Identification of antibiotic resistance genes in the multidrug-resistant Acinetobacter baumannii strain, MDR-SHH02, using whole-genome sequencing

Wang,Hualiang; Wang,Jinghua; Yu,Peijuan; Ge,Ping; Jiang,Yanqun; Xu,Rong; Chen,Rong; Liu,Xuejie

doi:10.3892/ijmm.2016.2844

Identification of antibiotic resistance genes in the multidrug-resistant Acinetobacter baumannii strain, MDR-SHH02, using whole-genome sequencing

Authors:
- Hualiang Wang
- Jinghua Wang
- Peijuan Yu
- Ping Ge
- Yanqun Jiang
- Rong Xu
- Rong Chen
- Xuejie Liu
View Affiliations

Affiliations: Department of Molecular Biology Laboratory, Shanghai Centre for Clinical Laboratory, Shanghai 200126, P.R. China, Department of Microbiology Laboratory, Shanghai Centre for Clinical Laboratory, Shanghai 200126, P.R. China, Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China, Department of Clinical Laboratory, The Sixth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200233, P.R. China
Published online on: December 30, 2016 https://doi.org/10.3892/ijmm.2016.2844
Pages: 364-372
Copyright: © Wang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

This study aimed to investigate antibiotic resistance genes in the multidrug-resistant (MDR) Acinetobacter baumannii (A. baumanii) strain, MDR-SHH02, using whole‑genome sequencing (WGS). The antibiotic resistance of MDR-SHH02 isolated from a patient with breast cancer to 19 types of antibiotics was determined using the Kirby‑Bauer method. WGS of MDR-SHH02 was then performed. Following quality control and transcriptome assembly, functional annotation of genes was conducted, and the phylogenetic tree of MDR-SHH02, along with another 5 A. baumanii species and 2 Acinetobacter species, was constructed using PHYLIP 3.695 and FigTree v1.4.2. Furthermore, pathogenicity islands (PAIs) were predicted by the pathogenicity island database. Potential antibiotic resistance genes in MDR-SHH02 were predicted based on the information in the Antibiotic Resistance Genes Database (ARDB). MDR-SHH02 was found to be resistant to all of the tested antibiotics. The total draft genome length of MDR-SHH02 was 4,003,808 bp. There were 74.25% of coding sequences to be annotated into 21 of the Clusters of Orthologous Groups (COGs) of protein terms, such as ‘transcription’ and ‘amino acid transport and metabolism’. Furthermore, there were 45 PAIs homologous to the sequence MDRSHH02000806. Additionally, a total of 12 gene sequences in MDR-SHH02 were highly similar to the sequences of antibiotic resistance genes in ARDB, including genes encoding aminoglycoside‑modifying enzymes [e.g., aac(3)-Ia, ant(2'')‑Ia, aph33ib and aph(3')-Ia], β-lactamase genes (bl2b_tem and bl2b_tem1), sulfonamide-resistant dihydropteroate synthase genes (sul1 and sul2), catb3 and tetb. These results suggest that numerous genes mediate resistance to various antibiotics in MDR-SHH02, and provide a clinical guidance for the personalized therapy of A. baumannii-infected patients.

