Applying sputum as a diagnostic tool in pneumonia: limited yield, minimal impact on treatment decisions

Diagnostic accuracy of point-of-care tests for acute respiratory infection: a systematic review of reviews

Background

Acute respiratory infections are a common reason for consultation with primary and emergency healthcare services. Identifying individuals with a bacterial infection is crucial to ensure appropriate treatment. However, it is also important to avoid overprescription of antibiotics, to prevent unnecessary side effects and antimicrobial resistance. We conducted a systematic review to summarise evidence on the diagnostic accuracy of symptoms, signs and point-of-care tests to diagnose bacterial respiratory tract infection in adults, and to diagnose two common respiratory viruses, influenza and respiratory syncytial virus.

Methods

The primary approach was an overview of existing systematic reviews. We conducted literature searches (22 May 2023) to identify systematic reviews of the diagnostic accuracy of point-of-care tests. Where multiple reviews were identified, we selected the most recent and comprehensive review, with the greatest overlap in scope with our review question. Methodological quality was assessed using the Risk of Bias in Systematic Reviews tool. Summary estimates of diagnostic accuracy (sensitivity, specificity or area under the curve) were extracted. Where no systematic review was identified, we searched for primary studies. We extracted sufficient data to construct a 2 × 2 table of diagnostic accuracy, to calculate sensitivity and specificity. Methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies version 2 tool. Where possible, meta-analyses were conducted. We used GRADE to assess the certainty of the evidence from existing reviews and new analyses.

Results

We identified 23 reviews which addressed our review question; 6 were selected as the most comprehensive and similar in scope to our review protocol. These systematic reviews considered the following tests for bacterial respiratory infection: individual symptoms and signs; combinations of symptoms and signs (in clinical prediction models); clinical prediction models incorporating C-reactive protein; and biological markers related to infection (including C-reactive protein, procalcitonin and others). We also identified systematic reviews that reported the accuracy of specific tests for influenza and respiratory syncytial virus. No reviews were found that assessed the diagnostic accuracy of white cell count for bacterial respiratory infection, or multiplex tests for influenza and respiratory syncytial virus. We therefore conducted searches for primary studies, and carried out meta-analyses for these index tests. Overall, we found that symptoms and signs have poor diagnostic accuracy for bacterial respiratory infection (sensitivity ranging from 9.6% to 89.1%; specificity ranging from 13.4% to 95%). Accuracy of biomarkers was slightly better, particularly when combinations of biomarkers were used (sensitivity 80-90%, specificity 82-93%). The sensitivity and specificity for influenza or respiratory syncytial virus varied considerably across the different types of tests. Tests involving nucleic acid amplification techniques (either single pathogen or multiplex tests) had the highest diagnostic accuracy for influenza (sensitivity 91-99.8%, specificity 96.8-99.4%).

Limitations

Most of the evidence was considered low or very low certainty when assessed with GRADE, due to imprecision in effect estimates, the potential for bias and the inclusion of participants outside the scope of this review (children, or people in hospital).

Future work

Currently evidence is insufficient to support routine use of point-of-care tests in primary and emergency care. Further work must establish whether the introduction of point-of-care tests adds value, or simply increases healthcare costs.

Funding

This article presents independent research funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme as award number NIHR159948.

The agreement between bronchoalveolar lavage, bronchial wash and sputum culture: a retrospective study

PURPOSE

Bronchoalveolar lavage is commonly used in clinical practice for unresolved pneumonia. However, bronchoalveolar lavage is not suitable for all patients as it is an invasive procedure and can worsen oxygenation. The diagnostic value of bronchial wash and sputum has been debated extensively over the years. In this study, we aim to compare the diagnostic value in several pathogens of bronchoalveolar lavage and bronchial wash, and secondarily bronchoalveolar lavage and sputum.

METHODS

We retrospectively included all adult patients in our hospital who underwent bronchoalveolar lavage, bronchial wash, and where sputum sampling was done between January 1st of 2018 and December 31st of 2021. The intraclass correlation coefficient was computed for the three tests.

RESULTS

In total, 308 patients were included. We found a level of correlation of 0.819 and 0.865, respectively, between bronchoalveolar lavage and bronchial wash for two pathogens: Staphylococcus aureus and Pseudomonas aeruginosa. For Stenotrophomonas maltophilia and Aspergillus fumigatus, we found an intraclass correlation coefficient of 0.568 and 0.624, respectively. Between bronchoalveolar lavage and sputum, we found varying levels of agreement.

CONCLUSION

Our study shows reasonably well agreement levels between bronchoalveolar lavage and bronchial wash, suggesting that bronchial wash could potentially be an alternative to bronchoalveolar lavage.

Evaluation of point-of-care multiplex polymerase chain reaction in guiding antibiotic treatment of patients acutely admitted with suspected community-acquired pneumonia in Denmark: A multicentre randomised controlled trial

BACKGROUND

Rapid and accurate detection of pathogens is needed in community-acquired pneumonia (CAP) to enable appropriate antibiotics and to slow the development of antibiotic resistance. We aimed to compare the effect of point-of-care (POC) polymerase chain reaction (PCR) detection of respiratory pathogens added to standard care with standard care only (SCO) on antibiotic prescriptions after acute hospital admission.

METHODS AND FINDINGS

We performed a superiority, parallel-group, open-label, multicentre, randomised controlled trial (RCT) in 3 Danish medical emergency departments (EDs) from March 2021 to February 2022. Adults acutely admitted with suspected CAP during the daytime on weekdays were included and randomly assigned (1:1) to POC-PCR (The Biofire FilmArray Pneumonia Panel plus added to standard care) or SCO (routine culture and, if requested by the attending physician, target-specific PCR) analysis of respiratory samples. We randomly assigned 294 patients with successfully collected samples (tracheal secretion 78.4% or expectorated sputum 21.6%) to POC-PCR (n = 148, 50.4%) or SCO (146, 49.6%). Patients and investigators owning the data were blinded to the allocation and test results. Outcome adjudicators and clinical staff at the ED were not blinded to allocation and test results but were together with the statistician, blinded to data management and analysis. Laboratory staff performing standard care analyses was blinded to allocation. The study coordinator was not blinded. Intention-to-treat and per protocol analysis were performed using logistic regression with Huber-White clustered standard errors for the prescription of antibiotic treatment. Loss to follow-up comprises 3 patients in the POC-PCR (2%) and none in the SCO group. Intention-to-treat analysis showed no difference in the primary outcome of prescriptions of no or narrow-spectrum antibiotics at 4 h after admission for the POC-PCR (n = 91, 62.8%) odds ratio (OR) 1.13; (95% confidence interval (CI) [0.96, 1.34] p = 0.134) and SCO (n = 87, 59.6%). Secondary outcomes showed that prescriptions were significantly more targeted at 4-h OR 5.68; (95% CI [2.49, 12.94] p < 0.001) and 48-h OR 4.20; (95% CI [1.87, 9.40] p < 0.001) and more adequate at 48-h OR 2.11; (95% CI [1.23, 3.61] p = 0.006) and on day 5 in the POC-PCR group OR 1.40; (95% CI [1.18, 1.66] p < 0.001). There was no difference between the groups in relation to intensive care unit (ICU) admissions OR 0.54; (95% CI [0.10, 2.91] p = 0.475), readmission within 30 days OR 0.90; (95% CI [0.43, 1.86] p = 0.787), length of stay (LOS) IRR 0.82; (95% CI [0.63, 1.07] p = 0.164), 30 days mortality OR 1.24; (95% CI [0.32, 4.82] p = 0.749), and in-hospital mortality OR 0.98; (95% CI [0.19, 5.06] p = 0.986).

CONCLUSIONS

In a setting with an already restrictive use of antibiotics, adding POC-PCR to the diagnostic setup did not increase the number of patients treated with narrow-spectrum or without antibiotics. POC-PCR may result in a more targeted and adequate use of antibiotics. A significant study limitation was the concurrent Coronavirus Disease 2019 (COVID-19) pandemic resulting in an unusually low transmission of respiratory virus.

TRIAL REGISTRATION

ClinicalTrials.gov (NCT04651712).

