1
|
Ramachandran K, Sethuraman N, Yuvaraj G, Chokkalingam V. Mycoplasma salivarium in a Retropharyngeal abscess - nidus in a niche! Diagn Microbiol Infect Dis 2024; 110:116416. [PMID: 38943820 DOI: 10.1016/j.diagmicrobio.2024.116416] [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: 04/17/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Retropharyngeal abscess (RPA) is considered one of the life threatening conditions which can present either as dysphagia or dyspnoea. Timely management for the airway obstruction along with etiology identification plays a pivotal role in saving a patient's life. Here we present a case of RPA due to a rare pathogen.
Collapse
Affiliation(s)
- Krithiga Ramachandran
- Department of Microbiology, Apollo Main Hospital, Greams Road, Chennai 600006, India
| | - Nandini Sethuraman
- Department of Microbiology, Apollo Main Hospital, Greams Road, Chennai 600006, India.
| | | | | |
Collapse
|
2
|
Hu H, Ding H, Lyu J, Chen Y, Huang C, Zhang C, Li W, Fang X, Zhang W. Detection of rare microorganisms in bone and joint infections by metagenomic next-generation sequencing. Bone Joint Res 2024; 13:401-410. [PMID: 39142657 PMCID: PMC11324352 DOI: 10.1302/2046-3758.138.bjr-2023-0420.r1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/16/2024] Open
Abstract
Aims This aim of this study was to analyze the detection rate of rare pathogens in bone and joint infections (BJIs) using metagenomic next-generation sequencing (mNGS), and the impact of mNGS on clinical diagnosis and treatment. Methods A retrospective analysis was conducted on 235 patients with BJIs who were treated at our hospital between January 2015 and December 2021. Patients were divided into the no-mNGS group (microbial culture only) and the mNGS group (mNGS testing and microbial culture) based on whether mNGS testing was used or not. Results A total of 147 patients were included in the no-mNGS group and 88 in the mNGS group. The mNGS group had a higher detection rate of rare pathogens than the no-mNGS group (21.6% vs 10.2%, p = 0.016). However, the mNGS group had lower rates of antibiotic-related complications, shorter hospital stays, and higher infection control rates compared with the no-mNGS group (p = 0.017, p = 0.003, and p = 0.028, respectively), while there was no significant difference in the duration of antibiotic use (p = 0.957). In culture-negative cases, the mNGS group had lower rates of antibiotic-related complications, shorter hospital stays, and a higher infection control rate than the no-mNGS group (p = 0.036, p = 0.033, p = 0.022, respectively), while there was no significant difference in the duration of antibiotic use (p = 0.748). Conclusion mNGS improves detection of rare pathogens in BJIs. mNGS testing reduces antibiotic-related complications, shortens hospital stay and antibiotic use duration, and improves treatment success rate, benefits which are particularly evident in culture-negative cases.
Collapse
Affiliation(s)
- Hongxin Hu
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Haiqi Ding
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jianhua Lyu
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yang Chen
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Changyu Huang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Chaofan Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xinyu Fang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| |
Collapse
|
3
|
Jiang L, Liang TW, Al-Odaini N, Hu Y, Huang M, Wei L, Li XY, Pan KS, Zheng DY, Jiang ZW, Wei G, Cao CW. Metagenomic Next-Generation Sequencing as an Effective Diagnostic Tool for Talaromycosis in HIV-Negative Patients. Mycopathologia 2024; 189:63. [PMID: 38985209 DOI: 10.1007/s11046-024-00866-x] [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: 02/04/2024] [Accepted: 06/05/2024] [Indexed: 07/11/2024]
Abstract
The diagnosis of Talaromyces marneffei infection in HIV-negative patients remains challenging. There is an urgent need for rapid and convenient methods to diagnose this complicated disease. The aim of this study was to evaluate the diagnostic efficiency of metagenomic next-generation sequencing (mNGS) for talaromycosis in non-HIV-infected patients by comparing mNGS with traditional microbial culture. In total, 66 samples from 57 patients were analyzed via both mNGS and microbial culture. The ROC curve showed a sensitivity for mNGS of 97.22%, which was greater than that of microbial culture (61.11%). Samples from the respiratory tract, infectious skin lesions, and lymph nodes are recommended as routine samples for talaromycosis detection via mNGS. Furthermore, mNGS significantly reduced the diagnostic time compared to microbial culture. Overall, our study demonstrated that mNGS is a promising tool for rapid and accurate pathogenic detection in HIV-negative patients with talaromycosis.
Collapse
Affiliation(s)
- Li Jiang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Tian-Wei Liang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Najwa Al-Odaini
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Yuan Hu
- Richardson Medical Fungal Laboratory, Guangzhou Centre for Fungal Diagnostics and Research, Guangzhou, China
| | - Minli Huang
- Department of Ophthalmology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lili Wei
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Xiu-Ying Li
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Kai-Su Pan
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Dong-Yan Zheng
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Zhi-Wen Jiang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Gao Wei
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China.
| | - Cun-Wei Cao
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China.
| |
Collapse
|
4
|
Zhu N, Zhou D, Xiong W, Zhang X, Li S. Performance of mNGS in bronchoalveolar lavage fluid for the diagnosis of invasive pulmonary aspergillosis in non-neutropenic patients. Front Cell Infect Microbiol 2023; 13:1271853. [PMID: 38029249 PMCID: PMC10644336 DOI: 10.3389/fcimb.2023.1271853] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023] Open
Abstract
The diagnosis of invasive pulmonary aspergillosis (IPA) diseases in non-neutropenic patients remains challenging. It is essential to develop optimal non-invasive or minimally invasive detection methods for the rapid and reliable diagnosis of IPA. Metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) can be a valuable tool for identifying the microorganism. Our study aims to evaluate the performance of mNGS in BALF in suspected IPA patients and compare it with other detection tests, including serum/BALF galactomannan antigen (GM) and traditional microbiological tests (BALF fungal culture and smear and lung biopsy histopathology). Ninety-four patients with suspicion of IPA were finally enrolled in our study. Thirty-nine patients were diagnosed with IPA, and 55 patients were non-IPA. There was significance between the IPA and non-IPA groups, such as BALF GM (P < 0.001), history of glucocorticoid use (P = 0.004), and pulmonary comorbidities (P = 0.002), as well as no significance of the other demographic data including age, sex, BMI, history of cigarette, blood GM assay, T-SPOT.TB, and NEUT#/LYMPH#. The sensitivity of the BALF mNGS was 92.31%, which was higher than that of the traditional tests or the GM assays. The specificity of BALF mNGS was 92.73%, which was relatively similar to that of the traditional tests. The AUC of BALF mNGS was 0.925, which presented an excellent performance compared with other traditional tests or GM assays. Our study demonstrated the important role of BALF detection by the mNGS platform for pathogen identification in IPA patients with non-neutropenic states, which may provide an optimal way to diagnose suspected IPA disease.
Collapse
Affiliation(s)
| | | | | | | | - Shengqing Li
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
5
|
Li H, Niu E, Fu J, Huang Y, Gao Y, Chai W, Chen J. The Clinical Impact of Metagenomic Next-Generation Sequencing for the Diagnosis of Periprosthetic Joint Infection. Infect Drug Resist 2023; 16:6521-6533. [PMID: 37809036 PMCID: PMC10557970 DOI: 10.2147/idr.s420325] [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: 05/07/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023] Open
Abstract
Background Synovial fluid metagenomic next-generation sequencing was introduced into the diagnosis of periprosthetic joint infection (PJI) in recent years. However, the clinical impact of mNGS remains unknown. Therefore, we performed a prospective cohort study to evaluate the clinical impact of mNGS for PJI diagnosis. Materials and Methods Between April 2019 and April 2021, a total of 201 patients with suspected PJI were recruited in a high-volume PJI revision center. All patients underwent joint aspiration before surgeries and the obtained synovial fluids were sent to tests for the diagnosis of PJI. Based on the clinical evaluation of these patients, the patients were categorized into three groups: Group A: the mNGS reports were not acted upon. Group B: mNGS confirmed the standard diagnostic tests of PJI and generated identical clinical impact compared to standard diagnostic tests. Group C: mNGS results guided clinical therapy. Then, the concordance between synovial mNGS and cultures was analyzed. After that, multivariate regressions were performed to explore the "targeted populations" of mNGS tests. Results A total of 107 patients were diagnosed with PJI based on the 2014 MSIS criteria and there were 33, 123, 45 patients in the group A, B, C respectively. The predictive factors of mNGS inducing clinical impact compared to standard diagnostic tests were negative culture results (adjusted OR: 5.88), previous history of joint infection (adjusted OR: 5.97), polymicrobial PJI revealed by culture (adjusted OR: 4.39) and PJI identified by MSIS criteria (adjusted OR: 17.06). Conclusion When standard diagnostic tests for PJI were performed, about 22% of synovial fluid mNGS tests can change the treatment protocols built on standard diagnostic tests and affect the clinical practice. Thus, the use of synovial fluid mNGS in some "target" populations is more valuable compared to others such as patients with previous joint infection, polymicrobial PJI, and culture-negative PJI. Evidence Level Level I.
