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Gong J, Yang J, Liu L, Chen X, Yang G, He Y, Sun R. Evaluation and clinical practice of pathogens and antimicrobial resistance genes of BioFire FilmArray Pneumonia panel in lower respiratory tract infections. Infection 2024; 52:545-555. [PMID: 38123753 PMCID: PMC10955009 DOI: 10.1007/s15010-023-02144-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Existing panels for lower respiratory tract infections (LRTIs) are slow and lack quantification of important pathogens and antimicrobial resistance, which are not solely responsible for their complex etiology and antibiotic resistance. BioFire FilmArray Pneumonia (PN) panels may provide rapid information on their etiology. METHODS The bronchoalveolar lavage fluid of 187 patients with LRTIs was simultaneously analyzed using a PN panel and cultivation, and the impact of the PN panel on clinical practice was assessed. The primary endpoint was to compare the consistency between the PN panel and conventional microbiology in terms of etiology and drug resistance, as well as to explore the clinical significance of the PN panel. The secondary endpoint was pathogen detection using the PN panel in patients with community-acquired pneumonia (CAP) or hospital-acquired pneumonia (HAP). RESULTS Fifty-seven patients with HAP and 130 with CAP were included. The most common pathogens of HAP were Acinetobacter baumannii and Klebsiella pneumoniae, with the most prevalent antimicrobial resistance (AMR) genes being CTX-M and KPC. For CAP, the most common pathogens were Haemophilus influenzae and Staphylococcus aureus, with the most frequent AMR genes being CTX-M and VIM. Compared with routine bacterial culture, the PN panel demonstrated an 85% combined positive percent agreement (PPA) and 92% negative percent agreement (NPA) for the qualitative identification of 13 bacterial targets. PN detection of bacteria with higher levels of semi-quantitative bacteria was associated with more positive bacterial cultures. Positive concordance between phenotypic resistance and the presence of corresponding AMR determinants was 85%, with 90% positive agreement between CTX-M-type extended-spectrum beta-lactamase gene type and phenotype and 100% agreement for mecA/C and MREJ. The clinical benefit of the PN panel increased by 25.97% compared with traditional cultural tests. CONCLUSION The bacterial pathogens and AMR identified by the PN panel were in good agreement with conventional cultivation, and the clinical benefit of the PN panel increased by 25.97% compared with traditional detection. Therefore, the PN panel is recommended for patients with CAP or HAP who require prompt pathogen diagnosis and resistance identification.
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Affiliation(s)
- Jinru Gong
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jiasheng Yang
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Lihong Liu
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoxuan Chen
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Guangyu Yang
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yaowei He
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Ruilin Sun
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.
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Yang H, Xu N, Yan M, Yang L, Wen S, Wang S, Qu C, Xu K, Yang X, Wang G. Comparison of metagenomic next-generation sequencing and conventional culture for the diagnostic performance in febrile patients with suspected infections. BMC Infect Dis 2024; 24:350. [PMID: 38532348 DOI: 10.1186/s12879-024-09236-w] [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: 11/23/2023] [Accepted: 03/19/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Timely and accurate identification of pathogens is crucial for appropriate treatment and prognosis of infectious diseases. As an increasingly popular pathogen detection method, the performance of metagenomic next-generation sequencing (mNGS) in detecting pathogens in febrile patients with suspected infection requires further exploration. METHODS This study included 368 febrile patients with suspected infections who were admitted to the Infectious Disease Department of Qilu Hospital, Shandong University between January 5, 2021 and April 14, 2023. Both mNGS testing and conventional culture were performed in all patients. Clinical data of enrolled patients were collected, and the diagnostic performances of mNGS and culture were compared. RESULTS Of the 368 enrolled patients, 231 were finally diagnosed with infection and 137 were with diseases other than infection. The sensitivity (58.01% vs. 21.65%, p < 0.001) and negative predictive value (54.67% vs. 42.9%) of mNGS were superior to those of culture. In contrast, the culture exhibited higher specificity (99.27% vs. 85.40%, p < 0.001) and positive predictive value (98.84% vs. 87.01%) than mNGS. Among infected patients with positive mNGS results, 64 received adjusted antibiotic therapy including treatment transitions, antibiotic downgrading, and combination therapy. Among them, 9 had additional antifungal drugs and 21 patients had a treatment turning point based on the mNGS results and these patients recovered and discharged due to timely antibiotic adjustment. Both positive rates of puncture fluid mNGS and tissue mNGS were higher than those of culture in the patients who had prior antibiotic use, and this difference was statistically significant (p = 0.000). CONCLUSION mNGS is more sensitive and accurate than traditional culture, making it ideal for identifying pathogens and screening infectious diseases, especially for those with uncultivated or difficult-to-cultivate species. Early diagnosis allows for prompt treatment with targeted antibiotics, and mNGS is recommended when samples are limited.
