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.

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 bla 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.

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.

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.

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