Phylogenetic analysis of blaNDM genes of carbapenem resistant uropathogens isolated from federal tertiary care hospital, Pakistan: insights into the evolution and dissemination of drug resistance
-
Muhammad Shafiq
,
Amnah Akhtar Khan
,
Muhammad Zeeshan Hyder
,
Umme Farwa
,
Farhan Kursheed
,
Sana Khan
,
Ayesha Siddiqa
,
Iftikhar Ahmed
,
Muhammad Saeed
,
Muhammad Fiaz
Abstract
Background and Objectives: Global health is seriously threatened by the rise of carbapenem-resistant Enterobacterales (CRE). The blaNDM gene, a key carbapenemase coding gene, causes global health concern due to its multidrug resistance and easy spread through mobile genetic elements. This study aimed to identify and genetically characterize the blaNDM genes from uropathogens, its antibiotic susceptibility, and its correlation with global sequences.
Materials and Methods: Urine samples were processed following microbiological guidelines. Isolates were identified using API-20E. Antibiotic susceptibility was tested using disc diffusion method, and bacterial DNAs were extracted for blaNDM gene sequencing for phylogenetic analysis.
Results: CREs were detected in 11.92% (n=51) of the 428 Enterobacterales. Among CRE isolates, 45% (n=23) were positive for blaNDM gene harbored by Klebsiella pneumoniae (57%), followed by Escherichia coli (26%). Uropathogenic CRE, harboring blaNDM, revealed susceptibility of 34.78%, 60.87%, and 65.22% to amikacin, nitrofurantoin, and fosfomycin respectively. The blaNDM-5 variant was most common (69.57%), followed by blaNDM-1 (26.09%) and blaNDM-7 (4.35%). Phylogenetic analysis revealed that blaNDM variants exhibit diverse relationships with Pakistani and worldwide sequences.
Conclusion: The significant presence of blaNDM in uropathogens, along with extensive antibiotic resistance, underscores the urgent need for continuous monitoring and antibiotic stewardship programs to manage the growing threat of CRE infections.
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8. Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, et al. Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother 2009; 53: 5046-5054.
9. Junaid K. Molecular Diversity of NDM-1, NDM-5, NDM-6, and NDM-7 Variants of New Delhi Metallo-β-Lactamases and their impact on Drug Resistance. Clin Lab 2021; 67: 10.7754/Clin.Lab.2021.201214.
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11. CLSI (2022). Clinical and laboratory standard institute. Performance Standards for Antimicrobial Susceptibility Testing. 32nd ed. CLSI supplement M100. https://clsi.org/about/news/clsi-publishes-m100-performance-standards-for-antimicrobial-susceptibility-testing-32nd-edition/
12. Bilal H, Rehman TU, Khan MA, Hameed F, Jian ZG, Han J, et al. Molecular Epidemiology of mcr-1, bla(KPC-2,) and bla(NDM-1) Harboring Clinically Isolated Escherichia coli from Pakistan. Infect Drug Resist 2021; 14: 1467-1479.
13. Abdullah S, Almusallam A, Li M, Mahmood MS, Mushtaq MA, Eltai NO, et al. Whole genome-based genetic insights of bla(NDM) producing clinical E. coli isolates in hospital settings of Pakistan. Microbiol Spectr 2023; 11(5): e0058423.
14. Masseron A, Poirel L, Jamil Ali B, Syed MA, Nordmann P. Molecular characterization of multidrug-resistance in Gram-negative bacteria from the Peshawar teaching hospital, Pakistan. New Microbes New Infect 2019; 32: 100605.
15. Mathlouthi N, Al-Bayssari C, El Salabi A, Bakour S, Ben Gwierif S, Zorgani AA, et al. Carbapenemases and extended-spectrum β-lactamases producing Enterobacteriaceae isolated from Tunisian and Libyan hospitals. J Infect Dev Ctries 2016; 10: 718-727.
16. Awoke T, Teka B, Aseffa A, Sebre S, Seman A, Yeshitela B, et al. Detection of blaKPC and blaNDM carbapenemase genes among Klebsiella pneumoniae isolates in Addis Ababa, Ethiopia: Dominance of blaNDM. PLoS One 2022; 17(4): e0267657.
17. Naeem S, Bilal H, Muhammad H, Khan MA, Hameed F, Bahadur S, et al. Detection of blaNDM-1 gene in ESBL producing Escherichia coli and Klebsiella pneumoniae isolated from urine samples. J Infect Dev Ctries 2021; 15: 516-522.
18. Rahman M, Shukla SK, Prasad KN, Ovejero CM, Pati BK, Tripathi A, et al. Prevalence and molecular characterisation of New Delhi metallo-β-lactamases NDM-1, NDM-5, NDM-6 and NDM-7 in multidrug-resistant Enterobacteriaceae from India. Int J Antimicrob Agents 2014; 44: 30-37.
19. Thapa A, Upreti MK, Bimali NK, Shrestha B, Sah AK, Nepal K, et al. Detection of NDM Variants (bla(NDM-1), bla(NDM-2), bla(NDM-3)) from Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae: First Report from Nepal. Infect Drug Resist 2022; 15: 4419-4434.
