{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T15:15:10Z","timestamp":1789139710497,"version":"build-2803163510"},"reference-count":48,"publisher":"American Society for Microbiology","issue":"5","license":[{"start":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T00:00:00Z","timestamp":1697500800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T00:00:00Z","timestamp":1697500800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"National Infectious Disease Medical Center startup fund","award":["B2022011-1"],"award-info":[{"award-number":["B2022011-1"]}]},{"name":"Jinan Microecological Biomedicine Shandong Laboratory project","award":["JNL-2022050B"],"award-info":[{"award-number":["JNL-2022050B"]}]},{"name":"Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang","award":["No. 2021R01012"],"award-info":[{"award-number":["No. 2021R01012"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2023,10,17]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    <jats:italic toggle=\"yes\">Providencia rettgeri<\/jats:italic>\n                    is a clinically significant opportunistic pathogen that is involved in urinary tract infections. Due to the resolution limitations of identification, distinguishing\n                    <jats:italic toggle=\"yes\">P. rettgeri<\/jats:italic>\n                    from closely related species is challenging by commercial biochemical test systems. Here, we first reported a novel species,\n                    <jats:italic toggle=\"yes\">Providencia hangzhouensis<\/jats:italic>\n                    , which had been misidentified as\n                    <jats:italic toggle=\"yes\">P. rettgeri<\/jats:italic>\n                    . Exhibiting \u226491.97% average nucleotide identity (ANI) and \u226446.10% in silico DNA-DNA hybridization values with all known\n                    <jats:italic toggle=\"yes\">Providencia<\/jats:italic>\n                    species,\n                    <jats:italic toggle=\"yes\">P. hangzhouensis<\/jats:italic>\n                    falls well beneath the established species-defining thresholds. We conducted a population genomics analysis of\n                    <jats:italic toggle=\"yes\">P. hangzhouensis<\/jats:italic>\n                    isolates worldwide. Our study revealed that\n                    <jats:italic toggle=\"yes\">P. hangzhouensis<\/jats:italic>\n                    has emerged in many countries and has formed several transmission clusters. We found that\n                    <jats:italic toggle=\"yes\">P. hangzhouensis<\/jats:italic>\n                    shared the highest ANI values (91.54% and 91.97%) with\n                    <jats:italic toggle=\"yes\">P. rettgeri<\/jats:italic>\n                    and\n                    <jats:italic toggle=\"yes\">P. huaxiensis<\/jats:italic>\n                    , respectively. The pan-genome analysis revealed that these three species possessed a similar component of pan-genomes. Two genes associated with metabolism,\n                    <jats:italic toggle=\"yes\">folE2<\/jats:italic>\n                    and\n                    <jats:italic toggle=\"yes\">ccmM<\/jats:italic>\n                    , were identified to be specific to\n                    <jats:italic toggle=\"yes\">P. hangzhouensis<\/jats:italic>\n                    . Furthermore, we also observed that carbapenem-resistance genes frequently occur in\n                    <jats:italic toggle=\"yes\">P. hangzhouensis<\/jats:italic>\n                    with the\n                    <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                    <jats:sub>IMP-27<\/jats:sub>\n                    being the most prevalent (46.15%; 36\/78). The emergence of\n                    <jats:italic toggle=\"yes\">P. hangzhouensis<\/jats:italic>\n                    is often accompanied by extended-spectrum \u03b2-lactamase and carbapenem-resistance genes, and calls for tailored surveillance of this species as a clinically relevant species in the future.\n                  <\/jats:p>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Our study has identified and characterized a novel species,\n                      <jats:italic toggle=\"yes\">Providencia hangzhouensis<\/jats:italic>\n                      , which is associated with urinary tract infections and was previously misidentified as\n                      <jats:italic toggle=\"yes\">Providencia rettgeri<\/jats:italic>\n                      . Through this study, we have identified specific genes unique to\n                      <jats:italic toggle=\"yes\">P. hangzhouensis<\/jats:italic>\n                      , which could serve as marker genes for rapid PCR identification. Additionally, our findings suggest that the emergence of\n                      <jats:italic toggle=\"yes\">P. hangzhouensis<\/jats:italic>\n                      is often accompanied by extended-spectrum \u03b2-lactamase and carbapenem-resistance genes, emphasizing the need for attention to clinical management and the importance of accurate species identification and proper drug use.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01227-23","type":"journal-article","created":{"date-parts":[[2023,9,21]],"date-time":"2023-09-21T09:01:23Z","timestamp":1695286883000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":21,"title":["Whole-genome sequencing provides insights into a novel species:\n                    <i>Providencia hangzhouensis<\/i>\n                    associated with urinary tract infections"],"prefix":"10.1128","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8568-5106","authenticated-orcid":false,"given":"Xu","family":"Dong","sequence":"first","affiliation":[{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuyun","family":"Yu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaying","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Cao","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanghui","family":"Xiang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kefan","family":"Bi","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Yuan","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengchao","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiantian","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5908-307X","authenticated-orcid":false,"given":"Ying","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.3904\/kjim.2015.30.2.167"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ophtha.2006.03.047"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1177\/089686081403400501"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13104-017-2866-4"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1099\/00207713-44-4-846"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2010.02181.x"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2017.10.013"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.002809"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.64483-0"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0906412106"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-60"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.001755"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.002516"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.005474"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2005.09.006"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2008.09.006"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cellsig.2006.05.034"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2018.02.018"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00382-20"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2019.07.013"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00527-20"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02945-15"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2022.05.005"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt086"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkf436"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.000760"},{"key":"e_1_3_4_30_2","first-page":"103.","volume-title":"Methods for general and molecular Bacteriology. edited by P. Gerhardt, R. G. E. Murray, W. A. wood and N. R. Krieg. 791 pages, numerous figures and tables. American society for Microbiology, Washington, D.C., 1994. price: 55.00 \u00a3","author":"Kamlage B","year":"1996","unstructured":"Kamlage B . 1996. Methods for general and molecular Bacteriology. edited by P. Gerhardt, R. G. E. Murray, W. A. wood and N. R. Krieg. 791 pages, numerous figures and tables. American society for Microbiology, Washington, D.C., 1994. price: 55.00 \u00a3, Vol. 40, p 103."},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.crmeth.2021.100085"},{"key":"e_1_3_4_34_2","volume-title":"ggplot2: Elegant Graphics for data analysis","author":"H W","year":"2016","unstructured":"H W . 2016. ggplot2: Elegant Graphics for data analysis. Springer-Verlag New York."},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msab293"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp348"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msz189"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.12628"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msj030"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22760-6"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx066"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.12688\/wellcomeopenres.14694.1"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkj014"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp105"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1080\/14756366.2017.1344235"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw313"},{"key":"e_1_3_4_49_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq413"}],"updated-by":[{"DOI":"10.1128\/spectrum.00905-24","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2024,5,23]],"date-time":"2024-05-23T00:00:00Z","timestamp":1716422400000}}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01227-23","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01227-23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:28:31Z","timestamp":1788222511000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.01227-23"}},"subtitle":[],"editor":[{"given":"Bonnie Chase","family":"Prokesch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,10,17]]},"references-count":48,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2023,10,17]]}},"alternative-id":["10.1128\/spectrum.01227-23"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.01227-23","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,17]]},"assertion":[{"value":"2023-03-21","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-07-25","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-09-21","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01227-23"}}