Genetic Analysis of mcr-1-Carrying Plasmids From Gram-Negative Bacteria in a Dutch Tertiary Care Hospital: Evidence for Intrapatient and Interspecies Transmission Events

Abstract

The role of plasmids in the complex pandemic of antimicrobial resistance is increasingly being recognized. In this respect, multiple mobile colistin resistance (mcr) gene-carrying plasmids have been described. However, the characteristics and epidemiology of these plasmids within local healthcare settings are largely unknown. We retrospectively characterized the genetic composition and epidemiology of plasmids from mcr-1-positive bacterial isolates identified from patients from a large academic hospital in the Netherlands. Clinical Gram-negative bacteria with an MIC > 2 μg/mL for colistin, obtained from patients hospitalized at the Erasmus MC University Medical Center Rotterdam during the years 2010–2018, were screened for presence of the mcr-1 gene. Extracted plasmids from mcr-1-positive isolates were sequenced using a combination of short- and long-read sequencing platforms, characterized by incompatibility type and genetic composition and compared to publicly available mcr-1-carrying plasmid sequences. In 21 isolates from 14 patients, mcr-1 was located on a plasmid. These plasmids were of diverse genetic background involving Inc types IncX4, IncI2(delta), IncHI2, as well as double Inc types IncHI2/IncN and IncHI2/IncQ. mcr-1-carrying plasmids were found in Escherichia coli, Klebsiella pneumoniae, and Kluyvera georgiana, and within the chromosome of an ST147 K. pneumoniae isolate. In depth analysis indicated intrapatient, interpatient, and interspecies transmission events of mcr-1-carrying plasmids. In addition, our results show that the mcr-1 gene resides in a rich environment full of other (mcr-1 negative) plasmids and of many different Inc types, enabling interplasmidal transfer events and facilitating widespread dissemination of the mcr-1 gene. Multiple mcr-1-carrying plasmid transmission events had likely occurred among isolates from hospitalized patients. Recognition and identification of plasmid transmission events within hospitals is necessary in order to design and implement effective infection control measures.

Plasmidome in mcr-1 harboring carbapenem-resistant enterobacterales isolates from human in Thailand

“…Among such plasmids in our study, the IncX4 and IncI2 plasmid types were genetically similar, with the least variability, whereas the IncHI2/IncN plasmid type was divergent due to the fact that this type of double-Inc type plasmid contains multiple antimicrobial-resistant genes. This was consistent with the results of the two plasmids merging to perhaps increase the range of host species, plasmid fitness, and/or the acquisition of multiple antimicrobial-resistant genes 45 . Another study demonstrated that IncHI2-type plasmids are genetically divergent due to containing an MDR region which comprises a variable combination of antimicrobial-resistance genes and insertion sequences, such as Tn 6330 , in the IncHI2 type that is still highly active and is often transposable 37 .…”

Spread of the mcr-1 colistin-resistance gene in Escherichia coli through plasmid transmission and chromosomal transposition in French goats

“…This was also the case in the IncHI2 and IncX4plasmid sequenced in this study, which, respectively, presented either the truncated IS Apl1 - mcr-1 element or only the mcr-1 - pap2 genes with no trace of the original IS Apl1 sequences. Our results reinforce the hypothesis that the loss of the IS Apl1 sequences might favor the stabilization of the mcr-1 in a plasmidic backbone ( Strepis et al, 2021 ).…”

Klebsiella, a Hitherto Underappreciated Zoonotic Pathogen of Importance to One Health: A Short Review

“…In this study 21 isolates from 14 patients were shown to be positive for mcr-1-containing plasmids, including IncX4, IncI2(delta), IncHI2, IncHI2/IncN, and IncHI2/IncQ. These plasmids were found in K. pneumoniae, Escherichia coli, and Kluyvera georgiana, and on the chromosome of K. pneumoniae ST147 [an ST of international high-risk] [61]. These Klebsiellaassociated plasmid transmission events carrying the broadest AMR gene repertoires amongst humans, animals, and the environment is an evolutionary process in need of urgent remedial action.…”