Antimicrobial resistant bacteria ~ Escherichia coll, Klebsiella pneumonlae carriage and transmission In avian species

Abstract

Antimicrobial resistance has emerged as an enormous threat to public health in the recent years. In particular, the Gram-negative Enterobacteriaceae family comprising several clinically important disease-causing species dominate reports of human infections have been frequently identified as carriers of genes conferring resistance to critically important antimicrobials. This further elevates the risk associated to human health as critically important antimicrobials are the last line of treatment available for treating serious life-threatening infections in humans and development of resistance towards this group of antimicrobials limits treatment options. One of the major human health crises with AMR is the propensity for Gram-negative bacteria to readily acquire and disseminate resistance genes further increasing the risk of bi-directional transmission of these bacteria into the wider environment and other animal species through anthropogenic activities or as zoonoses. This PhD thesis was designed to clarify the carriage and transmission of antimicrobial resistant bacteria in the wider environment especially amongst certain wild bird species that share proximity with humans, have access to remote ecological niches and interact with other avian species that are generally far from human contact. The main highlights of the experiments performed and recorded in this thesis were to reveal some of the important aspects of how the resistant bacteria are hosted by the specific avian species and how they are transmitted further between the species. The study also focussed on understanding if anthropogenic activities and proximity to human populations can potentially influence the carriage rates of critically important antimicrobial (CIA) resistant bacteria. The other important aspect investigated in this study was the potential for commensal strain sharing between the different avian species that have different foraging habits but share a common environment. The study initiated with investigation of the ecology, epidemiology and origins of CIA resistant Escherichia coli in Australian silver gulls. The Australia-wide cross-sectional survey of faecal flora of silver gulls demonstrated high levels of carriage of E. coli, resistant to two recognized critically important antimicrobials, extended spectrum cephalosporin (ceftriaxone) and fluoroquinolone (ciprofloxacin), 21.7% and 23.8% respectively. Further, genomic investigation revealed that majority of the E. coli isolated from gulls largely belonged to human-associated extra-intestinal pathogenic E. coli clones. The second study was designed to assess the implication of foraging and interspecies interaction of birds for carriage of E. coli demonstrated that gulls inhabiting areas of high anthropogenic activities can host, amplify and further disseminate the resistant E. coli strains to other bird species that share a common habitat for nesting and/or roosting. Genome sequencing results indicated that interspecies resistance transfer is facilitated by mobile genetic elements. The third study was conducted to investigate, how proximity of gulls to areas with high anthropogenic activities impact the overall CIA resistant E. coli carriage level and if the gulls can also act as a potential reservoir of other CIA resistant human health associated bacteria. The study revealed that silver gulls are not limited to hosting and disseminating critically important antimicrobial resistant E. coli only. They can also serve as potential reservoir of yet another significant human health associated member of Enterobacteriaceae family, Klebsiella pneumoniae known to acquire and harbour critically important antimicrobial resistance genes. A noteworthy observation of the study was that the frequency of carriage of both E. coli and K. pneumoniae by the gulls diminished as the proximity of the gulls from the anthropogenic activity and densely human populated areas gradually increased, thus indicating that gulls inhabiting urban areas are more often exposed to critically important antimicrobial resistant bacteria compared to those inhabiting sparsely human populated or remote areas. Furthermore, this study also investigated the potential of commensal E. coli strain sharing between three bird species, silver gulls, feral pigeons and little penguins that have different foraging habits but share the same environment. Although, the findings of this study indicated limited strain sharing of commensal E. coli and overall, very low levels of CIA resistance in the E. coli isolated from each bird species, this was attributed to not using enrichment and selective agar media to facilitate isolation of the resistant bacteria. This study also indicated that the resistant strains may not be dominant amongst the total E. coli population. Overall, the key findings of these studies indicate and further substantiate that silver gulls are ecological sponges with a propensity to indiscriminately acquire and disseminate CIA resistant bacteria. The detection of human health associated clinically important strains of E. coli and Klebsiella pneumoniae from gulls also indicates that anthropogenic activities and proximity of these birds to urban areas that are densely populated by humans contributes to the carriage levels and frequency CIA resistant bacteria. The foraging sites of urban birds on human leftovers, from hospital effluents and wastewater treatment plants represent the major exposure sites from where the avian species can acquire CIA resistant bacteria. It is also noteworthy that although the urban birds are implicated as carriers of CIA resistant E. coli, these strains are not always dominant and are detected at low CFU. To further select and encourage growth of these underrepresented CIA resistant commensal E. coli strains from amongst the dominant E. coli population, use of enrichment and selective agar medium is highly recommended. Considering the low representation of CIA resistant strains amongst the dominant commensal population, it would be worthwhile carrying out further investigations to determine if the risk of exposure to humans has been overestimated.