title: Identification of antibiotic resistance genes in the multidrug-resistant Acinetobacter baumannii strain, MDR-SHH02, using whole-genome sequencing.
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.
authors.affiliation: Department of Molecular Biology Laboratory, Shanghai Centre for Clinical Laboratory, Shanghai 200126, P.R. China.
authors.forename: Hualiang
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Microbiology Laboratory, Shanghai Centre for Clinical Laboratory, Shanghai 200126, P.R. China.
authors.forename: Jinghua
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P.R. China.
authors.forename: Peijuan
authors.initials: P
authors.lastname: Yu
authors.affiliation: Department of Microbiology Laboratory, Shanghai Centre for Clinical Laboratory, Shanghai 200126, P.R. China.
authors.forename: Ping
authors.initials: P
authors.lastname: Ge
authors.affiliation: Department of Clinical Laboratory, The Sixth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200233, P.R. China.
authors.forename: Yanqun
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Department of Microbiology Laboratory, Shanghai Centre for Clinical Laboratory, Shanghai 200126, P.R. China.
authors.forename: Rong
authors.initials: R
authors.lastname: Xu
authors.affiliation: Department of Microbiology Laboratory, Shanghai Centre for Clinical Laboratory, Shanghai 200126, P.R. China.
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.affiliation: Department of Microbiology Laboratory, Shanghai Centre for Clinical Laboratory, Shanghai 200126, P.R. China.
authors.forename: Xuejie
authors.initials: X
authors.lastname: Liu
mesh_terms: D040981:Acinetobacter baumannii / Q000187:drug effects* / Q000235:genetics*; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D024901:Drug Resistance, Multiple, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058977:Molecular Sequence Annotation; D010802:Phylogeny
chemical_list: D000900:Anti-Bacterial Agents