Collapse
Affiliation(s)
- Hao Li
- Medical School of Chinese PLA, Chinese PLA General Hospital, Beijing, People’s Republic of China
- Department of Orthopedic, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Erlong Niu
- Department of Orthopedics, 305 Hospital of PLA, Beijing, People’s Republic of China
| | - Jun Fu
- Department of Orthopedic, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Yinghao Huang
- School of Computer and Information Technology, Beijing Jiaotong University, Beijing, People’s Republic of China
| | - Yang Gao
- Department of Orthopedic, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Wei Chai
- Department of Orthopedic, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Jiying Chen
- Department of Orthopedic, Chinese PLA General Hospital, Beijing, People’s Republic of China
| |
Collapse
|
6
|
Rodriguez-Nava G, Epstein D, Nelson J. Sternal wound infection with Mycoplasma salivarium following bilateral lung transplant. Transpl Infect Dis 2023; 25:e14120. [PMID: 37622411 DOI: 10.1111/tid.14120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 08/26/2023]
Affiliation(s)
- Guillermo Rodriguez-Nava
- Division of Infectious Diseases & Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - David Epstein
- Division of Infectious Diseases & Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Joanna Nelson
- Division of Infectious Diseases & Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| |
Collapse
|
7
|
Abavisani M, Keikha M. Global analysis on the mutations associated with multidrug-resistant urogenital mycoplasmas and ureaplasmas infection: a systematic review and meta-analysis. Ann Clin Microbiol Antimicrob 2023; 22:70. [PMID: 37563660 PMCID: PMC10416482 DOI: 10.1186/s12941-023-00627-6] [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: 06/04/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND The emergence of multidrug-resistant (MDR) strains of genital pathogens, notably Mycoplasma genitalium and Ureaplasma spp., constitutes a significant global threat today. The present study aimed to evaluate the prevalence and trend of changes in MDR mycoplasma and ureaplasma strains. METHODS An exhaustive search was performed across the ISI Web of Science, PubMed, Scopus, ScienceDirect, and Google Scholar databases to accumulate relevant studies without restrictions until April 2023. We used event rate and corresponding 95% confidence intervals to determine the frequency of resistance-related mutations and examine the trend of antibiotic resistance changes. RESULTS The data from 27 studies, including 24,662 patients across 14 countries, were evaluated. Out of the total studies, 20 focused on M. genitalium infections, and five on Ureaplasma spp. The frequency of resistance-associated mutations to macrolides, tetracyclines, and fluoroquinolones in clinical strains of M. genitalium was 43.5%, 13.1%, and 18.6%, respectively. The prevalence of M. genitalium strains with double resistance and MDR was 11.0% and 17.4%, respectively. The incidence of both double-drug-resistant and MDR strains was higher in the World Health Organization (WHO) Western Pacific Region than in European and American populations. For Ureaplasma strains, resistance-associated mutations to macrolides, tetracyclines, and fluoroquinolones were 40.8%, 25.7%, and 90.3%, respectively. The rate of antibiotic resistance was higher in the African population compared to the European and WHO Western Pacific Regions. The rate of MDR Ureaplasma infections was 13.2%, with a higher incidence in the African population compared to the WHO Western Pacific and European regions. CONCLUSION The proliferation and spread of MDR Mycoplasma and Ureaplasma strains present a significant public health challenge. The situation is indeed alarming, and the rising trend of MDR M. genitalium and MDR Ureaplasma infections suggests that therapies involving macrolides and fluoroquinolones may become less effective.
Collapse
Affiliation(s)
- Mohammad Abavisani
- Student research committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Masoud Keikha
- Department of Medical Microbiology, School of Medicine, Iranshahr University of Medical Sciences, Iranshahr, Iran.
| |
Collapse
|
8
|
Patel R, Tsalik EL, Evans S, Fowler VG, Doernberg SB. Clinically Adjudicated Reference Standards for Evaluation of Infectious Diseases Diagnostics. Clin Infect Dis 2023; 76:938-943. [PMID: 36262037 PMCID: PMC10226744 DOI: 10.1093/cid/ciac829] [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: 08/31/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Lack of a gold standard can present a challenge for evaluation of diagnostic test accuracy of some infectious diseases tests, particularly when the test's accuracy potentially exceeds that of its predecessors. This approach may measure agreement with an imperfect reference, rather than correctness, because the right answer is unknown. Solutions consist of multitest comparators, including those that involve a test under evaluation if multiple new tests are being evaluated together, using latent class modeling, and clinically adjudicated reference standards. Clinically adjudicated reference standards may be considered as comparator methods when no predefined test or composite of tests is sufficiently accurate; they emulate clinical practice in that multiple data pieces are clinically assessed together.
Collapse
Affiliation(s)
- Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ephraim L Tsalik
- Emergency Medicine Service, Durham VA Health Care System, Durham, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Danaher Diagnostics, Washington, District of Columbia, USA
| | - Scott Evans
- Biostatistics Center and the Department of Biostatistics and Bioinformatics, George Washington Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, USA
| | - Vance G Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Sarah B Doernberg
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California, USA
| | | |
Collapse
|
9
|
Hong HL, Flurin L, Thoendel MJ, Wolf MJ, Abdel MP, Greenwood-Quaintance KE, Patel R. Targeted Versus Shotgun Metagenomic Sequencing-based Detection of Microorganisms in Sonicate Fluid for Periprosthetic Joint Infection Diagnosis. Clin Infect Dis 2023; 76:e1456-e1462. [PMID: 35944127 PMCID: PMC10169413 DOI: 10.1093/cid/ciac646] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/15/2022] [Accepted: 08/08/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is increasingly used for periprosthetic joint infection (PJI) diagnosis, but its clinical utility is poorly defined. Shotgun metagenomic sequencing (sNGS) has been reported to identify PJI pathogens undetected by culture in sonicate fluid. However, sNGS is complex and costly. Here, 16S ribosomal RNA (rRNA) gene-based targeted metagenomic sequencing (tNGS) was compared to sNGS of sonicate fluid for microbial detection and identification in patients with total hip arthroplasty (THA) and total knee arthroplasty (TKA) failure. METHODS A convenience sample of sonicate fluids derived from patients who had undergone THA or TKA removal, enriched with culture negative PJI cases, was tested. Samples had been previously tested by sNGS. For tNGS, samples were extracted, amplified by polymerase chain reaction targeting the V1 to V3 regions of the 16S rRNA gene, and sequenced on an Illumina MiSeq. RESULTS A total of 395 sonicate fluids, including 208 from subjects with PJI, were studied. Compared with sonicate fluid culture, tNGS had higher positive percent agreement (72.1 vs 52.9%, P < .001), detecting potential pathogens in 48.0% of culture-negative PJIs. There was no difference between the positive percent agreement of tNGS (72.1%) and sNGS (73.1%, P = .83). CONCLUSIONS 16S rRNA gene-based tNGS is a potential diagnostic tool for PJI pathogen identification in sonicate fluid from failed THAs and TKAs in culture-negative cases, with similar performance characteristics to sNGS.
Collapse
Affiliation(s)
- Hyo-Lim Hong
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Internal Medicine, Daegu Catholic University School of Medicine, Daegu, Republic of Korea
| | - Laure Flurin
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Intensive Care, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Matthew J Thoendel
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J Wolf
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Kerryl E Greenwood-Quaintance
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
10
|
Cai Y, Ding H, Chen X, Chen Y, Huang C, Zhang C, Huang Z, Huang Y, Li W, Zhang W, Fang X. Optimization and standardization of mNGS-based procedures for the diagnosis of Mycoplasma periprosthetic joint infection: A novel diagnostic strategy for rare bacterial periprosthetic joint infection. Front Cell Infect Microbiol 2023; 13:1089919. [PMID: 36936762 PMCID: PMC10014592 DOI: 10.3389/fcimb.2023.1089919] [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: 11/04/2022] [Accepted: 02/07/2023] [Indexed: 03/05/2023] Open
Abstract
Introduction The diagnosis of Mycoplasma periprosthetic joint infection (PJI) is rather difficult due to its rarity and difficult in isolation, there are not standardized diagnostic procedure for Mycoplasma PJI presently. This study aimed to reported a metagenomic next-generation sequencing (mNGS)-based diagnostic strategy for Mycoplasma PJI. Methods In the present study, we have reported the largest number of Mycoplasma PJI that were precisely diagnosed by mNGS and verified by optimized microbial culture methods and (or) 16S PCR polymerase chain reaction (PCR). Results The positive rate of optimized microbial culture methods and 16S PCR in the detection of Mycoplasma PJI was 57.14% and 71.43%, respectively. The infections were well controlled by targeted treatment in all cases. Conclusion The standardized and optimized procedure based on mNGS presented in this study is useful for the diagnosis of Mycoplasma PJI, which might also be provided as a novel diagnostic strategy for rare bacterial PJI.
Collapse
Affiliation(s)
- Yuanqing Cai
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Haiqi Ding
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiaoqing Chen
- Department of Orthopedics, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Yang Chen
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Changyu Huang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Chaofan Zhang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Zida Huang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Ying Huang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenbo Li
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenming Zhang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Wenming Zhang, ; Xinyu Fang,
| | - Xinyu Fang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Wenming Zhang, ; Xinyu Fang,
| |
Collapse
|
11
|
Metagenomic next-generation sequencing restores the diagnosis of a rare infectious complication of B cell depletion. Eur J Clin Microbiol Infect Dis 2022; 41:1269-1273. [PMID: 36001207 DOI: 10.1007/s10096-022-04484-7] [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: 11/24/2021] [Accepted: 08/12/2022] [Indexed: 11/03/2022]
Abstract
A 45-year-old female patient receiving rituximab for B cell non-Hodgkin follicular lymphoma presented unexplained recurrent fever, abdominal discomfort, and pollakiuria. We performed shotgun metagenomic sequencing from peri-kidney collection that identified a co-infection with Mycoplasma hominis and Ureaplasma urealyticum. The patient recovered with sequelae after appropriate antibiotic treatment was given.
Collapse
|
12
|
Xiao L, Totten AH, Crabb DM, Atkinson TP, Waites KB. Antimicrobial susceptibilities and mechanisms of resistance of commensal and invasive Mycoplasma salivarium isolates. Front Microbiol 2022; 13:914464. [PMID: 35979479 PMCID: PMC9376445 DOI: 10.3389/fmicb.2022.914464] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Mycoplasma salivarium, an oral commensal organism, can cause severe invasive infections in immunocompromised individuals. Currently there is no treatment guidance for such infections. We performed antimicrobial susceptibility tests on 39 commensal and invasive M. salivarium isolates and investigated the mechanisms of antimicrobial resistance. Clindamycin was the most active agent [minimum inhibition concentration (MIC) range: 0.004–128 mg/L, MIC50 = 0.031 mg/L, MIC90 = 0.125 mg/ml], followed by tetracycline and levofloxacin. All isolates were resistant to erythromycin (MIC ≥4 mg/L) due to the presence of 2057A (Escherichia coli numbering) in 23S rRNA. Three isolates with elevated clindamycin MICs (≥8 mg/L) harbored A2058T/G mutations in 23S rRNA gene; four sequential isolates from one patient developed C2611T and A2059G mutations accompanying the increase of clindamycin MICs. Five isolates with elevated tetracycline MICs (≥4 mg/L) had mutations in 16S rRNA gene (A965G/T, G966T, or A967C/T) and one of them harbored TetM. Nine isolates with elevated levofloxacin MICs (≥4 mg/L) had one or more mutations in gyrA, gyrB, parC, or parE. Susceptibility breakpoints for clindamycin, tetracycline and levofloxacin were suggested to be ≤0.125, ≤2, and ≤2 mg/L, respectively. Antimicrobial resistance to any of the three agents (clindamycin, tetracycline, or levofloxacin) was documented in 12 (34.3%) non-duplicate isolates, of which 10 were invasive. Levofloxacin resistance was most frequent (25.7%). Multi-drug resistance was also observed (14.3%). This study demonstrates the frequent occurrence of antimicrobial resistance in M. salivarium, emphasizing the need for culture and susceptibility testing to guide antimicrobial therapy.
