Severe Atypical Pneumonia Research Articles

Iron-depleting nutritional immunity controls extracellular bacterial replication in Legionella pneumophila infections

The accidental human pathogen Legionella pneumophila (Lp) is the etiological agent for a severe atypical pneumonia known as Legionnaires’ disease. In human infections and animal models of disease alveolar macrophages are the primary cellular niche that supports bacterial replication within a unique intracellular membrane-bound organelle. The Dot/Icm apparatus—a type IV secretion system that translocates ~300 bacterial proteins within the cytosol of the infected cell—is a central virulence factor required for intracellular growth. Mutant strains lacking functional Dot/Icm apparatus are transported to and degraded within the lysosomes of infected macrophages. The early foundational work from Dr. Horwitz’s group unequivocally established that Legionella does not replicate extracellularly during infection—a phenomenon well supported by experimental evidence for four decades. Our data challenges this paradigm by demonstrating that macrophages and monocytes provide the necessary nutrients and support robust Legionella extracellular replication. We show that the previously reported lack of Lp extracellular replication is not a bacteria intrinsic feature but rather a result of robust restriction by serum-derived nutritional immunity factors. Specifically, the host iron-sequestering protein Transferrin is identified here as a critical suppressor of Lp extracellular replication in an iron-dependent manner. In iron-overload conditions or in the absence of Transferrin, Lp bypasses growth restriction by IFNγ-primed macrophages though extracellular replication. It is well established that certain risk factors associated with development of Legionnaires’ disease, such as smoking, produce a chronic pulmonary environment of iron-overload. Our work indicates that iron-overload could be an important determinant of severe infection by allowing Lp to overcome nutritional immunity and replicate extracellularly, which in turn would circumvent intracellular cell intrinsic host defenses. Thus, we provide evidence for nutritional immunity as a key underappreciated host defense mechanism in Legionella pathogenesis.

The intracellular growth of the vacuolar pathogen Legionella pneumophila is dependent on the acyl chain composition of host membranes

Legionella pneumophila is an accidental human bacterial pathogen that infects and replicates within alveolar macrophages causing a severe atypical pneumonia known as Legionnaires’ disease. As a prototypical vacuolar pathogen L. pneumophila establishes a unique endoplasmic reticulum (ER)-derived organelle within which bacterial replication takes place. Bacteria-derived proteins are deposited in the host cytosol and in the lumen of the pathogen-occupied vacuole via a type IVb (T4bSS) and a type II (T2SS) secretion system respectively. These secretion system effector proteins manipulate multiple host functions to facilitate intracellular survival of the bacteria. Subversion of host membrane glycerophospholipids (GPLs) by the internalized bacteria via distinct mechanisms feature prominently in trafficking and biogenesis of the Legionella-containing vacuole (LCV). Conventional GPLs composed of a glycerol backbone linked to a polar headgroup and esterified with two fatty acids constitute the bulk of membrane lipids in eukaryotic cells. The acyl chain composition of GPLs dictates phase separation of the lipid bilayer and therefore determines the physiochemical properties of biological membranes - such as membrane disorder, fluidity and permeability. In mammalian cells, fatty acids esterified in membrane GPLs are sourced endogenously from de novo synthesis or via internalization from the exogenous pool of lipids present in serum and other interstitial fluids. Here, we exploited the preferential utilization of exogenous fatty acids for GPL synthesis by macrophages to reprogram the acyl chain composition of host membranes and investigated its impact on LCV homeostasis and L. pneumophila intracellular replication. Using saturated fatty acids as well as cis- and trans- isomers of monounsaturated fatty acids we discovered that under conditions promoting lipid packing and membrane rigidification L. pneumophila intracellular replication was significantly reduced. Palmitoleic acid – a C16:1 monounsaturated fatty acid – that promotes membrane disorder when enriched in GPLs significantly increased bacterial replication within human and murine macrophages but not in axenic growth assays. Lipidome analysis of infected macrophages showed that treatment with exogenous palmitoleic acid resulted in membrane acyl chain reprogramming in a manner that promotes membrane disorder and live-cell imaging revealed that the consequences of increasing membrane disorder impinge on several LCV homeostasis parameters. Collectively, we provide experimental evidence that L. pneumophila replication within its intracellular niche is a function of the lipid bilayer disorder and hydrophobic thickness.

Cellular cholesterol licenses Legionella pneumophila intracellular replication in macrophages.

