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Adewusi OO, Waldner CL, Hanington PC, Hill JE, Freeman CN, Otto SJG. Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review. J Vet Diagn Invest 2024; 36:400-417. [PMID: 38456288 PMCID: PMC11110769 DOI: 10.1177/10406387241235968] [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] [Indexed: 03/09/2024] Open
Abstract
Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.
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Affiliation(s)
- Olufunto O. Adewusi
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Janet E. Hill
- Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
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Martin T, Martinot P, Leclerc JT, Titécat M, Loïez C, Dartus J, Duhamel A, Migaud H, Chantelot C, Lafon Desmurs B, Amouyel T, Senneville E. Accuracy of the GeneXpert® MRSA/SA SSTI test to diagnose methicillin-resistant Staphylococcus spp. infection in bone fixation and fusion and management of infected non-unions. Orthop Traumatol Surg Res 2024:103820. [PMID: 38266672 DOI: 10.1016/j.otsr.2024.103820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/22/2023] [Accepted: 10/16/2023] [Indexed: 01/26/2024]
Abstract
INTRODUCTION The GeneXpert® MRSA/SA SSTI (Methicillin Resistant Staphylococcus aureus/S. aureus skin and soft tissue infection) PCR test allows early detection of methicillin resistance in staphylococci. This test was developed for skin infections and has been evaluated for prosthetic joint infections but, to our knowledge, has not been evaluated for hardware infections outside of arthroplasties. Furthermore, we conducted a retrospective study in patients with non-prosthetic osteosynthesis hardware aiming: (1) to identify the diagnostic values of the PCR test compared to conventional cultures and the resulting rate of appropriate antibiotic therapy; (2) to identify the rate of false negative (FN) results; (3) to identify and compare the rates of failure of infectious treatment (FN versus others); (4) to search for risk factors for FN of the PCR test. HYPOTHESIS The PCR test allowed early and appropriate targeting of antibiotic therapy. MATERIAL AND METHODS The results of PCR tests and conventional cultures for osteoarticular infections of non-prosthetic hardware over four years (2012-2016) were compared to identify the diagnostic values of using the results of conventional culture as a reference and the rate of appropriate antibiotic therapies. Infectious management failures between the results of the FN group and the others were compared, and variables associated with a FN of the PCR test were identified. RESULTS The analysis of 419 PCR tests allowed us to establish a sensitivity of 42.86%, a specificity of 96.82%, a positive predictive value of 60% and a negative predictive value of 93.83%. Using the results of the PCR test for the targeting of postoperative antibiotic therapy, it was suitable for staphylococcal coverage in 90.94% (381/419). The rates of patients for whom infectious treatment failed were not significantly different between the FN group and the other patients (20.8% versus 17.7%, respectively; Hazard Ratio=1.12 (95%CI 0.47-2.69, p=0.79)). A skin opening during the initial trauma (p=0.005) and a polymicrobial infection were significantly associated with a risk of FN from the PCR test (p<0.001). CONCLUSION The PCR test makes it possible to reduce the duration of empirical broad-spectrum antibiotic therapy during the treatment of an infection of osteosynthesis hardware but causes a lack of antibiotic coverage in 9.06% of cases. LEVEL OF EVIDENCE III; diagnostic case control study.
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Affiliation(s)
- Théo Martin
- Service d'orthopédie, hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France.
| | - Pierre Martinot
- Département de chirurgie orthopédique, groupement des hôpitaux de l'institut catholique de Lille, université catholique de Lille, Lomme, France
| | - Jean-Thomas Leclerc
- Service d'orthopédie, hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Département de chirurgie orthopédique, CHU de Québec-université Laval, Quebec, Canada
| | - Marie Titécat
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Microbiologie, centre de biologie pathologie Pierre-Marie Degand, CHU de Lille, boulevard du Pr Jules-Leclercq, 59000 Lille, France
| | - Caroline Loïez
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Microbiologie, centre de biologie pathologie Pierre-Marie Degand, CHU de Lille, boulevard du Pr Jules-Leclercq, 59000 Lille, France
| | - Julien Dartus
- Service d'orthopédie, hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France
| | - Alain Duhamel
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre d'étude et de recherche en informatique médicale, maison de la recherche clinique hospitalière et universitaire, CHU de Lille, 6, rue du Professeur-Laguesse, 59000 Lille, France
| | - Henri Migaud
- Service d'orthopédie, hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France
| | - Christophe Chantelot
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Service de traumatologie, hôpital Salengro, CHU de Lille, place de Verdun, 59000 Lille, France
| | - Barthélémy Lafon Desmurs
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Service universitaire des maladies infectieuses, CH de Dron, 155, rue du Président-Coty, 59200 Tourcoing, France
| | - Thomas Amouyel
- Service d'orthopédie, hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France
| | - Eric Senneville
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Service universitaire des maladies infectieuses, CH de Dron, 155, rue du Président-Coty, 59200 Tourcoing, France
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Mizusawa M, Carroll KC. Recent updates in the development of molecular assays for the rapid identification and susceptibility testing of MRSA. Expert Rev Mol Diagn 2023; 23:679-699. [PMID: 37419696 DOI: 10.1080/14737159.2023.2234823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/09/2023]
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of healthcare- and community-associated infections. Nasal carriage of MRSA is a risk factor for subsequent MRSA infections. Increased morbidity and mortality are associated with MRSA infections and screening and diagnostic tests for MRSA play an important role in clinical management. AREAS COVERED A literature search was conducted in PubMed and supplemented by citation searching. In this article, we provide a comprehensive review of molecular-based methods for MRSA screening and diagnostic tests including individual nucleic acid detection assays, syndromic panels, and sequencing technologies with a focus on their analytical performance. EXPERT OPINION Molecular based-assays for the detection of MRSA have improved in terms of accuracy and availability. Rapid turnaround enables earlier contact isolation and decolonization for MRSA. The availability of syndromic panel tests that include MRSA as a target has expanded from positive blood cultures to pneumonia and osteoarticular infections. Sequencing technologies allow detailed characterizations of novel methicillin-resistance mechanisms that can be incorporated into future assays. Next generation sequencing is capable of diagnosing MRSA infections that cannot be identified by conventional methods and metagenomic next-generation sequencing (mNGS) assays will likely move closer to implementation as front-line diagnostics in the near future.
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Affiliation(s)
- Masako Mizusawa
- Monmouth Medical Center, Rutgers University Robert Wood Johnson Medical School, Long Branch, NJ, USA
| | - Karen C Carroll
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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de la Rica-Martínez A, Andres-Franch M, Estan-Cerezo G, Ruiz-Garcia M, Rodríguez-Díaz JC, Gonzalo-Jimenez N, Galiana-Cabrera A. Clinical evaluation of a new molecular method for the detection of multidrug-resistant microorganisms. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:367-370. [PMID: 35550363 DOI: 10.1016/j.eimce.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/13/2020] [Accepted: 12/06/2020] [Indexed: 06/15/2023]
Abstract
INTRODUCTION The main objective of this work is to carry out the clinical validation of the trial with the AMR Direct Flow Chip starting from either nasal swabs, rectal swabs directly or from isolated strains to detect antibiotic resistance genes. METHODS We developed the preclinical validation of the assay with 104 known bacterial isolates. A total of 210 nasal or rectal swab samples were analyzed. The AMR assay is based on multiplex PCR followed by reverse dot blot hybridization on DNA arrays fully automated by using the HS24 platform. RESULTS Both the sensitivity and specificity of the preclinical assay were 100%, with the 104 samples correctly identified. In the clinical validation, the sensitivity was 100% and the specificity was between 100% in nasal swabs and 97% in rectal swabs. CONCLUSIONS The AMR Direct Flow Chip® is a rapid and effective assay for the detection of multidrug-resistant microorganisms (MDR) from nasal and rectal swab samples.
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Affiliation(s)
- Alba de la Rica-Martínez
- Servicio de Microbiología, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, Spain
| | - María Andres-Franch
- Servicio de Microbiología, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, Spain
| | - Gabriel Estan-Cerezo
- Unidad de Enfermedades Infecciosas, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, Spain
| | - Montserrat Ruiz-Garcia
- Servicio de Microbiología, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, Spain
| | - Juan Carlos Rodríguez-Díaz
- Servicio de Microbiología, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | - Nieves Gonzalo-Jimenez
- Servicio de Microbiología, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, Spain
| | - Antonio Galiana-Cabrera
- Servicio de Microbiología, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, Spain.
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Santopolo G, Clemente A, Rojo-Molinero E, Oliver A, Noé C, de la Rica R. Rapid Identification and Classification of Pathogens That Produce Carbapenemases and Cephalosporinases with a Colorimetric Paper-Based Multisensor. Anal Chem 2022; 94:9442-9449. [PMID: 35748103 DOI: 10.1021/acs.analchem.2c01724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Infections caused by bacteria that produce β-lactamases (BLs) are a major problem in hospital settings. The phenotypic detection of these bacterial strains requires culturing samples prior to analysis. This procedure may take up to 72 h, and therefore it cannot be used to guide the administration of the first antibiotic regimen. Here, we propose a multisensor for identifying pathogens bearing different types of β-lactamases above the infectious dose threshold within 90 min that does not require culturing samples. Instead, bacterial cells are preconcentrated in the cellulose scaffold of a paper-based multisensor. Then, 12 assays are performed in parallel to identify whether the pathogens produce carbapenemases and/or cephalosporinases, including metallo-β-lactamases, extended-spectrum β-lactamases (ESBLs), and AmpC enzymes. The multisensor generates an array of colored spots that can be quantified with image processing software and whose interpretation leads to the detection of the different enzymes depending on their specificity toward the hydrolysis of certain antibiotics, and/or their pattern of inhibition or cofactor activation. The test was validated for the diagnosis of urinary tract infections. The inexpensive paper platform along with the uncomplicated colorimetric readout makes the proposed prototypes promising for developing fully automated platforms for streamlined clinical diagnosis.
