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

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

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

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.</p

Prevalence and antibiotic susceptibility of Mannheimia haemolytica and Pasteurella multocida isolated from ovine respiratory infection: A study from Karnataka, Southern India

Background and Aim: Respiratory infection due to Mannheimia haemolytica and Pasteurella multocida are responsible for huge economic losses in livestock sector globally and it is poorly understood in ovine population. The study aimed to investigate and characterize M. haemolytica and P. multocida from infected and healthy sheep to rule out the involvement of these bacteria in the disease. Materials and Methods: A total of 374 healthy and infected sheep samples were processed for isolation, direct detection by multiplex PCR (mPCR), and antibiotic susceptibility testing by phenotypic and genotypic methods. Results: Overall, 55 Pasteurella isolates (27 [7.2%] M. haemolytica and 28 [7.4%] P. multocida) were recovered and identified by bacteriological tests and species-specific PCR assays. Significant correlation between the detection of M. haemolytica (66.6%) with disease condition and P. multocida (19.1%) exclusively from infected sheep was recorded by mPCR. In vitro antibiotic susceptibility testing of 55 isolates revealed higher multidrug resistance in M. haemolytica (25.9%) than P. multocida (7.1%) isolates. Descending resistance towards penicillin (63.6%), oxytetracycline (23.6%), streptomycin (14.5%), and gentamicin (12.7%) and absolute sensitivity towards chloramphenicol were observed in both the pathogens. The antibiotic resistance genes such as strA (32.7%) and sul2 (32.7%) associated with streptomycin and sulfonamide resistance, respectively, were detected in the isolates. Conclusion: The study revealed the significant involvement of M. haemolytica together with P. multocida in ovine respiratory infection and is probably responsible for frequent disease outbreaks even after vaccination against hemorrhagic septicemia in sheep population of Karnataka, southern province of India

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

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

Analyses of Extended-Spectrum-β-Lactamase, Metallo-β-Lactamase, and AmpC-β-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 β-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 β-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 β-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 β-lactamase producers among identified Enterobacteriaceae. This study highlights the presence of various prevalent β-lactamase genes in milk isolates, indicating the potential risk of antimicrobial-resistant bacteria in dairy products. The presence of β-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 β-lactam resistance

Temporal and Spatial Epidemiological Analysis of Peste Des Petits Ruminants Outbreaks from the Past 25 Years in Sheep and Goats and Its Control in India

This study was aimed to understand the temporal and spatial epidemiology of peste des petits ruminants (PPR) in India using national surveillance data available in the National Animal Diseases Referral Expert System (NADRES) along with its control plan undertaken. On analysis of the outbreaks/cases reports in sheep and goats in NADRES database from 1995 to 2019, it was observed that PPR features among the top ten diseases and stands first among viral diseases, and among reported deaths, PPR accounts for 36% of mortality in sheep and goats. PPR outbreaks occur round the year in all the seasons but are encountered most frequently during the lean period especially, in the winter season (January to February) in different regions/zones. The reported outbreaks have been progressively declined in most of the states in India due to the implementation of a mass vaccination strategic program since 2011. On state-wise analysis, the PPR risk-areas showed wide variations with different levels of endemicity. Andhra Pradesh, West Bengal, and Karnataka were the top three outbreaks reported states during 1995–2010, whereas Jharkhand and West Bengal states reported more outbreaks during 2011–2015 and 2016–2019 periods. The temporal and spatial distribution of PPR in India provides valuable information on the hotspot areas/zones to take appropriate policy decisions towards its prevention and control in different regions/zones of India. The study also identifies when and where intensive surveillance and vaccination along with biosecurity measures need to be implemented for the control and eradication of the disease from India in consonance with the PPR Global Control and Eradication Strategy