Cell-free plasma next-generation sequencing assists in the evaluation of secondary pneumonia in patients with COVID-19: a case series

Secondary pneumonia occurs in 8-24% of patients with Coronavirus 2019 (COVID-19) infection and is associated with increased morbidity and mortality. Diagnosis of secondary pneumonia can be challenging. The purpose of this study was to evaluate the use of plasma microbial cell free DNA sequencing (mcfNGS) in the evaluation of secondary pneumonia after COVID-19. We performed a single-center case series of patients with COVID-19 who underwent mcfNGS to evaluate secondary pneumonia and reported the organisms identified, concordance with available tests, clinical utility, and outcomes. In 8/13 (61%) cases, mcfNGS detected 1-6 organisms, with clinically significant organisms identified in 4 cases, including Pneumocystis jirovecii, and Legionella spp. Management was changed in 85% (11/13) of patients based on results, including initiation of targeted therapy, de-escalation of empiric antimicrobials, and avoiding contingent escalation of antifungals. mcfNGS may be helpful to identify pathogens causing secondary pneumonia, including opportunistic pathogens in immunocompromised patients with COVID-19. However, providers need to carefully interpret this test within the clinical context.

Diagnostic accuracy of the BioFire® FilmArray® pneumonia panel in COVID-19 patients with ventilator-associated pneumonia

BACKGROUND

Ventilator-Associated pneumonia (VAP) is one of the leading causes of morbidity and mortality in critically ill COVID-19 patients in lower-and-middle-income settings, where timely access to emergency care and accurate diagnostic testing is not widely available. Therefore, rapid microbiological diagnosis is essential to improve effective therapy delivery to affected individuals, preventing adverse outcomes and reducing antimicrobial resistance.

METHODS

We conducted a cross-sectional study of patients with suspected VAP and COVID-19, evaluating the diagnostic performance of the BioFire® FilmArray® Pneumonia Panel (FA-PP). Respiratory secretion samples underwent standard microbiological culture and FA-PP assays, and the results were compared.

RESULTS

We included 252 samples. The traditional culture method detected 141 microorganisms, and FA-PP detected 277, resulting in a sensitivity of 95% and specificity of 60%, with a positive predictive value of 68% and negative predictive value of 93%. In samples with high levels of genetic material (> 10^5 copies/mL), the panel had a sensitivity of 94% and specificity of 86%. In addition, 40% of the culture-negative samples had positive FA-PP® results, of which 35% had > 10^5 copies/mL of genetic material. The most prevalent bacteria were Gram-negative bacilli, followed by Gram-positive cocci. The panel identified 98 genes associated with antimicrobial resistance, predominantly extended-spectrum beta-lactamases (28%).

CONCLUSION

The FA-PP is a sensitive assay for identifying bacteria causing VAP in patients with COVID-19, with a greater capacity to detect bacteria than the conventional method. The timely microbiological recognition offered by this panel could lead to optimized decision-making processes, earlier tailored treatment initiation, and improved antibiotic stewardship practices.

Microbiology sampling in non-cystic fibrosis bronchiectasis cases from northern Alberta

Non-cystic fibrosis bronchiectasis (NCFB) is a chronic respiratory disease resulting in chronic cough, thick sputum, and lower airway microbial colonization, akin to patients with cystic fibrosis (CF). NCFB is a common, yet under recognized entity which inflicts significant morbidity and mortality particularly to older individuals, with a rising prevalence in the developed world. Given that sputum cultures are a non-invasive method to characterize the lower airway microbiota in NCFB patients, for which pathogenic organisms are associated with worsened outcomes, we sought to characterize the microbiological pattern and clinical outcomes associated with sputum culture in a cohort of NCFB patients from Western Canada. A total of 20 subjects were prospectively recruited from various bronchiectasis clinics across the Greater Edmonton area. A retrospective chart review and a symptoms questionnaire was performed, gathering information not limited to symptoms, comorbidities, exacerbations, hospitalizations, sputum production, and sputum culture results over the prior 5 years. Subjects reported frequent hospitalization alongside a significant burden of symptoms. A large majority of sputum cultures grew pathogenic organisms such as Haemophilus influenzae and Pseudomonas aeruginosa. We also note the considerable waste and inefficiency associated with sputum cultures, outlining areas for which this important diagnostic modality can be improved. Accurate characterization of the airway microbiota alongside efficient delivery of health services are key to ensuring the proper treatment of individuals with NCFB, given their high disease burden and frequent hospitalization.

A Retrospective Assessment of Sputum Samples and Antimicrobial Resistance in COVID-19 Patients

Data on bacterial or fungal pathogens and their impact on the mortality rates of Western Romanian COVID-19 patients are scarce. As a result, the purpose of this research was to determine the prevalence of bacterial and fungal co- and superinfections in Western Romanian adults with COVID-19, hospitalized in in-ward settings during the second half of the pandemic, and its distribution according to sociodemographic and clinical conditions. The unicentric retrospective observational study was conducted on 407 eligible patients. Expectorate sputum was selected as the sampling technique followed by routine microbiological investigations. A total of 31.5% of samples tested positive for Pseudomonas aeruginosa, followed by 26.2% having co-infections with Klebsiella pneumoniae among patients admitted with COVID-19. The third most common Pathogenic bacteria identified in the sputum samples was Escherichia coli, followed by Acinetobacter baumannii in 9.3% of samples. Commensal human pathogens caused respiratory infections in 67 patients, the most prevalent being Streptococcus penumoniae, followed by methicillin-sensitive and methicillin-resistant Staphylococcus aureus. A total of 53.4% of sputum samples tested positive for Candida spp., followed by 41.1% of samples with Aspergillus spp. growth. The three groups with positive microbial growth on sputum cultures had an equally proportional distribution of patients admitted to the ICU, with an average of 30%, compared with only 17.3% among hospitalized COVID-19 patients with negative sputum cultures (p = 0.003). More than 80% of all positive samples showed multidrug resistance. The high prevalence of bacterial and fungal co-infections and superinfections in COVID-19 patients mandates for strict and effective antimicrobial stewardship and infection control policies.

Gram Stain and Culture of Sputum Samples Detect Only Few Pathogens in Community-Acquired Lower Respiratory Tract Infections: Secondary Analysis of a Randomized Controlled Trial

Identification of the bacterial etiology of lower respiratory tract infections (LRTI) is crucial to ensure a narrow-spectrum, targeted antibiotic treatment. However, Gram stain and culture results are often difficult to interpret as they depend strongly on sputum sample quality. We aimed to investigate the diagnostic yield of Gram stain and culture from respiratory samples collected by tracheal suction and expiratory technique from adults admitted with suspected community-acquired LRTI (CA-LRTI). In this secondary analysis of a randomized controlled trial, 177 (62%) samples were collected by tracheal suction, and 108 (38%) by expiratory technique. We detected few pathogenic microorganisms, and regardless of sputum quality, there were no significant differences between the sample types. Common pathogens of CA-LRTI were identified by culture in 19 (7%) samples, with a significant difference between patients with or without prior antibiotic treatment (p = 0.007). The clinical value of sputum Gram stain and culture in CA-LRTI is therefore questionable, especially in patients treated with antibiotics.

Does etiological investigation have an impact on the outcomes of community-acquired pneumonia? - A prospective cohort study

INTRODUCTION

There is lack of evidence that etiological investigation influences outcomes in community-acquired pneumonia (CAP). Guidelines recommend diverse approaches to this matter. Our aim was to find if etiological investigation has an impact on CAP management and outcomes.

METHODS

Prospective cohort study, conducted over a two years' period, in a community-based hospital, including all adult patients with CAP. Univariate and multivariate logistic regression modeling were performed to understand the association of etiological identification with CAP outcomes, particularly hospital mortality.

RESULTS

A total of 660 cases of CAP were included, with a mean±sd age of 74±15 years and 58.9% of males. Etiology was documented in 33% of cases. Antibiotic (ATB) was modified in 148 patients, in 51 (34%) motivated by microbiological results. There was no significant impact on hospital mortality of microbiological documentation (35.5% vs 31.2%, p=0.352), or the fact that ATB was modified due to microbiological findings (27.0% vs 36.9%, p=0.272). When stratified by 3 subgroups of risk for drug-resistant pathogens (zero, one or two risk factors: being bed-ridden and/or ATB use within 90 days), etiology identification still did not influence mortality. When adjusted for CURB-65, Charlson's index, being bed-ridden, having had ATB or hospitalization within 90 days or coming from long-term care facilities, microbial identification was not associated with lower mortality.

CONCLUSION

Etiological investigation of patients with CAP does not have an association with hospital mortality, irrespective of the risk for drug-resistant pathogens.