Host membranes are inherently critical for niche homeostasis of vacuolar pathogens. Thus, intracellular bacteria frequently encode the capacity to regulate host lipogenesis as well as to modulate the lipid composition of host membranes. One membrane component that is often subverted by vacuolar bacteria is cholesterol - an abundant lipid that mammalian cells produce de novo at the endoplasmic reticulum (ER) or acquire exogenously from serum-derived lipoprotein carriers. Legionella pneumophila is an accidental human bacterial pathogen that infects and replicates within alveolar macrophages causing a severe atypical pneumonia known as Legionnaires' disease. From within a unique ER-derived vacuole L. pneumophila promotes host lipogenesis and experimental evidence indicates that cholesterol production might be one facet of this response. Here we investigated the link between cellular cholesterol and L. pneumophila intracellular replication and discovered that disruption of cholesterol biosynthesis or cholesterol trafficking lowered bacterial replication in infected cells. These growth defects were rescued by addition of exogenous cholesterol. Conversely, bacterial growth within cholesterol-leaden macrophages was enhanced. Importantly, the growth benefit of cholesterol was observed strictly in cellular infections and L. pneumophila growth kinetics in axenic cultures did not change in the presence of cholesterol. Microscopy analyses indicate that cholesterol regulates a step in L. pneumophila intracellular lifecycle that occurs after bacteria begin to replicate within an established intracellular niche. Collectively, we provide experimental evidence that cellular cholesterol promotes L. pneumophila replication within a membrane bound organelle in infected macrophages.

COVID-19: Artificial sputum, respiratory obstruction method and screening of pyolitic and antihypoxic drugs.

COVID-19 causes non-specific pneumonia, which has become a new cause of hypoxia, leading to the death of many patients. Today, there are no effective drugs that provide an urgent increase in blood oxygenation. Therefore, it is urgently necessary to develop drugs to increase blood oxygenation in order to save the lives of patients with the new coronavirus infection. Since hypoxia develops in this disease due to the blockage of respiratory tract with viscous mucus and sputum, an appropriate experimental model is needed for screening and finding new drugs. However this model is yet missing. Therefore, the development of an experimental model of respiratory obstruction by sputum with traces of blood can accelerate the discovery of drugs that eliminate hypoxia and prevent the death of patients with nonspecific pneumonia complicated by respiratory obstruction. The purpose of this letter was to present a model for evaluating the biological activity of drugs, which can become a new vector for the development of effective ways to increase blood oxygenation across pulmonary and save the lives of patients with severe atypical pneumonia complicated by respiratory obstruction in COVID-19.

Acute respiratory syndrome-2 (SARS-CoV-2): A solution of hydrogen peroxide and sodium bicarbonate as an expectorant for recanalization of the respiratory tract and blood oxygenation in respiratory obstruction (review)

The immediate cause of death of patients in the final stage of a new coronavirus infection is hypoxia, which develops due to respiratory obstruction. In accordance with the standard of treatment of patients with the most severe atypical pneumonia with COVID-19, artificial lung ventilation and extrapulmonary blood oxygenation are used to preserve their lives. However, these methods do not eliminate airway obstruction, one of the causes of which is mucus hypersecretion. The review shows that a new vector for the search and development of medicines for the drug elimination of hypoxia in respiratory obstruction has been identified in Russia. The high prospects of solutions of hydrogen peroxide and sodium bicarbonate with original physicochemical properties and local mechanisms of action providing urgent recanalization of the respiratory tract and oxygenation of blood in respiratory obstruction caused by blockage of the respiratory tract with thick sputum, mucus, pus and blood are shown. Domestic inventions are indicated, the essence of which is the basis of this scientific direction. Original formulations of solutions of hydrogen peroxide and sodium bicarbonate are given, as well as new technologies for their local application, providing urgent dissolution of mucus, sputum, pus and blood with simultaneous immediate release of oxygen gas.

A Call for Quality: Substandard Research in Male Sexual and Reproductive Medicine During the COVID-19 Pandemic

The coronavirus disease 2019 (COVID-19) pandemic has had a tremendous global economic impact and profound, long-lasting impact on people's lives. Since December 2019, when the first case of a severe atypical pneumonia caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) was described from Wuhan, China, COVID-19 has caused over 4 million deaths worldwide (https://coronavirus.jhu.edu/). The medical community responded quickly, addressing key knowledge gaps about COVID-19 and ultimately developing highly effective vaccines.

