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Su S, Wang R, Zhou R, Bai J, Chen Z, Zhou F. Higher diagnostic value of next-generation sequencing versus culture in periprosthetic joint infection: A systematic review and meta-analysis. Knee Surg Sports Traumatol Arthrosc 2024; 32:2277-2289. [PMID: 38713871 DOI: 10.1002/ksa.12227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND The next-generation sequencing (NGS) has developed rapidly in the past decade and is becoming a promising diagnostic tool for periprosthetic infection (PJI). However, its diagnostic value for PJI is still uncertain. The purpose of this systematic review and meta-analysis was to evaluate the diagnostic value of NGS compared to culture. METHODS In this systematic review and meta-analysis, electronic databases including PubMed, Embase, Cochrane Central Register of Controlled Trials, Web of Science and clinicaltrials.gov were searched for studies from inception to 12 November 2023. Diagnostic parameters, such as sensitivity, specificity, diagnostic odds ratio and area under the summary receiver-operating characteristic (SROC) curve (AUC), were calculated for the included studies. A systematic review and meta-analysis was performed. RESULTS A total of 22 studies with 2461 patients were included in our study. The pooled sensitivity, specificity and diagnostic odds ratio of NGS were 87% (95% confidence interval [CI]: 83-90), 94% (95% CI: 91-96) and 111 (95% CI: 70-177), respectively. On the other hand, the pooled sensitivity, specificity and diagnostic odds ratio of culture were 63% (95% CI: 58-67), 98% (95% CI: 96-99) and 93 (95% CI: 40-212), respectively. The SROC curve for NGS and culture showed that the AUCs are 0.96 (95% CI: 0.94-0.98) and 0.82 (95% CI: 0.79-0.86), respectively. CONCLUSION This systematic review and meta-analysis found NGS had higher sensitivity and diagnostic accuracy but slightly lower specificity than culture. Based on the pooled results, we suggested NGS may have the potential to be a new tool for the diagnosis of PJI. LEVEL OF EVIDENCE Level IV.
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Affiliation(s)
- Shilong Su
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Ruideng Wang
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Rubing Zhou
- Department of Orthopedics, Beijing friendship hospital, Capital Medical University, Xicheng, Beijing, China
| | - Jinwu Bai
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Zhengyang Chen
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Fang Zhou
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
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Delarbre D, Lavrard P, Elias A, Bossi V, Kacel I, Janvier F, Fournier PE. Bacterial DNA enrichment for low-inoculum fracture-related infection diagnostic using high-throughput sequencing. Diagn Microbiol Infect Dis 2024; 110:116411. [PMID: 39018934 DOI: 10.1016/j.diagmicrobio.2024.116411] [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: 01/18/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 07/19/2024]
Abstract
One of the main barriers for the implementation of metagenomic sequencing in routine diagnosis of infectious diseases is the presence of host DNA. While several enrichment methods are likely to overcome this issue, their effectiveness for specimens such as bone in the case of chronic infections remains to be determined. We compared the relevance of two methods for bacterial DNA enrichment when compared to a reference protocol during pretreatment of bone samples from fracture-related infections before HTS by both Illumina Miseq and Oxford Nanopore Technology (ONT). The bacterial/human DNA ratio was higher for either protocols than the reference technique (p = 0.00012), without any significant difference between them. HTS sensitivity over culture ranged from 21.7 % to 85 %. The ability of the studied protocols to improve the bacterial/human DNA ratio depends on the sequencing technique employed. In this context, there is room for improvement in enhancing the sensitivity of HTS for diagnostic purpose.
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Affiliation(s)
- David Delarbre
- Division of Internal Medicine and Infectious Diseases, Military Teaching Hospital Sainte-Anne, 2, boulevard Sainte-Anne, BP 600, Cedex 9, 83800, Toulon, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR (VITROME), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
| | - Philippe Lavrard
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR (VITROME), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Antoine Elias
- Centre Hospitalier Intercommunal Toulon - La Seyne sur Mer (C.H.I.T.S.), Toulon, France
| | | | - Idir Kacel
- Institut Méditerranée-Infection, Marseille, France
| | - Fréderic Janvier
- Division of microbiology, Military Teaching Hospital Sainte-Anne, 2, boulevard Sainte-Anne, BP 600, Cedex 9, 83800, Toulon, France
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR (VITROME), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
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Cao H, Chen Y, Ge L, Kwong JSW, Lai H, Hu F, Zhang R, Zhao H, Hu L, He R, Zheng W, Zhang J. An umbrella review of the diagnostic value of next-generation sequencing in infectious diseases. Int J Clin Pharm 2024; 46:780-794. [PMID: 38570474 DOI: 10.1007/s11096-024-01704-2] [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: 12/15/2023] [Accepted: 01/18/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND An increasing number of systematic reviews (SRs) have evaluated the diagnostic values of next-generation sequencing (NGS) in infectious diseases (IDs). AIM This umbrella analysis aimed to assess the potential risk of bias in existing SRs and to summarize the published diagnostic values of NGS in different IDs. METHOD We searched PubMed, Embase, and the Cochrane Library until September 2023 for SRs assessing the diagnostic validity of NGS for IDs. Two investigators independently determined review eligibility, extracted data, and evaluated reporting quality, risk of bias, methodological quality, and evidence certainty in the included SRs. RESULTS Eleven SRs were analyzed. Most SRs exhibited a moderate level of reporting quality, while a serious risk of bias was observed in all SRs. The diagnostic performance of NGS in detecting pneumocystis pneumonia and periprosthetic/prosthetic joint infection was notably robust, showing excellent sensitivity (pneumocystis pneumonia: 0.96, 95% CI 0.90-0.99, very low certainty; periprosthetic/prosthetic joint infection: 0.93, 95% CI 0.83-0.97, very low certainty) and specificity (pneumocystis pneumonia: 0.96, 95% CI 0.92-0.98, very low certainty; periprosthetic/prosthetic joint infection: 0.95, 95% CI 0.92-0.97, very low certainty). NGS exhibited high specificity for central nervous system infection, bacterial meningoencephalitis, and tuberculous meningitis. The sensitivity to these infectious diseases was moderate. NGS demonstrated moderate sensitivity and specificity for multiple infections and pulmonary infections. CONCLUSION This umbrella analysis indicates that NGS is a promising technique for diagnosing pneumocystis pneumonia and periprosthetic/prosthetic joint infection with excellent sensitivity and specificity. More high-quality original research and SRs are needed to verify the current findings.
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Affiliation(s)
- Hong Cao
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Yan Chen
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Long Ge
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Joey Sum-Wing Kwong
- Global Health Nursing, Graduate School of Nursing Science, St. Luke's International University, 10-1 Akashi-Cho, Chuo-Ku, Tokyo, 104-0044, Japan
| | - Honghao Lai
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Fangfang Hu
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, 550002, Guizhou Province, China
| | - Rui Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Huaye Zhao
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Linfang Hu
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Rui He
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Wenyi Zheng
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Jiaxing Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China.
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Zhou H, Yang Y, Zhang Y, Li F, Shen Y, Qin L, Huang W. Current Status and Perspectives of Diagnosis and Treatment of Periprosthetic Joint Infection. Infect Drug Resist 2024; 17:2417-2429. [PMID: 38912221 PMCID: PMC11192293 DOI: 10.2147/idr.s457644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
Periprosthetic joint infection (PJI) is a catastrophic complication following joint replacement surgery, posing significant challenges to orthopedic surgeons. Due to the lack of a definitive diagnostic gold standard, timely treatment initiation is problematic, resulting in substantial economic burdens on patients and society. In this review, we thoroughly analyze the complexities of PJI and emphasize the importance of accurate diagnosis and effective treatment. The article specifically focuses on the advancements in diagnostic techniques, ranging from traditional pathogen culture to advanced molecular diagnostics, and discusses their role in enhancing diagnostic accuracy. Additionally, we review the latest surgical management strategies, including everything from debridement to revision surgeries. Our summary aims to provide practical information for the diagnosis and treatment of PJI and encourages further research to improve diagnostic accuracy and treatment outcomes.