View Figures

View References

1	Lockhart SR, Abramson MA, Beekmann SE, Gallagher G, Riedel S, Diekema DJ, Quinn JP and Doern GV: Antimicrobial resistance among Gram-negative bacilli causing infections in intensive care unit patients in the United States between 1993 and 2004. J Clin Microbiol. 45:3352–3359. 2007. View Article : Google Scholar : PubMed/NCBI
2	Visca P, Seifert H and Towner KJ: Acinetobacter infection - an emerging threat to human health. IUBMB Life. 63:1048–1054. 2011. View Article : Google Scholar : PubMed/NCBI
3	Mortensen BL and Skaar EP: Host-microbe interactions that shape the pathogenesis of Acinetobacter baumannii infection. Cell Microbiol. 14:1336–1344. 2012. View Article : Google Scholar : PubMed/NCBI
4	Higgins PG, Pérez-Llarena FJ, Zander E, Fernández A, Bou G and Seifert H: OXA-235, a novel class D β-lactamase involved in resistance to carbapenems in Acinetobacter baumannii. Antimicrob Agents Chemother. 57:2121–2126. 2013. View Article : Google Scholar : PubMed/NCBI
5	Zander E, Nemec A, Seifert H and Higgins PG: Association between β-lactamase-encoding bla DiversiLab rep-PCR-based typing of Acinetobacter (OXA-51) variants and baumannii isolates. J Clin Microbiol. 50:1900–1904. 2012. View Article : Google Scholar : PubMed/NCBI
6	Krizova L, Poirel L, Nordmann P and Nemec A: TEM-1 β-lactamase as a source of resistance to sulbactam in clinical strains of Acinetobacter baumannii. J Antimicrob Chemother. 68:2786–2791. 2013. View Article : Google Scholar : PubMed/NCBI
7	Fournier PE, Vallenet D, Barbe V, Audic S, Ogata H, Poirel L, Richet H, Robert C, Mangenot S, Abergel C, et al: Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet. 2:e72006. View Article : Google Scholar : PubMed/NCBI
8	Ramírez MS, Vilacoba E, Stietz MS, Merkier AK, Jeric P, Limansky AS, Márquez C, Bello H, Catalano M and Centrón D: Spreading of AbaR-type genomic islands in multidrug resistance Acinetobacter baumannii strains belonging to different clonal complexes. Curr Microbiol. 67:9–14. 2013. View Article : Google Scholar : PubMed/NCBI
9	Šeputienė V, Povilonis J and Sužiedėlienė E: Novel variants of AbaR resistance islands with a common backbone in Acinetobacter baumannii isolates of European clone II. Antimicrob Agents Chemother. 56:1969–1973. 2012. View Article : Google Scholar : PubMed/NCBI
10	Taitt CR, Leski T, Stockelman MG, Craft DW, Zurawski DV, Kirkup BC and Vora GJ: Antimicrobial resistance determinants in Acinetobacter baumannii isolates taken from military treatment facilities. Antimicrob Agents Chemother. 58:767–781. 2014. View Article : Google Scholar :
11	Zhou H, Zhang T, Yu D, Pi B, Yang Q, Zhou J, Hu S and Yu Y: Genomic analysis of the multidrug-resistant Acinetobacter baumannii strain MDR-ZJ06 widely spread in China. Antimicrob Agents Chemother. 55:4506–4512. 2011. View Article : Google Scholar : PubMed/NCBI
12	Hornsey M, Loman N, Wareham DW, Ellington MJ, Pallen MJ, Turton JF, Underwood A, Gaulton T, Thomas CP, Doumith M, et al: Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy. J Antimicrob Chemother. 66:1499–1503. 2011. View Article : Google Scholar : PubMed/NCBI
13	Li H, Liu F, Zhang Y, Wang X, Zhao C, Chen H, Zhang F, Zhu B, Hu Y and Wang H: Evolution of carbapenem-resistant Acinetobacter baumannii revealed through whole-genome sequencing and comparative genomic analysis. Antimicrob Agents Chemother. 59:1168–1176. 2015. View Article : Google Scholar :
14	Atlas RM, Brown AE and Parks LC: Laboratory Manual of Experimental Microbiology. Mosby; St. Louis, MO: pp. 119–127. 1995
15	Watts JL: Performance Standards For Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals: Approved Standard. Clinical and Laboratory Standards Institute; 2008
16	Bauer AW, Kirby WM, Sherris JC and Turck M: Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol. 45:493–496. 1966.PubMed/NCBI
17	Delcher AL, Bratke KA, Powers EC and Salzberg SL: Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 23:673–679. 2007. View Article : Google Scholar : PubMed/NCBI
18	Schattner P, Brooks AN and Lowe TM: The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33(Web Server): W686–W689. 2005. View Article : Google Scholar : PubMed/NCBI
19	Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T and Ussery DW: RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100–3108. 2007. View Article : Google Scholar : PubMed/NCBI
20	Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al: The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 4:412003. View Article : Google Scholar : PubMed/NCBI
21	Mount DW: Using the basic local alignment search tool (BLAST). CSH Protoc. 2007:pdb. top172007.PubMed/NCBI
22	Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG and Thompson JD: Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497–3500. 2003. View Article : Google Scholar : PubMed/NCBI
