Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India.

Worldwide dissemination of extended-spectrum -lactamase (ESBL)-producing Escherichia coli constitutes an emerging global health issue, with animal food products contributing as potential reservoirs. ESBL E. coli infection is associated with the high mortality and mobility rate in developing countries due to less susceptibility to antibiotics. The present study aimed to elucidate the molecular characteristics and sequence-based analysis of ESBL E. coli in the Gujarat state of India. This study included 108 E. coli strains were isolated from different poultry farms (broiler and layer) in the Banaskantha District. PCR was employed to identify genotypic ESBL-producing antimicrobial resistance genes. Overall, a high occurrence of ESBL genes was found in poultry farms due to the high usage of antimicrobials. The PCR analysis revealed that 79.62% of isolates were detected positive with one or more ESBL genes. Among them, bla TEM (63.88%) was found to be the predominant genotype, followed by bla SHV (30.55%) and bla OXA (28.70%). In the bla CTX-M group, a higher occurrence was observed in bla CTX-M-9 (23.14%), followed by bla CTX-M-2 (24.07%) and bla CTX-M-1 (22.22%). We used the whole-genome sequencing (WGS) method to evaluate the antimicrobial resistance genes, virulence factors, single nucleotide polymorphisms (SNPs), plasmid replicons, and plasmid-mediated AMR genes of one ESBL E. coli isolated. We examined the genetic relatedness of a human pathogenic E. coli strain by comparing its sequence with the broad geographical reference E. coli sequences. Escherichia coli ST 681 was determined using multi-locus sequence typing. We compared our findings to the reference sequence of Escherichia coli str. K- 12 substr. MG1655. We found 24,937 SNPs with 21,792 in the genic region, 3,145 in the intergenic region, and six InDels across the genome. The WGS analysis revealed 46 antimicrobial resistance genes and seven plasmid-mediated AMR genes viz., tetA, qnrS1, dfrA14, sul2, aph(3")-lb, aph(6)-ld, and Aph(3')-la. The ST 681 was found to have Cib, traT, and terC virulence factors and two plasmid replicons, IncFII(pHN7A8) and IncI1-I(Alpha). This study revealed a higher occurrence of ESBL E. coli detected in poultry.

Virological, immunological and pathological findings of transplacentally transmitted bluetongue virus serotype 1 in IFNAR1-blocked mice during early and mid gestation.

Transplacental transmission (TPT) of wild-type Indian BTV-1 had never been experimentally proved. This study was first time investigated TPT of Indian BTV-1 (isolated from aborted and stillborn goat fetal spleens). The sequential pathology, virological and immune cell kinetics (CD4+, CD8+ T-lymphocytes and NK cells in spleen and PBMCs), and apoptosis in IFNAR1-blocked pregnant mice during early (infected on 1 GD) and mid (infected on 8 GD) gestation have been studied. There was higher rate of TPT during mid stage (71.43%) than early (57.14%) stage. In early stage reduced implantation sites, early embryonic deaths, abortions, and necro-haemorrhagic lesions had observed. Mid stage, congenital defects and neurological lesions in foetuses like haemorrhages, diffuse cerebral edema, necrotizing encephalitis and decreased bone size (Alizarin red staining) were noticed. BTV-1 antigen was first time demonstrable in cells of mesometrium, decidua of embryos, placenta, uterus, ovary, and brain of foetuses by immunohistochemistry and quantified by real-time qRT-PCR. BTV-inoculated mice were seroconverted by 7 and 5 dpi, and reached peak levels by 15 and 9 dpi in early and mid gestation, respectively. CD4+ and CD8+ cells were significantly decreased (increased ratio) on 7 dpi but subsequently increased on 15 dpi in early gestation. In mid gestation, increased CD8+ cells (decreased ratio) were observed. Apoptotic cells in PBMCs and tissues increased during peak viral load. This first time TPT of wild-type Indian BTV-1 deserves to be reported for implementation of control strategies. This model will be very suitable for further research into mechanisms of TPT, overwintering, and vaccination strategies.

Metagenomic of clinically diseased and healthy broiler affected with respiratory disease complex.

