Diagnostic performance of multiplex PCR on pulmonary samples versus nasopharyngeal aspirates in community-acquired severe lower respiratory tract infections

Update of guidelines for management of Community Acquired pneumonia in adults by the French Infectious Disease Society (SPILF) and the French-Speaking Society of Respiratory Diseases (SPLF): Endorsed by the French intensive care society (SRLF), the French microbiology society (SFM), the French radiology society (SFR) and the French emergency society (SFMU)

Community-Acquired Pneumonia (CAP) of Presumed Bacterial Origin: Updated Management Guidelines Community-acquired pneumonia (CAP) of presumed bacterial origin is a common condition with varying severity, requiring either outpatient, hospital, or even critical care management. The French Infectious Diseases Society (SPILF) and the French Language Pulmonology Society (SPLF), in collaboration with the French Societies of Microbiology (SFM), Emergency Medicine (SFMU), Radiology (SFR), and Intensive Care Medicine (SRLF), along with representatives of general practice, have coordinated an update of the previous management guidelines, which dated back to 2010. From a therapeutic perspective, the updated recommendations define the choice of initial empiric antibiotic therapy, indications for combination therapy, the use of anti-Pseudomonas beta-lactams, antibiotic treatment duration, and the indications and modalities for prescribing systemic corticosteroids. On a biological level, indications for biomarkers and microbiological investigations have been refined. Regarding imaging, the role of different modalities in the diagnosis and follow-up of CAP has been reassessed, including chest X-ray, pleuropulmonary ultrasound, and thoracic CT scan.

Impact of the COVID-19 pandemic on severe non-SARS-CoV-2 community-acquired pneumonia in Reunion Island: a multicenter retrospective observational study, 2016-2021

The Coronavirus 2019 (COVID-19) pandemic has had a considerable impact on the incidence of severe community-acquired pneumonia (CAP) worldwide. The aim of this study was to assess the early impact of the COVID-19 pandemic in the Reunion Island. This multicenter retrospective observational study was conducted from 2016 to 2021 in the hospitals of Reunion Island. The incidence of severe non-SARS-CoV-2 CAP, microorganisms, characteristics and outcomes of patients hospitalized in intensive care unit were compared between the pre-COVID-19 period (January 1, 2016 to February 29, 2020) and the early COVID-19 period (March 1, 2020 to October 31, 2021). Over the study period, 389 patients developed severe non-SARS-CoV-2 CAP. The incidence of severe non-SARS-CoV-2 CAP significantly decreased between the two periods (9.16 vs. 4.13 cases per 100,000 person-years). The influenza virus was isolated in 43.5% patients with severe non-SARS-CoV-2 CAP in the pre-COVID-19 period and in none of the 60 patients in the early COVID-19 period (P < 0.0001). The only virus that did not decrease was rhinovirus. Streptococcus pneumoniae was the most frequently isolated bacterial microorganism, with no significant difference between the two periods. In Reunion Island, the COVID-19 pandemic led to a significant decrease in the incidence of influenza, which likely explains the observed decrease in the incidence of severe non-SARS-CoV-2 CAP. The pandemic had no impact on the incidence of other viral and bacterial severe non-SARS-CoV-2 CAP. Monitoring influenza incidence is crucial now that COVID-19 control measures have been removed.

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.

Comparison of sputum specimens and nasopharyngeal swab specimens for diagnosis of acute human metapneumovirus-related lower respiratory tract infections in adults

BACKGROUND

To detect human metapneumovirus, tests besides reverse transcription-polymerase chain reaction (RT-PCR) on nasopharyngeal swab specimens are less accessible. Immunochromatography assays are rapid and simple without the need of any special equipment but sometimes are insufficiently sensitive. This study describes the usefulness of immunochromatography assays to detect human metapneumovirus in adult patients with human metapneumovirus-related acute lower respiratory tract infection using sputum specimens.

METHODS

This prospective single-center study enrolled adults and adolescents aged ≥16 years with signs and symptoms of an acute respiratory illness who were diagnosed with acute lower respiratory tract infection. The presence of human metapneumovirus infection was confirmed by seroconversion. Immunochromatography assays and real-time RT-PCR were performed to compare the efficacy of nasopharyngeal swab specimens and sputum specimens. Comparative results were obtained via McNemar's test.

