Life-threatening Pneumonia Research Articles

Noninvasive Early Detection of Systemic Inflammatory Response Syndrome of COVID-19 Inpatients Using a Piezoelectric Respiratory Rates Sensor

In 2020, 20% of patients with COVID-19 developed severe complications, including life-threatening pneumonia with systemic inflammatory response syndrome (SIRS). We developed a preliminary SIRS monitor that does not require blood sampling, is noninvasive, and can collect data 24 h per day. The proposed monitor comprises a piezoelectric respiratory sensor located beneath the patient’s mattress and a fingertip pulse sensor that determines ultra-high accuracy respiratory rate (mode of a 40-min frequency distribution of respiratory rates (M40FD-RR)). We assessed the clinical performance of the M40FD-RR preliminary SIRS monitor in 29 patients (12 female, 17 male, aged 15–90 years) hospitalized at Suwa Central Hospital with COVID-19, which was confirmed by a positive polymerase chain reaction test. SIRS was evaluated by logistic regression analysis using M40FD-RR, heart rate, age, and sex as explanatory variables. We compared the results of 109 examinations of 29 COVID-19 inpatients with SIRS against those determined by the proposed monitor. The proposed monitor achieved 75% sensitivity and 83% negative predictive value, making it a promising candidate for future 24 h noninvasive preliminary SIRS tests.

Metabolic modelling as a powerful tool to identify critical components of Pneumocystis growth medium.

Establishing suitable in vitro culture conditions for microorganisms is crucial for dissecting their biology and empowering potential applications. However, a significant number of bacterial and fungal species, including Pneumocystis jirovecii, remain unculturable, hampering research efforts. P. jirovecii is a deadly pathogen of humans that causes life-threatening pneumonia in immunocompromised individuals and transplant patients. Despite the major impact of Pneumocystis on human health, limited progress has been made in dissecting the pathobiology of this fungus. This is largely due to the fact that its experimental dissection has been constrained by the inability to culture the organism in vitro. We present a comprehensive in silico genome-scale metabolic model of Pneumocystis growth and metabolism, to identify metabolic requirements and imbalances that hinder growth in vitro. We utilise recently published genome data and available information in the literature as well as bioinformatics and software tools to develop and validate the model. In addition, we employ relaxed Flux Balance Analysis and Reinforcement Learning approaches to make predictions regarding metabolic fluxes and to identify critical components of the Pneumocystis growth medium. Our findings offer insights into the biology of Pneumocystis and provide a novel strategy to overcome the longstanding challenge of culturing this pathogen in vitro.

Development of RPA-Cas12a assay for rapid and sensitive detection of Pneumocystis jirovecii

Pneumocystis jirovecii is a prevalent opportunistic fungal pathogen that can lead to life-threatening Pneumocystis pneumonia in immunocompromised individuals. Given that timely and accurate diagnosis is essential for initiating prompt treatment and enhancing patient outcomes, it is vital to develop a rapid, simple, and sensitive method for P. jirovecii detection. Herein, we exploited a novel detection method for P. jirovecii by combining recombinase polymerase amplification (RPA) of nucleic acids isothermal amplification and the trans cleavage activity of Cas12a. The factors influencing the efficiency of RPA and Cas12a-mediated trans cleavage reaction, such as RPA primer, crRNA, the ratio of crRNA to Cas12a and ssDNA reporter concentration, were optimized. Our RPA-Cas12a-based fluorescent assay can be completed within 30–40 min, comprising a 25–30 min RPA reaction and a 5–10 min trans cleavage reaction. It can achieve a lower detection threshold of 0.5 copies/µL of target DNA with high specificity. Moreover, our RPA-Cas12a-based fluorescent method was examined using 30 artificial samples and demonstrated high accuracy with a diagnostic accuracy of 93.33%. In conclusion, a novel, rapid, sensitive, and cost-effective RPA-Cas12a-based detection method was developed and demonstrates significant potential for on-site detection of P. jirovecii in resource-limited settings.

