Etiology of community-acquired pneumonia and diagnostic yields of microbiological methods: a 3-year prospective study in Norway

Prevalence of gram negative bacteria causing community acquired pneumonia among adults in Mwanza City, Tanzania

BACKGROUND

Community acquired pneumonia (CAP) in adults is still a common and serious illness in the sub-Saharan Africa. Identification of the pathogens is crucial in the management of CAP. This study was done to determine the common bacterial pathogens, treatment outcomes and associated factors for microbiological confirmed CAP among adults attending the Bugando Medical Centre and Sekou Toure hospital in the city of Mwanza, Tanzania.

METHODS

This was a hospital based cross sectional study involving patients with community acquired pneumonia attending Bugando Medical Centre and Sekou Toure regional Hospital. Demographic and other data were collected using standardized data collection tool. Sputum culture was done followed by identification of the isolates and antibiotics susceptibility testing.

RESULTS

A total of 353 patients were enrolled in the study. Out of 353 sputum samples, 265(75%) were of good quality. Of 353 non-repetitive sputum cultures, 72/353 (20.4, 95% CI: 16.2-24.6) were positive for the bacterial pathogens with five patients having more than one pathogen. Good quality sputa had significantly higher yield of pathogenic bacteria than poor quality sputa (26.1% vs.3.4%, P = 0.001). The majority 64 (83.1%) of the isolates were gram negative bacteria. Common bacteria isolated were Klebsiella pneumoniae 23/77(29.9%), Streptococcus pyogenes 10/77 (13.0%), Pseudomonas aeruginosa 9/77 (11.7%) and Escherichia coli 7/77 (9.1%). Of 23 K. pneumoniae isolates, 20/23 (87.0%) were resistant to ceftriaxone. Resistance to ceftriaxone was found to be associated with prolongation of CAP symptoms (p = 0.009).

CONCLUSION

Gram negative bacteria resistant to ampicillin, amoxicillin/clavulanic acid and ceftriaxone were most frequently isolated bacteria among adults' patients with CAP attending BMC and Sekou Toure hospital. Routine sputum culture should be performed to guide appropriate treatment of CAP among adults in developing countries.

Empirical prescribing of penicillin G/V reduces risk of readmission of hospitalized patients with community-acquired pneumonia in Norway: a retrospective observational study

BACKGROUND

Norwegian guideline recommendations on first-line empirical antibiotic prescribing in hospitalised patients with community-acquired pneumonia (CAP) are penicillin G/V in monotherapy, or penicillin G in combination with gentamicin (or cefotaxime) in severely ill patients. The aim of this study was to explore how different empirical antibiotic treatments impact on length of hospital stay (LOS) and 30-day hospital readmission. A secondary aim was to describe median intravenous- and total treatment duration.

METHODS

We included CAP patients (≥18 years age) hospitalised in North Norway during 2010 and 2012 in a retrospective study. Patients with negative chest x-ray, malignancies or immunosuppression or frequent readmissions were excluded. We collected data on patient characteristics, empirical antibiotic prescribing, treatment duration and clinical outcomes from electronic patient records and the hospital administrative system. We used directed acyclic graphs for statistical model selection, and analysed data with mulitvariable logistic and linear regression.

RESULTS

We included 651 patients. Median age was 77 years [IQR; 64-84] and 46.5% were female. Median LOS was 4 days [IQR; 3-6], 30-day readmission rate was 14.4% and 30-day mortality rate was 6.9%. Penicillin G/V were empirically prescribed in monotherapy in 51.5% of patients, penicillin G and gentamicin in combination in 22.9% and other antibiotics in 25.6% of patients. Prescribing other antibiotics than penicillin G/V monotherapy was associated with increased risk of readmission [OR 1.9, 95% CI; 1.08-3.42]. Empirical antibiotic prescribing was not associated with LOS. Median intravenous- and total treatment duration was 3.0 [IQR; 2-5] and 11.0 [IQR; 9.8-13] days.

CONCLUSIONS

Our findings show that empirical prescribing with penicillin G/V in monotherapy in hospitalised non-severe CAP-patients, without complicating factors such as malignancy, immunosuppression and frequent readmission, is associated with lower risk of 30-day readmission compared to other antibiotic treatments. Median total treatment duration exceeds treatment recommendations.

Clinical factors influencing the performance of bacterial multiplex polymerase chain reaction in patients with community-onset pneumonia

The etiologic diagnostic yield of community-onset pneumonia (COP) using conventional methods is low. Bacterial multiplex polymerase chain reaction (mPCR) has been shown to be more sensitive than conventional methods. This study assessed the clinical factors influencing bacterial mPCR results in patients with COP. Patients with COP admitted to a tertiary care hospital between November 2015 and April 2016 were retrospectively assessed. Conventional methods included culture-based methods and serology for Mycoplasma pneumoniae. Bacterial mPCR that could identify Streptococcus pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, and Legionella pneumophilia was performed. Bacterial mPCR was performed in a total of 342 patients with COP in the study. Bacterial mPCR alone provided etiology in 99 patients. The total etiologic diagnosis rates improved from 22.2 to 51.1% when bacterial mPCR was added to conventional methods. Additional diagnostic benefits of bacterial mPCR were more prominent in the prior antibiotic non-exposure group (77.8% vs 63.5%, P = 0.015) and in the low-risk group with low CURB 65 score (62.6% vs 44.9%, P = 0.005). Patients who required ICU care, those with healthcare-associated pneumonia (HCAP), and patients with any underlying diseases were not associated with the additional pathogen detection rates using bacterial mPCR. By supplementing conventional diagnostic methods with bacterial mPCR-based methods, the overall pathogen detection rates improved in patients with COP. Moreover, the additional diagnostic usefulness of bacterial mPCR was significantly higher in patients without prior antibiotic exposure and in the mild-to-moderate-risk group with lower CURB 65 score.

RespiDisk: a point-of-care platform for fully automated detection of respiratory tract infection pathogens in clinical samples

The RespiDisk platform for automated detection of multiple viral and bacterial respiratory tract infection pathogens.

[The new comprehension of pulmonary infections]

Epidemiological data on the distribution of mostly bacterial pathogens are still the basis for empirical treatment recommendations on respiratory infections. Because of the dynamic technological developments in molecular multiplexing and sequencing procedures, the spectrum of potential pathogens is increased and challenges the current dogma of virulence and pathogenicity of certain pathogens. Classical pathogens of the lungs are thereby not questioned but are increasingly placed in a context that reflects co-infections with viruses and changes of the local microbiome in more depth. Recent data indicate that integration of this novel information is required for a better understanding of the seasonal differences in the frequency of particular lung infections and to find new approaches to risk stratification of patients. This becomes most obvious in the subgroup of immunosuppressed patients who are at risk of severe courses of diseases with higher morbidity and mortality from infections with viruses and facultative pathogens, such as nontuberculous mycobacteria (NTM). Based on the fundamental knowledge on the spectrum of pathogens of community-acquired and nosocomial lung infections, novel approaches in pathogen diagnostics and lung microbiome analytics are discussed and the applicability with respect to the current clinical routine is questioned.

Neutrophils in community-acquired pneumonia: parallels in dysfunction at the extremes of age

"Science means constantly walking a tight rope" Heinrich Rohrer, physicist, 1933. Community-acquired pneumonia (CAP) is the leading cause of death from infectious disease worldwide and disproportionately affects older adults and children. In high-income countries, pneumonia is one of the most common reasons for hospitalisation and (when recurrent) is associated with a risk of developing chronic pulmonary conditions in adulthood. Pneumococcal pneumonia is particularly prevalent in older adults, and here, pneumonia is still associated with significant mortality despite the widespread use of pneumococcal vaccination in middleand high-income countries and a low prevalence of resistant organisms. In older adults, 11% of pneumonia survivors are readmitted within months of discharge, often with a further pneumonia episode and with worse outcomes. In children, recurrent pneumonia occurs in approximately 10% of survivors and therefore is a significant cause of healthcare use. Current antibiotic trials focus on short-term outcomes and increasingly shorter courses of antibiotic therapy. However, the high requirement for further treatment for recurrent pneumonia questions the effectiveness of current strategies, and there is increasing global concern about our reliance on antibiotics to treat infections. Novel therapeutic targets and approaches are needed to improve outcomes. Neutrophils are the most abundant immune cell and among the first responders to infection. Appropriate neutrophil responses are crucial to host defence, as evidenced by the poor outcomes seen in neutropenia. Neutrophils from older adults appear to be dysfunctional, displaying a reduced ability to target infected or inflamed tissue, poor phagocytic responses and a reduced capacity to release neutrophil extracellular traps (NETs); this occurs in health, but responses are further diminished during infection and particularly during sepsis, where a reduced response to granulocyte colony-stimulating factor (G-CSF) inhibits the release of immature neutrophils from the bone marrow. Of note, neutrophil responses are similar in preterm infants. Here, the storage pool is decreased, neutrophils are less able to degranulate, have a reduced migratory capacity and are less able to release NETs. Less is known about neutrophil function from older children, but theoretically, impaired functions might increase susceptibility to infections. Targeting these blunted responses may offer a new paradigm for treating CAP, but modifying neutrophil behaviour is challenging; reducing their numbers or inhibiting their function is associated with poor clinical outcomes from infection. Uncontrolled activation and degranulation can cause significant host tissue damage. Any neutrophil-based intervention must walk the tightrope described by Heinrich Rohrer, facilitating necessary phagocytic functions while preventing bystander host damage, and this is a significant challenge which this review will explore.

