Yps Malik

Spatial molecular epidemiology of carbapenem‐resistant and New Delhi metallo beta‐lactamase (blaNDM)‐producing Escherichia coli in the piglets of organized farms in India

A cross‐sectional study was conducted in 10 government‐organized pig farms between 2014 and 2016 representing seven states of India to understand the epidemiology of carbapenem resistance in the Escherichia coli.

Molecular characterization of unusual bovine rotavirus A strains having high genetic relatedness with human rotavirus: evidence for zooanthroponotic transmission

We report here the genomic characterization of two rare rotavirus A (RVAs) G1P[11] and G9P[X] strains detected in cattle calves from two different geographical locations in India during routine rotavirus surveillance. These strains possessed unusual G types (VP7 gene) on a bovine/artiodactyl genotype constellation, G1‐P[11]‐I2‐Rx‐Cx‐Mx‐Ax‐N2‐T6‐E2‐H3 (HR‐B91) and G9‐P[X]‐I2‐Rx‐Cx‐Mx‐Ax‐N2‐T6‐E2‐H3 (WB‐H2). This is the first report on molecular characterization of G9 in cattle, and second report on G1 in cattle. The VP7 gene of HR‐B91 occupied lineage IIc within G1 while that of WB‐H2 occupied IIIb within G9 genotype. The latter was found to be very diverse from other RVA strains of G9 genotype, and this may emerge as a new genotype in due course. The study provides evidence of zooanthroponotic transmission of human G1 and G9 RVA genes to calves. Of note, the G9 genotype was found to serve as the ancestral genotype for G1. Phylogenetic analysis of remaining gene segments revealed close relatedness to artiodactyl or artiodactyl‐like human RVA strains. The findings of this study highlight the potential role of interspecies transmission and reassortment events in generating the rare rotavirus strains.

Experimental bovine rotavirus-A (RV-A)infection causes intestinal and extra-intestinal pathology in suckling mice

We describe here the intestinal and extra-intestinal spread of the species A rotavirus (RV-A) and associated lesions thereof in Swiss albino suckling mice pups, inoculated with a bovine-origin RV-A strain. In total, 35 suckling pups were used, wherein 20 pups received cell culture isolated RV-A @ 160 μL (TCID50/ml, 5 × 106.5) per pup [oral 80 μL and intra peritoneal (IP) 80 μL] and served as an infected group, while 15 pups were kept in the control group and inoculated the same volume of phosphate buffered saline (PBS) of neutral pH orally and IP. Four pups from the infected group and 3 from control group were sacrificed at 3, 5, 7, 9 and 12 day post infection (DPI). Of note, infected pups exhibited signs of dullness and restlessness till 5DPI, but none showed diarrhea at any point of time. No appreciable gross lesions were evident in any of the organs, except for mild congestion of the small intestine and yellowish catarrhal smearing over the luminal surface. However, light microscopic lesions in hematoxylin and eosin (H&E) stained sections of jejunum and ileum revealed vacuolation and pyknosis of nuclei of the mature enterocytes, their lysis and detachment, constriction and detachment of villi, mild mononuclear cells (MNCs) infiltration in the lamina propria and mildcell depletion of Peyers patches and mesenteric lymph nodes (MLN). The extra-intestinal lesions of the cellular degeneration and mild MNCs infiltration were identified in the liver and kidneys from 3 to 7 DPI, but no lesion was seen in the brain. Interstitial thickening with MNCs of lung parenchyma was visible from 3 to 7 DPI. The lesions in the intestine, lymphoid tissues and lungs resolved after 7 DPI. The presence of viral nucleic acid was seen in the intestinal contents from 3 to 5 DPI by using a RV-A specific reverse-transcription polymerase chain reaction (RT-PCR), while in the MLNs and the lungs it could be detected till 5 DPI by both the RT-PCR and direct fluorescent antigen test (dFAT). However, liver, spleen and brain were tested negative for the presence of RV-A by any of these tests. Nonetheless, the persistence of the RV-A was seen in the MLNs even after the absence of virus from the small intestines. Findings here conclusively indicates that heterologous host origin RV-A has an affinity not only to the intestine but also to extra-intestinal tissues like MLNs and lung tissues.

Clinicopathological characterization of experimental infection in chickens with sub-genotype VIIi Newcastle disease virus isolated from peafowl

Newcastle disease (ND) is an economically important viral disease distressing poultry industry across the globe. Herein, we report the clinicopathology of sub-genotype VIIi Newcastle disease virus (NDV) isolated from peafowl in chickens. The virus isolate produced systemic infection with prominent tropism in visceral organs in chicken, confirmed on the basis of gross and microscopic lesions, and immunohistochemistry findings. The experimentally infected chickens exhibited 100% mortality with severe hemorrhagic lesions in the proventriculus and intestine, especially marked lymphocytolysis in spleen and bursa. The virus could be re-isolated from the cloacal swabs of infected chickens during 4th to 6th dpi (on 6th dpi all birds died), and all were tested positive in conventional RT-PCR. This is the first report on clinicopathology of NDV isolated from peafowl and/or sub-genotype VIIi NDV in experimentally infected chickens. Explorative epidemiological and molecular studies are suggested to screen wild peafowls and poultry flocks of the country for establishing the occurrence of this sub-genotype and opting for appropriate prevention and control strategies.