In recent past, the respiratory infection has emerged as a great challenge to the poultry farmers. Various pathogens including Avian pneumovirus (APV), Avian influenza virus (AIV), Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV), Avibacterium paragallinarum, Ornithobacterium rhinotracheale (ORT), Mycoplasma synoviae (MS), Mycoplasma gallisepticum (MG) and Avian pathogenic Escherichia coli (APEC) are involved in the respiratory disease complex in birds [1], [2] (Bradbury, 1984; Roussan et al., 2008). Hence, respiratory disease complex is the most serious disease affecting to poultry and causes heavy economic losses in the poultry industry worldwide [3] (Murthy et al., 2008). In recent years, metagenomics is powerful analyzing tool for detection of pathogens directly from clinical samples without any prior knowledge of the organism in a given sample [4], [5] (Schuster, 2008; Pereira et al., 2010). High throughput Next-Generation-Sequencing technology was used for sequencing the isolated genomic DNA. These data provides an insight about taxonomic and functional status of microorganisms responsible for causing respiratory infection in broiler. The data of these metagenome are available in the BioSample Submission Portal as Bioproject PRJNA339659 and SRA accession number SRR5997823, SRR5992854, SRR6037376, SRR6024702, SRR6012248 and SRR6008913.

Complete Genome Sequence of Brucella abortus SKN 13 Isolated from Placenta of Aborted Cattle in Gujarat, India.

Brucella abortus is generally known to cause brucellosis in cattle and buffalo. Here, we report the draft genome sequence of Brucella abortus SKN 13, isolated from aborted cattle placenta in the area of Gujarat, India, providing precious resources for comparative genomic analyses of Brucella field strains.

Comparison of molecular and microscopic technique for detection of Theileria annulata from the field cases of cattle.

AIM: Tropical theileriosis is fatal hemoprotozoal disease of dairy animals caused by Theileria annulata. The aim of the present study was to detect the T. annulata and comparison of results of molecular and microscopic techniques. MATERIALS AND METHODS: A total of 52 blood samples were collected from the cattle suspected for theileriosis across the Banaskantha district. All the samples were screened for theileriosis using Giemsa's staining technique and polymerase chain reaction (PCR). RESULTS: Total of 17 (32.69%) and 24 (46.15%) samples were found positive for theileriosis by microscopic examination and PCR test, respectively. It revealed that the study area is endemic for theileriosis, and the microscopic technique has 70.83% sensitivity and 100% specificity with respect to PCR technique. CONCLUSION: It may be concluded from the present study that the PCR is comparatively sensitive technique than microscopic examination and may be recommended to use in the field for screening of theileriosis in the study area, where a high prevalence of diseases have been reported due to intensive dairy farming.

Isolation of bluetongue virus serotype 1 from aborted goat fetuses.

Abortions and stillbirths were noticed in pregnant goats on a farm in the state of Gujarat, India. About 50% of the pregnant goats aborted or gave birth to dead kids. Bluetongue virus (BTV) antibody in the sera of affected goats was detected using a competitive enzyme-linked immunosorbent assay (ELISA). Viral antigen in the blood of these goats and in the aborted fetal spleens was detected using a sandwich ELISA. Two viruses (SKN-9, SKN-10) were isolated in cell culture from aborted fetal spleens and were confirmed as Orbivirus by demonstration of ten bands in RNA polyacrylamide gel electrophoresis and identified as BTV-1 by sequencing of the VP2 gene. Sequence analyses revealed thatthese isolates were very closely related to a BTV-1 (strain SKN-8) isolated from Culicoides vectors captured on the same farm one month after the occurrence of abortion. Isolation of BTV-1 from fetuses is probably evidence of transplacental transmission of the wild-type strain, because attenuated or laboratory-adapted BTV-1 strains have never been used in this region. This may have important implications in the epidemiology of bluetongue, considering the presence of many BTV serotypes in India.

Efficacy of 'indigenous vaccine' using native 'Indian bison type' genotype of Mycobacterium avium subspecies paratuberculosis for the control of clinical Johne's disease in an organized goat herd.

