Common nucleotide sequence of structural gene encoding fibroblast growth factor 4 in eight cattle derived from three breeds

Fibroblast growth factor 4 (FGF4) is considered as a crucial gene for the proper development of bovine embryos. However, the complete nucleotide sequences of the structural genes encoding FGF4 in identified breeds are still unknown. In the present study, direct sequencing of PCR products derived from genomic DNA samples obtained from three Japanese Black, two Japanese Shorthorn and three Holstein cattle, revealed that the nucleotide sequences of the structural gene encoding FGF4 matched completely among these eight cattle. On the other hand, differences in the nucleotide sequences, leading to substitutions, insertions or deletions of amino acid residues were detected when compared with the already reported sequence from unidentified breeds. We cannot rule out a possibility that the structural gene elucidated in the present study is widely distributed in cattle. To the best of our knowledge, this is the first determination of the complete nucleotide sequence of the structural gene encoding bovine FGF4 in identified breeds.     

Haplotype C of growth hormone (GH) gene in Japanese Black cattle: Structure of GH protein and a novel method for detection of the gene

From a series of studies on single nucleotide polymorphisms (SNPs) in the bovine growth hormone (GH) gene of Japanese Black cattle, the type‐C (127^Val and 172^Met) that is specific for this breed has been intensively focused upon because of the economic importance for carcass traits, such as intramuscular oleic acid contents. In the present study, we intended to analyze the 3‐D structure of GH of haplotype C, and developed a novel method to detect the type C gene. Three‐D analysis of the type C protein showed that the amino acid residues (127^Val and 172^Met), which are present in the third and fourth helixes, respectively, and are important for binding with GH receptors, are shifted to deeper positions in the molecule compared with that for type A (127^Leu and 172^Thr), implying the alteration of binding interaction with receptors. A novel, efficient and cost‐effective method (Dot‐blot‐SNP technique) for type C genotyping was successfully established, of which the basal method was a reported genotyping of SNPs for a large number of plants, reducing the cost to 10% or less of direct sequencing.     

Determination of nucleotide sequence of SRY gene in sika deer (Cervus nippon)

The aim of the present study was to determine the whole nucleotide sequence of the open reading frame of the sex‐determining region Y (SRY‐ORF) in wild sika deer. The SRY gene of wild sika deer was obtained by polymerase chain reaction (PCR) with DNA from blood samples. The whole nucleotide sequence of the SRY‐ORF in wild sika deer consisted of 687 bp and encoded 229 deduced amino acids. In comparison with the bovine SRY gene, the percentage of nucleotide sequence homology was 91.0% in the overall ORF, and those of the N‐terminal, high mobility group (HMG) box, and C‐terminal regions within ORF were 88.9%, 96.2% and 87.9%, respectively. The nucleotide sequences of sika deer SRY‐ORF characterized in the present study can be used for phylogenetic analysis or sexing in wild sika deer.     

The polymorphism in the β4-defensin gene and its association with production and somatic cell count in Holstein-Friesian cows

The aim of this study was to find a polymorphism of the bovine β4‐defensin gene and search for its association with milk yield and composition and with the somatic cell count in milk. The data were from the years 1999 to 2004 on 212 Holstein‐Friesian (HF) dairy cows, descended from 70 sires. Based on the sequence of the bovine β4‐defensin gene (GenBank no. AF008307 ) the primers were designed for the amplification of the 924‐bp or 393‐bp long fragments. The 924‐bp long fragment was sequenced and the sequence was compared with that available in the GenBank. Ten putative nucleotide sequence polymorphisms were found in the intron of the bovine β4‐defensin gene. One of them, a C→T transition at position 2239, that creates a new NlaIII (Hin1II) restriction site, was genotyped with polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) in a cohort of 212 HF cows. The CC genotype was the most common (72%). The heterozygous CT genotype was found in 26% of the genotyped cows and four cows (2%) were TT homozygotes. In order to determine the relationship between the polymorphism of the β4‐defensin gene and milk production traits a multi‐trait repeatability test‐day animal model was used. The Derivative‐free Multivariate analysis program was used for computation. The differences between estimates for genotypes were checked using Student's t‐test. The model included the animal genotype, year‐season of calving and parity as fixed effects and the animal additive genetic effect and permanent environmental effect of individual cows as well as dates of the tests as random effects. Significant associations were found between the RFLP‐NlaIII and milk fat, protein and lactose contents. Also, a significant effect was shown of the defensin genotype on the somatic cell count in the milk.     

