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The co-existence of rats and humans in urban environments has long been a cause for concern regarding human health because of the potential for rats to harbor and transmit disease-causing pathogens. Here, we analyze whole-genome sequence (WGS) data from 41 Escherichia coli isolates collected from rat feces from 12 locations within the city of Chicago, IL, United States to determine the potential for rats to serve as a reservoir for pathogenic E. coli and describe its population structure. We identified 25 different serotypes, none of which were isolated from strains containing significant virulence markers indicating the presence of Shiga toxin-producing and other disease-causing E . coli . Nor did the E. coli isolates harbor any particularly rare stress tolerant or antimicrobial resistance genes. We then compared the isolates against a public database of approximately 100,000 E. coli and Shigella isolates of primarily food, food facility, or clinical origin. We found that only one isolate was genetically similar to genome sequences in the database. Phylogenetic analyses showed that isolates cluster by serotype, and there was little geographic structure (e.g., isolation by distance) among isolates. However, a greater signal of isolation by distance was observed when we compared genetic and geographic distancesmore »among isolates of the same serotype. This suggests that E. coli serotypes are independent lineages and recombination between serotypes is rare.« less

Abstract Frozen winters define life at high latitudes and altitudes. However, recent, rapid changes in winter conditions have highlighted our relatively poor understanding of ecosystem function in winter relative to other seasons. Winter ecological processes can affect reproduction, growth, survival, and fitness, whereas processes that occur during other seasons, such as summer production, mediate how organisms fare in winter. As interest grows in winter ecology, there is a need to clearly provide a thought-provoking framework for defining winter and the pathways through which it affects organisms. In the present article, we present nine maxims (concise expressions of a fundamentally held principle or truth) for winter ecology, drawing from the perspectives of scientists with diverse expertise. We describe winter as being frozen, cold, dark, snowy, less productive, variable, and deadly. Therefore, the implications of winter impacts on wildlife are striking for resource managers and conservation practitioners. Our final, overarching maxim, “winter is changing,” is a call to action to address the need for immediate study of the ecological implications of rapidly changing winters.