Resistome phylodynamics of multidrug-resistant Shigella isolated from diarrheal patients
ABSTRACT 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...
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American Society for Microbiology
2025-01-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01635-24 |
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| author | Asaduzzaman Asad Md. Abu Jaher Nayeem Md. Golam Mostafa Ruma Begum Shah Nayeem Faruque Suraia Nusrin Israt Jahan Shoma Hayat Zhahirul Islam |
| author_facet | Asaduzzaman Asad Md. Abu Jaher Nayeem Md. Golam Mostafa Ruma Begum Shah Nayeem Faruque Suraia Nusrin Israt Jahan Shoma Hayat Zhahirul Islam |
| author_sort | Asaduzzaman Asad |
| collection | DOAJ |
| description | ABSTRACT 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-blaCTX-M-15-ISEcp1 and blaTEM-1] and two macrolide-resistant mobile genomic islands (GIs) [mphA-mrx-mph(R)A-IS6100 and mphE-msrE-IS482-IS6] 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.IMPORTANCEThe 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. |
| format | Article |
| id | doaj-art-d7edd55d171b434a82ac55c5d4ae06de |
| institution | Kabale University |
| issn | 2165-0497 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj-art-d7edd55d171b434a82ac55c5d4ae06de2025-01-07T14:05:18ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972025-01-0113110.1128/spectrum.01635-24Resistome phylodynamics of multidrug-resistant Shigella isolated from diarrheal patientsAsaduzzaman Asad0Md. Abu Jaher Nayeem1Md. Golam Mostafa2Ruma Begum3Shah Nayeem Faruque4Suraia Nusrin5Israt Jahan6Shoma Hayat7Zhahirul Islam8Gut-Brain Axis Laboratory, Infectious Diseases Division (IDD), icddr, b, Dhaka, BangladeshGut-Brain Axis Laboratory, Infectious Diseases Division (IDD), icddr, b, Dhaka, BangladeshGut-Brain Axis Laboratory, Infectious Diseases Division (IDD), icddr, b, Dhaka, BangladeshGut-Brain Axis Laboratory, Infectious Diseases Division (IDD), icddr, b, Dhaka, BangladeshGut-Brain Axis Laboratory, Infectious Diseases Division (IDD), icddr, b, Dhaka, BangladeshDepartment of Genetic Engineering and Biotechnology, East West University, Dhaka, BangladeshGut-Brain Axis Laboratory, Infectious Diseases Division (IDD), icddr, b, Dhaka, BangladeshGut-Brain Axis Laboratory, Infectious Diseases Division (IDD), icddr, b, Dhaka, BangladeshGut-Brain Axis Laboratory, Infectious Diseases Division (IDD), icddr, b, Dhaka, BangladeshABSTRACT 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-blaCTX-M-15-ISEcp1 and blaTEM-1] and two macrolide-resistant mobile genomic islands (GIs) [mphA-mrx-mph(R)A-IS6100 and mphE-msrE-IS482-IS6] 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.IMPORTANCEThe 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.https://journals.asm.org/doi/10.1128/spectrum.01635-24Shigellamulti-drug resistancewhole-genome sequencingresistome phylodynamicsmobile genetic elementsconjugative plasmids |
| spellingShingle | Asaduzzaman Asad Md. Abu Jaher Nayeem Md. Golam Mostafa Ruma Begum Shah Nayeem Faruque Suraia Nusrin Israt Jahan Shoma Hayat Zhahirul Islam Resistome phylodynamics of multidrug-resistant Shigella isolated from diarrheal patients Microbiology Spectrum Shigella multi-drug resistance whole-genome sequencing resistome phylodynamics mobile genetic elements conjugative plasmids |
| title | Resistome phylodynamics of multidrug-resistant Shigella isolated from diarrheal patients |
| title_full | Resistome phylodynamics of multidrug-resistant Shigella isolated from diarrheal patients |
| title_fullStr | Resistome phylodynamics of multidrug-resistant Shigella isolated from diarrheal patients |
| title_full_unstemmed | Resistome phylodynamics of multidrug-resistant Shigella isolated from diarrheal patients |
| title_short | Resistome phylodynamics of multidrug-resistant Shigella isolated from diarrheal patients |
| title_sort | resistome phylodynamics of multidrug resistant shigella isolated from diarrheal patients |
| topic | Shigella multi-drug resistance whole-genome sequencing resistome phylodynamics mobile genetic elements conjugative plasmids |
| url | https://journals.asm.org/doi/10.1128/spectrum.01635-24 |
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