The application of epidemiology in national veterinary services: Challenges and threats in Brazil

Evolution and genomic profile of Salmonella enterica serovar Gallinarum biovar Pullorum isolates from Brazil

Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum (S. Pullorum) is a pathogenic bacterium that causes Pullorum disease (PD). PD is an acute systemic disease that affects young chickens, causing white diarrhea and high mortality. Although many sanitary programs have been carried out to eradicate S. Pullorum, PD outbreaks have been reported in different types of birds (layers, broilers, breeders) worldwide. This study aimed to evaluate the evolution and genetic characteristics of S. Pullorum isolated from PD in Brazil. Phylogenetic analysis of S. Pullorum genomes sequenced in this study and available genomic databases demonstrated that all isolates from Brazil are from sequence type 92 (ST92) and cluster into two lineages (III and IV). ColpVC, IncFIC(FII), and IncFII(S) were plasmid replicons frequently found in the Brazilian lineages. Two resistance genes (aac(6')-Iaa, conferring resistance to aminoglycoside, disinfecting agents, and antiseptics (mdf(A)) and tetracycline (mdf(A)) were detected frequently. Altogether, these results are important to understand the circulation of S. Pullorum and, consequently, to develop strategies to reduce losses due to PD.

Evolution and Epidemic Spread of the Avian Infectious Bronchitis Virus (IBV) GI-23 in Brazil

Infectious bronchitis virus (IBV) is a pathogen affecting poultry flocks worldwide. GI-23 is an IBV lineage with a rapid spread into different continents of the world, and it was reported for the first time in South American/Brazilian broiler farms last year. This study aimed to investigate the recent introduction and epidemic spread of IBV GI-23 in Brazil. Ninety-four broiler flocks infected with this lineage were evaluated from October 2021 to January 2023. IBV GI-23 was detected using real-time RT-qPCR, and the S1 gene hypervariable regions 1 and 2 (HVR1/2) were sequenced. S1 complete and HVR1/2 nucleotide sequence datasets were used to carry out phylogenetic and phylodynamic analyses. Brazilian IBV GI-23 strains clustered into two specific subclades (SA.1 and SA.2), both in tree branches with IBV GI-23 from Eastern European poultry-producing countries, suggesting two independent and recent introductions (around 2018). Viral phylodynamic analysis showed that the IBV GI-23 population increased from 2020 to 2021, remaining constant for one year and declining in 2022. S1 amino acid sequences from Brazilian IBV GI-23 presented specific and characteristic substitutions in the HVR1/2 for subclades IBV GI-23 SA.1 and SA.2. This study brings new insights into the introduction and recent epidemiology of IBV GI-23 in Brazil.

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.

Assessment of the foot-and-mouth disease surveillance system in Brazil

In 2021, the 88th General Session of the World Assembly of National Delegates to the World Organisation for Animal Health (OIE) recognized the estates of Acre, Paraná, the Rio Grande do Sul, and Rondônia as being free of foot-and-mouth disease (FMD) without vaccination. The certification was also extended to some cities in Amazonas and Mato Grosso. The new national strategic plan for 2026, which focuses on creating and maintaining sustainable conditions to expand FMD-free zones without vaccination, imposes new challenges and requires continuous evaluation of the FMD surveillance system. The objective of this research was to evaluate the FMD surveillance system in Brazil using quantitative models through Bayesian network approaches. The research was conducted using the Continental Surveillance and Information System (SivCont) database for Official Veterinary Services in Brazil, which refers to notified vesicular syndromes. The data on states, reported diseases, source of notification, disease confirmation, and timeliness (TL in days) of the delay by owners in notifying (TL.1) after a suspected case of the disease, and the response of Brazilian Veterinary Services after being notified (TL.2), were analysed. The collected data were analysed using Bayesian networks. It was observed that diseases with symptoms identical to FMD are the most notified events. TL.1 was long (mean of 18.96, CI: 18.33-19.59), and a low number of notifications was observed throughout the study period, which increases the chances of disseminating FMD in the population. Meanwhile, TL.2 suggests appropriate effectiveness of the Veterinary Services responding to suspected cases of FMD with interventions in less than 24 h (mean of 1, CI: 0.68-1.31). This study evaluated the performance of Brazilian Veterinary Services facing the report of vesicular diseases in the period 2004-2018. The results can help the states improve the surveillance system and the transition to the vaccination stop. Furthermore, the analytical method presented in the paper could serve as a model for other countries to evaluate the effectiveness of FMD surveillance systems.

