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Annals of Laboratory Medicine Mar 2019Real-time PCR is more sensitive than microscopic examination for detecting . We compared the performance of two assays for detecting DNA: the RealStar PCR Kit 1.0 CE... (Comparative Study)
Comparative Study
BACKGROUND
Real-time PCR is more sensitive than microscopic examination for detecting . We compared the performance of two assays for detecting DNA: the RealStar PCR Kit 1.0 CE (Altona Diagnostics, Hamburg, Germany) and the AmpliSens ()-FRT PCR kit (InterLabService Ltd., Moscow, Russia).
METHODS
We used 159 samples from the lower respiratory tract (112 bronchoalveolar lavage [BAL] fluid, 37 sputum, and 10 endotracheal aspirate [ETA] samples) of non-HIV immunocompromised patients. Nested PCR and sequencing were used to resolve discordant results. The performance of the two assays was evaluated according to clinical categories (clinical pneumonia [PCP], possible PCP, or unlikely PCP) based on clinical and radiological observations.
RESULTS
The positive and negative percent agreement values were 100% (95% confidence interval [CI], 85.4-100%) and 96.6% (95% CI, 90.9-98.9%), respectively, and kappa was 0.92 (95% CI, 0.84-0.99). DNA load was significantly higher in the clinical PCP group than in the other groups (<0.05). When stratified by sample type, the positive rate for BAL fluids from the clinical PCP group was 100% using either assay, whereas the positive rate for sputum/ETA samples was only 20%.
CONCLUSIONS
The two assays showed similar diagnostic performance and detected low burden in BAL fluids. Both assays may be useful as routine methods for detecting DNA in a clinical laboratory setting, though their results should be interpreted considering sample type.
Topics: Bronchoalveolar Lavage Fluid; DNA, Bacterial; Diagnostic Errors; Humans; Immunocompromised Host; Pneumocystis Infections; Pneumocystis carinii; Reagent Kits, Diagnostic; Real-Time Polymerase Chain Reaction; Respiratory Tract Diseases; Sputum
PubMed: 30430780
DOI: 10.3343/alm.2019.39.2.176 -
Frontiers in Cellular and Infection... 2021Differentiating infection from colonisation is crucial for appropriate therapy administration. In this study, we evaluated the performance of bronchoalveolar lavage...
BACKGROUND
Differentiating infection from colonisation is crucial for appropriate therapy administration. In this study, we evaluated the performance of bronchoalveolar lavage fluid (BAL) metagenomic next-generation sequencing (mNGS) and serum 1,3-β-D-glucan (BDG) tests in differentiating colonisation and infection with
METHODS
From January 2018 to March 2021, 47 patients were enrolled in this study at the Hunan Provincial People's Hospital. The final diagnosis was used as a reference, and cases were classified into the pneumonia (PJP) group or the colonisation (PJC) group. Clinical data were recorded. The performances of mNGS and BDG were compared.
RESULT
The fungal load significantly differed between patients with PJP and PJC, with median reads of 3,215.79 ± 1,797 . 5.61 ± 0.88 in the PJP and PJC groups, respectively ( < 0.0001). BDG also significantly differed between the two groups, with a median titre of 233.60 ± 39.65 pg/ml in the PJP group and 68.48 ± 19.21 pg/ml in the PJC group ( 0.0006). The area under the curve was 0.973 (95%CI: 0.868-1.007) for mNGS of the BAL and 0.879 (95%CI: 0.769-0.989) for the serum BDG. The optimal threshold value for discriminating infection from colonisation appeared to be 14 reads (sensitivity, 83.3%; specificity, 95.7%; positive likelihood ratio, 19.2) and BDG = 88.6 pg/ml (sensitivity, 79.2%; specificity, 92.9%; positive likelihood ratio, 18.2). No correlation between mNGS reads and the BDG titre was found in mNGS-positive patients ( = 0.0076, = 0.583). The levels of lactate dehydrogenase and C-reactive protein were significantly higher in the PJP group than in the PJC group.
CONCLUSION
BAL mNGS and serum BDG are useful adjunct tests that can assist with differentiating between colonisation and infection of .
