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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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Averbuch D, Moshkovitz L, Ilan S, Abu Ahmad W, Temper V, Strahilevitz J. Bacteremia with Carbapenemase-Producing Enterobacterales in Immunocompromised Patients Colonized with These Bacteria. Microb Drug Resist 2022; 28:593-600. [PMID: 35580283 DOI: 10.1089/mdr.2021.0253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We aimed to analyze rates and risk factors for carbapenemase-producing Enterobacterales (CPE) bloodstream infection (BSI) in CPE-colonized patients with malignancies or following hematopoietic cell transplantation. We retrospectively collected data on demography, underlying disease, colonizing CPE, treatment, intensive care unit (ICU) hospitalization, CPE-BSI, and mortality in CPE-colonized immunocompromised patients (2014-2020). Two hundred twenty-one patients were colonized with 272 CPE: 254 (93.4%) carried one carbapenemase [KPC (50.4%), NDM (34.6%), OXA-48-like (5.2%), and VIM (3.3%)]; 18 (6.6%) carried two carbapenemases. Twenty-eight (12.7%) patients developed CPE-BSI. Univariate analysis revealed CPE-BSI-associated factors: younger age, carbapenem or aminoglycoside exposure, ICU admission, neutropenia, carrying serine carbapenemase-producing, and specifically KPC-producing bacteria, colonization with several CPE, and detection of several carbapenemases. None of 23 auto-HSCT recipients developed CPE-BSI. In multivariate analysis, ICU hospitalization was significantly associated with CPE-BSI (odds ratio [OR] 2.82, 95% CI 1.10-7.20; p = 0.042); solid tumor diagnosis was protective (OR 0.21, 95% CI 0.05-1.01; p = 0.038). One-year crude mortality was 108/221 (48.8%), including 19/28 (67.9%) and 89/193 (46.1%) in patients with and without CPE-BSI, p = 0.104. To conclude, CPE-BSI is rare in CPE-colonized patients with solid tumors and following auto-HSCT. ICU hospitalization increased CPE-BSI risk. These data can help to guide empirical anti-CPE antibiotic therapy in patients colonized with these bacteria.
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Affiliation(s)
- Diana Averbuch
- Pediatric Infectious Diseases, Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical Center, Jerusalem, Israel
| | - Liya Moshkovitz
- Pediatric Infectious Diseases, Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical Center, Jerusalem, Israel
| | - Shlomi Ilan
- Pediatric Infectious Diseases, Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical Center, Jerusalem, Israel
| | - Wiessam Abu Ahmad
- Braun School of Public Health and Community Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Violeta Temper
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical Center, Jerusalem, Israel
| | - Jacob Strahilevitz
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical Center, Jerusalem, Israel
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3
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Chang E, Chang H, Shin I, Oh Y, Kang C, Choe P, Park W, Choi E, Oh M, Park K, Kim N. Investigation on the transmission rate of carbapenemase-producing carbapenem-resistant Enterobacterales among exposed persons in a tertiary hospital using whole-genome sequencing. J Hosp Infect 2022; 124:1-8. [DOI: 10.1016/j.jhin.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
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4
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Feng Y, Xue G, Feng J, Yan C, Cui J, Gan L, Zhang R, Zhao H, Xu W, Li N, Liu S, Du S, Zhang W, Yao H, Tai J, Ma L, Zhang T, Qu D, Wei Y, Yuan J. Rapid Detection of New Delhi Metallo-β-Lactamase Gene Using Recombinase-Aided Amplification Directly on Clinical Samples From Children. Front Microbiol 2021; 12:691289. [PMID: 34367092 PMCID: PMC8339468 DOI: 10.3389/fmicb.2021.691289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/30/2021] [Indexed: 11/26/2022] Open
Abstract
New Delhi metallo-β-lactamase, a metallo-β-lactamase carbapenemase type, mediates resistance to most β-lactam antibiotics including penicillins, cephalosporins, and carbapenems. Therefore, it is important to detect blaNDM genes in children’s clinical samples as quickly as possible and analyze their characteristics. Here, a recombinase-aided amplification (RAA) assay, which operates in a single one-step reaction tube at 39°C in 5−15 min, was established to target blaNDM genes in children’s clinical samples. The analytical sensitivity of the RAA assay was 20 copies, and the various bacterial types without blaNDM genes did not amplify. This method was used to detect blaNDM genes in 112 children’s stool samples, 10 of which were tested positive by both RAA and standard PCR. To further investigate the characteristics of carbapenem-resistant bacteria carrying blaNDM in children, 15 carbapenem-resistant bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Citrobacter freundii, Klebsiella oxytoca, Acinetobacter junii, and Proteus mirabilis) were isolated from the 10 samples. Notably, more than one bacterial type was isolated from three samples. Most of these isolates were resistant to cephalosporins, cefoperazone-sulbactam, piperacillin-tazobactam, ticarcillin-clavulanic acid, aztreonam, co-trimoxazole, and carbapenems. blaNDM–1 and blaNDM–5 were the two main types in these samples. These data show that the RAA assay has potential to be a sensitive and rapid blaNDM gene screening test for clinical samples. The common existence of blaNDM and multi-drug resistance genes presents major challenges for pediatric treatment.
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Affiliation(s)
| | - Guanhua Xue
- Capital Institute of Pediatrics, Beijing, China
| | - Junxia Feng
- Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Capital Institute of Pediatrics, Beijing, China
| | - Hanqin Zhao
- Capital Institute of Pediatrics, Beijing, China
| | - Wenjian Xu
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Nannan Li
- Capital Institute of Pediatrics, Beijing, China
| | - Shiyu Liu
- Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Capital Institute of Pediatrics, Beijing, China
| | | | - Hailan Yao
- Capital Institute of Pediatrics, Beijing, China
| | - Jun Tai
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Lijuan Ma
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Ting Zhang
- Capital Institute of Pediatrics, Beijing, China
| | - Dong Qu
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Yongxiang Wei
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Capital Institute of Pediatrics, Beijing, China
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Shanmugakani RK, Srinivasan B, Glesby MJ, Westblade LF, Cárdenas WB, Raj T, Erickson D, Mehta S. Current state of the art in rapid diagnostics for antimicrobial resistance. LAB ON A CHIP 2020; 20:2607-2625. [PMID: 32644060 PMCID: PMC7428068 DOI: 10.1039/d0lc00034e] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.
