Isolation and molecular characterization of Salmonella enterica and Escherichia coli from poultry samples

Isolation and molecular characterization of Salmonella enterica and Escherichia coli from poultry samples

Innumerable foodborne pathogens including Salmonella and Escherichia coli pose a serious threat to human health andfood safety. As perishable foods, poultry products are considered one of the most common sources of foodborne pathogens includingSalmonella and E. coli due to transmission of drug resistance, dissemination of organisms, and cross-contamination. In our study,phenotypic and genotypic characterizations of Salmonella enterica and E. coli isolated from packaged raw chicken products were carriedout. Samples belonging to different commercial brands were collected in Ankara in 2015. Among 15 out of 19 Salmonella enterica subsp.enterica strains isolated from different and/or same poultry samples were found as Infantis serotype, while 4 of them were identified asEnteritidis serotype by pulsed-field gel electrophoresis (PFGE) footprints. In addition, 19 out of 40 samples gave positive results for E.coli. In addition, PFGE types of Salmonella Infantis isolates were detected as PT 08, 45, and 50. Furthermore, multilocus sequence typingtypes of the samples were identified as ST 32. Results of the phenotypic and genotypic antimicrobial resistance profiles of SalmonellaInfantis and E. coli isolates revealed considerable resistance to nalidixic acid, tetracycline, streptomycin, sulfisoxazole and trimethoprim/sulfamethoxazole. On the other hand, 3 E. coli isolates showed antibiotic susceptibility. All in all, this study might enlighten somemolecular features of Salmonella and E. coli isolated from chicken products in Turkey.

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  • 1. Thorns CJ. Bacterial food-borne zoonoses. Revue Scientifique et Technique (International Office of Epizootics) 2000; 19 (1): 226-239.
  • 2. Zaidi MB, Campos FD, Estrada-García T, Gutierrez F, León M et al. Burden and transmission of zoonotic foodborne disease in a rural community in Mexico. Clinical Infectious Diseases 2012; 55 (1): 51-60. doi: 10.1093/cid/cis300
  • 3. Basler C, Nguyen TA, Anderson TC, Hancock T, Behravesh CB. Outbreaks of human Salmonella infections associated with live poultry, United States, 1990-2014. Emerging Infectious Diseases 2016; 22 (10): 1705-1711. doi: 10.3201/ eid2210.150765
  • 4. Dho-Moulin M, Fairbrother JM. Avian pathogenic Escherichia coli (APEC). Veterinary Research 1999; 30: 299-316.
  • 5. European Food Safety Authority. Shiga toxin-producing E. coli (STEC) O104:H4 2011 outbreaks in Europe: Taking Stock. EFSA Journal 2011; 9 (10): 2390.
  • 6. Santos RL, Zhang S, Tsolis RM, Kingsley RA, Adams GL et al. Animal models of Salmonella infections: Enteritis versus typhoid fever. Microbes and Infection 2001; 3 (14-15): 1335- 1344. doi: 10.1016/S1286-4579(01)01495-2
  • 7. European Food Safety Authority. The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2015. EFSA Journal 2016; 14 (12): 231. doi: 10.2903/j.efsa.2016.4634
  • 8. USDA-FSIS (2017). Serotypes profile of Salmonella isolates from meat and poultry products January 1998 through December 2014 [online]. Website https://www.fsis.usda.gov/ wps/wcm/connect/3866026a-582d-4f0e-a8ce-851b39c7390f/ Salmonella-Serotype-Annual-2014.pdf?MOD=AJPERES. [accessed 19 March 2019].
  • 9. European Food Safety Authority, European Centre for Disease Prevention and Control. The European Union Summary Report on antimicrobial resistance in Antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in the European Union in 2015. EFSA Journal 2017; 15 (2): 4694.
  • 10. Centers for Disease Control and Prevention.National Enteric Disease Surveillance: Salmonella Annual Report, 2016. Georgia, GA, USA: National Center for Emerging and Zoonotic Infectious Diseases; 2018.