Topics: Bronchoalveolar Lavage Fluid; Diagnosis, Differential; Glucans; Humans; Pneumocystis carinii; Pneumonia, Pneumocystis; Proteoglycans; Sensitivity and Specificity; beta-Glucans
PubMed: 35004353
DOI: 10.3389/fcimb.2021.784236 -
Antimicrobial Agents and Chemotherapy Oct 2020, the opportunistic fungus that causes pneumonia (PCP) in humans, is a significant contributor to morbidity and mortality in immunocompromised patients. Given the...
, the opportunistic fungus that causes pneumonia (PCP) in humans, is a significant contributor to morbidity and mortality in immunocompromised patients. Given the profound deleterious inflammatory effects of the major β-glucan cell wall carbohydrate constituents of through Dectin-1 engagement and downstream caspase recruitment domain-containing protein 9 (CARD9) immune activation, we sought to determine whether the pharmacodynamic activity of the known CARD9 inhibitor BRD5529 might have a therapeutic effect on macrophage innate immune signaling and subsequent downstream anti-inflammatory activity. The small-molecule inhibitor BRD5529 was able to significantly reduce both phospho-p38 and phospho-pERK1 signaling and tumor necrosis factor alpha (TNF-α) release during stimulation of macrophages with cell wall β-glucans.
Topics: CARD Signaling Adaptor Proteins; Humans; Immunity, Innate; Pneumocystis; Pneumocystis carinii; Pneumonia, Pneumocystis; beta-Glucans
PubMed: 32839216
DOI: 10.1128/AAC.01210-20 -
Annals of Clinical Microbiology and... Jun 2021Pneumocystis jirovecii and Aspergillus fumigatus, are opportunistic pathogenic fungus that has a major impact on mortality in patients with systemic lupus erythematosus....
Rapid and precise diagnosis of pneumonia coinfected by Pneumocystis jirovecii and Aspergillus fumigatus assisted by next-generation sequencing in a patient with systemic lupus erythematosus: a case report.
BACKGROUND
Pneumocystis jirovecii and Aspergillus fumigatus, are opportunistic pathogenic fungus that has a major impact on mortality in patients with systemic lupus erythematosus. With the potential to invade multiple organs, early and accurate diagnosis is essential to the survival of SLE patients, establishing an early diagnosis of the infection, especially coinfection by Pneumocystis jirovecii and Aspergillus fumigatus, still remains a great challenge.
CASE PRESENTATION
In this case, we reported that the application of next -generation sequencing in diagnosing Pneumocystis jirovecii and Aspergillus fumigatus coinfection in a Chinese girl with systemic lupus erythematosus (SLE). Voriconazole was used to treat pulmonary aspergillosis, besides sulfamethoxazole and trimethoprim (SMZ-TMP), and caspofungin acetate to treat Pneumocystis jirovecii infection for 6 days. On Day 10 of admission, her chest radiograph displayed obvious absorption of bilateral lung inflammation though the circumstance of repeated fever had not improved. Unfortunately, the patient discharged from the hospital since the financial burden, and during the follow-up, it was documented the patient died within one week after discharge.
CONCLUSIONS
This successful application of the next generation sequencing assisting the rapid diagnosis of Pneumocystis jirovecii and Aspergillus fumigatus coinfection provides a new perspective in the clinical approach against the systematic fungi infections and highlights the potential of this technique in rapid etiological diagnosis.
Topics: Adolescent; Aspergillus fumigatus; Caspofungin; Coinfection; Female; High-Throughput Nucleotide Sequencing; Humans; Lupus Erythematosus, Systemic; Opportunistic Infections; Pneumocystis carinii; Pneumonia; Sulfamethoxazole; Trimethoprim; Voriconazole
PubMed: 34174895
DOI: 10.1186/s12941-021-00448-5 -
PLoS Neglected Tropical Diseases Dec 2021Pneumocystis pneumonia (PCP) and pulmonary toxoplasmosis (PT) are caused by Pneumocystis jirovecii and Toxoplasma gondii. The clinical symptoms and imaging of PCP and PT...
