Definition and research guide
This page combines a MeSH definition, publication statistics and selected research abstracts. It is a starting point for reading the literature, not a medical textbook or a systematic evidence review.
Content available: 4 complete abstracts (784 words), 10 references. Full article text is not stored or reproduced here; follow the PMID, DOI or PMC links to read the original sources and their access terms.
Definition
Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.
Definition: NLM Medical Subject Headings (MeSH) scope note (Public domain (U.S. National Library of Medicine); attribution requested). View the MeSH record.
Also known as: Sequence Typing, Multilocus; Typing, Multilocus Sequence; Multilocus Sequence Analysis; Analyses, Multilocus Sequence; Analysis, Multilocus Sequence; Multilocus Sequence Analyses; Sequence Analyses, Multilocus; Sequence Analysis, Multilocus.
Where it fits in the MeSH classification
- Broader topics
- Molecular Typing; Sequence Analysis, DNA
Research landscape
PubMed indexes 10,024 records tagged with the MeSH heading “Multilocus Sequence Typing” (counts retrieved 2026-10-29). 3,956 of them (39.5%) were published from 2020 onward, and the busiest period so far is 2010-2019 with 6,200 records.
Reviews account for 150 records (1.5%) and meta-analyses for 8. Randomized controlled trials number 11 (0.1%) as a share of all records on the topic. Randomized trials make up only a small share of this literature, so much of what is known comes from laboratory, observational or descriptive work.
Show the data
| Period | Records |
|---|---|
| through 1999 | 0 |
| 2000-2009 | 12 |
| 2010-2019 | 6,200 |
| 2020 onward | 3,956 |
Publication-type chart data
| Type | Records | Share |
|---|---|---|
| Reviews | 150 | 1.5% |
| Meta-analyses | 8 | 0.1% |
| Randomized controlled trials | 11 | 0.1% |
Method: PubMed query "Multilocus Sequence Typing"[MeSH Terms] with publication-type and date filters, retrieved 2026-10-29.
Reading the evidence in genetics and genomics
Genetic findings vary widely in strength. A variant linked to a condition in one study may not replicate in other ancestries, and most common variants have small effects that are meaningful only in aggregate. Studies of rare, high-impact variants can support strong causal claims about a gene, while association studies describe statistical links that need functional and independent replication. Check the sample size, the ancestry of participants, whether results were replicated, and whether a laboratory or clinical outcome was actually measured.
Evidence from open-access studies
These open-access studies come from PubMed’s best-match results for this heading (papers whose main topic it is), ranked here by citation count, with one recent addition. Each abstract is reproduced in full under its recorded open licence so that you can read the authors’ own words. They illustrate the literature; they are not a systematic summary of it. Citation counts measure attention, not reliability or clinical benefit.
| Study / authors | Year | Source label / design | Europe PMC citations | Licence / source |
|---|---|---|---|---|
| Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage | 2015 | Research article Design not recorded in structured metadata | 177 | cc by PMID 26226598 · DOI · PMC4635312 |
| Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii | 2017 | Research article Design not recorded in structured metadata | 124 | cc by PMID 28594944 · DOI · PMC5464626 |
| Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates | 2017 | Research article Design not recorded in structured metadata | 116 | cc by PMID 28446571 · DOI · PMC5483910 |
| tidyGenR: tidy multilocus amplicon genotypes in R | 2026 | Research article Design not recorded in structured metadata | 1 | cc by PMID 42765074 · DOI · PMC13589960 |
Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage [1]
Abstract reading summary — source excerpts
- Opening excerpt
- ObjectivesNeisseria meningitidis is a leading cause of meningitis and septicaemia.