Evolution of serious and life-threatening COVID-19 pneumonia as the SARS-CoV-2 pandemic progressed: an observational study of mortality to 60 days after admission to a 15-hospital US health system

ObjectiveIn order to predict at hospital admission the prognosis of patients with serious and life-threatening COVID-19 pneumonia, we sought to understand the clinical characteristics of hospitalised patients at admission as...

The Prevalence, Predisposing Factors, and Outcomes of Pneumocystis jirovecii Pneumonia among Pediatric Inpatients, Northeastern Iran

Abstract Objective Pneumocystis jirovecii pneumonia (PJP), caused by Pneumocystis jirovecii, is one of the opportunistic fungal infections that can cause life-threatening pneumonia in children with underlying diseases. Due to the similarity of the symptoms of PJP with other lung infections, such as tuberculosis, differential and accurate diagnosis is necessary. The current study investigated the molecular diagnosis of P. jirovecii, predisposing factors and the outcomes, among pediatric inpatients in Northeastern Iran. Methods In this study, 180 bronchoalveolar lavage specimens were obtained from hospitalized children with respiratory disorders. The specimens were examined using Giemsa stain, and the genomic DNA was extracted according to the protocol of the AmpliSens kit. A real-time polymerase chain reaction (PCR) technique was used to detect P. jirovecii by the AmpliSens Pneumocystis jirovecii (carinii)-FRT PCR kit. Results Among the patients studied, 34 (18.9%) were positive and 8 (4.4%) were suspicious of the presence of P. jirovecii. Among the 34 positive cases, 12 (35%) were diagnosed before, and 22 (65%) during the coronavirus 2019 (COVID-19) pandemic. Only two cases (5.88%) among the positive ones detected by the real-time PCR method were observed using Giemsa staining. Also, no correlation was observed between positive cases of infection and the sex, the outcomes, and underlying diseases. Conclusion The results showed that PJP has a relatively high prevalence among pediatric inpatients with respiratory disorders. Neutropenia is a significant predisposing factor in these patients. However, there is no correlation between PJP cases and outcomes and underlying diseases. Most of the patients with PJP were affected during the COVID-19 pandemic, probably due to treatment with corticosteroids.

Electrolyte Imbalance and Impaired Kidney Functions in COVID-19 Hospitalized Patients

Abstract Objective: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as COVID-19, is a pandemic infection that first appeared in Wuhan, China and is responsible for acute respiratory illness. The symptoms of this infection range from being mild and restricted to developing fever, cough, and loss of smell or taste, to severe life-threatening pneumonia and acute respiratory distress syndrome, and the severity could reach beyond that level and convert to a multi-organ failure or death. Angiotensin-converting enzyme 2 (ACE2) is known to be the receptor that used by coronavirus to enter the cells, and hence, multi-organ infection could result. From that point, renal involvement, including impaired kidney function and electrolyte imbalance, is one of the complications that might develop. Materials and Methods: A total of 60 patients, 29 males and 31 females, were recruited in this study, where blood urea nitrogen (BUN), serum creatinine, sodium, potassium, and chloride were evaluated. Results: The results revealed elevated levels of BUN and serum creatinine and decreased levels of sodium and chloride and to some extent, potassium levels. Few samples were diagnosed with increased levels of serum electrolytes. Conclusion: The results revealed the presence of electrolyte imbalance and kidney dysfunction associated with COVID-19 infection. Further investigations need to be carried out to estimate to what extent the changes in these biochemical parameters could be risk factors for developing acute kidney injury (AKI) and eventually death.

IgG4-related disease and B-cell malignancy due to an IKZF1 gain-of-function variant