RESULTS

Overall, 337 patients were recruited in this study; 63 (18.7%) patients were seroconverted. Sputum specimens showed significantly higher positivity rates than nasopharyngeal swab specimens with both immunochromatography assays (p = 0.0008) and real-time RT-PCR (p = 0.014). Among 29 patients with pneumonia who had concordant positive real-time RT-PCR results for both nasopharyngeal swab specimens and sputum specimens, 21 (72.4%) had a higher viral load in the sputum specimens.

CONCLUSIONS

Sputum specimens are more useful in detecting human metapneumovirus than nasopharyngeal swab specimens in adult patients with acute lower respiratory tract infection.

Legionnaires' Disease: Update on Diagnosis and Treatment

Legionellosis is the infection caused by bacteria of the genus Legionella, including a non-pneumonic influenza-like syndrome, and Legionnaires’ disease is a more serious illness characterized by pneumonia. Legionellosis is becoming increasingly important as a public health problem throughout the world; although it is an underreported disease, studies have consistently documented a high incidence. In addition, health costs associated with the disease are high. Diagnosis of Legionnaires’ disease is based mainly on the detection of Legionella pneumophila serogroup 1 antigen in urine. However, there have been advances in detection tests for patients with legionellosis. New methodologies show greater sensitivity and specificity, detect more species and serogroups of Legionella spp., and have the potential for use in epidemiological studies. Testing for Legionella spp. is recommended at hospital admission for severe community-acquired pneumonia, and antibiotics directed against Legionella spp. should be included early as empirical therapy. Inadequate or delayed antibiotic treatment in Legionella pneumonia has been associated with a worse prognosis. Either a fluoroquinolone (levofloxacin or moxifloxacin) or a macrolide (azithromycin preferred) is the recommended first-line therapy for Legionnaires’ disease; however, little information is available regarding adverse events or complications, or about the duration of antibiotic therapy and its association with clinical outcomes. Most published studies evaluating antibiotic treatment for Legionnaires’ disease are observational and consequently susceptible to bias and confounding. Well-designed studies are needed to assess the usefulness of diagnostic tests regarding clinical outcomes, as well as randomized trials comparing fluoroquinolones and macrolides or combination therapy that evaluate outcomes and adverse events.

Severe Infections Due to Respiratory Viruses

Severe viral infections may result in severe illnesses capable of causing acute respiratory failure that could progress rapidly to acute respiratory distress syndrome (ARDS), related to worse outcomes, especially in individuals with a higher risk of infection, including the elderly and those with comorbidities such as asthma, diabetes mellitus and chronic respiratory or cardiovascular disease. In addition, in cases of severe viral pneumonia, co-infection with bacteria such as Streptococcus pneumoniae and Staphylococcus aureus is related to worse outcomes. Respiratory viruses like influenza, rhinovirus, parainfluenza, adenovirus, metapneumovirus, respiratory syncytial virus, and coronavirus have increasingly been detected. This trend has become more prevalent, especially in critically ill patients, due to the availability and implementation of molecular assays in clinical practice. Respiratory viruses have been diagnosed as a frequent cause of severe pneumonia, including cases of community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia. In this review, we will discuss the epidemiology, diagnosis, clinical characteristics, management, and prognosis of patients with severe infections due to respiratory viruses, with a focus on influenza viruses, non-influenza viruses, and coronaviruses.

Acute Respiratory Distress Syndrome Caused by Human Adenovirus in Adults: A Prospective Observational Study in Guangdong, China

Background

Viral causes of acute respiratory distress syndrome (ARDS) are mostly limited to influenza. However, adenovirus has been emerging as a cause of ARDS with a high mortality rate and described in adults are rare.

Methods

We conducted a prospective, single-center observational study of viral pneumonia with ARDS and confirmed adenovirus-associated ARDS in adults at our quaternary referral institution between March 2019 and June 2020. We prospectively analyzed clinical characteristics, laboratory test results, radiological characteristics, viral load from nasopharyngeal swabs and endotracheal aspirates, treatments, and outcomes for the study participants.

Results

The study enrolled 143 ARDS patients, including 47 patients with viral pneumonia-related ARDS, among which there were 14 adenovirus-associated ARDS patients, which accounted for 29.79% of the viral pneumonia-related ARDS cases. Among the adenovirus-associated ARDS patients, 78.57% were men with a mean age of 54.93 ± 19.04 years, younger than that of the non-adenovirus associated ARDS patients. Adenovirus-associated ARDS patients had no specific clinical characteristics, but they presented with decrease in the number of CD3+CD4+ T cells and higher serum creatinine during the early stage. The viral load and the positivity rate in the lower respiratory tract were higher than that of the upper respiratory tract in the patients with adenovirus-associated ARDS. All patients required invasive mechanical ventilation treatment. The average time from shortness of breath to the application of invasive ventilation was 24 h. Ten patients (71.43%) complicated by acute kidney injury, while 13 patients (71.43%) in the non-adenovirus associated ARDS group (P = 0.045). Additionally, 85.71% of the 14 adenovirus-associated ARDS patients survived. No significant differences were detected between the two groups regarding duration of ventilation, length of ICU stay and mortality.

