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
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!
New cgMLST scheme and LIN code classifications for Moraxella catarrhalis. Available on @pubmlst.org.
www.ndph.ox.ac.uk/news/new-stu...
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
New cgMLST scheme and LIN code classifications for Moraxella catarrhalis. Available on @pubmlst.org.
www.ndph.ox.ac.uk/news/new-stu...
www.ndph.ox.ac.uk/news/new-stu...
Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of Neisseria meningitidis and Salmonella enterica when accounting for methylation-related errors
journals.asm.org/doi/10.1128/...
Methylation errors affect results—RPB kit helps.
journals.asm.org/doi/10.1128/...
Methylation errors affect results—RPB kit helps.
Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of Neisseria meningitidis and Salmonella enterica when accounting for methylation-related err...
This study evaluates the suitability of Oxford Nanopore Technologies R10 sequencing
for core-genome multi-locus sequence typing (cgMLST), a widely used method in (clinical)
outbreak investigation and ...
journals.asm.org
October 15, 2025 at 8:04 AM
Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of Neisseria meningitidis and Salmonella enterica when accounting for methylation-related errors
journals.asm.org/doi/10.1128/...
Methylation errors affect results—RPB kit helps.
journals.asm.org/doi/10.1128/...
Methylation errors affect results—RPB kit helps.
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
• 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
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
• 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
🧬 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
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
🧬 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
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
Outbreak Investigation of Phytobacter diazotrophicus Using Fourier Transform Infrared Spectroscopy compared to cgMLST https://www.biorxiv.org/content/10.1101/2025.09.17.676977v1
September 19, 2025 at 1:17 PM
Outbreak Investigation of Phytobacter diazotrophicus Using Fourier Transform Infrared Spectroscopy compared to cgMLST https://www.biorxiv.org/content/10.1101/2025.09.17.676977v1
Outbreak Investigation of Phytobacter diazotrophicus Using Fourier Transform Infrared Spectroscopy compared to cgMLST https://www.biorxiv.org/content/10.1101/2025.09.17.676977v1
September 19, 2025 at 1:17 PM
Outbreak Investigation of Phytobacter diazotrophicus Using Fourier Transform Infrared Spectroscopy compared to cgMLST https://www.biorxiv.org/content/10.1101/2025.09.17.676977v1
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
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.
A team have launched PathoBase, announced in early 2025 in One Health Advances Built on the proven EnteroBase framework, PathoBase offers enhanced speed, accessibility, and analytical depth for researchers worldwide.
#cgMLST
Details: doi.org/10.1186/s442...
#cgMLST
Details: doi.org/10.1186/s442...
September 9, 2025 at 1:19 PM
A team have launched PathoBase, announced in early 2025 in One Health Advances Built on the proven EnteroBase framework, PathoBase offers enhanced speed, accessibility, and analytical depth for researchers worldwide.
#cgMLST
Details: doi.org/10.1186/s442...
#cgMLST
Details: doi.org/10.1186/s442...
Introducing PathoBase:
A new Asia-housed genomic platform for rapid analysis of zoonotic pathogens. Supports cgMLST typing & real-time outbreak tracing. Free access for global researchers. 🧬🔍
#PathogenGenomics #OneHealth
Link: pathobase.iotabiome.com
👉
onehealthadv.biomedcentral.com/articles/10....
A new Asia-housed genomic platform for rapid analysis of zoonotic pathogens. Supports cgMLST typing & real-time outbreak tracing. Free access for global researchers. 🧬🔍
#PathogenGenomics #OneHealth
Link: pathobase.iotabiome.com
👉
onehealthadv.biomedcentral.com/articles/10....
PathoBase: an integrated One Health approach for zoonotic pathogen genomics analysis - One Health Advances
The rapid identification and genomic analysis of zoonotic pathogens are essential for effective disease surveillance and outbreak response. PathoBase, an advanced computational platform developed for ...
onehealthadv.biomedcentral.com
September 9, 2025 at 11:56 AM
Introducing PathoBase:
A new Asia-housed genomic platform for rapid analysis of zoonotic pathogens. Supports cgMLST typing & real-time outbreak tracing. Free access for global researchers. 🧬🔍
#PathogenGenomics #OneHealth
Link: pathobase.iotabiome.com
👉
onehealthadv.biomedcentral.com/articles/10....
