Enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis as a reliable evidence for suspected Shigella spp. outbreaks

Bakhshi, Bita; Afshari, Nasim; Fallah, Fatemeh

doi:10.1016/j.bjm.2017.01.014

Cited by 20 publications

(14 citation statements)

References 21 publications

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“…pneumoniae isolates from beef samples were very similar despite the differences in their sampling stations and this was in accordance with a previous report [45]. e findings of several studies have revealed that ERIC fingerprinting is a reliable tool for discriminating among isolates from different sources and hence considered to be a powerful tool for surveillance and control of antibiotic resistant bacteria [28,46,47]; these data indicate the need to improve on farm management techniques as well as standard operational procedures in abattoirs. In addition, contamination of raw beef with these multi-drug resistant pathogens may have also occurred at sale points and this, therefore, amplifies the need to enforce proper hygiene practices in supermarkets.…”

Section: Genotypic Typing Of Esbl Producing E Coli and Klebsiella Pnsupporting

confidence: 91%

Antimicrobial Resistance Factors of Extended-Spectrum Beta-Lactamases Producing Escherichia coli and Klebsiella pneumoniae Isolated from Cattle Farms and Raw Beef in North-West Province, South Africa

Montso

Dlamini

Kumar

et al. 2019

BioMed Research International

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Background. Extended spectrum beta-lactamases (ESBLs) producing Enterobacteriaceae cause severe infections in humans which leads to complicated diseases. There is increasing evidence that cattle contribute to the development and spread of multidrug resistant pathogens and this raises public health concern. Despite this, data on the concurrence of ESBL producing pathogens in cattle, especially in the North-West province are rare. Therefore, the aim of the present study was to isolate, identify and characterise ESBL producing E. coli and K. pneumoniae species from cattle faeces and raw beef samples. Results. A total of 151 samples comprising 55 faeces samples and 96 raw beef samples were collected and 259 nonreplicative potential isolates of Enterobacteriaceae were obtained. One hundred and ninety-six isolates were confirmed as E. coli (114; 44%) and K. pneumoniae (82; 32%) species through amplification of uspA and uidA and ntrA gene fragments, respectively. Antimicrobial susceptibility test revealed that large proportions (66.7–100%) of the isolates were resistant to Amoxicillin, Aztreonam, Ceftazidime, Cefotaxime, and Piperacillin and were multidrug resistant isolates. Cluster analysis of antibiotic inhibition zone diameter data revealed close similarities between isolates from different sources or species thus suggested a link in antibiotic exposures. The isolates showing phenotypic resistance against ESBL antimicrobial susceptibility tests were screened for the presence of ESBL gene determinants. It was observed that 53.1% of the isolates harboured ESBL gene determinants. The blaTEM, blaSHV and blaCTX-M genes were detected in E. coli isolates (85.5%, 69.6%, and 58%, respectively) while blaCTX-M and blaOXA were detected in K. pneumoniae (40% and 42.9%, respectively). All the genetically confirmed ESBL producing E. coli and K. pneumoniae isolates were subjected to Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR analysis. Fingerprinting data revealed great similarities between isolates from different areas and sources which indicates cross-contamination between cattle and beef. Conclusion. This study revealed that cattle and its associated food products, beef in particular, harbour ESBL producing pathogens. And this warrants a need to enforce hygiene measures and to develop other mitigation strategies to minimise the spread of antibiotic resistant pathogens from animals to human.

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Section: Genotypic Typing Of Esbl Producing E Coli and Klebsiella Pnsupporting

confidence: 91%

Antimicrobial Resistance Factors of Extended-Spectrum Beta-Lactamases Producing Escherichia coli and Klebsiella pneumoniae Isolated from Cattle Farms and Raw Beef in North-West Province, South Africa

Montso

Dlamini

Kumar

et al. 2019

BioMed Research International

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“…It is noteworthy that the ERIC technique has been used in many different areas of research including veterinary microbiology, food microbiology and, in particular, various clinical areas dealing with human infections within the hospital environment and in the community [3–7]. Indeed, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) can be used to study human pathogens, in both Gram-positive and -negative bacterial isolates in order to determine their genetic diversity, and occasionally extended to bacterial pathogens in the animal kingdom.…”

Section: Introductionmentioning

confidence: 99%

Genetic relatedness in carbapenem-resistant isolates from clinical specimens in Ghana using ERIC-PCR technique

