Temporal variations in patterns of Escherichia coli strain diversity and antimicrobial resistance in the migrant Egyptian vulture

References

• Souza V, Rocha M, Valera A, et al. Genetic structure of natural populations of Escherichia coli in wild hosts on different continents. Appl Environ Microbiol. 1999;65:1–11.
   Web of Science ®Google Scholar
• Gordon DM, Cowling A. The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects. Microbiology. 2003;149:3575–3586.
   PubMed Web of Science ®Google Scholar
• Escobar-Paramo P, Le Menac’h A, Le Gall T, et al. Identification of forces shaping the commensal Escherichia coli genetic structure by comparing animal and human isolates. Environ Microbiol. 2006;8:1975–1984.
   PubMed Web of Science ®Google Scholar
• Tenaillon O, Skurnik D, Picard B, et al. The population genetics of commensal Escherichia coli. Nat Rev Microbiol. 2010;8:207–217.
   PubMed Web of Science ®Google Scholar
• Vittecoq M, Durand P, Brazier L, et al. Antimicrobial resistance in wildlife. J Appl Ecol. 2016;53:519–529.
   Web of Science ®Google Scholar
• Williams N, Sherlock C, Jones T, et al. The prevalence of antimicrobial-resistant Escherichia coli in sympatric wild rodents varies by season and host. J Appl Microbiol. 2011;110:962‒970.
   Web of Science ®Google Scholar
• Fluckey WM, Loneragan WGH, Warner R, et al. Antimicrobial drug resistance of Salmonella and Escherichia coli isolates from cattle feces, hides, and carcasses. J Food Prot. 2007;70:551–556.
   Web of Science ®Google Scholar
• Salehi TZ, Bonab SF. Antibiotics susceptibility pattern of Escherichia coli strains isolated from chickens with Colisepticemia in Tabriz province, Iran. Int J Poult Sci. 2006;5:677–684.
   Google Scholar
• Skurnik D, Ruimy R, Andremont A, et al. Effect of human vicinity on antimicrobial resistance and integrons in animal faecal Escherichia coli. J Antimicrob Chemother. 2006;57:1215–1219.
   PubMed Web of Science ®Google Scholar
• Blyton MDJ, Pi H, Vangchhia B, et al. Genetic structure and antimicrobial resistance of Escherichia coli and cryptic clades in birds with diverse human associations. Appl Environ Microbiol. 2015;81:5123–5133.
   Web of Science ®Google Scholar
• Allen HK, Donato J, Wang HH, et al. Call of the wild: antibiotic resistance genes in natural environments. Nat Rev Microbiol. 2010;8:251–259.
   PubMed Web of Science ®Google Scholar
• Radhouani H, Silva N, Poeta P, et al. Potential impact of antimicrobial resistance in wildlife, environment, and human health. Front Microbiol. 2014;5:1–12.
   PubMed Web of Science ®Google Scholar
• Gordon DM. Geographical structure and host specificity in bacteria and the implications for tracing the source of coliform contamination. Microbiol. 2001;147:1079–1085.
   PubMed Web of Science ®Google Scholar
• Sherley M, Gordon D, Cillingnon P. Variations in antibiotic resistance profiles of Enterobacteriaceae isolated from wild Australian mammals. Env Microbiol. 2000;2:620–631.
   PubMed Web of Science ®Google Scholar
• Carlos C, Pires MM, Stoppe NC, et al. Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination. BMC Microbiol. 2010;10:161.
   PubMed Web of Science ®Google Scholar
• Hernandez J, Bonnedahl J, Eliasson I, et al. Globally disseminated human path- ogenic Escherichia coli of O25b- ST131 clone, harbouring blaCTX- M-15, found in glaucous-winged gull at remote Commander Islands, Russia. Environ Microbiol Rep. 2010;2:329–332.
   PubMed Web of Science ®Google Scholar
• Guenther S, Ewers C, Wieler LH, et al. Extended-spectrum beta-lactamases producing E. coli in wildlife, yet another form of environmental pollution? Front Microbiol. 2011;2:1–13.
   Web of Science ®Google Scholar
• Iñigo A, Barov B, Orhun C, et al. Action plan for the Egyptian vulture Neophron percnopterus in the European union. BirdLife International for the European Commission2008;62 pp. .
   Google Scholar
• Margalida A, García D, Cortéz-Avizanda A. Factors influencing the breeding density of Bearded vultures, Egyptian vultures and Eurasian griffon vultures in Catalonia (NE Spain): management implications. Anim Biodiv Conserv. 2000;30:189–200.
