Massive detection of cryptic recessive genetic defects in dairy cattle mining millions of life histories.

BACKGROUND: Dairy cattle breeds are populations of limited effective size, subject to recurrent outbreaks of recessive defects that are commonly studied using positional cloning. However, this strategy, based on the observation of animals with characteristic features, may overlook a number of conditions, such as immune or metabolic genetic disorders, which may be confused with pathologies of environmental etiology. RESULTS: We present a data mining framework specifically designed to detect recessive defects in livestock that have been previously missed due to a lack of specific signs, incomplete penetrance, or incomplete linkage disequilibrium. This approach leverages the massive data generated by genomic selection. Its basic principle is to compare the observed and expected numbers of homozygotes for sliding haplotypes in animals with different life histories. Within three cattle breeds, we report 33 new loci responsible for increased risk of juvenile mortality and present a series of validations based on large-scale genotyping, clinical examination, and functional studies for candidate variants affecting the NOA1, RFC5, and ITGB7 genes. In particular, we describe disorders associated with NOA1 and RFC5 mutations for the first time in vertebrates. CONCLUSIONS: The discovery of these many new defects will help to characterize the genetic basis of inbreeding depression, while their management will improve animal welfare and reduce losses to the industry.

Pulsed-Field Gel Electrophoresis Analysis of Bovine Associated Staphylococcus aureus: A Review.

For decades now, DNA fingerprinting by means of pulsed-field gel electrophoresis (PFGE) continues to be the most widely used to separate large DNA molecules and distinguish between different strains in alternating pulses. This is done by isolating intact chromosomal DNA and using restriction enzymes with specific restriction sites to generate less than 30 restriction fragments from 50 Kb to 10 Mbp. These results make clone-specific band profiles easy to compare. Specialized equipment is required for the optimization of DNA separation and resolution, among which a contour-clamped homogeneous electric field (CHEF) apparatus is the most commonly used. As a result, the PFGE analysis of a bacterial genome provides useful information in terms of epidemiological investigations of different bacterial pathogens. For Staphylococcus aureus subtyping, despite its limitations and the emergence of alternative methods, PFGE analysis has proven to be an adequate choice and the gold standard for determining genetic relatedness, especially in outbreak detection and short-term surveillance in the veterinary field.

Monitoring Mycoplasma bovis Diversity and Antimicrobial Susceptibility in Calf Feedlots Undergoing a Respiratory Disease Outbreak.

Bovine respiratory diseases (BRD) are widespread in veal calf feedlots. Several pathogens are implicated, both viruses and bacteria, one of which, Mycoplasma bovis, is under-researched. This worldwide-distributed bacterium has been shown to be highly resistant in vitro to the main antimicrobials used to treat BRD. Our objective was to monitor the relative prevalence of M. bovis during BRD episodes, its diversity, and its resistance phenotype in relation to antimicrobial use. For this purpose, a two-year longitudinal follow-up of 25 feedlots was organized and 537 nasal swabs were collected on 358 veal calves at their arrival in the lot, at the BRD peak and 4 weeks after collective antimicrobial treatments. The presence of M. bovis was assessed by real-time PCR and culture. The clones isolated were then subtyped (polC subtyping and PFGE analysis), and their susceptibility to five antimicrobials was determined. The course of the disease and the antimicrobials used had no influence on the genetic diversity of the M. bovis strains: The subtype distribution was the same throughout the BRD episode and similar to that already described in France, with a major narrowly-variable subtype circulating, st2. The same conclusion holds for antimicrobial resistance (AMR) phenotypes: All the clones were already multiresistant to the main antimicrobials used (except for fluoroquinolones) prior to any treatments. By contrast, changes of AMR phenotypes could be suspected for Pasteurellaceae in two cases in relation to the treatments registered.

The role of Mycoplasma bovis in bovine respiratory disease outbreaks in veal calf feedlots.