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Affiliation(s)
- Giulia Santopolo
- Multidisciplinary Sepsis Group, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma de Mallorca 07120, Spain.,Department of Chemistry, University of the Balearic Islands, Palma de Mallorca 07122, Spain
| | - Antonio Clemente
- Multidisciplinary Sepsis Group, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma de Mallorca 07120, Spain
| | - Estrella Rojo-Molinero
- Microbiology Department, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma de Mallorca 07120, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid 28029, Spain
| | - Antonio Oliver
- Microbiology Department, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma de Mallorca 07120, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid 28029, Spain
| | - Camilla Noé
- Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino (POLITO), Torino 10129, Italy
| | - Roberto de la Rica
- Multidisciplinary Sepsis Group, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma de Mallorca 07120, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid 28029, Spain
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Ojha SC, Chen K, Sun C, Ahmed S, Sheng YJ, Deng CL. Clinical Relevance of Xpert MRSA/SA in Guiding Therapeutic Decisions for Staphylococcal Infections: A Diagnostic Test Accuracy Analysis. Infect Dis Ther 2022; 11:1205-1227. [PMID: 35451743 PMCID: PMC9124268 DOI: 10.1007/s40121-022-00632-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/30/2022] [Indexed: 11/12/2022] Open
Abstract
Introduction Rapid identification of the causal organism and antibiotic resistance is crucial for guiding targeted therapy in patients with suspected staphylococcal infection. A meta-analysis was carried out to evaluate the diagnostic relevance of Xpert™ MRSA/SA (Xpert) from clinical samples of various origins for limiting the use of unnecessary empirical methicillin-resistant Staphylococcus aureus (MRSA) therapy. Methods Five databases, including the Cochrane Library, Scopus, PubMed, Web of Science, and Embase, were comprehensively inspected from inception to October 12, 2021. The pooled summary estimates were evaluated using a bivariate random-effects model. Results Our inclusion criteria were met by 49 publications containing 68 datasets out of 735 citations. A total of 21 studies (n = 4996) examined the accuracy of Xpert in detecting methicillin-sensitive S. aureus (MSSA), while 47 studies (n = 45,430) examined the accuracy of Xpert in detecting MRSA. As compared to MRSA, Xpert’s diagnostic performance for MSSA detection was markedly higher [sensitivity: 0.97 (0.96–0.98), specificity: 0.97 (0.97–0.98), area under curve (AUC): 0.99 (0.99–1.0)]. Xpert’s pooled sensitivity and specificity differed marginally across sample types, including screening of colonization, lower respiratory tract (LRT), osteoarticular, and bloodstream samples. Notably, the Xpert pooled specificity was consistently ≥ 92% against microbiological culture across all sample types. The diagnostic efficiency heterogeneity was not explained by a meta-regression and subgroup analysis of research design, sample conditions, and sampling methods (P > 0.05). Conclusion Our findings suggest that Xpert could be used as the favoured screening test for the early detection of staphylococcal infection in a variety of sample types, with the goal of guiding therapeutic decisions. Supplementary Information The online version contains supplementary material available at 10.1007/s40121-022-00632-w.
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Affiliation(s)
- Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China. .,Southwest Medical University, Jiangyang District, Luzhou, 646000, China.
| | - Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China.,Southwest Medical University, Jiangyang District, Luzhou, 646000, China
| | - Changfeng Sun
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China.,Southwest Medical University, Jiangyang District, Luzhou, 646000, China
| | - Sarfraz Ahmed
- Department of Basic Sciences, University of Veterinary and Animal Sciences Lahore, Sub-campus, Narowal, 51600, Pakistan
| | - Yun-Jian Sheng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China.,Southwest Medical University, Jiangyang District, Luzhou, 646000, China
| | - Cun-Liang Deng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
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Almeida ST, Paulo AC, de Lencastre H, Sá-Leão R. Evaluation of Methicillin-Resistant Staphylococcus aureus Carriage in the Elderly in Portugal Using Selective Enrichment Followed by quantitative real-time PCR. Microb Drug Resist 2022; 28:585-592. [PMID: 35363078 DOI: 10.1089/mdr.2021.0383] [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] [Indexed: 11/12/2022] Open
Abstract
The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in hospitals in Portugal is worrisome and among the highest in Europe. Surprisingly, MRSA prevalence in the community was described as very low (<2%) based on studies that used classical culture-based methods (CCBM). We investigated whether the apparent limited spread of MRSA in the community in Portugal might result from low sensitivity of CCBM. Nasopharyngeal- and oropharyngeal-paired samples obtained from senior adults living in nursing (n = 299) or family homes (n = 300) previously characterized by CCBM were reanalyzed. Samples were inoculated in a semi-selective enrichment medium, and those showing visible growth were evaluated by qPCR targeting nuc, mecA, and mecC genes (SSE+qPCR). By SSE+qPCR, 34 of the 1,198 (2.8%) samples were MRSA positive compared with 21 (1.8%) by CCBM. SSE+qPCR improved non-significantly detection of MRSA carriers from 5.4% to 8.0% (p = 0.12) in the nursing home collection, and from 0.3% to 1.7% (p = 0.13) in the family home collection. MRSA isolates belonged to three HA-MRSA clones widely disseminated in Portuguese hospitals. In conclusion, use of semi-selective medium combined with qPCR did not change the overall scenario previously described. In Portugal, MRSA circulation in the community among senior adults is low.
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Affiliation(s)
- Sónia Tavares Almeida
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Ana Cristina Paulo
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
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Tenover FC, Tickler IA. Detection of Methicillin-Resistant Staphylococcus aureus Infections Using Molecular Methods. Antibiotics (Basel) 2022; 11:antibiotics11020239. [PMID: 35203841 PMCID: PMC8868555 DOI: 10.3390/antibiotics11020239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 02/01/2023] Open
Abstract
The application of molecular detection methods for bacterial pathogens has dramatically improved the outcomes of septic patients, including those with methicillin-resistant Staphylococcus aureus (MRSA) infections. Molecular methods can be applied to a variety of clinical specimens including nasal swabs, growth in blood culture bottles, and wounds. While data show that the overall accuracy of molecular tests for MRSA is high, results can be confounded by the presence of multiple staphylococcal species in a specimen, insertions and deletions of DNA in and around the Staphylococcal Cassette Chromosome mec (SCCmec) element, and point mutations in mecA. Herein, we explore the complexities of molecular approaches to MRSA detection and the instances where phenotypic methods should be pursued to resolve discrepancies between genotypic and phenotypic results.
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Coia JE, Wilson JA, Bak A, Marsden GL, Shimonovich M, Loveday HP, Humphreys H, Wigglesworth N, Demirjian A, Brooks J, Butcher L, Price JR, Ritchie L, Newsholme W, Enoch DA, Bostock J, Cann M, Wilson APR. Joint Healthcare Infection Society (HIS) and Infection Prevention Society (IPS) guidelines for the prevention and control of meticillin-resistant Staphylococcus aureus (MRSA) in healthcare facilities. J Hosp Infect 2021; 118S:S1-S39. [PMID: 34757174 DOI: 10.1016/j.jhin.2021.09.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 12/28/2022]
Affiliation(s)
- J E Coia
- Department of Clinical Microbiology, Hospital South West Jutland, Esbjerg, Denmark; Department of Regional Health Research IRS, University of Southern Denmark, Denmark; Healthcare Infection Society, London, UK
| | - J A Wilson
- Richard Wells Research Centre, University of West London, London, UK; Infection Prevention Society, Seafield, UK
| | - A Bak
- Healthcare Infection Society, London, UK.
| | | | - M Shimonovich
- Healthcare Infection Society, London, UK; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK
| | - H P Loveday
- Richard Wells Research Centre, University of West London, London, UK; Infection Prevention Society, Seafield, UK
| | - H Humphreys
- Healthcare Infection Society, London, UK; Department of Clinical Microbiology, The Royal College of Surgeons, Ireland; Department of Microbiology, Beaumont Hospital, Dublin, Ireland
| | - N Wigglesworth
- Infection Prevention Society, Seafield, UK; East Kent Hospitals University, NHS Foundation Trust, Canterbury, UK
| | - A Demirjian
- Healthcare-associated Infection and Antimicrobial Resistance, Public Health England, London, UK; Paediatric Infectious Diseases and Immunology, Evelina London Children's Hospital, London, UK; Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - J Brooks
- Infection Prevention Society, Seafield, UK; University Hospital Southampton NHS Foundation Trust, UK
| | - L Butcher
- Infection Prevention Society, Seafield, UK; Oxford University Hospitals NHS Foundation Trust, UK
| | - J R Price
- Healthcare Infection Society, London, UK; Imperial College Healthcare NHS Trust, London, UK
| | - L Ritchie
- Healthcare Infection Society, London, UK; NHS England and NHS Improvement, London, UK
| | - W Newsholme
- Healthcare Infection Society, London, UK; Guy's and St Thomas' NHS Foundation Trust, UK
| | - D A Enoch
- Healthcare Infection Society, London, UK; Clinical Microbiology & Public Health Laboratory, Public Health England, Addenbrooke's Hospital, Cambridge, UK
| | | | - M Cann
- Lay Member, UK; MRSA Action UK, Preston, UK
| | - A P R Wilson
- Healthcare Infection Society, London, UK; University College London Hospitals NHS Foundation Trust, UK.
