Metagenomic Next-Generation Sequencing Improves Diagnosis of Osteoarticular Infections From Abscess Specimens: A Multicenter Retrospective Study

Zhao, Mingwei; Tang, Kai; Liu, Fengsheng; Zhou, Weidong; Fan, Jia; Yan, Guangxuan; Qin, Songbing

doi:10.3389/fmicb.2020.02034

Cited by 19 publications

(21 citation statements)

References 23 publications

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“…In suspected bacterial infections, the main advantage of CMg over conventional methods is its capacity to identify (i) bacteria not detected by routine methods, (ii) antimicrobial resistance genetic determinants, and (iii) other genes of interest such as virulence factors–encoding genes. Six studies ( Ruppé et al, 2017 ; Street et al, 2017 ; Ivy et al, 2018 ; Sanderson et al, 2018 ; Thoendel et al, 2018 ; Zhao et al, 2020 ) investigated the performance of CMg in comparison to culture-based methods in diagnosing BJIs. The sensitivity of CMg varied from 58% at the species level in polymicrobial samples ( Ruppé et al, 2017 ) to 100% in monomicrobial samples ( Thoendel et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections

et al. 2022

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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.

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Section: Introductionmentioning

confidence: 99%

Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections

et al. 2022

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“…Comparable performances were found by other teams on samples drawn from prosthetic joints and other orthopaedic device infections or total knee arthroplasties [53,54]. CMg was also found suitable to detect (i) less common pathogens like M. tuberculosis or Brucella melitensis in a study conducted on patients with osteoarticular infections [55], or (ii) novel pathogens like Mycoplasma salivarium detected in a BJI [56].…”

Section: Reportmentioning

confidence: 70%

The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives

d’Humières

Salmona

Dellière

et al. 2021

Drugs

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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.

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“…Metagenomic next-generation sequencing (mNGS) is a new molecular diagnostic technology. mNGS application in TB of single organ has been reported, such as pulmonary TB, osteoarticular TB, and tuberculous meningitis, but rarely in disseminated TB until now (10)(11)(12). Here, we report a case of disseminated TB with a hepatic mass as the first manifestation.…”

Section: Introductionmentioning

confidence: 85%

Case Report: Metagenomic Next-Generation Sequencing in Diagnosis of Disseminated Tuberculosis of an Immunocompetent Patient

Yang

Zhou

et al. 2021

Front. Med.

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Disseminated tuberculosis (TB) is a rare disease and mainly occurs in immunodeficient patients. It is marked by hematogenous or lymphatic dissemination of Mycobacterium tuberculosis, causing tuberculous infection involving any organ system. Here, we report a case of disseminated TB involving lung, liver, spine, mediastinum, and prostate in an immunocompetent man. The present patient found a hepatic mass without any symptom during health examination. In the next 2 years, further examinations revealed multiple lesions in the lung, mediastinum, spine, and prostate. Imaging examinations, such as contrast-enhanced abdominal CT, F-18 FDG-PET/CT, and radionuclide bone scan, suggested the diagnosis of malignancy or metastatic tumor. Furthermore, histopathological results of the biopsies of the hepatic mass, mediastinal mass, and prostatic mass demonstrated granulomatous inflammation. Therefore, metagenomic next-generation sequencing (mNGS) was utilized to confirm the diagnosis. Mycobacterium tuberculosis complex was simultaneously detected in the spinal surgical resection specimens and bronchoalveolar lavage fluid (BALF), indicating the diagnosis of disseminated TB. mNGS is an emerging molecular diagnostic technology, and its application in disseminated TB has been rarely reported. We highlight that disseminated TB should be considered even in an immunocompetent patient, and mNGS can be performed when the diagnosis is difficult.

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Metagenomic Next-Generation Sequencing Improves Diagnosis of Osteoarticular Infections From Abscess Specimens: A Multicenter Retrospective Study

Cited by 19 publications

References 23 publications

Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections

Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections

The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives

Case Report: Metagenomic Next-Generation Sequencing in Diagnosis of Disseminated Tuberculosis of an Immunocompetent Patient

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