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Affiliation(s)
- Rathina Kumar Shanmugakani
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Balaji Srinivasan
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Marshall J. Glesby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Washington B. Cárdenas
- Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Guayas, Ecuador
| | - Tony Raj
- St. John’s Research Institute, Bangalore, Karnataka, India
| | - David Erickson
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
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Saliba R, Aho-Glélé LS, Karam-Sarkis D, Zahar JR. Evaluation of polymerase chain reaction assays for direct screening of carbapenemase-producing Enterobacteriaceae from rectal swabs: a diagnostic meta-analysis. J Hosp Infect 2020; 104:381-389. [DOI: 10.1016/j.jhin.2019.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 01/08/2023]
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7
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Soria Segarra C, Larrea Vera G, Berrezueta Jara M, Arévalo Mendez M, Cujilema P, Serrano Lino M, Soria Segarra C. Utility of CHROMagar mSuperCARBA for surveillance cultures of carbapenemase-producing Enterobacteriaceae. New Microbes New Infect 2018; 26:42-48. [PMID: 30224970 PMCID: PMC6138884 DOI: 10.1016/j.nmni.2018.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 07/16/2018] [Accepted: 08/03/2018] [Indexed: 12/19/2022] Open
Abstract
Culture of carbapenemase-producing Enterobacteriaceae (CPE) as part of active surveillance is one of the most useful strategies for successful infection control programmes. Our objective was to compare the recently introduced CHROMagar mSuperCARBA agar for CPE detection in surveillance cultures from perineal swabs with the US Centers for Disease Control and Prevention method. Our results showed that this agar is a useful and affordable alternative (sensitivity 93.05%, specificity 96.21%, diagnostic accuracy 95.2%) to detect CPE in hospital settings.
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Affiliation(s)
- Cl Soria Segarra
- Instituto Nacional de Investigación en Salud Pública 'Dr Leopoldo Izquieta Pérez,', Guayaquil, Ecuador.,Facultad de Ciencias Médicas, Universidad de Guayaquil, Guayaquil, Ecuador.,Laboratorio Clínico Sosegar, Guayaquil, Ecuador
| | | | - Ml Berrezueta Jara
- Instituto Nacional de Investigación en Salud Pública 'Dr Leopoldo Izquieta Pérez,', Guayaquil, Ecuador
| | - M Arévalo Mendez
- Instituto Nacional de Investigación en Salud Pública 'Dr Leopoldo Izquieta Pérez,', Guayaquil, Ecuador
| | - P Cujilema
- Instituto Nacional de Investigación en Salud Pública 'Dr Leopoldo Izquieta Pérez,', Guayaquil, Ecuador
| | - M Serrano Lino
- Instituto Nacional de Investigación en Salud Pública 'Dr Leopoldo Izquieta Pérez,', Guayaquil, Ecuador
| | - Ca Soria Segarra
- Facultad de Ciencias Médicas, Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
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8
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Pannala R, Baldwin B, Aluru V, Grys TE, Holmes J, Miller LJ, Harrison ME, Nguyen CC, Tenover FC, Persing D, Faigel DO. Prospective study of the feasibility of point-of-care testing strategy for carbapenem-resistant organism detection. Endosc Int Open 2018; 6:E58-E63. [PMID: 29340299 PMCID: PMC5766332 DOI: 10.1055/s-0043-122141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 10/10/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND/AIMS In an investigator-initiated, prospective study, we evaluated the feasibility of a five-gene sequence point-of-care (POC) testing strategy (Xpert CARBA-R Assay, Cepheid Inc., Sunnyvale, CA, USA), compared to reference laboratory PCR (48 - 72 hours turnaround time, two gene sequences), in patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) and in a hospital outbreak investigation. METHODS After informed consent, patients undergoing ERCP (September 2015 - April 2016, n = 191) at Mayo Clinic and potential hospital contacts (n = 9) of an index carbapenem-resistant organism (CRO)-positive inpatient were included. Two rectal swabs, one each for reference and POC assays were obtained. The Xpert CARBA-R Assay enables qualitative rapid detection of five beta-lactamase gene sequences associated with carbapenem-non-susceptibility in Gram-negative bacteria. Feasibility parameters (specimen processing and assay run time, ease of use) and percent agreement between the tests were calculated using JMP Pro11 (SAS Corp, Cary, NC, USA). RESULTS Mean age was 62 ± 15 years; 108 (54 %) were male. Both tests were successfully performed in all patients. The POC test was rated by endoscopy nurses as easy/very easy to conduct in 193 patients (97 %); median assay run time and median time for specimen collection and processing were 55 minutes (interquartile range IQR: 53 - 55 minutes) and 3 minutes (IQR: 3 - 6 minutes), respectively. In 200/201 (99.5 %) tests, there was agreement between the POC and reference PCR. CONCLUSIONS The more comprehensive POC CRO testing of patients in the endoscopy suite is feasible and results are available in < 1 hour. This strategy may enable rapid risk stratification of duodenoscope exposure to CRO and potentially improve operational efficiency and decrease costs.
