Epidemiology of lower respiratory tract infections in adults

Diagnostic value of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in patients with lower respiratory tract infections

BACKGROUND

Current diagnostic methods of lower respiratory tract infections (LRTIs) often lack specificity, underscoring the necessity for advanced technologies such as metagenomic next-generation sequencing (mNGS).

METHODS

This retrospective study compared bronchoalveolar lavage fluid (BALF) analysis using mNGS and conventional microbiological tests (CMT) to evaluate their effectiveness in pathogen identification and alignment with clinical diagnoses.

RESULTS

In this study involving 369 patients suspected of LTRIs, mNGS identified pathogens in 342 cases (92.7%), showing superior diagnostic performance compared to CMT (58.8%). The positive agreement and negative agreement rates of mNGS were 92.7% and 96.3%, respectively, both significantly higher than those of CMT (both p<0.001). The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were significantly higher than those of CMT, with values of 99.7% vs. 57.1%, 68.4% vs. 26.3%, 96.5% vs. 87.1%, and 96.3% vs. 6.3%, respectively (all p<0.001). Pathogen detection rates among the patients showed that 89.7% had evidence of LRTIs, with bacterial infections (20.1%), mycoplasma (13.6%), mycobacterium (4.3%), fungal (4.1%), viral (3.3%), and mixed infections (44.4%) being the most common. Furthermore, the study also differentiated the distribution of pathogens between adults and pediatric patients, and assessed the impact of pathogen types on severe outcomes using multivariate logistic regression, revealing that viral and fungal infections were more likely associated with severe symptoms, whereas mycoplasma infections typically presented with milder symptoms.

CONCLUSIONS

BALF mNGS proves effective for rapid, comprehensive pathogen detection in LRTIs, warranting its early use for enhanced diagnosis and management, especially across different age groups.

Relative Contribution of Diagnostic Testing to the Diagnosis of Respiratory Syncytial Virus in Hospitalized Adults in the United States

BACKGROUND

Respiratory syncytial virus (RSV) is a leading cause of acute respiratory illness (ARI) in older adults. Optimizing diagnosis could improve understanding of RSV burden.

METHODS

We enrolled adults ≥50 years of age hospitalized with ARI and adults of any age hospitalized with congestive heart failure or chronic obstructive pulmonary disease exacerbations at 2 hospitals during 2 respiratory seasons (2018-2020). We collected nasopharyngeal (NP) and oropharyngeal (OP) swabs (n = 1558), acute and convalescent sera (n = 568), and expectorated sputum (n = 153) from participants, and recorded standard-of-care (SOC) NP results (n = 805). We measured RSV antibodies by 2 immunoassays and performed BioFire testing on respiratory specimens.

RESULTS

Of 1558 eligible participants, 92 (5.9%) tested positive for RSV by any diagnostic method. Combined NP/OP polymerase chain reaction (PCR) testing yielded 58 positives, while separate NP and OP testing identified 11 additional positives (18.9% increase). Compared to study NP/OP PCR alone, the addition of paired serology increased RSV detection by 42.9% (28 vs 40) among those with both specimen types, while the addition of SOC swab PCR increased RSV detection by 25.9% (47 vs 59).

CONCLUSIONS

The addition of paired serology testing, SOC swab results, and separate testing of NP and OP swabs improved RSV diagnostic yield in hospitalized adults.

A Retrospective Analysis of Mortality Due to Pneumonia and Renal Disease in a Midwestern Patient Population

BACKGROUND

The impact of pneumonia (PNA) with concomitant renal disease (RD) has not been fully investigated in a United States Midwestern patient population, despite the morbidity and mortality associated with such diseases.

MATERIALS AND METHODS

A retrospective cohort study was performed on International Classification of Diseases, 10th Revision (ICD-10) data from a hospital system located in Southwest Missouri. Data was acquired from patients admitted between January 2019 and December 2021. Patients were separated into five groups (disease categories): acute kidney injury (AKI), chronic kidney disease (CKD), PNA, AKI with PNA, and CKD with PNA. The data were analyzed, and subset analysis was performed utilizing two-sample proportion tests (Wald test) to compare mortality rates. Informed consent was not needed due to the retrospective nature of the study.

RESULTS

 The mortality rate of patients with PNA with AKI and PNA with CKD was 36.08% (32.87% to 39.28%, 95% CI) and 24.97% (21.93% to 28.00%, 95% CI), respectively, revealing a significant increase in mortality for thosediagnosed with PNA and AKI -higher than any other disease category. For reference, PNA without (w/o) RD, CKD w/o PNA, and AKI w/o PNA had much lower mortality rates at 9.45%, 7.87% and 12.19%, respectively, with AKI w/o PNA having a 2.63% to 6.00% higher (p<0.0001) and 0.99% to 4.49% higher (p=0.0020), mortality alone than CKD w/o PNA or PNA w/o RD, respectively.

DISCUSSION AND CONCLUSION

Mortality associated with RD and PNA was examined in a predominantly rural, relatively poor, Midwestern patient population presenting to a tertiary center with the key finding that the presence of AKI correlates with a much greater mortality rate in both patients with and without PNA. Looking forward, future studies may include a broader population base(including urban, suburban, and rural areas), allowing not only for more statistical power but also a broader assessment of the population.Such knowledge is invaluable as we continue to prioritize healthcare resources for critically ill patients suffering from RD and PNA in different settings.

Sex differences in the impact of lower respiratory tract infections on older adults' health trajectories: a population-based cohort study

BACKGROUND

Lower respiratory tract infections (LRTIs) are a major global health concern, particularly among older adults, who have an increased risk of poorer health outcomes that persist beyond the acute infectious episode. We aimed to investigate the mid-term (up to 7 years) and long-term (up to 12 years) effects of LRTIs on the objective health status trajectories of older adults, while also considering potential sex differences.

METHODS

Cohort data of adults aged ≥ 60 years from the Swedish National study of Aging and Care in Kungsholmen (SNAC-K) collected between 2001 and 2016 was analyzed. Information on LRTIs was obtained from the Swedish National Patient Register, and objective health status was assessed using the Health Assessment Tool (HAT) which incorporates indicators of mild and severe disability, cognitive and physical functioning, and multimorbidity. The LRTI-exposed and -unexposed participants were matched using propensity score matching based on an expansive list of potential confounders. Mixed linear models were used to analyze the association between LRTIs and changes in HAT scores.

RESULTS

The study included 2796 participants, 567 of whom were diagnosed with a LRTI. LRTIs were independently associated with an excess annual decline of 0.060 (95% CI: -0.107, -0.013) in the HAT score over a 7-year period. The associations were stronger among males, who experienced an excess annual decline of 0.108 (95% CI: -0.177, -0.039) in up to 7-years follow-up, and 0.097 (95% CI: -0.173, -0.021) in up to 12-years follow-up. The associations were not statistically significant among females in either follow-up period.

CONCLUSION

LRTIs, even years after the acute infectious period, seem to have a prolonged negative effect on the health of older adults, particularly among males. Preventative public health measures aimed at decreasing LRTI cases among older adults could help in preserving good health and functioning in old age.

Protein and transcriptional biomarker profiling may inform treatment strategies in lower respiratory tract infections by indicating bacterial-viral differentiation

Lower respiratory tract infections (LRTIs) remain a significant global cause of infectious disease-related mortality. Accurate discrimination between acute bacterial and viral LRTIs is crucial for optimal patient care, prevention of unnecessary antibiotic prescriptions, and resource allocation. Plasma samples from LRTI patients with bacterial (n = 36), viral (n = 27; excluding SARS-CoV-2), SARS-CoV-2 (n = 22), and mixed bacterial-viral (n = 38) etiology were analyzed for protein profiling. Whole-blood RNA samples from a subset of patients (bacterial, n = 8; viral, n = 8; and SARS-CoV-2, n = 8) were analyzed for transcriptional profiling. Lasso regression modeling identified a seven-protein signature (CRP, IL4, IL9, IP10, MIP1α, MIP1β, and TNFα) that discriminated between patients with bacterial (n = 36) vs viral (n = 27) infections with an area under the curve (AUC) of 0.98. When comparing patients with bacterial and mixed bacterial-viral infections (antibiotics clinically justified; n = 74) vs patients with viral and SARS-CoV-2 infections (antibiotics clinically not justified; n = 49), a 10-protein signature (CRP, bFGF, eotaxin, IFNγ, IL1β, IL7, IP10, MIP1α, MIP1β, and TNFα) with an AUC of 0.94 was identified. The transcriptional profiling analysis identified 232 differentially expressed genes distinguishing bacterial (n = 8) from viral and SARS-CoV-2 (n = 16) etiology. Protein-protein interaction enrichment analysis identified 20 genes that could be useful in the differentiation between bacterial and viral infections. Finally, we examined the performance of selected published gene signatures for bacterial-viral differentiation in our gene set, yielding promising results. Further validation of both protein and gene signatures in diverse clinical settings is warranted to establish their potential to guide the treatment of acute LRTIs.

