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Hayotte A, Mariani-Kurkdjian P, Boizeau P, Dauger S, Riaud C, Lacarra B, Bourmaud A, Levy M. Viral Identification Using Multiplex Polymerase Chain Reaction Testing Does Not Reduce Antibiotic Prescribing in Paediatric Intensive Care Units. Microorganisms 2023; 11:microorganisms11040884. [PMID: 37110306 PMCID: PMC10143589 DOI: 10.3390/microorganisms11040884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/07/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
PCR tests for viral identification, performed on nasopharyngeal secretions, have experienced a major boom in the last few years. Their use is very frequent, but their indications are still not well defined, especially in Paediatric Intensive Care Units (PICU). These tests are used for the microbiological diagnosis of lower respiratory infections but can be used in other situations. The aim of the study was to investigate the effect of viral identification on antibiotic therapy management. We conducted a single-centre retrospective study from 1 October 2017 to 31 December 2019. This study included all consecutive FilmArray® Respiratory Panel tests performed in patients hospitalised in a PICU. Patients were identified using the microbiology laboratory prospective database and data were extracted from the medical record. 544 tests corresponding to 408 patients were included. The main reasons for testing were pneumonia (34%) and bronchiolitis (24%). In 70% of cases, at least one virus was identified, with Human Rhinovirus (56%) and Respiratory Syncytial Virus (28%) being the two predominant. Bacterial co-infection was present in 25% of cases. Viral identification was not associated with reduced antibiotic therapy. On multivariate analysis, antibiotic management was significantly associated with clinical gravity, CRP value or radiology findings regardless of virus identification. Viral identification has an epidemiological value, but antibiotic prescription relies on other factors.
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Yoshida K, Hatachi T, Okamoto Y, Aoki Y, Kyogoku M, Moon Miyashita K, Inata Y, Shimizu Y, Fujiwara F, Takeuchi M. Application of Multiplex Polymerase Chain Reaction for Pathogen Identification and Antibiotic Use in Children With Respiratory Infections in a PICU. Pediatr Crit Care Med 2021; 22:e644-e648. [PMID: 34224509 DOI: 10.1097/pcc.0000000000002794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVES To compare the pathogen identification rate and use of antibiotics before and after the implementation of multiplex polymerase chain reaction testing in children with respiratory infections in a PICU. DESIGN Single-center, pre-post study. SETTING PICU of Osaka Women's and Children's Hospital, Osaka, Japan. PATIENTS Consecutive children with respiratory infections who were admitted to the PICU between December 2017 and November 2018 (premultiplex polymerase chain reaction period) and between March 2019 and February 2020 (postmultiplex polymerase chain reaction period). INTERVENTIONS Conventional rapid antigen tests and bacterial culture tests were performed throughout the study period. Multiplex polymerase chain reaction testing using the FilmArray respiratory panel (BioFire Diagnostics, Salt Lake City, UT) was conducted to detect 17 viruses and three bacterial pathogens. During the postmultiplex polymerase chain reaction period, we did not recommend prescribing antibiotics for stable children, depending on the virus species and laboratory test results. MEASUREMENTS AND MAIN RESULTS Ninety-six and 85 children were enrolled during the pre- and postmultiplex polymerase chain reaction periods, respectively. Rapid antigen tests identified pathogens in 22% of the children (n = 21) during the premultiplex polymerase chain reaction period, whereas rapid antigen tests and/or multiplex polymerase chain reaction testing identified pathogens in 67% of the children (n = 57) during the postmultiplex polymerase chain reaction period (p < 0.001). The most commonly identified pathogen using multiplex polymerase chain reaction testing was human rhino/enterovirus. Bacterial pathogens were identified in 50% of the children (n = 48) and 60% of the children (n = 51) during the pre- and postmultiplex polymerase chain reaction periods (p = 0.18). There were no differences in antibiotic use (84% vs 75%; p = 0.14), broad-spectrum antibiotic use (33% vs 34%; p = 0.91), or the duration of antibiotic use within 14 days of admission (6.0 vs 7.0 d; p = 0.45) between the pre- and postmultiplex polymerase chain reaction periods. CONCLUSIONS Although the pathogen identification rate, especially for viral pathogens, increased using multiplex polymerase chain reaction testing, antibiotic use did not reduce in children with respiratory infections in the PICU. Definitive identification of bacterial pathogens and implementation of evidence-based antimicrobial stewardship programs employing multiplex polymerase chain reaction testing are warranted.
