Nanopore sequencing of cerebrospinal fluid of three patients with cryptococcal meningitis

Abstract Background Cryptococcal meningitis (CM) has a high morbidity and mortality due to the low detection of Cryptococcus in cerebrospinal fluid (CSF) during the early stage of the disease with traditional methods. Case presentation In addition to the traditional methods of India ink staining and cryptococcal antigen (CrAg), we used nanopore sequencing and next-generation sequencing (NGS) to detect pathogenic DNA in CSF samples of three patients with CM. The CSF samples of all three patients were positive by India ink staining and CrAg. NGS also detected Cryptococcus in all three CSF samples. Nanopore sequencing detected Cryptococcus in two CSF samples. Conclusion Nanopore sequencing may be useful in assisting with the clinical diagnosis of CM. Further research is needed to determine the sensitivity and specificity of nanopore sequencing of CSF.

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Case Report: Streptococcus Suis Meningitis Diagnosed in a HIV-Infected Patient With Cryptococcal Meningitis Using Next-Generation Sequencing

Frontiers in Medicine ◽

10.3389/fmed.2021.736064 ◽

2021 ◽

Vol 8 ◽

Author(s):

Yirui Xie ◽

Bing Ruan ◽

Guanjing Lang ◽

Biao Zhu

Keyword(s):

Next Generation Sequencing ◽

Cryptococcal Meningitis ◽

Infected Patient ◽

Early Stage ◽

Streptococcus Suis ◽

Antigen Test ◽

Next Generation ◽

Capsular Antigen ◽

India Ink ◽

Generation Sequencing

Background: Streptococcus suis has been recognized as a zoonotic pathogen that may cause infections in humans. Although rarely described, it is not surprising that both cryptococcal and streptococcus suis meningitis infections can co-exist in a HIV-infected patient with a low CD4 count. However, a fast and accurate diagnose of meningitis of multipathogenic infections is challenging. In this report, we describe such a case of a HIV-infected patient with meningitis of multipathogenic infections.Case Presentation: The patient was a 34-year-old Chinese male who was diagnosed with cryptococcal meningitis and HIV at the same time about 1 year ago. During the same time period, he had received (with good compliance) fluconazole and tenofovir-lamivudine- dolutegravir based antiretroviral therapy (ART). However, symptom of progressively worsening occipital headache appeared after he was exposed to a truck which was used for transporting pigs. Initial workup indicated an increase of the cerebrospinal fluid (CSF) opening pressure (OP) and an increase in the number of lymphocytes and proteins in CSF. A magnetic resonance imaging (MRI) scan revealed that partial cerebellar surface enhancement. The cryptococcus capsular antigen test of CSF was positive. The results of the India Ink microscopy for cryptococcus, nucleic acid of CMV and EBV and mycobacterium tuberculosis (MTB) tests of CSF were negative. The results of the bacteria and fungi smear and culture of CSF were also negative. Eventually, streptococcus suis was detected using next-generation sequencing (NGS) in CSF. The diagnosis of Streptococcus suis meningitis was made based on the patient's contact history with carrier pigs and the clinical findings addressed above. The treatment of 2 weeks of intravenous ceftriaxone and 1 week of oral moxifloxacin resulted in improvement of the condition of CSF. The anti-fungal treatment using fluconazole continued until the CFS OP went down to a normal level and the cryptococcus capsular antigen test of CSF was negative 6 months later.Conclusion: This case highlights that NGS might be beneficial to HIV-infected patients who have meningitis with negative CSF culture results. Multiple etiologies for such condition in the immunocompromised patients must be taken into consideration and early stage NGS is recommended.

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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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Microbiome Analysis of Biofilms of Silver Nanoparticle-Dispersed Silane-Based Coated Carbon Steel Using a Next-Generation Sequencing Technique

Antibiotics ◽

10.3390/antibiotics7040091 ◽

2018 ◽

Vol 7 (4) ◽

pp. 91 ◽

Cited By ~ 4

Author(s):

Akiko Ogawa ◽

Keito Takakura ◽

Katsuhiko Sano ◽

Hideyuki Kanematsu ◽

Takehiko Yamano ◽

...