Collapse
Affiliation(s)
- Li Xiao
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Li Xiao,
| | - Arthur H. Totten
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Donna M. Crabb
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Ken B. Waites
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
| |
Collapse
|
13
|
Fang X, Cai Y, Chen X, Huang C, Lin Y, Huang Z, Zhang C, Huang Y, Li W, Zhang W. The role of metagenomic next-generation sequencing in the pathogen detection of invasive osteoarticular infection. Int J Infect Dis 2022; 122:996-1001. [PMID: 35908720 DOI: 10.1016/j.ijid.2022.07.061] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/19/2022] [Accepted: 07/24/2022] [Indexed: 10/16/2022] Open
Abstract
OBJECTIVE This study aimed to analyzed the pathogenic bacteria spectrum in invasive and primary osteoarticular infection (IOI and POI), and compared the pathogen detection rate of metagenomic next-generation sequencing (mNGS) and microbial culture in IOI and POI. METHODS The suspected POI and IOI cases from 2008 to 2021 were included. The diagnosis of POI or IOI were made by at least two orthopaedic surgeons, two infectious diseases specialist and one senior microbiologist. Demographic characteristics, microbial culture results and so on were recorded. The pathogenic bacteria spectrum in IOI and POI were analyzed and the ability of mNGS and microbial culture in pathogen detection in IOI and POI were compared. RESULTS There were 63 POI cases and 92 cases, the common pathogen in POI and IOI were both Staphylococcus aureus. There are more cases with negative microbial culture results and multiple infections in IOI, and many cases were caused by rare and fastidious bacteria. The introduction of the mNGS could significantly increase the pathogen detection rate to 92.39% in IOI, which was 8.69% higher than that of microbial culture (P=0.007), while the improvement in POI was limited to about 2%. CONCLUSIONS mNGS was an ideal tool for IOI pathogen detection.
Collapse
Affiliation(s)
- Xinyu Fang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Yuanqing Cai
- Department of Orthopaedic Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Xiaoqing Chen
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China; Department of Orthopaedic Surgery, Quanzhou First Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China.
| | - Changyu Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Yiming Lin
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Zida Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Chaofan Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Ying Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Wenbo Li
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Wenming Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| |
Collapse
|
14
|
Bernard E, Peyret T, Plinet M, Contie Y, Cazaudarré T, Rouquet Y, Bernier M, Pesant S, Fabre R, Anton A, Maugis-Rabusseau C, François JM. The DendrisCHIP ® Technology as a New, Rapid and Reliable Molecular Method for the Diagnosis of Osteoarticular Infections. Diagnostics (Basel) 2022; 12:1353. [PMID: 35741163 PMCID: PMC9222036 DOI: 10.3390/diagnostics12061353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022] Open
Abstract
Osteoarticular infections are major disabling diseases that can occur after orthopedic implant surgery in patients. The management of these infections is very complex and painful, requiring surgical intervention in combination with long-term antibiotic treatment. Therefore, early and accurate diagnosis of the causal pathogens is essential before formulating chemotherapeutic regimens. Although culture-based microbiology remains the most common diagnosis of osteoarticular infections, its regular failure to identify the causative pathogen as well as its long-term modus operandi motivates the development of rapid, accurate, and sufficiently comprehensive bacterial species-specific diagnostics that must be easy to use by routine clinical laboratories. Based on these criteria, we reported on the feasibility of our DendrisCHIP® technology using DendrisCHIP®OA as an innovative molecular diagnostic method to diagnose pathogen bacteria implicated in osteoarticular infections. This technology is based on the principle of microarrays in which the hybridization signals between oligoprobes and complementary labeled DNA fragments from isolates queries a database of hybridization signatures corresponding to a list of pre-established bacteria implicated in osteoarticular infections by a decision algorithm based on machine learning methods. In this way, this technology combines the advantages of a PCR-based method and next-generation sequencing (NGS) while reducing the limitations and constraints of the two latter technologies. On the one hand, DendrisCHIP®OA is more comprehensive than multiplex PCR tests as it is able to detect many more germs on a single sample. On the other hand, this method is not affected by the large number of nonclinically relevant bacteria or false positives that characterize NGS, as our DendrisCHIP®OA has been designed to date to target only a subset of 20 bacteria potentially responsible for osteoarticular infections. DendrisCHIP®OA has been compared with microbial culture on more than 300 isolates and a 40% discrepancy between the two methods was found, which could be due in part but not solely to the absence or poor identification of germs detected by microbial culture. We also demonstrated the reliability of our technology in correctly identifying bacteria in isolates by showing a convergence (i.e., same bacteria identified) with NGS superior to 55% while this convergence was only 32% between NGS and microbial culture data. Finally, we showed that our technology can provide a diagnostic result in less than one day (technically, 5 h), which is comparatively faster and less labor intensive than microbial cultures and NGS.
Collapse
Affiliation(s)
- Elodie Bernard
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Thomas Peyret
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Mathilde Plinet
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Yohan Contie
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Thomas Cazaudarré
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Yannick Rouquet
- Laboratoire CBM-Inovie, F-31000 Toulouse, France; (Y.R.); (M.B.); (R.F.)
| | - Matthieu Bernier
- Laboratoire CBM-Inovie, F-31000 Toulouse, France; (Y.R.); (M.B.); (R.F.)
| | - Stéphanie Pesant
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Richard Fabre
- Laboratoire CBM-Inovie, F-31000 Toulouse, France; (Y.R.); (M.B.); (R.F.)
| | - Aurore Anton
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Cathy Maugis-Rabusseau
- Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, INSA, F-31077 Toulouse, France;
| | - Jean Marie François
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 Avenue de Rangueil, F-31077 Toulouse, France
| |
Collapse
|
15
|
d’Humières C, Gaïa N, Gueye S, de Lastours V, Leflon-Guibout V, Maataoui N, Duprilot M, Lecronier M, Rousseau MA, Gamany N, Lescure FX, Senard O, Deconinck L, Dollat M, Isernia V, Le Hur AC, Petitjean M, Nazimoudine A, Le Gac S, Chalal S, Ferreira S, Lazarevic V, Guigon G, Gervasi G, Armand-Lefèvre L, Schrenzel J, Ruppé E. Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections. Front Microbiol 2022; 13:863777. [PMID: 35531285 PMCID: PMC9069157 DOI: 10.3389/fmicb.2022.863777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/15/2022] [Indexed: 11/20/2022] Open
Abstract
Bone and joint infections (BJIs) are complex infections that require precise microbiological documentation to optimize antibiotic therapy. Currently, diagnosis is based on microbiological culture, sometimes complemented by amplification and sequencing of the 16S rDNA gene. Clinical metagenomics (CMg), that is, the sequencing of the entire nucleic acids in a sample, was previously shown to identify bacteria not detected by conventional methods, but its actual contribution to the diagnosis remains to be assessed, especially with regard to 16S rDNA sequencing. In the present study, we tested the performance of CMg in 34 patients (94 samples) with suspected BJIs, as compared to culture and 16S rDNA sequencing. A total of 94 samples from 34 patients with suspicion of BJIs, recruited from two sites, were analyzed by (i) conventional culture, (ii) 16S rDNA sequencing (Sanger method), and (iii) CMg (Illumina Technology). Two negative controls were also sequenced by CMg for contamination assessment. Based on the sequencing results of negative controls, 414 out of 539 (76.7%) bacterial species detected by CMg were considered as contaminants and 125 (23.2%) as truly present. For monomicrobial infections (13 patients), the sensitivity of CMg was 83.3% as compared to culture, and 100% as compared to 16S rDNA. For polymicrobial infections (13 patients), the sensitivity of CMg was 50% compared to culture, and 100% compared to 16S rDNA. For samples negative in culture (8 patients, 21 samples), CMg detected 11 bacteria in 10 samples from 5 different patients. In 5/34 patients, CMg brought a microbiological diagnosis where conventional methods failed, and in 16/34 patients, CMg provided additional information. Finally, 99 antibiotic resistance genes were detected in 24 patients (56 samples). Provided sufficient genome coverage (87.5%), a correct inference of antibiotic susceptibility was achieved in 8/8 bacteria (100%). In conclusion, our study demonstrated that the CMg provides complementary and potentially valuable data to conventional methods of BJIs diagnosis.
Collapse
Affiliation(s)
- Camille d’Humières
- AP-HP, Hôpital Bichat, Service de Bactériologie, Paris, France
- INSERM, Université de Paris Cité, IAME, Paris, France
- *Correspondence: Camille d’Humières,
| | - Nadia Gaïa
- Laboratoire de Recherche Génomique, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | - Signara Gueye
- AP-HP, Hôpital Bichat, Service de Bactériologie, Paris, France
| | - Victoire de Lastours
- INSERM, Université de Paris Cité, IAME, Paris, France
- AP-HP, Hôpital Beaujon, Service de Médecine Interne, Paris, France
| | | | - Naouale Maataoui
- AP-HP, Hôpital Beaujon, Laboratoire de Bactériologie, Paris, France
| | - Marion Duprilot
- AP-HP, Hôpital Beaujon, Laboratoire de Bactériologie, Paris, France
| | - Marie Lecronier
- AP-HP, Hôpital Beaujon, Service de Médecine Interne, Paris, France
| | | | - Naura Gamany
- AP-HP, Hôpital Beaujon, Service de Médecine Interne, Paris, France
| | - François-Xavier Lescure
- INSERM, Université de Paris Cité, IAME, Paris, France
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses, Site Bichat, Paris, France
| | - Olivia Senard
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses, Site Bichat, Paris, France
| | - Laurène Deconinck
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses, Site Bichat, Paris, France
| | - Marion Dollat
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses, Site Bichat, Paris, France
| | - Valentina Isernia
- AP-HP, Hôpital Bichat, Service de Maladies Infectieuses, Site Bichat, Paris, France
| | | | | | | | - Sylvie Le Gac
- AP-HP, Hôpital Bichat, Département d’Epidémiologie Biostatistique et Recherche Clinique, Paris, France
| | - Solaya Chalal
- AP-HP, Hôpital Bichat, Département d’Epidémiologie Biostatistique et Recherche Clinique, Paris, France
| | | | - Vladimir Lazarevic
- Laboratoire de Recherche Génomique, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | | | | | - Laurence Armand-Lefèvre
- AP-HP, Hôpital Bichat, Service de Bactériologie, Paris, France
- INSERM, Université de Paris Cité, IAME, Paris, France
| | - Jacques Schrenzel
- Laboratoire de Recherche Génomique, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | - Etienne Ruppé
- AP-HP, Hôpital Bichat, Service de Bactériologie, Paris, France
- INSERM, Université de Paris Cité, IAME, Paris, France
| |
Collapse
|
16
|
Chen Y, Huang C, Chen X, Cai Y, Li W, Fang X, Zhang W. Bone protein analysis via label-free quantitative proteomics in patients with periprosthetic joint infection. J Proteomics 2022; 252:104448. [PMID: 34883267 DOI: 10.1016/j.jprot.2021.104448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022]
Abstract
Periprosthetic joint infection (PJI) is a catastrophic complication of arthroplasty. The treatment of PJI often requires multiple operations and long-term use of antibiotics, making PJI a substantial health and economic burden for patients. Therefore, there is an urgent need to elucidate the pathological mechanism of PJI to explore new therapeutic methods. This study aimed to explore proteomics changes in bone tissue around the prosthesis during PJI development, to explain the pathological mechanism and to provide new treatment ideas. Ten patients who underwent revision surgery at our institution were included: 5 patients with Staphylococcus aureus PJI and 5 patients with aseptic failure. The proteomics changes in bone tissues after PJI were investigated by label-free quantitative proteomics, and the pathways affected by the differential proteins were analyzed by GO annotation, GO enrichment analysis, KEGG enrichment analysis and protein-protein interaction network analysis. We identified 435 differentially expressed proteins (DEPs), with 213 upregulated and 222 downregulated proteins. Analysis revealed activation of immune-related pathways, such as complement and coagulation cascades, phagocytosis, and neutrophil activation, and inhibition of energy metabolism pathways represented by the TCA cycle. We also observed an altered balance between osteoblasts and osteoclasts during S. aureus PJI. We hope that these processes will reveal new treatment ideas. SIGNIFICANCE: PJI is a catastrophic complication of arthroplasty. When infection occurs, bacteria may invade periprosthetic bone tissue to escape immunity and cause damage. So far, only few studies focused on the changes of proteomics associated to PJI. This is the first study to describe the proteomics changes of periprosthetic bone tissue of patients with PJI. We found that the pathological process of S. aureus PJI mainly involves activation of the immune system, decreased energy metabolism, and an altered balance of osteoblasts and osteoclasts.
