Characterization of NDM-5 Carbapenemase-Encoding Gene (bla NDM-5) - Positive Multidrug Resistant Commensal Escherichia coli from Diarrheal Patients

Goutam Chowdhury; Thandavarayan Ramamurthy; Bhabatosh Das; Debjani Ghosh; Keinosuke Okamoto; Shin-Ichi Miyoshi; Shanta Dutta; Asish K Mukhopadhyay

doi:10.2147/IDR.S364526

Characterization of NDM-5 Carbapenemase-Encoding Gene (bla _NDM-5) - Positive Multidrug Resistant Commensal Escherichia coli from Diarrheal Patients

Infect Drug Resist. 2022 Jul 8:15:3631-3642. doi: 10.2147/IDR.S364526. eCollection 2022.

Authors

Goutam Chowdhury^{1

2}, Thandavarayan Ramamurthy¹, Bhabatosh Das³, Debjani Ghosh¹, Keinosuke Okamoto², Shin-Ichi Miyoshi^{2

4}, Shanta Dutta¹, Asish K Mukhopadhyay¹

Affiliations

¹ Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.
² Collaborative Research Centre of Okayama University for Infectious Diseases, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.
³ Department of Infection and Immunology, Translational Health Science and Technology Institute, Faridabad, India.
⁴ Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.

Abstract

Purpose: The multidrug resistance Enterobacteriaceae cause many serious infections resulting in prolonged hospitalization, increased treatment charges and mortality rate. In this study, we characterized bla _NDM-5-positive multidrug resistance commensal Escherichia coli (CE) isolated from diarrheal patients in Kolkata, India.

Methods: Three CE strains were isolated from diarrheal stools, which were negative for different pathogroups of diarrheagenic E. coli (DEC). The presence of carbapenemases encoding genes and other antimicrobial resistance genes (ARGs) was detected using PCR. The genetic arrangement adjoining bla _NDM-5 was investigated by plasmid genome sequencing. The genetic relatedness of the strains was determined by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) methods.

Results: In addition to colistin, the bla _NDM-5-positive CE strains showed resistance to most of the antibiotics. Higher MICs were detected for ciprofloxacin (>32 mg/L) and imipenem (8 mg/L). Molecular typing revealed that three CE strains belonged to two different STs (ST 101 and ST 648) but they were 95% similar in the PFGE analysis. Screening for ARGs revealed that CE strains harbored Int-1, bla _TEM, bla_C _TX-M3, bla _OXA-1, bla _OXA-7, bla _OXA-9, tetA, strA, aadA1, aadB, sul2, floR, mph(A), and aac(6´)-Ib-cr. In conjugation experiment, transfer frequencies ranged from 2.5×10^-3 to 8.4x10^-5. The bla _NDM-5 gene was located on a 94-kb pNDM-TC-CE-89 type plasmid, which is highly similar to the IncFII plasmid harboring an IS26-IS30-bla _NDM-5-ble _MBL-trpF-dsbd-IS91-dhps structure.

Conclusion: To the best of our knowledge, this is the first report on carbapenem resistance involving the bla _NDM-5 gene in CE from diarrheal patients. The circulation of bla _NDM-5 gene in CE is worrisome, since it has the potential to transfer bla _NDM-5 gene to other enteric pathogens.

Keywords: antimicrobial resistance; carbapenem-resistance; commensal E. coli; plasmid; blaNDM-5.

Grants and funding

This study was supported in part by the Indian Council of Medical Research (ICMR), Government of India, New Delhi, India, the Japan Initiative for Global Research Network on Infectious Diseases (J-GRID), the Ministry of Education, Culture, Sports, Science and Technology in Japan, and the Japan Agency for Medical Research and Development (AMED; grant number JP21wm0125004 to SM).