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

Characterizing Neisseria meningitidis in Southern Vietnam between 2012 and 2021: A predominance of the chloramphenicol-resistant ST-1576 lineage

Objectives

Our goal was to describe Invasive Meningococcal Disease (IMD) in Southern Vietnam over the last 10 years. We characterized 109 Neisseria meningitidis strains in Southern Vietnam isolated between 1980s to 2021, that were collected from IMD (n = 44), sexually transmitted infections (n = 2), and healthy carriage (n = 63).

Methods

IMD were confirmed by bacterial culture and/or real-time polymerase chain reaction at the national reference laboratory in Pasteur Institute of Ho Chi Minh City (PIHCM). Antimicrobial resistance was determined on 31 IMD and two sexually transmitted infection isolates with E-test for chloramphenicol (CHL), penicillin (PEN), ciprofloxacin (CIP), ceftriaxone (CRO), and rifampicin (RIF). Sequencing was performed for analyzing of multilocus-sequence-typing (MLST), porA, fetA, and antibiotic resistance genes, including gyrA, penA, and rpoB.

Results

The incidence rate during this period was 0.02 per 100,000 persons/year. Serogroup B accounted for over 90% of cases (50/54). ST-1576 were mainly responsible for IMD, 27/42 MLST profiles, and associated with CHL resistance. Resistance was prevalent among IMD isolates. Thirteen were resistant to CHL (minimum inhibitory concentration [MIC] ≥16 mg/l), 12 were intermediate to PEN (MIC between 0.19 and 0.5 mg/l), and five were CIP-resistant (MIC between 0.19 and 0.5 mg/l). Particularly, one was non-susceptible to CRO (MIC at 0.125 mg/l), belonging to ST-5571 lineage. The resistance was due to carrying resistant alleles of penA and gyrA genes, and catP gene. Notably, seven isolates were resistant/non-susceptible to two or more antibiotics.

Conclusion

Our results suggest the persistence of the circulating ST-1576 in Southern Vietnam, with a spread of antimicrobial resistance across the community.

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

Background

Neisseria meningitidis 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 N. meningitidis B isolate from a military unit in Vietnam. Here, we extend these findings by sequencing two additional invasive N. meningitidis 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 N. meningitidis isolates from these units and other units in proximity.

Methods

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 N. meningitidis 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.

Results

Genome comparison revealed a high level of similarity among isolates both within and between units. All isolates showed resistance to chloramphenicol and carried identical catP 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 N. meningitidis 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 N. meningitidis in Vietnam.

Characteristics of Neisseria Species Colonized in the Human’s Nasopharynx

Context: Neisseria meningitidis is the causative agent of a life-threatening infection with high mortality and morbidity worldwide. The most common types of this bacterium are serogroups A, B, C, W135, X, and Y. Although in some countries, such as Iran, the meningococcal meningitis has been well monitored and controlled by the use of divalent and quadrivalent vaccines, other fatal infections caused by these bacteria are still an important threat. For the above reason, this review focused on the differences of Neisseria characteristics, particularly in capsular composition, pathogenic and commensal stages to a better understanding of how to manage Neisseria infections. Evidence Acquisition: In this review, PubMed, EMBASE, ScienceDirect, Scopus, and Google Scholar were searched for English-language publications on pathogenic or commensal strains of Neisseria, meningococcal disease, Neisseria biology, genetic diversity, molecular typing, serogroups, diagnostic, and epidemiology around the world up to July 2019. All articles and academic reports in the defined area of this research were considered too. The data were extracted and descriptively discussed. Results: We included 85 studies in the survey. The data analysis revealed that the distribution of meningococcal serogroups was different regionally. For example, the serogroups C and W-135 accounted for Africa and Latin America regions, serogroup B in the European countries, and rarely in the Western Pacific, and serogroups A and C were dominant in Asian countries. Although data set for laboratory-based diagnosis of N. meningitidis are available for all countries, only 30% of the countries rely on reference laboratories for serogroup determination, and more than half of the countries lack the ability of surveillance system. Nevertheless, molecular detection procedure is also available for all countries. The use of the meningococcal vaccine is a variable country by country, but most countries have applied the meningococcal vaccine, either divalent or quadrivalent, for the protection of high-risk groups. Conclusions: Owing to the geographical distribution of N. meningitidis serogroups in circulating, each country has to monitor for changes in serogroups diversity and its control management. Furthermore, laboratories should scale up the epidemiology and disease burden. It should be mentioned that quadrivalent meningococcal vaccines reduce the meningococcal disease burden sharply.

The spread of chloramphenicol-resistant Neisseria meningitidis in Southeast Asia

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Chloramphenicol resistant strains of Neisseria meningitidis are present in three countries across Southeast Asia.

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These strains are all closely related to each other and to resistant strains previously observed in Vietnam and France.

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This lineage has acquired other antimicrobial resistance genes during its spread.

Objectives

Invasive disease caused by Neisseria meningitidis is a significant health concern globally, but our knowledge of the prevailing serogroups, antimicrobial susceptibility patterns, and genetics of N. meningitidis in Southeast Asia is limited. Chloramphenicol resistance in N. meningitidis has rarely been reported, but was first described in isolates from Vietnam in 1998. We aimed to characterise eight chloramphenicol resistant meningococcal isolates collected between 2007 and 2018 from diagnostic microbiology laboratories in Cambodia, Thailand and the Lao People's Democratic Republic (Laos).

Methods

Whole-genome sequencing was used to generate genome sequences from 18 meningococcal isolates including the eight chloramphenicol resistant isolates. We identified antimicrobial resistance genes present in these strains, and examined the phylogenetic relationships between strains.

Results

The eight resistant strains all contain the same chloramphenicol resistance gene first described in 1998, and are closely related to each other. Strains resistant to penicillin, tetracycline, and ciprofloxacin were also observed, including a chloramphenicol-resistant strain which has acquired penicillin and ciprofloxacin resistance.

Conclusions

This study suggests that chloramphenicol-resistant N. meningitidis is more widespread than previously thought, and that the previously-identified resistant lineage is now found in multiple countries in Southeast Asia.