#cgMLST
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sylvainbrisse.bsky.social
Cumulative cgMLST : Our novel preprint is out @biorxiv doi.org/10.1101/2025...
Cumulative cgMLST provides increased discrimination of nested phylogenetic groups
Background Core genome multilocus sequence typing (cgMLST) is a powerful method for bacterial strain genotyping. However, the size of the core genome decreases as the phylogenetic breadth of the targe...
doi.org
November 26, 2025 at 2:27 PM
hughcottingham.bsky.social
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...
July 30, 2025 at 2:11 AM
sylvainbrisse.bsky.social
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇
Life Identification Numbers: A bacterial strain nomenclature approach
Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...
doi.org
November 30, 2025 at 7:51 PM
sylvainbrisse.bsky.social
The recordings of the 6-hour webinar on Bacterial Strain Taxonomy for Genomic Surveillance are now available through the @ecdc.europa.eu ECDC Learning portal: learning.ecdc.europa.eu/course/view.... - cgMLST, SNPs, K-mer based strain nomenclatures applications and more!
Course: GenEpi-BioTrain - Virtual training 21 - Bacterial Strain Taxonomy for Genomic Surveillance
learning.ecdc.europa.eu
October 24, 2025 at 6:42 AM
ecdc.europa.eu
🧬 New #GenEpiBioTrain course!

Bacterial Strain Taxonomy for Genomic Surveillance
📅 22–23.10, 09:00–12:00 (CEST)

Learn how bacterial pathogens are classified & named in genomic surveillance – from #MLST & #cgMLST to SNP-based & k-mer clustering.

Info: bit.ly/48qT5df
#ECDCTraining #IDsky #EpiSky
October 8, 2025 at 2:34 PM
hughcottingham.bsky.social
We found modern ONT data (R10.4.1, Dorado SUP) to generate perfect MLST profiles and AMR allelic variant profiles, ~99.5% cgMLST profiles and cgSNP profiles highly concordant with traditional Illumina methods /3
July 30, 2025 at 2:13 AM
josefdelgadoblas.bsky.social
Great work on the power of the cumulative cgMLST approach for the genotypic discrimination of Klebsiella pneumoniae phylogenetic groups! Happy to have participated in this fascinating study led by @armovse.bsky.social and @sylvainbrisse.bsky.social.
November 26, 2025 at 6:50 PM
bstevensonlab.bsky.social
The wild, wild west of plasmids: First insights into comparative genomics of Borrelia burgdorferi sensu lato

journals.plos.org/plosone/arti...

pubmed.ncbi.nlm.nih.gov/42102105/

#MicroSky
Fig 1. Maximum likelihood tree of the 86 genomes based on cgMLST and plasmid presence/absence matrix. Figure includes information about species, reservoir host, tick vector, pathogenicity and genome elements. Species are listed and colored in different colors. Reservoir hosts are shown as icons; unknown hosts are indicated by “?”; for insectivores and carnivores a hedgehog icon is used. Tick vector species are listed. Pathogenicity is shown in different colors (green: nonpathogenic, red: pathogenic, red and “?”: potentially pathogenic, white and “?”: unknown). Genome elements (chromosome and plasmids): presence is indicated in green (complete genome element) and red (incomplete genome element), absence is indicated in grey; “X”: fusion plasmid, “-”: linear plasmid that carry a PFam32 that is typically found on a circular plasmid, “O”: circular plasmid that carry a PFam32 that is typically found on a linear plasmid. “$”: cp32-28-4 (circular plasmid with syntenic gene contents to cp32 plasmid family but encodes a lp28−4 type PFam32 protein), “^”: inverted repeat plasmid, “~”: dimer fusion, “+”: sequence was additionally added, “2”: two cp9 plasmids with different PFam57 proteins. “(X)”: the same cp32−11 type PFam32 was found on a non-fused plasmid (cp32−11) and on a fusion plasmid (cp32−9 + 11); “!”: plasmid name used in this study differs to the published plasmid name (S3 Table). S2 Fig adds information about the continent, vls/vlsE located plasmid, fusion plasmids, and shows reservoir host and vector not as icons, but in separate color-coded columns. S1 Table presents this information in tabular form with additional information on plasmid length.
May 11, 2026 at 6:11 PM
monicamedhist.bsky.social
Important paper in Y pestis phylogeny. "W/ the cgMLST scheme developed here, the known population structure of Y. pestis could be reproduced." #histmed translation: the late medieval divergence (= Big Bang) is as historically important as has been postulated the past 20+ yrs. doi.org/10.3390/micr...
April 19, 2026 at 5:17 PM
pasteur.fr
Toward a unified taxonomy for bacterial strains

New essay in PLOS Biology explores the Life Identification Number system — a cgMLST‑based framework for stable, high‑resolution strain classification and global epidemiological tracking.

journals.plos.org/plosbiology/...

