Abstract
ObjectivesMDR bacteria have become a prevailing health threat worldwide. We here aimed to use optical DNA mapping (ODM) as a rapid method to trace nosocomial spread of bacterial clones and gene elements. We believe that this method has the potential to be a tool of pivotal importance for MDR control.MethodsTwenty-four Escherichia coli samples of ST410 from three different wards were collected at an Ethiopian hospital and their plasmids were analysed by ODM. Plasmids were specifically digested with Cas9 targeting the antibiotic resistance genes, stained by competitive binding and confined in nanochannels for imaging. The resulting intensity profiles (barcodes) for each plasmid were compared to identify potential clonal spread of resistant bacteria.ResultsODM demonstrated that a large fraction of the patients carried bacteria with a plasmid of the same origin, carrying the ESBL gene blaCTX-M-15, suggesting clonal spread. The results correlate perfectly with core genome (cg)MLST data, where bacteria with the same plasmid also had very similar cgMLST profiles.ConclusionsODM is a rapid discriminatory method for identifying plasmids and antibiotic resistance genes. Long-range deletions/insertions, which are challenging for short-read next-generation sequencing, can be easily identified and used to trace bacterial clonal spread. We propose that plasmid typing can be a useful tool to identify clonal spread of MDR bacteria. Furthermore, the simplicity of the method enables possible future application in low- and middle-income countries.
Highlights
The prevalence of MDR pathogens is increasing rapidly worldwide
The strains originated from patients that were treated in three different wards [paediatric (16), surgical (5) and medical (3)], and a potential outbreak would indicate transmission of bacteria between wards in the hospital
This study analysed plasmids from isolates collected from three different wards in a rural Ethiopian hospital using both Optical DNA mapping (ODM) and Next-generation sequencing (NGS)
Summary
The prevalence of MDR pathogens is increasing rapidly worldwide. It has been demonstrated that ICUs serve as long-term selection environments of MDR bacteria through selection of resistant strains in the microbiota, which can subsequently spread among patients and cause hospital-acquired infections.[2,3] The incidence of hospital-acquired infections is 5–10 times higher in ICUs than in general wards.[4]. Studies from Kenya,[5] Tanzania,[6] Uganda[7] and other countries reported high prevalence of AMR to different classes of antimicrobials.[8] A meta-analysis study on articles published from 2007 to 2017 reported that an average of 45% (range 27.5%–62.5%) of Escherichia coli strains were resistant to commonly prescribed antimicrobials in Ethiopia.[9] Another study from Jimma University Medical Center, Ethiopia, in 2014 reported that 28% of E. coli and 70% of Klebsiella pneumoniae were ESBL producing.[10] specific factors related to the cause and dissemination of AMR remain to be studied. An in-depth study requires an alternative to expensive and accurate diagnostic tools to study both local and regional outbreaks
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