The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures

All modern advances notwithstanding, pneumonia remains a common infection with substantial morbidity and mortality. Understanding of the etiology of pneumonia continues to evolve as new techniques enable identification of already known organisms and as new organisms emerge. We now review the etiology of pneumonia (at present often called "community-acquired pneumonia") beginning with classic bacteriologic techniques, which identified Streptococcus pneumoniae as the overwhelmingly common cause, to more modern bacteriologic studies, which emphasize Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Enterobacteriaceae, Pseudomonas, and normal respiratory flora. Urine antigen detection is useful in identifying Legionella and pneumococcus. The low yield of bacteria in recent studies is due to the failure to obtain valid sputum samples before antibiotics are administered. The use of high-quality sputum specimens enables identification of recognized ("typical") bacterial pathogens as well as a role for commensal bacteria ("normal respiratory flora"). Nucleic acid amplification technology for viruses has revolutionized diagnosis, showing the importance of viral pneumonia leading to hospitalization with or without coinfecting bacterial organisms. Quantitative PCR study of sputum is in its early stages of application, but regular detection of high counts of bacterial DNA from organisms that are not seen on Gram stain or grown in quantitative culture presents a therapeutic dilemma. This finding may reflect the host microbiome of the respiratory tract, in which case treatment may not need to be given for them. Finally, host transcriptional signatures might enable clinicians to distinguish between viral and bacterial pneumonia, an important practical consideration.

Expiratory Technique versus Tracheal Suction to Obtain Good-Quality Sputum from Patients with Suspected Lower Respiratory Tract Infection: A Randomized Controlled Trial

Microbiological diagnostics of good-quality sputum samples are fundamental for infection control and targeted treatment of lower respiratory tract infections (LRTI). This study aims to compare the expiratory technique and tracheal suction on the quality of sputa from adults acutely hospitalized with suspected LRTI. We performed an open-label, randomized controlled trial. Patients were randomized to sputum sampling by tracheal suction (standard care) or the expiratory technique. The primary outcome was quality of sputum evaluated by microscopy and was analysed in the intention-to-treat population. The secondary outcomes were adverse events and patients experience. In total, 280 patients were assigned to tracheal suction (n = 141, 50.4%) or the expiratory technique (n = 139, 49.6%). Sputum samples were collected from 122 (86.5%) patients with tracheal suction and 67 (48.2%) patients with expiratory technique. Good-quality sputa were obtained more often with tracheal suction than with expiratory technique (odds ratio 1.83 [95% CI 1.05 to 3.19]; p = 0.035). There was no statistical difference in adverse events (IRR 1.21 [95% CI, 0.94 to 1.66]; p = 0.136), but patient experience was better in the expiratory technique group (p < 0.0001). In conclusion, tracheal suction should be considered a routine procedure in emergency departments for patients with suspected LRTI.

Clinical value of serum sTREM-1 and HBP levels in combination with traditional inflammatory markers in diagnosing hospital-acquired pneumonia in elderly

Background

The clinical presentation of hospital-acquired pneumonia (HAP) in older patients is often complex and non-specific, posing a diagnostic challenge. This study evaluates the value of serum soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) and heparin-binding protein (HBP) in combination with traditional inflammatory markers procalcitonin (PCT) and C-reactive protein (CRP) in diagnosing HAP in older patients.

Methods

Thirty-eight elderly male patients with HAP (≥ 80 years old) and 46 age-matched controls, who were hospitalized for other reasons than HAP, were enrolled. The serum sTREM-1, HBP, PCT and CRP levels were measured by ELISA on the first day after enrollment. In addition, routine blood test, blood gas, sputum analysis, clinical pulmonary infection score (CPIS) assessment, and chest X-ray were performed, and the correlations with HAP were analyzed.

Results

The serum sTREM-1 (n = 38, 170.75 ± 158.33 pg/ml), HBP (2.08 ± 0.50), PCT (9.44 ± 17.73) and CRP (79.63 ± 71.37) were all significantly higher in the HAP group, when compared to the control group (P < 0.05). Furthermore, the values were positively correlated with the CPIS. The ROC curve analysis revealed that the AUC for sTREM-1 (0.667) and HBP (0.711) were lower, when compared to that for PCT (AUC = 0.839) and CRP (AUC = 0.840). The combination of PCT and CRP with sTREM-1 (AUC = 0.927) or HBP (AUC = 0.930) had the highest AUC values.

Conclusion

Serum sTREM-1, HBP, PCT and CRP can all be used as diagnostic markers for HAP in the elderly. The combination of traditional inflammatory markers PCT and CRP with novel inflammatory marker sTREM-1 or HBP further improves the diagnostic performance.

Comparative Analysis of Epidemiological and Clinical Characteristics Between Invasive Candida Infection versus Colonization in Critically Ill Patients in a Tertiary Hospital in Anhui, China

Objective

Invasive infections due to Candida spp. have unique epidemiology, strain distribution, antimicrobial susceptibility, and clinical features. This study aimed to compare and evaluate these characteristic variables between invasive Candida infection and colonization of critically ill patients in local China to potentially improve differential diagnosis and therapy.

Methods

A total of 193 critically ill patients were recruited and followed up for the study, and 133 Candida isolates were obtained from invasive Candida-infected or -colonized subjects. The strains were identified to species level through matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry, assisted by DNA sequencing. Candida susceptibility to common antifungals, including azoles, was determined by microbroth ATB Fungus 3 methodology. Azole resistance–related gene sequencing and homologous 3D-structure modeling were employed. Patient demographics and clinical risk factors were documented and comparatively analyzed from the hospital information-management system.

Results

Non–C. albicans Candida (56%) principally caused invasive Candida infections, while C. albicans (55.17%) contributed more to Candida colonization in critically ill patients. Additional risk factors exerted significant impact on both Candida cohorts, primarily including invasive interventions, cancers, and concurrent infections in common. Most colonized Candida spp. harbored relatively higher sensitivity to azoles. ERG11 gene mutations of T348A and A1309G, A395T and C461T, and a novel G1193T to our knowledge were identified in azole-resistant C. albicans, C. tropicalis, and C. parapsilosis respectively, and their corresponding homologous 3D-structure modeling was putatively achieved.

Conclusion

Distinct epidemiological and clinical characteristics existed between invasive Candida infection and colonization in critically ill patients. Multiple risk factors significantly involved both the Candida cohorts. Colonized Candida exhibited generally higher azole sensitivity than invasively infectious counterparts. ERG11 point mutations had mechanistically potential ties with local Candida resistance to azoles.

Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response: Application to the 2017 plague epidemic in Madagascar

During outbreaks, the lack of diagnostic "gold standard" can mask the true burden of infection in the population and hamper the allocation of resources required for control. Here, we present an analytical framework to evaluate and optimize the use of diagnostics when multiple yet imperfect diagnostic tests are available. We apply it to laboratory results of 2,136 samples, analyzed with 3 diagnostic tests (based on up to 7 diagnostic outcomes), collected during the 2017 pneumonic (PP) and bubonic plague (BP) outbreak in Madagascar, which was unprecedented both in the number of notified cases, clinical presentation, and spatial distribution. The extent of these outbreaks has however remained unclear due to nonoptimal assays. Using latent class methods, we estimate that 7% to 15% of notified cases were Yersinia pestis-infected. Overreporting was highest during the peak of the outbreak and lowest in the rural settings endemic to Y. pestis. Molecular biology methods offered the best compromise between sensitivity and specificity. The specificity of the rapid diagnostic test was relatively low (PP: 82%, BP: 85%), particularly for use in contexts with large quantities of misclassified cases. Comparison with data from a subsequent seasonal Y. pestis outbreak in 2018 reveal better test performance (BP: specificity 99%, sensitivity: 91%), indicating that factors related to the response to a large, explosive outbreak may well have affected test performance. We used our framework to optimize the case classification and derive consolidated epidemic trends. Our approach may help reduce uncertainties in other outbreaks where diagnostics are imperfect.

