Empyema caused by Streptococcus constellatus: a case report and literature review

Abstract Background Streptococcus constellatus is a member of Streptococcus anginosus group (SAG) that tends to cause pyogenic infections in various sites. However, Streptococcus constellatus is easily ignored by routine clinical laboratory tests for its prolonged anaerobic culture environment. Case presentation A 71-year-old man was admitted to our hospital due to productive cough, fever, chest pain and shortness of breath for 3 weeks. Chest computed tomography showed patchy opacities and right-sided pleural effusion, so a chest tube was inserted and purulent and hemorrhagic fluid was aspirated. The routine etiological examinations of the pleural effusion were all negative, and next-generation sequencing (NGS) detected Streptococcus constellatus. Intravenous piperacillin-tazobactam 4.5 g every 8 h was used accordingly. The patient recovered and subsequent chest computed tomography confirmed the improvement. Conclusions We reported a case of empyema secondary to Streptococcus constellatus infection, which was identified by NGS, instead of bacterial culture. This case highlights the utility of NGS in detecting pathogens negative in traditional bacterial tests.

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Pulmonary coinfection of Mycobacterium tuberculosis and Tropheryma whipplei: a case report

Journal of Medical Case Reports ◽

10.1186/s13256-021-02899-y ◽

2021 ◽

Vol 15 (1) ◽

Author(s):

Binghua Zhu ◽

Jing Tang ◽

Rong Fang ◽

Xuejie Fei ◽

Qing Wang ◽

...

Keyword(s):

Computed Tomography ◽

Mycobacterium Tuberculosis ◽

Next Generation Sequencing ◽

Tropheryma Whipplei ◽

Diagnostic Methods ◽

Next Generation ◽

Computed Tomography Scan ◽

Chest Computed Tomography ◽

Tomography Scan ◽

Generation Sequencing

Abstract Background We diagnosed a clinical case of pulmonary infection involving Mycobacterium tuberculosis and Tropheryma whipplei in a patient with acute respiratory distress syndrome. The diagnosis was assisted by metagenomic next-generation sequencing of bronchoalveolar lavage fluid. Case presentation A 44-year-old Han Chinese inmate was transferred to the emergency department because of dry cough, chest tightness, and shortness of breath. The patient’s body temperature rose to 39.3 °C following empirical cephalosporin treatment for 1 week. The blood CD4+/CD8+ ratio was 0.7, suggesting immunodeficiency. Routine microbiological tests were performed, and tuberculosis interferon gamma release assays were positive. Mycobacterium tuberculosis polymerase chain reaction was also positive. Chest computed tomography scan revealed miliary nodules and ground-glass opacifications, which were in accordance with tuberculosis. To fully examine the etiology, we performed routine laboratory tests and metagenomic sequencing, the results of which indicated the presence of Mycobacterium tuberculosis and Tropheryma whipplei. We administered anti-tuberculosis regimen in combination with trimethoprim/sulfamethoxazole. The patient recovered, with chest computed tomography scan showing absorption of lesions. Conclusions Compared with traditional diagnostic methods such as culture and serology, metagenomic next-generation sequencing has the advantage of detecting a wide array of microorganisms in a single test and therefore can be used for clinical diagnosis of rare pathogens and microbial coinfections. It is particularly useful for immunocompromised patients as they are more prone to infection by opportunistic microorganisms.

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SARS-CoV-2 infection in an infant with non-respiratory manifestations: a case report

Egyptian Pediatric Association Gazette ◽

10.1186/s43054-020-00047-7 ◽

2021 ◽

Vol 69 (1) ◽

Author(s):

Muhammad Adel ◽

Ahmed Magdy

Keyword(s):

Computed Tomography ◽

Aplastic Anemia ◽

Rt Pcr ◽

Positive Real ◽

Case Presentation ◽

Chest Computed Tomography ◽

High Incidence ◽

Laboratory Investigations ◽

High Index Of Suspicion ◽

Specific Symptoms

Abstract Background Coronavirus disease (COVID-19) presents in children usually with less severe manifestations than in adults. Although fever and cough were reported as the most common symptoms, children can have non-specific symptoms. We describe an infant with aplastic anemia as the main manifestation. Case presentation We describe a case of SARS-CoV-2 infection in an infant without any respiratory symptoms or signs while manifesting principally with pallor and purpura. Pancytopenia with reticulocytopenia was the predominant feature in the initial laboratory investigations, pointing to aplastic anemia. Chest computed tomography surprisingly showed typical findings suggestive of SARS-CoV-2 infection. Infection was later confirmed by positive real-time reverse transcription polymerase chain reaction assay (RT-PCR) for SARS-CoV-2. Conclusions Infants with COVID-19 can have non-specific manifestations and a high index of suspicion should be kept in mind especially in regions with a high incidence of the disease. Chest computed tomography (CT) and testing for SARS-CoV-2 infection by RT-PCR may be considered even in the absence of respiratory manifestations.