Estimating the True Burden of Legionnaires' Disease

Over the past decade, the reported incidence of Legionnaires' disease (LD) in the northeastern United States has increased, reaching 1-3 cases per 100,000 population. There is reason to suspect that this is an underestimate of the true burden, since LD cases may be underdiagnosed. In this analysis of pneumonia and influenza (P&I) hospitalizations, we estimated the percentages of cases due to Legionella, influenza, and respiratory syncytial virus (RSV) by age group. We fitted mixed-effects models to estimate attributable percents using weekly time series data on P&I hospitalizations in Connecticut from 2000 to 2014. Model-fitted values were used to calculate estimates of numbers of P&I hospitalizations attributable to Legionella (and influenza and RSV) by age group, season, and year. Our models estimated that 1.9%, 8.8%, and 5.1% of total (all-ages) inpatient P&I hospitalizations could be attributed to Legionella, influenza, and RSV, respectively. Only 10.6% of total predicted LD cases had been clinically diagnosed as LD during the study period. The observed incidence rate of 1.2 cases per 100,000 population was substantially lower than our estimated rate of 11.6 cases per 100,000 population. Our estimates of numbers of P&I hospitalizations attributable to Legionella are comparable to those provided by etiological studies of community-acquired pneumonia and emphasize the potential for underdiagnosis of LD in clinical settings.

Outpatient management of community-acquired pneumonia

PURPOSE OF REVIEW

The first guidelines on community-acquired pneumonia (CAP) were published in 1993, but since then many of the challenges regarding the outpatient management of CAP persist. These include the difficulty in establishing the initial clinical diagnosis, its risk stratification, which will dictate the place of treatment, the empirical choice of antibiotics, the relative scarcity of novel antibiotics and the importance of knowing local microbiological susceptibility patterns.

RECENT FINDINGS

New molecular biology methods have changed the etiologic perspective of CAP, especially the contribution of virus. Lung ultrasound and biomarkers might aid diagnosis and severity stratification in the outpatient setting. Antibiotic resistance is a growing problem that reinforces the importance of novel antibiotics. And finally, prevention and the use of anti-pneumococcal vaccine are instrumental in reducing the burden of disease.

SUMMARY

Most of CAP cases are managed in the community; however, most research comes from hospitalized severe patients. New and awaited advances might contribute to aid diagnosis, cause and assessment of patients with CAP in the community. This knowledge might prove decisive in the execution of stewardship programmes that maintain current antibiotics, safeguard future ones and reinforce prevention.

Health Care-Associated Pneumonia: Is It Still a Useful Concept?

"Health care-associated pneumonia (HCAP) was introduced into guidelines because of concerns about the increasing prevalence of drug-resistant pathogens (DRPs) not covered by standard empirical therapy. We now know that DRPs are very localized phenomena with low rates in most sites. Although HCAP risk factors are associated with a higher mortality, this is driven by comorbidities rather than the pathogens. Empirical coverage of DRPs has generally not resulted in better patient outcomes. A far more nuanced approach must be taken for patients with risk factors for DRPs taking into account the local cause and severity of disease.

Etiology and characteristics of community-acquired pneumonia in an influenza epidemic period

PURPOSE

The etiology of community-acquired pneumonia (CAP) in hospital patients is often ambiguous due to the limited pathogen detection. Lack of a microbiological diagnosis impairs precision treatment in CAP.

METHODS

Specimens collected from the lower respiratory tract of 195 CAP patients, viruses were measured by the Single-plex real-time PCR assay and the conventional culture method was exploited for bacteria.

RESULTS

Among the 195 patients, there were 46 (23.59%) pure bacterial infections, 20 (10.26%) yeast infections, 32 (16.41%) pure viral infections, 8 (4.10%) viral-yeast co-infections, and 17 (8.72%) viral-bacterial co-infections. The two most abundant bacteria were Acinetobacter baumannii and klebsiella pneumoniae, whereas the most common virus was influenza A.

CONCLUSIONS

Non-influenza respiratory microorganisms frequently co-circulated during the epidemic peaks of influenza, which easily being ignored in CAP therapy. In patients with bacterial and viral co-infections, identifying the etiologic agent is crucial for patient's therapy.

Pneumococcal Carriage, Serotype Distribution, and Risk Factors in Children With Community-Acquired Pneumonia, 5 Years After Introduction of the 10-Valent Pneumococcal Conjugate Vaccine in Ethiopia

Background

There is a scarcity of data on pneumococcal serotypes carried by children in Ethiopia. We studied pneumococcal nasopharyngeal carriage rate, serotypes, and risk factors among children with community acquired pneumonia (CAP).

Methods

A prospective observational cohort study was performed in children with CAP, aged 0–15 years, in 2 pediatric emergency departments in Addis Ababa, Ethiopia. Nasopharyngeal swabs were cultured, and serotypes of Streptococcus pneumoniae were determined by sequencing the cpsB gene and by the Quellung reaction. Risk factors were analyzed by using binary logistic regression.

Results

Nasopharyngeal swabs were collected from 362 children with CAP. Pneumococcal carriage rate was 21.5% (78 of 362). The most common serotypes were 19A (27%), 16F (8.5%), and 6A (4.9%). In addition, 8.5% of the pneumococcal isolates were nontypeable. In bivariate analysis, children with a parent that smokes were more likely to carry pneumococci (crude odds ratio, 3.9; 95% confidence interval [CI], 1.2–12.3; P = .023) than those with parents that do not smoke. In multivariable analysis, living in a house with ≥2 rooms (adjusted odds ratio [AOR], 0.48; 95% CI, 0.28–0.82; P = .007) and vaccination with ≥2 doses of 10-valent pneumococcal conjugate vaccine (PCV10) (AOR, 0.37; 95% CI, 0.15–0.92; P = .033) were protective of pneumococcal carriage.

Conclusions

Five years after introduction of PCV10 in Ethiopia, the vaccine-related serotype 19A was predominant in the nasopharynx of children with CAP. Continued evaluation of the direct and indirect impact of PCV10 on pneumococcal serotype distribution in Ethiopia is warranted.

Pneumococcal pneumonia prevalence among adults with severe acute respiratory illness in Thailand - comparison of Bayesian latent class modeling and conventional analysis

BACKGROUND

Determining the etiology of pneumonia is essential to guide public health interventions. Diagnostic test results, including from polymerase chain reaction (PCR) assays of upper respiratory tract specimens, have been used to estimate prevalence of pneumococcal pneumonia. However limitations in test sensitivity and specificity and the specimen types available make establishing a definitive diagnosis challenging. Prevalence estimates for pneumococcal pneumonia could be biased in the absence of a true gold standard reference test for detecting Streptococcus pneumoniae.

METHODS

We conducted a case control study to identify etiologies of community acquired pneumonia (CAP) from April 2014 through August 2015 in Thailand. We estimated the prevalence of pneumococcal pneumonia among adults hospitalized for CAP using Bayesian latent class models (BLCMs) incorporating results of real-time polymerase chain reaction (qPCR) testing of upper respiratory tract specimens and a urine antigen test (UAT) from cases and controls. We compared the prevalence estimate to conventional analyses using only UAT as a reference test.

RESULTS

The estimated prevalence of pneumococcal pneumonia was 8% (95% CI: 5-11%) by conventional analyses. By BLCM, we estimated the prevalence to be 10% (95% CrI: 7-16%) using binary qPCR and UAT results, and 11% (95% CrI: 7-17%) using binary UAT results and qPCR cycle threshold (Ct) values.

CONCLUSIONS

BLCM suggests a > 25% higher prevalence of pneumococcal pneumonia than estimated by a conventional approach assuming UAT as a gold standard reference test. Higher quantities of pneumococcal DNA in the upper respiratory tract were associated with pneumococcal pneumonia in adults but the addition of a second specific pneumococcal test was required to accurately estimate disease status and prevalence. By incorporating the inherent uncertainty of diagnostic tests, BLCM can obtain more reliable estimates of disease status and improve understanding of underlying etiology.

