{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:32:29Z","timestamp":1785407549948,"version":"3.56.0"},"reference-count":123,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T00:00:00Z","timestamp":1782777600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T00:00:00Z","timestamp":1782777600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100012190","name":"Ministry of Science and Higher Education of the Russian Federation","doi-asserted-by":"publisher","award":["075-15-2025-475"],"award-info":[{"award-number":["075-15-2025-475"]}],"id":[{"id":"10.13039\/501100012190","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSphere"],"published-print":{"date-parts":[[2026,6,30]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body sites, including the lungs, especially during severe illness. We applied Hi-C metagenomics to stool samples from 11 critically ill COVID-19 patients and analyzed microbial isolates from their lungs to investigate intra-host transmission of AMR genes. Plasmid-resolved microbial interaction networks revealed AMR gene sharing across 13 bacterial genera, primarily from Firmicutes and Proteobacteria, with evidence of plasmid-mediated transfer across phylum boundaries and between gut and lung compartments. Notably, we identified genetically identical\n                      <jats:italic toggle=\"yes\">Klebsiella pneumoniae<\/jats:italic>\n                      strains colonizing both the gut and lungs of a single patient, as well as shared plasmids carrying\n                      <jats:italic toggle=\"yes\">qnrS-1<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">blaCTX-M-231<\/jats:italic>\n                      resistance genes between gut\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      and lung\n                      <jats:italic toggle=\"yes\">K. pneumoniae<\/jats:italic>\n                      . In addition to bacterial pathogens,\n                      <jats:italic toggle=\"yes\">Candida<\/jats:italic>\n                      yeast species isolated from both niches harbored resistance genes to multiple antifungal classes, including azoles. These findings underscore the dynamic, cross-compartmental nature of AMR dissemination within the human body and highlight the importance of integrative surveillance strategies to control resistance in clinical settings.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>While COVID-19 itself caused severe illness, many deaths were ultimately due to secondary microbial infections\u2014often worsened by antibiotic resistance. Plasmids, which shuttle resistance genes between bacterial species, are key players in their spread, yet their roles in transmission, especially across body sites such as the gut and lungs, are to be elucidated. The use of Hi-C metagenomics allowed us to map bacterium-plasmid links in the guts of severe COVID-19 patients and reconstruct high-quality genomes of opportunistic fungi. Comparing these with lung-derived isolate genomes, we gained insight into possible intra-host dissemination routes of resistance genes. Preparing for future pandemics will require not only rapid pathogen detection but also tools to monitor microbiome health and resistance dynamics, and understanding how treatments and microbial imbalances shape infection risks.<\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/msphere.00139-26","type":"journal-article","created":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T12:56:52Z","timestamp":1779195412000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis"],"prefix":"10.1128","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6517-1375","authenticated-orcid":true,"given":"Anastasia Z.","family":"Revel-Muroz","sequence":"first","affiliation":[{"name":"Institute of Gene Biology Russian Academy of Sciences","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-7266-6657","authenticated-orcid":false,"given":"Ignat V.","family":"Sonets","sequence":"additional","affiliation":[{"name":"Institute of Gene Biology Russian Academy of Sciences","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander S.","family":"Chistyakov","sequence":"additional","affiliation":[{"name":"Institute of Gene Biology Russian Academy of Sciences","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petr A.","family":"Vasiluev","sequence":"additional","affiliation":[{"name":"Institute of Gene Biology Russian Academy of Sciences","place":["Moscow, Russia"]},{"id":[{"id":"https:\/\/ror.org\/03dhz7247","id-type":"ROR","asserted-by":"publisher"}],"name":"Research Center for Medical Genetics","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yury A.","family":"Surovoy","sequence":"additional","affiliation":[{"name":"I.I. Mechnikov Research Institute for Vaccines and Sera","place":["Moscow, Russia"]},{"id":[{"id":"https:\/\/ror.org\/010pmpe69","id-type":"ROR","asserted-by":"publisher"}],"name":"Faculty of Medicine, M.V. Lomonosov Moscow State University","place":["Moscow, Russia"]},{"name":"Clinical Hospital #1 MEDSI","place":["Otradnoe, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valeriia A.","family":"Ivanova","sequence":"additional","affiliation":[{"name":"Institute of Gene Biology Russian Academy of Sciences","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liubov I.","family":"Kozlovskaya","sequence":"additional","affiliation":[{"name":"FSASI Chumakov FSC R&D IBP RAS (Institute of Poliomyelitis)","place":["Moscow, Russia"]},{"name":"Sechenov First Moscow State Medical University","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga E.","family":"Khokhlova","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03vmrxk92","id-type":"ROR","asserted-by":"publisher"}],"name":"State Research Center for Applied Microbiology and Biotechnology","place":["Obolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikhail V.","family":"Fursov","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03vmrxk92","id-type":"ROR","asserted-by":"publisher"}],"name":"State Research Center for Applied Microbiology and