Comparing PFGE, MLST, and WGS in monitoring the spread of macrolide and rifampin resistant Rhodococcus equi in horse production.
Abstract: Rhodococcus equi (R. equi) infections are endemic in many horse facilities in the United States resulting significant economic loses annually. Currently, there is no commercial vaccine available and the emergence of isolates that are resistant to the current treatment and prophylaxis using antibiotics prompts closer surveillance of this pathogen. Objective: This study compares three different genotyping techniques, Pulsed Field Gel Electrophoresis (PFGE), Multilocus Sequence Typing (MLST) and whole genome SNP-based phylogeny to determine the most accurate method to monitor the spread of macrolide-and-rifampin-resistant R. equi. Methods: 16 macrolide and rifampin-resistant and 6 susceptible R. equi and their Illumina Miseq whole genome sequences were used in this study. The isolates were sub-typed by PFGE with VspI and a dendrogram based on their similarities generated. Additionally, three phylogenetic trees were constructed using CSI phylogeny on (i) whole genome sequences (WGS), (ii) in silico MLST sequences and (iii) MLST sequences obtained after PCR-amplification and Sanger sequencing. Results: PFGE identified 18 different genetic profiles and grouped the 22 isolates into 3 clusters independently of their susceptibilities. The phylogenetic trees built from WGS and MLST data showed similar topology, separating the isolates into 2 major clades in accordance with their susceptibility profiles (susceptible and resistant). However, only the trees generated with next generation sequencing data could detect the clonality of the resistant isolates.
Copyright © 2020 Elsevier B.V. All rights reserved.
Publication Date: 2019-12-28 PubMed ID: 32122585DOI: 10.1016/j.vetmic.2019.108571Google Scholar: Lookup
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- Comparative Study
- Journal Article
Summary
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This research investigates three techniques for monitoring the spread of a particular bacteria in horses which is becoming resistant to usual treatments. The team wanted to see which method gave the most accurate results.
Background
- Rhodococcus equi (R. equi) is a bacteria causing disease in horses and leading to major financial losses due to no current vaccine.
- Increasing antibiotic resistance in R. equi makes the need for accurate surveillance crucial to control its spread.
- The goal of the study was to compare three genotyping techniques, Pulsed Field Gel Electrophoresis (PFGE), Multilocus Sequence Typing (MLST) and whole genome SNP-based phylogeny for monitoring bacterial spread.
Methods
- 22 isolates of R. equi were used, including 16 resistant and 6 susceptible to macrolide and rifampin, common antibiotics used for its treatment.
- Their whole genome sequences were obtained using Illumina Miseq sequencing technology.
- The isolates were then sub-typed, using PFGE technique, identifying their genetic variability.
- Three phylogenetic trees, which trace and visually represent the genealogy of species, were created using WGS, in silico MLST sequences and MLST sequences obtained after PCR-amplification and Sanger sequencing.
Results
- PFGE identified 18 different genetic profiles and grouped the 22 isolates into 3 clusters, not depending on their susceptibilities to antibiotics.
- The phylogenetic trees generated with WGS and MLST data had similar topologies, dividing the isolates into 2 major groups consistent with their susceptibility profiles (i.e., susceptible and resistant isolates grouped separately).
- However, only the trees generated with next-generation sequencing data could identify the clonality, or genetic similarity, of the resistant isolates.
Conclusion
- In essence, this study suggests that genotyping methods using next-generation sequencing data, such as WGS, might provide more detailed and accurate insights into transmission of antibiotic-resistant R. equi.
- This could lead to more effective strategies for managing and preventing its spread.
Cite This Article
APA
Álvarez-Narváez S, Logue CM, Barbieri NL, Berghaus LJ, Giguère S.
(2019).
Comparing PFGE, MLST, and WGS in monitoring the spread of macrolide and rifampin resistant Rhodococcus equi in horse production.
Vet Microbiol, 242, 108571.
https://doi.org/10.1016/j.vetmic.2019.108571 Publication
Researcher Affiliations
- Department of Large Animal Medicine, University of Georgia, Athens 30605, USA. Electronic address: Sonsiray.Alvarez@uga.edu.
- Department of Population Health, University of Georgia, Athens 30602, USA.
- Department of Population Health, University of Georgia, Athens 30602, USA.
- Department of Large Animal Medicine, University of Georgia, Athens 30605, USA.
- Department of Large Animal Medicine, University of Georgia, Athens 30605, USA.
MeSH Terms
- Actinomycetales Infections / microbiology
- Actinomycetales Infections / veterinary
- Animals
- Anti-Bacterial Agents / pharmacology
- Bacterial Typing Techniques
- Drug Resistance, Multiple, Bacterial / genetics
- Electrophoresis, Gel, Pulsed-Field
- Genotyping Techniques
- Horse Diseases / microbiology
- Horses / microbiology
- Macrolides / pharmacology
- Microbial Sensitivity Tests
- Multilocus Sequence Typing
- Phylogeny
- Rhodococcus equi / classification
- Rhodococcus equi / drug effects
- Rifampin / pharmacology
- Sequence Analysis, DNA
- Whole Genome Sequencing
Citations
This article has been cited 2 times.- Zeng X, Xiong L, Wang W, Zhao Y, Xie Y, Wang Q, Zhang Q, Li L, Jia C, Liao Y, Zhou J. Whole-genome sequencing and comparative analysis of Helicobacter pylori GZ7 strain isolated from China.. Folia Microbiol (Praha) 2022 Dec;67(6):923-934.
- Álvarez-Narváez S, Huber L, Giguère S, Hart KA, Berghaus RD, Sanchez S, Cohen ND. Epidemiology and Molecular Basis of Multidrug Resistance in Rhodococcus equi.. Microbiol Mol Biol Rev 2021 May 19;85(2).
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