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Srivastava S, Sharad N, Kiro VV, Ningombam A, Shrivastava S, Farooque K, Mathur P. Utility of a multiplex pathogen detection system directly from respiratory specimens for treatment and diagnostic stewardship. Microbiol Spectr 2024:e0375923. [PMID: 38712971 DOI: 10.1128/spectrum.03759-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/29/2024] [Indexed: 05/08/2024] Open
Abstract
The availability of syndrome-based panels for various ailments has widened the scope of diagnostics in many clinical settings. These panels can detect a multitude of pathogens responsible for a particular condition, which can lead to a timely diagnosis and better treatment outcomes. In contrast to traditional identification methods based on pathogen growth on culture, syndrome-based panels offer a quicker diagnosis, which can be especially beneficial in situations requiring urgent care, such as intensive care units. One such panel is the Biofire Filmarray Pneumonia plus Panel (BFP), which we have compared against microbiological culture and identification. The lower respiratory samples from patients were tested with BFP, culture, and identification with culture considered the gold standard. The phenotypic antibiotic susceptibility results (Vitek 2) were compared with the antimicrobial resistance (AMR) genes detected in BFP. Statistical analysis was carried out using GraphPad 7.0 and MS Excel (Microsoft Inc.). The results showed a positive percent agreement of 100% and a negative percent agreement of 47.8% with an overall agreement of 76.72% compared to culture. BFP was better at identifying fastidious bacteria, and the agreement with culture was higher for high bacterial identification numbers (107 and 106). There was also a correlation between the number of pathogens detected and growth in culture. Carbapenemase genes were detected in around 80% of phenotypically resistant samples and correlated with in-house PCR 60% of the time. Hence, BFP results need to be interpreted with caution especially when multiple pathogens are detected. Similarly, the presence or absence of AMR genes should be used to guide the therapy while being watchful of unusual resistance or susceptibility. The cost constraints and low throughput call for patient selection criteria and prioritization in emergency or resource-limited conditions.IMPORTANCEApplication of syndrome-based panels in clinical microbiology is of huge support in infectious conditions requiring urgent interventions, such as pneumonia. Interpreting the results requires caution; hence, we have compared the results obtained from Biofire Filmarray Pneumonia plus Panel with standard microbiological methods.
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Affiliation(s)
| | - Neha Sharad
- Department of Microbiology, AIIMS, New Delhi, India
| | | | - Aparna Ningombam
- Department of Laboratory Medicine, JPNATC, AIIMS, New Delhi, India
| | | | | | - Purva Mathur
- Department of Laboratory Medicine, JPNATC, AIIMS, New Delhi, India
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Sharma M, Kiro VV, Srivastav S, Mansoori N, Lalwani P, Lathwal A, Agrawal R, Soni KD, Madaan N, Malhotra R, Trikha A, Lalwani S, Mathur P. SARS-CoV-2 antigen detection in deceased bodies: implications for infection prevention. Indian J Med Res 2023; 158:33-39. [PMID: 37602584 PMCID: PMC10550055 DOI: 10.4103/ijmr.ijmr_2794_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 08/03/2023] Open
Abstract
Background & objectives High transmissibility of the SARS-CoV-2 has significant implications on healthcare workers' safety, preservation, handling, transportation and disposal of the deceased bodies. The objective of this study was to detect SARS-CoV-2 antigen in nasopharyngeal samples and its implications in handling and care of COVID-19 deceased bodies. Methods A study was conducted at a dedicated COVID-19 centre on deceased individuals from April to December 2020. Rapid antigen test (RAT) and reverse transcription (RT)-PCR was compared on all the SARS-CoV-2 positive cadavers recruited in the study. Results A total of 115 deceased individuals were included in the study. Of these, 79 (68.7%) were male and 36 (31.3%) were female and majority were in the age group of 51-60 yr [31 (27%)]. SARS-CoV-2 antigen test was positive in 32 (27.8%) and negative in 83 (72.1%) individuals. The mean time interval between deaths to the sample collection was 13.2 h with interquartile range of eight to 20 h. Reverse transcription (RT)-PCR was used as the reference test and 24 (20.9%) cases were true positive; 93.6 per cent [95% confidence interval (CI) 88.8-98.4%] sensitivity, 45.2 per cent (95% CI 35.5-55%) specificity, 60.2 per cent (95% CI 50.6-69.8%) positive predictive value and 88.8 per cent (95% CI 82.7-95%) negative predictive value of antigen test was computed. Interpretation & conclusions SARS-CoV-2 antigen test was positive beyond 19 h in COVID-19 deceased individuals. Antigen test was found to be highly sensitive in the deceased. Patients, suspected of having died due to COVID-19, can be screened by this method. As infectiousness of the virus in the deceased bodies cannot be directly concluded from either the antigen or RT-PCR test, yet possible transmission cannot be completely ruled out. Strict infection control measures need to be followed during the handling and clearance of COVID-19 cadavers.