Evaluation of diagnostic tests' sensitivity, specificity and predictive values in bovine carcasses showing brucellosis suggestive lesions, condemned by Brazilian Federal Meat Inspection Service in the Amazon Region of Brazil

Cervical bursitis is a suggestive lesion of bovine brucellosis. Diagnostic sensitivity and specificity of two brucellosis serological tests, Rose Bengal (RB) and serum agglutination test with 2-mercaptoethanol (SAT/2-ME), and of isolation and identification (bacteriology) were evaluated through Bayesian latent class analysis (BLCA). A total of 165 paired serum and cervical bursitis samples detected at inspection by Brazilian federal meat inspection services were analyzed. The best model fit to the data occurred when accounting for the conditional dependence between serological tests. According to this model, RB and SAT/2-ME had almost the same sensitivity, 0.960 [0.903 - 0.992] and 0.963 [0.906 - 0.994] with 95 % Credible Interval (95 %CrI), respectively. Specificities were 0.9068 [0.562 - 0.997] and 0.875 [0.546 - 0.990] for RB and SAT/2-ME, respectively, also with 95 %CrI. Bacteriology had lower sensitivity than serological tests, 0.594 (95 %CrI: [0.525 - 0.794]) and the highest specificity of all evaluated tests, 0.992 (95 %CrI: [0.961-1.00]). Prevalence of infected animals was 0.829 (95 %CrI: [0.700-0.900]). BLCA showed that both RB and SAT/2-ME fitted to the purpose of initial screening the brucellosis suspect in carcasses with cervical bursitis in a reliable way. The results of RB or SAT/2-ME can guide the sanitary actions for brucellosis control and help the implementation of a risk-based surveillance system in the meat production chain. This strategy is especially true in remote areas with large beef cattle herds, raised extensively, where in vivo tests are rarely performed due to logistic and management constraints, as in the Northern region of Brazil.

Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil

Salmonella enterica serovar Heidelberg is isolated from poultry-producing regions around the world. In Brazil, S. Heidelberg has been frequently detected in poultry flocks, slaughterhouses, and chicken meat. The goal of the present study was to assess the population structure, recent temporal evolution, and some important genetic characteristics of S. Heidelberg isolated from Brazilian poultry farms. Phylogenetic analysis of 68 S. Heidelberg genomes sequenced here and additional whole-genome data from NCBI demonstrated that all isolates from the Brazilian poultry production chain clustered into a monophyletic group, here called S. Heidelberg Brazilian poultry lineage (SH-BPL). Bayesian analysis defined the time of the most recent common ancestor (tMRCA) as 2004, and the overall population size (N_e) was constant until 2008, when an ∼10-fold N_e increase was observed until circa 2013. SH-BPL presented at least two plasmids with replicons ColpVC (n = 68; 100%), IncX1 (n = 66; 97%), IncA/C2 (n = 65; 95.5%), ColRNAI (n = 43; 63.2%), IncI1 (n = 32; 47%), ColMG828, Col156, IncHI2A, IncHI2, IncQ1, IncX4, IncY, and TrfA (each with n < 4; <4% each). Antibiotic resistance genes were found, with high frequencies of fosA7 (n = 68; 100%), mdf(A) (n = 68; 100%), tet(34) (n = 68; 100%), sul2 (n = 64; 94.1%), and blaCMY-2 (n = 56; 82.3%), along with an overall multidrug resistance (MDR) profile. Ten Salmonella pathogenicity islands (SPI1 to SPI5, SPI9, and SPI11 to SPI14) and 139 virulence genes were also detected. The SH-BPL profile was like those of other previous S. Heidelberg isolates from poultry around the world in the 1990s. In conclusion, the present study demonstrates the recent introduction (2004) and high level of dissemination of an MDR S. Heidelberg lineage in Brazilian poultry operations. IMPORTANCE S. Heidelberg is the most frequent serovar in several broiler farms from the main Brazilian poultry-producing regions. Therefore, avian-source foods (mainly chicken carcasses) commercialized in the country and exported to other continents are contaminated with this foodborne pathogen, generating several national and international economic losses. In addition, isolates of this serovar are usually resistant to antibiotics and can cause human invasive and septicemic infection, representing a public health concern. This study demonstrates the use of whole-genome sequencing (WGS) to obtain epidemiological information for one S. Heidelberg lineage highly spread among Brazilian poultry farms. This information will help to define biosecurity measures to control this important Salmonella serovar in Brazilian and worldwide poultry operations.

