of genetically diverseY. ruckeriisolates from clinically healthy fish and environmental sources also suggests the widespread existence of less-virulent or avirulent strains.IMPORTANCEThis comprehensive population study substantially improves our understanding of the epizootiological history and nature of an internationally important fish-pathogenic bacterium. The MLVA assay developed and presented represents a high-resolution typing tool particularly well suited forYersinia ruckeriinfection tracing, selection of strains for vaccine inclusion, and risk assessment. The ability of the assay to separate isolates into geographically linked and/or possibly host-specific clusters reflects its potential utility for maintenance of national biosecurity. The MLVA is internationally applicable and robust, and it provides clear, unambiguous, and easily interpreted results. Typing is reasonably inexpensive, with a moderate technological requirement, and may be completed from a harvested colony within a single working day. As the resulting MLVA profiles are readily portable, anyY. ruckeristrain may rapidly be placed in a global epizootiological context.

scholarly journals Multiple-Locus Variable-Number Tandem Repeat Analysis of Dutch Bordetella pertussis Strains Reveals Rapid Genetic Changes with Clonal Expansion during the Late 1990s

2004 ◽  
Vol 186 (16) ◽  
pp. 5496-5505 ◽  
Author(s):  
Leo M. Schouls ◽  
Han G. J. van der Heide ◽  
Luc Vauterin ◽  
Paul Vauterin ◽  
Frits R. Mooi
Keyword(s):  
The Netherlands ◽  
Tandem Repeat ◽  
Bordetella Pertussis ◽  
Minimum Spanning Tree ◽  
Whooping Cough ◽  
Variable Number Tandem Repeat ◽  
Clonal Expansion ◽  
Variable Number ◽  
Multiple Locus ◽  
Repeat Analysis

ABSTRACT Bordetella pertussis, the causative agent of whooping cough, has remained endemic in The Netherlands despite extensive nationwide vaccination since 1953. In the 1990s, several epidemic periods have resulted in many cases of pertussis. We have proposed that strain variation has played a major role in the upsurges of this disease in The Netherlands. Therefore, molecular characterization of strains is important in identifying the causes of pertussis epidemiology. For this reason, we have developed a multiple-locus variable-number tandem repeat analysis (MLVA) typing system for B. pertussis. By combining the MLVA profile with the allelic profile based on multiple-antigen sequence typing, we were able to further differentiate strains. The relationships between the various genotypes were visualized by constructing a minimum spanning tree. MLVA of Dutch strains of B. pertussis revealed that the genotypes of the strains isolated in the prevaccination period were diverse and clearly distinct from the strains isolated in the 1990s. Furthermore, there was a decrease in diversity in the strains from the late 1990s, with a remarkable clonal expansion that coincided with the epidemic periods. Using this genotyping, we have been able to show that B. pertussis is much more dynamic than expected.

scholarly journals Examination of Taxonomic Uncertainties Surrounding Brucella abortus bv. 7 by Phenotypic and Molecular Approaches

2013 ◽  
Vol 80 (5) ◽  
pp. 1570-1579 ◽  
Author(s):  
Bruno Garin-Bastuji ◽  
Virginie Mick ◽  
Gilles Le Carrou ◽  
Sebastien Allix ◽  
Lorraine L. Perrett ◽  
...  
Keyword(s):  
Brucella Abortus ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Epidemiological Methods ◽  
Content Type ◽  
Phenotypic Profile ◽  
Molecular Approaches ◽  
Content Classification ◽  
Species Specific ◽  
Kenyan Strain

ABSTRACTBrucellataxonomy is perpetually being reshuffled, at both the species and intraspecies levels. Biovar 7 ofBrucella abortuswas suspended from theApproved Lists of Bacterial NamesBrucellaclassification in 1988, because of unpublished evidence that the reference strain 63/75 was a mixture ofB. abortusbiovars 3 and 5. To formally clarify the situation, all isolates previously identified asB. abortusbv. 7 in the AHVLA and ANSES strain collections were characterized by classical microbiological and multiple molecular approaches. Among the 14 investigated strains, including strain 63/75, only four strains, isolated in Kenya, Turkey, and Mongolia, were pure and showed a phenotypic profile in agreement with the former biovar 7, particularly agglutination with both anti-A/anti-M monospecific sera. These results were strengthened by molecular strategies. Indeed, genus- and species-specific methods allowed confirmation that the four pure strains belonged to theB. abortusspecies. The combination of most approaches excluded their affiliation with the recognized biovars (biovars 1 to 6 and 9), while some suggested that they were close to biovar 3.These assays were complemented by phylogenetic and/or epidemiological methods, such as multilocus sequence analysis (MLSA) and variable-number tandem repeat (VNTR) analysis. The results of this polyphasic investigation allow us to propose the reintroduction of biovar 7 into theBrucellaclassification, with at least three representative strains. Interestingly, the Kenyan strain, sharing the same biovar 7 phenotype, was genetically divergent from other three isolates. These discrepancies illustrate the complexity ofBrucellataxonomy. This study suggests that worldwide collections could include strains misidentified asB. abortusbv. 7, and it highlights the need to verify their real taxonomic position.

