Evaluating the relative resistance of different poultry breeds to Salmonella Typhimurium

Identification of SNPs Related to Salmonella Resistance in Chickens Using RNA-Seq and Integrated Bioinformatics Approach

Potential single nucleotide polymorphisms (SNPs) were detected between two chicken breeds (Kashmir favorella and broiler) using deep RNA sequencing. This was carried out to comprehend the coding area alterations, which cause variances in the immunological response to Salmonella infection. In the present study, we identified high impact SNPs from both chicken breeds in order to delineate different pathways that mediate disease resistant/susceptibility traits. Samples (liver and spleen) were collected from Salmonella resistant (K. favorella) and susceptible (broiler) chicken breeds. Salmonella resistance and susceptibility were checked by different pathological parameters post infection. To explore possible polymorphisms in genes linked with disease resistance, SNP identification analysis was performed utilizing RNA seq data from nine K. favorella and ten broiler chickens. A total of 1778 (1070 SNPs and 708 INDELs) and 1459 (859 SNPs and 600 INDELs) were found to be specific to K. favorella and broiler, respectively. Based on our results, we conclude that in broiler chickens the enriched pathways mostly included metabolic pathways like fatty acid metabolism, carbon metabolism and amino acid metabolism (Arginine and proline metabolism), while as in K. favorella genes with high impact SNPs were enriched in most of the immune-related pathways like MAPK signaling pathway, Wnt signaling pathway, NOD-like receptor signaling pathway, etc., which could be a possible resistance mechanism against salmonella infection. In K. favorella, protein-protein interaction analysis also shows some important hub nodes, which are important in providing defense against different infectious diseases. Phylogenomic analysis revealed that indigenous poultry breeds (resistant) are clearly separated from commercial breeds (susceptible). These findings will offer fresh perspectives on the genetic diversity in chicken breeds and will aid in the genomic selection of poultry birds.

Molecular Epidemiology of Salmonella enterica in Poultry in South Africa Using the Farm-to-Fork Approach

The presence of the zoonotic pathogen Salmonella in the food supply chain poses a serious public health threat. This study describes the prevalence, susceptibility profiles, virulence patterns, and clonality of Salmonella from a poultry flock monitored over six weeks, using the farm-to-fork approach. Salmonella was isolated using selective media and confirmed to the genus and species level by real-time polymerase chain reaction (RT-PCR) of the invA and iroB genes, respectively. Antimicrobial susceptibility profiles were determined using Vitek-2 and the Kirby–Bauer disk diffusion method against a panel of 21 antibiotics recommended by the World Health Organisation Advisory Group on Integrated Surveillance of Antimicrobial Resistance (WHO-AGISAR). Selected virulence genes were identified by conventional PCR, and clonality was determined using enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Salmonella was present in 32.1% of the samples: on the farm (30.9%), at the abattoir (0.6%), and during house decontamination (0.6%). A total of 210 isolates contained the invA and iroB genes. Litter, faeces, and carcass rinsate isolates were classified as resistant to cefuroxime (45.2%), cefoxitin (1.9%), chloramphenicol (1.9%), nitrofurantoin (0.4%), pefloxacin (11.4%), and azithromycin (11%). Multidrug resistance (MDR) was observed among 3.8% of the isolates. All wastewater and 72.4% of carcass rinsate isolates were fully susceptible. All isolates harboured the misL, orfL, pipD, stn, spiC, hilA, and sopB virulence genes, while pefA, spvA, spvB, and spvC were absent. In addition, fliC was only present among the wastewater isolates. Various ERIC-PCR patterns were observed throughout the continuum with different subtypes, indicating the unrelated spread of Salmonella. This study concluded that poultry and the poultry environment serve as reservoirs for resistant and pathogenic Salmonella. However, there was no evidence of transmission along the farm-to-fork continuum.

Crossbreeding impacts on caecal bacterial count and antibody titres in chickens

1. A crossbreeding experiment was conducted using 20 sires and 120 dams from each Fayoumi (F) and Rhode Island Red (R) breeds. The F₁ chicks of ½F½R and their reciprocal ½R½F crosses were used to estimate direct, maternal and heterotic effects.2. The caecal bacterial counts of Salmonella typhimurium and Enterococcus faecium and the IgA, IgG and IgM antibody titres were determined. Chicks of each genetic group (120 birds) were divided into three groups (40 birds per group) and chicks of the first group were assigned as the control group, while the second group was inoculated with S. typhimurium and E. faecium at 7 and 10 d of age (10⁶ cfu/chick) and the third was inoculated with S. typhimurium at 10 d of age (10⁶ cfu/chick).3. The generalised least square procedure was used to estimate cross-breeding effects. The S. typhimurium counts in the R breed was highly significant, followed by ½F½R cross, ½R½F cross, and F breed. The differences among genetic groups in E. faecium counts and caecal pH was not significant. The estimates of IgA, IgG, and IgM antibody titres were highly significant in the F breed, followed by ½R½F cross, ½F½R cross, and the R breed.4. The estimates of direct additive effects were highly significant F breed for the counts of S. typhimurium and antibody titres of IgA, IgG, and IgM. The maternal effects were highly significant F breed for S. typhimurium, E. faecium count, and antibody titres of IgA, IgG, and IgM. Estimates of direct heterosis were significant for S. typhimurium count and IgA antibody titre but not significant for E. faecium count, caecal pH, and antibody titres of IgG and IgM.5. The results showed that the Fayoumi breed could be used in breeding programmes to improve immunity traits against S. typhimurium in chickens.

Prevalence and Antibiogram Assessment of Staphylococcus aureus in Beef at Municipal Abattoir and Butcher Shops in Addis Ababa, Ethiopia

Objective

A cross-sectional study was conducted from October 2013 to April 2014 to determine the prevalence and antibiotic resistance of Staphylococcus aureus from beef of Addis Ababa Abattoir and butcher shops in Addis Ababa. Seven hundred sixty-eight swab samples were taken from the abattoir and butcher carcasses using a systematic random sampling. One hundred twenty swab samples were also taken from hooks, cutting tables, and knives from the abattoir. Staphylococcus aureus positive isolates were taken for antibiotic susceptibility test. A questionnaire survey was conducted in the abattoir and butcher workers to assess the hygienic practice and possible risk factors regarding the contamination of meat.

Results

The prevalence of S. aureus in the abattoir, butcher, cutting table, hook, and knife was 9.4%, 19.8%, 15%, 15%, and 22.5%, respectively. The prevalence of S. aureus in the knife and butcher was found to be 2.8 (OR = 2.8, CI = 1.2–6.4) and 2.4 (OR = 2.4, CI = 1.6–3.6) times that of the abattoir results (p < 0.01). The antimicrobial susceptibility testing was also conducted on 133 isolates of S. aureus using the disc diffusion susceptibility method. Bacitracin, neomycin, and methicillin were found to be 100% resistant to S. aureus. To avoid the presence of pathogenic Staphylococcus isolates, preventive measures using good hygienic practices during slaughtering and handling of the beef carcasses are recommended.