Goat farming in Pakistan depends on indigenous breeds that have adapted to specific agro-ecological conditions. Pakistan has a rich resource of goat breeds, and the genetic diversity of these goat breeds is largely unknown. In this study, genetic diversity and population structure were characterized from seven indigenous goat breeds using the goat 50K SNP chip. The genetic diversity analysis showed that Bugi toori goats have the highest inbreeding level, consistent with the highest linkage disequilibrium, lowest diversity and long run of heterozygosity segments. This indicates that this breed should be prioritized in future conservation activities. The population structure analysis revealed four fairly distinct clusters (including Bugi toori, Bari, Black Tapri and some Kamori) and three other breeds that are seemingly the results of admixture between these or related groups (some Kamori, Pateri, Tapri and White Tapri). The selection signatures were evaluated in each breed. A total of 2508 putative selection signals were reported. The 26 significant windows were identified in more than four breeds, and selection signatures spanned several genes that directly or indirectly influence traits included coat colour variation (KIT), reproduction (BMPR1B, GNRHR, INSL6, JAK2 and EGR4), body size (SOCS2), ear size (MSRB3) and milk composition (ABCG2, SPP1, CSN1S2, CSN2, CSN3 and PROLACTIN).

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| Escherichia coli is one of the common microbial flora of poultry gut. Most of E. coli isolates are nonpathogenic but are considered to be an indicator of fecal contamination in food industry. A study was carried-out on the prevalence, incidence, isolation and antibiogram of E. coli from table eggs. A total of 100 table eggs were collected from various locations of district Peshawar, Pakistan and divided into three parts viz., the egg-yolk, egg-white and eggshell. These were cultured on different media and identified organism was subjected to antibiogram study using the disk diffusion method. The overall prevalence of E. coli was found as 37%. While, incidence was recorded as 15% in eggshells, 12% in egg-whites and 10% in egg-yolks. It was concluded that the table eggs were contaminated with E. coli and higher incidence of E. coli was recorded in eggshells as compared to other components of the eggs. The antibiotics ciprofloxacin and enrofloxacin were recorded highly active against E. coli.

The Tibetan cashmere goat is one of the main goat breeds used by people living in the plateau. It exhibits the distinct phenotypic characteristics observed in lowland goats, allowing them to adapt to the challenging conditions at high altitudes. It provides an ideal model for understanding the genetic mechanisms underlying high-altitude adaptation and hypoxia-related diseases. Our previous exome sequencing of five Chinese cashmere breeds revealed a candidate gene, DSG3 (Desmoglein 3), responsible for the high-altitude adaptation of the Tibetan goat. However, the whole DSG3 gene (44 kbp) consisting of 16 exons in the goat genome was not entirely covered by the exome sequencing. In this study, we resequenced all the 16 exons of the DSG3 gene in ten Chinese native goat populations. Twenty-seven SNP variants were found between the lowland and highland goat populations. The genetic distance (FST) of significant SNPs between the lowland and highland populations ranged from 0.42 to 0.58. By using correlation coefficient analysis, linkage disequilibrium, and haplotype network construction, we found three non-synonymous SNPs (R597E, T595I, and G572S) in exon 5 and two synonymous SNPs in exons 8 and 16 in DSG3. These mutations significantly segregated high- and low-altitude goats in two clusters, indicating the contribution of DSG3 to the high-altitude hypoxia adaptation in the Tibetan goat.

Riemerella anatipestifer is a major pathogenic agent of duck septicemic and exudative diseases. Genetic analyses suggest that this pathogen has a novel protein secretion system, known as the “type IX secretion system” (T9SS). We previously reported that deletion of the AS87_RS08465 gene significantly reduced the bacterial virulence of the R. anatipestifer strain Yb2, but the mechanism remained unclear. The AS87_RS08465 gene is predicted to encode the gliding motility protein GldM (GldM) protein, a key component of the T9SS complex. In this study, Western blotting analysis demonstrated that R. anatipestifer GldM was localized to the cytomembrane. Further study revealed that the adhesion and invasion capacities of the mutant strain RA2281 (designated Yb2Δ gldM ) in Vero cells and the bacterial loads in the blood of infected ducks were significantly reduced. RNA-Seq and PCR analyses showed that six genes were upregulated and five genes were downregulated in the mutant strain Yb2Δ gldM and that these genes were mainly involved in the secretion of proteins. Yb2Δ gldM was also found to be defective in gliding motility and protein secretion. Liquid chromatography–tandem mass spectrometry analysis revealed that nine of the proteins had a conserved T9SS C-terminal domain and were differentially secreted by Yb2Δ gldM compared to Yb2. The complementation strain cYb2Δ gldM recovered the adhesion and invasion capacities in Vero cells and the bacterial loads in the blood of infected ducks as well as the bacterial gliding motility and most protein secretion in the mutant strain Yb2Δ gldM to the levels of the wild-type strain Yb2. Taken together, these results indicate that R. anatipestifer GldM is associated with T9SS and is important in bacterial virulence. Electronic supplementary material The online version of this article (10.1186/s13567-019-0660-0) contains supplementary material, which is available to authorized users.

Staphylococcus aureus, a normal flora of human and animals is recognized as an opportunistic pathogen that cause several infections. In present study, eighty S. aureus isolates were recovered from different animals such as sheep, goat, buffalo, camel, horse, cattle, dog and human. These isolates were exposed to in vitro antibiotic sensitivity test using eleven antimicrobial agents which included ampicillin (10µg), amikacin (30µg), chloramphenicol (30µg), sulfanilamide (30µg), erythromycin (15µg), gentamicin (10µg), kanamycin (30µg), neomycin (30µg), ofloxacin (5µg), penicillin G (10 IU) and tetracycline (30µg) by disc diffusion technique. Results indicated that camel isolates of S. aureus were found100% sensitive to tetracycline. While, ofloxacin and amikacin were found 100% effective against sheep and dog isolates respectively. Whereas, chloramphenicol showed 100% sensitivity against isolates of dog and horse. Ampicillin (0% sensitive to buffalo, cattle, goat, dog and horse isolates) and sulfanilamide (0% sensitive to buffalo, cattle, camel, goat and sheep isolates) showed least sensitivity as compared to other antimicrobial agents. However, poultry isolates showed least, while camel and horse isolates showed most response for the antimicrobial agents. These results indicates the host-microbe interaction and also probable role of host in progression of resistance in S. aureus against antimicrobial agents.

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