{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T03:37:33Z","timestamp":1792640253424,"version":"4.5.0"},"reference-count":49,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2025,2,4]],"date-time":"2025-02-04T00:00:00Z","timestamp":1738627200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,2,4]],"date-time":"2025-02-04T00:00:00Z","timestamp":1738627200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"Hospital Cayetano Heredia","award":["2017 Research Grant"],"award-info":[{"award-number":["2017 Research Grant"]}]},{"name":"Prociencia","award":["Grant No. 088-2018"],"award-info":[{"award-number":["Grant No. 088-2018"]}]},{"DOI":"10.13039\/501100019574","name":"Institut M\u00e9rieux","doi-asserted-by":"crossref","award":["Young Investigator Award"],"award-info":[{"award-number":["Young Investigator Award"]}],"id":[{"id":"10.13039\/501100019574","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Belgian Directorate of Development Cooperation and Humanitarian Aid"},{"name":"HHS | NIH | Fogarty International Center","award":["D43TW00934"],"award-info":[{"award-number":["D43TW00934"]}]},{"name":"HHS | NIH | Fogarty International Center","award":["D43TW007393"],"award-info":[{"award-number":["D43TW007393"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,2,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              The emergence of carbapenem-resistant\n              <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n              (CRKP) poses a significant public health threat, particularly in low- and middle-income countries (LMICs) with limited surveillance and treatment options. This study examines the genetic diversity, resistance patterns, and transmission dynamics of 66 CRKP isolates recovered over 5 years (2015\u20132019) after the first case of CRKP was identified at a tertiary care hospital in Lima, Peru. Our findings reveal a shift from\n              <jats:italic>bla<\/jats:italic>\n              <jats:sub>KPC-2<\/jats:sub>\n              to\n              <jats:italic>bla<\/jats:italic>\n              <jats:sub>NDM-1<\/jats:sub>\n              as the dominant carbapenemase gene after 2017. Lineage ST45 was the most prevalent and persisted for multiple years, followed by high-risk clones ST11 and ST147. The\n              <jats:italic>bla<\/jats:italic>\n              <jats:sub>NDM-1<\/jats:sub>\n              gene was carried almost exclusively by a Tn125-like transposon, similar to the one reported in previous studies from two Peruvian hospitals. Long-read sequencing revealed nearly identical\n              <jats:italic>bla<\/jats:italic>\n              <jats:sub>NDM<\/jats:sub>\n              -carrying plasmids across the four assessed lineages. A comparative analysis of 1,023 South American CRKP genomes confirmed a unique pattern in Peru, where\n              <jats:italic>bla<\/jats:italic>\n              <jats:sub>NDM-1<\/jats:sub>\n              (81.4%) outpaced\n              <jats:italic>bla<\/jats:italic>\n              <jats:sub>KPC-2<\/jats:sub>\n              , which remained dominant (59.4%) elsewhere. In addition, emerging clones ST45 and ST348 found in Peru were rarely found elsewhere in South America, suggesting potential regional adaptation. In conclusion, our study provides a comprehensive picture of the intra-hospital dynamics of these emerging pathogens and provides a framework for studying their genomic diversity in the understudied South American region.\n            <\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>\n                This study provides novel insights into the transmission and genetic diversity of carbapenem-resistant\n                <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                , a bacteria responsible for severe infections, with limited treatment options. By examining isolates recovered over 5 years at a major hospital in Lima, Peru, we demonstrated a shift from one type of resistance gene,\n                <jats:italic>bla<\/jats:italic>\n                <jats:sub>KPC<\/jats:sub>\n                , to another,\n                <jats:italic>bla<\/jats:italic>\n                <jats:sub>NDM<\/jats:sub>\n                , which is more challenging to treat. Our findings reveal that specific bacterial lineages carrying the\n                <jats:italic>bla<\/jats:italic>\n                <jats:sub>NDM<\/jats:sub>\n                gene in a specific plasmid are emerging in Peru, including well-known high-risk strains and others rarely found elsewhere in South America. This pattern highlights an urgent need for targeted surveillance and infection control as these strains pose a significant challenge to healthcare systems. Our study provides crucial data on\n                <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                in Peru, contributing to broader efforts to monitor and control antibiotic-resistant infections in South America and globally.