Mapping Heterogeneous Population Structure of Mannheimia haemolytica Associated with Pneumonic Infection of Sheep in Southern State Karnataka, India.

Mannheimia haemolytica is recognized as principal pathogen associated with pneumonic pasteurellosis leading to huge economic losses to small ruminant farmers. Even though the disease causes huge economic losses, epidemiology of M. haemolytica is less studied, hindering the formulation of effective control strategies. Current study aimed to highlight molecular characterisation of M. haemolytica strains isolated from ovine pneumonic infection. M. haemolytica 27 isolates with two reference strains were characterised using capsular and virulence gene typing, multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) methods. M. haemolytica serotype A2 recognized as predominant serotype (74%) followed by A6 (11%) and A1 (5%) serotypes. Virulence gene profiling by PCRs showed dominance of all five virulent genes [such as adh and gcp (100% each)] followed by gs60 (88.8%), lktC (85.2%), tbpB (51.9%) and least nmaA gene (14.8%). MLST profiling delineated M. haemolytic isolates into 11 sequence types (STs) with most prevalent being ST37 (27.9%) and ST16 (23%) and nine new STs (ST37, 38, 39, 40, 41, 42, 47, 48, and 49). These new STs did not belong to any of the three clonal complexes (CC4, CC8 and CC28). ST16 was exclusively noted in A1 and A6 serotypes. Amongst 25 isolates, 22 pulsotypes (GD 0.88) recorded indicated variability of the M. haemolytica isolates in PFGE analysis. In conclusion, the study suggested dominance of M. haemolytica serotype A2 harbouring different virulent genes, diverse STs and pulsotypes responsible for pneumonic pasteurellosis frequently encountered in sheep.

Genetic insights of antibiotic resistance, pathogenicity (virulence) and phylogenetic relationship of Escherichia coli strains isolated from livestock, poultry and their handlers - a one health snapshot.

BACKGROUND: Pathogenic and non-pathogenic strains of Escherichia coli harbouring antibiotic resistance genes (ARGs) from any source (clinical samples, animal settings, or environment) might be transmitted and contribute to the spread and increase of antibiotic resistance in the biosphere. The goal of this study was to investigate the genome to decipher the repertoire of ARGs, virulence genes carried by E. coli strains isolated from livestock, poultry, and their handlers (humans), and then unveil the genetic relatedness between the strains. METHODS: Whole genome sequencing was done to investigate the genetic makeup of E. coli isolates (n = 20) [swine (n = 2), cattle (n = 2), sheep (n = 4), poultry (n = 7), and animal handlers (n = 5)] from southern India. The detection of resistome, virulome, biofilm forming genes, mobile genetic elements (MGE), followed by multilocus sequence typing (MLST) and phylogenetic analyses, were performed. RESULTS: E. coli strains were found to be multi drug resistant, with a resistome encompassing > 20 ARGs, the virulome-17-22 genes, and > 20 key biofilm genes. MGE analysis showed four E. coli isolates (host: poultry, swine and cattle) harbouring composite transposons with ARGs/virulence genes (blaTEM, dfr, qnr/nleB, tir, eae,and esp) with the potential for horizontal transfer. MLST analyses revealed the presence of ST937 and ST3107 in both livestock/poultry and their handlers. Phylogenomic analyses with global E. coli isolates (human/livestock/poultry hosts) showed close relatedness with strains originating from different parts of the world (the United States, China, etc.). CONCLUSION: The current study emphasizes the circulation of strains of pathogenic sequence types of clinical importance, carrying a diverse repertoire of genes associated with antibiotic resistance, biofilm formation and virulence properties in animal settings, necessitating immediate mitigation measures to reduce the risk of spread across the biosphere.

Knowledge and practices related to antibiotics among poultry producers and veterinarians in two Indian states.

