304
Views
4
CrossRef citations to date
0
Altmetric
Original Research

Comparative Assessment of Different PCR-Based Typing Methods of Pseudomonas aeruginosa Isolates

ORCID Icon & ORCID Icon
Pages 1019-1035 | Published online: 17 Mar 2021

References

  • Pachori P, Gothalwal R, Gandhi P. Emergence of antibiotic resistance Pseudomonas aeruginosa in intensive care unit; a critical review. Genes Dis. 2019;6(2):109–119. doi:10.1016/j.gendis.2019.04.00131194018
  • Liu T, Zhang Y, Wan Q. Pseudomonas aeruginosa bacteremia among liver transplant recipients. Infect Drug Resist. 2018;11:2345–2356. doi:10.2147/IDR.S18028330532566
  • Li W, Raoult D, Fournier PE. Bacterial strain typing in the genomic era. FEMS Microbiol Rev. 2009;33(5):892–916. doi:10.1111/j.1574-6976.2009.00182.x19453749
  • MacCannell D. Bacterial strain typing. Clin Lab Med. 2013;33(3):629–650. doi:10.1016/j.cll.2013.03.00523931842
  • Ranjbar R, Karami A, Farshad S, Giammanco GM, Mammina C. Typing methods used in the molecular epidemiology of microbial pathogens: a how-to guide. New Microbiol. 2014;37(1):1–15.24531166
  • Aljindan R, Alsamman K, Elhadi N. ERIC-PCR genotyping of Acinetobacter baumannii isolated from different clinical specimens. Saudi J Med Med Sci. 2018;6(1):13–17. doi:10.4103/sjmms.sjmms_138_1630787810
  • Rodriguez JM, Lopez-Romalde S, Beaz R, Alonso MC, Castro D, Romalde JL. Molecular fingerprinting of Vibrio tapetis strains using three PCR-based methods: ERIC-PCR, REP-PCR and RAPD. Dis Aquat Organ. 2006;69(2):175–183. doi:10.3354/dao06917516724561
  • Uddin MS, Cheng Q. Recent application of biotechniques for the improvement of mango research. In: Poltronieri P, Hong Y, editors. Applied Plant Genomics and Biotechnology. Woodhead Publishing; 2015:195–212.
  • Waturangi DE, Joanito I, Yogi Y, Thomas S. Use of REP- and ERIC-PCR to reveal genetic heterogeneity of Vibrio cholerae from edible ice in Jakarta, Indonesia. Gut Pathog. 2012;4(1):2. doi:10.1186/1757-4749-4-224576322
  • Spacov ICG, Silva S, Júnior M, Morais M. Polymorphism of the rDNA and tDNA loci in clinical isolates of Pseudomonas aeruginosa: a perspective for molecular epidemiology surveillance. Genet Mol Biol. 2006;29(4):722–729. doi:10.1590/S1415-47572006000400023
  • Adzitey F, Huda N, Ali GR. Molecular techniques for detecting and typing of bacteria, advantages and application to foodborne pathogens isolated from ducks. 3 Biotech. 2013;3(2):97–107. doi:10.1007/s13205-012-0074-4
  • Van Looveren M, Ison CA, Ieven M, et al. Evaluation of the discriminatory power of typing methods for Neisseria gonorrhoeae. J Clin Microbiol. 1999;37(7):2183–2188. doi:10.1128/JCM.37.7.2183-2188.199910364583
  • Burucoa C, Lhomme V, Fauchere JL. Performance criteria of DNA fingerprinting methods for typing of Helicobacter pylori isolates: experimental results and meta-analysis. J Clin Microbiol. 1999;37(12):4071–4080. doi:10.1128/JCM.37.12.4071-4080.199910565934
  • Welsh J, McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990;18(24):7213–7218. doi:10.1093/nar/18.24.72132259619
  • Faria NA, Carrico JA, Oliveira DC, Ramirez M, de Lencastre H. Analysis of typing methods for epidemiological surveillance of both methicillin-resistant and methicillin-susceptible Staphylococcus aureus strains. J Clin Microbiol. 2008;46(1):136–144. doi:10.1128/JCM.01684-0717989188
  • Englen M, Kelley LC. A rapid DNA isolation procedure for the identification of Campylobacter jejuni by the polymerase chain reaction. Lett Appl Microbiol. 2008;31:421–426. doi:10.1046/j.1365-2672.2000.00841.x
  • Deligianni E, Pattison S, Berrar D, et al. Pseudomonas aeruginosa cystic fibrosis isolates of similar RAPD genotype exhibit diversity in biofilm forming ability in vitro. BMC Microbiol. 2010;10:38. doi:10.1186/1471-2180-10-3820141637
