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Brooks MR, Medley S, Ponder M, Alexander KA. Campylobacter in aquatic and terrestrial mammals is driven by life traits: A systematic review and meta-analysis. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1070519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
IntroductionCampylobacter spp. infections are responsible for significant diarrheal disease burden across the globe, with prevalence thought to be increasing. Although wild avian species have been studied as reservoirs of Campylobacter spp., our understanding of the role of wild mammalian species in disease transmission and persistence is limited. Host factors influencing infection dynamics in wild mammals have been neglected, particularly life traits, and the role of these factors in zoonotic spillover risk is largely unknown.MethodsHere, we conducted a systematic literature review, identifying mammalian species that had been tested for Campylobacter spp. infections (molecular and culture based). We used logistic regression to evaluate the relationship between the detection of Campylobacter spp. in feces and host life traits (urban association, trophic level, and sociality).ResultsOur analysis suggest that C. jejuni transmission is associated with urban living and trophic level. The probability of carriage was highest in urban-associated species (p = 0.02793) and the most informative model included trophic level. In contrast, C. coli carriage appears to be strongly influenced by sociality (p = 0.0113) with trophic level still being important. Detection of Campylobacter organisms at the genus level, however, was only associated with trophic level (p = 0.0156), highlighting the importance of this trait in exposure dynamics across host and Campylobacter pathogen systems.DiscussionWhile many challenges remain in the detection and characterization of Camploybacter spp., these results suggest that host life traits may have important influence on pathogen exposure and transmission dynamics, providing a useful starting point for more directed surveillance approaches.
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Townsend AK, Sewall KB, Leonard AS, Hawley DM. Infectious disease and cognition in wild populations. Trends Ecol Evol 2022; 37:899-910. [PMID: 35872026 DOI: 10.1016/j.tree.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/19/2022]
Abstract
Infectious disease is linked to impaired cognition across a breadth of host taxa and cognitive abilities, potentially contributing to variation in cognitive performance within and among populations. Impaired cognitive performance can stem from direct damage by the parasite, the host immune response, or lost opportunities for learning. Moreover, cognitive impairment could be compounded by factors that simultaneously increase infection risk and impair cognition directly, such as stress and malnutrition. As highlighted in this review, however, answers to fundamental questions remain unresolved, including the frequency, duration, and fitness consequences of infection-linked cognitive impairment in wild animal populations, the cognitive abilities most likely to be affected, and the potential for adaptive evolution of cognition in response to accelerating emergence of infectious disease.
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Affiliation(s)
- Andrea K Townsend
- Department of Biology, Hamilton College, 198 College Hill Road, Clinton, NY 13323, USA.
| | - Kendra B Sewall
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Anne S Leonard
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Dana M Hawley
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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Sen K, Berglund T, Patel N, Chhabra N, Ricci DM, Dutta S, Mukhopadhyay AK. Genotypic analyses and antimicrobial resistance profiles of Campylobacter jejuni from crows (Corvidae) of United States and India reflect their respective local antibiotic burdens. J Appl Microbiol 2021; 132:696-706. [PMID: 34260789 DOI: 10.1111/jam.15220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/29/2022]
Abstract
AIM The study examined the hypothesis that crow-borne Campylobacter can function as environmental reservoirs and indicators of antibiotic resistance (AR) determinants circulating in a human population. METHODS AND RESULTS Two species of crows from Washington (WA), United States, and Kolkata, India, respectively, were examined for their ability to carry antibiotic resistant Campylobacter. Campylobacter jejuni was the only species isolated by selective agar plating from crow faecal samples. Disk diffusion method used to compare the AR profile of the isolates showed tetracycline (TET) resistance to be the most prevalent (27%) among WA isolates, followed by ciprofloxacin (CIP; 24%). Among Kolkata isolates, nalidixic acid resistance was most common (36%), followed by CIP (27%). The AR profile demonstrated by crow isolates of WA reflects those reported by the US National Antimicrobial Resistance Monitoring System for human isolates (2007-2011), where resistance to TET was most prevalent (≈45%), followed by quinolones (≈24%). The Kolkata crow isolates reflected the AR profile of human clinical isolates from India, where 97% resistance was shown to quinolones, followed by TET (18%). Multilocus sequence typing of 37 isolates, including 11 water isolates from the crow roost area, showed 24 different sequence types (STs). Seventeen of these were previously found in wild birds, 2 in human diarrhoea, 4 in poultry and 8 in environmental water. One isolate was found in both water and faeces, though from different sites within WA. CONCLUSIONS The results indicate that crows most likely acquire the AR from anthropogenic sources. Although they are colonized by specific STs, rarely isolated from humans, they can facilitate the spread of AR. SIGNIFICANCE AND IMPACT OF THE STUDY By studying two areas in different continents, this research demonstrates that Campylobacter borne by crows can function as environmental reservoirs and indicators of AR determinants that circulate in a human population. This information will be of importance to scientists from the medical and poultry industries.
