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During the COVID-19 pandemic, detection of the virus in sewage water was used to determine disease spread in the community. Piggery effluent or waste is composed of faeces, urine, oronasal secretions, feed residues and other miscellaneous components which are diluted in water and released into the environment (Rate, 1997). This blended composition of effluent, along with evidence that several pathogenic bacteria have already been isolated from effluent (Chinivasagam et al., 2004) suggest that it could be useful to monitor pathogen prevalence in a herd at a given point in time. This monitoring could help in early detection and improved control of disease outbreaks that could potentially cause significant economic losses and decreased animal welfare. This point-of-management (POM) approach and better control of infectious diseases would also reduce the need for antimicrobials, improving the sustainability of intensive pig production and reducing the risk of antimicrobial resistance genes entering the food chain or the environment. The nucleic acid amplification-based assay known as Loop-mediated isothermal amplification (LAMP) has been widely adopted for POM diagnostics due to its high sensitivity, accuracy, affordability and quick turnaround time. Therefore, this study was designed to produce a proof-of-concept effluent testing methodology through LAMP-based POM assay, to determine if this tool is useful to monitor pathogens at the shed or herd level. Due to the composition of effluent and the ease of implementation and low cost of LAMP assays, it was hypothesised that LAMP assays could be used to detect a common pathogen in pig effluent for the purpose of POM diagnostics.

The current pandemic has ensured considerable attention has been paid to the role of the approach termed ‘Point of Care’ diagnostics. Indeed, the term ‘RAT’ (Rapid Antigen Test) and RAT hunting now have totally different meaning to that widely understood before 2020. In the veterinary field, including food safety, the term used for these types of rapid in situ assays is ‘Point of Management’ (POM) assays. In this article, we describe our recent research on low cost, low technology, in-house style POM assays in the field of food safety as applied to the poultry industries. We then discuss what are the advantages and disadvantages of these low cost, low technology POM assays.

Objective Pleurisy in pigs has economic impacts in the production stage and at slaughter. This study sought to establish if some micro-organisms can be found in high numbers in lungs with pleurisy by assessing batches of pigs at an abattoir in Queensland Australia. Design Samples of lung (including trachea/bronchus and lymph nodes) from a maximum of 5 pleurisy affected pigs were collected from 46 batches of pigs representing 46 Queensland farms. Procedure Pleurisy-affected lung areas were cultured by traditional bacteriological methods and bacteria quantified by plate scores. Additionally, tracheal or bronchial swabs and apical lobe fluid were tested for Mycoplasma hyopneumoniae DNA and the superior tracheobronchial lymph nodes were tested for porcine circovirus type 2 DNA by polymerase chain reaction (PCR). All apparently significant bacteria were identified via PCR or sequencing. Typing was undertaken on some of the bacterial isolates. Results The most prevalent pathogens were M. hyopneumoniae, Streptococcus suis and Porcine Circovirus type 2, being found in 34, 38 and 31 batches, respectively. Other bacteria found were Actinobacillus species (29 batches), Pasteurella multocida (24 batches), Mycoplasma flocculare (9 batches), Actinobacillus pleuropneumoniae (7 batches), Mycoplasma hyorhinis (4 batches), Bisgaard Taxon 10 (1 batch), Glaesserella parasuis (1 batch), Streptococcus minor (1 batch) and Streptococcus porcinus (1 batch). Most batches had more than one bacterial species. Conclusion The high percentage of batches infected with S. suis (83%), M. hyopneumoniae (74%) and PCV2 (70%) and clustering by a batch of these pathogens, as well as the presence of many secondary pathogens, suggests synergy between these organisms may have resulted in pleurisy.

A total of 22 Pasteurellaceae isolates obtained from the oral cavity of koalas (Phascolarctos cinereus) at different wildlife centers in Australia were investigated using amplification and sequencing of two housekeeping genes, rpoA and recN. The available sequences from the Lonepinella koalarum type strain (ACM3666T) and the recent isolates of Lonepinella-like bacteria obtained from human infected wounds associated with koala bites were also included. Phylogenetic analysis was performed on the concatenated rpoA-recN genes and genome relatedness was calculated based on the recN sequences. The oral cavity isolates, the koala bite wound isolates, and L. koalarum ACM3666T resulted in four clusters (Clusters 1-4). Clusters 1-3 were clearly not members of the genus Lonepinella. Cluster 1 was closely related to the genus Fredericksenia, and Clusters 2 and 3 appeared to be novel genera. Cluster 4 consisted of three subclusters: Cluster 4a with one koala bite wound isolate and L. koalarum ACM3666T, Cluster 4b with three oral cavity isolates and two Lonepinella-like wound isolates, and Cluster 4c with three nearly identical oral cavity isolates that may represent a different species within the genus Lonepinella. The rich Pasteurellaceae population, including potential novel taxa in the oral cavity of koalas supports an important role of these highly adapted microorganisms in the physiology of koalas. Moreover, the pathogenic potential of Lonepinella-like species is an important consideration when investigating infected koala bites in humans.

Aims Current culture-based methods for detection and determination of Campylobacter levels on processed chickens takes at least two days. Here, we sought to develop a new complete, low-cost and rapid (approximately 2·5 hours) detection system requiring minimal operator input. Methods and Results We observed a strong correlation between culture-based cell counts and our ability to detect either Campylobacter jejuni or Campylobacter coli by Loop mediated isothermal amplification (LAMP) from the same samples. This knowledge was used to develop a rapid and simple five-step assay to quantify Campylobacter, which was subsequently assessed for its specificity, reproducibility and accuracy in quantifying Campylobacter levels from processed chickens. The assay was found to be highly specific for C. jejuni and C. coli and was capable of distinguishing between samples that are either within or exceeding the industry set target of 6,000 Campylobacter colony forming units (cfu) per carcass (equivalent to 12 cfu ml-1 of chicken rinse) with> 90% accuracy relative to culture-based methods. Conclusions Our method can reliably quantify Campylobacter counts of processed chickens with an accuracy comparable to culture-based assays but provides results within hours as opposed to days. Significance and Impact of the Study The research presented here will help improve food safety by providing fast Campylobacter detection that will enable the implementation of real-time risk management strategies in poultry processing plants to rapidly test processed chickens and identify effective intervention strategies. This technology is a powerful tool that can be easily adapted for other organisms and thus could be highly beneficial for a broad range of industries.