Phylogenomic analysis of Mycoplasma bovis from Belgian veal, dairy and beef herds

Noninferiority trial in veal calves on the efficacy of oxytetracycline and florfenicol treatment for pneumonia guided by quick thoracic ultrasound

Purchase dependent calf rearing systems, such as the white veal industry, systematically rely on antimicrobial mass medication (metaphylaxis) to counter respiratory tract infections. Despite mounting criticism, the industry fears that without metaphylaxis, mortality would drastically increase. This randomized clinical trial aimed to compare the efficacy of a quick thoracic ultrasonography (qTUS) individualized treatment length between oxytetracycline (OTC) and florfenicol (FF). Regression of maximum consolidation depth <1 cm was used as a criterion for cure and to stop antimicrobial treatment. Additionally, the study assessed the associations of consolidation depth at treatment initiation with cure and treatment duration. The trial involved 320 veal calves, randomly assigned into one of 2 groups: one receiving OTC (n = 160) and the other FF (n = 160) on d 1 (2-d metaphylaxis). Clinical scoring and qTUS were done on d 1 and every 48 h for a 10-d period. After d 1, only calves with consolidations ≥1cm were given further treatment. On each time point, maximum consolidation depth was used to categorize calves into 4 qTUS categories: healthy (no consolidation), mild pneumonia (consolidation <1 cm), moderate pneumonia (consolidation 1-3 cm) and severe pneumonia (consolidation ≥3 cm). Cure, treatment duration and the number of antimicrobial dosages (NAD) were compared between treatment groups. In addition, pathogen identification and antimicrobial susceptibility testing was performed on isolates from nonendoscopic broncho-alveolar lavage fluid. On d 1, 30.0% (96/320) of the calves had consolidation ≥1cm, which increased to 50.9% (162/318) by d 9. After single metaphylactic treatment, cure was 20.9% (9/43) and 20.9% (9/43) in the OTC and FF group, respectively. Calves with severe pneumonia had lower odds to be cured after first treatment than calves with moderate pneumonia (odds ratio = 0.17; 95% CI: 0.04-0.63). By d 9, final cure of the initial cases was 27.9% in both the OTC and FF groups. In both groups, cure was similar at all observation points. Overall, final cure of all calves with either moderate or severe pneumonia during the trial was 41.2% (52/102) and 19.0% (12/63), respectively. Median (Med) treatment duration was 4 d (interquartile range [IQR] = 2-6; minimum [Min] = 2; maximum [Max] = 8) and was similar in both treatment groups. Treatment duration for calves with moderate pneumonia (Med = 6; IQR = 4-6; Min = 2; Max = 8) was lower than the median treatment duration of calves with severe pneumonia (Med = 8; IQR = 4-8; Min = 2; Max = 8). When compared with calves with mild pneumonia on d 1, calves with moderate and severe pneumonia had significantly longer treatment durations. In this study, cure was low and not different between both antimicrobials. Categorizing calves based on consolidation depth appears useful as both cure and treatment duration were different for the mild, moderate, and severe groups.

Characterisation and comparison of Mycoplasma bovis strain types from Irish and Scottish bovine isolates in a global context

Infection with Mycoplasma bovis (M. bovis) can present as a range of clinical manifestations of varying severity in beef and dairy cattle worldwide and can seriously impact cattle health and welfare. The objectives of this study were to characterise the strains and genetic diversity within isolates of M. bovis collected from bovine clinical samples in Ireland and Scotland, and to provide place these isolates a global phylogenetic context. We performed Illumina whole genome sequencing 19 M. bovis strains from 19 unique Irish animals and 5 M. bovis strains from 4 unique Scottish animals. The strains were then analysed against 117 downloaded Genbank assemblies to create a phylogenetic tree. The Irish strains clustered into 2 main groups which were identifiable as sequence type 29 (Group 1) and sequence type 21 (Group 2) using the pubMLST system. The Scottish strains all fell within Group 1 of our analysis and were identifiable as sequence type 29 using the pubMLST system. No novel sequence types were found. The Irish and Scottish strains are similar to the genetic variation of M. bovis currently seen in Europe and may suggest separate introductions. The impact of disease associated with M. bovis in cattle emphasises the importance of within and between herd biosecurity as well as the global nature of infectious disease due to widespread international cattle movement.

