Genomic Characteristics of Carbapenem-Resistant Klebsiella pneumoniae Isolated from Neonatal Patients in Southwest China During 2017–2021

References

• Diekema DJ, Hsueh PR, Mendes RE, et al. The microbiology of bloodstream infection: 20-year trends from the SENTRY antimicrobial surveillance program. Antimicrob Agents Chemother. 2019;63(7). doi:10.1128/AAC.00355-19
   PubMed Web of Science ®Google Scholar
• Paczosa MK, Mecsas J. Klebsiella pneumoniae: going on the offense with a strong defense. Microbiol Mol Biol Rev. 2016;80(3):629–661. doi:10.1128/MMBR.00078-15
   PubMed Web of Science ®Google Scholar
• Stewardson AJ, Marimuthu K, Sengupta S, et al. Effect of carbapenem resistance on outcomes of bloodstream infection caused by Enterobacteriaceae in low-income and middle-income countries (PANORAMA): a multinational prospective cohort study. Lancet Infect Dis. 2019;19(6):601–610. doi:10.1016/S1473-3099(18)30792-8
   PubMed Web of Science ®Google Scholar
• Zhou R, Fang X, Zhang J, et al. Impact of carbapenem resistance on mortality in patients infected with Enterobacteriaceae: a systematic review and meta-analysis. BMJ Open. 2021;11(12):e054971. doi:10.1136/bmjopen-2021-054971
   PubMed Web of Science ®Google Scholar
• World Health Organization. Global Antimicrobial Resistance and use Surveillance System (GLASS) Report 2021. Geneva: World Health Organization; 2021.
   Google Scholar
• Fupin HU, Yan GUO, Demei ZHU, et al. CHINET surveillance of antimicrobial resistance among the bacterial isolates in 2021. Chin J Infect Chemother. 2022;22(5):521–530. doi:10.16718/j.1009-7708.2022.05.001
   Google Scholar
• Fu P, Xu H, Jing C, et al. Bacterial epidemiology and antimicrobial resistance profiles in children reported by the ISPED program in China, 2016 to 2020. Microbiol Spectr. 2021;9(3):e0028321. doi:10.1128/Spectrum.00283-21
   PubMed Web of Science ®Google Scholar
• Ma J, Song X, Li M, et al. Global spread of carbapenem-resistant Enterobacteriaceae: epidemiological features, resistance mechanisms, detection and therapy. Microbiol Res. 2023;266:127249. doi:10.1016/j.micres.2022.127249
   PubMedGoogle Scholar
• Pitout JD, Nordmann P, Poirel L. Carbapenemase-producing Klebsiella pneumoniae, a key pathogen set for global nosocomial dominance. Antimicrob Agents Chemother. 2015;59(10):5873–5884. doi:10.1128/AAC.01019-15
   PubMed Web of Science ®Google Scholar
• Zhang R, Liu L, Zhou H, et al. Nationwide surveillance of clinical carbapenem-resistant Enterobacteriaceae (CRE) Strains in China. EBioMedicine. 2017;19:98–106. doi:10.1016/j.ebiom.2017.04.032
   PubMed Web of Science ®Google Scholar
• Gao F, Xiong Z, Liang B, et al. Molecular characterization and epidemiology of carbapenem-resistant Enterobacteriaceae isolated from pediatric patients in Guangzhou, Southern China. Can J Infect Dis Med Microbiol. 2023;2023:4762143. doi:10.1155/2023/4762143
   PubMed Web of Science ®Google Scholar
• Han R, Shi Q, Wu S, et al. Dissemination of carbapenemases (KPC, NDM, OXA-48, IMP, and VIM) among carbapenem-resistant Enterobacteriaceae isolated from adult and children patients in China. Front Cell Infect Microbiol. 2020;10:314. doi:10.3389/fcimb.2020.00314
   PubMed Web of Science ®Google Scholar
• Tao G, Tan H, Ma J, Chen Q. Resistance phenotype and molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae isolated from Nanjing children’s hospital in Jiangsu Province, China. Infect Drug Resist. 2022;15:5435–5447. doi:10.2147/IDR.S377068
   PubMed Web of Science ®Google Scholar
