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Karunakaran S, Pless LL, Ayres AM, Ciccone C, Penzelik J, Sundermann AJ, Martin EM, Griffith MP, Waggle K, Hodges JC, Harrison LH, Snyder GM. Impact of discontinuation of contact precautions on surveillance- and whole genome sequencing-defined methicillin-resistant Staphylococcus aureus healthcare-associated infections. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2024; 4:e97. [PMID: 38836046 PMCID: PMC11149034 DOI: 10.1017/ash.2024.89] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 06/06/2024]
Abstract
Objective Prior studies evaluating the impact of discontinuation of contact precautions (DcCP) on methicillin-resistant Staphylococcus aureus (MRSA) outcomes have characterized all healthcare-associated infections (HAIs) rather than those likely preventable by contact precautions. We aimed to analyze the impact of DcCP on the rate of MRSA HAI including transmission events identified through whole genome sequencing (WGS) surveillance. Design Quasi experimental interrupted time series. Setting Acute care medical center. Participants Inpatients. Methods The effect of DcCP (use of gowns and gloves) for encounters among patients with MRSA carriage was evaluated using time series analysis of MRSA HAI rates from January 2019 through December 2022, compared to WGS-defined attributable transmission events before and after DcCP in December 2020. Results The MRSA HAI rate was 4.22/10,000 patient days before and 2.98/10,000 patient days after DcCP (incidence rate ratio [IRR] 0.71 [95% confidence interval 0.56-0.89]) with a significant immediate decrease (P = .001). There were 7 WGS-defined attributable transmission events before and 11 events after DcCP (incident rate ratio 0.90 [95% confidence interval 0.30-2.55]). Conclusions DcCP did not result in an increase in MRSA HAI or, in WGS-defined attributable transmission events. Comprehensive analyses of the effect of transmission prevention measures should include outcomes specifically measuring transmission-associated HAI.
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Affiliation(s)
- Sharon Karunakaran
- Division of Pediatric Infectious Diseases, Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Lora Lee Pless
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ashley M. Ayres
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Carl Ciccone
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Joseph Penzelik
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Alexander J. Sundermann
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Elise M. Martin
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Veterans’ Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kady Waggle
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Lee H. Harrison
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Graham M. Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
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Wang Z, Pang Y, Chung CR, Wang HY, Cui H, Chiang YC, Horng JT, Lu JJ, Lee TY. A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology. Brief Bioinform 2023; 24:bbad330. [PMID: 37742050 DOI: 10.1093/bib/bbad330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/19/2023] [Accepted: 08/31/2023] [Indexed: 09/25/2023] Open
Abstract
The emergence of multidrug-resistant bacteria is a critical global crisis that poses a serious threat to public health, particularly with the rise of multidrug-resistant Staphylococcus aureus. Accurate assessment of drug resistance is essential for appropriate treatment and prevention of transmission of these deadly pathogens. Early detection of drug resistance in patients is critical for providing timely treatment and reducing the spread of multidrug-resistant bacteria. This study aims to develop a novel risk assessment framework for S. aureus that can accurately determine the resistance to multiple antibiotics. The comprehensive 7-year study involved ˃20 000 isolates with susceptibility testing profiles of six antibiotics. By incorporating mass spectrometry and machine learning, the study was able to predict the susceptibility to four different antibiotics with high accuracy. To validate the accuracy of our models, we externally tested on an independent cohort and achieved impressive results with an area under the receiver operating characteristic curve of 0. 94, 0.90, 0.86 and 0.91, and an area under the precision-recall curve of 0.93, 0.87, 0.87 and 0.81, respectively, for oxacillin, clindamycin, erythromycin and trimethoprim-sulfamethoxazole. In addition, the framework evaluated the level of multidrug resistance of the isolates by using the predicted drug resistance probabilities, interpreting them in the context of a multidrug resistance risk score and analyzing the performance contribution of different sample groups. The results of this study provide an efficient method for early antibiotic decision-making and a better understanding of the multidrug resistance risk of S. aureus.
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Affiliation(s)
- Zhuo Wang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong 518172, China
| | - Yuxuan Pang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong 518172, China
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong 518172, China
| | - Chia-Ru Chung
- Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan 333423, Taiwan
| | - Haiyan Cui
- Department of Clinical Laboratory, Longgang District People's Hospital of Shenzhen & The Second Affiliated Hospital of the Chinese University of Hong Kong, Shenzhen, China
| | - Ying-Chih Chiang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong, 518172, China
| | - Jorng-Tzong Horng
- Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan 333423, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan 33303, Taiwan
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 33303, Taiwan
| | - Tzong-Yi Lee
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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3
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Elbehiry A, Marzouk E, Moussa I, Anagreyyah S, AlGhamdi A, Alqarni A, Aljohani A, Hemeg HA, Almuzaini AM, Alzaben F, Abalkhail A, Alsubki RA, Najdi A, Algohani N, Abead B, Gazzaz B, Abu-Okail A. Using Protein Fingerprinting for Identifying and Discriminating Methicillin Resistant Staphylococcus aureus Isolates from Inpatient and Outpatient Clinics. Diagnostics (Basel) 2023; 13:2825. [PMID: 37685363 PMCID: PMC10486511 DOI: 10.3390/diagnostics13172825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
