scholarly journals Navigating Clinical Utilization of Direct-from-Specimen Metagenomic Pathogen Detection: Clinical Applications, Limitations, and Testing Recommendations

2020 ◽  
Vol 66 (11) ◽  
pp. 1381-1395
Author(s):  
Laura M Filkins ◽  
Alexandra L Bryson ◽  
Steve A Miller ◽  
Stephanie L Mitchell
Keyword(s):  
Clinical Studies ◽  
Pathogen Detection ◽  
Clinical Laboratory ◽  
Fungal Infections ◽  
Case Reports ◽  
Study Data ◽  
Community Acquired Pneumonia ◽  
Clinical Impact ◽  
Clinical Utilization ◽  
Clinical Indications

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.

scholarly journals Causes of eosinophilic ascites – A systematic review

2019 ◽  
Vol 57 (2) ◽  
pp. 110-124 ◽  
Author(s):  
Larisa Pinte ◽  
Cristian Baicuş
Keyword(s):  
Lupus Erythematosus ◽  
Clinical Laboratory ◽  
Fungal Infections ◽  
Case Reports ◽  
Hypereosinophilic Syndrome ◽  
Gastrointestinal Symptoms ◽  
Parasitic Infections ◽  
Medical Subject Headings ◽  
Mesh Terms ◽  
Eosinophilic Ascites

Abstract Background. In the last years an uprising interest for a relatively unknown entity, eosinophilic ascites (EA), has been recorded. Our aim is to investigate the potential causes of EA development, as well as clinical, laboratory, endoscopic and radiologic features, management and outcome in these patients. Methods. The following research was performed on PubMed (MEDLINE) database using the medical subject headings [Mesh] terms “Ascites” AND “Eosinophils”. Results. A total of 284 results, dating from 1962 onwards, were found and abstracts were examined. 131 papers were excluded and the remaining 153 publications, consisting in case reports and series of cases, were analyzed. From 171 patients with EA, 127 subjects (74%) had EGE, 17 (10%) parasitic and fungal infections, 11(7%) Hypereosinophilic syndrome and 16 patients (9%) less common diseases (eosinophilic pancreatitis, chronic eosinophilic leukemia, myelofibrosis, T-cell lymphoma, Churg Strauss Syndrome, Systemic lupus erythematosus, Familial paroxysmal polyserositis and Ménétrier’s disease). High eosinophil blood count and IgE levels as well as gastrointestinal symptoms are frequent. The diagnosis is based on ascitic fluid analysis, imaging and endoscopic biopsies. Therapy with corticosteroids results in resolution of eosinophilic ascites in almost all patients. Conclusion. In most cases, in the absence of allergy, parasitic infections, malignancy, hematological disorders, peritoneal tuberculosis, inflammatory bowel disease or autoimmune disease, EA develops as a manifestation of eosinophilic gastroenteritis.

scholarly journals Optimization of Microbiological Laboratory Detection Strategy for Patients in A Designated Hospital Treating Novel Coronavirus Pneumonia in Anhui Province

2020 ◽  
Author(s):  
Wenjiao Chang ◽  
Yuru Shi ◽  
Yingjie Qi ◽  
Jiaxing Liu ◽  
Ting Liu ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Pathogen Detection ◽  
Fungal Infections ◽  
Community Acquired Pneumonia ◽  
Anhui Province ◽  
Microbiological Analysis ◽  
Serologic Tests ◽  
Secondary Infections ◽  
Microbiological Laboratory ◽  
Novel Coronavirus