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Affiliation(s)
- Meenakshi Sharma
- Division of Forensic Pathology & Molecular DNA Laboratory, New Delhi, India
| | - Vandana Vijayeta Kiro
- Department of Microbiology (Laboratory Medicine), Jai Prakash Narayan Apex Trauma Centre, New Delhi, India
| | - Sharad Srivastav
- Department of Microbiology (Laboratory Medicine), Jai Prakash Narayan Apex Trauma Centre, New Delhi, India
| | - Nasim Mansoori
- Division of Forensic Pathology & Molecular DNA Laboratory, New Delhi, India
| | - Parin Lalwani
- Department of Anaesthesia & Critical Care, Jai Prakash Narayan Apex Trauma Centre, New Delhi, India
| | - Amit Lathwal
- Department of Hospital Administration, All India Institute of Medical Sciences, New Delhi, India
| | - Richa Agrawal
- Department of Anaesthesia & Critical Care, All India Institute of Medical Sciences, New Delhi, India
| | - Kapil Dev Soni
- Department of Anaesthesia & Critical Care, All India Institute of Medical Sciences, New Delhi, India
| | - Nirupam Madaan
- Department of Hospital Administration, All India Institute of Medical Sciences, New Delhi, India
| | - Rajesh Malhotra
- Department of Orthopaedics, Jai Prakash Narayan Apex Trauma Centre, New Delhi, India
| | - Anjan Trikha
- Department of Anaesthesia & Critical Care, Jai Prakash Narayan Apex Trauma Centre, New Delhi, India
| | - Sanjeev Lalwani
- Division of Forensic Pathology & Molecular DNA Laboratory, New Delhi, India
| | - Purva Mathur
- Department of Microbiology (Laboratory Medicine), Jai Prakash Narayan Apex Trauma Centre, New Delhi, India
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Srivastava S, Singh P, Sharad N, Kiro VV, Malhotra R, Mathur P. Infection Trends, Susceptibility Pattern, and Treatment Options for Stenotrophomonas maltophilia Infections in Trauma Patients: A Retrospective Study. J Lab Physicians 2022; 15:106-109. [PMID: 37064968 PMCID: PMC10104700 DOI: 10.1055/s-0042-1757413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Abstract
Introduction Stenotrophomonas maltophilia is an emerging environmental, gram-negative, multidrug-resistant organism, associated with risk factors such as prolonged hospitalization, invasive procedures, admission to the intensive care unit, mechanical ventilation, use of indwelling catheters, administration of immunosuppressants or corticosteroids, human immunodeficiency virus infection, underlying malignancy, and organ transplantation. The organism, despite being of low invasiveness in immune-competent individuals, is difficult to treat because of intrinsic resistance to several antimicrobial agents.
Materials and Methods This study focuses on commonly encountered resistance from among the isolates over a duration of 7 years from 2012 to 2018, analyzed retrospectively. Identification and susceptibility testing were performed using Vitek 2 (BioMérieux, Marcy-l'Etoile, France).
Results Bloodstream infections were found to be most common (52.02%), followed by respiratory infections (35.83%). The median age of the patients was 36 years, and male to female ratio was 143:27. The median duration of hospital stay was 18 days, and mortality was seen in 18.82% of patients. Susceptibility to cotrimoxazole and levofloxacin was seen in 97.1% of isolates (168 out of 173) and 90.1% of isolates (156 out of 173), respectively.
Conclusion Despite being effective in a majority of S. maltophilia isolates, both cotrimoxazole and levofloxacin have their shortcomings. Cotrimoxazole is bacteriostatic and can cause bone marrow suppression and resistance to levofloxacin sometimes develops during therapy. Thus, the therapy should be decided considering the characteristics of both of these drugs.
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Affiliation(s)
- Smriti Srivastava
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Parul Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Neha Sharad
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Vandana Vijayeta Kiro
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajesh Malhotra
- Department of Orthopaedic, All India Institute of Medical Sciences, New Delhi, India
| | - Purva Mathur
- Department of Laboratory Medicine, Jai Prakash Narayan Apex Trauma Centre (JPNATC), All India Institute of Medical Sciences, New Delhi, India
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Kiro VV, Singh P, Srivastav S, Aggarwal R, Soni KD, Singh Y, Singh A, Trikha A, Mathur P. SARS-CoV-2 Rapid Antigen Detection in Respiratory and Nonrespiratory Specimens in COVID-19 Patients. J Lab Physicians 2022; 14:369-372. [PMID: 36119430 PMCID: PMC9473930 DOI: 10.1055/s-0042-1742415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Rapid antigen testing for coronavirus disease 2019 (COVID-19) available at present provides immediate results at low cost with less expertise and without any need of sophisticated infrastructure. Most of these test kits available are for nasopharyngeal samples. This is a novel study to detect the presence of COVID antigen in samples other than throat and oropharyngeal. Various samples received from patients admitted in the COVID-19 dedicated center were tested for the presence of antigen. Same procedure was followed as done for the nasopharyngeal sample. A total of 150 samples were tested, which included ascitic fluid, pleural fluid, drain fluid, bile, bronchoalveolar lavage, cerebrospinal fluid, endotracheal tube aspirate, sputum, tissue, and urine. Out of 150, 11 (7.33%) were positive and 138 (92.66%) were negative for the antigen test. The COVID-19 antigen test kit, though designed for nasopharyngeal samples, was able to detect the presence of antigen in other clinical samples.