BackgroundMonoallelic loss-of-function IKZF1 (IKAROS) variants cause B-cell deficiency or combined immunodeficiency, whereas monoallelic gain-of-function IKZF1 variants have recently been reported to cause hypergammaglobulinemia, abnormal plasma cell differentiation, autoimmune and allergic manifestations, and infections. MethodsWe studied seven relatives with autoimmune/inflammatory diseases and lymphoproliferative diseases. We analysed biopsy results and performed whole-exome sequencing and immunological studies. ResultsDisease onset occurred at a mean age of 25.2 years (range: 10-64, years). Six patients suffered from autoimmune/inflammatory diseases, four had confirmed immunoglobulin G4-related disease (IgG4-RD), and five developed B-cell malignancies: lymphoma in four and multiple myeloma in the remaining patient. Patients without immunosuppression were not particularly prone to infectious diseases. Three patients suffered from life-threatening COVID-19 pneumonia, one of whom had autoantibodies neutralizing interferon (IFN)-α. The recently described IKZF1 gain-of-function p.R183H variant was found in the five affected relatives tested and in a six-year-old asymptomatic girl. Immunological analysis revealed hypergammaglobulinemia and high frequencies of certain lymphocyte subsets (exhausted B cells, effector memory CD4 T cells, TEMRA and CD28-CD57+ CD4+ and CD8+ T cells, Th2 and Tfh2 cells) attesting to immune dysregulation. Partial clinical responses to rituximab and corticosteroids were observed, and treatment with lenalidomide, which promotes IKAROS degradation, was initiated in three patients. ConclusionHeterozygosity for gain-of-function IKZF1 variants underlies autoimmunity/inflammatory diseases, IgG4-RD and B-cell malignancies, the onset of which may occur in adulthood. Clinical and immunological data are similar to those for patients with unexplained IgG4-RD. Patients may therefore benefit from treatments inhibiting pathways displaying IKAROS-mediated overactivity.

Comparison of the efficacy and tolerability of different repetitive transcranial magnetic stimulation modalities for post-stroke dysphagia: a systematic review and Bayesian network meta-analysis protocol

IntroductionUp to 78% of patients who had a stroke develop post-stroke dysphagia (PSD), a significant consequence. Life-threatening aspiration pneumonia, starvation, and water and electrolyte abnormalities can result. Several meta-analyses have...

Pneumocystis jirovecii pneumonia in paediatric acute lymphoblastic leukaemia: A report from the multi-international clinical trial AIEOP-BFM ALL 2009.

Pneumocystis jirovecii can cause life-threatening pneumonia (PjP), and patients with haematological malignancies are at high risk of this infection. Prophylactic measures have significantly decreased morbidity and mortality, but there is a paucity of contemporary data on the incidence and clinical course of PjP in well-defined and homogenous patient populations, such as children suffering from acute lymphoblastic leukaemia (ALL). In the multi-international trial AIEOP-BFM ALL2009, PjP was diagnosed in six children (incidence 1/1000) and was associated with insufficient prophylaxis in five of them. Although none of the patients died of PjP, the long-term impact of the infection is unclear.

Pneumocystis jirovecii pneumonia in people living with HIV: a review.

SUMMARYPneumocystis jirovecii is a ubiquitous opportunistic fungus that can cause life-threatening pneumonia. People with HIV (PWH) who have low CD4 counts are one of the populations at the greatest risk of Pneumocystis jirovecii pneumonia (PCP). While guidelines have approached the diagnosis, prophylaxis, and management of PCP, the numerous studies of PCP in PWH are dominated by the 1980s and 1990s. As such, most studies have included younger male populations, despite PCP affecting both sexes and a broad age range. Many studies have been small and observational in nature, with an overall lack of randomized controlled trials. In many jurisdictions, and especially in low- and middle-income countries, the diagnosis can be challenging due to lack of access to advanced and/or invasive diagnostics. Worldwide, most patients will be treated with 21 days of high-dose trimethoprim sulfamethoxazole, although both the dose and the duration are primarily based on historical practice. Whether treatment with a lower dose is as effective and less toxic is gaining interest based on observational studies. Similarly, a 21-day tapering regimen of prednisone is used for patients with more severe disease, yet other doses, other steroids, or shorter durations of treatment with corticosteroids have not been evaluated. Now with the widespread availability of antiretroviral therapy, improved and less invasive PCP diagnostic techniques, and interest in novel treatment strategies, this review consolidates the scientific body of literature on the diagnosis and management of PCP in PWH, as well as identifies areas in need of more study and thoughtfully designed clinical trials.