  • 11. Gal-Mor O, Valinsky L, Weinberger M, Guy S, Jaffe J et al. Multidrug-resistant Salmonella enterica serovar Infantis, Israel. Emerging Infectious Diseases 2010; 16 (11): 1754- 1757. doi: 10.3201/eid1611.100100
  • 12. Barco L, Barrucci F, Olsen JE, Ricci A. Salmonella source attribution based on microbial subtyping. International Journal of Food Microbiology 2013; 163 (2-3): 193-203. doi: 10.1016/j.ijfoodmicro.2013.03.005
  • 13. Fratamico PM, DebRoy C, Liu Y, Needleman DS, Baranzoni GM et al. Advances in molecular serotyping and subtyping of Escherichia coli. Frontiers in Microbiology 2016; 7: 644. doi: 10.3389/fmicb.2016.00644
  • 14. Zheng J, Keys CE, Zhao S, Ahmed R, Meng J et al. Simultaneous analysis of multiple enzymes increases accuracy of pulsedfield gel electrophoresis in assigning genetic relationships among homogeneous Salmonella strains. Journal of Clinical Microbiology 2011; 49 (1): 85-94. doi: 10.1128/JCM.00120-10
  • 15. Thong KL, Ngeow YF, Altwegg M, Navaratnam P, Pang T. Molecular analysis of SalmonellaEnteritidis by pulsedfield gel electrophoresis and ribotyping. Journal of Clinical Microbiology 1995; 33 (5): 1070-1074.
  • 16. Li W, Raoult D, Fournier PE. Bacterial strain typing in the genomic era. FEMS Microbiology Reviews 2009; 33 (5): 892- 916. doi: 10.1111/j.1574-6976.2009.00182.x
  • 17. Harbottle H, White DG, McDermott PF, Walker RD, Zhao S. Comparison of multilocus sequence typing, pulsed-field gel electrophoresis, and antimicrobial susceptibility typing for characterization of Salmonella enterica serotype Newport isolates. Journal of Clinical Microbiology 2006; 44 (7): 2449- 2457. doi:10.1128/JCM.00019-06
  • 18. Eichhorn I, Heidemanns K, Semmler T, Kinnemann B, Mellmann A et al. Highly virulent non-O157 enterohemorrhagic Escherichia coli (EHEC) serotypes reflect similar phylogenetic lineages, providing new insights into the evolution of EHEC. Applied and Environmental Microbiology 2015; 81 (20): 7041- 7047. doi: 10.1128/AEM.01921-15
  • 19. Kim JS, Lee GG, Park JS, Jung YH, Kwak HS et al. A novel multiplex PCR assay for rapid and simultaneous detection of five pathogenic bacteria: Escherichia coli O157:H7, Salmonella, Staphylococcus aureus, Listeria monocytogenes, and Vibrio parahaemolyticus. Journal of Food Protection 2007; 70 (7): 1656-1662.
  • 20. Osés SM, Rantsiou K, Cocolin L, Jaime I, Rovira J. Prevalence and quantification of Shiga-toxin producing Escherichia coli along the lamb food chain by quantitative PCR. International Journal of Food Microbiology 2010; 141: 163-169. doi: 10.1016/j.ijfoodmicro.2010.05.010
  • 21. Wang L, Rothemund D, Curd H, Reeves PR. Sequence diversity of the Escherichia coli H7 fliC genes: Implication for a DNAbased typing scheme for E. coli O157:H7. Journal of Clinical Microbiology 2000; 38 (5): 1786-1790.
