scholarly journals A Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme To Facilitate the Epidemiological Study of Cholera

2020 ◽  
Vol 202 (24) ◽  
Author(s):  
Kevin Y. H. Liang ◽  
Fabini D. Orata ◽  
Mohammad Tarequl Islam ◽  
Tania Nasreen ◽  
Munirul Alam ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Geographic Origin ◽  
Data Set ◽  
Epidemiological Research ◽  
Content Type ◽  
Typing Scheme ◽  
Subspecies Level ◽  
Allelic Differences

ABSTRACT Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies-level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive data set of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates that could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single-nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease of use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/). IMPORTANCE Toxigenic Vibrio cholerae isolates of the O1 and O139 serogroups are the causative agents of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing scheme for V. cholerae. Using this scheme, we have standardized the definition for subspecies-level classification, facilitating global collaboration in the surveillance of V. cholerae. In addition, this typing scheme allows for quick identification of outbreak-related isolates that can guide subsequent analyses, serving as an important first step in epidemiological research. This scheme is also easily scalable to analyze thousands of isolates at various levels of resolution, making it an invaluable tool for large-scale ecological and evolutionary analyses.

scholarly journals A Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme to Facilitate the Epidemiological Study of Cholera

2020 ◽  
Author(s):  
Kevin Y. H. Liang ◽  
Fabini D. Orata ◽  
Mohammad Tarequl Islam ◽  
Tania Nasreen ◽  
Munirul Alam ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Diarrheal Disease ◽  
Geographic Origin ◽  
Etiologic Agent ◽  
Ease Of Use ◽  
Epidemiological Surveillance ◽  
Typing Method ◽  
Allelic Differences

ABSTRACTCore genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive dataset of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates which could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease-of-use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/).IMPORTANCEToxigenic Vibrio cholerae of the O1 and O139 serogroups are the causative agent of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing (cgMLST) scheme for V. cholerae. Using cgMLST, we established an outbreak threshold that can efficiently identify outbreak related strains and potential sources of introduction. We also defined a sublineage threshold that is similar to traditional MLST sequence type which will provide context to this new typing method by relating it to previous MLST results. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease-of-use, making this scheme the most suitable method for V. cholerae typing and surveillance worldwide.

scholarly journals A Core Genome Multilocus Sequence Typing Scheme forEnterococcus faecalis

2019 ◽  
Vol 57 (3) ◽  
Author(s):  
Bernd Neumann ◽  
Karola Prior ◽  
Jennifer K. Bender ◽  
Dag Harmsen ◽  
Ingo Klare ◽  
...  
Keyword(s):  
Public Health ◽  
Multilocus Sequence Typing ◽  
One Health ◽  
Core Genome ◽  
Target Genes ◽  
Phylogenetic Analyses ◽  
Genome Sequences ◽  
Healthy Human ◽  
Content Type ◽  
Typing Scheme

ABSTRACTAmong enterococci,Enterococcus faecalisoccurs ubiquitously, with the highest incidence of human and animal infections. The high genetic plasticity ofE. faecaliscomplicates both molecular investigations and phylogenetic analyses. Whole-genome sequencing (WGS) enables unraveling of epidemiological linkages and putative transmission events between humans, animals, and food. Core genome multilocus sequence typing (cgMLST) aims to combine the discriminatory power of classical multilocus sequence typing (MLST) with the extensive genetic data obtained by WGS. By sequencing a representative collection of 146E. faecalisstrains isolated from hospital outbreaks, food, animals, and colonization of healthy human individuals, we established a novel cgMLST scheme with 1,972 gene targets within the Ridom SeqSphere+software. To test theE. faecaliscgMLST scheme and assess the typing performance, different collections comprising environmental and bacteremia isolates, as well as all publicly available genome sequences from the NCBI and SRA databases, were analyzed. In more than 98.6% of the tested genomes, >95% good cgMLST target genes were detected (mean, 99.2% target genes). Our genotyping results not only corroborate the known epidemiological background of the isolates but exceed previous typing resolution. In conclusion, we have created a powerful typing scheme, hence providing an international standardized nomenclature that is suitable for surveillance approaches in various sectors, linking public health, veterinary public health, and food safety in a true One Health fashion.