Performance of the Cepheid Methicillin-Resistant Staphylococcus aureus/S. aureus Skin and Soft Tissue Infection PCR Assay on Respiratory Samples from Mechanically Ventilated Patients for S. aureus Screening during the Phase 2 Double-Blind SAATELLITE Study

We investigated the performance of the Xpert methicillin-resistant Staphylococcus aureus (MRSA)/S. aureus skin and soft tissue (SSTI) quantitative PCR (qPCR) assay in SAATELLITE, a multicenter, double-blind, phase 2 study of suvratoxumab, a monoclonal antibody (MAb) targeting S. aureus alpha-toxin, for reducing the incidence of S. aureus pneumonia. The assay was used to detect methicillin-susceptible S. aureus (MSSA) and MRSA in lower respiratory tract (LRT) samples from mechanically ventilated patients. LRT culture results were compared with S. aureus protein A (spa) gene cycle threshold (C_T) values. Receiver operating characteristic (ROC) and Youden index were used to determine the C_T cutoff for best separation of culture-S. aureus-negative and S. aureus-positive patients. Of 720 screened subjects, 299 (41.5%) were S. aureus positive by qPCR, of whom 209 had culture data: 162 (77.5%) were S. aureus positive and 47 (22.5%) were S. aureus negative. Culture results were negatively affected by antibiotic use and cross-laboratory variability. An inverse linear correlation was observed between C_T values and quantitative S. aureus culture results. A spa C_T value of 29 (≈2 × 10³ CFU/mL) served as the best cutoff for separation between culture-negative and culture-positive samples. The associated area under the ROC curve was 83.8% (95% confidence interval [CI], 78 to 90%). Suvratoxumab provided greater reduction in S. aureus pneumonia or death than placebo in subjects with low S. aureus load (C_T ≥ 29; relative risk reduction [RRR], 50.0%; 90% CI, 2.7 to 74.4%) versus the total study population (RRR, 25.2%; 90% CI, -4.3 to 46.4%). The qPCR assay was easy to perform, sensitive, and standardized and provided better sensitivity than conventional culture for S. aureus detection. Quantitative PCR C_T output correlated with suvratoxumab efficacy in reducing S. aureus pneumonia incidence or death in S. aureus-colonized, mechanically ventilated patients.

Development and evaluation of a multiplex quantitative polymerase chain reaction assay for detecting bacteria associated with lower respiratory tract infection

OBJECTIVES

This study aimed to establish a multiplex quantitative polymerase chain reaction (MQ-PCR) assay for 12 bacterial pathogens found in lower respiratory tract infection (LRTI) and to evaluate its performance in a cohort of 211 patients with LRTI.

METHODS

The study was divided into two stages: a pilot study to establish the methodology and a clinical validation study to evaluate its performance. In the pilot study, we established the MQ-PCR and analyzed its performance regarding limits of detection, reproducibility, specificity, and efficiency. In the clinical validation study, we obtained 211 sputum and/or bronchoalveolar lavage fluid (BALF) samples and detected pathogens by MQ-PCR. The MQ-PCR time was 3 h from sample collection to complete pathogen detection.

RESULTS

The limit of detection was 1000 copies/ml, and the maximum efficiency was >95%. When cutoffs of ≥10⁵ copies/ml in sputum and ≥10⁴ copies/ml in BALF were applied, the sensitivity, specificity, and positive and negative predictive values of the MQ-PCR were 77% (95% confidence interval [CI] 67-88%), 94% (95% CI 93-95%), 25% (95% CI 19-31%), and 99% (95% CI 99-100%), respectively.

CONCLUSIONS

This study demonstrates that the new MQ-PCR assay is time-saving, more effective and sensitive, and brings us closer to mainstream adoption of quantitative molecular detection of bacteria.

Hyper-Virulent Listeria monocytogenes Strains Associated With Respiratory Infections in Central Italy

Listeria monocytogenes (Lm) is a foodborne pathogen causing listeriosis. Invasive forms of the disease mainly manifest as septicaemia, meningitis and maternal-neonatal infections. Lm-associated respiratory infections are very rare and little known. We reported two Lm respiratory infection cases occurred in Central Italy during the summer of 2020, in the midst of the SARS-CoV2 pandemic. In addition to collect the epidemiological and clinical characteristics of the patients, we used Whole Genome Sequencing to study the genomes of the Lm isolates investigating their virulence and antimicrobial profiles and the presence of genetic mobile elements. Both the strains belonged to hypervirulent MLST clonal complexes (CC). In addition to the Listeria Pathogenicity Island 1 (LIPI-1), the CC1 strain also carried LIPI-3 and the CC4 both LIPI-3 and LIPI-4. Genetic determinants for antimicrobial and disinfectants resistance were found. The CC1 genome presented prophage sequences but they did not interrupt the comK gene, involved in the phagosomal escape of Lm. None of the strains carried plasmids. Lm is an important, although rare, opportunistic pathogen for respiratory tract and lung infections. To avoid dangerous diagnostic delays of these severe clinical forms, it is important to sensitize hospital laboratories to this rare manifestation of listeriosis considering Lm in the differential diagnosis of respiratory infections.

Effectiveness of expiratory technique and induced sputum in obtaining good quality sputum from patients acutely hospitalized with suspected lower respiratory tract infection: a statistical analysis plan for a randomized controlled trial

Background

Targeted antimicrobial treatment is essential to avoid unnecessary use of broad-spectrum antibiotics and antimicrobial resistance. Targeted treatment relies on a precise microbiological diagnosis — in pneumonia, this poses a challenge as the usefulness of Gram stains and cultures is highly dependent on the quality of the sputum sample.

This study aims to examine adverse effects and quality of sputum samples obtained by expiratory techniques (forced expiratory technique and sputum induction) compared with tracheal suction. The hypothesis is that expiratory techniques are non-inferior to tracheal suction in obtaining samples from the lower respiratory tract. This statistical analysis plan (SAP) describes the study design, method, and data analysis of the trial to increase transparency, avoid reporting bias or data-driven analysis and increase the study’s reproducibility.

Method

The design is a pragmatic, non-inferiority, parallel-arm randomized controlled trial including 280 patients admitted with suspected lower respiratory infection to two emergency departments. Patients are randomized to a usual care group, where sputum samples are collected by tracheal suction or to an intervention group where sputum samples are collected by forced expiratory technique and sputum induction. The statistical analysis will follow an intention-to-treat protocol. This SAP is developed and submitted before the end of recruitment, database closure, and statistical analyses.

Discussion

The results of this study will provide valuable knowledge to clinical practice by comparing adverse effects and sputum sample quality associated with different sample methods.

Trial registration

Clinicaltrials.gov, NCT04595526. Submitted on October 19, 2020

Supplementary Information

The online version contains supplementary material available at 10.1186/s13063-021-05639-1.

[Management of Adult Community-Acquired Pneumonia and Prevention - Update 2021 - Guideline of the German Respiratory Society (DGP), the Paul-Ehrlich-Society for Chemotherapy (PEG), the German Society for Infectious Diseases (DGI), the German Society of Medical Intensive Care and Emergency Medicine (DGIIN), the German Viological Society (DGV), the Competence Network CAPNETZ, the German College of General Practitioneers and Family Physicians (DEGAM), the German Society for Geriatric Medicine (DGG), the German Palliative Society (DGP), the Austrian Society of Pneumology Society (ÖGP), the Austrian Society for Infectious and Tropical Diseases (ÖGIT), the Swiss Respiratory Society (SGP) and the Swiss Society for Infectious Diseases Society (SSI)]

The present guideline provides a new and updated concept of the management of adult patients with community-acquired pneumonia. It replaces the previous guideline dating from 2016.The guideline was worked out and agreed on following the standards of methodology of a S3-guideline. This includes a systematic literature search and grading, a structured discussion of recommendations supported by the literature as well as the declaration and assessment of potential conflicts of interests.The guideline has a focus on specific clinical circumstances, an update on severity assessment, and includes recommendations for an individualized selection of antimicrobial treatment.The recommendations aim at the same time at a structured assessment of risk for adverse outcome as well as an early determination of treatment goals in order to reduce mortality in patients with curative treatment goal and to provide palliation for patients with treatment restrictions.

Breath-Based Diagnosis of Infectious Diseases: A Review of the Current Landscape

Various analytical methods can be applied to concentrate, separate, and examine trace volatile organic metabolites in the breath, with the potential for noninvasive, rapid, real-time identification of various disease processes, including an array of microbial infections. Although biomarker discovery and validation in microbial infections can be technically challenging, it is an approach that has shown great promise, especially for infections that are particularly difficult to identify with standard culture and molecular amplification-based approaches. This article discusses the current state of breath analysis for the diagnosis of infectious diseases.

Sputum Gram Stain for Bacterial Pathogen Diagnosis in Community-acquired Pneumonia: A Systematic Review and Bayesian Meta-analysis of Diagnostic Accuracy and Yield

BACKGROUND

The clinical role of sputum Gram stain (SGS) in community-acquired pneumonia (CAP) diagnosis remains controversial. A 1996 meta-analysis of the diagnostic accuracy of SGS reported heterogeneous results. To update the available evidence, we performed a systematic review and a Bayesian standard and latent-class model meta-analysis.