  • 22. Bai J, Shi X, Nagaraja TG. A multiplex PCR procedure for the detection of six major virulence genes in Escherichia coli O157:H7. Journal of Microbiological Methods 2010; 82 (1): 85- 89. doi:10.1016/j.mimet.2010.05.003
  • 23. Fagan PK, Hornitzky MA, Bettelheim KA, Djordjevic SP. Detection of shiga-like toxin (stx1 and stx2), intimin (eaeA), and enterohemorrhagic Escherichia coli (EHEC) hemolysin (EHEC hlyA) genes in animal feces by multiplex PCR. Applied and Environmental Microbiology 1999; 65 (2): 868-872.
  • 24. Bertrand R, Roig B. Evaluation of enrichment-free PCR-based detection on the rfbE gene of Escherichia coli O157-Application to municipal wastewater. Water Research 2007; 41 (6): 1280- 1286. doi: 10.1016/j.watres.2006.11.027
  • 25. Botkin DJ, Galli L, Sankarapani V, Soler M, Rivas M et al. Development of a Multiplex PCR Assay for Detection of Shiga Toxin-Producing Escherichia coli, Enterohemorrhagic E. coli, and Enteropathogenic E. coli Strains. Frontiers in Cellular and Infection Microbiology 2012; 2: 1-10. doi: 10.3389/ fcimb.2012.00008
  • 26. Presterl E, Zwick RH, Reichmann S, Aichelburg A, Winkler S et al. Frequency and virulence properties of diarrheagenic Escherichia coli in children with diarrhea in Gabon. American Journal of Tropical Medicine and Hygiene 2003; 69 (4): 406- 410.
  • 27. Stacy-Phipps S, Mecca JJ, Weiss JB. Multiplex PCR assay and simple preparation method for stool specimens detect enterotoxigenic Escherichia coli DNA during course of infection. Journal of Clinical Microbiology 1995; 33 (5): 1054-1059.
  • 28. Guion CE, Ochoa TJ, Walker CM, Barletta F, Cleary TG. Detection of diarrheagenic Escherichia coli by use of meltingcurve analysis and real-time multiplex PCR. Journal of Clinical Microbiology 2008; 46 (5): 1752-1757. doi: 10.1128/ JCM.02341-07
  • 29. Ribot EM, Fair MA, Gautom R, Cameron DN, Hunter SB et al. Standardization of Pulsed-Field Gel Electrophoresis Protocols for the Subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathogens and Disease 2006; 3 (1): 59-67. doi:10.1089/fpd.2006.3.59
  • 30. Harbottle H, White DG, McDermott PF, Walker RD, Zhao S. Comparison of multilocus sequence typing, pulsed-field gel electrophoresis, and antimicrobial susceptibility typing for characterization of Salmonella enterica serotype Newport isolates. Journal of Clinical Microbiology 2006; 44 (7): 2449- 2457. doi:10.1128/JCM.00019-06
  • 31. Steenackers H, Hermans K, Vanderleyden J, De Keersmaecker SCJ. Salmonella biofilms: An overview on occurrence, structure, regulation and eradication. Food Research International 2012; 45 (2): 502-531. doi: 10.1016/j.foodres.2011.01.038
  • 32. Pavlickova S, Klancnik A, Dolezalova M, Mozina SS, Holko I. Antibiotic resistance, virulence factors and biofilm formation ability in Escherichia coli strains isolated from chicken meat and wildlife in the Czech Republic. Journal of Environmental Science and Health- Part B Pesticides, Food Contaminants, and Agricultural Wastes 2017; 52 (8): 570-576. doi: 10.1080/03601234.2017.1318637
  • 33. Rossi DA, Melo RT, Mendonça EP, Monteiro GP. Biofilms of Salmonella and Campylobacter in the poultry industry. Poultry Science InTech 2017; 93-113. doi: 10.5772/65254
  • 34. Stepanović S, Ćirković I, Ranin L, Švabić-Vlahović M. Biofilm formation by Salmonella spp. and Listeria monocytogenes on plastic surface. Letters in Applied Microbiology 2004; 38 (5): 428-432. doi: 10.1111/j.1472-765X.2004.01513.x
  • 35. CLSI. Clinical and Laboratory Standards Institute, Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated from Animals. Approved Standard— Second Edition 2002; 22 (6): M31-A2.
