The Use of Long-Read Sequencing Technologies in Infection Control: Horizontal Transfer of a blaCTX-M-27 Containing lncFII Plasmid in a Patient Screening Sample.

Vincent van Almsick,Alexander Mellmann,Franziska Schuler,Vera Schwierzeck

doi:10.3390/microorganisms10030491

Vincent van Almsick, Alexander Mellmann + Show 2 more

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https://doi.org/10.3390/microorganisms10030491

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Journal: Microorganisms	Publication Date: Feb 23, 2022
Citations: 7	License type: CC BY 4.0

Affiliation: University Hospital Münster

Abstract

Plasmid transfer is one important mechanism how antimicrobial resistance can spread between different species, contributing to the rise of multidrug resistant bacteria (MDRB) worldwide. Here were present whole genome sequencing (WGS) data of two MDRB isolates, an Escherichia coli and a Klebsiella quasipneumoniae, which were isolated from a single patient. Detailed analysis of long-read sequencing data identified an identical F2:A-:B- lncFII plasmid containing blaCTX-M-27 in both isolates, suggesting horizontal plasmid exchange between the two species. As the plasmid of the E. coli strain carried multiple copies of the resistance cassette, the genomic data correlated with the increased antimicrobial resistance (AMR) detected for this isolate. Our case report demonstrates how long-read sequencing data of MDRB can be used to investigate the role of plasmid mediate resistance in the healthcare setting and explain resistance phenotypes.

Highlights

The spread of multidrug resistant bacteria (MDRB) has become a serious threat for healthcare systems worldwide as antimicrobial resistance (AMR) limits treatment options even for life-threatening infections [1]
One limiting factor is the use of short-read sequencing, as the technology has difficulties to distinguish if antimicrobial resistance genes (ARG) are located on the chromosome or on a plasmid
During routine multidrug resistance (MDR) screening upon intensive care unit (ICU) admission, two MDR

Summary

Introduction

The spread of multidrug resistant bacteria (MDRB) has become a serious threat for healthcare systems worldwide as antimicrobial resistance (AMR) limits treatment options even for life-threatening infections [1]. Horizontal gene transfer enables bacteria to share antimicrobial resistance genes (ARG) between various species by exchanging AMR plasmids [2,3,4]. One limiting factor is the use of short-read sequencing, as the technology has difficulties to distinguish if ARGs are located on the chromosome or on a plasmid. Since long-read sequencing technology has been introduced into routine microbiology laboratories, this information has become more readily available [5,6] and can help in the detection and analyzation of ARG movement by plasmid conjugation and other mobile genetic elements [6]. We wanted to show how long-read sequencing data can be used to identify plasmid-mediated multidrug resistance (MDR) in a routine clinical sample. Detailed analysis of the MDR plasmid revealed an “artificial” multicopy of the AMR cassette, leading to a significantly higher minimum inhibitory concentration (MIC) against antibiotics

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