Circulation of emerging NDM‐5‐producing Escherichia coli among humans and dogs in Egypt

The emergence of NDM‐producing Escherichia coli has considerably threatened human and animal health worldwide. This study describes for the first time in Egypt, the draft genome sequences of emerging NDM‐5‐producing E. coli from humans and dogs, and investigates genetic relatedness between isolates from both sources. Two E. coli from human urine and seven from environmental clinical samples of dogs exhibited resistance to carbapenems and harbouring bla_NDM were subjected to Illumina Miseq whole‐genome sequencing (WGS). Assembly and analysis of the reads were performed to identify resistance genes, multilocus sequence types (MLST), plasmid replicon types (Inc) and insertion sequences (IS) of the bla_NDM region; core genome MLST (cgMLST) analysis was also performed. Two different NDM alleles were identified; bla_NDM‐5 in E. coli HR119 from the urine of a healthy person and environmental samples of dogs, and bla_NDM‐1 in E. coli HR135 from a human patient's urine. Multiple mobilizable resistance genes to different antimicrobial classes were identified except the colistin resistance gene, mcr. E. coli isolates from humans and dogs were assigned to different sequence types (STs). Using cgMLST, dog isolates clustered together with only 1–2 allellic differences; however, human E. coli showed 1,978 different allelles compared with dog isolates. Plasmidfinder results indicated the presence of an IncX3 replicon in bla_NDM‐5‐producing E. coli; however, bla_NDM‐1 was linked to IncCoIKP3. Notably, the NDM region (3 Kb) in all isolates from humans and dogs was highly similar with variable flanking sequences that represented different IS elements. This study reports the first emergence of NDM‐5‐producing E. coli from dogs in Egypt that shared some genetic features with human isolates and could be considered potential public health threats.     

Occurrence and Characteristics of CS31A Antigen‐Producing Escherichia coli in Calves with Diarrhoea and Septicaemia in Argentina

CS31A is a K88‐related non‐fimbrial adhesin first described on Escherichia coli strains isolated from diarrhoeic and septicaemic calves. In this report, CS31A antigen was screened by immunological methods and confirmed by PCR among bovine E. coli isolates. In addition, CS31A‐producing strains were characterized with respect to different fimbrial antigens, O‐serogroup and other properties related to virulence. Faecal or tissue specimens of 100 diarrhoeic or septicaemic calves and 27 older cattle with different pathologies from 71 outbreaks or individual cases that occurred in Buenos Aires province, Argentina, were examined. CS31A+ E. coli strains were isolated from 21 (21.0%) calves from 16 outbreaks or individual cases. No CS31A+ E. coli was detected in samples from cattle more than 1 year old. Fimbriae F5, F41, F17a and F17b were not detected among the CS31A‐producing strains. Three (14.3%) of the CS31A+ E. coli strains expressed the F17c fimbria. All of the 21 isolates exhibited at least one property of septicaemic strains (resistance to serum, production of aerobactin or colicins) but none of them demonstrated heat‐stable enterotoxigenic activity. CS31A+ E. coli isolates belonged to 10 serogroups, more commonly O8, O7, O17 and O21. The results obtained here confirm the worldwide distribution of CS31A antigen in bovine E. coli strains. However, CS31A+ or CS31A+/F17c+ E. coli were less frequently isolated than they were in North hemisphere countries.     