20. Wu W, Feng Y, Tang G, Qiao F, McNally A, Zong Z. NDM Metallo-β-Lactamases and their bacterial producers in health care settings. Clin Microbiol Rev 2019; 32(2): e00115-18.
21. Elbadawi HS, Elhag KM, Mahgoub E, Altayb HN, Ntoumi F, Elton L, et al. Detection and characterization of carbapenem resistant Gram-negative bacilli isolates recovered from hospitalized patients at Soba University Hospital, Sudan. BMC Microbiol 2021; 21: 136.
22. Zou H, Jia X, Liu H, Li S, Wu X, Huang S. Emergence of NDM-5-Producing Escherichia coli in a Teaching Hospital in Chongqing, China: IncF-Type Plasmids may Contribute to the Prevalence of blaNDM-5. Front Microbiol 2020; 11: 334.
23. Wang Q, Wang X, Wang J, Ouyang P, Jin C, Wang R, et al. Phenotypic and Genotypic Characterization of Carbapenem-resistant Enterobacteriaceae: Data from a Longitudinal Large-scale CRE study in China (2012-2016). Clin Infect Dis 2018; 67(suppl_2): S196-S205.
24. Dobhal S, Sen M, Yadav H, Agarwal J, Das A, Chandra A, et al. Role of ceftazidime-avibactam in urinary tract infections caused by carbapenem-resistant Enterobacterales. Cureus 2024; 16(12): e75221.
25. Ejaz H, Qamar MU, Farhana A, Younas S, Batool A, Lone D, et al. The rising tide of antibiotic resistance: A study on extended-spectrum beta-lactamase and carbapenem-resistant Escherichia coli and Klebsiella pneumoniae. J Clin Lab Anal 2024; 38(10): e25081.
26. Simon V, Viswam A, Alexander PS, James E, Sudhindran S. Colistin versus polymyxin B: A pragmatic assessment of renal and neurological adverse effects and effectiveness in multidrug-resistant Gram-negative bacterial infections. Indian J Pharmacol 2023; 55: 229-236.
27. Zhu X, Guo C, Xu S, Lv F, Guo Z, Lin S, et al. Clinical distribution of carbapenem genotypes and resistance to ceftazidime-avibactam in Enterobacteriaceae bacteria. Front Cell Infect Microbiol 2024; 14: 1345935.
2. Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 2022; 399: 629-655.
3. Alvarez-Uria G, Gandra S, Mandal S, Laxminarayan R. Global forecast of antimicrobial resistance in invasive isolates of Escherichia coli and Klebsiella pneumoniae. Int J Infect Dis 2018; 68: 50-53.
4. Frazee BW, Trivedi T, Montgomery M, Petrovic DF, Yamaji R, Riley L. Emergency Department Urinary tract infections Caused by Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae: many Patients have no Identifiable risk factor and Discordant Empiric Therapy Is Common. Ann Emerg Med 2018; 72: 449-456.
5. Sultan I, Rahman S, Jan AT, Siddiqui MT, Mondal AH, Haq QMR. Antibiotics, Resistome and resistance mechanisms: a bacterial perspective. Front Microbiol 2018; 9: 2066.
6. Aslam B, Rasool M, Muzammil S, Siddique AB, Nawaz Z, Shafique M, et al (2020). Carbapenem Resistance: Mechanisms and Drivers of Global Menace. In: Kırmusaoğlu S, Bhardwaj SB, editors. Pathogenic Bacteria. Rijeka: IntechOpen.
7. Qamar MU, Lopes BS, Hassan B, Khurshid M, Shafique M, Atif Nisar M, et al. The present danger of New Delhi metallo-β-lactamase: a threat to public health. Future Microbiol 2020; 15: 1759-1778.
8. Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, et al. Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother 2009; 53: 5046-5054.
9. Junaid K. Molecular Diversity of NDM-1, NDM-5, NDM-6, and NDM-7 Variants of New Delhi Metallo-β-Lactamases and their impact on Drug Resistance. Clin Lab 2021; 67: 10.7754/Clin.Lab.2021.201214.
10. Klein RD, Hultgren SJ. Urinary tract infections: microbial pathogenesis, host-pathogen interactions and new treatment strategies. Nat Rev Microbiol 2020; 18: 211-226.
11. CLSI (2022). Clinical and laboratory standard institute. Performance Standards for Antimicrobial Susceptibility Testing. 32nd ed. CLSI supplement M100. https://clsi.org/about/news/clsi-publishes-m100-performance-standards-for-antimicrobial-susceptibility-testing-32nd-edition/
12. Bilal H, Rehman TU, Khan MA, Hameed F, Jian ZG, Han J, et al. Molecular Epidemiology of mcr-1, bla(KPC-2,) and bla(NDM-1) Harboring Clinically Isolated Escherichia coli from Pakistan. Infect Drug Resist 2021; 14: 1467-1479.
