Nguyen M, Joshi SG. Carbapenem resistance in Acinetobacter baumannii, and their importance in hospital-acquired infections: a scientific review. J Appl Microbiol. 2021;131(6):2715–38. https://doi.org/10.1111/jam.15130.

Article  CAS  PubMed  Google Scholar 

Xie R, Zhang XD, Zhao Q, Peng B, Zheng J. Analysis of global prevalence of antibiotic resistance in Acinetobacter baumannii infections disclosed a faster increase in OECD countries. Emerg Microbes Infect. 2018;7(1):31. https://doi.org/10.1038/s41426-018-0038-9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dortet L, Bonnin RA, Bernabeu S, Escaut L, Vittecoq D, Girlich D, et al. First occurrence of OXA-72-Producing Acinetobacter baumannii in Serbia. Antimicrob Agents Chemother. 2016;60(10):5724–30. https://doi.org/10.1128/AAC.01016-16.

Article  PubMed  PubMed Central  Google Scholar 

Pfeifer Y, Wilharm G, Zander E, Wichelhaus TA, Göttig S, Hunfeld KP, et al. Molecular characterization of blaNDM-1 in an Acinetobacter baumannii strain isolated in Germany in 2007. J Antimicrob Chemother. 2011;66(9):1998–2001. https://doi.org/10.1093/jac/dkr256.

Article  CAS  PubMed  Google Scholar 

Zarrilli R, Pournaras S, Giannouli M, Tsakris A. Global evolution of multidrug-resistant Acinetobacter baumannii clonal lineages. Int J Antimicrob Agents. 2013;41(1):11–9. https://doi.org/10.1016/j.ijantimicag.2012.09.008.

Article  CAS  PubMed  Google Scholar 

Fitzpatrick MA, Ozer EA, Hauser AR. Utility of whole-genome sequencing in characterizing Acinetobacter epidemiology and analyzing Hospital outbreaks. J Clin Microbiol. 2016;54(3):593–612. https://doi.org/10.1128/JCM.01818-15.

Article  PubMed  PubMed Central  Google Scholar 

Performance Standards for Antimicrobial Susceptibility Testing. Twenty-seventh informational supplement M100-S27. Wayne, PA: Clinical and Laboratory Standards Institute; 2017.

Google Scholar 

Breakpoint tables for interpretation. Of MICs and zone diameters. Version 8.1. European Committee on Antimicrobial Susceptibility Testing; 2018.

Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect. 2012;18(3):268–81. https://doi.org/10.1111/j.1469-0691.2011.03570.x.

Article  CAS  PubMed  Google Scholar 

Andrews S. Babraham Bioinformatics - FastQC A Quality Control tool for High Throughput Sequence Data, 2010. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (Accessed May 29, 2023).

Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo Assembler. Curr Protoc Bioinf. 2020;70(1):e102. https://doi.org/10.1002/cpbi.102.

Article  CAS  Google Scholar 

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–2. https://doi.org/10.1093/bioinformatics/btv351.

Article  CAS  PubMed  Google Scholar 

Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–9. https://doi.org/10.1093/bioinformatics/btu153.

Article  CAS  PubMed  Google Scholar 

Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2020;48(D1):D517–25. https://doi.org/10.1093/nar/gkz935.

Article  CAS  PubMed  Google Scholar 

Liu B, Zheng D, Zhou S, Chen L, Yang J. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 2022;50(D1):D912–7. https://doi.org/10.1093/nar/gkab1107.

Article  CAS  PubMed  Google Scholar 

Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006;34(Database issue):D32–6. https://doi.org/10.1093/nar/gkj014.

Article  CAS  PubMed  Google Scholar 

Yoon SH, Park YK, Kim JF. PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands. Nucleic Acids Res. 2015;43(Database issue):D624–30. https://doi.org/10.1093/nar/gku985.

Article  CAS  PubMed  Google Scholar 

Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31(22):3691–3. https://doi.org/10.1093/bioinformatics/btv421.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genom. 2016;2(4):e000056. https://doi.org/10.1099/mgen.0.000056.

Article  PubMed  PubMed Central  Google Scholar 

Stamatakis A. Bioinformatics. 2014;30(9):1312–3. https://doi.org/10.1093/bioinformatics/btu033. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.

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):W293–6. https://doi.org/10.1093/nar/gkab301.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124. https://doi.org/10.12688/wellcomeopenres.14826.1.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun. 2020;11(1):2500. https://doi.org/10.1038/s41467-020-16366-7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Revell LJ. Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol. 2012;3(2):217–23. https://doi.org/10.1111/j.2041-210X.2011.00169.

Article  Google Scholar 

Chen CH, Kuo HY, Hsu PJ, Chang CM, Chen JY, Lu HH, et al. Clonal spread of carbapenem-resistant Acinetobacter baumannii across a community hospital and its affiliated long-term care facilities: a cross sectional study. J Microbiol Immunol Infect. 2018;51(3):377–84. https://doi.org/10.1016/j.jmii.2017.08.001.

Article  PubMed  Google Scholar 

Havenga B, Ndlovu T, Clements T, Reyneke B, Waso M, Khan W. Exploring the antimicrobial resistance profiles of WHO critical priority list bacterial strains. BMC Microbiol. 2019;19(1):303. https://doi.org/10.1186/s12866-019-1687-0.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Asadian M, Azimi L, Alinejad F, Ostadi Y, Lari AR. Molecular characterization of Acinetobacter baumannii isolated from Ventilator-Associated Pneumonia and burn Wound colonization by Random amplified polymorphic DNA polymerase chain reaction and the relationship between Antibiotic susceptibility and Biofilm Production. Adv Biomed Res. 2019;8:58. https://doi.org/10.4103/abr.abr_256_18.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kostyanev T, Xavier BB, García-Castillo M, Lammens C, Bravo-Ferrer Acosta J, Rodríguez-Baño J, et al. Phenotypic and molecular characterizations of carbapenem-resistant Acinetobacter baumannii isolates collected within the EURECA study. Int J Antimicrob Agents. 2021;57(6):106345. https://doi.org/10.1016/j.ijantimicag.2021.106345.

Article  CAS  PubMed  Google Scholar 

Weber RE, Pietsch M, Frühauf A, Pfeifer Y, Martin M, Luft D, et al. IS26-Mediated transfer of blaNDM-1 as the Main Route of Resistance Transmission during a polyclonal, multispecies Outbreak in a German hospital. Front Microbiol. 2019;10:2817. https://doi.org/10.3389/fmicb.2019.02817.

Article  PubMed  PubMed Central  Google Scholar 

Samuelsen Ø, Overballe-Petersen S, Bjørnholt JV, Brisse S, Doumith M, Woodford N, et al. Molecular and epidemiological characterization of carbapenemase-producing Enterobacteriaceae in Norway, 2007 to 2014. PLoS ONE. 2017;12(11):e0187832.