Whole-genome evaluation and prophages characterization associated with genome of carbapenem-resistant Acinetobacter baumannii UOL-KIMZ-24-2

Abouelfetouh A, Torky AS, Aboulmagd E (2019) Phenotypic and genotypic characterization of carbapenem-resistant Acinetobacter baumannii isolates from Egypt. Antimicrob Resist Infect Control 8:1–9. https://doi.org/10.1186/s13756-019-0611-6

Article  Google Scholar 

Adams MD, Wright MS, Karichu JK, Venepally P, Fouts DE, Chan AP, Richter SS, Jacobs MR, Bonomo RA (2019) Rapid replacement of Acinetobacter baumannii strains accompanied by changes in lipooligosaccharide loci and resistance gene repertoire. MBio 10. https://doi.org/10.1128/mbio00356– 00319

Al-Sehlawi ZS, Almohana AM, Al-Thahab AA (2014) Isolation and identification of Acinetobacter baumannii clinical isolates using novel methods. J Babylon University/Pure Appl Sci 22(3):1041–1050

Google Scholar 

Alcock BP, Raphenya AR, Lau TT, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen A-LV, Cheng AA, Liu S (2020) CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48:D517–D525. https://doi.org/10.1093/nar/gkz935

Article  CAS  PubMed  Google Scholar 

Alsan M, Klompas M (2010) Acinetobacter baumannii: an emerging and important pathogen. J Clin Outcomes Manag 17:363

PubMed  PubMed Central  Google Scholar 

Asif M, Alvi IA, Rehman SU (2018) Insight into Acinetobacter baumannii: pathogenesis, global resistance, mechanisms of resistance, treatment options, and alternative modalities. Infect Drug Resist 1249–1260. https://doi.org/10.2147/idr.s166750

Banerjee T, Mishra A, Das A, Sharma S, Barman H, Yadav G (2018) High prevalence and endemicity of multidrug resistant Acinetobacter spp. in intensive care unit of a tertiary care hospital, Varanasi, India. J Pathog 2018: 9129083. https://doi.org/10.1155/2018/9129083

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021

Article  CAS  PubMed  PubMed Central  Google Scholar 

Begum S, Hasan F, Hussain S, Shah AA (2013) Prevalence of multi drug resistant Acinetobacter baumannii in the clinical samples from Tertiary Care Hospital in Islamabad, Pakistan. Pak J Med Sci 29:1253. https://doi.org/10.12669/pjms.295.3695

PubMed  PubMed Central  Google Scholar 

Bergey DH (1994) Bergey’s manual of determinative bacteriology Lippincott Williams & Wilkins, pp. Pages.Bergogne-Berezin E (2001) The increasing role of Acinetobacter species asnosocomial pathogens. Curr Infect Dis Rep 3: 440–444

Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:W81–W87. https://doi.org/10.1093/nar/gkz310

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brown S, Young H, Amyes S (2005) Characterisation of OXA-51, a novel class D carbapenemase found in genetically unrelated clinical strains of Acinetobacter baumannii from Argentina. Clin Microbiol Infect 11:15–23. https://doi.org/10.1111/j.1469-0691.2004.01016.x

Article  CAS  PubMed  Google Scholar 

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:1–9. https://doi.org/10.1186/1471-2105-10-421

Article  CAS  Google Scholar 

Chopra T, Marchaim D, Awali RA, Krishna A, Johnson P, Tansek R, Chaudary K, Lephart P, Slim J, Hothi J (2013) Epidemiology of bloodstream infections caused by Acinetobacter baumannii and impact of drug resistance to both carbapenems and ampicillin-sulbactam on clinical outcomes. Antimicrob Agents Chemother 57:6270–6275. https://doi.org/10.1128/aac.01520-13

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chukamnerd A, Singkhamanan K, Chongsuvivatwong V, Palittapongarnpim P, Doi Y, Pomwised R, Sakunrang C, Jeenkeawpiam K, Yingkajorn M, Chusri S (2022) Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand. Comput Struct Biotechnol J 20:545–558. https://doi.org/10.1016/j.csbj.2021.12.038

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chung DR, Song J-H, Kim SH, Thamlikitkul V, Huang S-G, Wang H, So TM-k, Yasin RM, Hsueh P-R, Carlos CC (2011) High prevalence of multidrug-resistant nonfermenters in hospital-acquired pneumonia in Asia. Am J Respir Crit Care Med 184:1409–1417. https://doi.org/10.1164/rccm.201102-0349oc

Article  PubMed  Google Scholar 

CLCI (2021) Performance standards for Antmicrobial Susceptability Testing. CLSI M100-ED29 40:30thEdition–2020

Google Scholar 

De Nies L, Lopes S, Busi SB, Galata V, Heintz-Buschart A, Laczny CC, May P, Wilmes P (2021) PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. Microbiome 9:1–14. https://doi.org/10.1186/s40168-020-00993-9