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Severe pneumonia caused by Parvimonas micra: a case report

BMC Infectious Diseases ◽

10.1186/s12879-021-06058-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Qing Yu ◽

Lingling Sun ◽

Zuqing Xu ◽

Lumei Fan ◽

Yunbo Du

Keyword(s):

Bronchoalveolar Lavage Fluid ◽

Case Reports ◽

Severe Pneumonia ◽

Lavage Fluid ◽

Due Date ◽

Case Presentation ◽

Abdominal Abscesses ◽

Parvimonas Micra ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Background Parvimonas micra (P. micra) is a gram-positive anaerobic coccus that is detected widely on the skin, in the oral mucosa and in the gastrointestinal tract. In certain circumstances, P. micra can cause abdominal abscesses, bacteraemia and other infections. To the best of our knowledge, there have been no case reports describing the biological characteristics of P. micra-related pneumonia. These bacteria do not always multiply in an aerobic organ, such as the lung, and they could be easily overlooked because of the clinical mindset. Case presentation A 35-year-old pregnant woman was admitted to the emergency department 4 weeks prior to her due date who was exhibiting 5 points on the Glasgow coma scale. A computed tomography (CT) scan showed a massive haemorrhage in her left basal ganglia. She underwent a caesarean section and brain surgery before being admitted to the ICU. She soon developed severe pneumonia and hypoxemia. Given that multiple sputum cultures were negative, the patient’s bronchoalveolar lavage fluid was submitted for next-generation sequencing (NGS) to determine the pathogen responsible for the pneumonia; as a result, P. micra was determined to be the causative pathogen. Accordingly the antibiotic therapy was altered and the pneumonia improved. Conclusion In this case, we demonstrated severe pneumonia caused by the anaerobic organism P. micra, and the patient benefited from receiving the correct antibiotic. NGS was used as a method of quick diagnosis when sputum culture failed to distinguish the pathogen.

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Using a Next Generation Sequencing Panel to Discover the Obscure Causes of Hereditary Hemolytic Anemias

Blood ◽

10.1182/blood.v128.22.2433.2433 ◽

2016 ◽

Vol 128 (22) ◽

pp. 2433-2433 ◽

Cited By ~ 1

Author(s):

Archana M Agarwal ◽

N. Scott Reading ◽

Kimberly Frizzell ◽

Wei Shen ◽

Shelly Sorrells ◽

...

Keyword(s):

