Loading...
Assam Agricultural University, Jorhat
Assam Agricultural University is the first institution of its kind in the whole of North-Eastern Region of India. The main goal of this institution is to produce globally competitive human resources in farm sectorand to carry out research in both conventional and frontier areas for production optimization as well as to disseminate the generated technologies as public good for benefitting the food growers/produces and traders involved in the sector while emphasizing on sustainability, equity and overall food security at household level.
Genesis of AAU -
The embryo of the agricultural research in the state of Assam was formed as early as 1897 with the establishment of the Upper Shillong Experimental Farm (now in Meghalaya) just after about a decade of creation of the agricultural department in 1882. However, the seeds of agricultural research in today’s Assam were sown in the dawn of the twentieth century with the establishment of two Rice Experimental Stations, one at Karimganj in Barak valley in 1913 and the other at Titabor in Brahmaputra valley in 1923. Subsequent to these research stations, a number of research stations were established to conduct research on important crops, more specifically, jute, pulses, oilseeds etc. The Assam Agricultural University was established on April 1, 1969 under The Assam Agricultural University Act, 1968’ with the mandate of imparting farm education, conduct research in agriculture and allied sciences and to effectively disseminate technologies so generated. Before establishment of the University, there were altogether 17 research schemes/projects in the state under the Department of Agriculture. By July 1973, all the research projects and 10 experimental farms were transferred by the Government of Assam to the AAU which already inherited the College of Agriculture and its farm at Barbheta, Jorhat and College of Veterinary Sciences at Khanapara, Guwahati.
Subsequently, College of Community Science at Jorhat (1969), College of Fisheries at Raha (1988), Biswanath College of Agriculture at Biswanath Chariali (1988) and Lakhimpur College of Veterinary Science at Joyhing, North Lakhimpur (1988) were established. Presently, the University has three more colleges under its jurisdiction, viz., Sarat Chandra Singha College of Agriculture, Chapar, College of Horticulture, Nalbari & College of Sericulture, Titabar. Similarly, few more regional research stations at Shillongani, Diphu, Gossaigaon, Lakhimpur; and commodity research stations at Kahikuchi, Buralikson, Tinsukia, Kharua, Burnihat and Mandira were added to generate location and crop specific agricultural production packages.
Browse
5 results
Search Results
ThesisItem Open Access Biofilm production, associated genes and antimicrobial resistance of escerichia coli isolated from bovine mastitis(2022-09) Das, Himasri; Saikia, G KLivestock production sector acts as one of the greatest contributors towards economic development of the country. Mastitis is considered to be one of the most common diseases of high yielding dairy cows which can cause decline in the milk production that ultimately leads to great economic loss in both developed and developing countries. Bovine mastitis can be divided into two types, clinical mastitis and subclinical mastitis. The present study was undertaken on phenotypic and genotypic detection of biofilm producing E. coli isolated from bovine mastitic milk and their antimicrobial resistance profile against commonly used selected groups of antibiotics. To carry out the study, a total of 560 quarters from 140 animals of both organized and unorganized dairy farms in and around Guwahati were screened for mastitis by California Mastitis Test (CMT) out of which 108 animals were found positive for mastitis. The overall prevalence of mastitis including clinical (15%) and subclinical form (62.14%) in both types of farms was 77.14%. In quarter wise distribution of mastitis, involvement of hind quarter was found to be more frequent. A total of 33 E. coli were isolated from 108 milk samples of mastitic dairy cows. All the isolates were screened for biofilm producing ability when tested by using on qualitative as well as quantitative detection methods viz., Congo red agar, Christensen tube and Tissue culture plate methods and all of them were found to be biofilm producers. All the E. coli isolates