The atypical pneumonias: clinical diagnosis and importance

Imaging of pulmonary infections encountered in the emergency department in post-COVID 19 era- common, rare and exotic. Bacterial and viral

Pulmonary infections contribute substantially to emergency department (ED) visits, posing a considerable health burden. Lower respiratory tract infections are prevalent, particularly among the elderly, constituting a significant percentage of infectious disease-related ED visits. Timely recognition and treatment are crucial to mitigate morbidity and mortality. Imaging studies, primarily chest radiographs and less frequently CT chests, play a pivotal role in diagnosis. This article aims to elucidate the imaging patterns of both common and rare pulmonary infections (bacterial and viral) in the post COVID-19 era, emphasizing the importance of recognizing distinct radiological manifestations. The integration of clinical and microbiological evidence aids in achieving accurate diagnoses, and guiding optimal therapeutic interventions. Despite potential overlapping manifestations, a nuanced understanding of radiological patterns, coupled with comprehensive clinical and microbiological information, enhances diagnostic precision in majority cases.

Comparison of Mycoplasma pneumoniae infection in children admitted with community acquired pneumonia before and during the COVID-19 pandemic: a retrospective study at a tertiary hospital of southwest China

PURPOSE

The COVID-19 pandemic has notably altered the infection dynamics of various pathogens. This study aimed to evaluate the pandemic's impact on the infection spectrum of Mycoplasma pneumoniae (M. pneumoniae) among children with community acquired pneumonia (CAP).

METHODS

We enrolled pediatric CAP patients admitted to a tertiary hospital in southwest China to compare the prevalence and characteristics of M. pneumoniae infections before (2018-2019) and during (2020-2022) the COVID-19 pandemic. Detection of M. pneumoniae IgM antibodies in serum were conducted using either indirect immunofluorescence or passive agglutination methods.

RESULTS

The study included 1505 M. pneumoniae-positive and 3160 M. pneumoniae-negative CAP patients. Notable findings were the higher age and frequency of pneumonia-associated symptoms in M. pneumoniae-positive patients, alongside a lower male proportion and fewer respiratory co-infections. The year 2019 saw a notable increase in M. pneumoniae infections compared to 2018, followed by a decline from 2020 to 2022. The COVID-19 pandemic period witnessed significant alterations in age distribution, male proportion, and co-infections with specific pathogens in both M. pneumoniae-positive and negative patients. The M. pneumoniae infections were predominantly seasonal, peaking in autumn and winter during 2018 and 2019. Although there was a sharp drop in February 2020, the infection still peaked in cold months of 2020 and 2021. However, the typical seasonal pattern was nearly absent in 2022.

CONCLUSIONS

The COVID-19 pandemic has markedly changed the infection landscape of M. pneumoniae in pediatric CAP patients, with shifts observed in infection rates, demographic profiles, co-infections, and seasonal patterns.

In vitro modelling of bacterial pneumonia: a comparative analysis of widely applied complex cell culture models

Bacterial pneumonia greatly contributes to the disease burden and mortality of lower respiratory tract infections among all age groups and risk profiles. Therefore, laboratory modelling of bacterial pneumonia remains important for elucidating the complex host-pathogen interactions and to determine drug efficacy and toxicity. In vitro cell culture enables for the creation of high-throughput, specific disease models in a tightly controlled environment. Advanced human cell culture models specifically, can bridge the research gap between the classical two-dimensional cell models and animal models. This review provides an overview of the current status of the development of complex cellular in vitro models to study bacterial pneumonia infections, with a focus on air-liquid interface models, spheroid, organoid, and lung-on-a-chip models. For the wide scale, comparative literature search, we selected six clinically highly relevant bacteria (Pseudomonas aeruginosa, Mycoplasma pneumoniae, Haemophilus influenzae, Mycobacterium tuberculosis, Streptococcus pneumoniae, and Staphylococcus aureus). We reviewed the cell lines that are commonly used, as well as trends and discrepancies in the methodology, ranging from cell infection parameters to assay read-outs. We also highlighted the importance of model validation and data transparency in guiding the research field towards more complex infection models.

[Carcinoma, tuberculosis, atypical pneumonia - or may be pulmonary tularemia? Two case reports]

Tularemia is a rare zoonotic disease, endemic in rural areas all over Germany. It's clinical manifestation following inhalation of infectious aerosols may resemble pulmonary neoplasia, other atypical pneumonias or tuberculosis. Here we describe two representative cases with pulmonary tularemia.

Multiple pulmonary cavities in an immunocompetent patient: a case report and literature review

Legionella pneumonia (LP) is a relatively uncommon yet well-known type of atypical community-acquired pneumonia (CAP). It is characterized by a rapid progression to severe pneumonia and can be easily misdiagnosed. In most patients, chest computed tomography (CT) showed patchy infiltration, which may progress to lobar infiltration or even lobar consolidation. While pulmonary cavities are commonly observed in immunocompromised patients with LP, they are considered rare in immunocompetent individuals. Herein, we present a case of LP in an immunocompetent patient with multiple cavities in both lungs. Pathogen detection was performed using metagenomic next-generation sequencing (mNGS). This case highlights the unusual radiographic presentation of LP in an immunocompetent patient and emphasizes the importance of considering LP as a possible diagnosis in patients with pulmonary cavities, regardless of their immune status. Furthermore, the timely utilization of mNGS is crucial for early pathogen identification, as it provides multiple benefits in enhancing the diagnosis and prognosis of LP patients.

Legionella pneumonia in hospitalized adults with respiratory failure: Quinolones or macrolides?

The optimal antimicrobial regimen for adults with respiratory failure due to Legionella pneumonia remains controversial. A systematic review was performed to assess the impact on outcomes comparing quinolones versus macrolides. A literature search was conducted in PubMed, Cochrane Library and Web of Science between 2012 and 2022. It yielded 124 potentially articles and ten observational studies met the inclusion criteria. A total of 4271 patients were included, 2879 (67 %) were male. A total of 1797 (42 %) subjects required intensive care unit (ICU) admission and 942 (52 %) mechanical ventilation. Fluoroquinolones and macrolides alone were administered in 1397 (33 %) and 1500 (35 %) subjects, respectively; combined therapy in 204 (4.8 %) patients. Overall mortality was 7.4 % (319 patients), with no difference between antibiotics. When data from the three studies with severe pneumonia were pooled together, mortality with fluoroquinolones alone was statistically superior to macrolides alone (72.8 % vs 30.8 %, p value 0.027). Hospital length of stay and complications were comparable. Our findings suggest that macrolides and quinolones were comparable for hospitalized Legionella pneumonia. However, in severe pneumonia, a randomized clinical trial is an unmet clinical need. PROSPERO registration number: CRD42023389308.

Potential co-infection of influenza A, influenza B, respiratory syncytial virus, and Chlamydia pneumoniae: a case report with literature review

The occurrence of a co-infection involving four distinct respiratory pathogens could be underestimated. Here, we report the case of a 72-year-old woman who presented to a community hospital with a cough productive of sputum as her main clinical manifestation. Antibody detection of common respiratory pathogens revealed potential co-infection with influenza A, influenza B, respiratory syncytial virus, and Chlamydia pneumoniae. We treated her with 75 mg oseltamivir phosphate administered orally twice daily for 5 days, 0.5 g azithromycin administered orally for 5 days, and 0.3 g acetylcysteine aerosol inhaled twice daily for 3 days. The patient showed a favorable outcome on the eighth day after early diagnosis and treatment. Since co-infection with these four pathogens is rare, we performed an extensive PubMed search of similar cases and carried out a systematic review to analyze the epidemiology, clinical manifestations, transmission route, susceptible population, and outcomes of these four different pathogens. Our report highlights the importance for general practitioners to be vigilant about the possibility of mixed infections when a patient presents with respiratory symptoms. Although these symptoms may be mild, early diagnosis and timely treatment could improve outcomes. Additionally, further research is warranted to explore the potential influence of SARS-CoV-2 infection on the co-occurrence of multiple respiratory pathogens.

