Plasmid-mediated colistin resistance among human clinical Enterobacterales isolates: national surveillance in the Czech Republic

Abstract

The occurrence of colistin resistance has increased rapidly among Enterobacterales around the world. We performed a national survey of plasmid-mediated colistin resistance in human clinical isolates through a retrospective analysis of samples from 2009 to 2017 and a prospective sampling in 2018–2020. The aim of this study was to identify and characterize isolates with mcr genes from various regions of the Czech Republic using whole genome sequencing (WGS). Of all 1932 colistin-resistant isolates analyzed, 73 (3.8%) were positive for mcr genes. Most isolates carried mcr-1 (48/73) and were identified as Escherichia coli (n = 44) and Klebsiella pneumoniae (n = 4) of various sequence types (ST). Twenty-five isolates, including Enterobacter spp. (n = 24) and Citrobacter freundii (n = 1) carrying the mcr-9 gene were detected; three of them (Enterobacter kobei ST54) co-harbored the mcr-4 and mcr-9 genes. Multi-drug resistance phenotype was a common feature of mcr isolates and 14% (10/73) isolates also co-harbored clinically important beta-lactamases, including two isolates with carbapenemases KPC-2 and OXA-48. Phylogenetic analysis of E. coli ST744, the dominant genotype in this study, with the global collection showed Czech isolates belonged to two major clades, one containing isolates from Europe, while the second composed of isolates from diverse geographical areas. The mcr-1 gene was carried by IncX4 (34/73, 47%), IncHI2/ST4 (6/73, 8%) and IncI2 (8/73, 11%) plasmid groups. Small plasmids belonging to the ColE10 group were associated with mcr-4 in three isolates, while mcr-9 was carried by IncHI2/ST1 plasmids (4/73, 5%) or the chromosome (18/73, 25%). We showed an overall low level of occurrence of mcr genes in colistin-resistant bacteria from human clinical samples in the Czech Republic.

Plasmid-mediated colistin resistance from fresh meat and slaughtered animals in the Czech Republic: nation-wide surveillance 2020–2021

“…Several mcr-1 -associated STs including ST744, ST10, and ST162 also alarmingly overlap between livestock and clinical settings ( 51 , 52 ). We observed this phenomenon while comparing the data from our study and another project of our team that was focused on human patients in the Czech Republic ( 19 ). Despite no detection of a clonal pair of isolates with meat and human origin, we detected closely related isolates with a minimum of 38 SNPs in case of ST1011.…”

“…We compared our data with mcr- carrying E. coli strains coming from Czech patients sampled during 2010–2020 ( 19 ). We observed that several STs overlapped with our study including ST69, ST88, ST131, ST162, ST744, and ST1011 (Table S3).…”

“…The WGS-based estimation of mcr-1 location was supported by the conjugation experiment results and S1-PFGE size characterization (for the successfully transferred plasmids). The comparative analysis of mcr region for isolates from our set, our other studies focusing on mcr in Czech Republic ( 10 , 19 ), and relevant public data obtained from GenBank can be found in Supplementary Results: Genetic context of mcr -containing region .…”

Mobile Colistin-Resistant Genes mcr-1, mcr-2, and mcr-3 Identified in Diarrheal Pathogens among Infants, Children, and Adults in Bangladesh: Implications for the Future

“…The use of colistin as an antibiotic of last resort is greatly threatened by its overuse and the associated rise of plasmid-borne mobile colistin resistance genes [ 50 , 51 , 52 ], spreading rapidly via horizontal gene transfer [ 53 ]. Resistance to colistin is generated by the chromosomally mediated modification of lipopolysaccharide (LPS) [ 54 ].…”

“…This is important in Bangladesh, given extensive colistin-resistant Escherichia coli in broiler meat and chicken feces [39][40][41] exacerbating resistance among patients to colistin in Bangladesh [42][43][44][45]. Over-the-counter dispensing of antibiotics is also common in Bangladesh and is a concern, especially when this involves 'Reserve' antibiotics [46][47][48][49] The use of colistin as an antibiotic of last resort is greatly threatened by its overuse and the associated rise of plasmid-borne mobile colistin resistance genes [50][51][52], spreading rapidly via horizontal gene transfer [53]. Resistance to colistin is generated by the chromosomally mediated modification of lipopolysaccharide (LPS) [54].…”