Solithromycin monotherapy for treatment of community-acquired bacterial pneumonia: A meta-analysis of randomised controlled trials

OBJECTIVES

Solithromycin is a new monotherapy option for community-acquired bacterial pneumonia (CABP) patients. However, the efficacy and safety of solithromycin monotherapy for the treatment of CABP remains controversial. The aim of this meta-analysis was to evaluate the role that solithromycin played in the treatment of CABP.

METHODS

We systematically retrieved randomised controlled trials (RCTs) compared solithromycin with other antibiotics in the treatment of CABP, which were published on PubMed, ScienceDirect, Cochrane libary and the Clinical Trials.gov before July 2018. Ultimately, a meta-analysis of all RCTs eligible for inclusion criteria was performed.

RESULTS

Three RCTs, comprising 1855 patients, were included in the meta-analysis. There were no statistically significant differences between patients given solithromycin and those given other antibiotics with regard to early clinical response (ECR) [1855 patients, odds ratio (OR) = 1.00, 95% confidence interval (CI) 0.80 to 1.24, P = 0.99] and clinical success rates at short-term follow-up (SFU) (1855 patients, OR = 0.78, 95% CI 0.60 to 1.01, P = 0.06) in the intention-to-treat (ITT) population, as were the ECR (787 patients, OR = 0.90, 95% CI 0.64 to 1.27, P = 0.55) and clinical success rates at SFU (358 patients, OR = 0.73, 95% CI 0.41 to 1.31, P = 0.30) in microbiological intention-to-treat population (mITT). Similarly, with regard to the occurrence of treatment-emergent adverse events (TEAEs), drug-related adverse events (AEs), serious AEs, serious drug-related AEs and mortality, no statistically significant difference between patients given solithromycin and those given other antibiotics was observed.

CONCLUSION

In the treatment of CABP, solithromycin monotherapy is an effective and safe antibiotic regimen. Other advantages (ie anti-inflammatory effect, potent activity against expected pathogens of CABP and convenient clinical use) of solithromycin may make it a more fascinating option compared with the currently used regimens.

Respiratory viruses in adults hospitalised with Community-Acquired Pneumonia during the non-winter months in Melbourne: Routine diagnostic practice may miss large numbers of influenza and respiratory syncytial virus infections

Background Community-Acquired Pneumonia (CAP) is one of the highest health burden conditions in Australia. Disease notifications and other data from routine diagnosis suffers from selection bias that may misrepresent the true contribution of various aetiological agents. However existing Australian prospective studies of CAP aetiology have either under-represented elderly patients, not utilised Polymerase Chain Reaction (PCR) diagnostics or been limited to winter months. We therefore sought to re-evaluate CAP aetiology by systematically applying multiplex PCR in a representative cohort of mostly elderly patients hospitalised in Melbourne during non-winter months and compare diagnostic results with those obtained under usual conditions of care. Methods Seventy two CAP inpatients were prospectively enrolled over 2 ten-week blocks during non-winter months in Melbourne in 2016-17. Nasopharyngeal and oropharyngeal swabs were obtained at admission and analysed by multiplex-PCR for 7 respiratory viruses and 5 atypical bacteria. Results Median age was 74 (interquartile range 67-80) years, with 38 (52.8%) males and 34 (47.2%) females. PCR was positive in 24 (33.3%), including 12 Picornavirus (50.5% of those with a virus), 4 RSV (16.7%) and 4 influenza A (16.7%). CAP-Sym questionnaire responses were similar in those with and without viral infections. Most (80%) pathogens detected by the study, including all 8 cases of influenza and RSV, were not otherwise detected by treating clinicians during hospital admission. Conclusion One third of patients admitted with CAP during non-winter months had PCR-detectable respiratory viral infections, including many cases of influenza and RSV that were missed by existing routine clinical diagnostic processes. Keywords: Lower Respiratory Tract Infection (LRTI), Community-Acquired Pneumonia (CAP) Polymerase Chain Reaction (PCR), Influenza, Respiratory Syncytial Virus

[Austrian syndrome: A rare manifestation of invasive pneumococcal disease. A case report and bibliographic review]

The Austrian syndrome is a pathology caused by disseminated Streptococcus pneumoniae infection and characterized for the triad of pneumonia, endocarditis and meningitis. It has an estimated incidence of 0.9-7.8 cases per ten millions people each year, and a mortality of 32%. Alcohol abuse, as the main risk factor, appears only in four out of ten patients. Moreover, 14% of patientes do not have any risk factor. Two out of three patients are males and it occurs in the middle aged of life. It is more frequently on native valve, aortic valve is injured in the half of the cases. Severe regurgitation occurs in two per three patients. Appropriate antimicrobial treatment and early endocarditis surgery decrease mortality. It is possible that Austrian syndrome epidemiology is changing by the introduction of 13-valent pneumococcal conjugated vaccine in the children´s calendar.

Inflammatory biomarkers are associated with aetiology and predict outcomes in community-acquired pneumonia: results of a 5-year follow-up cohort study

Background

Biomarkers may facilitate clinical decisions in order to guide antimicrobial treatment and prediction of prognosis in community-acquired pneumonia (CAP). We measured serum C-reactive protein, procalcitonin (PCT) and calprotectin levels, and plasma pentraxin 3 (PTX3) and presepsin levels, along with whole-blood white cell counts, at three time-points, and examined their association with microbial aetiology and adverse clinical outcomes in CAP.

Methods

Blood samples were obtained at hospital admission, clinical stabilisation and 6-week follow-up from 267 hospitalised adults with CAP. Adverse short-term outcome was defined as intensive care unit admission and 30-day mortality. Long-term outcome was evaluated as 5-year all-cause mortality.

Results

Peak levels of all biomarkers were seen at hospital admission. Increased admission levels of C-reactive protein, PCT and calprotectin were associated with bacterial aetiology of CAP, while increased admission levels of PCT, PTX3 and presepsin were associated with adverse short-term outcome. In univariate and multivariate regression models, white blood cells and calprotectin at 6-week follow-up were predictors of 5-year all-cause mortality.

Conclusions

Calprotectin emerges as both a potential early marker of bacterial aetiology and a predictor for 5-year all-cause mortality in CAP, whereas PCT, PTX3 and presepsin may predict short-term outcome.

In 267 adults with community-acquired pneumonia, systemic calprotectin emerges as an early marker of bacterial aetiology and a predictor of 5-year mortality, whereas systemic procalcitonin, pentraxin 3 and presepsin are predictors of short-term outcomehttp://ow.ly/dz6S30nAFvn

Use of microbiology tests in the era of increasing AMR rates- a multicentre hospital cohort study

Background

Effective use of microbiology test results may positively influence patient outcomes and limit the use of broad-spectrum antibiotics. However, studies indicate that their potential is not fully utilized. We investigated microbiology test ordering practices and the use of test results for antibiotic decision-making in hospitals.

Methods

A multicentre cohort study was conducted during five months in 2014 in Medical departments across three hospitals in Western Norway. Patients treated with antibiotics for sepsis, urinary tract infections, skin and soft tissue infections, lower respiratory tract infections or acute exacerbations of chronic obstructive pulmonary disease were included in the analysis. Primary outcome measures were degree of microbiology test ordering, compliance with microbiology testing recommendations in the national antibiotic guideline and proportion of microbiology test results used to inform antibiotic treatment. Data was obtained from electronic- and paper medical records and charts and laboratory information systems.

Results

Of the 1731 patient admissions during the study period, mean compliance with microbiology testing recommendations in the antibiotic guideline was 89%, ranging from 81% in patients with acute exacerbations of chronic obstructive pulmonary disease to 95% in patients with sepsis. Substantial additional testing was performed beyond the recommendations with 298/606 (49%) of patients with lower respiratory tract infections having urine cultures and 42/194 (22%) of patients with urinary tract infections having respiratory tests. Microbiology test results from one of the hospitals showed that 18% (120/672) of patient admissions had applicable test results, but only half of them were used for therapy guidance, i.e. in total, 9% (63/672) of patient admissions had test results informing prescription of antibiotic therapy.

Conclusions

This study showed that despite a large number of microbiology test orders, only a limited number of tests informed antibiotic treatment. To ensure that microbiology tests are used optimally, there is a need to review the utility of existing microbiology tests, test ordering practices and use of test results through a more targeted and overarching approach.