scholarly journals Multilocus variable-number tandem repeat analysis of Vibrio cholerae O1 El Tor strains harbouring classical toxin B

2010 ◽  
Vol 59 (7) ◽  
pp. 763-769 ◽  
Author(s):  
Seon Young Choi ◽  
Je Hee Lee ◽  
Yoon-Seong Jeon ◽  
Hye Ri Lee ◽  
Eun Jin Kim ◽  
...  
Keyword(s):  
Cholera Toxin ◽  
Vibrio Cholerae ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Group Iii ◽  
Repeat Analysis ◽  
Group I ◽  
Ctx Prophage ◽  
El Tor

Atypical Vibrio cholerae O1 strains – hybrid strains (strains that cannot be classified either as El Tor or classical biotype) and altered strains (El Tor biotype strains that produce classical cholera toxin) – are currently prevalent in Asia and Africa. A total of 74 hybrid and altered strains that harboured classical cholera toxin were investigated by multilocus variable-number tandem repeat analysis (MLVA). The results showed that the hybrid/altered strains could be categorized into three groups and that they were distant from the El Tor strain responsible for the seventh cholera pandemic. Hybrid/altered strains with a tandem repeat of the classical CTX prophage on the small chromosome were divided into two MLVA groups (group I: Mozambique/Bangladesh group; group III: Vietnam group), and altered strains with the RS1–CTX prophage containing the El Tor type rstR and classical ctxB on the large chromosome were placed in two MLVA groups (group II: India/Bangladesh group; group III: India/Vietnam group).

scholarly journals Link between Geographical Origin and Occurrence of Brucella abortus Biovars in Cow and Water Buffalo Herds

2012 ◽  
Vol 79 (3) ◽  
pp. 1039-1043 ◽  
Author(s):  
Giorgia Borriello ◽  
Simone Peletto ◽  
Maria G. Lucibelli ◽  
Pier L. Acutis ◽  
Danilo Ercolini ◽  
...  
Keyword(s):  
Brucella Abortus ◽  
Water Buffalo ◽  
Geographical Origin ◽  
Variable Number Tandem Repeat ◽  
Geographic Origin ◽  
Variable Number ◽  
National Plan ◽  
Content Type ◽  
Repeat Analysis ◽  
Management Procedures

ABSTRACTSixty-threeBrucellaisolates from water buffaloes and cattle slaughtered within the Italian national plan for brucellosis control were characterized by multiple-locus variable-number tandem repeat analysis (MLVA). Genotyping indicated a strong influence of geographic origin on theBrucella abortusbiovar distribution in areas where brucellosis is endemic and highlighted the importance of rigorous management procedures aimed at avoiding inter- and intraherd spreading of pathogens.

scholarly journals Novel genotypes of Leptospira interrogans serogroup Sejroe isolated from human patients in Okinawa Prefecture, Japan

2020 ◽  
Vol 69 (4) ◽  
pp. 587-590
Author(s):  
Tetsuya Kakita ◽  
Hisako Kyan ◽  
Masato Miyahira ◽  
Taketoshi Takara ◽  
Eri Nakama ◽  
...  
Keyword(s):  
Type Species ◽  
Minimum Spanning Tree ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Public Health Issue ◽  
Content Type ◽  
Link Type ◽  
The Tropics ◽  
Sequence Types ◽  
Reference Strains

Leptospirosis is a zoonotic disease caused by pathogenic spirochetes of Leptospira species. It is a public health issue in the tropics, including Okinawa, the southernmost prefecture of Japan. This study reports the first isolation of L. interrogans serogroup Sejroe from two human patients in Japan, and describes its molecular characterization using multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). MLST on the two isolates, 168036 and 178129, showed that pfkB in 178129 is a novel allele, and that both isolates constitute novel sequence types (STs); ST286 for 168036 and ST287 for 178129. A minimum spanning tree based on seven alleles of L. interrogans indicates that both isolates are genetically close, but are distinct from known L. interrogans serogroup Sejroe strains. MLVA using 11 loci demonstrated that seven of the 11 loci were identical between the two isolates, whereas the identity between the isolates and the seven reference strains of L. interrogans serogroup Sejroe was zero to three loci. These results indicate that the isolates investigated in this study have novel genotypes, and are genetically closest to each other among the known L. interrogans serogroup Sejroe strains.

scholarly journals Surveillance of Circulating Bordetella pertussis Strains in Europe during 1998 to 2015

2018 ◽  
Vol 56 (5) ◽  
Author(s):  
Alex-Mikael Barkoff ◽  
Jussi Mertsola ◽  
Denis Pierard ◽  
Tine Dalby ◽  
Silje Vermedal Hoegh ◽  
...  
Keyword(s):  
Bordetella Pertussis ◽  
Virulence Genes ◽  
Genomic Structure ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Content Type ◽  
Present Collection ◽  
Genomic Analyses ◽  
The Common ◽  
Induced Immunity

