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Shahab SN, van Veen A, Büchler AC, Saharman YR, Karuniawati A, Vos MC, Voor In 't Holt AF, Severin JA. In search of the best method to detect carriage of carbapenem-resistant Pseudomonas aeruginosa in humans: a systematic review. Ann Clin Microbiol Antimicrob 2024; 23:50. [PMID: 38858708 PMCID: PMC11163693 DOI: 10.1186/s12941-024-00707-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Detection of carbapenem-resistant Pseudomonas aeruginosa (CR-PA) in humans is important to prevent transmission. However, the most optimal culture method to detect CR-PA is unknown. This systematic review aims to determine which culture method is most sensitive and which culture methods are used to detect CR-PA in humans. Second, to establish the most feasible culture method taking into account the turnaround time (TAT), and third, to provide an overview of the sampling sites used to detect carriage. METHODS We systematically searched the electronic databases Embase, Medline Ovid, Cochrane, Scopus, CINAHL, and Web of Science until January 27, 2023. All diagnostic accuracy studies comparing two or more culture methods to detect CR-PA and recent outbreak or surveillance reports on CR-PA carriage or infection in humans, which describe culture methods and their results, were eligible for inclusion. We used QUADAS-2 guideline for diagnostic accuracy studies and the STROBE or ORION guideline for outbreak-surveillance studies to assess the risk of bias. RESULTS Six diagnostic accuracy studies were included. An enrichment broth was found to increase the detection of CR-PA. Using an enrichment broth extended the TAT by 18-24 h, yet selective media could reduce the TAT by 24 h compared to routine media. In total, 124 outbreak-surveillance studies were included, of which 17 studies with surveillance samples and 116 studies with clinical samples. In outbreak-surveillance studies with surveillance samples, perianal, rectal swabs or stools were the most common sampling site/specimen (13/17, 76%). A large variety was observed in whether and which kind of enrichment broth and selective media were used. CONCLUSIONS We found a benefit of using an enrichment step prior to inoculation of the material onto selective media for the detection of CR-PA. More research is needed to determine the most sensitive sampling site and culture method. TRAIL REGISTRATION This study was registered in the PROSPERO International prospective register of systematic reviews (registration number: CRD42020207390, http://www.crd.york.ac.uk/PROSPERO/display_record.asp?ID=CRD42020207390 ).
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Affiliation(s)
- Selvi N Shahab
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia/Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Anneloes van Veen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Andrea C Büchler
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Yulia R Saharman
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia/Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Anis Karuniawati
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia/Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Anne F Voor In 't Holt
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Juliëtte A Severin
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
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Xu Y, Luo J, Lai W, Da J, Yang B, Luo X, Zhan L, Fei Y, Liu L, Zha Y. Multiplex lateral flow test strip for detection of carbapenemase genes using barcoded tetrahedral DNA capture probe-based biosensing interface. Mikrochim Acta 2023; 190:360. [PMID: 37606732 DOI: 10.1007/s00604-023-05903-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/04/2023] [Indexed: 08/23/2023]
Abstract
Carbapenem-resistant Enterobacterales pose significant global health challenges due to their rapid spread and ability to hydrolyse various beta-lactam antibiotics. Rapid tests for these carbapenemase genes are crucial to ensure appropriate prescription administration and infection control. In this study, we developed a rapid visual nanodiagnostic platform for multiplexed detection of carbapenemase genes using a lateral flow strip. The nanodiagnostic strip was designed with separate barcoded DNA tetrahedrons for the blaKPC and blaNDM genes. These tetrahedrons were distributed on a nitrocellulose membrane at two different test lines as capture probes. When tested against a panel of carbapenemase genes, the tetrahedral probes captured single-stranded amplicons of asymmetric PCR via strand hybridisation. The amplicons acted as bridging elements, binding the DNA-modified gold nanoparticles to the test line of the strip, resulting in clear visual readouts specific to the blaKPC and blaNDM genes. By employing barcoded tetrahedrons and asymmetric PCR in conjunction with the lateral flow strip, a single diagnostic test enabled the detection of multiple carbapenemase genes. The test yielded results as low as 0.12 fM for blaKPC and 0.05 fM for blaNDM within 75 min. Furthermore, the strip effectively identified specific carbapenemase genes in clinical isolates using real-time PCR, antibody-based lateral flow systems for carbapenemase detection, and carbapenemase phenotype experiments. Thus, the strip develop has a high potential for testing blaKPC and blaNDM genes in practice.
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Affiliation(s)
- Yongjie Xu
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Jie Luo
- Department of Laboratory Medicine, Guizhou Provincial Second People's Hospital, Guiyang, 550002, Guizhou, China
| | - Wei Lai
- School of Medical Laboratory, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jingjing Da
- Renal Division, Department of Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Bin Yang
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Xiangrong Luo
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Lin Zhan
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Ying Fei
- School of Medical Laboratory, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Lin Liu
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
| | - Yan Zha
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
- Renal Division, Department of Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
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Tarlton NJ, Wallace MA, Potter RF, Zhang K, Dantas G, Dubberke ER, Burnham CAD, Yarbrough ML. Evaluation of the NG-Test CARBA 5 Lateral Flow Assay with an IMP-27-Producing Morganella morganii and Other Morganellaceae. Microbiol Spectr 2023; 11:e0079323. [PMID: 37199652 PMCID: PMC10269506 DOI: 10.1128/spectrum.00793-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
An isolate of Morganella morganii (MMOR1) that tested susceptible to 3rd/4th-generation cephalosporins and intermediate to meropenem was characterized as positive for NDM and IMP carbapenemases by NG-Test CARBA 5. Our objective was to further investigate this result, given the inconsistent susceptibility profile and unusual epidemiological profile for our region. The MMOR1 isolate was retested for antimicrobial susceptibilities and characterized for carbapenemase production. MMOR1 tested susceptible to ceftazidime, ceftriaxone, cefepime, aztreonam, and ertapenem, and intermediate to meropenem and imipenem. The isolate tested positive by carbapenem inactivation method (CIM) and CIM+EDTA (eCIM) testing, indicating metallo-β-lactamase production. The isolate tested negative for all carbapenemase genes on Xpert Carba-R, but positive for IMP on repeat testing of NG-Test CARBA 5. Whole-genome sequencing revealed MMOR1 contained blaIMP-27, but no other carbapenemase genes. Additional testing with NG-Test CARBA 5 revealed a false-positive NDM band when the assay was overloaded with test inoculum. Supplementary isolates were tested with an overloaded inoculum (n = 6 M. morganii; n = 1 P. mirabilis; n = 1 IMP-27-producing P. rettgeri; n = 1 IMP-1-producing E. coli; n = 1 K. pneumoniae), and two non-carbapenemase-producing carbapenem non-susceptible M. morganii also generated a false-positive NDM band; though, this was not universal among this species. A dual IMP+/NDM+ M. morganii is an unusual result that should prompt additional investigation, especially in nonendemic regions and when the susceptibility profile is incompatible. IMP-27 is not detected by Xpert Carba-R but is variably detected by NG-Test CARBA 5. The microorganism inoculum used for NG-Test CARBA 5 must be carefully controlled for accurate results. IMPORTANCE The detection of carbapenemase-producing carbapenem-resistant Enterobacterales (CP-CRE) is an important function of the clinical microbiology laboratory, where positive identifications have immediate implications for infection control and surveillance strategies in the inpatient setting and can inform appropriate selection of therapy among the various novel anti-CP-CRE agents. NG-Test CARBA 5 is a relatively new lateral flow assay used for detection of carbapenemases in CP-CRE. Here, we describe the characterization of a Morganella morganii isolate that generated a false-positive NDM carbapenemase detection by this assay, and perform bacterial test inoculum experiments with additional isolates to further investigate a cause of false-positive results using the NG-Test CARBA 5. While a lateral flow assay like the NG-Test CARBA 5 is a very desirable test format for clinical laboratories, there are pitfalls to avoid when performing this test and interpreting results, including recognizing an overloaded test assay, which could lead to false-positive results.