Background: Antibiotics are frequently utilized in livestock, particularly poultry, for therapy and growth promotion, resulting in antimicrobial resistance. Multidrug-resistant bacteria are frequent in poultry samples from India. The purpose of this study was to better understand main antibiotic consumption patterns in poultry value chains, as well as antibiotic knowledge and practices among the stakeholders. Methods: A cross-sectional survey was conducted in Assam and Karnataka, India. The poultry farmers were interviewed on antibiotic usage, antibiotic knowledge, feeding practices, and preventive measures on the farm. Poultry farmers reported their veterinarians, and we also interviewed them on knowledge and practices related to antimicrobial use in poultry and antimicrobial resistance. Item response theory (IRT) was used to assess the association between the answers and demographic factors. Results: This survey interviewed 62 poultry farmers and 11 veterinarians. Small poultry farms with fewer than 4000 birds were owned by 51.6% of farmers. Most poultry farmers had heard about antibiotics, and 62.9% thought they cured all diseases. If one chicken is sick, 72.6% said others should be given antibiotics to prevent the disease. All veterinarians utilized tetracyclines, aminoglycosides, and cephalexin on the poultry farms. Over half (54.5%) stated antibiotics prevent diseases, and 72.7% said they treat and prevent diseases. Some (45.5%) said antibiotics boost growth. IRT analysis showed that 8 questions assessed a knowledge scale well. Univariable analysis showed that Assam farmers and women were likely to have have more knowledge. Conclusion: The poultry farmers were mostly unaware of the relation between antibiotic use and antimicrobial resistance. Despite being aware, the veterinarians agreed with use antibiotics as a prophylactic measure. It is vital that these stakeholders understand the repercussions of such widespread antibiotic use. In order to increase knowledge, frequent trainings and antimicrobial stewardship programmes with effective communication and incentives for behaviour change should be conducted.

Seroprevalence and associated risk factors of leptospirosis in bovine dairy farms in Telangana state, India.

The current cross-sectional study aimed to determine the seroprevalence of Leptospira infection in bovine dairy farms in the Telangana state of India, as well as the associated risk factors, in order to implement effective preventive measures for disease control. A total of 469 blood samples were collected from 67 herds/farms in different areas, covering 20 administrative districts in the state. These samples consisted of 253 from cattle and 216 from buffaloes. Questionnaires were used to collect data on host and epidemiological factors. The collected sera were tested using the gold standard serological test, the Microscopic Agglutination Test (MAT), which employed a panel of 18 reference serovars for Leptospira exposure. The statistical analysis of epidemiological data was carried out to identify the risk factors associated with Leptospira exposure. The overall observed seroprevalence at the animal and farm levels was 41.4% and 77.6%, respectively. The most prevalent anti-leptospiral antibodies were observed against the serogroups Icterohaemorrhagiae (32.4%), Pomona (22.2%), Javanica (19.1%), Australis (17.0%), Bataviae (15.5%), Autumnalis (12.9%), Hebdomadis (12.9%), and others, in the total reacting samples. At the animal level, the significant risk factors associated with exposure to Leptospira species were breed (p = 0.03) and health status (p = 0.03). Furthermore, the multivariate statistical analysis of farm factors revealed that farm size (p = 0.05), presence of dogs (p = 0.04) and rodents (p = 0.01) on the farm, use of fodder from wet soils (p = 0.04), and proximity to water bodies (p = 0.04) were significantly associated with exposure to Leptospira in the studied region. This study provides the first report from India highlighting the important risk factors at the herd/farm and animal level associated with Leptospira infections in cattle and buffaloes. The findings contribute to strengthening the one-health strategy by facilitating the design and planning of appropriate control measures to alleviate the burden of leptospirosis in bovines.

Analyses of Extended-Spectrum-ß-Lactamase, Metallo-ß-Lactamase, and AmpC-ß-Lactamase Producing Enterobacteriaceae from the Dairy Value Chain in India.

The consumption of milk contaminated with antibiotic-resistant bacteria poses a significant health threat to humans. This study aimed to investigate the prevalence of Enterobacteriaceae producing ß-lactamases (ESBL, MBL, and AmpC) in cow and buffalo milk samples from two Indian states, Haryana and Assam. A total of 401 milk samples were collected from dairy farmers and vendors in the specified districts. Microbiological assays, antibiotic susceptibility testing, and PCR-based genotyping were employed to analyze 421 Gram-negative bacterial isolates. The overall prevalence of ß-lactamase genes was 10% (confidence interval (CI) (7-13)), with higher rates in Haryana (13%, CI (9-19)) compared to Assam (7%, CI (4-11)). The identified ß-lactamase genes in isolates were blaCMY, blaMOX, blaFOX, blaEBC, and blaDHA, associated with AmpC production. Additionally, blaCTX-M1, blaSHV, and blaTEM were detected as ESBL producers, while blaVIM, blaIMP, blaSPM, blaSIM, and blaGIM were identified as MBL producers. Notably, Shigella spp. were the dominant ß-lactamase producers among identified Enterobacteriaceae. This study highlights the presence of various prevalent ß-lactamase genes in milk isolates, indicating the potential risk of antimicrobial-resistant bacteria in dairy products. The presence of ß-lactam resistance raises concern as this could restrict antibiotic options for treatment. The discordance between genotypic and phenotypic methods emphasizes the necessity for comprehensive approaches that integrate both techniques to accurately assess antibiotic resistance. Urgent collaborative action incorporating rational and regulated use of antibiotics across the dairy value chain is required to address the global challenge of ß-lactam resistance.

