Genotypic characterization and genome comparison reveal insights into potential vaccine coverage and genealogy of Neisseria meningitidis in military camps in Vietnam

• Published in: PeerJ (San Francisco, CA) Vol. 8; p. e9502
• Main Authors: Le, Trang Thu, Tran, Thach Xuan, Trieu, Long Phi, Austin, Christopher M, Nguyen, Huong Minh, Quyen, Dong Van
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 21-07-2020; PeerJ, Inc; PeerJ Inc
• Subjects: Analysis; Antibiotic resistance; Antibiotics; Camps; Cerebrospinal fluid; Chloramphenicol; DNA sequencing; Epidemiological characterization; Epidemiology; Genealogy; Genes; Genetic aspects; Genetic diversity; Genomes; Genomics; Genotypes; Infectious Diseases; Laboratories; Medical research; Meningitis; Meningococcal disease; Meropenem; Metadata; Microbial drug resistance; Microbiology; Military; Military camps; Neisseria meningitidis; Phylogenetics; Phylogeny; Preventive medicine; Sepsis; Strains (organisms); Tetracyclines; Vaccination; Vaccines; Vietnam; Virulence; Whole genome sequencing; Southeast Asia; Vietnam; Vietnam; Neisseria meningitidis; Whole genome sequencing; Epidemiological characterization; Antibiotic resistance; Military
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.9502

remains the main cause of sporadic meningitis and sepsis in military camps in Vietnam. Yet, very limited molecular data of their genotypic and epidemiological characteristics are available from Vietnam, and particularly the military environment. Whole genome sequencing (WGS) has proven useful for meningococcal disease surveillance and guiding preventative vaccination programs. Previously, we characterized key genetic and epidemiological features of an invasive
B isolate from a military unit in Vietnam. Here, we extend these findings by sequencing two additional invasive
B isolated from cerebrospinal fluid (CSF) of two meningitis cases at another military unit and compared their genomic sequences and features. We also report the sequence types and antigenic profiles of 25 historical and more recently emerged
isolates from these units and other units in proximity.
Strains were sequenced using the Illumina HiSeq platform, de novo assembled and annotated. Genomes were compared within and between military units, as well as against the global
collection and other isolates from the Southeast Asia region using PubMLST. Variations at the nucleotide level were determined, and phylogenetic relationships were estimated. Antigenic genotypes and vaccine coverage were analyzed using gMATS and PubMLST. Susceptibility of isolates against commonly used antibiotic agents was examined using E-test.
Genome comparison revealed a high level of similarity among isolates both within and between units. All isolates showed resistance to chloramphenicol and carried identical
gene with other Southeast Asian isolates, suggesting a common lineage. Their antigenic genotypes predicted no coverage by either Bexsero
or Trumenba
, and nucleotide variation analysis revealed diverse new, unassigned alleles at multiple virulence loci of all strains. Groups of singleton and unique novel sequence types extending beyond individual camps were found from epidemiological data of 25 other isolates. Our results add to the sparse published molecular data of
in the military units in Vietnam, highlight their diversity, distinct genetic features and antibiotic resistance pattern, and emphasize the need for further studies on the molecular characteristics of
in Vietnam.