{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T14:36:06Z","timestamp":1787582166594,"version":"build-2736575974"},"reference-count":92,"publisher":"AOSIS","issue":"1","license":[{"start":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T00:00:00Z","timestamp":1787616000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>Background:\u00a0Antimicrobial resistance (AMR) is a major global public health threat. ESKAPE pathogens\u00a0(Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and\u00a0Enterobacter\u00a0spp.) pose a major threat owing to resistance to last-line antibiotics. Genomic surveillance is crucial to understanding global and regional antimicrobial resistance genes (ARGs) in AMR transmission.\nAim:\u00a0This systematic review synthesised global genomic evidence to identify global and region-specific ARGs distribution among ESKAPE pathogens.\nMethods:\u00a0Following PRISMA guidelines, studies published January 2019 to December 2024 were identified from PubMed, Google Scholar, and Web of Science. Eligible studies reported genomic characteristics and resistance patterns of one or more ESKAPE pathogens from any source.\nResults:\u00a0Seventy-seven studies were included, with most originating from Asia, followed by Europe and Africa. Clinical isolates predominated\u00a0K. pneumoniae\u00a0was the most frequently investigated pathogen, followed by\u00a0S. aureus, P. aeruginosa, and\u00a0A. baumannii. The most reported resistance genes were\u00a0blaCTX-M,\u00a0blaNDM, and\u00a0blaSHV. Distinct regional patterns of antimicrobial resistance gene (ARG) distribution were observed, with tetracycline and quinolone resistance genes prevailing in Africa and South America, and\u00a0blaOXA variants dominating in Asia and Europe. Region-specific ARG patterns were identified through descriptive synthesis and comparative analysis of study-reported frequencies.\nConclusion:\u00a0This review provides a synthesised global map of ARG distribution in ESKAPE pathogens, highlighting surveillance gaps in underrepresented regions and non-clinical settings. Addressing these gaps will support targeted genomic surveillance and stewardship programmes.\nWhat this study adds:\u00a0This study contributes to the body of knowledge by mapping global and regional antimicrobial resistance gene patterns in ESKAPE pathogens, identifying key surveillance gaps and informing targeted AMR monitoring and stewardship strategies.<\/jats:p>","DOI":"10.4102\/ajlm.v15i1.2893","type":"journal-article","created":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T13:54:43Z","timestamp":1787579683000},"update-policy":"https:\/\/doi.org\/10.4102\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Systematic review on genomic insights into antimicrobial resistance in ESKAPE pathogens"],"prefix":"10.4102","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-4484-1166","authenticated-orcid":false,"given":"Husna F.","family":"Ibrahim","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04mb1pr47","id-type":"ROR","asserted-by":"publisher"}],"name":"Kano Independent Research Centre Trust"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8145-3399","authenticated-orcid":false,"given":"Nasiru","family":"Abdullahi","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04mb1pr47","id-type":"ROR","asserted-by":"publisher"}],"name":"Kano Independent Research Centre Trust"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6629-8685","authenticated-orcid":false,"given":"Ibrahim","family":"Yusuf","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04mb1pr47","id-type":"ROR","asserted-by":"publisher"}],"name":"Kano Independent Research Centre Trust"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-1832-5786","authenticated-orcid":false,"given":"Bashir I.","family":"Waziri","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04mb1pr47","id-type":"ROR","asserted-by":"publisher"}],"name":"Kano Independent Research Centre Trust"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-1215-9825","authenticated-orcid":false,"given":"Ahmad","family":"Abdulhadi","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04mb1pr47","id-type":"ROR","asserted-by":"publisher"}],"name":"Kano Independent Research Centre Trust"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-4720-9209","authenticated-orcid":false,"given":"Khadija","family":"Muhammad","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04mb1pr47","id-type":"ROR","asserted-by":"publisher"}],"name":"Kano Independent Research Centre Trust"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-7999-8489","authenticated-orcid":false,"given":"Maryam