Molecular Epidemiology of mcr-1, bla_KPC-2, and bla_NDM-1 Harboring Clinically Isolated Escherichia coli from Pakistan

Abstract

Purpose

The multiple-drug resistant Escherichia coli are among the deadliest pathogens causing life-threatening infections. This study was planned to determine the molecular epidemiology of mcr-1, bla_KPC-2, and bla_NDM-1 harboring clinically isolated E. coli from Pakistan.

Methods

In total, 545 strains of E. coli from clinical samples were collected from June 2018 to September 2019. All the isolates were screened for colistin-resistance, extended-spectrum-β-lactamases (ESBL), and carbapenemases through the micro-dilution method, Double-Disk-Synergy-Test (DDST), and Modified-Hodge-Test (MHT). The detection, sequence-typing, conjugal transfer, S1-PFGE, plasmid-replicon-typing, and southern-blotting for mcr, ESBL, and carbapenemase-encoding genes were performed.

Findings

A total of four (0.73%) colistin-resistant strains carrying alongside mcr-1 and bla_CTX-M-15 genes, three of these strains also had the bla_TEM-1 gene. The presence of ESBL genes was detected in 139 (25.5%) isolates harboring bla_CTXM-15 (74.82%), bla_TEM (34.53%), bla_SHV (28.06%) and bla_OXA-1 (28.78%). In 129 carbapenemase-producers, 35.83% possessed bla_NDM-1, 26.67% bla_KPC-2, 8.3% bla_OXA-48, 25% bla_VIM-1, and 20.83% bla_IMP-1 genes. The sequence typing revealed that mcr-1 harboring isolates belonged to ST405, ST117, and ST156. Fifty percent of bla_KPC-2 and 48.83% of bla_NDM-1 were found on ST131 and ST1196, respectively. Two rare types of STs, ST7584, and ST8671 were also identified in this study. The mcr-1 gene was located on Incl2 (60-kb) plasmid. The bla_KPC-2 was present on (140-kb) IncH12, (100-kb) IncN, (90-kb) Incl1, while bla_NDM-1 was located on (70-kb) IncFIIK, (140-kb) IncH12, (100-kb) IncN, (60-kb) IncA/C, and (45-kb) IncFII plasmids, which were successfully trans-conjugated. Among the plasmid types, the Incl1 carrying bla_KPC-2, IncH12 harboring bla_KPC-2 and bla_NDM-1, and IncFIIK carrying bla_NDM-1 were for the first time detected in Pakistan.

Conclusion

The mcr-1, bla_KPC-2, and bla_NDM-1 genes finding in various clonal and plasmids types indicate that a substantial selection of the resistance genes had occurred in our clinical strains.

Keywords:

• colistin-resistance
• extended-spectrum-β-lactamases
• carbapenemases
• mcr1
• bla_KPC-2
• bla_NDM-1
• plasmids
• E. coli

Acknowledgment

The authors are thankful to the Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Pakistan and Institute of Health sciences, Anhui University, China for supporting and facilitating this work.

Ethical Approval

This study was approved by Institutional review board of Anhui University; the ethical approval number is 2020KYNO. 19.

Author Contributions

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, took part in drafting, revising, gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work.

Disclosure

The authors report no conflicts of interest in this work.