Genome-Wide Association Study Reveals Genetic Markers for Antimicrobial Resistance in Mycoplasma bovis.

Mycoplasma bovis causes many health and welfare problems in cattle. Due to the absence of clear insights regarding transmission dynamics and the lack of a registered vaccine in Europe, control of an outbreak depends mainly on antimicrobial therapy. Unfortunately, antimicrobial susceptibility testing (AST) is usually not performed, because it is time-consuming and no standard protocol or clinical breakpoints are available. Fast identification of genetic markers associated with acquired resistance may at least partly resolve former issues. Therefore, the aims of this study were to implement a first genome-wide association study (GWAS) approach to identify genetic markers linked to antimicrobial resistance (AMR) in M. bovis using rapid long-read sequencing and to evaluate different epidemiological cutoff (ECOFF) thresholds. High-quality genomes of 100 M. bovis isolates were generated by Nanopore sequencing, and isolates were categorized as wild-type or non-wild-type isolates based on MIC testing results. Subsequently, a k-mer-based GWAS analysis was performed to link genotypes with phenotypes based on different ECOFF thresholds. This resulted in potential genetic markers for macrolides (gamithromycin and tylosin) (23S rRNA gene and 50S ribosomal unit) and enrofloxacin (GyrA and ParC). Also, for tilmicosin and the tetracyclines, previously described mutations in both 23S rRNA alleles and in one or both 16S rRNA alleles were observed. In addition, two new 16S rRNA mutations were possibly associated with gentamicin resistance. In conclusion, this study shows the potential of quick high-quality Nanopore sequencing and GWAS analysis in the evaluation of phenotypic ECOFF thresholds and the rapid identification of M. bovis strains with acquired resistance. IMPORTANCE Mycoplasma bovis is a leading cause of pneumonia but also causes other clinical signs in cattle. Since no effective vaccine is available, current M. bovis outbreak treatment relies primarily on the use of antimicrobials. However, M. bovis is naturally resistant to different antimicrobials, and acquired resistance against macrolides and fluoroquinolones is frequently described. Therefore, AST is important to provide appropriate and rapid antimicrobial treatment in the framework of AMR and to prevent the disease from spreading and/or becoming chronic. Unfortunately, phenotypic AST is time-consuming and, due to the lack of clinical breakpoints, the interpretation of AST in M. bovis is limited to the use of ECOFF values. Therefore, the objective of this study was to identify known and potentially new genetic markers linked to AMR phenotypes of M. bovis isolates, exploiting the power of a GWAS approach. For this, we used high-quality and complete Nanopore-sequenced M. bovis genomes of 100 isolates.

Combination of procedure for ultra rapid extraction (PURE) and loop-mediated isothermal amplification (LAMP) for rapid detection of Mycoplasma bovis in milk.

Polymerase chain reaction (PCR) is typically used for the early detection of mycoplasma in bovine milk; it requires 3 days to obtain results because of the necessary enrichment process. A more rapid, simple, and accurate detection method is required to directly detect the Mycoplasma bovis (M. bovis) gene in milk. In this study, we assess the utility of combining the following two methods to achieve this goal: the loop-mediated isothermal amplification (LAMP), which is more sensitive than PCR, and the procedure for ultra rapid extraction (PURE), which adsorbs and filters components that inhibit DNA amplification/detection. LAMP was examined using DNA extracts obtained by four methods. This showed that PURE had the highest sensitivity and specificity and that the combination of PURE and LAMP was able to detect M. bovis in milk. We then showed that the detection limit of M. bovis was 102 colony-forming units per milliliter of milk using the PURE-LAMP. Finally, the respective sensitivities of the PURE-LAMP and PCR were 57% and 86% for bulk tank milk, 89% and 74% for mature milk, 85% and 92% for colostrum/transitional milk, and 97% and 95% for mastitis milk. The specificity was 100% for all milk samples in both LAMP and PCR. We conclude that PCR was suitable for detecting mycoplasma in bulk tank milk and that the PURE-LAMP could detect mycoplasma within 2 hr and was also effective for mature and mastitis milk.

Dynamics of the within-herd prevalence of Mycoplasma bovis intramammary infection in endemically infected dairy herds.