Conclusion

Adenovirus infection is an important cause of virus-related ARDS. The positivity rate of adenovirus infection in lower respiratory tract secretions was higher than that in upper respiratory tract secretions in these patients. Age, lower CD3+CD4+ T cells, and high serum creatinine may be were associated with adenovirus induce ARDS in adults required mechanical ventilation. Early identification and intervention to prevent disease progression are essential for reducing the mortality rate in these patients.

MiR-181b serves as diagnosis and prognosis biomarker in severe community-acquired pneumonia

Severe community-acquired pneumonia (SCAP) is a common critical disease in the intensive care unit (ICU). This study aims to evaluate the clinical significance of miR-181b in SCAP, which has been revealed to be dysregulated in acute respiratory distress syndrome events due to SCAP. There were 50 SCAP patients and 26 healthy volunteers were recruited in this study. The expression of miR-181b was detected by RT-qPCR and the difference between SCAP and healthy controls was evaluated. The diagnosis and prognosis value of miR-181b was assessed by the receiver operating characteristics (ROC), Kaplan-Meier, and Cox regression analysis. miR-181b was significantly downregulated in SCAP compared with healthy controls. The downregulation of miR-181b showed a significant association with the white blood cell count, absolute neutrophils, and the C-reactive protein of patients. The downregulation of miR-181b could distinguish SCAP patients from healthy controls and predicate the poor prognosis of SCAP patients. Downregulated miR-181b serves as a diagnosis and prognosis biomarker for SCAP, which may be useful biological information for the early detection and risk estimation of SCAP.

Real-world antibiotic use in treating acute exacerbations of chronic obstructive pulmonary disease (AECOPD) in China: Evidence from the ACURE study

Background: The evidence for real-world antibiotic use in treating acute exacerbations of chronic obstructive pulmonary disease (AECOPD) is insufficient. This study aimed to investigate real-world antibiotic use in the management of AECOPD in China. Methods: All hospitalized AECOPD patients from the acute exacerbation of chronic obstructive pulmonary disease inpatient registry (ACURE) study conducted at 163 sites between January 2018 and December 2019 were screened according to the eligible criteria. The eligible study population was divided into secondary and tertiary hospital groups. Patients' baseline characteristics, antibiotic use, and bacterial pathogen characteristics were retrieved and analyzed using SPSS 23.0. Results: A total of 1663 patients were included in the study, including 194 patients from secondary hospitals and 1469 patients from tertiary hospitals. Among the 1663 AECOPD patients enrolled, 1434 (86.2%) received antibiotic treatment, comprising approximately 85.6% and 86.3% of patients in the secondary and tertiary hospital groups, respectively. The median antibiotic therapy duration was 9.0 (interquartile range [IQR]: 7.0 - 11.0)°days. Regarding the routes of antibiotic use, 1400 (97.6%) patients received intravenous antibiotics, 18 (1.3%) patients received oral antibiotics, 15 (1.0%) patients received both intravenous and oral antibiotics, and one (0.1%) patient received both oral and nebulized antibiotic treatment. In addition, cephalosporin, penicillin, and quinolone were the most commonly prescribed antibiotics (43.6%, 37.0%, and 34.2%, respectively). In total, 990 (56.5%) patients underwent pathogen examinations; the proportion of patients receiving pathogen examinations in the second hospital group was significantly lower than that in the tertiary hospital group (46.4% vs 61.3%, p < 0.001). Conclusion: This study demonstrates that an antibiotic overuse may exist in the treatment of AECOPD in China. Measures should be taken to prevent the overuse of antibiotics and potential antimicrobial resistance (AMR) in Chinese AECOPD patients.