Feasibility of a quantitative polymerase chain reaction assay for diagnosing pneumococcal pneumonia using oropharyngeal swabs

Streptococcus pneumoniae is the most important pathogen causing community-acquired pneumonia (CAP). The current diagnostic microbial standard detects S. pneumoniae in less than 30% of CAP cases. A quantitative polymerase chain reaction (PCR) targeting autolysin (lytA) is able to increase the rate of detection. The aim of this study is validation of this quantitative PCR in vitro using different available strains and in vivo using clinical samples (oropharyngeal swabs). The PCR autolysin (lytA) was validated by testing the intra- and inter-run variability. Also, the in vitro specificity and sensitivity, including the lower limit of detection was determined. In addition, a pilot-study was performed using samples from patients (n = 28) with pneumococcal pneumonia and patients (n = 28) with a pneumonia without detection of S. pneumoniae with the current diagnostic microbial standard, but with detection of either a viral and or another bacterial pathogen to validate this test further. The intra- and inter-run variability were relatively low (SD's ranging from 0.08 to 0.96 cycle thresholds). The lower limit of detection turned out to be 1-10 DNA copies/reaction. In-vitro sensitivity and specificity of the tested specimens (8 strains carrying lytA and 6 strains negative for lytA) were both 100%. In patients with pneumococcal and non-pneumococcal pneumonia a cut-off value of 6.000 copies/mL would lead to a sensitivity of 57.1% and a specificity of 85.7%. We were able to develop a quantitative PCR targeting lytA with good in-vitro test characteristics.

An international perspective on hospitalized patients with viral community-acquired pneumonia

BACKGROUND

Who should be tested for viruses in patients with community acquired pneumonia (CAP), prevalence and risk factors for viral CAP are still debated. We evaluated the frequency of viral testing, virus prevalence, risk factors and treatment coverage with oseltamivir in patients admitted for CAP.

METHODS

Secondary analysis of GLIMP, an international, multicenter, point-prevalence study of hospitalized adults with CAP. Testing frequency, prevalence of viral CAP and treatment with oseltamivir were assessed among patients who underwent a viral swab. Univariate and multivariate analysis was used to evaluate risk factors.

RESULTS

553 (14.9%) patients with CAP underwent nasal swab. Viral CAP was diagnosed in 157 (28.4%) patients. Influenza virus was isolated in 80.9% of cases. Testing frequency and viral CAP prevalence were inhomogeneous across the participating centers. Obesity (OR 1.59, 95%CI: 1.01-2.48; p = 0.043) and need for invasive mechanical ventilation (OR 1.62, 95%CI: 1.02-2.56; p = 0.040) were independently associated with viral CAP. Prevalence of empirical treatment with oseltamivir was 5.1%.

CONCLUSION

In an international scenario, testing frequency for viruses in CAP is very low. The most common cause of viral CAP is Influenza virus. Obesity and need for invasive ventilation represent independent risk factors for viral CAP. Adherence to recommendations for treatment with oseltamivir is poor.

Diagnosis of Haemophilus influenzae Pneumonia by Nanopore 16S Amplicon Sequencing of Sputum

We used deep sequencing of the 16S rRNA gene from sputum to identify Haemophilus influenza in a patient with community-acquired pneumonia. This method may be more effective than conventional diagnostic tests in pneumonia patients because of its speed and sensitivity.

Impact of microbial Aetiology on mortality in severe community-acquired pneumonia

BACKGROUND

The impact of different classes of microbial pathogens on mortality in severe community-acquired pneumonia is not well elucidated. Previous studies have shown significant variation in the incidence of viral, bacterial and mixed infections, with conflicting risk associations for mortality. We aimed to determine the risk association of microbial aetiologies with hospital mortality in severe CAP, utilising a diagnostic strategy incorporating molecular testing. Our primary hypothesis was that respiratory viruses were important causative pathogens in severe CAP and was associated with increased mortality when present with bacterial pathogens in mixed viral-bacterial co-infections.

METHODS

A retrospective cohort study from January 2014 to July 2015 was conducted in a tertiary hospital medical intensive care unit in eastern Singapore, which has a tropical climate. All patients diagnosed with severe community-acquired pneumonia were included.

RESULTS

A total of 117 patients were in the study. Microbial pathogens were identified in 84 (71.8%) patients. Mixed viral-bacterial co-infections occurred in 18 (15.4%) of patients. Isolated viral infections were present in 32 patients (27.4%); isolated bacterial infections were detected in 34 patients (29.1%). Hospital mortality occurred in 16 (13.7%) patients. The most common bacteria isolated was Streptococcus pneumoniae and the most common virus isolated was Influenza A. Univariate and multivariate logistic regression showed that serum procalcitonin, APACHE II severity score and mixed viral-bacterial infection were associated with increased risk of hospital mortality. Mixed viral-bacterial co-infections were associated with an adjusted odds ratio of 13.99 (95% CI 1.30-151.05, p = 0.03) for hospital mortality.

CONCLUSIONS

Respiratory viruses are common organisms isolated in severe community-acquired pneumonia. Mixed viral-bacterial infections may be associated with an increased risk of mortality.

Novel Immunoprotective Proteins of Streptococcus pneumoniae Identified by Opsonophagocytosis Killing Screen

The success of polysaccharide conjugate vaccines represents a major advance in the prevention of pneumococcal disease, but the power of these vaccines is limited by partial spectrum of coverage and high cost. Vaccines using immunoprotective proteins are a promising alternative type of pneumococcal vaccines. In this study, we constructed a library of antisera against conserved pneumococcal proteins predicted to be associated with cell surface or virulence using a combination of bioinformatic prediction and immunization of rabbits with recombinant proteins. Screening of the library by an opsonophagocytosis killing (OPK) assay identified the OPK-positive antisera, which represented 15 (OPK-positive) proteins. Further tests showed that virtually all of these OPK-positive antisera conferred passive protection against lethal infection of virulent pneumococci. More importantly, immunization with recombinant forms of three OPK-positive proteins (SP148, PBP2b, and ScpB), alone or in combination, conferred significant protection against lethal challenge of pneumococcal strains representing capsular serotypes 3, 4, and 6A in a mouse sepsis model. To our best knowledge, this work represents the first example in which novel vaccine candidates are successfully identified by the OPK screening. Our data have also provided further confirmation that the OPK activity may serve as a reliable in vitro surrogate for evaluating vaccine efficacy of pneumococcal proteins.

Incidence, Etiology, and Outcomes of Community-Acquired Pneumonia: A Population-Based Study

Background

The microbial etiology of community-acquired pneumonia (CAP) is often unclear in clinical practice, and previous studies have produced variable results. Population-based studies examining etiology and incidence are lacking. This study examined the incidence and etiology of CAP requiring hospitalization in a population-based cohort as well as risk factors and outcomes for specific etiologies.

Methods

Consecutive admissions due to CAP in Reykjavik, Iceland were studied. Etiologic testing was performed with cultures, urine-antigen detection, and polymerase chain reaction analysis of airway samples. Outcomes were length of stay, intensive care unit admission, assisted ventilation, and mortality.

Results

The inclusion rate was 95%. The incidence of CAP requiring hospitalization was 20.6 cases per 10000 adults/year. A potential pathogen was detected in 52% (164 of 310) of admissions and in 74% (43 of 58) with complete sample sets. Streptococcuspneumoniae was the most common pathogen (61 of 310, 20%; incidence: 4.1/10000). Viruses were identified in 15% (47 of 310; incidence: 3.1/10000), Mycoplasmapneumoniae were identified in 12% (36 of 310; incidence: 2.4/10000), and multiple pathogens were identified in 10% (30 of 310; incidence: 2.0/10000). Recent antimicrobial therapy was associated with increased detection of M pneumoniae (P < .001), whereas a lack of recent antimicrobial therapy was associated with increased detection of S pneumoniae (P = .02). Symptoms and outcomes were similar irrespective of microbial etiology.

Conclusions

Pneumococci, M pneumoniae, and viruses are the most common pathogens associated with CAP requiring hospital admission, and they all have a similar incidence that increases with age. Symptoms do not correlate with specific agents, and outcomes are similar irrespective of pathogens identified.

Low Levels of Immunoglobulins and Mannose-Binding Lectin Are Not Associated With Etiology, Severity, or Outcome in Community-Acquired Pneumonia

Background

Disease severity and outcome in community-acquired pneumonia (CAP) depend on the host and on the challenge of the causal microorganism(s). We measured levels of immunoglobulins (Igs) and complement in 257 hospitalized adults with CAP and examined the association of low levels of Igs or complement to microbial etiology, disease severity, and short-term and long-term outcome.

