Disseminated Coinfection by Mycobacterium fortuitum and Talaromyces marneffei in a Non-HIV Case

HIV-Negative Case of Talaromyces marneffei Pulmonary Infection with Liver Cirrhosis in China: A Case Report and Literature Review

Background

Talaromyces marneffei (TM) is the third most prevalent opportunistic infection in HIV-positive patients after tuberculosis and cryptococcosis. However, such infection of non-HIV individuals has rarely been reported.

Case Presentation

We describe a very rare case of a 52-year-old male who presented with a single space-occupying lesion on the right lung and was eventually diagnosed with pulmonary TM infection. The patient was HIV-negative and had liver cirrhosis with portal vein thrombosis. Lung tissue next-generation sequencing (NGS) revealed TM infection. We successfully treated the patient with voriconazole for 8 weeks and observed lesion absorption via subsequent CT. The patient consumed wild bamboo rats two months before admission. Mutations related to congenital immune deficiency were not detected by whole-exome sequencing.

Conclusion

Early and timely diagnosis is critical for improving patient prognosis. NGS plays a vital role in the diagnosis of pulmonary TM infection in patients. To our knowledge, this is the first published case of pulmonary TM infection in an HIV-negative patient with liver cirrhosis.

Clinical Evaluation of Metagenomic Next-Generation Sequencing and Identification of Risk Factors in Patients with Severe Community-Acquired Pneumonia

Purpose

Severe community-acquired pneumonia (SCAP) is the leading cause of death among patients with infectious diseases worldwide. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) through detecting pathogens in bronchoalveolar lavage fluid (BALF) and identifying risk factors for recovery in SCAP patients.

Patients and Methods

This prospective study recruited 158 SCAP patients admitted to respiratory intensive care unit that were randomly divided into control and study groups, with receiving conventional tests and the same conventional tests plus mNGS, respectively. The diagnostic efficiency of mNGS was evaluated by comparing with conventional tests. Furthermore, univariate and multivariate logistic regression analyses were performed to determine the independent risk factors for recovery in SCAP patients, and a nomogram prediction model was established based on these factors.

Results

Within the study group, the pathogen detection rate was significantly higher with mNGS than that with conventional tests (84.81% vs 45.57%, P < 0.001), with a positive coincidence rate of 94.44%. Acinetobacter baumannii (21.52%, 17/79), Candida albicans (17.72%, 14/79), and Klebsiella pneumonia (15.19%, 12/79) were the top three common pathogens detected by mNGS. Of note, the improvement rate of patients in the study group was significantly higher than that in the control group. The further analysis revealed that the increased levels of interleukin-6, blood urea nitrogen, procalcitonin, the longer length of hospital stay, and bacterial infection were independent risk factors for recovery of SCAP patients, while mNGS detection status was a protective factor. The predictive model showed a good performance for the modeling and validation sets.

Conclusion

Early mNGS exhibited a superior diagnostic efficiency to conventional tests in SCAP patients, which can reduce the risk of death in SCAP patients. Moreover, the clinical factors could also be used for the management and prognosis prediction of SCAP patients.

Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing for Pathogen Detection in Patients with Suspected Infectious Diseases: A Retrospective Study from a Large Tertiary Hospital

Purpose

Metagenomic next-generation sequencing (mNGS) is a powerful yet unbiased method to identify pathogens in suspected infections. However, little is known about its clinical effectiveness. The present study aimed to assess the efficacy of mNGS in routine clinical practice.

Patients and Methods

In this single-center retrospective cohort study, 518 patients with suspected infectious diseases were assessed for inclusion. Among them, each patient had undergone mNGS testing; 407 patients had undergone both microbial culture and mNGS testing. The result of mNGS testing was compared to microbial culture performed concurrently. The diagnostic performance of mNGS was evaluated using the comprehensive clinical diagnosis as the reference standard.

Results

There was a significant difference in the positive detection rates of pathogens between mNGS and culture (331/407, 81.3% vs 79/407, 19.4%, P < 0.001). The sensitivity of mNGS was much higher than the culture method (79.5% vs 21.3%, P < 0.001), especially in sample types of sputum and bronchoalveolar lavage fluid (BALF). Notably, the sensitivity of blood mNGS was relatively lower than other sample types (67.4% vs 88.9-93.8%). Pathogen cfDNA load based on standardized stringently mapped read number at the species level of microorganisms (SDSMRN) was significantly lower in blood than in other sample types from the same patient (P = 0.0003). Importantly, mNGS directly led to a change of treatment regimen in 142 (27.4%) cases, including antibiotic escalation (15.3%), antibiotic de-escalation (9.1%), and early definitive diagnosis to initiate appropriate treatment (3.1%).

