Sequence polymorphism in the ribosomal DNA internal transcribed spacers differs among Theileria species

The genomic region spanning the two ribosomal RNA internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene was cloned and sequenced from sixteen Theileria isolates. Each Theileria species possessed ITS1 and ITS2 of unique size(s) and species specific nucleotide sequences. Varying degrees of ITS1 and ITS2 intra- and inter-species sequence polymorphism were found among ruminant Theileria species. The spacers were most polymorphic in the agent of tropical theileriosis, Theileria annulata, and were more conserved in two benign species, Theileria buffeli and Theileria sergenti Chitose. Phylogenetic analysis of the rDNA ITS1-5.8S rRNA gene-ITS2 region clearly separated each taxon, placing them in three clusters. One held T. annulata, Theileria parva, and Theileria mutans, with the latter two most closely related. The second held T. sergenti Ikeda, T. sergenti Chitose, and T. buffeli, with the latter two most closely related. The third cluster held the Theileria ovis isolates.     

Detection and identification of equine Theileria and Babesia species by reverse line blotting: epidemiological survey and phylogenetic analysis

Specific oligonucleotide probes were designed to develop a new and highly sensitive reverse line blot assay to detect and identify simultaneously different Theileria and Babesia species in horses. The amplified hypervariable V4 region of the 18S rRNA gene was hybridised against different generic and species-specific probes. The survey was conducted over 243 samples of equine blood divided into three different groups: group 1, 24 horses presented as possible clinical piroplasmosis; group 2, 181 clinically healthy free-ranging horses exposed to ticks; group 3, 38 riding horses with unrelated pathologies and low or no contact with ticks. The study demonstrated a high piroplasm prevalence in the first two groups of animals. Two Theileria genotypes sharing 96.8% similarity between their 18S rRNA gene sequences and two Babesia genotypes sharing 97.4% similarity, were identified. The biologic meaning of such genotypes is discussed in terms of their phylogenetic relationships and potential pathogenicity.     

Identification of porcine intestinal spirochetes by PCR-restriction fragment length polymorphism analysis of ribosomal DNA encoding 23S rRNA

The Brachyspira (formerly Serpulina) species rrl gene encoding 23S ribosomal RNA (rRNA) was used as a target for amplification of a 517bp DNA fragment by polymerase chain reaction (PCR). The primers for PCR amplification had sequences that were conserved among Brachyspira 23S rRNA gene and were designed from nucleotide sequences of Brachyspira hyodysenteriae, Serpulina intermedia, Brachyspira innocens and Brachyspira pilosicoli available from the GenBank database. Digestion of PCR-generated products from reference and field isolates of swine intestinal spirochetes with restriction enzymes Taq I and Alu I revealed five restriction fragment length polymorphism (RFLP) patterns. Each RFLP pattern corresponded to previously established genetic groups including B. hyodysenteriae (I), S. intermedia/B. innocens (II), Brachyspira murdochii (III), B. pilosicoli (IV) and B. alvinipulli (V). The 23S rRNA PCR/RFLP provided a relatively simple genotypic method for identification of porcine pathogenic B. hyodysenteriae and B. pilosicoli.     

Pulsed-field gel electrophoresis genotyping of Salmonella gallinarum and comparison with random amplified polymorphic DNA

Salmonella gallinarum is gram-negative bacteria that cause fowl typhoid (FT) in chickens. Since the first outbreak of FT reported in 1992 in Korea, it has widely spread throughout the country. Today, FT is one of the most devastating diseases of poultry. The aim of the present study was to ascertain a genetic relationship among S. gallinarum isolates collected from different regions of Korea over a 10-year period. We examined a total of 38 isolates of S. gallinarum obtained in 29 regions of Korea from 1992 to 2001 including the 9R vaccine strain and the standard strain of S. gallinarum (ATCC 9184). The PFGE profiles produced 12 different patterns with the XbaI-digestion and 11 different patterns with the SpeI-digestion. The RAPD using URP-6 primers showed eight different genotypes with the same Salmonella isolates. The PFGE patterns of the 9R vaccine strain and ATCC 9184 of S. gallinarum were different from the identical type A, the most common genotype among field isolates in our study. In conclusion, a low genetic heterogeneity was observed among Korean S. gallinarum isolates. In addition, PFGE appeared to be a more accurate and reproducible method for genotyping of S. gallinarum isolates than RAPD.     