Methods

Serum Igs were analyzed in blood samples obtained at admission and at 6 weeks postdischarge if admission levels were low. Serum complement deficiencies were screened with a total complement activity enzyme-linked immunosorbent assay (ELISA), with further analyzes performed if justified. Disease severity was assessed by the CURB-65 severity score. Short-term outcome was defined as a composite end point of intensive care unit (ICU) admission and 30-day mortality, and long-term outcome as 5-year all-cause mortality.

Results

At admission, 87 (34%) patients had low levels of at least 1 Ig, with low IgG2 as the most prevalent finding (55/21%). IgG levels were lower in bacterial than viral CAP (8.48 vs 9.97 g/L, P = .023), but low Igs were not associated with microbial etiology. Fifty-five (21%) patients had low lectin pathway activity, of which 33 (13%) were mannose-binding lectin (MBL) deficient. Low admission levels of any Ig or MBL were not associated with disease severity, short-term outcome, or long-term outcome. Excluding patients defined as immunocompromised from analysis did not substantially affect these results.

Conclusion

In hospitalized adults with CAP, low admission levels of Igs or complement were in general not associated with microbial etiology, disease severity, short-term outcome, or long-term outcome.

Cytokine responses, microbial aetiology and short-term outcome in community-acquired pneumonia

BACKGROUND

The inflammatory response to community-acquired pneumonia (CAP) is orchestrated through activation of cytokine networks and the complement system. We examined the association of multiple cytokines and the terminal complement complex (TCC) with microbial aetiology, disease severity and short-term outcome.

MATERIALS AND METHODS

Plasma levels of 27 cytokines and TCC were analysed in blood samples obtained at hospital admission, clinical stabilization and 6-week follow-up from 247 hospitalized adults with CAP. Fourteen mediators were included in final analyses. Adverse short-term outcome was defined as intensive care unit (ICU) admission and 30-day mortality.

RESULTS

Cytokine and TCC levels were dynamic in the clinical course of CAP, with highest levels seen at admission for most mediators. Admission levels of cytokines and TCC did not differ between groups of microbial aetiology. High admission levels of IL-6 (odds ratio [OR] 1.47, 95% confidence interval [CI] 1.18-1.84, P = .001), IL-8 (OR 1.79, 95% CI 1.26-2.55, P = .001) and MIP-1β (OR 2.28, 95% CI 1.36-3.81, P = .002) were associated with a CURB-65 severity score of ≥3, while IL-6 (OR 1.37, 95% CI 1.07-1.74, P = .011) and MIP-1β (OR 1.86, 95% CI 1.03-3.36, P = .040) were associated with a high risk of an adverse short-term outcome.

CONCLUSIONS

In this CAP cohort, admission levels of IL-6, IL-8 and MIP-1β were associated with disease severity and/or adverse short-term outcome. Still, for most mediators, only nonsignificant variations in inflammatory responses were observed for groups of microbial aetiology, disease severity and short-term outcome.

The impact of virus infections on pneumonia mortality is complex in adults: a prospective multicentre observational study

Background

Various viruses are known to be associated with pneumonia. However, the impact of viral infections on adult pneumonia mortality remains unclear. This study aimed to clarify the effect of virus infection on pneumonia mortality among adults stratified by virus type and patient comorbidities.

Methods

This multicentre prospective study enrolled pneumonia patients aged ≥15 years from September 2011 to August 2014. Sputum samples were tested by in-house multiplex polymerase chain reaction assays to identify 13 respiratory viruses. Viral infection status and its effect on in-hospital mortality were examined by age group and comorbidity status.

Results

A total of 2617 patients were enrolled in the study and 77.8% was aged ≥65 years. 574 (21.9%) did not have comorbidities, 790 (30.2%) had chronic respiratory disease, and 1253 (47.9%) had other comorbidities. Viruses were detected in 605 (23.1%) patients. Human rhinovirus (9.8%) was the most frequently identified virus, followed by influenza A (3.9%) and respiratory syncytial virus (3.9%). Respiratory syncytial virus was more frequently identified in patients with chronic respiratory disease (4.7%) than those with other comorbidities (4.2%) and without comorbidities (2.1%) (p = 0.037). The frequencies of other viruses were almost identical between the three groups. Virus detection overall was not associated with increased mortality (adjusted risk ratio (ARR) 0.76, 95% CI 0.53–1.09). However, influenza virus A and B were associated with three-fold higher mortality in patients with chronic respiratory disease but not with other comorbidities (ARR 3.38, 95% CI 1.54–7.42). Intriguingly, paramyxoviruses were associated with dramatically lower mortality in patients with other comorbidities (ARR 0.10, 95% CI 0.01–0.70) but not with chronic respiratory disease. These effects were not affected by age group.

Conclusions

The impact of virus infections on pneumonia mortality varies by virus type and comorbidity status in adults.

Electronic supplementary material

The online version of this article (10.1186/s12879-017-2858-y) contains supplementary material, which is available to authorized users.

Assessment of the multiplex PCR-based assay Unyvero pneumonia application for detection of bacterial pathogens and antibiotic resistance genes in children and neonates

BACKGROUND

Pneumonia is a major healthcare problem. Rapid pathogen identification is critical, but often delayed due to the duration of culturing. Early, broad antibacterial therapy might lead to false-negative culture findings and eventually to the development of antibiotic resistances. We aimed to assess the accuracy of the new application Unyvero P50 based on multiplex PCR to detect bacterial pathogens in respiratory specimens from children and neonates.

METHODS

In this prospective study, bronchoalveolar lavage fluids, tracheal aspirates, or pleural fluids from neonates and children were analyzed by both traditional culture methods and Unyvero multiplex PCR.

RESULTS

We analyzed specimens from 79 patients with a median age of 1.8 (range 0.01-20.1). Overall, Unyvero yielded a sensitivity of 73.1% and a specificity of 97.9% compared to culture methods. Best results were observed for non-fermenting bacteria, for which sensitivity of Unyvero was 90% and specificity 97.3%, while rates were lower for Gram-positive bacteria (46.2 and 93.9%, respectively). For resistance genes, we observed a concordance with antibiogram of 75% for those specimens in which there was a cultural correlate.

CONCLUSIONS

Unyvero is a fast and easy-to-use tool that might provide additional information for clinical decision making, especially in neonates and in the setting of nosocomial pneumonia. Sensitivity of the PCR for Gram-positive bacteria and important resistance genes must be improved before this application can be widely recommended.

Systematic review of respiratory viral pathogens identified in adults with community-acquired pneumonia in Europe

Community-acquired pneumonia (CAP) is an important respiratory disease and the fifth leading cause of mortality in Europe. The development of molecular diagnostic tests has highlighted the contributions of respiratory viruses to the aetiology of CAP, suggesting the incidence of viral pneumonia may have been previously underestimated. We performed a systematic review and meta-analysis to describe the overall identification of respiratory viruses in adult patients with CAP in Europe, following PRISMA guidelines (PROSPERO; CRD42016037233). We searched EMBASE, MEDLINE, CINAHL, WHOLIS, COCHRANE library and grey literature sources for relevant studies, and screened these against protocol eligibility criteria. Two researchers performed data extraction and risk of bias assessments, independently, using a piloted form. Results were synthesised narratively, and random effects meta-analyses performed to calculate pooled estimates of effect; heterogeneity was quantified using I2. Twenty-eight studies met inclusion criteria of which 21 were included in the primary meta-analysis. The pooled proportion of patients with identified respiratory viruses was 22.0% (95% CI: 18.0%-27.0%), rising to 29.0% (25.0%-34.0%) in studies where polymerase chain reaction (PCR) diagnostics were performed. Influenza virus was the most frequently detected virus in 9% (7%-12%) of adults with CAP. Respiratory viruses make a substantial contribution to the aetiology of CAP in adult patients in Europe; one or more respiratory viruses are detected in about one quarter of all cases.

Hypothetical protein Cpn0423 triggers NOD2 activation and contributes to Chlamydia pneumoniae-mediated inflammation

BACKGROUND

Chlamydia pneumoniae (C. pneumoniae) is pathogenic to humans, by causing pulmonary inflammation or bronchitis in both adolescents and young adults. However, the molecular signals linking C. pneumoniae components to inflammation remain elusive. This study was to investigate the effect of Chlamydia-specific Cpn0423 of C. pneumoniae on C. pneumoniae-mediated inflammation.

RESULTS

Cpn0423 was detected outside of C. pneumoniae inclusions, which induced production of several cytokines including macrophage inflammatory protein-2 (MIP-2) and interleukins (ILs). Production of the Cpn0423-induced cytokines was markedly reduced in cells pretreated with NOD2-siRNA, but not with negative control oligonucleotides. Mice treated with Cpn0423 through intranasal administration exhibited pulmonary inflammation as evidenced by infiltration of inflammatory cells, increased inflammatory scores in the lung histology, recruitment of neutrophils and increased cytokines levels in the BALF.

