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Gopikrishnan M, Haryini S, C GPD. Emerging strategies and therapeutic innovations for combating drug resistance in Staphylococcus aureus strains: A comprehensive review. J Basic Microbiol 2024; 64:e2300579. [PMID: 38308076 DOI: 10.1002/jobm.202300579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/04/2024]
Abstract
In recent years, antibiotic therapy has encountered significant challenges due to the rapid emergence of multidrug resistance among bacteria responsible for life-threatening illnesses, creating uncertainty about the future management of infectious diseases. The escalation of antimicrobial resistance in the post-COVID era compared to the pre-COVID era has raised global concern. The prevalence of nosocomial-related infections, especially outbreaks of drug-resistant strains of Staphylococcus aureus, have been reported worldwide, with India being a notable hotspot for such occurrences. Various virulence factors and mutations characterize nosocomial infections involving S. aureus. The lack of proper alternative treatments leading to increased drug resistance emphasizes the need to investigate and examine recent research to combat future pandemics. In the current genomics era, the application of advanced technologies such as next-generation sequencing (NGS), machine learning (ML), and quantum computing (QC) for genomic analysis and resistance prediction has significantly increased the pace of diagnosing drug-resistant pathogens and insights into genetic intricacies. Despite prompt diagnosis, the elimination of drug-resistant infections remains unattainable in the absence of effective alternative therapies. Researchers are exploring various alternative therapeutic approaches, including phage therapy, antimicrobial peptides, photodynamic therapy, vaccines, host-directed therapies, and more. The proposed review mainly focuses on the resistance journey of S. aureus over the past decade, detailing its resistance mechanisms, prevalence in the subcontinent, innovations in rapid diagnosis of the drug-resistant strains, including the applicants of NGS and ML application along with QC, it helps to design alternative novel therapeutics approaches against S. aureus infection.
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Affiliation(s)
- Mohanraj Gopikrishnan
- Department of Integrative Biology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Sree Haryini
- Department of Biomedical Sciences, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - George Priya Doss C
- Department of Integrative Biology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
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A Multicenter Clinical Study To Demonstrate the Diagnostic Accuracy of the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panel. J Clin Microbiol 2021; 59:e0248420. [PMID: 34232066 PMCID: PMC8373019 DOI: 10.1128/jcm.02484-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteremia can progress to septic shock and death without appropriate medical intervention. Increasing evidence supports the role of molecular diagnostic panels in reducing the clinical impact of these infections through rapid identification of the infecting organism and associated antimicrobial resistance genes. We report the results of a multicenter clinical study assessing the performance of the GenMark Dx ePlex investigational-use-only blood culture identification Gram-negative panel (BCID-GN), a rapid diagnostic assay for detection of bloodstream pathogens in positive blood culture (PBC) bottles. Prospective, retrospective, and contrived samples were tested. Results from the BCID-GN were compared to standard-of-care bacterial identification methods. Antimicrobial resistance genes (ARGs) were identified using PCR and sequence analysis. The final BCID-GN analysis included 2,444 PBC samples, of which 926 were clinical samples with negative Gram stain results. Of these, 109 samples had false-negative and/or -positive results, resulting in an overall sample accuracy of 88.2% (817/926). After discordant resolution, overall sample accuracy increased to 92.9% (860/926). Pre- and postdiscordant resolution sample accuracy excludes 37 Gram-negative organisms representing 20 uncommon genera, 10 Gram-positive organisms, and 1 Candida species present in 5% of samples that are not targeted by the BCID-GN. The overall weighted positive percent agreement (PPA), which averages the individual PPAs from the 27 targets (Gram-negative and ARG), was 94.9%. The limit of detection ranged from 104 to 107 CFU/ml, except for one strain of Fusobacterium necrophorum at 108 CFU/ml.
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Dong T, Ma X, Sheng N, Qi X, Chu Y, Song Q, Zou B, Zhou G. Point-of-care DNA testing by automatically and sequentially performing extraction, amplification and identification in a closed-type cassette. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 327:128919. [PMID: 32963421 PMCID: PMC7497388 DOI: 10.1016/j.snb.2020.128919] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 05/06/2023]
Abstract
Nucleic acid detection is important for clinical diagnostics; however, it is challenging to perform genetic testing at the point-of-care due to the tedious steps involved in DNA extraction and the risk of cross-contamination from amplicons. To achieve a fully-automated and contamination-free nucleic acid detection, we propose a closed-type cassette system which enables the following steps to be operated automatically and sequentially: sample preparation based on magnetic beads, target amplification using multiplex polymerase chain reaction, and colorimetric detection of amplicons using a serial invasive reaction coupled with the aggregation of gold nanoparticle probes. The cassette was designed to be round and closed, and 10 targets in a sample could be simultaneously detected by the naked eye or using a spectrophotometer in the system. In addition, a cassette-driven device was fabricated to transfer reagents between wells, to control the temperature of each reaction, and to sense the colour in the detection wells. The cassette system was sensitive enough to detect 10 genotypes at 5 single nucleotide polymorphism sites related to the anticoagulant's usage, by using a 0.5 μL blood sample. The accuracy of the system was evaluated by detecting 12 whole blood samples, and the results obtained were consistent with those obtained using pyrosequencing. The cassette is airtight and the whole system is fully automatic; the only manual operation is the addition of the sample to the cassette, performing point-of-care genetic testing in a sample-in/answer-out way.