Quantifying the influence of climate, host and change in land-use patterns on occurrence of Crimean Congo Hemorrhagic Fever (CCHF) and development of spatial risk map for India.

Crimean Congo Hemorrhagic Fever (CCHF), is an emerging zoonosis globally and in India. The present study focused on identifying the risk factors for occurrence of CCHF in the Indian state of Gujarat and development of risk map for India. The past CCHF outbreaks in India were collated for the analyses. Influence of land use change and climatic factors in determining the occurrence of CCHF in Gujarat was assessed using Bayesian spatial models. Change in maximum temperature in affected districts was analysed to identify the significant change points over 110 years. Risk map was developed for Gujarat using Bayesian Additive Regression Trees (BART) model with remotely sensed environmental variables and host (livestock and human) factors. We found the change in land use patterns and maximum temperature in affected districts to be contributing to the occurrence of CCHF in Gujarat. Spatial risk map developed using CCHF occurrence data for Gujarat identified density of buffalo, minimum land surface temperature and elevation as risk determinants. Further, spatial risk map for the occurrence of CCHF in India was developed using selected variables. Overall, we found that combination of factors such as change in land-use patterns, maximum temperature, buffalo density, day time minimum land surface temperature and elevation led to the emergence and further spread of the disease in India. Mitigation measures for CCHF in India could be designed considering disease epidemiology and initiation of surveillance strategies based on the risk map developed in this study.

Management of bovine brucellosis in organized dairy herds through the identification of risk factors: A cross-sectional study from Karnataka, India.

Background and Aim: Brucellosis is an infectious disease caused by Brucella species. This study aimed to identify the risk factors associated with bovine brucellosis seropositivity in organized dairy farms to control the disease in unvaccinated adult bovine herds in Karnataka, India. Materials and Methods: In total, 3610 samples (3221 cattle and 389 buffaloes) were subjected to parallel testing using the Rose Bengal plate test and protein G-based enzyme-linked immunosorbent assay, followed by analyses of animal- and farm-level epidemiological datasets to identify the risk factors. Results: The apparent brucellosis prevalence at the animal level was higher in buffaloes (8.2%, 95% confidence interval [CI] = 5.9-11.4) than in cattle (6.1%, 95% CI = 5.3-7.0). In a multivariable logistic model, animals calved 3-5 times (odds ratio [OR] = 2.22, 95% CI = 1.50-3.1, reference [ref]: animals calved <2 times); animals with a history of abortion (OR = 54.73, 95% CI = 33.66-89.02), repeat breeding (OR = 19.46, 95% CI = 11.72-32.25), and placental retention (OR = 13.94, 95% CI = 4.92-39.42, ref: no clinical signs); and dogs on farms (OR = 2.55, 95% CI = 1.48-4.40, ref: absence of dogs); disposal of aborted fetus in open fields (OR = 4.97, 95% CI = 1.93-12.84) and water bodies (OR = 2.22, 95% CI = 1.50-3.1, ref: buried); purchase of animals from other farms (OR = 6.46, 95% CI = 1.01-41.67, ref: government farms); hand milking (OR = 1.98, 95% CI = 1.02-10.0, ref: machine milking); and use of monthly veterinary services (OR = 3.45, 95% CI = 1.28-9.29, ref: weekly services) were considered significant risk factors for brucellosis in organized bovine herds (p < 0.01). Conclusion: The study identified that the animals calved 3-5 times or with a history of abortion/repeat breeding/placental retention, and disposal of aborted fetus in open fields/water bodies as the potential risk factors for bovine brucellosis. These risk factors should be controlled through the implementation of best practices to reduce the brucellosis burden in bovine farms.