scholarly journals Use of Whole-Genus Genome Sequence Data To Develop a Multilocus Sequence Typing Tool That Accurately Identifies Yersinia Isolates to the Species and Subspecies Levels

2014 ◽  
Vol 53 (1) ◽  
pp. 35-42 ◽  
Author(s):  
Miquette Hall ◽  
Marie A. Chattaway ◽  
Sandra Reuter ◽  
Cyril Savin ◽  
Eckhard Strauch ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Multilocus Sequence Typing ◽  
Sequence Data ◽  
Species Level ◽  
Reference Laboratory ◽  
Whole Genome ◽  
Pathogenic Species ◽  
Data Set ◽  
Content Type ◽  
Genome Sequence Data

The genusYersiniais a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identifyYersiniastrains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic speciesYersinia enterocoliticato whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification ofYersiniaisolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available forY. enterocolitica.

scholarly journals Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Anna Janowicz ◽  
Fabrizio De Massis ◽  
Massimo Ancora ◽  
Cesare Cammà ◽  
Claudio Patavino ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Brucella Melitensis ◽  
Reference Sequence ◽  
Snp Analysis ◽  
Phylogenetic Distance ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type

ABSTRACT The use of whole-genome sequencing (WGS) using next-generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through single-nucleotide polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome multilocus sequence typing (cgMLST) has not been explored so far. The current study developed an allele-based cgMLST method and compared its performance to that of the genome-wide SNP approach and the traditional multilocus variable-number tandem repeat analysis (MLVA) on a defined sample collection. The data set was comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 isolates with unknown epidemiological status, composed of human and animal samples collected in Italy. The cgMLST scheme generated in this study contained 2,704 targets of the B. melitensis 16M reference genome. We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be ≤6 loci in the cgMLST and ≤7 in WGS SNP analysis. Higher phylogenetic distance resolution was achieved with cgMLST and SNP analysis than with MLVA, particularly for strains belonging to the same lineage, thereby allowing diverse and unrelated genotypes to be identified with greater confidence. The application of a cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen, and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.

Performance outcomes of environmental collaboration

2016 ◽  
Vol 11 (4) ◽  
pp. 430-451 ◽  
Author(s):  
Sini Laari ◽  
Tomi Solakivi ◽  
Juuso Töyli ◽  
Lauri Ojala
Keyword(s):  
Financial Performance ◽  
Service Providers ◽  
Geographic Origin ◽  
Road Transport ◽  
Performance Outcomes ◽  
Data Set ◽  
Financial Reports ◽  
Content Type ◽  
Transport Services ◽  
Internal Operations

Purpose Firms that need to address growing concerns about the environmental impact of their activities could benefit from collaborating internally and externally. The purpose of this paper is to develop and empirically test a theoretical model of the effects of internal and external environmental collaboration with customers on the firm performance of logistics service providers (LSPs). Design/methodology/approach Hierarchical multiple regression and generalised linear modelling are utilised to analyse 311 LSPs offering road transport services in Finland. The data set was collected from a Finnish nationwide logistics survey in 2012 and financial reports-based data. Findings External environmental collaboration with customers seems to be the most effective way to improve operational and financial performance, while internal environmental collaboration does not yield similar benefits. Research limitations/implications Research limitations include the concentrated geographic origin of the respondents and the exclusion of potential indirect effects of environmental collaboration on operational and financial performance through environmental performance. Practical implications Managers planning to implement environmental initiatives should extend their focus from internal operations to external partners in the supply chain. Originality/value This research is one of the first attempts to focus on performance outcomes with regard to the environmental activities of LSPs. The research provides quantified insights using both self-reported and financial reports-based data.

scholarly journals Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires' disease incidents

2015 ◽  
Vol 20 (28) ◽  
Author(s):  
J Moran-Gilad ◽  
K Prior ◽  
E Yakunin ◽  
T G Harrison ◽  
A Underwood ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Typing Scheme ◽  
Binary File ◽  
Legionnaires Disease ◽  
Design And Application

