Analysis of cattle olfactory subgenome: the first detail study on the characteristics of the complete olfactory receptor repertoire of a ruminant

BACKGROUND: Mammalian olfactory receptors (ORs) are encoded by the largest mammalian multigene family. Understanding the OR gene repertoire in the cattle genome could lead to link the effects of genetic differences in these genes to variations in olfaction in cattle. RESULTS: We report here a whole genome analysis of the olfactory receptor genes of Bos taurus using conserved OR gene-specific motifs and known OR protein sequences from diverse species. Our analysis, using the current cattle genome assembly UMD 3.1 covering 99.9% of the cattle genome, shows that the cattle genome contains 1,071 OR-related sequences including 881 functional, 190 pseudo, and 352 partial OR sequences. The OR genes are located in 49 clusters on 26 cattle chromosomes. We classified them into 18 families consisting of 4 Class I and 14 Class II families and these were further grouped into 272 subfamilies. Comparative analyses of the OR genes of cattle, pigs, humans, mice, and dogs showed that 6.0% (n = 53) of functional OR cattle genes were species-specific. We also showed that significant copy number variations are present in the OR repertoire of the cattle from the analysis of 10 selected OR genes. CONCLUSION: Our analysis revealed the almost complete OR gene repertoire from an individual cattle genome. Though the number of OR genes were lower than in pigs, the analysis of the genetic system of cattle ORs showed close similarities to that of the pig

Tropism and infectivity of duck-derived egg drop syndrome virus in chickens

<div><p>Egg drop syndrome virus (EDSV) can markedly decrease egg production in laying hens. Duck is the natural host of EDSV. EDSV derived from ducks abrogate egg drop in laying hens. We have previously confirmed that duck-derived EDSVs have a variety of replication activities in chick embryo liver (CEL) cells. However, it is currently unclear whether duck-derived EDSV could display tropism and adaptation in laying hens. This study assessed whether duck-derived EDSV can adapt to laying hens, and estimated the inducing factors. Complete genome sequences of duck-derived EDSVs (D11-JW-012, D11-JW-017, and D11-JW-032 isolates) with various replication efficiency in CEL cells and C10-GY-001 isolate causing disease in laying hens were analyzed to find their differences. Phylogenetic analysis of complete genome sequence revealed that C10-GY-001, D11-JW-032, and strain 127 virus as vaccine were clustered into the same group, with D11-JW-012 and D11-JW-017 clustered in another group. Comparison between D11-JW-012 isolate that poorly replicated and D11-JW-017 isolate that replicated well in CEL cells in same cluster revealed six amino acid differences on IVa2, DNA polymerase, endopeptidase, and DNA-binding protein. These amino acids might be key candidates enhancing cellular tropism in chicken. When the pathogenicities of these isolates in laying hens were compared, D11-JW-032 showed severe signs similar to 127 virus, D11-JW-017 showed intermediate signs, while D11-JW-012 showed almost no sign. Eleven amino acids differed between D11-JW-032 and D11-JW-017, and 17 amino acids were different between D11-JW-032 and D11-JW-012. These results suggest that EDSVs derived from ducks have various pathogenicities in laying hens. Key amino acid candidates might have altered their affinity to tropism of laying hens, causing difference pathogenicities.</p></div

Complete genome sequence analysis compared to that of the strain 127 virus and the characteristics of egg drop syndrome virus (EDSV) field strains used in this study.^a

<p>Complete genome sequence analysis compared to that of the strain 127 virus and the characteristics of egg drop syndrome virus (EDSV) field strains used in this study.<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177236#t001fn001" target="_blank">^a</a></p

Gross lesions change of the experimentally infected chickens.

<p>Reproductive system of ovary and oviduct of chicken inoculated with PBS control (A), D11-JW-012 (B), D11-JW-017 (C), D11-JW-032 (D), or 127 virus (E). Ruptured ovarian follicles and peritonitis were also found in chickens infected with 127 virus (F).</p

Phylogenetic analysis of complete genome sequences of four Korean egg drop syndrome virus (EDSV) isolates.

<p>The phylogenetic tree was prepared using the neighbor-joining method and bootstrap testing. Numbers over the branches indicate the percentage of 1,000 bootstrap replicates supporting the branch.</p

Serum antibody titers of laying chickens infected with EDSVs.

<p>Serum antibody titers of laying chickens infected with EDSVs.</p

Mean weight of laying chickens infected with EDSVs.

<p>Mean weight of laying chickens infected with EDSVs.</p

The use of embryonic chicken eggs as an alternative model to evaluate the virulence of Salmonella enterica serovar Gallinarum.