  • Scaccabarozzi L, Leoni L, Ballarini A, et al. Pseudomonas aeruginosa in dairy goats: genotypic and phenotypic comparison of intramammary and environmental isolates. PLoS One. 2015;10(11):e0142973. doi:10.1371/journal.pone.014297326606430
  • Jana T, Sharma TR, Prasad RD, Arora DK. Molecular characterization of Macrophomina phaseolina and Fusarium species by a single primer RAPD technique. Microbiol Res. 2003;158(3):249–257. doi:10.1078/0944-5013-0019814521235
  • Sazakli E, Leotsinidis M, Vantarakis A, Papapetropoulou M. Comparative typing of Pseudomonas species isolated from the aquatic environment in Greece by SDS-PAGE and RAPD analysis. J Appl Microbiol. 2005;99(5):1191–1203. doi:10.1111/j.1365-2672.2005.02691.x16238750
  • Eftekhar F, Nouri P. Correlation of RAPD-PCR profiles with ESBL production in clinical isolates of Klebsiella pneumoniae in Tehran. J Clin Diagn Res. 2015;9(1):DC01–03. doi:10.7860/JCDR/2015/10651.5373
  • Abou-Dobara MI, Deyab MA, Elsawy EM, Mohamed HH. Antibiotic susceptibility and genotype patterns of Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa isolated from urinary tract infected patients. Pol J Microbiol. 2010;59(3):207–212. doi:10.33073/pjm-2010-03221033585
  • Sumbria D, Singla LD, Sharma A, Moudgil AD, Bal MS. Equine trypanosomosis in central and western Punjab: prevalence, haemato-biochemical response and associated risk factors. Acta Trop. 2014;138:44–50. doi:10.1016/j.actatropica.2014.06.00324931285
  • Green LM, Worthington T, Hilton AC, Lambert PA. Genetic characterization of clinical isolates of Clostridium difficile using an optimized RAPD protocol and PCR ribotyping reveals strain diversity between two tertiary referral Trusts in the West Midlands, UK. J Med Microbiol. 2011;60(Pt 9):1287–1291. doi:10.1099/jmm.0.030999-021511887
  • Satpathy G, Patnayak D, Titiyal JS, et al. Post-operative endophthalmitis: antibiogram & genetic relatedness between Pseudomonas aeruginosa isolates from patients & phacoemulsifiers. Indian J Med Res. 2010;131:571–577.20424310
  • Wolska K, Szweda P. A comparative evaluation of PCR ribotyping and ERIC PCR for determining the diversity of clinical Pseudomonas aeruginosa isolates. Pol J Microbiol. 2008;57(2):157–163.18646404
  • Stehling EG, Leite DS, Silveira WD. Molecular typing and biological characteristics of Pseudomonas aeruginosa isolated from cystic fibrosis patients in Brazil. Braz J Infect Dis. 2010;14(5):462–467. doi:10.1016/S1413-8670(10)70094-521221474
  • Sornakili A, Rathinam P, Thiruvengadum R, Kuppusamy P. Comparative assessment of RAPD and ISSR markers to study genetic polymorphism in Colletotrichum gloeosorioides isolates of Mango. Asian J Plant Pathol. 2017;11:130–138. doi:10.3923/ajppaj.2017.130.138
  • Mariette S, Le Corre V, Austerlitz F, Kremer A. Sampling within the genome for measuring within-population diversity: trade-offs between markers. Mol Ecol. 2002;11(7):1145–1156. doi:10.1046/j.1365-294X.2002.01519.x12074722
  • Olenska E, Malek W. Genomic polymorphism of Trifolium repens root nodule symbionts from heavy metal-abundant 100-year-old waste heap in southern Poland. Arch Microbiol. 2019;201(10):1405–1414. doi:10.1007/s00203-019-01708-x31346652
  • 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):2465–2466. doi:10.1128/JCM.26.11.2465-2466.19883069867
  • Carrico JA, Silva-Costa C, Melo-Cristino J, et al. Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes. J Clin Microbiol. 2006;44(7):2524–2532. doi:10.1128/JCM.02536-0516825375
  • Singh JP, Verma R, Chaudhuri P. Random amplified polymorphic DNA (RAPD) analysis of Mycobacterium tuberculosis strains in India. J Vet Sci. 2006;7(2):181–187. doi:10.4142/jvs.2006.7.2.18116645345
  • Pethannan R, Kuppuswamy AC, Gupta R, et al. RAPD characterization of pseudomonas species identified from clinical samples. Recent Res Sci Technol. 2018;10:11–15.