et al. 2019

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AimEnterobacterial repetitive intergenic consensus (ERIC) sequence analysis is a powerful tool for epidemiological analysis of bacterial species. This study aimed to determine the genetic relatedness or variability in carbapenem-resistant isolates by species using this technique.MethodsA total of 111 non-duplicated carbapenem-resistant (CR) Gram-negative bacilli isolates from a three-year collection period (2012–2014) were investigated by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC–PCR) in four selected hospital laboratories in Ghana. The isolates were also screened for carbapenemase and extended spectrum β-lactamase genes by PCR.ResultsA proportion of 23.4% (26/111) of the genomic DNA extracts were carriers of PCR-positive carbapenemase genes, including 14.4% blaNDM-1, 7.2% blaVIM-1 and 1.8% blaOXA-48. The highest prevalence of carbapenemase genes was from non-fermenters, Acinetobacter baumannii and Pseudomonas aeruginosa. For the ESBL genes tested, 96.4% (107/111) of the CR isolates co-harboured both TEM-1 and SHV-1 genes. The ERIC-PCR gel analysis exhibited 1 to 8 bands ranging from 50 to 800 bp. Band patterns of 93 complex dissimilarities were visually distinguished from the 111 CR isolates studied, while the remaining 18 showed band similarities in pairs.ConclusionOverall, ERIC-PCR fingerprints have shown a high level of diversity among the species of Gram-negative bacterial pathogens and specimen collection sites in this study. ERIC-PCR optimisation assays may serve as a suitable genotyping tool for the assessment of genetic diversity or close relatedness of isolates that are found in clinical settings.

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“…So far, there were many reports on the molecular types of V. alginolyticus ( Kahla-Nakbi et al, 2006 ), V. tapetis ( Rodríguez et al, 2006 ), and V. parahaemolyticus ( Chen et al, 2012 ), but no reports on that of V. owensii . ERIC-PCR as an easy and cost-effective genotyping approach for discriminating different strains types ( Bakhshi et al, 2018 ) has urged us to use this technique to inspect phylogenetic closeness of V. owensii isolates. All 80 V. owensii isolates produced banding patterns after amplification by ERIC-PCR ( Supplementary Figure S2 ), indicating the complete type ability of V. owensii using this technology, which were clustered into four clusters (ET-1–ET-4) at 58% of similarity ( Figure 4 ).…”

Section: Discussionmentioning

confidence: 99%

“…The genetic patterns were calculated according to the molecular weights and quantification of the bands in each sample. Simpson’s Index of Diversity was used to calculated the discriminatory index of ERIC-PCR ( Pishbin and Mehrabian, 2020 ), and the “unweighted pair group method with dice similarity coefficient” option in NTSYS v. 12 program ( Bakhshi et al, 2018 ) was used to cluster the V. owensii isolates.…”

Section: Methodsmentioning

confidence: 99%

Community Structure of Protease-Producing Bacteria Cultivated From Aquaculture Systems: Potential Impact of a Tropical Environment

Wei

Long

et al. 2021

Front. Microbiol.

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Protease-producing bacteria play vital roles in degrading organic matter of aquaculture system, while the knowledge of diversity and bacterial community structure of protease-producing bacteria is limited in this system, especially in the tropical region. Herein, 1,179 cultivable protease-producing bacterial strains that belonged to Actinobacteria, Firmicutes, and Proteobacteria were isolated from tropical aquaculture systems, of which the most abundant genus was Bacillus, followed by Vibrio. The diversity and relative abundance of protease-producing bacteria in sediment were generally higher than those in water. Twenty-one genera from sediment and 16 genera from water were identified, of which Bacillus dominated by Bacillus hwajinpoensis in both and Vibrio dominated by Vibrio owensii in water were the dominant genera. The unique genera in sediment or water accounted for tiny percentage may play important roles in the stability of community structure. Eighty V. owensii isolates were clustered into four clusters (ET-1–ET-4) at 58% of similarity by ERIC-PCR (enterobacterial repetitive intergenic consensus-polymerase chain reaction), which was identified as a novel branch of V. owensii. Additionally, V. owensii strains belonged to ET-3 and ET-4 were detected in most aquaculture ponds without outbreak of epidemics, indicating that these protease-producing bacteria may be used as potential beneficial bacteria for wastewater purification. Environmental variables played important roles in shaping protease-producing bacterial diversity and community structure in aquaculture systems. In sediment, dissolved oxygen (DO), chemical oxygen demand (COD), and salinity as the main factors positively affected the distributions of dominant genus (Vibrio) and unique genera (Planococcus and Psychrobacter), whereas temperature negatively affected that of Bacillus (except B. hwajinpoensis). In water, Alteromonas as unique genus and Photobacterium were negatively affected by NO3−-N and NO2−-N, respectively, whereas pH as the main factor positively affected the distribution of Photobacterium. These findings will lay a foundation for the development of protease-producing bacterial agents for wastewater purification and the construction of an environment-friendly tropical aquaculture model.

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Enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis as a reliable evidence for suspected Shigella spp. outbreaks

Cited by 20 publications

References 21 publications

Antimicrobial Resistance Factors of Extended-Spectrum Beta-Lactamases Producing Escherichia coli and Klebsiella pneumoniae Isolated from Cattle Farms and Raw Beef in North-West Province, South Africa

Antimicrobial Resistance Factors of Extended-Spectrum Beta-Lactamases Producing Escherichia coli and Klebsiella pneumoniae Isolated from Cattle Farms and Raw Beef in North-West Province, South Africa

Genetic relatedness in carbapenem-resistant isolates from clinical specimens in Ghana using ERIC-PCR technique

Community Structure of Protease-Producing Bacteria Cultivated From Aquaculture Systems: Potential Impact of a Tropical Environment

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