Determination of the genetic similarities of fingerprints from Escherichia coli O157:H7 isolated from different sources in the North West Province, South Africa using ISR, BOXAIR and REP-PCR analysis

Abstract

The aim of this study was to determine the genetic relationships of Escherichia coli O157:H7 isolated from pigs, cattle, pork, beef, humans and water samples using REP, ISR and BOXAIR PCR analysis. A total of 94 isolates were subjected to the REP-PCR analysis while 95 were screened for ISR and BOXAIR PCR fingerprints. The band sizes for amplicons from the ISR-PCR analysis ranged from 0.173kb to 0.878kb. However, a large proportion of the isolates had four bands ranging from 0.447kb to 0.878kb. Cluster analysis of the BOXAIR PCR profiles based on banding patterns revealed seven main clusters. It was identified in the clusters III, IV and VII in the BOXAIR PCR that 17.9%, 16.8% and 18.9%, of E. coli O157:H7 isolates respectively were present from all the animal species, meat and water samples. REP-PCR analysis produced 9 different patterns with bands ranging from 0 to 12 per isolate. The band sizes ranged from 200bp to 8000bp. Nine major clusters (I-IX) were identified. From the three different species sampled cluster eight was the largest and a mixed cluster with 23.4% (22/94) of the E. coli O157:H7 isolates. These indicate that food products obtained from supermarkets in the study area are contaminated with E. coli O157:H7.

Fingerprints of resistant Escherichia coli O157:H7 from vegetables and environmental samples

“…Based on the results of the present study, some isolates from different sources/samples may have originated from a single source and been transmitted through different routes to vegetables or from diverse sources, as shown by similar and differing banding patterns. Our results are in agreement with previous studies reporting the similarity of fingerprints strains of E. coli O157:H7 obtained from different sources.…”

Genotypic diversity among multidrug resistant Pseudomonas aeruginosa and Acinetobacter species at Mulago Hospital in Kampala, Uganda

“…DNA fingerprints were analyzed with the BioNumerics software version 4 (Applied Maths NV, Sint-Martens-Latem, Belgium) as described elsewhere [34, 35, 45, 46]. The similarity-analysis of the results of each genotyping assay was calculated using Dice coefficient; cluster analysis of the similarity matrices was generated using Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithm.…”

Genetic Characterization Among Carbapenem-resistant Escherichia coli Strains Using Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) Fingerprinting in South Africa

“…Some selected E. coli strains were investigated genetically with the use of ERIC-PCR. Osińska et al [59] reported ERIC-PCR genomic ngerprinting technique as a vital tool for evaluating genetic relationships between bacterial strains isolated from environmental niches and some other studies reported ERIC-PCR genotypic diversity of multidrug resistant (MDR) bacterial strains isolated from different sources [60,61], However, in this study we analyzed selected E. coli strains comprising some CREC with the use of ERIC-ngerprinting in order to evaluate the links that exist between strains isolated from different sources. ERIC-PCR has been demonstrated to be an effective method in determining the genetic diversity or relatedness among bacterial species by grouping clusters according to band sizes [62].…”

“…A total of 243 different environmental samples ranging from surface water (47), WWTPs nal e uents (29), hospital e uents (27) to irrigation water (45), soil (60) and vegetables (35) were collected from January to September 2018. Water samples (1.5L) was collected in duplicate using sterile glass bottles and transported in an ice box to the research laboratory for bacteriological analyses within 6 hours of sampling.…”