Collapse
Affiliation(s)
- Yang Chen
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Changyu Huang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiaoqing Chen
- Department of Orthopedic Surgery, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Yuanqing Cai
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xinyu Fang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.
| | - Wenming Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.
| |
Collapse
|
17
|
Miller S, Chiu C. The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis. Clin Chem 2021; 68:115-124. [PMID: 34969106 DOI: 10.1093/clinchem/hvab173] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) for pathogen detection is becoming increasingly available as a method to identify pathogens in cases of suspected infection. mNGS analyzes the nucleic acid content of patient samples with high-throughput sequencing technologies to detect and characterize microorganism DNA and/or RNA. This unbiased approach to organism detection enables diagnosis of a broad spectrum of infection types and can identify more potential pathogens than any single conventional test. This can lead to improved ability to diagnose patients, although there remains concern regarding contamination and detection of nonclinically significant organisms. CONTENT We describe the laboratory approach to mNGS testing and highlight multiple considerations that affect diagnostic performance. We also summarize recent literature investigating the diagnostic performance of mNGS assays for a variety of infection types and recommend further studies to evaluate the improvement in clinical outcomes and cost-effectiveness of mNGS testing. SUMMARY The majority of studies demonstrate that mNGS has sensitivity similar to specific PCR assays and will identify more potential pathogens than conventional methods. While many of these additional organism detections correlate with the expected pathogen spectrum based on patient presentations, there are relatively few formal studies demonstrating whether these are true-positive infections and benefits to clinical outcomes. Reduced specificity due to contamination and clinically nonsignificant organism detections remains a major concern, emphasizing the importance of careful interpretation of the organism pathogenicity and potential association with the clinical syndrome. Further research is needed to determine the possible improvement in clinical outcomes and cost-effectiveness of mNGS testing.
Collapse
Affiliation(s)
- Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
18
|
Patel R. Advances in Testing for Infectious Diseases—Looking Back and Projecting Forward. Clin Chem 2021; 68:10-15. [DOI: 10.1093/clinchem/hvab110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/05/2021] [Indexed: 12/24/2022]
Affiliation(s)
- Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester MN
| |
Collapse
|
19
|
Wang H, Ren D, Li H, Wang S. Periprosthetic Joint Infection Caused by Mycoplasma hominis, Diagnosed Using Metagenomic Sequencing. Int J Gen Med 2021; 14:7003-7006. [PMID: 34707391 PMCID: PMC8544117 DOI: 10.2147/ijgm.s330924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/28/2021] [Indexed: 12/28/2022] Open
Abstract
To our knowledge, the periprosthetic joint infection (PJI) caused by Mycoplasma hominis is a rare postoperative complication after total knee arthroplasty (TKA). Just a few cases associated with Mycoplasma hominis infection after TKA were reported all over the world currently. In view of the difficulty involved in isolating this microorganism, Mycoplasma hominis infection may be under-recognized and should be considered in culture-negative cases where the microbial etiology is not easily identified. Metagenomic sequencing is a new tool to identify pathogens undetected by conventional methods. In this report, we present a case where metagenomic sequencing was used to identify Mycoplasma hominis as a novel PJI pathogen after TKA in our hospital.
Collapse
Affiliation(s)
- Haiying Wang
- Department of Orthopaedic Surgery, Baoding No.1 Central Hospital, Baoding, 071000, People's Republic of China
| | - Dongliang Ren
- Department of Orthopaedic Surgery, Baoding No.1 Central Hospital, Baoding, 071000, People's Republic of China
| | - Hui Li
- Department of Orthopaedic Surgery, Baoding No.1 Central Hospital, Baoding, 071000, People's Republic of China
| | - Shunyi Wang
- Department of Orthopaedic Surgery, Baoding No.1 Central Hospital, Baoding, 071000, People's Republic of China
| |
Collapse
|
20
|
Culture-Free Detection of Antibiotic Resistance Markers from Native Patient Samples by Hybridization Capture Sequencing. Microorganisms 2021; 9:microorganisms9081672. [PMID: 34442751 PMCID: PMC8398375 DOI: 10.3390/microorganisms9081672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 01/04/2023] Open
Abstract
The increasing incidence of antimicrobial resistance (AMR) is a major global challenge. Routine techniques for molecular AMR marker detection are largely based on low-plex PCR and detect dozens to hundreds of AMR markers. To allow for comprehensive and sensitive profiling of AMR markers, we developed a capture-based next generation sequencing (NGS) workflow featuring a novel AMR marker panel based on the curated AMR database ARESdb. Our primary objective was to compare the sensitivity of target enrichment-based AMR marker detection to metagenomics sequencing. Therefore, we determined the limit of detection (LOD) in synovial fluid and urine samples across four key pathogens. We further demonstrated proof-of-concept for AMR marker profiling from septic samples using a selection of urine samples with confirmed monoinfection. The results showed that the capture-based workflow is more sensitive and requires lower sequencing depth compared with metagenomics sequencing, allowing for comprehensive AMR marker detection with an LOD of 1000 CFU/mL. Combining the ARESdb AMR panel with 16S rRNA gene sequencing allowed for the culture-free detection of bacterial taxa and AMR markers directly from septic patient samples at an average sensitivity of 99%. Summarizing, the newly developed ARESdb AMR panel may serve as a valuable tool for comprehensive and sensitive AMR marker detection.
Collapse
|
21
|
Curren EJ, Lutgring JD, Kabbani S, Diekema DJ, Gitterman S, Lautenbach E, Morgan DJ, Rock C, Salerno RM, McDonald LC. Advancing Diagnostic Stewardship for Healthcare Associated Infections, Antibiotic Resistance, and Sepsis. Clin Infect Dis 2021; 74:723-728. [PMID: 34346494 DOI: 10.1093/cid/ciab672] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 01/14/2023] Open
Abstract
Diagnostic stewardship means ordering the right tests, for the right patient at the right time to inform optimal clinical care. Diagnostic stewardship is an integral part of antibiotic stewardship efforts to optimize antibiotic use and improve patient outcomes, including reductions in antibiotic resistance, and treatment of sepsis. CDC's Division of Healthcare Quality Promotion (DHQP) hosted a meeting on improving patient safety through diagnostic stewardship with a focus on the use of the laboratory. The meeting identified emerging issues in the field of diagnostic stewardship, raised awareness of these issues among stakeholders, and discussed strategies and interventions to address the issues-all with an emphasis on improved outcomes and patient safety. This white paper summarizes the key takeaways of the meeting including needs for diagnostic stewardship implementation, promising future avenues for diagnostic stewardship implementation, and areas of needed research.
Collapse
Affiliation(s)
- Emily J Curren
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Joseph D Lutgring
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Sarah Kabbani
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Daniel J Diekema
- Division of Infectious Diseases, Department of Medicine and Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Steven Gitterman
- Veterans Affairs Medical Center, Washington, D.C.,The George Washington University, Washington, D.C
| | - Ebbing Lautenbach
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Daniel J Morgan
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD
| | - Clare Rock
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Reynolds M Salerno
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA
| | - L Clifford McDonald
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| |
Collapse
|
22
|
d'Humières C, Salmona M, Dellière S, Leo S, Rodriguez C, Angebault C, Alanio A, Fourati S, Lazarevic V, Woerther PL, Schrenzel J, Ruppé E. The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives. Drugs 2021; 81:1453-1466. [PMID: 34328626 PMCID: PMC8323086 DOI: 10.1007/s40265-021-01572-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2021] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples to obtain clinically relevant information such as the identification of microorganisms and their susceptibility to antimicrobials. Over the last decades, sequencing and bioinformatic solutions supporting CMg have much evolved and an increasing number of case reports and series covering various infectious diseases have been published. Metagenomics is a new approach to infectious disease diagnosis that is currently being developed and is certainly one of the most promising for the coming years. However, most CMg studies are retrospective, and few address the potential impact CMg could have on patient management, including initiation, adaptation, or cessation of antimicrobials. In this narrative review, we have discussed the potential role of CMg in bacteriology, virology, mycology, and parasitology. Several reports and case-series confirm that CMg is an innovative tool with which one can (i) identify more microorganisms than with conventional methods in a single test, (ii) obtain results within hours, and (iii) tailor the antimicrobial regimen of patients. However, the cost-efficiency of CMg and its real impact on patient management are still to be determined.