Article  CAS  Google Scholar 

Diep DTH, Tuan HM, Ngoc KM, Vinh C, Dung TTN, Phat VV, Pham DT (2023) The clinical features and genomic epidemiology of carbapenem-resistant Acinetobacter baumannii infections at a tertiary hospital in Vietnam. J Global Antimicrob Resist 33:267–275

Article  CAS  Google Scholar 

Eigenbrod T, Reuter S, Gross A, Kocer K, Günther F, Zimmermann S, Heeg K, Mutters NT, Nurjadi D (2019) Molecular characterization of carbapenem-resistant Acinetobacter baumannii using WGS revealed missed transmission events in Germany from 2012–15. J Antimicrob Chemother 74:3473–3480. https://doi.org/10.1093/jac/dkz360

Article  CAS  PubMed  Google Scholar 

Farris JS (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106:645–668. https://doi.org/10.2307/2992359

Article  Google Scholar 

Freire M, de Oliveira Garcia D, Garcia C, Bueno MC, Camargo C, Magri AK, Francisco G, Reghini R, Vieira M, Ibrahim K (2016) Bloodstream infection caused by extensively drug-resistant Acinetobacter baumannii in cancer patients: high mortality associated with delayed treatment rather than with the degree of neutropenia. Clin Microbiol Infect 22:352–358. https://doi.org/10.1016/j.cmi.2015.12.010

Article  CAS  PubMed  Google Scholar 

Greene C, Vadlamudi G, Newton D, Foxman B, Xi C (2016) The influence of biofilm formation and multidrug resistance on environmental survival of clinical and environmental isolates of Acinetobacter baumannii. Am J Infect Control 44:e65–e71. https://doi.org/10.1016/j.ajic.2015.12.012

Article  CAS  PubMed  PubMed Central  Google Scholar 

Harding CM, Pulido MR, Di Venanzio G, Kinsella RL, Webb AI, Scott NE, Pachón J, Feldman MF (2017) Pathogenic Acinetobacter species have a functional type I secretion system and contact-dependent inhibition systems. J Biol Chem 292:9075–9087. https://doi.org/10.1074/jbc.m117.781575

Article  CAS  PubMed  PubMed Central  Google Scholar 

Héritier C, Poirel L, Fournier P-E, Claverie J-M, Raoult D, Nordmann P (2005) Characterization of the naturally occurring oxacillinase of Acinetobacter baumannii. Antimicrobi Agents Chemother 49:4174–4179. https://doi.org/10.1128/aac.49.10.4174-4179.2005

Article  Google Scholar 

Higgins PG, Dammhayn C, Hackel M, Seifert H (2010) Global spread of carbapenem-resistant Acinetobacter baumannii. J Antimicrob Chemother 65:233–238. https://doi.org/10.1093/jac/dkp428

Article  CAS  PubMed  Google Scholar 

Holt K, Kenyon JJ, Hamidian M, Schultz MB, Pickard DJ, Dougan G, Hall R (2016) Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1. Microb Genom 2:e000052. https://doi.org/10.1099/mgen.0.000052

Article  PubMed  PubMed Central  Google Scholar 

Ibrahim S, Al-Saryi N, Al-Kadmy IM, Aziz SN (2021) Multidrug-resistant Acinetobacter baumannii as an emerging concern in hospitals. Mol Biol Rep 48:6987–6998. https://doi.org/10.1007/s11033-021-06690-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Keegan KP, Glass EM, Meyer F (2016) MG-RAST, a metagenomics service for analysis of microbial community structure and function. Methods Mol Biol 207–233. https://doi.org/10.1007/978-1-4939-3369-3_13

Kenyon JJ, Arbatsky NP, Shneider MM, Popova AV, Dmitrenok AS, Kasimova AA, Shashkov AS, Hall RM, Knirel YA (2019) The K46 and K5 capsular polysaccharides produced by Acinetobacter baumannii NIPH 329 and SDF have related structures and the side-chain non-ulosonic acids are 4-O-acetylated by phage-encoded O-acetyltransferases. PLoS ONE 14:e0218461. https://doi.org/10.1371/journal.pone.0218461

Article  CAS  PubMed  PubMed Central  Google Scholar 

Khurshid M, Rasool MH, Ashfaq UA, Aslam B, Waseem M, Xu Q, Zhang X, Guo Q, Wang M (2020) Dissemination of blaOXA-23-harbouring carbapenem-resistant Acinetobacter baumannii clones in Pakistan. J Glob Antimicrob Resist 21:357–362. https://doi.org/10.1016/j.jgar.2020.01.001

Article  PubMed  Google Scholar 

Kim DH, Choi J-Y, Kim HW, Kim SH, Chung DR, Peck KR, Thamlikitkul V, So TM-K, Yasin RM, Hsueh P-R (2013) Spread of carbapenem-resistant Acinetobacter baumannii global clone 2 in Asia and AbaR-type resistance islands. Antimicrob Agents Chemother 57:5239–5246.

Comments (0)

No login
gif