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Affiliation(s)
- Nicole J. Tarlton
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Robert F. Potter
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kailun Zhang
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erik R. Dubberke
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Melanie L. Yarbrough
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Performance Evaluation of Diagnostic Assays for Detection and Classification of Carbapenemase-Producing Organisms. Antibiotics (Basel) 2021; 10:antibiotics10121457. [PMID: 34943669 PMCID: PMC8698775 DOI: 10.3390/antibiotics10121457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/12/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
Rapid and accurate detection can help optimize patient treatment and improve infection control against nosocomial carbapenemase-producing organisms (CPO). In this study, a total of 217 routine clinical isolates (Enterobacterales and A. baumannii), including 178 CPOs and 39 non-CPOs, were tested to evaluate the performance of six phenotypic carbapenemase detection and classification assays, i.e., BD Phoenix CPO detect panel, Rapidec Carba-NP, O.K.N detection kit, and three carbapenem inactivation methods (CIMs; mCIM, eCIM, sCIM). The overall detection sensitivity and specificity were 98.78% (95.21–99.79%) and 79.49% (63.06–90.13%), respectively, for the BD phoenix CPO P/N test; 91.93% (86.30–95.45%) and 100% (88.83–100%), respectively, for the Rapidec Carba-NP; 98.06% (94.00–99.50%) and 97.44% (84.92–99.87%), respectively, for mCIM; and 96.89% (92.52–98.85%) and 94.87% (81.37–99.11%), respectively, for sCIM. The classification sensitivity and specificity for the BD phoenix CPO Ambler test, the O.K.N detection kit, and the mCIM and eCIM were 56.71% (48.75–64.34%) and 94.87% (81.37–99.11%), 99.28% (95.43–99.96%) and 100% (88.83–100%), and 92.90% (87.35–96.23%) and 97.44% (84.92–99.87%), respectively. All detection assays were reliable in detecting carbapenemase. However, the Rapidec Carba-NP and mCIM were insufficient in detecting OXA-48-like enzymes. The BD phoenix CPO detect panel had a strong ability to detect carbapenemase but failed to classify 48/59 (81.36%) KPC, 8/52 (15.38%) NDM, 8/22 (36.36%) OXA-23-like, and 6/11 (54.55%) dual enzymes. The O.K.N detection kit accurately detected and differentiated KPC, NDM, and OXA-48-like enzymes existing alone or in combination. The results of this study will support reliable laboratory work tools and promote therapeutic and infection control decisions.
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Irum S, Naz K, Ullah N, Mustafa Z, Ali A, Arslan M, Khalid K, Andleeb S. Antimicrobial Resistance and Genomic Characterization of Six New Sequence Types in Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates from Pakistan. Antibiotics (Basel) 2021; 10:antibiotics10111386. [PMID: 34827324 PMCID: PMC8615273 DOI: 10.3390/antibiotics10111386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/06/2021] [Accepted: 08/13/2021] [Indexed: 01/13/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a major bacterial pathogen associated with a variety of infections with high mortality rates. Most of the clinical P. aeruginosa isolates belong to a limited number of genetic subgroups characterized by multiple housekeeping genes’ sequences (usually 5–7) through the Multi-Locus Sequence Typing (MLST) scheme. The emergence and dissemination of novel multidrug-resistant (MDR) sequence types (ST) in P. aeruginosa pose serious clinical concerns. We performed whole-genome sequencing on a cohort (n = 160) of MDR P. aeruginosa isolates collected from a tertiary care hospital lab in Pakistan and found six isolates belonging to six unique MLST allelic profiles. The genomes were submitted to the PubMLST database and new ST numbers (ST3493, ST3494, ST3472, ST3489, ST3491, and ST3492) were assigned to the respective allele combinations. MLST and core-genome-based phylogenetic analysis confirmed the divergence of these isolates and positioned them in separate branches. Analysis of the resistome of the new STs isolates revealed the presence of genes blaOXA-50, blaPAO, blaPDC, blaVIM-2, aph(3′)-IIb, aac(6′)-II, aac(3)-Id, fosA, catB7, dfrB2, crpP, merP and a number of missense and frame-shift mutations in chromosomal genes conferring resistance to various antipseudomonal antibiotics. The exoS, exoT, pvdE, rhlI, rhlR, lasA, lasB, lasI, and lasR genes were the most prevalent virulence-related genes among the new ST isolates. The different genotypic features revealed the adaptation of these new clones to a variety of infections by various mutations in genes affecting antimicrobial resistance, quorum sensing and biofilm formation. Close monitoring of these antibiotic-resistant pathogens and surveillance mechanisms needs to be adopted to reduce their spread to the healthcare facilities of Pakistan. We believe that these strains can be used as reference strains for future comparative analysis of isolates belonging to the same STs.
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Affiliation(s)
- Sidra Irum
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Kanwal Naz
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Nimat Ullah
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Zeeshan Mustafa
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Amjad Ali
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Muhammad Arslan
- Pakistan Institute of Medical Sciences (PIMS), Islamabad 44000, Pakistan;
| | - Kashaf Khalid
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
| | - Saadia Andleeb
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; (S.I.); (K.N.); (N.U.); (Z.M.); (A.A.); (K.K.)
