Validation of a real-time polymerase chain reaction for the detection and quantification of the nucleic acid of Histoplasma from equine clinical samples.

Histoplasma capsulatum var. farciminosum (HCF) is a dimorphic fungus that causes epizootic lymphangitis in equids. Current diagnostic approaches, including culture, microscopy, and clinical presentation, lack speed, sensitivity, and specificity when diagnosing clinical cases. In this study, equine blood and pus samples on Whatman FTA cards from Senegal (n = 3), The Gambia (n = 19), Ethiopia (n = 16), and Mali (n = 13) were tested using a real-time PCR (qPCR) protocol. The assay was optimized and tested for its suitability to detect and quantify HCF in blood and pus loaded onto Whatman FTA cards at sampling. Whatman FTA cards were tested for their suitability for use with qPCR and were found to recover DNA more efficiently than from direct extraction. Using TaqMan fluorescent probes and specific primers, the assay demonstrated 100% analytical specificity when detecting multiple strains of Histoplasma and no false positives with off-target organisms. The assay's diagnostic performance was measured against an existing nested internal transcribed spacer PCR protocol using a receiver operating characteristic curve. The test was found to have a diagnostic specificity and sensitivity of 100% and 71.4%, respectively, when analyzing pus samples using a cycle threshold (Ct) cutoff determined by Youden's index (27.75). Blood sample cutoff Ct value was proposed at 34.55. Further optimization is required to improve the performance of the protocol when applied to blood samples. This study has, for the first time, demonstrated the ability to detect and quantify the DNA of Histoplasma spp. in equine blood and pus samples with a high degree of accuracy, providing a platform to further investigate the pathogenesis and epidemiology of this disease. IMPORTANCE: Histoplasmosis is a neglected yet major cause of morbidity and mortality in both equids and people in resource-scarce settings. One of the major hindrances to the control of histoplasmosis is a lack of readily available diagnostic tests. Tests are needed to support clinical decision-making and to be applied in population-based research to further understand this disease in situ. This paper reports, for the first time, the validation and application of a qPCR to detect Histoplasma directly from equine clinical samples, bypassing the need to culture this notoriously difficult organism. We report and comment on the performance of the qPCR in comparison with our previously developed nested PCR.

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.

Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer.

Autonomous replication and segregation of mitochondrial DNA (mtDNA) creates the potential for evolutionary conflict driven by emergence of haplotypes under positive selection for 'selfish' traits, such as replicative advantage. However, few cases of this phenomenon arising within natural populations have been described. Here, we survey the frequency of mtDNA horizontal transfer within the canine transmissible venereal tumour (CTVT), a contagious cancer clone that occasionally acquires mtDNA from its hosts. Remarkably, one canine mtDNA haplotype, A1d1a, has repeatedly and recently colonised CTVT cells, recurrently replacing incumbent CTVT haplotypes. An A1d1a control region polymorphism predicted to influence transcription is fixed in the products of an A1d1a recombination event and occurs somatically on other CTVT mtDNA backgrounds. We present a model whereby 'selfish' positive selection acting on a regulatory variant drives repeated fixation of A1d1a within CTVT cells.

PPR Control in a Sahelian Setting: What Vaccination Strategy for Mauritania?

Peste des Petits Ruminants (PPR) is a viral disease affecting domestic and small wild ruminants. Endemic in large parts of the world, PPR causes severe damages to animal production and household economies. In 2015, FAO and OIE launched a global eradication program (GCSE) based on vaccination campaigns. The success of GCSE shall depend on the implementation of vaccination campaigns, accounting for husbandry practices, mobility and the periodicity of small ruminants' population renewal. In Mauritania, PPR outbreaks occur annually despite ongoing annual vaccination campaigns since 2008. Here, we developed a mathematical model to assess the impact of four vaccination strategies (including the GSCE one), the importance of their timing of implementation and the usefulness of individual animal identification on the reduction of PPR burden. The model was calibrated on data collected through ad-hoc surveys about demographic dynamics, disease impact, and national seroprevalence using Monte Carlo Markov Chain procedure. Numerical simulations were used to estimate the number of averted deaths over the next 12 years. The model results showed that the GSCE strategy prevented the largest number of deaths (9.2 million vs. 6.2 for random strategy) and provided one of the highest economic returns among all strategies (Benefit-Cost Ratio around 16 vs. 7 for random strategy). According to its current cost, identification would be a viable investment that could reduce the number of vaccine doses to distribute by 20-60%. Whilst the implementation of the identification system is crucial for PPR control, its success depends also on a coordinated approach at the regional level.

