Detection of the emergence of mcr-1–mediated colistin-resistant Escherichia coli and Klebsiella pneumoniae through a hospital-based surveillance in an oncology center in eastern India

To the Editor—The global emergence of colistin-resistant Enterobacteriaceae through the plasmid-mediated mcr gene has raised concerns with regard to spread of antimicrobial resistance and infection control.¹ There are several mechanisms of colistin resistance.² However, the molecular epidemiology of colistin resistance in clinically relevant gram-negative isolates is poorly defined in India, a country that is large and populous and is also a major trading center and an international tourism destination.^3,4 Here, we document 2 cases of mcr-gene–mediated colistin resistance in Enterobacteriaceae from an oncology center in eastern India.

Case 1

In June 2018, we isolated Escherichia coli in the urine of a 51-year-old woman from West Bengal, India, with metastatic carcinoma of lung. The E. coli isolate (detected while she was in the community) was positive for bla _OXA-48 and mcr-1 (confirmed by PCR and DNA sequencing).The minimum inhibitory concentration (MIC) for colistin was 4 µg/mL. In September 2019, while she was in the hospital, we detected Klebsiella pneumoniae from endotracheal aspirate which was bla _OXA-48 and mcr-1 positive (colistin MIC, 16 µg/mL). The patient was treated with fosfomycin. The patient had a diagnosis of diabetes mellitus and had several medical devices (urinary catheter, tracheostomy, central line). Carbapenemase-resistant isolates were detected previously, and she had received treatment in the past with meropenem and colistin.

Case 2

In an 8-year-old girl from Bangladesh with acute lymphoblastic leukemia, we detected, from left buttock wound swab, a carbapenem-sensitive but colistin-resistant Escherichia coli (positive for mcr-1) with an MIC of 8 µg/mL.

These 2 cases were part of a prospective surveillance for mcr-1–5 genes conducted in Tata Medical Center, Kolkata, India, a 183-bed oncology center where patients are mainly from the state of West Bengal in India but also from neighboring states in India and countries such as Bangladesh and Bhutan. The inclusion criteria for testing of mcr-1–5 genes by polymerase chain reaction (PCR) was the detection of colistin resistance (MIC ≥ 2 µg/mL) using the microbroth dilution method according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical Laboratory Standards Institute (CLSI) guidelines. If found to be carbapenem resistant, the isolates were also screened for the presence of the following carbapenemase-associated genes: bla _NDM-1, bla _VIM, bla _IMP, bla _{OXA48-like,23,24,58}, bla _KPC. Identification of the isolates was performed using the Vitek2 system (bioMèrieux, Marcy-l'Étoile, France), and mcr-1–5 genes were tested using in-house end-point multiplex PCR. If positive, they were confirmed by Sanger-based DNA sequencing. The results of this surveillance (conducted between August 2017 to October 2019) are presented in online Fig. 1 and Table 1.

Table 1. Distribution of Carbapenemase- and Colistin-Resistant mcr-1 Gene in the Samples Studied (N = 198)

Note: carbapenemase genes tested included: bla _NDM, bla _KPC, bla _IMP, bla _VIM, _{blaOXA-48, 23,24,58}.

Among colistin-resistant mechanisms, plasmid-mediated resistance is a major cause of global concern because of the potential for transfer of colistin-resistance genes to susceptible strains. These genes were first reported in E. coli isolated in China.¹ The mechanism of mcr-mediated colistin resistance is as follows. Encoded mcr-1 protein is a member of the phosphoethanolamine transferase enzyme family; mcr acquisition results in the addition of phosphoethanolamine to lipid A, and thereby to a more cationic lipopolysaccharide, which contributes to acquired colistin resistance in Enterobacteriaceae.⁵ Isolates carrying the mcr-1 gene demonstrate resistance to colistin displaying 4–8-fold increase in colistin MIC.⁵ Some plasmids containing the mcr-1 gene carry other genes that are resistant to antibiotics, such as β-lactams, aminoglycosides, quinolones, sulfonamides, tetracyclines, and fosfomycin.⁵ The mcr gene has also been identified in Enterobacteriaceae isolates, which carry such carbapenemase genes as bla _NDM1, bla _NDM5, bla _NDM9, bla _OXA48, bla _KPC2, and bla _VIM1.⁶ Studies have shown mcr-2–mediated colistin resistance in E. coli isolates from European countries, whereas mcr-3 has been widely identified in Enterobacteriaceae (mainly E. coli) and Aeromonas spp from Asia, Europe, and North America.^7,8 The mcr-4 and mcr-5 genes were first characterized in Salmonella and E. coli from European countries.^9,10 Currently from India, only 1 report of mcr-mediated colistin resistance in Klebsiella pneumoniae has been published.³ In 2017, Borowiak et al¹⁰ reported a new gene of the mcr family from Salmonella paratyphi B that were carried in transposons instead of plasmids.

The emergence of colistin resistance is a cause for concern for both clinicians and patients, particularly in countries with high rates of carbapenem- and/or colistin-resistant Enterobacteriaceae such as China and India. We are not aware of any report of the prevalence of mcr-mediated colistin resistance in the immunocompromised cancer patient population in India.

Because the mcr gene is plasmid mediated, the infection prevention and control challenges are significant. Using the PCR-based method, we have tried to develop a relatively low cost and feasible system to detect mcr-mediated mechanisms of colistin resistance. The cost of mcr gene detection is USD $7 for the multiplex screening PCR and USD $20 for Sanger-based DNA sequencing per isolate.

This study is important in several aspects. We have shown that mcr-1–mediated colistin resistance may occur independent of carbapenem resistance (i.e. case 2). The occurrence of these resistance mechanisms in immunocompromised cancer patients who have extensive healthcare and antibiotic exposure as well as hospital admission episodes increases the risk of infection spread in healthcare settings as well as in community (case 1). The second case shows that this resistance phenomenon can be found even in children. These cases are, to the best of our knowledge, the first reports of such infections from eastern India. Because of the proximity of this region to highly populous areas and to international trade, tourism, and travel, the likelihood of international dissemination may be high. Surveillance of mcr-mediated colistin resistance may reveal more cases and facilitate better infection control.