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Affiliation(s)
- Hui Yang
- Department of Infectious Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Nannan Xu
- Department of Infectious Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Meichen Yan
- Department of Intensive Care Unit, Qilu Hospital, Cheeloo College of Medicine, ShandongUniversity, Jinan, Shandong, 250012, China
| | - Lulu Yang
- Department of Infectious Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Sai Wen
- Department of Infectious Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Shanshan Wang
- Department of Infectious Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Chunmei Qu
- Department of Infectious Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ke Xu
- Department of Infectious Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xuying Yang
- Department of Scientific Affaires, Hugobiotech Co., Ltd., No.1, East Disheng Road, Beijing, 100176, China
| | - Gang Wang
- Department of Infectious Disease, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
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Zahid QUA, Khursheed N, Adnan F, Zafar A. Concordance and discordance of GeneXpert MTB/RIF and conventional culture method for diagnosis of Extra-Pulmonary Tuberculosis at a tertiary care hospital in Pakistan. Pak J Med Sci 2024; 40:S64-S69. [PMID: 38328643 PMCID: PMC10844911 DOI: 10.12669/pjms.40.2(icon).8967] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 10/16/2023] [Accepted: 11/12/2023] [Indexed: 02/09/2024] Open
Abstract
Objective To identify concordance and discordance between GeneXpert MTB/RIF assay and gold standard bacteriologic culture for the diagnosis of Mycobacterium tuberculosis (MTB) in Extra-Pulmonary tuberculosis (EPTB) specimens in our region. Methods This is a retrospective cross-sectional study conducted at the Indus Hospital and Health Network. Data from 1st January, 2020 to 31st December, 2021 was analyzed. A total of 1499 EPTB specimens were included for which GeneXpert was requested along with acid-fast bacteria (AFB) culture from the same specimen. Specimens were processed according to specimen type following standard operating procedures of the laboratory. Fluorescent staining was performed on all specimens along with bacteriologic culture. The GeneXpert MTB/RIF assay was carried out in exact accordance with the manufacturer's instructions. Results Out of 1499 EPTB specimens, 1370 (91.39%) specimens exhibited concordance between GeneXpert and conventional culture method, while 129 (8.60%) specimens showed discordance. GeneXpert exhibited sensitivity and specificity of 69.4% and 94.3% respectively in comparison to culture. Conclusion GeneXpert sensitivity for the diagnosis of EPTB varied with the site involved. Lower sensitivity was observed in ascitic and pleural fluids as compared to higher sensitivity observed among urine samples and pus aspirates. However, given the quick turnaround time and ease of use, it is a helpful tool in the diagnosis of EPTB when utilized in the appropriate clinical context. Caution is advised while interpreting negative GeneXpert results in endemic settings and should be interpreted along with other supporting clinical and diagnostic features.
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Affiliation(s)
- Qurat-ul-Ain Zahid
- Dr. Qurat-ul-Ain Zahid, Department of Pathology, Section of Microbiology Indus Hospital and Health Network, Karachi, Pakistan
| | - Nazia Khursheed
- Dr. Nazia Khursheed, FCPS. Department of Pathology, Section of Microbiology Indus Hospital and Health Network, Karachi, Pakistan
| | - Fareeha Adnan
- Dr. Fareeha Adnana, FCPS. Department of Pathology, Section of Microbiology Indus Hospital and Health Network, Karachi, Pakistan
| | - Adeel Zafar
- Dr. Adeel Zafar, Department of Pathology, Section of Microbiology Indus Hospital and Health Network, Karachi, Pakistan
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Hirai J, Mori N, Sakanashi D, Morishita Y, Kuge Y, Kishino T, Asai N, Hagihara M, Takahashi N, Mikamo H. Usefulness of the FilmArray blood culture identification panel for identifying causative pathogens of bone and joint infections. J Infect Chemother 2023; 29:722-725. [PMID: 37088145 DOI: 10.1016/j.jiac.2023.04.011] [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: 01/10/2023] [Revised: 03/24/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
As bone and joint infections (BJIs) require long-term treatment, identifying their causative pathogens is vital. However, the detection rate of conventional culturing remains inadequate. This study aimed to evaluate the usefulness of the FilmArray blood culture identification (BCID) panel for identifying causative pathogens in patients with BJIs. We tested a BCID panel using collected samples, in addition to conventional cultures. The primary outcome was to evaluate the diagnostic performance of the BCID panel, calculated using conventional culturing methods. A total of 44 patients who underwent BJI-related specimen collection were enrolled. Of the 44 patients, 22 were diagnosed with a BJI. Conventional culture identified 15 of 22 organisms (68.2%), whereas the BCID panel identified 14 of 22 organisms (63.4%). The overall sensitivity and specificity of the BCID panel were 73.3% and 57.1%, respectively, compared to those of the conventional culture. However, the sensitivity reached 100% when only pathogens included in the BCID panel were considered. In seven culture-negative cases, the BCID panel identified three organisms (42.9%). The BCID panel also indicated the appropriate therapy against a BJI caused by methicillin-resistant Staphylococcus aureus by detecting the mecA gene. This study demonstrated that the BCID panel has the potential for early and accurate diagnosis of the causative organism of BJI using specimens such as joint fluid and bone tissue. Our results suggest that BCID panels, in addition to routine culture, may improve our ability to diagnose the causative microorganisms of BJI in clinical practice, thereby contributing to the selection of appropriate antimicrobial agents.