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Affiliation(s)
- Keya Sen
- Division of Biological Sciences, STEM, University of Washington, Bothell, Washington, USA
| | - Tanner Berglund
- Division of Biological Sciences, STEM, University of Washington, Bothell, Washington, USA
| | - Nidhi Patel
- Division of Biological Sciences, STEM, University of Washington, Bothell, Washington, USA
| | - Neha Chhabra
- Division of Biological Sciences, STEM, University of Washington, Bothell, Washington, USA
| | - David M Ricci
- Division of Biological Sciences, STEM, University of Washington, Bothell, Washington, USA
| | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric disease, Kolkata, India
| | - Asish K Mukhopadhyay
- Division of Bacteriology, National Institute of Cholera and Enteric disease, Kolkata, India
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Wheeler SS, Taff CC, Reisen WK, Townsend AK. Mosquito blood-feeding patterns and nesting behavior of American crows, an amplifying host of West Nile virus. Parasit Vectors 2021; 14:331. [PMID: 34158103 PMCID: PMC8220764 DOI: 10.1186/s13071-021-04827-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/07/2021] [Indexed: 12/02/2022] Open
Abstract
Background Although American crows are a key indicator species for West Nile virus (WNV) and mount among the highest viremias reported for any host, the importance of crows in the WNV transmission cycle has been called into question because of their consistent underrepresentation in studies of Culex blood meal sources. Here, we test the hypothesis that this apparent underrepresentation could be due, in part, to underrepresentation of crow nesting habitat from mosquito sampling designs. Specifically, we examine how the likelihood of a crow blood meal changes with distance to and timing of active crow nests in a Davis, California, population. Methods Sixty artificial mosquito resting sites were deployed from May to September 2014 in varying proximity to known crow nesting sites, and Culex blood meal hosts were identified by DNA barcoding. Genotypes from crow blood meals and local crows (72 nestlings from 30 broods and 389 local breeders and helpers) were used to match mosquito blood meals to specific local crows. Results Among the 297 identified Culex blood meals, 20 (6.7%) were attributable to crows. The mean percentage of blood meals of crow origin was 19% in the nesting period (1 May–18 June 2014), but 0% in the weeks after fledging (19 June–1 September 2014), and the likelihood of a crow blood meal increased with proximity to an active nest: the odds that crows hosted a Culex blood meal were 38.07 times greater within 10 m of an active nest than > 10 m from an active nest. Nine of ten crow blood meals that could be matched to a genotype of a specific crow belonged to either nestlings in these nests or their mothers. Six of the seven genotypes that could not be attributed to sampled birds belonged to females, a sex bias likely due to mosquitoes targeting incubating or brooding females. Conclusion Data herein indicate that breeding crows serve as hosts for Culex in the initial stages of the WNV spring enzootic cycle. Given their high viremia, infected crows could thereby contribute to the re-initiation and early amplification of the virus, increasing its availability as mosquitoes shift to other moderately competent later-breeding avian hosts.![]() Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04827-x.
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Affiliation(s)
- Sarah S Wheeler
- Sacramento-Yolo Mosquito and Vector Control District, 8631 Bond Road, Elk Grove, CA, 95624, USA.
| | - Conor C Taff
- Cornell Lab of Ornithology and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - William K Reisen
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Andrea K Townsend
- Department of Biology, Hamilton College, 198 College Hill Rd, Clinton, NY, 13323, USA
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Bandoy DJDR, Weimer BC. Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation. Sci Rep 2021; 11:7380. [PMID: 33795722 PMCID: PMC8016908 DOI: 10.1038/s41598-021-86265-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/12/2021] [Indexed: 01/10/2023] Open
Abstract
The spread of SARS-CoV-2 created a pandemic crisis with > 150,000 cumulative cases in > 65 countries within a few months. The reproductive number (R) is a metric to estimate the transmission of a pathogen during an outbreak. Preliminary published estimates were based on the initial outbreak in China. Whole genome sequences (WGS) analysis found mutational variations in the viral genome; however, previous comparisons failed to show a direct relationship between viral genome diversity, transmission, and the epidemic severity. COVID-19 incidences from different countries were modeled over the epidemic curve. Estimates of the instantaneous R (Wallinga and Teunis method) with a short and standard serial interval were done. WGS were used to determine the populations genomic variation and that underpinned creation of the pathogen genome identity (GENI) score, which was merged with the outbreak curve in four distinct phases. Inference of transmission time was based on a mutation rate of 2 mutations/month. R estimates revealed differences in the transmission and variable infection dynamics between and within outbreak progression for each country examined. Outside China, our R estimates observed propagating dynamics indicating that other countries were poised to move to the takeoff and exponential stages. Population density and local temperatures had no clear relationship to the outbreak progression. Integration of incidence data with the GENI score directly predicted increases in cases as the genome variation increased that led to new variants. Integrating the outbreak curve, dynamic R, and SNP variation found a direct association between increasing cases and transmission genome evolution. By defining the epidemic curve into four stages and integrating the instantaneous country-specific R with the GENI score, we directly connected changes in individual outbreaks based on changes in the virus genome via SNPs. This resulted in the ability to forecast potential increases in cases as well as mutations that may defeat PCR screening and the infection process. By using instantaneous R estimations and WGS, outbreak dynamics were defined to be linked to viral mutations, indicating that WGS, as a surveillance tool, is required to predict shifts in each outbreak that will provide actionable decision making information. Integrating epidemiology with genome sequencing and modeling allows for evidence-based disease outbreak tracking with predictive therapeutically valuable insights in near real time.
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Affiliation(s)
- D J Darwin R Bandoy
- School of Veterinary Medicine, Population Health and Reproduction, 100K Pathogen Genome Project, University of California Davis, Davis, CA, 95616, USA.,Department of Veterinary Paraclinical Sciences, College of Veterinary Medicine, University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines
| | - Bart C Weimer
- School of Veterinary Medicine, Population Health and Reproduction, 100K Pathogen Genome Project, University of California Davis, Davis, CA, 95616, USA.
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Miller JJ, Weimer BC, Timme R, Lüdeke CHM, Pettengill JB, Bandoy DJD, Weis AM, Kaufman J, Huang BC, Payne J, Strain E, Jones JL. Phylogenetic and Biogeographic Patterns of Vibrio parahaemolyticus Strains from North America Inferred from Whole-Genome Sequence Data. Appl Environ Microbiol 2021; 87:e01403-20. [PMID: 33187991 PMCID: PMC7848924 DOI: 10.1128/aem.01403-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/04/2020] [Indexed: 11/20/2022] Open
Abstract
Vibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States. The draft genomes of 132 North American clinical and oyster V. parahaemolyticus isolates were sequenced to investigate their phylogenetic and biogeographic relationships. The majority of oyster isolate sequence types (STs) were from a single harvest location; however, four were identified from multiple locations. There was population structure along the Gulf and Atlantic Coasts of North America, with what seemed to be a hub of genetic variability along the Gulf Coast, with some of the same STs occurring along the Atlantic Coast and one shared between the coastal waters of the Gulf and those of Washington State. Phylogenetic analyses found nine well-supported clades. Two clades were composed of isolates from both clinical and oyster sources. Four were composed of isolates entirely from clinical sources, and three were entirely from oyster sources. Each single-source clade consisted of one ST. Some human isolates lack tdh, trh, and some type III secretion system (T3SS) genes, which are established virulence genes of V. parahaemolyticus Thus, these genes are not essential for pathogenicity. However, isolates in the monophyletic groups from clinical sources were enriched in several categories of genes compared to those from monophyletic groups of oyster isolates. These functional categories include cell signaling, transport, and metabolism. The identification of genes in these functional categories provides a basis for future in-depth pathogenicity investigations of V. parahaemolyticusIMPORTANCEVibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States and is frequently associated with shellfish consumption. This study contributes to our knowledge of the biogeography and functional genomics of this species around North America. STs shared between the Gulf Coast and the Atlantic seaboard as well as Pacific waters suggest possible transport via oceanic currents or large shipping vessels. STs frequently isolated from humans but rarely, if ever, isolated from the environment are likely more competitive in the human gut than other STs. This could be due to additional functional capabilities in areas such as cell signaling, transport, and metabolism, which may give these isolates an advantage in novel nutrient-replete environments such as the human gut.