were tested for presence of biofilm associated genes, viz., csgA, fimH and luxS. The csgA gene was detected in 30 (90.90%) isolates, fimH in 31(93.93%) isolates and luxS was found in 30 isolates (90.90%). On relative quantification of mRNA expression of csgD gene revealed that the ΔCT value is significantly and negatively associated with biofilm production (P value<0.05). The E. coli isolates showed 100% sensitivity to Gentamicin, Neomycin and Amoxicillin+Sulbactam followed by Streptomycin (96.97%), Colistin (84.85%), ciprofloxacin and Ceftriaxone+Sulbactam (72.73% to each), Cefoperazone+ Sulbactam (69.70), Enrofloxacin and amoxycillin (63.64% to each) and Ceftriaxone (39.39%). However 100% resistance was observed for Cloxacillin followed by Ampicillin (96.97%) and Sulfadiazine (90.91%) on Disc diffusion test. In the present study, a total of 15 (45.45%) isolates were found to be multidrug resistant. Among all the MDR biofilm producing isolates, 6 were strong biofilm producers, 5 were moderate and 4 were weak biofilm producers and a significant correlation has been found between the strength of biofilm production and presence of MDR isolates (p<0.01). Our present finding has shown that the MIC values of Ceftriaxone, Amoxycillin, Gentamicin, Streptomycin were significantly correlated with strength of biofilm (P value<0.05). Out of 33 E. coli isolates tested, 18 (54.54%) were confirmed as ESBL producers based on double disk synergy test (DDST) and E-test. Further genotypic characterization of ESBL producing E. coli showed that ESBL encoding gene blaCTX-M was detected in 13 (39.39%) isolates with a product size of 585bp, blaSHV gene was detected in 3 (9.09%) isolates with a product size of 393bp and blaTEM gene was detected in 6 (18.18%) isolates with a product size 506bp.ThesisItem Open Access PHENOTYPIC AND GENOTYPIC CHARACTERIZATION OF METHICILLIN SENSITIVE AND RESISTANT Staphylococcus aureus (MSSA & MRSA) ISOLATED FROM BOVINE MASTITIS(College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, 2020-12) ALI, ARFAN; SAIKIA, G. K.The present study was undertaken on characterization of Staphylococcus aureus isolated from bovine mastitic milk in respect of their phenotypic and genotypic characteristics more particularly resistance to methicillin (MSSA & MRSA) and other groups of antimicrobial agents, presence of methicillin resistance and other virulence genes. To carry out the study, a total of 1328 quarter milk samples from 812 animals of organized and unorganized dairy farms of Kamrup (M), Kamrup (R) and Nalbari districts of Assam were screened by California Mastitis Test (CMT) out of which 630 animals (1328 quarter) were found positive for mastitis. The 630 mastitic animals comprised 117 clinically and 513 subclinically affected dairy cows. The overall prevalence of mastitis including clinical (14.41%) and subclinical form (63.18%) mastitis in these three districts was 77.59%. Maximum number of animals had infection involving two quarters in both clinical (47.86%) and subclinical (52.44%) mastitis. Involvement of right hind quarters was higher (28.91%) than the left hind quarters (28.13%) in clinical mastitis, while it was higher in left hind quarters (29.10%) than right hind quarters (26.21%) in subclinical mastitis. Higher prevalence rate of clinical (15.36%) and subclinical (68.76%) mastitis was recorded in organized farms in comparison to clinical (12.13%) and subclinical (49.79%) mastitis in unorganized farms. A total of 194 isolates of staphylococci were obtained from 630 bovine mastitic milk, out of which 151 (77.84%) coagulase-positive isolates identified as Staphylococcus aureus by phenotypic tests were confirmed genotypically by detection of S. aureus specific aroA gene by PCR. Of the 151 isolates, 54 (35.76%) were from clinical and 97 (64.24%) from subclinical mastitis and all of them produced coagulase and fermented mannitol. The prevalence of S. aureus associated mastitis was found to be 46.15% and 18.91% for clinical and subclinical forms, respectively. The prevalence of MRSA was 9.27% (14) as determined by cefoxitin resistance in phenotypic tests and confirmed by detection of mecA gene by PCR. The MRSA isolates were completely resistant (100%) to methicillin, cloxacillin, cefoxitin, tetracycline, streptomycin, colistin and mupirocin followed by higher degree of resistance to gentamicin and oxytetracycline (85.71% each) and