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GÜMÜŞ H. Vankomisine Dirençli Enterococcus faecium: Kısa Bir Derleme. ARŞIV KAYNAK TARAMA DERGISI 2023. [DOI: 10.17827/aktd.1246260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Antimikrobiyal direnç (AMD) ile ilişkili morbidite ve mortalite küresel bir halk sağlığı sorunudur. Sağlık hizmeti ilişkili enfeksiyonlarda sık olarak görülen vankomisine dirençli Enterococcus faecium (VRE), Dünya Sağlık Örgütü’nün AMD’i olan öncelikli patojenler listesinde yüksek öncelik verdiği bir Gram pozitif koktur. Son zamanlarda Türkiye’de invaziv enfeksiyonlarda VRE izolasyon oranı %15.8 bildirilmiştir. Vankomisine direncin ana mekanizması, hedef bölgedeki D-Alanil-D-Alanin terminal molekülünün değişmesi ve ilacın affinitesinin azalmasıdır. Vankomisin direncinden sorumlu olan van geni kromozomal olarak kodlanmakta veya plazmid, transpozon gibi mobil genetik elemanlar ile kazanılmaktadır. Yayılımındaki ana mekanizma, mobil genetik elemanların Enterokoklar veya Staphylococcus aereus gibi farklı tür bakteriler arasında transfer edilebilmeleridir. Bu derlemede PubMed ve Web of Science veritabanlarında “Vankomisin-dirençli Enterococcus faecium”, “Vankomisin direnç mekanizmaları”, “Gram pozitif koklarda vankomisin direnci” terimleri ile arama yapılarak elde edilen literatür verileri özetlenmiş ve önerilerle birlikte kısaca tartışılmıştır.
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Tosun AI, Kolukirik M, Yılmaz M, Ötgün SN, Aygun G, Kolukirik CZK, Zeybek U, Ozgumus GG, Turan M, Kuskucu M, Ince O, Ince B, Kilic S. Development of a new multiplex real-time PCR assay for rapid screening of hospital-acquired infection agents. J Microbiol Methods 2023; 206:106690. [PMID: 36801238 DOI: 10.1016/j.mimet.2023.106690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023]
Abstract
AIMS A new multiplex real-time PCR (qPCR) assay was developed to detect antibiotic-resistant hospital-acquired infectious agents in nasal and rectal swab samples in 1.5 h without the need for nucleic acid extraction. METHODS Spiked negative clinical specimens were used for the analytical performance evaluation. Double-blind samples were collected from 1788 patients to assess the relative clinical performance of the qPCR assay to the conventional culture-based methods. Bio-Speedy® Fast Lysis Buffer (FLB) and 2× qPCR-Mix for hydrolysis probes (Bioeksen R&D Technologies, Istanbul, Turkey) and LightCycler® 96 Instrument (Roche Inc., Branchburg, NJ, USA) were used for all molecular analyses. The samples were transferred into 400 L FLB, homogenized and immediately used in qPCRs. The target DNA regions are vanA and vanB genes for vancomycin-resistant Enterococcus (VRE); blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-23, blaOXA-48, blaOXA-58 genes for carbapenem-resistant Enterobacteriaceae (CRE); and mecA, mecC and spa for methicillin-resistant Staphylococcus aureus (MRSA). RESULTS No qPCR tests produced positive results for the samples spiked with the potential cross-reacting organisms. The limit of detection (LOD) of the assay for all targets was 100 colony-forming unit (cfu)/swab-sample. Results of the repeatability studies in two different centers were in 96%-100% (69/72-72/72) agreement. The relative specificity and sensitivity of the qPCR assay were respectively 96.8% and 98.8% for VRE; 94.9% and 95.1% for CRE; 99.9% and 97.1% for MRSA. CONCLUSIONS The developed qPCR assay can screen antibiotic-resistant hospital-acquired infectious agents in infected/colonized patients with an equal clinical performance to the culture-based methods.