Conclusion

Our in-house mNGS platform significantly improved the sensitivity for the diagnosis of infectious diseases. mNGS has the potential to improve clinical outcomes by optimizing antimicrobial therapy.

Diagnostic value of metagenomics next-generation sequencing technology in disseminated strongyloidiasis

The symptoms of disseminated strongyloidiasis are not typical, and it is difficult for clinicians to identify strongyloidiasis in some non-endemic areas. We report a 70-year-old woman who was diagnosed with Guillain-Barré syndrome due to autonomic disturbance, symmetrical bulbar palsy, and lower-motor-nerve damage in the extremities; her symptoms continued to worsen after hormone and immunoglobulin therapy. Later, parasitic larvae were found in the patient’s gastric fluid, and metagenomic next generation sequencing (mNGS) detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms. The patient was diagnosed with disseminated strongyloidiasis. The patient was given albendazole for anthelmintic treatment, but died two days after being transferred to the intensive care unit due to the excessive strongyloidiasis burden. In recent years, mNGS has been increasingly used in clinical practice, and is becoming the main means of detecting strongyloides stercoralis in non-endemic areas. Especially during the corona virus disease 2019 pandemic, mNGS technology has irreplaceable value in identifying the source of infection.

Disseminated Strongyloidiasis Misdiagnosed as Guillain-Barré Syndrome: The Value of High-Throughput Genetic Sequencing of Pathogenic Microorganisms in Parasitic Infections

Background

With the widespread use of steroids and immunosuppressants in mainland China, disseminated strongyloidiasis is becoming a severely underestimated tropical disease due to the lack of disease-specific manifestations and well-established diagnostic methods.

Case Presentation

Here, we report a 70-year-old woman who was diagnosed with Guillain-Barré syndrome due to autonomic disturbance, symmetrical bulbar palsy, and lower-motor-nerve damage in the extremities; her symptoms continued to worsen after hormone and immunoglobulin therapy. Later, parasitic larvae were found in the patient’s gastric fluid, and metagenomic Next Generation Sequencing (mNGS) detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms. The patient was diagnosed with disseminated strongyloidiasis. The patient was given albendazole for anthelmintic treatment, but died two days after being transferred to the ICU due to the excessive strongyloidiasis burden.

Conclusion

This case highlights the combined application of mNGS and traditional testing in the clinical diagnosis of difficult and critical parasitic infections in immunocompromised patients. mNGS is a new, adjunct diagnostic method to rapidly screen for possible parasitic etiologies.

Disseminated alveolar echinococcosis in a patient diagnosed by metagenomic next-generation sequencing: A case report

Background

Alveolar echinococcosis (AE) is a parasitic zoonosis with high mortality and disability rates. Diverse clinical manifestations and mimicking of differential diagnoses such as tuberculosis and malignancy pose a diagnostic dilemma. With the rapid development of molecular diagnostic techniques in recent years, metagenomic next-generation sequencing (mNGS) has become an attractive approach for the etiological diagnosis of infectious diseases.

Case presentation

we report a case of 51-year-old Chinese Tibetan male presented with 3-year low-back pain and 4-month discomfort in the right upper quadrant of the abdomen. He had been in good health. He was diagnosed with tuberculosis and was given anti-tuberculosis treatment a month prior to the visit, but the symptoms were not relieved. Abdominal computerized tomography (CT) revealed a hypodense lesion with uneven enhancement in the liver, and two ring-enhancing cystic lesions in the right abdominal wall. Lumbar spine enhanced MRI showed lesions of mixed density with uneven enhancement in the L1 vertebra and paraspinal tissue. The pathological results of the liver biopsy revealed parasitic infection and possibly echinococcosis. The metagenomic next-generation sequencing (mNGS) of the puncture fluid of abdominal cysts using Illumina X10 sequencer revealed 585 sequence reads matching Echinococcus multilocularis. Disseminated AE was diagnosed. Albendazole (400 mg, twice daily) was used, and the patient was in stable condition during follow-up.