M.","family":"Ibrahim","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04mb1pr47","id-type":"ROR","asserted-by":"publisher"}],"name":"Kano Independent Research Centre Trust"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-5816-9399","authenticated-orcid":false,"given":"Aisha A.","family":"Abdullahi","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04mb1pr47","id-type":"ROR","asserted-by":"publisher"}],"name":"Kano Independent Research Centre Trust"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1767-4629","authenticated-orcid":false,"given":"Muhammad A.","family":"Abbas","sequence":"additional","affiliation":[{"name":"Kano Centre for Disease Control and Prevention"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7829-4200","authenticated-orcid":false,"given":"Hamisu M.","family":"Salihu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04mb1pr47","id-type":"ROR","asserted-by":"publisher"}],"name":"Kano Independent Research Centre Trust"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2580","published-online":{"date-parts":[[2026,8,25]]},"reference":[{"key":"ref0","unstructured":"WHO. Antimicrobial resistance [homepage on the Internet]. World Health Organization; 2023 [cited 2025 Mar 24]. Available from: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/antimicrobial-resistance"},{"key":"ref1","doi-asserted-by":"crossref","unstructured":"Founou RC, Founou LL, Allam M, Ismail A, Essack SY. Whole genome sequencing of extended spectrum \u03b2-lactamase (ESBL)-producing Klebsiella pneumoniae isolated from hospitalized patients in KwaZulu-Natal, South Africa. Sci Rep. 2019;9(1):6266. https:\/\/doi.org\/10.1038\/s41598-019-42672-2","DOI":"10.1038\/s41598-019-42672-2"},{"key":"ref2","unstructured":"World Health Organization. Global antimicrobial resistance and use surveillance system (GLASS) [homepage on the Internet]. 2026 [cited 2025 Mar 24]. Available from: https:\/\/www.who.int\/initiatives\/glass"},{"key":"ref3","doi-asserted-by":"crossref","unstructured":"GBD 2021 Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance 1990\u20132021: A systematic analysis with forecasts to 2050. Lancet. 2024;404(10459):1199\u20131226. https:\/\/doi.org\/10.1016\/S0140-6736(24)01867-1","DOI":"10.1016\/S0140-6736(24)01867-1"},{"key":"ref4","doi-asserted-by":"crossref","unstructured":"Mulani MS, Kamble EE, Kumkar SN, Tawre MS, Pardesi KR. Emerging strategies to combat ESKAPE pathogens in the era of antimicrobial resistance: A review. Front Microbiol. 2019;10:539. https:\/\/doi.org\/10.3389\/fmicb.2019.00539","DOI":"10.3389\/fmicb.2019.00539"},{"key":"ref5","unstructured":"WHO bacterial priority pathogens list, 2024: Bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance [homepage on the Internet]. 2024 [cited 2025 Mar 24]. Available from: https:\/\/www.who.int\/publications\/i\/item\/9789240093461"},{"key":"ref6","doi-asserted-by":"crossref","unstructured":"Santajit S, Indrawattana N. Mechanisms of antimicrobial resistance in ESKAPE pathogens. BioMed Res Int. 2016;2016:1\u20138. https:\/\/doi.org\/10.1155\/2016\/2475067","DOI":"10.1155\/2016\/2475067"},{"key":"ref7","doi-asserted-by":"crossref","unstructured":"De Oliveira DMP, Forde BM, Kidd TJ, et al. Antimicrobial resistance in ESKAPE pathogens. Clin Microbiol Rev. 2020;33(3):e00181-19. https:\/\/doi.org\/10.1128\/CMR.00181-19","DOI":"10.1128\/CMR.00181-19"},{"key":"ref8","doi-asserted-by":"crossref","unstructured":"Forero-Hurtado D, Corredor-Rozo ZL, Ruiz-Castellanos JS, et al. Worldwide dissemination of blaKPC gene by novel mobilization platforms in Pseudomonas aeruginosa: A systematic review. Antibiotics. 2023;12(4):658. https:\/\/doi.org\/10.3390\/antibiotics12040658","DOI":"10.3390\/antibiotics12040658"},{"key":"ref9","doi-asserted-by":"crossref","unstructured":"Tansarli GS, Poulikakos P, Kapaskelis A, Falagas ME. Proportion of extended-spectrum \u03b2-lactamase (ESBL)-producing isolates among Enterobacteriaceae in Africa: Evaluation of the evidence \u2013 Systematic review. J Antimicrob Chemother. 2014;69(5):1177\u20131184. https:\/\/doi.org\/10.1093\/jac\/dkt500","DOI":"10.1093\/jac\/dkt500"},{"key":"ref10","unstructured":"Martin J. Critical appraisal checklist for analytical cross sectional studies [homepage on the Internet]. Adelaide: Joanna Briggs Institute; 2017 [cited 2025 Apr 4]. Available from: https:\/\/jbi.global\/sites\/default\/files\/2019-05\/JBI_Critical_Appraisal-Checklist_for_Analytical_Cross_Sectional_Studies2017_0.pdf"},{"key":"ref11","doi-asserted-by":"crossref","unstructured":"Haddaway NR, Page MJ, Pritchard CC, McGuinness LA. PRISMA 2020: An R package and Shiny app for producing PRISMA 2020-compliant flow diagrams, with interactivity for optimised digital transparency and open synthesis. Campbell Syst. Rev. 2022;18(2):e1230. https:\/\/doi.org\/10.1002\/cl2.1230","DOI":"10.1002\/cl2.1230"},{"key":"ref12","doi-asserted-by":"crossref","unstructured":"Mairi A, Barraud O, Muggeo A, De Champs C, Touati A. Genomic analysis of a multidrug-resistant Klebsiella pneumoniae ST11 strain recovered from Barbary deer (Cervus elaphus barbarus) in Akfadou Forest, Algeria. J Glob Antimicrob Resist. 