Antibiotics and nano-antibiotics in treatment of lung infection: In management of COVID-19

The world has witnessed the cruelty of COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The association of COVID-19 with other secondary and bacterial co-infections has tremendously contributed to lung infections. An increased probability of having a secondary lung infection was observed among the post-COVID patients. The treatment of antibiotics has ameliorated the mortality rate. However, the stewardship of antibiotic treatment was linked to increased organ failure. Therefore, the paper discusses the interactions between the virus and host through the ACE2 receptors that contribute to COVID-19 development. Furthermore, the paper provides an invaluable compendium history of SARS-CoV-2 genomic composition. It revolves around most classes of antibiotics used to treat COVID-19 disease and post-COVID lung infections with the complete mechanism. This binds with the exertion of the antibiotics for bacterial infection associated with COVID-19 patients and how beneficial and effective responses have been recorded for the treatment. The application of nanotechnology and possible approaches of nanomedicines is also discussed to its potential usage.

Early discontinuation of combination antibiotic therapy in severe community-acquired pneumonia: a retrospective cohort study

BACKGROUND

Severe community-acquired pneumonia (SCAP) is commonly treated with an empiric combination therapy, including a macrolide, or a quinolone and a β-lactam. However, the risk of Legionella pneumonia may lead to a prolonged combination therapy even after negative urinary antigen tests (UAT).

METHODS

We conducted a retrospective cohort study in a French intensive care unit (ICU) over 6 years and included all the patients admitted with documented SCAP. All patients received an empirical combination therapy with a β-lactam plus a macrolide or quinolone, and a Legionella UAT was performed. Macrolide or quinolone were discontinued when the UAT was confirmed negative. We examined the clinical and epidemiological features of SCAP and analysed the independent factors associated with ICU mortality.

RESULTS

Among the 856 patients with documented SCAP, 26 patients had atypical pneumonia: 18 Legionella pneumophila (LP) serogroup 1, 3 Mycoplasma pneumonia (MP), and 5 Chlamydia psittaci (CP). UAT diagnosed 16 (89%) Legionella pneumonia and PCR confirmed the diagnosis for the other atypical pneumonia. No atypical pneumonia was found by culture only. Type of pathogen was not associated with a higher ICU mortality in the multivariate analysis.

CONCLUSION

Legionella pneumophila UAT proved to be highly effective in detecting the majority of cases, with only a negligible percentage of patients being missed, but is not sufficient to diagnose atypical pneumonia, and culture did not provide any supplementary information. These results suggest that the discontinuation of macrolides or quinolones may be a safe option when Legionella UAT is negative in countries with a low incidence of Legionella pneumonia.

Empirical antibiotic treatment for community-acquired pneumonia and accuracy for Legionella pneumophila, Mycoplasma pneumoniae, and Clamydophila pneumoniae: a descriptive cross-sectional study of adult patients in the emergency department

BACKGROUND

Many factors determine empirical antibiotic treatment of community-acquired pneumonia (CAP). We aimed to describe the empirical antibiotic treatment CAP patients with an acute hospital visit and to determine if the current treatment algorithm provided specific and sufficient coverage against Legionella pneumophila, Mycoplasma pneumoniae, and Clamydophila pneumoniae (LMC).

METHODS

A descriptive cross-sectional, multicenter study of all adults with an acute hospital visit in the Region of Southern Denmark between January 2016 and March 2018 was performed. Using medical records, we retrospectively identified the empirical antibiotic treatment and the microbiological etiology for CAP patients. CAP patients who were prescribed antibiotics within 24 h of admission and with an identified bacterial pathogen were included. The prescribed empirical antibiotic treatment and its ability to provide specific and sufficient coverage against LMC pneumonia were determined.

RESULTS

Of the 19,133 patients diagnosed with CAP, 1590 (8.3%) patients were included in this study. Piperacillin-tazobactam and Beta-lactamase sensitive penicillins were the most commonly prescribed empirical treatments, 515 (32%) and 388 (24%), respectively. Our analysis showed that 42 (37%, 95% CI: 28-47%) of 113 patients with LMC pneumonia were prescribed antibiotics with LMC coverage, and 42 (12%, 95% CI: 8-15%) of 364 patients prescribed antibiotics with LMC coverage had LMC pneumonia.

CONCLUSION

Piperacillin-tazobactam, a broad-spectrum antibiotic recommended for uncertain infectious focus, was the most frequent CAP treatment and prescribed to every third patient. In addition, the current empirical antibiotic treatment accuracy was low for LMC pneumonia. Therefore, future research should focus on faster diagnostic tools for identifying the infection focus and precise microbiological testing.

High specificity of metagenomic next-generation sequencing using protected bronchial brushing sample in diagnosing pneumonia in children

Background

Lower respiratory tract infections are the leading cause of morbidity and mortality in children worldwide. Timely and accurate pathogen detection is crucial for proper clinical diagnosis and therapeutic strategies. The low detection efficiency of conventional methods and low specificity using respiratory samples seriously hindered the accurate detection of pathogens.

Methods

In this study, we retrospectively enrolled 1,032 children to evaluate the performance of metagenomics next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) sample and protected bronchial brushing (BB) sample in diagnosing pneumonia in children. In addition, conventional tests (CTs) were also performed.

Results

The specificity of BB mNGS [67.3% (95% CI 58.6%-75.9%)] was significantly higher than that of BALF mNGS [38.5% (95% CI 12.0%-64.9%)]. The total coincidence rate of BB mNGS [77.6% (95% CI 74.8%-80.5%)] was slightly higher than that of BALF mNGS [76.5% (95% CI 68.8%-84.1%)] and CTs [38.5% (95% CI 35.2%-41.9%)]. During the epidemics of Mycoplasma pneumoniae, the detection rate of M. pneumoniae in the >6-year group (81.8%) was higher than that in the 3-6-year (78.9%) and <3-year groups (21.5%). The highest detection rates of bacteria, fungi, and viruses were found in the <3-year, >6-year, and 3-6-year groups, respectively. mNGS detection should be performed at the duration of 5-7 days after the start of continuous anti-microbial therapy or at the duration of 6-9 days from onset to mNGS test.

Conclusions

This is the first report to evaluate the performance of BB mNGS in diagnosing pulmonary infections in children on a large scale. Based on our findings, extensive application of BB mNGS could be expected.

Trends of legionellosis reported in Jeju Province, Republic of Korea, 2015-2022

BACKGROUND

The number of reported cases of Legionnaires' disease (LD) in the Republic of Korea surged nationally in 2016; however, in 2022, this number was higher in Jeju Province than the previous national peak. A descriptive epidemiological study was conducted to analyze trends in the incidence of reported LD cases in Jeju Island from 2015 to 2022.

METHODS

The data for this study were obtained from case reports submitted to the Korea Disease Control and Prevention Agency through its Disease and Health Integrated Management System. The selection criteria were cases or suspected cases of LD reported among Jeju residents between 2015 and 2022. The 95% confidence interval of the crude incidence rate was calculated using the Poisson distribution.

RESULTS

Since 2020, the incidence rate of LD in Jeju has risen sharply, showing a statistically significant difference from the national incidence rate. A particular medical institution in Jeju reported a significant number of LD cases. Screening with the urine antigen test (UAT) also increased significantly.

CONCLUSION

Our findings indicate that the rapid increase in cases of LD in Jeju Province since 2020 was due to the characteristics of medical-care use among Jeju residents, which were focused on a specific medical institution. According to their clinical practice guidelines, this medical institution conducted UATs to screen patients suspected of pneumonia.

