Genomic Characterization of mcr-1.1-Producing Escherichia coli Recovered From Human Infections in São Paulo, Brazil

Abstract

Polymyxins are one of most important antibiotics available for multidrug-resistant Gram-negative infections. Diverse chromosomal resistance mechanisms have been described, but the polymyxin resistance phenotype is not yet completely understood. The objective of this study was to characterize colistin resistant mcr-1-producing strains isolated from human infections over one year in a hospital setting (Hospital das Clínicas, São Paulo, Brazil). We isolated 490 colistin-resistant Gram-negative rods, of which eight were mcr-1.1-positive Escherichia coli, the only species with this result, indicating a low incidence of the mcr-1 production mechanism among colistin-resistant isolates. All mcr-1.1 positive isolates showed similarly low MICs for colistin and were susceptible to most antibiotics tested. The isolates showed diversity of MLST classification. The eight mcr-1.1-positive E. coli genomes were sequenced. In seven of eight isolates the mcr-1.1 gene is located in a contig that is presumed to be a part of an IncX4 plasmid; in one isolate, it is located in a contig that is presumed to be part of an IncHI2A plasmid. Three different genomic contexts for mcr-1.1 were observed, including a genomic cassette mcr-1.1-pap2 disrupting a DUF2806 domain-containing gene in six isolates. In addition, an IS1-family transposase was found inserted next to the mcr-1.1 cassette in one isolate. An mcr-1.1-pap2 genomic cassette not disrupting any gene was identified in another isolate. Our results suggest that plasmid dissemination of hospital-resident strains took place during the study period and highlight the need for continued genomic surveillance.

Screening of mcr-1 among Gram-Negative Bacteria from Different Clinical Samples from ICU Patients in Alexandria, Egypt: One-Year Study

“…Moreover, mcr-1.1 was reported in E. coli isolate obtained from wound drainage ( Eltai et al 2020 ) from Qatar. Girardello et al (2021) reported the presence of mcr-1.1 in E. coli clinical isolate in Sao Paulo, and mcr-1.1 was found in two K. pneumoniae clinical isolates by Rocha et al (2020) .…”

Antimicrobial resistance surveillance of Escherichia coli from chickens in the Qinghai Plateau of China

“…It is the diverse genetic mechanisms of the mcr-1-carrying IncI and IncHI2/HI2A plasmids that cause the high horizontal transfer rate of mcr-1, e.g., the mcr-1-related insertion element ISApl1 (1,070 bp; Zhong et al, 2018), which was originally discovered in Actinobacillus pleuropneumoniae (Tegetmeyer et al, 2008), is the most important mobile element of the IS30 family mediating the spread of mcr-1. The Tn6330 transposon (ISApl1-pap2-mcr-1-ISApl1) can mediate the horizontal transfer of mcr-1, in which ISApl1 forms a ringshaped intermediate in a "cut-and-paste" manner to mediate the spread of mcr-1 among different types of plasmids (Girardello et al, 2021). In the QH20-5D4-1 isolate, the transposon element ISApl1 was present downstream of mcr-1, and the pap2 gene present upstream of mcr-1 encodes the phospholipase closely related to the horizontal transmission of mcr-1 (Ma et al, 2021), both playing a very important role in mcr-1 mediated bacterial colistin resistance (Choi et al, 2020).…”

Detection and characterization of ESBL-producing Escherichia coli and additional co-existence with mcr genes from river water in northern Thailand

“…The genomic context analysis of the genome location of mcr-1.1 revealed that of the mcr-1.1 - pap2 cassette was present in this work. A variety of mcr-1.1 - pap2 cassette compositions have been shown, suggesting the ability of mcr-1 to mobilize across the genes ( Girardello et al, 2021 ; Snesrud et al, 2016 ). IS Apl1 flanking the mcr-1.1 - pap2 cassette conferred the transposition and was found to be lost after mobilization ( Snesrud et al, 2016 ).…”