Whole genome sequencing of Neisseria gonorrhoeae in two cities of Bangladesh reveals high genomic diversity and stable antimicrobial resistance among key populations

Background Neisseria gonorrhoeae is an obligate human pathogen causing gonorrhoea the second most reported bacterial sexually transmitted infection. High level genomic plasticity of this pathogen requires whole genome sequence (WGS) analysis for epidemiological investigations. The absence of N. gonorrhoeae genomic data from Bangladesh represents a critical gap in South Asian gonococcal genomic epidemiology. Here we report, a genomic investigation of N. gonorrhoeae from Bangladesh using WGS approach. Methods Twenty-four N. gonorrhoeae isolates (N = 24) were collected from key populations including female sex workers, male sex workers and hijra. These belong to two studies conducted in two districts of Bangladesh; a cross-sectional bio-behavioral survey 2014 (Dhaka) and sexual and reproductive health and rights 2022–2024 (Dhaka and Jashore). Antibiotic resistance data from disc-diffusion assay were available from specific study. Recovered isolates were sequenced using Illumina NextSeq550 instrument. Sequence typing, presence of virulence genes and antimicrobial resistance genes/mutations were determined using PubMLST, Pathogenwatch, and ABRicate. Phylogenetic analysis was conducted using Bayesian inference with globally reported selected sequences as well as WHO reference sequences. Results Genomic analysis for MLST revealed nine sequence types, with ST7363 predominating in 50% (12/24) of isolates, particularly among male sex workers (58.3%; 7/12). Phenotypic resistance was highest for ciprofloxacin (83.3%, 20/24), while all isolates remained sensitive to ceftriaxone. Novel NG-STAR types comprised 33.3% (8/24) of isolates, while novel NG-MAST types reached 62.5% (15/24). Genomic analysis predicted resistance to ciprofloxacin (100%), sulfonamides (91.7%) and tetracycline (79.2%), while 100% sensitivity was predicted for azithromycin, ceftriaxone and spectinomycin. Phylogenetic analysis showed four intra clusters for 18 isolates and 6 were distributed separately. Conclusions Here we report, high genomic diversity of N. gonorrhoeae from, however relatively stable antibiotic susceptibility pattern in comparison to previous studies. These findings emphasize the urgent need for genomic surveillance and antimicrobial stewardship in Bangladesh to preserve current treatment options.