Scientometric Analysis of Gastrointestinal Parasites Prevalence in Sheep and Goats of India.

PURPOSE: In the present study, gastrointestinal parasites (GIP) prevalence in sheep and goats from India was estimated by scientometrics. METHODS: The GIP prevalence studies (86) reported during 1998-2021 was obtained from online databases, and offline literatures, meta-analysis was undertaken by using "meta" package in R-Software. RESULTS: The pooled GIP prevalence in India was 65% (95% level CI 56-74%, PI 12-96%) in sheep, 74% (95% level CI 66-80%, PI 14-98%) in goats and 68% (95% level CI 62-73%, PI 15-96%) in sheep and goats. Period-wise analysis revealed a higher GIP prevalence during 1998-2010 than the recent periods. Among the zones, GIP prevalence was higher in the Central zone (79%) in sheep, North zone (82%) in goats, and Central zone (78%) in sheep and goats. Based on the state-wise analysis, a higher GIP prevalence was observed in Haryana for sheep, Himachal Pradesh for goats, and Uttarakhand for sheep and goats. In India, a higher prevalence was reported by nematodes than other parasite classes. Based on climatic regions, a higher GIP prevalence was observed in semi-arid Steppe type region (84%). CONCLUSION: The high prevalence zones, states, species, sample types, parasite classes, parasite species and climate regions of GIP will be useful in decision-making and resource use efficiency by policymakers and stake holders. There is an urgent need to prevent the occurrence of GIP infections in sheep and goats by adopting scientific management practices, effective therapeutic measures, and hygienic practices on farms to augment the economic benefits to sheep and goat farmers in India.

Characterization of humoral and cellular immune responses elicited by reduced doses of Brucella abortus S19 (calfhood) vaccine in cattle calves of India.

Brucella abortus S19 vaccine is a stable attenuated smooth strain, globally used as calfhood vaccine for the prevention of bovine brucellosis. Various agencies demonstrated different doses for vaccinating cattle and buffalo calves leading to ambiguity in selecting a suitable immune vaccine dose. The current study aimed at evaluating four graded doses of S19 vaccine to arrive at the dose which could produce comparable effectiveness as that of full dose prescribed by Indian Pharmacopeia among the Indian calves. Four vaccine doses of which the first dose consisted of full dose (40 × 109 CFU/dose) and the other three were 1/10th, 1/20th, 1/100th reduced doses along with control were tested. Each vaccine dose was administered to 13 cattle calves of 4-5 months of age maintained in separate groups. The blood samples were collected on 0 to 240 days post-vaccination (DPV) at the intervals of 0, 14, 28, 45, 60, 90, 150, 180 and 240 for assessment of vaccine-induced innate, humoral and cell-mediated immune responses. The sero-conversion of all vaccinated animals on DPV 45 and persistence of antibody till DPV 240 were noticed. No significant differences were observed in antibody response between animal groups that received full and 1/10th reduced doses. Innate and cell-mediated response by IL-6, TNF-α¸ IFN-γ, CD4+ and CD8+ cell counts showed dose-dependent responses with no significant difference between full dose and 1/10th reduced doses. The results suggest a possible one log reduction of full dose without compromising immune responses to aid larger vaccination coverage for creating herd immunity.

Evaluation of an in-house IgM/IgG lateral flow assay for serodiagnosis of human brucellosis.

This study aimed to evaluate the diagnostic efficacy of an in-house lateral flow assay (LFA) for the detection of IgM/IgG anti-Brucella antibodies for rapid serodiagnosis of human brucellosis. Three groups of sera samples including 476 from high-risk individuals, 27 from culture-confirmed patients, and 43 from healthy blood donors were used for evaluation of LFA. In comparison with iELISA, the sensitivity, specificity, and accuracy of LFA were >95%, >99%, and 99% respectively. Considering the very good agreement, accuracy, simplicity, and rapidity, LFAs might be useful as a point of care test for the diagnosis of human brucellosis in resource-limited laboratories.

Towards Eradication of PPR: Disease Status, Economic Cost and Perception of Veterinarians in Karnataka, India.

