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

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          Abstract

          Aim

          Enterobacterial 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.

          Methods

          A 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.

          Results

          A 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.

          Conclusion

          Overall, 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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          Most cited references30

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          The difficult-to-control spread of carbapenemase producers among Enterobacteriaceae worldwide.

          The spread of carbapenemase producers in Enterobacteriaceae has now been identified worldwide. Three main carbapenemases have been reported; they belong to three classes of β-lactamases, which are KPC, NDM, and OXA-48. The main reservoirs of KPC are Klebsiella pneumoniae in the USA, Israel, Greece, and Italy, those of NDM are K. pneumoniae and Escherichia coli in the Indian subcontinent, and those of OXA-48 are K. pneumoniae and Escherichia coli in North Africa and Turkey. KPC producers have been mostly identified among nosocomial isolates, whereas NDM and OXA-48 producers are both nosocomial and community-acquired pathogens. Control of their spread is still possible in hospital settings, and relies on the use of rapid diagnostic techniques and the strict implemention of hygiene measures.
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            Carbapenem resistance: overview of the problem and future perspectives.

            Carbapenem resistance, mainly among Gram-negative pathogens, is an ongoing public-health problem of global dimensions. This type of antimicrobial resistance, especially when mediated by transferable carbapenemase-encoding genes, is spreading rapidly causing serious outbreaks and dramatically limiting treatment options. In this article, important key points related to carbapenem resistance are reviewed and future perspectives are discussed.
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              The Acinetobacter baumannii Oxymoron: Commensal Hospital Dweller Turned Pan-Drug-Resistant Menace

              During the past few decades Acinetobacter baumannii has evolved from being a commensal dweller of health-care facilities to constitute one of the most annoying pathogens responsible for hospitalary outbreaks and it is currently considered one of the most important nosocomial pathogens. In a prevalence study of infections in intensive care units conducted among 75 countries of the five continents, this microorganism was found to be the fifth most common pathogen. Two main features contribute to the success of A. baumannii: (i) A. baumannii exhibits an outstanding ability to accumulate a great variety of resistance mechanisms acquired by different mechanisms, either mutations or acquisition of genetic elements such as plasmids, integrons, transposons, or resistant islands, making this microorganism multi- or pan-drug-resistant and (ii) The ability to survive in the environment during prolonged periods of time which, combined with its innate resistance to desiccation and disinfectants, makes A. baumannii almost impossible to eradicate from the clinical setting. In addition, its ability to produce biofilm greatly contributes to both persistence and resistance. In this review, the pathogenesis of the infections caused by this microorganism as well as the molecular bases of antibacterial resistance and clinical aspects such as treatment and potential future therapeutic strategies are discussed in depth.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: SupervisionRole: ValidationRole: Writing – original draft
                Role: ConceptualizationRole: InvestigationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: MethodologyRole: Project administrationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                12 September 2019
                2019
                : 14
                : 9
                : e0222168
                Affiliations
                [1 ] Department of Medical Laboratory Sciences, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Ghana
                [2 ] Biomolecular Science Research Centre, Sheffield Hallam University, Sheffield, England, United Kingdom
                [3 ] Department of Medical Microbiology, School of Biomedical & Allied Health Sciences, College of Health Sciences, University of Ghana, Ghana
                School of Pathology, National Health Laboratory Service (NHLS) and University of the Witwatersrand, South Africa, SOUTH AFRICA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-9368-0636
                Article
                PONE-D-19-09381
                10.1371/journal.pone.0222168
                6742460
                31513633
                e5044447-32b4-419a-9927-15943e5b21fa
                © 2019 Codjoe et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 2 April 2019
                : 19 August 2019
                Page count
                Figures: 2, Tables: 2, Pages: 11
                Funding
                Funded by: Office of Research, Innovation and Development, University of Ghana
                Award Recipient :
                The study was funded through a grant from the Office of Research, Innovation and Development of the University of Ghana to FSD, and a PhD sponsorship from the College of Health Sciences Endowment fund of the University of Ghana. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Bacterial Pathogens
                Pseudomonas Aeruginosa
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Bacterial Pathogens
                Pseudomonas Aeruginosa
                Biology and Life Sciences
                Organisms
                Bacteria
                Pseudomonas
                Pseudomonas Aeruginosa
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Genetic Fingerprinting and Footprinting
                Genetic Fingerprinting
                Research and Analysis Methods
                Molecular Biology Techniques
                Genetic Fingerprinting and Footprinting
                Genetic Fingerprinting
                Biology and Life Sciences
                Organisms
                Bacteria
                Acinetobacter
                Acinetobacter Baumannii
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Bacterial Pathogens
                Acinetobacter
                Acinetobacter Baumannii
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Bacterial Pathogens
                Acinetobacter
                Acinetobacter Baumannii
                Biology and Life Sciences
                Microbiology
                Microbial Control
                Antimicrobial Resistance
                Medicine and Health Sciences
                Pharmacology
                Antimicrobial Resistance
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Bacterial Pathogens
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Bacterial Pathogens
                Medicine and Health Sciences
                Infectious Diseases
                Bacterial Diseases
                Acinetobacter Infections
                Medicine and Health Sciences
                Infectious Diseases
                Bacterial Diseases
                Pseudomonas Infections
                Custom metadata
                Data will be available upon request. This is because the data contains potentially sensitive patient information. In view of this, the ethics committee has placed some restrictions on its sharing. Data request may be addressed to the Chair of the Ethical and Protocol Review Committee, College of Health Sciences, University of Ghana, Korle Bu Campus, Accra, Ghana; Email: eprc@ 123456chs.edu.gh

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