Whole-genome Study of Carbapenem-resistant Acinetobacter baumannii Virulence and Resistance

Author:

Shayea Rasha Hatem,Ali Munim Radwan, ,

Publisher

Farname, Inc.

Subject

Infectious Diseases,Microbiology (medical),Microbiology

Reference61 articles.

1. 1. Santajit, S.; Indrawattana, N. 2016. Mechanisms of antimicrobial resistance in ESKAPE pathogens. Biomed Res Int. ; 2016:2475067. doi: 10.1155/2016/2475067. 2. Kurihara, M.N.L.; Sales, R.O.; Silva, K.E.D.; Maciel, W.G.; Simionatto, S.2020. Multidrug-resistant Acinetobacter baumannii outbreaks: A global problem in healthcare settings. Rev. Soc. Bras. Med. Trop. ; 53:e20200248. doi: 10.1590/0037-8682-0248-2020. 3. Ayobami, O.; Willrich, N.; Harder, T.; Okeke, I.N.; Eckmanns, T.; Markwart, R .2019. The incidence and prevalence of hospital-acquired (carbapenem-resistant) Acinetobacter baumannii in Europe, eastern Mediterranean and Africa: a systematic review and meta-analysis. Emerg Microbes Infect;8(1):1747–1759. doi: 10.1080/22221751.2019.1698273. 4. Wareth, G.; Linde, J.; Hammer, P.; Nguyen, N.H.; Nguyen, T.N.M.; Splettstoesser, W.D. et al.2020 Phenotypic and WGS-derived antimicrobial resistance profiles of clinical and non-clinical Acinetobacter baumannii isolates from Germany and Vietnam. Int J Antimicrob Agents.;56(4):106127. 10.1016/j.ijantimicag.2020.106127. 5. Brovedan, M.A.; Cameranesi, M.M.; Limansky, A.S.; Morán-Barrio, J. ;Marchiaro ,P.; Repizo, G.D. 2020. What do we know about plasmids carried by members of the Acinetobacter genus? World J Microbiol Biotechnol. ;36(8):109. doi: 10.1007/s11274-020-02890-7. 6.Pagano, M.; Martins, A.F.; Barth, A. 2016. Mobile genetic elements related to carbapenem resistance in Acinetobacter baumannii. Brazilian J Microbiol. ;47(4):785–792. doi: 10.1016/j.bjm.2016.06.005. 7. Brandt, C; Braun, S.D.,;Stein, C.; Slickers, P.; Ehricht, R.; Pletz ,M.W.; Makarewicz, O.2017. In silico serine β-lactamases analysis reveals a huge potential resistome in environmental and pathogenic species. Sci Rep. ;7(1):43232. doi: 10.1038/srep43232. 8.Quainoo, S.; Coolen, J.P.; van Hijum, S.A.; Huynen, M.A.; Melchers, W.J.; van Schaik, W.; Wertheim, H.F.2017. Whole-genome se-quencing of bacterial pathogens: The future of nosocomial outbreak analysis. Clin. Microbiol. Rev. ;30: 1015–1063. 9.Durand, G.; Javerliat, F.; Bes, M.; Veyrieras, J.B.; Guigon, G.; Mugnier, N., Schicklin, S.; Kaneko, G.; Santiago-Allexant, E. 2018.Bouchiat Routine whole-genome sequencing for outbreak investigations of Staphylococcus aureus in a national reference center. Front. Microbiol.; 9: 511. 10.Lin ,M.F.; Lan, C.Y .2014. Antimicrobial resistance in Acinetobacter baumannii: from bench to bedside. World J Clin Cases. ;2(12):787–814. doi: 10.12998/wjcc.v2.i12.787. 11.Atlas RM, Brown AE and Parks LC .1997. Laboratory Manual of Experimental Microbiology. 1sted. Mosby, st. Louis U.S.A. 12.Clinical and Laboratory Standards Institute.2020. Performance standards for antimicrobial susceptibility testing, 30th ed CLSI supplement M100 CLSI., Wayne, PA. 13.Abed ES and Ali MR . 2020. Molecular Analysis of Efflux Pumps and Quorum Sensing Genes in MDR Acinetobacter baumannii. Biochemical and Cellular Archives, 20(1): 2259–2266. 14.Ridha DJ , Ali MR and Jassim KA.2019. Occurrence of Metallo-β-lactamase Genes among Acinetobacter baumannii Isolated from Different Clinical Samples. J Pure Appl Microbiol., 13(2): 1111-1119. 15. Turton JF, Gabriel SN ,Valderrey C , Kaufmann ME and Pitt TL . 