Mycoplasma bovis 5'-nucleotidase is a virulence factor conferring mammary fitness in bovine mastitis

Nucleases and 5' nucleotidase (5'-NT) play essential roles in cell biology and are often associated with bacterial virulence. In Mycoplasma spp., which have limited metabolic capacities and rely on nutrient availability, these enzymes are of significant importance for nucleotide salvage. This study explores the potential role of 2 membrane-associated lipoproteins, the major nuclease MnuA and 5'-NT, in Mycoplasma bovis mastitis. Mutants deficient in MnuA (mnuA::Tn) and in 5'-NT (0690::Tn) were identified through genome-wide transposon mutagenesis of M. bovis PG45 type strain and their fitness and virulence were assessed both in vitro, in axenic medium, and in vivo, using murine and cow mastitis models. The mnuA::Tn mutant demonstrated reduced nuclease activity, while 0690::Tn exhibited slow log-phase growth and impaired hydrolase activity towards nucleotides as well as deoxynucleotides (dAMP and dGMP). In comparison to the parent strain, the 0690::Tn mutant displayed markedly reduced fitness, as evidenced by a significant decrease or even absence in post-challenge mycoplasma counts in murine and cow mammary tissues, respectively. Moreover, the 0690::Tn mutant failed to induce mastitis in both experimental models. Conversely, the mnuA::Tn mutant induced inflammation in murine mammary glands, characterized by neutrophil infiltration and increased expression of major inflammatory genes. In cows, the mnuA::Tn was able to cause an increase in somatic cell counts in a manner comparable to the wild type, recruit neutrophils, and induce mastitis. Collectively, these findings provide complementary insights, revealing that disruption of 5'-NT significantly attenuated M. bovis pathogenicity, whereas a MnuA-deficient mutant retained the ability to cause mastitis.

Molecular characterisation of Mycoplasma bovis isolates from consecutive episodes of respiratory disease on Dutch veal farms

Mycoplasma bovis infections are wide spread in veal calf farms and a major contributor to respiratory disease. M. bovis are genetically diverse. It is unclear how this diversity influences the virulence and epidemiology of infections on veal calf farms over time. Therefore, the aim of this study was to follow the genetic composition of M. bovis isolates on veal farms over time in a fattening round and combine this with presence of disease and presence of other respiratory pathogens. For this, M. bovis isolates were obtained from healthy and diseased calves from ten different farms at different episodes of respiratory disease in the same groups in one fattening round. A new episode of respiratory disease was defined by the practitioner based on clinical diagnosis at least 7 days after end of a previous metaphylactic treatment. These isolates were sequenced using Illumina sequencing and analysed. This resulted in 148 sequenced isolates. The isolates belonged to 9 different clusters and to the known MLST sequence types ST4 (n=9), ST6 (n=2), ST7 (n=1), ST8 (n=1), ST21 (n=32), ST29 (n=30), ST32 (n=1), ST100 (n=36), ST122 (n=17) and ST135 (n=4), and new sequence types ST222 (n=8), ST223 (n=1), ST224 (n=5) and ST225 (n=1). Major sequence types are linked to types, found in other European countries. All farms showed presence of two or more different clusters, however with different distribution patterns. Farms did not show a major shift in type distribution over time. There was a relationship between M. bovis type and region of origin of the calves and the types differed with regards of presence of variable membrane surface lipoprotein (Vsp) genes. Types were not related to disease status of the calves or presence of other major respiratory pathogens. This study underlines the complexity of M. bovis infection on veal calf farms with persistent presence of different types together in both healthy and diseased calves with or without other respiratory pathogens. Prevention of introduction of M. bovis and biosecurity measures combined with optimisation of calf resilience should have priority.

