Microbiological surveillance in the Mid-West of Ireland

Microbial surveillance is crucial for tracking the emergence and prevalence of infectious diseases and antimicrobial resistance (AMR), enabling timely interventions to be made and health policies to be informed. The aim of this thesis is to provide a detailed epidemiological analysis of microbial pathogens and AMR in our region. This thesis presents a comprehensive analysis of the microbial pathology in the Mid-West region of Ireland over the past two decades, covering aspects of all three branches of One Health (humans, animals and the environment). Over the course of seven studies, retrospective data from the laboratory information system were extracted and analysed, looking for trends and patterns in the data. The first study (chapter two) explored the epidemiology of the fungal pathogens that cause skin, hair and nail infections. An interesting trend was identified: fungal infections from animals became less common, and there was a corresponding increase in infections from human source (less than 35% to more than 75%). The second study (chapter three) looked at the diagnostic methods commonly used around Ireland; limitations were found (many laboratories have been outsourcing testing, susceptibility testing is not being performed, and modern PCR tests have not been introduced), A roadmap was provided for optimising this service.

The third study (chapter four) was the first national study of public and private drinking water, and the first drinking water AMR study where all enterobacterales were included. Some concerning organisms were detected such as Yersinia enterocolitica. This organism was shown to be challenging to distinguish from other Yersinia species, so a follow-up study was performed (chapter five) which provides an analysis of Yersinia enterocolitica detection in our region, as well as a commentary on the detection and identification platforms available, and a framework for clinical laboratories to follow in order to improve detection.

The fifth study of this thesis (chapter six) investigated five specimens that are used in our hospital to help manage maternal sepsis (blood culture, urine, throat vaginal and placental swabs). Placenta swabs (an uncommonly requested specimen in other centres) were found to be useful in this context, by detecting pathogens that frequently cause perinatal infections while other specimens were often sterile or contained commensal organisms. In the sixth study (chapter seven), the epidemiology of neonatal bacteraemia was analysed. Details were available for 170 bacteraemia cases that occurred over a ten year period. Risk factors for neonatal bloodstream infection were reported for the first time from an Irish patient cohort.

Finally, a large One Health study (chapter eight) of antimicrobial resistance among a variety of clinical specimens from humans and animals was performed over a twelve year period. This study found a general decrease in both the use of antimicrobials and the resistance to those antimicrobials in that timeframe. Conversely, one antimicrobial showed an increase in both consumption and resistance. This provided important evidence for the utility of antimicrobial stewardship measures.

The studies performed in this thesis span a wide spectrum of organisms and their characteristics, including both bacteria and fungi, across all three domains of One Health: human medicine, animal medicine and the environment. Not only do they provide measurable data which in itself is an important function of retrospective epidemiological studies, but diagnostic deficiencies are pointed out, new and improved platforms are discussed and recommended, and future directions are proposed.