Genetic and genomic studies in ovine mastitis

Identifying selection strategies based on the practices and preferences of small ruminant farmers to improve the sustainability of their breeding systems

Small ruminant farming is of socio-economic and environmental importance to many rural communities around the world. The SMARTER H2020 project aims to redefine genetic selection criteria to increase the sustainability of the sector. The objective of this study was to analyse the selection and breeding management practices of small ruminant producers and breeders, linked with socio-technical elements that shape them. The study is based on farm surveys using semi-structured interviews conducted in five countries (France, Spain, Italy, Greece, and Uruguay) across 272 producers and breeders of 13 sheep and goat breeds, and 15 breed × system combinations. The information was collected in four sections. The first and second sections dealt with general elements of structure and management of the system and the flock/herd. The third section focused on selection and breeding management practices: criteria for culling and replacement of females, selection criteria for males, use of estimated breeding values and global indexes, and preferences for indexing new traits to increase the sustainability of their system. The fourth section aimed to collect socio-technical information. We used a data abstraction method to standardise the representation of these data. A mixed data factor analysis followed by a hierarchical ascending classification allowed the characterisation of three profiles of selection and breeding management: (1) a profile of producers (n = 93) of small flocks/herds, with little knowledge or use of genetic selection and improvement tools (selection index, artificial insemination, performance recording); these farmers do not feel that new traits are needed to improve the sustainability of their system. (2) a profile of producers (n = 34) of multibreed flocks/herds that rely significantly on grazing; they are familiar with genetic tools, they currently use AI; they would like the indexes to include more health and robustness characteristics, to make their animals more resistant and to increase the sustainability of their system. And (3) a profile of producers or breeders (n = 145) of large flocks/herds, with specific culling criteria; these farmers are satisfied with the current indexes to maintain the sustainability of their system. These results are elements that can be used by private breeding companies and associations to support the evolution of selection objectives to increase the resilience of animals and to improve the sustainability of the small ruminant breeding systems.

Genome-wide association study of health and production traits in meat sheep

Genotypes are currently widely used in animal breeding programmes to enhance the speed of genetic progress. With sufficient data, a Genome-Wide Association Study (GWAS) can be performed to identify informative markers. The aim of this study was to investigate the genetic background of health (footrot and mastitis) and production (birth weight, weaning weight, scan weight, and fat and muscle depth) traits using the available phenotypic and Single Nucleotide Polymorphism (SNP) data collected on the UK Texel sheep population. Initially, 10 193 genotypes were subject to quality control, leaving 9 505 genotypes for further analysis. Selected genotypes, recorded on four different Illumina chip types from low density (15 k SNPs) to high density (606 006 SNPs), were imputed to a subset of 45 686 markers from 50 k array, distributed on 27 chromosomes. Phenotypes collected on 32 farms across the UK for footrot and mastitis and extracted from the UK National database (iTexel) for the production traits were used along with pre-estimated variance components to obtain de-regressed breeding values and used to perform GWAS. Results showed three SNPs being significant on the genome-wise level ('OAR8_62240378.1' on chromosome 8 for birth weight, 's14444.1' on chromosome 19 for weaning weight and 's65197.1' on chromosome 23 for scan weight). Fourteen subsequent SNPs were found to be significant at the chromosome-wise level. These SNPs are located within or close to previously reported QTLs impacting on animal health (such as faecal egg count or somatic cell count) and production (such as body or carcass weight and fat amount). These results indicate that the studied traits are highly polygenic with complex genetic architecture.

Comparative genomic analysis of ovine and other host associated isolates of Staphylococcus aureus exhibit the important role of mobile genetic elements and virulence factors in host adaptation

Staphylococcus aureus is the main etiological agent of mastitis in small ruminants worldwide. This disease has a difficult cure and possible relapse, leading to significant economic losses in production, milk quality and livestock. This study performed comparative genomic analyses between 73 S. aureus genomes from different hosts (human, bovine, pig and others). This work isolated and sequenced 12 of these genomes from ovine. This study contributes to the knowledge of genomic specialization and the role of specific genes in establishing infection in ovine mastitis-associated S. aureus. The genomes of S. aureus isolated from sheep maintained a higher representation when grouped with clonal complexes 130 and 133. The genomes showed high genetic similarity, the species pan-genome consisting of 4200 genes (central = 2008, accessory = 1559 and unique = 634). Among these, 277 unique genes were related to the genomes isolated from sheep, with 39.6 % as hypothetical proteins, 6.4 % as phages, 6.4 % as toxins, 2.9 % as transporters, and 44.7 % as related to other proteins. Furthermore, at the pathogen level, they showed 80 genes associated with virulence factors and 19 with antibiotic resistance shared in almost all isolates. Although S. aureus isolated from ovine showed susceptibility to antimicrobials in vitro, ten genes were predicted to be associated with antibiotic inactivation and efflux pump, suggesting resistance to gentamicin and penicillin. This work may contribute to identifying genes acquired by horizontal transfer and their role in host adaptation, virulence, bacterial resistance, and characterization of strains affecting ovine.

Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission

BACKGROUND

The spread of infectious diseases in populations is controlled by the susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection), and recoverability (propensity to recover/die) of individuals. Estimating genetic risk factors for these three underlying host epidemiological traits can help reduce disease spread through genetic control strategies. Previous studies have identified important 'disease resistance single nucleotide polymorphisms (SNPs)', but how these affect the underlying traits is an unresolved question. Recent advances in computational statistics make it now possible to estimate the effects of SNPs on host traits from epidemic data (e.g. infection and/or recovery times of individuals or diagnostic test results). However, little is known about how to effectively design disease transmission experiments or field studies to maximise the precision with which these effects can be estimated.

RESULTS

In this paper, we develop and validate analytical expressions for the precision of the estimates of SNP effects on the three above host traits for a disease transmission experiment with one or more non-interacting contact groups. Maximising these expressions leads to three distinct 'experimental' designs, each specifying a different set of ideal SNP genotype compositions across groups: (a) appropriate for a single contact-group, (b) a multi-group design termed "pure", and (c) a multi-group design termed "mixed", where 'pure' and 'mixed' refer to groupings that consist of individuals with uniformly the same or different SNP genotypes, respectively. Precision estimates for susceptibility and recoverability were found to be less sensitive to the experimental design than estimates for infectivity. Whereas the analytical expressions suggest that the multi-group pure and mixed designs estimate SNP effects with similar precision, the mixed design is preferred because it uses information from naturally-occurring rather than artificial infections. The same design principles apply to estimates of the epidemiological impact of other categorical fixed effects, such as breed, line, family, sex, or vaccination status. Estimation of SNP effect precisions from a given experimental setup is implemented in an online software tool SIRE-PC.

CONCLUSIONS

Methodology was developed to aid the design of disease transmission experiments for estimating the effect of individual SNPs and other categorical variables that underlie host susceptibility, infectivity and recoverability. Designs that maximize the precision of estimates were derived.

High Milk Somatic Cell Counts and Increased Teladorsagia Burdens Overshadow Non-Infection-Related Factors as Predictors of Fat and Protein Content of Bulk-Tank Raw Milk in Sheep and Goat Farms

This paper presents the results of an extensive countrywide investigation performed in 325 dairy sheep flocks and 119 goat herds throughout Greece. The objectives of the study were (a) to investigate fat and protein content in the bulk-tank raw milk of small ruminant farms in Greece and (b) to identify factors potentially influencing that content and factors that can contribute to increased content. The mean fat/protein contents in bulk-tank raw milk of sheep and goats were 6.16 ± 0.05%/4.43 ± 0.01% and 4.77 ± 0.44%/3.23 ± 0.30%, respectively. Significant differences were seen in protein content between farms in the various parts of the country. For sheep, multivariable analyses revealed breed and age of lamb removal from dams as significant for fat content, and somatic cell counts, management system in the farm, administration of anthelmintic treatment during the last stage of pregnancy, and farmer education as significant for protein content. For goats, significant factors were month into lactation period, age of kid removal from dams, and breed for fat content, and somatic cell counts, month into lactation, grazing duration, and % Teladorsagia larvae in faecal samples for protein content. For concurrently high fat and protein content, in multivariable analyses, the following emerged as significant factors: somatic cell counts in milk, numbers of parasite eggs in faeces, and veterinary collaboration (sheep), and month into lactation and somatic cell counts in milk (goats). The results indicate that high somatic cell counts in milk (reflecting the presence of mastitis) and gastrointestinal parasitic infections (mainly Teladorsagia infection) appear to exert a more significant influence on fat and protein content of milk, in comparison to non-infection-related factors.

Long-Term Climatic Changes in Small Ruminant Farms in Greece and Potential Associations with Animal Health

The objectives of this work were (a) to present the changes in climatic parameters from 1989 to 2019, in 444 locations throughout Greece, where small ruminant farms have been based and (b) to present associations of the changes in the climatic parameters with clinical data related to small ruminant health. Climatic variables (1989–2019) were obtained for 444 locations with small ruminant farms throughout Greece. During this period, significant increases were noted in temperature-related parameters (annually 0.05 °C for average temperature and 0.14 °C for temperature range) and precipitation (annually 0.03 mm). There were significant differences in climatic conditions between locations of farms in accord with the management system applied therein, as well as in accord with the breed of animals on the farms (e.g., higher average temperature in locations with Greek breeds, higher temperature range in locations with imported breeds). There were significant associations of temperature-related parameters with the annual frequency of cases of neonatal hypothermia seen at a veterinary teaching hospital, as well as with the average proportion of Haemonchus contortus larvae in faecal samples and the frequency of cases of H. contortus resistance reported by a veterinary parasitology laboratory.