IMPORTANCE

Accurate differentiation between bacterial and viral lower respiratory tract infections (LRTIs) is vital for effective patient care and resource allocation. This study investigated specific protein signatures and gene expression patterns in plasma and blood samples from LRTI patients that distinguished bacterial and viral infections. The identified signatures can inform the design of point-of-care tests that can aid healthcare providers in making informed decisions about antibiotic prescriptions in order to reduce unnecessary use, thereby contributing to reduced side effects and antibiotic resistance. Furthermore, the potential for faster and more accurate diagnoses for improved patient management in acute LRTIs is compelling.

Clinical utility of bedside Contrast-Enhanced Ultrasound (CEUS) in the diagnosis of pneumonia in elderly patients: Comparison with clinical, -radiological and ultrasound diagnosis

AIMS

to measure the clinical impact of contrast-enhanced ultrasound (CEUS) in the diagnosis of -community-acquired pneumonia (CAP), compared to clinical, radiological and ultrasound diagnosis.

METHODS

84 patients (47/37 males/females, mean age:78,57±11,7 Y) with clinical suspicion of pneumonia and with ultrasound findings of peripheral lung lesions, were investigated with CEUS for a better characterization. Final diagnosis of 65 cap was obtained with complete disappearance of symptoms and pulmonary nodule(s); 19 neoplasms: 16 patients performed histologically with bronchoscopy; 3 refused (non-invasive diagnosis with basal CT-scan and positron emission tomography (PET) with fluorodeoxyglucose (FDG)). Sensitivity, specificity, overall diagnostic accuracy (ODA) (and corresponding AUROC) of clinical-data (CD), chest X-ray(CXR), Lung-ultrasound(LUS), CEUS were calculated with SPSS 26.0 software.

RESULTS

Final diagnosis: 65 CAP, and 19 chest cancers. 9/65 (13%) patients died, of these 7/9 with older age and heart disease as comorbidity. CD: True-Positive (TP):23, True-negative (TN): 17; False-Positive (FP):2; False-negative (FN):42 (sens:35,4% spec:89,5% ODA10%: PPV:92%, NPV:28,8%) (AUROC±SEauc:0,46±0,076); CXR: TP: 36, TN:14; FP:5, FN:29; (sens: 55,4%; spec: 73,7%; ODA: 32%; PPV:87,5%, NPV:32,66%) (AUROC±SEauc:0,645±0,068). US: TP:59; TN: 14; FP:5, FN:6 (sens: 90,8%, spec: 73,7%, ODA: 84,9%, PPV:92,2%, NPV:70%) (AUROC±SEauc:0,9417±0,024); CEUS: TP: 63; TN: 19; FP:0; FN:2 (sens: 96,9%; spec: 100% ODA: 97,5%; PPV: 100%, NPV:90,5%) (AUROC±SEauc:0,98±0,01).

CONCLUSIONS

Clinical-data and chest X-RAYS are insufficient to obtain a correct diagnosis of CAP in elderly population; US demonstrated a good accuracy to establish CAP, but with a relatively low specificity; in these cases, CEUS is able to give a correct characterization, allowing you to save the need for a chest contrast-enhanced-CT (CECT).

Impact of lower-respiratory tract infections on healthcare utilization and mortality in older adults: a Swedish population-based cohort study

BACKGROUND

Lower respiratory tract infections (LRTIs) have an immediate significant impact on morbidity and mortality among older adults. However, the impact following the infectious period of LRTI remains understudied. We aimed to assess the short- to long-term impact of LRTIs on hospitalization, mortality, and healthcare utilization in older adults.

METHODS

Data from the Swedish National Study of Aging and Care in Kungsholmen (SNAC-K) was analyzed, with data from 2001 to 2019 for mortality and 2001-2016 for healthcare utilization. LRTI-exposed participants were identified and matched with LRTI-nonexposed based on sociodemographics, lifestyle factors, and functional and clinical characteristics. Statistical models evaluated post-LRTI hospitalization risk, days of inpatient hospital admissions, healthcare visits, and mortality.

RESULTS

567 LRTIs-exposed participants during the study period and were matched with 1.701 unexposed individuals. LRTI-exposed individuals exhibited increased risk of hospitalization at 1-year (HR 2.14, CI 1.74, 2.63), 3-years (HR 1.74, CI 1.46, 2.07), and 5-years (HR 1.59, CI 1.33, 1.89). They also experienced longer post-LRTI hospital stays (IRR 1.40, CI 1.18, 1.66), more healthcare visits (IRR 1.47, CI 1.26, 1.71), specialist-care visits (IRR 1.46, CI 1.24, 1.73), and hospital admissions (IRR 1.57, CI 1.34, 1.83) compared to nonexposed participants over 16-years of potential follow-up. Additionally, the 19-year risk of mortality was higher among LRTI-exposed participants (HR 1.45, CI 1.24, 1.70). Men exhibited stronger associations with these risks compared to women.

CONCLUSIONS

LRTIs pose both short- and long-term risks for older adults, including increased risks of mortality, hospitalization, and healthcare visits that transpire beyond the acute infection period, although these effects diminish over time. Men exhibit higher risks across these outcomes compared to women. Given the potential preventability of LRTIs, further public health measures to mitigate infection risk are warranted.

Obstructive Sleep Apnea and Acute Lower Respiratory Tract Infections: A Narrative Literature Review

Both obstructive sleep apnea (OSA) and acute lower respiratory tract infections (LRTIs) are important global health issues. The pathophysiological links between OSA and LRTIs include altered immune responses due to chronic intermittent hypoxia and sleep fragmentation, increased aspiration risk, and a high burden of comorbidities. In this narrative review, we evaluated the current evidence on the association between OSA and the incidence and outcomes of acute LRTIs in adults, specifically community-acquired pneumonia and viral pneumonia caused by influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Studies have demonstrated that OSA patients are more likely to develop bacterial pneumonia and exhibit a higher risk of invasive pneumococcal disease. The risk intensifies with the severity of OSA, influencing hospitalization rates and the need for intensive care. OSA is also associated with an increased risk of contracting influenza and suffering more severe disease, potentially necessitating hospitalization. Similarly, OSA contributes to increased COVID-19 disease severity, reflected by higher rates of hospitalization, longer hospital stays, and a higher incidence of acute respiratory failure. The effect of OSA on mortality rates from these infections is, however, somewhat ambiguous. Finally, we explored antibiotic therapy for OSA patients with LRTIs, addressing care settings, empirical regimens, risks, and pharmacokinetic considerations. Given the substantial burden of OSA and its significant interplay with acute LRTIs, enhanced screening, targeted vaccinations, and optimized management strategies for OSA patients should be prioritized.

Model-based disease mapping using primary care registry data

BACKGROUND

Spatial modeling of disease risk using primary care registry data is promising for public health surveillance. However, it remains unclear to which extent challenges such as spatially disproportionate sampling and practice-specific reporting variation affect statistical inference.

METHODS

Using lower respiratory tract infection data from the INTEGO registry, modeled with a logistic model incorporating patient characteristics, a spatially structured random effect at municipality level, and an unstructured random effect at practice level, we conducted a case and simulation study to assess the impact of these challenges on spatial trend estimation.

RESULTS

Even with spatial imbalance and practice-specific reporting variation, the model performed well. Performance improved with increasing spatial sample balance and decreasing practice-specific variation.

CONCLUSION

Our findings indicate that, with correction for reporting efforts, primary care registries are valuable for spatial trend estimation. The diversity of patient locations within practice populations plays an important role.

Utilizing metagenomic next-generation sequencing for pathogen detection and diagnosis in lower respiratory tract infections in real-world clinical practice

BACKGROUND

Infectious etiologies of lower respiratory tract infections (LRTIs) by the conventional microbiology tests (CMTs) can be challenging. Metagenomic next-generation sequencing (mNGS) has great potential in clinical use for its comprehensiveness in identifying pathogens, particularly those difficult-to-culture organisms.

METHODS

We analyzed a total of 205 clinical samples from 201 patients with suspected LRTIs using mNGS in parallel with CMTs. mNGS results were used to guide treatment adjustments for patients who had negative CMT results. The efficacy of treatment was subsequently evaluated in these patients.

