Integrated population clustering and genomic epidemiology with PopPIPE DOI Creative Commons
M. McHugh, Samuel Horsfield, Johanna von Wachsmann

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 9, 2024

Abstract Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations, and as an additional source of information when detecting possible transmission events. Due their variable gene content order, reference-free methods offer more sensitive detection genetic differences, especially among samples found in outbreaks. However, across longer distances, frequent recombination make calculation interpretation these differences challenging, requiring significant bioinformatic expertise manual intervention during the analysis process. Here we present a Pop ulation PIPE line (PopPIPE) which combines rapid genome analyse genomes two scales, splitting whole subclusters plausible events within clusters. We use k-mer sketching split strains, followed by removal create alignments strains. first show that this approach creates high quality on population-wide dataset Streptococcus pneumoniae . When applied nosocomial vancomycin resistant Enterococcus faecium samples, PopPIPE finds clusters are epidemiologically than core or MLST-based approaches. Our pipeline is reproducible, interactive visualisations, easily reconfigured re-run new datasets. Therefore provides user-friendly for analyses spanning species-wide clustering outbreak investigations. Impact statement As time passes, accumulate small changes sequence due mutations, larger horizontal transfer. Using sequences, it phylogenetics work out most likely order happened, how long they took happen. Then, one estimate separates any – if short then may have been directly transmitted acquired from same source; but must separately. This determine chains, conjunction with dates locations infections. Understanding chains enables targeted infection control measures. correctly calculating evidence made difficult distinguishing different types changes, dealing large amounts data, need multiple complex tools. addressed gap creating computational workflow, PopPIPE, automates process transmissions using sequences. applies state-of-the-art tools fast easy run making technology will available wider audience researchers. Data summary The code at https://github.com/bacpop/PopPIPE docker image https://hub.docker.com/r/poppunk/poppipe Raw sequencing reads isolates deposited NCBI under BioProject accession number PRJNA997588.

Language: Английский

Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium DOI Creative Commons

Emma G. Mills,

Katharine Hewlett, Alexander B. Smith

et al.

Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: March 21, 2025

Gastrointestinal colonization by the nosocomial pathogen vancomycin-resistant Enterococcus faecium (VREfm) can lead to bloodstream infections with high mortality rates. Shifts in VREfm lineages found within healthcare settings occur, but reasons underlying these changes are not understood. Here we sequenced 710 clinical isolates collected between 2017 and 2022 from a large tertiary care centre. Genomic analyses revealed polyclonal population, although 46% of formed genetically related clusters, suggesting transmission rate. Comparing data global collection 15,631 publicly available genomes 2002 identified replacement sequence type (ST) 17 lineage emergent ST80 ST117 at local level. Comparative genomic functional that encoded bacteriocin T8, which conferred competitive advantage over T8-negative strains vitro upon mouse gut. Bacteriocin T8 carriage was also strongly associated strain emergence genome collection. These suggest T8-mediated competition may have contributed replacement. healthcare-associated reveal is enriched provides vivo.

Language: Английский

Citations

2
Integrated population clustering and genomic epidemiology with PopPIPE DOI Creative Commons
M. McHugh, Samuel Horsfield, Johanna von Wachsmann

et al.

Microbial Genomics, Journal Year: 2025, Volume and Issue: 11(4)

Published: April 28, 2025

Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations and as an additional source of information when detecting possible transmission events. Due their variable gene content order, reference-free methods offer more sensitive detection genetic differences, especially among samples found in outbreaks. However, across longer distances, frequent recombination make calculation interpretation these differences challenging, requiring significant bioinformatic expertise manual intervention during the analysis process. Here, we present a Pop ulation PIPE line (PopPIPE) which combines rapid genome analyse genomes two scales, splitting whole subclusters plausible events within clusters. We use k-mer sketching split strains, followed by removal create alignments strains. first show that this approach creates high-quality on population-wide dataset Streptococcus pneumoniae . When applied nosocomial vancomycin-resistant Enterococcus faecium samples, PopPIPE finds clusters are epidemiologically than core or multilocus sequence typing (MLST) approaches. Our pipeline is reproducible, interactive visualizations easily reconfigured re-run new datasets. Therefore, provides user-friendly for analyses spanning species-wide clustering outbreak investigations.