Use of Network Analysis and Spread Models to Target Control Actions for Bovine Tuberculosis in a State from Brazil

Livestock movements create complex dynamic interactions among premises that can be represented, interpreted, and used for epidemiological purposes. These movements are a very important part of the production chain but may also contribute to the spread of infectious diseases through the transfer of infected animals over large distances. Social network analysis (SNA) can be used to characterize cattle trade patterns and to identify highly connected premises that may act as hubs in the movement network, which could be subjected to targeted control measures in order to reduce the transmission of communicable diseases such as bovine tuberculosis (TB). Here, we analyzed data on cattle movement and slaughterhouse surveillance for detection of TB-like lesions (TLL) over the 2016-2018 period in the state of Rio Grande do Sul (RS) in Brazil with the following aims: (i) to characterize cattle trade describing the static full, yearly, and monthly snapshots of the network contact trade, (ii) to identify clusters in the space and contact networks of premises from which animals with TLL originated, and (iii) to evaluate the potential of targeted control actions to decrease TB spread in the cattle population of RS using a stochastic metapopulation disease transmission model that simulated within-farm and between-farm disease spread. We found heterogeneous densities of premises and animals in the study area. The analysis of the contact network revealed a highly connected (~94%) trade network, with strong temporal trends, especially for May and November. The TLL cases were significantly clustered in space and in the contact network, suggesting the potential for both local (e.g., fence-to-fence) and movement-mediated TB transmission. According to the disease spread model, removing the top 7% connected farms based on degree and betweenness could reduce the total number of infected farms over three years by >50%. In conclusion, the characterization of the cattle network suggests that highly connected farms may play a role in TB dissemination, although being close to infected farms was also identified as a risk factor for having animals with TLL. Surveillance and control actions based on degree and betweenness could be useful to break the transmission cycle between premises in RS.

Genomic Characterization of Salmonella Minnesota Clonal Lineages Associated with Poultry Production in Brazil

Salmonella serotype Minnesota has been increasingly detected in Brazilian poultry farms and food products (chicken meat, eggs) in recent years. In addition, S. Minnesota isolates from poultry are generally resistant to several antibiotics and persistent in farm environments. The present study aimed to assess phylogenomic diversity of S. Minnesota isolates from the poultry production chain in Brazil. In total, 107 worldwide S. Minnesota whole genomes (including 12 from Brazil) were analyzed using a comparative approach. Phylogenetic analysis demonstrated two clades more related to poultry production in Brazil: S. Minnesota poultry lineages I and II (SM-PLI and SM-PLII). Phylodynamic analysis demonstrated that SM-PLI had a common ancestor in 1915, while SM-PLII originated circa 1971. SM-PLII encompassed a higher number of isolates and presented a recent increase in effective population size (mainly from 2009 to 2012). Plasmids IncA/C2 and ColRNA, antimicrobial resistance genes (aph(3')-Ia, blaCMY-2, qnrB19, sul2, and tet(A)) and mainly a virulence genetic cluster (including the yersiniabactin operon) were detected in isolates from SM-PLI and/or SM-PLII. This study demonstrates the dissemination of two distinct S. Minnesota lineages with high resistance to antibiotics and important virulence genetic clusters in Brazilian poultry farms.

