Discrimination of Escherichia coli isolates recovered from mucosal contents of chicken intestines and different age by repetitive elements sequence-based PCR

Authors

  • Mohd Asrore Mohd Shaufi Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
  • Chin Chin Sieo
  • Yoke-Kqueen Cheah Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
  • Chun Wie Chong Department of Life Sciences, International Medical University, Jalan Jalil Perkasa 19, Taman Esplanade, 57000 Kuala Lumpur, Malaysia.
  • Abdul Rahman Omar Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
  • Yin Wan Ho Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
  • Geok Hun Tan Department of Agricultural Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.

DOI:

https://doi.org/10.54987/jobimb.v5i1.333

Keywords:

Rep-PCR, E. coli, Diversity, chicken intestines

Abstract

Repetitive sequence-based PCR (rep-PCR) is a distinctive typing approach that is used to differentiate between bacterial strains. This method is also useful for studying bacterial diversity from different sources. In this study, four rep-PCR which are enterobacterial repetitive intergenic consensus PCR (ERIC-PCR), BOX-PCR, repetitive extragenic palindromic PCR (REP-PCR) and polytrinucleotide (GTG)5-PCR were evaluated for differentiation of eighteen Escherichia coli isolates to correct source based on part of intestine and age. These isolates were recovered earlier from ileal and caecal mucosal contents of chickens at a different age. The purpose of this study was to investigate the efficacy of four rep-PCR methods and composite of rep-PCR patterns to differentiate E. coli isolates to original sources of part of intestines and age based on the D index (discriminatory power determined based on Simpson’s index of diversity calculated at similarity coefficient of 90%). The (GTG)5-PCR had the highest D index (0.9804) for part of intestine and age factors. The similar D index was observed in the composite of rep-PCR patterns. The lowest D index was observed in ERIC- and BOX-PCR at 0.9020 and 0.8039 for part of intestine and age factors, respectively. (GTG)5-PCR was also the most discriminative rep-PCR observed due to its ability to cluster 14I 3E and 14I 2X isolates, and 14C 1E and 14C 3E isolates correctly in part of intestine and age factors. It was concluded that (GTG)5-PCR is a promising tool for discriminating E. coli isolates extracted from chicken intestines.

References

Amit-Romach E, Sklan D, Uni Z. Microflora ecology of the chicken intestine using 16S Ribosomal DNA Primers. Poultry Sci. 2004;83(7):1093-8.

Lu J, Idris U, Harmon B, Hofacre C, Maurer JJ, Lee MD. Diversity and succession of the intestinal bacterial community of the maturing broiler chicken. Appl Environ Microbiol. 2003;69(11):6816-24.

Chambers JR, Gong J. The intestinal microbiota and its modulation for Salmonella control in chickens. Food Res Int. 2011;44(10):3149-59.

Zhu XY, Zhong T, Pandya Y, Joerger RD. 16S rRNA-Based analysis of microbiota from the cecum of broiler Chickens. Appl Environ Microbiol. 2002;68(1):124-37.

Kaper JB, Nataro JP, Mobley HLT. Pathogenic Escherichia coli. Nat Rev Micro. 2004;2(2):123-40.

Stavric S, Gleeson T, Blanchfield B, Pivnick H. Competitive exclusion of Salmonella from newly hatched chicks by mixtures of pure bacterial cultures isolated from fecal and cecal contents of adult birds. J Food Protect. 1985;48(9):778-82.

Pasquali F, Lucchi A, Braggio S, Giovanardi D, Franchini A, Stonfer M, et al. Genetic diversity of Escherichia coli isolates of animal and environmental origins from an integrated poultry production chain. Vet Microbiol. 2015;178(3-4):230-7.

Duan H, Chai T, Liu J, Zhang X, Qi C, Gao J, et al. Source identification of airborne Escherichia coli of swine house surroundings using ERIC-PCR and REP-PCR. Environ Res. 2009;109(5):511-7.

Sander A, Ruess M, Bereswill S, Schuppler M, Steinbrueckner B. Comparison of different DNA fingerprinting techniques for molecular typing of Bartonella henselae isolates. J Clin Microbiol. 1998;36(10):2973-81.

Abd-El-Haleem D, Layton AC, Sayler GS. Long PCR-amplified rDNA for PCR-RFLP- and Rep-PCR-based approaches to recognize closely related microbial species. J Microbiol Methods. 2002;49(3):315-9.

Simmons GM, Herbein SA, James CM. Managing nonpoint fecal coliform sources to tidal inlets. J Contemp Water Res Edu. 2011;100(1):1-11.

Hahm B-K, Maldonado Y, Schreiber E, Bhunia AK, Nakatsu CH. Subtyping of foodborne and environmental isolates of Escherichia coli by multiplex-PCR, rep-PCR, PFGE, ribotyping and AFLP. J Microbiol Methods. 2003;53(3):387-99.

