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Govind Ballabh Pant University of Agriculture and Technology, Pantnagar

After independence, development of the rural sector was considered the primary concern of the Government of India. In 1949, with the appointment of the Radhakrishnan University Education Commission, imparting of agricultural education through the setting up of rural universities became the focal point. Later, in 1954 an Indo-American team led by Dr. K.R. Damle, the Vice-President of ICAR, was constituted that arrived at the idea of establishing a Rural University on the land-grant pattern of USA. As a consequence a contract between the Government of India, the Technical Cooperation Mission and some land-grant universities of USA, was signed to promote agricultural education in the country. The US universities included the universities of Tennessee, the Ohio State University, the Kansas State University, The University of Illinois, the Pennsylvania State University and the University of Missouri. The task of assisting Uttar Pradesh in establishing an agricultural university was assigned to the University of Illinois which signed a contract in 1959 to establish an agricultural University in the State. Dean, H.W. Hannah, of the University of Illinois prepared a blueprint for a Rural University to be set up at the Tarai State Farm in the district Nainital, UP. In the initial stage the University of Illinois also offered the services of its scientists and teachers. Thus, in 1960, the first agricultural university of India, UP Agricultural University, came into being by an Act of legislation, UP Act XI-V of 1958. The Act was later amended under UP Universities Re-enactment and Amendment Act 1972 and the University was rechristened as Govind Ballabh Pant University of Agriculture and Technology keeping in view the contributions of Pt. Govind Ballabh Pant, the then Chief Minister of UP. The University was dedicated to the Nation by the first Prime Minister of India Pt Jawaharlal Nehru on 17 November 1960. The G.B. Pant University is a symbol of successful partnership between India and the United States. The establishment of this university brought about a revolution in agricultural education, research and extension. It paved the way for setting up of 31 other agricultural universities in the country.

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  • ThesisItemOpen Access
    Prevalence and characterization of non-typhoidal Salmonella isolates obtained from retail fish meat shops
    (G.B. Pant University of Agriculture and Technology, Pantnagar - 263145 (Uttarakhand), 2021-02) Sana Parveen; Sana Parveen; Sana Parveen; Maansi; Maansi; Maansi
    Non-Typhoidal salmonellosis stands among the major food illnesses. Outbreaks from contaminated fishes have been witnessed worldwide. This study was performed to assess the presence of Non -Typhoidal Salmonella in fishes and associated environmental samples of 22 retail fish meat shops of 4 locations of Uttarakhand. For this, a total of 368 samples (fish meat swabs(n=46), gill swabs(n=23), skin swabs(n=25), intestine swabs(n=23), hand swabs(n=44), knife swabs(n=27), rinsing water(n=22), fish water(n=41), floor swabs(n=22), chopping board swabs(n=24), utensil swabs(n=24) and container swabs(47) were collected. The overall occurrence of Non-Typhoidal Salmonella was found to be 4.35% (16/368). The highest prevalence of Salmonella was observed in rinsing water (18.18%,4/22) sample followed by knife swabs ( 11.11%, 3/27) , chopping board swabs (8.33%, 2/24) , meat swabs (6.52%, 3/46) , floor swab (4.54%,1/22) , gill and intestine swab (4.34%, 1/23), fishwater (2.43%,1/41). Geographically, the highest prevalence was observed in Lalkuan (6.52%, 3/46) followed by Haldwani (5.55%, 10/180), Kiccha (2.12%, 1/47) and Pantnagar (2.08%, 2/96). Of 16 Salmonella isolates, confirmed using ompC (204 bp) gene, 14 were revealed as S.Typhimurium (87.5%, 14/16) while 2 did not exhibit the typh gene (401bp) amplicon size. All the 16 isolates screened for the presence of virulence genes using PCR commonly harbored sipA gene (87.5%, 14/16) followed by stn (75%, 12/16), sopB ( 68.75%, 11/16), sopE1 ( 56.25%, 9/16) mgtC ( 43.75%, 7/16) and spvC and gipA ( 12.5%, 2/16) genes each. Highest resistance was observed against Tetracycline and Ampicillin (93.75%, 15/16), Nalidixic acid (50%, 8/16), Ciprofloxacin (37.5%, 6/16) Ofloxacin, Cefotaxime and Sulfisoxazole ( 25%, 4/16) each, Chloramphenicol (12.5%, 2/16) and Streptomycin ( 6.25%, 1/16). Ten Salmonella isolates were multi drug resistant (MDR). Ten different antimicrobial resistance patterns were observed. Of these, only one pattern (TE, AMP, NA, CTX , OF, SF) was found common in 2 Salmonella isolates belonging to knife and meat swab sample. All phenotypically resistant and intermediate resistant isolates were screened for 6 corresponding antimicrobial resistance genes. The most commonly occurring resistance gene was gyrA (92.30%, 12 /13), blaTEM (53.33%, 8/15), aadA1 and strA (50%, 2/4), sul1 (30.76 %, 4/13) while tetA was not found in any of the isolates. Overall, our study detected occurrence of Non-Typhoidal Salmonella in the fish retail meat shops. Resistance to critically important flouroquinolones and highly important Cephalosporin and Tetracycline antibiotic detected in Salmonella isolates is a serious threat to public health which highlights the indiscriminate use of antimicrobials.