Use of photodynamic therapy and photobiomodulation as alternatives for microbial control on clinical and subclinical mastitis in sheep

Evaluate the effects of antimicrobial photodynamic therapy (aPDT) and photobiomodulation (PBM) as alternatives in the treatment of mastitis in sheep. A total of 100 sheep were evaluated, and four teats with clinical mastitis and 16 teats with subclinical mastitis were selected. Milk was collected for isolation and identification of microorganisms. They were grown on TSA, EMB, and MacConkey agar for 24 h, and the microorganisms were identified by Gram stain and biochemical tests. The ceilings were subdivided into four groups: G1, treatment with photosensitizer; G2, treatment with PBM (diode laser λ = 660 nm); G3, aPDT with methylene blue, and G4, control group. Milk samples were collected before, 24 and 48 h after treatments. Cases of subclinical mastitis presented coagulase-negative Staphylococcus and Streptococcus spp, and clinical mastitis had Escherichia coli grow from the samples. The treatments decrease the total bacterial count of negative coagulase Staphylococcus, Streptococcus spp, and Escherichia coli. Comparing the treatments, aPDT stood out, as it was able to photoinactivate all bacteria. Treatment with methylene blue photosensitizer, PBM, and aPDT induced the initial microbial reduction, but aPDT was more effective 48 h after treatment.

Potential Novel Biomarkers for Mastitis Diagnosis in Sheep

Simple Summary

Inflammation of the mammary gland (mastitis) is an important disease of dairy sheep. Mastitis management depends mainly on the diagnosis. Conventional diagnostic methods including somatic cell count, California Mastitis Test, and microbial culture have limitations. Therefore researchers are looking for new diagnostic biomarkers of mastitis including specific proteins produced by the liver in case of disease (acute phase proteins), unique genetic sequences (miRNAs), or antimicrobial peptides produced by immune cells during inflammation (cathelicidines).

Abstract

This review aims to characterize promising novel markers of ovine mastitis. Mastitis is considered as one of the primary factors for premature culling in dairy sheep and has noticeable financial, productional, and animal welfare-related implications. Furthermore, clinical, and subclinical mammary infections negatively affect milk yield and alter the milk composition, thereby leading to lowered quality of dairy products. It is, therefore, crucial to control and prevent mastitis through proper diagnosis, treatment or culling, and appropriate udder health management particularly at the end of the lactation period. The clinical form of mastitis is characterized by abnormalities in milk and mammary gland tissue alteration or systemic symptoms consequently causing minor diagnostic difficulties. However, to identify ewes with subclinical mastitis, laboratory diagnostics is crucial. Mastitis control is primarily dependent on determining somatic cell count (SCC) and the California Mastitis Test (CMT), which aim to detect the quantity of cells in the milk sample. The other useful diagnostic tool is microbial culture, which complements SCC and CMT. However, all mentioned diagnostic methods have their limitations and therefore novel biomarkers of ovine subclinical mastitis are highly desired. These sensitive indicators include acute-phase proteins, miRNA, and cathelicidins measurements, which could be determined in ovine serum and/or milk and in the future may become useful in early mastitis diagnostics as well as a preventive tool. This may contribute to increased detection of ovine mammary gland inflammation in sheep, especially in subclinical form, and consequently improves milk quality and quantity.

Association of Breed of Sheep or Goats with Somatic Cell Counts and Total Bacterial Counts of Bulk-Tank Milk

The objective was to describe potential associations of somatic cell counts (SCC) and total bacterial counts (TBC) in bulk-tank milk from sheep and goat farms with breeds of these animals in Greece. In total, 325 dairy sheep flocks and 119 dairy goat herds were visited for the collection of milk; the breed of animals in farms was evaluated for a potential association with SCC or TBC. The most frequently seen sheep breeds were the Lacaune (95 flocks) and the Chios (44 flocks). The most frequently seen goat breeds were the indigenous Greek (Capra prisca) (50 herds) and the Murciano-Granadina (13 herds). In a multivariable analysis, the breed and the application of machine-milking in sheep flocks, and the breed and the management system in goat herds emerged as significant factors for increased SCC (>0.75 × 106 cells mL−1) in bulk-tank milk. Further, the month of lactation at sampling in sheep flocks emerged a significant factor for increased TBC (>1500 × 103 cfu mL−1) in bulk-tank milk.

