Co-Infection Pneumonia with Mycobacterium abscessus and Pneumocystis jiroveci in a Patient without HIV Infection Diagnosed by Metagenomic Next-Generation Sequencing

Abstract The transitions study examines HIV risk among adolescent girls and young women through their sexual life course from first sex, to past and current engagement in casual sex, transactional sex, and, for some, formal sex work (FSW). Understanding the timing of HIV infection and the circumstances around early infection in young females is critical to HIV prevention interventions. We inferred time since HIV infection using next-generation sequencing (NGS) of the HIV pol gene isolated from cross-sectional samples among high-risk young women in Dnipro, Ukraine. Dried blood spots were collected on Whatman 903 cards from young women aged 14–24 engaged in casual sex (n = 894), transactional sex (n = 464), and FSW (n = 452). The HIV pol gene was sequenced using an in-house NGS HIV drug resistance mutation genotyping assay. Time since HIV infection was inferred using an online tool as described by Puller et al. (2017) freely available at https://hiv.biozentrum.unibas.ch/ETI/. The mean estimated time since HIV infection (ETI) for participants engaged in casual sex, transactional sex, and FSW is 1.98, 1.84, and 3.01 years, respectively. ETI was used to determine the duration of HIV infection for each participant and compared to the number of sexually active years prior to FSW. Among FSW, 61 per cent of participants were infected with HIV prior to entry into sex work. In general, ETI from NGS data suggests that FSWs were infected with HIV before entry into FSW. Expansion of targeted prevention programs beyond FSW could play an important role in mitigating HIV transmission at the population level.

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Application of next generation sequencing in dual HIV infection studies

Journal of microbiology epidemiology immunobiology ◽

10.36233/0372-9311-153 ◽

2022 ◽

Vol 98 (6) ◽

pp. 627-638

Author(s):

I. A. Lapovok ◽

P. B. Baryshev ◽

D. V. Saleeva ◽

A. A. Kirichenko ◽

A. V. Shlykova (Murzakova) ◽

...

Keyword(s):

Next Generation Sequencing ◽

Hiv Infection ◽

Routine Practice ◽

Next Generation ◽

Genetic Characteristics ◽

Synonymous Mutations ◽

Operational Taxonomic Units ◽

Subtype B ◽

Generation Sequencing ◽

Hiv 1

Introduction. The aim of the study was to use comparative analysis for assessing efficiency of detection and confirmation of dual HIV infection, using conventional population sequencing (PS) and next generation sequencing (NGS) for an HIV-1 pol gene fragment, which encompasses protease and partially reverse transcriptase (positions 2253–3368).Materials and methods. The study was performed on intersubtype dual HIV infection model samples containing viruses of HIV-1 subtype B, sub-subtype A6 and recombinant form CRF63_02A1. Viruses were mixed pairwise in proportions from 10 to 90% to obtain 3 groups of model samples: CRF63vsB, CRF63vsA6, and A6vsB. The nucleotide sequences obtained by using PS and NGS technologies having 5, 10, 15, and 20% sensitivity thresholds for minor virus variants (NGS5–NGS20, respectively) were used to estimate the number of degenerate nucleotides or the degenerate base (DB) count and the number of synonymous mutations (SM) or the SM count. The fragment of the studied region (positions 2725–2981) was used for the analysis of operational taxonomic units.Results. The application of NGS5 proved highly efficient for detection of dual HIV infection in the model samples. The statistically significant (p < 0.01) increase in DB and SM counts was demonstrated by NGS5 compared to PS. As a result, NGS5 helped detect dual HIV infection in 25 out of 27 model samples, while with PS it was detected only in 15 samples. The analysis of operational taxonomic units confirmed dual HIV infection in all the groups of model samples.Discussion. The efficiency of detection and confirmation of dual HIV infection depends both on the content of each virus in the sample and on genetic characteristics of these viruses. Conclusion. Using NGS genetic testing in routine practice will be instrumental for efficient identification of genetic characteristics of infectious agents and for thorough analysis of the epidemiological situation.