Next Generation Sequencing ◽

Hemolytic Anemia ◽

Clinical Laboratory ◽

Single Gene ◽

Cytoskeletal Proteins ◽

Next Generation ◽

Pathogenic Variants ◽

Late Morbidity ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Hereditary hemolytic anemias are a heterogeneous group of disorders with consequences ranging from non-anemic hemolysis to severe life-threatening anemia. However, the late morbidity in patients without transfusions is often underappreciated because of erythropoietic compensatory stimulation inducing hematopoiesis by erythroferrone/hepcidin axis. Principal causes of hereditary hemolytic anemias are germline mutations of red cell cytoskeleton (e.g. hereditary spherocytosis and elliptocytosis/pyropoikilocytosis) or enzyme deficiencies (e.g. Glucose 6 phosphate dehydrogenase deficiency and pyruvate kinase deficiency). Routine morphological and biochemical analysis may be inconclusive and misleading particularly in transfusion-dependent infants and children. Molecular studies have not been extensively used to diagnose these disorders due to the complex genetic nature of these disorders, and multi-gene disorders. In these cases, patients may undergo multiple rounds of single gene testing, which can be very costly and time consuming. The advent of next generation sequencing (NGS) methods in the clinical laboratory has made diagnosing complex genetic disorders feasible. Our diagnostic panel includes 28 genes encoding cytoskeletal proteins and enzymes, and covers the complete coding region, splice site junctions, and, where appropriate, deep intronic or regulatory regions. Targeted gene capture and library construction for next-generation sequencing (NGS) was performed using Sure Select kit (Agilent Technologies, Santa Clara, USA). Prior to sequencing on the Illumina Next Seq, (Illumina Inc) instrument, indexed samples are quantified using qPCR and then pooled. Samples were sequenced using 2x150 paired end sequencing. We now report the first 68 patients evaluated using our NGS panel. The age of the patients ranged from newborn to 62 years. These patients presented with symptoms ranging from mild lifelong anemia to severe hemolytic anemia with extreme hyperbilirubinemia. Genetic variants were classified using the American College of Medical Genetics (ACMG) guidelines. We identified pathogenic variants in 11 patients and likely pathogenic variants in 12 others, the majority of these were novel. Many variants with unknown significance were also identified that could potentially contribute to disease. The most commonly mutated genes were SPTB and SPTA1, encoding spectrin subunits. Some complex interactions were uncovered i.e. SPTA1 mutations along with alpha LELY leading to hereditary pyropoikilocytosis; Spectrin variants along with Gilbert syndrome causing severe hyperbilirubinemia in neonates; and Spectrin variants in combination with PKLR and G6PD variants. Our results demonstrate that many patients with hemolytic anemia harbor complex combinations of known and novel mutations in RBC cytoskeleton/enzyme genes, but their clinical significance is further augmented by polymorphisms of UGT1A1 gene contributing to severe neonatal hyperbilirubinemia and its consequences. To conclude, next-generation sequencing provides a cost-effective and relatively rapid approach to molecular diagnosis, especially in instances where traditional testing failed. We have used this technology successfully to determine the molecular causes of hemolytic anemia in many cases with no prior family history. Disclosures Yaish: Octapharma: Other: Study investigator.

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Rapid screening for COVID-19 by applying artificial intelligence to chest computed tomography images: A feasibility study

Medicine Access Point of Care ◽

10.1177/23992026211013644 ◽

2021 ◽

Vol 5 ◽

pp. 239920262110136

Author(s):

Pedro Galván ◽

José Fusillo ◽

Felipe González ◽

Oraldo Vukujevic ◽

Luciano Recalde ◽

...

Keyword(s):

Artificial Intelligence ◽

Computed Tomography ◽

Pleural Effusion ◽

Feasibility Study ◽

Ct Images ◽

Public Hospitals ◽

Rt Pcr ◽

Chest Computed Tomography ◽

Computed Tomography Images ◽

Respiratory Conditions

Aim: The aim of the study was to present the results and impact of the application of artificial intelligence (AI) in the rapid diagnosis of COVID-19 by telemedicine in public health in Paraguay. Methods: This is a descriptive, multi-centered, observational design feasibility study based on an AI tool for the rapid detection of COVID-19 in chest computed tomography (CT) images of patients with respiratory difficulties attending the country’s public hospitals. The patients’ digital CT images were transmitted to the AI diagnostic platform, and after a few minutes, radiologists and pneumologists specialized in COVID-19 downloaded the images for evaluation, confirmation of diagnosis, and comparison with the genetic diagnosis (reverse transcription polymerase chain reaction (RT-PCR)). It was also determined the percentage of agreement between two similar AI systems applied in parallel to study the viability of using it as an alternative method of screening patients with COVID-19 through telemedicine. Results: Between March and August 2020, 911 rapid diagnostic tests were carried out on patients with respiratory disorders to rule out COVID-19 in 14 hospitals nationwide. The average age of patients was 50.7 years, 62.6% were male and 37.4% female. Most of the diagnosed respiratory conditions corresponded to the age group of 27–59 years (252 studies), the second most frequent corresponded to the group over 60 years, and the third to the group of 19–26 years. The most frequent findings of the radiologists/pneumologists were severe pneumonia, bilateral pneumonia with pleural effusion, bilateral pulmonary emphysema, diffuse ground glass opacity, hemidiaphragmatic paresis, calcified granuloma in the lower right lobe, bilateral pleural effusion, sequelae of tuberculosis, bilateral emphysema, and fibrotic changes, among others. Overall, an average of 86% agreement and 14% diagnostic discordance was determined between the two AI systems. The sensitivity of the AI system was 93% and the specificity 80% compared with RT-PCR. Conclusion: Paraguay has an AI-based telemedicine screening system for the rapid stratified detection of COVID-19 from chest CT images of patients with respiratory conditions. This application strengthens the integrated network of health services, rationalizing the use of specialized human resources, equipment, and inputs for laboratory diagnosis.