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Affiliation(s)
- John J Miller
- FDA, Biostatistics and Bioinformatics Staff, College Park, Maryland, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Bart C Weimer
- University of California-Davis, Institute for Veterinary Medicine, Davis, California, USA
| | - Ruth Timme
- FDA, Division of Microbiology, College Park, Maryland, USA
| | - Catharina H M Lüdeke
- FDA, Division of Seafood Science and Technology, Gulf Coast Seafood Laboratory, Dauphin Island, Alabama, USA
- University of Hamburg, Hamburg School of Food Science, Hamburg, Germany
| | - James B Pettengill
- FDA, Biostatistics and Bioinformatics Staff, College Park, Maryland, USA
| | - DJ Darwin Bandoy
- University of California-Davis, Institute for Veterinary Medicine, Davis, California, USA
| | - Allison M Weis
- University of California-Davis, Institute for Veterinary Medicine, Davis, California, USA
| | | | - B Carol Huang
- University of California-Davis, Institute for Veterinary Medicine, Davis, California, USA
| | - Justin Payne
- FDA, Division of Microbiology, College Park, Maryland, USA
| | - Errol Strain
- FDA, Biostatistics and Bioinformatics Staff, College Park, Maryland, USA
| | - Jessica L Jones
- FDA, Division of Seafood Science and Technology, Gulf Coast Seafood Laboratory, Dauphin Island, Alabama, USA
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Smith OM, Edworthy A, Taylor JM, Jones MS, Tormanen A, Kennedy CM, Fu Z, Latimer CE, Cornell KA, Michelotti LA, Sato C, Northfield T, Snyder WE, Owen JP. Agricultural intensification heightens food safety risks posed by wild birds. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13723] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Olivia M. Smith
- School of Biological Sciences Washington State University Pullman WA USA
- Department of Entomology University of Georgia Athens GA USA
| | - Amanda Edworthy
- Department of Entomology Washington State University Pullman WA USA
- Department of Forest and Conservation Sciences University of British Columbia Vancouver BC USA
| | - Joseph M. Taylor
- Department of Entomology University of Georgia Athens GA USA
- Department of Entomology Washington State University Pullman WA USA
| | - Matthew S. Jones
- Department of Entomology Washington State University Pullman WA USA
- WSU‐Tree Fruit Research and Extension Center Wenatchee WA USA
| | - Aaron Tormanen
- School of Biological Sciences Washington State University Pullman WA USA
- Department of Entomology Washington State University Pullman WA USA
- Department of Biological Sciences Arkansas Tech University Russellville AR USA
| | | | - Zhen Fu
- Department of Entomology Washington State University Pullman WA USA
- Department of Entomology Texas A&M University College Station TX USA
| | | | - Kevin A. Cornell
- School of Biological Sciences Washington State University Pullman WA USA
| | - Lucas A. Michelotti
- Department of Entomology University of Georgia Athens GA USA
- Department of Entomology Washington State University Pullman WA USA
| | - Chika Sato
- School of Biological Sciences Washington State University Pullman WA USA
| | - Tobin Northfield
- Department of Entomology Washington State University Pullman WA USA
- WSU‐Tree Fruit Research and Extension Center Wenatchee WA USA
- Centre for Tropical Environmental Sustainability Science James Cook University Brisbane Qld Australia
| | - William E. Snyder
- Department of Entomology University of Georgia Athens GA USA
- Department of Entomology Washington State University Pullman WA USA
| | - Jeb P. Owen
- Department of Entomology Washington State University Pullman WA USA
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Smith OM, Snyder WE, Owen JP. Are we overestimating risk of enteric pathogen spillover from wild birds to humans? Biol Rev Camb Philos Soc 2020; 95:652-679. [PMID: 32003106 PMCID: PMC7317827 DOI: 10.1111/brv.12581] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 01/07/2023]
Abstract
Enteric illnesses remain the second largest source of communicable diseases worldwide, and wild birds are suspected sources for human infection. This has led to efforts to reduce pathogen spillover through deterrence of wildlife and removal of wildlife habitat, particularly within farming systems, which can compromise conservation efforts and the ecosystem services wild birds provide. Further, Salmonella spp. are a significant cause of avian mortality, leading to additional conservation concerns. Despite numerous studies of enteric bacteria in wild birds and policies to discourage birds from food systems, we lack a comprehensive understanding of wild bird involvement in transmission of enteric bacteria to humans. Here, we propose a framework for understanding spillover of enteric pathogens from wild birds to humans, which includes pathogen acquisition, reservoir competence and bacterial shedding, contact with people and food, and pathogen survival in the environment. We place the literature into this framework to identify important knowledge gaps. Second, we conduct a meta‐analysis of prevalence data for three human enteric pathogens, Campylobacter spp., E. coli, and Salmonella spp., in 431 North American breeding bird species. Our literature review revealed that only 3% of studies addressed the complete system of pathogen transmission. In our meta‐analysis, we found a Campylobacter spp. prevalence of 27% across wild birds, while prevalence estimates of pathogenic E. coli (20%) and Salmonella spp. (6.4%) were lower. There was significant bias in which bird species have been tested, with most studies focusing on a small number of taxa that are common near people (e.g. European starlings Sturnus vulgaris and rock pigeons Columba livia) or commonly in contact with human waste (e.g. gulls). No pathogen prevalence data were available for 65% of North American breeding bird species, including many commonly in contact with humans (e.g. black‐billed magpie Pica hudsonia and great blue heron Ardea herodias), and our metadata suggest that some under‐studied species, taxonomic groups, and guilds may represent equivalent or greater risk to human infection than heavily studied species. We conclude that current data do not provide sufficient information to determine the likelihood of enteric pathogen spillover from wild birds to humans and thus preclude management solutions. The primary focus in the literature on pathogen prevalence likely overestimates the probability of enteric pathogen spillover from wild birds to humans because a pathogen must survive long enough at an infectious dose and be a strain that is able to colonize humans to cause infection. We propose that future research should focus on the large number of under‐studied species commonly in contact with people and food production and demonstrate shedding of bacterial strains pathogenic to humans into the environment where people may contact them. Finally, studies assessing the duration and intensity of bacterial shedding and survival of bacteria in the environment in bird faeces will help provide crucial missing information necessary to calculate spillover probability. Addressing these essential knowledge gaps will support policy to reduce enteric pathogen spillover to humans and enhance bird conservation efforts that are currently undermined by unsupported fears of pathogen spillover from wild birds.