In hospitals and other clinical settings, Methicillin-resistant Staphylococcus aureus (MRSA) is a particularly dangerous pathogen that can cause serious or even fatal infections. Thus, the detection and differentiation of MRSA has become an urgent matter in order to provide appropriate treatment and timely intervention in infection control. To ensure this, laboratories must have access to the most up-to-date testing methods and technology available. This study was conducted to determine whether protein fingerprinting technology could be used to identify and distinguish MRSA recovered from both inpatients and outpatients. A total of 326 S. aureus isolates were obtained from 2800 in- and outpatient samples collected from King Faisal Specialist Hospital and Research Centre in Riyadh, Saudi Arabia, from October 2018 to March 2021. For the phenotypic identification of 326 probable S. aureus cultures, microscopic analysis, Gram staining, a tube coagulase test, a Staph ID 32 API system, and a Vitek 2 Compact system were used. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), referred to as protein fingerprinting, was performed on each bacterial isolate to determine its proteomic composition. As part of the analysis, Principal Component Analysis (PCA) and a single-peak analysis of MALDI-TOF MS software were also used to distinguish between Methicillin-sensitive Staphylococcus aureus (MSSA) and MRSA. According to the results, S. aureus isolates constituted 326 out of 2800 (11.64%) based on the culture technique. The Staph ID 32 API system and Vitek 2 Compact System were able to correctly identify 262 (80.7%) and 281 (86.2%) S. aureus strains, respectively. Based on the Oxacillin Disc Diffusion Method, 197 (62.23%) of 326 isolates of S. aureus exhibited a cefoxitin inhibition zone of less than 21 mm and an oxacillin inhibition zone of less than 10 mm, and were classified as MRSA under Clinical Laboratory Standards Institute guidelines. MALDI-TOF MS was able to correctly identify 100% of all S. aureus isolates with a score value equal to or greater than 2.00. In addition, a close relationship was found between S. aureus isolates and higher peak intensities in the mass ranges of 3990 Da, 4120 Da, and 5850 Da, which were found in MRSA isolates but absent in MSSA isolates. Therefore, protein fingerprinting has the potential to be used in clinical settings to rapidly detect and differentiate MRSA isolates, allowing for more targeted treatments and improved patient outcomes.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
| | - Eman Marzouk
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sulaiman Anagreyyah
- Family Medicine Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Abdulaziz AlGhamdi
- Medical Director Office, North Area Armed Forces Hospital, King Khalid Military City 39747, Saudi Arabia
| | - Ali Alqarni
- Respiratory Therapy Department, Armed Forces Hospital Dhahran, Dhahran 34641, Saudi Arabia
| | - Ahmed Aljohani
- Patient Affairs Department, Sharourah Armed Forces Hospital, Sharourah 68372, Saudi Arabia
| | - Hassan A. Hemeg
- Department of Medical Technology/Microbiology, College of Applied Medical Science, Taibah University, Madina 30001, Saudi Arabia
| | - Abdulaziz M. Almuzaini
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Feras Alzaben
- Department of Food Service, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Roua A. Alsubki
- Department of Clinical Laboratory Science, College of Applied Medical Science, King Saud University, Riyadh 11433, Saudi Arabia
| | - Ali Najdi
- Northern Area Armed Forces Hospital, King Khalid Military City 39748, Saudi Arabia
| | - Nawaf Algohani
- Consultant Forensic Medicine, Forensic Medicine Center, Madina 42319, Saudi Arabia
| | - Banan Abead
- Support Service Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia;
| | - Bassam Gazzaz
- Patient Affairs Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Akram Abu-Okail
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
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Sonowal D, Ghatak S, Barua AG, Kandhan S, Hazarika RA, Sen A, Das S, Sonowal S, Sharma RK, Tamuly S, Phukan C, Sharma A, Hussain P. Livestock, pets and humans as carriers of methicillin-resistant Staphylococcusaureus and comparative evaluation of two PCR protocols for detection. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2023; 14:351-358. [PMID: 37564356 PMCID: PMC10410111 DOI: 10.30466/vrf.2023.1971891.3672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/19/2023] [Indexed: 08/12/2023]
Abstract
Staphylococcus aureus are Gram positive bacteria known to acquire antibiotic resistance rapidly and pose a major challenge to clinicians worldwide. Infections by methicillin resistant Staphylococcus aureus (MRSA) are usually associated with increased mortality and prolonging of treatment. Samples (n = 706) from diverse sources (livestock, pets, animal handlers, human hospital) were collected and screened for the presence of MRSA by phenotypic and genotypic methods. The incidence of Staphylococcus aureus was greater in goats (42.00%; 28.20 - 56.80%, confidence interval [CI] 95.00%) followed by cattle (13.50%; 9.20 - 18.80%, CI 95.00%), humans (12.90%; 9.30 - 17.40%, CI 95.00%) and dogs (12.90%; 8.10 - 19.20%, CI 95.00%). Significantly higher incidence of MRSA was observed in dogs (65.00%; 40.80 - 84.60%, CI 95.00%), compared to other hosts namely cattle (48.00%; 26.50 - 64.30%, CI 95.00%), humans (35.00%; 20.20 - 52.50%, CI 95.00%) and goats (10.00%; 1.20 - 30.40%, CI 95.00%). All the S. aureus isolates were further screened for thermostable nuclease (nuc gene) by polymerase chain reaction (PCR). The incidence of nuc gene in cattle, dog, goat and human were found to be 3.30% (1.30 - 6.60%, CI 95.00%), 5.20% (2.30 - 9.90%, CI 95.00%), 28.00% (16.20 - 42.50%, CI 95.00%) and 9.10% (6.00 - 13.00%, CI 95.00%), respectively. Comparative evaluation of two PCR primers (mecA-162 and mecA-310) indicated the former one as more rational choice for detection of MRSA. Overall, the results of our study indicated possible risk of zoonotic transmission of MRSA from canines.
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Affiliation(s)
- Dharitree Sonowal
- Department of Veterinary Public Health, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, India;
- These authors contributed equally.
| | - Sandeep Ghatak
- Department of Veterinary Public Health, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, India;
| | - Acheenta Gohain Barua
- Department of Veterinary Public Health, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, India;
| | - Srinivas Kandhan
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, India;
- These authors contributed equally.
| | - Razibuddin Ahmed Hazarika
- Department of Veterinary Public Health, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, India;
| | - Arnab Sen
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, India;
| | - Samir Das
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, India;
| | - Sarat Sonowal
- Department of Veterinary Public Health, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, India;
| | - Rajeev Kumar Sharma
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, India;
| | - Shantanu Tamuly
- Department of Veterinary Biochemistry, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, India;
| | - Chimanjita Phukan
- Department of Microbiology, Gauhati Medical College, Srimanta Sankaradeva University of Health Sciences, Guwahati, India.
| | - Ajanta Sharma
- Department of Microbiology, Gauhati Medical College, Srimanta Sankaradeva University of Health Sciences, Guwahati, India.
