{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:27:18Z","timestamp":1792787238417,"version":"4.5.0"},"reference-count":73,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2024,8,14]],"date-time":"2024-08-14T00:00:00Z","timestamp":1723593600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,8,14]],"date-time":"2024-08-14T00:00:00Z","timestamp":1723593600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","award":["AI137336"],"award-info":[{"award-number":["AI137336"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"crossref"}]},{"name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","award":["AI140754"],"award-info":[{"award-number":["AI140754"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"crossref"}]},{"name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","award":["AI105129"],"award-info":[{"award-number":["AI105129"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"crossref"}]},{"name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","award":["AI099394"],"award-info":[{"award-number":["AI099394"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"crossref"}]},{"name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","award":["AI143639"],"award-info":[{"award-number":["AI143639"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2024,8,14]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Severe COVID-19 has been associated with coinfections with bacterial and fungal pathogens. Notably, patients with COVID-19 who develop\n                      <jats:italic toggle=\"yes\">Staphylococcus aureus<\/jats:italic>\n                      bacteremia exhibit higher rates of mortality than those infected with either pathogen alone. To understand this clinical scenario, we collected and examined\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      blood and respiratory isolates from a hospital in New York City during the early phase of the pandemic from both SARS-CoV-2+ and SARS-CoV-2\u2212 patients. Whole genome sequencing of these\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      isolates revealed broad phylogenetic diversity in both patient groups, suggesting that SARS-CoV-2 coinfection was not associated with a particular\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      lineage. Phenotypic characterization of the contemporary collection of\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      isolates from SARS-CoV-2+ and SARS-CoV-2\u2212 patients revealed no notable differences in several virulence traits examined. However, we noted a trend toward overrepresentation of\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      bloodstream strains with low cytotoxicity in the SARS-CoV-2+ group. We observed that patients coinfected with SARS-CoV-2 and\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      were more likely to die during the acute phase of infection when the coinfecting\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      strain exhibited high or low cytotoxicity. To further investigate the relationship between SARS-CoV-2 and\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      infections, we developed a murine coinfection model. These studies revealed that infection with SARS-CoV-2 renders mice susceptible to subsequent superinfection with low cytotoxicity\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      . Thus, SARS-CoV-2 infection sensitizes the host to coinfections, including\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      isolates with low intrinsic virulence.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      The COVID-19 pandemic has had an enormous impact on healthcare across the globe. Patients who were severely infected with SARS-CoV-2, the virus causing COVID-19, sometimes became infected with other pathogens, which is termed coinfection. If the coinfecting pathogen is the bacterium\n                      <jats:italic toggle=\"yes\">Staphylococcus aureus<\/jats:italic>\n                      , there is an increased risk of patient death. We collected\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      strains that coinfected patients with SARS-CoV-2 to study the disease outcome caused by the interaction of these two important pathogens. We found that both in patients and in mice, coinfection with an\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      strain lacking toxicity resulted in more severe disease during the early phase of infection, compared with infection with either pathogen alone. Thus, SARS-CoV-2 infection can directly increase the severity of\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      infection.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.01667-24","type":"journal-article","created":{"date-parts":[[2024,7,22]],"date-time":"2024-07-22T09:10:21Z","timestamp":1721639421000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":19,"title":["SARS-CoV-2 infection predisposes patients to coinfection with\n                    <i>Staphylococcus aureus<\/i>"],"prefix":"10.1128","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0271-0562","authenticated-orcid":false,"given":"Ashira","family":"Lubkin","sequence":"first","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucie","family":"Bernard-Raichon","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]},{"name":"Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine","place":["Philadelphia, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley L.","family":"DuMont","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Mayela","family":"Valero Jimenez","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory G.","family":"Putzel","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]},{"name":"Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Gago","sequence":"additional","affiliation":[{"name":"Department of Population Health, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erin E.","family":"Zwack","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olufolakemi","family":"Olusanya","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]},{"name":"Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristina M.","family":"Boguslawski","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simone","family":"Dallari","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophie","family":"Dyzenhaus","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christin","family":"Herrmann","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juliana K.","family":"Ilmain","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georgia L.","family":"Isom","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miranda","family":"Pawline","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]},{"name":"Department of Medicine, NYU Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew I.","family":"Perault","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]},{"name":"Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sofya","family":"Perelman","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William E.","family":"Sause","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ifrah","family":"Shahi","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amelia","family":"St. John","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Tierce","sequence":"additional","affiliation":[{"name":"Division of Comparative Medicine, New York University Langone Health","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuhui","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunyi","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]},{"name":"Department of Medicine, NYU Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria G.","family":"Noval","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"O'Keeffe","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magda","family":"Podkowik","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]},{"name":"Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Gonzales","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth","family":"Inglima","sequence":"additional","affiliation":[{"name":"Department of Medicine, NYU Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ludovic","family":"Desvignes","sequence":"additional","affiliation":[{"name":"Department of Medicine, NYU Grossman School of Medicine","place":["New York, USA"]},{"name":"High Containment Laboratories, Office of Science and Research, NYU Langone Health","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah E.","family":"Hochman","sequence":"additional","affiliation":[{"name":"Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health","place":["New York, USA"]},{"name":"Department of Medicine, NYU Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7796-2254","authenticated-orcid":true,"given":"Kenneth A.","family":"Stapleford","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorna E.","family":"Thorpe","sequence":"additional","affiliation":[{"name":"Department of Population Health, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Pironti","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]},{"name":"Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Shopsin","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]},{"name":"Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health","place":["New York, USA"]},{"name":"Department of Medicine, NYU Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ken","family":"Cadwell","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine","place":["Philadelphia, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1741-7916","authenticated-orcid":true,"given":"Meike","family":"Dittmann","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7126-0489","authenticated-orcid":true,"given":"Victor J.","family":"Torres","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University Grossman School of Medicine","place":["New York, USA"]},{"name":"Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_6_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0272-5231(21)00101-5"},{"key":"e_1_3_6_3_2","doi-asserted-by":"publisher","DOI":"10.1002\/ppul.24699"},{"key":"e_1_3_6_4_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00134-020-06219-8"},{"key":"e_1_3_6_5_2","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofab065"},{"key":"e_1_3_6_6_2","doi-asserted-by":"publisher","DOI":"10.1007\/s15010-021-01602-z"},{"key":"e_1_3_6_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2021.100229"},{"key":"e_1_3_6_8_2","doi-asserted-by":"publisher","DOI":"10.1111\/myc.13096"},{"key":"e_1_3_6_9_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2711.211174"},{"key":"e_1_3_6_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofac083"},{"key":"e_1_3_6_11_2","doi-asserted-by":"publisher","DOI":"10.1111\/eci.13319"},{"key":"e_1_3_6_12_2","doi-asserted-by":"publisher","DOI":"10.3390\/jof6040211"},{"key":"e_1_3_6_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofaa518"},{"key":"e_1_3_6_14_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-021-06616-4"},{"key":"e_1_3_6_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.medcle.2023.05.007"},{"key":"e_1_3_6_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2021.03.018"},{"key":"e_1_3_6_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.idc.2008.10.003"},{"key":"e_1_3_6_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/microbiolspec.GPP3-0039-2018