Management of Complex Infections in Hemophagocytic Lymphohistiocytosis in Adults

Hemophagocytic lymphohistiocytosis (HLH) is a syndrome of excessive immune system activation and inflammatory response due to a variety of primary and secondary factors that can cause a range of clinical symptoms and, in severe cases, life-threatening conditions. Patients with HLH are at increased risk of infection due to their abnormal immune function as well as chemotherapy and immunosuppressive therapy at the time of treatment. At the same time, the lack of specific clinical features makes complex infections in HLH challenging to diagnose and treat. The management of complex infections in HLH requires a multidisciplinary and integrated approach including the early identification of pathogens, the development of anti-infection protocols and regimens, and the elimination of potential infection factors. Especially in HLH patients with septic shock, empirical combination therapy against the most likely pathogens should be initiated, and appropriate anti-infective regimens should be determined based on immune status, site of infection, pathogens, and their drug resistance, with timely antibiotic adjustment by monitoring procalcitonin. In addition, anti-infection prophylaxis for HLH patients is needed to reduce the risk of infection such as prophylactic antibiotics and vaccinations. In conclusion, complex infection in HLH is a serious and challenging disease that requires vigilance, early identification, and timely anti-infective therapy.

Atraumatic Splenic Rupture in Legionella pneumophila Pneumonia

A previously fit 46-year-old male handyman presented to a rural hospital with a cough, fever, and epigastric pain without peritonism. The patient was admitted medically with symptoms and radiological appearances consistent with atypical community-acquired pneumonia. During the first 48 hours of admission, he suffered a significant haemodynamic deterioration and was transferred to the intensive care unit (ICU) for vasoactive support. Following stabilisation, urgent abdominal CT imaging demonstrated splenic rupture with haematoma in the absence of historical trauma. Emergency splenectomy was performed; the histopathological examination was unremarkable. Investigations for the presenting complaint confirmed Legionella pneumophila serotype 1 pneumonia by urinary antigen testing. The patient was extubated on postoperative day 2 and stepped down from ICU to complete a 14-day course of azithromycin. Atraumatic splenic rupture is a rarely described clinical entity. The process can be subdivided into pathological and nonpathological (spontaneous) cases. Pathological atraumatic splenic rupture may occur in the context of wide-ranging aetiologies, including bacterial pneumonia; however, the association with Legionella pneumophila serotype 1 is exceptional, with this representing the eighth case in the medical literature.

Legionella-Induced Hepatitis: A Case Report

Legionnaires' disease is caused by a potentially life-threatening infection with the opportunistic Gram-negative bacilli species Legionella pneumophila, which is transmitted via inhalation or aspiration of water droplets. Legionnaires' commonly presents as atypical community-acquired pneumonia with accompanying diarrhea. Although hepatic and renal involvement are relatively uncommon, in this report, we present a case of Legionella pneumonia with acute hepatitis.

Diagnosis of asthmatic pneumonia in children by lung ultrasound vs. chest X-ray: an updated systematic review and meta-analysis

Introduction

Chest X-ray (CXR) is used as the standard diagnostic method in lung diseases, especially in pneumonia, but unfortunately, despite the high risk of receiving radiation, it also has a high false negative rate. Therefore, some researchers recommend ultrasound to diagnose pneumonia.

Aim

To investigate the accuracy of lung ultrasound compared to CXR for the diagnosis of pneumonia children by meta-analysis method.

Material and methods

Original articles which evaluated accuracy of lung ultrasound compared to chest X-ray for the diagnosis of pneumonia in children, published between 1 January 2010 and 20 March 2021, were identified in the PubMed, Web of Science, Embase, Scopus and Cochrane Library databases. Data synthesis and statistical analysis were carried out using STATA software. Odds ratios with 95% confidence interval (CI), fixed effect model and mean difference with 95% CI, random effect model (REM) were calculated.

Results

At the first step, 1016 potentially important research abstracts and titles were discovered in our electronic searches, 8 papers were in agreement with our inclusion criteria. The statistical analysis showed sensitivity of 95.5% (95% CI: 93.6-97.1%) and specificity of 96.3% (95% CI: 92.1-98.4%) for the lung ultrasound, and CXR sensitivity and specificity were 87.4% (95% CI: 84.3-90.0%) and 98.6% (95% CI: 95.8-99.6%), respectively.

Conclusions

The present study showed that ultrasound can be useful in diagnosing pneumonia in children, and due to the lack of risk of receiving radiation, this method is even more preferred.

Prostatitis as initial manifestation of Chlamydia psittaci pneumonia diagnosed by metagenome next-generation sequencing: A case report

Chlamydia psittaci (C. psittaci) pneumonia is a zoonotic infectious disease caused by C. psittaci, which is often underdiagnosed. The application of metagenomic next-generation sequencing (mNGS) provides an unbiased method for the detection of unknown pathogens. A 46-year-old man received empirical treatment with piperacillin-tazobactam and moxifloxacin after an initial diagnosis of prostatitis and pneumonia. However, he experienced recurrent symptoms and a cough, and a chest computed tomography (CT) showed aggravated pulmonary inflammation. Upon further questioning, the patient recalled a history of contact with pigeons, and a bronchoscope alveolar lavage fluid analysis with mNGS suggested C. psittaci infection. Following treatment with doxycycline, the patient's symptoms were rapidly alleviated, and chest CT showed pulmonary lesions absorption. The patient was followed up for 1 month without any discomfort. This case highlights that initial manifestations of C. psittaci pneumonia may present with atypical symptoms such as prostatitis. Furthermore, mNGS can be a useful tool for the detection of rare or unknown pathogens such as C. psittaci.

Atypical Pathogens in Adult Community-Acquired Pneumonia and Implications for Empiric Antibiotic Treatment: A Narrative Review

Atypical pathogens are intracellular bacteria causing community-acquired pneumonia (CAP) in a significant minority of patients. Legionella spp., Chlamydia pneumoniae and psittaci, Mycoplasma pneumoniae, and Coxiella burnetii are commonly included in this category. M. pneumoniae is present in 5-8% of CAP, being the second most frequent pathogen after Streptococcus pneumoniae. Legionella pneumophila is found in 3-5% of inpatients. Chlamydia spp. and Coxiella burnetii are present in less than 1% of patients. Legionella longbeachae is relatively frequent in New Zealand and Australia and might also be present in other parts of the world. Uncertainty remains on the prevalence of atypical pathogens, due to limitations in diagnostic means and methodological issues in epidemiological studies. Despite differences between CAP caused by typical and atypical pathogens, the clinical presentation alone does not allow accurate discrimination. Hence, antibiotics active against atypical pathogens (macrolides, tetracyclines and fluoroquinolones) should be included in the empiric antibiotic treatment of all patients with severe CAP. For patients with milder disease, evidence is lacking and recommendations differ between guidelines. Use of clinical prediction rules to identify patients most likely to be infected with atypical pathogens, and strategies of narrowing the antibiotic spectrum according to initial microbiologic investigations, should be the focus of future investigations.

Metagenomic next-generation sequencing clinches the diagnosis of Legionella pneumonia in a patient with acute myeloid leukemia: A case report and literature review

Legionella pneumonia caused by Legionella pneumophila is a multi-system disease that is a life-threatening, acute, and severe form of pneumonia. L. pneumophila is widespread and the clinical manifestations of Legionella pneumonia are similar to those of typical and atypical pneumonia. Current diagnostic scores and radiologic evidence have limited diagnostic value. Thus, it is likely that many cases of Legionella pneumonia remain unreported. We describe a woman with a medical history of acute myeloid leukemia who suffered from repeated fever, and no relief following initial empirical antibiotic treatment. Ultimately, she was diagnosed with Legionella pneumonia based on metagenomic next-generation sequencing (mNGS). We also performed a systematic review of the literature and identified 5 other patients who were diagnosed with Legionella pneumonia using mNGS, and reviewed their clinical characteristics, biological characteristics, epidemiological features, laboratory results, clinical findings, and treatments. This literature review showed that accurate etiological diagnosis is becoming increasingly essential for a definitive diagnosis and treatment strategies. The clinical manifestations of Legionella pneumonia are non-specific, and many routine laboratory diagnostic tests cannot identify Legionella. mNGS, an indispensable approach for identifying microorganisms, can provide a promising tool for the rapid and accurate etiological diagnosis methods contributing to early diagnosis, early treatment, and improved prognosis, especially for uncommon species such as L. pneumophila.

Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections

Although the fast-growing metagenomic next-generation sequencing (mNGS) has been used in diagnosing infectious diseases, low detection rate of mNGS in detecting pathogens with low loads limits its extensive application. In this study, 130 patients with suspected pulmonary infections were enrolled, from whom bronchoalveolar lavage fluid (BALF) samples were collected. The conventional tests and mNGS of cell-free DNA (cfDNA) and whole-cell DNA (wcDNA) using BALF were simultaneously performed. mNGS of cfDNA showed higher detection rate (91.5%) and total coincidence rate (73.8%) than mNGS of wcDNA (83.1% and 63.9%) and conventional methods (26.9% and 30.8%). A total of 70 microbes were detected by mNGS of cfDNA, and most of them (60) were also identified by mNGS of wcDNA. The 31.8% (21/66) of fungi, 38.6% (27/70) of viruses, and 26.7% (8/30) of intracellular microbes can be only detected by mNGS of cfDNA, much higher than those [19.7% (13/66), 14.3% (10/70), and 6.7% (2/30)] only detected by mNGS of wcDNA. After in-depth analysis on these microbes with low loads set by reads per million (RPM), we found that more RPM and fungi/viruses/intracellular microbes were detected by mNGS of cfDNA than by mNGS of wcDNA. Besides, the abilities of mNGS using both cfDNA and wcDNA to detect microbes with high loads were similar. We highlighted the advantage of mNGS using cfDNA in detecting fungi, viruses, and intracellular microbes with low loads, and suggested that mNGS of cfDNA could be considered as the first choice for diagnosing pulmonary infections.

Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of Children

Pneumonia is the leading cause of death in children; the pathogens are often difficult to diagnose. In this study, the performance of metagenomic next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from 112 children with confirmed pneumonia has been evaluated. mNGS performed a significantly higher positive detection rate (91.07%, 95% confidence interval [CI] 83.80% to 95.40%) and coincidence rate against the final diagnosis (72.32%, 95% CI 62.93% to 80.15%) than that of conventional methods (70.54%, 95% CI 61.06% to 78.58% and 56.25%, 95% CI 46.57% to 65.50%, respectively) (P < 0.01 and P < 0.05, respectively). Bacteria, viruses, and their mixed infections were common in children with pneumonia. Streptococcus pneumoniae was the most common bacterial pathogen in children with pneumonia, while Haemophilus parainfluenzae and Haemophilus influenzae seemed more likely to cause nonsevere pneumonia in children. In contrast, human cytomegalovirus (CMV) infection and the simultaneous bacterial infections could cause severe pneumonia, especially in children with underlying diseases. After adjustments of antibiotics based on mNGS and conventional methods, the conditions improved in 109 (97.32%) children. mNGS of BALF samples has shown great advantages in diagnosing the pathogenic etiology of pneumonia in children, especially when considering the limited volumes of BALF and the previous use of empirical antibiotics, contributing to the timely adjustment of antibiotic treatments, which can potentially improve the prognosis and decrease the mortality. IMPORTANCE Our study indicates high efficiency of mNGS using BALF for the detection of causative pathogens that cause pneumonia in children. mNGS can be a potential diagnostic tool to supplement conventional methods for children's pneumonia.

Atypical pneumonia caused by Chlamydia psittaci during the COVID-19 pandemic

OBJECTIVES

Here, we retrospectively described the diagnosis and treatment of 32 cases diagnosed with Chlamydia psittaci pneumonia during the COVID-19 pandemic.

METHODS

Clinical information was collected from all the patients. Reverse transcription-PCR and ELISAs were conducted for the detection of COVID-19 using nasal swabs and bronchoalveolar lavage fluid (BALF) samples. Metagenomic next-generation sequencing (mNGS) was performed for the identification of causative pathogens using BALF, peripheral blood and sputum samples. End-point PCR was performed to confirm the mNGS results.

RESULTS

All 32 patients showed atypical pneumonia and had infection-like symptoms that were similar to COVID-19. Results of reverse transcription-PCR and ELISAs ruled out COVID-19 infection. mNGS identified C. psittaci as the suspected pathogen in these patients within 48 hours, which was validated by PCR, except for three blood samples. The sequence reads that covered fragments of C. psittaci genome were detected more often in BALF than in sputum or blood samples. All patients received doxycycline-based treatment regimens and showed favorable outcomes.

CONCLUSION

This retrospective study, with the highest number of C. psittaci pneumonia enrolled cases in China so far, suggests that human psittacosis may be underdiagnosed and misdiagnosed clinically, especially in the midst of the COVID-19 pandemic.

Pneumocystis Pneumonia Mimicking Atypical Pneumonia in a Patient With Human Immunodeficiency Virus Infection

We report a case of pneumocystis pneumonia (PCP) that mimicked atypical pneumonia in a patient with human immunodeficiency virus (HIV) infection. A 44-year-old Japanese man with persistent fever and dyspnea for a month was diagnosed with atypical pneumonia because of bilateral ground-glass opacities on chest computed tomography (CT). Ground-glass opacities on chest CT diminished with three days treatment of azithromycin; however, his symptoms were persistent. Final diagnosis of HIV and PCP infection was eventually confirmed. Physicians should consider the possibility of PCP even when pulmonary manifestations resolve with azithromycin in patients with HIV infection.

Development of a Lateral Flow Strip-Based Recombinase-Aided Amplification for Active Chlamydia psittaci Infection

Chlamydia psittaci is the causative agent of psittacosis, a worldwide zoonotic disease. A rapid, specific, and sensitive diagnostic assay would be benefit for C. psittaci infection control. In this study, an assay combining recombinase-aided amplification and a lateral flow strip (RAA-LF) for the detection of active C. psittaci infection was developed. The RAA-LF assay targeted the CPSIT_RS02830 gene of C. psittaci and could be accomplished in 15 min at a single temperature (39°C). The analytical sensitivity of the assay was as low as 1 × 100 copies/μl and no cross-reaction with some other intracellular pathogens was observed. Moreover, all feces samples from mice infected with C. psittaci at day-1 post-infection were positive in the RAA-LF assay. In conclusion, the RAA-LF assay provides a convenient, rapid, specific and sensitive method for detection of active C. psittaci infection and it is also suitable for C. psittaci detection in field.

The Application Value of Metagenomic and Whole-Genome Capture Next-Generation Sequencing in the Diagnosis and Epidemiological Analysis of Psittacosis

Background

To evaluate the value of metagenomic next-generation sequencing (mNGS) for the early diagnosis of psittacosis, and to investigate its epidemiology by whole-genome capture.

Methods

Twenty-one bronchoalveolar lavage fluid (BALF) and blood samples of 16 psittacosis patients from multiple centers during August 2019 to September 2021 were analyzed retrospectively. mNGS with normal datasets (10 M 75-bp single-end reads after sequencing) and larger datasets (30 M 150-bp paired-end reads after sequencing) as well as quantitative real-time polymerase chain reaction (qPCR) were used to detect the pathogen. Also, whole-genome capture of Chlamydophila psittaci was applied to draw the phylogenetic tree.

Results

mNGS successfully detected the pathogen in all 16 cases (100%), while qPCR was positive only in 5 out of 10 cases (50%), indicating a significantly higher sensitivity of mNGS than qPCR (p &lt; 0.01). BALF-mNGS performed better than blood-mNGS (16/16 versus 3/5, p &lt; 0.05). In addition, larger datasets (the read counts have tripled, and the base number was 12-fold larger compared to clinical mNGS with a normal dataset) of mNGS showed significantly increased contents of human DNA (p &lt; 0.05) and decreased reads per million of the pathogen, suggesting no improvement. Whole-genome capture results of five samples (&gt;60% coverage and &gt;1 depth) were used to construct the phylogenetic tree.