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Affiliation(s)
- Kota Yoshida
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Takeshi Hatachi
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yuya Okamoto
- Department of Laboratory Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yoshihiro Aoki
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
- Department of Emergency and Critical Care Medicine, Aizawa Hospital, Nagano, Japan
| | - Miyako Kyogoku
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kazue Moon Miyashita
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yu Inata
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yoshiyuki Shimizu
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Futoshi Fujiwara
- Department of Laboratory Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Muneyuki Takeuchi
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
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Long Y, Zhang Y, Gong Y, Sun R, Su L, Lin X, Shen A, Zhou J, Caiji Z, Wang X, Li D, Wu H, Tan H. Diagnosis of Sepsis with Cell-free DNA by Next-Generation Sequencing Technology in ICU Patients. Arch Med Res 2017; 47:365-371. [PMID: 27751370 DOI: 10.1016/j.arcmed.2016.08.004] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 08/08/2016] [Indexed: 01/19/2023]
Abstract
BACKGROUND AND AIMS Bacteremia is a common serious manifestation of disease in the intensive care unit (ICU), which requires quick and accurate determinations of pathogens to select the appropriate antibiotic treatment. To overcome the shortcomings of traditional bacterial culture (BC), we have adapted next-generation sequencing (NGS) technology to identify pathogens from cell-free plasma DNA. METHODS In this study, 78 plasma samples from ICU patients were analyzed by both NGS and BC methods and verified by PCR amplification/Sanger sequencing and ten plasma samples from healthy volunteers were analyzed by NGS as negative controls to define or calibrate the threshold of the NGS methodology. RESULTS Overall, 1578 suspected patient samples were found to contain bacteria or fungi by NGS, whereas ten patients were diagnosed by BC. Seven samples were diagnosed with bacterial or fungal infection both by NGS and BC. Among them, two samples were diagnosed with two types of bacteria by NGS, whereas one sample was diagnosed with two types of bacteria by BC, which increased the detectability of bacteria or fungi from 11 with BC to 17 with NGS. Most interestingly, 14 specimens were also diagnosed with viral infection by NGS. The overall diagnostic sensitivity was significantly increased from 12.82% (10/78) by BC alone to 30.77% (24/78) by NGS alone for ICU patients, which provides more useful information for establishing patient treatment plans. CONCLUSION NGS technology can be applied to detect bacteria in clinical blood samples as an emerging diagnostic tool rich in information to determine the appropriate treatment of septic patients.
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Affiliation(s)
- Yun Long
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yinxin Zhang
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China; BGI-Shenzhen, Shenzhen, China
| | - Yanping Gong
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China; BGI-Shenzhen, Shenzhen, China
| | - Ruixue Sun
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China; BGI-Shenzhen, Shenzhen, China
| | - Longxiang Su
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Lin
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China; BGI-Shenzhen, Shenzhen, China
| | - Ao Shen
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China; BGI-Shenzhen, Shenzhen, China
| | - Jiali Zhou
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China; BGI-Shenzhen, Shenzhen, China
| | - Zhuoma Caiji
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China; BGI-Shenzhen, Shenzhen, China
| | - Xinying Wang
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China; BGI-Shenzhen, Shenzhen, China
| | - Dongfang Li
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China; BGI-Shenzhen, Shenzhen, China
| | - Honglong Wu
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China; BGI-Shenzhen, Shenzhen, China
| | - Hongdong Tan
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Complete Genomics, Inc., Mountain View, California, USA; Shenzhen Key Laboratory of Unknown Pathogen Identification, Shenzhen, China; BGI-Shenzhen, Shenzhen, China.
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