ArticlemSystems2022
Genomic Diversity of Hospital-Acquired Infections Revealed through Prospective Whole-Genome Sequencing-Based Surveillance.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
33 citing papers in PubMed, 40 citations in OpenAlex.
- Pangenome ofEcology and evolution · 2026Article
- Genetic Diversity and Hospital Circulation of Opportunistic Pathogens in COVID-19 ICUs: Whole-Genome Sequencing Data.Pathogens (Basel, Switzerland) · 2026Article
- A polyvalent phage shapes bacterial dynamics.Journal of virology · 2026Article
- Hospital-Associated Antimicrobial Resistant Bacteria on 95 Mobile Phones: An International Metagenomic "Phonome" Analysis.MicrobiologyOpen · 2026Article
- ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distances.Genome biology · 2026Article
- The regional landscape of the human colon culturome in health and cystic fibrosis.Microbiology spectrum · 2026Article
- Genome sequencing for prevention of health-care-associated bacterial infections.Nature reviews. Microbiology · 2026Review
- Real-Time Genomic Surveillance for Enhanced Healthcare Outbreak Detection and Control: Clinical and Economic Impact.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Evolution and rise of antimicrobial resistance in key public health bacteria within and across the One Health sectors.Future microbiology · 2026Review
- Genomics reveal Staphylococcus aureus persists during long-term urinary catheterization despite antimicrobial therapy and catheter exchanges.Nature communications · 2026Article
- Methods for cost-efficient, whole genome sequencing surveillance for enhanced detection of outbreaks in a hospital setting.PloS one · 2026Article
- Genomic phylogeny, taxonomic classification, genetic landscape, and antibiotic resistance of clinicalFrontiers in microbiology · 2026Article
- The changing epidemiology and long-term outcomes of patients with CRE infections.Antimicrobial stewardship & healthcare epidemiology : ASHE · 2026Article
- Molecular Epidemiological Surveillance of Carbapenem-Resistant Gram-Negative Bacteria in Southern Lebanon.Antibiotics (Basel, Switzerland) · 2025Article
- Methods for cost-efficient, whole genome sequencing surveillance for enhanced detection of outbreaks in a hospital setting.medRxiv : the preprint server for health sciences · 2025Article
- Comparison of core genome multi-locus sequencing typing pipelines for hospital outbreak detection of common bacterial pathogens.Journal of clinical microbiology · 2025Article
- The Regional Landscape of the Human Colon Culturome in Health and Cystic Fibrosis.bioRxiv : the preprint server for biology · 2025Article
- Genetic Characteristics ofPathogens (Basel, Switzerland) · 2025Article
- Stenotrophomonas maltophilia complex: A broadly distributed emerging pathogen.PLoS pathogens · 2025Article
- Genome-wide approaches to bacterial strain typing: a history and review of recent methodological advances.Current opinion in infectious diseases · 2025Review
Corrections and comments
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Authors and funding
12 authors at 1 institution in 1 country.
Funding
Abstract
Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of health care resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAIs using prospective whole-genome sequencing-based surveillance of bacterial pathogens collected from hospitalized patients. Here, we describe the diversity of bacteria sampled from hospitalized patients at a single center, as revealed through systematic analysis of bacterial isolate genomes. We sequenced the genomes of 3,004 bacterial isolates from hospitalized patients collected over a 25-month period. We identified bacteria belonging to 97 distinct species, which were distributed among 14 groups of related species. Within these groups, isolates could be distinguished from one another by both average nucleotide identity (ANI) and principal-component analysis of accessory genes (PCA-A). Core genome genetic distances and rates of evolution varied among species, which has practical implications for defining shared ancestry during outbreaks and for our broader understanding of the origins of bacterial strains and species. Finally, antimicrobial resistance genes and putative mobile genetic elements were frequently observed, and our systematic analysis revealed patterns of occurrence across the different species sampled from our hospital. Overall, this study shows how understanding the population structure of diverse pathogens circulating in a single health care setting can improve the discriminatory power of genomic epidemiology studies and can help define the processes leading to strain and species differentiation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.