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Affiliation(s)
- Rahul Pannala
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ, USA,Corresponding author Rahul Pannala, MD, MPH Mayo Clinic13400 E Shea BlvdScottsdaleAZ 85259USA+1-480-301-6737
| | - Bruce Baldwin
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ, USA
| | - Vijay Aluru
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ, USA
| | - Thomas E. Grys
- Division of Laboratory Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Jordan Holmes
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ, USA
| | - Laurence J. Miller
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ, USA
| | - M. Edwyn Harrison
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ, USA
| | - Cuong C. Nguyen
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ, USA
| | | | | | - Douglas O. Faigel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ, USA
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9
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van den Bijllaardt W, Janssens MM, Buiting AG, Muller AE, Mouton JW, Verweij JJ. Extended-spectrum β-lactamase (ESBL) polymerase chain reaction assay on rectal swabs and enrichment broth for detection of ESBL carriage. J Hosp Infect 2017; 98:264-269. [PMID: 29080706 DOI: 10.1016/j.jhin.2017.10.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Extended-spectrum β-lactamase (ESBL) screening and contact precautions on patients at high risk for ESBL carriage are considered important infection control measures. Since contact precautions are costly and may negatively impact patient care, rapid exclusion of ESBL carriage and therefore earlier discontinuation of contact precautions are desired. AIM In the present study, the performance of an ESBL polymerase chain reaction (PCR) targeting blaCTX-M genes was evaluated as a screening assay for ESBL carriage. METHODS Two methods were assessed: PCR performed directly on rectal swabs and PCR on enrichment broth after incubation overnight. The reference standard was culture of ESBL-producing Enterobacteriaceae on selective agar after overnight enrichment and confirmation by the combination disc diffusion method. Microarray was used for discrepancy analysis. A secondary analysis was performed to evaluate the added value of including a blaSHV target in the PCR. FINDINGS A total of 551 rectal swabs from 385 patients were included, of which 28 (5%) were ESBL positive in culture. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 86%, 98%, 67%, and 99%, respectively, for PCR directly on swabs, and 96%, 98%, 75%, and 100%, respectively, for PCR on enrichment broth. Adding a blaSHV target to the assay resulted in a lower PPV without increasing the sensitivity and NPV. CONCLUSION Screening for ESBL by PCR directly on rectal swabs has a high negative predictive value, is up to 48h faster than traditional culture and therefore facilitates earlier discontinuation of contact precautions, thereby improving patient care and saving valuable resources in the hospital.
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Affiliation(s)
- W van den Bijllaardt
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands; Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands.
| | - M M Janssens
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - A G Buiting
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - A E Muller
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands; Department of Medical Microbiology, Haaglanden Medical Centre, The Hague, The Netherlands
| | - J W Mouton
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - J J Verweij
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
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10
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Healthcare Antibiotic Resistance Prevalence - DC (HARP-DC): A Regional Prevalence Assessment of Carbapenem-Resistant Enterobacteriaceae (CRE) in Healthcare Facilities in Washington, District of Columbia. Infect Control Hosp Epidemiol 2017; 38:921-929. [PMID: 28615088 DOI: 10.1017/ice.2017.110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Carbapenem-resistant Enterobacteriaceae (CRE) are a significant clinical and public health concern. Understanding the distribution of CRE colonization and developing a coordinated approach are key components of control efforts. The prevalence of CRE in the District of Columbia is unknown. We sought to determine the CRE colonization prevalence within healthcare facilities (HCFs) in the District of Columbia using a collaborative, regional approach. DESIGN Point-prevalence study. SETTING This study included 16 HCFs in the District of Columbia: all 8 acute-care hospitals (ACHs), 5 of 19 skilled nursing facilities, 2 (both) long-term acute-care facilities, and 1 (the sole) inpatient rehabilitation facility. PATIENTS Inpatients on all units excluding psychiatry and obstetrics-gynecology. METHODS CRE identification was performed on perianal swab samples using real-time polymerase chain reaction, culture, and antimicrobial susceptibility testing (AST). Prevalence was calculated by facility and unit type as the number of patients with a positive result divided by the total number tested. Prevalence ratios were compared using the Poisson distribution. RESULTS Of 1,022 completed tests, 53 samples tested positive for CRE, yielding a prevalence of 5.2% (95% CI, 3.9%-6.8%). Of 726 tests from ACHs, 36 (5.0%; 95% CI, 3.5%-6.9%) were positive. Of 244 tests from long-term-care facilities, 17 (7.0%; 95% CI, 4.1%-11.2%) were positive. The relative prevalence ratios by facility type were 0.9 (95% CI, 0.5-1.5) and 1.5 (95% CI, 0.9-2.6), respectively. No CRE were identified from the inpatient rehabilitation facility. CONCLUSION A baseline CRE prevalence was established, revealing endemicity across healthcare settings in the District of Columbia. Our study establishes a framework for interfacility collaboration to reduce CRE transmission and infection. Infect Control Hosp Epidemiol 2017;38:921-929.
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11
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Richter SS, Marchaim D. Screening for carbapenem-resistant Enterobacteriaceae: Who, When, and How? Virulence 2017; 8:417-426. [PMID: 27813699 PMCID: PMC5477693 DOI: 10.1080/21505594.2016.1255381] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/23/2016] [Accepted: 10/25/2016] [Indexed: 10/20/2022] Open
Abstract
The global spread of carbapenem-resistant Enterobacteriaceae (CRE) has been fostered by the lack of preemptive screening of patients in healthcare facilities that could prevent patient-to-patient transmission. Outbreaks of CRE infections have led some institutions to implement rigorous screening programs, although controlled comparative data are frequently lacking. Resource limitations and uncertainty regarding the optimal approach has kept many facilities from enacting more active routine surveillance policies that could reduce the prevalence of CRE. The ideal population to target for screening, the frequency of testing, and the preferred test method are components of surveillance programs that remain open to debate. This review discusses the rationale for different screening policies in use and the performance characteristics of laboratory methods available to detect CRE carriage.