moderate resistance to neomycin (50%). The MSSA isolates exhibited higher degree of sensitivity (73.72 – 100%) to tetracycline, amoxyclav, cefotaxime, ciprofloxacin, colistin, neomycin, streptomycin, mupirocin, ceftriaxone, gentamicin, cloxacillin, oxytetracycline, teicoplanin except cefepime to which they were least sensitive (54.01%). Out of 151 S. aureus isolates, 55 (36.42%) were multidrug resistant (MDR) which exhibited resistance against 4-12 antimicrobial agents. Among the MDR isolates, 14 (25.45%) were MRSA which showed resistance to 9-12 antimicrobial agents. A comparative study on antimicrobial resistance spectrum of MRSA and MSSA strains was conducted by disc diffusion and E-test using 10 antimicrobial agents which included penicillin, ampicillin, oxacillin, amoxyclav, cefoxitin, cefotaxime, ceftriaxone, gentamicin, ciprofloxacin and teicoplanin. All the MRSA isolates (14) exhibited similar pattern of resistance to all the agents except cefotaxime to which three isolates showed variation. All of the 38 representative MSSA isolates were sensitive to cefoxitin, oxacillin and teicoplanin in both the tests. One to three isolates showed variation in resistance pattern to rest of the antimicrobial agents. The E-test was found to be more effective than disc diffusion method for determining sensitivity of clinical isolates to antimicrobial drugs. In phenotypic characterization, all the coagulase positive isolates (MSSA and MRSA) caused alpha or beta haemolysis on sheep blood agar and showed susceptibility to novobiocin and resistance to polymyxin B which are typical characteristics of S. aureus. All the 151 S. aureus isolates harboured the virulence associated nuc (thermonuclease) and spa (staphylococcal protein A) genes and lukF-PV by six (6) and bap by two (2) isolates as revealed by PCR assay. The isolates which showed presence of lukF-PV and bap genes were methicillin resistant strains of S. aureus (MRSA).ThesisItem Open Access CHARACTERIZATION OF OUTER MEMBRANE VESICLES (OMVs) OF Pasteurella multocida OF AVIAN ORIGIN(College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, 2020-01) Gogoi, Anamika; Sharma, R. K.The Fowl Cholera, an infectious disease of poultry, waterfowl and many other birds is caused by Pasteurella multocida. To overcome those hurdles in poultry industry, focus has been given to identify immunogenic subcomponent of the causative agent and their use in development of modern vaccines. The present study was undertaken with a view to evaluate immunogenic potential of Outer Membrane Vesicles (OMVs) of Pasteurella multocida as well as their release under the influence of various environmental and physico-chemical factors. The extraction of OMV fraction was made from a highly pathogenic strain of P. multocida capsular type A associated with Fowl Cholera. The release of OMVs by the selected isolates was found to be significantly (p˂0.001) highest under the influence of iron deficient condition (2, 2 bipyridyl), exhibiting a protein concentration of 18.3 mg/ml. Similarly, the influence of pH in iron restricted environment was also have an impact on OMV release, which was found to be significant (p˂0.05) in reverse direction. A positive correlation could also be made in respect to the oxidative and antibiotic stress with release of OMVs. The comparative protein profiling of OMVs, OMPs and whole cell lysate of the selected pathogenic P. multocida type A isolate could exhibit more distinct and prominent protein bands in OMV fraction. The OMV fraction could also reveal the ompA (37.7-38.1 kDa), which was not prominently observed in other two fractions. The immunogenic potential of the extracted OMV fraction revealed an increasing trend of the mean antibody titre in both the immunized groups, with (Group I) or without (Group II) booster. The immunized birds of group I exhibited a significantly rising trend (p<0.05) of the mean serum antibody titre from the day of the vaccination, until it reached its peak (5947.41±62.6). The peak titre was observed on 28th day of post primary immunization, following booster on 21st day post immunization. Similarly, the immunized birds of group II the mean serum antibody titre of 7th dpi was continued to increase significantly at every weeks of observation till it reached peak on 21st (4576.27±42.9). The declining trend of the mean serum antibody titre was observed in the birds of group