Molecular detection of Mycoplasma pneumoniae in Community acquired pneumonia

Community acquired pneumonia (CAP) remains a common and serious illness despite availability of potent anti-microbials and effective vaccine. Two types of CAP are commonly recognised - typical and atypical. Typical pneumonia is usually caused by bacteria such as Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catharralis, whereas, atypical pneumonia can be caused by Mycoplasma pneumoniae, Chlamydia pneumoniae, Legionella pneuomophila. Mycoplasma pneumoniae is found to be the most common cause of CAP among atypical pathogens and is called “Walking pneumonia”. It is a common atypical respiratory pathogen that produces diseases of varied severity ranging from mild upper respiratory tract infection to severe atypical pneumonia and is also responsible for producing a wide spectrum of non-pulmonary manifestations like neurological, hepatic, cardiac diseases, hemolytic anemia, polyarthritis and erythema multiforme which occur in as many as 25% of infected persons. As it lacks cell wall they are resistant to β lactam antibiotics, hence accurate and rapid diagnosis of M. pneumoniae infections is critical to initiate appropriate antibiotic treatment. Identification of M pneumoniae allows narrowing of initial empirical regimen which decreases antibiotic selection pressure and may lessen the risk of resistance. In view of this present study will be conducted in a tertiary care hospital for identification of M pneumoniae in cases of CAP by Polymerase chain reaction (PCR). 1. To detect proportion of Mycoplasma Pneumoniae among cases of CAP. 2. Detection of 16SrRNA Mycoplasma pneumoniae by PCR.Clinico-radiologically diagnosed 92 CAP patients were included in the study. Out of which 15 cases were caused by typical CAP pathogens like Streptococcus species, K.pneumoniae & M.tuberculosis. Samples (Sputum Bronchoalveolar lavages) from 77 suspected cases of atypical pneumonia are inoculated on PPLO broth (Difco) followed by identification of genus specific 16S rRNA Mycoplasma pneumoniae using PCR. PCR was found to be positive in 9 (11.68%) out of 77 CAP patients. PCR was found to be positive in 9 (11.68%) out of 77 CAP patients. Detection of M.pneumoniae is essential for prompt diagnosis and start of empirical therapy, thereby reducing antibiotic selection pressure.

English

Legionella pneumophila is an important pathogen and is involved in more than 95% of cases of severe atypical pneumonia. The current study focused on the ablution water in the grand mosque in Makkah as well as water tanks in hotels surrounding the holy mosque.  A total of 100 water samples were collected from ablution water in the Haram and the hotels in the central area around the grand mosque and sent to the research laboratory of microbiology, Faculty of Medicine, University of Umm Al Qura. Samples were filtrated and inoculated onto buffer charcoal-yeast extract agar base and incubated at 37°C in a CO2 incubator. The plates were examined after seven days of incubation. Isolated organisms were confirmed by using the “Microgen Legionella” (latex agglutination test). Out of the 100 water samples tested, 11 samples were positive for L. pneumophila. All positive water samples were from hotels water tanks. This indicates that this type of bacteria existing in the water sources. So requires further research to cover all sources of water to avoid an outbreak of this infection among the pilgrims. To avoid the possibility of this, constant maintenance of hotel water tanks regularly and the use of chlorine in specific proportions according to recommended specifications can help reduce the spread of these microbial infections.   Key words: Holy Mosque, Legionella pneumophila, water tanks, environmental.

Unfolded Protein Response Inhibition Reduces Middle East Respiratory Syndrome Coronavirus-Induced Acute Lung Injury.

ABSTRACTTissue- and cell-specific expression patterns are highly variable within and across individuals, leading to altered host responses after acute virus infection. Unraveling key tissue-specific response patterns provides novel opportunities for defining fundamental mechanisms of virus-host interaction in disease and the identification of critical tissue-specific networks for disease intervention in the lung. Currently, there are no approved therapeutics for Middle East respiratory syndrome coronavirus (MERS-CoV) patients, and little is understood about how lung cell types contribute to disease outcomes. MERS-CoV replicates equivalently in primary human lung microvascular endothelial cells (MVE) and fibroblasts (FB) and to equivalent peak titers but with slower replication kinetics in human airway epithelial cell cultures (HAE). However, only infected MVE demonstrate observable virus-induced cytopathic effect. To explore mechanisms leading to reduced MVE viability, donor-matched human lung MVE, HAE, and FB were infected, and their transcriptomes, proteomes, and lipidomes were monitored over time. Validated functional enrichment analysis demonstrated that MERS-CoV-infected MVE were dying via an unfolded protein response (UPR)-mediated apoptosis. Pharmacologic manipulation of the UPR in MERS-CoV-infected primary lung cells reduced viral titers and in male mice improved respiratory function with accompanying reductions in weight loss, pathological signatures of acute lung injury, and times to recovery. Systems biology analysis and validation studies of global kinetic transcript, protein, and lipid data sets confirmed that inhibition of host stress pathways that are differentially regulated following MERS-CoV infection of different tissue types can alleviate symptom progression to end-stage lung disease commonly seen following emerging coronavirus outbreaks.