METHODS

We searched Medline, Embase, and Cochrane Central by 23 August 2018 to identify studies reporting on the diagnostic accuracy, yield (percentage of patients with any pathogen[s] correctly identified by SGS), and clinical outcomes of SGS in adult patients with CAP. Two reviewers extracted the data. We quantitatively synthesized the diagnostic accuracy and yield, and descriptively analyzed other outcomes.

RESULTS

Twenty-four studies with 4533 patients were included. The methodological and reporting quality of the included studies was limited. When good-quality sputum specimens were selected, SGS had a summary sensitivity of 0.69 (95% credible interval [CrI], .56-.80) and specificity of 0.91 (CrI, .83-.96) for detecting Streptococcus pneumoniae, and a sensitivity of 0.76 (CrI, .60-.87) and specificity of 0.97 (CrI, .91-.99) for Haemophilus influenzae. Adjusted analyses accounting for imperfect reference standards provided higher-specificity estimates than the unadjusted analyses. Bacterial pathogens were identified in 73% (CrI, 26%-96%) of good-quality specimens, and 36% (CrI, 22%-53%) of all specimens regardless of quality. Evidence on other bacteria was sparse.

CONCLUSIONS

SGS was highly specific to diagnose S. pneumoniae and H. influenzae infections in patients with CAP. With good-quality specimens, SGS can provide clinically actionable information for pathogen-directed antibiotic therapies.

Appropriateness of antibiotic prescribing in the Emergency Department

Background

Antibiotics are some of the most commonly prescribed drugs in the Emergency Department (ED) and yet data describing the overall appropriateness of antibiotic prescribing in the ED is scarce.

Objectives

To describe the appropriateness of antibiotic prescribing in the ED.

Methods

A retrospective, observational study of current practice. All patients who presented to the ED during the study period and were prescribed at least one antibiotic were included. Specialists from Infectious Disease, Microbiology and Emergency Medicine and a Senior Pharmacist assessed antibiotic appropriateness against evidence-based guidelines.

Results

A total of 1019 (13.6%) of patient presentations involved the prescription of at least one antibiotic. Of these, 640 (62.8%) antibiotic prescriptions were assessed as appropriate, 333 (32.7%) were assessed as inappropriate and 46 (4.5%) were deemed to be not assessable. Adults were more likely to receive an inappropriate antibiotic prescription than children (36.9% versus 22.9%; difference 14.1%, 95% CI 7.2%–21.0%). Patients who met quick Sepsis-related Organ Failure Assessment (qSOFA) criteria were more likely to be prescribed inappropriate antibiotics (56.7% versus 36.1%; difference 20.5%, 95% CI, 2.4%–38.7%). There was no difference in the incidence of appropriate antibiotic prescribing based on patient gender, disposition (admitted/discharged), reason for antibiotic administration (treatment/prophylaxis) or time of shift (day/night).

Conclusions

Inappropriate administration of antibiotics can lead to unnecessary adverse events, treatment failure and antimicrobial resistance. With over one in three antibiotic prescriptions in the ED being assessed as inappropriate, there is a pressing need to develop initiatives to improve antibiotic prescribing to prevent antibiotic-associated patient and community harms.

Empirical Anti-MRSA vs Standard Antibiotic Therapy and Risk of 30-Day Mortality in Patients Hospitalized for Pneumonia

Importance

Use of empirical broad-spectrum antibiotics for pneumonia has increased owing to concern for resistant organisms, including methicillin-resistant Staphylococcus aureus (MRSA). The association of empirical anti-MRSA therapy with outcomes among patients with pneumonia is unknown, even for high-risk patients.

Objective

To compare 30-day mortality among patients hospitalized for pneumonia receiving empirical anti-MRSA therapy vs standard empirical antibiotic regimens.

Design, Setting, and Participants

Retrospective multicenter cohort study was conducted of all hospitalizations in which patients received either anti-MRSA or standard therapy for community-onset pneumonia in the Veterans Health Administration health care system from January 1, 2008, to December 31, 2013. Subgroups of patients analyzed were those with initial intensive care unit admission, MRSA risk factors, positive results of a MRSA surveillance test, and positive results of a MRSA admission culture. Primary analysis was an inverse probability of treatment-weighted propensity score analysis using generalized estimating equation regression; secondary analyses included an instrumental variable analysis. Statistical analysis was conducted from June 14 to November 20, 2019.

Exposures

Empirical anti-MRSA therapy plus standard pneumonia therapy vs standard therapy alone within the first day of hospitalization.

Main Outcomes and Measures

Risk of 30-day all-cause mortality after adjustment for patient comorbidities, vital signs, and laboratory results. Secondary outcomes included the development of kidney injury and secondary infections with Clostridioides difficile, vancomycin-resistant Enterococcus species, or gram-negative bacilli.

Results

Among 88 605 hospitalized patients (86 851 men; median age, 70 years [interquartile range, 62-81 years]), empirical anti-MRSA therapy was administered to 33 632 (38%); 8929 patients (10%) died within 30 days. Compared with standard therapy alone, in weighted propensity score analysis, empirical anti-MRSA therapy plus standard therapy was significantly associated with an increased adjusted risk of death (adjusted risk ratio [aRR], 1.4 [95% CI, 1.3-1.5]), kidney injury (aRR, 1.4 [95% CI, 1.3-1.5]), and secondary C difficile infections (aRR, 1.6 [95% CI, 1.3-1.9]), vancomycin-resistant Enterococcus spp infections (aRR, 1.6 [95% CI, 1.0-2.3]), and secondary gram-negative rod infections (aRR, 1.5 [95% CI, 1.2-1.8]). Similar associations between anti-MRSA therapy use and 30-day mortality were found by instrumental variable analysis (aRR, 1.6 [95% CI, 1.4-1.9]) and among patients admitted to the intensive care unit (aRR, 1.3 [95% CI, 1.2-1.5]), those with a high risk for MRSA (aRR, 1.2 [95% CI, 1.1-1.4]), and those with MRSA detected on surveillance testing (aRR, 1.6 [95% CI, 1.3-1.9]). No significant favorable association was found between empirical anti-MRSA therapy and death among patients with MRSA detected on culture (aRR, 1.1 [95% CI, 0.8-1.4]).

Conclusions and Relevance

This study suggests that empirical anti-MRSA therapy was not associated with reduced mortality for any group of patients hospitalized for pneumonia. These results contribute to a growing body of evidence that questions the value of empirical use of anti-MRSA therapy using existing risk approaches.

Diagnosis and Treatment of Adults with Community-acquired Pneumonia. An Official Clinical Practice Guideline of the American Thoracic Society and Infectious Diseases Society of America

Background: This document provides evidence-based clinical practice guidelines on the management of adult patients with community-acquired pneumonia.

Methods: A multidisciplinary panel conducted pragmatic systematic reviews of the relevant research and applied Grading of Recommendations, Assessment, Development, and Evaluation methodology for clinical recommendations.

Results: The panel addressed 16 specific areas for recommendations spanning questions of diagnostic testing, determination of site of care, selection of initial empiric antibiotic therapy, and subsequent management decisions. Although some recommendations remain unchanged from the 2007 guideline, the availability of results from new therapeutic trials and epidemiological investigations led to revised recommendations for empiric treatment strategies and additional management decisions.

Conclusions: The panel formulated and provided the rationale for recommendations on selected diagnostic and treatment strategies for adult patients with community-acquired pneumonia.

Evaluation of current practice of antimicrobial use and clinical outcome of patients with pneumonia at a tertiary care hospital in Ethiopia: A prospective observational study

BACKGROUND

Antimicrobial resistance, which is commonly observed in the management of pneumonia, is a major threat to public health and is driven by inappropriate antimicrobial use. The aim of this study was therefore to assess the current practice of antimicrobial utilization and clinical outcomes in the management of adult pneumonia at Tikur Anbessa Specialized Hospital.

METHOD

A prospective observational study was conducted in the internal medicine wards of Tikur Anbessa Specialized Hospital. The study was conducted from 1 September 2016 to 30 June 2017 and patients aged ≥ 14 years and diagnosed with pneumonia were included. Chart review and self-administered questionnaire were used to collect data regarding pneumonia diagnosis and management as well as clinical outcomes (stable, complications, and in-hospital mortality). Descriptive statistics and binary logistic regressions were performed for data analyses.