Genome-Wide Association Study Identifies New Candidate Markers for Somatic Cells Score in a Local Dairy Sheep

In the Mediterranean basin countries, the dairy sheep production is usually based on local breeds, which are very well-adapted to their production systems and environments and can indeed guarantee income, employment, and economic viability in areas where production alternatives are scarce or non-existent. Mastitis is still one of the greatest problems affecting commercial milk production. However, genetic evaluation of mastitis is particularly difficult because of its low heritability and the categorical nature of the trait. The aim of this study was to identify genomic regions putatively associated with somatic cells count (SCC) in the local economically important Valle del Belice sheep breed using of deregressed breeding values (DEBV) as response variables. All the samples were genotyped using the Illumina OvineSNP50K BeadChip. Genome-wide association analysis was carried out based on regression of DEBV. A total of eight markers were found to be significantly associated with log-transformed SCC. Several candidate genes associated with SCC were identified related to immunity system and udder conformation. The results can help improving the competitiveness of the local Valle del Belìce breed. Further studies considering a higher sample size or independent population will be needed to confirm our results.

Extensive Countrywide Field Investigation of Somatic Cell Counts and Total Bacterial Counts in Bulk-Tank Raw Milk in Sheep Flocks in Greece

Objectives were to investigate somatic cell counts (SCC) and total bacterial counts (TBC) in the raw bulk-tank milk of sheep flocks in Greece, to study factors potentially influencing increased SCC and TBC in the bulk-tank milk of sheep and to evaluate possible associations of SCC and TBC with milk content. Throughout Greece, 325 dairy sheep flocks were visited for collection of milk sampling for somatic cell counting, microbiological examination and composition measurement. Geometric mean SCC were 0.488 × 10⁶ cells mL^-1; geometric mean TBC were 398 × 10³ cfu mL^-1; 228 staphylococcal isolates were recovered form 206 flocks (63.4%). Multivariable analyses revealed annual incidence risk of clinical mastitis, age of the farmer and month into lactation period (among 53 variables) to be significant for SCC > 1.0 × 10⁶ cells mL^-1 and month into lactation period at sampling and availability of mechanical ventilators (among 58 variables) to be significant for TBC > 1500 × 10³ cfu mL^-1. Negative correlation of SCC with fat, total protein and lactose and positive correlation of SCC with added water were found. With SCC > 1.0 × 10⁶ cells mL^-1, significant reduction of protein content (2%) was observed, whilst in flocks with SCC > 1.5 × 10⁶ cells mL^-1, significantly lower annual milk production per ewe (42.9%) was recorded.

A genome-wide association analysis for body, udder, and leg conformation traits recorded in Murciano-Granadina goats

Morphological traits are of great importance to dairy goat production given their effect on phenotypes of economic interest. However, their underlying genomic architecture has not yet been extensively characterized. Herein, we aimed to identify genomic regions associated with body, udder, and leg conformation traits recorded in 825 Murciano-Granadina goats. We genotyped this resource population using the GoatSNP50 BeadChip (Illumina Inc., San Diego, CA) and performed genome-wide association analyses using the GEMMA software. We found 2 genome-wide significant associations between markers rs268273468 [Capra hircus (CHI) 16:69617700] and rs268249346 (CHI 28:18321523) and medial suspensory ligament. In contrast, we did not detect any genome-wide significant associations for body and leg traits. Moreover, we found 12, 19, and 7 chromosome-wide significant associations for udder, body, and leg traits, respectively. Comparison of our data with previous studies revealed a low level of positional concordance between regions associated with morphological traits. In addition to technical factors, this lack of concordance could be due to a substantial level of genetic heterogeneity among breeds or to the strong polygenic background of morphological traits, which makes it difficult to detect genetic factors that have small phenotypic effects.

Predisposing factors for bacterial mastitis in ewes

Objective of this review paper is the appraisal of predisposing factors for bacterial mastitis in ewes. Factors that predispose ewes to mastitis can be classified into non-animal-related factors (environmental and climatological factors, housing, nutrition, milking practices) and animal-related factors (anatomic, genetic, litter size-ethological factors, number and stage of lactation period, health problems). There are clear management-environment-animal interactions in mastitis development in ewes, which underline its multifactorial nature. Research and studies regarding risk factors are important, in order to develop strategies for their elimination, control or correction. Control measures for bacterial mastitis, which attempt to eliminate predisposing factors for infection, can thus be developed and implemented.