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Affiliation(s)
- Haotian Zhou
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yaji Yang
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yanhao Zhang
- College of Pharmacy, Army Military Medical University, Chongqing, 400038, People’s Republic of China
| | - Feilong Li
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yidong Shen
- Department of Orthopaedics, The First People’s Hospital of Yancheng, Yancheng, 224000, People’s Republic of China
| | - Leilei Qin
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Wei Huang
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
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Wang B, Wang Q, Li M, Yu J, Jiang F, Hu Y, Guo G, Chen X, Tang J, Han P, Shen H. Diagnostic Role of Metagenomic Next-Generation Sequencing in Tubercular Orthopedic Implant-Associated Infection. Infect Drug Resist 2024; 17:1951-1960. [PMID: 38774035 PMCID: PMC11107837 DOI: 10.2147/idr.s441940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
Objective The diagnosis of tubercular orthopedic implant-associated infection (TB-IAI) is challenging. This study evaluated the value of metagenomic next-generation sequencing (mNGS) for the diagnosis of TB-IAI and developed a standardized diagnostic procedure for TB-IAI. Methods The records of all patients with TB-IAI diagnosed and treated at our institution between December 2018 and September 2022 were retrospectively reviewed. Patient demographic characteristics, medical history, laboratory test, microbial culture, histopathology, and mNGS results, and time to diagnosis were recorded. The diagnostic efficiency of mNGS for TB-IAI was assessed by comparing the results and diagnostic time with that of other diagnostic modalities. Results Ten patients were included in the analysis, including eight with prosthetic joint infections and two with fracture-related infections. The mNGS positivity rate was 100% (10/10), which was higher than that of TB-antibody (11%, 1/9), real-time quantitative polymerase chain reaction (22%, 2/9), T-SPOT.TB (25%, 2/8), purified protein derivative (50%, 4/8), microbial culture (50%, 5/10), and histopathology (20%, 2/10). mNGS shortened the time to diagnosis of TB-IAI. A standardized diagnostic procedure for TB-IAI was developed based on the findings. Conclusion mNGS is useful for the diagnosis of TB-IAI. mNGS is recommended in cases where it is difficult to identify a pathogen using routine diagnostic tests. The standardized diagnostic procedure might improve TB-IAI diagnosis. Importance TB-IAI is a rare infection, which occurs after orthopedic surgery and hard to diagnose microbiologically. mNGS is a new detection technique not yet discussed in current literature as a means for TB-IAI diagnostics. Here we describe a cohort of patients with TB-IAI diagnosed by mNGS show high efficiency of mNGS for detection of this pathology and present a clinical algorithm supplementing conventional methods for TB-IAI assessment.
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Affiliation(s)
- Boyong Wang
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Qiaojie Wang
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Mingzhang Li
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Jinlong Yu
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Feng Jiang
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Yujie Hu
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Geyong Guo
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Xiaohua Chen
- Department of Infectious Diseases, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Jin Tang
- Clinical Laboratory, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Pei Han
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Hao Shen
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
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Shi T, Chen H, Liu Y, Wu Y, Lin F. Clinical applications of metagenomic next-generation sequencing in the identification of pathogens in periprosthetic joint infections: a retrospective study. J Orthop Surg Res 2024; 19:301. [PMID: 38760817 PMCID: PMC11102132 DOI: 10.1186/s13018-024-04745-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND This study aimed to evaluate the application of metagenomic next-generation sequencing (mNGS) technology to identify pathogens in periprosthetic joint infection (PJI). METHODS A retrospective analysis was conducted on 65 patients suspected of having PJI between April 2020 and July 2023. The patients were categorized into PJI (46 patients) and non-PJI (19 patients) groups based on the 2018 International Consensus Meeting criteria. Clinical data were collected, and both conventional bacterial culture and mNGS were performed. The diagnostic performance of the two methods was compared and analyzed. RESULTS mNGS exhibited a sensitivity of 89.13%, a specificity of 94.74%, a positive predictive value of 97.62%, a negative predictive value of 78.26%, and an overall diagnostic accuracy of 90.77%. Compared to microbial culture, mNGS demonstrated superior diagnostic sensitivity while maintaining similar specificity. A total of 48 pathogens were successfully identified using mNGS, with Coagulase-negative staphylococci, Streptococci, Staphylococcus aureus, and Cutibacterium acnes being the most common infectious agents. Notably, mNGS was used to identify 17 potential pathogens in 14 culture-negative PJI samples, highlighting its ability to detect rare infectious agents, including Cutibacterium acnes (n = 5), Granulicatella adiacens (n = 1), Mycobacterium tuberculosis complex (n = 1), and Coxiella burnetii (n = 1), among others, which are not detectable by routine culture methods. However, mNGS failed to detect the pathogen in 4 culture-positive PJI patients, indicating its limitations. Among the 46 PJI patients, 27 had positive culture and mNGS results. The results of mNGS were concordant with those of culture at the genus level in 6 patients with PJI and at the species level in 18 patients. Furthermore, the present study revealed a significantly greater proportion of Staphylococcus aureus in the sinus tract group (45.45%) than in the non-sinus tract group (14.29%), indicating the association of this pathogen with sinus formation in PJI (P = 0.03). Additionally, there was no significant difference in the occurrence of polymicrobial infections between the sinus tract group (27.27%) and the non-sinus tract group (33.33%) (P = 0.37). CONCLUSIONS Metagenomic next-generation sequencing can serve as a valuable screening tool in addition to traditional culture methods to improve diagnostic accuracy through optimized culture strategies.
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Affiliation(s)
- Tengfei Shi
- Department of Clinical Laboratory, Fuzhou Second General Hospital, Fuzhou, Fujian, China
| | - Huiyu Chen
- Department of Clinical Laboratory, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, China
| | - Yinhuan Liu
- Department of Clinical Laboratory, Fuzhou Second General Hospital, Fuzhou, Fujian, China
| | - Yexin Wu
- Department of Clinical Laboratory, Fuzhou Second General Hospital, Fuzhou, Fujian, China
| | - Feitai Lin
- Department of Orthopaedic Surgery, Fuzhou Second General Hospital, Shang Teng Road No. 47 Cang'shan District, Fuzhou, Fujian, China.