A case of chlamydia psittaci caused severe pneumonia and meningitis diagnosed by metagenome next-generation sequencing and clinical analysis: a case report and literature review

BackgroundPsittacosis, which is also known as parrot fever, is Chlamydia psittaci (C. psittaci) caused infectious disease. The clinical manifestations vary from asymptomatic infection to severe atypical pneumonia or even fatal meningitis. Early recognition of psittacosis is difficult because of its nonspecific clinical manifestations. Culture and gene probe techniques for C. psittaci are not available for routine clinical use, which makes the diagnosis difficult too. Although psittacosis has increasingly been recognized and reported in recent years, cure of severe pneumonia complicated with meningitis, with etiologic diagnosis aided by the use of metagenomic next-generation sequencing (mNGS), is still uncommon. So, it is necessary to report and review such potentially fatal case.Case presentationThis report describes a 54-year-old woman with C. psittaci caused severe atypical pneumonia and meningitis. She presented with symptoms of fever, dry cough and dyspnea, accompanied by prominent headache. Her condition deteriorated rapidly to respiratory failure and lethargy under the treatment of empirical antibacterial agents, and was treated with invasive mechanical ventilation soon. She denied contact with birds, poultry or horses, but unbiased mNGS of both the bronchoalveolar lavage fluid (BALF) and the cerebrospinal fluid (CSF) identified sequence reads corresponding to C. psittaci infection, and there was no sequence read corresponding to other probable pathogens. Combined use of targeted antimicrobial agents of tetracyclines, macrolides and fluoroquinolones was carried out, and the patient’s condition improved and she was discharged home 28 days later. Her status returned close to premorbid condition on day 60 of follow-up.ConclusionsWhen clinicians come across a patient with atypical pneumonia accompanied by symptoms of meningitis, psittacosis should be taken into consideration. mNGS is a promising detection method in such condition and is recommended.

COVID-19: la pandemia del olvido científico

COVID-19: la pandemia del olvido científico

Nursing Leadership in COVID-19 Education—Chronologic Indexing of Information and Assurance of Receipt of Information

ABSTRACT In December 2019, a cluster of patients in Wuhan, Hubei Province, China, presented with severe atypical pneumonia. Because of the association with a novel coronavirus strain, the disease was coined COVID-19. Preventing the spread of the virus through extensive education became the primary intervention point in the containment of COVID-19. Resource and labor mapping shifted to adapt to the pandemic. Nurse practitioners have transitioned to frontline community health and prevention roles in safety education and regulatory resource management.