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Bioinformatics for Clinical Next Generation Sequencing

Clinical Chemistry ◽

10.1373/clinchem.2014.224360 ◽

2015 ◽

Vol 61 (1) ◽

pp. 124-135 ◽

Cited By ~ 56

Author(s):

Gavin R Oliver ◽

Steven N Hart ◽

Eric W Klee

Keyword(s):

Next Generation Sequencing ◽

Service Providers ◽

Clinical Laboratory ◽

Work Flow ◽

Next Generation ◽

Sequencing Data ◽

Regulatory Requirements ◽

Bioinformatics Analyses ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract BACKGROUND Next generation sequencing (NGS)-based assays continue to redefine the field of genetic testing. Owing to the complexity of the data, bioinformatics has become a necessary component in any laboratory implementing a clinical NGS test. CONTENT The computational components of an NGS-based work flow can be conceptualized as primary, secondary, and tertiary analytics. Each of these components addresses a necessary step in the transformation of raw data into clinically actionable knowledge. Understanding the basic concepts of these analysis steps is important in assessing and addressing the informatics needs of a molecular diagnostics laboratory. Equally critical is a familiarity with the regulatory requirements addressing the bioinformatics analyses. These and other topics are covered in this review article. SUMMARY Bioinformatics has become an important component in clinical laboratories generating, analyzing, maintaining, and interpreting data from molecular genetics testing. Given the rapid adoption of NGS-based clinical testing, service providers must develop informatics work flows that adhere to the rigor of clinical laboratory standards, yet are flexible to changes as the chemistry and software for analyzing sequencing data mature.

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Effective quality management practices in routine clinical next-generation sequencing

Clinical Chemistry and Laboratory Medicine (CCLM) ◽

10.1515/cclm-2015-1190 ◽

2016 ◽

Vol 54 (5) ◽

Cited By ~ 15

Author(s):

Francine B. de Abreu ◽

Jason D. Peterson ◽

Christopher I. Amos ◽

Wendy A. Wells ◽

Gregory J. Tsongalis

Keyword(s):

Next Generation Sequencing ◽

Quality Management ◽

Patient Care ◽

Management Practices ◽

Clinical Laboratory ◽

Management Program ◽

Next Generation ◽

Ion Pgm ◽

Routine Clinical Laboratory ◽

Generation Sequencing

AbstractBackground:Molecular technologies have allowed laboratories to detect and establish the profiles of human cancers by identifying a variety of somatic variants. In order to improve personalized patient care, we have established a next-generation sequencing (NGS) test to screen for somatic variants in primary or advanced cancers. In this study, we describe the laboratory quality management program for NGS testing, and also provide an overview of the somatic variants identified in over 1000 patient samples as well as their implications in clinical practice.Methods:Over the past one-and-a-half years, our laboratory received a total of 1028 formalin-fixed, paraffin-embedded (FFPE) tumor tissues, which consisted of non-small-cell lung carcinomas (NSCLCs), colon adenocarcinomas, glioma/glioblastomas, melanomas, breast carcinomas, and other tumor types. During this time period, we implemented a series of quality control (QC) checks that included (1) pre-DNA extraction, (2) DNA quantification, (3) DNA quality, (4) library quantification, (5) post-emulsification PCR, and (6) post-sequencing metrics. At least 10 ng of genomic DNA (gDNA) were used to prepare barcoded libraries using the AmpliSeq CHPv2. Samples were multiplexed and sequenced on Ion Torrent 318 chips using the Ion PGM System. Variants were identified using the Variant Caller Plugin, and annotation and functional predictions were performed using the Golden Helix SVS.Results:A total of 1005 samples passed QC1–3, and following additional library preparation QC checkpoints, 877 samples were sequenced. Samples were classified into two categories: wild-type (127) and positive for somatic variants (750). Somatic variants were classified into clinically actionable (60%) and non-actionable (40%).Conclusions:The use of NGS in routine clinical laboratory practice allowed for the detection of tumor profiles that are essential for the selection of targeted therapies and identification of applicable clinical trials, contributing to the improvement of personalized patient care in oncology.