Versalovic J, Koeuth T, Lupski R. Distribution of repetitive DNA sequences in eubacteria and application to fingerpriting of bacterial genomes. Nucleic Acids Res. 1991;19(24):6823-31.

Versalovic J, de Bruijn F, Lupski J. Repetitive sequence-based PCR (rep-PCR) DNA fingerprinting of bacterial genomes. In: de Bruijn F, Lupski J, Weinstock G, editors. Bacterial Genomes: Springer US; 1998. p. 437-54.

Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J Clin Microbiol. 1988;26(11):2465-6.

Braem G, De Vliegher S, Supré K, Haesebrouck F, Leroy F, De Vuyst L. (GTG)5-PCR fingerprinting for the classification and identification of coagulase-negative Staphylococcus species from bovine milk and teat apices: a comparison of type strains and field isolates. Vet Microbiol. 2011;147(1-2):67-74.

Mohapatra BR, Broersma K, Mazumder A. Differentiation of fecal Escherichia coli from poultry and free-living birds by (GTG)5-PCR genomic fingerprinting. Int J Med Microbiol. 2008;298(3-4):245-52.

Rasschaert G, Houf K, Imberechts H, Grijspeerdt K, De Zutter L, Heyndrickx M. Comparison of five repetitive-sequence-based PCR typing methods for molecular discrimination of Salmonella enterica isolates. J Clin Microbiol. 2005;43(8):3615-23.

Švec P, Vancanneyt M, Seman M, Snauwaert C, Lefebvre K, Sedlá?ek I, et al. Evaluation of (GTG) 5?PCR for identification of Enterococcus spp. FEMS Microbiol Lett. 2005;247(1):59-63.

Gevers D, Huys G, Swings J. Applicability of rep?PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett. 2001;205(1):31-6.

Mohapatra B, Mazumder A. Comparative efficacy of five different rep-PCR methods to discriminate Escherichia coli populations in aquatic environments. Water Sci Technol. 2008;58(3):537-47.

Dombek PE, Johnson LK, Zimmerley ST, Sadowsky MJ. Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal Sources. Appl Environ Microbiol. 2000;66(6):2572-7.

Ma HJ, Fu LL, Li JR. Differentiation of fecal Escherichia coli from human, livestock, and poultry sources by rep-PCR DNA fingerprinting on the shellfish culture area of East China Sea. Curr Microbiol. 2011;62(5):1423-30.

Leung KT, Mackereth R, Tien YC, Topp E. A comparison of AFLP and ERIC-PCR analyses for discriminating Escherichia coli from cattle, pig and human sources. FEMS Microbiol Ecol. 2004;47(1):111-9.

Joerger RD, Ross T. Genotypic diversity of Escherichia coli isolated from cecal content and mucosa of one- to six-week-old broilers. Poult Sci. 2005;84(12):1902-7.

Mohd Shaufi MA, Sieo CC, Chong CW, Gan HM, Ho YW. Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses. Gut Pathog. 2015;7:4.

Stanley D, Hughes RJ, Moore RJ. Microbiota of the chicken gastrointestinal tract: influence on health, productivity and disease. Appl Microbiol Biotechnol. 2014;98(10):4301-10.

Lee CM, Sieo CC, Cheah Y-K, Abdullah N, Ho YW. Discrimination of probiotic Lactobacillus strains for poultry by repetitive sequenced-based PCR fingerprinting. J Sci Food Agric. 2012;92(3):660-6.

Johnson LK, Brown MB, Carruthers EA, Ferguson JA, Dombek PE, Sadowsky MJ. Sample Size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution. Appl Environ Microbiol. 2004;70(8):4478-85.

Chiou S-H, Huang M-F, Chang H-T. Separation of double-stranded DNA fragments by capillary electrophoresis: Impacts of poly(ethylene oxide), gold nanoparticles, ethidium bromide, and pH. Electrophoresis. 2004;25(14):2186-92.

Downloads

Published

31.07.2017

How to Cite

Mohd Shaufi, M. A., Sieo, C. C., Cheah, Y.-K., Chong, C. W., Omar, A. R., Ho, Y. W., & Tan, G. H. (2017). Discrimination of Escherichia coli isolates recovered from mucosal contents of chicken intestines and different age by repetitive elements sequence-based PCR. Journal of Biochemistry, Microbiology and Biotechnology, 5(1), 7–12. https://doi.org/10.54987/jobimb.v5i1.333

Issue

Vol. 5 No. 1 (2017)

Section

Articles

License

Authors who publish with this journal agree to the following terms:

    1. Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0) that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
    2. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
    3. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).