Etiopathology of intestinal affections in bovine calves

A variety of infectious agents are implicated in calf diarrhoea, and co-infection of multiple pathogens is not uncommon in diarrheic calves. Forty carcasses of bovine calves having history of diarrhoea were necropsied and the samples of intestine, lung, liver, kidney, heart and lymph nodes were collected in 10% neutral buffered formalin for histopathology and in -20°C for molecular diagnosis. Lesions of enteritis were observed histopathologically, and rotavirus was predominantly associated with enteritis along with other concomitant infections viz. pasteurellosis, FMD, parasites, aflatoxicosis and septicaemia etc. In most of the cases, the aetiologies were confirmed by PCR (rotavirus and FMD virus), bacterial culture (bacterial enteritis) and by pathological lesions in the intestines and other organs. It was observed that rotavirus enteritis usually found associatedalong with concomitant infections.

Reply to "May Newly Defined Genotypes XVII and XVIII of Newcastle Disease Virus in Poultry from West and Central Africa Be Considered a Single Genotype (XVII)?".

We read with great interest the article by Snoeck et al. (1), where the authors reported great genetic diversity among Newcastle disease virus (NDV) strains circulating in the poultry population of West and Central Africa along with two newly defined genotypes, genotypes XVII and XVIII, based on fusion (F) gene sequence analysis. More than 90% identity was noticed between the sequences belonging to genotypes XVII and XVIII in NCBI BLAST analysis. We analyzed the report and determined the mean distance within a genotype, mean distance between the genotypes, and net mean distances between genotypes XVII (n 56) and XVIII (n 15) using complete F gene sequences of NDVs, which were used in the report by Snoeck et al. (1). The mean evolutionary distance was calculated in MEGA6 software as follows. The number of nucleotide base substitutions per site from an estimation of the net average from comparisons between groups of sequences was analyzed using the maximum composite likelihood model (2). The rate of variation among sites was modeled with a gamma distribution (shape parameter 1). The analysis involved 71 gene sequences available in NCBI GenBank. The codon positions included were 1st plus 2nd plus 3rd plus noncoding. The nucleotide positions containing gaps and missing data were eliminated. The standard error estimate was obtained by a bootstrap procedure (500 replicates) (2). The analysis results revealed that the mean distance within genotype XVII is 0.031 (3.1%) with a standard error of 0.002 and within genotype XVII is 0.044 (4.4%) with a standard error of 0.004. The mean distance between genotypes XVII and XVIII was determined to be 0.108 (10.8%) with a standard error of 0.008, whereas the net mean distance between genotypes XVII and XVIII was determined to be 0.071 (7.1%) with a standard error of 0.007. The net mean distances between the genotypes showed agreement with the sequence identity determined in the NCBI BLAST analysis. A minimum of a 10% mean evolutionary distance between NDV genotypes has been recommended to define a new genotype (3). We conclude that newly defined genotypes XVII and XVIII of NDV (1) may be considered a single genotype, genotype XVII.

Ultra-structural changes in the thymus of chickens experimentally infected with chicken infectious anemia virus

The present investigation was undertaken to studythe ultra-structural changes in thymus following chicken infectious anemia virus (CIAV) infectionin chicks. Some thymocytes with electron-dense rings in their nuclei and few thymocytes showing chromatin aggregation were noticed in the cortex region with scarcity of the cells on 7 days post infection (DPI). At day 14, the cortex was severely depleted of thymocytes with some thymocytes showing apoptotic nuclei and some with broken nuclear fragments. The aggregations of virus-like particles surrounded by membrane like structures were also observed in the cortex region. The cortex started repopulating with thymocytes whereas some cells with apoptotic bodies were detected on day 21, whereas on day 28 the cortex area of infected group became comparable to the cortex of the control chickens after repopulation of cells. Findings of the study indicate that CIAV causes apoptotic death of the thymocytes following experimental infection.

Genetic Characterisation of Group-A Rotavirus Detected in Diarrhoeic Bovine Calves in Madhya Pradesh

Diarrhoeal disease continues to be an important cause of morbidity and mortality among neonates of various animal species worldwide. Amongst several viral agents associated with diarrhoea, rotavirus (RV) has been recognised as the major aetiological agent. In the following study, 184 faecal samples from diarrhoeic bovine claves were collected from different dairy farms of Madhya Pradesh (M.P), central India. Of these, 25 samples (13.6%) were found to be positive for RV infection using RNA polyacrylamide gel electrophoresis and reverse-transcription-polymerase chain reaction. One of the isolates (cow/C-32/IND/2008/G10) of predominant genotype (G10) was selected for sequence and SimPlot analysis. The results suggested occurrence of group-A RV in bovine population of central India, with circulation of a G10 genotype, which showed sequence identity of 63-98% with other bovine, human and porcine G10 isolates from India and other parts of the world. The C-32 isolate showed maximum sequence identity (98%) with a RV strain isolated from water buffaloes of Punjab (BRV 73Acc. No. EU311194). Our isolate showed minimum sequence identity (6372%) with G10 bovine isolates from the eastern region of the country (RUBVM135, EF200544 and EF200543). The results confirm circulation of divergent strains of G10 genotypes in India and warrants further molecular studies to understand the evolution of divergent G10 virus population in nature.