Higher COVID-19 pneumonia risk associated with anti-IFN-α than with anti-IFN-ω auto-Abs in children.

We found that 19 (10.4%) of 183 unvaccinated children hospitalized for COVID-19 pneumonia had autoantibodies (auto-Abs) neutralizing type I IFNs (IFN-α2 in 10 patients: IFN-α2 only in three, IFN-α2 plus IFN-ω in five, and IFN-α2, IFN-ω plus IFN-β in two; IFN-ω only in nine patients). Seven children (3.8%) had Abs neutralizing at least 10 ng/ml of one IFN, whereas the other 12 (6.6%) had Abs neutralizing only 100 pg/ml. The auto-Abs neutralized both unglycosylated and glycosylated IFNs. We also detected auto-Abs neutralizing 100 pg/ml IFN-α2 in 4 of 2,267 uninfected children (0.2%) and auto-Abs neutralizing IFN-ω in 45 children (2%). The odds ratios (ORs) for life-threatening COVID-19 pneumonia were, therefore, higher for auto-Abs neutralizing IFN-α2 only (OR [95% CI] = 67.6 [5.7-9,196.6]) than for auto-Abs neutralizing IFN-ω only (OR [95% CI] = 2.6 [1.2-5.3]). ORs were also higher for auto-Abs neutralizing high concentrations (OR [95% CI] = 12.9 [4.6-35.9]) than for those neutralizing low concentrations (OR [95% CI] = 5.5 [3.1-9.6]) of IFN-ω and/or IFN-α2.

Life-threatening Pneumocystis jiroveci Pneumonia with Cytomegalovirus Coinfection in a Follicular Lymphoma Patient During Rituximab-based Chemotherapy

Abstract In the era of target therapy, we face the challenge of the risk of opportunistic infection in patients with B-cell lymphoma who receiving rituximab-based chemotherapy. Opportunistic infections such as Pneumocystis jiroveci pneumonia (PJP) and Cytomegalovirus (CMV) pneumonia are life-threatening diseases. However, PJP with CMV coinfection is rare. Here, we report a follicular lymphoma patient who suffered from PJP with CMV coinfection after receiving three cycles of rituximab, cyclophosphamide, vincristine, and prednisone regimen and was successfully rescured after timely identification and treatment. We emphasize that physicians should be alert for the coinfection of PJP and CMV in lymphoma patients receiving rituximab-based chemotherapy and the timely recognition, and treatment that may avoid a deadly outcome.

Biochemical characterization of actinomycete from Namibia rocky crest mountainous soil and analyzing their bioactive metabolites for antagonistic effect against human respiratory pathogens.

the present study aimed at isolating and characterizing actinomycete from unexplored Windhoek rocky crest mountainous soil and extracting bioactive metabolites as possible therapeutics against common life-threatening Streptococcus pneumonia (S. pneumonia) and Stachybotrys chartarum (S. chartarum). chemotaxonomy and biochemical methods were used to identify the isolates. The solvent extraction method was used to extract bioactive compounds. Agar overlay and disc diffusion methods were used to determine the antimicrobial activity of isolates and extracted bioactive metabolites against S. pneumonia and S. chartarum. The antioxidant activity of the extracted bioactive metabolites was determined using 2.2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging method with ascorbic acid as a positive control. Comparison between groups was done using a Two-way ANOVA, followed by Bonferroni post-test. three distinct isolates from 3 soil samples were identified on starch casein agar and distinguished using biochemical tests. All three isolates showed strong inhibitory activity against S. pneumonia with average growth inhibition zones between 18.0±1.00 and 27±0.00 mm p< 0.005. All isolates showed potent inhibitory activity against S. chartarum with the average inhibition zones ranging between 42.0±1.00 and 48±0.00 mm, p< 0.005. The chloroform extracts showed potent DPPH activity of up to 73± 1.41%. growth conditions and extraction solvents can influence the antimicrobial and antioxidant properties of bioactive metabolites.