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Deng L, Wang J, Yang GY, Hou YZ, Li KW, Sun B, Wang SH. Different biomarker ratios in peripheral blood have limited value in diagnosing periprosthetic joint infection after total joint arthroplasty: a single-center, retrospective study. BMC Musculoskelet Disord 2024; 25:377. [PMID: 38741113 DOI: 10.1186/s12891-024-07499-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Periprosthetic joint infection (PJI) is a severe complication that can occur after total joint arthroplasty (TJA). The timely and accurate diagnosis of PJI is the key to treatment. This study investigated the diagnostic value of platelet to lymphocyte ratio (PLR), platelet count to mean platelet volume ratio (PVR), neutrophil to lymphocyte ratio (NLR) and monocyte to lymphocyte ratio (MLR) in PJI after total knee arthroplasty (TKA) and total hip arthroplasty (THA). METHODS We performed a retrospective analysis of the patients who underwent revision hip or knee arthroplasty at our Institute between June 2015 and June 2020. Of the 187 patients reviewed, 168 were included in the study. According to the diagnostic criteria of the Musculoskeletal Infection Society (MSIS), 58 patients were in the PJI group, and 110 patients were in the aseptic loosening (AL) group. We recorded and compared the preoperative peripheral blood white blood cell (WBC) count, platelet count (PLT), erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), PLR, PVR, NLR, and MLR in both groups. The diagnostic performance of the WBC, PLT, PLR, PVR, NLR, and MLR individually and in combination with the ESR and CRP for PJI diagnosis was evaluated by receiver operating characteristic (ROC) curves, and the sensitivity, specificity, positive predictive value, and negative predictive value were calculated. RESULTS Compared to those in the AL group, the mean WBC, PLT, ESR, CRP, PLR, PVR, NLR, and MLR in the peripheral blood of the PJI group were significantly greater (P < 0.05). The analysis of the ROC curve revealed that the ESR, CRP, PLR, PVR, NLR, and MLR in peripheral blood had moderate effectiveness in diagnosing PJI, with area under the curve (AUC) values of 0.760 (95% CI: 0.688-0.823), 0.758 (95% CI: 0.687-0.821), 0.714 (95% CI: 0.639-0.781), 0.709 (95% CI: 0.634-0.777), 0.723 (95% CI: 0.649-0.789), and 0.728 (95% CI: 0.654-0.793), respectively. Conversely, the WBC and PLT counts demonstrated poor diagnostic value for PJI, with AUC values of 0.578 (95% CI: 0.499-0.653) and 0.694 (95% CI: 0.619-0.763), respectively. The results of the prediction model calculations revealed that the combined AUC of the WBC, PLT, ESR, CRP, PLR, PVR, NLR, and MLR was the highest at 0.853 (95% CI, 0.790-0.909), indicating good value in the diagnosis of PJI, with a sensitivity of 82.8% and a specificity of 72.7%. Moreover, the novel composite of parameters improved the accuracy and reliability in diagnosing PJI compared to the traditional biomarkers ESR and CRP (P = 0.015). CONCLUSION Our study suggested that the diagnostic value of the peripheral blood biomarkers PLR, PVR, NLR, and MLR for diagnosing PJI is limited and not superior to that of the ESR or CRP. However, when the WBC, PLT, ESR, CRP, PLR, PVR, NLR, and MLR are combined, the diagnostic performance of PJI in TJA patients can be improved.
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Affiliation(s)
- Lei Deng
- The First School of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, 450052, People's Republic of China
- Department of Joint Surgery, Zhengzhou Orthopaedic Hospital, Zhengzhou, 450052, People's Republic of China
| | - Jie Wang
- Department of Orthopaedic, Beijing ChaoYang Hospital, Capital Medical University, Beijing, 100020, People's Republic of China
| | - Guang-Ya Yang
- The First School of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, 450052, People's Republic of China
- Department of Joint Surgery, Zhengzhou Orthopaedic Hospital, Zhengzhou, 450052, People's Republic of China
| | - Ying-Zhou Hou
- Department of Joint Surgery, Zhengzhou Orthopaedic Hospital, Zhengzhou, 450052, People's Republic of China
| | - Ke-Wei Li
- Department of Joint Surgery, Zhengzhou Orthopaedic Hospital, Zhengzhou, 450052, People's Republic of China
| | - Bo Sun
- Department of Joint Surgery, Zhengzhou Orthopaedic Hospital, Zhengzhou, 450052, People's Republic of China
| | - Shao-Hua Wang
- Department of Joint Surgery, Zhengzhou Orthopaedic Hospital, Zhengzhou, 450052, People's Republic of China.
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Liu Y, Qin S, Lan C, Huang Q, Zhang P, Cao W. Effectiveness of metagenomic next-generation sequencing in the diagnosis of infectious diseases: A systematic review and meta-analysis. Int J Infect Dis 2024; 142:106996. [PMID: 38458421 DOI: 10.1016/j.ijid.2024.106996] [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: 09/21/2023] [Revised: 02/25/2024] [Accepted: 03/02/2024] [Indexed: 03/10/2024] Open
Abstract
OBJECTIVES Early diagnosis of infectious diseases remains a challenge. This study assessed the diagnostic value of mNGS in infections and explored the effect of various factors on the accuracy of mNGS. METHODS An electronic article search of PubMed, Cochrane Library, and Embase was performed. A total of 85 papers were eligible for inclusion and analysis. Stata 12.0 was used for statistical calculation to evaluate the efficacy of mNGS for the diagnosis of infectious diseases. RESULTS The AUC of 85 studies was 0.88 (95%CI, 0.85-0.90). The AUC of the clinical comprehensive diagnosis and conventional test groups was 0.92 (95%CI, 0.89-0.94) and 0.82 (95%CI, 0.78-0.85), respectively. The results of subgroup analysis indicated that the PLR and NLR were 12.67 (95%CI, 6.01-26.70) and 0.05 (95%CI, 0.03-0.10), respectively, in arthrosis infections. The PLR was 24.41 (95%CI, 5.70-104.58) in central system infections and the NLR of immunocompromised patients was 0.08 (95%CI, 0.01-0.62). CONCLUSION mNGS demonstrated satisfactory diagnostic performance for infections, especially for bone and joint infections and central system infections. Moreover, mNGS also has a high value in the exclusion of infection in immunocompromised patients.
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Affiliation(s)
- Yusi Liu
- Department of Pharmacy, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China
| | - Sibei Qin
- Department of Pharmacy, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China
| | - Chunhai Lan
- Department of Orthopedic Surgery, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China
| | - Qinmiao Huang
- Department of Respiratory, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China
| | - Peng Zhang
- Department of Pharmacy, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China
| | - Weiling Cao
- Department of Pharmacy, Shenzhen Luohu People's Hospital, Shenzhen, Guangdong, PR China.
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Mahnic A, Rak M, Trebše R, Rupnik M, Cőr A. Identification of prosthetic joint infections with 16S amplicon metagenomic sequencing - comparison with standard cultivation approach. Diagn Microbiol Infect Dis 2024; 109:116188. [PMID: 38340614 DOI: 10.1016/j.diagmicrobio.2024.116188] [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: 09/08/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024]
Abstract
Prosthetic joint infections (PJIs) are commonly diagnosed via culture-based methods, which may miss hard-to-grow pathogens. This study contrasts amplicon metagenomic sequencing (16S AS) with traditional culture techniques for enhanced clinical decision-making. We analyzed sonicate fluid from 27 patients undergoing revision arthroplasty using both methods, emphasizing the distinction between contaminants and true positives. Our findings show moderate agreement between the two methods, with a Cohen's kappa of 0.490, varying across bacterial genera (Cohen's kappa -0.059 to 1). The sensitivity of 16S AS compared to culture was 81% (95% CI, 68% to 94%). Sequencing revealed greater microbial diversity, including anaerobic genera like Anaerococcus and Citrobacter. Interestingly, several culture-negative PJI samples showed diverse bacteria via 16S AS. Despite rigorous controls and algorithms to eliminate contaminants, confirming bacteria presence with 16S AS remains a challenge. This highlights the need for improved PJI diagnostic methods, while also pointing out the limitations of next-generation sequencing (NGS) as a clinical diagnostic tool.