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de la Rica-Martínez A, Andres-Franch M, Estan-Cerezo G, Ruiz-Garcia M, Rodríguez-Díaz JC, Gonzalo-Jimenez N, Galiana-Cabrera A. Clinical evaluation of a new molecular method for the detection of multidrug-resistant microorganisms. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00003-3. [PMID: 33573838 DOI: 10.1016/j.eimc.2020.12.001] [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: 07/17/2020] [Revised: 11/13/2020] [Accepted: 12/06/2020] [Indexed: 11/03/2022]
Abstract
INTRODUCTION The main objective of this work is to carry out the clinical validation of the trial with the AMR Direct Flow Chip® starting from either nasal swabs, rectal swabs directly or from isolated strains to detect antibiotic resistance genes. METHODS We developed the preclinical validation of the assay with 104 known bacterial isolates. A total of 210 nasal or rectal swab samples were analyzed. The AMR assay is based on multiplex PCR followed by reverse dot blot hybridization on DNA arrays fully automated by using the HS24 platform. The completion time of the full analysis is 3 hours. RESULTS Both the sensitivity and specificity of the preclinical assay were 100%, with the 104 samples correctly identified. In the clinical validation, the sensitivity was 100% and the specificity was between 100% in rectal swabs and 97% in nasal swabs. CONCLUSIONS The AMR Direct Flow Chip® is a rapid and effective assay for the detection of multidrug-resistant microorganisms from nasal and rectal swab samples.
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Affiliation(s)
- Alba de la Rica-Martínez
- Servicio de Microbiología, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, España
| | - María Andres-Franch
- Servicio de Microbiología, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, España
| | - Gabriel Estan-Cerezo
- Unidad de Enfermedades Infecciosas, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, España
| | - Montserrat Ruiz-Garcia
- Servicio de Microbiología, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, España
| | - Juan Carlos Rodríguez-Díaz
- Servicio de Microbiología, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, España
| | - Nieves Gonzalo-Jimenez
- Servicio de Microbiología, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, España
| | - Antonio Galiana-Cabrera
- Servicio de Microbiología, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Elche, Alicante, España.
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11
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Preparation of nature inspired indicator based agar for detection and identification of MRSA and MRSE. Talanta 2020; 219:121292. [DOI: 10.1016/j.talanta.2020.121292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 11/17/2022]
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Development and Evaluation of a Sensitive Bacteriophage-Based MRSA Diagnostic Screen. Viruses 2020; 12:v12060631. [PMID: 32545159 PMCID: PMC7354448 DOI: 10.3390/v12060631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022] Open
Abstract
Engineered luciferase reporter bacteriophages provide specific, sensitive, rapid and low-cost detection of target bacteria and address growing diagnostic needs in multiple industries. Detection of methicillin-resistant Staphylococcus aureus (MRSA) nasal colonization and antibiotic susceptibility play a critical supportive role in preventing hospital-acquired infections and facilitating antibiotic stewardship. We describe the development and evaluation of a novel phage-based MRSA diagnostic screen for nasal swab specimens. The screen utilizes two luciferase reporter phages capable of recognizing genetically-diverse Staphylococcus aureus. The beta-lactam antibiotic cefoxitin is included to differentiate between resistant (MRSA) and susceptible organisms. The screen positively identified 97.7% of 390 clinical MRSA isolates at low bacterial concentrations. At higher inoculums, 93.5% of 123 clinical non-MRSA Staphylococcus aureus yielded appropriate negative results. Although cross-reactivity of the phage cocktail was observed with other staphylococcal and bacillus species, these false positives were absent under selective conditions. MRSA remained detectable in the presence of 38 distinct competing species and was accurately identified in 100% of 40 spiked nasal specimens. Thus, this six-hour screen sensitively detected MRSA both in vitro and in human nasal matrix.
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Bouza E, Burillo A, de Egea V, Hortal J, Barrio JM, Vicente T, Muñoz P, Pérez-Granda MJ. Colonization of the nasal airways by Staphylococcus aureus on admission to a major heart surgery operating room: A real-world experience. Enferm Infecc Microbiol Clin 2019; 38:466-470. [PMID: 31668380 DOI: 10.1016/j.eimc.2019.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/11/2019] [Accepted: 07/18/2019] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Nasal swab culture is used to identify Staphylococcus aureus colonization, as this is a major risk factor for surgical site infection (SSI) in patients who are going to undergo major heart surgery (MHS). We determined nasal carriage of S. aureus in patients undergoing MHS by comparing the yield of a conventional culture with that of a rapid molecular test (Xpert® SA Nasal Complete, Cepheid). METHODS From July 2015 to April 2017, all patients who were to undergo MHS were invited to participate in the study. We obtained two nasal cultures from each patient just before entering the operating room, independently of a previous test for the determination of nasal colonization by this microorganism performed before surgery. One swab was used for conventional culture in the microbiology laboratory, and the other was used for the rapid molecular test. We defined nasal colonization as the presence of a positive culture for S. aureus using either of the two techniques. All patients were followed up until hospital discharge or death. RESULTS Overall, 57 out of 200 patients (28.5%) were colonized by S. aureus at the time of surgery. Thirty-three patients had both conventional culture- and PCR-positive results. Twenty-four patients had a negative culture and a positive PCR test. Only twenty-one percent (12/57) of colonized patients had undergone an attempt to decolonise before the surgical intervention. CONCLUSION A significant proportion of patients undergoing MHS are colonized by S. aureus in the nostrils on entering the operating room. New strategies to prevent SSI by this microorganism are needed. Rapid molecular tests immediately before MHS, followed by immediate decolonisation, must be evaluated. Trial Registration Clinical Trials.gov NCT02640001.
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Affiliation(s)
- Emilio Bouza
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; Department of Medicine, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain; CIBER de Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
| | - Almudena Burillo
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; Department of Medicine, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Viviana de Egea
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Javier Hortal
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; CIBER de Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain; Cardiac Surgery Postoperative Care Unit, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - José M Barrio
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; CIBER de Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain; Cardiac Surgery Postoperative Care Unit, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Teresa Vicente
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; Department of Medicine, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain; CIBER de Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
| | - María Jesús Pérez-Granda
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; Cardiac Surgery Postoperative Care Unit, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Department of Nursing, Faculty of nursing, physiotherapy and podiatry, Universidad Complutense de Madrid, Madrid, Spain.
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Ayebare A, Bebell LM, Bazira J, Ttendo S, Katawera V, Bangsberg DR, Siedner MJ, Firth PG, Boum Ii Y. Comparative assessment of methicillin resistant Staphylococcus aureus diagnostic assays for use in resource-limited settings. BMC Microbiol 2019; 19:194. [PMID: 31438852 PMCID: PMC6704615 DOI: 10.1186/s12866-019-1566-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The rise of methicillin-resistant Staphylococcus aureus (MRSA) is a global health concern. Paucity of data on MRSA carriage prevalence and diagnostic methods in resource-limited settings hampers efforts to define the problem and plan an appropriate response. Additionally, high variability in cost and logistical characteristics of MRSA screening methods may impede infection control efforts. We compared the performance of locally-available chromogenic agar BD CHROMagar MRSA II and two PCR-based assays (Hain GenoQuick MRSA and Cepheid Xpert SA Complete) for the detection of asymptomatic MRSA carriage in nasal swabs. RESULTS During 2015, we enrolled 500 patients from five hospital wards at a Ugandan regional referral hospital. We found 30% prevalence of methicillin-sensitive Staphylococcus aureus (MSSA) nasal carriage, and 5.4% MRSA nasal carriage prevalence. Compared to a composite reference standard defined as a positive test result on any one of the three assays, Hain GenoQuick MRSA demonstrated the highest sensitivity (96%) followed by direct plating on CHROMagar at (70%), with the lowest sensitivity observed with Xpert SA Complete (52%). Cepheid Xpert provided the most rapid results (< 1 h) but was the most expensive (US $45-50/test). Substantially more labor was required for the Hain GenoQuick MRSA compared to Xpert SA Complete or CHROMagar tests. CONCLUSION MRSA nasal carriage prevalence rates were low, and high diagnostic sensitivity was achieved using Hain GenoQuick MRSA. Chromogenic media had significantly lower sensitivity, but may represent a viable local option given its lower cost compared to PCR-based assays.
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Affiliation(s)
- A Ayebare
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda. .,Epicentre Mbarara Research Centre, Mbarara, Uganda.
| | - L M Bebell
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,Massachusetts General Hospital Center for Global Health, Boston, MA, USA
| | - J Bazira
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - S Ttendo
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - V Katawera
- World Health Organization, Monrovia, Liberia
| | - D R Bangsberg
- Oregon Health & Science University-Portland State University School of Public Health, Portland, OR, USA
| | - M J Siedner
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,Massachusetts General Hospital Center for Global Health, Boston, MA, USA
| | - P G Firth
- Massachusetts General Hospital Department of Anesthesia, Critical Care and Pain Medicine, Boston, MA, USA
| | - Y Boum Ii
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda. .,Epicentre Mbarara Research Centre, Mbarara, Uganda.
