Whole-genome sequencing and characterization of an antibiotic resistant Neisseria meningitidis B isolate from a military unit in Vietnam

• Published in: Annals of clinical microbiology and antimicrobials Vol. 18; no. 1; p. 16
• Main Authors: Tran, Thach Xuan, Le, Trang Thu, Trieu, Long Phi, Austin, Christopher M, Van Quyen, Dong, Nguyen, Huong Minh
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 06-05-2019; BioMed Central; BMC
• Subjects: Ampicillin; Antibiotic resistance; Antibiotics; Antigen sequence typing; Antigens; Assembly; Chloramphenicol; Chloromycetin; Control; Deoxyribonucleic acid; Diagnosis; DNA; DNA sequencing; Drug resistance; Epidemiological characterization; Epidemiology; Gene expression; Gene sequencing; Genes; Genetic aspects; Genomes; Health aspects; Health care; Immunization; Invasive meningococcal disease; Laboratories; Meningitis; Meningococcal disease; Methods; Microbial drug resistance; Microbiological techniques (Diagnosis); Military; Military personnel; Multilocus sequence typing; Neisseria meningitidis; Next generation sequencing; Nucleotide sequence; Prophages; Rifampin; Scaffolding; Vaccines; Vietnam; Vietnam; France; Vietnam; Neisseria meningitidis; Antigen sequence typing; Next generation sequencing; Epidemiological characterization; Antibiotic resistance
• ISSN: 1476-0711; 1476-0711
• DOI: 10.1186/s12941-019-0315-z

Invasive meningococcal disease (IMD) persists in military units in Vietnam despite the availability of antibiotics and vaccines. A hindrance to reducing the incidence of IMD in Vietnam is a lack of molecular data from isolates of the causative agent, Neisseria meningitidis from this country. Here, we characterized key genetic and epidemiological features of an invasive N. meningitidis isolate from a military unit in Vietnam using whole-genome sequencing.
Neisseria meningitidis was isolated from a conscript admitted for meningitis and tested against seven antibiotics. DNA from the isolate was extracted and sequenced using the Illumina HiSeq platform. Denovo assembly and scaffolding were performed to construct a draft genome assembly, from which genes were predicted and functionally annotated. Genome analysis included epidemiological characterization, genomic composition and identification of antibiotic resistance genes.
Susceptibility testing of the isolate showed high levels of resistance to chloramphenicol and diminished susceptibility to ampicillin and rifampicin. A draft genome of ~ 2.1 Mb was assembled, containing 2451 protein coding sequences, 49 tRNAs and 3 rRNAs. Fifteen coding sequences sharing ≥ 84% identity with known antibiotic resistance genes were identified. Genome analysis revealed abundant repetitive DNAs and two prophages. Epidemiological typing revealed newly described sequence type, antigenic finetype and Bexsero
Antigen Sequence Typing (BAST). The BAST profile showed no coverage by either Bexsero
or Trumenba
.
Our results present the first genome assembly of an invasive N. meningitidis isolate from a military unit in Vietnam. This study illustrates the usefulness of whole genome sequencing (WGS) analysis for epidemiological and antibiotic resistance studies and surveillance of IMD in Vietnam.