Biotechnology","place":["Obolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6053-2621","authenticated-orcid":true,"given":"Nadezhda K.","family":"Fursova","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03vmrxk92","id-type":"ROR","asserted-by":"publisher"}],"name":"State Research Center for Applied Microbiology and Biotechnology","place":["Obolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergey V.","family":"Ulianov","sequence":"additional","affiliation":[{"name":"Institute of Gene Biology Russian Academy of Sciences","place":["Moscow, Russia"]},{"id":[{"id":"https:\/\/ror.org\/010pmpe69","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7358-2537","authenticated-orcid":false,"given":"Alexander V.","family":"Tyakht","sequence":"additional","affiliation":[{"name":"Institute of Gene Biology Russian Academy of Sciences","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1206476"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-92220-0"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-82862-5"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13054-023-04412-x"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2019.00467"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-33395-6"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2020-323020"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1097\/MCC.0000000000000469"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.47387-0"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.01148-20"},{"key":"e_1_3_5_12_2","volume-title":"Microbiome metabolome brain vagus nerve circuit in disease and recovery","author":"Paley EL","year":"2023","unstructured":"Paley EL. 2023. Microbiome metabolome brain vagus nerve circuit in disease and recovery. Elsevier."},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2014.12.022"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0227139"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-11152-6"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2018.04.022"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13256-020-02583-7"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2021-325010"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13054-019-2604-5"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.4161\/gmic.21288"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.2147\/JIR.S506688"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiaa497"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-024-01041-1"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx488"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29096-9"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-021-00879-y"},{"key":"e_1_3_5_27_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18164-7"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201907-1487OC"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41385-020-00361-8"},{"key":"e_1_3_5_30_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34101-2"},{"key":"e_1_3_5_31_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35767-4"},{"key":"e_1_3_5_32_2","doi-asserted-by":"publisher","DOI":"10.1097\/01.CCM.0000055385.29232.11"},{"key":"e_1_3_5_33_2","doi-asserted-by":"publisher","DOI":"10.47278\/journal.ijvs\/2025.107"},{"key":"e_1_3_5_34_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature06244"},{"key":"e_1_3_5_35_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature13786"},{"key":"e_1_3_5_36_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.funeco.2015.01.006"},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1221789"},{"key":"e_1_3_5_38_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0071806"},{"key":"e_1_3_5_39_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00899-6"},{"key":"e_1_3_5_40_2","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-021-02036-x"},{"key":"e_1_3_5_41_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2020.06.048"},{"key":"e_1_3_5_42_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.083485-0"},{"key":"e_1_3_5_43_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003079"},{"key":"e_1_3_5_44_2","doi-asserted-by":"publisher","DOI":"10.3109\/1040841X.2013.813904"},{"key":"e_1_3_5_45_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00134-012-2690-1"},{"key":"e_1_3_5_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/0140-6736(91)91510-2"},{"key":"e_1_3_5_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dku092"},{"key":"e_1_3_5_48_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0309-z"},{"key":"e_1_3_5_49_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-019-0446-4"},{"key":"e_1_3_5_50_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.770323"},{"key":"e_1_3_5_51_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.fm.2024.104520"},{"key":"e_1_3_5_52_2","doi-asserted-by":"publisher","DOI":"10.1002\/0471142727.mb0204s56"},{"key":"e_1_3_5_53_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"e_1_3_5_54_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw569"},{"key":"e_1_3_5_55_2","unstructured":"St JohnJ. 2024. GitHub - jstjohn\/SeqPrep: Tool for stripping adaptors and\/or merging paired reads with overlap into single reads. GitHub [Internet]. https:\/\/github.com\/jstjohn\/SeqPrep."