   Google Scholar
• López-López P, García-Ripollés C, Urios V. Individual repeatability in timing and spatial flexibility of migration routes of trans-Saharan migratory raptors. Curr Zool. 2014;60:642‒652.
   Web of Science ®Google Scholar
• Ragg J, Mackintosh C, Moller H. The scavenging behaviour of ferrets (Mustela furo), feral cats (Felis domesticus), possums (Trichosurus vulpecula), hedgehogs (Erinaceus europaeus) and harrier hawks (Circus approximans) on pastoral farmland in New Zealand: implications for bovine tuberculosis transmission. N Z Vet J. 2000;48:166–175.
   PubMed Web of Science ®Google Scholar
• Kang H, Jeong Y, Oh J, et al. Characterization of antimicrobial resistance and class 1 integrons found in Escherichia coli isolates from humans and animals in Korea. J Antimicrob Chemother. 2005;55:639–644.
   PubMed Web of Science ®Google Scholar
• Barrow GI, Feltham RKA. Cowan and Steel’s manual for the identification of medical bacteria. London: Cambridge University Press; 2004.
   Google Scholar
• Cohen O, Gophan U, Pupko T. The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol. 2011;28:1481–1489.
   Web of Science ®Google Scholar
• Seurinck S, Verstraete W, Siciliano SD. Use of 16S-23S rRNA intergenic spacer region PCR and repetitive extragenic palindromic PCR analyses of Escherichia coli isolates to identify nonpoint fecal sources. Appl Environ Microbiol. 2003;69:4942–4950.
   PubMed Web of Science ®Google Scholar
• Buchan A, Alber M, Hodson RE. Strain-specific differentiation of environmental Escherichia coli isolates via denaturing gradient gel electrophoresis (DGGE) analysis of the 16S −23S intergenic spacer region. FEMS Microbiol Ecol. 2001;35:313–321.
   PubMed Web of Science ®Google Scholar
• Chen W, Kuo T. A simple and rapid method for the preparation of gram- negative bacterial genomic DNA. Nucleic Acids Res. 1993;21:2260.
   PubMed Web of Science ®Google Scholar
• Sambrook J, Russell DW. Molecular Cloning: A laboratory manual. 3rd ed. New York: Cold Spring Harbor Laboratory Press; 2001.
   Google Scholar
• Kostman JR, Edlind TD, LiPuma JJ, et al. Molecular epidemiology of Pseudomonas cepacia determined by polymerase chain reaction ribotyping. J Clin Microbiol. 1992;30:2084–2087.
   PubMed Web of Science ®Google Scholar
• Pavel AB, Vasile CI. PyElph - a software tool for gel images analysis and phylogenetics. BMC Bioinformatics. 2012;13:9.
   PubMed Web of Science ®Google Scholar
• Bauer A, Kirby W, Sherris J, et al. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol. 1966;45:493–496.
   PubMed Web of Science ®Google Scholar
• R Core Team. R: A language and environment for statistical computing [Computer Program]. R Foundation for Statistical Computing: Vienna; 2016 ISBN 3-900051-07-0, Available from: http://www.R-project.org/.
   Google Scholar
• Jombart T, Lyon D, Biome LD. adegenet : a R package for the multivariate analysis of genetic markers. Bioinformatics Appl Note. 2008;24:1403–1405.
   PubMed Web of Science ®Google Scholar
• Kamvar ZN, Tabima JF, Grünwald NJ. Poppr : an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ. 2014;2:e281.
   PubMed Web of Science ®Google Scholar
• Oksanen J, Blanchet F, Friendly M, et al. vegan: community ecology package [Computer Program]. R package version 2.4-1. 2016. Available from: https://CRAN.R-project.org/package=vegan.
   Google Scholar
• Jurasinski G, Retzer V simba: A collection of functions for similarity analysis of vegetation data [Computer program]. R package version 0.3-5. 2012. Available from: https://CRAN.R-project.org/package=simba.
   Google Scholar
• Baselga A, Orme C. betapart: an R package for the study of beta diversity. Methods Ecol Evol. 2012;3:802–812.
   Web of Science ®Google Scholar
• Dufrêne M, Legendre P. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol Monogr. 1997;67:354–366.
   Web of Science ®Google Scholar
• De Cáceres M, Legendre P, Wiser S, et al. Using species combinations in indicator value analyses. Methods Ecol Evol. 2012;3:973–982.