  • ThesisItemOpen Access
    Whole genome sequencing & bioinformatics of Campylobacter isolated from animals
    (G.B. Pant University of Agriculture and Technology, Pantnagar - 263145 (Uttarakhand), 2020-11) Roma; Upadhyay, A.K.
    Campylobacter species are one of the leading cause of bacterial foodborne zoonoses. Worldwide, Pathogenic Campylobacter species are responsible for causing over 400–500 million infections cases each year. These pathogenic Campylobacter species are grouped into major human enteric pathogens (C. jejuni, C. jejuni subsp. jejuni (Cjj), C. jejuni subsp. doyley (Cjd), C. coli and C. fetus) minor pathogens (C. concisus, C. upsaliensis, C. lari and C. hyointestinalis) and major veterinary pathogens (C. fetus subsp. venerealis (Cfv) and C. Fetus subsp. fetus (Cff)). A total of 498 samples consisting of poultry caeca (120), litter (40), poultry rectal swabs (24), poultry skin (24), water samples (38),faeces of pigs (30), meat swabs (32), clinical dog faecal ssample (20), goat (32) and lab animals faeces (92) were screened for the presence of C. jejuni and C. coli using conventional isolation and identification procedures. The overall occurence of Campylobacter was 8.83 %. The samples collected were screened for campylobacters. Highest isolation rate was observed from lab animals (19.56 %, 18/92) followed by poultry caeca (13.33%,16/120), pig faeces (10%,3/30), meat swabs (9.37 %, 3/32) ,poultry faeces (7.14%, 3/42) and litter (2.5%, 1/40). Since loads of virulence genes are responsible for bacterial pathogenecity, resilence, stress response and environmental persistence. The individual detection of every gene by techniques like PCR is a tedious process. The next generation sequencing concept play an extremely important role in this context. Among next generation sequencing also, whole genome sequencing (WGS) and assembly is best method for the characterization of isolates as it can detect every gene of the organism coding for it’s identification, virulence, pathogenicity and antibiotic resistance.The study characterised the entire genome of the infectious isolates by analysis of WGS sequence data via use of both web based and command based tools. Virulence genes pattern was observed using web based analysis tools namely VFDB Virulence Factor Database (http://www.mgc.ac.cn/VFs) and wgMLST (Whole-genome MLST) which is pangenome based tool was used using core genome genes/loci and all acessory genes/loci to detect lineage – specific genes/loci. A total of 23 genes were detected by VFDB and 33 virulence genes were detected via SRST2. Only resistance to beta – lactam were found. Overall, our study detected only one antimicrobial resistance gene that is blaₒₓₐ -₄₈₉ commonly found in Campylobacter spp. indicating good antibiotic management in areas of Pantnagar, Rudrapur and Barielly
  • ThesisItemOpen Access
    Molecular genotyping of multidrug-resistant Salmonella typhimurium isolates using repetitive sequence-based PCR fingerprinting technique
    (G.B. Pant University of Agriculture and Technology, Pantnagar - 263145 (Uttarakhand), 2020-08) Sivakumar, V.; Maansi
    Non-typhoidal salmonellae, responsible for salmonellosis in humans, are a threat to food safety impacting human health in the form of hospitalizations and in severe cases, fatalities. Such an impact also results in huge economic losses. Several food borne outbreaks resulting from zoonotic non- typhoidal Salmonella serovars have been reported, of which, S. Typhimurium has shown predominance. Epidemiological investigations of an outbreak requires accurate identification of the infection source and the transmission route for effective implementation of preventive measures against microbial food-borne pathogens. For this, techniques which can detect differences among the isolates at genomic level are applied. Therefore, in the present investigation, multidrug-resistant isolates of Salmonella Typhimurium were genotyped using repetitive sequence-based PCR (rep-PCR) fingerprinting. A total of 45 MDR S. Typhimurium isolates belonging to various sources and locations were procured from the Department of Veterinary Public Health and Epidemiology, CVASc, GBPUAT, Pantnagar. All the isolates were tested for purity and were confirmed on the basis of cultural, biochemical, serotyping and molecular (duplex PCR targeting genus specific ompC gene and serovar specific typh gene) assay. The isolates were subjected to ERIC, REP, BOX and GTG5-PCR analysis after DNA extraction