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Dewar S, Vass D, MacKenzie FM, Parcell BJ. Point-of-care testing by healthcare workers for detection of meticillin-resistant Staphylococcus aureus, Clostridioides difficile, and norovirus. J Hosp Infect 2019; 103:447-453. [PMID: 31404566 DOI: 10.1016/j.jhin.2019.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/01/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND The feasibility of introducing three separate Cepheid GeneXpert® assays was assessed: Xpert SA Nasal Complete, Xpert C. difficile, and Xpert Norovirus for point-of-care testing (POCT) on a ward in a district general hospital. AIM To establish a seven-day/24 h POCT service for meticillin-resistant Staphylococcus aureus (MRSA), Clostridioides difficile, and norovirus operated solely by healthcare workers (HCWs). METHODS The Cepheid GeneXpert assays performance characteristics were assessed by comparing the assays to traditional central laboratory methods in terms of clinical turnaround times, hands-on time, number of process steps, time to result and diagnostic accuracy. HCW feedback was collected to consider the potential added value of applying this technology to improve patient flow and clinical care. FINDINGS In total 1170 tests were carried out over the 16-month study period. The assays significantly reduced hands-on time, process steps, and time to result for identification of all three micro-organisms. Overall agreement with central laboratory testing was >98% for all three assays. Staff members fed back that POCT had a positive impact in terms of clinical utility. CONCLUSION Xpert SA Nasal Complete for MRSA detection, Xpert C. difficile, and Xpert Norovirus can be used as POCT solely by HCWs in a ward setting. Each assay was used throughout a seven-day/24 h period with potential positive impact on bed management and patient care.
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Affiliation(s)
- S Dewar
- Medical Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK.
| | - D Vass
- Stroke Ward & Acute Medical Admissions Unit, Dr Gray's Hospital, Elgin, UK
| | - F M MacKenzie
- Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - B J Parcell
- Medical Microbiology, Ninewells Hospital and Medical School, Dundee, UK
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Comparison of GeneXpert MRSA/SA ETA assay with semi-quantitative and quantitative cultures and nuc gene-based qPCR for detection of Staphylococcus aureus in endotracheal aspirate samples. Antimicrob Resist Infect Control 2019; 8:4. [PMID: 30627428 PMCID: PMC6321727 DOI: 10.1186/s13756-018-0460-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/21/2018] [Indexed: 11/10/2022] Open
Abstract
Introduction Staphylococcus aureus (S. aureus) is a common cause of ventilator-associated pneumonia. Rapid and accurate detection of lower respiratory tract colonization and/or infection with S. aureus may inform targeted preventive and therapeutic strategies. To investigate this, we compared semi-quantitative (SQ)-culture results from 79 endotracheal aspirates (ETA) collected from mechanically-ventilated patients, to two culture and two non-culture-based methods for detection of S. aureus. Methods ETA analyzed by routine SQ-culture on blood and colistin-nalidixic-acid agar was compared to: (i) quantitative (Q-) culture on chromogenic COLOREX™ Staph aureus; (ii) enrichment in brain-heart-infusion broth followed by plating on blood agar and COLOREX™; (iii) nuc-based TaqMan qPCR, and (iv) GeneXpert MRSA/SA ETA assay. Results Of the 79 ETA samples analyzed by SQ-culture, 39 samples were positive, and 40 negative for S. aureus. Two samples negative for S. aureus by SQ-culture were, however, S. aureus-positive by the other four methods and were considered positive. Appending these two samples as positive in the SQ-culture results, sensitivities-specificities for Q-culture, enrichment-culture, TaqMan qPCR and GeneXpert were 100-95, 100-92, 100-53% and 100% - 100, respectively. The lower specificities of Q-culture, enrichment-culture, and TaqMan qPCR was because of their higher sensitivities, although TaqMan qPCR also detected S. aureus-specific extracellular DNA. Conclusion This first evaluation of the GeneXpert MRSA/SA ETA assay with ETA samples found it to be highly sensitive, specific, user-friendly (hands-on time ~ 5 min.), and rapid (~ 66 min. assay time). Where this equipment is not available, we recommend implementing more sensitive culture-based methods for improved S. aureus detection in ETA samples.
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New Technologies for the Diagnosis of Infection. DIAGNOSTIC PATHOLOGY OF INFECTIOUS DISEASE 2018. [PMCID: PMC7152403 DOI: 10.1016/b978-0-323-44585-6.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Srinivasan A, Lee GC, Torres NS, Hernandez K, Dallas SD, Lopez-Ribot J, Frei CR, Ramasubramanian AK. High-throughput microarray for antimicrobial susceptibility testing. ACTA ACUST UNITED AC 2017; 16:44-47. [PMID: 29167758 PMCID: PMC5686425 DOI: 10.1016/j.btre.2017.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/20/2017] [Accepted: 10/30/2017] [Indexed: 12/03/2022]
Abstract
Developed a high-throughput microarray for anti-microbial susceptibility testing (AST). Demonstrated that the feasibility of the AST against clinical isolates of MRSA. Platform is a low sample volume, rapid, high-throughput alternative to traditional assays.
We describe the development of a novel, high-throughput, nano-scale microarray platform for antimicrobial susceptibility testing (AST). The platform allows to process 480 samples at 50 nL volume on a single chip, analyze by fluorescence read-out with an easy dunk-and-rinse step, and the ability to process multiple samples and chips simultaneously. We demonstrate the applicability of this chip for culturing community acquired methicillin resistant Staphylococcus aureus (CA-MRSA), and perform AST against clinical isolates of CA-MRSA. The chip platform holds promise for an impact in microbial biotechnology as an attractive high-throughput, lower sample volume and quicker alternative to conventional AST such as the traditional broth microdilution or the newer automated systems.
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Affiliation(s)
- Anand Srinivasan
- Department of Biomedical Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, United States
- BioBridge Global LLC, San Antonio, TX, 78201, United States
| | - Grace C. Lee
- College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, United States
- Department of Pathology, School of Medicine, The University of Texas Health Science Center, San Antonio, TX, 78229, United States
| | - Nelson S. Torres
- Department of Biomedical Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, United States
| | - Kevin Hernandez
- Department of Biomedical, Chemical and Materials Engineering, San José State University, San José, CA, 95192, United States
| | - Steven D. Dallas
- Department of Pathology, School of Medicine, The University of Texas Health Science Center, San Antonio, TX, 78229, United States
| | - Jose Lopez-Ribot
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, 78249, United States
| | - Christopher R. Frei
- College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, United States
- Department of Pathology, School of Medicine, The University of Texas Health Science Center, San Antonio, TX, 78229, United States
| | - Anand K. Ramasubramanian
- Department of Biomedical, Chemical and Materials Engineering, San José State University, San José, CA, 95192, United States
- Corresponding author at: Department of Biomedical, Chemical & Materials Engineering, San José State University, San José, United States.Department of BiomedicalChemical and Materials EngineeringSan José State UniversitySan JoséCA95192United States
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Genetic Mimetics of Mycobacterium tuberculosis and Methicillin-Resistant Staphylococcus aureus as Verification Standards for Molecular Diagnostics. J Clin Microbiol 2017; 55:3384-3394. [PMID: 28931561 DOI: 10.1128/jcm.01111-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/14/2017] [Indexed: 12/19/2022] Open
Abstract
Molecular diagnostics have revolutionized the management of health care through enhanced detection of disease or infection and effective enrollment into treatment. In recognition of this, the World Health Organization approved the rollout of nucleic acid amplification technologies for identification of Mycobacterium tuberculosis using platforms such as GeneXpert MTB/RIF, the GenoType MTBDRplus line probe assay, and, more recently, GeneXpert MTB/RIF Ultra. These assays can simultaneously detect tuberculosis infection and assess rifampin resistance. However, their widespread use in health systems requires verification and quality assurance programs. To enable development of these, we report the construction of genetically modified strains of Mycobacterium smegmatis that mimic the profile of Mycobacterium tuberculosis on both the GeneXpert MTB/RIF and the MTBDRplus line probe diagnostic tests. Using site-specific gene editing, we also created derivatives that faithfully mimic the diagnostic result of rifampin-resistant M. tuberculosis, with mutations at positions 513, 516, 526, 531, and 533 in the rifampin resistance-determining region of the rpoB gene. Next, we extended this approach to other diseases and demonstrated that a Staphylococcus aureus gene sequence can be introduced into M. smegmatis to generate a positive response for the SCCmec probe in the GeneXpert SA Nasal Complete molecular diagnostic cartridge, designed for identification of methicillin-resistant S. aureus These biomimetic strains are cost-effective, have low biohazard content, accurately mimic drug resistance, and can be produced with relative ease, thus illustrating their potential for widespread use as verification standards for diagnosis of a variety of diseases.
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Wu PJ, Jeyaratnam D, Tosas O, Cooper BS, French GL. Point-of-care universal screening for meticillin-resistant Staphylococcus aureus: a cluster-randomized cross-over trial. J Hosp Infect 2017; 95:245-252. [PMID: 27658666 PMCID: PMC5384532 DOI: 10.1016/j.jhin.2016.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/14/2016] [Indexed: 10/27/2022]
Abstract
BACKGROUND Meticillin-resistant Staphylococcus aureus (MRSA) is frequently endemic in healthcare settings and may be transmitted by person-to-person spread. Asymptomatic MRSA carriers are potential, unsuspected sources for transmission and some of them may be identified by admission screening. AIM To assess whether rapid point-of-care screening (POCS) for MRSA at hospital admission may be associated with a reduction in MRSA acquisition rates when compared with slower laboratory-based methods. METHODS A cluster-randomized cross-over trial was conducted in four admission wards of an acute London tertiary care hospital. Polymerase chain reaction-based POCS screening was compared with conventional culture screening. Patients were screened on ward admission and discharge, and the MRSA acquisition rate on the admission wards was calculated as the primary outcome measure. RESULTS In all, 10,017 patients were included; 4978 in the control arm, 5039 in the POCS arm. The MRSA carriage rate on admission was 1.7%. POCS reduced the median reporting time from 40.4 to 3.7 h (P < 0.001). MRSA was acquired on the admission wards by 23 (0.46%) patients in the control arm and by 24 (0.48%) in the intervention arm, acquisition rates of 5.39 and 4.60 per 1000 days respectively. After taking account of predefined confounding factors, the adjusted incidence rate ratio (IRR) for change in trend for MRSA acquisition was 0.961 (95% confidence interval: 0.766-1.206). The adjusted IRR for step change for MRSA acquisition was 0.98 (0.304-3.162). CONCLUSION POCS produces a significantly faster result but has no effect on MRSA acquisition on admission wards compared with culture screening. Where compliance with infection prevention and control is high and MRSA carriage is low, POCS has no additional impact on MRSA acquisition rates over the first one to four days of admission compared with conventional culture screening.