Diagnostic performance of Mycoplasmopsis bovis antibody ELISA tests on bulk tank milk from dairy herds

BACKGROUND

Testing of bulk tank milk (BTM) for Mycoplasmopsis bovis (previously Mycoplasma bovis) antibodies is increasingly popular. However the performance of some commercially available tests is unknown, and cutoff values possibly need to be adjusted in light of the purpose. Therefore, the aim of this study was to compare the diagnostic performance of three commercially available M. bovis antibody ELISAs on BTM, and to explore optimal cutoff values for screening purposes. A prospective diagnostic test accuracy study was performed on 156 BTM samples from Belgian and Swiss dairy farms using Bayesian Latent Class Analysis. Samples were initially classified using manufacturer cutoff values, followed by generated values.

RESULTS

Following the manufacturer's guidelines, sensitivity of 91.4%, 25.6%, 69.2%, and specificity of 67.2%, 96.8%, 85.8% were observed for ID-screen, Bio K432, and Bio K302, respectively. Optimization of cutoffs resulted in a sensitivity of 89.0%, 82.0%, and 85.5%, and a specificity of 83.4%, 75.1%, 77.2%, respectively.

CONCLUSIONS

The ID-screen showed the highest diagnostic performance after optimization of cutoff values, and could be useful for screening. Both Bio-X tests may be of value for diagnostic or confirmation purposes due to their high specificity.

Genome-wide phylodynamic approach reveals the epidemic dynamics of the main Mycoplasma bovis subtype circulating in France

Mycoplasma bovis is a major aetiological agent of bovine respiratory disease worldwide. Genome-based analyses are increasingly being used to monitor the genetic diversity and global distribution of M. bovis, complementing existing subtyping schemes based on locus sequencing. However, these analyses have so far provided limited information on the spatiotemporal and population dynamics of circulating subtypes. Here we applied a genome-wide phylodynamic approach to explore the epidemic dynamics of 88 French M. bovis strains collected between 2000 and 2019 in France and belonging to the currently dominant polC subtype 2 (st2). A strong molecular clock signal detected in the genomic data enabled robust phylodynamic inferences, which estimated that the M. bovis st2 population in France is composed of two lineages that successively emerged from independent introductions of international strains. The first lineage appeared around 2000 and supplanted the previously established antimicrobial-susceptible polC subtype 1. The second lineage, which is likely more transmissible, progressively replaced the first M. bovis st2 lineage population from 2005 onward and became predominant after 2010. Analyses also showed a brief decline in this second M. bovis st2 lineage population in around 2011, possibly due to the challenge from the concurrent emergence of M. bovis polC subtype 3 in France. Finally, we identified non-synonymous mutations in genes associated with lineages, which raises prospects for identifying new surveillance molecular markers. A genome-wide phylodynamic approach provides valuable resources for monitoring the evolution and epidemic dynamics of circulating M. bovis subtypes, and may prove critical for developing more effective surveillance systems and disease control strategies.

Antimicrobial susceptibility and molecular characteristics of Mycoplasma bovis isolated from cases of bovine respiratory disease in Australian feedlot cattle