A new Asia-housed genomic platform for rapid analysis of zoonotic pathogens. Supports cgMLST typing & real-time outbreak tracing. Free access for global researchers. 🧬🔍
#PathogenGenomics #OneHealth
Link: pathobase.iotabiome.com
👉
onehealthadv.biomedcentral.com/articles/10....
Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of Neisseria meningitidis and Salmonella enterica when accounting for methylation-related errors https://pubmed.ncbi.nlm.nih.gov/40844265/
August 23, 2025 at 12:25 PM
Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of Neisseria meningitidis and Salmonella enterica when accounting for methylation-related errors https://pubmed.ncbi.nlm.nih.gov/40844265/
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
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
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...
www.medrxiv.org/content/10.1...
July 30, 2025 at 2:11 AM
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...
www.medrxiv.org/content/10.1...
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
The cgMLST-based LIN code system provides a stable genomic taxonomy for strains of C. diphtheriae, C. rouxii and C. belfantii
New preprint describing a cgMLST scheme and LIN code system for Moraxella catarrhalis, with database hosted on @pubmlst.org. www.biorxiv.org/content/10.1...
Understanding the population structure of Moraxella catarrhalis using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system
Moraxella catarrhalis is an important cause of infectious exacerbations of chronic obstructive pulmonary disease and otitis media. Previously, seroresistant (SR) and serosensitive (SS) lineages that d...
www.biorxiv.org
May 7, 2025 at 7:03 AM
New preprint describing a cgMLST scheme and LIN code system for Moraxella catarrhalis, with database hosted on @pubmlst.org. www.biorxiv.org/content/10.1...
Understanding the population structure of Moraxella catarrhalis using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system https://www.biorxiv.org/content/10.1101/2025.04.30.651387v1
May 5, 2025 at 12:34 AM
Understanding the population structure of Moraxella catarrhalis using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system https://www.biorxiv.org/content/10.1101/2025.04.30.651387v1
Understanding the population structure of Moraxella catarrhalis using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system https://www.biorxiv.org/content/10.1101/2025.04.30.651387v1
May 5, 2025 at 12:34 AM
Understanding the population structure of Moraxella catarrhalis using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system https://www.biorxiv.org/content/10.1101/2025.04.30.651387v1
I am making one this week for the comparison of core genome SNP vs core genome MLST trees, to show the cgMLST is fine (so far cgSNPs used). So always useful to be able to make them quickly.
April 6, 2025 at 9:30 PM
I am making one this week for the comparison of core genome SNP vs core genome MLST trees, to show the cgMLST is fine (so far cgSNPs used). So always useful to be able to make them quickly.
Development of a core genome multilocus sequence typing (cgMLST) scheme and life identification number (LIN) code classification system for Staphylococcus aureus https://www.biorxiv.org/content/10.1101/2025.03.29.646111v1
April 3, 2025 at 6:33 PM
Development of a core genome multilocus sequence typing (cgMLST) scheme and life identification number (LIN) code classification system for Staphylococcus aureus https://www.biorxiv.org/content/10.1101/2025.03.29.646111v1
Development of a core genome multilocus sequence typing (cgMLST) scheme and life identification number (LIN) code classification system for Staphylococcus aureus https://www.biorxiv.org/content/10.1101/2025.03.29.646111v1
April 3, 2025 at 6:33 PM
Development of a core genome multilocus sequence typing (cgMLST) scheme and life identification number (LIN) code classification system for Staphylococcus aureus https://www.biorxiv.org/content/10.1101/2025.03.29.646111v1
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
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.
#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
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
#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
Used cgMLST and single-linkage clustering. Most clusters included humans and pets or pet contact. Wildlife->pets->people
MGen editors picks of the week!
A cgMLST scheme for pneumococcus
www.microbiologyresearch.org/content/jour...
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
MGen editors picks of the week!
A cgMLST scheme for pneumococcus
www.microbiologyresearch.org/content/jour...
A cgMLST scheme for pneumococcus
www.microbiologyresearch.org/content/jour...
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
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