II from the day 28th of post immunization (4219.12±64.5) and continued till end of the study, i.e. the 60th dpi (3813.83±148.5). No significant difference could be observed between the two preparations, with and without booster in respect to the mean serum antibody titre till 21st dpi. Challenge trial could establish 100 per cent protection of vaccinated birds against homologous challenge, while development of clinical signs in the immunized birds was observed, following heterologous challenge. There was no significant difference between OMVs administered group and control group was observed in terms of blood SOD and GPx activity.ThesisItem Open Access MOLECULAR DETECTION AND CHARACTERIZATION OF FOOT AND MOUTH DISEASE VIRUS (FMDV) AND STUDY OF CYTOKINE EXPRESSION IN NATURALLY INFECTED LOCAL/CROSSBRED CATTLE FROM ASSAM(College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, 2021-09) BRAHMA, DERHASAR; Sharma, K.Foot and mouth disease (FMD) is a transboundary and the most contagious disease of cloven-hoofed animals including domestic and wild ruminants and pig, and has a great potential for causing severe economic loss due to loss of production and deprivation from international trade of animal products to FMD free countries. FMDV may occur in all the secretions and excretions of acutely infected animals, including expired air. Following recovery from the acute stage of infection, infectious virus may persist in the oropharynx of some ruminants (carriers), where live virus or viral RNA may continue to be recovered from oropharyngeal fluids and cells for upto 6 months or more. In this study, besides Sandwich ELISA, molecular detection and typing of FMDV was done using multiplex Reverse Transcription Polymerase Chain Reaction (mRTPCR), Reverse Transcription Loopmediated Isothermal Amplification (RT-LAMP) and SYBR Green real-time PCR targeting 3D gene. Isolation and molecular characterization of FMDV by sequencing was done. Also, study of expression of cytokines like interferon (IFN-α, IFN-β, IFN-) as well as certain interleukins (IL-1α, IL-1β, IL-2, IL-6, IL-10 and IL-12) and tumour necrosis factor (TNF-α) was estimated at mRNA level by SYBR Green real-time PCR from whole blood (White Blood cells) samples during the natural infection and during the period of persistence. This study was carried out in a total of 129 animals, comprising of 93 crossbred (vaccinated) and 36 local (non-vaccinated) cattle and additionally 12 healthy in-contact animals were taken as control animals. For carrying out this study, Tissue (n=29), whole blood (n=36) and oropharyngeal fluid (n=190) samples were collected as per standard procedure in 50% glycerol, EDTA and 0.8 M PBS/transport media, respectively. OP fluid was collected from recovered animals until complete recovery (i.e. 1st, 3rd, 6thand 9thmonth) from FMD infection. All the RNA extractions were done using Qiagen RNA extraction kit. We found that, out of 29 tissue samples, 20 samples were positive for serotype O, 9 were positive for serotype A and none of the samples was positive for Asia-1 by the multiplex RT-PCR as well as RT-LAMP. FMDV could be detected in 86.21%, 100%, 100% and 100% of tissue samples by sandwich-ELISA, mRT-PCR, RT-LAMP and SYBR Green real-time PCR respectively. Sensitivity test was run using 10 fold serial dilution of RNA extracted from FMDV antigen and found that, the real-time PCR was more rapid and highly sensitive technique of all, secondly the RT-LAMP, followed by the mRT-PCR. From the follow-up cases of the FMD recovered cattle, 38 (23.75%), 47 (29.38%) and 49 (30.63%) OPF samples (n=178) were found to be positive for FMDV by the multiplex RT-PCR, RT-LAMP and SYBER Green real-time PCR respectively, indicating persistence (carriers).The SYBR green real-time PCR was very much useful for detection of persistence from the OPF samples.However, OPF (n=12) and blood (n=12) samples from all the healthy controls and blood (n=12) from persistent animals were negative for FMDV. All blood samples (100%, n=12) from the clinically FMD infected cattle were positive for FMDV. The persistence of FMDV in oropharyngeal region of cattle lasted for upto 3 to 4 months in most of the FMD infected cattle. Persistence in crossbred (vaccinated) cattle didn’t last for more than 4 months. Only 2 Local non-vaccinated cattle (1.6%) was found to have persistence upto 6-7 months after infection. The overall