- Correspondence: or
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Berneking L, Asar L, Both A, Berinson B, Aepfelbacher M, Lütgehetmann M, Rohde H. Performance of a loop-mediated isothermal amplification assay (Isoplex CRE-ART) to detect common carbapenemase-encoding genes in Gram-negative bacteria. J Med Microbiol 2021; 70. [PMID: 34251298 DOI: 10.1099/jmm.0.001379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbapenem-resistant Gram-negative bacteria (CR-GNB) are a major source of nosocomial infections worldwide. In this study, the ability of a loop-mediated isothermal amplification (LAMP)-based method (Isoplex CRE-ART) to rapidly detect carbapenemase-encoding genes bla OXA-48-like, bla OXA-23-like, bla OXA-24-like, bla KPC, bla VIM, bla NDM and bla IMP in 231 carbapenem-resistant Enterobacterales, Pseudomonas aeruginosa and Acinetobacter baumannii isolates was investigated. The accuracy of the LAMP test was compared to results of molecular isolate characterization using a Laboratory Developed Test multiplex carbapenemase PCR assay. The LAMP test correctly identified the presence of on-panel carbapenemases with a sensitivity of 99.16 % [95 % confidence interval (CI): 95.39-99.96 %] and a specificity of 98.21 % (95 % CI: 93.72-99.68 %) in 60 min. Our findings suggest that the Isoplex CRE-ART assay is able to rapidly identify carbapenemase genes in CR-GNB and improves options for pathogen characterization in the context of clinical microbiological and infection control diagnostics.
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Affiliation(s)
- Laura Berneking
- Universitätsklinikum Hamburg-Eppendorf, Medizinische Mikrobiologie, Virologie und Hygiene, Martinistraße 52, D-20246 Hamburg, Germany
| | - Lucia Asar
- Universitätsklinikum Hamburg-Eppendorf, Medizinische Mikrobiologie, Virologie und Hygiene, Martinistraße 52, D-20246 Hamburg, Germany
| | - Anna Both
- Universitätsklinikum Hamburg-Eppendorf, Medizinische Mikrobiologie, Virologie und Hygiene, Martinistraße 52, D-20246 Hamburg, Germany
| | - Benjamin Berinson
- Universitätsklinikum Hamburg-Eppendorf, Medizinische Mikrobiologie, Virologie und Hygiene, Martinistraße 52, D-20246 Hamburg, Germany
| | - Martin Aepfelbacher
- Universitätsklinikum Hamburg-Eppendorf, Medizinische Mikrobiologie, Virologie und Hygiene, Martinistraße 52, D-20246 Hamburg, Germany
| | - Marc Lütgehetmann
- Universitätsklinikum Hamburg-Eppendorf, Medizinische Mikrobiologie, Virologie und Hygiene, Martinistraße 52, D-20246 Hamburg, Germany
| | - Holger Rohde
- Universitätsklinikum Hamburg-Eppendorf, Medizinische Mikrobiologie, Virologie und Hygiene, Martinistraße 52, D-20246 Hamburg, Germany
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Evaluation of Xpert Carba-R Assay for the Detection of Carbapenemase Genes in Gram-Negative Bacteria. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6614812. [PMID: 33928150 PMCID: PMC8049809 DOI: 10.1155/2021/6614812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/23/2021] [Accepted: 03/19/2021] [Indexed: 11/18/2022]
Abstract
Introduction High mortality associated with carbapenemase-producing Gram-negative bacteria (CP-GNB) has evolved into a global health threat. Rapid and accurate detection as well as prompt treatment are of great significance in this case. Xpert Carba-R, a multiple qualitative analysis designed to detect five clinically relevant carbapenem-resistant gene families within one hour, is regarded as reliable, accurate, and easy-to-operate. This study is to present a systematic evaluation of the performance of Xpert Carba-R in detecting carbapenemase genes in GNB suspected for carbapenemase production. Methods We searched and screened the literature on “Xpert Carba-R” in the database of PubMed, Web of Science, Embase, and Cochrane Library, employing two independent evaluators to collect data, respectively. Then, statistical analysis of the data obtained was performed by the Stata 12.0 software to measure the accuracy of Xpert Carba-R assay in detecting the carbapenemase genes in GNB. Results We screened a total of 1767 Gram-negative bacillus isolates documented in 9 articles. The precision of the detection of OXA-48 carbapenemase genes was 100%; that of NDM = 100%; that of VIM = 100%. When it came to KPC, the precision rate was 100%; that of IMP = 99%. The overall accuracy of the detection of carbapenemase genes was 100%. Conclusions Xpert Carba-R assay demonstrates a 100% precision in identifying carbapenemase genes in GNB. It can be seen that Xpert Carba-R method is an effective tool for early clinical detection, which is suitable for the detection of carbapenase gene in GNB.
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Dulanto Chiang A, Dekker JP. From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics. J Infect Dis 2021; 221:S331-S340. [PMID: 31538184 DOI: 10.1093/infdis/jiz151] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized multiple areas in the field of infectious diseases, from pathogen discovery to characterization of genes mediating drug resistance. Consequently, there is much anticipation that NGS technologies may be harnessed in the realm of diagnostic methods to complement or replace current culture-based and molecular microbiologic techniques. In this context, much consideration has been given to hypothesis-free, culture-independent tests that can be performed directly on primary clinical samples. The closest realizations of such universal diagnostic methods achieved to date are based on targeted amplicon and unbiased metagenomic shotgun NGS approaches. Depending on the exact details of implementation and analysis, these approaches have the potential to detect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undiscovered and those that are uncultivatable. Shotgun metagenomics approaches additionally can provide information on the presence of virulence and resistance genetic elements. While many limitations to the use of NGS in clinical microbiology laboratories are being overcome with decreasing technology costs, expanding curated pathogen sequence databases, and better data analysis tools, there remain many challenges to the routine use and implementation of these methods. This review summarizes recent advances in applications of targeted amplicon and shotgun-based metagenomics approaches to infectious disease diagnostic methods. Technical and conceptual challenges are considered, along with expectations for future applications of these techniques.
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Affiliation(s)
- Augusto Dulanto Chiang
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
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Fahy S, O'Connor J, O'Brien D, Fitzpatrick L, O'Connor M, Crowley J, Bernard M, Sleator R, Lucey B. Carbapenemase screening in an Irish tertiary referral hospital: Best practice, or can we do better? Infect Prev Pract 2020; 2:100100. [PMID: 34368728 PMCID: PMC8335925 DOI: 10.1016/j.infpip.2020.100100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/26/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Carbapenems are a family of end line antibiotics with increasing levels of resistance that are a cause for concern. AIM To ascertain whether the CPE screening programme employed in an acute tertiary hospital is fit for purpose. METHOD We outlined the current working algorithm employed using a universal screening programme over a 26-month screening period. Rectal swabs are cultured on arrival. Those with suspicious growth are further investigated using NG-Carba 5 lateral flow tests and Vitek 2.0 sensitivity cards. These practices were compared with NHS guidelines. FINDINGS & CONCLUSIONS In all, 53 true positives were detected from 45 patients since the screening was implemented in early 2018 (46 OXA-48, 6 KPC, 1 NDM). As the rate of screening increased, the number of positive screens decreased over time. There were a lot of similarities between the HSE guidelines and the published NHS CPE toolkit. It was evident that there is no standard practice being employed across all hospitals. Comparing the MUH to national guidelines it appears to be quicker and more effective with universal screening in place at reducing the potential contacts and identifying carriers. Cost analysis indicates that the need to confirm all positive strains in a reference lab is costly, unnecessary and time consuming. There are adequate confirmatory tests available in-house for routine positive screens. It was concluded that infection prevention and control are key to identifying and controlling possible outbreaks in a hospital setting.