ABSTRACT One reason for increased pertussis incidence is the adaptation of Bordetella pertussis to vaccine-induced immunity by modulating its genomic structure. This study, EUpert IV, includes 265 isolates collected from nine European countries during 2012 to 2015 ( n = 265) and compares the results to previous EUpert I to III studies (1998 to 2009). The analyses included genotyping, serotyping, pulsed-field gel electrophoresis (PFGE), and multilocus variable-number tandem-repeat analysis (MLVA). Genotyping results showed only small variations among the common virulence genes of B. pertussis . The frequencies of serotypes Fim2 and Fim3 varied among the four collections. Genomic analyses showed that MLVA type 27 increased to 80% between the periods of 1998 to 2001 and 2012 to 2015. Two PFGE profiles, BpSR3 (29.4%) and BpSR10 (27.2%), constituted more than 50% of the circulating isolates in the present collection. Our study indicates that the European B. pertussis population is changing and became more homogenous after the introduction of acellular pertussis vaccines.

scholarly journals Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales

2012 ◽  
Vol 78 (18) ◽  
pp. 6433-6437 ◽  
Author(s):  
Chad W. Stratilo ◽  
Douglas E. Bader
Keyword(s):  
Bacillus Anthracis ◽  
National Park ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Phenotypic Characterization ◽  
Single Nucleotide ◽  
Content Type ◽  
Repeat Analysis ◽  
Typing Methods ◽  
Wood Buffalo National Park

ABSTRACTEnvironmental samples were collected from carcass sites during and after anthrax outbreaks in 2000 and 2001 in the bison (Bison bison) population within Wood Buffalo National Park and the Hook Lake Region north of Wood Buffalo National Park.Bacillus anthracisspores were isolated from these samples and confirmed using phenotypic characterization and real-time PCR. ConfirmedB. anthracisisolates were typed using multiple-locus variable-number tandem repeat analysis (MLVA15) and single-nucleotide-repeat analysis (SNRA).B. anthracisisolates split into two clades based on MLVA15, while SNRA allowed some isolates between carcass sites to be distinguished from each other. SNRA polymorphisms were also present within a single carcass site. Some isolates from different carcass sites having the same SNRA type had divergent MLVA types; this finding leads to questions about hierarchical typing methods and the robustness of the fine-scale typing ofBacillus anthracis.

scholarly journals New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae

2014 ◽  
Vol 81 (2) ◽  
pp. 688-698 ◽  
Author(s):  
L. Poulin ◽  
P. Grygiel ◽  
M. Magne ◽  
L. Gagnevin ◽  
L. M. Rodriguez-R ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Leaf Blight ◽  
Xanthomonas Oryzae ◽  
Bacterial Leaf Blight ◽  
Bacterial Leaf Streak ◽  
Content Type ◽  
Genetic Lineages ◽  
Repeat Analysis

ABSTRACTMultilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars ofXanthomonas oryzaecan cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused byX. oryzaepv. oryzicola, and bacterial leaf blight is caused byX. oryzaepv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the threeX. oryzaegenetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the threeX. oryzaelineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains ofX. oryzaerepresenting different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56X. oryzaestrains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales.

scholarly journals To Lump or To Split: Does Strain Lineage for Clostridioides difficile Matter?

2019 ◽  
Vol 57 (5) ◽  
Author(s):  
Scott R. Curry
Keyword(s):  
Observational Studies ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Clinical Severity ◽  
Ecological Studies ◽  
Causal Inferences ◽  
Content Type ◽  
Repeat Analysis ◽  
Clostridioides Difficile ◽  
Specific Virulence

ABSTRACT Since 2001, numerous descriptive ecological studies of Clostridioides difficile infections (CDI) have identified a single lineage (BI/NAP1/027) associated with the epidemics of CDI, increased severity of CDI, and increased likelihood of incident CDI to become recurrent. Establishing causality between the clinical severity and outcomes for CDI and the lineages of the infecting strains, however, has proved elusive, with many conflicting results in previous observational studies. In this issue of the Journal of Clinical Microbiology, J. R. Garneau, C. N. Abou Chakra, L.-C. Fortier, A.-C. Labbé, et al. (J Clin Microbiol 57:e01724-18, 2019, https://doi.org/10.1128/JCM.01724-18) performed multilocus variable-number tandem-repeat analysis (MLVA) on 450 isolates from epidemic strain CDI arising in 10 Canadian centers during a previously well-described epidemic to assess the hypothesis that subpopulations of this lineage are associated with adverse clinical outcomes. The authors’ key finding, however, was that MLVA genotyping grouped infections closely with associated hospital centers; CDI severity was not associated with any particular sublineage by MLVA. While the study does not support any causal inferences about strain-specific virulence of CDI, it does highlight the power of MLVA, a genotyping tool that remains valuable in tracking the geospatial transmission dynamics of CDI.

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