number of persistent animals and the rate of persistence in cattle (n=129) at 1st month, 3rd month and 6th month were 32 (24.81%), 15 (11.26%) and 2 (1.6%) respectively, and was slightly higher in the local non-vaccinated compared to the crossbred vaccinated cattle. No statistical significance was observed between the two groups as the P value was found to be 0.23 (>0.05) and the Chi-square value was 5.57. The sequencing results showed that the Serotype O sequence (MZ501211-G-02- 19, MZ501212-G-03-19 and MZ501213 Op) shared 98.81% identity with Pakistan isolate MN953620, 96.43% identity with India isolate KY579948.1 (Nagaland, submitted by RRC Assam) and 94.05% identity with India complete genome isolate MN983158.1; and theSerotype A sequence (MZ501214-Mg/01/19) shared 95.29% identity with Indian isolate HQ832583.1 and 94.24% identity with Bangladesh isolate KT982204. The identity range was 98.81%-96.43% and 95.29%-92.22% for type O and A respectively, based on the nucleotide sequence Blast search in NCBI. The multiple sequence alignment showed that there are some minor changes in the nucleotide sequences with the consensus sequences. There were nucleotide insertions in the 3953 and 3954 positions in two of the query sequences of FMDV type O. Whereas, in FMDV type A, there were nucleotide insertions at 3807, 3813-3815 and 3841 positions and deletions at 3771 and 3874 positions of the nucleotide sequences. The result from this study shows that cytokine genes had general trend of upregulation during acute infection and decreased level of expression or down regulation during persistence. Cytokines in blood were generally upregulated in both acute infection and persistence, but compared to acute, there was decreased mRNA level of expression of cytokines during persistence except the down regulation of IFN-β, IL-2 and IL-6, whereas, all but IFN-α and IL-1α were down regulated in OPF during persistence. These cytokines may have certain role in persistence of FMDV by suppression of immune response and also by having anti-inflammatory or immunomodulatory response in carrier cattle. Thus, from this study, we can conclude that, molecular detection techniques are the most sensitive and specific techniques for detection of FMDV and particularly for diagnosis of persistence from OPF samples. Persistence occurred in 32 cattle (25%) after 1st month of the FMDV infection, out of which the proportion of local non-vaccinated cattle was slightly higher. And that cytokines may have a role in persistence of FMDV in cattle.ThesisItem Open Access MOLECULAR DETECTION AND CHARACTERIZATION OF NEWCASTLE DISEASE VIRUS STRAINS FROM POULTRY(College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, 2021-10) NEOG, BHRIGU KUMAR; Sarma, D. K.Newcastle disease is a highly transmissible and acute fatal disease of poultry caused by virulent strains of Avian paramyxovirus type 1 (APMV-1) which is commonly known as the Newcastle disease virus (NDV). Avian paramyxovirus type 1 exhibit great variation in their pathogenicity and the severity of the disease produced varies with the host species and the strain of virus involved. Newcastle disease can have devastating effects on the poultry industry due to the high morbidity and mortality associated with virulent strains of the virus. A study was undertaken to detect and characterize different NDV strains circulating among the native poultry population. To investigate the presence of NDV in clinically suspected backyard chickens, a total of 289 tissue samples were collected from 74 birds at necropsy from nine districts of Assam and tested using haemagglutination inhibition (HI) and reverse transcriptase polymerase chain reaction (RT-PCR). Out of the 289 tissue samples, 24.57 % and 47.05 % samples were found to be positive for NDV in HI assay and RT-PCR respectively. Of the 74 clinically suspected chickens 52.70 % birds were found to be positive for NDV in HI assay while 91.89 % birds were found to be positive for NDV in RT-PCR. Among the different tissue samples tested for presence of NDV, a significantly higher number of tissue samples from spleen, trachea, lung, proventriculus and caecal tonsil tested positive for NDV irrespective of the test used. To detect NDV in apparently healthy chickens, 186 numbers of oropharyngeal swabs and 146 numbers of cloacal swabs were tested using HI assay and RT-PCR. Of the 186 oropharyngeal