Co-infection in patients with hypoxemic pneumonia due to COVID-19 in Reunion Island

This study aimed to evaluate the incidence of co-infection with different types of pathogens in patients with hypoxemic pneumonia due to coronavirus disease 2019 (COVID-19) in Reunion Island.This observational study using a prospectively collected database of hypoxemic pneumonia due to COVID-19 cases was conducted at Félix Guyon University Hospital in Reunion Island, France.Between 18 March 2020 and 15 April 2020, 156 patients were admitted to our hospital for COVID-19. A total of 36 patients had hypoxemic pneumonia (23.1%) due to COVID-19. Thirty of these cases (83.3%) were imported by travelers returning mainly from metropolitan France and Spain. Patients were screened for co-infection with other pathogens at admission: 31 (86.1%) by multiplex polymerase chain reaction (PCR) and 16 (44.4%) by cytobacteriological examination of sputum culture. Five patients (13.9%) were found to have co-infection: 1 with influenza virus A H1N1 (pdm09) associated with Branhamella catarrhalis, 1 with Streptococcus pneumoniae associated with Haemophilus influenzae, 1 with Human Coronavirus 229E, 1 with Rhinovirus, and 1 with methicillin-susceptible Staphylococcus aureus. Patients with co-infection had higher D-dimer levels than those without co-infection (1.36 [1.34-2.36] μg/mL vs 0.63 [0.51-1.12] μg/mL, P = .05).The incidence of co-infection in our cohort was higher than expected (13.9%). Three co-infections (with influenza virus A(H1N1) pdm09, Streptococcus pneumoniae, and Staphylococcus aureus) required specific treatment. Patients with hypoxemic pneumonia due to COVID-19 should be screened for co-infection using respiratory cultures or multiplex PCR. Whilst our study has a number of limitations, the results from our study suggest that in the absence of screening, patients should be commenced on treatment for co-infection in the presence of an elevated D-dimer.

Presenting characteristics, comorbidities, and outcomes of patients coinfected with COVID-19 and Mycoplasma pneumoniae in the USA

Coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome‐coronavirus 2 (SARS‐CoV‐2) is spreading at a rapid pace, and the World Health Organization declared it as pandemic on 11 March 2020. Mycoplasma pneumoniae is an "atypical" bacterial pathogen commonly known to cause respiratory illness in humans. The coinfection from SARS‐CoV‐2 and mycoplasma pneumonia is rarely reported in the literature to the best of our knowledge. We present a study in which 6 of 350 patients confirmed with COVID‐19 were also diagnosed with M. pneumoniae infection. In this study, we described the clinical characteristics of patients with coinfection. Common symptoms at the onset of illness included fever (six [100%] patients); five (83.3%) patients had a cough, shortness of breath, and fatigue. The other symptoms were myalgia (66.6%), gastrointestinal symptoms (33.3%‐50%), and altered mental status (16.7%). The laboratory parameters include lymphopenia, elevated erythrocyte sedimentation rate, C‐reactive protein, lactate dehydrogenase, interleukin‐6, serum ferritin, and D‐dimer in all six (100%) patients. The chest X‐ray at presentation showed bilateral infiltrates in all the patients (100%). We also described electrocardiogram findings, complications, and treatment during hospitalization in detail. One patient died during the hospital course.

The COVID‐19 pneumonia is a serious condition and can be associated with the common respiratory pathogens. Co‐infections with COVID‐19 can result in protracted respiratory symptoms, prolonged ICU stay, morbidity, and mortality if not detected and treated appropriately. The treatment of Co‐infection if y available might facilitate early recovery.

Method Comparison of the ImmuView L. pneumophila and L. longbeachae Urinary Antigen Test with the BinaxNOW Legionella Urinary Antigen Card for Detection of Legionella pneumophila Serogroup 1 Antigen in Urine

We compared the clinical performance of the ImmuView L. pneumophila and L. longbeachae urinary antigen test (SSI Diagnostica A/S, Hillerød, Denmark) to that of the BinaxNOW Legionella urinary antigen card (Binax; Abbott, Lake Buff, IL) using urine specimens from patients suspected of having pneumonia. In total, 100 frozen urine samples (derived from 50 Legionella cases and 50 noncases) were analyzed with both tests, as were 200 nonfrozen prospectively collected samples. For urine samples from five Legionella cases and two non-Legionella cases, analytical sensitivity (limit of detection) and repeatability were examined. The urine samples from the five Legionella cases were diluted with urine samples that tested Legionella urinary antigen negative with both tests. The analyses of the 100 frozen samples resulted in a sensitivity and specificity of both ImmuView and the BinaxNOW of 96.0% (48/50) and 100% (50/50), respectively. Of the 200 nonfrozen samples, there were three samples that showed a positive result for L. pneumophila by both tests. The analyses of reproducibility showed that for the 34 (diluted) samples that were tested at two consecutive times, 33 samples showed a consistent result for both the ImmuView and the BinaxNOW tests (Cohen's kappa values of 0.916 and 0.928). In addition, the ImmuView test may have detected two L. longbeachae-positive urine samples, although other diagnostic tests could not confirm this. Both ImmuView and BinaxNOW showed high sensitivity and specificity for the detection of L. pneumophila serogroup 1 antigen in urine samples from clinical patients with a suspected lower respiratory tract infection.