Conclusions

mNGS may be a useful tool for the diagnosis of AE. The case would help clinicians to improve their diagnostic skills.

Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: a Multicenter Retrospective Study

Metagenomic next-generation sequencing (mNGS) has been gradually applied to clinical practice due to its unbiased characteristics of pathogen detection. However, its diagnostic performance and clinical value in suspected pulmonary infection need to be evaluated. We systematically reviewed the clinical data of 246 patients with suspected pulmonary infection from 4 medical institutions between January 2019 and September 2021. The diagnostic performances of mNGS and conventional testing (CT) were systematically analyzed based on bronchoalveolar lavage fluid (BALF). The impacts of mNGS and CT on diagnosis modification and treatment adjustment were also assessed. The positive rates of mNGS and CT were 47.97% and 23.17%, respectively. The sensitivity of mNGS was significantly higher than that of CT (53.49% versus 23.26%, P < 0.01), especially for infections of Mycobacterium tuberculosis (67.86% versus 17.86%, P < 0.01), atypical pathogens (100.00% versus 7.14%, P < 0.01), viruses (92.31% versus 7.69%, P < 0.01), and fungi (78.57% versus 39.29%, P < 0.01). The specificity of mNGS was superior to that of CT, with no statistical difference (90.32% versus 77.42%, P = 0.167). The positive predictive value (PPV) and negative predictive value (NPV) of mNGS were 97.46% and 21.88%, respectively. Diagnosis modification and treatment adjustment were conducted in 32 (32/246, 13.01%) and 23 (23/246, 9.35%) cases, respectively, according to mNGS results only. mNGS significantly improved the diagnosis of suspected pulmonary infection, especially infections of M.tuberculosis, atypical pathogens, viruses, and fungi, and it demonstrated the pathogen distribution of pulmonary infections. It is expected to be a promising microbiological detection and diagnostic method in clinical practice.

IMPORTANCE Pulmonary infection is a heterogeneous and complex infectious disease with high morbidity and mortality worldwide. In clinical practice, a considerable proportion of the etiology of pulmonary infection is unclear, microbiological diagnosis being challenging. Metagenomic next-generation sequencing detects all nucleic acids in a sample in an unbiased manner, revealing the microbial community environment and organisms and improving the microbiological detection and diagnosis of infectious diseases in clinical settings. This study is the first multicenter, large-scale retrospective study based entirely on BALF for pathogen detection by mNGS, and it demonstrated the superior performance of mNGS for microbiological detection and diagnosis of suspected pulmonary infection, especially in infections of Mycobacterium tuberculosis, atypical pathogens, viruses, and fungi. It also demonstrated the pathogen distribution of pulmonary infections in the real world, guiding targeted treatment and improving clinical management and prognoses.

Strongyloidiasis in a Patient Diagnosed by Metagenomic Next-Generation Sequencing: A Case Report

Background

Strongylodiasis may be asymptomatic or cause mild gastrointestinal symptoms, and may be a fatal disseminated disease or Strongyloides hyperinfection syndrome. Non-specific clinical manifestations, such as pneumonia and gastroenteritis, pose a diagnostic dilemma.

Case Presentation

We report a case of a 67-year-old Chinese male who presented with abdominal pain, fever, headache, vomiting, constipation, and slight cough with sputum for nearly 2 months. He had been in good health and had no history of glucocorticoid use. He was diagnosed with enterococcal meningitis and intestinal obstruction at a local hospital and improved after treatment with vancomycin, but symptoms of headache and abdominal pain soon recurred. The metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid using Illumina X10 sequencer revealed seven sequence reads matching Strongyloides stercoralis. Strongyloidiasis was suspected. Microscopic examination of gastric fluid revealed the presence of S. stercoralis larvae, which was confirmed by PCR to amplify both S. stercoralis ribosomal DNA gene and mitochondrial cytochrome c oxidase subunit 1 gene and sequencing amplicons. Strongyloidiasis was diagnosed. Albendazole (400 mg, twice daily) was used, and the patient recovered gradually.

Conclusion

mNGS may be a useful tool for detecting uncommon infectious disease. The case would help clinicians to raise awareness of strongyloidiasis in non-endemic areas and reduce fatality.