Multiple Mechanisms Confer Resistance to Azithromycin in in Bangladesh: a Comprehensive Whole Genome-Based Approach.

is the second leading cause of diarrheal deaths worldwide. Azithromycin (AZM) is a potential treatment option for infection; however, the recent emergence of AZM resistance in threatens the current treatment strategy. Therefore, we conducted a comprehensive whole genome-based approach to identify the mechanism(s) of AZM resistance in . We performed antimicrobial susceptibility tests, polymerase chain reaction (PCR), Sanger (amplicon) sequencing, and whole genome-based bioinformatics approaches to conduct the study. Fifty-seven (38%) of the isolates examined were AZM resistant; Shigella sonnei exhibited the highest rate of resistance against AZM (80%). PCR amplification for 15 macrolide resistance genes (MRGs) followed by whole-genome analysis of 13 representative isolates identified two AZM-modifying genes, (A) (in all isolates resistant to AZM) and (E) (in 2 AZM-resistant isolates), as well as one 23S rRNA-methylating gene, (B) (41% of AZM-resistant isolates) and one efflux pump mediator gene, (E) [in the same two isolates that harbored the (E) gene]. This is the first report of (E) and (E) genes in . Moreover, we found that an IncFII-type plasmid predominates and can possess all four MRGs. We also detected two plasmid-borne resistance gene clusters: IS-(A)-(A)-(R)(A)-IS, which is linked to global dissemination of MRGs, and (E)-(E)-IS-IS, which is reported for the first time in . In conclusion, this study demonstrates that MRGs in association with pathogenic IS family insertion sequences generate resistance gene clusters that propagate through horizontal gene transfer (HGT) in . can frequently transform into a superbug due to uncontrolled and rogue administration of antibiotics and the emergence of HGT of antimicrobial resistance factors. The advent of AZM resistance in has become a serious concern in the treatment of shigellosis. However, there is an obvious scarcity of clinical data and research on genetic mechanisms that induce AZM resistance in , particularly in low- and middle-income countries. Therefore, this study is an approach to raise the alarm for the next lifeline. We show that two key MRGs [(A) and (B)] and the newly identified MRGs [(E) and (E)], with their origination in plasmid-borne pathogenic islands, are fundamental mechanisms of AZM resistance in in Bangladesh. Overall, this study predicts an abrupt decrease in the effectiveness of AZM against in the very near future and suggests prompt focus on seeking a more effective treatment alternative to AZM for shigellosis.