Сложность патогенеза коагулопатии при COVID-19

Введение. Коронавирус SARS-CoV-2 является новым вирусом, обладающим способностью осуществлять трансмиссию воздушно-капельным путем, вызывая тяжелое течение атипичной пневмонии, нередко сочетающейся с коагулопатиями. Роль структурных белков коронавируса в их патогенезе неизвестна. Цель исследования: с помощью биоинформационного анализа выявить в структурных белках коронавируса SARS-CoV-2 последовательности, гомологичные белкам системы гемостаза, и рассмотреть возможные сценарии их участия в патогенезе коагулопатий при COVID-19, а также объяснить существование вирусостатического эффекта гепарина. Материалы и методы. Для компьютерного анализа были использованы доступные в Интернете базы данных первичных структур белков коронавирусов и их рецепторов, а также поверхностных белков других вирусов, белков системы гемостаза и иммунной системы. Сравнивали аминокислотный состав белков и распределение оснόвных аминокислот (аргинина и лизина) в их первичных последовательностях. С целью выявления пептидного (иммуноэпитопного) родства структурных белков коронавирусов с белками системы гемостаза человека был выполнен поиск гомологичных последовательностей в их белках. Результаты. В структурных белках коронавируса SARS-CoV-2 выявлено множество последовательностей, гомологичных белкам системы гемостаза и иммунной системы. В отличие от коронавирусов SARS-CoV и MERS-CoV, S1-субъединица S-белка коронавируса SARS-CoV-2 имеет положительную полярность. Заключение. Множество последовательностей в структурных белках коронавируса SARS-CoV-2, гомологичных белкам системы гемостаза, потенциально способны вы- зывать различные сценарии патогенеза коагулопатий. Положительная полярность S1-субъединицы S-белка коронавируса SARS-CoV-2 позволяет объяснить неспецифическое взаимодействие ее с гепарином и его вирусостатический (неантикоагулянтный) эффект. Background. The coronavirus SARS-CoV-2 is a new virus capable of human-human transmission and inducing a severe atypical pneumonia often associated with coagulopathy. A role of SARS-CoV-2 structural proteins in coagulopathy pathogenesis is unknown. Objectives: to use a bioinformation analysis to identify SARS-CoV-2 sequences in the structural proteins that are homologous to hemostasis system proteins, regard their possible participation in coagulopathy pathogenesis and explain the antiviral effect of heparin. Materials / Methods. For computer analysis, Internet databases were used of the primary structures of coronavirus proteins and their receptors, as well as surface proteins of other viruses, proteins of hemostasis and immune systems. The amino acid composition of proteins and the distribution of basic amino acids (arginine and lysine) in their primary sequences were compared. For detection of peptide (immunoepitopic) relationship of coronaviruses structural proteins with human hemostasis proteins, a search for homologous sequences in their proteins was performed. Results. Many sequences have been identified in structural proteins of SARS-CoV-2 coronavirus that are homologous to the proteins of hemostasis and immune systems. In contrast with SARS-CoV and MERS-CoV coronaviruses, the S1-subunit of SARS-CoV-2 coronavirus S-protein has a positive polarity. Conclusions. Many sequences in SARS-CoV-2 structural proteins that homologous to hemostasis system proteins are potentially responsible for coagulopathy pathogenesis. The positive polarity of the S1-subunit of SARS-CoV-2 S-protein explains its nonspecific interaction with heparin and its virostatic (non-anticoagulant) effect.

A Review of the Preclinical and Clinical Efficacy of Remdesivir, Hydroxychloroquine, and Lopinavir-Ritonavir Treatments against COVID-19.

In December of 2019, an outbreak of a novel coronavirus flared in Wuhan, the capital city of the Hubei Province, China. The pathogen has been identified as a novel enveloped RNA beta-coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus SARS-CoV-2 is associated with a disease characterized by severe atypical pneumonia known as coronavirus 2019 (COVID-19). Typical symptoms of this disease include cough, fever, malaise, shortness of breath, gastrointestinal symptoms, anosmia, and, in severe cases, pneumonia.1 The high-risk group of COVID-19 patients includes people over the age of 60 years as well as people with existing cardiovascular disease and/or diabetes mellitus. Epidemiological investigations have suggested that the outbreak was associated with a live animal market in Wuhan. Within the first few months of the outbreak, cases were growing exponentially all over the world. The unabated spread of this deadly and highly infectious virus is a health emergency for all nations in the world and has led to the World Health Organization (WHO) declaring a pandemic on March 11, 2020. In this report, we consolidate and review the available clinically and preclinically relevant results emanating from in vitro animal models and clinical studies of drugs approved for emergency use as a treatment for COVID-19, including remdesivir, hydroxychloroquine, and lopinavir-ritonavir combinations. These compounds have been frequently touted as top candidates to treat COVID-19, but recent clinical reports suggest mixed outcomes on their efficacies within the current clinical protocol frameworks.