   Web of Science ®Google Scholar
• Kocijan I, Prukner-Radovčić E, Beck R, et al. Microflora and internal parasites of the digestive tract of Eurasian griffon vultures (Gyps fulvus) in Croatia. Eur J Wildl Res. 2009;55:71–74.
   Web of Science ®Google Scholar
• Bangert RL, Ward AC, Stauber EH, et al. A survey of the aerobic bacteria in the feces of captive raptors. Avian Dis. 1988;32:53–62.
   PubMed Web of Science ®Google Scholar
• Radhouani H, Pinto L, Coelho C, et al. Detection of Escherichia coli harbouring extended-spectrum {beta}-lactamases of the CTX-M classes in faecal samples of common buzzards (Buteo buteo). J Antimicrob Chemother. 2010;65:171–173.
   PubMed Web of Science ®Google Scholar
• Blanco G, Lemus JA, Grande J. Faecal bacteria associated with different diets of wintering red kites: influence of livestock carcass dumps in microflora alteration and pathogen acquisition. J Appl Ecol. 2006;43:990–998.
   Web of Science ®Google Scholar
• Bonnedahl J, Järhult JD. Antibiotic resistance in wild birds. Ups J Med Sci. 2014;119:113–116.
   PubMed Web of Science ®Google Scholar
• Guenther S, Grobbel M, Lubke- Becker A, et al. Antimicrobial resistance profiles of Escherichia coli from common European wild bird species. Vet Microbiol. 2010;144:219–225.
   PubMed Web of Science ®Google Scholar
• Schmitz F, Fluit A. Mechanisms of resistance. In: Armstrong D, Cohen S, editors. Infectious Diseases. London: Mosby Limited; 1999. p. 7.2.1–7.2.14.
   Google Scholar
• Alekshun MN, Levy SB. Review molecular mechanisms of antibacterial multidrug resistance. Cell. 2007;128:1037–1050.
   PubMed Web of Science ®Google Scholar
• Levy SB. Tetracycline resistance determinants are widespread. ASM News. 1988;54:418–421.
   Google Scholar
• Bush K, Palzkill T [Internet]. Beta-lactamase classification and amino acid sequences for TEM, SHV and OXA extended-spectrum and inhibitor resistant enzymes. [cited 2017 May 29]. Available from: www.lahey.org/studies/
   Google Scholar
• van den Bogaard AE, Stobberingh EE. Epidemiology of resistance to antibiotics. Links between animals and humans. Int J Antimicrob Agents. 2000;14:327–335.
   PubMed Web of Science ®Google Scholar
• Mammeri H, Galleni M, Nordmann P. Role of the Ser- 287-Asn replacement in the hydrolysis spectrum extension of AmpC betalactamases in Escherichia coli. Antimicrob Agents Chemother. 2009;53:323–326.
   Web of Science ®Google Scholar
• Deschamps C, Clermont O, Hipeaux MC, et al. Multiple acquisitions of CTX-M plasmids in the rare D2 genotype of Escherichia coli provide evidence for convergent evolution. Microbiology. 2009;155:1656–1668.
   Web of Science ®Google Scholar
• Johnson JR, Orskov I, Orskov F, et al. O, K, and H antigen predict virulence factors, carboxylesterase B pattern, antimicrobial resistance, and host compromise among Escherichia coli strains causing urosepsis. J Infect Dis J Infect Dis. 1994;169:119–126.
   Web of Science ®Google Scholar
• Sharma S, Mudgal N, Sharma P, et al. Phenotypic and genotypic characterization of Klebsiella pneumoniae obtained from Egyptian vultures and Steppes Eagles from India. Isr J Vet Med. 2015;69:122–128.
   Web of Science ®Google Scholar
• Sharma P, Faridi F, Mir IA, et al. Characterization of exo-s, exo-u, and alg virulence factors and antimicrobial resistance in Pseudomonas aeruginosa isolated from migratory Egyptian vultures from India. Infect Ecol Epidemiol. 2014;4:24553.
   Google Scholar
• Pedro JG, García De Los Ríos JE, Pozuelo MJ, et al. β-lactam resistance in Escherichia coli isolates from raptors in Spain. In: Mendez-Vilas A, editor. Current research topics in applied microbiology and microbial biotechnology. Singapore: World Scientific; 2009. p. 483–486.
   Google Scholar
• Literak I, Micudova M, Tausova D, et al. Plasmid-mediated quinolone resistance genes in fecal bacteria from rooks commonly wintering throughout Europe. Microb Drug Resist. 2012;18:567–573.
   Web of Science ®Google Scholar