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Affiliation(s)
- Olivia M Smith
- School of Biological Sciences, Washington State University, P.O. Box 644236, Pullman, WA, 99164, U.S.A
| | - William E Snyder
- Department of Entomology, Washington State University, 100 Dairy Road, P.O. Box 646382, Pullman, WA, 99164, U.S.A
| | - Jeb P Owen
- Department of Entomology, Washington State University, 100 Dairy Road, P.O. Box 646382, Pullman, WA, 99164, U.S.A
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Cockerham S, Lee B, Orben RA, Suryan RM, Torres LG, Warzybok P, Bradley R, Jahncke J, Young HS, Ouverney C, Shaffer SA. Microbial Ecology of the Western Gull (Larus occidentalis). MICROBIAL ECOLOGY 2019; 78:665-676. [PMID: 30891612 DOI: 10.1007/s00248-019-01352-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Avian species host diverse communities of microorganisms which have important roles in the life of birds, including increased metabolism, protection from disease, and immune system development. Along with high human populations and a diversity of human uses of coastal zones, anthropogenic food sources are becoming increasingly available to some species, including gulls. Anthropogenic associations increase the likelihood of encountering foreign or pathogenic bacteria. Diseases in birds caused by bacteria are a substantial source of avian mortality; therefore, it is essential to characterize the microbiome of seabirds. Here, we determined both core and environmentally derived microbial communities of breeding western gulls (Larus occidentalis) from six colonies in California and Oregon. Using DNA extracted from bacterial swabs of the bill, cloaca, and feet of gulls, 16S rRNA gene sequencing was performed targeting the V4 region. We identified a total of 8542 operational taxonomic units (OTUs) from 75 gulls. Sixty-eight OTUs were identified in gulls from all six colonies with the greatest representation from phyla's of Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Overall, microbial richness based on Chao's Abundance-based Coverage Estimator (ACE) index was similar for all colonies (mean = 2347 OTUs) with the smallest coastal colonies having the highest richness (mean = 2626 OTUs) and the largest colonies, located farther off-shore, having the lowest (mean = 2068 OTUs). This survey represents the most in-depth assessment to date of microbes associated with western gulls, and the first study to identify both species-specific and environmentally derived bacteria across multiple populations.
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Affiliation(s)
- Susan Cockerham
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA.
| | - Becky Lee
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA
| | - Rachael A Orben
- Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR, 97365, USA
| | - Robert M Suryan
- Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR, 97365, USA
- Alaska Fisheries Science Center, Auke Bay Laboratories, NOAA Fisheries, 17109 Pt. Lena Loop Rd, Juneau, AK, 99801, USA
| | - Leigh G Torres
- Department of Fisheries and Wildlife, Marine Mammal Institute, Oregon State University, Hatfield Marine Science Center, Newport, OR, 97365, USA
| | - Pete Warzybok
- Point Blue Conservation Science, 2030 SE Marine Science Dr., Petaluma, CA, USA
| | - Russell Bradley
- Point Blue Conservation Science, 2030 SE Marine Science Dr., Petaluma, CA, USA
| | - Jaime Jahncke
- Point Blue Conservation Science, 2030 SE Marine Science Dr., Petaluma, CA, USA
| | - Hillary S Young
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Cleber Ouverney
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA
| | - Scott A Shaffer
- Department of Biological Sciences, San José State University, One Washington Square, San Jose, CA, 95192-0100, USA
- Institute of Marine Sciences, University of California, Santa Cruz, CA, USA
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11
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Navarro J, Grémillet D, Afán I, Miranda F, Bouten W, Forero MG, Figuerola J. Pathogen transmission risk by opportunistic gulls moving across human landscapes. Sci Rep 2019; 9:10659. [PMID: 31337777 PMCID: PMC6650491 DOI: 10.1038/s41598-019-46326-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/21/2019] [Indexed: 01/19/2023] Open
Abstract
Wildlife that exploit human-made habitats hosts and spreads bacterial pathogens. This shapes the epidemiology of infectious diseases and facilitates pathogen spill-over between wildlife and humans. This is a global problem, yet little is known about the dissemination potential of pathogen-infected animals. By combining molecular pathogen diagnosis with GPS tracking of pathogen-infected gulls, we show how this knowledge gap could be filled at regional scales. Specifically, we generated pathogen risk maps of Salmonella, Campylobacter and Chlamydia based on the spatial movements of pathogen-infected yellow-legged gulls (Larus michahellis) equipped with GPS recorders. Also, crossing this spatial information with habitat information, we identified critical habitats for the potential transmission of these bacteria in southern Europe. The use of human-made habitats by infected-gulls could potentially increase the potential risk of direct and indirect bidirectional transmission of pathogens between humans and wildlife. Our findings show that pathogen-infected wildlife equipped with GPS recorders can provide accurate information on the spatial spread risk for zoonotic bacteria. Integration of GPS-tracking with classical epidemiological approaches may help to improve zoonosis surveillance and control programs.