To date, antimicrobial susceptibility has not been reported for Australian Mycoplasma bovis isolates. This study determined minimal inhibitory concentrations (MICs) for 12 different antimicrobials against Australian M. bovis isolates and used whole genome sequencing to screen those showing high macrolide MICs for point mutations in target genes. Most lung tissue/swab samples from bovine respiratory disease cases (61/76, 80.3%) tested positive for M. bovis. A set of 50 representative isolates (50/61, 82.0%) that showed adequate growth, was used for MIC testing. Uniformly, low MIC values were confirmed for enrofloxacin (≤ 4 μg/mL), florfenicol (≤ 8 μg/mL), gamithromycin (≤ 2 μg/mL), spectinomycin (≤ 4 μg/mL), tetracycline (≤ 8 μg/mL), tiamulin (≤ 4 μg/mL), and tulathromycin (≤ 0.5 μg/mL). A small proportion (10%) of isolates exhibited high MICs (≥ 32 μg/mL) for tildipirosin, tilmicosin, tylosin, and lincomycin, which were above the epidemiological cut-off values for each antimicrobial (≥ 4 μg/mL). These isolates, originating from three Australian states, underwent whole genome sequencing/multilocus sequencing typing and were compared with the reference strain PG45 to investigate mutations that might be linked with the high macrolide/lincosamide MICs. All five belonged to ST52 and two macrolide associated mutations were identified within the 23 S rRNA gene (A2058G in two sequenced isolates and G748A in all sequenced isolates). Four additional 23 S rRNA gene mutations did not appear to be linked to macrolide resistance. Whilst the majority of Australian M. bovis isolates appear susceptible to the tested antimicrobials, emerging macrolide resistance was detected in three Australian states and requires continued monitoring.

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

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.

Comparison and optimisation of screening cutoff values for Mycoplasma bovis antibody ELISAs using serum from youngstock

BACKGROUND

Mycoplasma bovis-associated disease can cause tremendous production losses, welfare issues and high antimicrobial use. Therefore, screening cattle for M. bovis antibodies before entering the herd is a popular and possibly cost-efficient way to reduce disease introduction. However, interpretation of results can be challenging due to variable accuracy between tests and populations. This study's objectives were to compare the diagnostic test accuracy of three commercially available M. bovis antibody ELISAs (ID-screen, Bio K302 and Bio K432) and to explore optimal cutoff values for screening purposes.

METHODS

A prospective diagnostic test accuracy study was performed on 170 serum samples from youngstock using Bayesian latent class modelling. Samples were categorised using manufacturer and generated cutoff values.

RESULTS

Using the manufacturers' guidelines, ID-screen, Bio K432 and Bio K302 showed 97.6%, 67.4% and 33.6% sensitivity, and 78.8%, 97.6% and 99.1% specificity, respectively. Optimised cutoffs resulted in 94.8%, 82.6% and 78.3% sensitivity, and 94.2%, 92.5% and 79.4% specificity, respectively.

CONCLUSIONS

The highest diagnostic accuracy for detecting M. bovis antibodies was obtained by ID-screen (≥110%). However, by adjusting cutoff values, the sensitivity of Bio-X tests could be markedly increased, making these tests also applicable as screening tools.

LIMITATIONS

Interpretation needs to be careful as antibodies may be linked to both infectious and non-infectious status.

Preparing Male Dairy Calves for the Veal and Dairy Beef Industry

Surplus male dairy calves experience significant health challenges after arrival at the veal and dairy beef facilities. To curb these challenges, the engagement of multiple stakeholders is needed starting with improved care on some dairy farms and better management of transportation. Differing management strategies are also needed if calves arrive at veal and dairy beef facilities under poor condition.

Prevalence and Molecular Characterization of Mycoplasma Species, Pasteurella multocida, and Staphylococcus aureus Isolated from Calves with Respiratory Manifestations