and PCR confirmation. ERIC, REP, BOX and GTG5-PCR fingerprinting generated reproducible band patterns ranging from 3-10, 1-5, 6-14 and 2-10 separate bands, respectively. Cluster analysis revealed 9 types from ERIC-PCR, 7 types from REP-PCR, 16 types from BOXPCR and 9 types from GTG5-PCR. Hundred percent typeability was obtained with all genotyping techniques except REP-PCR, which differentiated 39 Typhimurium isolates only (86.6%). The isolates’ sharing similar band patterns is suggestive of a genetic similarity between them directing towards the multifactor involvement in the transmission of Salmonella. Faecal isolates and meat swab isolates sharing identical band patterns and grouped into a single cluster is indicative of a likely cross contamination. No unique pattern was observed in penta resistant (ACSSuT) profile isolates by our typing techniques. DI value of BOX-PCR was highest (0.940) followed by GTG5-PCR (0.862), REP-PCR (0.846) and ERIC-PCR (0.843). On comparing the techniques, the BOX-PCR exhibited good DI value, typeability and complex band pattern on gel in differentiating the isolates. Hence, to conclude, the BOX-PCR fingerprinting technique was found useful in the genotyping of isolates suitable enough to find its application in an epidemiological investigation during an outbreak.
  • ThesisItemOpen Access
    Whole genome sequencing of nontyphoidal Salmonella isolates recovered from humans, swine and environment
    (G.B. Pant University of Agriculture and Technology, Pantnagar - 263145 (Uttarakhand), 2020-01) Pathak, Anubha Prashant; Upadhyay, A.K.
    Nontyphoidal Salmonella (NTS) is a serious zoonotic concern worldwide. It is one of the most important causes of diarrhea due to the consumption of food of animal origin such as pork, chicken and eggs. Armed with a battery of virulence factors and equipped with chromosomal and plasmid mediated antimicrobial resistance (AMR), Salmonella has established itself as successful zoonotic pathogen. Whole Genome Sequencing (WGS) is increasingly replacing various molecular typing and subtyping techniques used in bacteria as it offers highest resolution as well as detailed information on the accessory genes. Keeping these assertions in perspective, this work was designed to study the serotypes, AMR genes, virulence genes and plasmids in the Salmonella isolates (n=90) obtained from swine, human and swine rearing environment using WGS. The WGS of all the isolates (n=90) was conducted using Illumnia Miseq platform. The analysis of sequence data using various online and command-line based tools revealed a stereotypically diverse population of bacteria. A total of 15 serotypes were identified. The isolates were further classified using eBGSs (eBurst Groups), MLST (Multi Locus Sequence Typing) and rST (Ribosomal Sequence typing). Isolates grouped into 16 eBGs, 18STs and 25 rSTs offering more information than serotyping alone. The wgMLST was used to construct the phylogenetic tree which revealed serotype-based clustering and rST based sub-clustering. The virulence gene analysis revealed a highly conserved repertoire of genes. A total of 115 genes were detected, all the isolates (100%) carried genes encoding for type three secretion system one (T3SS1) and two (T3SS2) and their effectors, nonfimbrial adherence determinants, macrophage inducible genes and genes aiding in Mg2+transport. However, six genes constituting the T3SS2 effectors gogB, sseK1, sseK2, sseI, sspH1, sspH2 showed a serotype specific distribution pattern. A total of 27.7% of the isolates, all consisting of the serotype Typhimurium, from the three sources, were found to carry IncF plasmid mediated highly virulent genes spv, rck and pef. Typhoidal toxin gene cdtB was reported in 11.1% of NTS isolates. A total of 30 antimicrobial resistance genes encoding for resistance to 9 groups of antimicrobials were detected. The gene sul1 (45.5%) was most commonly detected, followed by tetA (30%) and ant(3'')-Ia (28%). Notably, two recently discovered genes encoding for resistance to the most crucial antibiotics Fosfomycin (fosA7) and Colistin (mcr9) were also reported. Out of the 19 plasmids identified, The pSPCV (IncFII) plasmid was found in 30% of the isolates followed by pSLT-BT (IncFIB) in 27.7% of isolates. A total of 8 groups of coexisting genes were found, ant(3'')-Ia blaCARB-2 floR_2 sul1 tet(G) which is responsible for the penta- resistance (ACSSuT) pattern of Salmonella Typhimurium was the most commonly reported group.