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Affiliation(s)
- Sandra S. Richter
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Dror Marchaim
- Division of Infectious Diseases, Assaf Harofeh Medical Center, Zerifin, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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12
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Nodari CS, Gales AC, Barth AL, Magagnin CM, Zavascki AP, Carvalhaes CG. Detection of OXA-370 directly from rectal swabs and blood culture vials using an immunochromatographic assay. J Microbiol Methods 2017; 139:92-94. [PMID: 28483549 DOI: 10.1016/j.mimet.2017.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/03/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
Abstract
We evaluated the performance of OXA-48 K-SeT assay for detecting OXA-370 directly from spiked rectal swabs and blood culture vials. The limit of detection of this test was 104UFC/mL for rectal swabs. Detection of the OXA-370-producing isolates was successfully achieved directly from positive blood culture vials independent of growing conditions.
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Affiliation(s)
- Carolina Silva Nodari
- Laboratório Alerta, Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, 781 Pedro de Toledo St, São Paulo, Brazil.
| | - Ana Cristina Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, 781 Pedro de Toledo St, São Paulo, Brazil
| | - Afonso Luís Barth
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Hospital de Clínicas de Porto Alegre, 2350 Ramiro Barcelos St, Porto Alegre, Brazil
| | - Cibele Massotti Magagnin
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Hospital de Clínicas de Porto Alegre, 2350 Ramiro Barcelos St, Porto Alegre, Brazil; Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, 2400 Ramiro Barcelos St, Porto Alegre, Brazil
| | - Alexandre Prehn Zavascki
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Hospital de Clínicas de Porto Alegre, 2350 Ramiro Barcelos St, Porto Alegre, Brazil; Infectious Diseases Service, Hospital de Clínicas de Porto Alegre, 2350 Ramiro Barcelos St, Porto Alegre, Brazil
| | - Cecília Godoy Carvalhaes
- Laboratório Alerta, Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, 781 Pedro de Toledo St, São Paulo, Brazil; Clinical Microbiology Section, Disciplina de Medicina Laboratorial, Universidade Federal de São Paulo, 715 Napoleão de Barros St, São Paulo, Brazil
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Fernández J, Cunningham SA, Fernández-Verdugo A, Viña-Soria L, Martín L, Rodicio MR, Escudero D, Vazquez F, Mandrekar JN, Patel R. Evaluation of a real-time PCR assay for rectal screening of OXA-48-producing Enterobacteriaceae in a general intensive care unit of an endemic hospital. Diagn Microbiol Infect Dis 2017; 88:252-258. [PMID: 28442306 DOI: 10.1016/j.diagmicrobio.2017.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/31/2017] [Accepted: 04/02/2017] [Indexed: 11/19/2022]
Abstract
Carbapenemase-producing Enterobacteriaceae are increasing worldwide. Rectal screening for these bacteria can inform the management of infected and colonized patients, especially those admitted to intensive care units (ICUs). A laboratory developed, qualitative duplex real-time polymerase chain reaction assay for rapid detection of OXA-48-like and VIM producing Enterobacteriaceae, performed on rectal swabs, was designed and evaluated in an intensive care unit with endemic presence of OXA-48. During analytical assay validation, no cross-reactivity was observed and 100% sensitivity and specificity were obtained for both blaOXA-48-like and blaVIM in all spiked clinical samples. During the clinical part of the study, the global sensitivity and specificity of the real-time PCR assay for OXA-48 detection were 95.7% and 100% (P=0.1250), respectively, in comparison with culture; no VIM-producing Enterobacteriaceae were detected. Clinical features of patients in the ICU who were colonized or infected with OXA-48 producing Enterobacteriaceae, including outcome, were analyzed. Most had severe underlying conditions, and had risk factors for colonization with carbapenemase-producing Enterobacteriaceae before or during ICU admission, such as receiving previous antimicrobial therapy, prior healthcare exposure (including long-term care), chronic disease, immunosuppression and/or the presence of an intravascular catheter and/or mechanical ventilation device. The described real-time PCR assay is fast (~2-3hours, if DNA extraction is included), simple to perform and results are easy to interpret, features which make it applicable in the routine of clinical microbiology laboratories. Implementation in endemic hospitals could contribute to early detection of patients colonized by OXA-48 producing Enterobacteriaceae and prevention of their spread.
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Affiliation(s)
- J Fernández
- Service of Microbiology, Hospital Universitario Central de Asturias, Oviedo, Spain; Department of Functional Biology, Section of Microbiology, University of Oviedo, Oviedo, Spain
| | - S A Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - A Fernández-Verdugo
- Service of Microbiology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - L Viña-Soria
- Intensive Care Unit, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - L Martín
- Intensive Care Unit, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - M R Rodicio
- Department of Functional Biology, Section of Microbiology, University of Oviedo, Oviedo, Spain
| | - D Escudero
- Intensive Care Unit, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - F Vazquez
- Service of Microbiology, Hospital Universitario Central de Asturias, Oviedo, Spain; Department of Functional Biology, Section of Microbiology, University of Oviedo, Oviedo, Spain; Fundación de Investigación Oftalmológica. Instituto Universitario Oftalmológico, Fernández-Vega
| | - J N Mandrekar
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN
| | - R Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN.