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Pneumocystis jiroveci pneumonia with cytomegalovirus infection diagnosed by metagenomic next-generation sequencing in a patient with nephrotic syndrome

Medicine ◽

10.1097/md.0000000000026842 ◽

2021 ◽

Vol 100 (31) ◽

pp. e26842

Author(s):

Qian Yu ◽

Xuchun Ding ◽

Wen Wang ◽

Yafang Lou

Keyword(s):

Nephrotic Syndrome ◽

Next Generation Sequencing ◽

Cytomegalovirus Infection ◽

Next Generation ◽

Pneumocystis Jiroveci ◽

Pneumocystis Jiroveci Pneumonia ◽

Generation Sequencing

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Next-Generation Sequencing of Small RNAs from HIV-Infected Cells Identifies Phased microRNA Expression Patterns and Candidate Novel microRNAs Differentially Expressed upon Infection

mBio ◽

10.1128/mbio.00549-12 ◽

2013 ◽

Vol 4 (1) ◽

Cited By ~ 37

Author(s):

Stewart T. Chang ◽

Matthew J. Thomas ◽

Pavel Sova ◽

Richard R. Green ◽

Robert E. Palermo ◽

...

Keyword(s):

Transcriptional Regulation ◽

Next Generation Sequencing ◽

Hiv Infection ◽

Small Rna ◽

Microrna Expression ◽

Rna Seq ◽

Next Generation ◽

Dynamic Changes ◽

Infected Cells ◽

Generation Sequencing

ABSTRACT HIV infection of CD4+ T cells induces a range of host transcriptional changes in mRNAs as well as microRNAs that may coordinate changes in mRNAs. To survey these dynamic changes, we applied next-generation sequencing, analyzing the small RNA fraction of HIV-infected cells at 5, 12, and 24 h postinfection (RNA-Seq). These time points afforded a view of the transcriptomic changes occurring both before and during viral replication. In the resulting small RNA-Seq data set, we detected a phased pattern of microRNA expression. Largely distinct sets of microRNAs were found to be suppressed at 5 and 12 h postinfection, and both sets of changes rebounded later in infection. A larger set of microRNA changes was observed at 24 h postinfection. When integrated with mRNA expression data, the small RNA-Seq data indicated a role for microRNAs in transcriptional regulation, T cell activation, and cell cycle during HIV infection. As a unique benefit of next-generation sequencing, we also detected candidate novel host microRNAs differentially expressed during infection, including one whose downregulation at 24 h postinfection may allow full replication of HIV to proceed. Collectively, our data provide a uniquely comprehensive view of the changes in host microRNAs induced by HIV during cellular infection. IMPORTANCE New sequencing technologies allow unprecedented views into changes occurring in virus-infected cells, including comprehensive and largely unbiased measurements of different types of RNA. In this study, we used next-generation sequencing to profile dynamic changes in cellular microRNAs occurring in HIV-infected cells. The sensitivity afforded by sequencing allowed us to detect changes in microRNA expression early in infection, before the onset of viral replication. A phased pattern of expression was evident among these microRNAs, and many that were initially suppressed were later overexpressed at the height of infection, providing unique signatures of infection. By integrating additional mRNA data with the microRNA data, we identified a role for microRNAs in transcriptional regulation during infection and specifically a network of microRNAs involved in the expression of a known HIV cofactor. Finally, as a distinct benefit of sequencing, we identified candidate nonannotated microRNAs, including one whose downregulation may allow HIV-1 replication to proceed fully.

