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Veterinary research2023; 54(1); 33; doi: 10.1186/s13567-023-01160-2

Whole genome sequencing to study antimicrobial resistance and RTX virulence genes in equine Actinobacillus isolates.

Abstract: Actinobacillus equuli is mostly associated with disease in horses and is most widely known as the causative agent of sleepy foal disease. Even though existing phenotypic tools such as biochemical tests, 16S rRNA gene sequencing, and Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) can be used to identify members of the Actinobacillus genus, these methods struggle to differentiate between certain species and do not allow strain, virulence, and antimicrobial susceptibility typing. Hence, we performed in-depth analysis of 24 equine Actinobacillus isolates using phenotypic identification and susceptibility testing on the one hand, and long-read nanopore whole genome sequencing on the other hand. This allowed to address strain divergence down to the whole genome single nucleotide polymorphism (SNP) level. While lowest resolution was observed for 16S rRNA gene classification, a new multi-locus sequence typing (MLST) scheme allowed proper classification up to the species level. Nevertheless, a SNP-level analysis was required to distinguish A. equuli subspecies equuli and haemolyticus. Our data provided first WGS data on Actinobacillus genomospecies 1, Actinobacillus genomospecies 2, and A. arthritidis, which allowed the identification of a new Actinobacillus genomospecies 1 field isolate. Also, in-depth characterization of RTX virulence genes provided information on the distribution, completeness, and potential complementary nature of the RTX gene operons within the Actinobacillus genus. Even though overall low prevalence of acquired resistance was observed, two plasmids were identified conferring resistance to penicillin-ampicillin-amoxicillin and chloramphenicol in one A. equuli strain. In conclusion our data delivered new insights in the use of long-read WGS in high resolution identification, virulence gene typing, and antimicrobial resistance (AMR) of equine Actinobacillus species.
© 2023. The Author(s).
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Publication Date: 2023-04-05 PubMed ID: 37020296PubMed Central: PMC10074821DOI: 10.1186/s13567-023-01160-2Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research used whole genome sequencing to deeply analyze Actinobacillus equuli, a bacteria commonly causing disease in horses, to better understand its resistance to antibiotics and its virulence genes. The study uncovers new insights on identification, virulence gene typing, and antimicrobial resistance of the bacteria.

Research Purpose and Approach

  • The study aimed to explore, with greater clarity and accuracy, the antimicrobial resistance and virulent characteristics of Actinobacillus equuli, a bacterium often associated with infections in horses. Traditional identification methods, while useful, have proven to be limited in differentiating between certain species and establishing virulence and antimicrobial susceptibility patterns.
  • To achieve this, the researchers carried out an extensive analysis of 24 equine Actinobacillus isolates. This analysis incorporated both phenotypic identification and susceptibility testing alongside long-read nanopore whole genome sequencing, permitting a thorough investigation down to single nucleotide polymorphisms.

Findings

  • The study discovered that the lowest resolution was found when employing 16S rRNA gene classification, whereas a new multi-locus sequence typing (MLST) scheme allowed for proper classification up to the species level. To distinguish between A. equuli subspecies equuli and haemolyticus, however, SNP-level analysis was necessary.
  • The first whole genome sequencing (WGS) data on Actinobacillus genomospecies 1, Actinobacillus genomospecies 2, and A. arthritidis was provided by the study, unveiling a new field isolate for Actinobacillus genomospecies 1.
  • The data also allowed robust characterization of RTX virulence genes – this provided further information on distribution, completeness, and the potential complementary nature of the RTX gene operons within the Actinobacillus genus.
  • Despite mostly low prevalence of acquired resistance, penicillin-ampicillin-amoxicillin and chloramphenicol resistance in one A. equuli strain were identified, facilitated by two different plasmids.

Conclusion

  • This research not only provided new insights into this bacterial genus, but also demonstrated the effectiveness of long-read whole genome sequencing in identifying, typing virulence genes, and determining antimicrobial resistance of equine Actinobacillus species. This can help develop better disease management in horses.

Cite This Article

APA
Vereecke N, Vandekerckhove A, Theuns S, Haesebrouck F, Boyen F. (2023). Whole genome sequencing to study antimicrobial resistance and RTX virulence genes in equine Actinobacillus isolates. Vet Res, 54(1), 33. https://doi.org/10.1186/s13567-023-01160-2

Publication

Veterinary research
ISSN: 1297-9716
NlmUniqueID: 9309551
Country: England
Language: English
Volume: 54
Issue: 1
Pages: 33
PII: 33

Researcher Affiliations

Vereecke, Nick
  • Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium. nick.vereecke@ugent.be.
  • PathoSense BV, Lier, Belgium. nick.vereecke@ugent.be.
Vandekerckhove, Arlette
  • Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
Theuns, Sebastiaan
  • PathoSense BV, Lier, Belgium.
Haesebrouck, Freddy
  • Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
Boyen, Filip
  • Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.

MeSH Terms

  • Animals
  • Horses
  • Actinobacillus / genetics
  • Anti-Bacterial Agents
  • Multilocus Sequence Typing / veterinary
  • RNA, Ribosomal, 16S / genetics
  • Virulence
  • Drug Resistance, Bacterial
  • Whole Genome Sequencing / veterinary

Grant Funding

  • HBC.2020.2889 / Agentschap Innoveren en Ondernemen
  • AUGE/15/05 / Research Foundation-Flanders (FWO)

Conflict of Interest Statement

None of the authors of this paper has a financial or personal relationship with other people or organisations that could inappropriately influence or bias the content of the paper. ST is co-founder and co-owner of PathoSense BV. NV is an employee at PathoSense BV.

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Citations

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