Application of metagenomic next-generation sequencing in cutaneous tuberculosis

A retrospective analysis comparing metagenomic next-generation sequencing with conventional microbiology testing for the identification of pathogens in patients with severe infections

Introduction

The application value of metagenomic next-generation sequencing (mNGS) in detecting pathogenic bacteria was evaluated to promote the rational and accurate use of antibiotics. A total of 180 patients with severe infections were included in this study.

Methods

Based on their different symptoms, bronchoalveolar lavage fluid (BALF) or blood samples were collected for conventional microbiological testing (CMT) and mNGS.

Results

The results indicated that the etiological diagnosis rate of mNGS (78.89%) was significantly higher than that of CMT (20%) (p<0.001). Notably, mNGS exhibited greater sensitivity towards rare pathogens such as Chlamydia pneumoniae, Mycobacterium tuberculosis complex, and Legionella pneumophila, which were undetectable by CMT. Additionally, 64 cases underwent blood culture, BALF culture, and mNGS testing. Analysis revealed that the positive rate of blood culture (3.1%) was lower than that of BALF (25%), and the positive rate of CMT from both types was significantly lower than that of mNGS (89.1%) (p<0.001). In this study, 168 mNGS results were accepted, and 116 patients had their antibiotic therapy adjustment based on mNGS. Paired analysis indicated that white blood cell count (WBC), procalcitonin (PCT), C-reactive protein (CRP), and neutrophil (NEU) percentage provided valuable therapeutic guidance. The survival rate of patients was 55.36%, influenced by patient physical condition and age.

Discussion

Our data indicated that mNGS had significant auxiliary value in the clinical diagnosis and treatment for critically ill patients, especially for those with negative CMT results and clinically undefined infections. mNGS could broaden the detection scope, especially for special pathogens, and improve the detection rate, providing powerful assistance for early clinical diagnosis and treatment.

Crohn's Disease With Latent Tuberculosis Infection or Intestinal Tuberculosis: Rapid Discrimination by Targeted Next-Generation Sequencing

BACKGROUND

Discriminating Crohn's disease (CD) with latent tuberculosis infection (LTBI) from intestinal tuberculosis (ITB) in tuberculosis-endemic regions remains challenging.

AIM

To assess whether targeted next-generation sequencing (tNGS) could be an efficient method for ITB diagnosis and discrimination from CD with LTBI.

METHODS

The study was conducted prospectively from September 2020 until December 2023. We recruited patients with undetermined intestinal ulcers and positive interferon-gamma release assay. We compared tNGS (using fresh biopsy tissue samples from ulcer bases) to pathological detection of caseous necrotising granuloma, acid-fast bacillus (AFB) staining, tuberculosis polymerase chain reaction (TB-PCR) for diagnostic efficiency. ITB was diagnosed based on cure by anti-tuberculosis therapy and comprehensive clinical evaluation.

RESULTS

Of the 100 patients included, 66 had ITB and 34 had CD with LTBI. The sensitivity, specificity, positive predictive value and negative predictive value of tNGS for ITB were 83% (72%-91%), 100% (87%-100%), 100% (92%-100%) and 76% (60%-87%), respectively. TNGS had significantly higher diagnostic sensitivity than AFB staining [15% (4%-39%), p < 0.05], TB-PCR [22% (12%-36%), p < 0.05] and detection of caseous necrotising granulomas [17% (9%-28%), p < 0.05]. The models combining multiclinical factors increased sensitivity (97% vs. 83%) than tNGS alone. No patients with CD and LTBI had positive tNGS.

CONCLUSIONS

TNGS using fresh biopsy tissue from ulcer bases is highly sensitive and specific, with superiority over other traditional diagnostic methods for ITB detection. TNGS could facilitate rapid diagnosis of ITB and discrimination from CD with LTBI, particularly in high TB-endemic countries.

Development of a clinical metagenomics workflow for the diagnosis of wound infections

BACKGROUND

Wound infections are a common complication of injuries negatively impacting the patient's recovery, causing tissue damage, delaying wound healing, and possibly leading to the spread of the infection beyond the wound site. The current gold-standard diagnostic methods based on microbiological testing are not optimal for use in austere medical treatment facilities due to the need for large equipment and the turnaround time. Clinical metagenomics (CMg) has the potential to provide an alternative to current diagnostic tests enabling rapid, untargeted identification of the causative pathogen and the provision of additional clinically relevant information using equipment with a reduced logistical and operative burden.

