New eight genes identified at the clinical multidrug-resistant Acinetobacter baumannii DMS06669 strain in a Vietnam hospital

Abstract

Background Acinetobacter baumannii is an important nosocomial pathogen that can develop multidrug resistance. In this study, we characterized the genome of the A. baumannii strain DMS06669 (isolated from the sputum of a male patient with hospital-acquired pneumonia) and focused on identification of genes relevant to antibiotic resistance.MethodsWhole genome analysis of A. baumannii DMS06669 from hospital-acquired pneumonia patients included de novo assembly; gene prediction; functional annotation to public databases; phylogenetics tree construction and antibiotics genes identification.ResultsAfter sequencing the A. baumannii DMS06669 genome and performing quality control, de novo genome assembly was carried out, producing 24 scaffolds. Public databases were used for gene prediction and functional annotation to construct a phylogenetic tree of the DMS06669 strain with 21 other A. baumannii strains. A total of 18 possible antibiotic resistance genes, conferring resistance to eight distinct classes of antibiotics, were identified. Eight of these genes have not previously been reported to occur in A. baumannii.ConclusionsOur results provide important information regarding mechanisms that may contribute to antibiotic resistance in the DMS06669 strain, and have implications for treatment of patients infected with A. baumannii. Electronic supplementary materialThe online version of this article (10.1186/s12941-017-0250-9) contains supplementary material, which is available to authorized users.

WGS-Based Analysis of Carbapenem-Resistant Acinetobacter baumannii in Vietnam and Molecular Characterization of Antimicrobial Determinants and MLST in Southeast Asia

“…All MDR strains ( n = 10) were carbapenem-resistant with MIC values of >8 µg/mL to imipenem (IMP) and >0.5 µg/mL to ertapenem (ERT). The MIC values to meropenem (MER) ranged from 32 to 128 µg/mL, higher than the MIC value (16 µg/mL) reported for the A. baumannii DMS06669 strain isolated in a Vietnam hospital [ 31 ]. From 2012 to 2014, resistance to cephalosporins, fluoroquinolones and carbapenems was >90% among 904 A. baumannii isolates from patients with hospital-acquired or ventilator-associated pneumonia in Vietnam [ 13 ], while colistin (MIC90, ≤0.25 mg/L) and tigecycline (MIC90, 4 mg/L) showed appreciable activity against A. baumannii.…”

Carbapenemase Genes and Multidrug Resistance of Acinetobacter Baumannii: A Cross Sectional Study of Patients with Pneumonia in Southern Vietnam

“…In Vietnam, multidrug-resistant Acinetobacter baumannii (MR- Ab ) has also had serious consequences, and the relationship between carbapenemase genes and antibiotics resistance are of great interest. There are many previous studies investigating this problem [23,26,27]. Our study aims to support those statements about the role of different genes and further analyze certain other factors, such as age and clinical wards.…”

“…Bacterial DNA was extracted using the AccuRive Bacteria DNA Prep Kit, following the manufacturer’s recommendations (Khoa Thuong Biotech, Ho Chi Minh, Vietnam). The presence of bla OXA-like genes was detected using multiplex Taq-man real-time PCR; and the presence of bla NDM-1 was determined using PCR because there was no available protocol for detecting new bla NDM-1 genes using real-time PCR [26]. A DTLite 4 amplifier (DNK-Tekhnologiva, Moscow, Russia) was applied to carry out the test.…”

Epidemiological and genomic characteristics of Acinetobacter baumannii from different infection sites using comparative genomics

“…For functional classi cation of the predicted genes, BLASTP was used to align amino acids of predicted genes against the Clusters of Orthologous Groups (COG) database with an expected threshold of 1e -3 using the Conserved Domains Database (CDD) [32]. We also performed sequence alignment of the amino acid sequences to the NCBI non-redundant (NR) database (E-value ≤1e -3 ).…”