Experimental infection of neonatal pigs with CNF toxin-producing strains of Escherichia coli

To examine and compare the pathogenicity of cytotoxic necrotising factor (CNF)-producing Escherichia coli, two litters of piglets were infected orally with 10¹⁰E coli O88 or 10¹⁰E coli O32 strains. Of the six piglets infected with E coli O88, two died within 24 hours and three developed blood-stained diarrhoea. The other piglets were killed one, five, six and eight days after infection, when bacterial cultures indicated an overwhelming bacteraemic infection with E coli O88 in the early stages followed by clearance through the large intestine. The pathological changes consisted of an early enteritis, progressing to enterocolitis and a bacteraemic spread to the lungs. The histopathological changes were characteristic of toxaemic effects in brain, heart, liver and kidney, and characterised by congestion, oedema and exudation. Infection with E coli O32 produced a milder but similar enterocolitis, also with bacterial colonisation in the lungs. The histopathological findings again reflected a toxaemia. The enteritis was more persistent after E coli O32 infection and the strain persisted in large numbers in the intestine. No evidence of bacterial adherence to the intestinal mucosa was found with either strain. Enteroinvasion was only evident in one E coli O884-nfected piglet, but the consistent occurrence of interstitial pneumonia showed the predilection of these organisms for the lung. The results confirm the toxigenic properties of CNF⁺E coli and suggest an important role for this organism in enteric infection of young pigs.     

Resistance patterns and detection of aac(3)-IV gene in apramycin-resistant Escherichia coli isolated from farm animals and farm workers in northeastern of China

The aminoglycoside apramycin has been used widely in animal production in China since 1999. This study was aimed to investigate the resistance pattern of apramycin-resistant Escherichia coli isolated from farm animals and farm workers in northeastern of China during 2004–2007 and to determine whether resistance to apramycin was mediated by plasmid containing the aac(3)-IV gene and the mode for the transfer of genetic information between bacteria of farm animals and farm workers. Thirty six E. coli isolates of swine, chicken, and human origins, chosen randomly from 318 apramycin-resistant E. coli isolates of six farms in northeastern of China during 2004–2007, were multi-resistant and carried the aac(3)-IV gene encoding resistance to apramycin. Conjugation experiments demonstrated that in all 36 cases, the gene encoding resistance to apramycin was borne on a mobilisable plasmid. Homology analysis of the cloned aac(3)-IV gene with the sequence (accession no. X01385) in GenBank showed 99.3% identity at a nucleotide level, but only with a deletion of guanosine in position 813 of the gene in all 36 cases. The results indicted that resistance to apramycin in these isolates was closely related to aac(3)-IV gene. Therefore, the multi-resistance of E. coli could complicate therapeutic practices for enteric infections in both farm animals and human.     

Polymorphism of 5'-region of the bovine growth hormone receptor gene

Genes coding for growth hormone (GH) and GH receptor (GHR) are candidates for quantitative trait markers in farm animals. This work describes a search for nucleotide sequence polymorphisms within the 5′‐region of the bovine GHR gene. Two new single nucleotide polymorphisms were found: restriction fragment length polymorphisms (RFLPs) at a Fnu4HI/TseI site (C/T transition at position ?1104), and at a Sau96I site (C/T transition at position ?262). The Fnu4HI/TseI polymorphic site is located within the 1.2‐kbp LINE‐1 retrotransposon upstream of the P1 promoter, while the Sau96I RFLP locates in the P1 promoter for exon 1A. The appearance of the Sau96I RFLP was studied in representatives of two bovine species, Bos taurus and Bos indicus. An absolute correlation was observed between Sau96I genotype and the insertion/deletion of LINE‐1.     