METHODS

This study presents the development and demonstration of a CMg workflow for wound swab samples. This workflow was applied to samples prospectively collected from patients with a suspected wound infection and the results were compared to routine microbiology and real-time quantitative polymerase chain reaction (qPCR).

RESULTS

Wound swab samples were prepared for nanopore-based DNA sequencing in approximately 4 h and achieved sensitivity and specificity values of 83.82% and 66.64% respectively, when compared to routine microbiology testing and species-specific qPCR. CMg also enabled the provision of additional information including the identification of fungal species, anaerobic bacteria, antimicrobial resistance (AMR) genes and microbial species diversity.

CONCLUSIONS

This study demonstrates that CMg has the potential to provide an alternative diagnostic method for wound infections suitable for use in austere medical treatment facilities. Future optimisation should focus on increased method automation and an improved understanding of the interpretation of CMg outputs, including robust reporting thresholds to confirm the presence of pathogen species and AMR gene identifications.

Facial cutaneous tuberculosis infected by non-tuberculous mycobacteria

BACKGROUND

Cutaneous infections caused by non-tuberculous mycobacteria (NTM) are extremely rare, particularly when they are localized to the facial area. This condition presents significant diagnostic challenges due to its unusual presentation and the need for precise microbiological identification.

CASE PRESENTATION

A two-year-old male patient presented with a progressively enlarging reddish-brown mass on the left side of his face. Despite the absence of systemic symptoms, the lesion's growth warranted investigation due to its growth. Ultrasonography showed a hypoechoic mass in the dermis, indicating an underlying abscess. The subsequent aspiration resulted in pale yellow pus, which upon testing and culture, confirmed the presence of Mycobacterium avium complex infection, a species of NTM. This case exemplifies the synergy between imaging modalities and microbiological analysis, highlighting the crucial role of both in achieving favorable clinical outcomes in patients with suspected cutaneous NTM infections. Ultrasound can expedite diagnosis, improve treatment planning, and enhance patient care by enabling targeted interventions and monitoring response to therapy in these scenarios. However, it is the combination of pathogen-specific diagnostics that ensures accurate etiological attribution and appropriate antimicrobial stewardship.

CONCLUSION

Although rare, facial cutaneous infections caused by NTM still deserve thorough investigation to determine the exact cause. Ultrasound is used to identify cutaneous lesions, measure their extent, and guide surgical procedures. The ultimate diagnosis is based on microbiological confirmation.

Persistently high plasma procalcitonin levels despite successful treatment of tuberculous pleuritis and tuberculous lymphadenitis patients

In a prospective cohort study, we evaluated plasma PCT levels in 48 TB lymphadenitis (TBLN) and 41 TB pleuritis (TBPE) patients. Measurements of PCT were done in unstimulated plasma of microbiologically and clinically confirmed TBLN and TBPE patients registered for anti-TB treatment at a tertiary care hospital in Lahore, Pakistan. Plasma levels of PCT were found to be raised in 89% of the patients at baseline with a median of 1.5 ng/ml. Levels were higher (p = 0.001) in TBLN as compared to TBPE (2.69, 0.96 ng/ml). PCT levels were not related to the bacterial burden depicted by culture positivity in these patients. PCT showed a negative correlation with the severity of constitutional symptoms (rho = - 0.238, p = 0.034), and inflammatory biomarkers; ferritin (rho = - 0.43, p < 0.001), INF-γ (rho = - 0.314, p = 0.003), TNF-α (rho = - 0.220, p = 0.039), IL-6 (rho = - 0.224, p = 0.035), and several chemokines of CCL and CCXL group. Raised plasma levels of PCT did not decrease with anti-TB treatment, indicating it is not a good biomarker to monitor treatment response in TBLN and TBPE patients. More studies with a larger number of confirmed EPTB cases are needed to define the role of PCT and its interaction with other biomarkers in EPTB.

