The rapid emergence of Salmonella Typhi with decreased ciprofloxacin susceptibility following an increase in ciprofloxacin prescriptions in Blantyre, Malawi

Ciprofloxacin is the first-line drug for treating typhoid fever in many high burden countries in Africa, but the emergence of non-susceptibility poses a grave challenge to public health programmes. Through enhanced surveillance as part of vaccine evaluation, we set out to investigate the occurrence and determinants of ciprofloxacin non-susceptibility in Blantyre, Malawi. We performed systematic typhoid fever and antibiotic prescription surveillance in two health centres in Blantyre, Malawi between 01/10/2016 and 31/10/2019, as part of the STRATAA and TyVAC studies. Blood culture isolates from study participants underwent i) pefloxacin screening and ciprofloxacin E-tests to identify ciprofloxcain non-susceptibility and ii) whole genome sequencing (WGS) to identify drug resistance mutations and phylogenetic relationships between non-susceptible and sensitive isolates. We constructed generalised linear regression models to investigate associations between ciprofloxacin prescription rates and S. Typhi isolates with Quinolone Resistance Determining Region (QRDR) mutations. We carried out 11295 blood cultures and microbiologically confirmed 239 cases of typhoid fever, with isolates from 193 participants sequenced (mean age of participants with sequenced genomes 12.8 years, 47% male). Between October 2016 and August 2019 2% (n=4/175) of WGS-confirmed typhoid fever cases were caused by S. Typhi with QRDR mutations, compared with 33% (n=6/18) in September and October 2019. Nine of the ten S. Typhi with QRDR mutations had a decreased ciprofloxacin susceptibility phenotype. Every additional prescription of ciprofloxacin given to study participants in the preceding month was associated with a 4.2% increase in the relative risk of isolating S. Typhi with a QRDR mutation (95% CI, 1.8-7.0%, p=0.0008). Phylogenetic analysis showed that S. Typhi isolates with QRDR mutations in September/October 2019 belonged to two distinct sub-clades encoding two different QRDR mutations, and were closely related (0-6 SNPs) to susceptible S. Typhi endemic to Blantyre. We have shown a close temporal association between empiric antimicrobial usage with an increase of fluoroquinolone non-susceptibility in S. Typhi, with two sub-clades responsible for the increase. Decreasing ciprofloxacin usage by improving typhoid diagnostics could help to limit the emergence of resistance.