2020;22:515\u2013518. https:\/\/doi.org\/10.1016\/j.jgar.2020.04.027","DOI":"10.1016\/j.jgar.2020.04.027"},{"key":"ref13","doi-asserted-by":"crossref","unstructured":"Olorunleke SO, Kirchner M, Duggett N, et al. Rapid detection and molecular epidemiology of \u03b2-lactamase producing Enterobacteriaceae isolated from food animals and in-contact humans in Nigeria. PLoS One. 2024;19(4):e0289190. https:\/\/doi.org\/10.1371\/journal.pone.0289190","DOI":"10.1371\/journal.pone.0289190"},{"key":"ref14","doi-asserted-by":"crossref","unstructured":"Rizk AM, Elsayed MM, Abd El Tawab AA, et al. Phenotypic and genotypic characterization of resistance and virulence in Pseudomonas aeruginosa isolated from poultry farms in Egypt using whole genome sequencing. Vet Microbiol. 2024;292:110063. https:\/\/doi.org\/10.1016\/j.vetmic.2024.110063","DOI":"10.1016\/j.vetmic.2024.110063"},{"key":"ref15","doi-asserted-by":"crossref","unstructured":"Salem M, Younis G, Sadat A, et al. Dissemination of mcr-1 and \u03b2-lactamase genes among Pseudomonas aeruginosa: Molecular characterization of MDR strains in broiler chicks and dead-in-shell chicks infections. Ann Clin Microbiol Antimicrob. 2024;23(1):9. https:\/\/doi.org\/10.1186\/s12941-024-00669-4","DOI":"10.1186\/s12941-024-00669-4"},{"key":"ref16","doi-asserted-by":"crossref","unstructured":"Zalegh I, Bourhia M, Zerouali K, et al. Molecular characterization of gene-mediated resistance and susceptibility of ESKAPE clinical isolates to Cistus monspeliensis L. and Cistus salviifolius L. Extracts. Ramanathan S, editor. Evid Based Complement Alternat Med. 2022;2022:1\u201316. https:\/\/doi.org\/10.1155\/2022\/7467279","DOI":"10.1155\/2022\/7467279"},{"key":"ref17","doi-asserted-by":"crossref","unstructured":"Altayb HN, Elbadawi HS, Baothman O, et al. Genomic analysis of multidrug-resistant hypervirulent (hypermucoviscous) Klebsiella pneumoniae strain lacking the hypermucoviscous regulators (rmpA\/rmpA2). Antibiotics. 2022;11(5):596. https:\/\/doi.org\/10.3390\/antibiotics11050596","DOI":"10.3390\/antibiotics11050596"},{"key":"ref18","doi-asserted-by":"crossref","unstructured":"Elgayar FA, Gouda MK, Badran AA, El Halfawy NM. Pathogenomics analysis of high-risk clone ST147 multidrug-resistant Klebsiella pneumoniae isolated from a patient in Egypt. BMC Microbiol. 2024;24(1):256. https:\/\/doi.org\/10.1186\/s12866-024-03389-z","DOI":"10.1186\/s12866-024-03389-z"},{"key":"ref19","doi-asserted-by":"crossref","unstructured":"Lewis JM, Mphasa M, Banda R, et al. Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi. Microb Genomics. 2022;8(3):000778. https:\/\/doi.org\/10.1099\/mgen.0.000778","DOI":"10.1099\/mgen.0.000778"},{"key":"ref20","doi-asserted-by":"crossref","unstructured":"Odewale G, Jibola-Shittu MY, Ojurongbe O, Olowe RA, Olowe OA. Genotypic determination of extended spectrum \u03b2-lactamases and carbapenemase production in clinical isolates of Klebsiella pneumoniae in Southwest Nigeria. Infect Dis Rep. 2023;15(3):339\u2013353. https:\/\/doi.org\/10.3390\/idr15030034","DOI":"10.3390\/idr15030034"},{"key":"ref21","doi-asserted-by":"crossref","unstructured":"Odih EE, Oaikhena AO, Underwood A, et al. High genetic diversity of carbapenem-resistant Acinetobacter baumannii isolates recovered in Nigerian Hospitals in 2016 to 2020. mSphere. 2023;8(3):e00098-23. https:\/\/doi.org\/10.1128\/msphere.00098-23","DOI":"10.1128\/msphere.00098-23"},{"key":"ref22","doi-asserted-by":"crossref","unstructured":"Eladawy M, Thomas JC, Hoyles L. Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital. Microb Genomics. 2023;9(10):001125. https:\/\/doi.org\/10.1099\/mgen.0.001125","DOI":"10.1099\/mgen.0.001125"},{"key":"ref23","doi-asserted-by":"crossref","unstructured":"Olalekan A, Bader BK, Iwalokun B, et al. High incidence of carbapenemase-producing Pseudomonas aeruginosa clinical isolates from Lagos, Nigeria. JAC-Antimicrob Resist. 2023;5(2):dlad038. https:\/\/doi.org\/10.1093\/jacamr\/dlad038","DOI":"10.1093\/jacamr\/dlad038"},{"key":"ref24","doi-asserted-by":"crossref","unstructured":"Rahman MH, El Zowalaty ME, Falgenhauer L, et al. Molecular identification and whole genome sequence analyses of methicillin-resistant and mastitis-associated Staphylococcus aureus sequence types 6 and 2454 isolated from dairy cows. J Genomics. 