Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 19

System / cell line: clinical ✕ Assay: mlst ✕ Clear

Environmental Burkholderia cepacia complex isolates in human infections.

PMID 17552100 · PMC2725883 · Emerging infectious diseases · 2007 · 6 claims · 4 setups

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More than 20% of clinical Bcc isolates examined are indistinguishable by MLST from environmental isolates, linking the natural environment to emergence of clinical infections

clinical environmental subset stabilis multilocus cloning pulsed-field
Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

PMID 18990211 · PMC2585095 · BMC microbiology · 2008 · 8 claims · 7 setups

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The 55 clinical B. cereus isolates were phylogenetically diverse, comprising 38 sequence types (STs) distributed across two of three previously described clades.

clinical concatenated cereus isolates multilocus phylogenetic pcr
Comparative genomic analysis of clinical strains of Campylobacter jejuni from South Africa.

PMID 18431496 · PMC2292242 · PloS one · 2008 · 8 claims · 4 setups

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South African HS:41 strains are clearly distinct from the other South African strains by comparative genomic analysis

clinical genomic jejuni multilocus microarray phylogenetic
Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

PMID 20021660 · PMC2810298 · BMC microbiology · 2009 · 8 claims · 6 setups

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A novel Multi-Locus Sequence Typing (MLST) scheme for O. anthropi was developed for the first time, based on 7 genes (3490 nucleotides) evolving mostly by neutral mutations

anthropi same candidate multi-locus pulsed-field antibiotyping
MLST clustering of Campylobacter jejuni isolates from patients with gastroenteritis, reactive arthritis and Guillain-Barré syndrome.

PMID 19702866 · PMC3985121 · Journal of applied microbiology · 2010 · 8 claims · 4 setups

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Danish C. jejuni isolates from gastroenteritis, RA and GBS patients are highly genetically diverse, comprising 51 STs within 18 clonal complexes among 122 isolates.

campylobacter concatenated clonal multilocus upgma clonalframe
Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

PMID 17535437 · PMC1892558 · BMC microbiology · 2007 · 8 claims · 6 setups

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Cjd strains are phylogenetically distinct from Cjj strains based on MLST and CGI analysis

geographically cjd novel jejuni multilocus comparative phenotypic
Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains.

PMID 18590534 · PMC2481270 · BMC genomics · 2008 · 8 claims · 6 setups

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B. pertussis strains carrying the ptxP3 allele gradually replaced ptxP1 strains and became predominant from 1998, coinciding with the Dutch pertussis resurgence

dutch additional pertussis ptxp3 multi-locus multiple-locus microarray-based
Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

streptococcus pyogenes emm values multilocus emm comparative
Lineage specific recombination rates and microevolution in Listeria monocytogenes.

PMID 18842152 · PMC2576243 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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Recombination is more prevalent in lineage II than in lineage I

listeria allelic unique monocytogenes multilocus sawyer's genealogical
Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia.

PMID 38711928 · PMC11070470 · Frontiers in cellular and infection microbiology · 2024 · 8 claims · 8 setups

Has reproduction · 69

Sequenced GBS isolates from Saudi Arabia show high genetic diversity, with 28 sequence types and nine distinct serotypes including uncommon serotypes VII and VIII

gbs whole-genome multilocus capsular
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

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A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

gbs clinical bioinformatic eburst kinetic
Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis.

PMID 18307777 · PMC2268939 · BMC microbiology · 2008 · 8 claims · 7 setups

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MLST of 26 C. trachomatis strains reveals three non-overlapping clonal complexes (groups I, II, III)

trachomatis pneumoniae chlamydiales mlst eburst upgma
Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

PMID 19852808 · PMC2770063 · BMC microbiology · 2009 · 8 claims · 6 setups

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A seven-locus MLST scheme (atpD, fusA, glnS, gltB, gyrB, infB, pps) reliably identifies and discriminates C. sakazakii and C. malonaticus strains

sakazakii cronobacter sequenced multilocus biotyping phylogenetic
Genetic diversity among Enterococcus faecalis.

PMID 17611618 · PMC1899230 · PloS one · 2007 · 7 claims · 7 setups

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Virulence and antibiotic resistance traits are distributed across many diverse E. faecalis lineages rather than confined to one clade

faecalis multi-locus dot pcr
Cryptococcus neoformans strains and infection in apparently immunocompetent patients, China.

PMID 18439357 · PMC2600263 · Emerging infectious diseases · 2008 · 8 claims · 8 setups

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71% (91/129) of Chinese cryptococcosis clinical isolates (1985-2006) came from patients with no apparent risk factor, versus only 8.5% from AIDS patients, contrasting sharply with other countries

clinical neoformans randomly balb pcr ura5 igs1-5.8s
Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

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A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

genome-sequenced trachomatis same concatenated whole-genome multilocus ompa
Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame.

PMID 30648934 · PMC6412060 · Microbial genomics · 2019 · 8 claims · 7 setups

Has reproduction · 100

WGS typing of the S. Adjame outbreak showed marked sub-clustering and genetic heterogeneity atypical of a point-source Salmonella outbreak

adjame first outbreak food genome snp-based core
Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States.

PMID 36314928 · PMC9769944 · Microbiology spectrum · 2022 · 8 claims · 6 setups

Has reproduction · 91

73 ruminant listeriosis isolates classified by WGS/cgMLST fall into three lineages: 31.5% lineage 1, 53.4% lineage 2, 15.1% lineage 3

monocytogenes isolate whole-genome core minimum
Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.

PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 8 claims · 8 setups

Has reproduction · 82

An isolate phenotypically identified as K. oxytoca was reclassified by genome-based taxonomy (GTDB-Tk, ANI, BLAST) as Klebsiella michiganensis

michiganensis a55848 african assembled whole-genome novo genome-based

Experiments

Environmental Burkholderia cepacia complex isolates in human infections.

Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

Comparative genomic analysis of clinical strains of Campylobacter jejuni from South Africa.

Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

MLST clustering of Campylobacter jejuni isolates from patients with gastroenteritis, reactive arthritis and Guillain-Barré syndrome.

Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains.

Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

Lineage specific recombination rates and microevolution in Listeria monocytogenes.

Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia.

Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis.

Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

Genetic diversity among Enterococcus faecalis.

Cryptococcus neoformans strains and infection in apparently immunocompetent patients, China.

Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame.

Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States.

Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.