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 Ruminant Rhombencephalitis-Associated Listeria monocytogenes Alleles Linked to a Multilocus Variable-Number Tandem-Repeat Analysis Complex

2011 ◽  
Vol 77 (23) ◽  
pp. 8325-8335 ◽  
Author(s):  
Lina Balandyté ◽  
Isabelle Brodard ◽  
Joachim Frey ◽  
Anna Oevermann ◽  
Carlos Abril
Keyword(s):  
Listeria Monocytogenes ◽  
Tandem Repeat ◽  
Genetic Relatedness ◽  
Clonal Complex ◽  
Variable Number Tandem Repeat ◽  
Virulence Gene ◽  
Variable Number ◽  
Content Type ◽  
Repeat Analysis ◽  
Cns Infections

ABSTRACTListeria monocytogenesis among the most important food-borne pathogens and is well adapted to persist in the environment. To gain insight into the genetic relatedness and potential virulence ofL. monocytogenesstrains causing central nervous system (CNS) infections, we used multilocus variable-number tandem-repeat analysis (MLVA) to subtype 183L. monocytogenesisolates, most from ruminant rhombencephalitis and some from human patients, food, and the environment. Allelic-profile-based comparisons groupedL. monocytogenesstrains mainly into three clonal complexes and linked single-locus variants (SLVs). Clonal complex A essentially consisted of isolates from human and ruminant brain samples. All but one rhombencephalitis isolate from cattle were located in clonal complex A. In contrast, food and environmental isolates mainly clustered into clonal complex C, and none was classified as clonal complex A. Isolates of the two main clonal complexes (A and C) obtained by MLVA were analyzed by PCR for the presence of 11 virulence-associated genes (prfA,actA,inlA,inlB,inlC,inlD,inlE,inlF,inlG,inlJ, andinlC2H). Virulence gene analysis revealed significant differences in theactA,inlF,inlG, andinlJallelic profiles between clinical isolates (complex A) and nonclinical isolates (complex C). The association of particular alleles ofactA,inlF, and newly described alleles ofinlJwith isolates from CNS infections (particularly rhombencephalitis) suggests that these virulence genes participate in neurovirulence ofL. monocytogenes. The overall absence ofinlGin clinical complex A and its presence in complex C isolates suggests that the InlG protein is more relevant for the survival ofL. monocytogenesin the environment.

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 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 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 Multilocus Variable-Number Tandem-Repeat Analysis for Genotyping of Escherichia coli Strains Isolated from Hospital Wastewater, Tehran, Iran

2020 ◽  
Author(s):  
Omid FARAHANI ◽  
Reza RANJBAR ◽  
Sahar HONARMAND JAHROMY ◽  
Bahareh ARABZADEH
Keyword(s):  
Escherichia Coli ◽  
Tandem Repeat ◽  
Bacterial Infections ◽  
Minimum Spanning Tree ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Hospital Wastewater ◽  
E Coli ◽  
Repeat Analysis ◽  
Hospital Wastewaters

Background: Escherichia coli is one of the most frequent causes of many common bacterial infections. As a potential reservoir, hospital wastewater is considered for the dissemination of bacterial pathogens such as E. coli. Therefore, research on hospital waste’s bacteria by low-cost, rapid and easy molecular typing methods such as multilocus variable-number tandem-repeat analysis (MLVA) can be helpful for the study of epidemics. Methods: E. coli strains were isolated from hospital wastewater sources in Tehran, Iran, over a 24-month sampling period (Jun 2014- Jun 2016) and identified by standard bacteriological methods. The diversity of repeated sequences of seven variable-number tandem-repeat (VNTR) loci was studied by MLVA method base on polymerase chain reaction (PCR). Results: Overall, 80 E. coli isolates were discriminated into 51 different genotypes. Analysis of the MLVA profiles using a minimum spanning tree (MST) algorithm showed two clonal complexes with 71 isolates and only nine isolates were stayed out of clonal complexes in the form of a singleton. High genotypic diversity was seen among E. coli strains isolated from hospital wastewaters; however, a large number of isolates showed a close genetic relationship. Conclusion: MLVA showed to be a rapid, inexpensive and useful tool for the analysis of the phylogenetic relationships between E. coli strains under the study

scholarly journals Multilocus Variable-Number Tandem-Repeat Analysis of Clostridioides difficile Clusters in Ribotype 027 Isolates and Lack of Association with Clinical Outcomes

2019 ◽  
Vol 57 (5) ◽  
Author(s):  
Julian R. Garneau ◽  
Claire Nour Abou Chakra ◽  
Louis-Charles Fortier ◽  
Annie-Claude Labbé ◽  
Andrew E. Simor ◽  
...  
Keyword(s):  
Clinical Outcomes ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Content Type ◽  
Repeat Analysis ◽  
Ribotype 027 ◽  
Clostridioides Difficile ◽  
Significant Difference ◽  
Pcr Ribotyping

ABSTRACT The epidemiology of Clostridioides difficile infection (CDI) has drastically changed since the emergence of the epidemic strain BI/NAP1/027, also known as ribotype 027 (R027). However, the relationship between the infecting C. difficile strain and clinical outcomes is still debated. We hypothesized that certain subpopulations of R027 isolates could be associated with unfavorable outcomes. We applied high-resolution multilocus variable-number tandem-repeat analysis (MLVA) to characterize C. difficile R027 isolates collected from confirmed CDI patients recruited across 10 Canadian hospitals from 2005 to 2008. PCR ribotyping was performed first to select R027 isolates that were then analyzed by MLVA (n = 450). Complicated CDI (cCDI) was defined by the occurrence of any of admission to an intensive care unit, colonic perforation, toxic megacolon, colectomy, and if CDI was the cause or contributed to death within 30 days after enrollment. Three major MLVA clusters were identified, MC-1, MC-3, and MC-10. MC-1 and MC-3 were exclusive to Quebec centers, while MC-10 was found only in Ontario. Fewer cases infected with MC-1 developed cCDI (4%) than those infected with MC-3 and MC-10 (15% and 16%, respectively), but a statistically significant difference was not reached. Our data did not identify a clear association between subpopulations of R027 and different clinical outcomes; however, the data confirmed the utility of MLVA’s higher discrimination potential to better characterize CDI populations in an epidemiological analysis. For a patient with CDI, the progression toward an unfavorable outcome is a complex process that probably includes several interrelated strain and host characteristics.