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Affiliation(s)
- Aleksander Mahnic
- National Laboratory of Health, Environment and Food, Department for Microbiological Research, Maribor, Slovenia.
| | - Mitja Rak
- National Laboratory of Health, Environment and Food, Medical Microbiology Department, Koper, Slovenia
| | - Rihard Trebše
- Orthopaedic Hospital Valdoltra, Ankaran, Slovenia; Faculty of Medicine, University of Ljubljana, Slovenia
| | - Maja Rupnik
- National Laboratory of Health, Environment and Food, Department for Microbiological Research, Maribor, Slovenia; Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Andrej Cőr
- Orthopaedic Hospital Valdoltra, Ankaran, Slovenia; University of Primorska, Faculty of Health Sciences, Izola, Slovenia
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10
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Tan J, Wu L, Zhan L, Sheng M, Tang Z, Xu J, Ma H. Optimal selection of specimens for metagenomic next-generation sequencing in diagnosing periprosthetic joint infections. Front Cell Infect Microbiol 2024; 14:1356804. [PMID: 38500507 PMCID: PMC10945027 DOI: 10.3389/fcimb.2024.1356804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Objective This study aimed to assess the diagnostic value of metagenomic next-generation sequencing (mNGS) across synovial fluid, prosthetic sonicate fluid, and periprosthetic tissues among patients with periprosthetic joint infection (PJI), intending to optimize specimen selection for mNGS in these patients. Methods This prospective study involved 61 patients undergoing revision arthroplasty between September 2021 and September 2022 at the First Affiliated Hospital of Zhengzhou University. Among them, 43 cases were diagnosed as PJI, and 18 as aseptic loosening (AL) based on the American Musculoskeletal Infection Society (MSIS) criteria. Preoperative or intraoperative synovial fluid, periprosthetic tissues, and prosthetic sonicate fluid were collected, each divided into two portions for mNGS and culture. Comparative analyses were conducted between the microbiological results and diagnostic efficacy derived from mNGS and culture tests. Furthermore, the variability in mNGS diagnostic efficacy for PJI across different specimen types was assessed. Results The sensitivity and specificity of mNGS diagnosis was 93% and 94.4% for all types of PJI specimens; the sensitivity and specificity of culture diagnosis was 72.1% and 100%, respectively. The diagnostic sensitivity of mNGS was significantly higher than that of culture (X2 = 6.541, P=0.011), with no statistically significant difference in specificity (X2 = 1.029, P=0.310). The sensitivity of the synovial fluid was 83.7% and the specificity was 94.4%; the sensitivity of the prosthetic sonicate fluid was 90.7% and the specificity was 94.4%; and the sensitivity of the periprosthetic tissue was 81.4% and the specificity was 100%. Notably, the mNGS of prosthetic sonicate fluid displayed a superior pathogen detection rate compared to other specimen types. Conclusion mNGS can function as a precise diagnostic tool for identifying pathogens in PJI patients using three types of specimens. Due to its superior ability in pathogen identification, prosthetic sonicate fluid can replace synovial fluid and periprosthetic tissue as the optimal sample choice for mNGS.
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Affiliation(s)
- Jun Tan
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
| | - Lingxiao Wu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lijuan Zhan
- Department of Neurology, People’s Hospital of Zhengzhou, Zhengzhou, Henan, China
| | - Minkui Sheng
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
| | - Zhongxin Tang
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jianzhong Xu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haijun Ma
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
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11
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Yang X, Zhou S, Chang Z, Xi X, Li J, Miao M, Chen Y, Chen W, Zhang H, Ding R, Hu Z. Nanopore targeted sequencing-based diagnosis of central nervous system infections in HIV-infected patients. Ann Clin Microbiol Antimicrob 2024; 23:22. [PMID: 38424544 PMCID: PMC10905896 DOI: 10.1186/s12941-024-00682-7] [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: 10/10/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Early and accurate etiological diagnosis is very important for improving the prognosis of central nervous system (CNS) infections in human immunodeficiency virus (HIV)-infected patients. The goal is not easily achieved by conventional microbiological tests. We developed a nanopore targeted sequencing (NTS) platform and evaluated the diagnostic performance for CNS infections in HIV-infected patients, with special focus on cryptococcal meningitis (CM). We compared the CM diagnostic performance of NTS with conventional methods and cryptococcal polymerase chain reaction (PCR). METHODS This study included 57 hospitalized HIV-infected patients with suspected CNS infections from September 2018 to March 2022. The diagnosis established during hospitalization includes 27 cases of CM, 13 CNS tuberculosis, 5 toxoplasma encephalitis, 2 cytomegalovirus (CMV) encephalitis and 1 Varicella-zoster virus (VZV) encephalitis. The 2 cases of CMV encephalitis also have co-existing CM. Target-specific PCR amplification was used to enrich pathogen sequences before nanopore sequencing. NTS was performed on stored cerebrospinal fluid (CSF) samples and the results were compared with the diagnosis during hospitalization. RESULTS 53 (93.0%) of the patients were male. The median CD4 cell count was 25.0 (IQR: 14.0-63.0) cells/uL. The sensitivities of CSF culture, India ink staining, cryptococcal PCR and NTS for CM were 70.4% (95%CI: 51.5 - 84.1%), 76.0% (95%CI: 56.6 - 88.5%), 77.8% (59.2 - 89.4%) and 85.2% (95%CI: 67.5 - 94.1%), respectively. All those methods had 100% specificity for CM. Our NTS platform could identify Cryptococcus at species level. Moreover, NTS was also able to identify all the 5 cases of toxoplasma encephalitis, 2 cases of CMV encephalitis and 1 VZV encephalitis. However, only 1 of 13 CNS tuberculosis cases was diagnosed by NTS, and so did Xpert MTB/RIF assay. CONCLUSIONS NTS has a good diagnostic performance for CM in HIV-infected patients and may have the ability of simultaneously detecting other pathogens, including mixed infections. With continuing improving of the NTS platform, it may be a promising alterative microbiological test for assisting with the diagnosis of CNS infections.
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Affiliation(s)
- Xihong Yang
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shuilian Zhou
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Pharmaceutical Co.,Ltd, Jiangsu Simcere Diagnostics Co.,Ltd., Nanjing, China
- Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Ziwei Chang
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaotong Xi
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Pharmaceutical Co.,Ltd, Jiangsu Simcere Diagnostics Co.,Ltd., Nanjing, China
- Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China
| | - Jiahui Li
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mengjiao Miao
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yaling Chen
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Chen
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongying Zhang
- Nanjing Center for Disease Control and Prevention, Nanjing Medical University, Nanjing, China.
| | - Ran Ding
- State Key Laboratory of Neurology and Oncology Drug Development, Jiangsu Simcere Pharmaceutical Co.,Ltd, Jiangsu Simcere Diagnostics Co.,Ltd., Nanjing, China.
- Nanjing Simcere Medical Laboratory Science Co., Ltd., Nanjing, China.
| | - Zhiliang Hu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China.
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
- Inovention Center for Infectious Disease of Jiangsu Province, Nanjing, China.
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12
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He S, Xiong Y, Tu T, Feng J, Fu Y, Hu X, Wang N, Li D. Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in cerebrospinal fluid in pediatric patients with central nervous system infection: a systematic review and meta-analysis. BMC Infect Dis 2024; 24:103. [PMID: 38238719 PMCID: PMC10797782 DOI: 10.1186/s12879-024-09010-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/10/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Detecting pathogens in pediatric central nervous system infection (CNSI) is still a major challenge in medicine. In addition to conventional diagnostic patterns, metagenomic next-generation sequencing (mNGS) shows great potential in pathogen detection. Therefore, we systematically evaluated the diagnostic performance of mNGS in cerebrospinal fluid (CSF) in pediatric patients with CNSI. METHODS Related literature was searched in the Web of Science, PubMed, Embase, and Cochrane Library. We screened the literature and extracted the data according to the selection criteria. The quality of included studies was assessed by the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool and the certainty of the evidence was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score system. Then, the pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odd's ratio (DOR), and area under the curve (AUC) of the summary receiver operating characteristic curve (sROC) were estimated in Stata Software and MetaDisc. Subgroup analyses were performed to investigate the potential factors that influence the diagnostic performance. RESULTS A total of 10 studies were included in the meta-analysis. The combined sensitivity was 0.68 (95% confidence interval [CI]: 0.59 to 0.76, I2 = 66.77%, p < 0.001), and the combined specificity was 0.89 (95% CI: 0.80 to 0.95, I2 = 83.37%, p < 0.001). The AUC of sROC was 0.85 (95% CI, 0.81 to 0.87). The quality level of evidence elevated by the GRADE score system was low. CONCLUSIONS Current evidence shows that mNGS presents a good diagnostic performance in pediatric CNSI. Due to the limited quality and quantity of the included studies, more high-quality studies are needed to verify the above conclusion.