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Affiliation(s)
- Joan Navarro
- Institut de Ciències del Mar - CSIC, Barcelona, Spain.
| | - David Grémillet
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS - Université de Montpellier, Université Paul-Valéry Montpellier - EPHE, Montpellier, France
- FitzPatrick Institute, University of Cape Town, Rondebosch, South Africa
| | - Isabel Afán
- Estación Biológica de Doñana - CSIC, Sevilla, Spain
| | | | - Willem Bouten
- Computational Geo-Ecology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | | | - Jordi Figuerola
- Estación Biológica de Doñana - CSIC, Sevilla, Spain
- CIBER Epidemiología y Salud Pública (CIBER-ESP), Sevilla, Spain
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12
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Ahlstrom CA, Bonnedahl J, Woksepp H, Hernandez J, Reed JA, Tibbitts L, Olsen B, Douglas DC, Ramey AM. Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial-resistant Escherichia coli on the Kenai Peninsula, Alaska. Mol Ecol 2019; 28:2531-2545. [PMID: 30980689 DOI: 10.1111/mec.15101] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/20/2022]
Abstract
Gulls (Larus spp.) have frequently been reported to carry Escherichia coli exhibiting antimicrobial resistance (AMR E. coli); however, the pathways governing the acquisition and dispersal of such bacteria are not well described. We equipped 17 landfill-foraging gulls with satellite transmitters and collected gull faecal samples longitudinally from four locations on the Kenai Peninsula, Alaska to assess: (a) gull attendance and transitions between sites, (b) spatiotemporal prevalence of faecally shed AMR E. coli, and (c) genomic relatedness of AMR E. coli isolates among sites. We also sampled Pacific salmon (Oncorhynchus spp.) harvested as part of personal-use dipnet fisheries at two sites to assess potential contamination with AMR E. coli. Among our study sites, marked gulls most commonly occupied the lower Kenai River (61% of site locations) followed by the Soldotna landfill (11%), lower Kasilof River (5%) and upper Kenai River (<1%). Gulls primarily moved between the Soldotna landfill and the lower Kenai River (94% of transitions among sites), which were also the two locations with the highest prevalence of AMR E. coli. There was relatively high spatial and temporal variability in AMR E. coli prevalence in gull faeces and there was no evidence of contamination on salmon harvested in personal-use fisheries. We identified E. coli sequence types and AMR genes of clinical importance, with some isolates possessing genes associated with resistance to as many as eight antibiotic classes. Our findings suggest that gulls acquire AMR E. coli at habitats with anthropogenic inputs and subsequent movements may represent pathways through which AMR is dispersed.
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Affiliation(s)
| | - Jonas Bonnedahl
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.,Department of Infectious Diseases, Kalmar County Council, Kalmar, Sweden
| | - Hanna Woksepp
- Research Section, Department of Development and Public Health, Kalmar County Hospital, Kalmar, Sweden
| | - Jorge Hernandez
- Department of Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden
| | - John A Reed
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska
| | - Lee Tibbitts
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska
| | - Björn Olsen
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - David C Douglas
- U.S. Geological Survey, Alaska Science Center, Juneau, Alaska
| | - Andrew M Ramey
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska
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13
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Kovanen S, Rossi M, Pohja-Mykrä M, Nieminen T, Raunio-Saarnisto M, Sauvala M, Fredriksson-Ahomaa M, Hänninen ML, Kivistö R. Population Genetics and Characterization of Campylobacter jejuni Isolates from Western Jackdaws and Game Birds in Finland. Appl Environ Microbiol 2019; 85:e02365-18. [PMID: 30552190 PMCID: PMC6365822 DOI: 10.1128/aem.02365-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/08/2018] [Indexed: 01/18/2023] Open
Abstract
Poultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterized Campylobacter jejuni from western jackdaws (n = 91, 43%), mallard ducks (n = 82, 76%), and pheasants (n = 9, 9%). Most of the western jackdaw and mallard duck C. jejuni isolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdaw C. jejuni isolates, e.g., a novel cdtABC gene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention.IMPORTANCE The roles of environmental reservoirs, including wild birds, in the molecular epidemiology of Campylobacter jejuni have not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they had C. jejuni genomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships of C. jejuni isolates.
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Affiliation(s)
- Sara Kovanen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mirko Rossi
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mari Pohja-Mykrä
- Ruralia Institute, Faculty of Agriculture and Forestry, University of Helsinki, Seinäjoki, Finland
| | - Timo Nieminen
- Ruralia Institute, Faculty of Agriculture and Forestry, University of Helsinki, Seinäjoki, Finland
| | | | - Mikaela Sauvala
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Maria Fredriksson-Ahomaa
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Rauni Kivistö
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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14
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Townsend AK, Taff CC, Jones ML, Getman KH, Wheeler SS, Hinton MG, Logsdon RM. Apparent inbreeding preference despite inbreeding depression in the American crow. Mol Ecol 2019; 28:1116-1126. [PMID: 30222228 DOI: 10.1111/mec.14866] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 08/18/2018] [Accepted: 09/04/2018] [Indexed: 11/28/2022]
Abstract
Although matings between relatives can have negative effects on offspring fitness, apparent inbreeding preference has been reported in a growing number of systems, including those with documented inbreeding depression. Here, we examined evidence for inbreeding depression and inbreeding preference in two populations (Clinton, New York, and Davis, California, USA) of the cooperatively breeding American crow (Corvus brachyrhynchos). We then compared observed inbreeding strategies with theoretical expectations for optimal, adaptive levels of inbreeding, given the inclusive fitness benefits and population-specific magnitude of inbreeding depression. We found that low heterozygosity at a panel of 33 microsatellite markers was associated with low survival probability (fledging success) and low white blood cell counts among offspring in both populations. Despite these costs, our data were more consistent with inbreeding preference than avoidance: The observed heterozygosity among 396 sampled crow offspring was significantly lower than expected if local adults were mating by random chance. This pattern was consistent across a range of spatial scales in both populations. Adaptive levels of inbreeding, given the magnitude of inbreeding depression, were predicted to be very low in the California population, whereas complete disassortative mating was predicted in the New York population. Sexual conflict might have contributed to the apparent absence of inbreeding avoidance in crows. These data add to an increasing number of examples of an "inbreeding paradox," where inbreeding appears to be preferred despite inbreeding depression.
