Bacteriophages to Control Campylobacter in Commercially Farmed Broiler Chickens, in Australia

© Copyright © 2020 The State of Queensland (through the Department Agriculture and Fisheries). This study describes the development and use of bacteriophage cocktails to control Campylobacter in broiler chickens, in a commercial setting, in Queensland Australia, following the birds from farm to the processing plant. The components of the bacteriophage cocktails were selected to be effective against the maximum number of Campylobacter jejuni and Campylobacter coli isolates encountered on SE Queensland farms. Farms were identified that had suitable Campylobacter target populations and phage were undetectable 1 week prior to the intended treatment. Cocktails of phages were administered at 47 days of age. Groups of study birds were slaughtered the following day, on-farm, at the end of flock transport to the plant, and at processing (approximately 28 h post-treatment). On Farm A, the phage treatment significantly reduced Campylobacter levels in the ceca at the farm in the range of 1–3 log10 CFU/g (p = 0.007), compared to mock treated controls. However, individual birds sampled on farm (1/10) or following transport (2/10) exhibited high cecal Campylobacter counts with low phage titers, suggesting that treatment periods > 24 h may be required to ensure phage replication for effective biocontrol in vivo. At the time of the trial the control birds in Farm B were phage positive despite having been negative one week earlier. There was no significant difference in the cecal Campylobacter counts between the treatment and control groups following treatment but a fall of 1.7 log10 CFU/g was observed from that determined from birds collected the previous week (p = 0.0004). Campylobacter isolates from both farms retained sensitivity to the treatment phages. These trials demonstrated bacteriophages sourced from Queensland farms have the potential to reduce intestinal Campylobacter levels in market ready broiler chickens

Moving from concept to control; use of phages for Campylobacter reduction

Poultry are a major source of Campylobacter with the organism having no impact on the bird. Irrespective of this situation, the important single source of campylobacteriosis is considered to be broiler meat (European Food Safety Authority 2016). The reported number of cases of campylobacteriosis in Australia in 2015 was 22,573 (Communicable Disease Intelligence 2019). Studies have suggested that a reduction in Campylobacter levels by greater than 2-log10 units would contribute to the reduction of the public health risk by more than 90% (European Food Safety Authority 2011). Overseas models have suggested that bacteriophage treatment has the greatest potential of all known/potential methods to reduce Campylobacter levels in the live chicken (Havelaar et al. 2007). Campylobacter naturally colonises the chicken gut, where it can reach high numbers and potentially contaminate the marketed product. A low number of organisms can cause human illness. This study is exploring a biocontrol option using bacteriophages (phages) to reduce Campylobacter numbers in chickens. Bacteriophages are viruses that infect and kill the target bacteria. These specific, Campylobacter-killing phages occur naturally in farm chickens, where they are already in a ‘predator–prey relationship’ with Campylobacter. The aim of this study is to better the outcome of this natural phenomenon. The study builds upon data from previous studies to progress the option of using Campylobacter bacteriophages to control Campylobacter levels in poultry. The report is targeted at the Australian Poultry Industry, those with a role of food-safety at an industry level and also have a regulatory role

Microsatellite discovery in an insular amphibian (Grandisonia alternans) with comments on cross-species utility and the accuracy of locus identification from unassembled Illumina data

The Seychelles archipelago is unique among isolated oceanic islands because it features an endemic radiation of caecilian amphibians (Gymnophiona). In order to develop population genetics resources for this system, we identified microsatellite loci using unassembled Illumina MiSeq data generated from a genomic library of Grandisonia alternans, a species that occurs on multiple islands in the archipelago. Applying a recently described method (PALFINDER) we identified 8001 microsatellite loci that were potentially informative for population genetics analyses. Of these markers, we screened 60 loci using five individuals, directly sequenced several amplicons to confirm their identity, and then used eight loci to score allele sizes in 64 G. alternans individuals originating from five islands. A number of these individuals were sampled using non-lethal methods, demonstrating the efficacy of non-destructive molecular sampling in amphibian research. Although two loci satisfied our criteria as diploid, neutrally evolving loci with the statistical power to detect population structure, our success in identifying reliable loci was very low. Additionally, we discovered some issues with primer redundancy and differences between Illumina and Sanger sequences that suggest some Illumina-inferred loci are invalid. We investigated cross-species utility for eight loci and found most could be successfully amplified, sequenced and aligned across other species and genera of caecilians from the Seychelles. Thus, our study in part supported the validity of using PALFINDER with unassembled reads for microsatellite discovery within and across species, but importantly identified major limitations to applying this approach to small datasets (ca. 1 million reads) and loci with small tandem repeat sizes