Keyword(s):

Next Generation Sequencing ◽

Silver Nanoparticle ◽

Biofilm Formation ◽

Early Stage ◽

Biofilm Reactor ◽

Next Generation ◽

Microbiome Analysis ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing ◽

Closed Laboratory

Previously, we demonstrated that silver nanoparticle-dispersed silane-based coating could inhibit biofilm formation in conditions where seawater was used as a bacterial source and circulated in a closed laboratory biofilm reactor. However, it is still unclear whether the microbiome of a biofilm of silver nanoparticle-dispersed silane-based coating samples (Ag) differs from that of a biofilm of non-dispersed silane-based coating samples (Non-Ag). This study aimed to perform a microbiome analysis of the biofilms grown on the aforementioned coatings using a next-generation sequencing (NGS) technique. For this, a biofilm formation test was conducted by allowing seawater to flow through a closed laboratory biofilm reactor; subsequently, DNAs extracted from the biofilms of Ag and Non-Ag were used to prepare 16S rRNA amplicon libraries to analyze the microbiomes by NGS. Results of the operational taxonomy unit indicated that the biofilms of Non-Ag and Ag comprised one and no phyla of archaea, respectively, whereas Proteobacteria was the dominant phylum for both biofilms. Additionally, in both biofilms, Non-Ag and Ag, Marinomonas was the primary bacterial group involved in early stage biofilm formation, whereas Anaerospora was primarily involved in late-stage biofilm formation. These results indicate that silver nanoparticles will be unrelated to the bacterial composition of biofilms on the surface of silane-based coatings, while they control biofilm formation there.

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

BMC Infectious Diseases ◽

10.1186/s12879-021-06955-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jingyan Xia ◽

Lexin Xia ◽

Hui Zhou ◽

Xiuhui Lin ◽

Feng Xu

Keyword(s):

Computed Tomography ◽

Pleural Effusion ◽

Clinical Laboratory ◽

Case Presentation ◽

Chest Computed Tomography ◽

Streptococcus Anginosus ◽

Streptococcus Constellatus ◽

Routine Clinical Laboratory ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

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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Genetic alterations of early-stage breast cancers by next-generation sequencing (NGS)

Annals of Oncology ◽

10.1093/annonc/mdy270.205 ◽

2018 ◽

Vol 29 ◽

pp. viii67

Author(s):

Y. Xu ◽

M. Zhang ◽

R. Chen ◽

X. Xia

Keyword(s):

Next Generation Sequencing ◽

Early Stage ◽

Genetic Alterations ◽

Breast Cancers ◽

Next Generation ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

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Case Report: Diagnosis of Klebsiella pneumoniae Invasive Liver Abscess Syndrome With Purulent Meningitis in a Patient From Pathogen to Lesions

Frontiers in Medicine ◽

10.3389/fmed.2021.714916 ◽

2021 ◽

Vol 8 ◽

Author(s):

Sheng Zeng ◽

Wei-qian Yan ◽

Xiao-mei Wu ◽

Hai-nan Zhang

Keyword(s):

Klebsiella Pneumoniae ◽

Liver Abscess ◽

Early Stage ◽

Disease Onset ◽

High Morbidity ◽

Antibiotic Administration ◽

Negative Results ◽

Purulent Meningitis ◽

Pathogen Diagnosis ◽

Generation Sequencing

As a determinant human pathogen, Klebsiella pneumoniae is known to cause rare K. pneumoniae liver abscess syndrome (KLAS) which was more common in Asia in early-stage and reported increasingly outside Asia now. Patients with KLAS who have septic metastatic ocular or central nervous system (CNS) lesions are associated with high morbidity and mortality. Relatively infrequent adult community-acquired K. pneumoniae meningitis have been documented and most were with poor prognosis. In this paper, we reported a case of KLAS presenting purulent meningitis as disease onset. While negative results were obtained in the bacterial culture of CSF, blood, or liver pus, metagenomic next-generation sequencing (mNGS) of CSF, and blood samples which were synchronously performed demonstrated Klebsiella pneumoniae as the pathogenic microorganism (13,470 and 5,318 unique reads, respectively). The ultimately cured patient benefited from rapid pathogen diagnosis, early percutaneous drainage of the abscess, and prompt appropriate antibiotic administration. Our case highlights the importance of clinicians using mNGS for early pathogen diagnosis of this disease.