\n              <\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/spectrum.01825-24","type":"journal-article","created":{"date-parts":[[2025,1,10]],"date-time":"2025-01-10T14:44:37Z","timestamp":1736520277000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":11,"title":["Emerging carbapenem-resistant\n            <i>Klebsiella pneumoniae<\/i>\n            in a tertiary care hospital in Lima, Peru"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8404-2827","authenticated-orcid":true,"given":"Fiorella","family":"Krapp","sequence":"first","affiliation":[{"name":"Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]},{"name":"Facultad de Medicina Alberto Hurtado, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]},{"name":"Department of Microbiology, Immunology and Transplantation, KU Leuven","place":["Leuven, Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diego","family":"Cuicapuza","sequence":"additional","affiliation":[{"name":"Facultad de Medicina Alberto Hurtado, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]},{"name":"Laboratorio de Gen\u00f3mica Microbiana, Facultad de Ciencias e Ingenier\u00eda, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6887-2599","authenticated-orcid":true,"given":"Guillermo","family":"Salvatierra","sequence":"additional","affiliation":[{"name":"Laboratorio de Gen\u00f3mica Microbiana, Facultad de Ciencias e Ingenier\u00eda, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean P.","family":"Buteau","sequence":"additional","affiliation":[{"name":"Facultad de Medicina Alberto Hurtado, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Amaro","sequence":"additional","affiliation":[{"name":"Department of Clinical Pathology, Hospital Nacional Cayetano Heredia","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lizeth","family":"Astocondor","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noem\u00ed","family":"Hinostroza","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Jacobs","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Transplantation, KU Leuven","place":["Leuven, Belgium"]},{"name":"Unit of Tropical Bacteriology, Department of Clinical Sciences, Institute of Tropical Medicine","place":["Antwerp, Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Coralith","family":"Garc\u00eda","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]},{"name":"Facultad de Medicina Alberto Hurtado, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]},{"name":"Department of Infectious, Tropical, and Dermatological Diseases, Hospital Nacional Cayetano Heredia","place":["Lima, Peru"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1669-2553","authenticated-orcid":true,"given":"Pablo","family":"Tsukayama","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]},{"name":"Laboratorio de Gen\u00f3mica Microbiana, Facultad de Ciencias e Ingenier\u00eda, Universidad Peruana Cayetano Heredia","place":["Lima, Peru"]},{"name":"Wellcome Sanger Institute","place":["Hinxton, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(17)30753-3"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(21)02724-0"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(18)30792-8"},{"key":"e_1_3_5_5_2","series-title":"Informe Resumido (PAHO\/CDE\/AR\/20-0031)","volume-title":"Magnitud y tendencias de la resistencia a los antimicrobianos en Latinoam\u00e9rica","author":"Pan American Health Organization","year":"2020","unstructured":"Pan American Health Organization. 2020. Magnitud y tendencias de la resistencia a los antimicrobianos en Latinoam\u00e9rica. Informe Resumido (PAHO\/CDE\/AR\/20-0031). RELAVRA 2014, 2015, 2016."},{"key":"e_1_3_5_6_2","volume-title":"Impact of the COVID pandemic in susceptibility patterns of Gram-negative organisms: a report from the SENTRY antimicrobial surveillance program","author":"Castanheira M","year":"2023","unstructured":"Castanheira M, Carvalhaes CG, DeVries S, Mendes RE, Sader HS. 2023. Impact of the COVID pandemic in susceptibility patterns of Gram-negative organisms: a report from the SENTRY antimicrobial surveillance program. ECCMID 2023, Copenhagen, Denmark."},{"key":"e_1_3_5_7_2","unstructured":"Pan American Health Organization. PLISA health information platform for the Americas. PAHO. Available from: https:\/\/www3.paho.org\/data\/index.php\/en\/mnu-topics\/antimicrobial-resistance\/571-amr-vig-en.html"},{"key":"e_1_3_5_8_2","unstructured":"Vel\u00e1squez J Hern\u00e1ndez R Pamo O Candiotti M Pinedo Y Sacsaquispe R Su\u00e1rez L Fern\u00e1ndez N. 2013. Klebsiella pneumoniae resistente a los carbapenemes. primer caso de carbapenemasa tipo KPC en Per\u00fa. Rev Soc Peru Med Interna. Vol. 26."},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.17843\/rpmesp.2018.352.3829"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3004129"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciab777"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-16322-5"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(19)30755-8"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000266"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0492-8"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofaa266"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms8091392"},{"key":"e_1_3_5_18_2","series-title":"CLSI Supplement M100","volume-title":"Performance standards for antimicrobial susceptibility testing","author":"CLSI","year":"2018","unstructured":"CLSI. 2018. Performance standards for antimicrobial susceptibility testing. 