{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T01:15:25Z","timestamp":1788225325771,"version":"build-2803163510"},"reference-count":43,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T00:00:00Z","timestamp":1770076800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T00:00:00Z","timestamp":1770076800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100014219","name":"National Science Fund for Distinguished Young Scholars","doi-asserted-by":"publisher","award":["82202541"],"award-info":[{"award-number":["82202541"]}],"id":[{"id":"10.13039\/501100014219","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008235","name":"Peking Union Medical College Hospital","doi-asserted-by":"publisher","award":["UHB12396"],"award-info":[{"award-number":["UHB12396"]}],"id":[{"id":"10.13039\/501100008235","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018594","name":"Central University Basic Research Fund of China","doi-asserted-by":"publisher","award":["3332022012"],"award-info":[{"award-number":["3332022012"]}],"id":[{"id":"10.13039\/501100018594","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,2,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      The\n                      <jats:italic toggle=\"yes\">Enterobacter cloacae<\/jats:italic>\n                      complex (ECC) is one of the major causes of hospital-acquired infections. However, achieving accurate species identification and comprehensive resistance profiling remains difficult in clinical practice, with a limited understanding of species-specific resistance patterns. ECC isolates were collected from patients with bloodstream infections at Peking Union Medical College Hospital between 2015 and 2020. Whole-genome sequencing (WGS) was performed to identify species, analyze antimicrobial resistance genes, and explore genomic variation in serial isolates. Multi-locus sequence typing (MLST) profiles were extracted from the WGS data. Phylogenetic analysis was conducted based on\n                      <jats:italic toggle=\"yes\">hsp60<\/jats:italic>\n                      sequences. Eleven\n                      <jats:italic toggle=\"yes\">hsp60<\/jats:italic>\n                      clusters were identified, with cluster VIII being the most prevalent (28\/108). Average nucleotide identity (ANI)-based species classification showed\n                      <jats:italic toggle=\"yes\">Enterobacter hormaechei<\/jats:italic>\n                      (31.5%) and\n                      <jats:italic toggle=\"yes\">Enterobacter xiangfangensis<\/jats:italic>\n                      (15.7%) were dominant species. Five clade-cluster pairs (B-VIII, A-VI, G-XI, D-III, R-IX) accounted for 74% of isolates. A total of 90 sequence types (STs) were detected, including 29 novel STs. Resistance gene analysis revealed a high prevalence of\n                      <jats:italic toggle=\"yes\">\n                        bla\n                        <jats:sub>ACT<\/jats:sub>\n                      <\/jats:italic>\n                      , with distinct distribution patterns observed among different species. Twenty isolates were carbapenem-resistant, with three carrying\n                      <jats:italic toggle=\"yes\">\n                        bla\n                        <jats:sub>NDM-1\/5<\/jats:sub>\n                        . Enterobacter roggenkampii\n                      <\/jats:italic>\n                      was the most common species (5\/20) among all carbapenem-resistant isolates, and 83.3% of the isolates showed resistance to both carbapenems and colistin. Comparative genomics of longitudinal isolates from individual patients revealed adaptive single-nucleotide polymorphisms (SNPs) in\n                      <jats:italic toggle=\"yes\">pco<\/jats:italic>\n                      genes. This study provides a detailed genomic characterization of ECC isolates from bloodstream infections, highlighting species diversity, resistance gene distribution, and potential within-host evolution. These insights advocate genome-based surveillance in managing ECC infections and understanding resistance evolution in clinical contexts.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        <jats:italic toggle=\"yes\">Enterobacter cloacae<\/jats:italic>\n                        complex (ECC) is a major cause of hospital-acquired bloodstream infections, yet species-level identification and resistance profiling remain challenging. As one of the largest whole-genome sequencing (WGS)-based studies of ECC bloodstream isolates in northern China to date, we performed whole-genome sequencing of 108 ECC isolates, revealing high genetic diversity and identifying 29 novel sequence types. We clarified the correspondence between species, clades, and clusters and highlighted\n                        <jats:italic toggle=\"yes\">Enterobacter roggenkampii<\/jats:italic>\n                        as a potential high-risk species linked to carbapenem and colistin resistance. Our findings not only improve the understanding of ECC population structure and resistance evolution in China but also provide valuable genomic data for future epidemiological surveillance and species-level diagnostics.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.02865-25","type":"journal-article","created":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T12:21:08Z","timestamp":1765974068000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["Precise species identification and whole-genome sequencing analysis of\n                    <i>Enterobacter cloacae<\/i>\n                    complex causing bloodstream infections in China"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-4141-8534","authenticated-orcid":false,"given":"Yanbing","family":"Li","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02drdmm93","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College","place":["Beijing, People\u2019s Republic of China"]},{"id":[{"id":"https:\/\/ror.org\/02drdmm93","id-type":"ROR","asserted-by":"publisher"}],"name":"Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences","place":["Beijing, People\u2019s Republic of 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