Bovine respiratory disease (BRD) is a complex syndrome associated with high mortality in young calves and causes severe economic losses in the cattle industry worldwide. The current study investigated the prevalence and molecular characterization of common bacterial pathogens associated with respiratory symptoms in young calves from Sadat City, one of the largest industrial cities in Menoufiya Governorate, Egypt. In between December 2020 and March 2021, 200 mixed-breed young calves of 6–12 months were examined clinically. Of them, sixty (30%) calves showed signs of respiratory manifestations, such as coughing, serous to mucopurulent nasal discharges, fever, and abnormal lung sound. Deep nasal (Nasopharyngeal) swabs were collected from the affected calves for bacteriological investigation. Phenotypic characterization and identification revealed Mycoplasma bovis, Mycoplasma bovigenitalium, Pasteurella multocida, and Staphylococcus aureus in 8.33%, 5%, 5%, and 5% of the tested samples, respectively. The PCR technique using species-specific primer sets successfully amplified the target bacterial DNA in all culture-positive samples, confirming the identity of the isolated bacterial species. Partial gene sequencing of 16S rRNA gene of M. bovigenitalium, P. multocida, and S. aureus, and mb-mp 81 gene of M. bovis revealed high nucleotide similarity and genetic relationship with respective bacterial species reported from Egypt and around the world, suggesting transmission of these bacterial species between animal host species and localities. Our study highlights the four important bacterial strains associated with respiratory disorders in calves and suggests the possible spread of these bacterial pathogens across animal species and different geographic locations. Further studies using WGS and a large number of isolates are required to investigate the realistic lineage of Egyptian isolates and globally.

Randomized field trial comparing the efficacy of florfenicol and oxytetracycline in a natural outbreak of calf pneumonia using lung reaeration as a cure criterion

Background

Respiratory infections are the main indication for antimicrobial use in calves. Optimal treatment duration currently is unknown, but shorter duration would likely decrease selection for antimicrobial resistance.

Hypothesis/Objectives

Determine differences in cure rate and healing time between animals treated with florfenicol and oxytetracycline in a natural outbreak of respiratory disease using reaeration observed on thoracic ultrasound examination as healing criterion.

Animals

Commercial farm housing 130, 3 to 9 month old Belgian blue beef calves.

Methods

Randomized clinical trial during an outbreak of respiratory disease. Metaphylactic treatment was initiated, randomly treating animals with either florfenicol or oxytetracycline. Ultrasonographic follow‐up was done the first day and every other day for a 14‐day period. At the individual animal level, treatment was discontinued when reaeration of the lungs occurred. Differences in cure rate and healing time were determined.

Results

Of the 130 animals studied, 67.7% developed a lung consolidation ≥0.5 cm. The mean ultrasonographic healing time was 2.5 days in the florfenicol group compared to 3.1 days in the oxytetracycline group (P = .04). After single treatment, 80.6% and 60.3% had no consolidations in the florfenicol and oxytetracycline groups, respectively (P = .01). A Mycoplasma bovis strain was genetically and phenotypically determined to be susceptible to both antimicrobials.

Conclusions and Clinical Importance

Ultrasonographic lung reaeration shows potential as a cure criterion to rationalize antimicrobial use for outbreaks of pneumonia. In our study, florfenicol resulted in a faster cure and higher reduction in antimicrobial usage than did oxytetracycline.

Evaluation of Nanopore Sequencing as a Diagnostic Tool for the Rapid Identification of Mycoplasma bovis from Individual and Pooled Respiratory Tract Samples

Rapid identification of Mycoplasma bovis infections in cattle is a key factor to guide antimicrobial therapy and biosecurity measures. Recently, Nanopore sequencing became an affordable diagnostic tool for both clinically relevant viruses and bacteria, but the diagnostic accuracy for M. bovis identification is undocumented. Therefore, in this study Nanopore sequencing was compared to rapid identification of M. bovis with matrix-assisted laser desorption ionization-time of flight mass spectrometry (RIMM) and a triplex real-time PCR assay in a Bayesian latent class model (BLCM) for M. bovis in bronchoalveolar lavage fluid (BALf) samples obtained from calves. In practice, pooling of samples is often used to save money, but the influence on diagnostic accuracy has not been described for M. bovis. Therefore, a convenience sample of 17 pooled samples containing 5 individual BALf samples per farm was analyzed as well. The results for the pooled samples were compared with those for the individual samples to determine sensitivity and specificity. The BLCM showed good sensitivity (77.3% [95% credible interval, 57.8 to 92.8%]) and high specificity (97.4% [91.5 to 99.7%]) for Nanopore sequencing, compared to RIMM (sensitivity, 93.0% [76.8 to 99.5%]; specificity, 91.3% [82.5 to 97.0%]) and real-time PCR (sensitivity, 94.6% [89.7 to 97.7%]; specificity, 86.0% [76.1 to 93.6%]). Sensitivity and specificity of pooled analysis for M. bovis were 85.7% (95% confidence interval, 59.8 to 111.6%) and 90.0% (71.4 to 108.6%%), respectively, for Nanopore sequencing and 100% (100% to 100%) and 88.9% (68.4 to 109.4%) for RIMM. In conclusion, Nanopore sequencing is a rapid, reliable tool for the identification of M. bovis. To reduce costs and increase the chance of M. bovis identification, pooling of 5 samples for Nanopore sequencing and RIMM is possible.

