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 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 Draft Genome Sequences of 13 Vibrio cholerae Strains from the Rio Grande Delta

2021 ◽  
Vol 10 (22) ◽  
Author(s):  
Jeffrey W. Turner ◽  
Jorge Duran-Gonzalez ◽  
David A. Laughlin ◽  
Daniel Unterweger ◽  
David Silva ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Diarrheal Disease ◽  
Draft Genome ◽  
Rio Grande ◽  
Etiologic Agent ◽  
Genome Sequences ◽  
Content Type

Vibrio cholerae is the etiologic agent of cholera, an acute and often fatal diarrheal disease that affects millions globally. We report the draft genome sequences of 13 non-O1/O139 V. cholerae strains isolated from the Rio Grande Delta, TX, USA. These genomes will aid future analyses of environmental serovars.

scholarly journals High resolution typing of Staphylococcus epidermidis based on cgMLST to investigate the hospital spread of multidrug resistant clones

2020 ◽  
pp. JCM.02454-20
Author(s):  
Anne Jamet ◽  
Julien Guglielmini ◽  
Bryan Brancotte ◽  
Mathieu Coureuil ◽  
Daniel Euphrasie ◽  
...  
Keyword(s):  
High Resolution ◽  
Staphylococcus Epidermidis ◽  
Core Genome ◽  
Genetic Relatedness ◽  
Multidrug Resistant ◽  
Epidemiological Surveillance ◽  
Typing Method ◽  
Health Care Associated Infections ◽  
French Hospital ◽  
Core Genes

Staphylococcus epidermidis is a pathogen emerging worldwide as a leading cause of health-care associated infections. A standardized high-resolution typing method to document transmission and dissemination of multidrug-resistant S. epidermidis strains is needed. Our aim was to provide a core genome multilocus sequence typing (cgMLST) typing scheme for S. epidermidis to improve the international surveillance of S. epidermidis.We defined a cgMLST scheme based on 699 core genes and used it to investigate the population structure of the species, and the genetic relatedness of isolates recovered from infants hospitalized in several wards of a French hospital. Our results show the long-lasting endemic persistence of S. epidermidis clones within and across wards of hospitals and demonstrate the ability of our cgMLST approach to identify and track these clones.We made the scheme publicly available through the Institut Pasteur BIGSdb server (http://bigsdb.pasteur.fr/epidermidis/). This tool should enable international harmonization of the epidemiological surveillance of multidrug-resistant S. epidermidis clones. By comparing gene distribution among infection and commensal isolates, we also confirmed the association of the mecA locus with infection isolates and of the fdh gene with commensal isolates.

scholarly journals A Core Genome Multilocus Sequence Typing Scheme for Streptococcus mutans

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Shanshan Liu ◽  
Xiaoliang Li ◽  
Zhenfei Guo ◽  
Hongsheng Liu ◽  
Yu Sun ◽  
...  
Keyword(s):  
Dental Caries ◽  
Streptococcus Mutans ◽  
Molecular Typing ◽  
Multilocus Sequence Typing ◽  
Phylogenetic Trees ◽  
Core Genome ◽  
Typing Method ◽  
Content Type ◽  
Mlst Scheme ◽  
Molecular Typing Method

ABSTRACT Streptococcus mutans is one of the primary pathogens responsible for the development of dental caries. Recent whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) approaches have been employed in epidemiological studies of specific human pathogens. However, this approach has not been reported in studies of S. mutans. Here, we therefore developed a cgMLST scheme for S. mutans. We surveyed 199 available S. mutans genomes as a means of identifying cgMLST targets, developing a scheme that incorporated 594 targets from the S. mutans UA159 reference genome. Sixty-eight sequence types (STs) were identified in this cgMLST scheme (cgSTs) in 80 S. mutans isolates from 40 children that were sequenced in this study, compared to 35 STs identified by multilocus sequence typing (MLST). Fifty-six cgSTs (82.35%) were associated with a single isolate based on our cgMLST scheme, which is significantly higher than in the MLST scheme (11.43%). In addition, 58.06% of all MLST profiles with ≥2 isolates were further differentiated by our cgMLST scheme. Topological analyses of the maximum likelihood phylogenetic trees revealed that our cgMLST scheme was more reliable than the MLST scheme. A minimum spanning tree of 145 S. mutans isolates from 10 countries developed based upon the cgMLST scheme highlighted the diverse population structure of S. mutans. This cgMLST scheme thus offers a new molecular typing method suitable for evaluating the epidemiological distribution of this pathogen and has the potential to serve as a benchmark for future global studies of the epidemiological nature of dental caries. IMPORTANCE Streptococcus mutans is regarded as a major pathogen responsible for the onset of dental caries. S. mutans can transmit among people, especially within families. In this study, we established a new epidemiological approach to S. mutans classification. This approach can effectively differentiate among closely related isolates and offers superior reliability relative to that of the traditional MLST molecular typing method. As such, it has the potential to better support effective public health strategies centered around this bacterium that are aimed at preventing and treating dental caries.

scholarly journals Establishment of a Publicly Available Core Genome Multilocus Sequence Typing Scheme for Clostridium perfringens

2021 ◽  
Author(s):  
Mostafa Y. Abdel-Glil ◽  
Prasad Thomas ◽  
Jörg Linde ◽  
Keith A. Jolley ◽  
Dag Harmsen ◽  
...  
Keyword(s):  
High Resolution ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clostridium Perfringens ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Epidemiological Surveillance ◽  
Whole Genome ◽  
Bacterial Strains

Global epidemiological surveillance of bacterial pathogens is enhanced by the availability of standard tools and sharing of typing data. The use of whole-genome sequencing has opened the possibility for high-resolution characterization of bacterial strains down to the clonal and subclonal levels.