"},{"key":"e_1_3_6_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.semcdb.2017.04.003"},{"key":"e_1_3_6_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2017.27"},{"key":"e_1_3_6_21_2","doi-asserted-by":"publisher","DOI":"10.1086\/345476"},{"key":"e_1_3_6_22_2","doi-asserted-by":"publisher","DOI":"10.1177\/0310057X0903700320"},{"key":"e_1_3_6_23_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-695X.2011.00830.x"},{"key":"e_1_3_6_24_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiu554"},{"key":"e_1_3_6_25_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12014-017-9178-5"},{"key":"e_1_3_6_26_2","doi-asserted-by":"publisher","DOI":"10.1086\/595963"},{"key":"e_1_3_6_27_2","doi-asserted-by":"publisher","DOI":"10.1086\/669866"},{"key":"e_1_3_6_28_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-695X.2012.00937.x"},{"key":"e_1_3_6_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2022.12.003"},{"key":"e_1_3_6_30_2","doi-asserted-by":"publisher","DOI":"10.1128\/microbiolspec.GPP3-0031-2018"},{"key":"e_1_3_6_31_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.2007\/011874-0"},{"key":"e_1_3_6_32_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1099930"},{"key":"e_1_3_6_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00204-06"},{"key":"e_1_3_6_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00055-13"},{"key":"e_1_3_6_35_2","doi-asserted-by":"publisher","DOI":"10.1080\/21505594.2020.1793525"},{"key":"e_1_3_6_36_2","doi-asserted-by":"publisher","DOI":"10.1159\/000513346"},{"key":"e_1_3_6_37_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2011.07942.x"},{"key":"e_1_3_6_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02012-06"},{"key":"e_1_3_6_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2023.105975"},{"key":"e_1_3_6_40_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-33395-6"},{"key":"e_1_3_6_41_2","doi-asserted-by":"publisher","DOI":"10.4103\/ijmr.IJMR_957_20"},{"key":"e_1_3_6_42_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12941-021-00444-9"},{"key":"e_1_3_6_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2020.110698"},{"key":"e_1_3_6_44_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M111.238147"},{"key":"e_1_3_6_45_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2020.583897"},{"key":"e_1_3_6_46_2","doi-asserted-by":"publisher","DOI":"10.12659\/MSM.894238"},{"key":"e_1_3_6_47_2","doi-asserted-by":"publisher","DOI":"10.12968\/bjon.2018.27.10.565"},{"key":"e_1_3_6_48_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2022.01.004"},{"key":"e_1_3_6_49_2","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.159422"},{"key":"e_1_3_6_50_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02068-16"},{"key":"e_1_3_6_51_2","doi-asserted-by":"publisher","DOI":"10.3390\/toxins11120734"},{"key":"e_1_3_6_52_2","doi-asserted-by":"publisher","DOI":"10.1097\/INF.0b013e3181eb7315"},{"key":"e_1_3_6_53_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jiph.2021.02.001"},{"key":"e_1_3_6_54_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa524"},{"key":"e_1_3_6_55_2","doi-asserted-by":"publisher","DOI":"10.2217\/fmb-2021-0008"},{"key":"e_1_3_6_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2021.106324"},{"key":"e_1_3_6_57_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chest.2021.04.002"},{"key":"e_1_3_6_58_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0010146"},{"key":"e_1_3_6_59_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2011.07720.x"},{"key":"e_1_3_6_60_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-02448-6"},{"key":"e_1_3_6_61_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"e_1_3_6_62_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"e_1_3_6_63_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_3_6_64_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz848"},{"key":"e_1_3_6_65_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab776"},{"key":"e_1_3_6_66_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.6995"},{"key":"e_1_3_6_67_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.5261"},{"key":"e_1_3_6_68_2","unstructured":"Seemann T. 2015. snippy: fast bacterial variant calling from NGS reads. Available from: https:\/\/github.com\/tseemann\/snippy"},{"key":"e_1_3_6_69_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"e_1_3_6_70_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab301"},{"key":"e_1_3_6_71_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01334-21"},{"key":"e_1_3_6_72_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00095-13"},{"key":"e_1_3_6_73_2","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v032.i06"},{"key":"e_1_3_6_74_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01819-20"}],"container-title":["mBio"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.01667-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.01667-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T13:39:33Z","timestamp":1791553173000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mbio.01667-24"}},"subtitle":[],"editor":[{"given":"Nancy E.","family":"Freitag","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,8,14]]},"references-count":73,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2024,8,14]]}},"alternative-id":["10.1128\/mbio.01667-24"],"URL":"https:\/\/doi.org\/10.1128\/mbio.01667-24","relation":{},"ISSN":["2150-7511"],"issn-type":[{"value":"2150-7511","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,14]]},"assertion":[{"value":"2024-05-31","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-06-27","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-07-22","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01667-24"}}