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Affiliation(s)
- S. Fahy
- Department of Clinical Microbiology, Mercy University Hospital, Cork, Ireland
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - J.A. O'Connor
- Department of Clinical Microbiology, Mercy University Hospital, Cork, Ireland
| | - D. O'Brien
- Department of Clinical Microbiology, Mercy University Hospital, Cork, Ireland
| | - L. Fitzpatrick
- Department of Clinical Microbiology, Mercy University Hospital, Cork, Ireland
| | - M. O'Connor
- Infection Prevention & Control Department, Mercy University Hospital, Cork, Ireland
| | - J. Crowley
- Infection Prevention & Control Department, Mercy University Hospital, Cork, Ireland
| | - M. Bernard
- Infection Prevention & Control Department, Mercy University Hospital, Cork, Ireland
| | - R.D. Sleator
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - B. Lucey
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
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11
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Gajdács M, Ábrók M, Lázár A, Jánvári L, Tóth Á, Terhes G, Burián K. Detection of VIM, NDM and OXA-48 producing carbapenem resistant Enterobacterales among clinical isolates in Southern Hungary. Acta Microbiol Immunol Hung 2020; 67:209-215. [PMID: 33258795 DOI: 10.1556/030.2020.01181] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/04/2020] [Indexed: 02/06/2023]
Abstract
Infections caused by carbapenem-resistant Enterobacterales (CRE) present an important therapeutic problem, as there are limited number of effective therapeutic alternatives available. In this study, phenotypic and genotypic methods were used to characterize carbapenemase-production and other resistance-determinants (AmpC and ESBL-production, efflux pump-overexpression) in 50 isolates (Klebsiella spp. n = 35, Escherichia coli n = 12 and Enterobacter cloacae complex n = 3) collected at the Albert Szent-Györgyi Clinical Center (University of Szeged) between 2014 and 2017. Minimum inhibitory concentrations of meropenem, sulfamethoxazole/trimethoprim, tigecycline, amikacin, moxifloxacin, colistin and fosfomycin were also determined. 24% of isolates were AmpC-producers, while 30% carried blaCTX-M ESBL-genes. Carbapenemase-genes were detected in 18 (36%) of the tested isolates: in 2 isolates blaNDM, in 6 isolates blaOXA-48-like and in 12 isolates, blaVIM was detected by PCR. The species-distribution for isolates positive for carbapenemase-genes was the following: Klebsiella pneumoniae n = 11, Klebsiella oxytoca n = 1, E. coli n = 5, E. cloacae complex n = 1. Efflux pump-overexpression based on the PAβN-screening agar was shown in n = 3 of the tested strains. In nine isolates (18%), carbapenemase and ESBL-genes were detected simultaneously. Highest levels of resistance were noted for fosfomycin (74%) and moxifloxacin (70%), while all isolates were susceptible to colistin. Among applied phenotypic tests in this study the modified carbapenem inactivation method (mCIM) proved to be the most accurate one compared to that of PCR results.
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Affiliation(s)
- Márió Gajdács
- 1Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, Eötvös utca 6., 6720 Szeged, Hungary
| | - Marianna Ábrók
- 2Institute of Clinical Microbiology, Albert Szent-Györgyi Clinical Center, University of Szeged, Semmelweis utca 6., 6725 Szeged, Hungary
| | - Andrea Lázár
- 2Institute of Clinical Microbiology, Albert Szent-Györgyi Clinical Center, University of Szeged, Semmelweis utca 6., 6725 Szeged, Hungary
| | - Laura Jánvári
- 3Department of Bacteriology, Mycology and Parasitology, National Public Health Centre, Albert Flórián út 2-6., 1097 Budapest, Hungary
| | - Ákos Tóth
- 3Department of Bacteriology, Mycology and Parasitology, National Public Health Centre, Albert Flórián út 2-6., 1097 Budapest, Hungary
| | - Gabriella Terhes
- 3Department of Bacteriology, Mycology and Parasitology, National Public Health Centre, Albert Flórián út 2-6., 1097 Budapest, Hungary
| | - Katalin Burián
- 2Institute of Clinical Microbiology, Albert Szent-Györgyi Clinical Center, University of Szeged, Semmelweis utca 6., 6725 Szeged, Hungary
- 4Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, Dóm tér 10., 6720 Szeged, Hungary
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12
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Cai Z, Tao J, Jia T, Fu H, Zhang X, Zhao M, Du H, Yu H, Shan B, Huang B, Chen L, Tang YW, Jia W, Qu F. Multicenter Evaluation of the Xpert Carba-R Assay for Detection and Identification of Carbapenemase Genes in Sputum Specimens. J Clin Microbiol 2020; 58:e00644-20. [PMID: 32522829 PMCID: PMC7448655 DOI: 10.1128/jcm.00644-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
Rapid diagnosis of infections caused by carbapenem-resistant Enterobacteriaceae (CRE) is crucial for proper treatment and infection control. The Xpert Carba-R assay is a qualitative multiplex real-time PCR method that qualitatively detects and differentiates five common carbapenemase genes (blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP) directly from rectal swabs or purified colonies within approximately 1 h. We performed a multicenter evaluation of the investigational use of the Carba-R assay for detection and differentiation of carbapenemase genes from sputum specimens in patients with a clinical diagnosis of pneumonia. The intra- and interassay coefficients of variation values for the Carba-R assay were 0.2% to 2.0% and 1.4% to 2.3%, respectively. A total of 301 sputum specimens were collected and tested. Compared to bacterial culture followed by PCR identification of resistance genes from colonies, the Carba-R assay reduced turnaround time from 56 to 84 h to less than 2 h. Carbapenemase genes were detected by the Carba-R assay in Klebsiella pneumoniae (n = 236), Escherichia coli (n = 22), Enterobacter cloacae (n = 23), Klebsiella oxytoca (n = 8), Serratia marcescens (n = 6), Citrobacter freundii (n = 4), and Klebsiella aerogenes (n = 2). The Carba-R assay detected 112 blaKPC (33.5%), 70 blaNDM (21.0%), 8 blaIMP (2.4%), and 2 blaVIM (0.6%) genes, with positive percent agreement, negative percent agreement, and concordance rates of 92.9%, 86.7%, and 88.3%, respectively, for the dominant blaKPC and 85.0%, 87.8%, and 87.4%, respectively, for the blaNDM genes. Neither method detected the blaOXA-48 carbapenemase gene. The convenient, rapid, and simple characteristics of the Xpert Carba-R assay make it a potential tool for CRE detection and identification directly in sputum specimens.