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Affiliation(s)
- P J Wu
- Department of Infection, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - D Jeyaratnam
- Department of Microbiology, King's College Hospital NHS Foundation Trust, London, UK.
| | - O Tosas
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, London, UK
| | - B S Cooper
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, London, UK
| | - G L French
- Department of Infection, Guy's and St Thomas' NHS Foundation Trust, London, UK; Department of Infectious Disease, King's College London, School of Medicine, London, UK
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Rabaan AA, Bazzi AM. Variation in MRSA identification results from different generations of Xpert MRSA real-time PCR testing kits from nasal swabs. J Infect Public Health 2017; 10:799-802. [PMID: 28185823 DOI: 10.1016/j.jiph.2017.01.007] [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: 08/20/2016] [Revised: 12/01/2016] [Accepted: 01/07/2017] [Indexed: 11/17/2022] Open
Abstract
GeneXpert MRSA kits (Cepheid) are based on a multiplex, real-time PCR method for methicillin-resistant Staphylococcus aureus (MRSA) detection, with primers to detect each SCCmec type and the chromosomal orfX-SCCmec junction. Modifications in recent kit versions were proposed to help overcome false-positive issues in earlier kit versions. The main objective of this study was to determine whether use of any version of the GeneXpert MRSA multiplex, real-time PCR kits yielded higher than expected MRSA+ results. We also estimated the level of MRSA in our healthcare facility as a proportion of total S. aureus between 2010 and 2015. We examined results from five generations of the kits used between 2008 and 2015. Results were from nasal swab samples from 16,431 patients in the Johns Hopkins Aramco Healthcare facility in Saudi Arabia. The percentage of isolates scored as MRSA+ for the original Xpert MRSA kit was 18.57%, compared to 6.93±1.12% (mean±SD) for the other four kits. The Xpert MRSA-SA Nasal kit yielded 6.48% Invalid results, compared to 0.73±0.28% for the other four kits. The succeeding Xpert MRSA-SA Nasal G3 and Xpert MRSA-SA Nasal Complete G3 kits yielded Invalid results rates of 0.29% and 1.04% respectively. Levels of MRSA-positive isolates as a percentage of total S. aureus-containing samples ranged between 19.81% and 26.74%. In conclusion, the original Xpert MRSA kit yielded higher than expected rates of MRSA+. Issues with over-estimation of MRSA+ and/or numerous Invalid results have been overcome in the most recent modified kits.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.
| | - Ali M Bazzi
- Microbiology Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
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Lymperopoulou DS, Coil DA, Schichnes D, Lindow SE, Jospin G, Eisen JA, Adams RI. Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72. Stand Genomic Sci 2017; 12:17. [PMID: 28163826 PMCID: PMC5282799 DOI: 10.1186/s40793-017-0223-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/08/2016] [Indexed: 11/10/2022] Open
Abstract
We report here the draft genome sequences of eight bacterial strains of the genera Staphylococcus, Microbacterium, Mycobacterium, Plantibacter, and Pseudomonas. These isolates were obtained from aerosol sampling of bathrooms of five residences in the San Francisco Bay area. Taxonomic classifications as well as the genome sequence and gene annotation of the isolates are described. As part of the "Built Environment Reference Genome" project, these isolates and associated genome data provide valuable resources for studying the microbiology of the built environment.
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Affiliation(s)
| | - David A. Coil
- Genome Center, University of California Davis, Davis, USA
| | - Denise Schichnes
- CNR Biological Imaging Facility, University of California Berkeley, Berkeley, USA
| | - Steven E. Lindow
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA USA
| | | | - Jonathan A. Eisen
- Genome Center, University of California Davis, Davis, USA
- Department of Evolution and Ecology, University of California Davis, Davis, USA
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA USA
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Preoperative Staphylococcus aureus Carriage and Risk of Surgical Site Infection After Cardiac Surgery in Children Younger than 1 year: A Pilot Cohort Study. Pediatr Cardiol 2017; 38:176-183. [PMID: 27844091 DOI: 10.1007/s00246-016-1499-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 10/25/2016] [Indexed: 10/20/2022]
Abstract
Surgical site infections (SSI) increase length of stay, morbidity, mortality and cost of hospitalization. Staphylococcus aureus (SA) carriage is a known risk factor of SSI in adults, but its role in pediatrics remains uncertain. The main objective of this pilot prospective monocentric cohort study was to describe the prevalence of SA colonization in children under 1 year old before cardiac surgery. The secondary objectives were to compare the incidence of SSI and other nosocomial infections (NI) between preoperative carriers and non-carriers. From May 2012 to November 2013, all children <1 year old undergoing cardiac surgery under cardiopulmonary bypass underwent preoperative methicillin-resistant (MRSA) and methicillin-sensitive SA (MSSA) screening using real-time PCR. The only exclusion criterion was invalid PCR. All patients were followed up to 1 year after the surgery regarding SSI and other nosocomial infections. Among the 68 studied patients, SA colonization prevalence was 26.5%, comprising 23.5% MSSA and 2.9% MRSA. There was no significant difference between colonized and non-colonized children regarding SSI rate (16.7 vs 20%; p = 0.53), but ventilator-associated pneumonia rate was significantly higher among the SA carriers (22.2 vs 2%; p < 0.05). The colonization rate was different depending on the age of the patients (p < 0.05). This pilot study highlights that colonization with MSSA is frequent whereas MRSA prevalence is low in our population. In this cohort, there was no association between SA colonization and SSI incidence but further studies are needed to analyze this association.
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Lee JT, Frank DN, Ramakrishnan V. Microbiome of the paranasal sinuses: Update and literature review. Am J Rhinol Allergy 2016; 30:3-16. [PMID: 26867525 DOI: 10.2500/ajra.2016.30.4255] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Our understanding of the resident microbiome of the paranasal sinuses has changed considerably in recent years. Once presumed to be sterile, healthy sinus cavities are now known to harbor a diverse assemblage of microorganisms, and, it is hypothesized that alterations in the kinds and quantities of these microbes may play a role in the pathogenesis of chronic rhinosinusitis (CRS). OBJECTIVES To review the current literature regarding the sinus microbiome and collate research findings from relevant studies published to date. METHODS A systematic literature review was performed on all molecular studies that investigated the microbial communities of the paranasal sinuses. Methods of detection, microbiome composition, and comparative profiling between patients with and without CRS were explored. RESULTS A complex consortium of microorganisms has been demonstrated in the sinuses of both patients with and without CRS. However, the latter generally have been characterized by reduced biodiversity compared with controls, with selective enrichment of particular microbes (e.g., Staphylococcus aureus). Such disruptions in the resident microbiome may contribute to disease pathogenesis by enhancing the virulence of potential pathogens and adversely modulating immune responses. CONCLUSION The advent of culture-independent molecular approaches has led to a greater appreciation of the intricate microbial ecology of the paranasal sinuses. Microbiota composition, distribution, and abundance impact mucosal health and influence pathogen growth and function. A deeper understanding of the host-microbiome relationship and its constituents may encourage development of new treatment paradigms for CRS, which target restoration of microbiome homeostasis and cultivation of optimal microbial communities.
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Affiliation(s)
- Jivianne T Lee
- Department of Otolaryngology-Head and Neck Surgery, Orange County Sinus Institute, Southern California Permanente Medical Group, Irvine, California, USA
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26
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Kelley SO. New Technologies for Rapid Bacterial Identification and Antibiotic Resistance Profiling. SLAS Technol 2016; 22:113-121. [PMID: 27879409 DOI: 10.1177/2211068216680207] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Conventional approaches to bacterial identification and drug susceptibility testing typically rely on culture-based approaches that take 2 to 7 days to return results. The long turnaround times contribute to the spread of infectious disease, negative patient outcomes, and the misuse of antibiotics that can contribute to antibiotic resistance. To provide new solutions enabling faster bacterial analysis, a variety of approaches are under development that leverage single-cell analysis, microfluidic concentration and detection strategies, and ultrasensitive readout mechanisms. This review discusses recent advances in this area and the potential of new technologies to enable more effective management of infectious disease.
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Affiliation(s)
- Shana O Kelley
- 1 Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.,2 Department of Chemistry, Faculty of Arts and Science, University of Toronto, Toronto, ON, Canada.,3 Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.,4 Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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Abstract
The automation of specimen processing and culture workup has rapidly emerged in clinical microbiology laboratories throughout the world and more recently in the United States. While many U.S. laboratories have implemented some form of automated specimen processing and some have begun performing digital plate reading, automated colony analysis is just beginning to be utilized clinically. In this issue of the Journal of Clinical Microbiology, M. L. Faron et al. (J Clin Microbiol 54:2470-2475, 2016, http://dx.doi.org/10.1128/JCM.01040-16) report the results of their evaluation of the performance of the WASPLab Chromogenic Detection Module (CDM) for categorizing chromogenic agar plates as negative or "nonnegative" for vancomycin-resistant enterococci (VRE). Their major finding was 100% sensitivity for detection of "nonnegative" specimens using CDM compared to manual methods for specimens plated on two different types of VRE chromogenic agar plates. Additionally, utilization of digital plate reading in conjunction with automated colony analysis was predicted to result in significant savings based on greatly reduced labor costs.
