Development of core competencies for field veterinary epidemiology training programs.

A workforce with the adequate field epidemiology knowledge, skills and abilities is the foundation of a strong and effective animal health system. Field epidemiology training is conducted in several countries to meet the increased global demand for such a workforce. However, core competencies for field veterinary epidemiology have not been identified and agreed upon globally, leading to the development of different training curricula. Having a set of agreed core competencies can harmonize field veterinary epidemiology training. The Food and Agriculture Organization of the United Nations (FAO) initiated a collective, iterative, and participative process to achieve this and organized two expert consultative workshops in 2018 to develop core competencies for field veterinary epidemiology at the frontline and intermediate levels. Based on these expert discussions, 13 competencies were identified for the frontline and intermediate levels. These competencies were organized into three domains: epidemiological surveillance and studies; field investigation, preparedness and response; and One Health, communication, ethics and professionalism. These competencies can be used to facilitate the development of field epidemiology training curricula for veterinarians, adapted to country training needs, or customized for training other close disciplines. The competencies can also be useful for mentors and employers to monitor and evaluate the progress of their mentees, or to guide the selection process during the recruitment of new staff.

Investigation of Campylobacter fetus in breeding bulls of private farms in Bangladesh.

BACKGROUND: Bovine genital campylobacteriosis (BGC) is a venereal disease caused by Campylobacter fetus that has a negative impact on animal reproduction. The bull is considered to be a symptomless carrier that spreads the disease agent to breeding cows, causing infertility and sporadic abortion. AIM: The study aims to estimate the prevalence, identify risk factors of Campylobacter fetus (C. fetus) infection and antimicrobial resistance pattern of the C. fetus isolates. METHOD: A cross-sectional survey was conducted in Mymensingh district of Bangladesh. Bull smegma samples (single sample from each bull) were collected from 300 bulls from four farms and tested via culture, biochemical identification and finally 16S rRNA and cdtA gene-based molecular assays (PCR) for herd and animal-level prevalence estimation. Herd- and animal-level data on risk factors were collected from the farmers using a pretested questionnaire and analysed by univariable and multivariable logistic regression models with a p value of <0.05 was taken statistically significant for both analyses. RESULTS: Among the surveyed farms, 75% (95% CI: 19.4%-99.4%) were confirmed to have bulls infected with Campylobacter fetus at herd level. However, animal-level occurrence of C. fetus was estimated to be 8.7% (26/300) (95% CI: 5.7%-12.4%). Natural service increases the odds of campylobacteriosis 38.18 times (95% CI: 13.89-104.94) in comparison to artificial insemination for C. fetus infection in bulls. Significantly, half of the isolates (50%, n = 13) were identified to be multidrug resistant (MDR) for three to five antimicrobial agents. CONCLUSION: This study highlights the need to develop official guidelines for C. fetus control and prevention in Bangladesh including mandatory artificial insemination in reproductive cows and heifers, routine screening of breeding bulls for C. fetus free status.

Molecular characterization of new emerging sub-genotype VIIh Newcastle disease viruses in China.

Newcastle disease (ND) has been enzootic in China for several decades since the first recognition of the disease in 1946 in China. Continuous surveillance revealed that the sub-genotype VIId Newcastle disease virus (NDV) has been predominantly responsible for most of ND outbreak in China in recent years. But in the present study, three virulent NDVs isolated from poultry in southern China were classified as sub-genotype VIIh, which is highly related to the viruses circulating in some Southeast Asia countries. Continuous isolation of genotype VIIh NDV strains in the region suggests its panzootic potential. This is the first report of the sub-genotype VIIh NDVs in domestic poultry in China. The complete genome length of the three isolates was 15,192 nucleotides, and the motif at the cleavage site of F protein was 112RRRRR/F117 or 112RRRKR/F117, which was typical of virulent NDV. Phylogenetic analysis based on the F gene revealed that the three viruses had close relationship with the sub-genotype VIIh virus isolated from wild bird in 2011 in China. These viruses might have formed a stable lineage in poultry during 2012-2016 and have the potential to cause enzootic in China. Our study revealed the genetic and phylogenetic characteristics of the three sub-genotype VIIh isolates, which could help us to better understand the epidemiological context of these viruses.

Geographical and Historical Patterns in the Emergences of Novel Highly Pathogenic Avian Influenza (HPAI) H5 and H7 Viruses in Poultry.