Pneumocystis pneumonia (PCP) and pulmonary toxoplasmosis (PT) are caused by Pneumocystis jirovecii and Toxoplasma gondii. The clinical symptoms and imaging of PCP and PT are indistinguishable. A duplex qPCR was developed to differentiate between these two pathogens. In testing 92 clinical samples to validate the performance of this method for P. jirovecii detection, it identified 31 positive samples for P. jirovecii infection, consistent with clinical diagnosis. Among the remainder of the 61 clinical samples with suspected PCP, yet showing as negative by the conventional PCR diagnosis approach, 6 of them proved positive using our new assay. Our new approach also produced similar results in identification of T. gondii infections, giving a result of 2 positive and 20 negative in clinical samples. An investigation was undertaken on the prevalence of P. jirovecii and T. gondii infections using 113 samples from lung infection patients. 9% (10/113) were shown to be positive with infections of P. jirovecii, 2% with T. gondii (2/113) and 5% (6/113) were co-infected with both pathogens. Although this duplex qPCR can detect individual P. jirovecii and T. gondii infection, and co-infection of both pathogens, further large-scale investigations are needed to validate its performance, especially in T. gondii detection. Our assay provides a rapid and accurate tool for PCP and PT diagnosis in immunocompromised population and clinical surveillance of these infections in patients with no immune defects.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Child; Child, Preschool; Female; Humans; Immunocompromised Host; Infant; Lung; Lung Diseases; Male; Middle Aged; Pneumocystis carinii; Pneumonia, Pneumocystis; Polymerase Chain Reaction; Toxoplasma; Toxoplasmosis; Young Adult
PubMed: 34919557
DOI: 10.1371/journal.pntd.0010025 -
Frontiers in Immunology 2021is one of the most common fungal pathogens in immunocompromised individuals. Pneumocystis jirovecii pneumonia (PJP) causes a significant host immune response that is... (Review)
Review
is one of the most common fungal pathogens in immunocompromised individuals. Pneumocystis jirovecii pneumonia (PJP) causes a significant host immune response that is driven greatly by the organism's cell wall components including β-glucans and major surface glycoprotein (Msg). These ligands interact with a number of C-type lectin receptors (CLRs) leading to downstream activation of proinflammatory signaling pathways. This minireview provides a brief overview summarizing known CLR/ interactions.
Topics: Animals; Fungal Proteins; Host-Pathogen Interactions; Humans; Immunity, Innate; Inflammation Mediators; Lectins, C-Type; Ligands; Membrane Glycoproteins; Pneumocystis carinii; Pneumonia, Pneumocystis; Signal Transduction; beta-Glucans
PubMed: 34975910
DOI: 10.3389/fimmu.2021.798214 -
Polish Journal of Microbiology Feb 2022is an opportunistic fungus that can cause severe and potentially fatal pneumonia (PCP) in immunodeficient patients. In this study, we investigated the genetic...
is an opportunistic fungus that can cause severe and potentially fatal pneumonia (PCP) in immunodeficient patients. In this study, we investigated the genetic polymorphisms of at eight different loci, including six nuclear genes (ITS, 26S rRNA, , , and β-Tub) and two mitochondrial genes (mtLSU-rRNA and ) in three PCP cases, including two patients with HIV infection and one without HIV infection in Shanxi Province, P.R. China. The gene targets were amplified by PCR followed by sequencing of plasmid clones. The HIV-negative patient showed a coinfection with two genotypes of at six of the eight loci sequenced. Of the two HIV-positive patients, one showed a coinfection with two genotypes of at the same two of the six loci as in the HIV-negative patient, while the other showed a single infection at all eight loci sequenced. None of the three drug target genes ( and ) showed mutations known to be potentially associated with drug resistance. This is the first report of genetic polymorphisms of in PCP patients in Shanxi Province, China. Our findings expand our understanding of the genetic diversity of in China.
Topics: AIDS-Related Opportunistic Infections; China; Coinfection; HIV Infections; Humans; Pneumocystis carinii; Pneumonia, Pneumocystis; Polymorphism, Genetic
PubMed: 35635165
DOI: 10.33073/pjm-2022-002 -
Emerging Infectious Diseases Oct 2004Pneumocystis pneumonia (PCP) caused by the opportunistic fungal agent Pneumocystis jirovecii (formerly P. carinii) continues to cause illness and death in HIV-infected... (Review)
Review
Pneumocystis pneumonia (PCP) caused by the opportunistic fungal agent Pneumocystis jirovecii (formerly P. carinii) continues to cause illness and death in HIV-infected patients. In the absence of a culture system to isolate and maintain live organisms, efforts to type and characterize the organism have relied on polymerase chain reaction-based approaches. Studies using these methods have improved understanding of PCP epidemiology, shedding light on sources of infection, transmission patterns, and potential emergence of antimicrobial resistance. One concern, however, is the lack of guidance regarding the appropriateness of different methods and standardization of these methods, which would facilitate comparing results reported by different laboratories.