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Bialvaei AZ, Kafil HS, Asgharzadeh M, Yousef Memar M, Yousefi M. Current methods for the identification of carbapenemases. J Chemother 2017; 28:1-19. [PMID: 26256147 DOI: 10.1179/1973947815y.0000000063] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Detection of carbapenemases in clinical microbiology labs is a challenging issue. Comparison of the results of susceptibility testing with the breakpoint values of carbapenems is the first step in the screening of carbapenemase producers. To date, screening of carbapenemase-producing (CP) bacteria has been mostly performed by a selective medium. Although these media are practical for the detection of most CP isolates, the inoculated plates have to be incubated overnight. Subsequently, we need the confirmation of the carbapenemase producers present in the culture medium by additional testing [e.g. inhibition studies with liquid or solid media, modified Hodge test (MHT), or gradient strips], which can take up to another 48 hours. Despite the lack of discrimination between the three different classes of carbapenemases (KPC, MBL and OXA) and difficulties in the interpretation of the results, the MHT is usually deemed as the phenotypic reference method for the confirmation of carbapenemase production. Molecular techniques, such as real-time polymerase chain reaction (PCR) assays, in contrast to phenotypic methods that are very time consuming, are faster and allow for the quick identification of carbapenemase genes. These techniques can detect and characterize carbapenemases, including NDM- and KPC-mediated resistance, which is critical for epidemiological investigations. The aim of this review is to gather a summary of the available methods for carbapenemase detection and describe the strengths and weaknesses of each method.
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Affiliation(s)
- Abed Zahedi Bialvaei
- a Drug Applied Research Center, Faculty of Medical Sciences , Tabriz University of Medical Sciences , Iran
| | - Hossein Samadi Kafil
- a Drug Applied Research Center, Faculty of Medical Sciences , Tabriz University of Medical Sciences , Iran
| | | | - Mohammad Yousef Memar
- c Infectious Disease and Tropical Medicine Research Center , Tabriz University of Medical Sciences , Iran
| | - Mehdi Yousefi
- d Immunology Research Center , Tabriz University of Medical Sciences , Iran
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Aguirre-Quiñonero A, Martínez-Martínez L. Non-molecular detection of carbapenemases in Enterobacteriaceae clinical isolates. J Infect Chemother 2017; 23:1-11. [DOI: 10.1016/j.jiac.2016.09.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/28/2016] [Accepted: 09/28/2016] [Indexed: 01/11/2023]
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Evaluation of a Multiplex PCR Assay To Rapidly Detect Enterobacteriaceae with a Broad Range of β-Lactamases Directly from Perianal Swabs. Antimicrob Agents Chemother 2016; 60:6957-6961. [PMID: 27600053 DOI: 10.1128/aac.01458-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/01/2016] [Indexed: 11/20/2022] Open
Abstract
We developed and evaluated multiplexed molecular beacon probes in a real-time PCR assay to identify prominent extended-spectrum-β-lactamase, plasmid-mediated AmpC β-lactamase (pAmpC) and carbapenemase genes directly from perianal swab specimens within 6 h. We evaluated this assay on 158 perianal swabs collected from hematopoietic stem cell transplant recipients and found that this assay was highly sensitive and specific for detection of CTX-M-, pAmpC-, and KPC-producing Enterobacteriaceae compared to culture on chromogenic agar.
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Intestinal Carriage of Carbapenemase-Producing Organisms: Current Status of Surveillance Methods. Clin Microbiol Rev 2016; 29:1-27. [PMID: 26511484 DOI: 10.1128/cmr.00108-14] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Carbapenemases have become a significant mechanism for broad-spectrum β-lactam resistance in Enterobacteriaceae and other Gram-negative bacteria such as Pseudomonas and Acinetobacter spp. Intestinal carriage of carbapenemase-producing organisms (CPOs) is an important source of transmission. Isolation of carriers is one strategy that can be used to limit the spread of these bacteria. In this review, we critically examine the clinical performance, advantages, and disadvantages of methods available for the detection of intestinal carriage of CPOs. Culture-based methods (Centers for Disease Control and Prevention [CDC] protocols, chromogenic media, specialized agars, and double-disk synergy tests) for detecting carriage of CPOs are convenient due to their ready availability and low cost, but their limited sensitivity and long turnaround time may not always be optimal for infection control practices. Contemporary nucleic acid amplification techniques (NAATs) such as real-time PCR, hybridization assays, loop-mediated isothermal amplification (LAMP), or a combined culture and NAAT approach may provide fast results and/or added sensitivity and specificity compared with culture-based methods. Infection control practitioners and clinical microbiologists should be aware of the strengths and limitations of available methods to determine the most suitable approach for their medical facility to fit their infection control needs.
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Yang Q, Rui Y. Two Multiplex Real-Time PCR Assays to Detect and Differentiate Acinetobacter baumannii and Non- baumannii Acinetobacter spp. Carrying blaNDM, blaOXA-23-Like, blaOXA-40-Like, blaOXA-51-Like, and blaOXA-58-Like Genes. PLoS One 2016; 11:e0158958. [PMID: 27391234 PMCID: PMC4938629 DOI: 10.1371/journal.pone.0158958] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 06/26/2016] [Indexed: 01/01/2023] Open
Abstract
Nosocomial infections caused by Acinetobacter spp. resistant to carbapenems are increasingly reported worldwide. Carbapenem-resistant Acinetobacter (CRA) is becoming a serious concern with increasing patient morbidity, mortality, and lengths of hospital stay. Therefore, the rapid detection of CRA is essential for epidemiological surveillance. Polymerase chain reaction (PCR) has been extensively used for the rapid identification of most pathogens. In this study, we have developed two multiplex real-time PCR assays to detect and differentiate A. baumannii and non-A. baumannii Acinetobacter spp, and common carbapenemase genes, including blaNDM, blaOXA-23-like, blaOXA-40-like, blaOXA-51-like, and blaOXA-58-like. We demonstrate the potential utility of these assays for the direct detection of blaNDM-, blaOXA-23-like-, blaOXA-40-like-, blaOXA-51-like-, and blaOXA-58-like-positive CRA in clinical specimens. Primers were specifically designed, and two multiplex real-time PCR assays were developed: multiplex real-time PCR assay1 for the detection of Acinetobacter baumannii 16S–23S rRNA internal transcribed spacer sequence, the Acinetobacter recA gene, and class-B-metalloenzyme-encoding gene blaNDM; and multiplex real-time PCR assay2 to detect class-D-oxacillinase-encoding genes (blaOXA-23-like, blaOXA-40-like, blaOXA-51-like,and blaOXA-58-like). The assays were performed on an ABI Prism 7500 FAST Real-Time PCR System. CRA isolates were used to compare the assays with conventional PCR and sequencing. Known amounts of CRA cells were added to sputum and fecal specimens and used to test the multiplex real-time PCR assays. The results for target and nontarget amplification showed that the multiplex real-time PCR assays were specific, the limit of detection for each target was 10 copies per 20 μL reaction volume, the assays were linear over six log dilutions of the target genes (r2 > 0.99), and the Ct values of the coefficients of variation for intra- and interassay reproducibility were less than 5%. The multiplex real-time PCR assays showed 100% concordance with conventional PCR when tested against 400 CRA isolates and their sensitivity for the target DNA in sputum and fecal specimens was 102 CFU/mL. Therefore, these novel multiplex real-time PCR assays allow the sensitive and specific characterization and differentiation of blaNDM-, blaOXA-23-like-, blaOXA-40-like-, blaOXA-51-like-, and blaOXA-58-like-positive CRA, making them potential tools for the direct detection of CRA in clinical specimens and the surveillance of nosocomial infections.