Case of Life-Threatening Pneumonia during the Treatment of a Patient with Acute Bacterial Prostatitis

Case of Life-Threatening Pneumonia during the Treatment of a Patient with Acute Bacterial Prostatitis

Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency

Patients with autoimmune polyendocrinopathy syndrome type 1 (APS-1) caused by autosomal recessive AIRE deficiency produce autoantibodies that neutralize type I interferons (IFNs)1,2, conferring a predisposition to life-threatening COVID-19 pneumonia3. Here we report that patients with autosomal recessive NIK or RELB deficiency, or a specific type of autosomal-dominant NF-κB2 deficiency, also have neutralizing autoantibodies against type I IFNs and are at higher risk of getting life-threatening COVID-19 pneumonia. In patients with autosomal-dominant NF-κB2 deficiency, these autoantibodies are found only in individuals who are heterozygous for variants associated with both transcription (p52 activity) loss of function (LOF) due to impaired p100 processing to generate p52, and regulatory (IκBδ activity) gain of function (GOF) due to the accumulation of unprocessed p100, therefore increasing the inhibitory activity of IκBδ (hereafter, p52LOF/IκBδGOF). By contrast, neutralizing autoantibodies against type I IFNs are not found in individuals who are heterozygous for NFKB2 variants causing haploinsufficiency of p100 and p52 (hereafter, p52LOF/IκBδLOF) or gain-of-function of p52 (hereafter, p52GOF/IκBδLOF). In contrast to patients with APS-1, patients with disorders of NIK, RELB or NF-κB2 have very few tissue-specific autoantibodies. However, their thymuses have an abnormal structure, with few AIRE-expressing medullary thymic epithelial cells. Human inborn errors of the alternative NF-κB pathway impair the development of AIRE-expressing medullary thymic epithelial cells, thereby underlying the production of autoantibodies against type I IFNs and predisposition to viral diseases.

Purification, characterization, and cloning of a novel pro-inflammatory secreted protein from Staphylococcus aureus.

Staphylococcus aureus causes a myriad of human diseases, ranging from relatively mild soft tissue infections to highly fatal pneumonia, sepsis, and toxic shock syndrome. The organisms primarily cause diseases across mucosal and skin barriers. In order to facilitate penetration of barriers, S. aureus causes harmful inflammation by inducing chemokines from epithelial cells. We report the cloning and characterization of a novel secreted S. aureus protein that induces chemokine production from epithelial cells as its major demonstrable function. This secreted protein possibly helps S. aureus and its secreted proteins to penetrate host barriers.

Fungal antigenic variation using mosaicism and reassortment of subtelomeric genes’ repertoires

Surface antigenic variation is crucial for major pathogens that infect humans. To escape the immune system, they exploit various mechanisms. Understanding these mechanisms is important to better prevent and fight the deadly diseases caused. Those used by the fungus Pneumocystis jirovecii that causes life-threatening pneumonia in immunocompromised individuals remain poorly understood. Here, though this fungus is currently not cultivable, our detailed analysis of the subtelomeric sequence motifs and genes encoding surface proteins suggests that the system involves the reassortment of the repertoire of ca. 80 non-expressed genes present in each strain, from which single genes are retrieved for mutually exclusive expression. Dispersion of the new repertoires, supposedly by healthy carrier individuals, appears very efficient because identical alleles are observed in patients from different countries. Our observations reveal a unique strategy of antigenic variation. They also highlight the possible role in genome rearrangements of small imperfect mirror sequences forming DNA triplexes.

Identification of repurposable drug targets in Mycoplasma pneumoniae using subtractive genomics, molecular docking and dynamics simulation

Mycoplasma pneumoniae is a significant causative agent of community-acquired pneumonia, causing acute inflammation in the upper and lower respiratory tract as well as extrapulmonary syndromes. In particular, the elderly and infants are at greater risk of developing severe, life-threatening pneumonia caused by M. pneumoniae. Yet, the global increase in antimicrobial resistance against antibiotics for the treatment of M. pneumoniae infection highlights the urgent need to explore novel drug targets. To this end, bioinformatics approaches, such as subtractive genomics, can be employed to identify specific metabolic pathways and essential proteins unique to the pathogen that could be potential targets for new drugs. In this study, we implemented a subtractive genomics approach to identify 61 metabolic pathways and 42 essential proteins that are unique to M. pneumoniae. A subsequent screening in the DrugBank database revealed three druggable proteins with similarity to FDA-approved small-molecule drugs, and finally, the compound CHEBI:97093 was identified as a promising novel putative drug target. These findings can provide crucial insights for the development of highly effective drugs that selectively inhibit the pathogen-specific metabolic pathways, leading to better management and treatment of M. pneumoniae infections.