RESULTS

mNGS-detected microorganisms in 91.7% (188/205) of the clinical samples, whereas CMTs demonstrated a lower detection rate, identifying microorganisms in only 37.6% (77/205) of samples. Compared to CMT results, mNGS exhibited a detection sensitivity of 93.5% and 95.4% in all 205 clinical samples and 180 bronchoalveolar lavage fluid (BALF) samples, respectively. A total of 114 patients (114/201; 56.7%) showed negative CMT results, among which 92 received treatment adjustments guided by their positive mNGS results. Notably, 67.4% (62/92) of patients demonstrated effective treatment, while 25% (23/92) experienced a stabilized condition. Subgroup analysis of cancer patients revealed that 41.9% (13/31) exhibited an effective response to treatment, and 35.5% (11/31) maintained a stable condition following medication adjustments guided by mNGS.

CONCLUSION

mNGS demonstrated great potential in identifying microorganisms of clinical significance in LRTIs. The rapid turnaround time and reduced susceptibility to the impact of antimicrobial administration make mNGS a valuable supplementary tool for diagnosis and treatment decision-making for suspected LRTIs in clinical practice.

Bacterial pathogens in Xpert MTB/RIF Ultra-negative sputum samples of patients with presumptive tuberculosis in a high TB burden setting: a 16S rRNA analysis

In patients with presumptive tuberculosis (TB) in whom the diagnosis of TB was excluded, understanding the bacterial etiology of lower respiratory tract infections (LRTIs) is important for optimal patient management. A secondary analysis was performed on a cohort of 250 hospitalized patients with symptoms of TB. Bacterial DNA was extracted from sputum samples for Illumina 16S rRNA sequencing to identify bacterial species based on amplicon sequence variant level. The bacterial pathogen most likely to be responsible for the patients' LRTI could only be identified in a minority (6.0%, 13/215) of cases based on 16S rRNA amplicon sequencing: Mycoplasma pneumoniae (n = 7), Bordetella pertussis (n = 2), Acinetobacter baumanii (n = 2), and Pseudomonas aeruginosa (n = 2). Other putative pathogens were present in similar proportions of Xpert Ultra-positive and Xpert Ultra-negative sputum samples. The presence of Streptococcus (pseudo)pneumoniae appeared to increase the odds of radiological abnormalities (aOR 2.5, 95% CI 1.12-6.16) and the presence of S. (pseudo)pneumoniae (aOR 5.31, 95% CI 1.29-26.6) and Moraxella catarrhalis/nonliquefaciens (aOR 12.1, 95% CI 2.67-72.8) increased the odds of 6-month mortality, suggesting that these pathogens might have clinical relevance. M. pneumoniae, B. pertussis, and A. baumanii appeared to be the possible causes of TB-like symptoms. S. (pseudo)pneumoniae and M. catarrhalis/nonliquefaciens also appeared of clinical relevance based on 16S rRNA amplicon sequencing. Further research using tools with higher discriminatory power than 16S rRNA sequencing is required to develop optimal diagnostic and treatment strategies for this population.IMPORTANCEThe objective of this study was to identify possible bacterial lower respiratory tract infection (LRTI) pathogens in hospitalized patients who were initially suspected to have TB but later tested negative using the Xpert Ultra test. Although 16S rRNA was able to identify some less common or difficult-to-culture pathogens such as Mycoplasma pneumoniae and Bordetella pertussis, one of the main findings of the study is that, in contrast to what we had hypothesized, 16S rRNA is not a method that can be used to assist in the management of patients with presumptive TB having a negative Xpert Ultra test. Even though this could be considered a negative finding, we believe it is an important finding to report as it highlights the need for further research using different approaches.

Rates of Lower Respiratory Tract Illness in US Adults by Age and Comorbidity Profile

INTRODUCTION

While it is widely recognized that older adults, adults with chronic medical conditions (CMC), and adults with immunocompromising conditions (IC) are at increased risk of lower respiratory tract illness (LRTI), evidence of the magnitude of increased risk is limited. This study was thus undertaken to characterize rates of hospitalized and ambulatory LRTI among United States (US) adults by age and comorbidity profile.

METHODS

A retrospective cohort design and US healthcare claims database (2016-2019) were employed. Study population included adults aged ≥ 18 years and was stratified by age and comorbidity profile (CMC-, CMC+ , IC). LRTI was ascertained overall and by pathogen pathogen (e.g., respiratory syncytial virus [RSV]), and was classified by care setting (hospital, emergency department [ED], physician office/hospital outpatient [PO/HO]).

RESULTS

Relative rates (RR) of LRTI generally increased with older age across care settings (vs. 18-49 years), with the most marked increase for hospitalizations: for LRTI-hospitalized, RRs ranged from 3.3 for 50-64 years to 46.6 for ≥ 85 years; for LRTI-ED and LRTI-PO/HO, RRs ranged from 1.0 to 2.7 and from 1.3 to 1.5, respectively. Within age groups, LRTI rates were also consistently higher among CMC+ and IC adults (vs. CMC- adults). Age-specific RRs of LRTI patients hospitalized due to RSV were largely comparable to overall LRTI; age-specific RRs for other care settings, and RRs for CMC+ and IC adults (vs. CMC- adults), were generally higher for LRTI due to RSV.

CONCLUSIONS

Incidence of LRTI, including that due to RSV, especially for events requiring acute inpatient care, is markedly higher among older adults and adults of all ages with CMC or IC.

Global burden of influenza lower respiratory tract infections in older people from 1990 to 2019

BACKGROUND

Infections with influenza viruses cause severe illness, substantial number of hospitalization and death, especially in older adults. However, few studies have focused on the burden of influenza lower respiratory tract infections (LRTIs) solely in older adults, particularly in low-resource settings.

AIMS

We aimed to estimate the mortality and DALYs of influenza LRTIs for people aged 55 years and older in 204 countries and territories from 1990 to 2019.

METHODS

The Global Burden of Disease (GBD) 2019 study was used to obtain data on mortality and DALYs of influenza LRTIs at the global, regional, and country levels.

RESULTS

In 2019, the global rates for mortality and DALYs of influenza LRTIs were 6.46 per 100,000 [95% uncertainty interval (UI): 2.37-12.62] and 97.39 per 100,000 (95% UI: 34.70-187.03). Although the rates for mortality and DALYs in people aged 55 years and older decreased from 1990 to 2019, the absolute numbers for both increased by 85.84% and 66.56%, respectively. Both the absolute numbers and rates of deaths and DALYs of influenza LRTIs were higher in male than in female in all age groups. Although low-socio-demographic index (SDI) regions experienced the largest declines for the rates of mortality and DALYs of influenza LRTIs over the past three decades, they still had the highest rates for mortality and DALYs in all age groups. Moreover, the absolute numbers and rates of deaths and DALYs of influenza LRTIs showed an increasing trend with age, reaching the peak in the people over 85 years old.

DISCUSSION

Burden of influenza LRTIs in older adults is still high and could continue to grow along with global aging.

CONCLUSION

Efforts to improve vaccination for influenza are needed for preparedness of another influenza pandemic, especially in low-SDI regions.

Impact of patient characteristics on innate immune responses and inflammasome activation in ex vivo human lung tissues infected with influenza A virus

Background

Influenza A virus (IAV) infection poses a persistent global health challenge, necessitating a nuanced grasp of host immune responses for optimal interventions. While the interplay between aging, immunosenescence, and IAV is recognized as key in severe lower respiratory tract infections, the role of specific patient attributes in shaping innate immune reactions and inflammasome activity during IAV infection remains under-investigated. In this study, we utilized an ex vivo infection model of human lung tissues with H3N2 IAV to discern relationships among patient demographics, IAV nucleoprotein (NP) expression, toll-like receptor (TLR) profiles, PD-1/PD-L1 markers, and cytokine production.

Methods

Our cohort consisted of thirty adult patients who underwent video-assisted thoracoscopic surgery during 2018-2019. Post-surgical lung tissues were exposed to H3N2 IAV for ex vivo infections, and the ensuing immune responses were profiled using flow cytometry.

Results

We observed pronounced IAV activity within lung cells, as indicated by marked NP upregulation in both epithelial cells (P = 0.022) and macrophages (P = 0.003) in the IAV-exposed group relative to controls. Notably, interleukin-2 levels correlated with variations in TLR1 expression on epithelial cells and PD-L1 markers on macrophages. Age emerged as a modulating factor, dampening innate immune reactions, as evidenced by reduced interleukin-2 and interferon-γ concentrations (both adjusted P < 0.05). Intriguingly, a subset of participants with pronounced tumor necrosis factor-alpha post-mock infection (Cluster 1) showed attenuated cytokine responses in contrast to their counterparts in Cluster 2 and Cluster 3 (all adjusted P < 0.05). Individuals in Cluster 2, characterized by a low post-mock infection NP expression in macrophages, exhibited reduced variations in both NP and TLR1-3 expressions on these cells and a decreased variation in interleukin-2 secretion in comparison to their Cluster 3 counterparts, who were identified by their elevated NP macrophage expression (all adjusted P < 0.05).