| | - Poznur Hussain
- Department of Veterinary Public Health, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, India;
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5
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Chen C, Zhou Z, Cong L, Shan M, Zhu Z, Li Y. Rapid identification of methicillin-resistant Staphylococcus aureus by MALDI-TOF MS: A meta-analysis. Biotechnol Appl Biochem 2022. [PMID: 36575908 DOI: 10.1002/bab.2433] [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: 02/02/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022]
Abstract
Invasive infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are associated with high mortality and morbidity. The sooner the pathogen is determined, the better it is beneficial to patient. However, routine laboratory inspections are time-consuming and laborious. A thorough research was conducted in PubMed and Web of Science (until June 2021) to identify studies evaluating the accuracy of MRSA identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). STATA 15.0 software was used to analyze the pooled results of sensitivity, specificity, and 95% confidence intervals (CI). The summary receiver operating characteristic curves (SROC) and area under the curve (AUC) were utilized to show the overall performance of MALDI-TOF MS. Fifteen studies involving 2471 isolates were included in this study after the final selection in this meta-analysis. Using the random effects model forest plot to summarize the overall statistics, the sensitivity of MALDI-TOF MS for identifying MRSA was 92% (95% CI: 81%-97%), and the specificity was 97% (95% CI: 89%-99%). In the SROC curve, the AUC reached 0.99 (95% CI: 97%-99%). Deeks' test showed no significant publication bias in this meta-analysis. Compared with clinical reference methods, MALDI-TOF MS identification of MRSA shows a higher degree of sensitivity and specificity.
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Affiliation(s)
- Chaoqun Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
| | - Zheng Zhou
- Department of Clinical Laboratory, Shandong Provincial Public Health Clinical Center, Shandong University Affiliated Hospital, Jinan, Shandong, People's Republic of China
| | - Liu Cong
- School of Medical Technology, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
| | - Mingzhu Shan
- Department of Clinical Laboratory, The Central Hospital of Xuzhou City, Xuzhou, Jiangsu, People's Republic of China
| | - Zuobin Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
| | - Ying Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
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6
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Deb M, Hunter R, Taha M, Abdelbary H, Anis H. Rapid detection of bacteria using gold nanoparticles in SERS with three different capping agents: Thioglucose, polyvinylpyrrolidone, and citrate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 280:121533. [PMID: 35752039 DOI: 10.1016/j.saa.2022.121533] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The increase in outbreaks of emerging and re-emerging bacterial infections over the last few decades calls for their rapid detection and treatment. Surface-enhanced Raman spectroscopy (SERS) is a technique that can be applied to develop fast screening systems for bacterial presence in biological samples. Optimizing the capping agents in nanoparticle synthesis is important because capping agents are responsible for controlling the morphological features and chemical properties of the nanoparticles that are essential for SERS. To the best of our knowledge, this paper is the first to study the application of gold nanoparticles capped with thioglucose and polyvinylpyrrolidone (PVP) in SERS detection of bacteria as an alternative to the citrate-capped gold nanoparticles that are often used in SERS detection of bacteria. Three different species of bacteria were used in this study: Cutibacterium acnes, Escherichia coli and Staphylococcus aureus (methicillin-sensitive and methicillin-resistant). This study demonstrates that the thioglucose, citrate both show good contribution in bacterial species identification and the thioglucose shows the best among the three capping agents in two types of S. aureus identification. Moreover, although PVP showed high Raman peaks in the SERS spectrum for each type of bacteria, it showed least contribution in identifying species and strains due to its low efficacy in producing responses from different nucleic acid components in the bacteria cells.
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Affiliation(s)
- Mahamaya Deb
- School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | - Robert Hunter
- Ottawa-Carleton Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Mariam Taha
- The Ottawa Hospital Research Institute, Ottawa, Ontario K1Y 4E9, Canada
| | - Hesham Abdelbary
- The Ottawa Hospital Research Institute, Ottawa, Ontario K1Y 4E9, Canada
| | - Hanan Anis
- School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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7
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Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics. Int J Mol Sci 2022; 23:ijms23179834. [PMID: 36077231 PMCID: PMC9456280 DOI: 10.3390/ijms23179834] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/21/2022] Open
Abstract
Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.
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8
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Wang Y, Liang X, Xu J, Nan L, Liu F, Duan G, Yang H. Rapid and Ultrasensitive Detection of Methicillin-Resistant Staphylococcus aureus Based on CRISPR-Cas12a Combined With Recombinase-Aided Amplification. Front Microbiol 2022; 13:903298. [PMID: 35722329 PMCID: PMC9204182 DOI: 10.3389/fmicb.2022.903298] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/09/2022] [Indexed: 12/26/2022] Open
Abstract
Staphylococcus aureus is one of the main pathogens causing hospital and community-acquired infections, in particular, infections caused by methicillin-resistant Staphylococcus aureus (MRSA) cause a higher mortality rate than those caused by methicillin-sensitive strains, which poses a serious global public health problem. Therefore, rapid and ultrasensitive detection of patients with clinical MRSA infection and timely control of infection are essential. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) based on nucleic acid detection methods are well-known for its high specificity and sensitivity and programmability. Here, we successfully proposed a method based on CRISPR-Cas12a combined with recombinase-aided amplification (RAA) through fluorescent readout to achieve accurate identification and highly sensitive detection of MRSA in clinical samples. Results showed that the limit of detection (LoD) of the RAA-Cas12a method could reach 10 copies/μl at 60 min of reaction. Specificity tests showed that the method could distinguish MRSA from clinically common bacteria. The results of RAA-Cas12a were consistent with that of antimicrobial susceptibility tests (AST) and polymerase chain reaction (PCR) in 83 clinical samples. These results indicated that the detection method based on RAA-Cas12a has high sensitivity and specificity, and provides important value for rapid detection of MRSA.