Somatic evolution and global expansion of an ancient transmissible cancer lineage.

The canine transmissible venereal tumor (CTVT) is a cancer lineage that arose several millennia ago and survives by "metastasizing" between hosts through cell transfer. The somatic mutations in this cancer record its phylogeography and evolutionary history. We constructed a time-resolved phylogeny from 546 CTVT exomes and describe the lineage's worldwide expansion. Examining variation in mutational exposure, we identify a highly context-specific mutational process that operated early in the cancer's evolution but subsequently vanished, correlate ultraviolet-light mutagenesis with tumor latitude, and describe tumors with heritable hyperactivity of an endogenous mutational process. CTVT displays little evidence of ongoing positive selection, and negative selection is detectable only in essential genes. We illustrate how long-lived clonal organisms capture changing mutagenic environments, and reveal that neutral genetic drift is the dominant feature of long-term cancer evolution.

Molecular Characterization of Escherichia coli Isolated from Chickens with Colibacillosis in Senegal.

Avian pathogenic Escherichia coli (APEC), a subset of extraintestinal pathogenic E. coli (ExPEC), are the etiologic agent of avian colibacillosis, one of the main causes of economic losses in the poultry industry. The aim of this study was to characterize E. coli isolated from diseased chickens in Senegal to elucidate their virulence potential and antimicrobial resistance (AMR). A total of 58 isolates, each from a separate farm, were characterized for AMR, virulence, and AMR genes, phylogroup, serogroup, biofilm formation, and pulsed-field gel electrophoresis, and for two isolates, whole-genome sequencing (WGS). Fifty isolates (86.2%) were multidrug resistant. Many AMR genes were detected, including variants of blaCTX-M encoding resistance to third-generation cephalosporins (five isolates [8.6%]). Most fluoroquinolone-nonsusceptible isolates (21/26) were carriers of mutations in gyrA (Ser83Leu, Asp87Asn, and/or Asp87Tyr) and/or parC (Ser80Ile) genes. Forty-nine (84.5%) isolates exhibited at least one of the virulence markers of APEC, among which 23 (39.7%) were defined as potential virulent APEC. In addition, 10 isolates, of which 9 were defined as APEC, carried virulence profiles corresponding to ExPEC. Seven isolates, of which six were classified as ExPEC, belonged to phylo-serogroup F-O25, and following WGS of two of these isolates, were found to belong to the serotype O25:H1 and to the sequence type ST624. Some isolates classified as ExPEC, including F-O25, were found to strongly produce biofilm, suggesting their capability to persist for long time in the environment. F-O25-isolates, although found in different widely separated farms, formed a single cluster that included clones, suggesting that these isolates may have originated from a common source. Taken together, these results suggest that some E. coli involved in chicken colibacillosis in Senegal may pose a human health risk.

Effects of an experimental Trypanosoma congolense infection on the reproductive performance of West African Dwarf goats.

Thirty-six West African Dwarf (WAD) goats were used to assess the effects of an experimental Trypanosoma congolense infection on their reproductive system. Estrous cycles were synchronised and when confirmed pregnant (n = 31), the does were randomly allocated into control and trypanosome-infected groups. After infection, the animals were carefully observed till parturition. Trypanosome infection caused an increase of rectal temperature, a significant drop in PCV (infected: 23.3 +/- 0.3%; control: 28.5 +/- 0.4%; P < 0.0001) and abortions in 27.8% of the infected does. Kids born from infected does had a lower birth weight than kids born from control goats (0.9 +/- 0.1 kg versus 1.6 +/- 0.1 kg; P < 0.0001). Eight out of 13 kids (61.5%) that were born alive from infected does died during their first week of life. Plasma pregnancy-associated glycoprotein (PAG) and progesterone concentrations were lower in the infected animals than in the controls. In general, PAG concentration in does which aborted dropped before abortion. Our results revealed that artificial T. congolense infection affected reproductive performance of WAD goats with abortions, premature births and perinatal losses being observed. Neither transplacental transmission of T. congolense nor histopathological lesions of the placenta could be demonstrated.