In this study, we assessed the PPR disease status, its economic cost, the financial viability of vaccination, and the perspectives of field veterinarians on the PPR vaccination programme implemented in Karnataka state, India. In addition to secondary data, cross-sectional surveys undertaken during 2016-17 (survey I) and 2018-19 (survey II) from 673 sheep and goat flocks and data collected from 62 veterinarians were analysed. The economic costs and perceptions of veterinarians were analysed using deterministic models and the Likert scale, respectively, and the financial viability of vaccination programmes under the best (15%), base (20%), and worst-case (25%) PPR incidence scenarios, considering two different vaccination plans (plan I and plan II), was assessed. The disease incidence in sheep and goats was found to be 9.8% and 4.8% in survey I and survey II, respectively. In consonance with the increased vaccination coverage, the number of reported PPR outbreaks in the state declined significantly. The estimated farm-level loss of PPR varied between the surveyed years. Even under the best-incidence scenario, under vaccination plan-I and plan-II, the estimated benefit-cost ratio (18.4:1; 19.7:1), the net present value (USD 932 million; USD 936 million) and the internal rate of return (412%) implied that the vaccination programmes were financially viable and the benefits outweighed the cost. Though the majority of veterinarians perceived that the control programme was well planned and rolled out in the state, a few of them disagreed or were neutral towards the plan per se, towards the coordination between functionaries, the availability of funding, and the programme acceptance by farmers. Despite many years of vaccination, PPR still persists in the Karnataka state for various reasons and in order to eradicate the disease, a review of the existing control programme with strong facilitation from the federal government is needed.

Elevation determines the spatial risk of Anthrax outbreaks in Karnataka, India.

Anthrax is an economically important livestock disease affecting subsistence farmers and it is of zoonotic importance. Anthrax is endemic in many states of India including Karnataka. Identification of spatial risk factors for occurrence of anthrax and development of predictive risk maps are required for planning adequate vaccination in high-risk areas as well as targeted surveillance activities in animals, humans and environment. In this study, village level anthrax outbreak locations from Karnataka (1997-2016) were geo-referenced and predictive risk map was developed using temporally Fourier Processed remotely sensed variables. A non-linear discriminant analysis approach was used to develop the risk map for Karnataka. Elevation was identified as top predictor variable in the 10 variables selected. The predicted risk map showed good accuracy and validation statistics when evaluated using different metrics (Kappa, sensitivity, specificity, AUC). The predicted risk map also showed good correspondence with past outbreaks. Further, we used Bayesian Penalised spline method to estimate species response curves for top 10 variables selected. The validated risk map can be used in planning vaccination strategy and surveillance in high-risk areas.

The first study on analysis of the codon usage bias and evolutionary analysis of the glycoprotein envelope E2 gene of seven Pestiviruses.

Background and Aim: Pestivirus, a genus of the Flaviviridae family, comprises viruses that affect bovines, sheep, and pigs. Symptoms, including hemorrhagic syndromes, abortion, respiratory complications, and deadly mucosal diseases, are produced in infected animals, which cause huge economic losses to the farmers. Bovine viral diarrhea virus-1, bovine viral diarrhea virus-2, classical swine fever virus, border disease virus, Bungowannah, Hobi-like, and atypical porcine pestivirus belonging to the Pestivirus genus were selected for the study. This study aimed to estimate the codon usage bias and the rate of evolution using the glycoprotein E2 gene. Furthermore, codon usage bias analysis was performed using publicly available nucleotide sequences of the E2 gene of all seven Pestiviruses. These nucleotide sequences might elucidate the disease epidemiology and facilitate the development of designing better vaccines. Materials and Methods: Coding sequences of the E2 gene of Pestiviruses A (n = 89), B (n = 60), C (n = 75), D (n = 10), F (n = 07), H (n = 52), and K (n = 85) were included in this study. They were analyzed using different methods to estimate the codon usage bias and evolution. In addition, the maximum likelihood and Bayesian methodologies were employed to analyze a molecular dataset of seven Pestiviruses using a complete E2 gene region. Results: The combined analysis of codon usage bias and evolutionary rate analysis revealed that the Pestiviruses A, B, C, D, F, H, and K have a codon usage bias in which mutation and natural selection have played vital roles. Furthermore, while the effective number of codons values revealed a moderate bias, neutrality plots indicated the natural selection in A, B, F, and H Pestiviruses and mutational pressure in C, D, and K Pestiviruses. The correspondence analysis revealed that axis-1 significantly contributes to the synonymous codon usage pattern. In this study, the evolutionary rate of Pestiviruses B, H, and K was very high. The most recent common ancestors of all Pestivirus lineages are 1997, 1975, 1946, 1990, 2004, 1990, and 1990 for Pestiviruses A, B, C, D, F, H, and K, respectively. This study confirms that both mutational pressure and natural selection have played a significant role in codon usage bias and evolutionary studies. Conclusion: This study provides insight into the codon usage bias and evolutionary lineages of pestiviruses. It is arguably the first report of such kind. The information provided by the study can be further used to elucidate the respective host adaptation strategies of the viruses. In turn, this information helps study the epidemiology and control methods of pestiviruses.