Polymorphisms in the bovine hemoglobin‐beta gene provide evidence for gene‐flow between wild species of Bos (Bibos) and domestic cattle in Southeast Asia

The electrophoretic variation in bovine hemoglobin‐beta (HBB) is one of the most investigated genetic markers. The presence of a unique HBB variant, HBB^X, in Southeast Asian cattle has been reputed as a sign of gene‐flow from wild bovine species. In this study, we analyzed the DNA sequences of HBB genes in domestic and wild bovine species to verify this belief. Isoelectric focusing of HBB chain revealed that the HBB^X in domestic cattle had dimorphism and was separated into HBB^X1 and HBB^X2. The HBB^X1 had the same DNA sequence of the common HBB variant in gayal (Bos gaurus frontalis), while some of the HBB^X2 were identical with that of Cambodian banteng (Bos javanicus birmanicus). As a result, we confirmed that the bovine HBB variants can be a good indicator of introgression between wild and domestic cattle. The HBB^X1 was always predominant to HBB^X2 in the continental populations, suggesting that the gaur had contributed to the gene pool of domestic cattle in this region much more than the banteng. On the other hand, the mitochondrial DNA analysis could not detect gene‐flow from wild species. Autosomal markers that can trace the phylogeny between alleles are suitable for the assessment of bovine interspecific introgression.     

Molecular cloning and expression of FGF2 gene in pre‐implantation developmental stages of in vitro‐produced sheep embryos

Early embryonic mortality is one of the main sources of reproductive loss in domestic ruminants including sheep. Fibroblast growth factor‐2 (FGF‐2) is a member of FGFs family that mediates trophoblast activities and regulates embryonic development in various species. In this study, we have cloned, characterized sheep FGF2 cDNA (KU316368) and studied the expression in sheep embryos. Ovaries of non‐pregnant sheep were collected from local abattoir and matured in culture medium at 38.5ºC, 5% CO₂, 95% humidity for 22–24 hr. The matured oocytes were inseminated with capacitated spermatozoa in Brackett and Oliphant medium and resulted embryos were cultured in CO₂ incubator for 6–7 days to complete the developmental stages from two cells to blastocyst stage. Total RNA was extracted from immature oocytes (n = 100), mature oocytes (n = 100) and different stages of embryos such as 2 cell (n = 50), 4 cell (n = 25), 8 cell (n = 12), 16 cell (n = 6), morula (n = 5) and blastocyst (n = 3). The total RNA isolated from the oocytes and embryos was reverse transcribed and subjected to real‐time polymerase chain reaction using sequence‐specific primers and SYBR green as the DNA dye. On sequence analysis, the nucleotide sequence of sheep FGF2 exhibited highest sequence similarity with cattle (100%) and least with rat and mouse (69.2%). At the deduced amino acid level, a highest degree of similarity was noticed with cattle, buffalo, goat, pig, camel and horse (100%) and lowest degree of identity with rat, human and mouse (98.2%). The FGF2 mRNA expression was higher in immature and mature oocytes and gradually decreases from 2‐cell stage of embryo to the blastocyst stage. More over a significant differences in FGF2 mRNA expression (p < .05) were observed between immature oocytes and all pre‐implantation stages of embryo. It can be concluded that FGF‐2 plays a significant role in pre‐implantation and early development of embryos in sheep.     

Genotypic Prevalence of the Adhesin Involved in Diffuse Adherence in Escherichia coli Isolates in Pre‐weaned Pigs with Diarrhoea in Korea

A total of 1002 Escherichia coli strains isolated from pre‐weaned pigs with diarrhoea on 1114 swine farms were screened for the presence of the adhesin involved in diffuse adherence (AIDA) gene by polymerase chain reaction (PCR). Escherichia coli isolates that carried AIDA genes were also tested by PCR for the detection of five fimbriae (F4, F5, F6, F18 and F41), heat‐stable (STa, STb) and heat‐labile (LT) enterotoxin, enteroaggregative E. coli heat‐stable enterotoxin 1 (EAST1), and Shiga toxin 2 oedema disease (Stx2e) genes. Twenty‐three (2.3%) of the 1002 E. coli isolates carried the gene for AIDA. Among 23 isolates shown to carry genes for AIDA, three carried the AIDA gene as the only shown virulence factor. Other isolates carried other virulence factor genes in addition to AIDA. Four isolates carried genes for at least one of the fimbrial adhesins and enterotoxins. Sixteen isolates carried genes for enterotoxins only. The AIDA may represent an additional virulence determinant in pre‐weaned pigs with diarrhoea.     