Collapse
Affiliation(s)
- Camille d'Humières
- Université de Paris, IAME, INSERM, 75018, Paris, France.,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France
| | - Maud Salmona
- Unité de Paris, INSERM U976, Insight Team, 75010, Paris, France.,AP-HP, Hôpital Saint-Louis, Laboratoire de Virologie, 75010, Paris, France
| | - Sarah Dellière
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Stefano Leo
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Christophe Rodriguez
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Cécile Angebault
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Alexandre Alanio
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Slim Fourati
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Vladimir Lazarevic
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Paul-Louis Woerther
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Jacques Schrenzel
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Etienne Ruppé
- Université de Paris, IAME, INSERM, 75018, Paris, France. .,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France.
| |
Collapse
|
23
|
Flurin L, Wolf MJ, Greenwood-Quaintance KE, Sanchez-Sotelo J, Patel R. Targeted next generation sequencing for elbow periprosthetic joint infection diagnosis. Diagn Microbiol Infect Dis 2021; 101:115448. [PMID: 34224945 DOI: 10.1016/j.diagmicrobio.2021.115448] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 11/18/2022]
Abstract
16S ribosomal RNA (rRNA) gene PCR followed by next-generation sequencing (NGS) was compared to culture of sonicate fluid derived from total elbow arthroplasty for periprosthetic joint infection (PJI) diagnosis. Sonicate fluids collected from 2007 to 2019 from patients who underwent revision of a total elbow arthroplasty were retrospectively analyzed at a single institution. PCR amplification of the V1-V3 region of the 16S rRNA gene was performed, followed by NGS using an Illumina MiSeq. Results were compared to those of sonicate fluid culture using McNemar's test of paired proportions. Forty-seven periprosthetic joint infections and 58 non-infectious arthroplasty failures were studied. Sensitivity of targeted NGS was 85%, compared to 77% for culture (P = 0.045). Specificity and positive and negative predictive values of targeted NGS were 98, 98 and 89%, respectively, compared to 100, 100 and 84%, respectively, for culture. 16S rRNA gene-based targeted metagenomic analysis of sonicate fluid was more sensitive than culture.
Collapse
Affiliation(s)
- Laure Flurin
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA; Department of Intensive care, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Matthew J Wolf
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Robin Patel
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA; Infectious Diseases, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
24
|
Filkins LM, Bryson AL, Miller SA, Mitchell SL. Navigating Clinical Utilization of Direct-from-Specimen Metagenomic Pathogen Detection: Clinical Applications, Limitations, and Testing Recommendations. Clin Chem 2021; 66:1381-1395. [PMID: 33141913 DOI: 10.1093/clinchem/hvaa183] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Metagenomic next generation sequencing (mNGS) is becoming increasingly available for pathogen detection directly from clinical specimens. These tests use target-independent, shotgun sequencing to detect potentially unlimited organisms. The promise of this methodology to aid infection diagnosis is demonstrated through early case reports and clinical studies. However, the optimal role of mNGS in clinical microbiology remains uncertain. CONTENT We reviewed studies reporting clinical use of mNGS for pathogen detection from various specimen types, including cerebrospinal fluid, plasma, lower respiratory specimens, and others. Published clinical study data were critically evaluated and summarized to identify promising clinical indications for mNGS-based testing, to assess the clinical impact of mNGS for each indication, and to recognize test limitations. Based on these clinical studies, early testing recommendations are made to guide clinical utilization of mNGS for pathogen detection. Finally, current barriers to routine clinical laboratory implementation of mNGS tests are highlighted. SUMMARY The promise of direct-from-specimen mNGS to enable challenging infection diagnoses has been demonstrated through early clinical studies of patients with meningitis or encephalitis, invasive fungal infections, community acquired pneumonia, and other clinical indications. However, the proportion of patient cases with positive clinical impact due to mNGS testing is low in published studies and the cost of testing is high, emphasizing the importance of improving our understanding of 'when to test' and for which patients mNGS testing is appropriate.
Collapse
Affiliation(s)
- Laura M Filkins
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Alexandra L Bryson
- Department of Pathology, Virginia Commonwealth University Health System, Richmond, VA
| | - Steve A Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA
| | - Stephanie L Mitchell
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| |
Collapse
|
25
|
Karczewski D, Müllner M, Perka C, Müller M. Clostridium difficile septic arthritis and periprosthetic joint infection in a patient with acute lymphoblastic leukaemia, T-/B-lymphocytopenia and hypogammaglobulinemia - a case report and review of the literature. Access Microbiol 2021; 3:000233. [PMID: 34151183 PMCID: PMC8209633 DOI: 10.1099/acmi.0.000233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/11/2021] [Indexed: 11/29/2022] Open
Abstract
To the best of our knowledge, we report the first Clostridium difficile infection in a native hip joint with subsequent prosthetic joint infection in a patient at a state of hypogammaglobulinemia. The infection developed following chemotherapy for B-cell precursor acute lymphoblastic leukaemia (BCP-ALL). After chemotherapy, hip arthroplasty was performed for destructive septic arthritis. However, infection in the hip persisted with several failing revisions for more than 3 years, until ultimately hypogammaglobulinemia and T-/B-lymphocytopenia were diagnosed, and supplementation with i.v. immunoglobulins was able to achieve infection control.
Collapse
Affiliation(s)
- Daniel Karczewski
- Department of Orthopaedics, Center for Musculoskeletal Surgery, Charité - University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Maximilian Müllner
- Department of Orthopaedics, Center for Musculoskeletal Surgery, Charité - University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Carsten Perka
- Department of Orthopaedics, Center for Musculoskeletal Surgery, Charité - University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Michael Müller
- Department of Orthopaedics, Center for Musculoskeletal Surgery, Charité - University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany
| |
Collapse
|
26
|
Totten AH, Xiao L, Crabb DM, Ratliff AE, Waites KB, Hwangpo T, Atkinson TP. Septic polyarthritis with Mycoplasma salivarium in a patient with common variable immunodeficiency: case report and review of the literature. Access Microbiol 2021; 3:000221. [PMID: 34151172 PMCID: PMC8208761 DOI: 10.1099/acmi.0.000221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/15/2021] [Indexed: 11/18/2022] Open
Abstract
Mycoplasma salivarium is a common mycoplasma usually isolated from human oropharynx, particularly from individuals with periodontal disease. It is also among the more common mycoplasmal contaminants of eukaryotic cell cultures. Although M. salivarium has been isolated occasionally from abscesses and other sterile sites, to our knowledge, only three cases of septic arthritis have been documented in the past due to this organism, all in patients with humoral immunodeficiency. We now report a fourth case of septic polyarthritis in a patient with profound hypoimmunoglobulinemia who had experienced dental abscesses within the preceding 2 years. Our case highlights the importance of considering invasive mycoplasmal infection in hypogammaglobulinemic patients. It is likely of significance that the patient had suffered recurrent dental abscesses as a source of infection with M. salivarium .
Collapse
Affiliation(s)
- Arthur H Totten
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA.,Present address: Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Li Xiao
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Donna M Crabb
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amy E Ratliff
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ken B Waites
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tracy Hwangpo
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| |
Collapse
|
27
|
Gómez Rufo D, García Sánchez E, García Sánchez JE, García Moro M. [Clinical implications of the genus Mycoplasma]. REVISTA ESPANOLA DE QUIMIOTERAPIA 2021; 34:169-184. [PMID: 33735544 PMCID: PMC8179937 DOI: 10.37201/req/014.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Dentro del género Mycoplasma, las especies que tradicionalmente se han relacionado con cuadros infecciosos han sido principalmente M. pneumoniae, M. genitalium, M. hominis o U. urealyticum. Sin embargo, existen otras muchas que están implicadas y, que muchas veces, son desconocidas para los profesionales sanitarios. El objetivo de esta revisión es identificar todas las especies del género Mycoplasma que se han aislado en el hombre y determinar su participación en la patología infecciosa humana.
Collapse
Affiliation(s)
| | - E García Sánchez
- Enrique García Sánchez, Departamento de Ciencias Biomédicas. Facultad de Medicina. Universidad de Salamanca. Spain.
| | | | | |
Collapse
|
28
|
Evaluation of a commercial microbial enrichment kit used prior DNA extraction to improve the molecular detection of vector-borne pathogens from naturally infected dogs. J Microbiol Methods 2021; 188:106163. [PMID: 33581169 DOI: 10.1016/j.mimet.2021.106163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/28/2023]
Abstract
Accurate detection of vector-borne pathogens (VBPs) is extremely important as the number of reported cases in humans and animals continues to rise in the US and abroad. Validated PCR assays are currently the cornerstone of molecular diagnostics and can achieve excellent analytical sensitivity and specificity. However, the detection of pathogens at low parasitemia still presents a challenge for VBP diagnosis, especially given the very low volume of specimens tested by molecular methods. The objective of this study is to determine if a commercially available microbial enrichment kit, used prior DNA extraction, is capable of expanding the overall microbial community and increasing detectable levels of VBPs in canine blood samples through host DNA depletion. This study used EDTA-whole blood samples from dogs naturally infected with varying parasitemia levels of either Anaplasma phagocytophilum, Babesia gibsoni, or Ehrlichia ewingii. For two VBPs, EDTA-blood samples were diluted to determine the effect of microbial concentration at low parasitemia. Paired EDTA-blood samples from each dog were subjected to traditional, automated DNA extraction with or without the microbial concentrating kit (MolYsis®) prior to DNA extraction. Relative amounts of pathogen DNA in paired samples were determined by real-time PCR and Next-Generation Sequencing targeting conserved regions of 16S rRNA (for bacteria) and 18S rRNA (for protozoa). Results from the three molecular methods suggest that the microbial concentrating kit did not improve the detection of VBPs, although significantly reduced the presence of host DNA. Alternative methods for VBP enrichment in clinical samples prior to molecular testing should continue to be investigated, as it may significantly improve clinical sensitivity and reduce the number of false-negative results.
Collapse
|
29
|
Dulanto Chiang A, Dekker JP. From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics. J Infect Dis 2021; 221:S331-S340. [PMID: 31538184 DOI: 10.1093/infdis/jiz151] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized multiple areas in the field of infectious diseases, from pathogen discovery to characterization of genes mediating drug resistance. Consequently, there is much anticipation that NGS technologies may be harnessed in the realm of diagnostic methods to complement or replace current culture-based and molecular microbiologic techniques. In this context, much consideration has been given to hypothesis-free, culture-independent tests that can be performed directly on primary clinical samples. The closest realizations of such universal diagnostic methods achieved to date are based on targeted amplicon and unbiased metagenomic shotgun NGS approaches. Depending on the exact details of implementation and analysis, these approaches have the potential to detect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undiscovered and those that are uncultivatable. Shotgun metagenomics approaches additionally can provide information on the presence of virulence and resistance genetic elements. While many limitations to the use of NGS in clinical microbiology laboratories are being overcome with decreasing technology costs, expanding curated pathogen sequence databases, and better data analysis tools, there remain many challenges to the routine use and implementation of these methods. This review summarizes recent advances in applications of targeted amplicon and shotgun-based metagenomics approaches to infectious disease diagnostic methods. Technical and conceptual challenges are considered, along with expectations for future applications of these techniques.
