Merging Metagenomics and Spatial Epidemiology To Understand the Distribution of Antimicrobial Resistance Genes from Enterobacteriaceae in Wild Owls

Abstract

Antimicrobial resistance (AMR) is a well-documented phenomenon in bacteria from many natural ecosystems, including wild animals. However, the specific determinants and spatial distribution of resistant bacteria and resistance genes (ARGs) in the environment remain incompletely understood. In particular, the relative importance of anthropogenic sources of AMR are lacking, compared to other biological and ecological influences. Here we conduct a cross-sectional study of AMR in great horned owls (Bubo virginianus) and barred owls (Strix varia) admitted to a rehabilitation center in the midwestern United States. A combination of selective culture enrichment and shotgun metagenomic sequencing was used to identify ARGs from Enterobacteriaceae. Overall, AMR prevalence was comparable to past studies of resistant Enterobacteriaceae in raptors, with acquired ARGs identified in 23% of samples. Multi-model regression analyses identified seasonality and owl age as important predictors of ARG likelihood, with birds sampled during warmer months more likely to harbor ARGs compared to those from cooler months, and hatch year birds more likely to harbor β-lactam ARGs than adults. Beyond host-specific determinants, ARG-positive owls were also more likely to be recovered from areas of high agricultural land cover. Spatial clustering analyses identified a significant high-risk cluster of tetracycline ARG-positive owls in the southern sampling range, but this could not be explained by any predictor variables. Taken together, these results highlight the complex distribution of AMR in natural environments and suggest that both biological and anthropogenic factors play important roles in determining the emergence and persistence of AMR in wildlife. IMPORTANCE Antimicrobial resistance (AMR) is a multifaceted problem that poses a worldwide threat to human and animal health. Recent reports suggest that wildlife may play an important role in the emergence, dissemination, and persistence of AMR. As such, there have been calls for better integration of wildlife into current research of AMR, including the use of wild animals as bio-sentinels of AMR contamination in the environment. A One Health approach can be used to gain a better understanding of all AMR sources and pathways, particularly those at the human-animal-environment interface. Our study focuses on this interface in order to assess the effect of human-impacted landscapes on AMR in a wild animal. This work highlights the value of wildlife rehabilitation centers for environmental AMR surveillance and demonstrates how metagenomic sequencing within a spatial epidemiology framework can be used to address questions surrounding AMR complexity in natural ecosystems.

Occurrence and Characteristics of ESBL- and Carbapenemase- Producing Escherichia coli from Wild and Feral Birds in Greece

“…Four species; Common buzzard, Short-toed snake eagle, Steppe eagle and Eurasian sparrow hawk, are raptors and two; Steppe eagle and Eurasian magpie, can be considered omnivores and scavengers. Their diet, which is commonly in direct contact with anthropogenic environments and agricultural animals and waste, constitutes a major potential route for ESBL acquisition [41]. Another alternative pathway is the environment inhabited by the aforementioned species, as also applies to the Grey heron, a waterbird.…”

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

“…New methodologies to help elucidate the complexity of the environmental metagenome are being developed and applied (Gupta et al, 2019;Li et al, 2020;Miller et al, 2020;Stanton et al, 2020;Sun et al, 2020;Xu et al, 2020;Zhao et al, 2020;Liu et al, 2021;Zhang et al, 2021). There are, however, few studies that have used optimised sampling and analytical methodologies to identify and quantify the full complexity of the environmental resistome in a representative way (Agunos et al, 2021;de Almeida Kumlien et al, 2021;Strange et al, 2021), particularly in food production settings.…”

Characteristics of Wild Bird Resistomes and Dissemination of Antibiotic Resistance Genes in Interconnected Bird-Habitat Systems Revealed by Similarity of blaTEM Polymorphic Sequences

“…Several studies have characterized resistant bacteria isolated from wild birds, including pigeons, ducks and geese, − cormorants, gulls, − passerines and rooks . Of most concern are bacteria carrying multidrug resistance ARGs such as New Delhi metallo-β-lactamase encoding gene NDM-1 and colistin resistance mcr -1, , which respectively confer resistance to clinically relevant β-lactams and colistin. ,− Several studies have documented that wild birds living in environments affected by human activities generally harbor more ARGs than those in remote areas. , Moreover, bird gut microbiota are influenced by host phylogeny, age, sex, health, diet and other environmental factors, resulting in diverse and dynamic fecal ARG profiles. Birds are exposed to microbes at their foraging or nesting sites and dispose of fecal microbes broadly, representing a potentially important link in ARG exchange and dissemination.…”

“…39,44−50 Several studies have documented that wild birds living in environments affected by human activities generally harbor more ARGs than those in remote areas. 19,51 Moreover, bird gut microbiota are influenced by host phylogeny, age, sex, health, diet and other environmental factors, 52 resulting in diverse and dynamic fecal ARG profiles. Birds are exposed to microbes at their foraging or nesting sites and dispose of fecal microbes broadly, representing a potentially important link in ARG exchange and dissemination.…”