Resistome phylodynamics of multidrug-resistant
Shigella
isolated from diarrheal patients
Authors: Asad Asaduzzaman , Nayeem Md. Abu Jaher , Mostafa Md. Golam , Begum Ruma , Faruque Shah Nayeem , Nusrin Suraia , Jahan Israt , Hayat Shoma , Islam Zhahirul 
Published: November 2024

Multi-drug resistance (MDR) in
Shigella
continues to pose a significant public health challenge, particularly in developing countries. Recent advances in genomics strengthen the surveillance of MDR-pathogens and antimicrobial resistance (AMR) mediators. However, genome-based investigations into resistome dynamics in
Shigella
are limited, specifically in Bangladesh. Therefore, we investigated MDR-
Shigella
resistomes to evaluate their AMR transmission and phylodynamics. Clinical
Shigella
strains were screened for MDR phenotypes through susceptibility tests against 28 antibiotics from 10 different classes. Whole-genome sequencing (WGS) and bioinformatics approaches were performed to unveil the resistome dynamics: >500 global plasmid entities and >1,000 plasmid-mediated resistance gene clusters from global databases were included in this study. We identified 28 distinct antimicrobial resistance genes (ARGs) from nine antibiotic classes, with 75% originating from plasmids. Notably, two conjugative MDR plasmids included nearly all potential ARGs, conferring resistance to first-line drugs for shigellosis. Two third-generation cephalosporin-resistant [

wubC-bla
CTX-M-15

-ISEcp
1
and

bla
TEM-1

] and two macrolide-resistant mobile genomic islands (GIs) [
mphA-mrx-mph(R)A
-IS
6100
and
mphE-msrE
-IS
482
-IS
6
] had emerged in
Shigella
in Bangladesh. In addition, trimethoprim-aminoglycoside-streptothricin-sulfonamide-resistant
dfrA1-sat1-aadA1
and
aph3-dfrA14-aph6-sul2
were in conjugative plasmids in Bangladesh. The MDR plasmids and resistant GIs were phylogenetically relevant to Europe, USA, or China-derived isolates, indicating carry-over of the emerging ARGs from heavily industrialized countries and MSM-burdened (men who have sex with men) populations. The global burden of resistance GIs has increased sharply, especially after 2014. Emerging resistance mediators were most frequent (>80%) in human-associated
Escherichia coli
and
Klebsiella pneumoniae
. We infer ARGs horizontally propagate among Enteropathogens: informing treatment strategies and supporting policymakers in strengthening AMR-containment efforts utilizing the phylodynamics network.

IMPORTANCE

The world is suffering from a high burden of MDR enteropathogens. Healthcare providers in low- and middle-income countries (LMICs) often face trouble finding effective drugs among the many antibiotics introduced in diarrheal treatment. Resistance-mediated drug inactivation is more rapid than the advent of new antimicrobials, leaving enteritis treatment on the edge. In Bangladesh, where one-third of users are self-prescribing antibiotics and thousands are dying due to resistance-related treatment failure, phylogenomic evidence of AMR transmission root is scarce. Therefore, investigating the resistomes of MDR-
Shigella
, the leading cause of diarrheal deaths in Bangladesh, is crucial. We identified several emerging resistance mediators and their phylogenetic links to global entities, which is significant for improving shigellosis treatment and enhancing AMR containment strategies. Understanding the MDR mechanism in
Shigella
will help physicians choose effective drugs and anticipate resistance-mediated changes in treatment approaches; the spatiotemporal phylodynamics of AMR mediators aid policymakers in setting effective checkpoints in the AMR transmission network.