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Affiliation(s)
- Zhen Cai
- China Aviation General Hospital of China Medical University, Beijing, China
| | - Jia Tao
- Center of Medical Laboratory, the General Hospital of Ningxia Medical University, Yinchuan, China
| | - Tianye Jia
- The Center of Clinical Diagnosis Laboratory, 302 Hospital of PLA, Beijing, China
| | - Hongyu Fu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xin Zhang
- Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mei Zhao
- Center of Medical Laboratory, the General Hospital of Ningxia Medical University, Yinchuan, China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Hua Yu
- Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Bin Shan
- Department of Laboratory Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liang Chen
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Seton Hall University, Nutley, New Jersey, USA
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
- Cepheid, Shanghai, China
| | - Wei Jia
- Center of Medical Laboratory, the General Hospital of Ningxia Medical University, Yinchuan, China
| | - Fen Qu
- China Aviation General Hospital of China Medical University, Beijing, China
- The Center of Clinical Diagnosis Laboratory, 302 Hospital of PLA, Beijing, China
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13
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McMullen AR, Wallace MA, LaBombardi V, Hindler J, Campeau S, Humphries R, Procop GW, Richter SS, Wise MG, Burnham CAD. Multicenter evaluation of the RAPIDEC® CARBA NP assay for the detection of carbapenemase production in clinical isolates of Enterobacterales and Pseudomonas aeruginosa. Eur J Clin Microbiol Infect Dis 2020; 39:2037-2044. [PMID: 32577953 DOI: 10.1007/s10096-020-03937-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/29/2020] [Indexed: 01/25/2023]
Abstract
Carbapenem-resistant Gram-negative bacilli are a major public health problem. Accurate and rapid detection of carbapenemase-producing organisms can facilitate appropriate infection prevention measures. The objective was to evaluate the performance of the RAPIDEC® CARBA NP assay (RAPIDEC), a screening assay that utilizes a pH indicator to detect carbapenem hydrolysis within 2 h. A multicenter study evaluated 306 clinical bacterial strains of Enterobacterales (n = 257) and Pseudomonas aeruginosa (n = 49). The RAPIDEC was compared to a composite reference standard-the Clinical Laboratory Standards Institute (CLSI) Carba NP assay, PCR for specific carbapenemase genes (blaKPC, blaNDM, blaOXA-48-like, blaVIM and blaIMP), and phenotypic carbapenem susceptibility testing. The assay was evaluated using two culture incubation times for the bacterial isolates: "routine"(cultures incubated 18-24 h) and "short" (cultures incubated 4-5 h). For the routine incubation, the overall percent agreement was 98.7% with a positive percent agreement (PPA) of 99.6% and a negative percent agreement (NPA) of 97.4%; there were five false positives and one false negative. For the short incubation, the overall percent agreement was 98.0% with a PPA of 98.5% and a NPA of 97.3%; there were five false positives and four false negatives. RAPIDEC results for the P. aeruginosa isolates were 100% concordant with the reference standard for both incubation times. The RAPIDEC assay is an accurate and rapid (≤ 2 h) assay for the detection of the most common carbapenemases in clinical isolates. Growth from a short incubation culture may be used to reliably detect carbapenemase production in clinical strains.
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Affiliation(s)
- Allison R McMullen
- Washington University in St. Louis Medical School, St Louis, MO, USA.
- Augusta University, Augusta, GA, USA.
| | - Meghan A Wallace
- Washington University in St. Louis Medical School, St Louis, MO, USA
| | | | - Janet Hindler
- University of California Los Angeles, Los Angeles, CA, USA
| | - Shelley Campeau
- University of California Los Angeles, Los Angeles, CA, USA
- Accelerate Diagnostics, Tuscon, AZ, USA
| | - Romney Humphries
- University of California Los Angeles, Los Angeles, CA, USA
- Accelerate Diagnostics, Tuscon, AZ, USA
| | | | - Sandra S Richter
- Cleveland Clinic, Cleveland, OH, USA
- bioMérieux, Inc., Durham, NC, USA
| | - Mark G Wise
- International Health Management Associates, Schaumburg, IL, USA
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14
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Howard J, Creighton J, Ikram R, Werno A. Comparison of the performance of three variations of the Carbapenem Inactivation Method (CIM, modified CIM [mCIM] and in-house method (iCIM)) for the detection of carbapenemase-producing Enterobacterales and non-fermenters. J Glob Antimicrob Resist 2020; 21:78-82. [DOI: 10.1016/j.jgar.2020.03.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/23/2020] [Accepted: 03/21/2020] [Indexed: 10/24/2022] Open
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15
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Evaluation of the Revogene Carba C Assay for Detection and Differentiation of Carbapenemase-Producing Gram-Negative Bacteria. J Clin Microbiol 2020; 58:JCM.01927-19. [PMID: 31996448 PMCID: PMC7098745 DOI: 10.1128/jcm.01927-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/24/2020] [Indexed: 11/20/2022] Open
Abstract
The Revogene Carba C assay (formerly GenePOC Carba assay) is a multiplex nucleic acid-based in vitro diagnostic test intended for the detection of carbapenemase-producing Enterobacterales (CPE) from cultured colonies. This assay was evaluated directly on colonies of 118 well-characterized Enterobacterales with reduced susceptibility to carbapenems and on 49 multidrug-resistant (MDR) Pseudomonas aeruginosa and 40 MDR Acinetobacter baumannii isolates. The Revogene Carba C assay's performance was high, as it was able to detect the five major carbapenemases (NDM, VIM, IMP, KPC, and OXA-48). In Enterobacterales, sensitivity and specificity were 100%. When extrapolating the results to the French CPE epidemiology between 2012 and 2018, this assay would have detected 99.28% of the 9,624 CPE isolates sent to the French NRC, missing 69 CPE isolates (2 GES-5, 10 OXA-23, 2 TMB-1, 1 SME-4, 53 IMI, and 1 FRI). The overall sensitivity and specificity for CP P. aeruginosa were 93.7 and 100%, respectively, as two rare IMP variants (IMP-31 and -46) were not detected. Extrapolating these results to the French epidemiology of CP P. aeruginosa in 2017, 93.3% would have been identified, missing only 1 DIM and 10 GES variants. The Revogene Carba C assay accurately identified the targeted carbapenemase genes in A. baumannii, but when extrapolating these results to the French CP A. baumannii epidemiology of 2017, only 12.50% of them could be detected, as OXA-23 is the most prevalent carbapenemase in CP A. baumannii The Revogene Carba C assay showed excellent sensitivity and specificity for the five most common carbapenemases regardless of the bacterial host. It is well adapted to the CPE and CP P. aeruginosa epidemiology of many countries worldwide, which makes it suitable for use in the routine microbiology laboratory, with a time to result of ca. 85 min for eight isolates simultaneously.
