{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:34:17Z","timestamp":1785429257618,"version":"3.56.0"},"reference-count":40,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T00:00:00Z","timestamp":1761091200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T00:00:00Z","timestamp":1761091200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32072327"],"award-info":[{"award-number":["32072327"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2025,10,22]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Cronobacter<\/jats:italic>\n                      spp. is an important foodborne pathogen that causes serious neonatal infections. The prevalence of the colistin resistance gene\n                      <jats:italic toggle=\"yes\">mcr-9<\/jats:italic>\n                      in\n                      <jats:italic toggle=\"yes\">Cronobacter<\/jats:italic>\n                      spp. strains isolated from foods has been reported; however, there are no reports for isolates from clinical infections. Surveillance of\n                      <jats:italic toggle=\"yes\">Cronobacter<\/jats:italic>\n                      infection was conducted at a prominent children\u2019s hospital in China during 2015\u20132023 and also in a tertiary hospital in 2023. There were a total of seven\n                      <jats:italic toggle=\"yes\">Cronobacter sakazakii<\/jats:italic>\n                      infection cases, and\n                      <jats:italic toggle=\"yes\">mcr-9.1<\/jats:italic>\n                      was detected in one ST13 and two ST256 strains. After adding the publicly available sequence data, the backbones of IS\n                      <jats:italic toggle=\"yes\">1R-mcr-9.1-wbuc-qsec<\/jats:italic>\n                      in\n                      <jats:italic toggle=\"yes\">C. sakazakii<\/jats:italic>\n                      ST13 and IS\n                      <jats:italic toggle=\"yes\">903B-mcr-9.1-wbuc<\/jats:italic>\n                      -IS\n                      <jats:italic toggle=\"yes\">26<\/jats:italic>\n                      in ST256 strains are proposed to be associated with IncFIB and IncHI2 plasmids, respectively. More importantly, the\n                      <jats:italic toggle=\"yes\">mcr-9.1<\/jats:italic>\n                      -positive IncHI2 plasmid in\n                      <jats:italic toggle=\"yes\">C. sakazakii<\/jats:italic>\n                      ST256 clinical strain can be transferred to\n                      <jats:italic toggle=\"yes\">Escherichia coli<\/jats:italic>\n                      J53, conferring multiple drug resistance. These ST13 and ST256 strains were assigned to 19 CRISPR types (CTs), and\n                      <jats:italic toggle=\"yes\">mcr-9.1<\/jats:italic>\n                      -positive strains belonged to specific CTs in China. While ST256 has not been detected in contaminated food, its presence in insect and environmental samples suggests a potential transmission route requiring further investigation. Combined phylodynamic and CRISPR spacer analyses suggested phage interactions shaped\n                      <jats:italic toggle=\"yes\">C. sakazakii<\/jats:italic>\n                      ST13 evolution. The relatively high-risk lineage bridging clinical (\n                      <jats:italic toggle=\"yes\">mcr-9.1<\/jats:italic>\n                      -positive CT212) and food chain (CT208) reservoirs displayed CRISPR adaptation signatures: selective type 1 ancestral spacer loss coupled with type 2 ancestral preservation. Plasmid-mediated\n                      <jats:italic toggle=\"yes\">mcr-9.1<\/jats:italic>\n                      gene transfer in\n                      <jats:italic toggle=\"yes\">C. sakazakii<\/jats:italic>\n                      poses a potential threat to public health, thereby necessitating vigilant clinical monitoring.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        <jats:italic toggle=\"yes\">Cronobacter<\/jats:italic>\n                        spp. is ubiquitous in food and the environment, although the infection incidence of this pathogen is low, the case-fatality rate is high in premature and immunocompromised infants. In this study, we first report that the silent dissemination of\n                        <jats:italic toggle=\"yes\">mcr-9.1<\/jats:italic>\n                        in\n                        <jats:italic toggle=\"yes\">Cronobacter sakazakii<\/jats:italic>\n                        ST13 and ST256 strains was associated with IncFIB and IncHI2 plasmids, respectively. The\n                        <jats:italic toggle=\"yes\">mcr-9.1<\/jats:italic>\n                        -encoding IncHI2 plasmid was transferable from the ST256 strain, suggesting significant dissemination potential among clinically relevant bacteria. Taking into account the temporal organization of spacers, we first used CRISPR diversity to trace the origins of\n                        <jats:italic toggle=\"yes\">mcr-9.1<\/jats:italic>\n                        -positive\n                        <jats:italic toggle=\"yes\">C. sakazakii<\/jats:italic>\n                        strains and deduce their divergent evolution through the preserved spacer information targeting specific phages. Our CRISPR-enhanced molecular epidemiology approach enables robust phylogenetic inferences despite limited clinical isolates, demonstrating a transferable framework applicable to other emerging pathogens with surveillance data.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/aem.01379-25","type":"journal-article","created":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T12:52:49Z","timestamp":1756817569000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["Emergence of transmissible\n                    <i>mcr-9.1<\/i>\n                    plasmids in clinical\n                    <i>Cronobacter sakazakii<\/i>\n                    : CRISPR typing unravels phage-driven evolution and high-risk 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