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Affiliation(s)
- Sike He
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Ying Xiong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Department of Periodical Press/Chinese Evidence-Based Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Teng Tu
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Yu Fu
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Xu Hu
- Department of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Neng Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Dapeng Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, China.
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13
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Williams A, Webster WZ, Cai C, Milgrom A, Al-Hasan M, Bookstaver PB. Evaluation of the diagnostic utility of metagenomic next-generation sequencing testing for pathogen identification in infected hosts: a retrospective cohort study. Ther Adv Infect Dis 2024; 11:20499361241232854. [PMID: 38404751 PMCID: PMC10893884 DOI: 10.1177/20499361241232854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) testing identifies thousands of potential pathogens in a single blood test, though data on its real-world diagnostic utility are lacking. Objectives Determine the diagnostic utility of mNGS testing in practice and factors associated with high clinical utility. Design Retrospective cohort study of mNGS tests ordered from June 2018 through May 2020 at a community teaching hospital. Methods Tests were included if ordered for diagnostic purposes in patients with probable or high clinical suspicion of infection. Exclusions included patient expiration, hospice care, or transfer outside of the institution. Utility criteria were established a priori by the research team. Two investigators independently reviewed each test and categorized it to either high or low diagnostic utility. Reviewer discordance was referred to a third investigator. The stepwise multiple regression method was used to identify clinical factors associated with high diagnostic utility. Results Among 96 individual tests from 82 unique patients, 80 tests met the inclusion criteria for analysis. At least one potential pathogen was identified in 58% of tests. Among 112 pathogens identified, there were 74 bacteria, 25 viruses, 12 fungi, and 1 protozoon. In all, 46 tests (57.5%) were determined to be of high diagnostic utility. Positive mNGS tests were identified in 36 (78.3%) and 11 (32.4%) of high and low diagnostic utility tests, respectively (p < 0.001). Antimicrobials were changed after receiving test results in 31 (67.4%) of high utility tests and 4 (11.8%) of low utility tests (p < 0.0001). In the multiple regression model, a positive test [odds ratio (OR) = 10.9; 95% confidence interval (CI), 3.2-44.4] and consultation with the company medical director (OR = 3.6; 95% CI, 1.1-13.7) remained significantly associated with high diagnostic utility. Conclusion mNGS testing resulted in high clinical utility in most cases. Positive mNGS tests were associated with high diagnostic utility. Consultation with the Karius® medical director is recommended to maximize utility.
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Affiliation(s)
- Austin Williams
- Department of Pharmacy, Prisma Health Midlands, Columbia, SC, USA
| | - William Zach Webster
- Division of Infectious Diseases, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - Chao Cai
- Department of Clinical Pharmacy and Outcomes Sciences, University of South Carolina College of Pharmacy, Columbia, SC, USA
| | - Alexander Milgrom
- Division of Infectious Diseases, Prisma Health Richland, Columbia, SC, USA
| | - Majdi Al-Hasan
- Division of Infectious Diseases, Prisma Health Richland, Columbia, SC, USA
| | - P. Brandon Bookstaver
- Department of Clinical Pharmacy and Outcomes Sciences, University of South Carolina College of Pharmacy, Columbia, SC 29208, USA
- Department of Pharmacy, Prisma Health Richland, 5 Medical Park Dr., Columbia, SC 29203, USA
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14
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Xiang ZB, Leng EL, Cao WF, Liu SM, Zhou YL, Luo CQ, Hu F, Wen A. A systematic review and meta-analysis of the diagnostic accuracy of metagenomic next-generation sequencing for diagnosing tuberculous meningitis. Front Immunol 2023; 14:1223675. [PMID: 37822937 PMCID: PMC10562686 DOI: 10.3389/fimmu.2023.1223675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023] Open
Abstract
Objective The utility of metagenomic next-generation sequencing (mNGS) in the diagnosis of tuberculous meningitis (TBM) remains uncertain. We performed a meta-analysis to comprehensively evaluate its diagnostic accuracy for the early diagnosis of TBM. Methods English (PubMed, Medline, Web of Science, Cochrane Library, and Embase) and Chinese (CNKI, Wanfang, and CBM) databases were searched for relevant studies assessing the diagnostic accuracy of mNGS for TBM. Review Manager was used to evaluate the quality of the included studies, and Stata was used to perform the statistical analysis. Results Of 495 relevant articles retrieved, eight studies involving 693 participants (348 with and 345 without TBM) met the inclusion criteria and were included in the meta-analysis. The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the summary receiver-operating characteristic curve of mNGS for diagnosing TBM were 62% (95% confidence interval [CI]: 0.46-0.76), 99% (95% CI: 0.94-1.00), 139.08 (95% CI: 8.54-2266), 0.38 (95% CI: 0.25-0.58), 364.89 (95% CI: 18.39-7239), and 0.97 (95% CI: 0.95-0.98), respectively. Conclusions mNGS showed good specificity but moderate sensitivity; therefore, a more sensitive test should be developed to assist in the diagnosis of TBM.
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Affiliation(s)
- Zheng-Bing Xiang
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Er-Ling Leng
- Department of Pediatrics, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
| | - Wen-Feng Cao
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Shi-Min Liu
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Yong-Liang Zhou
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Chao-Qun Luo
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Fan Hu
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - An Wen
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of Neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
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15
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Baek YJ, Lee YJ, Lee JA, Kim JH, Kwon HM, Yeom JS, Park KK, Jeong SJ. Role of α-Defensin and the Microbiome in Prosthetic Joint Infection: A Prospective Cohort Study in Korea. J Clin Med 2023; 12:5964. [PMID: 37762905 PMCID: PMC10532201 DOI: 10.3390/jcm12185964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The utility of α-defensin (AD), leukocyte esterase (LE) levels, and metagenomics sequencing as diagnostic tools for prosthetic joint infection (PJI) has been suggested, but there are few studies among the Asian population. This study aimed to evaluate the diagnostic performance of various biomarkers for PJI and the role of the microbiome in the synovial fluid of patients with prostheses. Patients with suspected knee PJI were enrolled, and their blood and synovial fluid were collected. The cases were classified into the PJI and non-PJI groups. Significant differences between the two groups were observed in the levels of AD (4698 µg/L vs. 296 µg/L, p < 0.001) and positivity for LE (62.5% vs. 21.1%, p = 0.01). AD had 94.4% sensitivity and 89.5% specificity for diagnosing PJI, whereas LE had 37.5% sensitivity and 100% specificity. Microbiome taxonomic profiling showed high sensitivity. The number of operational taxonomic units and the richness of the microbiome in the synovial fluid were higher in the non-PJI than in the PJI group. AD has shown encouraging results in the Asian population as a diagnostic biomarker for PJI, and LE can be used as a diagnostic adjunct. The bacterial richness of the synovial fluid is likely associated with infections.