Molecular Alterations Prompted by SARS-CoV-2 Infection: Induction of Hyaluronan, Glycosaminoglycan and Mucopolysaccharide Metabolism

BackgroundThe SARS-CoV-2 is the etiological agent causing COVID-19 which has infected more than 2 million people with more than 200000 deaths since its emergence in December 2019. In the majority of cases patients are either asymptomatic or show mild to moderate symptoms and signs of a common cold. A subset of patients, however, develop a severe atypical pneumonia, with the characteristic ground-glass appearance on chest x-ray and computerized tomography, which evolves into an acute respiratory distress syndrome, that requires mechanical ventilation and eventually results in multiple organ failure and death. The Molecular pathogenesis of COVID-19 is still unknown.Aim of the studyIn the present work we performed a stringent metanalysis from the publicly available RNAseq data from bronchoalveolar cells and peripheral blood mononuclear cells to elucidate molecular alterations and cellular deconvolution to identify immune cell profiles.ResultsAlterations in genes involved in hyaluronan, glycosaminoglycan and mucopolysaccharides metabolism were over-represented in bronchoalveolar cells infected by SARS-CoV-2, as well as potential lung infiltration with neutrophils, T CD4+ cell and macrophages. The blood mononuclear cells presented a proliferative state. Dramatic reduction of NK and T lymphocytes, whereas an exacerbated increase in monocytes.ConclusionsIn summary our results revealed molecular pathogenesis of the SARS-CoV-2 infection to bronchoalveolar cells inducing the hyaluronan and glycosaminoglycan metabolism that could shape partially the components of the ground-glass opacities observed in CT. And the potential immune response profile in COVID-19.

Methods of An Open - Label Proof - of - Concept Trial of Intravenous Valproic Acid for Severe COVID-19

Introduction. Coronavirus disease 2019 (COVID-19) is the systemic entity caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that may cause death through severe atypical pneumonia and acute lung injury. Valproic acid (VPA) has shown anti-inflammatory activity and intrinsic antiviral effect. These properties warrant the study of VPA as a possible active treatment in people with severe COVID-19. Material and Methods. Consecutive adult patients needing invasive mechanical ventilation (IMV) will be given intravenous (IV) VPA at a starting dose of 20 mg/kg/day and up to 60/kg/day (in 60 min IV infusions in 250 mL normal saline) as needed to reach plasma VPA concentrations of 50-100 μg/mL (measured every 72 h). These patients will be followed-up for 10 days for the primary outcome and for a further period of 30 days after treatment completion for the secondary outcome of recurrence. The primary study outcome is the reduction in the case fatality rate (CFR) of at least 50 % after 10 days of treatment (as compared with natural history). Secondary outcomes are the reduction of length of stay (LOS) of at least 50 %, as well as COVID-19 recurrence at 30-day follow-up. The most important safety outcomes are acute liver failure, acute pancreatitis, and thrombocytopenia. Conclusions. Although long-term adverse effects and even pro-inflammatory consequences have been reported with the chronic use of VPA, the study of VPA is justified from a scientific standpoint given the urgent need for a drug against COVID-19 to shorten the high mortality and LOS.

Molecular Insights into Severe Acute Respiratory Syndrome Coronavirus 2 Pathobiology: Dissecting the Interplay between Cellular Innate Immunity and Immune Evasion.

In December 2019, outbreak of a novel coronavirus flared in Wuhan, the capital city of Hubei province, China. The identified pathogen was an enveloped RNA betacoronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The outbreak was declared a pandemic by the World Health Organization (WHO), because the continual spread of this deadly and highly infectious virus is a health emergency for all world nations. SARS-CoV-2 is associated with severe atypical pneumonia coronavirus disease-19. Typical symptoms of this disease include fever, malaise, cough, shortness of breath, and in severe cases, death. As the virus continues to invade host cells deep into alveoli, infection severity mostly depends on the undeterred immune response that is triggered by elevated levels of inflammation-inducing cytokines, called a cytokine storm. In this article, we provide a comprehensive review of the viral life cycle and immunological responses associated with the SARS-CoV-2 infection.

Severe atypical pneumonia in critically ill patients: a retrospective multicenter study