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16
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Miltgen G, Cholley P, Martak D, Thouverez M, Seraphin P, Leclaire A, Traversier N, Roquebert B, Jaffar-Bandjee MC, Lugagne N, Cimon CB, Ramiandrisoa M, Picot S, Lignereux A, Masson G, Allyn J, Allou N, Mavingui P, Belmonte O, Bertrand X, Hocquet D. Carbapenemase-producing Enterobacteriaceae circulating in the Reunion Island, a French territory in the Southwest Indian Ocean. Antimicrob Resist Infect Control 2020; 9:36. [PMID: 32075697 PMCID: PMC7031992 DOI: 10.1186/s13756-020-0703-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/14/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The spread of carbapenemase-producing Enterobacteriaceae (CPE) in the Southwest Indian Ocean area (SIOA) is poorly documented. Reunion Island is a French overseas territory located close to Madagascar and connected with Southern Africa, Indian sub-continent and Europe, with several weekly flights. Here we report the results of the CPE surveillance program in Reunion Island over a six-year period. METHODS All CPE were collected between January 2011 and December 2016. Demographics and clinical data of the carrier patients were collected. We determined their susceptibility to antimicrobials, identified the carbapenemases and ESBL by PCR and sequencing, and explored their genetic relationship using pulsed-field gel electrophoresis and multi-locus sequence typing. RESULTS A total of 61 CPEs isolated from 53 patients were retrieved in 6 public or private laboratories of the island. We found that 69.8% of CPE patients were linked to a foreign country of SIOA and that almost half of CPE cases (47.2%) reached the island through a medical evacuation. The annual number of CPE cases strongly increased over the studied period (one case in 2011 vs. 21 cases in 2016). A proportion of 17.5% of CPE isolates were non-susceptible to colistin. blaNDM was the most frequent carbapenemase (79.4%), followed by blaIMI (11.1%), and blaIMP-10 (4.8%). Autochtonous CPE cases (30.2%) harboured CPE isolates belonging to a polyclonal population. CONCLUSIONS Because the hospital of Reunion Island is the only reference healthcare setting of the SIOA, we can reasonably estimate that its CPE epidemiology reflects that of this area. Mauritius was the main provider of foreign CPE cases (35.5%). We also showed that autochthonous isolates of CPEs are mostly polyclonal, thus unrelated to cross-transmission. This demonstrates the local spread of carbapenemase-encoding genes (i.e. blaNDM) in a polyclonal bacterial population and raises fears that Reunion Island could contribute to the influx of NDM-carbapenemase producers into the French mainland territory.
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Affiliation(s)
- Guillaume Miltgen
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France. .,UMR Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France.
| | - Pascal Cholley
- Laboratoire d'Hygiène Hospitalière, CHRU Jean Minjoz, Besançon, France.,UMR Chrono-Environnement, CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France
| | - Daniel Martak
- Laboratoire d'Hygiène Hospitalière, CHRU Jean Minjoz, Besançon, France.,UMR Chrono-Environnement, CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France
| | | | - Paul Seraphin
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France
| | - Alexandre Leclaire
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France
| | - Nicolas Traversier
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France
| | - Bénédicte Roquebert
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France.,UMR Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Marie-Christine Jaffar-Bandjee
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France.,UMR Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Nathalie Lugagne
- Service d'hygiène hospitalière, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | | | | | - Sandrine Picot
- Laboratoire de Bactériologie, Groupe Hospitalier Sud Réunion, Saint-Pierre, La Réunion, France
| | - Anne Lignereux
- Laboratoire de biologie, Centre Hospitalier Gabriel Martin, Saint-Paul, La Réunion, France
| | - Geoffrey Masson
- Laboratoire de biologie, Groupe Hospitalier Est Réunion, Saint-Benoit, La Réunion, France
| | - Jérôme Allyn
- Service de Réanimation polyvalente. Département d'Informatique clinique, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - Nicolas Allou
- Service de Réanimation polyvalente. Département d'Informatique clinique, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - Patrick Mavingui
- UMR Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Olivier Belmonte
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France
| | - Xavier Bertrand
- Laboratoire d'Hygiène Hospitalière, CHRU Jean Minjoz, Besançon, France.,UMR Chrono-Environnement, CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France
| | - Didier Hocquet
- Laboratoire d'Hygiène Hospitalière, CHRU Jean Minjoz, Besançon, France.,UMR Chrono-Environnement, CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France
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17
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Girlich D, Oueslati S, Bernabeu S, Langlois I, Begasse C, Arangia N, Creton E, Cotellon G, Sauvadet A, Dortet L, Fortineau N, Naas T. Evaluation of the BD MAX Check-Points CPO Assay for the Detection of Carbapenemase Producers Directly from Rectal Swabs. J Mol Diagn 2020; 22:294-300. [DOI: 10.1016/j.jmoldx.2019.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/02/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
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18
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Bhattacharyya RP, Bandyopadhyay N, Ma P, Son SS, Liu J, He LL, Wu L, Khafizov R, Boykin R, Cerqueira GC, Pironti A, Rudy RF, Patel MM, Yang R, Skerry J, Nazarian E, Musser KA, Taylor J, Pierce VM, Earl AM, Cosimi LA, Shoresh N, Beechem J, Livny J, Hung DT. Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination. Nat Med 2019; 25:1858-1864. [PMID: 31768064 PMCID: PMC6930013 DOI: 10.1038/s41591-019-0650-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/11/2019] [Indexed: 12/13/2022]
Abstract
Multidrug resistant organisms (MDROs) are a serious threat to human health1,2. Fast, accurate antibiotic susceptibility testing (AST) is a critical need in addressing escalating antibiotic resistance, since delays in identifying MDROs increase mortality3,4 and use of broad-spectrum antibiotics, further selecting for resistant organisms. Yet current growth-based AST assays, such as broth microdilution5, require several days before informing key clinical decisions. Rapid AST would transform the care of infected patients while ensuring that our antibiotic arsenal is deployed as efficiently as possible. Growth-based assays are fundamentally constrained in speed by doubling time of the pathogen, and genotypic assays are limited by the ever-growing diversity and complexity of bacterial antibiotic resistance mechanisms. Here, we describe a rapid assay for combined Genotypic and Phenotypic AST through RNA detection, GoPhAST-R, that classifies strains with 94–99% accuracy by coupling machine learning analysis of early antibiotic-induced transcriptional changes with simultaneous detection of key genetic resistance determinants to increase accuracy of resistance detection, facilitate molecular epidemiology, and enable early detection of emerging resistance mechanisms. This two-pronged approach provides phenotypic AST 24–36 hours faster than standard workflows, with <4 hour assay time on a pilot instrument for hybridization-based multiplexed RNA detection implemented directly from positive blood cultures.