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Affiliation(s)
- Yae Jee Baek
- Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul 04401, Republic of Korea;
| | - Youn-Jung Lee
- Division of Infectious Diseases, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung Ah Lee
- Division of Infectious Diseases, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung Ho Kim
- Division of Infectious Diseases, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyuck Min Kwon
- Department of Orthopedic Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Joon-Sup Yeom
- Division of Infectious Diseases, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Kwan Kyu Park
- Department of Orthopedic Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Su Jin Jeong
- Department of Orthopedic Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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16
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Tekin A, Truong HH, Rovati L, Lal A, Gerberi DJ, Gajic O, O’Horo JC. The Diagnostic Accuracy of Metagenomic Next-Generation Sequencing in Diagnosing Pneumocystis Pneumonia: A Systemic Review and Meta-analysis. Open Forum Infect Dis 2023; 10:ofad442. [PMID: 37674635 PMCID: PMC10478158 DOI: 10.1093/ofid/ofad442] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
Background Pneumocystis pneumonia (PCP) is a growing concern as the immunocompromised population expands. Current laboratory approaches are limited. This systematic review aimed to evaluate metagenomic next-generation sequencing (MNGS) tests' performance in detecting PCP. Methods Five databases were searched through December 19, 2022, to identify original studies comparing MNGS with clinically diagnosed PCP. To assess the accuracy, symmetric hierarchical summary receiver operating characteristic models were used. Results Eleven observational studies reporting 1442 patients (424 with PCP) were included. Six studies focused exclusively on recipients of biologic immunosuppression (none with HIV-associated immunosuppression). Six were exclusively on bronchoalveolar lavage, while 1 was on blood samples. The sensitivity of MGNS was 0.96 (95% CI, 0.90-0.99), and specificity was 0.96 (95% CI, 0.92-0.98), with negative and positive likelihood ratios of 0.02 (95% CI, 0.01-0.05) and 19.31 (95% CI, 10.26-36.36), respectively. A subgroup analysis of studies exclusively including bronchoalveolar lavage (BAL) and blood samples demonstrated a sensitivity of 0.94 (95% CI, 0.78-0.99) and 0.93 (95% CI, 0.80-0.98) and a specificity of 0.96 (95% CI, 0.88-0.99) and 0.98 (95% CI, 0.76-1.00), respectively. The sensitivity analysis on recipients of biologic immunosuppression showed a sensitivity and specificity of 0.96 (95% CI, 0.90-0.98) and 0.94 (95% CI, 0.84-0.98), respectively. The overall confidence in the estimates was low. Conclusions Despite the low certainty of evidence, MNGS detects PCP with high sensitivity and specificity. This also applies to recipients of biologic immunosuppression and tests performed exclusively on blood samples without the need for BAL. Further studies are required in individuals with HIV-associated immunosuppression.
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Affiliation(s)
- Aysun Tekin
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Hong Hieu Truong
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Lucrezia Rovati
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Danielle J Gerberi
- Mayo Clinic Library Services, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, Minnesota, USA
| | - Ognjen Gajic
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - John C O’Horo
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
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17
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Kato H, Hagihara M, Asai N, Umemura T, Hirai J, Yamagishi Y, Iwamoto T, Mikamo H. Comparison of microbial detection rates in microbial culture methods versus next-generation sequencing in patients with prosthetic joint infection: a systematic review and meta-analysis. J Orthop Surg Res 2023; 18:604. [PMID: 37587529 PMCID: PMC10428596 DOI: 10.1186/s13018-023-03973-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/03/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Accurate diagnosis of prosthetic joint infection (PJI) enables early and effective treatment. However, there is currently no gold standard test for microbial detection of PJI and traditional synovial fluid culture is relatively insensitive. Recently, it has been reported that sonicating fluid culture and next-generation sequencing (NGS) improve microbial detection rates. Hence, we performed a systematic review and meta-analysis to compare microbial detection rates in microbial culture methods with and without sonication versus NGS. METHODS We systematically searched EMBASE, PubMed, Scopus, CINAHL, and Ichushi databases and other sources (previous reviews) until August 2022. We evaluated the detection rates of pathogens in NGS and microbial cultures using samples of synovial or sonicated fluid. RESULTS Of the 170 citations identified for screening, nine studies were included. Pooled analysis indicated that NGS had the highest detection rate among the microbial detection methods (NGS vs. sonicated, odds ratios [OR] 5.09, 95% confidential interval [CI] 1.67-15.50; NGS vs. synovial, OR 4.52, 95% CI 2.86-7.16). Sonicated fluid culture showed a higher detection rate than synovial fluid culture (OR 2.11, 95% CI 1.23-3.62). CONCLUSION NGS might be useful as a screening tool for culture-negative patients. In clinical settings, sonicated fluid culture is a practical method for diagnosing PJI.
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Affiliation(s)
- Hideo Kato
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
- Department of Pharmacy, Mie University Hospital, Mie, Japan
- Division of Clinical Medical Science, Department of Clinical Pharmaceutics, Mie University Graduate School of Medicine, Mie, Japan
| | - Mao Hagihara
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
- Department of Molecular Epidemiology and Biomedical Sciences, Aichi Medical University Hospital, Aichi, Japan
| | - Nobuhiro Asai
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Takumi Umemura
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Jun Hirai
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Yuka Yamagishi
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Takuya Iwamoto
- Department of Pharmacy, Mie University Hospital, Mie, Japan
- Division of Clinical Medical Science, Department of Clinical Pharmaceutics, Mie University Graduate School of Medicine, Mie, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan.
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Zhang H, Shen D, Zhou J, Yang Q, Ying Y, Li N, Cao L, Wang W, Ma X. The Utility of Metagenomic Next-Generation Sequencing (mNGS) in the Management of Patients With Bronchiectasis: A Single-Center Retrospective Study of 93 Cases. Open Forum Infect Dis 2023; 10:ofad425. [PMID: 37663088 PMCID: PMC10470666 DOI: 10.1093/ofid/ofad425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023] Open
Abstract
Background Bronchiectasis is a chronic inflammatory respiratory disease mainly caused by pathogenic infections. However, standard methods of pathogen detection show prolonged cycle durations and unsatisfactory sensitivity and detection rates. Macrogenomic next-generation sequencing (mNGS) emerges as a promising technique for swift, effective, and unbiased pathogen detection and subsequent data interpretation. Methods Here, a retrospective analysis of 93 patients with suspected bronchiectasis was performed to assess the clinical applicability of mNGS. Bronchoalveolar alveolar lavage fluid (BALF) samples were collected from these subjects, followed by standard assays and mNGS separately. The turnaround time, detection rate, and pathogen identification using mNGS were compared with those of standard methods. Results mNGS identified a greater number of bacteria (72 vs 16), fungi (26 vs 19), and viruses (14 vs 0) than standard methods. Specifically, the commonly identified bacteria were Haemophilus, Mycobacterium intracellulare, Pseudomonas, and Streptococcus pneumoniae, while the most detected fungi were Aspergillus and the most prevalent viruses were human herpesviruses. Of note, 29 out of 30 patients (96.67%) who received optimized treatment strategies based on mNGS results experienced recovery. Conclusions Collectively, these findings suggest that mNGS has the potential to improve the diagnosis and treatment of bronchiectasis patients by enabling rapid and precise pathogen detection, which can lead to timely and effective treatment strategies.