Binary file ES_Abstracts_Final_ECDC.txt matches

scholarly journals Development and validation of a Burkholderia pseudomallei core genome multilocus sequence typing scheme to facilitate molecular surveillance

2021 ◽  
Author(s):  
Sabine Lichtenegger ◽  
Trung T. Trinh ◽  
Karoline Assig ◽  
Karola Prior ◽  
Dag Harmsen ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Burkholderia Pseudomallei ◽  
Core Genome ◽  
Target Genes ◽  
Severe Disease ◽  
Recent Infection ◽  
Fast Analysis ◽  
Typing Scheme ◽  
Typing Methods ◽  
Good Concordance

Objectives: Burkholderia pseudomallei causes the severe disease melioidosis. Whole genome-sequencing (WGS) based typing methods currently offer the highest resolution for molecular investigations of this genetically diverse pathogen. Still, its routine application in diagnostic laboratories is limited by the need for high computing power, bioinformatic skills and variable bioinformatic approaches, the latter affecting the results. We therefore aimed to establish and validate a WGS-based core genome multilocus sequence typing (cgMLST) scheme, applicable in routine diagnostic settings. Methods: A soft defined core genome was obtained by challenging the B. pseudomallei reference genome K96243 with 469 environmental and clinical genomes, resulting in 4,221 core and 1,359 accessory targets. The scheme was validated with 320 WGS datasets. We compared our novel typing scheme with single nucleotide polymorphism based-approaches investigating closely and distantly related strains. Finally, we applied our scheme for tracking the environmental source of a recent infection. Results: The validation of the scheme detected >95% good cgMLST target genes in 98.4% of the genomes. Comparison with existing typing methods revealed very good concordance. Our scheme proved to be applicable to investigate not only closely related strains, but also the global B. pseudomallei population structure. We successfully utilized our scheme to identify a sugar cane field as the presumable source of a recent melioidosis case. Conclusion: We developed a robust cgMLST typing scheme which integrates high resolution, maximized standardization and fast analysis for the non-bioinformatician. Our typing scheme has the potential to serve as a routinely applicable classification system in B. pseudomallei molecular epidemiology.

scholarly journals Hash-Based Core Genome Multilocus Sequence Typing for Clostridium difficile

2019 ◽  
Vol 58 (1) ◽  
Author(s):  
David W. Eyre ◽  
Tim E. A. Peto ◽  
Derrick W. Crook ◽  
A. Sarah Walker ◽  
Mark H. Wilcox
Keyword(s):  
Clostridium Difficile ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Genetic Relationships ◽  
Nucleotide Polymorphisms ◽  
Content Type ◽  
Recent Transmission ◽  
A Genome ◽  
Performance Penalty

ABSTRACT Pathogen whole-genome sequencing has huge potential as a tool to better understand infection transmission. However, rapidly identifying closely related genomes among a background of thousands of other genomes is challenging. Here, we describe a refinement to core genome multilocus sequence typing (cgMLST) in which alleles at each gene are reproducibly converted to a unique hash, or short string of letters (hash-cgMLST). This avoids the resource-intensive need for a single centralized database of sequentially numbered alleles. We test the reproducibility and discriminatory power of cgMLST/hash-cgMLST compared to those of mapping-based approaches in Clostridium difficile, using repeated sequencing of the same isolates (replicates) and data from consecutive infection isolates from six English hospitals. Hash-cgMLST provided the same results as standard cgMLST, with minimal performance penalty. Comparing 272 replicate sequence pairs using reference-based mapping, there were 0, 1, or 2 single-nucleotide polymorphisms (SNPs) between 262 (96%), 5 (2%), and 1 (<1%) of the pairs, respectively. Using hash-cgMLST, 218 (80%) of replicate pairs assembled with SPAdes had zero gene differences, and 31 (11%), 5 (2%), and 18 (7%) pairs had 1, 2, and >2 differences, respectively. False gene differences were clustered in specific genes and associated with fragmented assemblies, but were reduced using the SKESA assembler. Considering 412 pairs of infections with ≤2 SNPS, i.e., consistent with recent transmission, 376 (91%) had ≤2 gene differences and 16 (4%) had ≥4. Comparing a genome to 100,000 others took <1 min using hash-cgMLST. Hash-cgMLST is an effective surveillance tool for rapidly identifying clusters of related genomes. However, cgMLST/hash-cgMLST generate more false variants than mapping-based approaches. Follow-up mapping-based analyses are likely required to precisely define close genetic relationships.