- Closing excerpt
- ConclusionsHigh resolution 'genomic' multilocus sequence typing is necessary to resolve and monitor the spread of diverse cc11 lineages globally.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (195 words)
ObjectivesNeisseria meningitidis is a leading cause of meningitis and septicaemia. The hyperinvasive ST-11 clonal complex (cc11) caused serogroup C (MenC) outbreaks in the US military in the 1960s and UK universities in the 1990s, a global Hajj-associated serogroup W (MenW) outbreak in 2000-2001, and subsequent MenW epidemics in sub-Saharan Africa. More recently, endemic MenW disease has expanded in South Africa, South America and the UK, and MenC cases have been reported among European and North American men who have sex with men (MSM). Routine typing schemes poorly resolve cc11 so we established the population structure at genomic resolution.MethodsRepresentatives of these episodes and other geo-temporally diverse cc11 meningococci (n = 750) were compared across 1546 core genes and visualised on phylogenetic networks.ResultsMenW isolates were confined to a distal portion of one of two main lineages with MenB and MenC isolates interspersed elsewhere. An expanding South American/UK MenW strain was distinct from the 'Hajj outbreak' strain and a closely related endemic South African strain. Recent MenC isolates from MSM in France and the UK were closely related but distinct.ConclusionsHigh resolution 'genomic' multilocus sequence typing is necessary to resolve and monitor the spread of diverse cc11 lineages globally.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 26226598 · DOI · PMC4635312
Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii [2]
Abstract reading summary — source excerpts
- Opening excerpt
- We have employed whole genome sequencing to define and evaluate a core genome multilocus sequence typing (cgMLST) scheme for Acinetobacter baumannii.
- Closing excerpt
- Moreover, because a standardised cgMLST nomenclature is used, the system will allow inter-laboratory exchange of data.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (193 words)
We have employed whole genome sequencing to define and evaluate a core genome multilocus sequence typing (cgMLST) scheme for Acinetobacter baumannii. To define a core genome we downloaded a total of 1,573 putative A. baumannii genomes from NCBI as well as representative isolates belonging to the eight previously described international A. baumannii clonal lineages. The core genome was then employed against a total of fifty-three carbapenem-resistant A. baumannii isolates that were previously typed by PFGE and linked to hospital outbreaks in eight German cities. We defined a core genome of 2,390 genes of which an average 98.4% were called successfully from 1,339 A. baumannii genomes, while Acinetobacter nosocomialis, Acinetobacter pittii, and Acinetobacter calcoaceticus resulted in 71.2%, 33.3%, and 23.2% good targets, respectively. When tested against the previously identified outbreak strains, we found good correlation between PFGE and cgMLST clustering, with 0-8 allelic differences within a pulsotype, and 40-2,166 differences between pulsotypes. The highest number of allelic differences was between the isolates representing the international clones. This typing scheme was highly discriminatory and identified separate A. baumannii outbreaks. Moreover, because a standardised cgMLST nomenclature is used, the system will allow inter-laboratory exchange of data.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 28594944 · DOI · PMC5464626
Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates [3]
Abstract reading summary — source excerpts
- Opening excerpt
- Human campylobacteriosis, caused by Campylobacter jejuni and C.
- Closing excerpt
- In addition to the rapid and effective high-resolution analysis of large numbers of diverse isolates, the cgMLST scheme enabled the efficient identification of very closely related isolates from a well-defined single-source campylobacteriosis outbreak.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (247 words)
Human campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterization methods. Whole-genome sequencing (WGS) data enable the improvement of sequence-based typing approaches, such as multilocus sequence typing (MLST), by substantially increasing the number of loci examined. A core genome MLST (cgMLST) scheme defines a comprehensive set of those loci present in most members of a bacterial group, balancing very high resolution with comparability across the diversity of the group. Here we propose a set of 1,343 loci as a human campylobacteriosis cgMLST scheme (v1.0), the allelic profiles of which can be assigned to core genome sequence types. The 1,343 loci chosen were a subset of the 1,643 loci identified in the reannotation of the genome sequence of C. jejuni isolate NCTC 11168, chosen as being present in >95% of draft genomes of 2,472 representative United Kingdom campylobacteriosis isolates, comprising 2,207 (89.3%) C. jejuni isolates and 265 (10.7%) C. coli isolates. Validation of the cgMLST scheme was undertaken with 1,478 further high-quality draft genomes, containing 150 or fewer contiguous sequences, from disease isolate collections: 99.5% of these isolates contained ≥95% of the 1,343 cgMLST loci. In addition to the rapid and effective high-resolution analysis of large numbers of diverse isolates, the cgMLST scheme enabled the efficient identification of very closely related isolates from a well-defined single-source campylobacteriosis outbreak.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 28446571 · DOI · PMC5483910
tidyGenR: tidy multilocus amplicon genotypes in R [4]
Abstract reading summary — source excerpts
- Opening excerpt
- Multiplexed amplicon sequencing has become an important tool in phylogenetics and conservation genetics.