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Affiliation(s)
- Ayse Istanbullu Tosun
- Medical Microbiology, School of Medicine, Istanbul Medipol University, İIstanbu, Turkey.
| | - Mustafa Kolukirik
- Bioeksen R&D Technologies Ltd., Istanbul Technical University Ari-3 Technopark, Istanbul, Turkey
| | - Mesut Yılmaz
- Infectious Diseases and Clinical Microbiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Selin Nar Ötgün
- Public Health General Directorate, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
| | - Gokhan Aygun
- Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | | | - Umit Zeybek
- Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Gozde Girgin Ozgumus
- Bioeksen R&D Technologies Ltd., Istanbul Technical University Ari-3 Technopark, Istanbul, Turkey
| | - Meral Turan
- Public Health General Directorate, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
| | - Mert Kuskucu
- Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Orhan Ince
- ENGY Environmental and Energy Technologies Biotechnology R&D Ltd., Bogazici University Technopark, Istanbul, Turkey
| | - Bahar Ince
- ENGY Environmental and Energy Technologies Biotechnology R&D Ltd., Bogazici University Technopark, Istanbul, Turkey
| | - Selcuk Kilic
- Public Health General Directorate, Department of Microbiology Reference Laboratories and Biological Products, Ankara, Turkey
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Zerrouki H, Rebiahi SA, Hadjadj L, Rolain JM, Diene SM. Real-Time PCR Assay for Rapid and Simultaneous Detection of vanA and vanB Genes in Clinical Strains. Diagnostics (Basel) 2021; 11:diagnostics11112081. [PMID: 34829428 PMCID: PMC8618848 DOI: 10.3390/diagnostics11112081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022] Open
Abstract
Here, we develop a robust and sensitive real-time PCR assay which allows the simultaneous detection of vanA and vanB genes using common primers. The system was designed using the Primer3 online software. The specificity of primers and probes was first checked by in silico PCR and by BlastN analysis. The genomic DNA of 255 bacterial isolates, including Enterococcus spp., Gram-negative, and Gram-positive strains, as well as a collection of 50 stool and 50 rectal swab samples, were tested to evaluate the specificity of the new real-time PCR (RT-PCR) system. The results of the designed RT-PCR were 100% specific and 100% positive on tested vancomycin resistant isolates harboring either the vanA or vanB gene. RT-PCR assays were negative for all other bacterial species tested including vancomycin-sensitive Enterococci and Enterococcus strains harboring vanC genes. The limit of detection of vanA and vanB genes by RT-PCR assay was 47 CFU/mL and 32 CFU/mL, respectively. The rapid and accurate detection of vancomycin-resistant Enterococci is the cornerstone for minimizing the risk of nosocomial transmissions and outbreaks. We believe that this assay will strengthen routine diagnostics and surveillance programs.
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Affiliation(s)
- Hanane Zerrouki
- Laboratoire de microbiologie appliquée à l’agroalimentaire, au biomédical et à l’environnement, Université de Tlemcen, Tlemcen 13000, Algeria; (H.Z.); (S.-A.R.)
- Aix-Marseille Univ., MEPHI, IRD, APHM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.H.); (J.-M.R.)
| | - Sid-Ahmed Rebiahi
- Laboratoire de microbiologie appliquée à l’agroalimentaire, au biomédical et à l’environnement, Université de Tlemcen, Tlemcen 13000, Algeria; (H.Z.); (S.-A.R.)
| | - Linda Hadjadj
- Aix-Marseille Univ., MEPHI, IRD, APHM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.H.); (J.-M.R.)
| | - Jean-Marc Rolain
- Aix-Marseille Univ., MEPHI, IRD, APHM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.H.); (J.-M.R.)
| | - Seydina M. Diene
- Aix-Marseille Univ., MEPHI, IRD, APHM, IHU-Méditerranée Infection, 13005 Marseille, France; (L.H.); (J.-M.R.)