Over the years, the emergence of novel H5 and H7 highly pathogenic avian influenza viruses (HPAI) has been taking place through two main mechanisms: first, the conversion of a low pathogenic into a highly pathogenic virus, and second, the reassortment between different genetic segments of low and highly pathogenic viruses already in circulation. We investigated and summarized the literature on emerging HPAI H5 and H7 viruses with the aim of building a spatio-temporal database of all these recorded conversions and reassortments events. We subsequently mapped the spatio-temporal distribution of known emergence events, as well as the species and production systems that they were associated with, the aim being to establish their main characteristics. From 1959 onwards, we identified a total of 39 independent H7 and H5 LPAI to HPAI conversion events. All but two of these events were reported in commercial poultry production systems, and a majority of these events took place in high-income countries. In contrast, a total of 127 reassortments have been reported from 1983 to 2015, which predominantly took place in countries with poultry production systems transitioning from backyard to intensive production systems. Those systems are characterized by several co-circulating viruses, multiple host species, regular contact points in live bird markets, limited biosecurity within value chains, and frequent vaccination campaigns that impose selection pressures for emergence of novel reassortants. We conclude that novel HPAI emergences by these two mechanisms occur in different ecological niches, with different viral, environmental and host associated factors, which has implications in early detection and management and mitigation of the risk of emergence of novel HPAI viruses.

Genomic Characterizations of a Newcastle Disease Virus Isolated from Ducks in Live Bird Markets in China.

One class I Newcastle disease virus (NDV), designated as duck/Guangxi/1261/2015 (GX1261), was isolated from asymptomatic ducks in live bird markets (LBM) from southern China during the national active surveillance for NDVs in 2015. The complete genome length of GX1261 isolate was 15,198 nucleotides with the gene order of 3'-NP-P-M-F-HN-L-5'. The motif at the cleavage site of F protein was 112ERQER/L117, which was typical of low virulence NDV. Several mutations were identified in the functional domains of F and HN proteins, including fusion peptide, heptad repeat region, transmembrane domains and neutralizing epitopes. Phylogenetic analysis based on the complete F gene revealed that the isolate was clustered into sub-genotype 1c in class I, and showed a high level of similarity with the strains isolated from waterfowl in the United States of America. This is the first report of this kind of virus in the mainland of China. These results demonstrated that GX1261-like viruses might exist in asymptomatic waterfowl, and remain undetected or unidentified. Thus, more investigation needs to be done in order to identify the source of the virus. This study revealed the genetic and phylogenetic characteristics of GX1261 isolate and could help us to better understand the epidemiological context of class I NDV in China.

Clade-level Spatial Modelling of HPAI H5N1 Dynamics in the Mekong Region Reveals New Patterns and Associations with Agro-Ecological Factors.

The highly pathogenic avian influenza (HPAI) H5N1 virus has been circulating in Asia since 2003 and diversified into several genetic lineages, or clades. Although the spatial distribution of its outbreaks was extensively studied, differences in clades were never previously taken into account. We developed models to quantify associations over time and space between different HPAI H5N1 viruses from clade 1, 2.3.4 and 2.3.2 and agro-ecological factors. We found that the distribution of clades in the Mekong region from 2004 to 2013 was strongly regionalised, defining specific epidemiological zones, or epizones. Clade 1 became entrenched in the Mekong Delta and was not supplanted by newer clades, in association with a relatively higher presence of domestic ducks. In contrast, two new clades were introduced (2.3.4 and 2.3.2) in northern Viet Nam and were associated with higher chicken density and more intensive chicken production systems. We suggest that differences in poultry production systems in these different epizones may explain these associations, along with differences in introduction pressure from neighbouring countries. The different distribution patterns found at the clade level would not be otherwise apparent through analysis treating all outbreaks equally, which requires improved linking of disease outbreak records and genetic sequence data.

Development and application of a vaccination planning tool for avian influenza.

The vaccination planning tool for avian influenza supports evidence-based planning and preparedness for vaccinating poultry at national and regional levels. This study describes the development, testing, and application of a vaccination planning tool for H5N1 highly pathogenic avian influenza (HPAI) used in two South Asian countries. The tool consists of eight planning clusters, 37 planning elements, and 303 referenced planning criteria. Both countries attained a score of 52% among planning clusters as a measure of preparedness. The highest and lowest planning cluster scores included vaccination strategies and financial readiness, respectively. The comprehensive vaccination program was identified as the most-useful planning cluster for assessing preparedness, and 86% of participants indicated that the objectives of the planning tool were achieved. Based on these results, the planning tool provides a structured approach for decision makers to develop their national vaccination program for HPAI as part of an overall strategy for the progressive reduction and control of endemic influenza viruses in poultry.

Spatio-temporal epidemiology of highly pathogenic avian influenza (subtype H5N1) in poultry in eastern India.