2024;12:19\u201325. https:\/\/doi.org\/10.7150\/jgen.90833","DOI":"10.7150\/jgen.90833"},{"key":"ref25","doi-asserted-by":"crossref","unstructured":"Sivakumar R, Pranav PS, Annamanedi M, et al. Genome sequencing and comparative genomic analysis of bovine mastitis-associated Staphylococcus aureus strains from India. BMC Genomics. 2023;24(1):44. https:\/\/doi.org\/10.1186\/s12864-022-09090-7","DOI":"10.1186\/s12864-022-09090-7"},{"key":"ref26","doi-asserted-by":"crossref","unstructured":"Sivaraman GK, Sivam V, Ganesh B, Elangovan R, Vijayan A, Mothadaka MP. Whole genome sequence analysis of multi drug resistant community associated methicillin resistant Staphylococcus aureus from food fish: Detection of clonal lineage ST 28 and its antimicrobial resistance and virulence genes. PeerJ. 2021;9:e11224. https:\/\/doi.org\/10.7717\/peerj.11224","DOI":"10.7717\/peerj.11224"},{"key":"ref27","doi-asserted-by":"crossref","unstructured":"Khan MM, Mushtaq MA, Abbas N, et al. Occurrence, antimicrobial resistance and genomic features of Klebsiella pneumoniae from broiler chicken in Faisalabad, Pakistan. Front Vet Sci. 2024;11:1433124. https:\/\/doi.org\/10.3389\/fvets.2024.1433124","DOI":"10.3389\/fvets.2024.1433124"},{"key":"ref28","doi-asserted-by":"crossref","unstructured":"Shen J, Long X, Jiang Q, et al. Genomic characterization of a vancomycin-resistant strain of Enterococcus faecium harboring a rep2 Plasmid. Infect Drug Resist. 2023;16:1153\u20131158. https:\/\/doi.org\/10.2147\/IDR.S398913","DOI":"10.2147\/IDR.S398913"},{"key":"ref29","doi-asserted-by":"crossref","unstructured":"Ballah FM, Hoque MN, Islam MdS, et al. Genomic insights of a methicillin-resistant biofilm-producing Staphylococcus aureus strain isolated from food handlers. BioMed Res Int. 2024;2024(1):5516117. https:\/\/doi.org\/10.1155\/2024\/5516117","DOI":"10.1155\/2024\/5516117"},{"key":"ref30","doi-asserted-by":"crossref","unstructured":"Batool N, Shamim A, Chaurasia AK, Kim KK. Genome-wide analysis of Staphylococcus aureus sequence Type 72 isolates provides insights into resistance against antimicrobial agents and virulence potential. Front Microbiol. 2021;11:613800. https:\/\/doi.org\/10.3389\/fmicb.2020.613800","DOI":"10.3389\/fmicb.2020.613800"},{"key":"ref31","doi-asserted-by":"crossref","unstructured":"Chopjitt P, Wongsurawat T, Jenjaroenpun P, et al. Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus harboring staphylococcal cassette chromosome mec Type IX, Isolated from a fatal bacteremic pneumonia case. Dunning Hotopp JC, editor. Microbiol Resour Announc. 2021;10(30):e00616-21. https:\/\/doi.org\/10.1128\/MRA.00616-21","DOI":"10.1128\/MRA.00616-21"},{"key":"ref32","doi-asserted-by":"crossref","unstructured":"Islam S, Nasrin N, Tithi NS, et al. Antimicrobial Susceptibility and Genomic profiles of multidrug-resistant Staphylococcus aureus from nasopharynx of asymptomatic children in Dhaka, Bangladesh. Life. 2024;14(8):971. https:\/\/doi.org\/10.3390\/life14080971","DOI":"10.3390\/life14080971"},{"key":"ref33","doi-asserted-by":"crossref","unstructured":"Balushi MA, Kumar R, Al-Rashdi A, et al. Genomic analysis of the emerging carbapenem-resistant Klebsiella pneumoniae sequence type 11 harbouring Klebsiella pneumoniae carbapenemase (KPC) in Oman. J Infect Public Health. 2022;15(10):1089\u20131096. https:\/\/doi.org\/10.1016\/j.jiph.2022.08.014","DOI":"10.1016\/j.jiph.2022.08.014"},{"key":"ref34","doi-asserted-by":"crossref","unstructured":"Chen L, Zhou Y, Wang S, et al. Genomic analysis of carbapenem-resistant hypervirulent Klebsiella pneumoniae in a Chinese tertiary hospital. Infect Drug Resist. 2023;16:6385\u20136394. https:\/\/doi.org\/10.2147\/IDR.S425949","DOI":"10.2147\/IDR.S425949"},{"key":"ref35","doi-asserted-by":"crossref","unstructured":"Chukamnerd A, Pomwised R, Jeenkeawpiam K, Sakunrang C, Chusri S, Surachat K. Genomic insights into blaNDM-carrying carbapenem-resistant Klebsiella pneumoniae clinical isolates from a university hospital in Thailand. Microbiol Res. 2022;263:127136. https:\/\/doi.org\/10.1016\/j.micres.2022.127136","DOI":"10.1016\/j.micres.2022.127136"},{"key":"ref36","doi-asserted-by":"crossref","unstructured":"Cienfuegos-Gallet AV, Zhou Y, Ai W, Kreiswirth BN, Yu F, Chen L. Multicenter genomic analysis of carbapenem-resistant Klebsiella pneumoniae from Bacteremia in China. Microbiol Spectr. 2022;10(2):e02290-21. https:\/\/doi.org\/10.1128\/spectrum.02290-21","DOI":"10.1128\/spectrum.02290-21"},{"key":"ref37","doi-asserted-by":"crossref","unstructured":"Liu Z, Chen R, Xu P, Wang Z, Li R. Characterization of a blaNDM-1-bearing IncHI5-like plasmid from Klebsiella pneumoniae of infant origin. Front Cell Infect Microbiol. 