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Novel approaches for managing and controlling antimicrobial resistance in pigs

Laird, Tanya Jane (2021) Novel approaches for managing and controlling antimicrobial resistance in pigs. PhD thesis, Murdoch University.

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Antimicrobial resistance (AMR) continues to threaten One Health with a projected 10 million deaths per year by 2050 if left uncontrolled. While the human medical field has historically demonstrated poor control in the use of antimicrobials, usage in livestock, both historic and current, is also of concern. Resistance to critically important antimicrobials (CIA’s), those reserved for use in life-threatening human infections, has been detected in swine globally. This resistance has the potential to transfer between animals and into humans, and with the accelerated growth of AMR, investigation into novel control strategies for AMR and bacterial infections is now equally as important as surveillance.

This thesis determined the diversity of AMR in commensal Escherichia coli (E. coli) within and between pigs and farms, hypothesising that this diversity results in underrepresentation of the true prevalence of AMR by current national AMR surveillance approaches. Secondly, this thesis investigated novel approaches for the control of AMR E. coli and a ubiquitous pathogen, enterotoxigenic E. coli (ETEC), in swine. Postbiotics in the form of Lactobacillus acidophilus fermentation products (LFP) and Saccharomyces cerevisiae fermentation products (SFP) have demonstrated potential effects in alleviating symptoms induced by ETEC infection and in reducing AMR. The thesis evaluated LFP and SFP, as well as their combined effects, on weaner pigs challenged with F4-ETEC, and in a second experimental trial, on weaner pigs challenged with extended-spectrum cephalosporin (ESC) resistant E. coli. Following these trials, a large-scale field-based trial was completed analysing the effects of these postbiotics on AMR E. coli. Finally, the combination of bacteriophages and competitive exclusion clones (CECs) were evaluated in vitro as a novel and targeted approach for the control of ESC-resistant E. coli. The high throughput robotics platform, Robotic Antimicrobial Susceptibility Platform (RASP), was used throughout the project to determine its future application in AMR surveillance and evaluation of control strategies.

High levels of phenotypic and genotypic diversity were detected in commensal E coli at both the host and farm level. This was evident in 89% of pigs harbouring more than a single AMR index in the eight E. coli colonies subjected to antimicrobial susceptibility testing (AST). Furthermore, 58 different multi-locus sequence types (MSLTs) were identified from the 151 isolates subjected to whole genome sequencing. This diversity highlights the low reliability of current national surveillance methods that use 1 isolate per farm and less than 200 isolates per animal species.

Supplementation with LFP and SFP demonstrated indirect benefits in ETEC-challenged weaner pigs. This was detected as increased growth performance and modulation of the faecal microbiome through increased alpha diversity and abundance in the beneficial bacterial family Lactobacillaceae. However, the postbiotics demonstrated no direct impact on ETEC infection measured through bacterial quantification and faecal consistency scores. Furthermore, the effect of these postbiotics on growth performance and faecal shedding of resistant E. coli were also studied in healthy weaner pigs. The postbiotics demonstrated no impact on growth performance of healthy weaner pigs. Although the postbiotics demonstrated a reduction in ESC-resistant E. coli in pigs challenged with ESC-resistant E. coli, no effects on ciprofloxacin, tetracycline and ESC-resistant E. coli were detected in the farm-based trial. These conflicting results highlight the importance of evaluating strategies in field trials, however, both studies provided a detailed examination of the natural reduction in AMR-carriage over time, whether in experimental models or on farm. Finally, a targeted approach for controlling ESC-resistant E. coli was analysed. The combination of bacteriophages and CECs demonstrated a complimentary relationship, significantly reducing and possibly eliminating ESC-resistant E. coli in vitro. Overall, the high-through put robotics platform, RASP, provided cost-effective bacterial quantification and testing of selected bacterial strains across the project. The sample number in experiments is often restricted due to labour constraints especially during these already labour-intensive trials, however implementation of RASP allowed a high number of samples to be processed and tested, demonstrating future use in AMR research.

In conclusion, a more in-depth sampling model for AMR surveillance is necessary to account for the heterogeneity of AMR. Application of robotic platforms, such as the RASP, in AMR surveillance offers a highly economic and low laborious approach for processing this increased sample size. The RASP additionally demonstrated use in investigation of AMR and ETEC control methods, demonstrated by its high resolution into the dynamics of AMR E. coli and ETEC in faecal contents of pigs. Lastly, an in vitro combination approach, using both targeted and preventative therapies, demonstrated superiority in reduction of ESC-resistant E. coli. This novel combined approach requires future analysis to determine if these results are replicated on farm.

Item Type: Thesis (PhD)
Murdoch Affiliation(s): Medical, Molecular and Forensic Sciences
Supervisor(s): O'Dea, Mark, Sahibzada, Shafi and Abraham, Sam
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