Characterization of Necrotoxigenic Escherichia coli (NTEC) Strains Isolated from Healthy Calves in Poland

Faecal samples from 132 healthy, 4–8‐week‐old calves from four different farms were examined for necrotoxigenic Escherichia coli (NTEC) producing the cytotoxic necrotizing factors type 1 (CNF1) and type 2 (CNF2). CNF2 genes were detected by polymerase chain reaction in 24 (6.1%) of the 396 E. coli strains tested; these strains were found in 18 (13.6%) calves used in the study. None of the 396 E. coli isolates examined possessed the gene encoding CNF1. Overall, 28.8% of E. coli examined expressed the F17 fimbrial antigen. A strong association between CNF2 toxin and F17 fimbriae was found (62.5% of CNF2‐positive strains were F17‐positive). Moreover, six out of 24 NTEC strains had the Stx1 or the Stx2 shiga toxin genes, and three additional isolates possessed the eae genetic marker of the intimin protein.     

Flow Cytometry for the Detection of Enterohaemorrhagic Escherichia coli O157 : H7 with Latex Beads Sensitized with Specific Antibody

To detect low concentrations of enterohaemorrhagic Escherichia coli O157 : H7 rapidly, flow cytometry (FCM) was carried out with specific IgG‐sensitized latex beads (IgG‐Lx). It was found that test samples for FCM can be prepared for much shorter periods by culturing E. coli O157 : H7 in trypto‐soya broth at 42°C and by treatment with 0.5 % formalin at 37°C. FCM with IgG‐Lx performed with E. coli O157 : H7 prepared by such a procedure revealed that the lowest number of E. coli O157 : H7 prepared in pure culture detected by FCM was 10³/ml. Because similar findings have already been reported by FCM with immunomagnetic beads, FCM with IgG‐Lx is also suggested to be a valuable technique to detect low numbers of E. coli O157 : H7 rapidly in food stuffs.     

Survival of Escherichia coli,Enterococci and Campylobacter jejuni in Canada Goose Faeces on Pasture

Freshly excreted Canada goose faeces pose a public health risk as they contain pathogenic microorganisms. Accordingly, a study was carried out on the growth and survival of resident indicator bacteria (enterococci and Escherichia coli) and inoculated Campylobacter jejuni in freshly excreted faeces over summer and winter. Canada goose faeces were collected, mixed thoroughly and inoculated with 10⁸ g^?1C. jejuni. The faeces were mixed again before making the Canada goose dropping. The simulated goose droppings (N = 70) were placed on pasture, and the concentrations of E. coli, enterococci and the pathogen, C. jejuni, were monitored. In summer only, the molecular marker of E. coli LacZ and the avian‐associated bacteria E2 was also monitored. Results of the survival study indicated that significant growth of enterococci and E. coli occurred in summer, before concentrations decreased to less than 15% of the original concentration (day 77) for enterococci and 0.01% for E. coli. LacZ followed a similar pattern to E. coli, while the E2 marker dropped to below 0.1% of the original concentration within 4 days. In winter, enterococci grew slightly, while no growth of E. coli occurred. In both summer and winter, C. jejuni was rapidly inactivated. This research highlights the ability of bacterial indicators to replicate and survive in the environment when harboured by avian faeces, and the limited risk aged Canada goose faeces pose as an environmental source of Campylobacter spp.     

