References
- Sarshar M, Behzadi P, Scribano D, et al. Acinetobacter baumannii: an ancient commensal with weapons of a pathogen. Pathogens. 2021;10(4):387.
- Whiteway C, Breine A, Philippe C, et al. Acinetobacter baumannii. Trends Microbiol. 2021;30(2):199–200.
- Oh K, Kim K, Islam M, et al. Transcriptional regulation of the outer membrane protein A in Acinetobacter baumannii. Microorganisms. 2020;8(5):706.
- Zilberberg MD, Shorr AF. Secular trends in gram-negative resistance among urinary tract infection hospitalizations in the United States, 2000–2009. Infect Control & Hosp Epidemiol. 2013;34(9):940–946.
- Goel N, Wattal C, Oberoi JK, et al. Trend analysis of antimicrobial consumption and development of resistance in non-fermenters in a tertiary care hospital in Delhi, India. J Antimicrob Chemother. 2011;66(7):1625–1630.
- Li S, Duan X, Peng Y, et al. Molecular characteristics of carbapenem-resistant Acinetobacter spp. from clinical infection samples and fecal survey samples in southern China. BMC Infect Dis. 2019;19(1):900.
- Yang J, Chen Y, Jia X, et al. Dissemination and characterization of NDM-1-producing Acinetobacter pittii in an intensive care unit in China. Clin Microbiol Infect. 2012;18(12):E506–E513.
- Lim SMS, Abidin AZ, Liew SM, et al. The global prevalence of multidrug-resistance among Acinetobacter baumannii causing hospital-acquired and ventilator-associated pneumonia and its associated mortality: A systematic review and meta-analysis. J Infect. 2019;79(6):593–600.
- Pormohammad A, Mehdinejadiani K, Gholizadeh P, et al. Global prevalence of colistin resistance in clinical isolates of Acinetobacter baumannii: A systematic review and meta-analysis. Microb Pathog. 2020;139:103887.
- Hagihara M, Housman S, Nicolau D, et al. In vitro pharmacodynamics of polymyxin B and tigecycline alone and in combination against carbapenem-resistant Acinetobacter baumannii. Antimicrob Agents Chemother. 2014;58(2):874–879.
- Wang L, Liu D, Lv Y, et al. Novel plasmid-mediated tet (X5) gene conferring resistance to tigecycline, eravacycline, and omadacycline in a clinical Acinetobacter baumannii isolate. Antimicrob Agents Chemother. 2019;64(1):e01326–e01319.
- Wang Z, Li H, Zhang J, et al. Identification of a novel plasmid-mediated tigecycline resistance-related gene, tet (Y), in Acinetobacter baumannii. J Antimicrob Chemother. 2022;77(1):58–68.
- Sun B, Liu H, Jiang Y, et al. New mutations involved in colistin resistance in Acinetobacter baumannii. mSphere. 2020;5(2):e00895-19.
- Chen Q, Li X, Zhou H, et al. Decreased susceptibility to tigecycline in Acinetobacter baumannii mediated by a mutation in trm encoding SAM-dependent methyltransferase. J Antimicrob Chemother. 2014;69(1):72–76.
- He T, Wang R, Liu D, et al. Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans. Nature Microbiol. 2019;4(9):1450–1456.
- Wang Y, Wang J, Wang R, et al. Resistance to ceftazidime-avibactam and underlying mechanisms. J Glob Antimicrob Resist. 2020;22:18–27.
- Yahav D, Giske C, Grāmatniece A, et al. New β-lactam-β-lactamase inhibitor combinations. Clin Microbiol Rev. 2020;34(1):e00115-20.
- CLSI. Performance standards for antimicrobial susceptibility testing. 30th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2020. (CLSI supplement M100).
- Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120.
- 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.
- Li R, Xie M, Dong N, et al. Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data. Gigascience. 2018;7(3):gix132.
