Incremental value of metagenomic next generation sequencing for the diagnosis of suspected focal infection in adults

doi:10.1016/j.jinf.2019.08.012

Journal of Infection

Volume 79, Issue 5, November 2019, Pages 419-425

https://doi.org/10.1016/j.jinf.2019.08.012 Get rights and content

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.

Introduction

Focal infection is a cluster of diseases during which infections were localized in a specific part of organs and can occur in virtually every organ of a human body, such as eyes, bones, etc.1, 2, 3, 4 Focal infection can be divided into two parts, purulent infections and non-purulent necrotizing tissue infections. Rapid and precise microbiological diagnosis is one of the keystones of the management of diseases to improve patient prognosis. The golden standard for bacterial pathogen diagnosis is undoubtedly culture, but weakness of which still exists in that fastidious bacteria culture is relatively difficult and the culture time consumption fluctuated among different pathogens. Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF)5, 6 has been shown to further increase positive percent agreement through direct identification of pathogens from samples like urine, but it is still more widely used in identifying pathogens from culture-positive specimens.7, 8 Multiplex PCR assays (Filmarray, etc.)9, 10, 11, 12 usually could only detect a limited range of microorganisms. Therefore, new techniques, which had the capability to overcome limitations of current diagnostic tests and allows for advantages of hypothesis-free, culture-independent, and direct pathogen detection from clinical specimens, will further assist clinicians' approaches to focal infection.

Hypothesis-free testing metagenomics next generation sequencing (mNGS) offers a relatively unprejudiced and unlimited diagnostic tool for all microorganisms whose sequencing data was included in database library. Up till now, multiple articles have highlighted its value in pathogen detection from blood,13, 14, 15 respiratory tract,16, 17 cerebral spinal fluid samples18, 19, 20 and prosthetic joint infection.21, 22 However, data of the diagnostic efficacy of mNGS still lacks in the field of focal infection in all parts of the body, and this cohort study aimed to establish an mNGS analysis platform to evaluate its diagnostic value in localized infection further.

Section snippets

Study design and participants

This single-center retrospective cross-section study was conducted in Huashan Hospital, Shanghai, China from March 2017 to December 2017. Patients, aged over 16, who met the diagnostic criteria of suspected focal infection (Table 1A) were consecutively enrolled. All of the collected samples were sent for culture and smear, and the tissue samples were also sent for pathology and imprint cytology. The physicians prescribed other conventional tests such as Xpert MTB/RIF and smear tests according

General characteristics of the enrolled cohort

A total of 98 patients with suspected focal infection were consented for sample collection and went through screening. Three patients were lost to follow up, and three samples failed quality testing during deep sequencing. Finally, 95 patients were enrolled, among which, 67 patients were diagnosed as definite focal infection, six patients were diagnosed as possible focal infection, and 22 patients had non-infectious diseases including vasculitis, tumor, etc. (Fig. 1) (Supplementary material 2).

Discussion

Here, we conducted a single-center retrospective cross-section study to evaluate the use of metagenomic shotgun sequencing applied to focal infection specimens. Accurate pathogen detection is essential to guide clinical management of focal infection, and studies have reported the use of mNGS in identification of causative agents in different kinds of focal tissues.21, 22^,24, 25, 26 Therefore, the overall pro and cons of the usage of mNGS during clinical approach to focal infections is much

Conclusion

We conducted a focal infection cohort and evaluated the diagnostic ability of mNGS in focal infection. mNGS could be administered on a variety of focal tissues and provide credible results during suspected focal infections. The positive percent agreement of mNGS compared to clinical diagnosis is significantly higher than that of conventional methods and culture, resulting in a notably extra increase in pathogen identification. Antimicrobial treatment prior to sample collection may decrease

Acknowledgments

We thank the patients for cooperating with our investigation and acknowledge the professionalism and compassion demonstrated by all the healthcare workers involved in patients’ care.

Declaration of Competing Interest

Authors had no potential conflicts of interest.

Funding

This work was supported by the New and Advanced Technology Project of Shanghai Municipal Hospital: Application of next generation sequencing technique in precise diagnosis of infectious diseases under Grant SHDC12017104; Key Technologies Research and Development Program for Infectious Diseases of China under Grant 2018ZX10305-409-001-003.

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¹: These authors contributed equally to this manuscript.

View full text

Incremental value of metagenomic next generation sequencing for the diagnosis of suspected focal infection in adults

Abstract

Objectives

Methods

Results

Conclusions

Introduction

Section snippets

Study design and participants

General characteristics of the enrolled cohort

Discussion

Conclusion

Acknowledgments

Declaration of Competing Interest

Funding

Lancet

Clin Microbiol Infect

Clin Res Hepatol Gastroenterol

Bladder cystitis following focal infection of group a streptococci

Nature

Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology

FEMS Microbiol Rev

Rapid direct susceptibility testing from positive blood cultures by the matrix-assisted laser desorption ionization-time of flight mass spectrometry-based direct-on-target microdroplet growth assay

J Clin Microbiol

Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection

Anal Bioanal Chem

A novel lab-on-chip platform with integrated solid phase PCR and supercritical angle fluorescence (SAF) microlens array for highly sensitive and multiplexed pathogen detection

Biosens Bioelectron

Comparison of ePlex respiratory pathogen panel with laboratory-developed real-time PCR assays for detection of respiratory pathogens

J Clin Microbiol

The FilmArray® respiratory panel: an automated, broadly multiplexed molecular test for the rapid and accurate detection of respiratory pathogens

Exp Rev Mol Diagn

Coinfections of Zika and Chikungunya viruses in Bahia, Brazil, identified by metagenomic next-generation sequencing

J Clin Microbiol

Next-generation sequencing diagnostics of bacteremia in septic patients

Genome Med

Next-generation sequencing diagnostics of bacteremia in sepsis (Next GeneSiS-Trial): study protocol of a prospective, observational, noninterventional, multicenter, clinical trial

Medicine

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Am J Respir Crit Care Med