Quantitative real‐time PCR monitoring of Escherichia coli and Clostridium perfringens with oral administration of Lactobacillus plantarum strain Lq80 to weaning piglets

Levels of fecal or intestinal lactobacilli, Escherichia coli and Clostridium perfringens, and the prevalence of clostridial alpha toxin gene and heat‐stable toxin (ST) gene of enterotoxigenic E. coli (ETEC) were monitored in weaned piglets before (day 0) and during (days 7, 14, and 21) the administration of Lactobacillus plantarum strain Lq80. Lactobacilli were enumerated in a culture‐dependent method. The remainders were determined by quantitative real‐time PCR. In this quantitative real‐time PCR method, the detection limit was proved to be as low as 10³ cells/g feces or intestinal contents. Number of lactobacilli increased from day 0 to day 7 (P < 0.05), to day 14 (P < 0.05), and to day 21 (P = 0.07) in the Lq80‐administered group. L. plantarum contributed to as low as 10% of the lactobacillal population in the Lq80‐administered group. The number of E. coli and C. perfringens, and the prevalence of alpha toxin gene in feces or intestinal contents of the Lq80‐administered group decreased, at least in the first week of the postweaning period. Oral administration of L. plantarum strain Lq80 can stimulate the growth of indigenous lactobacilli and decrease ST‐producing ETEC and C. perfringens in the intestine of postweaning piglets.     

Survival of Pathogenic Escherichia Coli on Basil,Lettuce, and Spinach

The contamination of lettuce, spinach and basil with pathogenic E. coli has caused numerous illnesses over the past decade. E. coli O157:H7, E. coli O104:H4 and avian pathogenic E. coli (APECstx‐ and APECstx+) were inoculated on basil plants and in promix substrate using drip and overhead irrigation. When overhead inoculated with 7 log CFU/ml of each strain, E. coli populations were significantly (P = 0.03) higher on overhead‐irrigated plants than on drip‐irrigated plants. APECstx‐, E. coli O104:H4 and APECstx+ populations were recovered on plants at 3.6, 2.3 and 3.1 log CFU/g at 10 dpi (days post‐inoculation), respectively. E. coli O157:H7 was not detected on basil after 4 dpi. The persistence of E. coli O157:H7 and APECstx‐ were similar when co‐inoculated on lettuce and spinach plants. On spinach and lettuce, E. coli O157:H7 and APEC populations declined from 5.7 to 6.1 log CFU/g and 4.5 log CFU/g, to undetectable at 3 dpi and 0.6–1.6 log CFU/g at 7 dpi, respectively. The detection of low populations of APEC and E. coli O104:H4 strains 10 dpi indicates these strains may be more adapted to environmental conditions than E. coli O157:H7. This is the first reported study of E. coli O104:H4 on a produce commodity.     

Partial characterization of structure and function of a xylanase gene from the rumen hemicellulolytic bacterium Eubacterium ruminantium

A gene encoding for xylanase activity in the rumen hemicellulolytic bacterium Eubacterium ruminantium was cloned into pBR322 in Escherichia coli (E. coli ). The primary clone had a 5.7 kb insert produced by Eco RI partial digestion. Subcloning followed by sequencing allowed for the discovery that this enzyme has a glycosyl‐hydrolase family 10 catalytic domain with a family 9 carbohydrate binding module at C‐terminus and a region partially homologous to a family 22 carbohydrate binding module at N‐terminus. Cloned xylanase is specifically active against xylan and oligoxyloside to produce xylobiose and xylotriose, showing optimal pH and temperature at 7.0 and 50°C, respectively. Molecular size of the xylanase (91 kDa) was confirmed by zymogram analysis of the E. coli clone, which agreed with the predicted size from the DNA sequence. Functions of the two modules at C‐ and N‐termini were evaluated by using xylanase variants with and without the respective module and the C‐terminal module was found to be functional in binding to acid‐swollen cellulose and insoluble oat‐spelt xylan, whereas the N‐terminal module was inactive for binding them.