Collapse
Affiliation(s)
- Augusto Dulanto Chiang
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| |
Collapse
|
30
|
Esteban J, Gómez-Barrena E. An update about molecular biology techniques to detect orthopaedic implant-related infections. EFORT Open Rev 2021; 6:93-100. [PMID: 33828851 PMCID: PMC8022009 DOI: 10.1302/2058-5241.6.200118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Despite different criteria to diagnose a prosthetic joint infection (PJI), aetiological diagnosis of the causing microorganism remains essential to guide treatment.Molecular-biology-based PJI diagnosis is progressing (faster, higher specificity) in different techniques, from the experimental laboratory into clinical use.Multiplex polymerase chain reaction techniques (custom-made or commercial) provide satisfactory results in clinical series of cases, with specificity close to 100% and sensitivity over 70-80%.Next-generation metagenomics may increase sensitivity while maintaining high specificity.Molecular biology techniques may represent, in the next five years, a significant transformation of the currently available microbiological diagnosis in PJI. Cite this article: EFORT Open Rev 2021;6:93-100. DOI: 10.1302/2058-5241.6.200118.
Collapse
Affiliation(s)
- Jaime Esteban
- Servicio de Microbiología Clínica, Hospital Universitario Fundación Jiménez Díaz-IIS-Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Enrique Gómez-Barrena
- Servicio de Cirugía Ortopédica y Traumatología, Hospital Universitario La Paz-IdiPaz, Universidad Autónoma de Madrid, Madrid, Spain
| |
Collapse
|
31
|
Fang X, Cai Y, Mei J, Huang Z, Zhang C, Yang B, Li W, Zhang W. Optimizing culture methods according to preoperative mNGS results can improve joint infection diagnosis. Bone Joint J 2021; 103-B:39-45. [PMID: 33380187 DOI: 10.1302/0301-620x.103b1.bjj-2020-0771.r2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AIMS Metagenomic next-generation sequencing (mNGS) is useful in the diagnosis of infectious disease. However, while it is highly sensitive at identifying bacteria, it does not provide information on the sensitivity of the organisms to antibiotics. The purpose of this study was to determine whether the results of mNGS can be used to guide optimization of culture methods to improve the sensitivity of culture from intraoperative samples. METHODS Between July 2014 and October 2019, patients with suspected joint infection (JI) from whom synovial fluid (SF) was obtained preoperatively were enrolled. Preoperative aspirated SF was analyzed by conventional microbial culture and mNGS. In addition to samples taken for conventional microbial culture, some samples were taken for intraoperative culture to optimize the culture method according to the preoperative mNGS results. The demographic characteristics, medical history, laboratory examination, mNGS, and culture results of the patients were recorded, and the possibility of the optimized culture methods improving diagnostic efficiency was evaluated. RESULTS A total of 56 cases were included in this study. There were 35 cases of JI and 21 cases of non-joint infection (NJI). The sensitivity, specificity, and accuracy of intraoperative microbial culture after optimization of the culture method were 94.29%, 76.19%, and 87.5%, respectively, while those of the conventional microbial culture method were 60%, 80.95%, and 67.86%, respectively. CONCLUSION Preoperative aspirated SF detected via mNGS can provide more aetiological information than preoperative culture, which can guide the optimization and improve the sensitivity of intraoperative culture. Cite this article: Bone Joint J 2021;103-B(1):39-45.
Collapse
Affiliation(s)
- Xinyu Fang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yuanqing Cai
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jian Mei
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Chaofan Zhang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| |
Collapse
|
32
|
Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
Collapse
Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| |
Collapse
|
33
|
Ebinger A, Fischer S, Höper D. A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics. Comput Struct Biotechnol J 2020; 19:732-742. [PMID: 33552445 PMCID: PMC7822954 DOI: 10.1016/j.csbj.2020.12.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/16/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Metagenomics is a powerful tool to identify novel or unexpected pathogens, since it is generic and relatively unbiased. The limit of detection (LOD) is a critical parameter for the routine application of methods in the clinical diagnostic context. Although attempts for the determination of LODs for metagenomics next-generation sequencing (mNGS) have been made previously, these were only applicable for specific target species in defined samples matrices. Therefore, we developed and validated a generalized probability-based model to assess the sample-specific LOD of mNGS experiments (LODmNGS). Initial rarefaction analyses with datasets of Borna disease virus 1 human encephalitis cases revealed a stochastic behavior of virus read detection. Based on this, we transformed the Bernoulli formula to predict the minimal necessary dataset size to detect one virus read with a probability of 99%. We validated the formula with 30 datasets from diseased individuals, resulting in an accuracy of 99.1% and an average of 4.5 ± 0.4 viral reads found in the calculated minimal dataset size. We demonstrated by modeling the virus genome size, virus-, and total RNA-concentration that the main determinant of mNGS sensitivity is the virus-sample background ratio. The predicted LODmNGS for the respective pathogenic virus in the datasets were congruent with the virus-concentration determined by RT-qPCR. Theoretical assumptions were further confirmed by correlation analysis of mNGS and RT-qPCR data from the samples of the analyzed datasets. This approach should guide standardization of mNGS application, due to the generalized concept of LODmNGS.
Collapse
Affiliation(s)
- Arnt Ebinger
- Institute for Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Mecklenburg-Western Pomerania, Germany
| | - Susanne Fischer
- Institute of Infectology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Mecklenburg-Western Pomerania, Germany
| | - Dirk Höper
- Institute for Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Mecklenburg-Western Pomerania, Germany
| |
Collapse
|
34
|
Oral mucosa infection by Mycoplasma salivarium in a patient with chronic graft-versus-host disease: A diagnostic challenge. Hematol Transfus Cell Ther 2020; 44:259-263. [PMID: 32912839 PMCID: PMC9123595 DOI: 10.1016/j.htct.2020.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/15/2020] [Accepted: 08/12/2020] [Indexed: 11/22/2022] Open
|
35
|
Zhang C, Wang C, Chen F, Huang Z, Fang X, Li W, Yang B, Zhang W. Metagenomic Next-Generation Sequencing Technique Helps Identify Cryptococcal Infection in the Rib: A Report of 2 Cases and Review of the Literature. JBJS Case Connect 2020; 9:e0367. [PMID: 31821204 DOI: 10.2106/jbjs.cc.19.00367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CASE Two patients presented with pathological lytic bone lesions in the rib and associated soft tissue mass believed initially to represent soft tissue neoplasm. However, further consideration of infectious etiologies led to the identification of cryptococcal osteomyelitis. In one case, the microbiological culture was negative, but Cryptococcus neoformans was identified with the help of the metagenomic next-generation sequencing (mNGS) technique. Both patients received oral fluconazole-only treatment, and the infections were successfully eradicated. CONCLUSIONS The mNGS technique helps identify cryptococcal infection in the rib.
Collapse
Affiliation(s)
- Chaofan Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Chaoxin Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Fei Chen
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Zida Huang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Xinyu Fang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Wenbo Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Wenming Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| |
Collapse
|
36
|
Detecting the presence of bacteria in low-volume preoperative aspirated synovial fluid by metagenomic next-generation sequencing. Int J Infect Dis 2020; 99:108-116. [PMID: 32721535 DOI: 10.1016/j.ijid.2020.07.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES Preoperative diagnosis is important for patients who need revision surgery due to PJI. Microbial culture plays an important role in PJI diagnosis, but the sensitivity of cultures is low when the sample amount is limited or when a patient is treated with antibiotics before sample collection. In this study, metagenomic next-generation sequencing (mNGS) was used to detect bacteria in preoperative puncture synovial fluid samples from patients with suspected PJI, and the preoperative and intraoperative culture results were compared to estimate its diagnostic efficiency. METHODS From July 2016 to December 2018, patients with suspected PJI who underwent prosthetic joint revision surgery were included, and the results of those who had been tested by preoperative synovial fluid culture and mNGS were obtained. The demographic characteristics, medical history, laboratory test results, culture results, and mNGS results of each patient were recorded. Then, the efficiency of preoperative synovial fluid mNGS was compared to that of synovial fluid culture for diagnosing PJI. RESULTS A total of 37 patients were included, and 24 patients (25 joints) were diagnosed with PJI. The sensitivity, specificity, and accuracy of preoperative synovial fluid mNGS were 92%, 91.7%, and 83.7%, respectively. The sensitivity, specificity, and accuracy of preoperative synovial fluid culture were 52%, 91.7%, and 43.7%, respectively. CONCLUSIONS With a low volume of synovia (1 ml), mNGS can be performed with higher sensitivity and specificity compared to synovial culture. Thus, mNGS can be a useful supplemental method to improve diagnostic efficiency during the preoperative period.
Collapse
|
37
|
Peiffer-Smadja N, Dellière S, Rodriguez C, Birgand G, Lescure FX, Fourati S, Ruppé E. Machine learning in the clinical microbiology laboratory: has the time come for routine practice? Clin Microbiol Infect 2020; 26:1300-1309. [PMID: 32061795 DOI: 10.1016/j.cmi.2020.02.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Machine learning (ML) allows the analysis of complex and large data sets and has the potential to improve health care. The clinical microbiology laboratory, at the interface of clinical practice and diagnostics, is of special interest for the development of ML systems. AIMS This narrative review aims to explore the current use of ML In clinical microbiology. SOURCES References for this review were identified through searches of MEDLINE/PubMed, EMBASE, Google Scholar, biorXiv, arXiV, ACM Digital Library and IEEE Xplore Digital Library up to November 2019. CONTENT We found 97 ML systems aiming to assist clinical microbiologists. Overall, 82 ML systems (85%) targeted bacterial infections, 11 (11%) parasitic infections, nine (9%) viral infections and three (3%) fungal infections. Forty ML systems (41%) focused on microorganism detection, identification and quantification, 36 (37%) evaluated antimicrobial susceptibility, and 21 (22%) targeted the diagnosis, disease classification and prediction of clinical outcomes. The ML systems used very diverse data sources: 21 (22%) used genomic data of microorganisms, 19 (20%) microbiota data obtained by metagenomic sequencing, 19 (20%) analysed microscopic images, 17 (18%) spectroscopy data, eight (8%) targeted gene sequencing, six (6%) volatile organic compounds, four (4%) photographs of bacterial colonies, four (4%) transcriptome data, three (3%) protein structure, and three (3%) clinical data. Most systems used data from high-income countries (n = 71, 73%) but a significant number used data from low- and middle-income countries (n = 36, 37%). Performance measures were reported for the 97 ML systems, but no article described their use in clinical practice or reported impact on processes or clinical outcomes. IMPLICATIONS In clinical microbiology, ML has been used with various data sources and diverse practical applications. The evaluation and implementation processes represent the main gap in existing ML systems, requiring a focus on their interpretability and potential integration into real-world settings.