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Affiliation(s)
- Ying Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xuan Liang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Jie Xu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Lan Nan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Fang Liu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haiyan Yang
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9
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Montagut EJ, Acosta G, Albericio F, Royo M, Godoy-Tena G, Lacoma A, Prat C, Salvador JP, Marco MP. Direct Quantitative Immunochemical Analysis of Autoinducer Peptide IV for Diagnosing and Stratifying Staphylococcus aureus Infections. ACS Infect Dis 2022; 8:645-656. [PMID: 35175740 PMCID: PMC8922274 DOI: 10.1021/acsinfecdis.1c00670] [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] [Indexed: 11/29/2022]
Abstract
An immunochemical strategy to detect and quantify AIP-IV, the quorum sensing (QS) signaling molecule produced by Staphylococcus aureus agr type IV, is reported here for the first time. Theoretical calculations and molecular modeling studies have assisted on the design and synthesis of a suitable peptide hapten (AIPIVS), allowing to obtain high avidity and specific antibodies toward this peptide despite its low molecular weight. The ELISA developed achieves an IC50 value of 2.80 ± 0.17 and an LOD of 0.19 ± 0.06 nM in complex media such as 1/2 Tryptic Soy Broth. Recognition of other S. aureus AIPs (I-III) is negligible (cross-reactivity below 0.001%), regardless of the structural similarities. A pilot study with a set of clinical isolates from patients with airways infection or colonization demonstrates the potential of this ELISA to perform biomedical investigations related to the role of QS in pathogenesis and the association between dysfunctional agr or the agr type with unfavorable clinical outcomes. The AIP-IV levels could be quantified in the low nanomolar range in less than 1 h after inoculating agr IV-genotyped isolates in the culture broth, while those genotyped as I-III did not show any immunoreactivity after a 48 h growth, pointing to the possibility to use this technology for phenotyping S. aureus. The research strategy here reported can be extended to the rest of the AIP types of S. aureus, allowing the development of powerful multiplexed chips or point-of-care (PoC) diagnostic devices to unequivocally identify its presence and its agr type on samples from infected patients.
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Affiliation(s)
- Enrique-J. Montagut
- Nanobiotechnology for Diagnostics (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), 08750 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid Spain
| | - Gerardo Acosta
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid Spain
- Multivalent Systems for Nanomedicine (MS4N), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), 08750 Barcelona, Spain
| | - Fernando Albericio
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid Spain
- Multivalent Systems for Nanomedicine (MS4N), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), 08750 Barcelona, Spain
- Department of Organic Chemistry, Faculty of Chemistry, University of Barcelona, 08028 Barcelona, Spain
- School of Chemistry and Physics, University of KwaZulu-Natal, 4000 Durban, South Africa
| | - Miriam Royo
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid Spain
- Multivalent Systems for Nanomedicine (MS4N), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), 08750 Barcelona, Spain
| | - Gerard Godoy-Tena
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d’Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Alicia Lacoma
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d’Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
| | - Cristina Prat
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d’Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), 28029 Madrid, Spain
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, 3584 Utrecht, the Netherlands
| | - Juan-Pablo Salvador
- Nanobiotechnology for Diagnostics (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), 08750 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid Spain
| | - María-Pilar Marco
- Nanobiotechnology for Diagnostics (Nb4D), Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC) of the Spanish Council for Scientific Research (CSIC), 08750 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid Spain
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10
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Recent Developments in Phenotypic and Molecular Diagnostic Methods for Antimicrobial Resistance Detection in Staphylococcus aureus: A Narrative Review. Diagnostics (Basel) 2022; 12:diagnostics12010208. [PMID: 35054375 PMCID: PMC8774325 DOI: 10.3390/diagnostics12010208] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen responsible for a wide range of infections in humans, such as skin and soft tissue infections, pneumonia, food poisoning or sepsis. Historically, S. aureus was able to rapidly adapt to anti-staphylococcal antibiotics and become resistant to several classes of antibiotics. Today, methicillin-resistant S. aureus (MRSA) is a multidrug-resistant pathogen and is one of the most common bacteria responsible for hospital-acquired infections and outbreaks, in community settings as well. The rapid and accurate diagnosis of antimicrobial resistance in S. aureus is crucial to the early initiation of directed antibiotic therapy and to improve clinical outcomes for patients. In this narrative review, I provide an overview of recent phenotypic and molecular diagnostic methods for antimicrobial resistance detection in S. aureus, with a particular focus on MRSA detection. I consider methods for resistance detection in both clinical samples and isolated S. aureus cultures, along with a brief discussion of the advantages and the challenges of implementing such methods in routine diagnostics.
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11
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Zhao L, Huang X, Zhang T, Zhang X, Jiang M, Lu H, Sui G, Zhao Y, Zhao W, Liu X. A point-of-care test device for MRSA rapid detection. J Pharm Biomed Anal 2021; 209:114464. [PMID: 34915322 DOI: 10.1016/j.jpba.2021.114464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/18/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
Staphylococcus aureus (SA) is one of the most common pathogenic bacteria, and methicillin-resistant SA (MRSA) is an equally common drug-resistant bacteria. MRSA detection is of great significance for clinical diagnosis, medication guidance, and prevention of antibiotic abuse. Traditional MRSA detection using the culture method is time-consuming, laborious, and difficult to conduct rapid on-site detection. In this research, we developed a device for rapid MRSA detection, which can detect the nuc gene in SA and mecA gene in MRSA simultaneously for 30-40 min. After simple sample processing, the mixture can be directly loaded onto the chip device. The detection results can be directly determined by a color change, with a limitation of approximately 102 copies. This isothermal amplification chip device can be widely applied in many fields, with simple operation and low contamination.
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Affiliation(s)
- Linlin Zhao
- Department of Gastroenterology, Shanghai Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, PR China
| | - Xiaochun Huang
- Department of Laboratory, Shanghai Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, PR China
| | - Tong Zhang
- Shanghai Key laboratory of Atmospheric Particle Pollution Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China
| | - Xinlian Zhang
- Shanghai Key laboratory of Atmospheric Particle Pollution Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China
| | - Mengni Jiang
- Department of Gastroenterology, Shanghai Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, PR China
| | - Huijun Lu
- Shanghai Key laboratory of Atmospheric Particle Pollution Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China
| | - Guodong Sui
- Shanghai Key laboratory of Atmospheric Particle Pollution Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China
| | - Yue Zhao
- Liaocheng Center for Disease Control and Prevention, 2 East Hunan Road, Liaocheng 252000, Shandong, PR China
| | - Wang Zhao
- Shanghai Key laboratory of Atmospheric Particle Pollution Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, 2005 Songhu Road, Shanghai 200438, PR China.
| | - Xiao Liu
- Department of Gastroenterology, Shanghai Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, PR China.