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Affiliation(s)
- Qiu Yang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongyu Rui
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
- * E-mail:
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New Delhi metallo-β-lactamase-1: structure, inhibitors and detection of producers. Future Med Chem 2016; 8:993-1012. [PMID: 27253479 DOI: 10.4155/fmc-2016-0015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Since its discovery in 2008, New Delhi metallo-β-lactamase-1 (NDM-1)-producing Enterobacteriaceae have disseminated globally, facilitated predominantly by gut colonization and the spread of plasmids carrying the bla NDM-1 gene. With few effective antibiotics against NDM-1 producers, and resistance developing to those which remain, there is an urgent need to develop new treatments. To date, most drug design in this area has been focused on developing an NDM-1 inhibitor and has been aided by the wealth of structural and mechanistic information available from high resolution x-ray crystallography and molecular modeling. This review aims to summarize current knowledge regarding the detection of NDM-1 producers, the mechanism of action of NDM-1 and to highlight recent attempts toward the development of clinically useful inhibitors.
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An Immunocompromised Child with Bloodstream Infection Caused by Two Escherichia coli Strains, One Harboring NDM-5 and the Other Harboring OXA-48-Like Carbapenemase. Antimicrob Agents Chemother 2016; 60:3270-5. [PMID: 27217442 DOI: 10.1128/aac.03118-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We describe a 16-year-old neutropenic patient from the Middle East with bloodstream infection caused by two carbapenemase-producing Escherichia coli isolates that we characterized by whole-genome sequencing. While one displayed meropenem resistance and was blaNDM positive, the other demonstrated meropenem susceptibility yet harbored blaOXA181 (which encodes a blaOXA48-like enzyme). This report highlights the challenge of laboratory detection of blaOXA48-like enzymes and the clinical implications of genotypic resistance detection in carbapenemase-producing Enterobacteriaceae.
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Laboratory Detection of Carbapenemases in Gram-Negative Bacteria. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2016. [DOI: 10.5812/archcid.32816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Overview of Molecular Diagnostics in Multiple-Drug-Resistant Organism Prevention: Focus on Multiple-Drug-Resistant Gram-Negative Bacterial Organisms. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch17] [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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Continuing Challenges for the Clinical Laboratory for Detection of Carbapenem-Resistant Enterobacteriaceae. J Clin Microbiol 2015; 53:3712-4. [PMID: 26468504 DOI: 10.1128/jcm.02668-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Detecting carbapenem-resistant Enterobacteriaceae (CRE) can be difficult. In particular, the absence of FDA-cleared automated antimicrobial susceptibility test (AST) devices that use revised Clinical and Laboratory Standards Institute (CLSI) carbapenem breakpoints for Enterobacteriaceae and the lack of active surveillance tests hamper the clinical laboratory. In this issue of the Journal of Clinical Microbiology, Lau and colleagues (A. F. Lau, G. A. Fahle, M. A. Kemp, A. N. Jassem, J. P. Dekker, and K. M. Frank, J Clin Microbiol 53:3729-3737, 2015, http://dx.doi.org/10.1128/JCM.01921-15) evaluate the performance of a research-use-only PCR for the detection of CRE in rectal surveillance specimens.
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Clinical Performance of Check-Direct CPE, a Multiplex PCR for Direct Detection of bla(KPC), bla(NDM) and/or bla(VIM), and bla(OXA)-48 from Perirectal Swabs. J Clin Microbiol 2015; 53:3729-37. [PMID: 26338860 DOI: 10.1128/jcm.01921-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/23/2015] [Indexed: 12/13/2022] Open
Abstract
We evaluated the clinical performance of Check-Direct CPE for carbapenemase detection directly from 301 perirectal swabs (258 patients) in a nonoutbreak setting. Culture of a PCR-confirmed, carbapenemase-containing organism, or history of colonization with such organism within the previous 2 weeks, was used as the reference standard. Check-Direct CPE demonstrated a sensitivity value, specificity value, positive predictive value (PPV), and negative predictive value (NPV) of 100% (all bla(KPC)), 88%, 21%, and 100%, respectively. False positives accounted for 79% (n = 34) of samples for which a cycle threshold (C(T)) value was reached. Simulated studies to evaluate specimen pooling as an approach to minimize costs showed no difference in C(T) values for pooled groups of three or five that each contained a single specimen spiked with ∼1,500 CFU bla(KPC) Klebsiella pneumoniae; however, the detection rate dropped to 60% at a seeded concentration of ∼150 CFU. When data were pooled, C(T) values for bla(KPC) were higher for heavy-feces-containing than for light-feces-containing liquid-suspended specimens. Furthermore, C(T) values for liquid-suspended specimens were 4 to 5 C(T) values lower (i.e., represented greater sensitivity) than those seen in direct swab analysis. Culture was equivalent to or better than Check-Direct CPE for 13/15 (87%) isolates tested in a limit-of-detection analysis. Detection of a carbapenemase gene at a C(T) cutoff value of ≤35 was culture confirmed in 23/24 (96%) of cases; however, C(T) values of >35 overlapped broadly between culture-positive (n = 21) and culture-negative (n = 36) specimens. Check-Direct CPE will likely prove most useful in high-prevalence areas or in outbreak settings where rapid carbapenemase detection is critical for infection control management.