2007. Use of sequence-based typing and multiplex PCR to identify clonal lineages of outbreak strains of Acinetobacter baumannii. Clin Microbiol Infect., 13(8):807–15. 16.Coudron PE , Moland ES and Thomson KS .2000. Occurrence and detection of AmpC beta-lactamases among Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis isolates at a veterans medical center. J Clin Microbiol., 38:1791–6. 17. García-Soto, S.; Abdel-Glil, M.Y.;Tomaso, H.; Linde ,J.; Methner, U.2020. Emergence of multidrug-resistant Salmonella enterica Subspecies enterica serovar infantis of multilocus sequence type 2283 in German broiler farms. Front. Microbiol. ;11:1741. doi: 10.3389/fmicb.2020.01741. 18.Andrews, S.2020. FastQC: A Quality Control Tool for High Throughput Sequence Data. v. 0.11.5. (accessed on 1 August 2020); Available online: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 19. Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski; A.D., et al.2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. J. Comput. Mol. Cell Biol. ;19:455–477. doi: 10.1089/cmb.2012.0021. 20.Gurevich, A.; Saveliev, V.; Vyahhi, N.; Tesler, G. 2013.QUAST: Quality assessment tool for genome assemblies. Bioinformatics. ;29:1072–1075. doi: 10.1093/bioinformatics/btt086. 21. Wood ,D.E.; Lu, J.; Langmead ,B. 2019.Improved metagenomic analysis with Kraken 2. Genome. Biol. ;20:257. doi: 10.1186/s13059-019-1891-0. 22.Feldgarden, M.; Brover, V.; Haft, D.H.; Prasad, A.B.; Slotta, D.J.; Tolstoy, I.; Tyson, G.H.; Zhao , S.; Hsu, C.H.; McDermott, P.F.; et al.2019. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob. Agents Chemother. ;63 . doi: 10.1128/AAC.00483-19. 23. Zankari ,E.; Hasman, H.;Cosentino, S.; Vestergaard ,M.; Rasmussen, S.; Lund, O.; Aarestrup, F.M.; Larsen, M.V.2012. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. ;67:2640–2644. doi: 10.1093/jac/dks261. 24. Jia, B.; Raphenya, A.R.; Alcock, B.; Waglechner, N.; Guo ,P.; Tsang K.K.; Lago, B.A.; Dave, B.M.; Pereira, S.; Sharma, A.N., et al.2017. CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. ;45:D566–D573. doi: 10.1093/nar/gkw1004. 25.Liu, B.; Zheng, D.; Jin, Q. Chen, L.; Yang, J.2019. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res;47:D687– 92 26.Lowe ,T.M.and Eddy, S.R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955–964. 27.Lagesen, K.; Hallin, P.and Rodland ,E.A. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35: 3100–3108. 28.Gao, F.and Zhang, C.T. 2006. GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res 34: W686–691. 29.Arndt ,D.; Grant ,J.R.; Marcu, A.; Sajed, T.; Pon ,A.; Liang ,Y. et al.2016 PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. ;44(W1):W16. 30.Couvin , D.; Bernheim, A.; Tofano-Nioche, C.; Touchon, M.; Michalik, J.; Néron, B. et al.2018. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res.;46(W1):W246–51. 31.Carattoli, A.; Zankari, E.; García-Fernández, A.; Voldby- Larsen ,M.; Lund, O.; Villa, L.; Møller- Aarestrup, F.; Hasman, H.2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequencetyping. Antimicrob. Agents Chemother. ;58:3895–3903. doi: 10.1128/AAC.02412-14. 32.Schwengers ,O.; Barth, P.; Falgenhauer, L.; Hain, T.; Chakrabort,y T.; Goesmann, A. 2020.Platon: Identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microb. Genom. 2020:6. doi: 10.1099/mgen.0.000398. 33.Schramm , A.T.J; Place,K. ; Montaña,S. ; Almuzara, M. ; Fung,S. ; Fernandez , J.S.;Tuttobene,M.R.; Golic,A. ; Altilio,M. ; Traglia,G.M. ; Vay,C. ; Mussi,M.A. ; Iriarte,A. and Ramirez,M.S. 2019. Genetic and Phenotypic Features of a Novel Acinetobacter Species, Strain A47, Isolated From the Clinical Setting. Frontiers in Microbiology; 10:1375. doi: 10.3389/fmicb.2019.01375. 