Conclusion

Significant advantages of mNGS with normal datasets were demonstrated in early diagnosing psittacosis. It is the first study to use whole-genome capture to analyze C. psittaci epidemiological information.

Global Perspective of Legionella Infection in Community-Acquired Pneumonia: A Systematic Review and Meta-Analysis of Observational Studies

Legionnaires’ disease (LD) (Legionella) is a common cause of community-acquired pneumonia (CAP) in those requiring hospitalization. Geographical variation in the importance of Legionella species as an aetiologic agent of CAP is poorly understood. We performed a systematic review and meta-analysis of population-based observational studies that reported the proportion of Legionella infection in patients with CAP (1 January 1990 to 31 May 2020). Using five electronic databases, articles were identified, appraised and reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. The quality of the included studies was assessed using the Newcastle–Ottawa Scale. Univariate and multivariate meta-regression analyses were conducted using study design, WHO region, study quality and healthcare setting as the explanatory variables. We reviewed 2778 studies, of which 219 were included in the meta-analysis. The mean incidence of CAP was 46.7/100,000 population (95% CI: 46.6–46.8). The mean proportion of Legionella as the causative agent for CAP was 4.6% (95% CI: 4.4 to 4.7). Consequently, the mean Legionella incidence rate was 2.8/100,000 population (95% CI: 2.7–2.9). There was significant heterogeneity across all studies I² = 99.27% (p < 0.0001). After outliers were removed, there was a decrease in the heterogeneity (I² = 43.53%). Legionella contribution to CAP has a global distribution. Although the rates appear highest in high income countries in temperate regions, there are insufficient studies from low- and middle-income countries to draw conclusions about the rates in these regions. Nevertheless, this study provides an estimate of the mean incidence of Legionella infection in CAP, which could be used to estimate the regional and global burden of LD to support efforts to reduce the impact of this infection as well as to fill important knowledge gaps.

Development of Multiplex RT-PCR with Immobilized Primers for Identification of Infectious Human Pneumonia Pathogens

A prototype of a system for the detection of infectious human pneumonia pathogens based on multiplex solid-phase reverse transcription PCR (RT-PCR) was developed. Primers were designed to identify the DNA of six bacterial pneumonia pathogen strains, and the RNA of two viral pathogens of pneumonia: influenza A and SARS-CoV-2. The signal accumulation of elongated immobilized primers occurs due to the incorporation of fluorescently labeled nucleotides in the chain. The signal is detected after all the components of the mixture are removed, which significantly reduces the background signal and increases the sensitivity of the analysis. The use of a specialized detector makes it possible to read the signals of elongated primers directly through the transparent cover film of the reaction chamber. This solution is designed to prevent cross-contamination and is suitable for simultaneous testing of a large number of test samples. The proposed platform is able to detect the presence of several pathogens of pneumonia in a sample and has an open architecture that allows expansion of the range of pathogenic bacteria and viruses that can be detected.

Lefamulin in Patients with Community-Acquired Bacterial Pneumonia Caused by Atypical Respiratory Pathogens: Pooled Results from Two Phase 3 Trials

Lefamulin was the first systemic pleuromutilin antibiotic approved for intravenous and oral use in adults with community-acquired bacterial pneumonia based on two phase 3 trials (Lefamulin Evaluation Against Pneumonia [LEAP]-1 and LEAP-2). This pooled analysis evaluated lefamulin efficacy and safety in adults with community-acquired bacterial pneumonia caused by atypical pathogens (Mycoplasma pneumoniae, Legionella pneumophila, and Chlamydia pneumoniae). In LEAP-1, participants received intravenous lefamulin 150 mg every 12 h for 5–7 days or moxifloxacin 400 mg every 24 h for 7 days, with optional intravenous-to-oral switch. In LEAP-2, participants received oral lefamulin 600 mg every 12 h for 5 days or moxifloxacin 400 mg every 24 h for 7 days. Primary outcomes were early clinical response at 96 ± 24 h after first dose and investigator assessment of clinical response at test of cure (5–10 days after last dose). Atypical pathogens were identified in 25.0% (91/364) of lefamulin-treated patients and 25.2% (87/345) of moxifloxacin-treated patients; most were identified by ≥1 standard diagnostic modality (M. pneumoniae 71.2% [52/73]; L. pneumophila 96.9% [63/65]; C. pneumoniae 79.3% [46/58]); the most common standard diagnostic modality was serology. In terms of disease severity, more than 90% of patients had CURB-65 (confusion of new onset, blood urea nitrogen > 19 mg/dL, respiratory rate ≥ 30 breaths/min, blood pressure <90 mm Hg systolic or ≤60 mm Hg diastolic, and age ≥ 65 years) scores of 0–2; approximately 50% of patients had PORT (Pneumonia Outcomes Research Team) risk class of III, and the remaining patients were more likely to have PORT risk class of II or IV versus V. In patients with atypical pathogens, early clinical response (lefamulin 84.4–96.6%; moxifloxacin 90.3–96.8%) and investigator assessment of clinical response at test of cure (lefamulin 74.1–89.7%; moxifloxacin 74.2–97.1%) were high and similar between arms. Treatment-emergent adverse event rates were similar in the lefamulin (34.1% [31/91]) and moxifloxacin (32.2% [28/87]) groups. Limitations to this analysis include its post hoc nature, the small numbers of patients infected with atypical pathogens, the possibility of PCR-based diagnostic methods to identify non-etiologically relevant pathogens, and the possibility that these findings may not be generalizable to all patients. Lefamulin as short-course empiric monotherapy, including 5-day oral therapy, was well tolerated in adults with community-acquired bacterial pneumonia and demonstrated high clinical response rates against atypical pathogens.

A practical artificial intelligence system to diagnose COVID-19 using computed tomography: A multinational external validation study

Computed tomography has gained an important role in the early diagnosis of COVID-19 pneumonia. However, the ever-increasing number of patients has overwhelmed radiology departments and has caused a reduction in quality of services. Artificial intelligence (AI) systems are the remedy to the current situation. However, the lack of application in real-world conditions has limited their consideration in clinical settings. This study validated a clinical AI system, COVIDiag, to aid radiologists in accurate and rapid evaluation of COVID-19 cases. 50 COVID-19 and 50 non-COVID-19 pneumonia cases were included from each of five centers: Argentina, Turkey, Iran, Netherlands, and Italy. The Dutch database included only 50 COVID-19 cases. The performance parameters namely sensitivity, specificity, accuracy, and area under the ROC curve (AUC) were computed for each database using COVIDiag model. The most common pattern of involvement among COVID-19 cases in all databases were bilateral involvement of upper and lower lobes with ground-glass opacities. The best sensitivity of 92.0% was recorded for the Italian database. The system achieved an AUC of 0.983, 0.914, 0.910, and 0.882 for Argentina, Turkey, Iran, and Italy, respectively. The model obtained a sensitivity of 86.0% for the Dutch database. COVIDiag model could diagnose COVID-19 pneumonia in all of cohorts with AUC of 0.921 (sensitivity, specificity, and accuracy of 88.8%, 87.0%, and 88.0%, respectively). Our study confirmed the accuracy of our proposed AI model (COVIDiag) in the diagnosis of COVID-19 cases. Furthermore, the system demonstrated consistent optimal diagnostic performance on multinational databases, which is critical to determine the generalizability and objectivity of the proposed COVIDiag model. Our results are significant as they provide real-world evidence regarding the applicability of AI systems in clinical medicine.