- Closing excerpt
- In addition, tidyGenR offers greater flexibility and interoperability.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (149 words)
Multiplexed amplicon sequencing has become an important tool in phylogenetics and conservation genetics. Amplicon sequencing reads need to be processed to get final haplotypes. The bioinformatics involved is often limiting for embarking on these kind of projects and there are few tools designed to handle this type of data. tidyGenR is an R package for reproducible multilocus amplicon genotyping workflows from sequencing reads. It provides a modular workflow that starts by demultiplexing loci, variant determination with DADA2, and ends with genotyping. Input data can be raw single-end or paired-end FASTQ reads and the main outputs are haplotypes in tidy tables. Results can also be exported as FASTA files. We successfully tested tidyGenR on amplicon libraries of 27 loci from a population genetics study in a rodent. The results from tidyGenR were reliable and robust across a wide range of read depths. In addition, tidyGenR offers greater flexibility and interoperability.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 42765074 · DOI · PMC13589960
Key reviews and meta-analyses
The most cited review-type papers among PubMed’s best-match results for this heading, listed with bibliographic details only. Follow the links for the full text and access terms.
- Research article MLST revisited: the gene-by-gene approach to bacterial genomics [5]
- Research article Multilocus sequence analysis (MLSA) in prokaryotic taxonomy [6]
- Research article Multi-locus species delimitation in closely related animals and fungi: one marker is not enough [7]
- Research article Pathogen typing in the genomics era: MLST and the future of molecular epidemiology [8]
- Research article Molecular approaches for a better understanding of the epidemiology and population genetics of Leishmania [9]
- Research article Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review [10]
References
- Lucidarme J, Hill DM, Bratcher HB, Gray SJ, du Plessis M, Tsang RS, et al.. Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage. . 2015. PMID 26226598 · DOI · PMC4635312
- Higgins PG, Prior K, Harmsen D, Seifert H. Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii. . 2017. PMID 28594944 · DOI · PMC5464626
- Cody AJ, Bray JE, Jolley KA, McCarthy ND, Maiden MCJ. Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates. . 2017. PMID 28446571 · DOI · PMC5483910
- Camacho-Sanchez M, Leonard JA. tidyGenR: tidy multilocus amplicon genotypes in R. . 2026. PMID 42765074 · DOI · PMC13589960
- Maiden MC, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, et al.. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol. 2013. PMID 23979428 · DOI · PMC3980634
- Glaeser SP, Kämpfer P. Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol. 2015. PMID 25959541 · DOI
- Dupuis JR, Roe AD, Sperling FA. Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Mol Ecol. 2012. PMID 22891635 · DOI
- Pérez-Losada M, Cabezas P, Castro-Nallar E, Crandall KA. Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infect Genet Evol. 2013. PMID 23357583 · DOI
- Schönian G, Kuhls K, Mauricio IL. Molecular approaches for a better understanding of the epidemiology and population genetics of Leishmania. Parasitology. 2011. PMID 21078222 · DOI
- Tagini F, Greub G. Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review. Eur J Clin Microbiol Infect Dis. 2017. PMID 28639162 · DOI · PMC5653721
About this article
- Sources
- NLM Medical Subject Headings (definition, synonyms); NCBI PubMed (counts, identifiers); Europe PMC (open-access abstracts and citation counts).
- Verification
- Every reference was resolved against PubMed on 2026-10-31; title, year and DOI matched.
- Review state
- automated source verified; no human expert review has been recorded yet.
- Version
- 1, last updated 2026-10-29.
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Evidence strength
EvidenceHelix's computed view of the study designs behind this topic: how common meta-analyses, randomized trials and reviews are, how recent the literature is, and a plain-language reading. It describes the design mix of the literature. It is not a quality appraisal of any study, and it is not medical advice.