Comparing the Effectiveness of Different Approaches to Raise Awareness About Antimicrobial Resistance in Farmers and Veterinarians of India.

Background: Antimicrobial resistance (AMR) is a global public health threat. The indiscriminate use of antibiotics in the animal health sector contributes to increasing rates of AMR and studies involving dairy farmers in India have found knowledge levels regarding antibiotics and AMR to be very low. The purpose of this study was to assess different methods to raise awareness and knowledge about AMR and antibiotic use among dairy farmers, paravets (veterinary assistants), and veterinarians. Materials and Methods: The study was conducted in September-December of 2018 in some parts of Haryana, Assam, Karnataka, and West Bengal. It had two parts: an intervention meeting (September-October 2018) which consisted of focus group discussions (FGD) with farmers, key informant interviews (KII) with veterinary professionals along with distribution of information packages, and then a follow-up survey (November-December 2018). The villages were randomly allocated to either one of the four intervention approaches (1-FGD/KII and information package on AMR; 2-FGD/KI and information on animal health; 3- FGD/KII and information package on animal health plus information on AMR; or 4- only the FGD/KII). A follow-up survey was done to assess the effect of interventions. Results: In total, 274 dairy farmers and 51 veterinary professionals (21 veterinarians and 30 paravets) participated in the follow-up survey. Many of the farmers and veterinary professionals who participated in the follow-up survey had been part of the intervention meetings. The average knowledge score of farmers was 7.8. It was found that the knowledge score was higher amongst farmers who had participated in the intervention meetings (p < 0.05), had received intervention approach 2 (p = 0.03) or approach 3 (p = 0.01), and amongst female farmers (p = 0.03) compared to male. The veterinary professionals had good knowledge but lacked interest in training the farmers about antimicrobial resistance. Conclusion: Our research demonstrated that a higher percentage of farmers and veterinary professionals who attended the intervention meeting had improved knowledge. Dairy farmers should be regularly educated on antibiotic usage and how to avoid misusing them. Also, veterinary experts should be provided with tools and strategies to educate farmers on the use of antimicrobials.

Seroprevalence of sheeppox and goatpox virus in Asia and African continent: A systematic review and meta-analysis (Scientometrics).

Background and Aim: Two endemic capripox infectious diseases, sheeppox (SP) and goatpox (GP) are common in Asia, Africa, and the Middle East. Sheep and goats, in general, are considered current assets of small and marginal farmers and have significant economic value in terms of meat, wool, and skin/hide production. Sheep and goat populations in India total 148.88 million and 74.26 million, respectively. Capripox caused US$ 2.3 million (Indian Rupee [INR] 105 million) in economic damages in Maharashtra (India) alone, and it took over 6 years for a flock to recover from the outbreak. The projected yearly loss at the national level is US$ 27.47 million (INR 1250 million). As a result, Capripox diseases put small and marginal farmers under much financial strain. The present study estimates the seroprevalence of SP and GP diseases in the Asian and African continents using systematic review and meta-analysis. The results of the study will help researchers and policymakers to understand the spatial and temporal distribution of the disease and its burden. In addition, the results are also helpful to design and implement location-specific prevention and eradication measures against these diseases. Materials and Methods: Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines of Cochran collaborations were used for systematic review and subsequently meta-analysis were used. The literature was collected from various databases. Initial search string resulted in more than nine thousand articles for the period 2000 to 2020 using the different combinations of keywords and Boolean operators (or not) asterisk* and quotation marks. Out of 9398 papers, 80 studies were chosen for complete test reviews and quality bias evaluation using the inclusion and exclusion criteria. Finally, 21 articles were used for the meta-analysis. The statistical study employed fixed effects and random effects models using R. Results: Seroprevalence of SP and GP was calculated using studies with a cumulative sample size of 4352, out of which sheep and goats' samples together contribute 48%, followed by sheep (32%) and goat (21%). The result of the meta-regression revealed that detection techniques had a significant impact on the overall effect size at 5% level (Qm=14.12). Subgroup analysis of polymerase chain reaction (PCR) test with samples was further grouped into two categories based on the median, and it revealed that 62% of samples used PCR as a detecting test followed by group-II. Conclusion: From the study, it is concluded that SP and GP diseases are highly prevalent; hence, effective vaccines, proper education to farmers through extension activity, and transboundary disease movement restriction are necessary for the control and eradication of the disease.