Conclusion

Our work elucidates the multifaceted interplay of patient factors, innate immunity, and inflammasome responses in lung tissues subjected to ex vivo H3N2 IAV exposure, reflecting real-world lower respiratory tract infections. While these findings provide a foundation for tailored therapeutic strategies, supplementary studies are requisite for thorough validation and refinement.

Clinical Efficiency of Metagenomic Next-Generation Sequencing in Sputum for Pathogen Detection of Patients with Pneumonia According to Disease Severity and Host Immune Status

Purpose

Severe pneumonia causes the highest mortality rate in immunocompromised patients. This study aimed to investigate the pathogen diagnostic efficacy of metagenomic next-generation sequencing (mNGS) using sputum sample in patients with pneumonia according to patients' disease severity and immune conditions.

Patients and Methods

A total of 180 patients suffering from pneumonia were recruited, and sputum samples were collected in duplicate for pathogen detection by both conventional microbiological tests (CMT) and mNGS. Then, the performance of pathogen identification was examined between two methods, according to disease severity and patients' immune status.

Results

In comparison to CMT, mNGS had higher positivity rates in all patients with pneumonia (85.0% vs 62.2%, P=9.445e-07). The most commonly detected microorganism in sputum of pneumonia patients was Acinetobacter baumannii (42/180, 23.3%) in bacterum level, Candida albicans in fungus level (44/180, 24.4%), and Human herpesvirus 1 (39/180, 27.5%) in virus level. However, for mNGS results, Candida albicans in 34.9% of positive patients, and Human herpesvirus 1 in 7.7% of positive cases were confirmed as pathogens causing pneumonia. Acinetobacter baumannii detected by mNGS in 75% of positive patients was diagnosed as pathogen of pneumonia. The microorganism profile of sputum mNGS differed according to disease severity and immune status of patients. Pneumocystis jirovecii was more likely to infect immunocompromised patients (P=0.002). Pseudomonas aeruginosa (14.8% vs 0.0%, P=0.008) and Human herpesvirus 1 (26.1% vs 5.3%, P=0.004) had higher infection rate in patients with severe pneumonia compared with non-severe cases. mNGS had overwhelming advantages over CMT in detecting a lot of microorganisms including Streptococcus pneumoniae, Enterococcus faecium, Pneumocystis jirovecii, and majority of viruses.

Conclusion

mNGS is a complementary tool of CMT for detecting suspected pathogens for patients with lower respiratory infections. The interpretation of opportunistic pathogens identified by mNGS is challenging, and needs comprehensive consideration of sequencing data and clinical factors.

Seasonal influence on respiratory tract infection severity including COVID-19 quantified through Markov Chain modeling

Respiratory tract infections (RTIs) are a burden to global health, but their characterization is complicated by the influence of seasonality on incidence and severity. The Re-BCG-CoV-19 trial (NCT04379336) assessed BCG (re)vaccination for protection from coronavirus disease 2019 (COVID-19) and recorded 958 RTIs in 574 individuals followed over 1 year. We characterized the probability of RTI occurrence and severity using a Markov model with health scores (HSs) for four states of symptom severity. Covariate analysis on the transition probability between HSs explored the influence of demographics, medical history, severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), or influenza vaccinations, which became available during the trial, SARS-CoV-2 serology, and epidemiology-informed seasonal influence of infection pressure represented as regional COVID-19 pandemic waves, as well as BCG (re)vaccination. The infection pressure reflecting the pandemic waves increased the risk of RTI symptom development, whereas the presence of SARS-CoV-2 antibodies protected against RTI symptom development and increased the probability of symptom relief. Higher probability of symptom relief was also found in participants with African ethnicity and with male biological gender. SARS-CoV-2 or influenza vaccination reduced the probability of transitioning from mild to healthy symptoms. Model diagnostics over calendar-time indicated that COVID-19 cases were under-reported during the first wave by an estimated 2.76-fold. This trial was performed during the initial phase of the COVID-19 pandemic in South Africa and the results reflect that situation. Using this unique clinical dataset of prospectively studied RTIs over the course of 1 year, our Markov Chain model was able to capture risk factors for RTI development and severity, including epidemiology-informed infection pressure.

Importance of Skeletal Muscle and Interdisciplinary Team Approach in Managing Pneumonia in Older People

Pneumonia is the most frequent lower respiratory tract disease and a major cause of morbidity and mortality globally [...].

Adherence to evidence-based guidelines for the management of pneumonia in a tertiary teaching hospital in Riyadh

Background

Adherence to therapeutic guidelines is crucial when treating pneumonia, as it reduces mortality rate, length of hospital stay and duration of antibiotic therapy. However, the high non-adherence rate to treatment guidelines, in general, and to the Infectious Disease Society of America (IDSA) guidelines, are still reported globally. According to our knowledge, no existing data is available regarding the rate of physicians' adherence to the IDSA guidelines for managing pneumonia in Saudi Arabia. Therefore, we aim to assess the adherence rate and the clinical outcomes among patients treated according to the IDSA guidelines, in a tertiary care center in Riyadh.

Methods

A single-centered, retrospective, cross-sectional, observational study was conducted at King Khalid University Hospital, Riyadh, Saudi Arabia. All data were extracted from the hospital's electronic information system, known as Esihi. Adult patients (≥18 years old) diagnosed and treated in the hospital for community-acquired pneumonia, hospital-acquired pneumonia, or ventilator-associated pneumonia from Nov 2019 to Nov 2021 were included.

Results

A total of 148 patients were included in this study, and the management of 50% of them (74 patients) adhered to the guidelines' recommendations. Even though the patients who received guidelines-adhered management were older (70 ± 16 vs 59 ± 22; p = 0.001), and had a higher CURB-65 score for pneumonia severity (1.86 ± 1.03 vs 1.39 ± 1.26; p = 0.026) and an average calculated Charlson comorbidity index (4.62 ± 2.19 vs 3.28 ± 2.80; p = 0.001) than patients who were treated irrespectively of the guidelines, yet they had a better cure rate (95% vs 84%; adjusted OR, 3.9; 95% CI, 0.82-18.58), lower mortality (5% vs 14%; adjusted OR, 0.38; 95% CI, 0.04-4.05) and shorter length of hospital stay (LOS) (6.5 vs 8 days; p = 0.082); compared to patients who were treated irrespectively of the guidelines.

Conclusions

Comparable to previous literature, non-adherence to evidence-based guidelines has been observed in 50% of patients treated for pneumonia. Despite being nonsignificant, higher clinical cure rates, shorter LOS, and lower mortality rates have been observed in patients who were treated based on evidence-based guidelines. Further measures to improve guidelines compliance in pneumonia treatment are needed.

Determinants of Flu Vaccine Uptake Among the General Population in Saudi Arabia: A Study Based on the Health Belief Model

Background and objective Recently, influenza has emerged as a significant public health concern worldwide, including in Saudi Arabia. Vaccination against the flu is widely recognized as a crucial preventive measure to reduce morbidity and mortality associated with the virus. However, the uptake of flu vaccines among the general population in Saudi Arabia still remains low. In light of this, this study aimed to examine the determinants of influenza vaccine uptake in Saudi Arabia by using the Health Belief Model (HBM). Methods This cross-sectional study was conducted among adults living in all regions of Saudi Arabia by using an online self-administered questionnaire based on the HBM. The questionnaire inquired about demographics, knowledge about influenza, knowledge about vaccines, and beliefs/barriers. It was distributed via social media platforms, including WhatsApp, Twitter, and Instagram. IBM SPSS Statistics software version 29 (IBM Corp., Armonk, NY) was used for statistical analyses, and both the Chi-square test and logic regression analyses were applied to determine associations between explanatory and response variables, with the level of significance set at p<0.05. Results This study enrolled a total of 1040 participants, and the majority were Saudi nationals (96.9%). Of note, 66.2% of the participants were males, and the rest were females. Most of the participants were employed by governmental institutions (42.0%), had bachelor's degrees (58.4%), had never worked in the health sector (70.2%), and earned above 10,000 Saudi riyals per month (62.1%). Over half (55.7%) of participants had taken the flu vaccine at the time of this study. Working in the healthcare sector was associated with increased flu vaccine uptake [adjusted odds ratio (aOR): 3.84, p<0.001]. The likelihood of getting the flu vaccines was greater among men (aOR: 1.38, p=0.027), and obesity was associated with lower flu vaccine uptake (aOR: 0.29, p=0.034). Having contact with people with flu, having had flu in the past, and experiencing severe flu complications (aOR: 4.71, p=0.029; aOR: 0.13, p=0.006; and aOR: 0.29, p=0.033, respectively) were significantly associated with the flu vaccine uptake among our study participants. Perceived potential risks of the flu vaccine were also associated with taking the flu vaccine (aOR: 0.213, p=0.042). There was a significant association between seeing an advertisement for the flu vaccine and the likelihood of taking the vaccine (aOR: 5.488, p=0.042). Conclusion This study found that certain sociodemographic factors are associated with flu vaccine uptake. These factors included contact with flu-infected individuals, past experiences with flu, perceived risks, and exposure to flu vaccine advertisements. Improving healthcare accessibility, conducting awareness campaigns, and implementing workplace initiatives are recommended to address the issues related to flu vaccine uptake.