2021;11:738053. https:\/\/doi.org\/10.3389\/fcimb.2021.738053","DOI":"10.3389\/fcimb.2021.738053"},{"key":"ref38","doi-asserted-by":"crossref","unstructured":"Pei N, Liu X, Jian Z, et al. Genome sequence and genomic analysis of liver abscess caused by hypervirulent Klebsiella pneumoniae. 3 Biotech. 2023;13(3):76. https:\/\/doi.org\/10.1007\/s13205-023-03458-6","DOI":"10.1007\/s13205-023-03458-6"},{"key":"ref39","doi-asserted-by":"crossref","unstructured":"Sheng J, Cave R, Ter-Stepanyan MM, et al. Emergence of mcr-8.1 -bearing MDR-hypervirulent Klebsiella pneumoniae ST307. Microbiol Spectr. 2024;13(1):e01910-24. https:\/\/doi.org\/10.1128\/spectrum.01910-24","DOI":"10.1128\/spectrum.01910-24"},{"key":"ref40","doi-asserted-by":"crossref","unstructured":"Shi Q, Han X, Huang Q, et al. The genetic characteristics and carbapenem resistance mechanism of ST307 Klebsiella pneumoniae coharbouring blaCMY-6, blaOXA-48, and a Truncated blaNDM-1. Antibiotics. 2022;11(11):1616. https:\/\/doi.org\/10.3390\/antibiotics11111616","DOI":"10.3390\/antibiotics11111616"},{"key":"ref41","doi-asserted-by":"crossref","unstructured":"Tian X, Zhang L, Li C, Xia D, Ying J. Genome sequence of a sequence type 1 NDM-5-producing carbapenem-resistant Klebsiella pneumoniae in China. J Glob Antimicrob Resist. 2024;38:271\u2013274. https:\/\/doi.org\/10.1016\/j.jgar.2024.05.001","DOI":"10.1016\/j.jgar.2024.05.001"},{"key":"ref42","doi-asserted-by":"crossref","unstructured":"Wang L, Zhu M, Yan C, et al. Class 1 integrons and multiple mobile genetic elements in clinical isolates of the Klebsiella pneumoniae complex from a tertiary hospital in eastern China. Front Microbiol. 2023;14:985102. https:\/\/doi.org\/10.3389\/fmicb.2023.985102","DOI":"10.3389\/fmicb.2023.985102"},{"key":"ref43","doi-asserted-by":"crossref","unstructured":"Xu J, Zhao Z, Ge Y, He F. Unravelling the genome sequence of NDM-1 and KPC-2 co-producing Klebsiella pneumoniae ST11 isolated from a bloodstream infection. J Glob Antimicrob Resist. 2020;20:339\u2013341. https:\/\/doi.org\/10.1016\/j.jgar.2020.01.021","DOI":"10.1016\/j.jgar.2020.01.021"},{"key":"ref44","doi-asserted-by":"crossref","unstructured":"Yang Q, Jia X, Zhou M, et al. Emergence of ST11-K47 and ST11-K64 hypervirulent carbapenem-resistant Klebsiella pneumoniae in bacterial liver abscesses from China: A molecular, biological, and epidemiological study. Emerg Microbes Infect. 2020;9(1):320\u2013331. https:\/\/doi.org\/10.1080\/22221751.2020.1721334","DOI":"10.1080\/22221751.2020.1721334"},{"key":"ref45","doi-asserted-by":"crossref","unstructured":"Zhang W, Wang Y, Wang K, et al. Hybrid sequencing-based genomic analysis of Klebsiella pneumoniae from urinary tract infections among inpatients at a tertiary hospital in Beijing. Infect Drug Resist. 2024;17:1447\u20131457. https:\/\/doi.org\/10.2147\/IDR.S448253","DOI":"10.2147\/IDR.S448253"},{"key":"ref46","doi-asserted-by":"crossref","unstructured":"Farlow J, Nozadze M, Mitaishvili N, et al. Comparative genomic analysis of four multidrug-resistant isolates of Acinetobacter baumannii from Georgia. J Glob Antimicrob Resist. 2020;21:363\u2013368. https:\/\/doi.org\/10.1016\/j.jgar.2019.11.002","DOI":"10.1016\/j.jgar.2019.11.002"},{"key":"ref47","doi-asserted-by":"crossref","unstructured":"Khan MAS, Chaity SC, Hosen MA, Rahman SR. Genomic epidemiology of multidrug-resistant clinical Acinetobacter baumannii in Bangladesh. Infect Genet Evol. 2024;123:105656. https:\/\/doi.org\/10.1016\/j.meegid.2024.105656","DOI":"10.1016\/j.meegid.2024.105656"},{"key":"ref48","doi-asserted-by":"crossref","unstructured":"He J, Lu X, Yuan C, et al. Genetic characteristics of novel IncpSE5381-aadB plasmids, integrative and mobilizable elements, and integrative and conjugative elements in Pseudomonas aeruginosa. Infect Drug Resist. 2024;17:2053\u20132068. https:\/\/doi.org\/10.2147\/IDR.S462670","DOI":"10.2147\/IDR.S462670"},{"key":"ref49","doi-asserted-by":"crossref","unstructured":"Amoudizaj FF, Aghayi E, Matin MG, Soltani N, Mala P. Antibiotic resistance pattern and frequency of PER-1, SHV-1 and AMPC Type B-lactamase genes in Pseudomonas aeruginosa isolated from clinical samples. Open Microbiol J. 2019;13(1):308\u2013312. https:\/\/doi.org\/10.2174\/1874285801913010308","DOI":"10.2174\/1874285801913010308"},{"key":"ref50","doi-asserted-by":"crossref","unstructured":"Chukamnerd A, Pomwised R, Chusri S, et al. Antimicrobial susceptibility and molecular features of colonizing isolates of Pseudomonas aeruginosa and the report of a novel sequence type (ST) 3910 from Thailand. Antibiotics. 