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Rapid Detection of KPC, NDM, and OXA-48-Like Carbapenemases by Real-Time PCR from Rectal Swab Surveillance Samples. J Clin Microbiol 2015; 53:2731-3. [PMID: 26019195 DOI: 10.1128/jcm.01237-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 05/20/2015] [Indexed: 01/06/2023] Open
Abstract
We describe a multiplex real-time PCR assay for use on the ABI 7500 Fast TaqMan platform to detect all currently described Klebsiella pneumoniae carbapenemases (KPC), New Delhi metallo-β-lactamases (NDM), and the OXA-48-like family of carbapenemases from bacterial culture lysates or sample enrichment broth lysates.
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Rodríguez-Baño J, Cisneros JM, Cobos-Trigueros N, Fresco G, Navarro-San Francisco C, Gudiol C, Horcajada JP, López-Cerero L, Martínez JA, Molina J, Montero M, Paño-Pardo JR, Pascual A, Peña C, Pintado V, Retamar P, Tomás M, Borges-Sa M, Garnacho-Montero J, Bou G. Diagnosis and antimicrobial treatment of invasive infections due to multidrug-resistant Enterobacteriaceae. Guidelines of the Spanish Society of Infectious Diseases and Clinical Microbiology. Enferm Infecc Microbiol Clin 2015; 33:337.e1-337.e21. [DOI: 10.1016/j.eimc.2014.11.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 12/21/2022]
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Abstract
Carbapenemase-producing Enterobacteriaceae (CPE) were almost nonexistent up to the 1990s, but are today encountered routinely in hospitals and other healthcare facilities in many countries including the United States. KPC-producing Klebsiella pneumoniae was the first to emerge and spread globally and is endemic in the United States, Israel, Greece, and Italy. Recently, NDM-producing Enterobacteriaceae and OXA-48-producing K. pneumoniae appear to be disseminating from South Asia and Northern Africa, respectively. They are almost always resistant to all β-lactams including carbapenems and many other classes. Mortality from invasive CPE infections reaches up to 40%. To obtain the maximal benefit from the limited options available, dosing of antimicrobial agents should be optimized based on pharmacokinetic data, especially for colistin and carbapenems. In addition, multiple observational studies have associated combination antimicrobial therapy with lower mortality compared with monotherapy for these infections. The outcomes appear to be especially favorable when patients are treated with a carbapenem and a second agent such as colistin, tigecycline, and gentamicin, but the best approach is yet to be defined.
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Affiliation(s)
- Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David L Paterson
- The University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, Brisbane, Australia
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Huang TD, Bogaerts P, Ghilani E, Heinrichs A, Gavage P, Roisin S, Willems E, Verbruggen AM, Francart H, Denis O, Senterre JM, Glupczynski Y. Multicentre evaluation of the Check-Direct CPE® assay for direct screening of carbapenemase-producing Enterobacteriaceae from rectal swabs. J Antimicrob Chemother 2015; 70:1669-73. [PMID: 25637518 DOI: 10.1093/jac/dkv009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 01/05/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The objective of this study was to evaluate in a multicentre survey the analytical performance of the Check-Direct CPE® assay (CDCPE), a multiplex PCR assay for the detection of carbapenemase-producing Enterobacteriaceae (CPE), directly from rectal swabs. METHODS Adult patients admitted to a high-risk unit in four participating centres were prospectively screened for CPE carriage by rectal swabbing. Samples were cultured on chromogenic CPE-selective media in the local laboratories. All growing Enterobacteriaceae strains were transferred for confirmation of carbapenemase production by multiplex PCR, together with the faecal swabs for CDCPE, to the coordinating laboratory. RESULTS Overall, 38 of the 394 samples analysed (9.6%; range 3%-20% per centre) yielded a positive signal for a carbapenemase gene with CDCPE, including 17 samples (4.3%; range 0%-15% per centre) that grew a total of 25 CPE-confirmed isolates (all OXA-48-like producers, including one isolate that simultaneously harboured a VIM-type carbapenemase). No CPE culture-positive samples were missed by CDCPE. Among the 21 samples that were CPE-positive with CDCPE but negative on culture, five were collected from previously known CPE carriers and 6/9 OXA-48-positive signals were detected at one participating centre that was undergoing a hospital-wide outbreak of OXA-48 CPE. When compared with the selective culture, the sensitivity and specificity of CDCPE were 100% and 94%, respectively. CONCLUSIONS This study showed the value of CDCPE as a tool for screening CPE carriage in an epidemiological setting with a high prevalence of OXA-48 CPE. However, the potential added value for infection control management remains to be demonstrated.