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Liu Y, Zhang J, Ji Y. PCR-based Approaches for the Detection of Clinical Methicillin-resistant Staphylococcus aureus. Open Microbiol J 2016; 10:45-56. [PMID: 27335617 PMCID: PMC4899539 DOI: 10.2174/1874285801610010045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 11/22/2022] Open
Abstract
Staphylococcus aureus is an important pathogen that can cause a variety of infections, including superficial and systematic infections, in humans and animals. The persistent emergence of multidrug resistant S. aureus, particularly methicillin-resistant S. aureus, has caused dramatically economic burden and concerns in the public health due to limited options of treatment of MRSA infections. In order to make a correct choice of treatment for physicians and understand the prevalence of MRSA, it is extremely critical to precisely and timely diagnose the pathogen that induces a specific infection of patients and to reveal the antibiotic resistant profile of the pathogen. In this review, we outlined different PCR-based approaches that have been successfully utilized for the rapid detection of S. aureus, including MRSA and MSSA, directly from various clinical specimens. The sensitivity and specificity of detections were pointed out. Both advantages and disadvantages of listed approaches were discussed. Importantly, an alternative approach is necessary to further confirm the detection results from the molecular diagnostic assays.
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Affiliation(s)
- Ying Liu
- Shanghai Vocational College of Agriculture and Forestry, Shanghai, China; Department of Veterinary Biomedical Science, College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
| | - Jiang Zhang
- Shanghai Vocational College of Agriculture and Forestry, Shanghai, China
| | - Yinduo Ji
- Department of Veterinary Biomedical Science, College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
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Edmiston CE, Ledeboer NA, Buchan BW, Spencer M, Seabrook GR, Leaper D. Is Staphylococcal Screening and Suppression an Effective Interventional Strategy for Reduction of Surgical Site Infection? Surg Infect (Larchmt) 2016; 17:158-66. [DOI: 10.1089/sur.2015.257] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Charles E. Edmiston
- Departments of Surgery (Vascular), Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Nathan A. Ledeboer
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Blake W. Buchan
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Gary R. Seabrook
- Departments of Surgery (Vascular), Medical College of Wisconsin, Milwaukee, Wisconsin
| | - David Leaper
- Infection Prevention Consultants, Boston, Massachusetts
- Institute of Skin Integrity and Infection Prevention, University of Huddersfield, Huddersfield, United Kingdom
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Hernandez DR, Newton DW, Ledeboer NA, Buchan B, Young C, Clark AE, Connoly J, Wolk DM. Multicenter Evaluation of MRSASelect II Chromogenic Agar for Identification of Methicillin-Resistant Staphylococcus aureus from Wound and Nasal Specimens. J Clin Microbiol 2016; 54:305-11. [PMID: 26582836 PMCID: PMC4733205 DOI: 10.1128/jcm.02410-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/12/2015] [Indexed: 12/15/2022] Open
Abstract
Hospitals strive to reduce methicillin-resistant Staphylococcus aureus (MRSA) prevalence via active surveillance of inpatient populations. Rapid and inexpensive screening methods are utilized when molecular methods are not operationally feasible. In this multisite clinical trial, the utility of Bio-Rad's MRSASelect II was evaluated for MRSA identification from remnant nares and wound swabs. The prevalence of MRSA was 11.1% (n = 1,384) from nares samples and 18.1% (n = 842) from wound samples. MRSASelect II had an overall concordance of 95.4% (confidence interval [CI] = 94.5% to 96.2%) compared to a broth-enriched reference standard. Comparisons between results, stratified by examination times, exhibited a nonsignificant trend toward increased positivity at prolonged incubation times. Cefoxitin screening of colonies directly from MRSASelect II was 96.7% (95.8% to 97.3%) concordant compared to testing of colonies following broth enrichment. A comparison of MRSASelect and MRSASelect II revealed no statistical differences; however, the latter exhibited earlier positivity, greater selectivity, and more intense indicator staining, which resulted in facilitated differentiation of positive results. MRSASelect II agar is a simple, rapid, and robust method to routinely screen patients for MRSA colonization without the need for additional testing.
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Affiliation(s)
| | - Duane W Newton
- University of Michigan Health System, Ann Arbor, Michigan, USA
| | | | - Blake Buchan
- Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Carol Young
- University of Michigan Health System, Ann Arbor, Michigan, USA
| | | | | | - Donna M Wolk
- Geisinger Health System, Danville, Pennsylvania, USA
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Bacterial Infections. MOLECULAR PATHOLOGY IN CLINICAL PRACTICE 2016. [PMCID: PMC7123846 DOI: 10.1007/978-3-319-19674-9_49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular techniques have revolutionized the detection and identification of microorganisms. Real-time PCR has allowed for the rapid and accurate detection of MRSA, VRE, and group B Streptococcus. The identification of difficult and slow-growing organisms has been expedited by sequence-based methods such as 16S rRNA gene sequencing. Rapid identification of organisms and detection of resistance markers directly from positive blood culture bottles has become a reality. Finally, a transformation is taking place with the introduction of MALDI-TOF into clinical laboratories that promises to improve the accuracy and speed of bacterial and fungal identifications by days. The advantages of these methodologies and their associated clinical applications, along with their inherent pitfalls and problems, are elucidated in this chapter.
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Weiser MC, Moucha CS. The Current State of Screening and Decolonization for the Prevention of Staphylococcus aureus Surgical Site Infection After Total Hip and Knee Arthroplasty. J Bone Joint Surg Am 2015; 97:1449-58. [PMID: 26333741 PMCID: PMC7535098 DOI: 10.2106/jbjs.n.01114] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The most common pathogens in surgical site infections after total hip and knee arthroplasty are methicillin-sensitive Staphylococcus aureus (MSSA), methicillin-resistant S. aureus (MRSA), and coagulase-negative staphylococci. Patients colonized with MSSA or MRSA have an increased risk for a staphylococcal infection at the site of a total hip or knee arthroplasty. Most colonized individuals who develop a staphylococcal infection at the site of a total hip or total knee arthroplasty have molecularly identical S. aureus isolates in their nares and wounds. Screening and nasal decolonization of S. aureus can potentially reduce the rates of staphylococcal surgical site infection after total hip and total knee arthroplasty.
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Affiliation(s)
- Mitchell C. Weiser
- Department of Orthopaedics, Icahn School of Medicine at Mount Sinai, 5 East 98th Street, 9th Floor, Box 1188, New York, NY 10029. E-mail address for M.C. Weiser: . E-mail address for C.S. Moucha:
| | - Calin S. Moucha
- Department of Orthopaedics, Icahn School of Medicine at Mount Sinai, 5 East 98th Street, 9th Floor, Box 1188, New York, NY 10029. E-mail address for M.C. Weiser: . E-mail address for C.S. Moucha:
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Evaluation of BD Max StaphSR and BD Max MRSAXT Assays Using ESwab-Collected Specimens. J Clin Microbiol 2015; 53:2525-9. [PMID: 26019193 DOI: 10.1128/jcm.00970-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/20/2015] [Indexed: 12/13/2022] Open
Abstract
The BD Max MRSAXT and the BD Max StaphSR assays were validated for the detection of methicillin-resistant Staphylococcus aureus (MRSA) in ESwab samples. In addition, the BD Max StaphSR assay was evaluated for its ability to detect and differentiate S. aureus and MRSA in the same sample. A total of 255 ESwab samples collected from the anterior nares of patients were tested by each of three BD Max assays, including the BD Max MRSA first-generation assay. The results were compared to those of direct and enrichment culture. Additionally, a challenge panel comprising 14 control strains was evaluated to determine the ability of these assays to correctly identify MRSA and also appropriately differentiate S. aureus by the BD Max StaphSR assay. Out of 255 clinical samples tested, 161 were negative and 30 were positive for MRSA, and 45 were positive for S. aureus (by BD Max StaphSR) and negative for MRSA by all three PCR assays and culture. Nineteen samples had discrepant results; all of them were retested by additional laboratory testing. All strains from the challenge panel were correctly identified or excluded by the BD Max MRSAXT and BD Max StaphSR assays. The results showed that the BD Max StaphSR and the BD MRSAXT assays have excellent sensitivity (94.3%) and specificity (97.7%) for detecting MRSA. The BD Max StaphSR assay demonstrated excellent sensitivity (96.4%) and specificity (93.6%) for detecting S. aureus.
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Patel PA, Robicsek A, Grayes A, Schora DM, Peterson KE, Wright MO, Peterson LR. Evaluation of multiple real-time PCR tests on nasal samples in a large MRSA surveillance program. Am J Clin Pathol 2015; 143:652-8. [PMID: 25873498 DOI: 10.1309/ajcpmdy32ztdxpfc] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES We evaluated the LightCycler MRSA Advanced Test (Roche Molecular Diagnostics, Pleasanton, CA), the BD MAX MRSA assay (Becton Dickinson, Franklin Lakes, NJ), and the Xpert MRSA assay (Cepheid, Sunnyvale, CA) on nasal samples using the same population. METHODS Admission and discharge nasal swabs were collected from inpatients using a double-headed swab. One swab was plated onto CHROMagar MRSA (CMA; Becton Dickinson, Sparks, MD) and then broken off into tryptic soy broth (TSB) for enrichment. TSB was incubated for 24 hours and then plated to CMA. The molecular tests were performed on the second swab. We analyzed the cost benefit of testing to evaluate what parameters affect hospital resources. RESULTS A total of 27,647 specimens were enrolled. The sensitivity/specificity was 98.3%/98.9% for the LightCycler MRSA Advanced Test and 95.7%/98.8% for the Xpert MRSA assay, but the difference was not significant. The positive predictive value was 86.7% for the LightCycler MRSA Advanced Test, 82.7% for the Xpert MRSA assay (P > .1), and 72.2% and for the BD MAX MRSA test (P < .001 compared with the LightCycler MRSA Advanced Test). All three assays were cost-effective, with the LightCycler MRSA Advanced Test having the highest economic return. CONCLUSIONS Our results suggest that the performance of the three commercial assays is similar. When assessing economic cost benefit of methicillin-resistant Staphylococcus aureus screening, the two measures with the most impact are the cost of the test and the specificity of the assay results.
