Nguyen Si-Tuan1, Hua My Ngoc2, Le Duy Nhat3, Cuong Nguyen4, Huy Quang Pham5, Nguyen Thuy Huong6. 1. Department of Biotechnology, Faculty of Chemical Engineering, Ho Chi Minh City University of Technology, HCM National University, Vietnam; Department of Medical Microbiology, Thongnhat General Hospital of Dongnai Province, Vietnam. Electronic address: nsituan@gmail.com. 2. Department of Medical Biochemistry, Thongnhat General Hospital of Dongnai Province, Vietnam. 3. Department of Medical Microbiology, Thongnhat General Hospital of Dongnai Province, Vietnam. 4. Vinmec HiTech Center, Hanoi, Vietnam. 5. School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea. 6. Department of Biotechnology, Faculty of Chemical Engineering, Ho Chi Minh City University of Technology, HCM National University, Vietnam.
Abstract
OBJECTIVES: Acinetobacter baumannii is a major cause of ventilator-associated-pneumonia (VAP) worldwide due to its impressive propensity to rapidly acquire resistance elements to a wide range of antibacterial agents. We sought to explore the genomic features of this pathogen from a sputum specimen of a VAP male patient. METHODS: Whole genome analysis of A. baumannii DMS06670 included de novo assembly; functional annotation, whole-genome-phylogenetic analysis, antibiotics genes identification, prophage regions, virulent factor and pan-genome analysis. RESULTS: Assembly of whole-genome shotgun sequences of strain DMS06670 yielded an estimated genome size of 3.8 Mb with Sequence Type 447. Functional annotation and orthologous protein cluster analysis identified several potential antibiotic resistance genes was conducted (with 1 novel gene), prophage regions, virulent factors. The clusters of orthologous groups (COGs) analysis in protein sequence of the A. baumannii strain was compared with the other five genomes showed that the orthologous protein clusters responsible for multi-drug exist inside highly antimicrobial resistant strains. Whole-genome phylogenetic and in silico MLST analysis revealed that this A. baumannii strain is in the same clade as strains LAC-4 and BJAB0715. Comparative analysis of 23 available genomes of A. baumannii revealed a pan-genome consisting of 15,883 genes. CONCLUSION: Our findings provide insight into the virulence-associated genes and then compared with the genomes of other A. baumannii strains by calculation of ANI values and pan-genome analysis. Functional studies of these pathogens are required to validate these findings.
OBJECTIVES:Acinetobacter baumannii is a major cause of ventilator-associated-pneumonia (VAP) worldwide due to its impressive propensity to rapidly acquire resistance elements to a wide range of antibacterial agents. We sought to explore the genomic features of this pathogen from a sputum specimen of a VAP male patient. METHODS: Whole genome analysis of A. baumannii DMS06670 included de novo assembly; functional annotation, whole-genome-phylogenetic analysis, antibiotics genes identification, prophage regions, virulent factor and pan-genome analysis. RESULTS: Assembly of whole-genome shotgun sequences of strain DMS06670 yielded an estimated genome size of 3.8 Mb with Sequence Type 447. Functional annotation and orthologous protein cluster analysis identified several potential antibiotic resistance genes was conducted (with 1 novel gene), prophage regions, virulent factors. The clusters of orthologous groups (COGs) analysis in protein sequence of the A. baumannii strain was compared with the other five genomes showed that the orthologous protein clusters responsible for multi-drug exist inside highly antimicrobial resistant strains. Whole-genome phylogenetic and in silico MLST analysis revealed that this A. baumannii strain is in the same clade as strains LAC-4 and BJAB0715. Comparative analysis of 23 available genomes of A. baumannii revealed a pan-genome consisting of 15,883 genes. CONCLUSION: Our findings provide insight into the virulence-associated genes and then compared with the genomes of other A. baumannii strains by calculation of ANI values and pan-genome analysis. Functional studies of these pathogens are required to validate these findings.
Authors: Gamal Wareth; Jörg Linde; Ngoc H Nguyen; Tuan N M Nguyen; Lisa D Sprague; Mathias W Pletz; Heinrich Neubauer Journal: Antibiotics (Basel) Date: 2021-05-11