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  • Cage-free housing is increasingly chosen in Europe, North America, and Australia as an animal-welfare friendly farm system for laying hens. However, hens are kept in large numbers in those systems which makes checking for health and welfare difficult and individuals cannot be identified. Tracking systems like radio frequency identification allow researchers to monitor these individuals almost continuously. Individual tracking data has revealed substantial individual variation in movement patterns, however, in recent studies, only a subset of animals per flock was tracked. We applied an RFID tracking system to monitor all 1125 laying hens of a flock, which were divided into 5 pens of 225 birds each in a barn with an aviary system. In each pen, 26 antennas were placed on the edges of three tiers and in the litter. For validation purposes, 3 hens in 2 connected pens were fitted with colored backpacks. They were recorded on video and their location throughout the pen was taken from the video and compared with registrations from the RFID system. For 93% of compared transitions, the RFID data matched the observational data regarding the tier or litter whereas the value fell to 39%  for specific antennae. When the antennae on the litter were excluded for the validation, the match on tier-level was at least 98% but on antenna-level it remained lower than 50%. The sensitivity of the detection of tiers/litter but not antennae differed among the three hens. We conclude that the RFID tracking system was suitable for studying the movement pattern of individual hens among tiers in an aviary system in a reliable way but tracking birds on the litter needs to be improved.

  • Rivers, creeks, streams are integrators of biological, chemical and physical processes occurring in a catchment linking land cover from the headwaters to the outlet.  The dynamics of human and animal pathogens in catchments have been widely studied in a large variety of contexts allowing the optimization of disease risk reduction. In parallel, there is an emerging awareness that crop pathogens might also be disseminated via surface waters especially when they are used for irrigation. However, there are no studies on the extent to which potential plant pathogens are present – nor about their dynamics - along the full course of a catchment. Here we have compared the seasonal dynamics of populations of the Pseudomonas syringae (Psy) and the Soft Rot Pectobacteriaceae (SRP) species complexes along a 270 km stretch of the Durance River from the upstream alpine reaches to the downstream agricultural production areas at the confluence with the Rhone River at Avignon. Among 168 samples collected at 21 sites in fall, winter, spring and summer of 2016 and 2017, Psy strains were detected at all sampling sites and in 156 of the samples at population densities up to 105 bacteria L-1. In contrast, SRP strains were detected in 98 of the samples, mostly from the southern part of the river, at population densities that did not exceed 3 ´ 104 bacteria L-1. Among the biological and chemical parameters that were characterized at each sampling site, temperature was the only factor that explained a significant amount of the variability in population size for both species complexes. Psy densities decreased with increasing temperature whereas SRP densities increased with increasing temperature. River-borne populations of SRP were composed mainly of Pectobacterium versatile and P. aquaticum that have little known epidemiological importance. Only a few strains of Pectobacterium and Dickeya species reputed for their epidemiological impact were observed. In contrast, Psy populations at all sites were dominated by a genetic lineage of phylogroup 2 known from other studies for its broad host range and its geographic and habitat ubiquity. Our observations suggest that surveillance of river water for SRP could be leveraged to signal diagnostic and management reactions to avoid disease outbreaks.  In contrast, the constant presence of Psy throughout the catchment in absence of regular and widespread disease outbreaks due to this group of bacteria suggests that surveillance should focus on future changes in land use, river water conditions and agronomic practices that could destabilize the mechanisms currently holding Psy outbreaks in check.

  • Mathematical & Computational Biology

    General encoding of canonical k-mers

    10.24072/pcjournal.323 - Peer Community Journal, Volume 3 (2023), article no. e87.

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    To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are often encoded as integers, e.g., applying some bijective mapping between all possible σk k-mers and the interval [0, σk −1], where σ is the alphabet size. In many applications, e.g., when the reading direction of a DNA-sequence is ambiguous, canonical k-mers are considered, i.e., the lexicographically smaller of a given k-mer and its reverse (or reverse complement) is chosen as a representative. In naive encodings, canonical k-mers are not evenly distributed within the interval [0, σk −1]. We present a minimal encoding of canonical k-mers on alphabets of arbitrary size, i.e., a mapping to the interval [0, σk/2−1]. The approach is introduced for canonicalization under reversal and extended to canonicalization under reverse complementation. We further present a space and time efficient bit-based implementation for the DNA alphabet.

  • A tailor-made health plan is a set of recommendations for a farmer to achieve and maintain a high health and welfare status. Tailored to each farm, it is intended to be an effective way of triggering change. This study aimed to assess the effectiveness of tailor-made health plans in pig farms, designed in various situations after a systematic biosecurity and herd health audit. An intervention study was carried out in 20 farrow-to-finish pig farms. An initial standardized audit and discussion between the farm veterinarian and the farmer resulted in a specific plan. Compliance with recommendations was monitored during 8 months. Changes in health, performances and antimicrobial use were monitored. We defined two categories of plans: i) 14 plans targeting a given health disorder present in a farm; ii) 17 plans to improve prevention, not targeting a specific health disorder (a farm could have both types of plans). A small number of priority recommendations were made per farm. In 18 farms, farmers implemented 1 to 4 recommendations (none in 2 farms). Of the 17 non-disorder-specific plans, 11 were considered effective (>50% recommendations implemented), 3 intermediate (at least one but less than half of the recommendations implemented) and 3 ineffective (no implementation). Of the 14 disorder-specific plans, 9 were followed with full or good compliance (>50% recommendations implemented), 2 with intermediate compliance (1 recommendation implemented out of 2) and 3 with no compliance (no recommendation implemented). When at least one recommendation was implemented, change in clinical, performance and antimicrobial use indicators was assessed if a biological association with the disorder was deemed plausible and if their initial value showed room for improvement. Improvement was evidenced 4/9, 1/6 and 1/6 times for these indicators, respectively. Independently, veterinarians concluded that 8/14 plans were effective. Overall, tailor-made health plans were effective in triggering changes in farm management. Three key points were identified for future assessments of the effectiveness of tailor-made health plans. Compliance should be the first indicator of assessment. Outcome indicators and their monitoring periods should be adapted to each farm and to the targeted health disorder. Indicators should be combined to have a holistic description of the evolution of a health disorder. Further research is needed to identify how to select indicators to combine and how to combine them, according to health disorders.

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