AbstractNovel coronavirus pneumonia (NCP) is an emerging, highly contagious community acquired pneumonia (CAP) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Highly efficient and accurate microbiological laboratory assay is essential to confirm the SARS-CoV-2 infection, rule out other pathogens that can cause CAP, and monitor secondary infections. Here, we enrolled and provide microbiological analysis for 129 suspected and 52 transferred confirmed NCP patients hospitalized in the First Affiliated Hospital of University of Science and Technology of China (USTC) from Jan 21 to Feb 29, 2020. By analyzing the dual swab samples (sputum and pharyngeal) from 129 suspected patients with realtime RT-PCR, we confirmed 33 SARS-CoV-2 infections, with two co-infection cases with adenovirus or rhinovirus. We also used multiplex PCR to detect 13 common respiratory tract pathogens in 96 non-NCP patients, and found that 30 patients (31.25%) were infected with at least one respiratory tract pathogen that may cause CAP. Further, we performed bacterial and fungal cultures as well as fungal serologic tests and found that there is no secondary bacterial/fungal infections in confirmed NCP patients. Our studies suggest that, during the epidemic of NCP in Anhui province, there was a certain proportion of infection and co-infection of other common pathogens of CAP, and the secondary bacterial and fungal infection is not detectable in NCP patients. In comparison with SARS-CoV-2 detection alone, this optimized strategy combining multiple pathogen detection for identification of NCP and other CAP patients as well as cultures and serologic tests for confirmed patients increases the diagnosis efficiency and facilitates the personalized medication.

scholarly journals Cardio-Pulmonary Sequelae in Recovered COVID-19 Patients: Considerations for Primary Care

2021 ◽  
Vol 12 ◽  
pp. 215013272110237
Author(s):  
Zouina Sarfraz ◽  
Azza Sarfraz ◽  
Alanna Barrios ◽  
Radhika Garimella ◽  
Asimina Dominari ◽  
...  
Keyword(s):  
Primary Care ◽  
Primary Infection ◽  
Clinical Laboratory ◽  
Point Of Care ◽  
Case Reports ◽  
Case Series ◽  
Infectious Complications ◽  
Care Physician ◽  
Cross Sectional ◽  
Infection Period

Background: Current literature lacks characterization of the post-recovery sequelae among COVID-19 patients. This review characterizes the course of clinical, laboratory, radiological findings during the primary infection period, and the complications post-recovery. Primary care findings are presented for long-COVID care. Methods: Adhering to PRISMA guidelines, 4 databases were searched (PubMed, Embase, CINAHL Plus, Scopus) through December 5, 2020, using the keywords “COVID-19 and/or recovered and/or cardiovascular and/or long-term and/or sequelae and/or sub-acute and/or complication.” We included published peer-reviewed case reports, case series, and cross-sectional studies providing the clinical course of COVID-19 infection, and cardiopulmonary complications of patients who recovered from COVID-19, while making healthcare considerations for primary care workers. Results: We identified 29 studies across 9 countries including 37.9% Chinese and 24.1% U.S. studies, comprising 655 patients (Mean Age = 45) with various ethnical backgrounds including Asian and European. Based on the WHO COVID-19 severity classification scale, initial disease severity was mild for 377 patients and severe for 52 patients. Treatments during primary infection included corticosteroids, oxygen support, and antivirals. The mean value (in days) for complication onset after acute recovery was 28 days. Complete blood counts and RT-PCR tests were the most common laboratory results described. In 22 of the studies, patients showed signs of clinical improvement and were prescribed medications such as anticoagulants or corticosteroids. Conclusion: Post-recovery infectious complications are common in long-COVID-19 patients ranging from mild infections to life-threatening conditions. International thoracic and cardiovascular societies need to develop guidelines for patients recovering from COVID-19 pneumonia, while focused patient care by the primary care physician is crucial to curb preventable adverse events. Recommendations for real-time and lab-quality diagnostic tests are warranted to establish point-of-care testing, detect early complications, and provide timely treatment.

scholarly journals A Pandemic Early Warning System Decision Analysis Concept Utilizing a Distributed Network of Air Samplers via Electrostatic Air Precipitation

2021 ◽  
Vol 11 (11) ◽  
pp. 5308
Author(s):  
Joseph J. Bango ◽  
Sophia A. Agostinelli ◽  
Makayla Maroney ◽  
Michael Dziekan ◽  
Ruba Deeb ◽  
...  
Keyword(s):  
Early Warning ◽  
Early Warning System ◽  
Pathogen Detection ◽  
Clinical Laboratory ◽  
Culture Media ◽  
Morphological Characteristics ◽  
Warning System ◽  
Ambient Air ◽  
Aerosol Sampling ◽  
Distributed Network