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12
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Rousseau AN, Faure N, Rol F, Sedaghat Z, Le Galudec J, Mallard F, Josso Q. Fast Antibiotic Susceptibility Testing via Raman Microspectrometry on Single Bacteria: An MRSA Case Study. ACS OMEGA 2021; 6:16273-16279. [PMID: 34235297 PMCID: PMC8246468 DOI: 10.1021/acsomega.1c00170] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/05/2021] [Indexed: 05/14/2023]
Abstract
Despite recent advances in molecular diagnostics, ultrafast determination of the antibiotic susceptibility phenotype of pathogenic microorganisms is still a major challenge of in vitro diagnostics (IVD) of infectious diseases. Raman microspectroscopy has been proposed as a means to achieve this goal. Previous studies have shown that susceptibility phenotyping could be done through Raman analysis of microbial cells, either in large clusters or down to the single-cell level in the case of Gram-negative rods. Gram-positive cocci such as Staphylococcus aureus pose several challenges due to their size and their different metabolic and chemical characteristics. Using a tailored automated single-cell Raman spectrometer and a previously proposed sample preparation protocol, we acquired and analyzed 9429 S. aureus single cells belonging to three cefoxitin-resistant strains and two susceptible strains during their incubation in the presence of various concentrations of cefoxitin. We observed an effect on S. aureus spectra that is weaker than what was detected on previous bacteria/drug combinations, with a higher cell-to-cell response variability and an important impact of incubation conditions on the phenotypic resistance of a given strain. Overall, the proposed protocol was able to correlate strains' phenotype with a specific modification of the spectra using majority votes. We, hence, confirm that our previous results on single-cell Raman antibiotic susceptibility testing can be extended to the S. aureus case and further clarify potential limitations and development requirements of this approach in the move toward industrial applications.
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Affiliation(s)
| | - Nicolas Faure
- bioMérieux,
R&D Microbiology, 5 rue des Berges, 38024 Grenoble, France
| | - Fabian Rol
- Bioaster, 40 avenue Tony Garnier, 69007 Lyon, France
| | | | - Joël Le Galudec
- bioMérieux,
R&D Microbiology, 5 rue des Berges, 38024 Grenoble, France
| | - Frédéric Mallard
- bioMérieux,
R&D Microbiology, 5 rue des Berges, 38024 Grenoble, France
| | - Quentin Josso
- bioMérieux,
R&D Microbiology, 376 Chemin de l’Orme, 69280 Marcy-l’Etoile, France
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13
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Abstract
The nasopharyngeal microbiome is a dynamic microbial interface of the aerodigestive tract, and a diagnostic window in the fight against respiratory infections and antimicrobial resistance. As its constituent bacteria, viruses and mycobacteria become better understood and sampling accuracy improves, diagnostics of the nasopharynx could guide more personalized care of infections of surrounding areas including the lungs, ears and sinuses. This review will summarize the current literature from a clinical perspective and highlight its growing importance in diagnostics and infectious disease management.
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Affiliation(s)
- Matthew Flynn
- School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
- Otolaryngology Department, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - James Dooley
- School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
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14
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Suea‐Ngam A, Choopara I, Li S, Schmelcher M, Somboonna N, Howes PD, deMello AJ. In Situ Nucleic Acid Amplification and Ultrasensitive Colorimetric Readout in a Paper-Based Analytical Device Using Silver Nanoplates. Adv Healthc Mater 2021; 10:e2001755. [PMID: 33251714 DOI: 10.1002/adhm.202001755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/04/2020] [Indexed: 12/16/2022]
Abstract
A rapid, highly sensitive, and quantitative colorimetric paper-based analytical device (PAD) based on silver nanoplates (AgNPls) and loop-mediated isothermal amplification (LAMP) is presented. It is shown that cauliflower-like concatemer LAMP products can mediate crystal etching of AgNPls, with a threefold signal enhancement versus linear dsDNA. Methicillin-resistant Staphylococcus aureus (MRSA), an antimicrobial resistant bacterium that poses a formidable risk with persistently high mortality, is used as a model pathogen. Due to the excellent color contrast provided by AgNPls, the PAD allows qualitative analysis by the naked eye and quantitative analysis using a smartphone camera, with detection limits down to a single copy in just 30 min, and a linear response from 1 to 104 copies (R2 = 0.994). The entire assay runs in situ on the paper surface, which drastically simplifies operation of the device. This is the first demonstration of single copy detection using a colorimetric readout, and the developed PAD shows great promise for translation into an ultrasensitive gene-based point-of-care test for any infectious disease target, via modification of the LAMP primer set.
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Affiliation(s)
- Akkapol Suea‐Ngam
- Institute for Chemical and Bioengineering Department of Chemistry and Applied Biosciences ETH Zürich Zürich 8093 Switzerland
| | - Ilada Choopara
- Program in Biotechnology Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
| | - Shangkun Li
- Institute for Chemical and Bioengineering Department of Chemistry and Applied Biosciences ETH Zürich Zürich 8093 Switzerland
| | - Mathias Schmelcher
- Institute of Food, Nutrition and Health ETH Zürich Zürich 8092 Switzerland
| | - Naraporn Somboonna
- Department of Microbiology Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
- Microbiome Research Unit for Probiotics in Food and Cosmetics Chulalongkorn University Bangkok 10330 Thailand
| | - Philip D. Howes
- Institute for Chemical and Bioengineering Department of Chemistry and Applied Biosciences ETH Zürich Zürich 8093 Switzerland
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering Department of Chemistry and Applied Biosciences ETH Zürich Zürich 8093 Switzerland
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15
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Graphene for Biosensing Applications in Point-of-Care Testing. Trends Biotechnol 2021; 39:1065-1077. [PMID: 33573848 DOI: 10.1016/j.tibtech.2021.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 02/06/2023]
Abstract
Graphene and graphene-related materials (GRMs) exhibit a unique combination of electronic, optical, and electrochemical properties, which make them ideally suitable for ultrasensitive and selective point-of-care testing (POCT) devices. POCT device-based applications in diagnostics require test results to be readily accessible anywhere to produce results within a short analysis timeframe. This review article provides a summary of methods and latest developments in the field of graphene and GRM-based biosensing in POCT and an overview of the main applications of the latter in nucleic acids and enzymatic biosensing, cell detection, and immunosensing. For each application, we discuss scientific and technological advances along with the remaining challenges, outlining future directions for widespread use of this technology in biomedical applications.