Multilocus sequence typing of Vibrio cholerae strains with differing pandemic importance

2015 ◽  
Vol 30 (2) ◽  
pp. 85-92
Author(s):  
L. V. Mironova ◽  
M. V. Afanas’ev ◽  
E. G. Goldapel ◽  
S. V. Balakhonov
Keyword(s):  
Vibrio Cholerae ◽  
Multilocus Sequence Typing

Development and evaluation of a core genome multilocus sequence typing (cgMLST) scheme for Brucella spp.

2019 ◽  
Vol 67 ◽  
pp. 38-43 ◽  
Author(s):  
Jagadesan Sankarasubramanian ◽  
Udayakumar S. Vishnu ◽  
Paramasamy Gunasekaran ◽  
Jeyaprakash Rajendhran
Keyword(s):  
Multilocus Sequence Typing ◽  
Core Genome

scholarly journals Evaluation of WGS-subtyping methods for epidemiological surveillance of foodborne salmonellosis.

2020 ◽  
Author(s):  
Manal Mohammed ◽  
Salina Thapa
Keyword(s):  
Salmonella Typhimurium ◽  
Multilocus Sequence Typing ◽  
Bacterial Infections ◽  
Outbreak Investigation ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Whole Genome ◽  
Salmonella Dublin ◽  
Source Of Infection ◽  
Investigation Methods

Abstract Background: Salmonellosis is one of the most common foodborne diseases worldwide. Although human infection by non-typhoidal Salmonella (NTS) enterica subspecies enterica is associated primarily with a self-limiting diarrhoeal illness, invasive bacterial infections (such as septicaemia, bacteraemia and meningitis) were also reported. Human outbreaks of NTS were reported in several countries all over the world including developing as well as high-income countries. Conventional laboratory methods such as pulsed field gel electrophoresis (PFGE) do not display adequate discrimination and have their limitations in epidemiological surveillance. It is therefore very crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological characterisation and outbreak investigation. Methods: Here, we used different whole genome sequence (WGS)-based subtyping methods for retrospective investigation of two different outbreaks of Salmonella Typhimurium and Salmonella Dublin that occurred in 2013 in UK and Ireland respectively. Results: Single nucleotide polymorphism (SNP)-based cluster analysis of Salmonella Typhimurium genomes revealed well supported clades, that were concordant with epidemiologically defined outbreak and confirmed the source of outbreak is due to consumption of contaminated mayonnaise. SNP-analyses of Salmonella Dublin genomes confirmed the outbreak however the source of infection could not be determined. The core genome multilocus sequence typing (cgMLST) was discriminatory and separated the outbreak strains of Salmonella Dublin from the non-outbreak strains that were concordant with the epidemiological data however cgMLST could neither discriminate between the outbreak and non-outbreak strains of Salmonella Typhimurium nor confirm that contaminated mayonnaise is the source of infection, On the other hand, other WGS-based subtyping methods including multilocus sequence typing (MLST), ribosomal MLST (rMLST), whole genome MLST (wgMLST), clustered regularly interspaced short palindromic repeats (CRISPRs), prophage sequence profiling, antibiotic resistance profile and plasmid typing methods were less discriminatory and could not confirm the source of the outbreak. Conclusions: Foodborne salmonellosis is an important concern for public health therefore, it is crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological surveillance and outbreak investigation. In this study, we showed that SNP-based analyses do not only have the ability to confirm the occurrence of the outbreak but also to provide definitive evidence of the source of the outbreak in real-time.

scholarly journals Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period

2018 ◽  
Author(s):  
Angus Angermeyer ◽  
Moon Moon Das ◽  
Durg Vijai Singh ◽  
Kimberley D. Seed
Keyword(s):  
Vibrio Cholerae ◽  
Bay Of Bengal ◽  
Core Genome ◽  
Coastal Areas ◽  
Lytic Bacteriophage ◽  
Large Core ◽  
Accessory Genome ◽  
El Tor ◽  
Endemic Cholera ◽  
Over Time

AbstractThe Vibrio cholerae biotype ‘El Tor’ is responsible for all current epidemic and endemic cholera outbreaks worldwide. These outbreaks are clonal and are hypothesized to originate from the coastal areas near the Bay of Bengal where the lytic bacteriophage ICP1 specifically preys upon these pathogenic outbreak strains. ICP1 has also been the dominant bacteriophage found in cholera patient stool since 2001. However, little is known about its genomic differences between ICP1 strains collected over time. Here we elucidate the pan-genome and phylogeny of ICP1 strains by aligning, annotating and analyzing the genomes of 19 distinct isolates collected between 2001 and 2012. Our results reveal that ICP1 isolates are highly conserved and possess a large core-genome as well as a smaller, somewhat flexible accessory-genome. Despite its overall conservation, ICP1 strains have managed to acquire a number of unknown genes as well as a CRISPR-Cas system, which is known to be critical for its ongoing struggle for co-evolutionary dominance over its host. This study describes a foundation on which to construct future molecular and bioinformatic studies of this V. cholerae-associated bacteriophages.

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