Microbial Status of Meat Chicken Flocks in Population Level Samples

Abstract

<p>Poultry meat is one of the most widely consumed meats throughout the world, with increasing demands for it to match the growing world population. Because of increasing public concern, antimicrobials that had been commonly used in poultry feed to enhance bird growth and performance have been banned or strictly regulated in many countries. This has resulted in the increase of clinical and subclinical enteric diseases in chicken meat flocks with significant losses in productive performance. The two major enteric diseases on the rise in meat chickens are necrotic enteritis, caused by the bacterium <i>Clostridium perfringens</i>, and coccidiosis, caused by <i>Eimeria</i> species. Monitoring for both diseases is usually based on post-mortem evaluation and scoring of gut lesions which requires skilled personnel as the scoring can be subjective and this method is unable to detect subclinical infections.</p> <p>In addition to monitoring specific enteric diseases, current research is moving towards the development of tools for monitoring general gut health. Among the tools to assess gut health, the gut microbiota has gained attention as shifts in microbial community composition have been associated with productive performance. The assessment of gut microbiota is usually restricted to research settings as it is an expensive and time-consuming technique which is complicated by the multiple microbial profiles that have been associated with poor or high performance. This is fuelled by the high variability of the microbial composition of individual birds, which leads to the need of terminal sampling of a large number of birds for collection of gut contents. Some of the current research has shown that non-invasive samples such as caecal droppings and boot socks, a composite sample type that contains a mixture of litter and excreta, could be used as an alternative to caecal contents to study flock microbiota composition longitudinally. Boot sock samples, also known as boot swabs, are collected by walking through a poultry house with a boot cover/sock worn over the shoe. The excreta and litter materials adhered to the socks is then collected and used for testing. Non-invasive and easy to collect population level samples such as dust, pooled excreta and litter do not require terminal sampling and have the potential to provide flock-level metrics on microbial composition and burden of enteric pathogens using a reduced number of samples and therefore reducing costs. However, the usefulness of population level sampling approaches to monitor microbiota composition or the load of the specific gut disruptors such as <i>Eimeria</i> species and <i>C. perfringens</i> and their association with flock productive performance is unclear.</p> <p>In response to these challenges, this PhD project was designed with 3 broad objectives, namely, 1) evaluating the usefulness of non-invasive population level samples (dust, pooled excreta) to detect specific gut disruptors, <i>C. perfringens</i> and <i>Eimeria</i> spp and the association of the detected pathogen load with flock productive performance; 2) investigating the bacterial signatures correlated with flock productive performance in non-invasive population-level samples; and 3) evaluating the extent to which the microbiota of non-invasive samples (dust, excreta and litter) is similar to invasive samples (caecal and ileal contents). To achieve the first objective reported in Chapter 2 (study 1), poultry house dust and pooled excreta were collected weekly from high or low productive performance farms of two Australian integrator companies. The association of the DNA levels of <i>C. perfringens</i> and associated virulence factor <i>net</i>B plasmid gene, and five <i>Eimeria</i> spp (<i>E. necatrix</i>, <i>E. acervulina</i>, <i>E. brunetti</i>, <i>E. maxima</i> and <i>E. tenella</i>) with flock productive performance was investigated using PCR. To achieve the second objective reported in Chapter 3 (study 2), the microbiota of dust and pooled excreta of the same farms used in study 1 was assessed using 16S ribosomal RNA gene amplicon sequencing and the bacterial signatures associated with flock productive performance were identified. To achieve the third objective reported in Chapter 4 (study 3), invasive (caecal and ileal contents) and non-invasive (dust, excreta and litter) samples were collected from experimental meat chickens fed with an industry standard diet. The microbiota of invasive and non-invasive samples was assessed using 16S ribosomal RNA gene amplicon sequencing and the extent of similarity of the microbial composition between non-invasive and invasive samples were evaluated.</p> <p>In study 1, dust and pooled excreta were shown to be useful to detect <i>Eimeria</i> spp, C. perfringens and <i>net</i>B DNA; however, there was no association between pathogen load and flock production performance. There was a strong association between the DNA level of <i>Eimeria</i> species in excreta and dust suggesting that the latter could be used for screening flocks for these pathogens. In study 2, performance explained the least amount of variation in the microbial communities within each sample type, while company and age explained a larger amount of variation. Despite that, some specific bacterial taxa were found to be associated with high and low performance in both dust and excreta. The bacteria taxa associated with high-performing farms in dust or excreta found in this study were <i>Enterococcus</i> and<i> Candidatus</i> Arthromitus whereas bacterial taxa associated with lowperforming farms included <i> Nocardia, Lapillococcus, Brachybacterium, Ruania, Dietzia Brevibacterium, Jeotgalicoccus, Corynebacterium</i> and <i>Aerococcus</i>. In study 3, the non-invasive samples tested (dust, litter, excreta) could be used to detect the presence or absence of the majority of the microbial taxa present in invasive samples but did not reflect the microbial community composition of invasive samples. The outcomes of this thesis enhanced our understanding of the use of non-invasive population level samples for monitoring gut disruptors and microbiota at a flock level. Specifically, it led to the development of a practical and economical method to monitor the DNA load of the microorganisms causing necrotic enteritis and coccidiosis, and to detect bacterial signatures of flock productive performance in commercial meat chicken flocks using dust samples.</p>