  • Daly M, Power E, Bjorkroth J, et al. Molecular analysis of Pseudomonas aeruginosa: epidemiological investigation of mastitis outbreaks in Irish dairy herds. Appl Environ Microbiol. 1999;65(6):2723–2729. doi:10.1128/AEM.65.6.2723-2729.199910347067
  • Kostman JR, Alden MB, Mair M, Edlind TD, LiPuma JJ, Stull TL. A universal approach to bacterial molecular epidemiology by polymerase chain reaction ribotyping. J Infect Dis. 1995;171(1):204–208. doi:10.1093/infdis/171.1.2047528251
  • Garcia-Martinez J, Acinas SG, Anton AI, Rodriguez-Valera F. Use of the 16S–23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiol Methods. 1999;36(1–2):55–64. doi:10.1016/S0167-7012(99)00011-110353800
  • Azimirad M, Alebouyeh M, Rashidan M, Aslani MM, Zali MR. Comparison of common molecular typing methods for differentiation of Clostridium difficile strains in the study of hospital acquired diarrhea. Arch Clin Infect Dis. 2018;13:5.
  • Collier JG, Fraser GA, Marmion PB, Simmons A. Practical medical microbiology. Churchill Livingstone, NY. 1996;4:413–418.
  • Martin C, Ichou MA, Massicot P, Goudeau A, Quentin R. Genetic diversity of Pseudomonas aeruginosa strains isolated from patients with cystic fibrosis revealed by restriction fragment length polymorphism of the rRNA gene region. J Clin Microbiol. 1995;33(6):1461–1466. doi:10.1128/JCM.33.6.1461-1466.19957544364
  • Liu Y, Davin-Regli A, Bosi C, Charrel RN, Bollet C. Epidemiological investigation of Pseudomonas aeruginosa nosocomial bacteraemia isolates by PCR-based DNA fingerprinting analysis. J Med Microbiol. 1996;45(5):359–365. doi:10.1099/00222615-45-5-3598918952
  • Ekundayo T, Okoh A. Molecular characterization, intra-species diversity and abundance of freshwater Plesiomonas shigelloides isolates. Microorganisms. 2020;8(7):1081. doi:10.3390/microorganisms8071081
  • Ekundayo TC, Okoh AI, Sibai AM. A global bibliometric analysis of Plesiomonas-related research (1990–2017). PLoS One. 2018;13(11):e0207655. doi:10.1371/journal.pone.020765530496198
  • Ekundayo TC, Okoh AI. Modelling the effects of physicochemical variables and anthropogenic activities as ecological drivers of Plesiomonas shigelloides distribution and freshwaters quality. Sci Total Environ. 2019;682:765–778. doi:10.1016/j.scitotenv.2019.05.12931132640
  • Bilung LM, Pui CF, Su’ut L, Apun K. Evaluation of BOX-PCR and ERIC-PCR as molecular typing tools for pathogenic leptospira. Dis Markers. 2018;2018:1351634. doi:10.1155/2018/135163430154937
  • Ghazi F, Kihal M, Altay N, Gürakan GC. Comparison of RAPD-PCR and PFGE analysis for the typing of Streptococcus thermophilus strains isolated from traditional Turkish yogurts. Ann Microbiol. 2016;66:1013–1026. doi:10.1007/s13213-015-1185-z
  • Hernández M, Castillo G, Ramos OC, et al. Molecular characterization of Pseudomonas aeruginosa clinical isolates among patients of the Hospital Del Niño, Republic Of Panama. Internet J Microbiol. 2016;14(1).
  • Han MM, Mu LZ, Liu XP, Zhao J, Liu XF, Liu H. ERIC-PCR genotyping of Pseudomonas aeruginosa isolates from haemorrhagic pneumonia cases in mink. Vet Rec Open. 2014;1(1):e000043. doi:10.1136/vropen-2014-00004326392878
  • Saha O, Hoque MN, Islam OK, Rahaman MM, Sultana M, Hossain MA. Multidrug-resistant avian pathogenic Escherichia coli strains and association of their virulence genes in Bangladesh. Microorganisms. 2020;8(8):1135. doi:10.3390/microorganisms8081135
  • Khosravi AD, Hoveizavi H, Mohammadian A, Farahani A, Jenabi A. Genotyping of multidrug-resistant strains of Pseudomonas aeruginosa isolated from burn and wound infections by ERIC-PCR. Acta Cir Bras. 2016;31(3):206–211. doi:10.1590/S0102-86502016003000000927050792
  • Zarei O, Shokoohizadeh L, Hossainpour H, Alikhani MY. Molecular analysis of Pseudomonas aeruginosa isolated from clinical, environmental and cockroach sources by ERIC-PCR. BMC Res Notes. 2018;11(1):668. doi:10.1186/s13104-018-3765-z30219108
  • Clark CG, Taboada E, Grant CC, et al. Comparison of molecular typing methods useful for detecting clusters of Campylobacter jejuni and C. coli isolates through routine surveillance. J Clin Microbiol. 2012;50(3):798–809. doi:10.1128/JCM.05733-1122162562