RESULTS

Out of 200 enrolled patients, clinical diagnosis was supported by microbiologic testing and imaging in 75 (37.5%) and 122 (61.0%) cases, respectively. The treatment approach in almost all patients (99.5%) was empirical and no de-escalation therapy was made even after acquiring culture results. The total duration of antimicrobial therapy was 12.05±5.09 days and vancomycin was the most commonly prescribed antimicrobial agent (25%), with 70% of the patients receiving this drug empirically. Nearly, 30% of the patients missed their antimicrobial doses during the course of treatment and stock-out (36.7%) was the major reason. Close to 113 (66%) of the treating physicians used reference books to prescribe antimicrobial agents. Patients' outcomes were found to be stable (66%), in-hospital mortality (18.5%), and ending up in complications (17%). Poor clinical outcome (death and complicated cases) was found to be associated with recent antimicrobial use history (p = 0.007, AOR 2.86(1.33-6.13)), cancer (p = 0.023, AOR 3.46(1.18-10.13)), recent recurrent upper respiratory tract infection (p = 0.046, AOR 3.70(1.02-13.40)), respiratory rate >24 breaths/min or <12 breaths/min (p = 0.013, AOR 2.45(1.21-4.95)) and high level of serum creatinine after initiation of antimicrobial therapy (>1.4mg/dl) (p = 0.032, AOR 2.37(1.07-5.20)).

CONCLUSION

Antimicrobials are empirically prescribed without sufficient evidence of indication and microbiological or radiological findings. The practice also is not based on local guidelines and no multidisciplinary approach is apparent. [How about: "It is likely that these factors contributed to higher rates of mortality (18.5%) when compared with similar studies in other countries" instead of this "As a result, there were higher rates of mortality (18.5%) when compared with other similar studies"]. Hence, the hospital requires a coordinated intervention to improve rational use of antimicrobials and clinical outcomes through establishing an antimicrobial stewardship program.

Seasonal Incidence of Community-acquired Pneumonia: A Retrospective Study in a Tertiary Care Hospital in Kathmandu, Nepal

Introduction

Community-acquired pneumonia (CAP) is the major cause of death in adult and elderly persons with a variety of presentations. Seasonal variation in the incidence of the disease is essential for clinicians and epidemiologists who deal with such diseases. The study was aimed at analysing the clinical profile and outcomes of community-acquired pneumonia during different seasons of the year in a tertiary care hospital, Manmohan Memorial Teaching Hospital (MMTH), of Kathmandu, Nepal.

Method

The aetiology and clinical profile of 378 patients with CAP who were admitted to MMTH over a period of one year were taken into account in this retrospective cross-sectional hospital-based study. Data were retrieved from the hospital medical records section and the Department of Pathology. All patients with a primary diagnosis of CAP admitted to the hospital were included in the study. Monthly and seasonal trends, aetiology, comorbidities, and mortality rates were analysed.

Results 

Of 378 patients with CAP, 160 patients (42.3%) had associated chronic obstructive pulmonary disease (COPD), 92 patients (24.3%) had hypertension (HTN), 59 patients (15.6%) had diabetes, 12 patients (3.1%) had active pulmonary tuberculosis, seven patients (1.85%) had kidney disease, and the remaining 48 patients (12.6%) had only CAP. Seasonal variation of CAP was noted in 131 patients (35%) in the winter, 98 (26%) in autumn, 86 (23%) in spring, and 63 patients (16%) in summer seasons. None of the patients were vaccinated against influenza and pneumococcus. The most common organism isolated in CAP was Acinetobacter calcoaceticus baumannii (ACB) complex (4.7%), which was more distinguished in the winter season. The second most isolated organism was Pseudomonas aeruginosa (2.6%). The most common clinical presentation was fever (63%), followed by cough (47%) and shortness of breath (47%). Sputum culture was found to be positive in 51 cases (13.4%). Among 378 patients, 78 patients (20.6%) received treatment in the Intensive Care Unit (ICU) and the rest of the patients received treatment in the general medical ward. The mortality rate was found to be 6.6%.

Conclusion

An incidence of sputum-positive CAP was found in 51 cases (13.4%). The most common organism was ACB complex, followed by Pseudomonas aeruginosa, which were sensitive to polymyxins. Both of them were predominant in the winter and spring.

Airway mycosis in allergic airway disease

The allergic airway diseases, including chronic rhinosinusitis (CRS), asthma, allergic bronchopulmonary mycosis (ABPM) and many others, comprise a heterogeneous collection of inflammatory disorders affecting the upper and lower airways and lung parenchyma that represent the most common chronic diseases of humanity. In addition to their shared tissue tropism, the allergic airway diseases are characterized by a distinct pattern of inflammation involving the accumulation of eosinophils, type 2 macrophages, innate lymphoid cells type 2 (ILC2), IgE-secreting B cells, and T helper type 2 (Th2) cells in airway tissues, and the prominent production of type 2 cytokines including interleukin (IL-) 33, IL-4, IL-5, IL-13, and many others. These factors and related inflammatory molecules induce characteristic remodeling and other changes of the airways that include goblet cell metaplasia, enhanced mucus secretion, smooth muscle hypertrophy, tissue swelling and polyp formation that account for the major clinical manifestations of nasal obstruction, headache, hyposmia, cough, shortness of breath, chest pain, wheezing, and, in the most severe cases of lower airway disease, death due to respiratory failure or disseminated, systemic disease. The syndromic nature of the allergic airway diseases that now include many physiological variants or endotypes suggests that distinct endogenous or environmental factors underlie their expression. However, findings from different perspectives now collectively link these disorders to a single infectious source, the fungi, and a molecular pathogenesis that involves the local production of airway proteinases by these organisms. In this review, we discuss the evidence linking fungi and their proteinases to the surprisingly wide variety of chronic airway and systemic disorders and the immune pathogenesis of these conditions as they relate to environmental fungi. We further discuss the important implications these new findings have for the diagnosis and future therapy of these common conditions.

Usefulness of sputum gram stain for etiologic diagnosis in community-acquired pneumonia: a systematic review and meta-analysis

Background

Implementation of sputum Gram stain in the initial assessment of community-acquired pneumonia (CAP) patients is still controversial. We performed a systematic review and meta-analysis to investigate the usefulness of sputum Gram stain for defining the etiologic diagnosis of CAP in adult patients.

Methods

We systematically searched the Medline, Embase, Science Direct, Scopus and LILACS databases for full-text articles. Relevant studies were reviewed by at least three investigators who extracted the data, pooled them using a random effects model, and carried out quality assessment. For each bacterium (Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, and Gram-negative bacilli), pooled sensitivity, specificity, positive and negative likelihood ratios were reported.

Results

After a review of 3539 abstracts, 20 articles were included in the present meta-analysis. The studies included yielded 5619 patients with CAP. Pooled sensitivity and pooled specificity of sputum Gram stain were 0.59 (95% CI, 0.56–0.62) and 0.87 (95% CI, 0.86–0.89) respectively for S. pneumoniae, 0.78 (95% CI, 0.72–0.84) and 0.96 (95% CI, 0.94–0.97) for H. influenzae, 0.72 (95% CI, 0.53–0.87) and 0.97 (95% CI, 0.95–0.99) for S. aureus, and 0.64 (95% CI, 0.49–0.77) and 0.99 (95% CI, 0.97–0.99) for Gram-negative bacilli.

Conclusion

Sputum Gram stain test is sensitive and highly specific for identifying the main causative pathogens in adult patients with CAP.

Trial registration

This study has been registered at PROSPERO International prospective register of systematic reviews under registration no. CRD42015015337.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4048-6) contains supplementary material, which is available to authorized users.

Culture of all sputum samples irrespective of quality adds value to the diagnosis of pneumococcal community-acquired pneumonia in the elderly

Culture of expectorated sputum in the microbiological diagnosis of community-acquired pneumonia (CAP) is considered valid only if high-quality (HQ) samples are obtained, but evidence regarding pneumococcal etiology specifically is lacking. We studied 323 radiologically confirmed CAP cases in patients aged ≥ 65 years. Sputum samples were assessed for quality microscopically and cultured. Two quality criteria sets were applied to delineate HQ from low-quality (LQ) sputa: leukocytes/epithelial cells ratio > 5 and ≤ 2.5 epithelial cells/400× magnification field (HQ1), or leukocytes/epithelial cells ratio > 1 (HQ2). A sputum sample was obtained and the quality assessed in 224 cases; 47% were HQ1 and 76% HQ2. Encapsulated pneumococci (EPnc) were cultured in 25 (24%), 14 (12%), 35 (21%), and 4 (7%) of the HQ1-, LQ1-, HQ2-, and LQ2-samples, respectively. If another pneumococcal test (blood culture, urine antigen, or ≥ twofold increase in CbpA or PsaA antibodies) was positive, EPnc were cultured at similar proportions in HQ1- and LQ1-sputa; if the other test was negative, EPnc were cultured less often in LQ1- than HQ1-sputa. EPnc were found less often in LQ2- than in HQ2-sputa. Our results suggest similar specificity in LQ- and HQ-sputum cultures. All sputum samples add value to the pneumococcal CAP-diagnosis in the elderly.