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Affiliation(s)
| | - Conor C Taff
- Cornell University Laboratory of Ornithology, Ithaca, New York
| | - Melissa L Jones
- Avian Sciences Graduate Group, University of California, Davis, California
| | | | - Sarah S Wheeler
- Sacramento-Yolo Mosquito and Vector Control District, Elk Grove, California
| | - Mitch G Hinton
- Animal Behavior Graduate Group, University of California, Davis, California
| | - Ryane M Logsdon
- Animal Behavior Graduate Group, University of California, Davis, California
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15
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Townsend AK, Taff CC, Wheeler SS, Weis AM, Hinton MG, Jones ML, Logsdon RM, Reisen WK, Freund D, Sehgal RNM, Saberi M, Suh YH, Hurd J, Boyce WM. Low heterozygosity is associated with vector‐borne disease in crows. Ecosphere 2018. [DOI: 10.1002/ecs2.2407] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
| | - Conor C. Taff
- Cornell University Laboratory of Ornithology Ithaca New York 14850 USA
| | - Sarah S. Wheeler
- Sacramento‐Yolo Mosquito and Vector Control District Elk Grove California 95624 USA
| | - Allison M. Weis
- Department of Population Health and Reproduction School of Veterinary Medicine 100K Pathogen Genome Project University of California Davis California 95616 USA
| | - Mitch G. Hinton
- Animal Behavior Graduate Group University of California Davis California 95616 USA
| | - Melissa L. Jones
- Avian Sciences Graduate Group University of California Davis California 95616 USA
| | - Ryane M. Logsdon
- Animal Behavior Graduate Group University of California Davis California 95616 USA
| | - William K. Reisen
- Department of Pathology, Microbiology, and Immunology School of Veterinary Medicine University of California Davis California 95616 USA
| | - David Freund
- Department of Biology San Francisco State University San Francisco California 94132 USA
| | - Ravinder N. M. Sehgal
- Department of Biology San Francisco State University San Francisco California 94132 USA
| | - Mojan Saberi
- Department of Wildlife, Fish, and Conservation Biology University of California Davis California 95616 USA
| | - Young Ha Suh
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York 14853 USA
| | - Jacqueline Hurd
- Department of Wildlife, Fish, and Conservation Biology University of California Davis California 95616 USA
| | - Walter M. Boyce
- Department of Pathology, Microbiology, and Immunology School of Veterinary Medicine University of California Davis California 95616 USA
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16
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Schapheer C, Sandoval G, Villagra CA. Pest Cockroaches May Overcome Environmental Restriction Due to Anthropization. JOURNAL OF MEDICAL ENTOMOLOGY 2018; 55:1357-1364. [PMID: 29889262 DOI: 10.1093/jme/tjy090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Our species have altered their surroundings since its early dispersion on Earth. Unfortunately, thanks to human-modified habitats, several pest organisms such as domiciliary insects have expanded their distributions. Moreover, pest-related microorganisms may also be aided by anthropization. Pest cockroaches are globally distributed and capable of carrying several diseases. We explored if urbanization may buffer environmental conditions allowing pest insects to expand their distribution. Specifically, we suggest that human settlements may generate suitable microhabitats for synanthropic cockroaches, helping them to survive and establish with disregard to overall climatic restrictions. To test this idea we studied the distribution of pest cockroaches spanning the length of Chilean territory. Chile, along its 4270 km length north to south extent, is a country offering a formidable sampling of Earth's climatic diversity accompanied by dense urbanizations. We studied entomological collections and spatially analyzed pest cockroach distribution found in Chile and discovered that synanthropic cockroach populations are consistently concentrated near most urban developed zones of the country and not limited by overall temperature. Furthermore, health-concern pest cockroach species were widely distributed in Chilean territory, found even in its most southern urban centers as well as Easter Island. Therefore, these disease vectors could exist even in isolated and extreme climatic zones as long as urbanization provides the adequate microhabitat. We discuss the need for further research in order to assess if these distributions can be extrapolated to the pathogenic strains these pest insects may be carrying as reported in other regions of the planet.
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Affiliation(s)
- Constanza Schapheer
- Laboratorio de Sistemática y Evolución de Plantas, Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Avenida Santa Rosa, La Pintana, Santiago, Chile
| | - Gino Sandoval
- Departamento de Historia y Geografía, Facultad de Historia, Geografía y Letras, Universidad Metropolitana de Ciencias de la Educación, Ñuñoa, Santiago de Chile
| | - Cristian A Villagra
- Instituto de Entomología, Facultad de Ciencias Básicas, Universidad Metropolitana de Ciencias de la Educación, Ñuñoa, Santiago de Chile
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17
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Bulbow H, Wu J, Turner D, McEntire M, Tizard I. Campylobacter colonization is not associated with proventricular dilatation disease in psittacines. VETERINARY MEDICINE-RESEARCH AND REPORTS 2018; 8:37-40. [PMID: 30050854 PMCID: PMC6042502 DOI: 10.2147/vmrr.s137213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Psittacine proventricular dilatation disease (PDD) is a neurological disease caused by parrot bornaviruses. A competing theory suggests that intestinal colonization by Campylobacter species may also be a potential cause of PDD or that their presence may be required for disease development. This theory proposes that PDD results from the activities of antiganglioside antibodies on enteric neurons in a manner similar to the pathogenesis of Guillain–Barré syndrome in humans. We therefore cultured feces from domestic chickens as well as from multiple parrot species to determine whether Campylobacter spp. could be detected in the latter. We failed to detect Campylobacter in a flock of cockatiels known to be highly susceptible to experimental parrot bornavirus-induced PDD. Even in naturally infected psittacines suffering from clinical PDD, no Campylobacter species were detected. Conversely, Campylobacter was readily cultured from domestic poultry samples and confirmed by using matrix-associated laser desorption ionization mass spectroscopy/real-time polymerase chain reaction. We conclude that not only are Campylobacter infections of psittacines uncommon, but also that infection by Campylobacter species is not related to the etiology of PDD.