scholarly journals Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum

2017 ◽  
Vol 56 (1) ◽  
Author(s):  
Mostafa Ghanem ◽  
Leyi Wang ◽  
Yan Zhang ◽  
Scott Edwards ◽  
Amanda Lu ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Phylogenetic Trees ◽  
Core Genome ◽  
Sequence Data ◽  
Mycoplasma Gallisepticum ◽  
Content Type ◽  
Next Generation Sequencing Technology ◽  
Animal Pathogens ◽  
Conserved Genes ◽  
Outbreak Investigations

ABSTRACT Mycoplasma gallisepticum is the most virulent and economically important Mycoplasma species for poultry worldwide. Currently, M. gallisepticum strain differentiation based on sequence analysis of 5 loci remains insufficient for accurate outbreak investigation. Recently, whole-genome sequences (WGS) of many human and animal pathogens have been successfully used for microbial outbreak investigations. However, the massive sequence data and the diverse properties of different genes within bacterial genomes results in a lack of standard reproducible methods for comparisons among M. gallisepticum whole genomes. Here, we proposed the development of a core genome multilocus sequence typing (cgMLST) scheme for M. gallisepticum strains and field isolates. For development of this scheme, a diverse collection of 37 M. gallisepticum genomes was used to identify cgMLST targets. A total of 425 M. gallisepticum conserved genes (49.85% of M. gallisepticum genome) were selected as core genome targets. A total of 81 M. gallisepticum genomes from 5 countries on 4 continents were typed using M. gallisepticum cgMLST. Analyses of phylogenetic trees generated by cgMLST displayed a high degree of agreement with geographical and temporal information. Moreover, the high discriminatory power of cgMLST allowed differentiation between M. gallisepticum strains of the same outbreak. M. gallisepticum cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation among M. gallisepticum isolates. cgMLST provides stable and expandable nomenclature, allowing for comparison and sharing of typing results among laboratories worldwide. cgMLST offers an opportunity to harness the tremendous power of next-generation sequencing technology in applied avian mycoplasma epidemiology at both local and global levels.

scholarly journals Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
Richard A. Stanton ◽  
Gillian McAllister ◽  
Jonathan B. Daniels ◽  
Erin Breaker ◽  
Nicholas Vlachos ◽  
...  
Keyword(s):  
Health Care ◽  
Pseudomonas Aeruginosa ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Health Care Environment ◽  
Content Type ◽  
Health Care Associated Infections ◽  
Opportunistic Human Pathogen ◽  
The Stability ◽  
Core Genes

ABSTRACT Pseudomonas aeruginosa is an opportunistic human pathogen that frequently causes health care-associated infections (HAIs). Due to its metabolic diversity and ability to form biofilms, this Gram-negative nonfermenting bacterium can persist in the health care environment, which can lead to prolonged HAI outbreaks. We describe the creation of a core genome multilocus sequence typing (cgMLST) scheme to provide a stable platform for the rapid comparison of P. aeruginosa isolates using whole-genome sequencing (WGS) data. We used a diverse set of 58 complete P. aeruginosa genomes to curate a set of 4,440 core genes found in each isolate, representing ∼64% of the average genome size. We then expanded the alleles for each gene using 1,991 contig-level genome sequences. The scheme was used to analyze genomes from four historical HAI outbreaks to compare the phylogenies generated using cgMLST to those of other means (traditional MLST, pulsed-field gel electrophoresis [PFGE], and single-nucleotide variant [SNV] analysis). The cgMLST scheme provides sufficient resolution for analyzing individual outbreaks, as well as the stability for comparisons across a variety of isolates encountered in surveillance studies, making it a valuable tool for the rapid analysis of P. aeruginosa genomes.

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