CONCLUSION

Cpn0423 could be sensed by NOD2, which was identified as an essential element in a pathway contributing to the development of C. pneumoniae -mediated inflammation.

Burden of vaccine-preventable pneumococcal disease in hospitalized adults: A Canadian Immunization Research Network (CIRN) Serious Outcomes Surveillance (SOS) network study

BACKGROUND

Pneumococcal community acquired pneumonia (CAP_Spn) and invasive pneumococcal disease (IPD) cause significant morbidity and mortality worldwide. Although childhood immunization programs have reduced the overall burden of pneumococcal disease, there is insufficient data in Canada to inform immunization policy in immunocompetent adults. This study aimed to describe clinical outcomes of pneumococcal disease in hospitalized Canadian adults, and determine the proportion of cases caused by vaccine-preventable serotypes.

METHODS

Active surveillance for CAP_Spn and IPD in hospitalized adults was performed in hospitals across five Canadian provinces from December 2010 to 2013. CAP_Spn were identified using sputum culture, blood culture, a commercial pan-pneumococcal urine antigen detection (UAD), or a serotype-specific UAD. The serotype distribution was characterized using Quellung reaction, and PCR-based serotyping on cultured isolates, or using a 13-valent pneumococcal conjugate vaccine (PCV13) serotype-specific UAD assay.

RESULTS AND CONCLUSIONS

In total, 4769 all-cause CAP cases and 81 cases of IPD (non-CAP) were identified. Of the 4769 all-cause CAP cases, a laboratory test for S. pneumoniae was performed in 3851, identifying 14.3% as CAP_Spn. Of CAP cases among whom all four diagnostic test were performed, S. pneumoniae was identified in 23.2% (144/621). CAP_Spn cases increased with age and the disease burden of illness was evident in terms of requirement for mechanical ventilation, intensive care unit admission, and 30-day mortality. Of serotypeable CAP_Spn or IPD results, predominance for serotypes 3, 7F, 19A, and 22F was observed. The proportion of hospitalized CAP cases caused by a PCV13-type S. pneumoniae ranged between 7.0% and 14.8% among cases with at least one test for S. pneumoniae performed or in whom all four diagnostic tests were performed, respectively. Overall, vaccine-preventable pneumococcal CAP and IPD were shown to be significant causes of morbidity and mortality in hospitalized Canadian adults in the three years following infant PCV13 immunization programs in Canada.

Nasopharyngeal polymicrobial colonization during health, viral upper respiratory infection and upper respiratory bacterial infection

OBJECTIVES

We sought to understand how polymicrobial colonization varies during health, viral upper respiratory infection (URI) and acute upper respiratory bacterial infection to understand differences in infection-prone vs. non-prone patients.

METHODS

Nasopharyngeal (NP) samples were collected from 74 acute otitis media (AOM) infection-prone and 754 non-prone children during 2094 healthy visits, 673 viral URI visits and 631 AOM visits. Three otopathogens Streptococcus pneumoniae (Spn), Nontypeable Haemophilus influenzae (NTHi), and Moraxella catarrhalis (Mcat) were identified by culture.

RESULTS

NP colonization rates of multiple otopathogens during health were significantly lower than during viral URI, and during URI they were lower than at onset of upper respiratory bacterial infection in both AOM infection-prone and non-prone children. AOM infection-prone children had higher polymicrobial colonization rates than non-prone children during health, viral URI and AOM. Polymicrobial colonization rates of AOM infection-prone children during health were equivalent to that of non-prone children during viral URI, and during viral URI were equivalent to that of non-prone during AOM infection. Spn colonization was positively associated with NTHi and Mcat colonization during health, but negatively during AOM infection.

CONCLUSION

The infection-prone patients more frequently have multiple potential bacterial pathogens in the NP than the non-prone patients. Polymicrobial interaction in the NP differs during health and at onset of infection.

Viral infection in community-acquired pneumonia: a systematic review and meta-analysis

The advent of PCR has improved the identification of viruses in patients with community-acquired pneumonia (CAP). Several studies have used PCR to establish the importance of viruses in the aetiology of CAP.We performed a systematic review and meta-analysis of the studies that reported the proportion of viral infection detected via PCR in patients with CAP. We excluded studies with paediatric populations. The primary outcome was the proportion of patients with viral infection. The secondary outcome was short-term mortality.Our review included 31 studies. Most obtained PCR via nasopharyngeal or oropharyngeal swab. The pooled proportion of patients with viral infection was 24.5% (95% CI 21.5-27.5%). In studies that obtained lower respiratory samples in >50% of patients, the proportion was 44.2% (95% CI 35.1-53.3%). The odds of death were higher in patients with dual bacterial and viral infection (OR 2.1, 95% CI 1.32-3.31).Viral infection is present in a high proportion of patients with CAP. The true proportion of viral infection is probably underestimated because of negative test results from nasopharyngeal or oropharyngeal swab PCR. There is increased mortality in patients with dual bacterial and viral infection.

Serotype Replacement in Adult Pneumococcal Pneumonia after the Introduction of Seven-Valent Pneumococcal Conjugate Vaccines for Children in Japan: a Systematic Literature Review and Pooled Data Analysis

Streptococcus pneumoniae is the major causative agent for adult pneumonia. Following the introduction of pneumococcal conjugate vaccines (PCV) for children, serotype replacement has been reported in adult invasive pneumococcal diseases but has not been well studied for cases of pneumococcal pneumonia in adults in Asia. To investigate serotype replacement in adult pneumococcal pneumonia in Japan, we conducted a systematic review of the literature across 5 databases using terms, including pneumococcus, serotype, their synonyms, and derivatives. After the assessment of the identified articles, data on the pneumococcal serotype distribution among adult pneumonia cases were extracted from relevant studies. Twenty-two studies were reviewed, and 4 relevant articles were included in the pooled data analysis. The proportion of the 7-valent PCV (PCV7)-covered serotypes from before and after the introduction of PCV7 for children (－18.1%, p ＜ 0.001) significantly decreased; moreover, the proportions of serotypes covered by PCV13 but not PCV7 (＋9.9%, p = 0.003) and those covered by the 23-valent polysaccharide vaccine but not PCV7 (＋9.4%, p = 0.007) significantly increased. Serotype replacement occurred in adult cases of pneumococcal pneumonia following vaccination of children with PCV7 in Japan. Further nationwide surveillance is warranted to investigate serotype replacement in the post-PCV13 phase.

Utility of oropharyngeal real-time PCR for S. pneumoniae and H. influenzae for diagnosis of pneumonia in adults

A lack of sensitive tests and difficulties obtaining representative samples contribute to the challenge in identifying etiology in pneumonia. Upper respiratory tract swabs can be easily collected and analyzed with real-time PCR (rtPCR). Common pathogens such as S. pneumoniae and H. influenzae can both colonize and infect the respiratory tract, complicating the interpretation of positive results. Oropharyngeal swabs were collected (n = 239) prospectively from adults admitted to hospital with pneumonia. Analysis with rtPCR targeting S. pneumoniae and H. influenzae was performed and results compared with sputum cultures, blood cultures, and urine antigen testing for S. pneumoniae. Different Ct cutoff values were applied to positive tests to discern colonization from infection. Comparing rtPCR with conventional testing for S. pneumoniae in patients with all tests available (n = 57) resulted in: sensitivity 87 %, specificity 79 %, PPV 59 % and NPV 94 %, and for H. influenzae (n = 67): sensitivity 75 %, specificity 80 %, PPV 45 % and NPV 94 %. When patients with prior antimicrobial exposure were excluded sensitivity improved: 92 % for S. pneumoniae and 80 % for H. influenzae. Receiver operating characteristic curve analysis demonstrated for S. pneumoniae: AUC = 0.65 (95 % CI 0.51-0.80) and for H. influenzae: AUC = 0.86 (95 % CI 0.72-1.00). Analysis of oropharyngeal swabs using rtPCR proved both reasonably sensitive and specific for diagnosing pneumonia caused by S. pneumoniae and H. influenzae. This method may be a useful diagnostic adjunct to other methods and of special value in patients unable to provide representative lower airway samples.

