Genotyping Techniques for Determining the Diversity of Microorganisms

Wolska, Katarzyna; Szweda, Piotr

doi:10.5772/35101

Cited by 12 publications

(13 citation statements)

References 201 publications

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“…Therefore, it is essential to generate a prior knowledge about the prevalence of pathogens especially E. coli in different source. Understanding their occurrence also the genetic diversity analysis in various potential host sources of contamination would help us to assess the health risk posed by such strains of E. coli and epidemiological surveillance of bacterial infections [ 5 ]. High genetic diversity among E. coli populations potentially influence the accuracy of the results, thus, more information is necessary on the genetic diversity of E. coli populations in a host source of interest.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of Escherichia coli isolated from ice cube production sites

et al. 2018

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ObjectiveThe prevalence of Escherichia coli including from ice cubes in Indonesia is quite high. Unfortunately, little is known about the genetic diversity of E. coli from ice cube production site. Genotypic variation in E. coli populations is a major barrier to control public health risk associated with foodborne pathogen. The aims of this study were to analyze the genotypic diversity of E. coli strains isolated from various samples in order to determine the genetic relationship between those strains. This study is also important to understand the occurrence, prevalence and profile picture of different pathogenic E. coli in various sources which potentially cause disease.ResultsEnterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic palindromic polymerase chain reaction (REP-PCR) dendrogram showed high genetic diversity of 120 E. coli isolates in majority of sampling sites. DNA fingerprint patterns showed 26 and 21 clusters with 11 and 3 fingerprints individual lineages for ERIC and REP-PCR respectively. There was no correlation observed between phylogenetic relationship and virulence genes. The result indicated a variation of E. coli isolates in ice cube manufacturers. ERIC-PCR method is more discriminative compared with REP-PCR to analyze the genetic diversity of E. coli from ice cubes production sites.

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Section: Introductionmentioning

confidence: 99%

Genetic diversity of Escherichia coli isolated from ice cube production sites

et al. 2018

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“…Another important advantage of proposed methods is high discriminatory power, which has been confirmed in the presented research. Both methods exhibit comparable (RFLP-PCR) or higher (MLST) potential for differentiation of the strains tested in comparison to the BOX-PCR method, which is widely used for genotyping of different pathogenic bacteria, including E. coli [15,21,22]. The differentiation of the strains tested with the BOX-PCR method revealed 31 different genotypes, while 29 and 47 clusters were revealed with the fliC RFLP-PCR and MLST methods, respectively.…”

Section: Discussionmentioning

confidence: 96%

“…In recent years, significant progress has been observed in the development of new techniques for the genotyping of pathogenic microorganisms [22,25,33]. Pulsed-field gel electrophoresis (PFGE) is still considered as the gold standard.…”

Section: Discussionmentioning

confidence: 99%

New Approaches for Escherichia coli Genotyping

et al. 2020

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Easy-to-perform, fast, and inexpensive methods of differentiation of Escherichia coli strains beyond the species level are highly required. Herein two new, original tools for genotyping of E. coli isolates are proposed. The first of the developed method, a PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) test uses a highly variable fliC gene, encoding the H antigen as a molecular target. The designing of universal pair of primers and selection of the optimal restriction enzyme RsaI was preceded by in silico comparative analysis of the sequences of the genes coding for 53 different serotypes of H-antigen (E. coli flagellin). The target fragments of E. coli genomes for MLST method were selected on the basis of bioinformatics analysis of complete sequences of 16 genomes of E. coli. Initially, seven molecular targets were proposed (seven pairs of primers) and five of them were found useful for effective genotyping of E. coli strains. Both developed methods revealed high differentiation power, and a high genetic diversity of the strains tested was observed. Within the group of 71 strains tested, 29 and 47 clusters were revealed with fliC RFLP-PCR and MLST methods, respectively. Differentiation of the strains with the reference BOX-PCR method revealed 31 different genotypes. The in silico analysis revealed that the discriminatory power of the new MLST method is comparable to the Pasteur and Achtman schemes and is higher than the discriminatory power of the method developed by Clermont. From the epidemiology point of view, the outcomes of our investigation revealed that in most cases, the patients were infected with unique strains, probably from environmental sources. However, some strains isolated from different patients of the wards of pediatrics, internal medicine, and neurology were classified to the same genotype when the results of all three methods were taken into account. It could suggest that they were transferred between the patients.

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“…The relationship between isolates was calculated by numerical analysis of genetic features determined by ERIC-PCR. This molecular genotyping is much faster and more cost-effective; furthermore, it possesses a higher discriminatory ability than other typing techniques (Wolska and Szweda 2012). ERIC-PCR was used successfully, for example, for typing of clinical P. aeruginosa (Wolska and Szweda 2008) and to determine the link between pathogenic and non-pathogenic isolates (Yang et al 2005).…”

Section: Discussionmentioning

confidence: 99%

“…PCR-based genotyping methods have played an important role in bacterial typing schemes (Wolska and Szweda 2012). One of the PCR-based methods, is Rep-PCR.…”

Section: Inntroductionmentioning

confidence: 99%

Motility activity, slime production, biofilm formation and genetic typing by ERIC-PCR for Pseudomonas aeruginosa strains isolated from bovine and other sources (human and environment)

Wolska¹,

Szweda²,

Lada³

et al. 2014

Polish Journal of Veterinary Sciences

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The molecular-typing strategy, ERIC-PCR was used in an attempt to determine the genomic relationship of 28 P. aeruginosa strains isolated from faeces of healthy bovine, bovine mastitis and from faeces of hospital patients as well as from environment. ERIC-PCR fingerprinting revealed large molecular differentiation within this group of isolates. Twenty two out of 28 strains tested generated unique patterns of DNA bands and only three genotypes consisted of two isolates each were identified.We also tested the P. aeruginosa isolates for their ability to form a biofilm on abiotic surfaces including polyvinylchloride and polystyrene. Different biofilm-forming abilities were demonstrated among strains; however, most of them (64.3%) showed moderate-biofilm forming ability. The strains with increased swimming and twitching motility displayed elevated biofilm formation. However, a negative correlation was found between slime and initial biofilm production. On the basis of the results obtained, we suggest that there are no major differences in phenotypic properties between P. aeruginosa strains isolated from different sources.

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Genotyping Techniques for Determining the Diversity of Microorganisms

Cited by 12 publications

References 201 publications

Genetic diversity of Escherichia coli isolated from ice cube production sites

Genetic diversity of Escherichia coli isolated from ice cube production sites

New Approaches for Escherichia coli Genotyping

Motility activity, slime production, biofilm formation and genetic typing by ERIC-PCR for Pseudomonas aeruginosa strains isolated from bovine and other sources (human and environment)

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