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Osuolale, Olayinka O.ORCID iD iconorcid.org/0000-0001-6525-8502
Publications (2 of 2) Show all publications
Danko, D., Bezdan, D., Afshin, E. E., Ahsanuddin, S., Bhattacharya, C., Butler, D. J., . . . Mason, C. E. (2021). A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell, 184(13), 3376-3393
Open this publication in new window or tab >>A global metagenomic map of urban microbiomes and antimicrobial resistance
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2021 (English)In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 184, no 13, p. 3376-3393Article in journal (Refereed) Published
Abstract [en]

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-196175 (URN)10.1016/j.cell.2021.05.002 (DOI)000665547300006 ()34043940 (PubMedID)
Available from: 2021-09-07 Created: 2021-09-07 Last updated: 2022-02-25Bibliographically approved
Chng, K. R., Li, C., Bertrand, D., Ng, A. H., Kwah, J. S., Low, H. M., . . . Mason, C. E. (2020). Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nature Medicine, 26, 941-951
Open this publication in new window or tab >>Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
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2020 (English)In: Nature Medicine, ISSN 1078-8956, E-ISSN 1546-170X, Vol. 26, p. 941-951Article in journal (Refereed) Published
Abstract [en]

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections. Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.
National Category
Biological Sciences Infectious Medicine
Identifiers
urn:nbn:se:su:diva-183662 (URN)10.1038/s41591-020-0894-4 (DOI)000538976400005 ()32514171 (PubMedID)
Available from: 2020-07-26 Created: 2020-07-26 Last updated: 2022-02-26Bibliographically approved
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-6525-8502

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