Comparison of phenotypic and genotypic methods for the species identification of coagulase-negative staphylococcal isolates from bovine intramammary infections

Coagulase-negative staphylococci (CNS) are the most frequently isolated pathogens from cows with intramammary infection (IMI). Although API STAPH ID 20, a commercially available identification system, and PCR-restriction fragment length polymorphism (PCR-RFLP) of the gap gene (gap PCR-RFLP) have been successfully applied for the identification of CNS isolates from human specimens, their accuracy in the identification of veterinary isolates has not been fully established. In this study, we identified 263 CNS isolates from bovine IMI at species level by partial 16S rRNA gene sequence analysis as the definitive test. Species identification obtained using partial 16S rRNA gene sequence analysis was compared to results from the API STAPH ID 20 and gap PCR-RFLP analysis. Eleven different CNS species were identified by partial 16S rRNA gene sequence analysis. Only 76.0% (200/263) of the species identification results obtained by API STAPH ID 20 matched those obtained by partial 16S rRNA gene sequence analysis, whereas 97.0% (255/263) of the species identification results obtained by the gap PCR-RFLP analysis matched those obtained by partial 16S rRNA gene sequence analysis. The gap PCR-RFLP analysis could be a useful and reliable alternative method for the species identification of CNS isolates from bovine IMI and appears to be a more accurate method of species identification than the API STAPH ID 20 system.     

Molecular characterization of Blastocystis isolates from children and rhesus monkeys in Kathmandu, Nepal

To investigate the possible transmission of Blastocystis organisms between local rhesus monkeys and children in Kathmandu, Nepal, we compared the subtype (ST) and sequence of Blastocystis isolates from children with gastrointestinal symptoms and local rhesus monkeys. Twenty and 10 Blastocystis isolates were established from 82 and 10 fecal samples obtained from children and monkeys, respectively. Subtype analysis with seven sequence-tagged site (STS) primers indicated that the prevalence of Blastocystis sp. ST1, ST2 and ST3 was 20%, 20% and 60% in the child isolates, respectively. In contrast to human isolates, ST3 was not found in monkey isolates and the prevalence of ST1 and ST2 was 50% and 70%, respectively, including three mixed STs1 and 2 and one isolate not amplified by any STS primers, respectively. Since Blastocystis sp. ST2 has been reported as the most dominant genotype in the survey of Blastocystis infection among the various monkey species, sequence comparison of the 150 bp variable region of the small subunit rRNA (SSU rRNA) gene was conducted among ST2 isolates of humans and monkeys. Sequence alignment of 24 clones developed from ST2 isolates of 4 humans and 4 monkeys showed three distinct subgroups, defined as ST2A, ST2B and ST2C. These three subgroups were shared between the child and monkey isolates. These results suggest that the local rhesus monkeys are a possible source of Blastocystis sp. ST2 infection of humans in Kathmandu.     

Genotyping of infectious bronchitis viruses isolated in Japan during 2008−2019

Seventeen isolates of infectious bronchitis virus (IBV) were obtained from various prefectures of Japan during 2008–2019 and genetically analyzed. The IBV isolates were classified into six genetic groups, based on phylogenetic analysis of the S1 gene. The S1 genotypes were distinguishable by a newly developed restriction fragment length polymorphism (RFLP) method using three endonucleases, Hae II, Hpa I, and Fok I. Moreover, the isolates were classified into four genetic groups, based on phylogenetic analysis of the S2 gene. However, novel genetic groups based on a combination of S1 and S2 genotypes, which were undetected previously, were confirmed in this study, indicating that various recombinant IBV strains were prevalent in poultry in Japan.     