Single Cell Cryo-Soft X-ray Tomography Shows That Each Chlamydia Trachomatis Inclusion Is a Unique Community of Bacteria

Chlamydiae are strict intracellular pathogens residing within a specialised membrane-bound compartment called the inclusion. Therefore, each infected cell can, be considered as a single entity where bacteria form a community within the inclusion. It remains unclear as to how the population of bacteria within the inclusion influences individual bacterium. The life cycle of Chlamydia involves transitioning between the invasive elementary bodies (EBs) and replicative reticulate bodies (RBs). We have used cryo-soft X-ray tomography to observe individual inclusions, an approach that combines 40 nm spatial resolution and large volume imaging (up to 16 µm). Using semi-automated segmentation pipeline, we considered each inclusion as an individual bacterial niche. Within each inclusion, we identifyed and classified different forms of the bacteria and confirmed the recent finding that RBs have a variety of volumes (small, large and abnormal). We demonstrate that the proportions of these different RB forms depend on the bacterial concentration in the inclusion. We conclude that each inclusion operates as an autonomous community that influences the characteristics of individual bacteria within the inclusion.

Clinical Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage in the Diagnosis and Management of Pneumonia: A Multicenter Prospective Observational Study

Rapid and accurate pathogen identification is necessary for appropriate treatment of pneumonia. Here, we describe the use of shotgun metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage for pathogen identification in pneumonia in a large-scale multicenter prospective study with 159 patients enrolled. We compared the results of mNGS with standard methods including culture, staining, and targeted PCR, and evaluated the clinical impact of mNGS. A positive impact was defined by a definitive diagnosis made using the mNGS results, or change of management because of the mNGS results, leading to a favorable clinical outcome. Overall, mNGS identified more organisms than standard methods (117 versus 72), detected 17 pathogens that consistently were missed in all cases by standard methods, and had an overall positive clinical impact in 40.3% (64 of 159) of cases. mNGS was especially useful in identification of fastidious and atypical organisms causing pneumonia, contributing to detection of definitive pathogens in 45 (28.3%) cases in which standard results were either negative or insufficient. mNGS also helped reassure antibiotic de-escalation in 19 (11.9%) cases. Overall, mNGS led to a change of treatment in 59 (37.1%) cases, including antibiotic de-escalation in 40 (25.2%) cases. This study showed the significant value of mNGS of bronchoalveolar lavage for improving the diagnosis of pneumonia and contributing to better patient care.

Understanding the Molecular Biology of SARS-CoV-2 and the COVID-19 Pandemic: A Review

Coronaviruses are named after the crown-like spike proteins on their surface. In the 21st century, three coronaviruses, namely severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-CoV, and Middle East respiratory syndrome related coronavirus (MERS-CoV), have emerged in the human population, presumably evolving from pathogens infecting other animals. Coronaviruses are enveloped viruses responsible for 15-30% of the atypical pneumonia cases in humans worldwide. The current coronavirus disease 2019 (COVID-19) pandemic is caused by the newest SARS virus, SARS-CoV-2, an enveloped, positive-sense, single-stranded RNA betacoronavirus of the family Coronaviridae. As of April 2021, the World Health Organization has reported more than 3 million deaths from COVID-19 and more than 140 million people have been infected with the virus, thereby making it the worst SARS pandemic of all time. Here, I review the current understanding of the molecular biology of coronaviruses and their host interactions, bringing together knowledge of the infection process to aid in the development of therapeutic drugs and/or vaccines against SARS-CoV-2. I also briefly overview the current situation of available treatments, vaccinations, and emerging strains.

Clinical Analysis of Metagenomic Next-Generation Sequencing Confirmed Chlamydia psittaci Pneumonia: A Case Series and Literature Review

Introduction

Chlamydia psittaci infection is a zoonotic infectious disease, which mainly inhaled through the lungs when exposed to the secretions of poultry that carry pathogenic bacteria. The traditional respiratory specimens or serological antibody testing is slow, and the false-negative rate is high. Metagenomic next-generation sequencing (mNGS) gives a promising rapid diagnosis tool.

Methods

We retrospectively summarized the clinical characteristics of five C. psittaci pneumonia patients diagnosed by mNGS, conducted a literature review summarizing the clinical characteristics of patients with C. psittaci pneumonia reported since 2010.

Results

Five C. psittaci pneumonia patients confirmed by mNGS aged from 36 to 66 years with three males. About 60% of patients had a history of contact with avian or poultry. All patients had a high fever over 38.5 °C, cough, hypodynamia, hypoxemia, and dyspnea on admission. Two patients had invasive ventilator support and extracorporeal membrane oxygenation support. Inflammatory index levels on admission and follow-up were all higher than normal values. Doxycycline or moxifloxacin and their combination therapy were used in patients. Four patients improved and were discharged, and one patient died due to multiple organ failures and disseminated intravascular coagulation. We summarized 19 articles including 69 C. psittaci pneumonia patients and patients in 11 publications were identified by mNGS, and most patients are treated with tetracycline and quinolone with good outcomes.

Conclusion

mNGS is a promising rapid diagnosis tool, which may increase the detection rate and shorten the diagnosis time of C. psittaci pneumonia. Further case-control studies are needed to confirm.

Atypical Pneumonia: Definition, Causes, and Imaging Features

Pneumonia is among the most common causes of death worldwide. The epidemiologic and clinical heterogeneity of pneumonia results in challenges in diagnosis and treatment. There is inconsistency in the definition of the group of microorganisms that cause "atypical pneumonia." Nevertheless, the use of this term in the medical and radiologic literature is common. Among the causes of community-acquired pneumonia, atypical bacteria are responsible for approximately 15% of cases. Zoonotic and nonzoonotic bacteria, as well as viruses, have been considered among the causes of atypical pneumonia in a patient who is immunocompetent and have been associated with major community outbreaks of respiratory infection, with relevant implications in public health policies. Considering the difficulty of isolating atypical microorganisms and the significant overlap in clinical manifestations, a targeted empirical therapy is not possible. Imaging plays an important role in the diagnosis and management of atypical pneumonia, as in many cases its findings may first suggest the possibility of an atypical infection. Clarifying and unifying the definition of atypical pneumonia among the medical community, including radiologists, are of extreme importance. The prompt diagnosis and prevention of community spread of some atypical microorganisms can have a relevant impact on local, regional, and global health policies. ^©RSNA, 2021.

Characterization and comparison of differentially expressed genes involved in Chlamydia psittaci persistent infection in vitro and in vivo

Chlamydia psittaci is an obligate intracellular zoonotic pathogen that can enter a persistence state in host cells. While the exact pathogenesis is not well understood, this persistence state may play an important role in chronic Chlamydia disease. Here, we assess the effects of chlamydial persistence state in vitro and in vivo by transmission electron microscopy (TEM) and cDNA microarray assays. First, IFN-γ-induced C. psittaci persistence in HeLa cells resulted in the upregulation of 68 genes. These genes are involved in protein translation, carbohydrate metabolism, nucleotide metabolism, lipid metabolism and general stress. However, 109 genes were downregulated following persistent C. psittaci infection, many of which are involved in the TCA cycle, expression regulation and transcription, protein secretion, proteolysis and transport, membrane protein, presumed virulence factor, cell division and late expression. To further study differential gene expression of C. psittaci persistence in vivo, we established an experimentally tractable mouse model of C. psittaci persistence. The C. psittaci-infected mice were gavaged with either water or amoxicillin (amox), and the results indicated that the 20 mg/kg amox-exposed C. psittaci were viable but not infectious. Differentially expressed genes (DEGs) screened by cDNA microarray were detected, and interestingly, the results showed upregulation of three genes (euo, ahpC, prmC) and downregulation of five genes (pbp3, sucB_1, oppA_4, pmpH, ligA) in 20 mg/kg amox-exposed C. psittaci, which suggests that antibiotic treatment in vivo can induce chlamydial persistence state and lead to differential gene expression. However, the discrepancy on inducers between the two models requires more research to supplement. The results may help researchers better understand survival advantages during persistent infection and mechanisms influencing C. psittaci pathogenesis or evasion of the adaptive immune response.

Hepcidin and Ferritin Predict Microbial Etiology in Community-Acquired Pneumonia

Background

Iron is crucial for survival and growth of microbes. Consequently, limiting iron availability is a human antimicrobial defense mechanism. We explored iron and iron-related proteins as potential biomarkers in community-acquired pneumonia and hypothesized that infection-induced changes in these potential biomarkers differ between groups of pathogens and could predict microbial etiology.