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Affiliation(s)
- Vandana Vijayeta Kiro
- Department of Microbiology, Jai Prakash Narayan Apex Trauma Center (JPNATC), All India Institute of Medical Sciences, New Delhi, India
| | - Parul Singh
- Department of Microbiology, Jai Prakash Narayan Apex Trauma Center (JPNATC), All India Institute of Medical Sciences, New Delhi, India
| | - Sharad Srivastav
- Junior Research Fellow Program, Jai Prakash Narayan Apex Trauma Center (JPNATC), All India Institute of Medical Sciences, New Delhi, India
| | - Richa Aggarwal
- Department of Anaesthesia and Critical Care, All India Institute of Medical Sciences IIMS, New Delhi, India
| | - Kapil Dev Soni
- Department of Anaesthesia and Critical Care, All India Institute of Medical Sciences IIMS, New Delhi, India
| | - Yudhyavir Singh
- Department of Anaesthesia and Critical Care, All India Institute of Medical Sciences IIMS, New Delhi, India
| | - Abhishek Singh
- Department of Anaesthesia and Critical Care, All India Institute of Medical Sciences IIMS, New Delhi, India
| | - Anjan Trikha
- Department of Anaesthesia and Critical Care, All India Institute of Medical Sciences IIMS, New Delhi, India
| | - Purva Mathur
- Division of Clinical Microbiology, Department of Laboratory Medicine, Jai Prakash Narayan Apex Trauma Center (JPNATC), All India Institute of Medical Sciences, New Delhi, India
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Kiro VV, Gupta A, Singh P, Sharad N, Khurana S, Prakash S, Dar L, Malhotra R, Wig N, Kumar A, Trikha A, Mathur P. Evaluation of COVID-19 Antigen Fluorescence Immunoassay Test for Rapid Detection of SARS-CoV-2. J Glob Infect Dis 2021; 13:91-93. [PMID: 34194176 PMCID: PMC8213088 DOI: 10.4103/jgid.jgid_316_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/28/2020] [Accepted: 12/01/2020] [Indexed: 11/04/2022] Open
Abstract
Introduction Tests detecting SARS-CoV-2-specific antigen have recently been developed, and many of them are now commercially available. However, the real-world performance of these assays is uncertain; therefore, their validation is important. In this study, we have evaluated the performance of STANDARD F COVID-19 antigen fluorescence immunoassay (FIA) kit. Methods Nasopharyngeal samples collected from patients were subjected to the test as per manufacturer's instructions. The performance of the kit was compared with the gold standard real-time polymerase chain reaction. Results A total of 354 patients were tested with STANDARD F COVID-19 antigen FIA test kit. The overall sensitivity, specificity, positive predictive value, and negative predictive value of this test were found to be 38%, 99%, 96.2%, and 72%, respectively, with a diagnostic accuracy of 75.7%. Conclusion STANDARD F COVID-19 antigen FIA showed high specificity and positive predictive value but low sensitivity and negative predictive value.
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Affiliation(s)
| | - Ankesh Gupta
- Department of Infectious Diseases, AIIMS, New Delhi, India
| | - Parul Singh
- Department of Microbiology (Laboratory Medicine), AIIMS, New Delhi, India
| | - Neha Sharad
- Department of Microbiology (Laboratory Medicine), AIIMS, New Delhi, India
| | - Surbhi Khurana
- Department of Laboratory Medicine, AIIMS, New Delhi, India
| | - S Prakash
- Department of Hospital Administration, AIIMS, New Delhi, India
| | - Lalit Dar
- Department of Microbiology, AIIMS, New Delhi,, India
| | | | - Naveet Wig
- Department of Medicine, AIIMS, New Delhi,, India
| | - Arvind Kumar
- Department of Medicine, AIIMS, New Delhi,, India
| | - Anjan Trikha
- Department of Anaesthesia and Critical Care, AIIMS, New Delhi,, India
| | - Purva Mathur
- Department of Laboratory Medicine (Microbiology Division), JPNATC, AIIMS, New Delhi,, India
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