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Affiliation(s)
- Tianhui Dong
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Nan Sheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Qinxin Song
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Guohua Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, China
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Mancini S, Bodendoerfer E, Kolensnik-Goldmann N, Herren S, Röthlin K, Courvalin P, Böttger EC. Evaluation of standardized automated rapid antimicrobial susceptibility testing of Enterobacterales-containing blood cultures: a proof-of-principle study. J Antimicrob Chemother 2020; 75:3218-3229. [DOI: 10.1093/jac/dkaa336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/01/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Rapid antimicrobial susceptibility testing (RAST) of bacteria causing bloodstream infections is critical for implementation of appropriate antibiotic regimens.
Objectives
We have established a procedure to prepare standardized bacterial inocula for Enterobacterales-containing clinical blood cultures and assessed antimicrobial susceptibility testing (AST) data generated with the WASPLabTM automated reading system.
Methods
A total of 258 blood cultures containing Enterobacterales were examined. Bacteria were enumerated by flow cytometry using the UF-4000 system and adjusted to an inoculum of 106 cfu/mL. Disc diffusion plates were automatically streaked, incubated for 6, 8 and 18 h and imaged using the fully automated WASPLabTM system. Growth inhibition zones were compared with those obtained with inocula prepared from primary subcultures following the EUCAST standard method. Due to time-dependent variations of the inhibition zone diameters, early AST readings were interpreted using time-adjusted tentative breakpoints and areas of technical uncertainty.
Results and conclusions
Inhibition zones obtained after 18 h incubation using an inoculum of 106 cfu/mL prepared directly from blood cultures were highly concordant with those of the EUCAST standard method based on primary subcultures, with categorical agreement (CA) of 95.8%. After 6 and 8 h incubation, 89.5% and 93.0% of the isolates produced interpretable results, respectively, with CA of >98.5% and very low numbers of clinical categorization errors for both the 6 h and 8 h readings. Overall, with the standardized and automated RAST method, consistent AST data from blood cultures containing Enterobacterales can be generated after 6–8 h of incubation and subsequently confirmed by standard reading of the same plate after 18 h.
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Affiliation(s)
- Stefano Mancini
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | - Elias Bodendoerfer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | | | - Sebastian Herren
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | - Kim Röthlin
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | | | - Erik C Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
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Malli E, Papagiannitsis CC, Xitsas S, Tsilipounidaki K, Petinaki E. Implementation of the Rapid Polymyxin™ NP test directly to positive blood cultures bottles. Diagn Microbiol Infect Dis 2019; 95:114889. [DOI: 10.1016/j.diagmicrobio.2019.114889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/29/2019] [Accepted: 08/17/2019] [Indexed: 12/24/2022]
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Dubourg G, Raoult D, Fenollar F. Emerging methodologies for pathogen identification in bloodstream infections: an update. Expert Rev Mol Diagn 2019; 19:161-173. [DOI: 10.1080/14737159.2019.1568241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
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Duncan R, Grigorenko E, Fisher C, Hockman D, Lanning B. Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls - an update. Expert Rev Mol Diagn 2018; 19:15-25. [DOI: 10.1080/14737159.2019.1559055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Robert Duncan
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | | | - Carolyn Fisher
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | | | - Bryan Lanning
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
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She RC, Bender JM. Advances in Rapid Molecular Blood Culture Diagnostics: Healthcare Impact, Laboratory Implications, and Multiplex Technologies. J Appl Lab Med 2018; 3:617-630. [PMID: 31639730 DOI: 10.1373/jalm.2018.027409] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/28/2018] [Indexed: 01/11/2023]
Abstract
BACKGROUND For far too long, the diagnosis of bloodstream infections has relied on time-consuming blood cultures coupled with traditional organism identification and susceptibility testing. Technologies to define the culprit in bloodstream infections have gained sophistication in recent years, notably by application of molecular methods. CONTENT In this review, we summarize the tests available to clinical laboratories for molecular rapid identification and resistance marker detection in blood culture bottles that have flagged positive. We explore the cost-benefit ratio of such assays, covering aspects that include performance characteristics, effect on patient care, and relevance to antibiotic stewardship initiatives. SUMMARY Rapid blood culture diagnostics represent an advance in the care of patients with bloodstream infections, particularly those infected with resistant organisms. These diagnostics are relatively easy to implement and appear to have a positive cost-benefit balance, particularly when fully incorporated into a hospital's antimicrobial stewardship program.
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Affiliation(s)
- Rosemary C She
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA;
| | - Jeffrey M Bender
- Division of Infectious Diseases of the Department of Pediatrics, Keck School of Medicine of the University of Southern California, Los Angeles, CA
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