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Affiliation(s)
- Roby P Bhattacharyya
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nirmalya Bandyopadhyay
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Peijun Ma
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sophie S Son
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jamin Liu
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lorrie L He
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lidan Wu
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Rich Boykin
- NanoString Technologies, Inc., Seattle, WA, USA
| | - Gustavo C Cerqueira
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Personal Genome Diagnostics, Ellicott City, MD, USA
| | - Alejandro Pironti
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Robert F Rudy
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Milesh M Patel
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rui Yang
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jennifer Skerry
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kimberly A Musser
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jill Taylor
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Virginia M Pierce
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lisa A Cosimi
- Infectious Diseases Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Noam Shoresh
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Deborah T Hung
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
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19
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Breakpoint beware: reliance on historical breakpoints for Enterobacteriaceae leads to discrepancies in interpretation of susceptibility testing for carbapenems and cephalosporins and gaps in detection of carbapenem-resistant organisms. Eur J Clin Microbiol Infect Dis 2019; 39:187-195. [PMID: 31679102 DOI: 10.1007/s10096-019-03711-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/13/2019] [Indexed: 10/25/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are an important public health and infection prevention threat. CRE are typically detected via phenotypic antimicrobial susceptibility testing (AST), for which interpretive standards were modified in recent years. Our objective was to measure the impact of breakpoint changes on AST interpretation for CRE. Zone sizes from disk diffusion AST for Enterobacteriaceae isolates recovered from clinical cultures over a 1-year period (n = 10,183) and CRE from clinical and environmental sources from the USA and Pakistan (n = 342) were evaluated. Results were interpreted according to historical (CLSI M100-S19) and current (CLSI M100-S29) breakpoints. Interpretive errors were calculated according to the FDA definitions. Using current breakpoints as the reference standard, 56 (17%) very major (false susceptibility) errors occurred for cefepime and 13 (45%) very major errors for meropenem interpretation using historical breakpoints in clinical isolates of Enterobacteriaceae, corresponding to 12 carbapenemase-producing CRE that would have been missed during the 1-year period. For confirmed blaKPC CP-CRE clinical and environmental isolates (n = 149), the very major error rate for historic breakpoints was 8%, 30%, 63%, and 0% for cefepime, meropenem, imipenem, and ertapenem, respectively. For blaKPC isolates, the use of historical breakpoints would have led to 42 (28%) reports of false susceptibility to meropenem. Failure to adopt updated AST breakpoints may lead to reports of false susceptibility for antimicrobials commonly used to treat Gram-negative infections and preclude recognition of CRE. Such errors could negatively impact patient care and hamper infection control and public health efforts.
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Villegas MV, Jiménez A, Esparza G, Appel TM. Carbapenemase-producing Enterobacteriaceae: A diagnostic, epidemiological and therapeutic challenge. INFECTIO 2019. [DOI: 10.22354/in.v23i4.808] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Davoudi-Monfared E, Khalili H. The threat of carbapenem-resistant gram-negative bacteria in a Middle East region. Infect Drug Resist 2018; 11:1831-1880. [PMID: 30425536 PMCID: PMC6203168 DOI: 10.2147/idr.s176049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Data on the status of carbapenem-resistant microorganisms in the Middle East countries are scarce. The aim of this review was to collect available data regarding resistance to carbapenems in a Middle East region. Available data regarding carbapenem-resistant isolates were considered for evaluation in this review. Biomedical electronic databases were systematically searched to find related articles. The key terms used were "carbapenem-resistant, resistant gram-negative bacilli, Enterobacteriaceae, fermenting and non-fermenting gram-negative bacilli, Pseudomonas, Acinetobacter, Klebsiella and Iran". After primary screening, 275 relevant articles were selected to be assessed thoroughly. Resistance rate to carbapenems was reported between 1% and 86% during years 2006-2018. Most of the carbapenem-resistant microorganisms were isolated from burn patients. Modified Hodge test was a commonly used phenotypic test. Only in few studies, genotypic assays were considered. Pattern of antibiotic use can affect emergence of resistant microorganisms. Rational use of drugs, and specifically, antibiotics is a challenging issue in developing countries. Mean number of drugs per prescription in these countries was higher than the World Health Organization standards. Overuse of antibiotics, especially injectable ones, and easy access to antibiotics without prescription is a warning alarm for future antibiotic resistance in developing countries. Establishing antimicrobial stewardship's programs is new in the hospitals. Unfortunately, rules and regulatory issues to restrict antibiotic access in community pharmacies and prescription by general physicians are limited.
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Affiliation(s)
- Effat Davoudi-Monfared
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran,
| | - Hossein Khalili
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran,
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Britt NS, Ritchie DJ, Kollef MH, Burnham CAD, Durkin MJ, Hampton NB, Micek ST. Clinical epidemiology of carbapenem-resistant gram-negative sepsis among hospitalized patients: Shifting burden of disease? Am J Infect Control 2018; 46:1092-1096. [PMID: 29706365 DOI: 10.1016/j.ajic.2018.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/13/2018] [Accepted: 03/13/2018] [Indexed: 01/10/2023]
Abstract
BACKGROUND Infections caused by carbapenem-resistant gram-negative bacilli are an emerging public health threat. However, there is a paucity of data examining comparative incidence rates, risk factors, and outcomes in this population. METHODS This single-center retrospective cohort study was conducted at an urban tertiary-care academic medical center. We included patients admitted from 2012 to 2015 who met the following criteria: i) age ≥ 18 years; and ii) culture positive for carbapenem-resistant Enterobacteriaceae (CRE) or carbapenem-resistant non-Enterobacteriaceae (CRNE) from any site. Exclusion criteria were: i) < 2 systemic inflammatory response criteria; ii) cystic fibrosis; and iii) no targeted treatment. We evaluated hospital survival by Cox regression and year-by-year differences in the distribution of cases by the Cochran-Armitage test. RESULTS 448 patients were analyzed (CRE, n = 111 [24.8%]; CRNE, n = 337 [75.2%]). CRE sepsis cases increased significantly over the study period (P <.001), driven primarily by increasing incidence of Enterobacter spp. infection (P = .004). No difference was observed in hospital survival between patients with CRE versus CRNE sepsis (hazard ratio [HR], 1.29; 95% confidence interval [CI], 0.83-2.02; P = .285), even after adjusting for confounding factors (adjusted HR, 1.08; 95% CI, 0.62-1.87; P = .799). CONCLUSIONS Clinical outcomes did not differ between patients with CRE versus CRNE sepsis. Dramatic increases in CRE, particularly Enterobacter spp., appear to be causing a shift in the burden of clinically significant carbapenem-resistant gram-negative infection.