Occurrence of Theileria and Babesia species in water buffalo (Bubalus babalis, Linnaeus, 1758) in the Hubei province, South China

The presence and prevalence of tick-borne haemoparasites in water buffalo from the Hubei province, south China was investigated using the reverse line blot (RLB) hybridization assay and phylogenetic analysis of the parasite 18S rRNA gene. Theileria buffeli (19.1%) was the most frequently found species in all of the locations, followed by Babesia orientalis (8.9%), Babesia bovis (1.0%) and Babesia bigemina (0.7%). Only 12 (3.9%) of the samples had mixed infections. Eleven samples with single infections were selected for further characterization using 18S rRNA gene sequence analysis. Phylogenetic analysis showed that the eight T. buffeli 18S rRNA gene sequences obtained grouped into four clusters, of which three grouped with the known T. buffeli types B and D. The remaining five grouped separately from the previously describe T. buffeli types, constituting new T. buffeli types. The two B. bigemina 18S rRNA gene sequences obtained grouped closely with B. bigemina Kunming; this serves as the first report of B. bigemina in the Hubei province. The B. orientalis Daye 18S rRNA gene sequence obtained grouped closely with the previously reported B. orientalis Wuhan strain and with Babesia sp. Kashi 1 and Kashi 2.     

健康与腹泻仔猪源A型产气荚膜梭菌的多位点序列分型

A型产气荚膜梭菌(CpA)存在于健康仔猪肠道,同时也是仔猪肠毒血症的关键病原.为研究两者的差异,本试验在江西省4个地区采集健康和腹泻仔猪粪便样本分离得到CpA,通过16S rRNA鉴定所有CpA分离株,并通过多重PCR确定分离株的毒素分型.采用MLST多位点序列分型技术对选取的24株CpA(腹泻或健康来源CpA各12株...     

Characterisation of a novel Mannheimia sp from Australian feedlot cattle

OBJECTIVE: To characterise eight isolates of a Gram-negative organism obtained from the upper respiratory tract of cattle showing evidence of mild upper respiratory tract disease. DESIGN: The isolates were compared with the five recognised species within the genus Mannheimia - M haemolytica, M glucosida, M granulomatis, M ruminalis and M varigena--using a range of phenotypic and genotypic methods. RESULTS: Phenotypic characterisation indicated that the isolates belonged to the trehalose-negative [Pasteurella] haemolytica complex. This complex has recently been reorganised into five species within the new genus Mannheimia. Ribotyping performed using HindIII and a computerised analysis system indicated that the eight Australian isolates formed a distinct cluster that was related to, but different from, the five recognised species of Mannheimia. The 16S rRNA sequence of one isolate (BNO311) was determined and a phylogenetic analysis performed. Isolate BNO311 was distinct from the five named Mannheimia spp but did join a larger cluster consisting of rRNA cluster IV (M varigena) and the unnamed rRNA cluster V of Mannheimia. DNA:DNA hybridisation between isolate BNO311 and M haemolytica NCTC 9380T, M granulomatis P411 and Actinobacillus ligniersii NCTC 4189T all suggested similarities of approximately 30%. CONCLUSIONS: These phenotypic and genotypic characterisation studies suggest that the eight Australian isolates represent a new species of Mannheimia. Until further characterisation studies are performed, we are unwilling to propose a name for this taxon, preferring to refer to this possible new species as Bisgaard taxon 39 of cluster V of Mannheimia.     

Multilocus enzyme electrophoresis for identification and typing of Treponema hyodysenteriae and related spirochaetes

An assessment was made of multilocus enzyme electrophoresis as a means of identifying and typing spirochaetes isolated from pigs. Using five enzyme systems, 36 isolates from Australia, the U.K. and the U.S.A. were divided into 12 electrophoretic types or multilocus genotypes, comprising four major, genetically distinct groups. All 26 isolates of Treponema hyodysenteriae fell into one group, members of which showed relatively little genetic diversity. Ten isolates of non-pathogenic spirochaetes fell into three genetically different groups. Although the technique was capable of typing organisms within the groups, it was not always as discriminatory as DNA-restriction endonuclease analysis. Examination of additional enzyme loci should increase the sensitivity of the method for typing and for overall assessment of genetic relationships between spirochaetes.     

Amplification of 16S rRNA genes of Anaplasma species in China for phylogenetic analysis

In this study, a phylogenetic tree was inferred through comparing five 16S rRNA gene sequences of four isolates of Anaplasma ovis and one of Anaplasma marginale in China with all nineteen 16S rRNA gene sequences deposited in GenBank (12 A. marginale, 3 A. ovis and 4 Anaplasma centrale derived from America, Uruguay, South Africa, Zimbabwe, Australia, Isreal and Japan). The analysis showed that all A. ovis isolated in China were separated into an A. ovis cluster, while the A. marginale in China was separated into an A. marginale cluster (see Fig. 1). This analysis demonstrated that there are at least two different Anaplasma species widespread among ruminants in North China.     

