Antimicrobial Resistance in Vibrio cholerae: Insights from a 2023 Outbreak

The 2023 Khyber Pakhtunkhwa cholera outbreak revealed extensive multidrug resistance that materially complicated clinical management and increased the risk of treatment failure. Investigators used Vibrio cholerae whole genome sequencing to identify resistance determinants linked to clinical nonresponse, prompting rapid reassessment of empirical regimens early in the outbreak.

Among 70 confirmed isolates—uniformly the Ogawa serotype—34 met MDR criteria, and 13 were XDR. Six isolates were selected for sequencing, which identified multiple antimicrobial-resistance genes and quinolone-associated mutations. Phenotypic susceptibility testing largely matched genomic predictions, with limited genotype–phenotype discordance. Collectively, the data indicate first-line tetracycline and trimethoprim–sulfamethoxazole are unreliable without local susceptibility confirmation.

Sequencing guided empiric changes by pinpointing agents with retained activity and flagging those to avoid, supporting targeted use of macrolides or alternative agents when indicated. The investigation used centralized MiSeq processing after targeted sample selection, demonstrating that actionable genomic data can arrive during an outbreak when logistics and laboratory capacity permit—shortening the interval to evidence-based antimicrobial selection when sequencing is integrated into response workflows.

Taken together, the highest-confidence findings support routine incorporation of genomic surveillance into outbreak planning, prioritization of targeted susceptibility testing for admitted cases, and investment in laboratory turnaround capacity to enable near–real-time guidance.