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16
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Kadri SS, Lai YL, Warner S, Strich JR, Babiker A, Ricotta EE, Demirkale CY, Dekker JP, Palmore TN, Rhee C, Klompas M, Hooper DC, Powers JH, Srinivasan A, Danner RL, Adjemian J. Inappropriate empirical antibiotic therapy for bloodstream infections based on discordant in-vitro susceptibilities: a retrospective cohort analysis of prevalence, predictors, and mortality risk in US hospitals. THE LANCET. INFECTIOUS DISEASES 2021; 21:241-251. [PMID: 32916100 PMCID: PMC7855478 DOI: 10.1016/s1473-3099(20)30477-1] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/14/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND The prevalence and effects of inappropriate empirical antibiotic therapy for bloodstream infections are unclear. We aimed to establish the population-level burden, predictors, and mortality risk of in-vitro susceptibility-discordant empirical antibiotic therapy among patients with bloodstream infections. METHODS Our retrospective cohort analysis of electronic health record data from 131 hospitals in the USA included patients with suspected-and subsequently confirmed-bloodstream infections who were treated empirically with systemic antibiotics between Jan 1, 2005, and Dec 31, 2014. We included all patients with monomicrobial bacteraemia caused by common bloodstream pathogens who received at least one systemic antibiotic either on the day blood cultures were drawn or the day after, and for whom susceptibility data were available. We calculated the prevalence of discordant empirical antibiotic therapy-which was defined as receiving antibiotics on the day blood culture samples were drawn to which the cultured isolate was not susceptible in vitro-overall and by hospital type by using regression tree analysis. We used generalised estimating equations to identify predictors of receiving discordant empirical antibiotic therapy, and used logistic regression to calculate adjusted odds ratios for the relationship between in-hospital mortality and discordant empirical antibiotic therapy. FINDINGS 21 608 patients with bloodstream infections received empirical antibiotic therapy on the day of first blood culture collection. Of these patients, 4165 (19%) received discordant empirical antibiotic therapy. Discordant empirical antibiotic therapy was independently associated with increased risk of mortality (adjusted odds ratio 1·46 [95% CI, 1·28-1·66]; p<0·0001), a relationship that was unaffected by the presence or absence of resistance or sepsis or septic shock. Infection with antibiotic-resistant species strongly predicted receiving discordant empirical therapy (adjusted odds ratio 9·09 [95% CI 7·68-10·76]; p<0·0001). Most incidences of discordant empirical antibiotic therapy and associated deaths occurred among patients with bloodstream infections caused by Staphylococcus aureus or Enterobacterales. INTERPRETATION Approximately one in five patients with bloodstream infections in US hospitals received discordant empirical antibiotic therapy, receipt of which was closely associated with infection with antibiotic-resistant pathogens. Receiving discordant empirical antibiotic therapy was associated with increased odds of mortality overall, even in patients without sepsis. Early identification of bloodstream pathogens and resistance will probably improve population-level outcomes. FUNDING US National Institutes of Health, US Centers for Disease Control and Prevention, and US Agency for Healthcare Research and Quality.
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Affiliation(s)
- Sameer S Kadri
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
| | - Yi Ling Lai
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarah Warner
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Jeffrey R Strich
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD, USA; United States Public Health Service, Commissioned Corps, Rockville, MD, USA
| | - Ahmed Babiker
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Emily E Ricotta
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cumhur Y Demirkale
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - John P Dekker
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tara N Palmore
- Hospital Epidemiology Service, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Chanu Rhee
- Brigham and Women's Hospitals, Boston, MA, USA; Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Michael Klompas
- Brigham and Women's Hospitals, Boston, MA, USA; Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - David C Hooper
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - John H Powers
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Arjun Srinivasan
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert L Danner
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Jennifer Adjemian
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; United States Public Health Service, Commissioned Corps, Rockville, MD, USA
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17
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Broddrick JT, Szubin R, Norsigian CJ, Monk JM, Palsson BO, Parenteau MN. High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. Front Microbiol 2020; 11:596626. [PMID: 33281796 PMCID: PMC7688782 DOI: 10.3389/fmicb.2020.596626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/19/2020] [Indexed: 11/13/2022] Open
Abstract
Advances in nanopore-based sequencing techniques have enabled rapid characterization of genomes and transcriptomes. An emerging application of this sequencing technology is point-of-care characterization of pathogenic bacteria. However, genome assessments alone are unable to provide a complete understanding of the pathogenic phenotype. Genome-scale metabolic reconstruction and analysis is a bottom-up Systems Biology technique that has elucidated the phenotypic nuances of antimicrobial resistant (AMR) bacteria and other human pathogens. Combining these genome-scale models (GEMs) with point-of-care nanopore sequencing is a promising strategy for combating the emerging health challenge of AMR pathogens. However, the sequencing errors inherent to the nanopore technique may negatively affect the quality, and therefore the utility, of GEMs reconstructed from nanopore assemblies. Here we describe and validate a workflow for rapid construction of GEMs from nanopore (MinION) derived assemblies. Benchmarking the pipeline against a high-quality reference GEM of Escherichia coli K-12 resulted in nanopore-derived models that were >99% complete even at sequencing depths of less than 10× coverage. Applying the pipeline to clinical isolates of pathogenic bacteria resulted in strain-specific GEMs that identified canonical AMR genome content and enabled simulations of strain-specific microbial growth. Additionally, we show that treating the sequencing run as a mock metagenome did not degrade the quality of models derived from metagenome assemblies. Taken together, this study demonstrates that combining nanopore sequencing with GEM construction pipelines enables rapid, in situ characterization of microbial metabolism.
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Affiliation(s)
- Jared T Broddrick
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA, United States
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Charles J Norsigian
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Mary N Parenteau
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA, United States
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18
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Tang K, Tang D, Wang Q, Li C. MALDI-TOF MS platform combined with machine learning to establish a model for rapid identification of methicillin-resistant Staphylococcus aureus. J Microbiol Methods 2020; 180:106109. [PMID: 33271209 DOI: 10.1016/j.mimet.2020.106109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/10/2020] [Accepted: 11/25/2020] [Indexed: 12/01/2022]
Abstract
MALDI-TOF MS is an effective potential tool to distinguish between MSSA and MRSA. By combining the ClinProTools3.0 software and manual grouping intervention, we proposed a model optimization method for the first time. The cross validation of the model increased from 95.82% to 96.68%, and the accuracy of the model increased from 88.89% to 91.98%. Finally, we reported nine characteristic peaks of rapid detection of MRSA.
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Affiliation(s)
- Kewen Tang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, China
| | - Dongling Tang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, China
| | - Qianyu Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, China
| | - Congrong Li
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, China.