Advances in Rodent Experimental Models of Sepsis

In the development of therapeutic strategies for human diseases, preclinical experimental models have a key role. However, the preclinical immunomodulatory therapies developed using rodent sepsis were not successful in human clinical trials. Sepsis is characterized by a dysregulated inflammation and redox imbalance triggered by infection. Human sepsis is simulated in experimental models using methods that trigger inflammation or infection in the host animals, most often mice or rats. It remains unknown whether the characteristics of the host species, the methods used to induce sepsis, or the molecular processes focused upon need to be revisited in the development of treatment methods that will succeed in human clinical trials. Our goal in this review is to provide a survey of existing experimental models of sepsis, including the use of humanized mice and dirty mice, and to show how these models reflect the clinical course of sepsis. We will discuss the strengths and limitations of these models and present recent advances in this subject area. We maintain that rodent models continue to have an irreplaceable role in studies toward discovering treatment methods for human sepsis.

Evaluation of safety and efficacy of inhaled ambroxol in hospitalized adult patients with mucopurulent sputum and expectoration difficulty

Background

Ambroxol is a widely used mucoactive drug in sputum clearance of respiratory diseases taken orally and by injection. However, there is a paucity of evidence for inhaled ambroxol in sputum clearance.

Methods

This study performed a multicenter, randomized, double-blind, placebo-controlled, phase 3 trial at 19 centers in China. Hospitalized adult patients with mucopurulent sputum and expectoration difficulty were recruited. Patients were randomized by 1:1 to receive inhalation of either ambroxol hydrochloride solution 3 mL (22.5 mg) + 0.9% sodium chloride 3 mL or 0.9% sodium chloride 6 mL twice daily for 5 days, with an interval of more than 6 h. The primary efficacy endpoint was the absolute change in the sputum property score after treatment compared to the baseline in the intention-to-treat population.

Results

Between 10 April 2018 and 23 November 2020, 316 patients were recruited and assessed for eligibility, of whom 138 who received inhaled ambroxol and 134 who received a placebo were included. Patients who received inhaled ambroxol had a significantly greater decrease in the sputum property score compared with patients who received inhalation of placebo (difference: -0.29; 95% CI: -0.53 to -0.05; p = 0.0215). Compared with the placebo, inhaled ambroxol also significantly reduced more expectoration volume in 24 h (difference: -0.18; 95% CI: -0.34 to -0.03; p  = 0.0166). There was no significant difference in the proportion of adverse events between the two groups, and no deaths were reported.

Discussion

In hospitalized adult patients with mucopurulent sputum and expectoration difficulty, inhaled ambroxol was safe and effective for sputum clearance compared with a placebo.

Clinical trial registration

[https://www.chictr.org.cn/showproj.html?proj=184677], Chinese Clinical Trial Registry [ChiCTR2200066348].

Utility of the BioFire® FilmArray® Pneumonia Panel plus assay for syndromic testing of lower respiratory tract infections in a low/middle-income setting

Background

Determining lower respiratory tract infection (LRTI) aetiology is complex. Culture-based methods are laborious with poor sensitivity. Molecular assays improve detection of potential pathogens, but incorrect interpretation of results may lead to inappropriate antimicrobial therapy.

Methods

The utility of the BioFire^® FilmArray^® Pneumonia Panel plus (FA-PP) to detect LRTI pathogens, and the potential impact on antimicrobial stewardship in a low-resource setting, were assessed. Routine LRT samples were included from adult patients with clinically suspected LRTI or with a concomitant blood culture at Groote Schuur Hospital and referring facilities. Culture and FA-PP results were compared, and pharmacy data analysed to determine appropriateness of antibiotic therapy.

Results

There was an 80% correlation between cultured LRTI pathogens and the FA-PP bin ≥10⁷ results. Compared with culture, the FA-PP detected substantially more pathogens (86.6% versus 17.9%) and produced a combined 100% positive percent agreement, and 88% negative percent agreement. The FA-PP detected bacterial/viral coinfections in 27% of samples. Correlation of FA-PP results with pharmacy data (n = 69) indicated a potential antibiotic change in 75% of cases, but this is difficult to accurately characterize without a 'gold standard' for treatment or complete clinical data.

Conclusions

The FA-PP increased the number of positive samples with typical bacteria, but the semi-quantitative reporting algorithm does not describe the correlation between the different bin values and colonization versus infection. This complicates result interpretation and may lead to inappropriate antimicrobial treatment. This study highlights the potential positive impact of rapid molecular assays for routine care in lower-income settings, but also underscores the interpretive challenges associated with these tests.

The application of targeted nanopore sequencing for the identification of pathogens and resistance genes in lower respiratory tract infections

Objectives

Lower respiratory tract infections (LRTIs) are one of the causes of mortality among infectious diseases. Microbial cultures commonly used in clinical practice are time-consuming, have poor sensitivity to unculturable and polymicrobial patterns, and are inadequate to guide timely and accurate antibiotic therapy. We investigated the feasibility of targeted nanopore sequencing (TNPseq) for the identification of pathogen and antimicrobial resistance (AMR) genes across suspected patients with LRTIs. TNPseq is a novel approach, which was improved based on nanopore sequencing for the identification of bacterial and fungal infections of clinical relevance.

Methods

This prospective study recruited 146 patients suspected of having LRTIs and with a median age of 61 years. The potential pathogens in these patients were detected by both TNPseq and the traditional culture workups. We compared the performance between the two methods among 146 LRTIs-related specimens. AMR genes were also detected by TNPseq to prompt the proper utilization of antibiotics.

Results

At least one pathogen was detected in 133 (91.1%) samples by TNPseq, but only 37 (25.3%) samples contained positive isolates among 146 cultured specimens. TNPseq possessed higher sensitivity than the conventional culture method (91.1 vs. 25.3%, P < 0.001) in identifying pathogens. It detected more samples with bacterial infections (P < 0.001) and mixed infections (P < 0.001) compared with the clinical culture tests. The most frequent AMR gene identified by TNPseq was bla _TEM (n = 29), followed by bla _SHV (n = 4), bla _KPC (n = 2), bla _CTX-M (n = 2), and mecA (n = 2). Furthermore, TNPseq discovered five possible multi-drug resistance specimens.

Conclusion

TNPseq is efficient to identify pathogens early, thus assisting physicians to conduct timely and precise treatment for patients with suspected LRTIs.

The diagnostic value of nasal microbiota and clinical parameters in a multi-parametric prediction model to differentiate bacterial versus viral infections in lower respiratory tract infections

Background

The ability to accurately distinguish bacterial from viral infection would help clinicians better target antimicrobial therapy during suspected lower respiratory tract infections (LRTI). Although technological developments make it feasible to rapidly generate patient-specific microbiota profiles, evidence is required to show the clinical value of using microbiota data for infection diagnosis. In this study, we investigated whether adding nasal cavity microbiota profiles to readily available clinical information could improve machine learning classifiers to distinguish bacterial from viral infection in patients with LRTI.

Results

Various multi-parametric Random Forests classifiers were evaluated on the clinical and microbiota data of 293 LRTI patients for their prediction accuracies to differentiate bacterial from viral infection. The most predictive variable was C-reactive protein (CRP). We observed a marginal prediction improvement when 7 most prevalent nasal microbiota genera were added to the CRP model. In contrast, adding three clinical variables, absolute neutrophil count, consolidation on X-ray, and age group to the CRP model significantly improved the prediction. The best model correctly predicted 85% of the ‘bacterial’ patients and 82% of the ‘viral’ patients using 13 clinical and 3 nasal cavity microbiota genera (Staphylococcus, Moraxella, and Streptococcus).