The COVID-19 pandemic has highlighted the need for improved airborne infectious disease monitoring capability. A key challenge is to develop a technology that captures pathogens for identification from ambient air. While pathogenic species vary significantly in size and shape, for effective airborne pathogen detection the target species must be selectively captured from aerosolized droplets. Captured pathogens must then be separated from the remaining aerosolized droplet content and characterized in real-time. While improvements have been made with clinical laboratory automated sorting in culture media based on morphological characteristics of cells, this application has not extended to aerosol samples containing bacteria, viruses, spores, or prions. This manuscript presents a strategy and a model for the development of an airborne pandemic early warning system using aerosol sampling. 

scholarly journals Bittersweet: infective complications of drug-induced glycosuria in patients with diabetes mellitus on SGLT2-inhibitors: two case reports

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Caroline Bartolo ◽  
Victoria Hall ◽  
N. Deborah Friedman ◽  
Chloe Lanyon ◽  
Andrew Fuller ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Fungal Infections ◽  
Case Reports ◽  
Sglt2 Inhibitor ◽  
Sglt2 Inhibitors ◽  
Urogenital Tract ◽  
Hypoglycemic Agents ◽  
Drug Induced ◽  
First Case ◽  
Increased Risk

Abstract Background Sodium-glucose co-transporter 2 (SGLT2) inhibitors are novel hypoglycemic agents which reduce reabsorption of glucose at the renal proximal tubule, resulting in significant glycosuria and increased risk of genital mycotic infections (GMI). These infections are typically not severe as reported in large systematic reviews and meta-analyses of the medications. These reviews have also demonstrated significant cardiovascular benefits through other mechanisms of action, making them attractive options for the management of Type 2 diabetes mellitus (T2DM). We present two cases with underlying abnormalities of the urogenital tract in which the GMI were complicated and necessitated cessation of the SGLT2 inhibitor. Case presentations Both cases are patients with T2DM on empagliflozin, an SGLT2 inhibitor. The first case is a 64 year old man with Candida albicans balanitis and candidemia who was found to have an obstructing renal calculus and prostatic abscess requiring operative management. The second case describes a 72 year old man with Candida glabrata candidemia who was found to have prostatomegaly, balanitis xerotica obliterans with significant urethral stricture and bladder diverticulae. His treatment was more complex due to fluconazole resistance and concerns about urinary tract penetration of other antifungals. Both patients recovered following prolonged courses of antifungal therapy and in both cases the SGLT2 inhibitor was ceased. Conclusions Despite their cardiovascular benefits, SGLT2 inhibitors can be associated with complicated fungal infections including candidemia and patients with anatomical abnormalities of the urogenital tract may be more susceptible to these infections as demonstrated in these cases. Clinicians should be aware of their mechanism of action and associated risk of infection and prior to prescription, assessment of urogenital anatomical abnormalities should be performed to identify patients who may be at risk of complicated infection.

scholarly journals 2019 novel coronavirus disease with secondary ischemic stroke: two case reports

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Bin Fu ◽  
Yun Chen ◽  
Ping Li
Keyword(s):  
Ischemic Stroke ◽  
Acute Ischemic Stroke ◽  
Clinical Laboratory ◽  
Case Reports ◽  
Small Vessel ◽  
Vessel Occlusion ◽  
Aged Patients ◽  
Health Crisis ◽  
Physical Examinations ◽  
Novel Coronavirus

Abstract Background The COVID-19 pandemic, which broke out in Wuhan in 2019, has become the global health crisis of our time. Elderly patients with certain fundamental diseases are more likely to develop severe cases. The secondary lesion following viral infection have only rarely been reported. Case presentation We here report two cases of coronavirus-infected pneumonia with acute ischemic stroke in middle-aged patients. In both COVID-19 cases, neurological physical examinations showed normal results before infection. Lymphocytopenia, accompanied by elevated cytokines and D-dimers, were found from serum clinical laboratory examination at admission. Dysarthria and limb muscle weakness are initial manifestations, occurring one week after infect-causative pathogen, SARS-CoV-2. The head CT and head/neck arterial CTA showed small-vessel occlusion. The patients were diagnosed with coronavirus diseases with secondary acute ischemic stroke. They were treated with tirofiban and followed up with daily aspirin and atorvastatin. Conclusions These cases suggested that secondary ischemic stroke, mainly manifested as small-vessel occlusion, should be considered for COVID-19 patients and diagnosed and treated promptly.