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Affiliation(s)
- Holden Bulbow
- Schubot Exotic Bird Health Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA,
| | - Jing Wu
- Schubot Exotic Bird Health Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA,
| | - Debra Turner
- Schubot Exotic Bird Health Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA,
| | - Michael McEntire
- Schubot Exotic Bird Health Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA,
| | - Ian Tizard
- Schubot Exotic Bird Health Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA,
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18
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Janecko N, Halova D, Jamborova I, Papousek I, Masarikova M, Dolejska M, Literak I. Occurrence of plasmid-mediated quinolone resistance genes in Escherichia coli and Klebsiella spp. recovered from Corvus brachyrhynchos and Corvus corax roosting in Canada. Lett Appl Microbiol 2018; 67:130-135. [PMID: 29675942 DOI: 10.1111/lam.12993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 11/28/2022]
Abstract
The spread of antimicrobial resistance from human activity derived sources to natural habitats implicates wildlife as potential vectors of antimicrobial resistance transfer. Wild birds, including corvid species can disseminate mobile genetic resistance determinants through faeces. This study aimed to determine the occurrence of plasmid-mediated quinolone resistance (PMQR) genes in Escherichia coli and Klebsiella spp. isolates obtained from winter roosting sites of American crows (Corvus brachyrhynchos) and common ravens (Corvus corax) in Canada. Faecal swabs were collected at five roosting sites across Canada. Selective media isolation and multiplex PCR screening was utilized to identify PMQR genes followed by gene sequencing, pulse-field gel electrophoresis and multilocus sequence typing to characterize isolates. Despite the low prevalence of E. coli containing PMQR (1·3%, 6/449), qnrS1, qnrB19, qnrC, oqxAB and aac(6')-Ib-cr genes were found in five sequence types (ST), including E. coli ST 131. Conversely, one isolate of Klebsiella pneumoniae contained the plasmid-mediated resistance gene qnrB19. Five different K. pneumoniae STs were identified, including two novel types. The occurrence of PMQR genes and STs of public health significance in E. coli and Klebsiella pneumoniae recovered from corvids gives further evidence of the anthropogenic derived dissemination of antimicrobial resistance determinants at the human activity-wildlife-environment interface. SIGNIFICANCE AND IMPACT OF THE STUDY This study examined large corvids as possible vector species for the dissemination of antimicrobial resistance in indicator and pathogenic bacteria as a means to assess the anthropogenic dissemination of plasmid-mediated quinolone resistance (PMQR) genes. Although rare, PMQR genes were found among corvid populations across Canada. The clinically important Escherichia coli strain ST131 containing aac(6')-Ib-cr gene along with a four-class phenotypic antimicrobial resistance (AMR) pattern as well as one Klebsiella pneumoniae strain containing a qnrB19 gene were identified in one geographical location. Corvids are a viable vector for the circulation of PMQR genes and clinically important clones in wide-ranging environments.
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Affiliation(s)
- N Janecko
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,Department of Population Medicine, University of Guelph, Guelph, ON, Canada
| | - D Halova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - I Jamborova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - I Papousek
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - M Masarikova
- CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - M Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - I Literak
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
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19
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Lawton SJ, Weis AM, Byrne BA, Fritz H, Taff CC, Townsend AK, Weimer BC, Mete A, Wheeler S, Boyce WM. Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing. J Vet Diagn Invest 2018; 30:354-361. [PMID: 29528812 PMCID: PMC6505823 DOI: 10.1177/1040638718762562] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared to conventional biochemical testing methods and nucleic acid analyses (16S rDNA sequencing, hippurate hydrolysis gene testing, whole genome sequencing [WGS]) for species identification of Campylobacter isolates obtained from chickens ( Gallus gallus domesticus, n = 8), American crows ( Corvus brachyrhynchos, n = 17), a mallard duck ( Anas platyrhynchos, n = 1), and a western scrub-jay ( Aphelocoma californica, n = 1). The test results for all 27 isolates were in 100% agreement between MALDI-TOF MS, the combined results of 16S rDNA sequencing, and the hippurate hydrolysis gene PCR ( p = 0.0027, kappa = 1). Likewise, the identifications derived from WGS from a subset of 14 isolates were in 100% agreement with the MALDI-TOF MS identification. In contrast, biochemical testing misclassified 5 isolates of C. jejuni as C. coli, and 16S rDNA sequencing alone was not able to differentiate between C. coli and C. jejuni for 11 sequences ( p = 0.1573, kappa = 0.0857) when compared to MALDI-TOF MS and WGS. No agreement was observed between MALDI-TOF MS dendrograms and the phylogenetic relationships revealed by rDNA sequencing or WGS. Our results confirm that MALDI-TOF MS is a fast and reliable method for identifying Campylobacter isolates to the species level from wild birds and chickens, but not for elucidating phylogenetic relationships among Campylobacter isolates.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Walter M. Boyce
- Walter M. Boyce, Department
of Pathology, Microbiology and Immunology, University of California, Davis, 1
Shields Avenue, Davis, CA 95616.
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20
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Okamura M, Kaneko M, Ojima S, Sano H, Shindo J, Shirafuji H, Yamamoto S, Tanabe T, Yoshikawa Y, Hu DL. Differential Distribution of Salmonella Serovars and Campylobacter spp. Isolates in Free-Living Crows and Broiler Chickens in Aomori, Japan. Microbes Environ 2018; 33:77-82. [PMID: 29491247 PMCID: PMC5877346 DOI: 10.1264/jsme2.me17183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 12/26/2017] [Indexed: 11/12/2022] Open
Abstract
Salmonella and Campylobacter cause foodborne enteritis mainly via the consumption of raw/undercooked contaminated poultry meat and products. Broiler flocks are primarily colonized with these bacteria; however, the underlying etiology remains unclear. The present study was conducted in order to obtain further information on the prevalence and genotypic distribution of Salmonella and Campylobacter in free-living crows and broiler flocks in a region for 2 years, thereby facilitating estimations of the potential risk of transmission of C. jejuni from crows to broiler flocks. Salmonella serovars Bredeney and Derby were isolated from 8 and 3 out of 123 captured crows, respectively, both of which are not common in broiler chickens. Campylobacter were isolated from all 89 crows tested and C. jejuni was prevalent (85 crows). Pulsed field gel electrophoresis showed broad diversity in the crow isolates of C. jejuni. However, 3 crow isolates and 2 broiler isolates showing similar banding patterns were assigned to different sequence types in multi-locus sequence typing. These results indicate that crows do not share Salmonella serovars with broilers, and harbor various genotypes of C. jejuni that differ from those of broiler flocks. Thus, our results indicate that crows are not a potential vector of these bacteria to broiler flocks in this region.