scholarly journals Subtyping of a Large Collection of Historical Listeria monocytogenes Strains from Ontario, Canada, by an Improved Multilocus Variable-Number Tandem-Repeat Analysis (MLVA)

2013 ◽  
Vol 79 (20) ◽  
pp. 6472-6480 ◽  
Author(s):  
S. Saleh-Lakha ◽  
V. G. Allen ◽  
J. Li ◽  
F. Pagotto ◽  
J. Odumeru ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Tandem Repeat ◽  
Food Chain ◽  
Diversity Index ◽  
Variable Number Tandem Repeat ◽  
Diversity Indices ◽  
Variable Number ◽  
Typing Method ◽  
Content Type ◽  
Repeat Analysis

ABSTRACTListeria monocytogenesis responsible for severe and often fatal food-borne infections in humans. A collection of 2,421L. monocytogenesisolates originating from Ontario's food chain between 1993 and 2010, along with Ontario clinical isolates collected from 2004 to 2010, was characterized using an improved multilocus variable-number tandem-repeat analysis (MLVA). The MLVA method was established based on eight primer pairs targeting seven variable-number tandem-repeat (VNTR) loci in two 4-plex fluorescent PCRs. Diversity indices and amplification rates of the individual VNTR loci ranged from 0.38 to 0.92 and from 0.64 to 0.99, respectively. MLVA types and pulsed-field gel electrophoresis (PFGE) patterns were compared using Comparative Partitions analysis involving 336 clinical and 99 food and environmental isolates. The analysis yielded Simpson's diversity index values of 0.998 and 0.992 for MLVA and PFGE, respectively, and adjusted Wallace coefficients of 0.318 when MLVA was used as a primary subtyping method and 0.088 when PFGE was a primary typing method. Statistical data analysis using BioNumerics allowed for identification of at least 8 predominant and persistentL. monocytogenesMLVA types in Ontario's food chain. The MLVA method correctly clustered epidemiologically related outbreak strains and separated unrelated strains in a subset analysis. An MLVA database was established for the 2,421L. monocytogenesisolates, which allows for comparison of data among historical and new isolates of different sources. The subtyping method coupled with the MLVA database will help in effective monitoring/prevention approaches to identify environmental contamination by pathogenic strains ofL. monocytogenesand investigation of outbreaks.

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 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

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Sabrina Cadel-Six ◽  
Marie-Leone Vignaud ◽  
Manal Mohammed
Keyword(s):  
Tandem Repeat ◽  
Salmonella Enterica ◽  
Draft Genome ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Genome Sequences ◽  
Content Type ◽  
Repeat Analysis

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.

scholarly journals Effective Surveillance Using Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Enterohemorrhagic Escherichia coli O157

2019 ◽  
Vol 85 (17) ◽  
Author(s):  
Kenichi Lee ◽  
Hidemasa Izumiya ◽  
Sunao Iyoda ◽  
Makoto Ohnishi
Keyword(s):  
Escherichia Coli ◽  
Tandem Repeat ◽  
Core Genome ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Whole Genome ◽  
Single Nucleotide ◽  
Molecular Surveillance ◽  
Content Type ◽  
Repeat Analysis

ABSTRACT Due to the potential of enterohemorrhagic Escherichia coli (EHEC) serogroup O157 to cause large food borne outbreaks, national and international surveillance is necessary. For developing an effective method of molecular surveillance, a conventional method, multilocus variable-number tandem-repeat analysis (MLVA), and whole-genome sequencing (WGS) analysis were compared. WGS of 369 isolates of EHEC O157 belonging to 7 major MLVA types and their relatives were subjected to comprehensive in silico typing, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) analyses. The typing resolution was the highest in cgSNP analysis. However, determination of the sequence of the mismatch repair protein gene mutS is necessary because spontaneous deletion of the gene could lead to a hypermutator phenotype. MLVA had sufficient typing resolution for a short-term outbreak investigation and had advantages in rapidity and high throughput. cgMLST showed less typing resolution than cgSNP, but it is less time-consuming and does not require as much computer power. Therefore, cgMLST is suitable for comparisons using large data sets (e.g., international comparison using public databases). In conclusion, screening using MLVA followed by cgMLST and cgSNP analyses would provide the highest typing resolution and improve the accuracy and cost-effectiveness of EHEC O157 surveillance. IMPORTANCE Intensive surveillance for enterohemorrhagic Escherichia coli (EHEC) serogroup O157 is important to detect outbreaks and to prevent the spread of the bacterium. Recent advances in sequencing technology made molecular surveillance using whole-genome sequence (WGS) realistic. To develop rapid, high-throughput, and cost-effective typing methods for real-time surveillance, typing resolution of WGS and a conventional typing method, multilocus variable-number tandem-repeat analysis (MLVA), was evaluated. Nation-level systematic comparison of MLVA, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) indicated that a combination of WGS and MLVA is a realistic approach to improve EHEC O157 surveillance.

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