Methods

Blood samples from a prospective cohort of 267 patients with community-acquired pneumonia were analyzed for hepcidin, ferritin, iron, transferrin, and soluble transferrin receptor at admission, clinical stabilization, and a 6-week follow-up. A total of 111 patients with an established microbiological diagnosis confined to 1 microbial group (atypical bacterial, typical bacterial, or viral) were included in predictive analyses.

Results

High admission levels of ferritin predicted atypical bacterial versus typical bacterial etiology (odds ratio [OR], 2.26; 95% confidence interval [CI], 1.18–4.32; P = .014). Furthermore, hepcidin and ferritin predicted atypical bacterial versus viral etiology (hepcidin: OR = 3.12, 95% CI = 1.34–7.28, P = .008; ferritin: OR = 2.38, 95% CI = 1.28–4.45, P = .006). The findings were independent of C-reactive protein and procalcitonin.

Conclusions

Hepcidin and ferritin are potential biomarkers of microbial etiology in community-acquired pneumonia.

Severe Sepsis With Septic Shock as a Consequence of a Severe Community-Acquired Pneumonia Resulting From a Combined Legionella pneumophila and Streptococcus pneumoniae Infection

Community-acquired pneumonia (CAP) is a frequent cause of intensive care unit (ICU) admission in adults and the sixth leading cause of death worldwide. Although co-infections have been previously reported, the co-existence of Streptococcus pneumoniae and Legionella pneumophila is exceedingly rare. Despite the fact that Streptococcus pneumoniae is the most common etiology in the majority of cases, atypical organisms such as Legionella pneumophila should be considered as etiologic agents among all CAP cases that require hospitalization. Unlike Legionella, extra-pulmonary findings are uncommon in patients with Streptococcus pneumoniae pneumonia. In this report, the authors describe an unusual case of septic shock resulting from a combined Legionella pneumophila and Streptococcus pneumoniae infection associated with rhabdomyolysis, acute kidney injury, acute hypoxemic respiratory failure, pancreatitis, and acute liver injury.

Application of deep learning technique to manage COVID-19 in routine clinical practice using CT images: Results of 10 convolutional neural networks

Fast diagnostic methods can control and prevent the spread of pandemic diseases like coronavirus disease 2019 (COVID-19) and assist physicians to better manage patients in high workload conditions. Although a laboratory test is the current routine diagnostic tool, it is time-consuming, imposing a high cost and requiring a well-equipped laboratory for analysis. Computed tomography (CT) has thus far become a fast method to diagnose patients with COVID-19. However, the performance of radiologists in diagnosis of COVID-19 was moderate. Accordingly, additional investigations are needed to improve the performance in diagnosing COVID-19. In this study is suggested a rapid and valid method for COVID-19 diagnosis using an artificial intelligence technique based. 1020 CT slices from 108 patients with laboratory proven COVID-19 (the COVID-19 group) and 86 patients with other atypical and viral pneumonia diseases (the non-COVID-19 group) were included. Ten well-known convolutional neural networks were used to distinguish infection of COVID-19 from non-COVID-19 groups: AlexNet, VGG-16, VGG-19, SqueezeNet, GoogleNet, MobileNet-V2, ResNet-18, ResNet-50, ResNet-101, and Xception. Among all networks, the best performance was achieved by ResNet-101 and Xception. ResNet-101 could distinguish COVID-19 from non-COVID-19 cases with an AUC of 0.994 (sensitivity, 100%; specificity, 99.02%; accuracy, 99.51%). Xception achieved an AUC of 0.994 (sensitivity, 98.04%; specificity, 100%; accuracy, 99.02%). However, the performance of the radiologist was moderate with an AUC of 0.873 (sensitivity, 89.21%; specificity, 83.33%; accuracy, 86.27%). ResNet-101 can be considered as a high sensitivity model to characterize and diagnose COVID-19 infections, and can be used as an adjuvant tool in radiology departments.

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Ten CNNs were used to distinguish infection of COVID-19 from non-COVID-19 groups.

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ResNet-101 and Xception represented the best performance with an AUC of 0.994.

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Deep learning technique can be used as an adjuvant tool in diagnosing COVID-19.

Immunochromatography for the diagnosis of Mycoplasma pneumoniae infection: A systematic review and meta-analysis

The aim of this study was to evaluate the diagnostic performance of immunochromatographic tests (ICTs) for the detection of Mycoplasma pneumoniae. Medline/Pubmed, Embase, the Cochrane Library, and ISI Web of Science were searched through June 12, 2019 for relevant studies that used ICTs for the detection of M. pneumoniae infection with polymerase chain reaction (PCR) or microbial culturing as reference standards. Pooled diagnostic accuracy with 95% confidence interval (CI) was calculated using a bivariate random effects model. We also constructed summary receiver operating characteristic curves and calculated the area under the curve (AUC). Statistical heterogeneity was evaluated by χ² test or Cochrane’s Q test. Thirteen studies including 2,235 samples were included in the meta-analysis. The pooled sensitivity and specificity for diagnosing M. pneumoniae infection were 0.70 (95% CI: 0.59–0.79) and 0.92 (95% CI: 0.87–0.95), respectively. The positive likelihood ratio (LR) was 8.94 (95% CI: 4.90–14.80), negative LR 0.33 (95% CI: 0.22–0.46), diagnostic odds ratio 29.20 (95% CI: 10.70–64.20), and AUC 0.904. In subgroup analysis, ICTs demonstrated similar pooled sensitivities and specificities in populations of children only and mixed populations (children + adults). Specimens obtained from oropharyngeal swabs exhibited a higher sensitivity and specificity than those of nasopharyngeal swab. Moreover, pooled estimates of sensitivity and accuracy for studies using PCR as a reference standard were higher than those using culture. The pooled sensitivity and specificity of Ribotest Mycoplasma^®, the commercial kit most commonly used in the included studies, were 0.66 and 0.89, respectively. Overall, ICT is a rapid user-friendly method for diagnosing M. pneumoniae infection with moderate sensitivity, high specificity, and high accuracy. This suggests that ICT may be useful in the diagnostic workup of M. pneumoniae infection; however, additional studies are needed for evaluating the potential impact of ICT in clinical practice.

Development of loop-mediated isothermal amplification coupled with nanoparticle-based lateral flow biosensor assay for Mycoplasma pneumoniae detection

Mycoplasma pneumoniae (MP) is one of the most common pathogens causing respiratory tract infection, especially for community-acquired pneumonia (CAP) in school-age children. There was considerable amount of studies on loop-mediated isothermal amplification (LAMP) assay for MP detection. However, the result interpretation of these developed LAMP assays was sophisticated and subjective. Therefore, we developed and evaluated a LAMP coupled with nanoparticle-based lateral flow biosensor (LFB) assay (LAMP-LFB) for simple, reliable, and objective identification of MP (MP-LAMP-LFB). Six primers specific to P1 gene of MP were designed, and the preferred temperature for this assay was confirmed to be 65 °C. The amplification products could be visually interpreted by LFB within 2 min. The MP-LAMP-LFB assay specifically identified DNA templates of MP, and no cross-reactivity with other pathogens was obtained. The limit of the detection for this assay was 600 fg of DNA templates in pure cultures, which was in complete accordance with colorimetric indicator detection and agarose gel electrophoresis analysis. This assay was applied to 209 oropharyngeal swab specimens collected from children with acute respiratory tract infection for clinical evaluation, and compared to real-time PCR detection. Using the LAMP-LFB and real-time PCR assay, the positive rates of MP were 47.8% and 31.6%, respectively. Results suggested that the LAMP-LFB assay displayed high sensitivity compared to real-time PCR method. In summary, LAMP-LFB assay established here was a simple, objective, and sensitive assay for MP detection, which can be widely applied in clinical settings, especially in rural areas.