Genetic characterization and comparative genomics of a multi drug resistant (MDR) Escherichia coli SCM-21 isolated from a subclinical case of bovine mastitis.

Escherichia coli is one of the major pathogens causing mastitis that adversely affects the dairy industry worldwide. This study employed whole genome sequence (WGS) approach to characterize the repertoire of antibiotic resistance genes (resistome), virulence genes (virulome), phylogenetic relationship and genome wide comparison of a multi drug resistant (MDR) E. coli(SCM-21) isolated from a case of subclinical bovine mastitis in Bangalore, India. The genome of E. coli SCM- 21 was found to be of 4.29 Mb size with 50.6% GC content, comprising a resistome of 22 genes encoding beta-lactamases (blaTEM,blaAmpC), polymyxin resistance (arnA) and various efflux pumps (acr, ade, emr,rob, mac, mar, rob), attributing to the bacteria's overall antibiotic resistance genetic profile. The virulome of E. coli SCM-21 consisted of genes encoding different traits [adhesion (ecp, fim, fde), biofilm formation (csg) and toxin production (ent, esp, fep, gsp)], necessary for manifestation of the infection. Phylogenetic relationship of E. coli SCM- 21 with other global E. coli strains (n = 4867) revealed its close genetic relatedness with E. coli strains originating from different hosts of varied geographical regions [human (Germany) bos taurus (USA, Belgium and Scotland) and chicken (China)]. Further, genome wide comparative analysis with E. coli (n = 6) from human and other animal origins showed synteny across the genomes. Overall findings of this study provided a comprehensive insight of the hidden genetic determinants/power of E. coli SCM-21 that might be responsible for manifestation of mastitis and failure of antibiotic treatment. Aforesaid strain forms a reservoir of antibiotic resistance genes (ARGs) and can integrate to one health micro biosphere.

Countrywide cross-sectional study of swine brucellosis sero-prevalence in Indian subcontinent during 2018-2019.

Brucellosis in swine is a contagious disease with greater zoonotic potential caused by Brucella suis. The study describes PAN India swine brucellosis sero-prevalence in 5431 stratified random serum samples collected during 2018-2019 from 26 out of 29 states and two out of seven union territories. The serum samples were tested for anti-Brucella antibodies by indirect ELISA and overall, 4.33% apparent prevalence (AP) was recorded. The AP is ≥ 10% in five states among 26 states, P ≥ 50% in four districts out of 117 districts screened and cent percent prevalence in two epi units out of 264 sampled. Significantly high seropositivity (p < 0.05) in male (6.08%) than female pigs (3.46%) and in ≥ 24-month-old pigs indicated older and male pigs as potential carriers of the disease. The study recorded endemicity of the swine brucellosis in few regions of India requiring periodical surveillance for control of the disease. Brucella testing of boars before breeding and awareness among farmers and veterinarians will aid in reduction of disease burden in the absence of vaccination policy.

Whole genome global insight of antibiotic resistance gene repertoire and virulome of high - risk multidrug-resistant Uropathogenic Escherichiacoli.

