[Preprints, 1 December 2022]

Agent-based models (ABMs) are computational models for simulating the actions and interactions of autonomous agents in time and space. These models allow users to simulate the complex interactions between individual agents and the landscapes they inhabit and are increasingly used in epidemiology to understand complex phenomena and make predictions. However, as the complexity of the simulated systems increases, notably when disease control interventions are considered, model flexibility and processing speed can become limiting. Here we introduce SamPy, an open-source Python library for stochastic agent-based modeling of epidemics. SamPy is a modular toolkit for model development, providing adaptable modules that capture host movement, disease dynamics, and disease control interventions. Memory optimization and design provide high computational efficiency allowing modelling of large, spatially-explicit populations of agents over extensive geographical areas. In this article, we demonstrate the high flexibility and processing speed of this new library.

The version of SamPy considered in this paper is available at:

https://github.com/sam...

[Mathematical Biosciences and Engineering, 24 March 2022]

Tick infestation and tick-borne disease spread in a region of multiple adjacent patches with different environmental conditions depend heavily on the host mobility and patch-specific suitability for tick growth. Here we introduce a two-patch model where environmental conditions differ in patches and yield different tick developmental delays, and where feeding adult ticks can be dispersed by the movement of larger mammal hosts. We obtain a coupled system of four delay differential equations with two delays, and we examine how the dynamical behaviours depend on patch-specific basic reproduction numbers and host mobility by using singular perturbation analyses and monotone dynamical systems theory. Our theoretical results and numerical simulations provide useful insights for tick population control strategies.

[Journal of Veterinary Diagnostic Investigation, 27 June 2023]

Surveillance for SARS-CoV-2 in American mink (Neovison vison) is a global priority because outbreaks on mink farms have potential consequences for animal and public health. Surveillance programs often focus on screening natural mortalities; however, significant knowledge gaps remain regarding sampling and testing approaches. Using 76 mink from 3 naturally infected farms in British Columbia, Canada, we compared the performance of 2 reverse-transcription real-time PCR (RT-rtPCR) targets (the envelope [E] and RNA-dependent RNA polymerase [RdRp] genes) as well as serology. We also compared RT-rtPCR and sequencing results from nasopharyngeal, oropharyngeal, skin, and rectal swabs, as well as nasopharyngeal samples collected using swabs and interdental brushes. We found that infected mink were generally RT-rtPCR–positive on all samples; however, Ct values differed significantly among sample types (nasopharyngeal < oropharyngeal < skin < rectal). There was no difference in the results of nasopharyngeal samples collected using swabs or interdental brushes. For most mink (89.4%), qualitative (i.e., positive vs. negative) serology and RT-rtPCR results were concordant. However, mink were positive on RT-rtPCR and negative on serology and vice versa, and there was no significant correlation between Ct values on RT-rtPCR and percent inhibition on serology. Both the E and RdRp targets were detectable in all sample types, albeit with a small difference in Ct values. Although SARS-CoV-2 RNA can be detected in multiple sample types, passive surveillance programs in mink should focus on multiple target RT-rtPCR testing of nasopharyngeal samples in combination with serology.

[eLife, 4 April 2023]

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a generalist virus, infecting and evolving in numerous mammals, including captive and companion animals, free-ranging wildlife, and humans. Transmission among non-human species poses a risk for the establishment of SARS-CoV-2 reservoirs, makes eradication difficult, and provides the virus with opportunities for new evolutionary trajectories, including the selection of adaptive mutations and the emergence of new variant lineages. Here, we use publicly available viral genome sequences and phylogenetic analysis to systematically investigate the transmission of SARS-CoV-2 between human and non-human species and to identify mutations associated with each species. We found the highest frequency of animal-to-human transmission from mink, compared with lower transmission from other sampled species (cat, dog, and deer). Although inferred transmission events could be limited by sampling biases, our results provide a useful baseline for further studies. Using genome-wide association studies, no single nucleotide variants (SNVs) were significantly associated with cats and dogs, potentially due to small sample sizes. However, we identified three SNVs statistically associated with mink and 26 with deer. Of these SNVs, approx ⅔ were plausibly introduced into these animal species from local human populations, while the remaining approx ⅓ were more likely derived in animal populations and are thus top candidates for experimental studies of species-specific adaptation. Together, our results highlight the importance of studying animal-associated SARS-CoV-2 mutations to assess their potential impact on human and animal health.

[Preventive Veterinary Medicine, 30 May 2023]

Antimicrobial resistance (AMR) in animals, including dairy cattle, is a significant concern for animal and public health worldwide. In this study, we used data collected through the Canadian Dairy Network for Antimicrobial Stewardship and Resistance (CaDNetASR) to: (1) describe the proportions of AMR in fecal E. coli, and (2) investigate the relationship between antimicrobial use (AMU) (intramammary and systemic routes, while accounting for confounding by other variables) and AMR/multidrug resistance (MDR – resistance to ≥ 3 antimicrobial classes) in fecal E. coli from Canadian dairy farms. We hypothesized that an increase of the AMU was associated with an increase in AMR in E. coli isolates. A total of 140 dairy farms across five provinces in Canada were included in the study. Fecal samples from pre-weaned calves, post-weaned heifers, lactating cows, and farm manure storage were cultured, and E. coli isolates were identified using MALDI-TOF MS. The minimum inhibitory concentrations (MIC) to 14 antimicrobials were evaluated using a microbroth dilution methodology. AMU was quantified in Defined Course Dose (DCD - the dose for a standardized complete treatment course on a standard size animal) and converted to a rate indicator - DCD/100 animal-years. Of 1134 fecal samples collected, the proportion of samples positive for E. coli in 2019 and 2020 was 97.1% (544/560) and 94.4% (542/574), respectively. Overall, 24.5% (266/1086) of the E. coli isolates were resistant to at least one antimicrobial. Resistance towards tetracycline was commonly observed (20.7%), whereas resistance to third-generation cephalosporins, fluoroquinolones, and carbapenems was found in 2.2%, 1.4%, and 0.1% of E. coli isolates, respectively. E. coli isolates resistant to two or ≥ 3 antimicrobial classes (MDR) was 2.7% and 15%, respectively. Two multilevel models were built to explore risk factors associated with AMR with AMU being the main exposure. Systemic AMU was associated with increased E. coli resistance. For an increase in systemic AMU equivalent to its IQR, the odds of resistance to any antimicrobial in the model increased by 18%. Fecal samples from calves had higher odds of being resistant to any antimicrobial when compared to other production ages and farm manure storage. The samples collected in 2020 were less likely to be resistant when compared to samples collected in 2019. Compared to previous studies in dairy cattle in North America, AMR in E. coli was lower.