Pathogen Surveillance in Swallows (family Hirundinidae): Investigation into Role as Avian Influenza Vector in Eastern Canada Agricultural Landscapes.

First detected in Atlantic Canada in December 2021, highly pathogenic avian influenza virus (HPAIV) subtype H5N1 clade 2.3.4.4b, A/Goose/Guangdong/1/96 lineage, has caused massive mortality in wild birds and domestic poultry in North America. Swallows (Hirundinidae), abundant in North American agricultural ecosystems, have been proposed as possible (bridge) species for HPAIV transmission between wild and domestic birds. We aimed to seek evidence of the potential role of swallows in bridging AIV infection between wild bird reservoirs and poultry flocks in eastern Canada. During a wide-scale outbreak of HPAIV in wild birds and poultry farms across eastern Canada, 200 samples were collected from swallow breeding sites in the Canadian provinces of New Brunswick, Nova Scotia, Ontario, and Quebec, June-August 2022. Samples came from Barn Swallow (Hirundo rustica; n=142), Tree Swallow (Tachycineta bicolor; n=56), and Cliff Swallow (Petrochelidon pyrrhonota; n=2) nests. All samples tested negative for AIV, suggesting that HPAIV and low pathogenic AIV (LPAIV) strains were probably not circulating widely in swallows during the 2022 breeding season in eastern Canada; thus swallows may present a low risk of transmitting AIV. Within a management context, these findings suggest that removing nests of Barn Swallows, a species at risk in Canada, from the exterior of biosecure domestic poultry facilities may not significantly reduce risks of HPAI transmission to poultry.

Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes.

Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.

Microbiology in the Field: Construction and Validation of a Portable Incubator for Real-Time Quantification of Coliforms and Other Bacteria.

Performing microbiological assays on environmental samples in field settings poses logistical challenges with respect to the availability of suitable equipment or the ability to get samples to the laboratory in a timely fashion. For example, the viability of some bacteria can decrease greatly between sampling and arrival to the laboratory for processing. We developed and constructed rugged, reliable, and cost-effective portable incubators that were used by 10 independent field teams to perform microbiological assays on surface water samples from lakes across Canada. Rigorous testing and validation of our incubators ensured that incubation conditions were consistent within and across all 10 field teams and 2 sampling years. Samples from all sites were processed in duplicate and bacterial counts were highly repeatable within and across sampling teams. Bacterial counts were also found to be statistically equivalent to counts obtained with standard laboratory techniques using a conventional incubator. Using this method, thermotolerant coliforms (TTCs) and Escherichia coli were quantified from 432 lakes, allowing comparison to both historical datasets that relied on TTCs and those following current guidelines that use E. coli counts. We found higher loads at the shoreline than the middle of lakes and different patterns between ecozones. E. coli was not frequently detected, but many lakes exceeded Canadian guideline values for activities such as swimming and some even exceeded the guideline value for secondary recreational activities such as boating. To the best of our knowledge, this is the largest bacteriological water quality assessment of freshwater lakes to date in terms of both spatial scale and the number of lakes sampled. Our incubator design can be easily adapted for a wide variety of researcher goals and represents a robust platform for field studies and other applications, including those in remote or low-resources settings.

Influenza A viruses remain infectious for more than seven months in northern wetlands of North America.

In this investigation, we used a combination of field- and laboratory-based approaches to assess if influenza A viruses (IAVs) shed by ducks could remain viable for extended periods in surface water within three wetland complexes of North America. In a field experiment, replicate filtered surface water samples inoculated with duck swabs were tested for IAVs upon collection and again after an overwintering period of approximately 6-7 months. Numerous IAVs were molecularly detected and isolated from these samples, including replicates maintained at wetland field sites in Alaska and Minnesota for 181-229 days. In a parallel laboratory experiment, we attempted to culture IAVs from filtered surface water samples inoculated with duck swabs from Minnesota each month during September 2018-April 2019 and found monthly declines in viral viability. In an experimental challenge study, we found that IAVs maintained in filtered surface water within wetlands of Alaska and Minnesota for 214 and 226 days, respectively, were infectious in a mallard model. Collectively, our results support surface waters of northern wetlands as a biologically important medium in which IAVs may be both transmitted and maintained, potentially serving as an environmental reservoir for infectious IAVs during the overwintering period of migratory birds.