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.

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 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 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 Comparison between Salmonella enterica Serotype Enteritidis Genotyping Methods and Phage Type

2015 ◽  
Vol 53 (9) ◽  
pp. 3021-3031 ◽  
Author(s):  
Alessandra De Cesare ◽  
Keshav Krishnamani ◽  
Antonio Parisi ◽  
Antonia Ricci ◽  
Ida Luzzi ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Phage Type ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Quantitative Comparison ◽  
Pulsed Field Gel Electrophoresis ◽  
Typing Method ◽  
Content Type ◽  
Repeat Analysis ◽  
Automated Ribotyping

A quantitative comparison between discriminatory indexes and concordance among multilocus variable-number tandem-repeat analysis (MLVA), pulsed-field gel electrophoresis (PFGE), automated ribotyping, and phage typing has been performed, testing 238Salmonella entericaserotype Enteritidis isolates not epidemiologically correlated. The results show that MLVA is the best choice, but each typing method provides a piece of information for establishing clonal relationships between the isolates.

scholarly journals Virulence Traits of Environmental and ClinicalLegionella pneumophilaMultilocus Variable-Number Tandem-Repeat Analysis (MLVA) Genotypes

2018 ◽  
Vol 84 (10) ◽  
Author(s):  
Yehonatan Sharaby ◽  
Sarah Rodríguez-Martínez ◽  
Marina Pecellin ◽  
Rotem Sela ◽  
Avi Peretz ◽  
...  
Keyword(s):  
Drinking Water ◽  
Health Risks ◽  
Legionella Pneumophila ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Content Type ◽  
Clinical Strains ◽  
Repeat Analysis ◽  
Public Health Risks ◽  
Virulence Traits

ABSTRACTLegionella pneumophilacauses water-based infections resulting in severe pneumonia. Recently, we showed that different MLVA-8 (multilocus variable-number tandem-repeat analysis using 8 loci) genotypes dominated different sites of a drinking-water distribution system. Each genotype displayed a unique temperature-dependent growth behavior. Here we compared the pathogenicity potentials of different MLVA-8 genotypes of environmental and clinical strains. The virulence traits studied were hemolytic activity and cytotoxicity toward amoebae and macrophages. Clinical strains were significantly more hemolytic than environmental strains, while their cytotoxicity toward amoebae was significantly lower at 30°C. No significant differences were detected between clinical and environmental strains in cytotoxicity toward macrophages. Significant differences in virulence were observed between the environmental genotypes (Gt). Gt15 strains showed a significantly higher hemolytic activity. In contrast, Gt4 and Gt6 strains were more infective towardAcanthamoeba castellanii. Moreover, Gt4 strains exhibited increased cytotoxicity toward macrophages and demonstrated a broader temperature range of amoebal lysis than Gt6 and Gt15 strains. Understanding the virulence traits ofLegionellagenotypes may improve the assessment of public health risks ofLegionellain drinking water.IMPORTANCELegionella pneumophilais the causative agent of a severe form of pneumonia. Here we demonstrated that clinical strains were significantly more cytotoxic toward red blood cells than environmental strains, while their cytotoxicity toward macrophages was similar. Genotype 4 (Gt4) strains were highly cytotoxic toward amoebae and macrophages and lysed amoebae in a broader temperature range than to the other studied genotypes. The results can explain the relatively high success of Gt4 in the environment and in clinical samples; thus, Gt4 strains should be considered a main factor for the assessment of public health risks ofLegionellain drinking water. Our findings shed light on the ecology, virulence, and pathogenicity potential of differentL. pneumophilagenotypes, which can be a valuable parameter for future modeling and quantitative microbial risk assessment ofLegionellain drinking-water systems.

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.

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