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Affiliation(s)
| | - Ari Robicsek
- NorthShore University HealthSystem, Evanston, IL
- NorthShore University of Chicago Pritzker School of Medicine, Chicago, IL
| | | | | | | | | | - Lance R. Peterson
- NorthShore University HealthSystem, Evanston, IL
- NorthShore University of Chicago Pritzker School of Medicine, Chicago, IL
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Huang ZG, Zheng XZ, Guan J, Xiao SN, Zhuo C. Direct detection of methicillin-resistant Staphylococcus aureus in sputum specimens from patients with hospital-associated pneumonia using a novel multilocus PCR assay. Pathogens 2015; 4:199-209. [PMID: 25942570 PMCID: PMC4493470 DOI: 10.3390/pathogens4020199] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/23/2015] [Accepted: 04/28/2015] [Indexed: 01/27/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a significant cause of hospital-associated pneumonia (HAP). The rapid identification of MRSA would be beneficial for early diagnosis. The study aimed to evaluate a multilocus, fluorescence-based PCR assay based on the detection of mecA and nuc genes for identification of S. aureusin lower respiratory tract (LRT) specimens. Sensitivity and specificity of the PCR assay were analyzed. Clinical evaluation for the assay was performed using LRT specimens from patients with HAP, and the sensitivity, specificity, positive and negative predictive values (PPV and NPV) were evaluated in comparison with semi-quantitative culture methods. The result showed the assay provided positive identification of all MRSA reference strains with a limit of detection for MRSA of 4 × 103 CFU/mL. Compared with semi-quantitative culture, the sensitivity, specificity, PPV and NPV were 100%, 89.6%, 75.0%, and 100%, respectively. A positive correlation between MRSA bacterial colonies and PCR copy number was found. The specificity and PPV reached 96.6% and 89.7% respectively, if the PCR copy number reached a definite positive threshold of 5.96 × 105. It suggested that this novel multilocus, fluorescence-based PCR assay proved to be a fast, sensitive and specific tool for direct detection of MRSA from LRT specimens.
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Affiliation(s)
- Zeng-Guang Huang
- State Key Laboratory of Respiratory Diseases, the first affiliated hospital of Guangzhou Medical University, Guangzhou, 510120, China.
| | - Xing-Zheng Zheng
- Peking University Health Science Center, Beijing, 100191, China.
| | - Jing Guan
- State Key Laboratory of Respiratory Diseases, the first affiliated hospital of Guangzhou Medical University, Guangzhou, 510120, China.
| | - Shu-Nian Xiao
- State Key Laboratory of Respiratory Diseases, the first affiliated hospital of Guangzhou Medical University, Guangzhou, 510120, China.
| | - Chao Zhuo
- State Key Laboratory of Respiratory Diseases, the first affiliated hospital of Guangzhou Medical University, Guangzhou, 510120, China.
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Identification of methicillin-susceptible or methicillin-resistant Staphylococcus aureus carrier status preoperatively using polymerase chain reaction in patients undergoing elective surgery with hardware implantation. Infect Control Hosp Epidemiol 2015; 36:738-41. [PMID: 25732409 DOI: 10.1017/ice.2015.34] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We compared bedside polymerase chain reaction to culture for identifying Staphylococcus aureus in patients about to undergo surgery with hardware implantation. Patients were screened for S. aureus carrier status at the preoperative clinic and on the day of surgery. The sensitivity, specificity, positive and negative predictive values, and accuracy were calculated.
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Creamer E, Dolan A, Sherlock O, Thomas T, Walsh J, Moore J, Smyth E, O'Neill E, Shore A, Sullivan D, Rossney AS, Cunney R, Coleman D, Humphreys H. The Effect of Rapid Screening for Methicillin-ResistantStaphylococcus aureus(MRSA) on the Identification and Earlier Isolation of MRSA-Positive Patients. Infect Control Hosp Epidemiol 2015; 31:374-81. [DOI: 10.1086/651093] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Objectives.(1) To determine whether rapid screening with polymerase chain reaction (PCR) assays leads to the earlier isolation of patients at risk for methicillin-resistantStaphylococcus aureus(MRSA) colonization, (2) to assess compliance with routine MRSA screening protocols, (3) to confirm the diagnostic accuracy of the Xpert MRSA real-time PCR assay (Cepheid) by comparison with culture, and (4) to compare turnaround times for PCR assay results with those for culture results.Design.Before-and-after study conducted in a 700-bed acute tertiary care referral hospital. Study periods were (1) a 5-week period before PCR testing began, (2) a 10-week period when the PCR assay was used, and (3) a 5-week period after PCR testing was discontinued.Results.Among 489 at-risk patients, MRSA was isolated from 20 (33%) of 60 patients during period 1, 77 (22%) of 349 patients during period 2, and 18 (23%) of 80 patients during period 3. Twenty-two (27%) of 82 at-risk patients were not screened during period 1, compared with 40 (10%) of 389 at-risk patients not screened during period 2 (P< .001). More MRSA-positive patients were preemptively isolated during periods 1 and 3 compared with period 2 (34 [24%] of 140 vs 28 [8%] of 389;P< .001); however, more MRSA-positive patients were isolated after notification of MRSA-positive results during period 2 (47 [13%] of 349) compared with periods 1 and 3 (2 [1%] of 140;P< .001). The sensitivity, specificity, positive predictive value, and negative predictive value of the PCR assay were 95%, 97%, 82%, and 99%, respectively. The mean turnaround time from receipt of specimens in the laboratory to PCR assay result was 2.6 hours.Conclusions.Rapid screening with the Xpert MRSA PCR assay facilitated compliance with screening policies and the earlier isolation of MRSA-positive Patients. Discrepant results confirm that PCR testing should be used as a screening tool rather than as a diagnostic tool.
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Chan WS, Chan TM, Lai TW, Chan JFW, Lai RWM, Lai CKC, Tang BSF. Complementary use of MALDI-TOF MS and real-time PCR-melt curve analysis for rapid identification of methicillin-resistant staphylococci and VRE. J Antimicrob Chemother 2014; 70:441-7. [PMID: 25336164 DOI: 10.1093/jac/dku411] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To develop a rapid method for routine screening of methicillin-resistant staphylococci and VRE for clinical isolates and positive blood cultures. METHODS Our method consisted of two parts: MALDI-TOF MS was used for identification of staphylococci and enterococci, followed by antibiotic resistance detection by real-time PCR-melt curve analysis without DNA extraction. The latter part included a triplex reaction for staphylococcal culture isolates (mecA, mecALGA251 and Panton-Valentine leucocidin genes), dual PCR of mecA/mecALGA251 and nuc genes for staphylococcal blood cultures, and a duplex reaction for enterococci (vanA and vanB genes). A total of 124 clinical isolates and 56 positive blood cultures were tested. MALDI-TOF MS was performed using Microflex LT (Bruker Daltonik, Bremen, Germany) and Rotor-Gene Q (Qiagen, Hilden, Germany) was used for real-time PCR-melt curve analysis. The total assay time was <2.5 h. RESULTS The results revealed 100% concordance with antibiotic susceptibility testing or other reference methods for all culture isolates and enterococcal blood cultures. The percentage of concordance for staphylococcal blood cultures was 97.5%. CONCLUSIONS The method described herein was fast, economical, reliable and capable of detecting mecALGA251, vanB1 and vanB2 genotypes, which are not included in most commercial assays. Large-scale screening is required to further test the performance of this protocol, especially for genotypes that are infrequently encountered.
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Affiliation(s)
- Wai-Sing Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Tsz-Ming Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Tsz-Wan Lai
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | | | | | - Bone Siu-Fai Tang
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
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Eigner U, Veldenzer A, Holfelder M. Validation of the FluoroType® MRSA assay for the rapid identification of methicillin-resistant Staphylococcus aureus directly from patient material. J Microbiol Methods 2014; 107:71-3. [PMID: 25193437 DOI: 10.1016/j.mimet.2014.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/15/2014] [Accepted: 08/16/2014] [Indexed: 11/18/2022]
Abstract
We performed the first evaluation study of the new HyBeacon based FluoroType(®) MRSA assay for the detection of MRSA directly from 617 patient specimens. Using culture as the reference method sensitivity and specificity were higher than 95%. Results were available within 2.5h, including DNA extraction.