scholarly journals Herb–Drug Interactions: Worlds Intersect with the Patient at the Center

Medicines ◽  
2021 ◽  
Vol 8 (8) ◽  
pp. 44
Author(s):  
Mary Beth Babos ◽  
Michelle Heinan ◽  
Linda Redmond ◽  
Fareeha Moiz ◽  
Joao Victor Souza-Peres ◽  
...  
Keyword(s):  
Drug Interaction ◽  
Case Report ◽  
Drug Interactions ◽  
Clinical Studies ◽  
Drug Information ◽  
Case Reports ◽  
Full Information ◽  
Information Need ◽  
Herbal Products ◽  
Reduce Risk

This review examines three bodies of literature related to herb–drug interactions: case reports, clinical studies, evaluations found in six drug interaction checking resources. The aim of the study is to examine the congruity of resources and to assess the degree to which case reports signal for further study. A qualitative review of case reports seeks to determine needs and perspectives of case report authors. Methods: Systematic search of Medline identified clinical studies and case reports of interacting herb–drug combinations. Interacting herb–drug pairs were searched in six drug interaction resources. Case reports were analyzed qualitatively for completeness and to identify underlying themes. Results: Ninety-nine case-report documents detailed 107 cases. Sixty-five clinical studies evaluated 93 mechanisms of interaction relevant to herbs reported in case studies, involving 30 different herbal products; 52.7% of these investigations offered evidence supporting reported reactions. Cohen’s kappa found no agreement between any interaction checker and case report corpus. Case reports often lacked full information. Need for further information, attitudes about herbs and herb use, and strategies to reduce risk from interaction were three primary themes in the case report corpus. Conclusions: Reliable herb–drug information is needed, including open and respectful discussion with patients.

scholarly journals Moraxella lacunata infection accompanied by acute glomerulonephritis

Open Medicine ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. 962-967
Author(s):  
Nami Sawada ◽  
Tamaki Morohashi ◽  
Tomokazu Mutoh ◽  
Tsukasa Kuwana ◽  
Junko Yamaguchi ◽  
...  
Keyword(s):  
Clinical Laboratory ◽  
Case Reports ◽  
Laboratory Data ◽  
Inflammatory Cells ◽  
Final Diagnosis ◽  
Renal Tissue ◽  
Acute Glomerulonephritis ◽  
Pathological Findings ◽  
Complement Activity ◽  
Moraxella Lacunata

AbstractMoraxella lacunata (M. lacunata) is a Gram-negative bacterium, which rarely causes serious infection. This is a rare case report of acute glomerulonephritis diagnosed by pathological findings in a child accompanied by M. lacunata infection. The patient showed hematuria, proteinuria and hyperkalemia requiring emergency hemodialysis. After hospitalization, M. lacunata bacteremia became apparent. Pathological findings showed an increase in glomerulus inflammatory cells and glomerular C3 deposition was observed in the renal tissue biopsy. Final diagnosis was endocapillary proliferative glomerulonephritis. Clinical reports of M. lacunata infection requiring emergency hemodialysis in children are rare. Previous reports have suggested that lowered immune competency with chronic kidney disease may be a risk factor associated with serious invasive cases of M. lacunata infection. However, detailed clinical laboratory data and pathological findings have not been identified in previous case reports. Our case directly indicated complement activity and acute glomerulonephritis with M. lacunata infection. Although there are various causes for acute glomerulonephritis, infection-related glomerulonephritis (IRGN) is an important concept. M. lacunata infection might have a potential risk for IRGN with dysregulation of complement activity leading to serious and invasive clinical conditions than previously considered.