Conclusions

We developed high-accuracy multi-parametric machine learning classifiers to differentiate bacterial from viral infections in LRTI patients of various ages. We demonstrated the predictive value of four easy-to-collect clinical variables which facilitate personalized and accurate clinical decision-making. We observed that nasal cavity microbiota correlate with the clinical variables and thus may not add significant value to diagnostic algorithms that aim to differentiate bacterial from viral infections.

Can bacterial lysates be useful in prevention of viral respiratory infections in childhood? The results of experimental OM-85 studies

Respiratory tract infections (RTI) are mainly viral in origin and among the leading cause of childhood morbidity globally. Associated wheezing illness and asthma are still a clear unmet medical need. Despite the continuous progress in understanding the processes involved in their pathogenesis, preventive measures and treatments failed to demonstrate any significant disease-modifying effect. However, in the last decades it was understood that early-life exposure to microbes, may reduce the risk of infectious and allergic disorders, increasing the immune response efficacy. These results suggested that treatment with bacterial lysates (BLs) acting on gut microbiota, could promote a heterologous immunomodulation useful in the prevention of recurrent RTIs and of wheezing inception and persistence. This hypothesis has been supported by clinical and experimental studies showing the reduction of RTI frequency and severity in childhood after oral BL prophylaxis and elucidating the involved mechanisms. OM-85 is the product whose anti-viral effects have been most extensively studied in vitro, animal, and human cell studies and in translational animal infection/disease models. The results of the latter studies, describing the potential immune training-based activities of such BL, leading to the protection against respiratory viruses, will be reported. In response to human rhinovirus, influenza virus, respiratory syncytial virus and severe acute respiratory coronavirus-2, OM-85 was effective in modulating the structure and the functions of a large numbers of airways epithelial and immune cells, when administered both orally and intranasally.

Molecular Diagnosis of Pneumonia (Including Multiplex Panels)

Background

Pneumonia is a common illness, accounting for a staggering amount of worldwide morbidity and mortality. The diagnosis of pneumonia is challenging given the variety of responsible pathogens. Diagnostic testing for bacterial pneumonia has traditionally relied on time-consuming culture-based methods, though recently multiplexed molecular approaches have been described. Multiplexed molecular assays for pneumonia have the potential to provide broad diagnostic information in a rapid timeframe. Much has yet to be learned about these assays regarding analytical performance, potential impact, and optimal implementation strategy.

Content

Herein we provide a summary of what is known and what has yet to be learned about multiplexed molecular pneumonia assays. We provide a comparison of the different commercially available assays and summarize the most current performance data for each. We further describe outcome data and lessons learned from those who have implemented these assays worldwide. Finally, based on the current state of performance and outcome data, we provide informed strategies and considerations for laboratories contemplating implementation.

Summary

Multiplexed molecular assays for the diagnosis of pneumonia boast high accuracy though the diagnostic information gained from these assays is inherently different from culture and must be interpreted in cultural context. Despite this, these assays can be powerful and effective diagnostic tools with a potential to positively impact patient care. The extent to which this is realized varies from setting to setting, though is dependent on thoughtful implementation and a focus on delivering clear, rapid, and actionable results that can be interpreted in the appropriate context.

The spectrum of Cefditoren for Lower Respiratory Tract Infections (LRTIs) in Surabaya

Background:

Empirical antibiotics among outpatients with Lower Respiratory Tract Infections (LRTIs) are scarcely allocated in Indonesia. The study aims to evaluate the pathogens causing LRTIs, drug sensitivity test and the minimum inhibitory concentrations of 90% (MIC90) of Cefditoren, Azithromycin, Amoxicillin-Clavulanic Acid, and Cefixime

Methods:

The study was performed in adult outpatients with LRTI that can be expectorated. Patients with diabetes mellitus, HIV, lung tuberculosis, renal or hepatic failure, and hemoptysis were excluded. We performed bacterial culture, antibiotic sensitivity, and MIC measurement of four antibiotics.

Results:

There were 126 patients with LRTIs, and 61 patients were eligible for the study. We identified 69 bacteria. We found Klebsiella pneumonia (n=16; 26.23%), Staphylococcus aureus (n=11; 18%), Pseudomonas aeruginosa (n=8; 13.11%), Acinetobacter baumanii complex (n= 4; 6.55%), Streptococcus pneumonia (n=3; 4.9%) and others bacteria as causa of LRTI. Testing MIC90 of Cefditoren and three empiric antibiotics on LRTI found that Cefditoren has a lower MIC of 90 for K. pneumonia (0.97(2.04) µg.mL-1) and S. pneumonia (0.06(0.00)µg.mL-1) than other antibiotics, but almost the same as Cefixime ((0.05(0.16)µg.mL-1) and (0.38(0.17)µg.mL-1). MIC90 Cefditoren for S.aureus (3.18(3.54)µg.mL-1) and P.aeruginosa (9.2(3.53)µg.mL-1) is lower than Cefixime but higher than Azithromycin and Amoxicillin-Clavulanic acid. Reference data MIC90 of Cefditoren for LRTI bacteria is lower than the other three oral empirical antibiotics.

Conclusions:

In vitro studies of an outpatient LRTI in Surabaya found gram-negative bacteria dominant. Cefditoren can inhibit K.pneumonia and S.pneumonia has lower MIC90 compared to other antibiotics. Cefditoren can inhibit gram-negative and positive bacteria causing LRTI.

Prevalence and Clinical Significance of Occult Pulmonary Infection in Elderly Patients with Type 2 Diabetes Mellitus

The occult pulmonary infection is the most common complications in elderly patients with type 2 diabetes mellitus (T2DM). Since its etiological characteristics has not been clarified, infection control remains a serious problem for public health. To investigate the prevalence and clinical significance of occult pulmonary infection in elderly T2DM patients, in this study, 573 elderly patients cochallenged with T2DM and community-acquired pulmonary infection from January 2018 to December 2020 were selected in the hospitals and divided into occult pneumonia group (OP, n = 249) and nonoccult pneumonia group (NOP, n = 324) according to the nature of infection. Clinical medical records were analyzed retrospectively to summarize the infection characteristics of elderly diabetics with occult pneumonia. The prevalence of the cases (278/324, 85.8%) in NOP group was not higher than that in OP group (206/249, 82.7%; P > 0.05). Also, there was not significant difference in the distribution of isolated pathogens among the positive patients. The length of hospitalization and mortality of OP patients were significantly higher than those NOP patients. Multivariate logistic regression showed that advanced age, comorbidities, hypothyroidism, senile dementia, and prolonged bed rest were independent risk factors for occult pneumonia in elderly diabetic patients. Therefore, the results demonstrated that the pulmonary infection in elderly patients with diabetes mellitus is often occult. Gram-negative bacteria are the predominant pathogens and cause poor prognosis. Advanced age, comorbidities (senile dementia, hypothyroidism), and prolonged bed rest are the independent risk factors for occult pneumonia.

Effectiveness of Pharmacist-Led Brief Educational Intervention for Adherence to the Antibiotics for Lower Respiratory Tract Infections (EATSA) in Post-Conflict Rural Areas of Pakistan: Study Protocol for a Randomized Controlled Trial

Globally, lower respiratory infections (LRTIs) are one of the most common infectious diseases whichaffect majority of the population and as a result of inappropriate antibiotics practices lead to antibiotic resistance (AR). An individual randomized control trial will be conducted in the post-conflict areas of Swat, Pakistan, through a random sampling method. Patients aged > 18 years will be recruited from five community pharmacies and assigned to equally sized groups to receive either pharmacist-led education interventions or usual care with no intervention. A total of 400 (control = 200, study = 200) patients will be included, with prescriptions comprised of antibiotics for LRTIs. The outcomes measured in both groups will be a combination of treatment cure rate and adherence, which will be assessed using the Morisky Medication Adherence Scale and pill count. The trial comprises pharmacist-led educational interventions to improve treatment outcomes for patients with LRTIs. This study might establish the groundwork for pharmaceutical care of LRTIs patients with antibacterial therapy and the future delivery of a care strategy for the improvement of LRTIs treatment outcomes in post-conflict, remote areas of the third world and LMICs.

The clinical role of host and bacterial-derived extracellular vesicles in pneumonia

Pneumonia is among the leading causes of morbidity and mortality worldwide. Due to constant evolution of respiratory bacteria and viruses, development of drug resistance and emerging pathogens, it constitutes a considerable health care threat. To enable development of novel strategies to control pneumonia, a better understanding of the complex mechanisms of interaction between host cells and infecting pathogens is vital. Here, we review the roles of host cell and bacterial-derived extracellular vesicles (EVs) in these interactions. We discuss clinical and experimental as well as pathogen-overarching and pathogen-specific evidence for common viral and bacterial elicitors of community- and hospital-acquired pneumonia. Finally, we highlight the potential of EVs for improved management of pneumonia patients and discuss the translational steps to be taken before they can be safely exploited as novel vaccines, biomarkers, or therapeutics in clinical practice.