Retrospective review of epidemic viral pneumonia cases in Turkey: A multicenter study

Influenza A (H1N1) caused its first pandemic in 2009 in USA and Mexico. Since then, clinicians have exercised great care in order to make an early diagnosis of viral pneumonias. This is due in part to pandemic influenza A infection having greater impact on populations <65 years old than other viral strains, including seasonal influenza. Chest radiographies of those affected displayed a rapid progression of patchy infiltrates, and a large proportion of individuals required admission to intensive care units (ICU). Despite efforts, patients infected with the virus had a high mortality rate. The present multicenter study aimed to retrospectively evaluate the clinical, demographic and prognostic characteristics of patients diagnosed with epidemic viral pneumonia in Turkey. A total of 92 patients were included in the study. The Student's t-test and Chi-square tests were performed to analyze quantitative data, assuming a normal distribution, and to analyze qualitative data, respectively. Stepwise logistic regression was used to evaluate the effects of demographic variables and laboratory values on the virus mortality rate. The male/female ratio was 42/50 and the mean age was 48.74±16.65 years. A total of 69 (75%) patients were unvaccinated against influenza. The most common symptoms were cough (87%) and fever (63%). Chest computed tomography showed peripheral patchy areas of the lungs of ground glass density in 38 patients (41.3%). A total of 22 (59.4%) patients had H1N1, 5 (12.5%) patients had influenza B, and 38 (41.3%) patients met the criteria for admission to the ICU. Of these patients, 20 (52.63%) were monitored with a mechanical ventilator, with a noninvasive ventilator being adequate for 10 (26.32%) of patients. The length of stay in the ICU was 6.45±5.97 days and the duration of mechanical ventilation was 5.06±4.69 days. A total of 12 (13.04%) patients in the ICU succumbed. Logistic regression analysis revealed that among the parameters possibly associated with mortality, being an active smoker increased the risk of mortality 7.08-fold compared to other groups (P=0.005). In conclusion, viral pneumonia remains a significant health problem during the winter period. Considering the high number of ICU admissions and high rate of mortality for patients in the present study, earlier initiation of antiviral therapy is necessary. Active smoking increased mortality in viral pneumonia.

Seasonality, risk factors and burden of community-acquired pneumonia in COPD patients: a population database study using linked health care records

Background

Community-acquired pneumonia (CAP) is more common in patients with COPD than in the adult general population, with studies of hospitalized CAP patients consistently reporting COPD as a frequent comorbidity. However, despite an increasing recognition of its importance, large studies evaluating the incidence patterns over time, risk factors and burden of CAP in COPD are currently lacking.

Methods

A retrospective observational study using a large UK-based database of linked primary and secondary care records was conducted. Patients with a diagnosis of COPD aged ≥40 years were followed up for 5 years from January 1, 2010. CAP and exacerbation episodes were identified from hospital discharge data and primary care coding records, and rates were calculated per month, adjusting for mortality, and displayed over time. In addition, baseline factors predicting future risk of CAP and hospital admission with CAP were identified.

Results

A total of 14,513 COPD patients were identified: 13.4% (n=1,938) had ≥1 CAP episode, of whom 18.8% suffered from recurrent (≥2) CAP. Highest rates of both CAP and exacerbations were seen in winter. A greater proportion of frequent, compared to infrequent, exacerbators experienced recurrent CAP (5.1% versus 2.0%, respectively, P<0.001); 75.6% of CAP episodes were associated with hospital admission compared to 22.1% of exacerbations. Older age and increasing grade of airflow limitation were independently associated with increased odds of CAP and hospital admission with CAP. Other independent predictors of future CAP included lower body mass index, inhaled corticosteroid use, prior frequent exacerbations and comorbidities, including ischemic heart disease and diabetes.

Conclusion

CAP in COPD demonstrates clear seasonal patterns, with patient characteristics predictive of the odds of future CAP and hospital admission with CAP. Highlighting this burden of COPD-associated CAP during the winter period informs us of the likely triggers and the need for more effective preventive strategies.

Multiplex Urinary Antigen Detection for 13 Streptococcus pneumoniae Serotypes Improves Diagnosis of Pneumococcal Pneumonia in South African HIV-Infected Adults

A serotype-specific urinary antigen detection (UAD) assay for 13 serotypes included in the pneumococcal conjugate vaccine (PCV13) was recently reported as a useful diagnostic tool for pneumococcal pneumonia. We aimed to assess the diagnostic accuracy of the UAD in HIV-infected South African adults. Urine specimens from a well-defined cohort of HIV-infected South African adults with pneumonia were evaluated retrospectively in the UAD assay. Pneumonia was considered pneumococcal if either sputum Gram stain, sputum culture, blood culture, or the immunochromatographic (ICT) BinaxNow S. pneumoniae test (composite diagnostic) was positive. Among 235 enrolled pneumonia patients, the UAD assay was more frequently positive (104 [44.3%]) than the composite diagnostic (71 [30.2%]; P < 0.001) and increased the pneumococcal etiology from 30.2% by an additional 22.6% to 52.8%. The UAD assay detected more pneumococcal etiologies (45.0%) than the serotype-independent ICT (23.4%, P < 0.001). UAD identified 6/7 patients with PCV13 serotype bacteremia without misclassification of bacteremia episodes due to non-PCV13 serotypes. UAD was positive for 5.1% of asymptomatic HIV-infected persons, with higher rates among those with nasopharyngeal carriage. Concordance between serotypes identified by UAD and by Quellung reaction and PCR serotyping was 70/86 (81.4%). UAD identified the dominant serotype in multiple serotype carriage. This study confirms the utility of the UAD assay for HIV-infected adults comparing favorably with other diagnostic tests. A highly valent UAD may become a new standard for detection of pneumococcal pneumonia in adults. Prior to PCV introduction, at least 53% of pneumonia cases were due to pneumococci in HIV-infected South African adults.

Vitamin D Status and Long-Term Mortality in Community-Acquired Pneumonia: Secondary Data Analysis from a Prospective Cohort

Background

Low vitamin D status has been associated with short-term (30-day) mortality in hospitalized adults with community-acquired pneumonia (CAP). Data on its prevalence in these patients are scarce, and impact on long-term prognosis is unknown. We examined the prevalence of vitamin D deficiency and inadequacy and their effect on long-term mortality in hospitalized adults with CAP.

Methods

Secondary follow-up analysis of data from a prospectively recruited (January 2008–January 2011) well-defined cohort of 241 hospital survivors of CAP (Norway, latitude 60°N). Serum 25-hydroxyvitamin D levels, demographic, clinical, and laboratory data were measured within 48 hours of admission. The etiology of CAP was established in 63% of patients through extensive microbiological investigations. Mortality data were obtained from the national Cause of Death Registry. Explanatory strategy and Cox regression models were used to explore the association between vitamin D status and all-cause mortality.

Results

Median age was 66 years. Eighty-seven (36%) patients were vitamin D deficient (<30 nmol/L), 81 (34%) were inadequate (30–49 nmol/L), and 73 (30%) were sufficient (≥50 nmol/L). Seventy-two patients died over a median of 1839 days (range 1–2520 days), corresponding to cumulative 5-year survival rates of 66.2% (95% CI 56.2–76.2%), 77.0% (67.6–86.4%), and 77.8% (67.8–87.8%) for vitamin D deficient, inadequate, and sufficient patients, respectively. After adjusting for confounders (age, chronic obstructive pulmonary disease, immunocompromization and season), vitamin D deficiency, but not inadequacy, was significantly associated with higher mortality compared to patients with sufficiency (HR 1.91, 95% CI 1.06–3.45; P = .031).

Conclusions

There is a high prevalence of vitamin D deficiency and inadequacy among hospitalized adults with CAP. The results of this study also suggest that vitamin D deficiency is associated with an increased risk of mortality way beyond the short-term in these patients.

Underdiagnosing of Mycoplasma pneumoniae infections as revealed by use of a respiratory multiplex PCR panel

We compared a multiplex PCR diagnostic approach against specific PCR diagnosis for detection of Mycoplasma pneumoniae infection. Seventy-five percent of all M. pneumoniae infections were only detected "unintentionally" by the use of the multiplex PCR indicating underdiagnosing of M. pneumoniae due to absence of clinical suspicion.

Mycoplasma pneumoniae: Current Knowledge on Nucleic Acid Amplification Techniques and Serological Diagnostics

Mycoplasma pneumoniae (M. pneumoniae) belongs to the class Mollicutes and has been recognized as a common cause of respiratory tract infections (RTIs), including community-acquired pneumonia (CAP), that occur worldwide and in all age groups. In addition, M. pneumoniae can simultaneously or sequentially lead to damage in the nervous system and has been associated with a wide variety of other acute and chronic diseases. During the past 10 years, the proportion of LRTI in children and adults, associated with M. pneumoniae infection has ranged from 0 to more than 50%. This variation is due to the age and the geographic location of the population examined but also due to the diagnostic methods used. The true role of M. pneumoniae in RTIs remains a challenge given the many limitations and lack of standardization of the applied diagnostic tool in most cases, with resultant wide variations in data from different studies. Correct and rapid diagnosis and/or management of M. pneumoniae infections is, however, critical to initiate appropriate antibiotic treatment and is nowadays usually done by PCR and/or serology. Several recent reviews, have summarized current methods for the detection and identification of M. pneumoniae. This review will therefore provide a look at the general principles, advantages, diagnostic value, and limitations of the most currently used detection techniques for the etiological diagnosis of a M. pneumoniae infection as they evolve from research to daily practice.

