The emergence of azithromycin-resistant Salmonella Typhi in Nepal

Abstract

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. In mid-2019, three azithromycin-resistant (AzithR) S. Typhi isolates were isolated from typhoid fever patients attending Patan Hospital, Kathmandu, Nepal. These organisms were whole genome sequenced and compared with a global collection. We found that the three AzithR isolates belonged to the H58 lineage and were genetically identical; they were distantly related to contemporaneous S. Typhi from Nepal and AzithR S. Typhi recently described in Bangladesh. Azithromycin resistance was mediated by nonsynonymous mutation in the acrB gene (R717L). Clinical information from one patient suggested non-response to azithromycin treatment. Further investigations are needed to evaluate treatment responses to azithromycin, predict the evolutionary trajectories of AzithR S. Typhi, and track the transmission of these organisms.

Tracking the Emergence of Azithromycin Resistance in Multiple Genotypes of Typhoidal Salmonella

“…To gain further genomic and evolutionary insight into the AcrB-717 mutations of Salmonella Typhi, we contextualized 33 AcrB-R717Q/L and 47 AcrB-717WT isolates collected in the same study in a maximum-likelihood phylogenetic tree against 750 Salmonella Typhi genomes reported from Bangladesh in previous studies ( 14 , 18 , 21 , 22 ) (see Table S2 ). These previous studies included 12 genomes with AcrB-R717Q/L mutations.…”

“…These previous studies included 12 genomes with AcrB-R717Q/L mutations. In addition, the tree also included five AcrB-717 mutants previously identified in the United Kingdom, Nepal, and Pakistan ( 16 – 18 ). The final tree contained 50 Salmonella Typhi genomes with AcrB-R717Q/L.…”

“…The presence of this single nucleotide polymorphism (SNP) raises the MICs of Salmonella Typhi and Paratyphi A for azithromycin to ≥32 μg/ml, the Clinical and Laboratory Standards Institute (CLSI) breakpoint of resistance ( 15 ). Since the report from Bangladesh in 2019, at least six AzmR Salmonella Typhi cases mediated by this mutation have been reported from Nepal, India, and Pakistan, the epicenter of the XDR typhoid outbreak ( 16 – 18 ). However, no further AzmR Salmonella Paratyphi A has been described.…”

Proximal binding pocket Arg717 substitutions in Escherichia coli AcrB cause clinically relevant divergencies in resistance profiles

“…Specifically, they found 13 out of 1,082 strains with azithromycin resistance levels between 32-64 μg/ml, of which 12 harbored the R717Q/L mutation in the AcrB multidrug efflux pump (19). Similarly, in a recent study, S. Typhi isolates from Nepal from 2019 harboring the R717L mutation were non-susceptible to azithromycin (15). Genomic analysis of 133 S. Typhi strains collected in India between 1993 and 2016 showed that the two azithromycin non-susceptible strains contained the R717Q mutation in AcrB (20).…”

“…These substitutions are present in the efflux pump's proximal binding pocket (11)(12)(13) at the Channel 2 entrance (12)(13)(14). This is a concerning development, as in many countries, azithromycin is the last available and effective oral drug to treat typhoid (15,16). In 2010, the first azithromycin-resistant S. Serovars Paratyphi A strains unresponsive to azithromycin treatment isolated from Pakistan were reported (17).…”