Repertoire of bacterial species cultured from the human oral cavity and respiratory tract

While the gut microbiota is currently in the spotlight, the airway microbiome has been recently associated with several pulmonary diseases and carcinogenesis. As there are several biases associated with high-throughput sequencing methods, cultivation techniques are crucial for the investigation of the human microbiome. We thus aimed to build an exhaustive database, including a list of microbes isolated by culture from respiratory specimens, by performing a review of the literature. Herein, we have listed a total of 756 species cultured from the human respiratory tract. This represents 27.23% of the overall bacterial richness captured from human being by culture methods. This repertoire could be valuable for the elucidation of the interactions between the respiratory microbiome and human health.

Impact of Procalcitonin Guidance with an Educational Program on Management of Adults Hospitalized with Pneumonia

BACKGROUND

Community-acquired pneumonia and healthcare-associated pneumonia are often treated with prolonged antibiotic therapy. Procalcitonin (PCT) has effectively and safely reduced antibiotic use for pneumonia in controlled studies. However, limited data exist regarding PCT guidance in real-world settings for management of pneumonia.

METHODS

A retrospective, preintervention/postintervention study was conducted to compare management for patients admitted with pneumonia before and after implementation of PCT guidance at 2 teaching hospitals in Pittsburgh, Pennsylvania. The preintervention period was March 1, 2014 through October 31, 2014, and the postintervention period was March, 1 2015 through October 31, 2015.

RESULTS

A total of 152 and 232 patients were included in the preintervention and postintervention cohorts, respectively. When compared with the preintervention group, mean duration of therapy decreased (9.9 vs 6.0 days; P < .001). More patients received an appropriate duration of 7 days or less (26.9% vs 66.4%; P < .001). Additionally, mean hospital length of stay decreased in the postintervention group (4.9 vs 3.5 days; P = .006). Pneumonia-related 30-day readmission rates (7.2% vs 4.3%; P = .26) were unaffected. In the postintervention group, patients with PCT levels <0.25 µg/L received shorter mean duration of therapy compared with patients with levels >0.25 µg/L (4.6 vs 8.0 days; P < .001), as well as reduced hospital length of stay (3.2 vs 3.9 days; P = .02).

CONCLUSIONS

In this real-world study, PCT guidance led to shorter durations of total antibiotic therapy and abridged inpatient length of stay without affecting hospital readmissions.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past 25 years due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation in the clinical microbiology laboratory as well as user-friendly software and robust laboratory informatics systems have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting [3, 4]. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, has benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods continues to lag behind. The purpose of this chapter is to review, update, and discuss the interpretation and relevance of results produced by these advanced molecular techniques.

Diagnosis and treatment of community-acquired pneumonia in adults: 2016 clinical practice guidelines by the Chinese Thoracic Society, Chinese Medical Association

Community‐acquired pneumonia (CAP) in adults is an infectious disease with high morbidity in China and the rest of the world. With the changing pattern in the etiological profile of CAP and advances in medical techniques in diagnosis and treatment over time, Chinese Thoracic Society of Chinese Medical Association updated its CAP guideline in 2016 to address the standard management of CAP in Chinese adults. Extensive and comprehensive literature search was made to collect the data and evidence for experts to review and evaluate the level of evidence. Corresponding recommendations are provided appropriately based on the level of evidence. This updated guideline covers comprehensive topics on CAP, including aetiology, antimicrobial resistance profile, diagnosis, empirical and targeted treatments, adjunctive and supportive therapies, as well as prophylaxis. The recommendations may help clinicians manage CAP patients more effectively and efficiently. CAP in pediatric patients and immunocompromised adults is beyond the scope of this guideline. This guideline is only applicable for the immunocompetent CAP patients aged 18 years and older. The recommendations on selection of antimicrobial agents and the dosing regimens are not mandatory. The clinicians are recommended to prescribe and adjust antimicrobial therapies primarily based on their local etiological profile and results of susceptibility testing, with reference to this guideline.

Using Standardized Interpretation of Chest Radiographs to Identify Adults with Bacterial Pneumonia--Guatemala, 2007-2012

Background

Bacterial pneumonia is a leading cause of illness and death worldwide, but quantifying its burden is difficult due to insensitive diagnostics. Although World Health Organization (WHO) protocol standardizes pediatric chest radiograph (CXR) interpretation for epidemiologic studies of bacterial pneumonia, its validity in adults is unknown.

Methods

Patients (age ≥15 years) admitted with respiratory infections to two Guatemalan hospitals between November 2007 and March 2012 had urine and nasopharyngeal/oropharyngeal (NP/OP) swabs collected; blood cultures and CXR were also performed at physician clinical discretion. ‘Any bacterial infection’ was defined as a positive urine pneumococcal antigen test, isolation of a bacterial pneumonia pathogen from blood culture, or detection of an atypical bacterial pathogen by polymerase chain reaction (PCR) of nasopharyngeal/oropharyngeal (NP/OP) specimens. ‘Viral infection’ was defined as detection of viral pathogens by PCR of NP/OP specimens. CXRs were interpreted according to the WHO protocol as having ‘endpoint consolidation’, ‘other infiltrate’, or ‘normal’ findings. We examined associations between bacterial and viral infections and endpoint consolidation.

Findings

Urine antigen and/or blood culture results were available for 721 patients with CXR interpretations; of these, 385 (53%) had endpoint consolidation and 253 (35%) had other infiltrate. Any bacterial infection was detected in 119 (17%) patients, including 106 (89%) pneumococcal infections. Any bacterial infection (Diagnostic Odds Ratio [DOR] = 2.9; 95% confidence Interval (CI): 1.3–7.9) and pneumococcal infection (DOR = 3.4; 95% CI: 1.5–10.0) were associated with ‘endpoint consolidation’, but not ‘other infiltrate’ (DOR = 1.7; 95% CI: 0.7–4.9, and 1.7; 95% CI: 0.7–4.9 respectively). Viral infection was not significantly associated with ‘endpoint consolidation’, ‘other infiltrate,’ or ‘normal’ findings.

Interpretation

‘Endpoint consolidation’ was associated with ‘any bacterial infection,’ specifically pneumococcal infection. Therefore, endpoint consolidation may be a useful surrogate for studies measuring the impact of interventions, such as conjugate vaccines, against bacterial pneumonia.

Impact of infant 13-valent pneumococcal conjugate vaccine on serotypes in adult pneumonia

Infant 13-valent pneumococcal conjugate vaccination (PCV13) was introduced to the UK in 2010. Its impact on serotypes implicated in adult non-bacteraemic pneumococcal pneumonia is not known. Beginning in 2008, a 5-year prospective cohort study of adults admitted to hospital with community-acquired pneumonia (CAP) was conducted. Pneumococcal serotype was established using a validated multiplex immunoassay (Bio-Plex; Bio-Rad, Hercules, CA, USA). The overall incidence for hospitalised CAP and pneumococcal CAP was 79.9 (95% CI 76.6-83.3) and 23.4 (95% CI 21.6-25.3) per 100,000 population, respectively. A decline in CAP (incidence rate ratio (IRR) per year 0.96, 95% CI 0.94-0.99; p=0.016) and pneumococcal CAP (IRR per year 0.84, 95% CI 0.80-0.89; p<0.001) was observed over the 5-year period of the study. Between the pre- and post-PCV13 periods of the study, the incidence of CAP due to serotypes included in the PCV7 declined by 88% (IRR 0.12, 95% CI 0.08-0.20; p<0.001), and CAP due to the additional 6 serotypes in PCV13 declined by 30% (IRR 0.70, 95% CI 0.51-0.96; p=0.024). Incidence of adult pneumococcal pneumonia declined over the last 5 years, with serotypes included in PCV13 declining post-PCV13 introduction, indicating early herd protection effects from PCV13 infant vaccination on adult non-bacteraemic disease. These effects may accrue over the coming years with implications for national pneumococcal vaccination policies in adults.