Intraspecific variation in the 16S rRNA gene sequences of Mycoplasma agalactiae and Mycoplasma bovis strains

Intraspecific variation in the 16S rRNA genes of 17 Mycoplasma agalactiae and eight Mycoplasma bovis isolates was investigated to determine the degree of sequence variation in these two species and to determine whether the polymorphisms in the 16S rRNA genes could be used for the construction of an evolutionary tree and as epidemiological markers. A high degree of variation was found within isolates (between operons) and between isolates of both species. In contrast to M. capripneumoniae no distinct evolutionary pattern could be seen, probably because there are functional systems for gene conversion in M. agalactiae and M. bovis. However, the non-European isolates of M. agalactiae shared three characteristic nucleotides and European isolates from the same or neighbouring countries were very similar. Differences within isolates included both polymorphic positions and sequence length differences between operons. The amount of variation within isolates of the respective species ranged from zero to seven polymorphisms for M. agalactiae and from zero to four polymorphisms for M. bovis. The high degree of variation suggests the potential for misdiagnosis of species in diagnostic PCR assays based on the 16S rRNA gene sequences. All isolates of both species had a thymidine in position 912 (E. coli numbering) that causes streptomycin resistance in several bacterial species and which is characteristic for the members of the hominis group. As expected, when five M. agalactiae and three M. bovis isolates were tested for streptomycin susceptibility, they all demonstrated streptomycin resistance. M. agalactiae and M. bovis were found to have high intraspecific variation in their 16S rRNA gene and the polymorphisms patterns indicate that gene conversion takes place.     

Strains of avian paramyxovirus type 1 of low pathogenicity for chickens isolated from poultry and wild birds in Denmark

Twenty-one strains of avian paramyxovirus type 1 of low virulence for chickens were isolated in Denmark between 1996 and the beginning of 2003. The low virulence of the strains was demonstrated by sequencing the fusion (F) gene at the cleavage site motif and in some cases by determining the intracerebral pathogenicity index in day-old chicks. By using a panel of monoclonal antibodies it was shown that the isolates belonged to four different antigenic groups (five C2 isolates, six E isolates, six H isolates and four G/Q isolates). They were placed in three distinguishable genetic groups by phylogenetic analysis of a partial sequence of the F gene. The origin of the six E isolates was probably contaminated vaccines; the other viruses were isolated from wild birds and from poultry which probably came into contact with wild birds.     

Molecular characterization of Streptococcus suis strains by 16S–23S intergenic spacer polymerase chain reaction and restriction fragment length polymorphism analysis

We developed a new molecular method of typing Streptococcus suis based on polymerase chain reaction (PCR) amplification of a large fragment of rRNA genes, including a part of the 16S and 23S genes and the 16S-23S intergenic spacer region (ISR), followed by restriction fragment length polymorphism (RFLP) analysis with RsaI or MboII endonuclease. The 16S-23S ISRs of 5 S. suis isolates were sequenced and compared. Size and sequence polymorphisms were observed between the S735 reference strain and the 4 wild-type strains. The genetic relationships between 138 independent S. suis strains belonging to various serotypes, isolated from swine or human cases, were determined. The discriminatory power of the method was > 0.95, the threshold value for interpreting typing results with confidence (0.954 with RsaI and 0.984 with RsaI plus MboII). The in vitro reproducibility was 100%. The strains isolated from humans were less genetically diverse than the strains isolated from pigs. For the first time, 2 molecular patterns (R6, M9) were significantly associated with S. suis serotype 2 strains. This genetic tool could be valuable in distinguishing individual isolates of S. suis during epidemiologic investigations.     