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19
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Vasala A, Hytönen VP, Laitinen OH. Modern Tools for Rapid Diagnostics of Antimicrobial Resistance. Front Cell Infect Microbiol 2020; 10:308. [PMID: 32760676 PMCID: PMC7373752 DOI: 10.3389/fcimb.2020.00308] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/22/2020] [Indexed: 12/18/2022] Open
Abstract
Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard methods. Many rapid diagnostic techniques can already provide pathogen identification. Some of them can additionally detect the presence of resistance genes or resistance proteins, but usually isolated pure cultures are needed for AST. We discuss the value of the technologies applying nucleic acid amplification, whole genome sequencing, and hybridization as well as immunodiagnostic and mass spectrometry-based methods and biosensor-based AST. Additionally, we evaluate the potential of integrated systems applying microfluidics to integrate cultivation, lysis, purification, and signal reading steps. We discuss technologies and commercial products with potential for Point-of-Care Testing (POCT) and their capability to analyze polymicrobial samples without pre-purification steps. The purpose of this critical review is to present the needs and drivers for AST development, to show the benefits and limitations of AST methods, to introduce promising new POCT-compatible technologies, and to discuss AST technologies that are likely to thrive in the future.
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Affiliation(s)
- Antti Vasala
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa P. Hytönen
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
| | - Olli H. Laitinen
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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20
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Schulz M, Calabrese S, Hausladen F, Wurm H, Drossart D, Stock K, Sobieraj AM, Eichenseher F, Loessner MJ, Schmelcher M, Gerhardts A, Goetz U, Handel M, Serr A, Haecker G, Li J, Specht M, Koch P, Meyer M, Tepper P, Rother R, Jehle M, Wadle S, Zengerle R, von Stetten F, Paust N, Borst N. Point-of-care testing system for digital single cell detection of MRSA directly from nasal swabs. LAB ON A CHIP 2020; 20:2549-2561. [PMID: 32568322 DOI: 10.1039/d0lc00294a] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We present an automated point-of-care testing (POCT) system for rapid detection of species- and resistance markers in methicillin-resistant Staphylococcus aureus (MRSA) at the level of single cells, directly from nasal swab samples. Our novel system allows clear differentiation between MRSA, methicillin-sensitive S. aureus (MSSA) and methicillin-resistant coagulase-negative staphylococci (MR-CoNS), which is not the case for currently used real-time quantitative PCR based systems. On top, the novel approach outcompetes the culture-based methods in terms of its short time-to-result (1 h vs. up to 60 h) and reduces manual labor. The walk-away test is fully automated on the centrifugal microfluidic LabDisk platform. The LabDisk cartridge comprises the unit operations swab-uptake, reagent pre-storage, distribution of the sample into 20 000 droplets, specific enzymatic lysis of Staphylococcus spp. and recombinase polymerase amplification (RPA) of species (vicK) - and resistance (mecA) -markers. LabDisk actuation, incubation and multi-channel fluorescence detection is demonstrated with a clinical isolate and spiked nasal swab samples down to a limit of detection (LOD) of 3 ± 0.3 CFU μl-1 for MRSA. The novel approach of the digital single cell detection is suggested to improve hospital admission screening, timely decision making, and goal-oriented antibiotic therapy. The implementation of a higher degree of multiplexing is required to translate the results into clinical practice.
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Affiliation(s)
- Martin Schulz
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
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21
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Shalizi A, Wiegers TN, Maamar H. Click-to-Capture: A method for enriching viable Staphylococcus aureus using bio-orthogonal labeling of surface proteins. PLoS One 2020; 15:e0234542. [PMID: 32555702 PMCID: PMC7299360 DOI: 10.1371/journal.pone.0234542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/27/2020] [Indexed: 11/30/2022] Open
Abstract
Staphylococcus aureus is one of the principal causative agents of bacteremia which can progress to sepsis. Rapid diagnostic tests for identification and antibiotic resistance profiling of S. aureus would improve patient outcomes and antibiotic stewardship, but existing methods require a lengthy culture step to obtain enough material for testing. Complexity of the host matrix, where pathogenic microbes are often present, also interferes with many diagnostic methods. Here, we describe a straightforward and rapid method for enriching viable S. aureus using bio-orthogonal, or “click,” chemistry methods. Bacteria labeled in this manner can potentially be cultured, interrogated using molecular methods for pathogen identification, or used to test antibiotic susceptibility.
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Affiliation(s)
- Aryaman Shalizi
- Department of Assay Development, Talis Biomedical Corporation, California, United States of America
| | - Toni N. Wiegers
- Department of Assay Development, Talis Biomedical Corporation, California, United States of America
| | - Hédia Maamar
- Department of Assay Development, Talis Biomedical Corporation, California, United States of America
- * E-mail:
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22
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Dailey PJ, Elbeik T, Holodniy M. Companion and complementary diagnostics for infectious diseases. Expert Rev Mol Diagn 2020; 20:619-636. [PMID: 32031431 DOI: 10.1080/14737159.2020.1724784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Companion diagnostics (CDx) are important in oncology therapeutic decision-making, but specific regulatory-approved CDx for infectious disease treatment are officially lacking. While not approved as CDx, several ID diagnostics are used as CDx. The diagnostics community, manufacturers, and regulatory agencies have made major efforts to ensure that diagnostics for new antimicrobials are available at or near release of new agents. AREAS COVERED This review highlights the status of Complementary and companion diagnostic (c/CDx) in the infectious disease literature, with a focus on genotypic antimicrobial resistance testing against pathogens as a class of diagnostic tests. EXPERT OPINION CRISPR, sepsis markers, and narrow spectrum antimicrobials, in addition to current and emerging technologies, present opportunities for infectious disease c/CDx. Challenges include slow guideline revision, high costs for regulatory approval, lengthy buy in by agencies, discordant pharmaceutical/diagnostic partnerships, and higher treatment costs. The number of patients and available medications used to treat different infectious diseases is well suited to support competing diagnostic tests. However, newer approaches to treatment (for example, narrow spectrum antibiotics), may be well suited for a small number of patients, i.e. a niche market in support of a CDx. The current emphasis is rapid and point-of-care (POC) diagnostic platforms as well as changes in treatment.