We aimed to identify the dynamics of the within-herd prevalence of Mycoplasma (M.) bovis intramammary infection (IMI) in four dairy herds, estimate prevalence of M. bovis in colostrum and clinical mastitis cases and compare M. bovis strains from calves' respiratory and cow clinical mastitis samples. Within a six-month study period, cow composite milk samples (CMS) were collected three times during routine milk recording, first milking colostrum samples from all calving cows and udder quarter milk samples from clinical mastitis cases. Calf respiratory samples were collected from calves with respiratory disease. Pooled milk samples were analysed for M. bovis with the Mastitis 4B polymerase chain reaction (PCR) test kit (DNA Diagnostic A/S). Prevalence estimates were calculated with Bayesian framework in R statistical programme. cg-MLST was used for M. bovis genotyping. In Herd I and II first testing M. bovis IMI within-herd prevalence (95 % credibility interval (CI)) was 4.7 % (2.9; 6.8) and 3.4 % (2.3; 4.6), changing to 1.0 % (0.1; 1.7) and 0.8 % (0.1; 1.4) in Herd I and 0.4 % (0.0; 0.7) in Herd II at the next samplings. In Herd III and IV first testing M. bovis IMI within-herd prevalence was 12.3 % (9.7; 15.2) and 7.8 % (6.2; 9.5), changing to 4.6 % (3.0; 6.4) and 3.2 % (1.9; 4.8) in Herd III and to 2.8 % (1.9; 3.8) and 4.9 % (3.6; 6.4) in Herd IV at the next samplings. The estimated prevalence of M. bovis in colostrum ranged between 1.7 % (0.2; 2.8) and 4.7 % (2.7; 7.1) and in clinical mastitis cases between 3.7 % (1.7; 6.4) and 11.0 % (7.5; 15.2) in the study herds. M. bovis strains isolated from cows and calves clustered within herds indicating possible transmission of M. bovis between dairy cows and calves. Prevalence of M. bovis in colostrum and clinical mastitis cases as well as the within-herd prevalence of M. bovis IMI was low in endemically infected dairy herds.

The effect of antimicrobial treatment and preventive strategies on bovine respiratory disease and genetic relatedness and antimicrobial resistance of Mycoplasma bovis isolates in a western Canadian feedlot.

Feedlot calves (n = 3784) were systematically randomized and allocated in a 2 × 2 factorial study to receive metaphylactic oxytetracycline (OTC) on arrival or no antimicrobial, as well as florfenicol once subcutaneously or twice intramuscularly (48 h apart) if diagnosed with bovine respiratory disease (BRD). Calves of different treatment groups were comingled and followed from placement to re-implantation (~100 days). Animals receiving OTC had a reduced risk of BRD, an increased risk of arthritis, and no significant differences in average daily gain, BRD relapse, overall mortality, or BRD mortality. There were no significant differences between treatment protocols. Deep nasal swabs (n = 233) taken at arrival (n = 122), treatment (n = 77), and swabs from lungs and joints at postmortem (n = 34) were cultured for Mycoplasma bovis from 61 animals ill or dying of chronic pneumonia and arthritis and from 61 healthy calves. There was significant variation in diversity among isolates (n = 51) between study years and different cattle. Metaphylaxis or antimicrobial treatment did not affect the diversity of isolates. Except for tilmicosin, isolates were largely susceptible to tested antimicrobials.

Effet du traitement antimicrobien et des stratégies préventives sur le complexe respiratoire bovin ainsi que la relation génétique et l'antibiorésistance des isolats deMycoplasma bovisdans un parc d'engraissement de l'Ouest canadien. Les veaux d'un parc d'engraissement (n = 3784) ont été systématiquement randomisés et répartis dans une étude factorielle 2 × 2 pour recevoir de l'oxytétracycline métaphylactique (OTC) à l'arrivée ou pas d'antimicrobien, ainsi qu'une injection sous-cutanée ou deux injections intramusculaires (à intervalle de 48 h) de florfénicol s'ils étaient diagnostiqués avec le complexe respiratoire bovin (CRB). Les veaux de différents groupes de traitement ont été regroupés pêle-mêle et suivis du placement à la réimplantation (~100 jours). Les animaux recevant l'OTC avaient un risque réduit de CRB, un risque accru d'arthrite et ne présentaient pas de différences significatives pour le gain de poids quotidien moyen, la rechute du CRB, la mortalité globale ou la mortalité associée au CRB. Il n'y avait aucune différence significative entre les protocoles de traitement. Des écouvillonnages nasaux profonds (n = 233) prélevés à l'arrivée (n = 122), au traitement (n = 77) et des écouvillonnages des poumons et des articulations post mortem (n = 34) ont été cultivés pour Mycoplasma bovis à partir de 61 animaux malades ou mourants de pneumonie chronique et d'arthrite et de 61 veaux en santé. Il n'y avait aucune variation significative dans la diversité des isolats (n = 51) entre les années d'étude et les différents bovins. La métaphylaxie ou le traitement antimicrobien n'a pas affecté la diversité des isolats. Sauf pour la tilmicosine, les isolats étaient largement sensibles aux antimicrobiens testés.(Traduit par Isabelle Vallières).