Tag: cgMLST

Investigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing | Antimicrobial Resistance & Infection Control

Isolate characteristics From June 2020 to October 2021, our analysis included a total of 28 isolates from patient and environmental samples, all subjected to Whole Genome Sequencing (WGS) (refer to Table 1). To ensure robustness and minimize the influence of sequencing errors on our findings, all 28 WGS datasets maintained a…

Continue Reading Investigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing | Antimicrobial Resistance & Infection Control

Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century

Distributed cgMLST scheme and the species tree based on a global dataset of 70,000 Neisseria genomes To set up the new dcgMLST scheme, we established a global collection of genomic sequences for 69,994 Neisseria strains (Supplementary Data 1), consisting of 4411 assembled genomes from GenBank, 65,434 genomes assembled based on short…

Continue Reading Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century

How divergent is c. coli when compared to c. jejuni based on cgmlst data?

What are the major chicken diseases that impact poultry meat production? 3 answers Microbiota, Gut Health and Chicken Productivity: What Is the Connection? 5 answers Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study 3 answers What is the role of FitA in Klebsiella? 5…

Continue Reading How divergent is c. coli when compared to c. jejuni based on cgmlst data?

Core-genome multilocus sequence typing and core-SNP analysis of Clostridium neonatale strains isolated in different spatio-temporal settings

Clostridium neonatale was described as a new species within the Clostridium genus cluster I sensu stricto. It was recovered from the gut microbiota of infants and has been associated with necrotizing enterocolitis (NEC), a severe gastrointestinal disease affecting preterm neonates. In the absence of molecular typing methods, we developed a…

Continue Reading Core-genome multilocus sequence typing and core-SNP analysis of Clostridium neonatale strains isolated in different spatio-temporal settings

Minimum spanning tree based on cgMLST allelic profiles

Minimum spanning tree based on cgMLST allelic profiles 0 Hi, I want to build a Minimum spanning tree based on cgMLST allelic profiles for e.coli isolates. I ran an analysis using pubMLST – for each genome I have a list of genes. The lists are not identical – i.e. they…

Continue Reading Minimum spanning tree based on cgMLST allelic profiles

A core-genome multilocus sequence typing scheme for the detection of genetically related Streptococcus pyogenes clusters

doi: 10.1128/jcm.00558-23. Online ahead of print. Affiliations Expand Affiliation 1 Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. Item in Clipboard Myrthe M A Toorop et al. J Clin Microbiol. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1128/jcm.00558-23. Online ahead of print. Affiliation 1 Department…

Continue Reading A core-genome multilocus sequence typing scheme for the detection of genetically related Streptococcus pyogenes clusters

Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA

Salmonella enterica is a leading cause of bacterial foodborne and zoonotic illnesses in the United States. For this study, we applied four different whole genome sequencing (WGS)-based subtyping methods: high quality single-nucleotide polymorphism (hqSNP) analysis, whole genome multilocus sequence typing using either all loci [wgMLST (all loci)] and only chromosome-associated…

Continue Reading Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA

Comparative genomic analysis of Fusobacterium nucleatum reveals high intra-species diversity and cgmlst marker construction | Gut Pathogens

Summary of genomic data A total of 105 Fusobacterium nucleatums’ genome sequences were downloaded from the NCBI, quality controlled and evaluated for core genes. Finally, 93 genomes were selected for further analysis (Additional file 5: Table S1). The number of scaffolds ranged from 1 to 379, with a maximum N50…

Continue Reading Comparative genomic analysis of Fusobacterium nucleatum reveals high intra-species diversity and cgmlst marker construction | Gut Pathogens

Core-genome multilocus sequence typing for epidemiological and evolutionary analyses of phytopathogenicXanthomonas citri

Xanthomonas citri subsp. citri is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry. X. citri subspecies and pathovars are responsible for diseases in soybean, common bean, mango, pomegranate, and cashew. X. citri disease has been tracked using several typing methods, but recent studies…

Continue Reading Core-genome multilocus sequence typing for epidemiological and evolutionary analyses of phytopathogenicXanthomonas citri

Comparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environments

Core genomes of Listeria species strongly differ between natural and food-associated environments and can accurately predict isolation sources at a lineage level To assess the relationship between the core genome of L. monocytogenes (which entails genomes of all three L. monocytogenes lineages identified in this study – lineage I, II,…

Continue Reading Comparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environments

Microorganisms | Free Full-Text | Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin

1. Introduction Staphylococcus aureus is an important pathogen in healthcare and community settings that can cause a broad spectrum of diseases, ranging from skin and soft-tissue infections to invasive diseases such as pneumonia, septicemia, and endocarditis [1]. In the 1960s [2], soon after the introduction of methicillin into the healthcare…

Continue Reading Microorganisms | Free Full-Text | Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin

Chewbbaca – explanation of the output

Chewbbaca – explanation of the output 0 Hello! I’m new in the field and I need to use Chewbbaca In the end of the analysis, I get in a visualization folder, a file, cgMLST.tsv. Is the values in this file represent the allele distance of each specie from the schema…

Continue Reading Chewbbaca – explanation of the output

Whole strains vs MGEs in short and longterm transmission of ESBL genes between healthcare and community settings in Uganda

ESBL carriage Of the 1556 samples analyzed, 81.9% (1275) yielded suspected ESBL producing bacteria. The antimicrobial susceptibility testing of the obtained isolates showed that many of the strains were resistant to critical cephalosporin and carbapenem antimicrobials such as Cefepime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem and Imipenem in both healthcare and community…

Continue Reading Whole strains vs MGEs in short and longterm transmission of ESBL genes between healthcare and community settings in Uganda

Whole-genome sequencing of Listeria monocytogenes isolated from the first listeriosis foodborne outbreak in South Korea

Introduction Although globalization has provided opportunities for consumers to enjoy a wide range of products and expanded global food trade, the complexity of the international food supply has contributed to an increase in foodborne outbreaks (Quested et al., 2010; Hussain and Dawson, 2013). Worldwide efforts have ensured food safety by…

Continue Reading Whole-genome sequencing of Listeria monocytogenes isolated from the first listeriosis foodborne outbreak in South Korea

Whole genome sequencing of Ethiopian Brucella abortus isolates expands the known diversity of an early branching sub-Saharan African lineage

1. Introduction Brucellosis is a zoonotic infection caused by bacteria of the genus Brucella, which affects domestic livestock and a wide range of wild mammals (Ducrotoy et al., 2017). The disease is amongst the most common zoonotic infections globally, with an estimated 500,000 human cases annually (Pappas et al., 2006),…

Continue Reading Whole genome sequencing of Ethiopian Brucella abortus isolates expands the known diversity of an early branching sub-Saharan African lineage

Working to tackle antibiotic resistant bacteria

The emergence of an XDR S. sonnei outbreak in the United Kingdom. A cgMLST dendrogram (midpoint rooted) of clinical isolates from the UK (n = 2,820) and genomic subtype references (n = 120) with the scale bar indicating distance in cgMLST alleles. Metadata tracks show patient and genomic features for isolates colored according to…

Continue Reading Working to tackle antibiotic resistant bacteria

Application of a core genome sequence typing (cgMLST) pipeline for surveillance of Clostridioides difficile in China

Front Cell Infect Microbiol . 2023 Mar 13;13:1109153. doi: 10.3389/fcimb.2023.1109153. eCollection 2023. Affiliations Expand Affiliations 1 State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. 2 Research Center for Micro-Ecological Agent Engineering and…

Continue Reading Application of a core genome sequence typing (cgMLST) pipeline for surveillance of Clostridioides difficile in China

Public health implications of Yersinia enterocolitica investigation: an ecological modeling and molecular epidemiology study | Infectious Diseases of Poverty

Epidemic profile of Yersinia during 2007–2019 A total of 9031 samples were monitored from 2007 to 2019, with the detection rate of Yersinia ranging from 0.9% to 7.6% (Table 1). The highest detection rate was in 2014 (7.6%), eightfold higher than in 2013 (0.5%). The difference in positivity rates between…

Continue Reading Public health implications of Yersinia enterocolitica investigation: an ecological modeling and molecular epidemiology study | Infectious Diseases of Poverty

Whole-Genome Sequencing-Based Characterization of Clinical Isolates in China, 2013-2019.