13. Abdullah S, Almusallam A, Li M, Mahmood MS, Mushtaq MA, Eltai NO, et al. Whole genome-based genetic insights of bla(NDM) producing clinical E. coli isolates in hospital settings of Pakistan. Microbiol Spectr 2023; 11(5): e0058423.
14. Masseron A, Poirel L, Jamil Ali B, Syed MA, Nordmann P. Molecular characterization of multidrug-resistance in Gram-negative bacteria from the Peshawar teaching hospital, Pakistan. New Microbes New Infect 2019; 32: 100605.
15. Mathlouthi N, Al-Bayssari C, El Salabi A, Bakour S, Ben Gwierif S, Zorgani AA, et al. Carbapenemases and extended-spectrum β-lactamases producing Enterobacteriaceae isolated from Tunisian and Libyan hospitals. J Infect Dev Ctries 2016; 10: 718-727.
16. Awoke T, Teka B, Aseffa A, Sebre S, Seman A, Yeshitela B, et al. Detection of blaKPC and blaNDM carbapenemase genes among Klebsiella pneumoniae isolates in Addis Ababa, Ethiopia: Dominance of blaNDM. PLoS One 2022; 17(4): e0267657.
17. Naeem S, Bilal H, Muhammad H, Khan MA, Hameed F, Bahadur S, et al. Detection of blaNDM-1 gene in ESBL producing Escherichia coli and Klebsiella pneumoniae isolated from urine samples. J Infect Dev Ctries 2021; 15: 516-522.
18. Rahman M, Shukla SK, Prasad KN, Ovejero CM, Pati BK, Tripathi A, et al. Prevalence and molecular characterisation of New Delhi metallo-β-lactamases NDM-1, NDM-5, NDM-6 and NDM-7 in multidrug-resistant Enterobacteriaceae from India. Int J Antimicrob Agents 2014; 44: 30-37.
19. Thapa A, Upreti MK, Bimali NK, Shrestha B, Sah AK, Nepal K, et al. Detection of NDM Variants (bla(NDM-1), bla(NDM-2), bla(NDM-3)) from Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae: First Report from Nepal. Infect Drug Resist 2022; 15: 4419-4434.
20. Wu W, Feng Y, Tang G, Qiao F, McNally A, Zong Z. NDM Metallo-β-Lactamases and their bacterial producers in health care settings. Clin Microbiol Rev 2019; 32(2): e00115-18.
21. Elbadawi HS, Elhag KM, Mahgoub E, Altayb HN, Ntoumi F, Elton L, et al. Detection and characterization of carbapenem resistant Gram-negative bacilli isolates recovered from hospitalized patients at Soba University Hospital, Sudan. BMC Microbiol 2021; 21: 136.
22. Zou H, Jia X, Liu H, Li S, Wu X, Huang S. Emergence of NDM-5-Producing Escherichia coli in a Teaching Hospital in Chongqing, China: IncF-Type Plasmids may Contribute to the Prevalence of blaNDM-5. Front Microbiol 2020; 11: 334.
23. Wang Q, Wang X, Wang J, Ouyang P, Jin C, Wang R, et al. Phenotypic and Genotypic Characterization of Carbapenem-resistant Enterobacteriaceae: Data from a Longitudinal Large-scale CRE study in China (2012-2016). Clin Infect Dis 2018; 67(suppl_2): S196-S205.
24. Dobhal S, Sen M, Yadav H, Agarwal J, Das A, Chandra A, et al. Role of ceftazidime-avibactam in urinary tract infections caused by carbapenem-resistant Enterobacterales. Cureus 2024; 16(12): e75221.
25. Ejaz H, Qamar MU, Farhana A, Younas S, Batool A, Lone D, et al. The rising tide of antibiotic resistance: A study on extended-spectrum beta-lactamase and carbapenem-resistant Escherichia coli and Klebsiella pneumoniae. J Clin Lab Anal 2024; 38(10): e25081.
26. Simon V, Viswam A, Alexander PS, James E, Sudhindran S. Colistin versus polymyxin B: A pragmatic assessment of renal and neurological adverse effects and effectiveness in multidrug-resistant Gram-negative bacterial infections. Indian J Pharmacol 2023; 55: 229-236.
27. Zhu X, Guo C, Xu S, Lv F, Guo Z, Lin S, et al. Clinical distribution of carbapenem genotypes and resistance to ceftazidime-avibactam in Enterobacteriaceae bacteria. Front Cell Infect Microbiol 2024; 14: 1345935.
| Files | ||
| Issue | Vol 17 No 5 (2025) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v17i5.19883 | |
| Keywords | ||
| Urine NDM Carbapenem resistance Colistin Enterobacteriaceae | ||
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How to Cite
1.
Shafiq M, Khan A, Hyder M, Farwa U, Kursheed F, Khan S, Siddiqa A, Ahmed I, Saeed M, Fiaz M. Phylogenetic analysis of blaNDM genes of carbapenem resistant uropathogens isolated from federal tertiary care hospital, Pakistan: insights into the evolution and dissemination of drug resistance. Iran J Microbiol. 2025;17(5):741-750.