Outcomes of severe human metapneumovirus-associated community-acquired pneumonia in adults

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We compared severe human metapneumovirus-associated community-acquired pneumonia (CAP) and influenza virus-associated CAP.

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Human metapneumovirus accounted for 3.2% of severe CAP cases.

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Influenza virus accounted for 7.0% of severe CAP cases.

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Coinfection was more common in severe influenza virus-associated CAP patients.

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The two groups had similar overall mortality rates.

Background

The outcomes of severe human metapneumovirus (HMPV)-associated pneumonia have not been adequately evaluated.

Objectives

We aimed to investigate the incidence and outcomes of severe HMPV-associated CAP and to compare them with those of severe IFV associated CAP.

Study design

From March 2010 to August 2017, all consecutive adult patients with severe HMPV-associated CAP and severe influenza virus (IFV)-associated CAP who required intensive care unit admission were prospectively identified and followed in a 2,700-bed tertiary care hospital. The characteristics and outcomes of severe HMPV-associated CAP patients were compared with those of severe IFV-associated CAP patients.

Results

HMPV and IFV were identified in 3.2% (50) and 7.0% (109) of the 1559 patients with severe CAP, respectively. The mortality rates were not significantly different between the HMPV and IFV groups (30-day mortality: 24.0% vs. 32.1%, p = 0.30; 60-day mortality: 32.0% vs. 38.5%, p = 0.43). Oral ribavirin therapy was not associated with improved outcome (60-day mortality: ribavirin therapy group 35.0% [7/20] vs. no ribavirin therapy group 30.0% [9/30], p = 0.71). Subgroup analyses showed no significant differences in mortality among non-immunocompromised (60-day mortality: HMPV 25.6% vs. IFV 31.1%, p = 0.55) and immunocompromised patients (60-day mortality; HMPV 54.5% vs. 54.3%, p = 0.99). The length of ICU and hospital stay did not differ between groups.

Conclusions

The incidence of HMPV infection was approximately half that of IFV infection in a cohort of patients with severe CAP. The mortality rate of severe HMPV-associated CAP was similar to that of severe IFV associated CAP.

Respiratory Pathogens in Infants Diagnosed with Acute Lower Respiratory Tract Infection in a Tertiary Care Hospital of Western India Using Multiplex Real Time PCR

OBJECTIVE

To determine the frequency of respiratory pathogens in infants diagnosed with acute lower respiratory tract infections.

METHODS

A prospective cross-sectional observational study was conducted in infants hospitalized with a diagnosis of acute lower respiratory tract infection (ALRTI), in a tertiary care hospital in a metropolitan city of Western India. Nasopharyngeal swabs were analyzed by multiplex real time polymerase chain reaction, for 18 viruses and 3 bacteria (H. influenzae type b, C. pneumoniae and M. pneumoniae). The entire data was entered in Microsoft excel sheet and frequencies were determined.

RESULTS

One hundred eligible infants were enrolled. Pathogens were detected in 82 samples, which included Respiratory syncytial viruses (RSV) A / B (35.4%), Human rhinovirus (25.6%), Adenovirus (22%), Human Parainfluenza viruses (11%), Human bocavirus (9.8), Human metapneumovirus A / B (8.5%), Influenza A (H1N1) pdm 09 (6.1%), Parechovirus (3.7%), Human coronaviruses (3.66%), Haemophilus influenzae type b (6.1%), Chlamydia pneumoniae (2.4%) and Mycoplasma pneumoniae (2.4%). Influenza A (other than H1N1), Influenza B, Human Coronavirus 229E and Enterovirus were not detected. The rate of coinfection was 34% and rhinovirus was the most common of the multiple pathogens.

CONCLUSIONS

Spectrum of viral etiologies of ALRTI is highlighted. Etiological diagnosis of ALRTI would enable specific antiviral therapy, restrict antibiotic use and help in knowing burden of disease.