Timeliness of vesicular disease notification system in Brazilian foot-and-mouth disease surveillance programme

Animal health surveillance programmes should be reliable and informative to ensure their effective implementation. As such, the regular assessment of those aiming to demonstrate the absence of disease, as well as the ability to detect outbreaks on time, is of vital importance. Several criteria make it possible to assess the performance of surveillance systems, including timeliness, which represents the speed between steps in a surveillance system. Therefore, the objective of this study was to evaluate the variability in the timeliness, within and between states, of the surveillance programme of the Brazilian Veterinary Services (BVS) for foot-and-mouth disease (FMD), for the notification of vesicular disease. A total of 14 years (2004-2017) of data relating to vesicular syndromes from the Brazilian Continental Information and Surveillance System (SivCont) were included. A categorical variable was created with four classes to group the notified vesicular processes in the SivCont, according to two criteria, the similarity of the symptoms of the diseases reported with FMD and aetiology (viral, bacterial, fungal and non-infectious). The three timeliness values (TL-1, TL-2 and TL-3) related to different portions of the FMD surveillance system were analysed as a response in a generalized linear model in which the states of Brazil were the explanatory variables. The analyses were performed separately for each notification class (FMD, vesicular stomatitis, similar symptoms and similar non-infectious symptoms) and included comparisons within and between states. The study results provide an understanding and evaluation of the timeliness of the Brazilian FMD surveillance system, thereby providing a base of knowledge from which involved agents and decision-makers can evaluate BVS and reinforce surveillance measures in the states with poorer timeliness than permitted.

A Proposed New Strain of Avian Picornavirus in Broiler Chicken from Brazil

A new strain of avian picornavirus was identified in fecal samples from broiler chickens in a commercial farm in the municipality of Benevides, Pará, Brazil. Genomic analysis showed it to have a nucleotide identity of 78.4% with the family Picornaviridae, genus Avisivirus, and species Avisivirus A, suggesting that this is a possible new strain within this species.

Molecular and phylogenetic analyses of Salmonella Gallinarum trace the origin and diversification of recent outbreaks of fowl typhoid in poultry farms

Fowl typhoid (FT) and pullorum disease (PD) are two important poultry infections caused by Salmonella enterica subsp. enterica serotype Gallinarum (S. Gallinarum). S. Gallinarum strains are adapted to birds and classified into biovars Gallinarum (bvGA) and Pullorum (bvPU) as they are the causative agent of FT and PD, respectively. In Brazil, FT/PD outbreaks have been reported along the last 50 years, but there was a recent increase of FT field reports with the suspicion it could be due to virulence reversion of the attenuated live vaccine SG9R. In this study, we applied molecular biology assays and phylogenetic methods to detect and investigate S. Gallinarum isolates from commercial poultry flocks in order to understand the evolutionary history and origin of the recent FT outbreaks in Brazil. S. Gallinarum isolates were obtained from thirteen different poultry flocks with clinical signs of FT/PD from 2013 to 2015. These isolates were serotyped, tested with three specific PCR (for the detection of bvGA, bvPU and live vaccine strain SG9R) and submitted to sequencing of a variable genome region (ISR analysis). The complete genome of one bvGA strain (BR_RS12) was also compared to other S. Gallinarum complete genomes (including other two Brazilian ones: bvGA 287/91 and bvPU FCVA198). PCR detected all thirteen isolates as S. Gallinarum (eight bvGA and five bvPU), none positive for SG9R strain. ISR analysis revealed that all eight bvGA isolates showed exactly the same nucleotide sequences with 100% similarity to reference strains, while two patterns were observed for bvPU. Genome phylogeny demonstrated distinct clades for bvGA and bvPU, with the bvGA clade showing a clear subdivision including three genomes: SG9R vaccine, the respective SG9 parent strain and one SG9R revertant field isolate (MB4523). The evolutionary rate of the total S. Gallinarum genome was calculated at 6.15×10^-7 substitutions/site/year, with 2.8 observed substitutions per year per genome (1 SNP per 4292 bases). Phylodynamics analysis estimated that at least two introductions of S. Gallinarum bvGA happened in Brazil, the first in 1885 and the second in 1950. The Brazilian bvGA genomes 287/91 and BR_RS12 analyzed here were related to the early and the late introductions, respectively. In conclusion, these results indicate the occurrence of S. Gallinarum strains associated with FT outbreaks that have been circulating for more than 50 years in Brazil and are not originated from virulence reversion of the SG9R vaccine.