BackgroundChlamydophila pneumoniae (CP) and Mycoplasma pneumoniae (MP) patients could require intensive care unit (ICU) admission for acute respiratory failure.MethodsAdults admitted between 2000 and 2015 to 20 French ICUs with proven atypical pneumonia were retrospectively described. Patients with MP were compared to Streptococcus pneumoniae (SP) pneumonia patients admitted to ICUs.ResultsA total of 104 patients were included, 71 men and 33 women, with a median age of 56 [44–67] years. MP was the causative agent for 76 (73%) patients and CP for 28 (27%) patients. Co-infection was documented for 18 patients (viruses for 8 [47%] patients). Median number of involved quadrants on chest X-ray was 2 [1–4], with alveolar opacities (n = 61, 75%), interstitial opacities (n = 32, 40%). Extra-pulmonary manifestations were present in 34 (33%) patients. Mechanical ventilation was required for 75 (72%) patients and vasopressors for 41 (39%) patients. ICU length of stay was 16.5 [9.5–30.5] days, and 11 (11%) patients died in the ICU. Compared with SP patients, MP patients had more extensive interstitial pneumonia, fewer pleural effusion, and a lower mortality rate [6 (8%) vs. 17 (22%), p = 0.013]. According MCA analysis, some characteristics at admission could discriminate MP and SP. MP was more often associated with hemolytic anemia, abdominal manifestations, and extensive chest radiograph abnormalities. SP-P was associated with shock, confusion, focal crackles, and focal consolidation.ConclusionIn this descriptive study of atypical bacterial pneumonia requiring ICU admission, mortality was 11%. The comparison with SP pneumonia identified clinical, laboratory, and radiographic features that may suggest MP or CP pneumonia.

Detection of respiratory bacterial pathogens causing atypical pneumonia by multiplex Lightmix® RT-PCR

Pneumonia is a severe infectious disease. In addition to common viruses and bacterial pathogens (e.g. Streptococcus pneumoniae), fastidious respiratory pathogens like Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella spp. can cause severe atypical pneumonia. They do not respond to penicillin derivatives, which may cause failure of antibiotic empirical therapy. The same applies for infections with B. pertussis and B. parapertussis, the cause of pertussis disease, that may present atypically and need to be treated with macrolides. Moreover, these fastidious bacteria are difficult to identify by culture or serology, and therefore often remain undetected. Thus, rapid and accurate identification of bacterial pathogens causing atypical pneumonia is crucial. We performed a retrospective method evaluation study to evaluate the diagnostic performance of the new, commercially available Lightmix® multiplex RT-PCR assay that detects these fastidious bacterial pathogens causing atypical pneumonia. In this retrospective study, 368 clinical respiratory specimens, obtained from patients suffering from atypical pneumonia that have been tested negative for the presence of common agents of pneumonia by culture and viral PCR, were investigated. These clinical specimens have been previously characterized by singleplex RT-PCR assays in our diagnostic laboratory and were used to evaluate the diagnostic performance of the respiratory multiplex Lightmix® RT-PCR. The multiplex RT-PCR displayed a limit of detection between 5 and 10 DNA copies for different in-panel organisms and showed identical performance characteristics with respect to specificity and sensitivity as in-house singleplex RT-PCRs for pathogen detection. The Lightmix® multiplex RT-PCR assay represents a low-cost, time-saving and accurate diagnostic tool with high throughput potential. The time-to-result using an automated DNA extraction device for respiratory specimens followed by multiplex RT-PCR detection was below 4 h, which is expected to significantly improve diagnostics for atypical pneumonia-associated bacterial pathogens.

Assessment of Chlamydia psittaci Shedding and Environmental Contamination as Potential Sources of Worker Exposure throughout the Mule Duck Breeding Process.

Chlamydia psittaci is an obligate intracellular bacterium responsible for avian chlamydiosis, otherwise known as psittacosis, a zoonotic disease that may lead to severe atypical pneumonia. This study was conducted on seven mule duck flocks harboring asymptomatic birds to explore the circulation and persistence of C. psittaci during the entire breeding process and assess the potential sources of worker exposure. Cloacal swabs and air samples were taken on each occasion requiring humans to handle the birds. In parallel, environmental samples, including dust, water, and soil, were collected. Specific real-time PCR analyses revealed the presence of C. psittaci in all flocks but with three different shedding patterns involving ducks about the age of 4, 8, and 12 weeks with heavy, moderate, and low excretion levels, respectively. Air samples were only positive in flocks harboring heavy shedders. Dust in flocks with heavy or moderate shedders carried chlamydial loads strongly associated with the loads detected in avian and soil samples. Environmental contamination, significantly correlated with shedding dynamics, was considered to be the most probable source of exposure. The high prevalence of bacteriophage Chp1 in all flocks, mostly jointly present with chlamydia, suggests an important factor in C. psittaci persistence, thus creating a greater risk for humans. A survey conducted in these flocks regarding farming practices and activities showed that disinfection seems to be the most promising practice for reducing C. psittaci prevalence in ducks and that the place and the duration of action during operations seem to be potential risk factors. Strict adherence to good practices is strongly recommended.