34.Hamidian ,M.; Nigro, S.J. 2019.Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii. Microb. Genom. 2019:5. doi: 10.1099/mgen.0.000306. 35.Thirapanmethee ,K.; Srisiri ,A.N.T.; Houngsaitong, J.;Montakantikul ,P.; Khuntayaporn ,P.; Chomnawang, M.T.2020. Prevalence of OXA-Type β-Lactamase genes among carbapenem-resistant Acinetobacter baumannii clinical isolates in Thailand. Antibiotics.; 9:864. doi: 10.3390/antibiotics9120864 36.Tada ,T.; Uchida, H.; Hishinuma ,T.; Watanabe, S.; Tohya , M.; Kuwahara-Arai , K.; Mya, S.; Zan ,K.N.; Kirikae ,T.; Tin; H.H.2020. Molecular epidemiology of multidrug-resistant Acinetobacter baumannii isolates from hospitals in Myanmar. J. Glob. Antimicrob. Resist.;22:122–125. doi: 10.1016/j.jgar.2020.02.011. 37.Gaiarsa ,S.; Batisti Biffignandi, G.; Esposito, E.P.; Castelli ,M.; Jolley, K.A.; Brisse, S.; Sassera, D.; Zarrilli, R.2019. Comparative analysis of the two Acinetobacter baumannii multilocus sequence typing (MLST) schemes. Front. Microbiol. 2019;10:930. doi: 10.3389/fmicb.2019.00930 38.Kunin, V. A.; Copeland, A. ;Lapidus, K. ;Mavromatis, and Hugenholtz,P. 2008. A Bioinformatician's Guide to Metagenomics. Microbiology and Molecular Biology Reviews; 72:557-578. 39.Jennings, L.J. M.E.; Arcila, C.; Corless, S.; Kamel-Reid, I.M.; Lubin, J. ; Pfeifer, R.L. ;Temple Smolkin, K.V.; Voelkerding, and Nikiforova,M.N. 2017. Guidelines for validation of next-generation sequencing–based oncology panels: a joint consensus recommendation of the Association for Molecular Pathology and College of American Pathologists. The Journal of molecular diagnostics. 19:341-365. 40.Ma, X. Y.; Shao, L.; Tian, D.A. ;Flasch, H.L.; Mulder, M.N.; Edmonson, Y.; Liu, X. ; Chen, S. ; Newman, and Nakitandwe,J. 2019. Analysis of error profiles in deep nextgeneration sequencing data. Genome biology. 20:1-15. 41.Sims, D. I. ; Sudbery, N.E.; Ilott, A. ; Heger, and Ponting,C.P. 2014. Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews Genetics. 15:121- 132 42.Kauser,A.(2020). Resistome Identification from Whole Genome Sequencing Data of Norwegian Isolates. Master’s Thesis .Inland Norway University of Applied Science. Norway. 43.Agaras ,B.C.; Iriarte ,A.; Valverde, C.F.2018. Genomic insights into the broad antifungal activity, plant-probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6. PLoS One 2018;13:e0194088. 44.Ten,K.E ; Zoqratt,M.Z.H.M.D; Ayub,Q. and Tan,H.S.(2021). Characterization of multidrug-resistant Acinetobacter baumannii strain ATCC BAA1605 using whole-genome sequencing. BMC Research Notes; 14:83. https://doi.org/10.1186/s13104-021-05493-z 45.Roca, I.; Espinal, P.; Vila-Farrés, X. and Vila, J.2012. The Acinetobacter baumannii Oxymoron: Commensal Hospital Dweller Turned Pan Drug-Resistant Menace. Front. Microbiol. 3: 148 . 46.Wright, M. S.; Iovleva, A.; Jacobs, M. R.; Bonomo, R. A. and Adams, M. D. (2016).Genome dynamics of multidrug-resistant Acinetobacter baumannii during infection and treatment. Genome Med. 8 :26 . 47.Rao, M.; Rashid, F.A.; Shukor, S.; Hashim, R.; Ahmad, N .2020. Detection of antimicrobial resistance genes associated with carbapenem resistance from the whole-genome sequence of Acinetobacter baumannii isolates from Malaysia. Can. J. Infect. Dis. Med. Microbiol. ; 2020:5021064. doi: 10.1155/2020/5021064. 