23	Yoon SH, Park Y-K, Lee S, Choi D, Oh TK, Hur C-G and Kim JF: Towards pathogenomics: a web-based resource for pathogenicity islands. Nucleic Acids Res. 35(Database): D395–D400. 2007. View Article : Google Scholar
24	Liu B and Pop M: ARDB - Antibiotic Resistance Genes Database. Nucleic Acids Res. 37(Database): D443–D447. 2009. View Article : Google Scholar
25	Pósfai G, Koob MD, Kirkpatrick HA and Blattner FR: Versatile insertion plasmids for targeted genome manipulations in bacteria: isolation, deletion, and rescue of the pathogenicity island LEE of the Escherichia coli O157:H7 genome. J Bacteriol. 179:4426–4428. 1997. View Article : Google Scholar : PubMed/NCBI
26	Tauschek M, Strugnell RA and Robins-Browne RM: Characterization and evidence of mobilization of the LEE pathogenicity island of rabbit-specific strains of enteropathogenic Escherichia coli. Mol Microbiol. 44:1533–1550. 2002. View Article : Google Scholar : PubMed/NCBI
27	Harrison EM, Carter ME, Luck S, Ou H-Y, He X, Deng Z, O'Callaghan C, Kadioglu A and Rajakumar K: Pathogenicity islands PAPI-1 and PAPI-2 contribute individually and synergistically to the virulence of Pseudomonas aeruginosa strain A14. Infect Immun. 78:1437–1446. 2010. View Article : Google Scholar : PubMed/NCBI
28	Towner KJ: Acinetobacter: an old friend, but a new enemy. J Hosp Infect. 73:355–363. 2009. View Article : Google Scholar : PubMed/NCBI
29	Ramirez MS and Tolmasky ME: Aminoglycoside modifying enzymes. Drug Resist Updat. 13:151–171. 2010. View Article : Google Scholar : PubMed/NCBI
30	Nemec A, Dolzani L, Brisse S, van den Broek P and Dijkshoorn L: Diversity of aminoglycoside-resistance genes and their association with class 1 integrons among strains of pan-European Acinetobacter baumannii clones. J Med Microbiol. 53:1233–1240. 2004. View Article : Google Scholar : PubMed/NCBI
31	Cho YJ, Moon DC, Jin JS, Choi CH, Lee YC and Lee JC: Genetic basis of resistance to aminoglycosides in Acinetobacter spp. and spread of armA in Acinetobacter baumannii sequence group 1 in Korean hospitals. Diagn Microbiol Infect Dis. 64:185–190. 2009. View Article : Google Scholar : PubMed/NCBI
32	Ploy MC, Denis F, Courvalin P and Lambert T: Molecular characterization of integrons in Acinetobacter baumannii: description of a hybrid class 2 integron. Antimicrob Agents Chemother. 44:2684–2688. 2000. View Article : Google Scholar : PubMed/NCBI
33	Waterman PE, McGann P, Snesrud E, Clifford RJ, Kwak YI, Munoz-Urbizo IP, Tabora-Castellanos J, Milillo M, Preston L, Aviles R, et al: Bacterial peritonitis due to Acinetobacter baumannii sequence type 25 with plasmid-borne new delhi metallo-β-lactamase in Honduras. Antimicrob Agents Chemother. 57:4584–4586. 2013. View Article : Google Scholar : PubMed/NCBI
34	Akers KS, Chaney C, Barsoumian A, Beckius M, Zera W, Yu X, Guymon C, Keen EF III, Robinson BJ, Mende K, et al: Aminoglycoside resistance and susceptibility testing errors in Acinetobacter baumannii-calcoaceticus complex. J Clin Microbiol. 48:1132–1138. 2010. View Article : Google Scholar : PubMed/NCBI
35	Kostić T, Ellis M, Williams MR, Stedtfeld TM, Kaneene JB, Stedtfeld RD and Hashsham SA: Thirty-minute screening of antibiotic resistance genes in bacterial isolates with minimal sample preparation in static self-dispensing 64 and 384 assay cards. Appl Microbiol Biotechnol. 99:7711–7722. 2015. View Article : Google Scholar
36	Hatosy SM and Martiny AC: The ocean as a global reservoir of antibiotic resistance genes. Appl Environ Microbiol. 81:7593–7599. 2015. View Article : Google Scholar : PubMed/NCBI
37	Chang-Tai Z, Yang L, Zhong-Yi H, Chang-Song Z, Yin-Ze K, Yong-Ping L and Chun-Lei D: High frequency of integrons related to drug-resistance in clinical isolates of Acinetobacter baumannii. Indian J Med Microbiol. 29:118–123. 2011. View Article : Google Scholar : PubMed/NCBI
38	Martí S, Fernández-Cuenca F, Pascual A, Ribera A, Rodríguez-Baño J, Bou G, Miguel Cisneros J, Pachón J, Martínez-Martínez L and Vila J; Grupo de Estudio de Infección Hospitalaria (GEIH): Prevalence of the tetA and tetB genes as mechanisms of resistance to tetracycline and minocycline in Acinetobacter baumannii clinical isolates. Enferm Infecc Microbiol Clin. 24:77–80. 2006.In Spanish. View Article : Google Scholar
39	Post V and Hall RM: AbaR5, a large multiple-antibiotic resistance region found in Acinetobacter baumannii. Antimicrob Agents Chemother. 53:2667–2671. 2009. View Article : Google Scholar : PubMed/NCBI
40	Agersø Y and Petersen A: The tetracycline resistance determinant Tet 39 and the sulphonamide resistance gene sulII are common among resistant Acinetobacter spp. isolated from integrated fish farms in Thailand. J Antimicrob Chemother. 59:23–27. 2007. View Article : Google Scholar