To assess the prevalence and relative importance of Mycoplasma bovis among the pathological agents implicated in bovine respiratory disease (BRD), we surveyed 135 veal calves from nine feedlots in eastern France during naturally occurring outbreaks of respiratory disease. Occurrence of respiratory pathogens, M. bovis, bovine viral diarrhoea (BVD) virus, bovine respiratory syncytial (BRS) virus and parainfluenza-3 (PI3) virus was investigated by seroconversion and isolation of bacteria and viruses from broncho-alveolar fluids. M. bovis and pathogenic respiratory bacteria were isolated in eight of the nine feedlots, and from 106 and 32, respectively, of the 135 tested animals. Seroconversion to PI3 virus occurred in four lots. BVD and BRS viruses were detected in eight and one lot, respectively. M. bovis was the most frequently isolated aetiologic agent in these BRD outbreaks, spreading early and widely throughout the affected units (60-100% rate of isolation and seroconversion). These results stress the importance of M. bovis in the BRD complex.

Diagnosis of bovine dictyocaulosis by bronchoalveolar lavage technique: A comparative study using a Bayesian approach.

Bovine dictyocaulosis is a pulmonary parasitic disease present in temperate countries, with potential important clinical and economic impacts. The Baermann technique is routinely used despite its low sensitivity in adult cows. Recently developed serological tests seem to offer better sensitivity, but validations of these tests in field conditions are few. We aimed to study two non-previously evaluated diagnosis methods of dictyocaulosis based on bronchoalveolar lavage sampling (BAL), which allows finding lungworm stages in the lungs as well as determination of eosinophilia. We compared them to the Baermann technique and serological tests. As no gold standard was available, we performed a Bayesian analysis by the simultaneous use of latent class and mixture models. The study was carried out during the 2015 pasture season on 60 adult cows originating from 11 herds with clinical signs of dictyocaulosis, and 10 apparently healthy cows originating from the teaching herd of VetAgro Sup, in France. Prevalence of infection was highly variable among herds with clinical signs (10-90%). Despite a maximal specificity (100%), the sensitivity of parasitological methods was low (7.4% for the Baermann sedimentation and 24.7% for the examination of BAL fluids). Better results were observed with serology (Se = 74.9%, Sp = 85.5%) with an optimal cut-off value estimated at 0.397 for the optical density ratio. Even better results were obtained with the count of eosinophil in BAL (Se = 89.4%, Sp = 85.2%) with an optimal cut-off value estimated at 4.77% for the eosinophil proportion. The BAL is a relevant diagnostic method of dictyocaulosis for practitioners due to the opportunity to perform two analyses (direct parasitic research and the eosinophil count) and to its good sensitivity and specificity.

Loss of diversity within Mycoplasma bovis isolates collected in France from bovines with respiratory diseases over the last 35 years.

Mycoplasma (M.) bovis has recently emerged as a major, worldwide etiological agent of bovine respiratory diseases leading to huge economic losses mainly due to high morbidity and mortality as well as poor growth rates. The spread of M. bovis infections between different animals, herds, regions or countries has been often reported to be connected to the movement of animals. However, despite recent considerable efforts, no universal subtyping method is yet available to trace M. bovis isolates circulation at an international scale. Moreover in France, the overall population diversity of M. bovis isolates has not been assessed since the early 1990s. This study was conducted to fill in these gaps. The genotypic diversity between sixty isolates collected in France over the last 35 years was assessed using two molecular subtyping methods that addressed either the long-term epidemiological relationships (Multi Locus Sequence Typing, MLST) or the genetic microvariations (Multiple Locus VNTR Analysis, MLVA) between isolates. Phenotypic diversity was also analyzed by using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) to compare the main protein patterns of isolates. All proposed subtyping approaches were optimized and led to the same pattern in the French M. bovis population that consisted of two clusters, the first one comprising isolates collected before 2000 and the second, those collected after 2000. Recent strains were further shown to be more homogeneous than older ones, which is consistent with the spread of a single clone throughout the country. Because this spread was concomitant with the emergence of multiresistant M. bovis isolates, several hypotheses are discussed to explain the homogeneity of M. bovis isolates in France, even though the M. bovis species is fully equipped to generate diversity.