In India, majority outbreaks of highly pathogenic avian influenza (HPAI) H5N1 have occurred in eastern states of West Bengal, Assam and Tripura. This study aimed to identify disease clusters and risk factors of HPAI H5N1 in these states, for targeted surveillance and disease control. A spatial scan statistic identified two significant disease clusters in West Bengal and Assam, occurring during January and November-December 2008, respectively. Key risk factors were identified at sub-district level using bootstrapped logistic regression and boosted regression trees model. With both methods, HPAI H5N1 outbreaks in backyard poultry were associated with accessibility in terms of time taken to access a city with >50,000 persons, human population density and duck density (P<0.005). In addition, areas at lower elevation were also identified as high risk by BRT model. It is recommended that risk-based surveillance should be implemented in high duck density areas and all live-bird markets in high-throughput locations.

Longitudinal monitoring of two commercial layer flocks and their environments for Salmonella enterica serovar enteritidis and other Salmonellae.

Between August 20, 2001, and September 17, 2002, 1429 samples including drag swabs, egg belt or egg rollout swabs, fan-blade swabs, rodent organ and intestinal pools, beetle (Alphitobius diaperinus) pools, housefly (Musca domestica) pools, chicken organ and intestinal pools, and egg pools were obtained for Salmonella culture from two flocks from two different commercial layer ranches. The two ranches were purposefully selected for the study based on their previous status of Salmonella Enteritidis isolation using environmental drag swabs in cooperation with practicing veterinarians. Salmonella sp. was isolated from 337 out of 979 (34.42%) non-egg samples. No Salmonella was isolated from 450 egg pools collected from either ranch. S. enteritidis was isolated from samples obtained from ranch 1 from manure drag swabs, 4/284 (1.4%); rodent organs, 1/24 (4.2%); and housefly pool cultures 1/21 (4.8%). Salmonella Enteritidis was isolated from ranch 2 from mouse organ and intestinal pool samples, 1/24 (4.2%). Salmonella group B was isolated from all sample types except the insects. There was a statistically significant difference in isolation rates among seven serogroups of Salmonella: groups B, C1, C2, D, E, K, and untypeable (Pearson chi-square 18.96, P = 0.002). Overall, statistically significant differences were observed with respect to Salmonella isolation among the types of samples taken (Pearson chi-square 118.54, P < 0.0001). Intensive monitoring for Salmonella Enteritidis can be used to optimize a Salmonella reduction program for an individual poultry biosecurity unit.

Descriptive study of California egg layer premises and analysis of risk factors for Salmonella enterica serotype enteritidis as characterized by manure drag swabs.

This cross-sectional, double-blind study reports the prevalence of Salmonella enterica serotype enteritidis (SE) on California egg layer premises using single vs. pooled manure drag swabs and presents a description of egg production and management systems in the state and an initial analysis of risk factors for SE. The study included 91% of all known eligible egg premises in California, representing the majority of eggs produced in the state. The overall prevalence of SE on California egg layer premises was 10.5%, while 1.1% of all rows sampled were positive for SE. The percentage of positive rows for SE on any premises never exceeded 25% of the 16 swabs collected per premises. A description of egg production and management on California egg layer premises is presented. Statistically significant associations for SE were not evident and were limited because of sample size and the low prevalence of SE on California egg layer premises. Several biological and management factors, such as flock health, stage of production, manure management, ventilation, and watering systems, show trend associations with premises positive for SE and require further investigation. Manure drag swabs serve as a useful tool to validate the core components of an egg quality assurance program for SE based on process control principles.

The occurrence and distribution of Salmonella enteritidis and other serovars on California egg laying premises: a comparison of two sampling methods and two culturing techniques.

Between the summer of 1998 and the winter of 2000, Salmonella analysis was performed on 2128 single and 532 pooled manure drag swabs obtained from 133 California commercial egg laying farms. The isolation of Salmonella from all rows and from all flocks using single or pooled swabs was 80% and 92%, respectively. Hence, there was no statistical difference between single vs. pooled swabs in terms of identifying Salmonella on a row or flock basis. A total of 14 serogroups comprising 44 serotypes were isolated from 123 of 133 farms. When the top 10 serotypes were considered, there was no significant difference in the range of serotypes isolated by the two culturing methods. The overall S. enteritidis prevalence for California flocks was 10.5% (14/133). The overall row prevalence for S. enteritidis for all the farms was 1.1% (24/2128), and the overall pool prevalence was 2.4% (13/532). Sixty percent (12/20) of the S. enteritidis isolates from the positive farms were phage type 4, and 40% (8/20) represented five other phage types (1, 6B, 7, 8, and 28).