Pneumonia by Listeria monocytogenes: A Common Infection by an Uncommon Pathogen

Infections by Listeria monocytogenes typically occur in infants, the elderly, pregnant women, and immunosuppressed subjects. Pulmonary infections in adults are extremely uncommon and only few reports can be found in the literature. We here report a case of Listeria pneumonia in an 85-year-old female patient and we discuss our diagnostic and therapeutic approach. Despite being rare and in most cases difficult to be identified, Listeria pneumonia should always be considered in immunosuppressed patients, presenting with fever and symptoms from the lower respiratory system.

Validation of sputum Gram stain for treatment of community-acquired pneumonia and healthcare-associated pneumonia: a prospective observational study

BACKGROUND

The usefulness of sputum Gram stain in patients with community-acquired pneumonia (CAP) is controversial. There has been no study to evaluate the diagnostic value of this method in patients with healthcare-associated pneumonia (HCAP). The purpose of this study was to evaluate the usefulness of sputum Gram stain in etiological diagnosis and pathogen-targeted antibiotic treatment of CAP and HCAP.

METHODS

We conducted a prospective observational study on hospitalized patients with pneumonia admitted to our hospital from August 2010 to July 2012. Before administering antibiotics on admission, Gram stain was performed and examined by trained physicians immediately after sputum samples were obtained. We analyzed the quality of sputum samples and the diagnostic performance of Gram stain. We also compared pathogen-targeted antibiotic treatment guided by sputum Gram stain with empirical treatment.

RESULTS

Of 670 patients with pneumonia, 328 were CAP and 342 were HCAP. Sputum samples were obtained from 591 patients, of these 478 samples were good quality. The sensitivity and specificity of sputum Gram stain were 62.5% and 91.5% for Streptococcus pneumoniae, 60.9% and 95.1% for Haemophilus influenzae, 68.2% and 96.1% for Moraxella catarrhalis, 39.5% and 98.2% for Klebsiella pneumoniae, 22.2% and 99.8% for Pseudomonas aeruginosa, 9.1% and 100% for Staphylococcus aureus. The diagnostic yield decreased in patients who had received antibiotics or patients with suspected aspiration pneumonia. Pathogen-targeted treatment provided similar efficacy with a decrease in adverse events compared to empirical treatment.

CONCLUSIONS

Sputum Gram stain is highly specific for the etiologic diagnosis and useful in guiding pathogen-targeted antibiotic treatment of CAP and HCAP.

[First epidemiologic data on pneumonia in Cambodia]

About 15% of deaths in adults are related to lung infections in Cambodia. Some knowledge on microbial epidemiology is crucial for deciding first-line antibiotic treatment. However, to date, these data are not available in Cambodia. Consequently, antibiotic prescription relies on French or neighborhood's countries guidelines, which are possibly not suitable. This cases-series aimed to provide data on microbial ecology in pneumonia. Medical charts of patients newly admitted for lung infection in the pulmonology unit of Preah Kossamak Hospital were retrospectively reviewed. Ninety-four patients were included and 29% had a complete microbiological diagnosis. Main germs isolated were: Gram-negative bacilli (n=20; 70.4%) and M. tuberculosis infections (n=7; 25.9%). There was one case of myeloïdosis. No S. pneumonia was isolated, possibly due to sample shipping tropical conditions. Antibiograms showed high resistance profiles. Although this study bring new data in the field, it also showed that European guidelines for antibiotic are not relevant in such countries and stress the need for further dedicated and prospective studies.

Evaluation of yield of currently available diagnostics by sample type to optimize detection of respiratory pathogens in patients with a community-acquired pneumonia

BACKGROUND

For the detection of respiratory pathogens, the sampling strategy may influence the diagnostic yield. Ideally, samples from the lower respiratory tract are collected, but they are difficult to obtain.

OBJECTIVES

In this study, we compared the diagnostic yield in sputum and oropharyngeal samples (OPS) for the detection of respiratory pathogens in patients with community-acquired pneumonia (CAP), with the objective to optimize our diagnostic testing algorithm.

METHODS

Matched sputum samples, OPS, blood cultures, serum, and urine samples were taken from patients (>18 years) with CAP and tested for the presence of possible respiratory pathogens using bacterial cultures, PCR for 17 viruses and five bacteria and urinary antigen testing.

RESULTS

When using only conventional methods, that is, blood cultures, sputum culture, urinary antigen tests, a pathogen was detected in 49·6% of patients (n = 57). Adding molecular detection assays increased the yield to 80%. A pathogen was detected in 77 of the 115 patients in OPS or sputum samples by PCR. The sensitivity of the OPS was lower than that of the sputum samples (57% versus 74%). In particular, bacterial pathogens were more often detected in sputum samples. The sensitivity of OPS for the detection of most viruses was higher than in sputum samples (72% versus 66%), except for human rhinovirus and respiratory syncytial virus.

CONCLUSION

Addition of PCR on both OPS and sputum samples significantly increased the diagnostic yield. For molecular detection of bacterial pathogens, a sputum sample is imperative, but for detection of most viral pathogens, an OPS is sufficient.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past two decades due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation and user-friendly software have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, have benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods has lagged somewhat behind. The purpose of this chapter is to review and discuss the interpretation and relevance of results produced by these advanced molecular techniques. Moreover, this chapter will address the “myths” of NAATs, as these myths can markedly influence the interpretation and relevance of these results.

Usefulness of gram-stained sputum obtained just after administration of antimicrobial agents as the earliest therapeutic indicator for evaluating the effectiveness of empiric therapy in community-acquired pneumonia caused by pneumococcus or Moraxella catarrhalis

We present here three cases in which morphological changes and/or a decreased number of Streptococcus pneumoniae or Moraxella catarrhalis could be observed in gram-stained sputum obtained just after the first administration of an antimicrobial agent. Case 1 was a 53-year-old man with pneumonia caused by gram-positive diplococcus, identified as S. pneumoniae, who was administered 2 g of ampicillin over a period of 1 h. Gram-stained sputum showed smaller or gram-negative pneumococci at the completion of administration of the agent, a decreased number of cocci at 1 h after administration, and almost no cocci at 12 h after the completion of administration. Case 2 was a 72-year-old woman with pneumonia caused by diplococcus, identified as S. pneumoniae, who was administered 2 g of ampicillin over a period of 1 h. Gram-stained sputum showed weakly stained, small cocci at the completion of administration of the agent and few cocci at 1 h after the completion of administration. Case 3 was a 58-year-old woman with pneumonia caused by a gram-negative diplococcus, identified as Moraxella catarrhalis, who was administered 1 g of cefotaxime over a period of 30 min. Gram-stained sputum showed few extracellular cocci and some intracellular cocci inside neutrophils 1 h after administration and no cocci 2 h after the completion of administration. These three cases showed that gram-stained sputum obtained just after and/or 1 h after administration of the first antimicrobial agent were suitable as the quickest therapeutic indicator of the effectiveness of empiric therapy, with the effectiveness of the agent being shown much earlier than with markers such as the white blood cell count and C-reactive protein level.

Clinical, epidemiological, and etiological profile of inpatients with community-acquired pneumonia at a general hospital in the Sumaré microregion of Brazil

OBJECTIVE

To analyze the clinical, etiological, and epidemiological aspects of community-acquired pneumonia (CAP) in hospitalized individuals.

METHODS

We prospectively studied 66 patients (> 14 years of age) with CAP admitted to the Hospital Estadual Sumaré, located in the Sumaré microregion of Brazil, between October of 2005 and September of 2007. We collected data related to clinical history, physical examination, pneumonia severity index (PSI) scores, and laboratory tests (blood culture; sputum smear microscopy and culture; serology for Chlamydophila pneumoniae, Mycoplasma pneumoniae, and Legionella pneumophila; and detection of Legionella sp. and Streptococcus pneumoniae antigens in urine).

RESULTS

The mean age of patients was 53 years. Most had a low level of education, and 55.7% presented with at least one comorbidity at the time of hospitalization. The proportion of elderly people vaccinated against influenza was significantly lower among the inpatients than in the general population of the Sumaré microregion (52.6% vs. > 70%). Fever was less common among the elderly patients (p < 0.05). The clinical evolution was associated with the PSI scores but not with age. The etiology was confirmed in 31 cases (50.8%) and was attributed to S. pneumoniae, principally detected by the urinary antigen test, in 21 (34.4%), followed by C. pneumoniae, in 5 (8.2%). The mortality rate was 4.9%, and 80.3% of the patients were classified as cured at discharge.

CONCLUSIONS

The knowledge of the etiologic profile of CAP at the regional level favors the appropriate choice of empirical treatment, which is particularly relevant in elderly patients and in those with comorbidities. The lack of influenza vaccination in elderly patients is a risk factor for hospitalization due to CAP.