Collapse
Affiliation(s)
- N Peiffer-Smadja
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK; Université de Paris, IAME, INSERM, F-75018 Paris, France
| | - S Dellière
- Université de Paris, Laboratoire de Parasitologie-Mycologie, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - C Rodriguez
- Department of Prevention, Diagnosis and Treatment of Infections, Henri-Mondor Hospital, APHP, Université Paris-Est Créteil, IMRB, INSERM U955, Créteil, France
| | - G Birgand
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - F-X Lescure
- Université de Paris, IAME, INSERM, F-75018 Paris, France
| | - S Fourati
- Department of Prevention, Diagnosis and Treatment of Infections, Henri-Mondor Hospital, APHP, Université Paris-Est Créteil, IMRB, INSERM U955, Créteil, France
| | - E Ruppé
- Université de Paris, IAME, INSERM, F-75018 Paris, France.
| |
Collapse
|
38
|
Abstract
Purpose of Review Major technologic advances in two main areas of molecular infectious disease diagnostics have resulted in accelerated adoption or ordering, outpacing implementation, and clinical utility studies. Physicians must understand the limitations to and appropriate utilization of these technologies in order to provide cost-effective and well-informed care for their patients. Recent Findings Rapid molecular testing and, to a lesser degree, clinical metagenomics are now being routinely used in clinical practice. While these tests allow for a breadth of interrogation not possible with conventional microbiology, they pose new challenges for diagnostic and antimicrobial stewardship programs. This review will summarize the most recent literature on these two categories of technologic advances and discuss the few studies that have looked at utilization and stewardship approaches. This review also highlights the future directions for both of these technologies. Summary The appropriate utilization of rapid molecular testing and clinical metagenomics has not been well established. More studies are needed to assess their prospective impacts on patient management and antimicrobial stewardship efforts as the future state of infectious disease diagnostics will see continued expansion of these technologic advances.
Collapse
|
39
|
Diagnosis and treatment of mycoplasmal septic arthritis: a systematic review. INTERNATIONAL ORTHOPAEDICS 2019; 44:199-213. [PMID: 31792575 DOI: 10.1007/s00264-019-04451-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/11/2019] [Indexed: 12/15/2022]
Abstract
PURPOSE Septic arthritis caused by Mycoplasma is rare. The diagnosis and effective treatment of mycoplasmal septic arthritis remains a serious problem for clinicians. The aim of this systematic review was to document the available evidence on the diagnosis and treatment methods for mycoplasmal septic arthritis and to provide guidance for clinicians. METHODS The PubMed, EMBASE, and Cochrane Library databases were searched in December 2018.The searches were limited to the English language. Article screening and data extraction and compilation were conducted by two independent reviewers. All the included studies were assessed using the Methodological Index for Non-randomized Studies (MINORS) tool. RESULTS There was a total of 33 articles including 34 cases of mycoplasmal septic arthritis and eight of them were periprosthetic joint infection (PJI). Twenty-four patients (70.6%) were immunocompromised, and the synovial fluid white blood cell (WBC) count was significantly lower in the immunocompromised group than in the immunocompetent group (48,527 × 106/L vs. 100,640 × 106/L; P = 0.009). The traditional culture method took longer, and the positivity rate was lower than that of nucleic acid testing (50% vs. 100%; P = 0.016). Only 19.2% (5/26) of patients treated with empiric antibiotics were relieved of symptoms, while 82.4% (28/34) of patients achieved satisfactory results after being treated with antibiotics against Mycoplasma. CONCLUSION The possibility of mycoplasmal septic arthritis should be considered if patients with joint infections have a history of immunocompromised, repeated negative cultures, and poor empiric antibiotic treatment results. The rational use of nucleic acid testing technologies can help in the clinical diagnosis and treatment of mycoplasmal septic arthritis.
Collapse
|
40
|
Han D, Li Z, Li R, Tan P, Zhang R, Li J. mNGS in clinical microbiology laboratories: on the road to maturity. Crit Rev Microbiol 2019; 45:668-685. [PMID: 31691607 DOI: 10.1080/1040841x.2019.1681933] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical laboratories for unbiased culture-independent diagnosis. Whether it can be a next routine pathogen identification tool has become a topic of concern. We review the current implementation of this new technology for infectious disease diagnostics and discuss the feasibility of transforming mNGS into a routine diagnostic test. Since 2008, numerous studies from over 20 countries have revealed the practicality of mNGS in the work-up of undiagnosed infectious diseases. mNGS performs well in identifying rare, novel, difficult-to-detect and coinfected pathogens directly from clinical samples and presents great potential in resistance prediction by sequencing the antibiotic resistance genes, providing new diagnostic evidence that can be used to guide treatment options and improve antibiotic stewardship. Many physicians recognized mNGS as a last resort method to address clinical infection problems. Although several hurdles, such as workflow validation, quality control, method standardisation, and data interpretation, remain before mNGS can be implemented routinely in clinical laboratories, they are temporary and can be overcome by rapidly evolving technologies. With more validated workflows, lower cost and turnaround time, and simplified interpretation criteria, mNGS will be widely accepted in clinical practice. Overall, mNGS is transforming the landscape of clinical microbiology laboratories, and to ensure that it is properly utilised in clinical diagnosis, both physicians and microbiologists should have a thorough understanding of the power and limitations of this method.
Collapse
Affiliation(s)
- Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ziyang Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| |
Collapse
|
41
|
Thoendel MJ, Jeraldo PR, Greenwood-Quaintance KE, Yao JZ, Chia N, Hanssen AD, Abdel MP, Patel R. Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach. Clin Infect Dis 2019; 67:1333-1338. [PMID: 29648630 DOI: 10.1093/cid/ciy303] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 04/09/2018] [Indexed: 12/14/2022] Open
Abstract
Background Metagenomic shotgun sequencing has the potential to change how many infections, particularly those caused by difficult-to-culture organisms, are diagnosed. Metagenomics was used to investigate prosthetic joint infections (PJIs), where pathogen detection can be challenging. Methods Four hundred eight sonicate fluid samples generated from resected hip and knee arthroplasties were tested, including 213 from subjects with infections and 195 from subjects without infection. Samples were enriched for microbial DNA using the MolYsis basic kit, whole-genome amplified, and sequenced using Illumina HiSeq 2500 instruments. A pipeline was designed to screen out human reads and analyze remaining sequences for microbial content using the Livermore Metagenomics Analysis Toolkit and MetaPhlAn2 tools. Results When compared to sonicate fluid culture, metagenomics was able to identify known pathogens in 94.8% (109/115) of culture-positive PJIs, with additional potential pathogens detected in 9.6% (11/115). New potential pathogens were detected in 43.9% (43/98) of culture-negative PJIs, 21 of which had no other positive culture sources from which these microorganisms had been detected. Detection of microorganisms in samples from uninfected aseptic failure cases was conversely rare (7/195 [3.6%] cases). The presence of human and contaminant microbial DNA from reagents was a challenge, as previously reported. Conclusions Metagenomic shotgun sequencing is a powerful tool to identify a wide range of PJI pathogens, including difficult-to-detect pathogens in culture-negative infections.
Collapse
Affiliation(s)
- Matthew J Thoendel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Janet Z Yao
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Nicholas Chia
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Arlen D Hanssen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota.,Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
42
|
Zhang C, Fang X, Huang Z, Li W, Zhang CF, Yang B, Zhang W. Value of mNGS in sonication fluid for the diagnosis of periprosthetic joint infection. ARTHROPLASTY 2019; 1:9. [PMID: 35240758 PMCID: PMC8796449 DOI: 10.1186/s42836-019-0006-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/09/2019] [Indexed: 12/24/2022] Open
Abstract
Objective To evaluate the effectiveness of metagenomics next-generation sequencing (mNGS) for the detection of pathogenic microorganisms in periprosthetic joint infection (PJI) using the sonication fluid from removed prosthesis. Methods In this prospective diagnostic cohort study, 44 patients who underwent revision arthroplasty in our hospital from December 2016 to December 2018 were screened. Seven cases were excluded due to incomplete clinical data, insufficient synovial fluid or failure of sequencing. According to the PJI diagnostic criteria recommended by the Musculoskeletal Infection Society (MSIS), the patients were defined as PJI or aseptic failure (AF). Conventional culture, sonication fluid culture and mNGS were performed, in order to assess the value of mNGS using sonication fluid for the diagnosis of PJI, and the mNGS results were analyzed and compared with the conventional and sonication fluid culture. Results Among the 37 patients, 24 were diagnosed with PJI (64.86%), while 13 were diagnosed with aseptic failure. Among the 24 patients diagnosed with PJI, 15 cases (62.5%), 17 cases (70.8%) and 24 cases (100%) yielded positive results in conventional culture, sonication fluid culture and mNGS, respectively. In addition, mNGS detected the same pathogenic microorganisms in 16 out of the 17 (94.12%) culture-positive (conventional + sonication fluid) PJI cases. In the only one discrepancy case, Enterococcus faecalis was identified in the cultures, while Enterobacter cloacae was detected by mNGS. In the AF group, the results of the conventional culture were all negative. Nevertheless, Staphylococcus epidermidis was detected in the sonication fluid culture and mNGS in one case. The diagnostic sensitivity of mNGS for PJI was 100%, which was significantly higher than 70.83% (P = 0.039) of the sonication fluid culture and 62.5% (P = 0.021) of the conventional culture. The diagnostic specificity of mNGS for PJI was 92.31%, which was not significantly different (P > 0.05) from those of the conventional culture (100%) and sonication fluid culture (92.31%). Conclusion We demonstrated that mNGS using sonication fluid can improve the detection rate of pathogenic microorganisms and provide valuable information for the diagnosis of PJI. In addition, mNGS can effectively identify pathogenic microorganisms in culture-negative PJIs cases, especially for the cases who have been treated with antibiotics before sample acquisition or have fastidious microorganisms. Therefore, this method can potentially help to guide the clinical use of antibiotics.