Topics: DNA, Fungal; Humans; Membrane Glycoproteins; Molecular Epidemiology; Mycological Typing Techniques; Pneumocystis carinii; Pneumonia, Pneumocystis; Polymorphism, Genetic; RNA, Fungal; Reproducibility of Results; Sensitivity and Specificity
PubMed: 15504257
DOI: 10.3201/eid1010.030981 -
PloS One May 2007Members of the genus Pneumocystis are fungal pathogens that cause pneumonia in a wide variety of mammals with debilitated immune systems. Little is known about their...
Members of the genus Pneumocystis are fungal pathogens that cause pneumonia in a wide variety of mammals with debilitated immune systems. Little is known about their basic biological functions, including life cycle, since no species can be cultured continuously outside the mammalian lung. To better understand the pathological process, about 4500 ESTS derived from sequencing of the poly(A) tail ends of P. carinii mRNAs during fulminate infection were annotated and functionally characterized as unassembled reads, and then clustered and reduced to a unigene set with 1042 members. Because of the presence of sequences from other microbial genomes and the rat host, the analysis and compression to a unigene set was necessarily an iterative process. BLASTx analysis of the unassembled reads (UR) vs. the Uni-Prot and TREMBL databases revealed 56% had similarities to existing polypeptides at E values of
carinii gene products. In contrast, similarities to proteins of the yeast-like fungi, Schizosaccharomyces pombe and Saccharomyces cerevisiae, predominated in the unigene set. Gene Ontology analysis using BLAST2GO revealed P. carinii dedicated most of its transcripts to cellular and physiological processes ( approximately 80%), molecular binding and catalytic activities (approximately 70%), and were primarily derived from cell and organellar compartments (approximately 80%). KEGG Pathway mapping showed the putative P. carinii genes represented most standard metabolic pathways and cellular processes, including the tricarboxylic acid cycle, glycolysis, amino acid biosynthesis, cell cycle and mitochondrial function. Several gene homologs associated with mating, meiosis, and sterol biosynthesis in fungi were identified. Genes encoding the major surface glycoprotein family (MSG), heat shock (HSP70), and proteases (PROT/KEX) were the most abundantly expressed of known P. carinii genes. The apparent presence of many metabolic pathways in P. carinii, sexual reproduction within the host, and lack of an invasive infection process in the immunologically intact host suggest members of the genus Pneumocystis may be adapted parasites and have a compatible relationship with their mammalian hosts. This study represents the first characterization of the expressed genes of a non-culturable fungal pathogen of mammals during the infective process. Topics: Carbohydrate Metabolism; Citric Acid Cycle; Expressed Sequence Tags; Gene Expression Profiling; Gluconeogenesis; Glycolysis; Glyoxylates; Pentose Phosphate Pathway; Pneumocystis carinii; RNA, Fungal; RNA, Messenger
PubMed: 17487271
DOI: 10.1371/journal.pone.0000423 -
Memorias Do Instituto Oswaldo Cruz Dec 2005Basic aspects of cell biology of Pneumocystis carinii are reviewed with major emphasis on its life cycle and the structural organization of the trophozoites and cyst... (Review)
Review
Basic aspects of cell biology of Pneumocystis carinii are reviewed with major emphasis on its life cycle and the structural organization of the trophozoites and cyst forms. Initially considered as a protozoan it is now established that Pneumocystis belongs to the Fungi Kingdom. Its life cycle includes two basic forms: (a) trophozoites, which are haploid cells that divide by binary fission and may conjugate with each other forming an early procyst and (b) cysts where division takes place through a meiotic process with the formation of eight nuclei followed by cytoplasmic delimitation and formation of intracystic bodies which are subsequently released and transformed into trophozoites. Basic aspects of the structure of the two developmental stages of P. carinii are reviewed.
Topics: Animals; Cell Division; Life Cycle Stages; Microscopy, Electron; Pneumocystis carinii
PubMed: 16444423
DOI: 10.1590/s0074-02762005000800013