The Legionella autoinducer LAI-1 is delivered by outer membrane vesicles to promote interbacterial and interkingdom signaling

Legionella pneumophila is an environmental bacterium, which replicates in amoeba but also in macrophages, and causes a life-threatening pneumonia called Legionnaires' disease. The opportunistic pathogen employs the α-hydroxy-ketone compound Legionella autoinducer-1 (LAI-1) for intraspecies and interkingdom signaling. LAI-1 is produced by the autoinducer synthase Legionella quorum sensing A (LqsA), but it is not known, how LAI-1 is released by the pathogen. Here, we use a Vibrio cholerae luminescence reporter strain and liquid chromatography-tandem mass spectrometry to detect bacteria-produced and synthetic LAI-1. Ectopic production of LqsA in Escherichia coli generated LAI-1, which partitions to outer membrane vesicles (OMVs) and increases OMV size. These E.coli OMVs trigger luminescence of the V.cholerae reporter strain and inhibit the migration of Dictyostelium discoideum amoeba. Overexpression of lqsA in L.pneumophila under the control of strong stationary phase promoters (PflaA or P6SRNA), but not under control of its endogenous promoter (PlqsA), produces LAI-1, which is detected in purified OMVs. These L. pneumophila OMVs trigger luminescence of the Vibrio reporter strain and inhibit D.discoideum migration. L.pneumophila OMVs are smaller upon overexpression of lqsA or upon addition of LAI-1 to growing bacteria, and therefore, LqsA affects OMV production. The overexpression of lqsA but not a catalytically inactive mutant promotes intracellular replication of L.pneumophila in macrophages, indicating that intracellularly produced LA1-1 modulates the interaction in favor of the pathogen. Taken together, we provide evidence that L.pneumophila LAI-1 is secreted through OMVs and promotes interbacterial communication and interactions with eukaryotic host cells.

A comprehensive immunoinformatic analysis of chitin deacetylase’s and MP88 for designing multi-epitope vaccines against Cryptococcus neoformans

Cryptococcus neoformans causes life-threatening pneumonia and meningitis and is regarded as one of the leading killers of immunocompromised individuals. There is currently no vaccine against this pathogen. Recently, WHO placed it at the top among the critical priority groups in the fungal priority pathogens to accelerate the development of effective treatments. Numerous studies suggested the potential of subunit vaccines to overcome the challenges associated with live and inactivated whole-cell vaccines. Therefore, this study exploited integrated reverse vaccinology and immunoinformatic approach to construct and characterize multi-epitope vaccines targeting chitin deacetylases (Cda1, Cda2, Cda3) and MP88 of C. neoformans. 4 CTL, 8 HTL and 6 B cell epitopes were fused with different adjuvants and appropriate linkers to design two multi-epitope vaccines (VC1 and VC2). Both chimeric constructs were predicted to be highly antigenic, non-allergenic, non-toxic, soluble and had satisfactory physicochemical properties. Molecular docking and binding free energy calculation revealed strong binding interactions between vaccine constructs and human TLRs (TLR-2 and TLR-4). Classical MD Simulation and Normal mode analysis verified the stability of the vaccine-TLR complex in the biological environment. Codon adaptation, cloning and in silico expression suggested the efficient expression of recombinant vaccine proteins in E. coli. Both candidates also generated robust immune profiles comprising innate, adaptive and humoral immune responses. Taken together, experimental validations of our findings through extensive in vitro and in vivo testing might provide an effective vaccine for prophylactic control of C. neoformans. Communicated by Ramaswamy H. Sarma