- Correspondence: ; Tel.: +(33)4-91-83-56-49
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Benkova M, Soukup O, Marek J. Antimicrobial susceptibility testing: currently used methods and devices and the near future in clinical practice. J Appl Microbiol 2020; 129:806-822. [DOI: 10.1111/jam.14704] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- M. Benkova
- Department of Epidemiology Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
| | - O. Soukup
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
- Department of Toxicology and Military Pharmacy Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
| | - J. Marek
- Department of Epidemiology Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
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Haghi F, Lohrasbi V, Zeighami H. High incidence of virulence determinants, aminoglycoside and vancomycin resistance in enterococci isolated from hospitalized patients in Northwest Iran. BMC Infect Dis 2019; 19:744. [PMID: 31455296 PMCID: PMC6712822 DOI: 10.1186/s12879-019-4395-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/20/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multidrug resistant (MDR) enterococci are important nosocomial pathogens causing serious problem in hospitalized patients. The aim of present study was to investigate the frequency of high-level aminoglycoside-resistant and vancomycin-resistant enterococci (VRE) and virulence encoding genes in enterococci isolated from hospitalized patients. METHODS A total of 100 enterococci isolated from urine samples of hospitalized patients with symptomatic urinary tract infections were investigated for antimicrobial susceptibility, the frequency of aminoglycoside and vancomycin resistance genes (including aac (6')-Ie-aph (2")-Ia, aph (3')-IIIa, ant (4')-Ia, aph (2")-Ic, aph (2")-Ib, aph (2")-Id, ant (3″)-III, ant (6')-Ia, vanA, vanB and vanC) and virulence encoding genes (including gelE, PAI, esp, ace, cyl, hyl and sprE). RESULTS Enterococcus faecalis species was identified as predominant enterococci (69%), followed by "other" Enterococcus species (21%) and E. faecium (10%). Ninety three percent of isolates were resistant to one or more antimicrobial agents, with the most frequent resistance found against tetracycline (86%), ciprofloxacin (73%) and quinupristin-dalfopristin (53%). Gentamicin and streptomycin resistance were detected in 50 and 34% of isolates, respectively. The most prevalent aminoglycoside resistance genes were ant (3″)-III (78%) and aph (3')-IIIa (67%). Vancomycin resistance was detected in 21% of isolates. All E. faecium isolates carried vanA gene, whereas, the vanB gene was not detected in Enterococcus species. The most frequent virulence gene was ace (88.6%), followed by esp (67.1%), PAI (45.5%) and sprE (41.7%). CONCLUSION Our study revealed the high frequency of gentamycin resistance and VRE in E. faecium isolates, with a high prevalence and heterogeneity of virulence and resistance genes. Due to high frequency of MDR enterococci, it seems that the appropriate surveillance and control measures are essential to prevent the emergence and transmission of these isolates in hospitals.
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Affiliation(s)
- Fakhri Haghi
- Department of Microbiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Vahid Lohrasbi
- Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, Zanjan, Iran.,Department of Microbiology, Iran University of Medical Sciences, Tehran, Iran
| | - Habib Zeighami
- Department of Microbiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran. .,Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, Zanjan, Iran.
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He YH, Ruan GJ, Hao H, Xue F, Ma YK, Zhu SN, Zheng B. Real-time PCR for the rapid detection of vanA, vanB and vanM genes. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 53:746-750. [PMID: 30926279 DOI: 10.1016/j.jmii.2019.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND/PURPOSE To evaluate the ability of quadruple Taqman probe real-time PCR to the detection of vanA, vanB and vanM in enterococcal isolates. METHODS A total of 343 strains, including 253 vancomycin-resistant enterococcus (VRE) strains and 90 non-VRE strains, were tested by both quadruple Taqman probe real-time PCR and gel-based PCR assay. RESULTS When differentiating among three genotypes of vanA, vanB and vanM in VRE strains, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic accuracy and consistency of the quadruple Taqman probe real-time PCR were all 100%. Minimum. Inhibitory concentration (MIC) results showed that there was a wide MIC range of vancomycin and teicoplanin for the strains that harboring vanA/vanM gene respectively or harboring vanA and vanM genes simultaneously. However, the VRE strains with vanB genotype all were sensitive to teicoplanin. CONCLUSION Considering the excellent PPV and low NPV, real-time PCR would be useful to monitor VRE-colonized or infected patients. However, further evaluation of the assay's performance in the clinical specimens is required, especially when considering that high level of PCR inhibitors present in these samples.
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Affiliation(s)
- Yuan-Hui He
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Gen-Jie Ruan
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Hui Hao
- IPE Biotechnology Co. Ltd, Beijing, China
| | - Feng Xue
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Ya-Kun Ma
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Sai-Nan Zhu
- Department of Biostatistics, Peking University First Hospital, Beijing, China
| | - Bo Zheng
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China.