  • 36. CLSI. Clinical and Laboratory Standards Institute, Performance Standards for Antimicrobial Susceptibility Testing. Twenty- First Informational Supplement 2011; 31 (1): M100-S21.
  • 37. Chen S, Zhao S, White DG, Schroeder CM, Lu R et al. Characterization of Multiple-Antimicrobial-Resistant Salmonella Serovars Isolated from Retail Meats. Applied and Environmental Microbiology 2004; 70 (1): 1-7.
  • 38. Pérez-Pérez FJ, Hanson ND. Detection of plasmid-mediated AmpC beta-lactamase genes in clinical isolates by using multiplex PCR. Journal of Clinical Microbiology 2002; 40 (6): 2153-2162.
  • 39. Randall LP, Cooles SW, Osborn MK, Piddock LJV, Woodward MJ. Antibiotic resistance genes, integrons and multiple antibiotic resistance in thirty-five serotypes of Salmonella enterica isolated from humans and animals in the UK. Journal of Antimicrobial Chemotherapy 2004; 53 (2): 208-216. doi: 10.1093/jac/dkh070
  • 40. Gebreyes WA, Altier C. Molecular Characterization of multidrug-resistant Salmonella enterica subsp. enterica serovar typhimurium isolates from Swine. Journal of Clinical Microbiology 2002; 40 (8): 2813-2822.
  • 41. Frana TS, Carlson SA, Griffith RW. Relative distribution and conservation of genes encoding aminoglycoside-modifying enzymes in Salmonella enterica serotype typhimurium phage type DT104. Applied and Environmental Microbiology 2001; 67 (1): 445-448. doi: 10.1128/AEM.67.1.445-448.2001
  • 42. Kaper JB, Nataro JP, Mobley HL. Pathogenic Escherichia coli, review. Nature Reviews Microbiology 2004; 2 (2): 123-140. doi: 10.1038/nrmicro818
  • 43. Allocati N, Masulli M, Alexeyev MF, Di Ilio C. Escherichia coli in Europe: An overview. International Journal of Environmental Research and Public Health 2013; 10 (12): 6235-6254. doi: 10.3390/ijerph10126235
  • 44. Farrokh C, Jordan K, Auvray F, Glass K, Oppegaard H et al. Review of Shiga-toxin-producing Escherichia coli (STEC) and their significance in dairy production. International Journal of Food Microbiology 2013; 162 (2): 190-212. doi: 10.1016/j. ijfoodmicro.2012.08.008
  • 45. Almeida F, Pitondo-Silva A, Oliveira MA, Falcão JP. Molecular epidemiology and virulence markers of Salmonella Infantis isolated over 25 years in São Paulo State, Brazil. Journal of Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases 2013; 19: 145-151. doi: 10.1016/j. meegid.2013.07.004
  • 46. Ed-Dra A, Karraouan B, Allaoui AE, Khayatti M, Ossmani HE et al. Isolation, antimicrobial resistance and genetic diversity of Salmonella Infantis isolates from foods and human samples in Morocco. Journal of Global Antimicrobial Resistance 2018; 14: 297-301. doi: 10.1016/j.jgar.2018.05.019
  • 47. Nógrády N, Király M, Davies R, Nagy B. Multidrug resistant clones of Salmonella Infantis of broiler origin in Europe. International Journal of Food Microbiology 2012; 157 (1): 108- 112. doi:10.1016/j.ijfoodmicro.2012.04.007
  • 48. Shahada F, Sugiyama H, Chuma T, Sueyoshi M, Okamoto K. Genetic analysis of multi-drug resistance and the clonal dissemination of β-lactam resistance in Salmonella Infantis isolated from broilers. Veterinary Microbiology 2010; 140 (1- 2): 136-141. doi: 10.1016/j.vetmic.2009.07.007
  • 49. Miller T, Prager R, Rabsch W, Fehlhaber K, Voss M. Epidemiological relationship between Salmonella Infantis isolates of human and broiler origin. Lohmann Information 2010; 2: 27-31.