Therapeutic efficacy of a new 'Indigenous vaccine' prepared from native highly pathogenic 'Indian Bison Type' genotype of Mycobacterium avium subspecies paratuberculosis (MAP) of goat origin has been evaluated with respect to control of clinical Johne's disease in naturally infected Mehsana breed of goat in North Gujarat. Fifty goats from Sheep and Goats Research Station, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, were randomly divided into 2 groups viz.,'Vaccinated'(n = 35) and 'Control'(n = 15). After vaccination, goats were monitored for physical condition, morbidity, mortality, body weights, shedding of MAP in feces, internal condition, gross lesions and humoral immune responses up to 120 days (at each interval of 30 days). At the end of 120 days trial, there was marked overall improvement in physical condition and body weights of vaccinated goats as compared to 'Control' goats. Vaccinated goats gained significantly (P < 0.05) higher body weights, hardly exhibited any lesions characteristic of JD, had significantly higher (P < 0.01) antibody titers and shedding of MAP was significantly (P < 0.01) reduced. Few of the vaccinated goats were positive for MAP DNA in faecal PCR and blood PCR before vaccination. However, all were found as negative at 120 days post vaccination (DPV). Overall vaccine exhibited effective in restriction of MAP infection and significant improvement in production parameters and reduction in mortality and morbidity due to JD. The trial in the herd will be continued.

Isolation of bluetongue virus serotype 1 from Culicoides vector captured in livestock farms and sequence analysis of the viral genome segment-2.

Bluetongue virus serotype-1 (BTV-1) was isolated from Culicoides oxystoma vectors captured on livestock farms in two places of Gujarat, India. The viruses were isolated on BHK-21 cells, which produced characteristic BTV-related cytopathic effects between 24 and 48 h post-infection. Virus antigen was demonstrated in infected cells at different passage by a BTV-specific sandwich ELISA. Further, polyacrylamide gel electrophoresis and silver staining of viral genomic RNA revealed ten double-stranded RNA segments characteristic of BTV. Serotype of the isolates was identified by virus neutralization and PCR coupled with sequencing. The isolates were designated as SKN-7 and SKN-8 and their genome segment-2 (VP2) were sequenced. Phylogenetic analyses revealed very close relationship between them although they are not identical. SKN-8 showed closer relationship with a recently isolated BTV-1 from goat. Bluetongue virus was earlier isolated from Culicoides in adjacent state more than 20 years ago, although the serotype of the virus was not determined.

Zoonotic infections of buffalopox in India.

Four outbreaks of buffalopox in domestic buffaloes, with considerable mortality with high case fatality rates in young buffalo calves and high morbidity with significant productivity loss in terms of reduction in milk yield in adult animals along with severe zoonotic infection in milk attendants were recorded at various places in India, during 2006-2008. In buffaloes, the pox lesions were confined to udder and teats of the majority of the affected animals, and in few animals the lesions were appeared on the hindquarters, indicating generalized infection. The overall disease morbidity, mortality and case fatality rate were 6.8%, 0.7% and 11.4% respectively. Milkers developed pox-like lesions on the hands, forearms and forehead accompanied by fever, axillary lymphadenopathy and general malaise. The causative agent of the outbreaks, buffalopox virus (BPXV), was confirmed upon virus isolation in cell culture, electron microscopy, A-type inclusion (ATI) and ankyrin repeat protein (C18L) gene-specific polymerase chain reactions (PCR). Further, sequence analysis of the BPXV isolates from human and buffalo showed more identity of ATI and C18L genes sequences with that of other orthopoxviruses at nucleotide and amino acid levels and confirmed a close relationship of BPXV with Vaccinia virus (VACV) or VACV-like viruses. Considering the zoonotic impact and productivity losses of buffalopox infection, the control measures are imperative in curtailing economic and public health impact of the disease.

Comparison of the standard AGID test and competitive ELISA for detecting bluetongue virus antibodies in camels in Gujarat, India.

The performance of the standard agar gel immunodiffusion (AGID) test and the competitive enzyme-linked immunosorbent assay (cELISA) for the detection of serum antibody against bluetongue virus (BTV) in clinically healthy and diseased camels in Gujarat state were compared. Out of 176 sera tested, 22 (12.5%) and 34 (19.3%) were positive for group-specific bluetongue antibodies by AGID and cELISA, respectively. Maximum seropositivities of 18.0% by AGID and 25.8% by cELISA were recorded in the Kutchhi breed, and of 6.9% and 12.6%, respectively, in the Marwari breed. The seroprevalence detected by AGID and cELISA in clinically healthy and diseased camels did not differ significantly with regard to bluetongue disease in these breeds.