• Shon AS, Bajwa RP, Russo TA. Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: a new and dangerous breed. Virulence. 2013;4(2):107–118. doi:10.4161/viru.22718
   PubMed Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120. doi:10.1093/bioinformatics/btu170
   PubMed Web of Science ®Google Scholar
• Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–477. doi:10.1089/cmb.2012.0021
   PubMed Web of Science ®Google Scholar
• Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–2069. doi:10.1093/bioinformatics/btu153
   PubMed Web of Science ®Google Scholar
• Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–1313. doi:10.1093/bioinformatics/btu033
   PubMed Web of Science ®Google Scholar
• Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49(W1):W293–W296. doi:10.1093/nar/gkab301
   PubMed Web of Science ®Google Scholar
• Yin L, He L, Miao J, et al. Actively surveillance and appropriate patients placements’ contact isolation dramatically decreased Carbapenem-Resistant Enterobacteriaceae infection and colonization in pediatric patients in China. J Hosp Infect. 2020;105(3):486–494. doi:10.1016/j.jhin.2020.03.031
   Web of Science ®Google Scholar
• Wang J, Lv Y, Yang W, Zhao P, Yin C. Epidemiology and clinical characteristics of infection/colonization due to carbapenemase-producing Enterobacterales in neonatal patients. BMC Microbiol. 2022;22(1):177. doi:10.1186/s12866-022-02585-z
   PubMed Web of Science ®Google Scholar
• Darda VM, Iosifidis E, Antachopoulos C, et al. Modifiable risk factors associated with later gut decolonization of carbapenem-resistant Gram-negative bacteria in children: a prospective cohort study. J Hosp Infect. 2023;136:75–84. doi:10.1016/j.jhin.2023.03.024
   PubMed Web of Science ®Google Scholar
• Yen CS, Hsiao HL, Lee CC, et al. Carbapenem-resistant Enterobacteriaceae infection in children less than one year old in an Asian medical center. Pediatr Neonatol. 2023;64(2):168–175. doi:10.1016/j.pedneo.2022.05.016
   PubMed Web of Science ®Google Scholar
• Yin L, He L, Miao J, et al. Carbapenem-resistant Enterobacterales colonization and subsequent infection in a neonatal intensive care unit in Shanghai, China. Infect Prev Pract. 2021;3(3):100147. doi:10.1016/j.infpip.2021.100147
   PubMedGoogle Scholar
• Scamardo MS, Dolce P, Esposito EP, Raimondi F, Triassi M, Zarrilli R. Trends, risk factors and outcomes of healthcare-associated infections in a neonatal intensive care unit in Italy during 2013–2017. Ital J Pediatr. 2020;46(1):34. doi:10.1186/s13052-020-0799-3
   PubMed Web of Science ®Google Scholar
• Zhang X, Xue J, Shen MJ, An WH, Chen ZQ, Wu KF. Molecular typing and drug resistance analysis of carbapenem-resistant Klebsiella pneumoniae from paediatric patients in China. J Infect Dev Ctries. 2022;16(11):1726–1731. doi:10.3855/jidc.17003
   PubMed Web of Science ®Google Scholar
• Yin L, Yan G, Lu L, et al. Molecular characteristics and virulence factors of carbapenem-resistant Klebsiella pneumoniae among pediatric patients in Shanghai, China. Infect Genet Evol. 2023;112:105451. doi:10.1016/j.meegid.2023.105451
   PubMed Web of Science ®Google Scholar
• Fu P, Luo X, Shen J, et al. The molecular and epidemiological characteristics of carbapenemase-producing Enterobacteriaceae isolated from children in Shanghai, China, 2016–2021. J Microbiol Immunol Infect. 2023;56(1):48–56. doi:10.1016/j.jmii.2022.07.012
   PubMedGoogle Scholar
• Shields RK, Nguyen MH, Chen L, et al. Ceftazidime-avibactam is superior to other treatment regimens against carbapenem-resistant Klebsiella pneumoniae bacteremia. Antimicrob Agents Chemother. 2017;61(8). doi:10.1128/AAC.00883-17