2023;12(1):165. https:\/\/doi.org\/10.3390\/antibiotics12010165","DOI":"10.3390\/antibiotics12010165"},{"key":"ref51","doi-asserted-by":"crossref","unstructured":"Hu Z, Zhou L, Tao X, et al. Antimicrobial resistance survey and whole-genome analysis of nosocomial P. Aeruginosa isolated from eastern Province of China in 2016\u20132021. Ann Clin Microbiol Antimicrob. 2024;23(1):12. https:\/\/doi.org\/10.1186\/s12941-023-00656-1","DOI":"10.1186\/s12941-023-00656-1"},{"key":"ref52","doi-asserted-by":"crossref","unstructured":"Dong X, Zhu M, Li Y, et al. Whole-genome sequencing-based species classification, multilocus sequence typing, and antimicrobial resistance mechanism analysis of the Enterobacter cloacae complex in Southern China. Microbiol Spectr. 2022;10(6):e02160-22. https:\/\/doi.org\/10.1128\/spectrum.02160-22","DOI":"10.1128\/spectrum.02160-22"},{"key":"ref53","doi-asserted-by":"crossref","unstructured":"Gaber Y, TumAllah HM, AbdelAllah NH, et al. Emergence and genomic characterization of a spa Type t4407 ST6-SCCmec Type IVa methicillin-resistant Staphylococcus aureus strain isolated from Al-Karak Hospital, Jordan. Medicina (Mex). 2024;60(2):295. https:\/\/doi.org\/10.3390\/medicina60020295","DOI":"10.3390\/medicina60020295"},{"key":"ref54","doi-asserted-by":"crossref","unstructured":"Yasir M, Subahi AM, Shukri HA, et al. Bacterial community and genomic analysis of carbapenem-resistant Acinetobacter baumannii isolates from the environment of a health care facility in the western region of Saudi Arabia. Pharmaceuticals. 2022;15(5):611. https:\/\/doi.org\/10.3390\/ph15050611","DOI":"10.3390\/ph15050611"},{"key":"ref55","doi-asserted-by":"crossref","unstructured":"Chang J, Zhang Y, Zhang Z, et al. Prevalence, antimicrobial resistance, and genetic characteristics of Staphylococcus aureus isolates in frozen flour and rice products in Shanghai, China. Curr Res Food Sci. 2023;7:100631. https:\/\/doi.org\/10.1016\/j.crfs.2023.100631","DOI":"10.1016\/j.crfs.2023.100631"},{"key":"ref56","doi-asserted-by":"crossref","unstructured":"Zendri F, Isgren CM, Devaney J, Schmidt V, Rankin R, Timofte D. Resistome-based surveillance identifies ESKAPE pathogens as the predominant gram-negative organisms circulating in veterinary hospitals. Front Microbiol. 2023;14:1252216. https:\/\/doi.org\/10.3389\/fmicb.2023.1252216","DOI":"10.3389\/fmicb.2023.1252216"},{"key":"ref57","doi-asserted-by":"crossref","unstructured":"Torres RT, Cunha MV, Ferreira H, Fonseca C, Palmeira JD. A high-risk carbapenem-resistant Pseudomonas aeruginosa clone detected in red deer (Cervus elaphus) from Portugal. Sci Total Environ. 2022;829:154699. https:\/\/doi.org\/10.1016\/j.scitotenv.2022.154699","DOI":"10.1016\/j.scitotenv.2022.154699"},{"key":"ref58","doi-asserted-by":"crossref","unstructured":"Lopes J, De Lencastre H, Concei\u00e7\u00e3o T. Genomic analysis of Enterococcus faecium from non-clinical settings: Antimicrobial resistance, virulence, and clonal population in livestock and the urban environment. Front Microbiol. 2024;15:1466990. https:\/\/doi.org\/10.3389\/fmicb.2024.1466990","DOI":"10.3389\/fmicb.2024.1466990"},{"key":"ref59","doi-asserted-by":"crossref","unstructured":"Coppens J, Xavier BB, Vlaeminck J, et al. Genomic analysis of methicillin-resistant Staphylococcus aureus clonal complex 239 isolated from Danish patients with and without an international travel history. Front Microbiol. 2022;13:1016829. https:\/\/doi.org\/10.3389\/fmicb.2022.1016829","DOI":"10.3389\/fmicb.2022.1016829"},{"key":"ref60","doi-asserted-by":"crossref","unstructured":"Wolff N, Hendling M, Schroeder F, et al. Full pathogen characterisation: Species identification including the detection of virulence factors and antibiotic resistance genes via multiplex DNA-assays. Sci Rep. 2021;11(1):6001. https:\/\/doi.org\/10.1038\/s41598-021-85438-5","DOI":"10.1038\/s41598-021-85438-5"},{"key":"ref61","doi-asserted-by":"crossref","unstructured":"Fox V, Mangioni D, Renica S, et al. Genomic characterization of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) strains circulating in three university hospitals in Northern Italy over three years. Antimicrob Resist Infect Control. 2024;13(1):70. https:\/\/doi.org\/10.1186\/s13756-024-01429-x","DOI":"10.1186\/s13756-024-01429-x"},{"key":"ref62","doi-asserted-by":"crossref","unstructured":"Garcia-Gonzalez N, Fuster B, Tormo N, Salvador C, Gimeno C, Gonzalez-Candelas F. Genomic analysis of the initial dissemination of carbapenem-resistant Klebsiella pneumoniae clones in a tertiary hospital. Microb Genom. 2023;9(6):mgen001032. https:\/\/doi.org\/10.1099\/mgen.0.001032","DOI":"10.1099\/mgen.0.001032"},{"key":"ref63","doi-asserted-by":"crossref","unstructured":"Kuzina ES, Kislichkina AA, Sizova AA, et al. High-molecular-weight plasmids carrying carbapenemase genes blaNDM-1, blaKPC-2, and blaOXA-48 coexisting in clinical Klebsiella pneumoniae strains of ST39. Microorganisms. 