The clinical management of lower respiratory tract infections

The 2010 Global Burden of Disease Study reported that lower respiratory tract infections, including pneumonia, are the fourth most common cause of death globally. The etiology of acute bronchitis and asthma exacerbations is mostly viral and the therapy is symptomatic. Management decisions in community acquired pneumonia regarding site of care, extent of assessment, and level of treatment are based primarily on disease severity (outpatient, inpatient, ICU admission). Antibiotics are the main choice of treatment for patients with pneumonia, acute exacerbations (AE) of COPD (including increased sputum purulence and worsening shortness of breath) and AE of non-CF bronchiectasis. Inhaled antibiotics may represent a more optimal approach for the treatment and prevention of AE of non-CF bronchiectasis. Approved strategies for the prevention of exacerbations include smoking cessation and rehabilitation programs, drug therapy and vaccination.

Cost effectiveness of adherence to IDSA/ATS guidelines in elderly patients hospitalized for Community-Aquired Pneumonia

BACKGROUND

Adherence to guidelines for the treatment of hospitalized elderly patients with community-acquired pneumonia (CAP) has been associated with improved clinical outcomes. This study evaluated the cost-effectiveness of adherence to guidelines for the treatment of CAP in an elderly hospitalized patient cohort.

METHODS

Data from an international, multicenter observational study for patients age 65 years or older hospitalized with CAP from 2001 to 2007 were used to estimate transition probabilities for a multi-state Markov model traversing multiple health states during hospitalization for CAP. Empiric antibiotic therapy was classified as adherent, over-treated, and under-treated according to 2007 Infectious Disease Society of America/American Thoracic Society IDSA/ATS guidelines. Utilities were estimated from an expert panel of active clinicians. Costs were estimated from a tertiary referral hospital and adjusted for inflation to 2013 US dollars. Costs, utilities, and transition probabilities were all modeled using probability distributions to handle their inherit uncertainty. Cost-effectiveness analysis was based on the first 14 days of hospitalization. Patients admitted to the intensive care unit (ICU) were analyzed separately from those admitted to the ward. Sensitivity analyses with regards to time frame (out to 30 days hospitalization), cost estimates, and willingness to pay values were performed.

RESULTS

The model parameters were estimated using data from 1635 patients (1438 admitted to the ward and 197 admitted to the ICU). For the ward model, adherence to antibiotic guidelines was the dominant strategy and associated with lower costs (-$1379 and -$799) and improved quality of life compared to over- and under-treatment. In the ICU model, however, adherence to guidelines was associated with greater costs (+$13,854 and + $3461 vs. over- and under-treatment, respectively) and lower quality of life. Acceptance rates across the willingness to pay ranges evaluated were 42-48 % for guideline adherence on the ward and 61-64 % for over-treatment on the ICU. Results were robust over sensitivity analyses concerning cost and utility estimates.

CONCLUSIONS

While adherence to antibiotic guidelines was the most cost-effective strategy for elderly patients hospitalized with CAP and admitted to the ward, in the ICU over-treatment of patients relative to the guidelines was the most cost-effective strategy.

An audit and feedback intervention study increased adherence to antibiotic prescribing guidelines at a Norwegian hospital

Background

Appropriate antibiotic prescribing is associated with favourable levels of antimicrobial resistance (AMR) and clinical outcomes. Most intervention studies on antibiotic prescribing originate from settings with high level of AMR. In a Norwegian hospital setting with low level of AMR, the literature on interventions for promoting guideline-recommended antibiotic prescribing in hospital is scarce and requested. Preliminary studies have shown improvement potentials regarding antibiotic prescribing according to guidelines. We aimed to promote appropriate antibiotic prescribing in patients with community-acquired pneumonia (CAP) and acute exacerbations of chronic obstructive pulmonary disease (AECOPD) at a respiratory medicine department in a Norwegian University hospital. Our specific objectives were to increase prescribing of appropriate empirical antibiotics, reduce high-dose benzylpenicillin and reduce total treatment duration.

Methods

We performed an audit and feedback intervention study, combined with distribution of a recently published pocket version of the national clinical practice guideline. We included patients discharged with CAP or AECOPD and prescribed antibiotics during hospital stay, and excluded those presenting with aspiration, nosocomial infection and co-infections. The pre- and post-intervention period was 9 and 6 months, respectively. Feedback was provided orally to the department physicians at an internal-educational meeting. To explore the effect of the intervention on appropriate empirical antibiotics and mean total treatment duration we applied before-after analysis (Student’s t-test) and interrupted time series (ITS). We used Pearson’s χ2 to compare dose changes.

Results

In the pre-and post-intervention period we included 253 and 155 patients, respectively. Following the intervention, overall mean prescribing of appropriate empirical antibiotics increased from 61.7 to 83.8 % (P < 0.001), overall mean total treatment duration decreased from 11.2 to 10.4 days (P = 0.015), and prescribing of high-dose benzylpenicillin decreased from 48.8 to 38.6 % (P = 0.125). With ITS we found that six months post-intervention, the effect on appropriate empirical antibiotic prescribing had increased and sustained, while the effect on treatment duration was at pre-intervention level.

Conclusion

The combination of audit and feedback plus distribution of a pocket version of guideline recommendations led to a substantial increase in prescribing of appropriate empirical antibiotics, which is important due to favourable effect on AMR and clinical outcomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-016-1426-1) contains supplementary material, which is available to authorized users.

Efficacy and safety of oral solithromycin versus oral moxifloxacin for treatment of community-acquired bacterial pneumonia: a global, double-blind, multicentre, randomised, active-controlled, non-inferiority trial (SOLITAIRE-ORAL)

BACKGROUND

Community-acquired bacterial pneumonia (CABP) is a leading cause of morbidity and mortality, and treatment recommendations, each with specific limitations, vary globally. We aimed to compare the efficacy and safety of solithromycin, a novel macrolide, with moxifloxacin for treatment of CABP.

METHODS

We did this global, double-blind, double-dummy, randomised, active-controlled, non-inferiority trial at 114 centres in North America, Latin America, Europe, and South Africa. Patients (aged ≥18 years) with clinically and radiographically confirmed pneumonia of Pneumonia Outcomes Research Team (PORT) risk class II, III, or IV were randomly assigned (1:1), via an internet-based central block randomisation procedure (block size of four), to receive either oral solithromycin (800 mg on day 1, 400 mg on days 2-5, placebo on days 6-7) or oral moxifloxacin (400 mg on days 1-7). Randomisation was stratified by geographical region, PORT risk class (II vs III or IV), and medical history of asthma or chronic obstructive pulmonary disease. The study sponsor, investigators, staff, and patients were masked to group allocation. The primary outcome was early clinical response, defined as an improvement in at least two of four symptoms (cough, chest pain, sputum production, dyspnoea) with no worsening in any symptom at 72 h after the first dose of study drug, with a 10% non-inferiority margin. The primary analysis was by intention to treat. This trial is registered with ClinicalTrials.gov, number NCT-01756339.

FINDINGS

Between Jan 3, 2013, and Sept 24, 2014, we randomly assigned 860 patients to receive solithromycin (n=426) or moxifloxacin (n=434). Patients were followed up to days 28-35 after first dose. Solithromycin was non-inferior to moxifloxacin in achievement of early clinical response: 333 (78·2%) patients had an early clinical response in the solithromycin group versus 338 (77·9%) patients in the moxifloxacin group (difference 0·29, 95% CI -5·5 to 6·1). Both drugs had a similar safety profile. 43 (10%) of 155 treatment-emergent adverse events in the solithromycin group and 54 (13%) of 154 such events in the moxifloxacin group were deemed to be related to study drug. The most common adverse events, mostly of mild severity, were gastrointestinal disorders, including diarrhoea (18 [4%] patients in the solithromycin group vs 28 [6%] patients in the moxifloxacin group), nausea (15 [4%] vs 17 [4%] patients) and vomiting (ten [2%] patients in each group); and nervous system disorders, including headache (19 [4%] vs 11 [3%] patients) and dizziness (nine [2%] vs seven [2%] patients).

INTERPRETATION

Oral solithromycin was non-inferior to oral moxifloxacin for treatment of patients with CABP, showing the potential to restore macrolide monotherapy for this indication.

FUNDING

Cempra.