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Next generation sequencing in early diagnosis of pneumocystis jirovecii pneumonia after chemotherapy: a case report

International Journal of Research in Medical Sciences ◽

10.18203/2320-6012.ijrms20193948 ◽

2019 ◽

Vol 7 (9) ◽

pp. 3561

Author(s):

Donghua Zheng ◽

Kai Chen ◽

Fang Xiao ◽

Na Liu

Keyword(s):

Case Report ◽

Next Generation Sequencing ◽

Early Stage ◽

Severe Pneumonia ◽

Pneumocystis Pneumonia ◽

Pneumocystis Jirovecii Pneumonia ◽

Next Generation ◽

Pneumocystis Jiroveci ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

The incidence of Pneumocystis pneumonia is increasing in immunosuppressive patients. How to diagnose and treat Pneumocystis pneumonia in the early stage has become an important issue for clinicians. The development of Next-generation Sequencing (NGS) provides technical support for the diagnosis of Pneumocystis pneumonia. Case report: A 14-year-old male patient was diagnosed with T lymphoblastoma and treated with chemotherapy. After chemotherapy, the patient developed bone marrow suppression and was complicated with severe pneumonia. He was given endotracheal intubation and ventilator assisted respiration. Samples of patients' alveolar lavage fluid were obtained, and Next-generation Sequencing (NGS) was used for diagnosis, confirming the pathogen as Pneumocystis jiroveci, which was treated by TMP/SMX. The patient's condition gradually improved, and was finally removed from ventilator and endotracheal tube. Pneumocystis jiroveci is a common opportunistic pathogen in immunosuppressive patients, and Next-generation Sequencing (NGS) can be used for rapid diagnosis of Pneumocystis pneumonia, thus improving the clinical therapeutic effect.

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Case Report: Next-Generation Sequencing in Diagnosis of Pneumonia Due to Pneumocystis jirovecii and Cytomegalovirus in a Patient With HIV Infection

Frontiers in Medicine ◽

10.3389/fmed.2021.653294 ◽

2021 ◽

Vol 8 ◽

Author(s):

Yirui Xie ◽

Bing Ruan ◽

Lingxiao Jin ◽

Biao Zhu

Keyword(s):

Next Generation Sequencing ◽

Hiv Infection ◽

Lavage Fluid ◽

Pneumocystis Jirovecii ◽

Next Generation ◽

Combined Application ◽

Bacteria And Fungi ◽

Bilateral Lung ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Background: Pulmonary infections remain a significant cause of morbidity and mortality in immunocompromised patients. The pathogens spectrum of pulmonary infection that can affect patients with human immunodeficiency virus (HIV) is wide such as bacterial, fungal, viral, parasitic organisms, and so on. The risk of multi-pathogenic pneumonia is higher in HIV-infected patients. However, the fast and accurate diagnosis of multi-pathogenic pneumonia is challenging because of the limitations of current conventional tests.Case Presentation: Here, we report a case of pneumonia due to Pneumocystis jirovecii and cytomegalovirus (CMV) in a 22-year-old male with newly diagnosed HIV infection. Blood tests revealed a low CD4 count, a chest computed tomography (CT) scan showed extensive ground-glass opacities in the bilateral lung with multiple cavity lesions in the left upper lung. Microscopic examination of stained sputum and bronchoalveolar lavage fluid (BALF) smear specimens did not find any pathogens. There was also no evidence of pathogens known to cause pneumonia in bacteria and fungi culture tests and virus antibodies such as EBV, CMV, and COVID-19. The nucleic acid of CMV in blood was reported by quantitative PCR. Next-generation sequencing (NGS) analysis of BALF specimens identified a large number of P. jirovecii and CMV reads, and confirmed the diagnosis of pneumonia due to P. jirovecii and CMV. Following the patient's treatment with anti-PCP and anti-CMV, the patient was cured and discharged.Conclusions: This case highlights the combined application of NGS in the clinical diagnosis of multi-pathogenic pneumonia in an HIV-infected patient. NGS is proposed as an important adjunctive diagnostic approach for identifying pathogens of multi-pathogenic pneumonia in HIV-infected patients.

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