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This approach has been focused on targeted pathogenic taxa, such as <jats:italic>Mycobacteria<\/jats:italic>, and diseases corresponding to different modes of transmission, including food-and-water-borne diseases (FWDs) and sexually transmitted infections (STIs). In addition, major healthcare-associated pathogens such as methicillin-resistant <jats:italic>\n                     <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.11043\" xlink:type=\"simple\">Staphylococcus aureus<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic>, vancomycin-resistant enterococci and carbapenemase-producing <jats:italic>\n                     <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.10789\" xlink:type=\"simple\">Klebsiella pneumoniae<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> are the focus of research projects and initiatives to understand transmission dynamics and temporal trends on both local and global scales. Here, we discuss current and future public health priorities relating to genome-based surveillance of major healthcare-associated pathogens. We highlight the specific challenges for the surveillance of healthcare-associated infections (HAIs), and how recent technical advances might be deployed most effectively to mitigate the increasing public health burden they cause.<\/jats:p>","DOI":"10.1099\/mgen.0.001008","type":"journal-article","created":{"date-parts":[[2023,4,26]],"date-time":"2023-04-26T18:16:24Z","timestamp":1682532984000},"source":"Crossref","is-referenced-by-count":14,"title":["Taking hospital pathogen surveillance to the next level"],"prefix":"10.1099","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5081-151X","authenticated-orcid":false,"given":"Guido","family":"Werner","sequence":"first","affiliation":[{"name":"Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Germany"}]},{"given":"Natacha","family":"Couto","sequence":"additional","affiliation":[{"name":"Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford OX3 7LF, UK"},{"name":"The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK"}]},{"given":"Edward J.","family":"Feil","sequence":"additional","affiliation":[{"name":"The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK"}]},{"given":"Angela","family":"Novais","sequence":"additional","affiliation":[{"name":"Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal"},{"name":"UCIBIO-Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal"}]},{"given":"Kristin","family":"Hegstad","sequence":"additional","affiliation":[{"name":"Research Group for Host\u2013Microbe Interactions, Department of Medical Biology, UiT the Arctic University of Norway, Troms\u00f8, Norway"},{"name":"Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Troms\u00f8, Norway"}]},{"given":"Benjamin P.","family":"Howden","sequence":"additional","affiliation":[{"name":"Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia"}]},{"given":"Alexander W.","family":"Friedrich","sequence":"additional","affiliation":[{"name":"Medical Faculty, University Hospital, Westphalia-Wilhelms-University Muenster, Germany"}]},{"given":"Sandra","family":"Reuter","sequence":"additional","affiliation":[{"name":"Institute for Infection Prevention and Hospital Hygiene, University Hospital Freiburg, Germany"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.38.10.3527-3533.2000"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1086\/315752"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.41.4.1574-1585.2003"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1002\/elps.200500096"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.6.3140"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.14826.1"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.000700"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(12)70268-2"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2019.00317"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.02351"},{"key":"R11","article-title":"ECDC strategic framework for the integration of molecular and genomic typing into European surveillance and multi-country outbreak investigations 2019\u20132021","year":"2019"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.2903\/j.efsa.2021.6506"},{"key":"R13","article-title":"Whole Genome Sequencing Program"},{"key":"R14","article-title":"GLASS whole-genome sequencing for surveillance of antimicrobial resistance","year":"2020"},{"key":"R15","article-title":"Tuberculosis surveillance and monitoring in Europe 2021 \u20132019 data; Report of the ECDC and WHO. 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