48.Khurshid, M.; Rasool, M.H.; Ashfaq, U.A.; Aslam ,B.; Waseem, M.; Xu, Q.; Zhang, X; Guo, Q.; Wang, M .2020. Dissemination of bla(OXA-23)-harbouring carbapenem-resistant Acinetobacter baumannii clones in Pakistan. J. Glob. Antimicrob. Resist. ;21:357–362. doi: 10.1016/j.jgar.2020.01.001. 49. Lee, S.Y.; Oh, M.H.; Yun, S.H.; Choi, C.W.; Park ,E.C.; Song, H.S.; Lee, H.; Yi, Y.S.; Shin, J.; Chung, C., et al.2018. Genomic characterization of extensively drug-resistant Acinetobacter baumannii strain, KAB03 belonging to ST451 from Korea. Infect. Genet. Evol. ;65:150–158. 50.Mortazavi, S.M.; Farshadzadeh, Z.; Janabadi, S.; Musavi, M.; Shahi, F.; Moradi, M.; Khoshnood, S.2020. Evaluating the frequency of carbapenem and aminoglycoside resistance genes among clinical isolates of Acinetobacter baumannii from Ahvaz, south-west Iran. New Microbes New Infect.;38:100779. doi: 10.1016/j.nmni.2020.100779. 51.Ostrer, L.; Khodursky, R. F.; Johnson, J. R.; Hiasa, H. and Khodursky, A. (2019). Analysis of mutational patterns in quinolone resistance-determining regions of GyrA and ParC of clinical isolates. Int. J. Antimicrob. Agents 53, 318–324. doi: 10.1016/j.ijantimicag.2018.12.004 52.Leus, I.V.; Weeks , J.W.; Bonifay, V.; Smith, L.; Richardson, S.; Zgurskaya, H.I. 2018.Substrate specificities and efflux efficiencies of RND efflux pumps of Acinetobacter baumannii. J. Bacteriol. 2018:200. doi: 10.1128/jb.00049-18. 53.Coyne, S.; Courvalin, P.; Perichon ,B.2011. Efflux-mediated antibiotic resistance in Acinetobacter spp. Antimicrob. Agents Chemother. ;55:947–953. doi: 10.1128/AAC.01388-10. 54. Sharma ,A.; Sharma, R.; Bhattacharyya, T.; Bhando, T.; Pathania, R.2017. Fosfomycin resistance in Acinetobacter baumannii is mediated by efflux through a major facilitator superfamily (MFS) transporter-AbaF. J. Antimicrob. Chemother. ;72:68–74. doi: 10.1093/jac/dkw382. 55.Yakkala, H.; Samantarrai, D.; Gribskov, M.; Siddavattam, D. 2019.Comparative genome analysis reveals niche-specifc genome expansion in Acinetobacter baumannii strains . (Research Article) (Report). PLoS ONE.;14(6):e0218204. 56.Choi ,C.H.; Hyun, S.H.; Lee ,J.Y. 2008. Acinetobacter baumannii outer membrane protein A targets the nucleus and induces cytotoxicity. Cell Microbiol 10: 309–319. 57.Tipton, K.A.; Dimitrova, D.; Rather, P.N. 2015.Phase-variable control of multiple phenotypes in Acinetobacter baumannii strain AB5075. J Bacteriol;197:2593–9. 58.Andersen, S.B.; Ghoul, M.; Griffin, A.S.; Petersen, B.; Johansen, H.K.; Molin, S. 2017. Diversity, prevalence, and longitudinal occurrence of type II toxin-antitoxin systems of Pseudomonas aeruginosa infecting cystic fibrosis lungs. Front Microbiol 8:1180. doi:10.3389/fmicb.2017.01180 59.Bobay, L.M.; Rocha, E.P.; Touchon ,M. 2013.The adaptation of temperate bacteriophages to their host genomes. Mol Biol Evol;30:737–51. 60.Touchon, M.; Bernheim, A.; Rocha, E.P.2016. Genetic and life-history traits associated with the distribution of prophages in bacteria. ISME J;10:2744–54.

2. Mechanisms of Antimicrobial Resistance in ESKAPE Pathogens

3. Multidrug-resistant Acinetobacter baumannii outbreaks: a global problem in healthcare settings

4. The incidence and prevalence of hospital-acquired (carbapenem-resistant) Acinetobacter baumannii in Europe, Eastern Mediterranean and Africa: a systematic review and meta-analysis

5. Phenotypic and WGS-derived antimicrobial resistance profiles of clinical and non-clinical Acinetobacter baumannii isolates from Germany and Vietnam

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3