2023;11(2):459. https:\/\/doi.org\/10.3390\/microorganisms11020459","DOI":"10.3390\/microorganisms11020459"},{"key":"ref64","doi-asserted-by":"crossref","unstructured":"Martin MJ, Corey BW, Sannio F, et al. Anatomy of an extensively drug-resistant Klebsiella pneumoniae outbreak in Tuscany, Italy. Proc Natl Acad Sci USA. 2021;118(48):e2110227118. https:\/\/doi.org\/10.1073\/pnas.2110227118","DOI":"10.1073\/pnas.2110227118"},{"key":"ref65","doi-asserted-by":"crossref","unstructured":"Chapartegui-Gonz\u00e1lez I, L\u00e1zaro-D\u00edez M, Redondo-Salvo S, Navas J, Ramos-Vivas J. Antimicrobial resistance determinants in genomes and plasmids from Acinetobacter baumannii clinical isolates. Antibiotics. 2021;10(7):753. https:\/\/doi.org\/10.3390\/antibiotics10070753","DOI":"10.3390\/antibiotics10070753"},{"key":"ref66","doi-asserted-by":"crossref","unstructured":"Valcek A, Nesporova K, Whiteway C, et al. Genomic analysis of a strain collection containing Multidrug-, extensively drug-, pandrug-, and carbapenem-resistant modern clinical isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 2022;66(9):e00892-22. https:\/\/doi.org\/10.1128\/aac.00892-22","DOI":"10.1128\/aac.00892-22"},{"key":"ref67","doi-asserted-by":"crossref","unstructured":"Hern\u00e1ndez-Garc\u00eda M, Gonz\u00e1lez De Aledo M, Ponce-Alonso M, et al. Simultaneous clonal spread of NDM-1\u2013producing Pseudomonas aeruginosa ST773 from Ukrainian patients in the Netherlands and Spain. IJID Reg. 2024;12:100415. https:\/\/doi.org\/10.1016\/j.ijregi.2024.100415","DOI":"10.1016\/j.ijregi.2024.100415"},{"key":"ref68","doi-asserted-by":"crossref","unstructured":"Torrens G, Van Der Schalk TE, Cortes-Lara S, et al. Susceptibility profiles and resistance genomics of Pseudomonas aeruginosa isolates from European ICUs participating in the ASPIRE-ICU trial. J Antimicrob Chemother. 2022;77(7):1862\u20131872. https:\/\/doi.org\/10.1093\/jac\/dkac122","DOI":"10.1093\/jac\/dkac122"},{"key":"ref69","doi-asserted-by":"crossref","unstructured":"Valenza G, Eisenberger D, Esse J, et al. High prevalence of the recently identified clonal lineage ST1299\/CT3109 vanA among vancomycin-resistant Enterococcus faecium strains isolated from municipal wastewater. mSphere. 2024;9(9):e00396-24. https:\/\/doi.org\/10.1128\/msphere.00396-24","DOI":"10.1128\/msphere.00396-24"},{"key":"ref70","doi-asserted-by":"crossref","unstructured":"Di Cesare A, Cornacchia A, Sbaffi T, et al. Treated wastewater: A hotspot for multidrug- and colistin-resistant Klebsiella pneumoniae. Environ Pollut. 2024;359:124598. https:\/\/doi.org\/10.1016\/j.envpol.2024.124598","DOI":"10.1016\/j.envpol.2024.124598"},{"key":"ref71","doi-asserted-by":"crossref","unstructured":"Sakkas H, Bozidis P, Ilia A, Mpekoulis G, Papadopoulou C. Antimicrobial resistance in bacterial pathogens and detection of carbapenemases in Klebsiella pneumoniae isolates from hospital wastewater. Antibiotics. 2019;8(3):85. https:\/\/doi.org\/10.3390\/antibiotics8030085","DOI":"10.3390\/antibiotics8030085"},{"key":"ref72","doi-asserted-by":"crossref","unstructured":"Belloso Daza MV, Milani G, Cortimiglia C, Pietta E, Bassi D, Cocconcelli PS. Genomic insights of Enterococcus faecium UC7251, a multi-drug resistant strain from ready-to-eat food, highlight the risk of antimicrobial resistance in the food chain. Front Microbiol. 2022;13:894241. https:\/\/doi.org\/10.3389\/fmicb.2022.894241","DOI":"10.3389\/fmicb.2022.894241"},{"key":"ref73","doi-asserted-by":"crossref","unstructured":"Naushad S, Nobrega DB, Naqvi SA, Barkema HW, De Buck J. Genomic analysis of bovine Staphylococcus aureus isolates from milk to elucidate diversity and determine the distributions of antimicrobial and virulence genes and their association with mastitis. mSystems. 2020;5(4):e00063-20. https:\/\/doi.org\/10.1128\/mSystems.00063-20","DOI":"10.1128\/mSystems.00063-20"},{"key":"ref74","doi-asserted-by":"crossref","unstructured":"Selvaraj Anand S, Wu CT, Bremer J, et al. Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA. Microb Genomics. 2024;10(2):001201. https:\/\/doi.org\/10.1099\/mgen.0.001201","DOI":"10.1099\/mgen.0.001201"},{"key":"ref75","doi-asserted-by":"crossref","unstructured":"VanNatta M, Grier L, Khan MH, et al. In vivo emergence of pandrug-resistant Acinetobacter baumannii strain: Comprehensive resistance characterization and compassionate use of sulbactam-durlobactam. Open Forum Infect Dis. 2023;10(10):ofad504. https:\/\/doi.org\/10.1093\/ofid\/ofad504","DOI":"10.1093\/ofid\/ofad504"},{"key":"ref76","doi-asserted-by":"crossref","unstructured":"Souza G\u00c1AD, Almeida ACD, Xavier MADS, et al. Characterization and molecular epidemiology of Staphylococcus aureus strains resistant to beta-lactams isolated from the milk of cows diagnosed with subclinical mastitis. Vet World. 