   Web of Science ®Google Scholar
• Carmeli Y, Armstrong J, Laud PJ, et al. Ceftazidime-avibactam or best available therapy in patients with ceftazidime-resistant Enterobacteriaceae and Pseudomonas aeruginosa complicated urinary tract infections or complicated intra-abdominal infections (REPRISE): a randomised, pathogen-directed, Phase 3 study. Lancet Infect Dis. 2016;16(6):661–673. doi:10.1016/S1473-3099(16)30004-4
   PubMed Web of Science ®Google Scholar
• Ipek MS, Aktar F, Okur N, Celik M, Ozbek E. Colistin use in critically ill neonates: a case-control study. Pediatr Neonatol. 2017;58(6):490–496. doi:10.1016/j.pedneo.2016.10.002
   PubMed Web of Science ®Google Scholar
• Cagan E, Kiray Bas E, Asker HS. Use of colistin in a neonatal intensive care unit: a cohort study of 65 patients. Med Sci Monit. 2017;23:548–554. doi:10.12659/msm.898213
   PubMed Web of Science ®Google Scholar
• Abrahams I, Dramowski A, Moloto K, Lloyd L, Whitelaw A, Bekker A. Colistin use in a carbapenem-resistant Enterobacterales outbreak at a South African neonatal unit. S Afr J Infect Dis. 2023;38(1):487. doi:10.4102/sajid.v38i1.487
   PubMed Web of Science ®Google Scholar
• Yin D, Zhang L, Wang A, et al. Clinical and molecular epidemiologic characteristics of carbapenem-resistant Klebsiella pneumoniae infection/colonization among neonates in China. J Hosp Infect. 2018;100(1):21–28. doi:10.1016/j.jhin.2018.05.005
   PubMed Web of Science ®Google Scholar
• Hu Y, Yang Y, Feng Y, et al. Prevalence and clonal diversity of carbapenem-resistant Klebsiella pneumoniae causing neonatal infections: a systematic review of 128 articles across 30 countries. PLoS Med. 2023;20(6):e1004233. doi:10.1371/journal.pmed.1004233
   PubMed Web of Science ®Google Scholar
• Khan AU, Maryam L, Zarrilli R. Structure, genetics and worldwide spread of new delhi metallo-beta-lactamase (NDM): a threat to public health. BMC Microbiol. 2017;17(1):101. doi:10.1186/s12866-017-1012-8
   PubMedGoogle Scholar
• Kong Z, Cai R, Cheng C, et al. First reported nosocomial outbreak of NDM-5-Producing Klebsiella pneumoniae In A neonatal unit in China. Infect Drug Resist. 2019;12:3557–3566. doi:10.2147/IDR.S218945
   PubMed Web of Science ®Google Scholar
• Qiao F, Wei L, Feng Y, et al. Handwashing sink contamination and carbapenem-resistant Klebsiella infection in the intensive care unit: a prospective multicenter study. Clin Infect Dis. 2020;71(Suppl 4):S379–S385. doi:10.1093/cid/ciaa1515
   PubMed Web of Science ®Google Scholar
• Wei L, Feng Y, Wen H, Ya H, Qiao F, Zong Z. NDM-5-producing carbapenem-resistant Klebsiella pneumoniae of sequence type 789 emerged as a threat for neonates: a multicentre, genome-based study. Int J Antimicrob Agents. 2022;59(2):106508. doi:10.1016/j.ijantimicag.2021.106508
   PubMed Web of Science ®Google Scholar
• Fu B, Yin D, Sun C, et al. Clonal and Horizontal Transmission of bla(NDM) among Klebsiella pneumoniae in Children’s Intensive Care Units. Microbiol Spectr. 2022;10(4):e0157421. doi:10.1128/spectrum.01574-21
   PubMed Web of Science ®Google Scholar
• Kopotsa K, Osei Sekyere J, Mbelle NM. Plasmid evolution in carbapenemase-producing Enterobacteriaceae: a review. Ann N Y Acad Sci. 2019;1457(1):61–91. doi:10.1111/nyas.14223
   PubMed Web of Science ®Google Scholar
• Wu W, Feng Y, Tang G, Qiao F, McNally A, Zong Z. NDM metallo-beta-lactamases and their bacterial producers in health care settings. Clin Microbiol Rev. 2019;32(2). doi:10.1128/CMR.00115-18
   PubMed Web of Science ®Google Scholar