Lung ultrasound may support internal medicine physicians in predicting the diagnosis, bacterial etiology and favorable outcome of community-acquired pneumonia

To assess the usefulness of lung ultrasound (LUS) for identifying community-acquired pneumonia (CAP) among adult patients with suspected lower respiratory tract infection (LRTI) and for discriminating between CAP with different cultural statuses, etiologies, and outcomes. LUS was performed at internal medicine ward admission. The performance of chest X-ray (CXR) and LUS in diagnosing CAP in 410 patients with suspected LRTI was determined. All possible positive results for pneumonia on LUS were condensed into pattern 1 (consolidation + / − alveolar-interstitial syndrome) and pattern 2 (alveolar-interstitial syndrome). The performance of LUS in predicting culture-positive status, bacterial etiology, and adverse outcomes of CAP was assessed in 315 patients. The area under the receiver operating characteristic curve for diagnosing CAP by LUS was significantly higher than for diagnosis CAP by CXR (0.93 and 0.71, respectively; p < 0.001). Pattern 1 predicted CAP with bacterial and mixed bacterial and viral etiologies with positive predictive values of 99% (95% CI, 94–100%) and 97% (95% CI, 81–99%), respectively. Pattern 2 ruled out mortality with a negative predictive value of 95% (95% CI, 86–98%), respectively. In this study, LUS was useful in predicting a diagnosis of CAP, the bacterial etiology of CAP, and favorable outcome in patients with CAP.

Results from the Survey of Antibiotic Resistance (SOAR) 2015-17 in Turkey: data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints

OBJECTIVES

To determine antibiotic susceptibility of Streptococcus pneumoniae and Haemophilus influenzae isolates from community-acquired respiratory tract infections (CA-RTIs) collected in 2015-17 from Turkey.

METHODS

MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

RESULTS

A total of 179 S. pneumoniae and 239 H. influenzae isolates were collected. Few (27.9%) pneumococci were penicillin susceptible by CLSI oral or EUCAST low-dose breakpoints, but by EUCAST high-dose or CLSI IV breakpoints 84.4% were susceptible. The most active antibiotics (excluding penicillin IV) by CLSI breakpoints were fluoroquinolones (98.9% of isolates susceptible), ceftriaxone (83.2%), amoxicillin (78.8%) and amoxicillin/clavulanic acid (78.8%). Pneumococcal susceptibility to amoxicillin and amoxicillin/clavulanic acid was lower using EUCAST low-dose breakpoints (49.7%), although susceptibility increased when using EUCAST high-dose (57.0%-58.1%) and PK/PD (78.8%-87.7%) breakpoints. Twenty-three H. influenzae isolates were β-lactamase positive, with 11 characterized as β-lactamase negative and ampicillin resistant following EUCAST criteria and 5 by CLSI criteria. Generally antibiotic susceptibility was high using CLSI breakpoints: ≥92.9% for all antibiotics except ampicillin (87% by CLSI and EUCAST breakpoints) and trimethoprim/sulfamethoxazole (67.4% and 72% by CLSI and EUCAST breakpoints, respectively). Susceptibility using EUCAST breakpoints (where these are published) was similar, except for cefuroxime (oral) with 3.8% of isolates susceptible. PK/PD breakpoints indicated low susceptibility to macrolides (5.9%-10%) and cefaclor (13%). The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified.

CONCLUSIONS

Antibiotic susceptibility of S. pneumoniae was generally low, which is in keeping with evidence of inappropriate and high antibiotic use in Turkey. H. influenzae susceptibility was high. These data are important for empirical therapy of CA-RTIs.

Results from the Survey of Antibiotic Resistance (SOAR) 2015-17 in Latin America (Argentina, Chile and Costa Rica): data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints

OBJECTIVES

To determine antibiotic susceptibility of Streptococcus pneumoniae and Haemophilus influenzae isolates from community-acquired respiratory tract infections (CA-RTIs) collected in 2015-17 from Argentina, Chile and Costa Rica.

METHODS

MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

RESULTS

A total of 170 S. pneumoniae and 218 H. influenzae isolates were collected at five centres in Argentina, Chile and Costa Rica in 2015-17. Small S. pneumoniae isolate numbers from Costa Rica (n = 2) meant that these could only be included in the penicillin susceptibility analysis; they were excluded from further country analyses. Around one-third of pneumococcal isolates from Argentina and two-thirds from Chile were non-susceptible to penicillin by CLSI oral or EUCAST low-dose IV breakpoints, but most (≥89%) were susceptible by CLSI IV or EUCAST high-dose breakpoints. Amongst pneumococci from Argentina, about 80% or more were susceptible to most other antibiotics except cefaclor (all breakpoints), cefixime (PK/PD breakpoints), cefuroxime (EUCAST breakpoints) and trimethoprim/sulfamethoxazole (CLSI and PK/PD breakpoints). S. pneumoniae isolates from Chile showed significantly lower susceptibility (P < 0.05) using CLSI breakpoints compared with those from Argentina for many of the antibiotics tested. Among isolates of H. influenzae from Latin America, more than 90% were susceptible to amoxicillin/clavulanic acid (high dose), cefixime, cefpodoxime, ceftriaxone and fluoroquinolones, irrespective of the breakpoints used. The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified.

CONCLUSIONS

Antibiotic susceptibility of H. influenzae isolates was generally high in the Latin American countries studied; however, susceptibility profiles varied for S. pneumoniae by country and depending on the breakpoints used, especially for cefaclor. These factors are important in decision making for empirical therapy of bacterial infections.

Results from the Survey of Antibiotic Resistance (SOAR) 2016-17 in Ukraine: data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints

OBJECTIVES

To determine antibiotic susceptibility of Streptococcus pneumoniae and Haemophilus influenzae isolates from community-acquired respiratory tract infections (CA-RTIs) collected in 2016-17 from Ukraine.

METHODS

MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

RESULTS

A total of 177 viable clinical isolates, including 78 S. pneumoniae and 99 H. influenzae, were collected. Overall, ∼98% of S. pneumoniae isolates were susceptible to penicillin by CLSI IV or EUCAST high-dose breakpoints and 73.1% were susceptible by CLSI oral or EUCAST low-dose IV breakpoints. Susceptibility rates of 76.9%-100% were observed for most antibiotics by all breakpoints except trimethoprim/sulfamethoxazole (41%-69.2%) and cefaclor, which showed the greatest difference between breakpoints: 0% by EUCAST, 28.2% by PK/PD and 73.1% by CLSI. All S. pneumoniae isolates were susceptible to amoxicillin/clavulanic acid by CLSI and PK/PD breakpoints. H. influenzae isolates were almost all β-lactamase negative (90.9%). One isolate was β-lactamase negative and ampicillin resistant (BLNAR) by CLSI and four isolates were BLNAR by EUCAST criteria. Susceptibility of isolates was high (≥90.9%) by CLSI breakpoints for all antibiotics tested except trimethoprim/sulfamethoxazole (61.6%). Susceptibility using EUCAST breakpoints was similar for ampicillin (90.9%) and amoxicillin/clavulanic acid (95%) but was low for cefuroxime (oral), where only 10.1% of isolates were susceptible. All S. pneumoniae and H. influenzae isolates were susceptible to the fluoroquinolones by all breakpoints. Susceptibility to ceftriaxone was also 100% for H. influenzae and ≥91% for S. pneumoniae isolates by all breakpoints. The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified.

CONCLUSIONS

Antibiotic susceptibility in these respiratory tract pathogens was generally high in Ukraine. These data are important for empirical therapy choices in the treatment of CA-RTIs.

Results from the Survey of Antibiotic Resistance (SOAR) 2015-17 in the Middle East (Kuwait, Lebanon and Saudi Arabia): data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints

OBJECTIVES

To determine antibiotic susceptibility of Streptococcus pneumoniae and Haemophilus influenzae isolates from community-acquired respiratory tract infections (CA-RTIs) collected in 2015-17 from Kuwait, Lebanon and Saudi Arabia.