  • 50. Nógrády N, Tóth Á, Kostyák Á, Pászti J, Nagy B. Emergence of multidrug-resistant clones of Salmonella Infantis in broiler chickens and humans in Hungary. Journal of Antimicrobial Chemotherapy 2007; 60 (3): 645-648. doi: 10.1093/jac/dkm249
  • 51. Murgia M, Bouchrif B, Timinouni M, Al-Qahtani A, Al-Ahdal MN et al. Antibiotic resistance determinants and genetic analysis of Salmonella enterica isolated from food in Morocco. International Journal of Food Microbiology 2015; 215: 31-39. doi: 10.1016/j.ijfoodmicro.2015.08.003
  • 52. Ceyssens PJ, Mattheus W, Vanhoof R, Bertrand S. Trends in serotype distribution and antimicrobial susceptibility in Salmonella enterica isolates from humans in Belgium, 2009 to 2013. Antimicrobial Agents and Chemotherapy 2015; 59 (1): 544-552. doi:10.1128/AAC.04203-14
  • 53. Liang Z, Ke B, Deng X, Liang J, Ran L et al. Serotypes, seasonal trends, and antibiotic resistance of non-typhoidal Salmonella from human patients in Guangdong Province, China, 2009- 2012. BMC Infectious Diseases 2015; 15 (1): 53. doi: 10.1186/ s12879-015-0784-4
  • 54. Zhu Y, Lai H, Zou L, Yin S, Wang C et al. Antimicrobial resistance and resistance genes in Salmonella strains isolated from broiler chickens along the slaughtering process in China. International Journal of Food Microbiology 2017; 259: 43-51. doi: 10.1016/j.ijfoodmicro.2017.07.023
  • 55. Shigemura H, Matsui M, Sekizuka T, Onozuka D, Noda T et al. Decrease in the prevalence of extended-spectrum cephalosporin-resistant Salmonella following cessation of ceftiofur use by the Japanese poultry industry. International Journal of Food Microbiology 2018; 274: 45-51. doi: 10.1016/j. ijfoodmicro.2018.03.011
  • 56. Dionisi AM, Lucarelli C, Benedetti I, Owczarek S, Luzzi I. Molecular characterisation of multidrug-resistant Salmonella enterica serotype Infantis from humans, animals and the environment in Italy. International Journal of Antimicrobial Agents 2011; 38 (5): 384-389. doi: 10.1016/j. ijantimicag.2011.07.001
  • 57. Chuah LO, Shamila Syuhada AK, Mohamad Suhaimi I, Farah Hanim T, Rusul G. Genetic relatedness, antimicrobial resistance and biofilm formation of Salmonella isolated from naturally contaminated poultry and their processing environment in northern Malaysia. Food Research International 2018; 105: 743-751. doi: 10.1016/j.foodres.2017.11.066
  • 58. Papadopoulos T, Petridou E, Zdragas A, Mandilara G, Vafeas G et al. Multiple clones and low antimicrobial resistance rates for Salmonella enterica serovar Infantis populations in Greece. Comparative Immunology, Microbiology and Infectious Diseases 2017; 51: 54-58. doi: 10.1016/j.cimid.2017.02.002
  • 59. Raffatellu M, Tukel C, Chessa D, Wilson RP, Baumler AJ. The intestinal phase of Salmonella infections. In: Rhen M, Maskell D, Mastroeni P, Threlfall EJ, editor. Salmonella: Molecular Biology and Pathogenesis. Norfolk, United Kingdom: Horizon Bioscience; 2007. pp. 30-51.