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.

IMPORTANCEMycoplasma 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.

Application of Four Genotyping Methods to Mycoplasma bovis Isolates Derived from Western Canadian Feedlot Cattle

Mycoplasma bovis is a significant pathogen of feedlot cattle, responsible for chronic pneumonia and polyarthritis syndrome (CPPS). M. bovis isolates (n = 129) were used to compare four methods of phylogenetic analysis and to determine if the isolates' genotypes were associated with phenotypes. Metadata included the health status of the animal from which an isolate was derived (healthy, diseased, or dead), anatomical location (nasopharynx, lung, or joint), feedlot, and production year (2006 to 2018). Four in silico phylogenetic typing methods were used: multilocus sequence typing (MLST), core genome MLST (cgMLST), core genome single nucleotide variant (cgSNV) analysis, and whole-genome SNV (wgSNV) analysis. Using Simpson's diversity index (D) as a proxy for resolution, MLST had the lowest resolution (D = 0.932); cgSNV (D = 0.984) and cgMLST (D = 0.987) generated comparable results; and wgSNV (D = 1.000) provided the highest resolution. Visual inspection of the minimum spanning trees found that the memberships of the clonal complexes and clades had similar structural appearances. Although MLST had the lowest resolution, this methodology was intuitive and easy to apply, and the PubMLST database facilitates the comparison of sequence types across studies. The cg methods had higher resolution than MLST, and the graphical interface software was user-friendly for nonbioinformaticians, but the proprietary software is relatively expensive. The wgSNV approach was the most robust for processing poor-quality sequence data while offering the highest resolution; however, application of its software requires specialized training. None of the four methods could associate genotypes with phenotypes.

Antimicrobial Susceptibility of Mycoplasma bovis Isolates from Veal, Dairy and Beef Herds

Mycoplasma bovis is an important pathogen causing mostly pneumonia in calves and mastitis in dairy cattle. In the absence of an effective vaccine, antimicrobial therapy remains the main control measure. Antimicrobial use in veal calves is substantially higher than in conventional herds, but whether veal calves also harbor more resistant M. bovis strains is currently unknown. Therefore, we compared antimicrobial susceptibility test results of M. bovis isolates from different cattle sectors and genomic clusters. The minimum inhibitory concentration of nine antimicrobials was determined for 141 Belgian M. bovis isolates (29 dairy, 69 beef, 12 mixed, 31 veal farms), and was used to estimate the epidemiological cut-off. Acquired resistance was frequently observed for the macrolides, while no acquired resistance to oxytetracycline and doxycycline, minimal acquired resistance to florfenicol and tiamulin, and a limited acquired resistance to enrofloxacin was seen. M. bovis isolates from beef cattle or genomic cluster III had higher odds of being gamithromycin-resistant than those from dairy cattle or genomic clusters IV and V. In this study, no cattle industry could be identified as source of resistant M. bovis strains. A single guideline for antimicrobial use for M. bovis infections, with a small remark for gamithromycin, is likely sufficient.