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Comparison of KRAS mutation analysis of colorectal cancer samples by standard testing and next-generation sequencing

Journal of Clinical Pathology ◽

10.1136/jclinpath-2014-202405 ◽

2014 ◽

Vol 67 (9) ◽

pp. 764-767 ◽

Cited By ~ 21

Author(s):

Nishi Kothari ◽

Michael J Schell ◽

Jamie K Teer ◽

Timothy Yeatman ◽

David Shibata ◽

...

Keyword(s):

Colorectal Cancer ◽

Next Generation Sequencing ◽

Clinical Laboratory ◽

Clinical Care ◽

Next Generation ◽

Illumina Platform ◽

Kras Mutations ◽

Standard Testing ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

AimsBased on KRAS testing, the subset of patients with metastatic colorectal cancer (CRC) that could benefit from anti-EGFR therapy can be better delineated. Though KRAS testing has become significantly more prevalent over the last few years, methods for testing remain heterogeneous and discordance has been reported between methods.MethodsIn this study, we examined a CRC patient population and compared KRAS testing done in Clinical Laboratory Improvement Amendments (CLIA) approved laboratories as part of standard clinical care and by next-generation sequencing (NGS) using the Illumina platform. Discordances were further evaluated with manual review of the NGS testing.ResultsOut of 468 CRC patient samples, 77 had KRAS testing done by both CLIA assay and NGS. There were concordant results between testing methodologies in 74 out of 77 patients, or 96% (95% CI 89% to 99%). There were three patient samples that showed discordant results between the two methods of testing. Upon further investigation of the NGS results for the three discordant cases, one sample showed a low level of the mutation seen in the standard testing, one sample showed low tumour fraction and a third did not show any evidence of the mutation that was found with the standard assay. Five patients had KRAS mutations not typically tested with standard testing.ConclusionsOverall there was a high concordance rate between NGS and standard testing for KRAS. However, NGS revealed mutations that are not tested for with standard KRAS assays that might have clinical impact with regards to the role for anti-EGFR therapy.

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A mass in the upper abdomen derived from Talaromyces marneffei infected lymphadenopathy: a case report

BMC Infectious Diseases ◽

10.1186/s12879-021-06489-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xue Chen ◽

Lin Jia ◽

Yongfeng Wu ◽

Jing Chang ◽

Tong Zhang ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Case Report ◽

Abdominal Mass ◽

Case Presentation ◽

Talaromyces Marneffei ◽

Immunodeficiency Virus ◽

Upper Abdominal ◽

Upper Abdomen ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Background An upper abdominal mass without tenderness often indicates a benign or malignant tumor once liver or spleen hyperplasia has been excluded. A lymphadenopathic mass from Talaromyces marneffei infection is rare. Case presentation We report the case of a 29-year-old human immunodeficiency virus (HIV) infected man who presented with an upper abdominal mass and without any symptoms related with infection. Histopathology and next-generation sequencing (NGS) following biopsy of the mass confirmed T. marneffei-infected lymphadenopathy, and the patient was successfully treated with amphotericin B and itraconazole. Conclusions This case report suggests that potential fungal infection should be considered during the diagnostic workup of a mass in clinical practice.

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Hodgkin’s Lymphoma Presenting as Multiple Cavitary Lung Lesions

European Journal of Case Reports in Internal Medicine ◽

10.12890/2020_003024 ◽

2021 ◽

Author(s):

Esha Jain ◽

Ali Hani Al-Tarbsheh ◽

Jozef Oweis ◽

Erik Jacobson ◽

Boris Shkolnik

Keyword(s):

Computed Tomography ◽

Critical Care ◽

Hodgkin Lymphoma ◽

Care Setting ◽

Clinical Laboratory ◽

Critical Care Setting ◽

Productive Cough ◽

Chest Computed Tomography ◽

Atypical Presentations ◽

Infectious Etiology

Hodgkin Lymphoma (HL) typically presents similarly to an infectious etiology, thus awareness of its atypical presentations is essential. We present a case of an adult woman who was found to have HL after presenting with a dry, non-productive cough and showing cavitary lesions on chest computed tomography (CT). We also describe the clinical, laboratory, and radiological workup done leading to the diagnosis and management of HL in a critical care setting.

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