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Recombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus. PLoS One 2014; 9:e101419. [PMID: 24972080 PMCID: PMC4074205 DOI: 10.1371/journal.pone.0101419] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 06/06/2014] [Indexed: 01/31/2023] Open
Abstract
Clinical laboratories are increasingly using molecular tests for methicillin-resistant Staphylococcus aureus (MRSA) screening. However, primers have to be targeted to a variable chromosomal region, the staphylococcal cassette chromosome mec (SCCmec). We initially screened 726 MRSA isolates from a single UK hospital trust by recombinase polymerase amplification (RPA), a novel, isothermal alternative to PCR. Undetected isolates were further characterised using multilocus sequence, spa typing and whole genome sequencing. 96% of our tested phenotypically MRSA isolates contained one of the six orfX-SCCmec junctions our RPA test and commercially available molecular tests target. However 30 isolates could not be detected. Sequencing of 24 of these isolates demonstrated recombinations within the SCCmec element with novel insertions that interfered with the RPA, preventing identification as MRSA. This result suggests that clinical laboratories cannot rely solely upon molecular assays to reliably detect all methicillin-resistance. The presence of significant recombinations in the SCCmec element, where the majority of assays target their primers, suggests that there will continue to be isolates that escape identification. We caution that dependence on amplification-based molecular assays will continue to result in failure to diagnose a small proportion (∼4%) of MRSA isolates, unless the true level of SCCmec natural diversity is determined by whole genome sequencing of a large collection of MRSA isolates.
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Use of Xpert® MRSA PCR point-of-care testing beyond the laboratory. J Hosp Infect 2014; 87:119-21. [DOI: 10.1016/j.jhin.2014.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 04/03/2014] [Indexed: 11/21/2022]
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43
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May L, McCann C, Brooks G, Rothman R, Miller L, Jordan J. Dual-site sampling improved detection rates for MRSA colonization in patients with cutaneous abscesses. Diagn Microbiol Infect Dis 2014; 80:79-82. [PMID: 24958641 DOI: 10.1016/j.diagmicrobio.2014.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/29/2014] [Accepted: 05/03/2014] [Indexed: 10/25/2022]
Abstract
Extranasal sites are common reservoirs of Staphylococcus aureus colonization and may be relevant for methicillin-resistant S. aureus (MRSA) screening and infection control strategies. The objective here was to determine whether inguinal specimens could also be screened using Xpert SA Nasal Complete assay for MRSA. Results were compared to broth enrichment culture. Among 162 consented adults seeking care in the emergency department for cutaneous abscesses, inguinal specimens were found positive for MRSA more often than nares specimens, 24% and 26% by PCR or culture, respectively, compared to 19% each by PCR or culture. Overall, 6% of adults colonized with MRSA would have been missed by nares screening alone. Compared to culture, Xpert SA Nasal Complete assay demonstrated sensitivity and specificity of 89% and 97%, respectively, for detecting nares and/or inguinal MRSA colonization. In conclusion, inguinal specimens were a more common reservoir for MRSA than nares specimens in this population of patients.
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Affiliation(s)
- L May
- Department of Emergency Medicine, The George Washington University Medical Faculty Associates, Washington, DC; Department of Epidemiology and Biostatistics, School of Public Health and Health Services, The George Washington University, Washington, DC.
| | - C McCann
- Department of Epidemiology and Biostatistics, School of Public Health and Health Services, The George Washington University, Washington, DC
| | - G Brooks
- Department of Emergency Medicine, The George Washington University Medical Faculty Associates, Washington, DC; Department of Epidemiology and Biostatistics, School of Public Health and Health Services, The George Washington University, Washington, DC
| | - R Rothman
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD
| | - L Miller
- Infectious Disease Clinical Outcomes Research Unit, Division of Infectious Disease, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA
| | - J Jordan
- Department of Epidemiology and Biostatistics, School of Public Health and Health Services, The George Washington University, Washington, DC
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Abstract
A comparison between the BD MAX MRSA and Xpert MRSA assays was performed using 239 nares samples. A 97.9% overall agreement between the two molecular assays was observed. The BD MAX MRSA assay proved to be a reliable alternative for a highly automated system to detect methicillin-resistant Staphylococcus aureus (MRSA) in patient nares samples.
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45
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Comparison of ESwab with traditional swabs for detection of methicillin-resistant Staphylococcus aureus using two different walk-away commercial real-time PCR methods. J Clin Microbiol 2014; 52:2641-3. [PMID: 24759722 DOI: 10.1128/jcm.00315-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The ESwab system (Copan Diagnostics) was evaluated as a nasopharyngeal specimen collection device to be used for methicillin-resistant Staphylococcus aureus (MRSA) detection by the GeneXpert and BD Max MRSA assays. Different MRSA strains and dilutions of each strain were tested in triplicate. ESwabs proved to be a suitable collection system for the two assays tested.
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46
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Saeidi S, Ravan H, Sanadgol N, Khaleghi M, Bazi S, Shojaei P. Methicillin-resistance Staphylococcus aureus in Southeast Iran: Herbal
Control and Detection Methods Comparison. JOURNAL OF MEDICAL SCIENCES 2014. [DOI: 10.3923/jms.2014.123.129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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47
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Chan WS, Tang BS, Boost MV, Chow C, Leung PH. Detection of methicillin-resistant Staphylococcus aureus using a gold nanoparticle-based colourimetric polymerase chain reaction assay. Biosens Bioelectron 2014; 53:105-11. [DOI: 10.1016/j.bios.2013.09.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/12/2013] [Accepted: 09/14/2013] [Indexed: 01/27/2023]
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48
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Concordance of PCR and culture from nasal swabs for detection of methicillin-resistant Staphylococcus aureus in a setting of concurrent antistaphylococcal antibiotics. J Clin Microbiol 2014; 52:1235-7. [PMID: 24452168 DOI: 10.1128/jcm.02972-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effect of concurrent administration of antibiotics on the detection of methicillin-resistant Staphylococcus aureus (MRSA) remains unresolved. Here, we assessed the concordance of paired nasal swabs processed using commercial PCR and culture and found high concordance in both the absence and presence of antibiotics with activity against MRSA (93.7% [95% confidence interval [CI], 88.1%, 96.8%] and 90.9% [95% CI, 84.8%, 94.7%], respectively), although PCR was more likely to be positive in the presence of antibiotics. (This study has been registered at ClinicalTrials.gov under registration no. NCT01234831.).
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Abstract
Antimicrobial susceptibility test methods such as disk diffusion, broth microdilution, and oxacillin screen plate require 24 h of incubation after having the organism growing in pure culture. Rapid and accurate identification of MRSA isolates is essential not only for patient care, but also for effective infection control programs to limit the spread of MRSA. In the last few years, several commercial rapid tests for detection of MRSA directly from nasal swabs and blood cultures have been developed for use in clinical laboratories. Real-time PCR and other molecular tests are gaining popularity as MRSA screening tests to identify patients who are candidates for contact precaution at the time of admission decreasing the risk for nosocomial transmission. These new methodologies have the advantage of a lower turnaround time than that of traditional culture and susceptibility testing and they are capable of detecting MRSA directly from nasal or wound swabs allowing rapid identification of colonized or infected patients. In addition, molecular methods able to detect and differentiate S. aureus and MRSA (SA/MRSA) directly from blood cultures are becoming a useful tool for rapid detection of bacteremia caused by MSSA and MRSA. This review focuses on the procedures for performing testing using rapid methods currently available for detection of MRSA directly from clinical specimens.
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Valour F, Blanc-Pattin V, Freydière AM, Bouaziz A, Chanard E, Lustig S, Ferry T, Laurent F. Rapid detection of Staphylococcus aureus and methicillin resistance in bone and joint infection samples: evaluation of the GeneXpert MRSA/SA SSTI assay. Diagn Microbiol Infect Dis 2013; 78:313-5. [PMID: 24374309 DOI: 10.1016/j.diagmicrobio.2013.11.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 11/23/2013] [Accepted: 11/24/2013] [Indexed: 11/16/2022]
Abstract
The GeneXpert MRSA/SA SSTI assay was compared to conventional cultures to detect Staphylococcus aureus and methicillin-resistance from 91 bone and joint infection samples. Sensitivity and specificity were 94.4% and 100%. Three false-positive results were observed, in fact providing from patients known to be infected by S. aureus on the basis of other concomitant osteoarticular samples, which suggests that PCR was more sensitive than culture. This diagnosis accuracy may help shorten toxic and non-optimal empirical therapies such as glycopeptides in case of methicillin-susceptible strains.
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Affiliation(s)
- Florent Valour
- International Center for Research in Infectiology, INSERM U1111, Lyon, France; Laboratory of bacteriology, North Lyon University Hospital, Hospices Civils de Lyon, Lyon, France; Department of infectious diseases, North Lyon University Hospital, Hospices Civils de Lyon, Lyon, France; Lyon I Claude Bernard University, Lyon, France.
| | - Viviane Blanc-Pattin
- Laboratory of bacteriology, North Lyon University Hospital, Hospices Civils de Lyon, Lyon, France
| | - Anne-Marie Freydière
- Laboratory of bacteriology, East Lyon University Hospital, Hospices Civils de Lyon, Lyon, France
| | - Anissa Bouaziz
- Department of infectious diseases, North Lyon University Hospital, Hospices Civils de Lyon, Lyon, France
| | | | - Sébastien Lustig
- Lyon I Claude Bernard University, Lyon, France; Orthopedic surgery department, North Lyon University Hospital, Hospices Civils de Lyon, Lyon, France
| | - Tristan Ferry
- International Center for Research in Infectiology, INSERM U1111, Lyon, France; Department of infectious diseases, North Lyon University Hospital, Hospices Civils de Lyon, Lyon, France; Lyon I Claude Bernard University, Lyon, France
| | - Frédéric Laurent
- International Center for Research in Infectiology, INSERM U1111, Lyon, France; Laboratory of bacteriology, North Lyon University Hospital, Hospices Civils de Lyon, Lyon, France; Lyon I Claude Bernard University, Lyon, France; French National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
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