- Wick RR, Judd LM, Gorrie CL, et al. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13(6):e1005595.
- Overbeek R, Olson R, Pusch GD, et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 2013;42(D1):D206–D214.
- Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–2644.
- Kwong JC, Mercoulia K, Tomita T, et al. Prospective whole-genome sequencing enhances national surveillance of Listeria monocytogenes. J Clin Microbiol. 2016;54(2):333–342.
- Price MN, Dehal PS, Arkin AP. Fasttree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641–1650.
- Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44(W1):W242–W245.
- Cheng L, Connor TR, Sirén J, et al. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol Biol Evol. 2013;30(5):1224–1228.
- Gorrie CL, Da Silva AG, Ingle DJ, et al. Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis. Lancet Microbe. 2021;2(11):e575–e583.
- Nigro SJ, Hall RM. Structure and context of Acinetobacter transposons carrying the oxa23 carbapenemase gene. J Antimicrob Chemother. 2016;71(5):1135–1147.
- Robledo IE, Aquino EE, Santé MI, et al. Detection of KPC in Acinetobacter spp. in Puerto Rico. Antimicrob Agents Chemother. 2010;54(3):1354–1357.
- Abdulzahra AT, Khalil MA, Elkhatib WF. First report of colistin resistance among carbapenem-resistant Acinetobacter baumannii isolates recovered from hospitalized patients in Egypt. New Microbes New Infect. 2018;26:53–58.
- Wieczorek P, Sacha P, Hauschild T, et al. Multidrug resistant Acinetobacter baumannii–the role of AdeABC (RND family) efflux pump in resistance to antibiotics. Folia Histochem Cytobiol. 2008;46(3):257–267.
- Nordmann P, Poirel L. Epidemiology and diagnostics of carbapenem resistance in gram-negative bacteria. Clin Infect Dis. 2019;69(Suppl 7):S521–s528.
- Hwang SM, Cho HW, Kim TY, et al. Whole-genome sequencing for investigating a health care-associated outbreak of carbapenem-resistant Acinetobacter baumannii. Diagnostics. 2021;11(2):201.
- Shinohara DR, dos Santos Saalfeld SM, Martinez HV, et al. Outbreak of endemic carbapenem-resistant Acinetobacter baumannii in a coronavirus disease 2019 (COVID-19)–specific intensive care unit. Infect Control & Hosp Epidemiol. 2021;43(6):815–817.
- World Health Organization. Prioritization of pathogens to guide discovery, research and development of new antibiotics for drug-resistant bacterial infections, including tuberculosis. World health organization; 2017. https://www.who.int/publications/i/item/WHO-EMP-IAU-2017.12.
- Koenig SM, Truwit JD. Ventilator-associated pneumonia: diagnosis, treatment, and prevention. Clin Microbiol Rev. 2006;19(4):637–657.
- Hamidian M, Nigro S. Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii. Microbial Genomics. 2019;5(10):e000306.
- Maiden MC, Van Rensburg MJJ, Bray JE, et al. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol. 2013;11(10):728–736.
- Pearce ME, Alikhan N-F, Dallman TJ, et al. Comparative analysis of core genome MLST and SNP typing within a European salmonella serovar enteritidis outbreak. Int J Food Microbiol. 2018;274:1–11.
- Forster D, Daschner F. Acinetobacter species as nosocomial pathogens. Eur J Clin Microbiol Infect Dis. 1998;17(2):73–77.
- Zhang R, Dong N, Zeng Y, et al. Chromosomal and plasmid-borne tigecycline resistance genes tet (X3) and tet (X4) in dairy cows on a Chinese farm. Antimicrob Agents Chemother. 2020;64(11):e00674–e00620.
- Hua X, Shu J, Ruan Z, et al. Multiplication of bla OXA-23 is common in clinical Acinetobacter baumannii, but does not enhance carbapenem resistance. J Antimicrob Chemother. 2016;71(12):3381–3385.