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Affiliation(s)
- Jun Hirai
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Aichi, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, Aichi, Japan.
| | - Nobuaki Mori
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Aichi, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, Aichi, Japan
| | - Daisuke Sakanashi
- Department of Infection Control and Prevention, Aichi Medical University Hospital, Aichi, Japan
| | - Yusuke Morishita
- Department of Orthopedic Surgery, Aichi Medical University, Aichi, Japan
| | - Yuji Kuge
- Department of Emergency and Critical Care Medicine, Aichi Medical University Hospital, Nagakute, Aichi, Japan
| | - Takaaki Kishino
- Department of Emergency and Critical Care Medicine, Aichi Medical University Hospital, Nagakute, Aichi, Japan
| | - Nobuhiro Asai
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Aichi, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, Aichi, Japan
| | - Mao Hagihara
- Department of Molecular Epidemiology and Biomedical Sciences, Aichi Medical University Hospital, Aichi, Japan
| | - Nobunori Takahashi
- Department of Orthopedic Surgery, Aichi Medical University, Aichi, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Aichi, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, Aichi, Japan
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Pongsachareonnont P, Honglertnapakul W, Chatsuwan T. Comparison of methods for identifying causative bacterial microorganisms in presumed acute endophthalmitis: conventional culture, blood culture, and PCR. BMC Infect Dis 2017; 17:165. [PMID: 28222703 PMCID: PMC5320661 DOI: 10.1186/s12879-017-2264-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/11/2017] [Indexed: 11/20/2022] Open
Abstract
Background Identification of bacterial pathogens in endophthalmitis is important to inform antibiotic selection and treatment decisions. Hemoculture bottles and polymerase chain reaction (PCR) analysis have been proposed to offer good detection sensitivity. This study compared the sensitivity and accuracy of a blood culture system, a PCR approach, and conventional culture methods for identification of causative bacteria in cases of acute endophthalmitis. Methods Twenty-nine patients with a diagnosis of presumed acute bacterial endophthalmitis who underwent vitreous specimen collection at King Chulalongkorn Memorial Hospital were enrolled in this study. Forty-one specimens were collected. Each specimen was divided into three parts, and each part was analyzed using one of three microbial identification techniques: conventional plate culture, blood culture, and polymerase chain reaction and sequencing. The results of the three methods were then compared. Results Bacteria were identified in 15 of the 41 specimens (36.5%). Five (12.2%) specimens were positive by conventional culture methods, 11 (26.8%) were positive by hemoculture, and 11 (26.8%) were positive by PCR. Cohen’s kappa analysis revealed p-values for conventional methods vs. hemoculture, conventional methods vs. PCR, and hemoculture vs. PCR of 0.057, 0.33, and 0.009, respectively. Higher detection rates of Enterococcus faecalis were observed for hemoculture and PCR than for conventional methods. Conclusions Blood culture bottles and PCR detection may facilitate bacterial identification in cases of presumed acute endophthalmitis. These techniques should be used in addition to conventional plate culture methods because they provide a greater degree of sensitivity than conventional plate culture alone for the detection of specific microorganisms such as E. faecalis. Trial registration Thai Clinical Trial Register No. TCTR20110000024.
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Affiliation(s)
- Pear Pongsachareonnont
- Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University; and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand.
| | - Worawalun Honglertnapakul
- Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University; and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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