Farrell, M. L. | bioRxiv Science

bioRxiv2025

Avian Influenza in Ireland: A Spatiotemporal, Subtype, and Host-Based Analysis (1983-2024)

Avian influenza virus (AIV) is a significant global concern, causing widespread mortality in wild birds, domestic poultry and most recently wild and domestic mammals. This study presents a retrospective analysis of AIV detections in the Republic of Ireland. Data was sourced from official surveillance databases, peer-reviewed literature and grey literature sources. Spatio-temporal, host-specific and subtype patterns were assessed using descriptive statistics, chi-square tests, linear regression and kernel density estimations. A total of 2,888 confirmed AIV detections were recorded from 25 of Irelands 26 counties. Wild birds accounted for 98.7% of detections, with domestic birds comprising 1.3% and two detections in foxes. H5N1 was the most prevalent subtype (96.7%) followed by H5N8 and H6N1. Spatial clustering was observed in urban areas, particularly Dublin. The highest seasonal peak occurred during summer, contrasting with traditional winter-associated patterns. Several detections occurred in migratory species outside of typical residency periods, suggesting potential climate-related shifts in migration behaviour. This study represents the first review of AIV surveillance data in Ireland to date. The findings highlight evolving patterns in virus distribution, seasonality and host dynamics, with implications for national surveillance strategies. Continued cross-species monitoring and integration of ecological data are essential to inform effective management strategies.

microbiology↗

bioRxiv2022

First reported detection of the mobile colistin resistance genes, mcr-8 and mcr-9, in the Irish environment

The emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collected were assessed for the presence of antimicrobial resistant bacteria using Brilliance ESBL, Brilliance CRE, mSuperCARBA and McConkey agar containing a ciprofloxacin disc. All water and integrated constructed wetland influent and effluent samples were filtered and enriched in buffered peptone water prior to culture, while wastewater samples were cultured directly. Isolates collected were identified via MALDI-TOF, were tested for susceptibility to 16 antimicrobials, including colistin, and subsequently underwent whole genome sequencing. Overall, eight mcr positive Enterobacterales (one mcr-8 and seven mcr-9) were recovered from six samples (freshwater (n=2), healthcare facility wastewater (n=2), wastewater treatment plant influent (n=1) and integrated constructed wetland influent (piggery farm waste) (n=1)). While the mcr-8 positive K. pneumoniae displayed resistance to colistin, all seven mcr-9 harbouring Enterobacterales remained susceptible. All isolates demonstrated multi-drug resistance and through whole genome sequencing analysis, were found to harbour a wide variety of antimicrobial resistance genes i.e., 30 {+/-} 4.1 (10-61), including the carbapenemases, blaOXA-48 (n=2) and blaNDM-1 (n=1), which were harboured by three of the isolates. The mcr genes were located on IncHI2, IncFIIK and IncI1-like plasmids. The findings of this study highlight potential sources and reservoirs of mcr genes in the environment and illustrate the need for further research to gain a better understanding of the role the environment plays in the persistence and dissemination of antimicrobial resistance.

microbiology↗