@sylvainbrisse.bsky.social
Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens
Unified bacterial strain taxonomies are needed for coherent communication of findings in microbiological research. This Essay provides an overview of a novel bacterial strain taxonomy and describes ho...
journals.plos.org
June 5, 2026 at 8:43 AM
kasiamparfitt.bsky.social
Really happy to share this new pre print on the development of a cgMLST and LIN code for Streptococcus pyogenes, led by Yan Ryan at @ukhsa.bsky.social

www.biorxiv.org/content/10.6...
High resolution Streptococcus pyogenes core genome MLST and LIN coding scheme for outbreak detection
Streptococcus pyogenes is a globally important pathogen responsible for at least 500,000 deaths a year, causing significant burden on healthcare systems. It is the causative agent for ailments such as...
www.biorxiv.org
July 12, 2026 at 8:29 PM
kjolley.bsky.social
Just published - A new cgMLST scheme for Borrelia burgdorferi, the causative agent of Lyme disease. www.cell.com/cell-reports.... Scheme is available on @pubmlst.org.
A core genome MLST scheme for Borrelia burgdorferi sensu lato improves insights into the evolutionary history of the species complex
Hepner et al. develop a 639-loci core genome multi-locus sequence typing (cgMLST) scheme for Borrelia burgdorferi sensu lato that extends the traditional 8-loci MLST to a genomic scale. The cgMLST scheme gains higher reliability, robustness, and resolution, enabling improved insights into the evolutionary history of the species complex.
www.cell.com
December 19, 2024 at 9:06 AM
microbiologysociety.org
Genetic traits of IncK2 plasmids and the Escherichia coli host underlying the association to the chicken gut. Available to read in MGen: https://doi.org/10.1099/mgen.0.001535 #MGen
An MST of the cgMLST analysis of 57 E. coli isolates. Nodes are colour-coded according to sources. The cluster definition was set at ten allelic differences.
April 17, 2026 at 9:00 AM
alanmcn1.bsky.social
MGen editors picks of the week!

A cgMLST scheme for pneumococcus

www.microbiologyresearch.org/content/jour...
Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal popu...
Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermor...
www.microbiologyresearch.org
August 16, 2024 at 12:31 PM
sylvainbrisse.bsky.social
A taxonomic system needs to be created and updated in a coordinated manner. The cgMLST LIN code strain taxonomy is implemented in @kjolley.bsky.social 's BIGSdb, and is deployed at two main sites, PubMLST (at Oxford University) and BIGSdb-Pasteur (at Institut Pasteur, Paris)
November 30, 2025 at 7:51 PM
mgabrielaite.bsky.social
Taxonomy matters and if we call the same strain different names in different countries, we quickly run into problems not knowing what’s happening around us. @sylvainbrisse.bsky.social is defining the main requirements and offers a solution using cgMLST and LIN codes.
September 18, 2025 at 8:21 AM
rlsdvm.bsky.social
#ISVEE17 session on One Health starts with Chiara Crestani on genomic epi of C ulcerans (zoonotic cause of diptheria)

Used cgMLST and single-linkage clustering. Most clusters included humans and pets or pet contact. Wildlife->pets->people
November 15, 2024 at 4:29 AM
biorxiv-genomic.bsky.social
Development and Implementation of a Core Genome Multilocus Sequence Typing (cgMLST) scheme for Haemophilus influenzae https://www.biorxiv.org/content/10.1101/2024.04.15.589521v1
Development and Implementation of a Core Genome Multilocus Sequence Typing (cgMLST) scheme for Haemophilus influenzae https://www.biorxiv.org/content/10.1101/2024.04.15.589521v1
Haemophilus influenzae is part of the human nasopharyngeal microbiota and a pathogen causing invasiv
www.biorxiv.org
April 17, 2024 at 12:33 AM
alanmcn1.bsky.social
A cgMLST scheme for H. influenzae

www.microbiologyresearch.org/content/jour...
Development and implementation of a core genome multilocus sequence typing scheme for Haemophilus influenzae
Haemophilus influenzae is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in H. influenzae necessitates discriminatory ana...
www.microbiologyresearch.org
August 16, 2024 at 12:32 PM
ecdc.europa.eu
Participants will:

• Understand MLST, cgMLST, SNP-based, LIN and k-mer systems
• Apply these to classify bacterial isolates at species, lineage and outbreak level
• Design or adapt cgMLST schemes
• Evaluate pros and cons for public health surveillance

#GenomicEpidemiology #Bioinformatics
October 8, 2025 at 2:34 PM
sylvainbrisse.bsky.social
The wide adoption of cgMLST LIN code strain taxonomies has the potential to result in a universal approach for standardized bacterial genotyping that could greatly enhance microbial biodiversity studies, international genomic epidemiology and infectious disease surveillance
November 30, 2025 at 7:51 PM
sylvainbrisse.bsky.social
Core genome multilocus sequence typing (cgMLST) enables standardized high-resolution strain genotyping. Life Identification Number (LIN) codes are series of numeric codes that reflect genomic similarity between organisms, from left to right down to strain identity.
November 30, 2025 at 7:51 PM
sylvainbrisse.bsky.social
The recognition of sub-populations associated with distinct phenotypes is an important “raison d’être” of taxonomies. cgMLST LIN codes strain taxonomies will advance our understanding of the links between genotypes and clinical phenotypes, vaccine coverage and antimicrobial resistance
November 30, 2025 at 7:51 PM
kjolley.bsky.social
New cgMLST scheme and LIN code classifications for Moraxella catarrhalis. Available on @pubmlst.org.
www.ndph.ox.ac.uk/news/new-stu...
New study confirms genetic lineages of common bacterium
Oxford Population Health study confirms two genetic lineages of M. catarrhalis and unveils a global tool to track strains and resistance.
www.ndph.ox.ac.uk
October 17, 2025 at 7:24 PM
sylvainbrisse.bsky.social
The cgMLST-based LIN code system provides a stable genomic taxonomy for strains of C. diphtheriae, C. rouxii and C. belfantii
June 23, 2025 at 1:29 PM