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Affiliation(s)
- Hui Zhang
- Department of Respiratory Medicine, The First Hospital of Jiaxing (the Affiliated Hospital of Jiaxing University), The Key Laboratory of Precision Therapy for Lung Cancer, Jiaxing, Zhejiang, China
| | - Dongfeng Shen
- Department of Respiratory Medicine, The First Hospital of Jiaxing (the Affiliated Hospital of Jiaxing University), The Key Laboratory of Precision Therapy for Lung Cancer, Jiaxing, Zhejiang, China
| | - Jiaqi Zhou
- Department of Respiratory Medicine, The First Hospital of Jiaxing (the Affiliated Hospital of Jiaxing University), The Key Laboratory of Precision Therapy for Lung Cancer, Jiaxing, Zhejiang, China
| | - Qingyue Yang
- Biological Medicine Research and Development Center, Yangtze Delta of Zhejiang, Hangzhou, Zhejiang, China
| | - Ying Ying
- Department of Respiratory Medicine, The First Hospital of Jiaxing (the Affiliated Hospital of Jiaxing University), The Key Laboratory of Precision Therapy for Lung Cancer, Jiaxing, Zhejiang, China
| | - Na Li
- Department of Respiratory Medicine, The First Hospital of Jiaxing (the Affiliated Hospital of Jiaxing University), The Key Laboratory of Precision Therapy for Lung Cancer, Jiaxing, Zhejiang, China
| | - Linfeng Cao
- Department of Respiratory Medicine, The First Hospital of Jiaxing (the Affiliated Hospital of Jiaxing University), The Key Laboratory of Precision Therapy for Lung Cancer, Jiaxing, Zhejiang, China
| | - Wenmin Wang
- Biological Medicine Research and Development Center, Yangtze Delta of Zhejiang, Hangzhou, Zhejiang, China
| | - Xiaolong Ma
- Department of Respiratory Medicine, The First Hospital of Jiaxing (the Affiliated Hospital of Jiaxing University), The Key Laboratory of Precision Therapy for Lung Cancer, Jiaxing, Zhejiang, China
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Wang Y, Wang R, Zhang X, Li L, Liu H, Chang Y, Li Q, Wang Y, Qi E, Hao L, Chai W, Yao S, Shi Y, Yan W, Shao W, Zhang J, Chen J, Tian J. Diagnostic efficiency of [68 Ga]Ga-DOTA-FAPI-04 in differentiating periprosthetic hip joint infection and aseptic failure. Eur J Nucl Med Mol Imaging 2023; 50:1919-1928. [PMID: 36813979 DOI: 10.1007/s00259-023-06146-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023]
Abstract
PURPOSE To assess the efficiency of [68 Ga]Ga-DOTA-FAPI-04 in diagnosing periprosthetic hip joint infection and establish a diagnostic standard of clinical significance based on uptake pattern. METHODS [68 Ga]Ga-DOTA-FAPI-04 PET/CT was performed in patients with symptomatic hip arthroplasty from December 2019 to July 2022. The reference standard was based on the 2018 Evidence-Based and Validation Criteria. Two diagnostic criteria, SUVmax and uptake pattern, were used to diagnose PJI. Meanwhile, original data were imported into IKT-snap to draw the view of interest, A.K. was used to extract features of clinical cases, and unsupervised clustering analysis was applied according to the groups. RESULTS A total of 103 patients were included, 28 of whom had PJI. The area under the curve of SUVmax was 0.898, which was better than that of all of the serological tests. The cutoff value of SUVmax was 7.53, and the sensitivity and specificity were 100 and 72%, respectively. The sensitivity, specificity and accuracy of the uptake pattern were 100, 93.1 and 95%, respectively. In radiomics analysis, the features of PJI were significantly different from those of aseptic failure. CONCLUSION The efficiency of [68 Ga]Ga-DOTA-FAPI-04 PET/CT in diagnosing PJI showed promising results, and the diagnostic criteria of the uptake pattern were more clinically instructive. Radiomics also showed certain application prospects in the field of PJI. TRIAL REGISTRATION NUMBER Trial registration: ChiCTR2000041204. Registered 24 September 2019.
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Affiliation(s)
- Yiqun Wang
- Department of Nuclear Medicine, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China
| | - Ruimin Wang
- Department of Nuclear Medicine, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China
| | - Xiaojun Zhang
- Department of Nuclear Medicine, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China
| | - La Li
- Department of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Institute of Sports Medicine of Peking University, Beijing, People's Republic of China
| | - Honghong Liu
- Department of Nuclear Medicine, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China
| | - Yan Chang
- Department of Nuclear Medicine, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China
| | - Qingxiao Li
- Department of Nuclear Medicine, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China
| | - Yanmei Wang
- General Electric (GE) Healthcare China, Shanghai, People's Republic of China
| | - Erpeng Qi
- Department of Interventional Ultrasound, The First Medical Centre, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Libo Hao
- Department of Orthopedics, The First Medical Centre, Chinese PLA General Hospital, Beijing, People's Republic of China
- Department of Orthopedics, The Fourth Medical Centre, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Wei Chai
- Department of Orthopedics, The First Medical Centre, Chinese PLA General Hospital, Beijing, People's Republic of China
- Department of Orthopedics, The Fourth Medical Centre, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Shulin Yao
- Department of Nuclear Medicine, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China
| | - Yuanyuan Shi
- Department of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Institute of Sports Medicine of Peking University, Beijing, People's Republic of China
| | - Wenqiang Yan
- Department of Sports Medicine, Peking University Third Hospital, Beijing Key Laboratory of Sports Injuries, Institute of Sports Medicine of Peking University, Beijing, People's Republic of China
| | - Wuguo Shao
- Fangshan District, HighTech Atom Co., Ltd, No. 1 Sanqiang Road, Xinzhen, Beijing, People's Republic of China
- China Isotope & Radiation Corporation, Haidian District, No. 66 Changwa Zhongjie, Beijing, People's Republic of China
| | - Jinming Zhang
- Department of Nuclear Medicine, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China.
| | - Jiying Chen
- Department of Orthopedics, The First Medical Centre, Chinese PLA General Hospital, Beijing, People's Republic of China.
- Department of Orthopedics, The Fourth Medical Centre, Chinese PLA General Hospital, Beijing, People's Republic of China.
| | - Jiahe Tian
- Department of Nuclear Medicine, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China.
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Ponraj DS, Lund M, Lange J, Poehlein A, Himmelbach A, Falstie-Jensen T, Jørgensen NP, Ravn C, Brüggemann H. Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent. Front Cell Infect Microbiol 2023; 13:1165017. [PMID: 37265503 PMCID: PMC10229904 DOI: 10.3389/fcimb.2023.1165017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/02/2023] [Indexed: 06/03/2023] Open
Abstract
Orthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed on sonication fluid (SF) specimens derived from 24 implants. These were divided into three groups, based on culture results: group I, culture-negative (n = 4); group II, culture-positive for C. acnes (n = 10); and group III, culture-positive for other bacteria (n = 10). In group I, sequence reads from C. acnes were detected in only one SF sample, originating from a suspected case of OIAIs, which was SF and tissue culture-negative. In group II, C. acnes sequences were detected in 7/10 samples. In group III, C. acnes sequence reads were found in 5/10 samples, in addition to sequence reads that matched the bacterial species identified by culture. These samples could represent polymicrobial infections that were missed by culture. Taken together, mNGS was able to detect C. acnes DNA in more samples compared to culture and could be used to identify cases of suspected C. acnes OIAIs, in particular regarding possible polymicrobial infections, where the growth of C. acnes might be compromised due to a fast-growing bacterial species. However, since SF specimens are usually low-biomass samples, mNGS is prone to DNA contamination, possibly introduced during DNA extraction or sequencing procedures. Thus, it is advisable to set a sequence read count threshold, taking into account project- and NGS-specific criteria.