},{"key":"e_1_3_5_56_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_5_57_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01688-w"},{"key":"e_1_3_5_58_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-019-5699-9"},{"key":"e_1_3_5_59_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_5_60_2","unstructured":"Bushnell B. 2014. BBMap: a fast accurate splice-aware aligner. Available from: https:\/\/escholarship.org\/content\/qt1h3515gn\/qt1h3515gn.pdf?t=p0juuw"},{"key":"e_1_3_5_61_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_3_5_62_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_3_5_63_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7359"},{"key":"e_1_3_5_64_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv638"},{"key":"e_1_3_5_65_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1643-1"},{"key":"e_1_3_5_66_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz848"},{"key":"e_1_3_5_67_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186072.114"},{"key":"e_1_3_5_68_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0541-1"},{"key":"e_1_3_5_69_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-018-0171-1"},{"key":"e_1_3_5_70_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1008839"},{"key":"e_1_3_5_71_2","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.02243-25"},{"key":"e_1_3_5_72_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-023-01347-5"},{"key":"e_1_3_5_73_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001030"},{"key":"e_1_3_5_74_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkj014"},{"key":"e_1_3_5_75_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2021.0439"},{"key":"e_1_3_5_76_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.04645-22"},{"key":"e_1_3_5_77_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00419-13"},{"key":"e_1_3_5_78_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac920"},{"key":"e_1_3_5_79_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa490"},{"key":"e_1_3_5_80_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000206"},{"key":"e_1_3_5_81_2","doi-asserted-by":"publisher","unstructured":"Cs\u00e1rdi G Nepusz T M\u00fcller K Horv\u00e1t S Traag V Zanini F et al.. 2025. Igraph for R: R interface of the igraph library for graph theory and network analysis. doi:10.5281\/zenodo.17470081","DOI":"10.5281\/zenodo.17470081"},{"key":"e_1_3_5_82_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"e_1_3_5_83_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa015"},{"key":"e_1_3_5_84_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005944"},{"key":"e_1_3_5_85_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000685"},{"key":"e_1_3_5_86_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa892"},{"key":"e_1_3_5_87_2","doi-asserted-by":"publisher","DOI":"10.1109\/MCSE.2007.55"},{"key":"e_1_3_5_88_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009490"},{"key":"e_1_3_5_89_2","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.14826.1"},{"key":"e_1_3_5_90_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"e_1_3_5_91_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1568-0"},{"key":"e_1_3_5_92_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv033"},{"key":"e_1_3_5_93_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-9173-0_8"},{"key":"e_1_3_5_94_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-023-01547-z"},{"key":"e_1_3_5_95_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw924"},{"key":"e_1_3_5_96_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.4958"},{"key":"e_1_3_5_97_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_3_5_98_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2016.07.002"},{"key":"e_1_3_5_99_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aal3327"},{"key":"e_1_3_5_100_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-9173-0_14"},{"key":"e_1_3_5_101_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34630-w"},{"key":"e_1_3_5_102_2","doi-asserted-by":"publisher","DOI":"10.1093\/jacamr\/dlad026"},{"key":"e_1_3_5_103_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-020-00834-3"},{"key":"e_1_3_5_104_2","doi-asserted-by":"publisher","DOI":"10.3390\/jof9101020"},{"key":"e_1_3_5_105_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0052218"},{"key":"e_1_3_5_106_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01827-22"},{"key":"e_1_3_5_107_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.759408"},{"key":"e_1_3_5_108_2","doi-asserted-by":"publisher","DOI":"10.1007\/s12223-025-01298-w"},{"key":"e_1_3_5_109_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-025-02238-z"},{"key":"e_1_3_5_110_2","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics11070886"},{"key":"e_1_3_5_111_2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaf589"},{"key":"e_1_3_5_112_2","doi-asserted-by":"publisher","DOI":"10.3389\/978-2-8325-6238-3"},{"key":"e_1_3_5_113_2","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2025.1693964"},{"key":"e_1_3_5_114_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-025-03246-7"},{"key":"e_1_3_5_115_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000306"},{"key":"e_1_3_5_116_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02263-09"},{"key":"e_1_3_5_117_2","doi-asserted-by":"publisher","DOI":"10.1128\/aac.01424-22"},{"key":"e_1_3_5_118_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-023-01159-6"},{"key":"e_1_3_5_119_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00555-17"},{"key":"e_1_3_5_120_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-019-0709-7"},{"key":"e_1_3_5_121_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms26094407"},{"key":"e_1_3_5_122_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02946"},{"key":"e_1_3_5_123_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.01523"},{"key":"e_1_3_5_124_2","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2023.1242622"}],"container-title":["mSphere"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msphere.00139-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msphere.00139-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T13:02:25Z","timestamp":1783688545000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/msphere.00139-26"}},"subtitle":[],"editor":[{"given":"Raffaele","family":"Zarrilli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,6,30]]},"references-count":123,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6,30]]}},"alternative-id":["10.1128\/msphere.00139-26"],"URL":"https:\/\/doi.org\/10.1128\/msphere.00139-26","relation":{},"ISSN":["2379-5042"],"issn-type":[{"value":"2379-5042","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,30]]},"assertion":[{"value":"2026-03-23","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-04-13","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-05-19","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00139-26"}}