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Affiliation(s)
- Te-Din Huang
- National Reference Laboratory for Monitoring of Antimicrobial Resistance in Gram-negative bacteria, CHU Dinant Godinne UCL Namur, Université catholique de Louvain (UCL), 1 Avenue Docteur Gaston Therasse, 5530 Yvoir, Belgium
| | - Pierre Bogaerts
- National Reference Laboratory for Monitoring of Antimicrobial Resistance in Gram-negative bacteria, CHU Dinant Godinne UCL Namur, Université catholique de Louvain (UCL), 1 Avenue Docteur Gaston Therasse, 5530 Yvoir, Belgium
| | - Enes Ghilani
- National Reference Laboratory for Monitoring of Antimicrobial Resistance in Gram-negative bacteria, CHU Dinant Godinne UCL Namur, Université catholique de Louvain (UCL), 1 Avenue Docteur Gaston Therasse, 5530 Yvoir, Belgium
| | - Amélie Heinrichs
- National Reference Laboratory for Monitoring of Antimicrobial Resistance in Gram-negative bacteria, CHU Dinant Godinne UCL Namur, Université catholique de Louvain (UCL), 1 Avenue Docteur Gaston Therasse, 5530 Yvoir, Belgium
| | - Pierre Gavage
- Centre Hospitalier Régional de la Citadelle, 1 Boulevard du 12ème de Ligne, 4000 Liège, Belgium
| | - Sandrine Roisin
- Associated National Reference Laboratory for Monitoring of Antimicrobial Resistance in Gram-negative bacteria, Hôpital Erasme, Université Libre de Bruxelles (ULB), 808 Route de Lennik, 1070 Brussels, Belgium
| | - Elise Willems
- Algemeen Ziekenhuis Nikolaas, 1 Moerlandstraat, 9100 Sint-Niklaas, Belgium
| | | | - Hugo Francart
- Algemeen Ziekenhuis Nikolaas, 1 Moerlandstraat, 9100 Sint-Niklaas, Belgium
| | - Olivier Denis
- Associated National Reference Laboratory for Monitoring of Antimicrobial Resistance in Gram-negative bacteria, Hôpital Erasme, Université Libre de Bruxelles (ULB), 808 Route de Lennik, 1070 Brussels, Belgium
| | - Jean-Marc Senterre
- Centre Hospitalier Régional de la Citadelle, 1 Boulevard du 12ème de Ligne, 4000 Liège, Belgium
| | - Youri Glupczynski
- National Reference Laboratory for Monitoring of Antimicrobial Resistance in Gram-negative bacteria, CHU Dinant Godinne UCL Namur, Université catholique de Louvain (UCL), 1 Avenue Docteur Gaston Therasse, 5530 Yvoir, Belgium
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Vasoo S, Madigan T, Cunningham SA, Mandrekar JN, Porter SB, Johnston B, Sampathkumar P, Tosh PK, Johnson JR, Patel R, Banerjee R. Prevalence of rectal colonization with multidrug-resistant Enterobacteriaceae among international patients hospitalized at Mayo Clinic, Rochester, Minnesota. Infect Control Hosp Epidemiol 2014; 35:182-6. [PMID: 24442082 DOI: 10.1086/674853] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Rectal colonization with multidrug-resistant Enterobacteriaceae was found in 23 of 94 consecutively enrolled international patients hospitalized at Mayo Clinic, Rochester, Minnesota. No carbapenemase producers were detected. Twenty-one isolates were extended-spectrum β-lactamase-producing Escherichia coli. Colonization was associated with gastrointestinal disease and central venous catheter placement within the antecedent year.
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Affiliation(s)
- Shawn Vasoo
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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Lowman W, Marais M, Ahmed K, Marcus L. Routine active surveillance for carbapenemase-producing Enterobacteriaceae from rectal swabs: diagnostic implications of multiplex polymerase chain reaction. J Hosp Infect 2014; 88:66-71. [DOI: 10.1016/j.jhin.2014.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 06/27/2014] [Indexed: 11/29/2022]
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Huang L, Hu X, Zhou M, Yang Y, Qiao J, Wang D, Yu J, Cui Z, Zhang Z, Zhang XE, Wei H. Rapid detection of New Delhi metallo-β-lactamase gene and variants coding for carbapenemases with different activities by use of a PCR-based in vitro protein expression method. J Clin Microbiol 2014; 52:1947-53. [PMID: 24671780 PMCID: PMC4042754 DOI: 10.1128/jcm.03363-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/19/2014] [Indexed: 11/20/2022] Open
Abstract
New Delhi metallo-β-lactamase (NDM)-producing bacteria are considered potential global health threats. It is necessary to monitor NDM-1 and its variants in clinical isolates in order to understand the NDM-1 epidemic and the impact of its variants on β-lactam resistance. To reduce the lengthy time needed for cloning and expression of NDM-1 variants, a novel PCR-based in vitro protein expression (PCR-P) method was used to detect blaNDM-1 and its variants coding for carbapenemases with different activities (functional variants). The PCR-P method combined a long-fragment real-time quantitative PCR (LF-qPCR) with in vitro cell-free expression to convert the blaNDM-1 amplicons into NDM for carbapenemase assay. The method could screen for blaNDM-1 within 3 h with a detection limit of 5 copies and identify functional variants within 1 day. Using the PCR-P to analyze 5 recent blaNDM-1 variants, 2 functional variants, blaNDM-4 and blaNDM-5, were revealed. In the initial testing of 23 clinical isolates, the PCR-P assay correctly found 8 isolates containing blaNDM-1. This novel method provides the first integrated approach for rapidly detecting the full-length blaNDM-1 and revealing its functional variants in clinical isolates.
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Affiliation(s)
- Li Huang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China University of Chinese Academy of Sciences, Beijing, China
| | - Xiumei Hu
- Clinical Laboratory Department, Guangzhou First Municipal People's Hospital, Affiliated Hospital of Guangzhou Medical College, Guangzhou, China Southern Medical University, Guangzhou, China
| | - Man Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yinmei Yang
- Clinical Laboratory Department, Guangzhou First Municipal People's Hospital, Affiliated Hospital of Guangzhou Medical College, Guangzhou, China
| | - Jinjuan Qiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China University of Chinese Academy of Sciences, Beijing, China
| | - Dianbing Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Junping Yu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zhiping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xian-En Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Hongping Wei
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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