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MicroRNA Profile of Patients with Chronic Limb-Threatening Ischemia

Diagnostics ◽

10.3390/diagnostics10040230 ◽

2020 ◽

Vol 10 (4) ◽

pp. 230 ◽

Cited By ~ 2

Author(s):

Muzammil H. Syed ◽

Abdelrahman Zamzam ◽

Jason Valencia ◽

Hamzah Khan ◽

Shubha Jain ◽

...

Keyword(s):

Early Stage ◽

P Value ◽

Discovery Phase ◽

Genome Wide ◽

A Genome ◽

Microrna Profile ◽

Mirna Sequencing ◽

Next Generation Sequencing Ngs ◽

Confirmatory Phase ◽

Generation Sequencing

Chronic limb-threatening ischemia (CLTI) results in devastating complications such as lower-limb amputations. In this study, a genome-wide plasma microRNAs (miRNA) sequencing was performed to identify miRNA(s) associated with CLTI. Blood samples were collected from early stage CLTI patients (ABI < 0.9) and non-PAD controls (ABI ≥ 0.9) for 3 experiments: discovery phase (n = 23), confirmatory phase (n = 52) and validation phase (n = 20). In the discovery phase, next generation sequencing (NGS) was used to identify miRNA circulating in the plasma CLTI (n = 13) patients, compared to non-PAD controls (n = 10). Two down-regulated miRNAs (miRNA-6843-3p and miRNA-6766-5p) and three upregulated miRNAs (miRNA-1827, miRNA-320 and miRNA-98-3p) were identified (≥2-fold change). In the confirmatory phase, these 5 deregulated miRNAs were further investigated in non-PAD (n = 21) and CTLI (n = 31) patients using qRT-PCR. Only miRNA-1827 was found to be significantly upregulated (≥3-fold, p-value < 0. 001) in the CLTI group. Lastly, to minimize the influence of confounding factors, miRNA-1827 plasma levels were validated in a third cohort of CLTI patients (n = 10) matched to non-PAD controls (n = 10). Our analysis demonstrated that miRNA-1827 expression was increased in the CLTI cohort (≥2-folds, p-value < 0.001). In summary, circulating miRNA-1827 is significantly elevated in patients with CLTI.

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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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Acute Lymphocytic Leukemia With KMT2A-ELL Fusion Mutation in a Patient With Untreated Chronic Lymphocytic Leukemia: A Case Report and Literature Review

10.21203/rs.3.rs-290097/v1 ◽

2021 ◽

Author(s):

Shilin Zhang ◽

Sennan Qiao ◽

Wei Han ◽

Ruiping Hu ◽

Zhonghua Du ◽

...

Keyword(s):

Chronic Lymphocytic Leukemia ◽

Fusion Gene ◽

Tp53 Gene ◽

Lymphocytic Leukemia ◽

Lower Limbs ◽

Case Presentation ◽

Coding Sequence ◽

Patient Reported ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Background: The concurrent of chronic lymphocytic leukemia (CLL) and acute myeloid leukemia (AML) in a patient is a rare situation, and has caused obstacles in clinical management. Case presentation: In the current study, we described a 64-year old female who was characterized by intermittent fatigue, edema of both lower limbs, dyspnea, and occasionally fever up to 39°C. The admission blood routine detections and the flow cytometry showed the patient was impaired by both CLL and AML. In RT-qPCR molecular detection, KMT2A-ELL fusion gene t (11:10) (q23:p13.1) was detected, which was verified by FISH detections. The next-generation sequencing (NGS) revealed a missense mutation of p.V157F in the coding sequence of TP53 gene, and frameshift mutations of p.V220fs and p.A382fs in the coding sequence of WT1. Conclusions: Collectively, the patient reported in this case was simultaneously impaired by CLL and AML. Our findings also inferred that the concurrent of CLL and AML might be attributed to the fusion mutation in KMT2A-ELL gene.

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