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Pereckaite L, Tatarunas V, Giedraitiene A. Current antimicrobial susceptibility testing for beta-lactamase-producing Enterobacteriaceae in clinical settings. J Microbiol Methods 2018; 152:154-164. [PMID: 30063958 DOI: 10.1016/j.mimet.2018.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 07/16/2018] [Accepted: 07/27/2018] [Indexed: 11/17/2022]
Abstract
The worldwide prevalence of beta-lactamase-producing Enterobacteriaceae (BL-E) is increasing. Bacterial infections involving ESBLs can be more difficult to treat because of antibiotic resistance, as there are fewer effective antibiotics left to be used. Moreover, treatment failure is often observed. Thus, quick and accurate identification of β-lactamases is imperative to minimize it. This review article describes most commonly used phenotypic techniques and molecular methods for the detection of ESBLs, acquired AmpC β-lactamases, and carbapenemases produced by Enterobacteriaceae. Phenotypic detection tests remain useful and relevant in clinical laboratories while molecular diagnostic methods are less affordable, more technically demanding, and not standardized. Molecular methods could be used to speed up results of bacterial antibiotic resistance or to clarify the results of phenotypic β-lactamases confirmation tests.
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Affiliation(s)
- Laura Pereckaite
- Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vacis Tatarunas
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Agne Giedraitiene
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania.
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Bassetti M, Vena A, Croxatto A, Righi E, Guery B. How to manage Pseudomonas aeruginosa infections. Drugs Context 2018; 7:212527. [PMID: 29872449 PMCID: PMC5978525 DOI: 10.7573/dic.212527] [Citation(s) in RCA: 409] [Impact Index Per Article: 68.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 02/07/2023] Open
Abstract
Infections with Pseudomonas aeruginosa have become a real concern in hospital-acquired infections, especially in critically ill and immunocompromised patients. The major problem leading to high mortality lies in the appearance of drug-resistant strains. Therefore, a vast number of approaches to develop novel anti-infectives is currently pursued. Diverse strategies range from killing (new antibiotics) to disarming (antivirulence) the pathogen. In this review, selected aspects of P. aeruginosa antimicrobial resistance and infection management will be addressed. Many studies have been performed to evaluate the risk factors for resistance and the potential consequences on mortality and attributable mortality. The review also looks at the mechanisms associated with resistance – P. aeruginosa is a pathogen presenting a large genome, and it can develop a large number of factors associated with antibiotic resistance involving almost all classes of antibiotics. Clinical approaches to patients with bacteremia, ventilator-associated pneumonia, urinary tract infections and skin soft tissue infections are discussed. Antibiotic combinations are reviewed as well as an analysis of pharmacokinetic and pharmacodynamic parameters to optimize P. aeruginosa treatment. Limitations of current therapies, the potential for alternative drugs and new therapeutic options are also discussed.
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Affiliation(s)
- Matteo Bassetti
- Infectious Diseases Clinic, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Integrata, Udine, Italy
| | - Antonio Vena
- Infectious Diseases Clinic, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Integrata, Udine, Italy
| | - Antony Croxatto
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Elda Righi
- Infectious Diseases Clinic, Department of Medicine, University of Udine and Azienda Sanitaria Universitaria Integrata, Udine, Italy
| | - Benoit Guery
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
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Fleece ME, Pholwat S, Mathers AJ, Houpt ER. Molecular diagnosis of antimicrobial resistance in Escherichia coli. Expert Rev Mol Diagn 2018; 18:207-217. [PMID: 29431523 DOI: 10.1080/14737159.2018.1439381] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Antimicrobial resistance is a growing global public health threat. The complexities of antimicrobial resistance in gram-negative bacteria such as Escherichia coli pose significant diagnostic and therapeutic challenges. Molecular diagnostics are emerging in this field. Areas covered: The authors review the clinical importance of pathogenic E. coli and discuss the mechanisms of resistance to common antibiotics used to treat these infections. We review the literature on antimicrobial susceptibility testing and discuss the current state of phenotypic as well as molecular methodologies. Clinical vignettes are presented to highlight how molecular diagnostics may be used for patient care. Expert commentary: The future use of molecular diagnostics for detection of antimicrobial resistance will be tailored to the context, whether hospital epidemiology, infection control, antibiotic stewardship, or clinical care. Further clinical research is needed to understand how to best apply molecular diagnostics to these settings.
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Affiliation(s)
- Molly E Fleece
- a Division of Infectious Diseases & International Health , University of Virginia , Charlottesville , VA , USA
| | - Suporn Pholwat
- a Division of Infectious Diseases & International Health , University of Virginia , Charlottesville , VA , USA
| | - Amy J Mathers
- a Division of Infectious Diseases & International Health , University of Virginia , Charlottesville , VA , USA
| | - Eric R Houpt
- a Division of Infectious Diseases & International Health , University of Virginia , Charlottesville , VA , USA
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Evaluation of a Modified Carbapenem Inactivation Method for Detection of Carbapenemases in Pseudomonas aeruginosa. J Clin Microbiol 2017; 56:JCM.01234-17. [PMID: 29070655 DOI: 10.1128/jcm.01234-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Verification of the Cepheid Xpert Carba-R assay for the detection of carbapenemase genes in bacterial isolates cultured on alternative solid culture media. J Hosp Infect 2017; 97:254-257. [DOI: 10.1016/j.jhin.2017.06.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 06/27/2017] [Indexed: 11/18/2022]
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Draft Genome Sequence of the blaOXA-436- and blaNDM-1-Harboring Shewanella putrefaciens SA70 Isolate. GENOME ANNOUNCEMENTS 2017; 5:5/29/e00644-17. [PMID: 28729267 PMCID: PMC5522934 DOI: 10.1128/genomea.00644-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We sequenced a carbapenem-resistant Shewanella putrefaciens isolate cultured from the sink handle of a Pakistan hospital room. Assembly annotation indicates that the isolate has a chromosomal blaOXA-436 carbapenemase and a plasmid-borne blaNDM-1 gene. To our knowledge, this is the first report of a Shewanella species harboring blaNDM.
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