2019;12(12):1931\u20131939. https:\/\/doi.org\/10.14202\/vetworld.2019.1931-1939","DOI":"10.14202\/vetworld.2019.1931-1939"},{"key":"ref77","doi-asserted-by":"crossref","unstructured":"Vasconcelos PC, Leite EL, Saraiva MMS, et al. Genomic analysis of a community-acquired methicillin-resistant Staphylococcus aureus sequence Type 1 associated with caprine mastitis. Pathogens. 2023;13(1):23. https:\/\/doi.org\/10.14202\/vetworld.2019.1931-1939","DOI":"10.3390\/pathogens13010023"},{"key":"ref78","doi-asserted-by":"crossref","unstructured":"Davies YM, Cunha MPV, Dropa M, et al. Pandemic clones of CTX-M-15 producing Klebsiella pneumoniae ST15, ST147, and ST307 in companion parrots. Microorganisms. 2022;10(7):1412. https:\/\/doi.org\/10.3390\/microorganisms10071412","DOI":"10.3390\/microorganisms10071412"},{"key":"ref79","doi-asserted-by":"crossref","unstructured":"Guill\u00e9n R, Salinas C, Mendoza-\u00c1lvarez A, et al. Genomic epidemiology of the primary methicillin-resistant Staphylococcus aureus clones causing invasive infections in Paraguayan children. Microbiol Spectr. 2024;12(4):e03012-23. https:\/\/doi.org\/10.1128\/spectrum.03012-23","DOI":"10.1128\/spectrum.03012-23"},{"key":"ref80","doi-asserted-by":"crossref","unstructured":"Jure MA, Albarracin L, Vargas JM, et al. Draft genome sequences of two hypermucoviscous carbapenem-resistant ST25 Klebsiella pneumoniae strains causing respiratory and systemic infections. J Glob Antimicrob Resist. 2021;26:174\u2013176. https:\/\/doi.org\/10.1016\/j.jgar.2021.05.018","DOI":"10.1016\/j.jgar.2021.05.018"},{"key":"ref81","doi-asserted-by":"crossref","unstructured":"Veloso M, Arros P, Acosta J, et al. Antimicrobial resistance, pathogenic potential, and genomic features of carbapenem-resistant Klebsiella pneumoniae isolated in Chile: High-risk ST25 clones and novel mobile elements. 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Antimicrob Resist Infect Control. 2021;10(1):63. https:\/\/doi.org\/10.1186\/s13756-021-00931-w","DOI":"10.1186\/s13756-021-00931-w"},{"key":"ref85","doi-asserted-by":"crossref","unstructured":"Malik SS, Mundra S. Increasing consumption of antibiotics during the COVID-19 pandemic: Implications for patient health and emerging anti-microbial resistance. Antibiotics. 2022;12(1):45. https:\/\/doi.org\/10.3390\/antibiotics12010045","DOI":"10.3390\/antibiotics12010045"},{"key":"ref86","unstructured":"World Health Organization. WHO reports widespread overuse of antibiotics in patients hospitalized with COVID-19 [homepage on the Internet]. 2024 [cited 2025 Apr 4]. Available from: https:\/\/www.who.int\/news\/item\/26-04-2024-who-reports-widespread-overuse-of-antibiotics-in-patients--hospitalized-with-covid-19"},{"key":"ref87","doi-asserted-by":"crossref","unstructured":"Abdelaziz Abdelmoneim S, Mohamed Ghazy R, Anwar Sultan E, Hassaan MA, Anwar Mahgoub M. Antimicrobial resistance burden pre and post-COVID-19 pandemic with mapping the multidrug resistance in Egypt: A comparative cross-sectional study. Sci Rep. 2024;14(1):7176. https:\/\/doi.org\/10.1038\/s41598-024-56254-4","DOI":"10.1038\/s41598-024-56254-4"},{"key":"ref88","doi-asserted-by":"crossref","unstructured":"Somda NS, Nyarkoh R, Kotey FCN, Tetteh-Quarcoo PB, Donkor ES. A systematic review and meta-analysis of carbapenem-resistant Enterobacteriaceae in West Africa. BMC Med Genomics. 2024;17(1):267. https:\/\/doi.org\/10.1186\/s12920-024-02043-x","DOI":"10.1186\/s12920-024-02043-x"},{"key":"ref89","doi-asserted-by":"crossref","unstructured":"Navon-Venezia S, Kondratyeva K, Carattoli A. Klebsiella pneumoniae: A major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol Rev. 2017;41(3):252\u2013275. https:\/\/doi.org\/10.1093\/femsre\/fux013","DOI":"10.1093\/femsre\/fux013"},{"key":"ref90","doi-asserted-by":"crossref","unstructured":"Teixeira P, Tac\u00e3o M, Pureza L, et al. Occurrence of carbapenemase-producing Enterobacteriaceae in a Portuguese river: blaNDM, blaKPC and blaGES among the detected genes. Environ Pollut. 2020;260:113913. https:\/\/doi.org\/10.1016\/j.envpol.2020.113913","DOI":"10.1016\/j.envpol.2020.113913"},{"key":"ref91","doi-asserted-by":"crossref","unstructured":"Hazen TH, Mettus R, McElheny CL, et al. Diversity among blaKPC-containing plasmids in Escherichia coli and other bacterial species isolated from the same patients. 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