The emergence of azithromycin-resistant Salmonella Typhi in Nepal

Abstract

Background: Typhoid fever remains a significant cause of morbidity and mortality in Asia and Africa. The emergence of azithromycin resistance in South Asia is concerning, as azithromycin is one of the last effective oral drugs for treating typhoid.

Objectives: To describe the molecular mechanism and phylogenetics of azithromycin-resistant (Azith^R) Salmonella Typhi isolates from Patan Hospital, Kathmandu, Nepal.

Methods: Whole-genome sequences of three Azith^R S. Typhi isolates (MIC >256 mg/L) were analysed and compared with a global collection to investigate the azithromycin resistance mechanism and phylogenetic structure. Clinical information is reported for one of the three patients infected with Azith^R S. Typhi.

Results: The three Azith^R isolates belonged to the H58 lineage and were genetically identical; they were distantly related to contemporaneous S. Typhi from Nepal and Azith^R S. Typhi recently described in Bangladesh. Azithromycin resistance was mediated by a non-synonymous mutation in the acrB gene (R717L). The three Azith^R isolates showed reduced susceptibility to ciprofloxacin (double mutation in the gyrA: S83F and D87G), and were susceptible to ampicillin, chloramphenicol and co-trimoxazole. Clinical information from one patient suggested non-response to azithromycin treatment.

Conclusions: This is the first molecular description of Azith^R S. Typhi in Nepal. These organisms showed no phylogenetic link to Azith^R S. Typhi in Bangladesh. Our data suggest that increasing use of azithromycin may pose a strong selective pressure driving the emergence of Azith^R S. Typhi in South Asia. Further investigations are needed to evaluate treatment responses to azithromycin, predict evolutionary trajectories, and track the transmission of these organisms.

Figure 1.

Phylogenetic relationships between azithromycin-resistant Nepali H58 isolates and global H58 isolates. Rooted maximum likelihood tree (CT18 was used as an outgroup to root the tree and pruned for visualization) reconstructed based on the SNPs of 1512 H58 isolates. Branches indicating three major H58 lineages are coloured in orange (lineage Bd), green (lineage I), and blue (lineage II). The red terminal branch (also highlighted with a red star) shows the three azithromycin-resistant isolates described in this study. Branches highlighted in pink show different clusters associated with fluoroquinolone resistance, extensive drug resistance, and azithromycin resistance reported recently in Nepal, Pakistan and Bangladesh, respectively. The ring around the phylogeny indicates the location from which each isolate originates. The outside purple arc indicates the Nepali cluster containing most contemporaneous Nepali S. Typhi H58 isolates. The scale bar indicates 0.003 SNPS/site. QRDR, quinolone resistance-determining regions.