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Both A, Franke GC, Mirwald N, Lütgehetmann M, Christner M, Klupp EM, Belmar Campos C, Büttner H, Aepfelbacher M, Rohde H. Two-tier approach combining molecular and culture-based techniques for optimized detection of vancomycin-resistant enterococci. Diagn Microbiol Infect Dis 2017; 89:253-257. [DOI: 10.1016/j.diagmicrobio.2017.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/15/2017] [Accepted: 08/17/2017] [Indexed: 11/29/2022]
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Detection of Vancomycin-Resistant Enterococci. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Real-time PCR is the traditional face of nucleic acid detection in the diagnostic microbiology laboratory and is now generally regarded as robust enough to be widely adopted. Methods based on nucleic acid detection of this type are bringing increased accuracy to diagnosis in areas where culture is difficult and/or expensive, and these methods are often effective partners to other rapid molecular diagnostic tools such as matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS). This change in practice has particularly affected the recognition of viruses and fastidious or antibiotic-exposed bacteria, but has been also shown to be effective in the recognition of troublesome or specialised phenotypes such as antiviral resistance and transmissible antibiotic resistance in the Enterobacteriaceae. Quantitation and high-intensity sequencing (of multiple whole genomes) has brought new opportunities as well as new challenges to the microbiology community. Diagnostic microbiologists currently training might be expected to deal less with the culture-based techniques of the last half-century than with the high-volume data and complex analyses of the next.
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Evaluation of the NanoCHIP® Infection Control Panel test for direct detection and screening of methicillin-resistant Staphylococcus aureus (MRSA), Klebsiella pneumoniae carbapenemase (KPC)-producing bacteria and vancomycin-resistant Enterococcus (VRE). Infection 2015; 43:331-8. [DOI: 10.1007/s15010-015-0754-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 02/19/2015] [Indexed: 11/26/2022]
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Huh HJ, Jang MA, Seo JY, Kim JY, Ki CS, Kim JW, Lee NY. Evaluation of the iNtRON VRE vanA/vanB real-time PCR assay for detection of vancomycin-resistant enterococci. Ann Lab Med 2014; 35:76-81. [PMID: 25553284 PMCID: PMC4272969 DOI: 10.3343/alm.2015.35.1.76] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/28/2014] [Accepted: 10/13/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Recently, the iNtRON VRE vanA/vanB real-time PCR (iNtRON; iNtRON Biotechnology, Korea) assay, a multiplex real-time PCR method, was introduced. In this prospective study, we compared the iNtRON assay with the Seeplex VRE ACE detection kit (Seeplex; Seegene, Korea), a conventional multiplex PCR assay. METHODS A chromogenic agar-based culture, in which pre-selected vancomycin-resistant enterococci (VRE) was grown and subsequently plated on blood agar with vancomycin disks, was regarded as the reference method. A total of 304 consecutive rectal swab specimens were tested for VRE by culture and by iNtRON and Seeplex PCR assays. For the PCR assays, specimens were enriched for 16-24 hr before PCR. RESULTS VRE were isolated from 44 (14.5%) specimens by chromogenic agar-based culture. The clinical sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the iNtRON assay were 100% (95% confidence interval: 89.8%-100%), 99.2% (96.9%-99.9%), 95.6% (83.6%-99.2%), and 100% (98.2%-100%), respectively, while those of the Seeplex assay were 97.7% (86.2%-99.9%), 99.6% (97.5%-99.9%), 97.7% (86.2%-99.9%), and 99.6% (97.5%-99.9%), respectively. The iNtRON assay had a detection limit of 3,159 copies/µL and 13,702 copies/µL for the vanA and vanB genes, respectively. No cross-reactivity was observed in 11 non-VRE bacterial culture isolates. CONCLUSIONS The overall performance of the iNtRON assay was comparable to that of a chromogenic agar-based culture method for prompt identification of VRE-colonized patients in hospitals. This assay could be an alternative or supportive method for the effective control of nosocomial VRE infection.
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Affiliation(s)
- Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ja Young Seo
- Department of Laboratory Medicine, Gachon University Gil Hospital, Incheon, Korea
| | - Ji-Youn Kim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, Korea
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