Language: Английский

Citations

0
Genomic Surveillance for Enhanced Healthcare Outbreak Detection and Control DOI Creative Commons
Alexander Sundermann, Praveen Kumar, M. Patrick Griffith

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 22, 2024

ABSTRACT Background Current methods are insufficient alone for outbreak detection in hospitals. Real-time genomic surveillance using offers the potential to detect otherwise unidentified outbreaks. We initiated and evaluated Enhanced Detection System Healthcare-associated Transmission (EDS-HAT), a real-time program mitigation. Methods This study was conducted at UPMC Presbyterian Hospital from November 2021 October 2023. Whole genome sequencing (WGS) performed weekly on healthcare-associated clinical bacterial isolates identify undetected Interventions were implemented based identified transmission. A economic impact analysis estimate infections averted net cost savings. Results There 3,921 patient that underwent WGS, of which 476 (12.1%) clustered into 172 outbreaks (size range 2-16 patients). Of isolates, 292 (61.3%) had an epidemiological link. Among with interventions, 95.6% showed no further transmission intervened route. The estimated that, over two-year period, 62 averted, gross savings $1,011,146, $695,706, translates 3.2-fold return investment. Probabilistic sensitivity EDS-HAT cost-saving more effective 98% simulations. Conclusion enabled rapid control our hospital resulted benefits improvement safety. demonstrates feasibility effectiveness integrating routine infection prevention practice, offering paradigm shift healthcare control.

Language: Английский

Citations

3
Bacteriocin production facilitates nosocomial emergence of vancomycin-resistantEnterococcus faecium DOI Creative Commons

Emma G. Mills,

Alexander B. Smith, M. Patrick Griffith

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 3, 2024

ABSTRACT Vancomycin-resistant Enterococcus faecium (VREfm) is a prevalent healthcare-acquired pathogen. Gastrointestinal colonization can lead to difficult-to-treat bloodstream infections with high mortality rates. Prior studies have investigated VREfm population structure within healthcare centers. However, little known about how and why hospital-adapted populations change over time. We sequenced 710 healthcare-associated clinical isolates from 2017-2022 large tertiary care center as part of the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT) program. Although in our was polyclonal, 46% formed genetically related clusters, suggesting transmission rate. compared collection 15,631 publicly available genomes spanning 20 years. Our findings describe drastic shift lineage replacement nosocomial at both local global level. Functional genomic analysis revealed, antimicrobial peptide, bacteriocin T8 may be driving feature strain emergence persistence hospital setting. Summary This study shows vancomycin-resistant . Bacteriocin enriched emergent lineages provides strong competitive advantage vitro vivo

Language: Английский

Citations

1
Integrated population clustering and genomic epidemiology with PopPIPE DOI Creative Commons
M. McHugh, Samuel Horsfield, Johanna von Wachsmann

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 9, 2024

Abstract Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations, and as an additional source of information when detecting possible transmission events. Due their variable gene content order, reference-free methods offer more sensitive detection genetic differences, especially among samples found in outbreaks. However, across longer distances, frequent recombination make calculation interpretation these differences challenging, requiring significant bioinformatic expertise manual intervention during the analysis process. Here we present a Pop ulation PIPE line (PopPIPE) which combines rapid genome analyse genomes two scales, splitting whole subclusters plausible events within clusters. We use k-mer sketching split strains, followed by removal create alignments strains. first show that this approach creates high quality on population-wide dataset Streptococcus pneumoniae . When applied nosocomial vancomycin resistant Enterococcus faecium samples, PopPIPE finds clusters are epidemiologically than core or MLST-based approaches. Our pipeline is reproducible, interactive visualisations, easily reconfigured re-run new datasets. Therefore provides user-friendly for analyses spanning species-wide clustering outbreak investigations. Impact statement As time passes, accumulate small changes sequence due mutations, larger horizontal transfer. Using sequences, it phylogenetics work out most likely order happened, how long they took happen. Then, one estimate separates any – if short then may have been directly transmitted acquired from same source; but must separately. This determine chains, conjunction with dates locations infections. Understanding chains enables targeted infection control measures. correctly calculating evidence made difficult distinguishing different types changes, dealing large amounts data, need multiple complex tools. addressed gap creating computational workflow, PopPIPE, automates process transmissions using sequences. applies state-of-the-art tools fast easy run making technology will available wider audience researchers. Data summary The code at https://github.com/bacpop/PopPIPE docker image https://hub.docker.com/r/poppunk/poppipe Raw sequencing reads isolates deposited NCBI under BioProject accession number PRJNA997588.

Language: Английский

Citations

0