Invasive listeriosis is a rare but serious foodborne disease that causes maternal-neonatal, central nervous system, and bloodstream infections. The aim of this study was to assess the whole-genome sequencing (WGS)-based genetic diversity of clinical isolates over a 7-year period and prove the effect of WGS application in food vehicle investigation….

Continue Reading Whole-Genome Sequencing-Based Characterization of Clinical Isolates in China, 2013-2019.

The genomic epidemiology of Escherichia albertii infecting humans and birds in Great Britain

Summary of the human isolates Between January 2014 (when routine WGS was first implemented at the GBRU) and December 2021, 83 isolates from human cases were confirmed as E. albertii. Over this 8-year period, between 4 and 23 isolates were identified per year (Supplementary Fig. 1). Metadata regarding patient gender, age…

Continue Reading The genomic epidemiology of Escherichia albertii infecting humans and birds in Great Britain

A 10-year microbiological study of Pseudomonas aeruginosa strains revealed the circulation of populations resistant to both carbapenems and quaternary ammonium compounds

P. aeruginosa bacterial strains Reference strains Four well-described and genome-available reference strains were used in the present study, ATCC27853 and ATCC15442, obtained from the American Type Culture Collection (ATCC), and PAO1 and PA14, from the collection of Institut Pasteur (Paris, France). Strain ATCC15442 is recommended for disinfectant susceptibility testing44, strain…

Continue Reading A 10-year microbiological study of Pseudomonas aeruginosa strains revealed the circulation of populations resistant to both carbapenems and quaternary ammonium compounds

Institut Pasteur MLST databases and software

LIN codes General presentation The cgMLST-based Life Identification Numbers (LIN) codes (cgLIN codes, or LIN codes for short) constitute the basis of a novel bacterial strain taxonomy system proposed in 2022. An implementation was initially developed for the Klebsiella pneumoniae species complex (KpSC) by Hennart et al. 2022. This system…

Continue Reading Institut Pasteur MLST databases and software

Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil

Bacterial isolate Adolfo Lutz Institute is a regional reference laboratory for Salmonella isolates from São Paulo, Brazil. Thus, all isolates received are submitted to classical serotyping, antimicrobial susceptibility testing, and molecular-typing by PFGE and next-generation sequencing. Isolate 288_18 was recovered from a blood sample from a patient with clinical symptoms…

Continue Reading Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil

Development and Evaluation of a Core Genome Multilocus Sequencing Typing (cgMLST) Scheme for Serratia marcescens Molecular Surveillance and Outbreak Investigations

Serratia marcescens can cause a range of severe infections and contributes to nosocomial outbreaks. Although whole-genome sequencing (WGS)-based typing is the standard method for molecular surveillance and outbreak investigation, there is no standardized analytic scheme for S. marcescens core genome multilocus sequence typing (cgMLST). Here, the development and evaluation of…

Continue Reading Development and Evaluation of a Core Genome Multilocus Sequencing Typing (cgMLST) Scheme for Serratia marcescens Molecular Surveillance and Outbreak Investigations

A core genome MLST (cgMLST) scheme for Mycobacterium abscessus complex subspecies

Dataset for manuscript “The use of comparative genomic analysis for the development of subspecies-specific PCR assays for the Mycobacterium abscessus complex” by Winifred Akwani et al. A core genome MLST scheme was developed for Mycobacterium abscessus complex (MABC) subspecies M. abscessus, M. bolletii and M. massiliense, using chewBBACA version 2.8.5…

Continue Reading A core genome MLST (cgMLST) scheme for Mycobacterium abscessus complex subspecies

Genomic Characterization of Clinical Listeria monocytogenes Isolates in Beijing, China

Listeria monocytogenes is a foodborne human pathogen that affects public health worldwide. Whole-genome sequencing (WGS) can classify L. monocytogenes isolates and identify virulence islands and resistance genes potentially influencing infectivity. Herein, WGS was used to assess 151 L. monocytogenes isolates from 120 cases of clinical infection in Beijing, China, between…

Continue Reading Genomic Characterization of Clinical Listeria monocytogenes Isolates in Beijing, China