Whole-Genome Sequencing of Clinically Isolated Carbapenem-Resistant Enterobacterales Harboring mcr Genes in Thailand, 2016–2019

Abstract

Mobile colistin-resistant genes (<i>mcr</i>) have become an increasing public health concern. Since the first report of <i>mcr-1</i> in Thailand in 2016, perspective surveillance was conducted to explore the genomic characteristics of clinical carbapenem-resistant Enterobacterales (CRE) isolates harboring <i>mcr</i> in 2016-2019. Thirteen (0.28%) out of 4,516 CRE isolates were found to carry <i>mcr</i> genes, including 69.2% (9/13) of <i>E. coli</i> and 30.8% (4/13) of <i>K. pneumoniae</i> isolates. Individual <i>mcr-1.1</i> was detected in eight <i>E. coli</i> (61.5%) isolates, whereas the co-occurrence of <i>mcr-1.1</i> and <i>mcr-3.5</i> was seen in only one <i>E. coli</i> isolate (7.7%). No CRE were detected carrying <i>mcr-2, mcr-4</i>, or <i>mcr-5</i> through to <i>mcr-9</i>. Analysis of plasmid replicon types carrying <i>mcr</i> revealed that IncX4 was the most common (61.5%; 8/13), followed by IncI2 (15.4%; 2/13). The minimum inhibitory concentration values for colistin were in the range of 4-16 μg/ml for all CRE isolates harboring <i>mcr</i>, suggesting they have 100% colistin resistance. Clermont phylotyping of nine <i>mcr</i>-harboring carbapenem-resistant <i>E. coli</i> isolates demonstrated phylogroup C was predominant in ST410. In contrast, ST336 belonged to CC17, and the KL type 25 was predominant in carbapenem-resistant <i>K. pneumoniae</i> isolates. This report provides a comprehensive insight into the prevalence of <i>mcr</i>-carrying CRE from patients in Thailand. The information highlights the importance of strengthening official active surveillance efforts to detect, control, and prevent <i>mcr</i>-harboring CRE and the need for rational drug use in all sectors.