Diagnosis of swine dysentery and spirochaetal diarrhea. 2. Effort of macrorestriction analysis for differentiation of intestinal Serpulina relative to determination by culture-biochemical markers following species classification]

Genotypic differentiation by means of macrorestriction fragment profile analysis using Mlul restriction enzyme was carried out differentiating 41 Serpulina field strains from swine (38), dog (2) and a rat as well as ten type and reference strains into 40 electrophoretic types. A dendrogram was created using the average linkage between groups method. At a level of 50% similarity the patterns could be divided into six groups that roughly corresponded to the results yielded by cultural and biochemical methods formerly (FELTRUP et al. 1999). Five of these clusters corresponded to the five known porcine Serpulina species, one cluster contained the S. pilosicoli isolates from dog and rat included in this study. Interestingly all nine investigated indole negative, strongly haemolytic isolates were clustered together in one group with the S. hyodysenteriae strains, so that incidence of indole negative variants of S. hyodysenteriae was confirmed. Because of being grouped together with two S. intermedia isolates, the suitability of B 256 as S. innocens type strain is--in accord to investigations carried out by PETTERSSON et al (1996)--called in question.     

Phylogenetic analysis of Blastocystis isolates from animal and human hosts in the Philippines

To study the genetic diversity and cross-transmissibility of Blastocystis species in naturally infected hosts, 12 Blastocystis isolates from animal and human hosts in the Philippines were analyzed by sequencing the full-length small subunit ribosomal RNA (SSU rRNA) genes. Each sequence showed very high similarity (from 97% to 100%) to homologous sequences of other Blastocystis isolates reported previously. Phylogenetic analysis revealed that the 12 isolates were classified into 4 genetically distinct subtypes: 1, 2, 3, and 6. Results showed that Blastocystis subtypes 1, 2, and 3 were shared by isolates from varied hosts. This study confirms the remarkable heterogeneity of SSU rRNA gene among different Blastocystis isolates. The findings of this study agree with previous reports that the different Blastocystis subtypes have low host-specificity, comprising isolates from humans and various animal hosts. This study also suggests evidence for zoonotic transmission of the parasite and cross-transmissibility among heterogeneous hosts.     

Heterogeneity of ruminant pestiviruses: academic interest or important basis for the development of vaccines and diagnostics?

Pestiviruses cause economically important diseases of farm animals. Members of the Pestiviruses are bovine viral diarrhea virus 1 (BVDV-1), BVDV-2, classical swine fever virus (CSFV) and border disease virus (BDV). Phylogenetic analyses based on the entire nucleic acid sequence encoding the Npro allow a statistically significant segregation of established species and of subgroups within the species. BVDV-1 strains isolated in Germany can be associated with at least five different subgroups. In contrast all BVDV-2 isolates detected in Germany so far are closely related, belonging to one subgroup. A group of virus isolates from sheep and zoo animals is clearly different from established pestivirus species and can be designated as BDV-2. Antigenetic relatedness of pestiviruses was studied using defined virus isolates and antisera in cross-neutralization assays. Six antigenic groups were distinguished corresponding to the genetic clusters BVDV-1, BVDV-2, CSFV, BDV-1, BDV-2 and Giraffe-1. A significant antigenic difference was also observed between members of subgroups 1a and 1b of BVDV-1. Studies on the genetic and antigenic heterogeneity of pestiviruses are important for the development of new vaccines, diagnostic tests and for eradication programs.     

Effect of ochratoxin A on broiler chicks challenged with Salmonella gallinarum

1. A study was conducted to evaluate the effects of ochratoxin A (OA) on broiler chicks challenged with Salmonella gallinarum. 2. One hundred and seventy-six 1-d-old broiler chicks were divided into two groups of 88 chicks each, with one group fed on a control mash diet and the other given a mash diet containing 2 ppm OA. On d 14, each group was further subdivided into two groups with one group infected with S. gallinarum and the other uninfected. 3. Following S. gallinarum inoculation on d 14, 4 birds from each group were killed at 1, 2, 3, 5, 7, 10, 14 and 21 d post inoculation. 4. S. gallinarum infection caused dullness, depression, weakness, increased thirst, droopy wings, ruffled feathers and greenish-yellow diarrhoea. S. gallinarum infection in the absence of OA caused 11.5% mortality which increased to 28.8% in the presence of OA. 5. Decreased body weight and reduced feed intake were observed in chicks fed on the diet containing OA. S. gallinarum infection also reduced the body weights of chicks, with the effects being more marked in chicks receiving OA. The OA diet led to increased serum levels of aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, uric acid and creatinine, and decreased levels of total proteins, albumin, globulins, calcium and phosphorus. S. gallinarum infection did not cause significant alteration in any of the serum biochemical parameters. 6. Mortality and the severity of S. gallinarum infection in broiler chicks were increased by the presence of OA in the diet.