swabs tested, 24.57 % and 15.05 % swab samples were found to be positive for NDV in HI assay and RT-PCR respectively. Further, out of 146 cloacal swabs tested, 6.16 % and 21.23 % swab samples were found to be positive for NDV in HI assay and RT-PCR respectively. A total of 18 tissue samples, identified as NDV positive using HI assay and RT-PCR, were processed for isolation of NDV using SPF embryonated chicken eggs (ECEs) of 9-11 days of incubation. The presence of the virus in the allantoic fluid of the inoculated ECEs was confirmed by two RT-PCR techniques, one of which targeted a 767 bp sequence of the F gene while the other targeted a 426 bp sequence of the HN gene of NDV. NDV from all the 18 tissue samples (100 %) was detected in the allantoic fluid of ECEs using the RT-PCR techniques. Six representative NDV isolates were sequenced by outsourcing and subjected to phylogenetic study. The consensus sequences of the isolates were subjected to multiple sequence alignment with reference sequences from GenBank databases. A phylogenetic tree was then constructed where five of the isolates clustered with genotype XIII of Class II NDV while one clustered with genotype II of Class II NDV cluster. Evaluation of the amino acid composition of the F0 cleavage site revealed the presence of the consensus sequence 112R-R-Q-K-R-F117 in case of the five genotype XIII isolates whereas the genotype II NDV isolate possessed the sequence 112G-R-Q-G-R-L117 at the F0 cleavage site of the fusion gene. Thus, five isolates from the present study were identified as virulent NDV strains while one isolate was identified as an avirulent strain. A multiplex reverse transcriptase-polymerase chain reaction (mRT-PCR) was standardized for simultaneous detection and differentiation of different pathotypes of NDV. Three specific oligonucleotide primers were used in the mRT-PCR for amplification of the target sequences of the F gene of NDV. The pathotypes of NDV was differentiated based on the products generated by the mRT-PCR. A product in size of 364 bp was obtained in case of the lentogenic strains while for mesogenic strains two products in size of 364 bp and 204 bp were generated. In case of velogenic strains only one product in size of 204 bp was generated. All the 18 NDV isolates from the present study was characterized using the mRT-PCR. Out of the eighteen isolates one isolate was identified as a lentogenic and two were identified as mesogenic. The other 15 isolates were identified as velogenic strains. A standard RFLP technique was also used to validate the results of the mRT-PCR. The RFLP involved digestion of a RT-PCR amplified 363 bp fusion gene product by HinfI restriction enzyme. The virulent and avirulent strains of NDV were differentiated based on the HinfI digestion patterns exhibited on 3 % agarose gels. The results of pathotyping obtained using RFLP analysis, corroborated the results of the mRT-PCR. A local isolate of NDV (AS/KM/CG 01) from non-vaccinated backyard chicken was subjected to complete genome sequencing by outsourcing. Evaluation of the genomic data revealed that the genome of the NDV isolate AS/KM/CG 01 consists of six genes arranged in tandem that encodes for six structural proteins namely, the nucleocapsid protein (NP), the phosphoprotein (P), the matrix protein (M), the fusion protein (F), the hemagglutinin-neuraminidase protein (HN), and the polymerase protein (L). The isolate possessed a genome of approximately 15 kb. Evaluation of the F0 cleavage site within the fusion gene of the isolate revealed the presence of the consensus amino acid sequence 112G-R-Q-G-R-L117 which is typical of lentogenic strains of NDV. Phylogenetic study revealed that the NDV isolate belong to genotype II of class II NDV cluster. It was also found that the isolate has close relationship with previously reported genotype II NDV isolates from India and China. The isolate also showed more than 97 % homology with NDV vaccine strain LaSota. The study was summarized with the findings that genotype XIII NDV of class II cluster is predominant among the poultry flocks of Assam. Detection of genotype II NDV of class II closely related to NDV vaccine strain LaSota in the present study suggests a possible spillover of vaccine-type viruses from vaccinated poultry or feral avian reservoirs to non-vaccinated backyard chickens. However further studies are needed on this aspect.