28th ed. CLSI Supplement M100. Clinical and Laboratory Standards Institute, Wayne, PA.","edition":"28"},{"key":"e_1_3_5_19_2","volume-title":"M\u00e9todo de Screening \u201cCOLISTIN AGAR-SPOT\u201d","author":"Servicio Antimicrobianos LNdReA, INEI-ANLIS \u201cDr. Carlos G. Malbr\u00e1n\"","year":"2017","unstructured":"Servicio Antimicrobianos LNdReA, INEI-ANLIS \u201cDr. Carlos G. Malbr\u00e1n\". 2017. M\u00e9todo de Screening \u201cCOLISTIN AGAR-SPOT\u201d"},{"key":"e_1_3_5_20_2","series-title":"CLSI Supplement M100","volume-title":"Performance standards for antimicrobial susceptibility testing","author":"Clinical and Laboratory Standards Institute (CLSI)","year":"2021","unstructured":"Clinical and Laboratory Standards Institute (CLSI). 2021. Performance standards for antimicrobial susceptibility testing. 31st ed. CLSI Supplement M100. Clinical and Laboratory Standards Institute, Wayne, PA.","edition":"31"},{"key":"e_1_3_5_21_2","unstructured":"Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24448-3"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-91456-0"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts565"},{"key":"e_1_3_5_27_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02090-4"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"e_1_3_5_30_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"e_1_3_5_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab301"},{"key":"e_1_3_5_32_2","unstructured":"Seeman T. 2018. Pairwise SNP distance matrix from a FASTA sequence alignment"},{"key":"e_1_3_5_33_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciac791"},{"key":"e_1_3_5_34_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1616248114"},{"key":"e_1_3_5_35_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-023-05332-x"},{"key":"e_1_3_5_36_2","unstructured":"National Library of Medicine (US) NCfBI. 2016. The NCBI pathogen detection project [Internet]. Bethesda MD. Available from: https:\/\/www.ncbi.nlm.nih.gov\/pathogens\/isolates\/"},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23091-2"},{"key":"e_1_3_5_38_2","doi-asserted-by":"publisher","DOI":"10.1089\/mdr.2021.0128"},{"key":"e_1_3_5_39_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiw282"},{"key":"e_1_3_5_40_2","doi-asserted-by":"publisher","unstructured":"Lee J Sunny S Nazarian E Fornek M Abdallah M Episcopia B Rowlinson MC Quale J. 2016. Carbapenem-resistant Klebsiella pneumoniae in large public acute-care healthcare system New York New York USA 2016-2022 29:1973\u20131978. doi:10.3201\/eid2910.230153","DOI":"10.3201\/eid2910.230153"},{"key":"e_1_3_5_41_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciad428"},{"key":"e_1_3_5_42_2","doi-asserted-by":"publisher","unstructured":"Mendes AC Novais A Campos J Rodrigues C Santos C Antunes P Ramos H Peixe L. 2016. mcr-1 in carbapenemase-producing Klebsiella pneumoniae with hospitalized patients Portugal 2016-2017 24:762\u2013766. doi:10.3201\/eid2404.171787","DOI":"10.3201\/eid2404.171787"},{"key":"e_1_3_5_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02290-21"},{"key":"e_1_3_5_44_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2022.10.006"},{"key":"e_1_3_5_45_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2018.06.012"},{"key":"e_1_3_5_46_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.581711"},{"key":"e_1_3_5_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciad151"},{"key":"e_1_3_5_48_2","unstructured":"Ministerio de Salud. 2011. Gu\u00eda T\u00e9cnica de Procedimientos de Limpieza y Desinfecci\u00f3n de Ambientes en los Establecimientos de Salud y Servicios M\u00e9dicos de Apoyo"},{"key":"e_1_3_5_49_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000613"},{"key":"e_1_3_5_50_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00399-23"}],"container-title":["Microbiology Spectrum"],"original-title":[],"contributor":[{"given":"Zhen","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"reviewer"}]}],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01825-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01825-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,4]],"date-time":"2025-02-04T14:08:59Z","timestamp":1738678139000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.01825-24"}},"subtitle":[],"editor":[{"given":"Silvia T.","family":"Cardona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,2,4]]},"references-count":49,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2025,2,4]]}},"alternative-id":["10.1128\/spectrum.01825-24"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.01825-24","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,4]]},"assertion":[{"value":"2024-07-24","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-11-30","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-01-10","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01825-24"}}