Elucidation of genetic determinants via whole genome sequence (WGS) analyses can help understand the high risk multidrug-resistant (MDR) Uropathogenic Escherichia coli (UPEC) associated with urinary tract infections (UTI) and its evasion strategies from treatment. We investigated the WGS of 30 UPEC strains from UTI samples across the world (2016-2019) and found 25 UPEC strains carrying 2-23 antibiotic resistance genes (ARGs) scattered across 1-3 plasmids per strain. Different ARGs (blaTEM, blaCTXM, blaNDM, blaOXA, blaCMY) encoding extended-spectrum beta-lactamases (TEM, CTXM, CMY) and carbapenemases (NDM, OXA) were found in 24/30, ARGs encoding aminoglycoside modifying enzymes (AAC, APH, AAD) variants in 23/30, trimethoprim ARGs (dfrA17, dfrA12, dfrA5, dfrB4 variants) encoding dihydrofolate reductase in 19/30 and sulfonamide ARGs (sul1, sul2, sul3) encoding dihydropteroate synthase and macrolide ARGs (mph1) encoding macrolide 2' phosphotransferase in 15/30 UPEC strains. Collectively the ARGs were distributed in different combinations in 40 plasmids across UPEC strains with 20 plasmids displaying co-occurrence of multiple ARGs conferring resistance to beta lactam, aminoglycoside, sulfonamide, trimethoprim and macrolide antibiotics. These resistance plasmids belonged to seven incompatibility groups (IncF, IncI, IncC, IncH, IncN, IncB and Col), with IncFI and IncFII being the predominant resistance plasmids. Additionally, we observed co-occurrence of specific mutation pattern in quinolone resistance determining region (QRDR) viz., DNA gyrase (gyrA: S83L, D87N), and topoisomerase IV (parC: S80I, E84V; parE: I529L) in 18/30 strains. The strains also harbored diverse virulence genes, such as fimH, gad, iss, iha, ireA, iroN, cnf1 and san. Multilocus sequence typing (MLST) reconfirmed ST131(n = 10) as the predominant global high-risk clonal strain causing UTI. In summary, our findings contribute to better understand the plasmid mediated ARGs and its encoded enzymes that may contribute in antibiotic inactivation/modification or alteration in the antibiotic target site in high risk MDR hypervirulent UPEC strains causing UTI. The study reinforces the need to characterize and design appropriate inhibitors to counterattack different enzymes and devise strategies to curtail resistance plasmid.

Analysis of codon usage bias of classical swine fever virus.

BACKGROUND AND AIM: Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5' and 3' end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment. This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern. MATERIALS AND METHODS: The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern. RESULTS: The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias. CONCLUSION: The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India.

Comparative evaluation of the immunodominant proteins of Brucella abortus for the diagnosis of cattle brucellosis.

BACKGROUND AND AIM: The present serodiagnosis of brucellosis in livestock is based on the whole cell or smooth lipopolysaccharide of the Brucella organism in which specificity is hampered by the cross-reactivity, especially with the antibodies against Yersinia enterocolitica O:9 organism. The problem can be addressed by screening for better immunodominant antigens. Hence, the present study was undertaken to screen protein antigens of Brucella abortus for their diagnostic potential in cattle brucellosis. MATERIALS AND METHODS: Protein antigens of B. abortus (n=10) non-reactive to antibodies against Y. enterocolitica O:9 were selected, expressed in Escherichia coli, assessed the reactivity of expressed recombinant proteins by Western blot, standardized indirect-enzyme-linked immunosorbent assay (ELISA) for detecting Brucella antibodies in cattle serum, and comparative evaluation was done. RESULTS: All the selected protein antigens were expressed and in the Western blot with Brucella antibodies positive cattle serum, six recombinant (Brucella protein 26 [BP26], Cu-Zn Superoxide dismutase [SodC], B. abortus I-1885, Serine protease, Bacterioferritin, and Brucella Lumazine Synthase [BLS]) proteins showed reaction whereas none of the proteins showed reactivity with Brucella negative cattle serum. ELISA has been done using known Brucella positive and negative cattle sera samples (n=113 each) in which the performance of recombinant proteins in diagnosing brucellosis was in the order of BP26 > BLS > SodC followed by rest of the proteins. BP26 based ELISA was found to be better with area under the curve as 0.953, and diagnostic sensitivity, diagnostic specificity, and Youden's index of 90.27%, 95.58%, and 0.8584, respectively, with the excellent agreement (k=0.85). CONCLUSION: BP26 could be a potential diagnostic antigen among the immunodominant proteins of B. abortus in ruling out Y. enterocolitica O:9 infection while diagnosing brucellosis in cattle herds.