Retrospective clinical and microbiologic analysis of metagenomic next-generation sequencing in the microbiological diagnosis of cutaneous infectious granulomas

BACKGROUND

Cutaneous infectious granulomas (CIG) are localized and chronic skin infection caused by a variety of pathogens such as protozoans, bacteria, worms, viruses and fungi. The diagnosis of CIG is difficult because microbiological examination shows low sensitivity and the histomorphological findings of CIG caused by different pathogens are commonly difficult to be distinguished.

OBJECTIVE

The objective of this study is to explore the application of mNGS in tissue sample testing for CIG cases, and to compare mNGS with traditional microbiological methods by evaluating sensitivity and specificity.

METHODS

We conducted a retrospective study at the Department of Dermatology of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from January 1st, 2020, to May 31st, 2024. Specimens from CIG patients with a clinical presentation of cutaneous infection that was supported by histological examination were retrospectively enrolled. Specimens were delivered to be tested for microbiological examinations and mNGS.

RESULTS

Our data show that mNGS detected Non-tuberculosis mycobacteria, Mycobacterium tuberculosis, fungi and bacteria in CIG. Compared to culture, mNGS showed a higher positive rate (80.77% vs. 57.7%) with high sensitivity rate (100%) and negative predictive value (100%). In addition, mNGS can detect more pathogens in one sample and can be used to detect variable samples including the samples of paraffin-embedded tissue with shorter detective time. Of the 21 patients who showed clinical improvement within a 30-day follow-up, eighteen had their treatments adjusted, including fifteen who continued treatment based on the results of mNGS.

CONCLUSIONS

mNGS could provide a potentially rapid and effective alternative detection method for diagnosis of cutaneous infectious granulomas and mNGS results may affect the clinical prognosis resulting from enabling the patients to initiate timely treatment.

Clinical applications and challenges of metagenomic next-generation sequencing in the diagnosis of pediatric infectious disease

Infectious diseases seriously threaten the lives of children. Timely and accurate detection of pathogenic microorganisms and targeted medication are the keys to the diagnosing and treatment of infectious diseases in children. The next-generation metagenomic sequencing technology has attracted great attention in infectious diseases because of its characteristics such as no culture, high throughput, short detection cycle, wide coverage, and a good application prospect. In this paper, we review the studies of metagenomic next-generation sequencing in pediatric infectious diseases and analyze the challenges of its application in pediatric diseases.

Progressive Facial Ulcer: A Case Report of Pyoderma gangrenosum

Pyoderma gangrenosum (PG) is a rare neutrophilic dermatosis characterized by rapidly developing and painful skin ulcers with distinctive features. As far as we are concerned, there is no previous case report on facial PG in East-Asia. In this case, we describe a case of a 79-year-old man with a 3-month history of progressive painful ulcers on his cheek and upper lip. Initial suspicion of atypical mycobacterium infection led to an ineffective treatment regimen. Comprehensive infectious testing yielded negative results, and a positive pathergy test indicated a potential diagnosis of PG. A skin biopsy confirmed the diagnosis, and the patient showed significant improvement with intravenous methylprednisolone and oral cyclosporine treatment. After three months, complete resolution of the lesions was achieved without recurrence. The case highlights the diagnostic challenges associated with PG, which is often misdiagnosed due to its resemblance to other conditions. Thorough evaluation is crucial to exclude alternative diagnoses, particularly cutaneous infections. Clinical morphology, tissue biopsy, and culture are essential for accurate diagnosis. The presence of pathergy, the development of new lesions following minor trauma, can also be a diagnostic clue.

Application of next-generation sequencing to identify different pathogens

Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry, biochemical tests, molecular testing, and culture-based methods, are limited in application and are time-consuming. Next generation sequencing (NGS) has emerged as an essential technology for identifying pathogens. NGS is a cutting-edge sequencing method with high throughput that can create massive volumes of sequences with a broad application prospects in the field of pathogen identification and diagnosis. In this review, we introduce NGS technology in detail, summarizes the application of NGS in that identification of different pathogens, including bacteria, fungi, and viruses, and analyze the challenges and outlook for using NGS to identify clinical pathogens. Thus, this work provides a theoretical basis for NGS studies and provides evidence to support the application of NGS in distinguishing various clinical pathogens.