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Affiliation(s)
| | - Michael Lund
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jeppe Lange
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Orthopaedic Surgery, Regional Hospital, Horsens, Denmark
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | | | - Christen Ravn
- Department of Orthopaedic Surgery, Aarhus University Hospital, Aarhus, Denmark
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Indelli PF, Ghirardelli S, Valpiana P, Bini L, Festini M, Iannotti F. Debridement, Antibiotic Pearls, and Retention of the Implant (DAPRI) in the Treatment of Early Periprosthetic Joint Infections: A Consecutive Series. Pathogens 2023; 12:pathogens12040605. [PMID: 37111491 PMCID: PMC10143842 DOI: 10.3390/pathogens12040605] [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: 03/23/2023] [Revised: 04/10/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
INTRODUCTION Periprosthetic joint infections (PJI) represent a devastating consequence following total joint arthroplasty (TJA). In this study, the authors describe a modified surgical technique developed to enhance the classical irrigation and debridement procedure (DAIR) to improve the possibilities of retaining an acutely infected TJA. MATERIALS AND METHODS This technique, debridement antibiotic pearls and retention of the implant (DAPRI), aims to remove the intra-articular biofilm allowing a higher and prolonged local antibiotic concentration by using calcium sulphate antibiotic-added beads in a setting of acute (<4 weeks from symptoms onset) PJI with pathogen identification. The combination of three different surgical techniques (tumor-like synovectomy, argon beam/acetic acid application and chlorhexidine gluconate brushing) aims to remove the bacterial biofilm from the implant without explanting the original hardware. RESULTS In total, 62 patients met the acute infection criteria (<4 weeks of symptoms); there were 57 males and five females. The patients' average age at the time of treatment was 71 years (62-77) and the average BMI was 37 kg/m2. The micro-organism, always identified through synovial fluid analysis (culture, multiplex PCR or Next Generation Sequencing), was an aerobic Gram + in 76% (S. Coag-Neg 41%; S. aureus 16%), Gram-in 10% (E. coli 4%) and anaerobic Gram + in 4%. The DAPRI treatment was performed at an average of 3 days from symptoms onset (1-7 days). All patients underwent a 12-week course of post-operative antibiotic therapy (6 weeks I.V. and 6 weeks oral). All patients were available at the 2-year minimum FU (24-84 months). A total of 48 (77.5%) patients were infection-free at the final FU, while 14 patients underwent 2-stage revision for PJI recurrence. In total, four patients (6.4%) had a prolonged drainage from the wound after placement of the calcium sulphate beads. CONCLUSIONS This study suggests that the DAPRI technique could represent a valid alternative to the classic DAIR procedure. The current authors do not recommend this procedure outside of the main inclusive criteria (acute scenario micro-organism identification).
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Affiliation(s)
- Pier Francesco Indelli
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Redwood City, CA 94063, USA
- Südtiroler Sanitätsbetrieb, 39042 Brixen, Italy
| | - Stefano Ghirardelli
- Orthoapedic Sports Medicine, University of Toronto, Toronto, ON M5S 1B2, Canada
- Institute for Biomechanics, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Pieralberto Valpiana
- Südtiroler Sanitätsbetrieb, 39042 Brixen, Italy
- Institute for Biomechanics, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Lorenzo Bini
- School of Medicine, University of Genova, 16132 Genova, Italy
| | | | - Ferdinando Iannotti
- Department of Orthopaedic and Trauma Surgery, San Paolo Hospital, 00053 Civitavecchia, Italy
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A case for investment in clinical metagenomics in low-income and middle-income countries. THE LANCET. MICROBE 2023; 4:e192-e199. [PMID: 36563703 DOI: 10.1016/s2666-5247(22)00328-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics is the diagnostic approach with the broadest capacity to detect both known and novel pathogens. Clinical metagenomics is costly to run and requires infrastructure, but the use of next-generation sequencing for SARS-CoV-2 molecular epidemiology in low-income and middle-income countries (LMICs) offers an opportunity to direct this infrastructure to the establishment of clinical metagenomics programmes. Local implementation of clinical metagenomics is important to create relevant systems and evaluate cost-effective methodologies for its use, as well as to ensure that reference databases and result interpretation tools are appropriate to local epidemiology. Rational implementation, based on the needs of LMICs and the available resources, could ultimately improve individual patient care in instances in which available diagnostics are inadequate and supplement emerging infectious disease surveillance systems to ensure the next pandemic pathogen is quickly identified.
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23
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Vrancianu CO, Serban B, Gheorghe-Barbu I, Czobor Barbu I, Cristian RE, Chifiriuc MC, Cirstoiu C. The Challenge of Periprosthetic Joint Infection Diagnosis: From Current Methods to Emerging Biomarkers. Int J Mol Sci 2023; 24:ijms24054320. [PMID: 36901750 PMCID: PMC10002145 DOI: 10.3390/ijms24054320] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Due to the increase in the life span and mobility at older ages, the number of implanted prosthetic joints is constantly increasing. However, the number of periprosthetic joint infections (PJIs), one of the most severe complications after total joint arthroplasty, also shows an increasing trend. PJI has an incidence of 1-2% in the case of primary arthroplasties and up to 4% in the case of revision operations. The development of efficient protocols for managing periprosthetic infections can lead to the establishment of preventive measures and effective diagnostic methods based on the results obtained after the laboratory tests. In this review, we will briefly present the current methods used in PJI diagnosis and the current and emerging synovial biomarkers used for the prognosis, prophylaxis, and early diagnosis of periprosthetic infections. We will discuss treatment failure that may result from patient factors, microbiological factors, or factors related to errors during diagnosis.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Bogdan Serban
- University Emergency Hospital, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Correspondence: (B.S.); (I.G.-B.)
| | - Irina Gheorghe-Barbu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- Correspondence: (B.S.); (I.G.-B.)
| | - Ilda Czobor Barbu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Roxana Elena Cristian
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- Romanian Academy, 010071 Bucharest, Romania
| | - Catalin Cirstoiu
- University Emergency Hospital, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
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Molecular Diagnosis of Osteoarticular Implant-Associated Infection: Available Techniques and How We Can Use Them. PROSTHESIS 2022. [DOI: 10.3390/prosthesis5010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite recent advances during the last few years, microbiological diagnosis of prosthetic joint infections remains a challenge. Molecular biology techniques have been developed to try to overcome this problem, and recently, many of them have become available for many laboratories. Some of them, especially commercial multiplex PCR-based assays and universal 16S rDNA homemade PCR assays, are now available in many laboratories. Moreover, new technologies have appeared, especially metagenomics and next-generation sequencing. These techniques have demonstrated their potential in many studies but appear to be experimental at present. A few studies have evaluated the possible use of these methods in the clinical routine, and a review of the critical aspects for the selection of a molecular method (accuracy, complexity, cost) was performed. Finally, a proposal for a protocol that includes molecular biology techniques was made according to the literature published in this field. In conclusion, molecular biology techniques are ready to be used in the clinical routine of a microbiology laboratory, but their use must be carried out in accordance with the many special characteristics of each laboratory. In all cases, the interpretation of the results must be conducted by a multidisciplinary team with experience in the management of these patients.
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Yagupsky P. The Past, Present, and Future of Kingella kingae Detection in Pediatric Osteoarthritis. Diagnostics (Basel) 2022; 12:diagnostics12122932. [PMID: 36552939 PMCID: PMC9777514 DOI: 10.3390/diagnostics12122932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
As a result of the increasing use of improved detection methods, Kingella kingae, a Gram-negative component of the pediatric oropharyngeal microbiota, is increasingly appreciated as the prime etiology of septic arthritis, osteomyelitis, and spondylodiscitis in children aged 6 to 48 months. The medical literature was reviewed to summarize the laboratory methods required for detecting the organism. Kingella kingae is notoriously fastidious, and seeding skeletal system samples onto solid culture media usually fails to isolate it. Inoculation of synovial fluid aspirates and bone exudates into blood culture vials enhances Kingella kingae recovery by diluting detrimental factors in the specimen. The detection of the species has been further improved by nucleic acid amplification tests, especially by using species-specific primers targeting Kingella kingae's rtxA, groEL, and mdh genes in a real-time PCR platform. Although novel metagenomic next-generation technology performed in the patient's plasma sample (liquid biopsy) has not yet reached its full potential, improvements in the sensitivity and specificity of the method will probably make this approach the primary means of diagnosing Kingella kingae infections in the future.
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Affiliation(s)
- Pablo Yagupsky
- Clinical Microbiology Laboratory, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer Sheva 8410500, Israel
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