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Affiliation(s)
- Masashi Okamura
- Laboratory of Zoonoses, Kitasato University School of Veterinary MedicineTowada, AomoriJapan
| | - Miyuki Kaneko
- Laboratory of Zoonoses, Kitasato University School of Veterinary MedicineTowada, AomoriJapan
| | - Shinjiro Ojima
- Laboratory of Zoonoses, Kitasato University School of Veterinary MedicineTowada, AomoriJapan
| | - Hiroki Sano
- Laboratory of Zoonoses, Kitasato University School of Veterinary MedicineTowada, AomoriJapan
| | - Junji Shindo
- Laboratory of Wildlife Science, Kitasato University School of Veterinary MedicineTowada, AomoriJapan
| | - Hiroaki Shirafuji
- Subtropical Disease Control Unit, Division of Transboundary Animal Diseases, Kyusyu Research Station, National Institute of Animal Health, National Agriculture and Food Research OrganizationChuzan, KagoshimaJapan
| | - Satomi Yamamoto
- Laboratory of Microbiology, Kitasato University School of Veterinary MedicineTowada, AomoriJapan
| | - Taishi Tanabe
- Laboratory of Microbiology, Kitasato University School of Veterinary MedicineTowada, AomoriJapan
| | - Yasuhiro Yoshikawa
- Faculty of Risk and Crisis Management, Chiba Institute of ScienceChoshi, ChibaJapan
| | - Dong-Liang Hu
- Laboratory of Zoonoses, Kitasato University School of Veterinary MedicineTowada, AomoriJapan
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21
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Abstract
The 100K Pathogen Genome Project is producing draft and closed genome sequences from diverse pathogens. This project expanded globally to include a snapshot of global bacterial genome diversity. The genomes form a sequence database that has a variety of uses from systematics to public health.
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22
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Draft Genome Sequence of Multidrug-Resistant Abortive Campylobacter jejuni from Northern California. GENOME ANNOUNCEMENTS 2017; 5:5/15/e00171-17. [PMID: 28408683 PMCID: PMC5391421 DOI: 10.1128/genomea.00171-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Campylobacter jejuni is an enteric bacterium that can cause abortion in livestock. This is the release of a multidrug-resistant Campylobacter jejuni genome from an isolate that caused an abortion in a cow in northern California. This isolate is part of the 100K Pathogen Genome Project.
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23
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Large-Scale Release of Campylobacter Draft Genomes: Resources for Food Safety and Public Health from the 100K Pathogen Genome Project. GENOME ANNOUNCEMENTS 2017; 5:5/1/e00925-16. [PMID: 28057746 PMCID: PMC5255908 DOI: 10.1128/genomea.00925-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Campylobacter is a food-associated bacterium and a leading cause of foodborne illness worldwide, being associated with poultry in the food supply. This is the initial public release of 202 Campylobacter genome sequences as part of the 100K Pathogen Genome Project. These isolates represent global genomic diversity in the Campylobacter genus.
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24
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Draft Genome Sequences of Campylobacter jejuni Strains That Cause Abortion in Livestock. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01324-16. [PMID: 27908990 PMCID: PMC5137404 DOI: 10.1128/genomea.01324-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. This publication announces the public release of 15 Campylobacter jejuni genome sequences from isolates linked to abortion in livestock. These isolates are part of the 100K Pathogen Genome Project and are from clinical cases at the University of California (UC) Davis.
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25
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Genomic Comparison of Campylobacter spp. and Their Potential for Zoonotic Transmission between Birds, Primates, and Livestock. Appl Environ Microbiol 2016; 82:7165-7175. [PMID: 27736787 DOI: 10.1128/aem.01746-16] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/30/2016] [Indexed: 12/30/2022] Open
Abstract
Campylobacter is the leading cause of human gastroenteritis worldwide. Wild birds, including American crows, are abundant in urban, suburban, and agricultural settings and are likely zoonotic vectors of Campylobacter Their proximity to humans and livestock increases the potential spreading of Campylobacter via crows between the environment, livestock, and humans. However, no studies have definitively demonstrated that crows are a vector for pathogenic Campylobacter We used genomics to evaluate the zoonotic and pathogenic potential of Campylobacter from crows to other animals with 184 isolates obtained from crows, chickens, cows, sheep, goats, humans, and nonhuman primates. Whole-genome analysis uncovered two distinct clades of Campylobacter jejuni genotypes; the first contained genotypes found only in crows, while a second genotype contained "generalist" genomes that were isolated from multiple host species, including isolates implicated in human disease, primate gastroenteritis, and livestock abortion. Two major β-lactamase genes were observed frequently in these genomes (oxa-184, 55%, and oxa-61, 29%), where oxa-184 was associated only with crows and oxa-61 was associated with generalists. Mutations in gyrA, indicative of fluoroquinolone resistance, were observed in 14% of the isolates. Tetracycline resistance (tetO) was present in 22% of the isolates, yet it occurred in 91% of the abortion isolates. Virulence genes were distributed throughout the genomes; however, cdtC alleles recapitulated the crow-only and generalist clades. A specific cdtC allele was associated with abortion in livestock and was concomitant with tetO These findings indicate that crows harboring a generalist C. jejuni genotype may act as a vector for the zoonotic transmission of Campylobacter IMPORTANCE: This study examined the link between public health and the genomic variation of Campylobacter in relation to disease in humans, primates, and livestock. Use of large-scale whole-genome sequencing enabled population-level assessment to find new genes that are linked to livestock disease. With 184 Campylobacter genomes, we assessed virulence traits, antibiotic resistance susceptibility, and the potential for zoonotic transfer to observe that there is a "generalist" genotype that may move between host species.
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