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Affiliation(s)
- Peter J Dailey
- School of Public Health, University of California, Berkeley , Berkeley, CA, USA.,The Foundation for Innovative New Diagnostics (FIND) , Geneva, Switzerland
| | - Tarek Elbeik
- VA Palo Alto Health Care System, Department of Veterans Affairs , Palo Alto, CA, USA
| | - Mark Holodniy
- VA Palo Alto Health Care System, Department of Veterans Affairs , Palo Alto, CA, USA.,Division of Infectious Diseases and Geographic Medicine, Stanford University , Stanford, CA, USA
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23
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Innovative and rapid antimicrobial susceptibility testing systems. Nat Rev Microbiol 2020; 18:299-311. [PMID: 32055026 DOI: 10.1038/s41579-020-0327-x] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance (AMR) is a major threat to human health worldwide, and the rapid detection and quantification of resistance, combined with antimicrobial stewardship, are key interventions to combat the spread and emergence of AMR. Antimicrobial susceptibility testing (AST) systems are the collective set of diagnostic processes that facilitate the phenotypic and genotypic assessment of AMR and antibiotic susceptibility. Over the past 30 years, only a few high-throughput AST methods have been developed and widely implemented. By contrast, several studies have established proof of principle for various innovative AST methods, including both molecular-based and genome-based methods, which await clinical trials and regulatory review. In this Review, we discuss the current state of AST systems in the broadest technical, translational and implementation-related scope.
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Boattini M, Bianco G, Iannaccone M, Charrier L, Almeida A, De Intinis G, Cavallo R, Costa C. Accuracy of the ELITe MGB assays for the detection of carbapenemases, CTX-M, Staphylococcus aureus and mecA/C genes directly from respiratory samples. J Hosp Infect 2020; 105:306-310. [PMID: 31931044 DOI: 10.1016/j.jhin.2019.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/30/2019] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Bacterial lower respiratory tract infections (BLRTI) may represent serious clinical conditions which can lead to respiratory failure, intensive care unit admission and high hospital costs. The detection of carbapenemase- and extended-spectrum β-lactamase (ESBL)-producing Enterobacterales, as well as meticillin-resistant Staphylococcus aureus (MRSA), has become a major issue, especially in healthcare-associated infections. This study aimed to determine whether molecular assays could detect genes encoding carbapenemases, ESBL and MRSA directly from respiratory samples in order to expedite appropriate therapy and infection control for patients with BLRTI. METHODS The carbapenem-resistant enterobacterales (CRE), ESBL and MRSA/SA ELITe MGB assays were performed directly on 354 respiratory specimens sampled from 318 patients admitted with BLRTI. Molecular results were compared with routine culture-based diagnostics results. RESULTS Positive (PPV) and negative (NPV) predictive values of the CRE ELITe MGB kit were 75.9% [95% confidence interval (CI) 60.3-86.7] and 100%, respectively. PPV and NPV of the ESBL ELITe MGB kit were 80.8% (95% CI 63.6-91.0) and 99.1% (95% CI 96.6-99.8), respectively. PPV and NPV of the MRSA/SA ELITe MGB kit were 91.7% (95% CI 73.7-97.7)/100% and 98.3% (95% CI 89.8-99.3)/96.8% (95% CI 81.6-99.5), respectively. DISCUSSION Validity assessment of molecular assays detecting the main antibiotic resistance genes directly from respiratory samples showed high accuracy compared with culture-based results. Molecular assays detecting the main carbapenemase, ESBL, S. aureus and meticillin resistance encoding genes provide an interesting tool with potential to expedite optimization of antibiotic therapy and infection control practices in patients with BLRTI.
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Affiliation(s)
- M Boattini
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy.
| | - G Bianco
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - M Iannaccone
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - L Charrier
- Department of Public Health and Paediatrics, University of Torino, Turin, Italy
| | - A Almeida
- Department of Internal Medicine 4, Hospital de Santa Marta, Central Lisbon Hospital Centre, Lisbon, Portugal; NOVA Medical School, Universidade Nova de Lisboa, Lisbon, Portugal
| | - G De Intinis
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - R Cavallo
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - C Costa
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
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25
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Abstract
Traditional antimicrobial susceptibility test methods for detection of S. aureus resistant to oxacillin (MRSA) such as disk diffusion, broth microdilution, and oxacillin screen plate require 18-24 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 and wound swabs, as well as from positive blood cultures, have been developed for use in clinical laboratories. Chromogenic agar plates and real-time PCR and other molecular tests are gaining popularity as MRSA screening tests because they 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 and 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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26
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Kim JM, Kim I, Chung SH, Chung Y, Han M, Kim JS. Rapid Discrimination of Methicillin-Resistant Staphylococcus aureus by MALDI-TOF MS. Pathogens 2019; 8:pathogens8040214. [PMID: 31683799 PMCID: PMC6963962 DOI: 10.3390/pathogens8040214] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/20/2019] [Accepted: 10/31/2019] [Indexed: 02/07/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a serious pathogen in clinical settings and early detection is critical. Here, we investigated the MRSA discrimination potential of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) using 320 clinical S. aureus isolates obtained in 2005–2014 and 181 isolates obtained in 2018. We conducted polymerase chain reactions (PCR) for staphylococcal cassette chromosome mec (SCCmec) typing and MALDI-TOF MS to find specific markers for methicillin resistance. We identified 21 peaks with significant differences between MRSA and methicillin-susceptible S. aureus (MSSA), as determined by mecA and SCCmec types. Each specific peak was sufficient to discriminate MRSA. We developed two methods for simple discrimination according to these peaks. First, a decision tree for MRSA based on six MRSA-specific peaks, three MSSA-specific peaks, and two SCCmec type IV peaks showed a sensitivity of 96.5%. Second, simple discrimination based on four MRSA-specific peaks and one MSSA peak had a maximum sensitivity of 88.3%. The decision tree applied to 181 S. aureus isolates from 2018 had a sensitivity of 87.6%. In conclusion, we used specific peaks to develop sensitive MRSA identification methods. This rapid and easy MALDI-TOF MS approach can improve patient management.
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Affiliation(s)
- Jung-Min Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul 05355, Korea.
| | - Inhee Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul 05355, Korea.
| | - Sung Hee Chung
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul 05355, Korea.
| | - Yousun Chung
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Korea.
| | - Minje Han
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Korea.
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul 05355, Korea.
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