scholarly journals Clinical metagenomics assessments improve diagnosis and outcomes in community-acquired pneumonia

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fei Xie ◽  
Zhimei Duan ◽  
Weiqi Zeng ◽  
Shumei Xie ◽  
Mingzhou Xie ◽  
...  
Keyword(s):  
Patient Outcomes ◽  
Clinical Management ◽  
Pathogen Detection ◽  
Community Acquired Pneumonia ◽  
Diagnostic Methods ◽  
Trial Registration ◽  
Clinical Trial Registry ◽  
Registration Number ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background Identifying the causes of community-acquired pneumonia (CAP) is challenging due to the disease’s complex etiology and the limitations of traditional microbiological diagnostic methods. Recent advances in next generation sequencing (NGS)-based metagenomics allow pan-pathogen detection in a single assay, and may have significant advantages over culture-based techniques. Results We conducted a cohort study of 159 CAP patients to assess the diagnostic performance of a clinical metagenomics assay and its impact on clinical management and patient outcomes. When compared to other techniques, clinical metagenomics detected more pathogens in more CAP cases, and identified a substantial number of polymicrobial infections. Moreover, metagenomics results led to changes in or confirmation of clinical management in 35 of 59 cases; these 35 cases also had significantly improved patient outcomes. Conclusions Clinical metagenomics could be a valuable tool for the diagnosis and treatment of CAP. Trial registration Trial registration number with the Chinese Clinical Trial Registry: ChiCTR2100043628.

Oral Terbinafine: A New Antifungal Agent

1997 ◽  
Vol 31 (4) ◽  
pp. 445-456 ◽  
Author(s):  
Susan M Abdel-Rahman ◽  
Milap C Nahata
Keyword(s):  
Adverse Effects ◽  
Drug Interactions ◽  
Fungal Infections ◽  
Case Reports ◽  
Current Standard ◽  
Open Label ◽  
Double Blind ◽  
Pathogenic Yeast

Objective To review the pharmacology, pharmacokinetics, efficacy, adverse effects, drug interactions, and dosage guidelines of terbinafine. Available comparative data of terbinafine and other antimycotic agents are described for understanding the potential role of terbinafine in patient care. Data Sources A MEDLINE search restricted to English language during 1966–1996 and extensive review of journals was conducted to prepare this article. MeSH headings included allylamines, terbinafine, SF 86–327, dermatophytosis, dermatomycosis. Data Extraction The data on pharmacokinetics, adverse effects, and drug interactions were obtained from open-label and controlled studies and case reports. Controlled single- or double-blind studies were evaluated to describe the efficacy of terbinafine in the treatment of various fungal infections. Data Synthesis Terbinafine is the first oral antimycotic in the allylamines class: a fungicidal agent that inhibits ergosterol synthesis at the stage of squalene epoxidation. Terbinafine demonstrates excellent in vitro activity against the majority of dermatophyte species including Trichophyton rubrum, Trichophyton mentagrophytes, and Epidermophyton floccosum; less activity is seen against Dematiaceae and the filamentous fungi. It is least active against the pathogenic yeast and this correlates with the relatively poor efficacy against these organisms in vivo. High concentrations of terbinafine are achieved in keratinous tissues, the site of superficial infections, and these concentrations are maintained for up to 3 months. The clinical efficacy of terbinafine against a number of dermatophyte infections exceeds that of the current standard of therapy, griseofulvin. The efficacy of terbinafine may be as good or better than that of the azole antifungals. Additional studies are required to confirm these observations. Terbinafine demonstrates a good safety profile, and relatively few drug interactions have been identified. Conclusions Terbinafine is more effective than the gold standard, griseofulvin, in the treatment of tinea pedis and tinea unguinum, with considerably shorter treatment duration in the latter. It has been proven as effective as griseofulvin in the treatment of tinea capitis, tinea corporis, and tinea cruris. Terbinafine does not appear to offer any advantage in the treatment of nondermatophyte infections; its utility in the treatment of systemic infections has yet to be established. Depending on individual institutional costs, terbinafine may be a front-line drug for some superficial infections responding poorly to the current standard of therapy.

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