Evolution of chloramphenicol resistance, with emergence of cross-resistance to florfenicol, in bovine Salmonella Typhimurium strains implicates definitive phage type (DT) 104.

The prevalence of resistance to florfenicol, a phenicol drug newly introduced in veterinary therapy, was determined in 86 chloramphenicol-resistant Salmonella Typhimurium isolates from cattle collected during 1985-1995. All were highly resistant to chloramphenicol (MICs > or = 128 mg/L) and 38 were simultaneously resistant to florfenicol (MICs >16 mg/L) and to beta-lactam agents, spectinomycin, streptomycin, sulphonamides and tetracyclines. The isolates susceptible to florfenicol harboured the chloramphenicol acetyl transferase gene, cat of type I. All the florfenicol-resistant isolates harboured the floR resistance gene and the characteristic multiple resistance genetic locus, previously characterised in a S. Typhimurium DT104 strain and identified by a multiplex PCR. Plasmid profiles and ribotype patterns were determined for all the isolates. The florfenicol-resistant isolates were grouped into the same ribotyping pattern and presented similar plasmid profiles, whereas the florfenicol-susceptible isolates showed a wider genetic diversity that is usual for S. Typhimurium. Thus, the florfenicol-resistant isolates could represent a clonal cluster, closely related to, if not of DT104 phage type, which appeared in 1989 and is now predominant within chloramphenicol-resistant S. Typhimurium. The multiplex PCR provided a useful tool to survey further evolution of multiresistant S. Typhimurium strains.

Transmission dynamics of Mycoplasma bovis in newly received beef bulls at fattening operations.

Mycoplasma bovis is an important cause of bovine respiratory disease (BRD) in newly received cattle at fattening operations. However, little information on its within-pen transmission dynamics during a BRD outbreak is available. Such information is nevertheless crucial to adapt control measures during M. bovis-associated BRD outbreaks. The objective of the current study was to determine whether single or multiple clones of M. bovis are present within a pen during a BRD outbreak that occurs early in the feeding period. Sixteen BRD outbreaks that naturally occurred in 12 pens of 8-12 bulls each (n = 112) newly received at 3 fattening operations were investigated. Two hundred and thirty-nine transtracheal aspirations (TTA) were performed during the outbreaks, and the M. bovis isolates obtained were characterized by pulsed-field gel electrophoresis (PFGE). Mycoplasma bovis isolates were recovered from TTA in 8 of the 16 BRD outbreaks that occurred. The within-pen prevalence of bulls positive for M. bovis during these outbreaks ranged from 8% to 100%. The PFGE analysis revealed that, even though bulls came from multiple origins, a single clone of M. bovis was present within a pen during BRD outbreaks with a high prevalence of M. bovis infection. The study therefore indicates that, even if M. bovis can recrudesce from carriers after stressful events such as transportation and commingling, the increased prevalence of M. bovis pulmonary infection observed during BRD outbreaks that are early occurring in the feeding period seems primarily due to the horizontal transmission of only 1 clone among cattle.

The use of pulsed-field gel electrophoresis to investigate the epidemiology of Mycoplasma bovis in French calf feedlots.

Mycoplasma bovis is a major cause of respiratory outbreaks in cattle feedlots. In this study pulsed-field gel electrophoresis (PFGE) was used to trace field strains and provide information on M. bovis patterns of spread in calf feedlots. The suitability of KpnI, MluI and SmaI restriction enzymes was assessed on different sets of strains. The discriminative power of the first two enzymes was first assessed using 28 epidemiologically unrelated strains; stability was 100% on multiple isolates from in vivo experimental infection. Thirty-nine field isolates from six feedlots were then evaluated. In contrast to the unique fingerprints displayed by the unrelated strains, the isolates from the feedlots showed identical patterns at the time of the outbreak of respiratory disease and 4 weeks later. The PFGE typing results suggest that M. bovis strains follow a clonal epidemic spread pattern at the herd level and that the same strain persists in calves of the herd after the clinical signs have disappeared.