Bactericidal efficacies of food additive grade calcium hydroxide toward Legionella pneumophila

Food additive grade calcium hydroxide (FdCa(OH)₂) in the solution of 0.17% was evaluated for its bactericidal efficacies toward Legionella pneumophila with or without sodium hypochlorite (NaOCl) at a concentration of 200 ppm total residual chlorine, at room temperature (RT) (25°C ± 2°C) and 42°C, either with or without 5% fetal bovine serum (FBS). Besides, FdCa(OH)₂ in different concentration solutions were prepared in field water samples (hot spring and bath tab water) and evaluated for their bactericidal efficacies at 42°C. FdCa(OH)₂ (0.17%) inactivated the L. pneumophila to the undetectable level (<2.6 log CFU/ml) within 5 min and 3 min, respectively, at RT and 42°C, with 5% FBS. At RT and 42°C, NaOCl inactivated L. pneumophila to the undetectable level within 5 min, without 5% FBS, but with 5% FBS, it could only inactivate this bacterium effectively (≥3 log reductions). Conversely, at RT and 42°C, the mixture of 0.17% FdCa(OH)₂ and 200 ppm NaOCl could inactivate L. pneumophila to the undetectable level, respectively, within 3 min and 1 min, even with 5% FBS, and it was elucidated that FdCa(OH)₂ has a synergistic bactericidal effect together with NaOCl. FdCa(OH)₂ 0.05% solution prepared in hot spring water could inactivate L. pneumophila to the undetectable within 3 min at 42°C. So, FdCa(OH)₂ alone could show nice bactericidal efficacy at 42°C, even with 5% FBS, as well as in field water samples.

Atypical and Typical Bacteria in Children with Community Acquired Pneumonia

This study seeks to determine the pathogens in respiratory specimens and blood serum obtained from children who present with community acquired pneumonia (CAP) diagnosed on the basis of clinical and radiological evidence. The study group consisted of 46 hospitalized children aged 1-11 years. The material for research consisted of pharyngeal swabs and samples of blood serum. One hundred and thirty eight pharyngeal swabs were examined for the presence of C. pneumoniae antigen, C. pneumoniae DNA, and for typical pathogens. C. pneumoniae DNA was detected in pharyngeal swabs with nested PCR. Classical microbiological culture was used for detection of typical bacteria. ELISA test were used for detection anti-C. pneumoniae and anti-M. pneumoniae antibodies in the serum. C. pneumoniae DNA was identified in 10.9% of children. Positive culture for typical pathogens was observed in 8.7% of children. Specific anti-C. pneumoniae IgM antibodies were found in 8.7% of children, and IgG and IgA antibodies in 1 child each. Specific anti-M. pneumoniae IgG antibodies were found in 13.1% of children and IgM antibodies in 1 child. We conclude that the underlying bacterial etiology of CAP is rather rarely conclusively confirmed in children. Nonetheless, determining the etiology of CAP is essential for the choice of treatment to optimize the use and effectiveness of antimicrobials and to avoid adverse effect. Due to considerable variations in the power of detection of the type of atypical bacteria causing CAP, the search for the optimum diagnostic methods continues.

Diagnosis of mycoplasma pneumoniae by loop-mediated isothermal amplification: systematic review and meta-analysis

Background

A novel method, termed loop-mediated isothermal amplification (LAMP), was developed by Notomi et al. (2000). Individually published results have been reported that this technology has been successfully applied to the detection of a variety of pathogens. However, the overall diagnostic accuracy of LAMP for Mycoplasma pneumoniae (MP) remains unclear. A meta-analysis was therefore performed to review the accuracy of LAMP for Mycoplasma pneumoniae.

Methods

Cochrane Library and PubMed were systematically searched and checked for studies using LAMP for detecting mycoplasma pneumoniae. We used PCR as a reference standard to evaluate the quality of the studies eligible for inclusion in the meta-analysis. Then, the data from the studies were extracted by two independent assessors. Meta-DiSc 1.4 software was utilized to test the heterogeneity of sensitivity (SEN), specificity (SP), positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnosis odds ratio (DOR). The pooled analysis results were plotted, and the summary receiver operating characteristic (SROC) curve was plotted by calculating the area under the curve (AUC). Generated pooled summary estimates (95% CIs) were calculated for the overall accuracy, and a bivariate meta-regression model was used for the meta-analysis.

Results

Seven studies with nine fourfold tables were included in this meta-analysis. The pooled SEN and SPE for diagnosing Mycoplasma pneumoniae were 0.90 (95% CI: 0.87–0.93) and 0.98 (95% CI: 0.96–0.99), respectively. The PLR was 31.25 (95% CI: 14.83–65.87), NLR 0.10 (95% CI: 0.05–0.22), DOR 399.32 (95% CI: 172.01–927.00), and AUC 0.9892.

Conclusions

In conclusion, compared with PCR, LAMP is a valuable alternative method for Mycoplasma pneumoniae diagnosis in clinic with high sensitivity and specificity. However, more evidence is required to confirm that LAMP can fully replace other methods in the clinical diagnosis of MP.

The use of multiplex PCR for the detection of atypical pathogens in Egyptian children with CAP: a high rate of Bordetella pertussis in early infancy

Background

Atypical pathogen infections played an important role in community-acquired pneumonia (CAP) in children. Pathogen-specific clinical symptoms are often lacking, and it is difficult to detect atypical pathogens by culture methods. The use of multiplex polymerase chain reaction (PCR) methods enables testing for many pathogens simultaneously in a single analysis.

Aim

To determine the role of atypical pathogens in children hospitalized with CAP.

Patients and methods

This cross-sectional study was conducted throughout a 2-year period from August 2015 to September 2017. It included 400 Egyptian children hospitalized with clinical diagnosis of CAP at a tertiary hospital in Cairo, Egypt. Sputum samples were collected from lower respiratory tract of all enrolled patients by mucus trap catheter for identification of Bordetella pertussis, Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella pneumophilia by using multiplex real-time PCR.

Results

Among the 400 CAP patients enrolled in this study, atypical pathogens were detected in 12/400 (3%) patients. Bordetella pertussis was detected in 2% of cases, and it was responsible for CAP in 8/104 (7.69%) infants in the age stratum ≤ 4 months; compared with pertussis-negative cases, pertussis-positive cases were younger and incompletely vaccinated (P values were 0.001 and 0.007, respectively). Mycoplasma pneumoniae was detected in 1% of cases, all were among the age stratum > 4 months ≤ 59 months in 4/272 (1.47%) children.

Conclusion

In early infancy, Bordetella pertussis causes a significant proportion of hospitalized CAP cases; all were ≤ 4 months old and incompletely vaccinated. This finding could suggest the role of maternal immunization in developing countries.

Acute Bronchitis Caused by Bordetella Pertussis Possibly Co-Infected with Mycoplasma Pneumoniae

BACKGROUND Mycoplasma pneumoniae and Bordetella pertussis are among the causative pathogens of human acute bronchitis, which usually has mild symptoms. However, if there is a co-infection, the symptoms often can be prolonged and occasionally can lead to severe respiratory complications. CASE REPORT A 49-year-old Japanese female, who had not been vaccinated for B. pertussis, developed a persistent productive cough which became vigorous, and occasionally caused difficulty breathing and vomiting. Since serum IgM to M. pneumoniae was positive and IgG to B. pertussis was significantly elevated, and there were no findings of pneumonia on a chest x-ray film, we made a diagnosis of acute bronchitis caused by B. pertussis with possible co-infection with M. pneumoniae. The use of garenoxacin, a quinolone derivative, failed to work; however, a macrolide antibiotic clarithromycin dramatically improved her symptoms shortly after its administration. CONCLUSIONS In this patient case, because of the lymphocyte-stimulatory nature of M. pneumoniae and B. pertussis, an increased immunological response was likely to be involved in the pathogenesis of the symptoms. The immunosuppressive effect of clarithromycin was considered to repress the increased lymphocyte activity, facilitating the remission of the disease.