Collapse
|
43
|
Zhang HC, Ai JW, Cui P, Zhu YM, Hong-Long W, Li YJ, Zhang WH. Incremental value of metagenomic next generation sequencing for the diagnosis of suspected focal infection in adults. J Infect 2019; 79:419-425. [PMID: 31442461 DOI: 10.1016/j.jinf.2019.08.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/15/2019] [Accepted: 08/18/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVES Microbiological diagnosis is essential during clinical management of focal infections. Metagenomic next generation sequencing (mNGS) has been reported as a promising diagnostic tool in infectious diseases. However, little is known about the clinical utility of mNGS in focal infections. METHODS We conducted a single-center retrospective study to investigate impact of mNGS on focal infection diagnosis and compared it with conventional methods, including culture, pathological examination, Xpert MTB/RIF, etc. 98 suspected focal infections cases were enrolled, and medical records were reviewed to determine their rates of detection, time-to-identification, and clinical outcomes. RESULTS mNGS showed a satisfying diagnostic positive percent agreement of 86.30% (95% CI: 75.79-92.88%) in a variety of tissues, compared to 45.21% (95% CI: 33.68-57.24%) for culture and 57.53% (95% CI: 45.43-68.84%)f for conventional methods (p < 0.0125), and detected an extra 34 pathogenic microorganisms. Time requirement for pathogen identification using mNGS ranges from 31 h to 55 h, which showed an advantage over culture. (82.36 h; 95%CI: 65.83, 98.89; P < 0.05) CONCLUSIONS: mNGS showed promising potential in pathogenic diagnosis during focal infections and might enable clinicians to make more timely and targeted therapeutic decisions.
Collapse
Affiliation(s)
- Hao-Cheng Zhang
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Jing-Wen Ai
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Peng Cui
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Yi-Min Zhu
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
| | - Wu Hong-Long
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Yong-Jun Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Wen-Hong Zhang
- Department of Infectious Disease, Huashan Hospital of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China.
| |
Collapse
|
44
|
Trousdale WH, Salib CG, Reina N, Lewallen EA, Viste A, Berry DJ, Morrey ME, Sanchez-Sotelo J, van Wijnen AJ, Abdel MP. A Drug Eluting Scaffold for the Treatment of Arthrofibrosis. Tissue Eng Part C Methods 2019; 24:514-523. [PMID: 30101668 DOI: 10.1089/ten.tec.2018.0136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
INTRODUCTION The inflammatory cascade and production of prostaglandins may play a role in the pathogenesis of arthrofibrosis, a debilitating condition after joint replacement and other orthopedic procedures. Cyclooxygenase 2 (COX-2) inhibitors may mitigate the inflammatory response and formation of arthrofibrosis, but oral delivery is associated with risk of systemic side effects in many patients. The nonsteroidal anti-inflammatory drug, celecoxib, may have therapeutic benefits for arthrofibrosis, but current methods for its local delivery (e.g., biologically derived microspheres) are not translatable to immediate clinical use. Therefore, we investigated the use of a drug scaffold for sustainable intra-articular delivery of therapeutic doses of celecoxib. MATERIALS AND METHODS Celecoxib was eluted from clinically approved biodegradable collagen membranes over 7 days as measured by UV spectroscopy and high-performance liquid chromatography/mass spectroscopy. Eluted concentrations of celecoxib were examined for toxicity (live/dead staining) and profibrotic gene expression (real-time-quantitative polymerase chain reaction) in rabbit knee capsular fibroblasts in vitro. RESULTS Sustained concentrations of celecoxib eluted from the membrane over 7 days from both a wet and dry scaffold, with a burst release (30-45%) of celecoxib in the first 2 h. Rabbit cells treated with eluted concentrations experienced a toxic response to the burst release doses, and inhibitory effects on profibrotic genes were seen in response to the sustained doses eluted from the scaffold. CONCLUSIONS This study characterized the novel use of collagen scaffolds for intra-articular drug delivery to treat arthrofibrosis. Scaffolds exhibit celecoxib release through an initial burst release followed by sustained release of antifibrotic doses over 7 days. Thus, collagen scaffolds are promising for clinician-directed treatment of arthrofibrosis.
Collapse
Affiliation(s)
| | | | - Nicolas Reina
- 1 Department of Orthopedic Surgery, Mayo Clinic , Rochester, Minnesota
| | - Eric A Lewallen
- 1 Department of Orthopedic Surgery, Mayo Clinic , Rochester, Minnesota.,2 Department of Biological Sciences, Hampton University , Hampton, Virginia
| | - Anthony Viste
- 1 Department of Orthopedic Surgery, Mayo Clinic , Rochester, Minnesota
| | - Daniel J Berry
- 1 Department of Orthopedic Surgery, Mayo Clinic , Rochester, Minnesota
| | - Mark E Morrey
- 1 Department of Orthopedic Surgery, Mayo Clinic , Rochester, Minnesota
| | | | | | - Matthew P Abdel
- 1 Department of Orthopedic Surgery, Mayo Clinic , Rochester, Minnesota
| |
Collapse
|
45
|
Evaluation of the CosmosID Bioinformatics Platform for Prosthetic Joint-Associated Sonicate Fluid Shotgun Metagenomic Data Analysis. J Clin Microbiol 2019; 57:JCM.01182-18. [PMID: 30429253 DOI: 10.1128/jcm.01182-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
We previously demonstrated that shotgun metagenomic sequencing can detect bacteria in sonicate fluid, providing a diagnosis of prosthetic joint infection (PJI). A limitation of the approach that we used is that data analysis was time-consuming and specialized bioinformatics expertise was required, both of which are barriers to routine clinical use. Fortunately, automated commercial analytic platforms that can interpret shotgun metagenomic data are emerging. In this study, we evaluated the CosmosID bioinformatics platform using shotgun metagenomic sequencing data derived from 408 sonicate fluid samples from our prior study with the goal of evaluating the platform vis-à-vis bacterial detection and antibiotic resistance gene detection for predicting staphylococcal antibacterial susceptibility. Samples were divided into a derivation set and a validation set, each consisting of 204 samples; results from the derivation set were used to establish cutoffs, which were then tested in the validation set for identifying pathogens and predicting staphylococcal antibacterial resistance. Metagenomic analysis detected bacteria in 94.8% (109/115) of sonicate fluid culture-positive PJIs and 37.8% (37/98) of sonicate fluid culture-negative PJIs. Metagenomic analysis showed sensitivities ranging from 65.7 to 85.0% for predicting staphylococcal antibacterial resistance. In conclusion, the CosmosID platform has the potential to provide fast, reliable bacterial detection and identification from metagenomic shotgun sequencing data derived from sonicate fluid for the diagnosis of PJI. Strategies for metagenomic detection of antibiotic resistance genes for predicting staphylococcal antibacterial resistance need further development.
Collapse
|
46
|
Huang Z, Zhang C, Li W, Fang X, Wang Q, Xing L, Li Y, Nie X, Yang B, Zhang W. Metagenomic next-generation sequencing contribution in identifying prosthetic joint infection due to Parvimonas micra: a case report. J Bone Jt Infect 2019; 4:50-55. [PMID: 30755848 PMCID: PMC6367198 DOI: 10.7150/jbji.30615] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/13/2019] [Indexed: 11/17/2022] Open
Abstract
Identifying fastidious pathogens in patients with prosthetic joint infection (PJI) by culture is challenging. Metagenomic next-generation sequencing (mNGS) is a novel culture-independent approach that is associated with a higher likelihood for identifying pathogens. We present a case where mNGS was implemented to identify Parvimonas micra, a rarely reported and difficult-to-culture PJI pathogen.
Collapse
Affiliation(s)
- Zida Huang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Chongjing Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Wenbo Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Xinyu Fang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Qijin Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Li Xing
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yingzhen Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xifang Nie
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Wenming Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| |
Collapse
|
47
|
Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing. mSphere 2019; 4:4/1/e00529-18. [PMID: 30651402 PMCID: PMC6336080 DOI: 10.1128/msphere.00529-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms. Culture-independent methods that target genome fragments have shown promise in identifying certain pathogens, but the holy grail of comprehensive pathogen genome detection from microbiologically complex samples for subsequent forensic analyses remains a challenge. In the context of an investigation of a nosocomial outbreak, we used shotgun metagenomic sequencing of a human fecal sample and a neural network algorithm based on tetranucleotide frequency profiling to reconstruct microbial genomes and tested the same approach using rectal swabs from a second patient. The approach rapidly and readily detected the genome of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in the patient fecal specimen and in the rectal swab sample, achieving a level of strain resolution that was sufficient for confident transmission inference during a highly clonal outbreak. The analysis also detected previously unrecognized colonization of the patient by vancomycin-resistant Enterococcus faecium, another multidrug-resistant bacterium. IMPORTANCE The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms.
Collapse
|
48
|
|
49
|
Mercuri LG. Prevention and detection of prosthetic temporomandibular joint infections-update. Int J Oral Maxillofac Surg 2018; 48:217-224. [PMID: 30316660 DOI: 10.1016/j.ijom.2018.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/25/2018] [Indexed: 10/28/2022]
Abstract
Prosthetic joint infections are not only distressing complications for patients and surgeons, but also have an enormous financial impact on healthcare systems. The reported incidence of prosthetic joint infection is likely underestimated due to difficulties in their diagnosis. This unfortunate complication has challenged joint replacement surgeons for years, despite all the advances made in this surgical discipline. Since eradication of these infections can be very difficult, prevention remains the primary objective. Identifying recipient risk factors, adopting a proper surgical technique, appropriate wound care, optimizing the operating room environment, and appropriate postoperative care have become some of the core elements that can help to minimize the overall incidence of this complication. The purpose of this article is to provide the temporomandibular joint replacement surgeon with an update on the prevention and detection of prosthetic joint infections based on a review of the most recent information published in the orthopedic and surgical literature.
Collapse
Affiliation(s)
- L G Mercuri
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, Illinois, USA.
| |
Collapse
|
50
|
Huang Z, Zhang C, Fang X, Li W, Zhang C, Zhang W, Yang B. Identification of musculoskeletal infection with non-tuberculous mycobacterium using metagenomic sequencing. J Infect 2018; 78:158-169. [PMID: 30312646 DOI: 10.1016/j.jinf.2018.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 09/29/2018] [Accepted: 10/01/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Zida Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, No.20 Chazhong Road, Fuzhou 350005, China
| | - Chongjing Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, No.20 Chazhong Road, Fuzhou 350005, China
| | - Xinyu Fang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, No.20 Chazhong Road, Fuzhou 350005, China
| | - Wenbo Li
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, No.20 Chazhong Road, Fuzhou 350005, China
| | - Chaofan Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, No.20 Chazhong Road, Fuzhou 350005, China
| | - Wenming Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, No.20 Chazhong Road, Fuzhou 350005, China.
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, No.20 Chazhong Road, Fuzhou 350005, China.
| |
Collapse
|