Salmonella enterica serovar Gallinarum (S. Gallinarum) can cause fowl typhoid, a severe systemic disease responsible for considerable economic losses. Chicken pathogenicity test is the traditional method for assessing the virulence of S. Gallinarum. However, this method is limited by several factors, including ethical considerations, costs, and the need for specialized facilities. Hence, we established a chicken embryo lethality assay (ELA) model to determine the virulence of S. Gallinarum. Three virulent and three avirulent representative strains, which were confirmed by the chicken pathogenicity test, were used to perform the ELA. The most significant difference between the virulent and avirulent strains could be observed when 13-day-old embryos were inoculated via the AC route and incubated for 5 days. Based on a 50% embryo lethal dose (ELD50), isolates considered to be virulent had a Log10ELD50 of ≤ 4.0, moderately virulent strains had a Log10ELD50 of 4.0-6.1, and avirulent isolates had a Log10ELD50 of ≥ 6.1. Different abilities to invade the liver of embryos were found between the virulent and avirulent strains by a growth curve experiment in vitro. The maximum colony-forming units (CFU) of the virulent strain was about 10,000 times higher than that of the avirulent strain in the liver at 5 days post infection. The ELA results of 42 field strains showed that thirty-two strains (76.2%) were virulent, nine were moderately virulent (21.4%), and one strain was avirulent (2.4%). In conclusion, these results suggest that the ELA can be used as an alternative method to assess the virulence of S. Gallinarum, which will contribute to the study of virulence genes, virulence evolution, pathogenic mechanisms and vaccine development

Clonal dissemination of Salmonella enterica serovar albany with concurrent resistance to ampicillin, chloramphenicol, streptomycin, sulfisoxazole, tetracycline, and nalidixic acid in broiler chicken in Korea

ABSTRACT: The aim of this study was to determine the prevalence, serovar distribution, antimicrobial resistance, and genotypic analyses of the dominating serovars of Salmonella in chickens from a national study in Korea. Between 2017 and 2018, a total of 550 chicken samples were collected from the top 12 integrated broiler chicken operations in Korea. Salmonella was isolated from 117 (32.5%) chicken feces and 19 (10.0%) retail chicken meat sources. Ten serovars were identified, and the most common Salmonella serovar was Salmonella ser. Albany (50 isolates, 36.8%), followed by S. Enteritidis (38 isolates, 27.9%), and S. Montevideo (23 isolates, 16.9%) isolated from 6, 10, and 6 operations, respectively. A total of 35 (25.7%) isolates were with the ACSSuTN (ampicillin, chloramphenicol, streptomycin, sulfisoxazole, tetracycline, and nalidixic acid) resistance pattern, with high prevalence of this resistance pattern in S. Albany (29 isolates, 58.0%). A total of 35 PFGE types were identified among Salmonella isolates of the serovars Albany, Enteritidis, Virchow, Montevideo, and Senftenberg, while 11 distinct types of PFGE patterns were found among S. Albany isolates, which showed an overall homology similarity of higher than 85%. Among these 35 PFGE types, 22 PFGE types corresponded to 32 isolates from samples limited to one operation, and the other 13 PFGE types corresponded to 72 isolates from samples widely distributed among different operations. These results highlighted rapid colony dissemination of multidrug-resistant S. Albany in chicken all over Korea after it first appeared in 2016; furthermore, the spread of Salmonella colonies between various integrated operations was common, and several operations played an important role in Salmonella carriage and transmission in Korea

Conjugative Plasmid-Mediated Extended Spectrum Cephalosporin Resistance in Genetically Diverse Escherichia coli from a Chicken Slaughterhouse

ESC-resistant E. coli isolates were collected from broiler chickens, a slaughterhouse, and retail meat to assess their dispersion and their involvement in cross-contamination. ESBL-/AmpC-producing E. coli were isolated during the slaughter process of all six investigated chicken flocks from scalding, feather removal, first conveyor, evisceration, second washing, third conveyor, and third washing areas, and from handling workers in the slaughterhouse. ESC-resistant E. coli isolates with the same pulsed-field gel electrophoresis type were found in the same site (scalding) on different sampling days. ESBL/AmpC-producing E. coli isolates were absent in the lairage area in the slaughterhouse, but present in the retail markets in 36.8% (7/19) of the chicken flocks. The blaCTX-M genes and blaCMY-2 were conjugated to recipient E. coli J53 in 67.5% (27/40) and 56.1% (23/41) of ESBL-producing and AmpC-producing E. coli isolates, respectively. The presence of the same conjugative plasmids was found in genetic diversity ESC-resistant E. coli colonies collected on different sampling days. Our study emphasizes that cross-contamination of ESBL/AmpC-producing E. coli in slaughterhouse has a crucial impact on the occurrence of ESC resistance in retail chicken meat