CLINICAL METAGENOMICS FOR THE DIAGNOSIS OF STAPHYLOCOCCAL INFECTIONS IN THE DOG

THE REDUCTION AND RATIONAL USE OF ANTIBIOTICS IN VETERINARY MEDICINE IS ONE OF THE MAIN STRATEGIES TO REDUCE BACTERIAL RESISTANCE AND IS ADVOCATED BY HEALTH ORGANIZATIONS. ONE OF THE MAIN REASONS FOR PRESCRIBING ANTIMICROBIALS IN VETERINARY MEDICINE IS BACTERIAL SKIN INFECTION IN DOGS (CANINE PYODERMA), MAINLY CAUSED BY STAPHYLOCOCCUS PSEUDINTERMEDIUS. THE HIGH PREVALENCE OF METHICILLIN-RESISTANT S. PSEUDINTERMEDIUS IS A GROWING CONCERN, AND ITS EMERGENCE ASSOCIATED WITH EVEN BROADER DRUG RESISTANCE HAS BECOME A WORLDWIDE CHALLENGE. FURTHERMORE, S. PSEUDINTERMEDIUS HAS A ZOONOTIC IMPACT BECAUSE IT CAN CAUSE INFECTION IN HUMANS, AND THE ANTIBIOTIC-RESISTANCE GENES CAN BE TRANSMITTED TO OTHER STAPHYLOCCOCUS SPECIES THAT ARE HUMAN PATHOGENS. THE PRESENT PROJECT SEEKS TO EXPLORE THE POSSIBILITY OF INTRODUCING A METHODOLOGICAL CHANGE IN THE DIAGNOSIS OF INFECTIOUS DISEASES BASED ON THE RECENT ADVANCES IN WHOLE GENOME SEQUENCING. OUR HYPOTHESIS IS THAT A CLINICAL METAGENOMICS ASSAY USING NANOPORE SEQUENCING WILL BE SUITABLE FOR THE RAPID DIAGNOSIS OF SKIN INFECTIONS IN DOGS, ALLOWING THE IDENTIFICATION OF THE BACTERIAL PATHOGEN AND THE CHARACTERIZATION OF ITS ASSOCIATED ANTIMICROBIAL RESISTANCE AND VIRULENCE FACTORS. STAPHYLOCOCCUS SKIN INFECTIONS IN DOGS ARE AN IDEAL MODEL FOR THIS STUDY. FIRSTLY, BECAUSE IT IS A MODEL WE KNOW WELL AND HAVE PREVIOUSLY CHARACTERIZED IN ANOTHER RESEARCH PROJECT (PROYECTO RTI2018-101991-B-100). SECONDLY, BECAUSE S. PSEUDINTERMEDIUS IS VERY SIMILAR TO S. AUREUS, AN IMPORTANT HUMAN PATHOGEN, SO THE RESULTS CAN BE EASILY EXTRAPOLATED TO HUMAN MEDICINE. HOWEVER, TO FULLY REPLACE CULTURE AND ANTIMICROBIAL SUSCEPTIBILITY TESTING, SOME PROBLEMS MUST BE SOLVED, SUCH AS: 1) IMPROVING EXTRACTION OF BACTERIAL DNA AND SEQUENCING - OBTAINING A SAMPLE OF ENOUGH QUALITY FOR LONG-READS METAGENOMICS SEQUENCING. 2) BEING ABLE TO DISCRIMINATE BETWEEN THE PATHOGEN AND THE COMMENSAL BACTERIA PRESENT IN THE CLINICAL SAMPLE. 3) DEMONSTRATING A GOOD CORRELATION BETWEEN THE ANTIMICROBIAL PHENOTYPE (RESISTANCE/SUSCEPTIBILITY USING MIC) AND GENOTYPE (PRESENCE/ABSENCE OF ANTIMICROBIAL RESISTANCE GENES AND POINT MUTATIONS). 4) DEVELOPING A USER-FRIENDLY WAY TO REPORT THE RESULTS OF METAGENOMICS SEQUENCING TO THE VETERINARY CLINICIAN. THE AIM OF THE PRESENT PROJECT IS TO OVERCOME THESE BARRIERS BY DEVELOPING AN IMPLEMENTABLE CLINICAL METAGENOMICS METHOD BASED ON NANOPORE SEQUENCING ON PORTABLE SEQUENCERS. IF SUCCESSFUL, IT WOULD ALLOW A REDUCTION IN THE EMPIRICAL PRESCRIPTION OF ANTIBIOTICS IN VETERINARY MEDICINE AND SERVE AS A MODEL TO IMPLEMENT A SIMILAR CHANGE IN HUMAN MEDICINE. THE BENEFITS OF OUR PROPOSAL CAN BE SUMMARISED IN THE FOLLOWING POINTS: 1) SPECIFICALLY, IT MAY ALLOW THE DEVELOPMENT OF A RAPID METHOD TO IDENTIFY AND CHARACTERISE THE CAUSATIVE BACTERIA OF SKIN INFECTIONS IN VETERINARY MEDICINE, REDUCING THE EMPIRICAL PRESCRIPTION OF ANTIBIOTICS. OUR METHODOLOGY, IF SUCCESSFUL, WOULD BE TRANSFERRED TO LARGE VETERINARY DIAGNOSTIC LABORATORIES FOR LARGE-SCALE IMPLEMENTATION. 2) IN ADDITION, IT WILL SOLVE SOME OF THE PROBLEMS THAT IMPEDE THE PROGRESS OF CLINICAL METAGENOMICS AND, THEREFORE, MAY FACILITATE ITS IMPLEMENTATION IN OTHER ANIMAL OR HUMAN INFECTIOUS DISEASES. IT IS THEREFORE A TRANSLATIONAL PROPOSAL, ORIENTED TOWARDS PROVIDING SOLUTIONS DERIVED FROM SCIENTIFIC AND TECHNOLOGICAL ADVANCES TO A MAJOR HEALTH PROBLEM.