Genomic characterization of Mycoplasma edwardii isolated from a dog bite induced cat wound reveals multiple horizontal gene transfer events and loss of the CRISPR/Cas system

A domestic short hair cat (Felis catus) suffering from a purulent wound infection resulting from a dog bite was sampled for bacterial culture and isolation as the wound had been unresponsive to prolonged antimicrobial treatment. A mycoplasma was isolated from the wound. Whole genome sequencing of the isolate was performed using short-read Illumina and long-read Oxford Nanopore chemistry, and the organism was identified as Mycoplasma edwardii. Comparison of the genome sequence of the isolate to a reference M. edwardii genome sequence (canid isolate) identified the loss of several key bacterial factors involved in genome editing, as well the insertion of several novel ORFs most closely related to those found in other canine mycoplasmas, specifically Mycoplasma canis, M. cynos, M. molare and M. maculosa. This is only the second known report of disease caused by M. edwardii in a non-canid species, and the first report of it infecting and causing clinical disease in a cat.

DNA microarray chip assay in new use: early diagnostic value in cutaneous mycobacterial infection

Introduction

The clinical practicability of DNA microarray chip in detecting the presence of mycobacterial species/isolates directly in the skin tissues has not been evaluated, nor the efficacy of DNA microarray chip as a novel diagnostic tool for the early diagnosis of cutaneous mycobacterial infections is known.

Methods

The present study analyzed the incidence of cutaneous mycobacterial infections in Shanghai and explored the efficacy of a novel DNA microarray chip assay for the clinical diagnosis of the disease from skin tissue specimens compared to traditional detection methods. A total of 60 participants fulfilling the defined diagnostic criteria and confirmed positive for cutaneous mycobacterial infections from 2019 to 2021 were enrolled in the study. Subsequent to recording the participants' medical history and clinical characteristics, the skin tissue specimens were collected for analyses. The specimens underwent histopathological analyses, skin tissue culture, and DNA microarray chip assay.

Results

Increased incidence of cutaneous mycobacterial infection was detected from 2019 to 2021. The most common infecting pathogen was M. marinum followed by M. abscessus. The sensitivity, specificity and accuracy of the skin tissue culture method were 70%, 100% and 76.62%, respectively, while that of the DNA microarray chip assay were 91.67%, 100% and 93.51%, respectively. The sensitivity and accuracy of the DNA microarray chip assay were significantly higher than those of the skin tissue culture method. The positive likelihood and diagnostic odds ratio were >10 and >1, respectively for both the methods. The negative likelihood ratio was significantly higher (30% vs 8.33%) and the Youden's index was significantly lower (70.00% vs 91.67%) in the skin culture method compared to that of the DNA microarray chip assay. There was a significant association of false negative results with a history of antibiotic use in the skin tissue culture method.

Discussion

Given the increasing incidence of cutaneous mycobacterial infections, early diagnosis remains a prime clinical focus. The DNA microarray chip assay provides a simple, rapid, high-throughput, and reliable method for the diagnosis of cutaneous mycobacterial infections with potential for clinical application.

Rapid diagnostics for skin and soft tissue infections: the current landscape and future potential

PURPOSE OF REVIEW

Managing antimicrobial therapy in patients with complicated skin and soft tissue infections (SSTI) constitutes a growing challenge due to the wide spectrum of potential pathogens and resistance phenotypes. Today, microbiological documentation relies on cultural methods. This review summarizes the available evidence regarding the clinical input of rapid microbiological diagnostic tools (RMDT) and their impact on the management of antimicrobial therapy in SSTI.

RECENT FINDINGS

Accurate tools are already available for the early detection of methicillin-resistant Staphylococcus aureus (MRSA) in SSTI samples and may help avoiding or shortening empirical anti-MRSA coverage. Further research is necessary to develop and evaluate RMDT detecting group A streptococci (e.g., antigenic test) and Gram-negative pathogens (e.g., multiplex PCR assays), including through point-of-care utilization. Next-generation sequencing (NGS) methods could provide pivotal information for the stewardship of antimicrobial therapy, especially in case of polymicrobial or fungal SSTI and in the immunocompromised host; however, a shortening in the turnaround time and prospective data regarding their therapeutic input are needed to better appraise the clinical positioning of these promising approaches.

SUMMARY

The clinical input of RMDT in SSTI is currently limited due to the scarcity of available dedicated assays and the polymicrobial feature of certain cases. NGS appears as a relevant tool but requires further developments before its implementation in routine clinical practice.