  • 60. Pasquali F, Lucchi A, Braggio S, Giovanardi D, Franchini A et al. Genetic diversity of Escherichia coli isolates of animal and environmental origins from an integrated poultry production chain. Veterinary Microbiology 2015; 178 (3-4): 230-237. doi: 10.1016/j.vetmic.2015.05.007
  • 61. Guo S, Tay MYF, Aung KT, Seow KLG, Ng LC et al. Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods. Food Control 2019; 99: 89-97. doi: 10.1016/j.foodcont.2018.12.043
  • 62. Ferreira JC, Penha Filho RAC, Andrade LN, Berchieri Junior A, Darini ALC. Evaluation and characterization of plasmids carrying CTX-M genes in a non-clonal population of multidrugresistant Enterobacteriaceae isolated from poultry in Brazil. Diagnostic Microbiology and Infectious Disease 2016; 85 (4): 444-448. doi: 10.1016/j.diagmicrobio.2016.05.011
  • 63. Rasmussen MM, Opintan JA, Frimodt- Møller N, Styrishave B. Beta-lactamase producing Escherichia coli isolates in imported and locally produced chicken meat from Ghana. PLoS ONE 2015; 10 (10): e0139706. doi: 10.1371/journal.pone.0139706
  • 64. Li L, Wang B, Feng S, Li J, Wu C et al. Prevalence and characteristics of extended-spectrum β-lactamase and plasmidmediated fluoroquinolone resistance genes in Escherichia coli isolated from chickens in Anhui Province, China. PLoS ONE 2014; 9 (8): e104356. doi: 10.1371/journal.pone.0104356
  • 65. Toszeghy M, Phillips N, Reeves H, Wu G, Teale C et al. Molecular and phenotypic characterisation of Extended Spectrum β-lactamase CTX-M Escherichia coli from farm animals in Great Britain. Research in Veterinary Science 2012; 93 (3): 1142-1150. doi: 10.1016/j.rvsc.2012.05.001
  • 66. Oikarainen PE, Pohjola LK, Pietola ES, Heikinheimo A. Direct vertical transmission of ESBL/pAmpC-producing Escherichia coli limited in poultry production pyramid. Veterinary Microbiology 2019; 231: 100-106. doi: 10.1016/j.vetmic.2019.03.001
  • 67. Bush K. Alarming beta-lactamase-mediated resistance in multidrug-resistant Enterobacteriaceae. Current Opinion in Microbiology 2010; 13 (5): 558-564. doi: 10.1016/j. mib.2010.09.006
  • 68. Liebana E, Carattoli A, Coque TM, Hasman H, Magiorakos AP, et al. Public health risks of enterobacterial isolates producing extended-spectrum β-lactamases or AmpC β-lactamases in food and food-producing animals: an EU perspective of epidemiology, analytical methods, risk factors, and control Options. Clinical Infectious Diseases 2013; 56 (7): 1030-1037. doi: 10.1093/cid/ cis1043
  • 69. Ewers C, Bethe A, Semmler T, Guenther S, Wieler LH. Extended-spectrum beta-lactamase-producing and AmpCproducing Escherichia coli from livestock and companion animals, and their putative impact on public health: a global perspective. Clinical Microbiology and Infection 2012; 18 (7): 646-655. doi: 10.1111/j.1469-0691.2012.03850.x
  • 70. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005; 307: 1915-1920. doi: 10.1126/science.1104816
  • 71. Jernberg C, Löfmark S, Edlund C, Jansson JK. Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 2010; 156: 3216-3223. doi: 10.1099/mic.0.040618-0
  • 72. Casals-Pascual C, Vergara A, Vila J. Intestinal microbiota and antibiotic resistance: Perspectives and solutions. Human Microbiome Journal 2018; 37: 1-27. doi: 10.1016/j. humic.2018.05.002
  • 73. Penders J, Stobberingh EE, Savelkoul PHM, Wolffs PFG. The human microbiome as a reservoir of antimicrobial resistance. Frontiers in Microbiology 2013; 4: 87. doi: 10.3389/ fmicb.2013.00087