METHODS

MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

RESULTS

A total of 139 S. pneumoniae isolates were collected from four centres in Kuwait, Lebanon and Saudi Arabia in 2015-17 and 55 H. influenzae isolates were collected and analysed from Saudi Arabia over the same time period. Pneumococci from all three countries were commonly non-susceptible to penicillin based on CLSI oral or low-dose IV penicillin using EUCAST breakpoints (39% in Kuwait to 57.1% in Lebanon) but by CLSI IV and EUCAST high-dose breakpoints most isolates were susceptible (∼90% in Kuwait and Saudi Arabia, and 100% in Lebanon). Isolates from Lebanon were highly susceptible to most other antibiotics (>90%) except cefaclor, oral cefuroxime and cefpodoxime (EUCAST breakpoints only). Overall, susceptibility was significantly lower in Kuwait and Saudi Arabia than Lebanon. Although all H. influenzae isolates (Saudi Arabia only) were β-lactamase negative, 3.6% and 12.7% were ampicillin resistant by CLSI and EUCAST breakpoints, respectively. Otherwise susceptibility was high in H. influenzae. The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified.

CONCLUSIONS

Relatively low antibiotic susceptibility was observed in S. pneumoniae from Kuwait and Saudi Arabia in contrast to Lebanon, where rates of susceptibility were generally higher. Isolates of H. influenzae from Saudi Arabia were susceptible to most antibiotics. These factors are important in decision making for empirical therapy of CA-RTIs.

Results from the Survey of Antibiotic Resistance (SOAR) 2015-17 in Pakistan: data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints

OBJECTIVES

To determine antibiotic susceptibility of community-acquired respiratory tract infection (CA-RTI) isolates of Streptococcus pneumoniae and Haemophilus influenzae collected in 2015-17 from Pakistan.

METHODS

MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

RESULTS

A total of 94 S. pneumoniae and 122 H. influenzae isolates were collected. Susceptibility to penicillin was noted in 23.4% of the S. pneumoniae isolates by CLSI oral/EUCAST low-dose IV breakpoints, although by CLSI IV and EUCAST high-dose breakpoints all isolates were characterized as susceptible. Susceptibility to trimethoprim/sulfamethoxazole (10.6%), macrolides (33%) and cefaclor (28.7%) was low but higher susceptibility was observed to ceftriaxone (100%), amoxicillin and amoxicillin/clavulanic acid (98.9%), cefuroxime (oral, 97.9%), cefpodoxime (96.8%), fluoroquinolones (93.6%-96.8%) and cefdinir (76.6%) by CLSI breakpoints. However, using EUCAST breakpoints, susceptibility to cefpodoxime (70.2%) and cefuroxime (oral, 61.7%) was reduced. H. influenzae isolates were almost all β-lactamase negative (96.7%). Using CLSI breakpoints, ≥93.4% of isolates were susceptible to all antibiotics tested except fluoroquinolones (75.4%-77.1%) and trimethoprim/sulfamethoxazole (41%). The proportion of isolates susceptible using EUCAST breakpoints was similar or identical for penicillins, trimethoprim/sulfamethoxazole and the cephalosporins that have EUCAST breakpoints; the proportion of isolates susceptible using EUCAST breakpoints was similar or identical to that using CSLI breakpoints except for cefuroxime (oral), where only 1.6% of isolates were considered susceptible. Susceptibility of H. influenzae to fluoroquinolones was also lower by EUCAST breakpoints (33.6%-34.4%). The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified.

CONCLUSIONS

Antibiotic susceptibility in these important respiratory tract pathogens varied in Pakistan based on different breakpoints. These data are important for empirical therapy choices in the treatment of CA-RTIs.

Effects of select dietary supplements on the prevention and treatment of viral respiratory tract infections: a systematic review of randomized controlled trials

Introduction: Viral respiratory tract infections (RTIs) have been recognized as a global public health burden. Despite current theories about their effectiveness, the true benefits of dietary supplements on the prevention and treatment of viral RTIs remain elusive, due to contradictory reports. Hence, we aimed to evaluate the effectiveness of dietary supplements on the prevention and treatment of viral RTIs.Areas covered: We systematically searched databases of PubMed, Web of Science, Scopus, and Google Scholar through 4 March 2020, to identify randomized controlled trials that evaluated the effects of consuming selected dietary supplements on the prevention or treatment of viral RTIs.Expert opinion: Thirty-nine randomized controlled trials (n = 16,797 participants) were eligible and included. Namely, vitamin D supplementation appeared to improve viral RTIs across cohorts particulate in those with vitamin D deficiency. Among the evaluated dietary supplements, specific lactobacillus strains were used most commonly with selected prebiotics that showed potentially positive effects on the prevention and treatment of viral RTIs. Further, ginseng extract supplementation may effectively prevent viral RTIs as adjuvant therapy. However, longitudinal research is required to confirm these observations and address the optimal dose, duration, and safety of dietary supplements being publicly recommended.

Flow Cytometry: From Experimental Design to Its Application in the Diagnosis and Monitoring of Respiratory Diseases

Recent advances in the field of flow cytometry (FCM) have highlighted the importance of incorporating it as a basic analysis tool in laboratories. FCM not only allows the identification of cell subpopulations by detecting the expression of molecules in the cell membrane or cytoplasm, but it can also quantify and identify soluble molecules. The proper functioning of the FCM requires six fundamental systems, from those related to the transport of events to the systems dedicated to the analysis of information. In this review, we have identified the main considerations that every FCM user must know for an optimal antibody panel design, the quality systems that must govern the FCM protocols to guarantee reproducible results in research or clinical laboratories. Finally, we have introduced the current evidence that highlights the relevance of FCM in the investigation and clinical diagnosis of respiratory diseases, establishing important advances in the basic and clinical study of diseases as old as Tuberculosis along with the recent proposals for the monitoring and classification of patients infected with the new SARS-CoV2 virus.

Carbapenemase Producers Among Extensive Drug-Resistant Gram-Negative Pathogens Recovered from Febrile Neutrophilic Patients in Egypt

Purpose

This study aimed to detect the prevalence of carbapenemase producers (CPs) among extensive drug-resistant (XDR)-carbapenemase producing Gram-negative bacteria (GNB) recovered from various clinical specimens of hospitalized neutrophilic febrile patients in two major tertiary care hospitals in Egypt.

Methods

Standard methods were used to evaluate the antimicrobial susceptibility of clinical isolates according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Phenotypic and genotypic analysis of CPs were carried out and statistically analyzed using standard methods.

Results

Three hundred and forty-two GNB were obtained from 342 clinical specimens during the period of the study, where 162 (47%) were enterobacterial isolates, including, 63 (18.4%) Escherichia coli, 87 (25.4%) Klebsiella spp., 5 (1.46%) Enterobacter cloacae, 5 (1.46%) Salmonella spp. and 2 (0.6%) Proteus and 180 (53%) were non-fermentative bacilli including, 129 (37.7%), Acinetobacter baumannii, and 51 (14.9%), Pseudomonas spp. Out of the 342 GNB, 188 (54.9%) isolates were multi-drug resistant (MDR). Of these, 52 (27.6%) were XDR as well as CPs as confirmed phenotypically. The MIC of imipenem against the XDR GNB against showed either low (11 isolates; 21.1%; MIC range =4–32 µg/mL) or high levels of resistance (41 isolates; 78.8%; MIC range = 64-≥1024). The most prevalent carbapenem resistance (CR) genes were blaKPC (63.5%) followed by blaOXA-48 (55.7%) and blaVIM (28.8%). No significant association could be observed between the MIC level and the presence of CR genes (P value >0.05).

Conclusion

High prevalence of MDR (54.9%) and XDR (27.6%) GNB pathogens associated with high levels of resistance to carbapenems were observed. All XDR GNB were CPs and tested positive for at least one of the CR genes. However, most of them (78.8%) showed a high level of CR (MIC range = 64-≥1024) with no significant association with the CR genes.

Platelets and Their Role in the Pathogenesis of Cardiovascular Events in Patients With Community-Acquired Pneumonia

Community-acquired pneumonia (CAP) remains an important cause of morbidity and mortality throughout the world with much recent and ongoing research focused on the occurrence of cardiovascular events (CVEs) during the infection, which are associated with adverse short-term and long-term survival. Much of the research directed at unraveling the pathogenesis of these events has been undertaken in the settings of experimental and clinical CAP caused by the dangerous, bacterial respiratory pathogen, Streptococcus pneumoniae (pneumococcus), which remains the most common bacterial cause of CAP. Studies of this type have revealed that although platelets play an important role in host defense against infection, there is also increasing recognition that hyperactivation of these cells contributes to a pro-inflammatory, prothrombotic systemic milieu that contributes to the etiology of CVEs. In the case of the pneumococcus, platelet-driven myocardial damage and dysfunction is exacerbated by the direct cardiotoxic actions of pneumolysin, a major pore-forming toxin of this pathogen, which also acts as potent activator of platelets. This review is focused on the role of platelets in host defense against infection, including pneumococcal infection in particular, and reviews the current literature describing the potential mechanisms by which platelet activation contributes to cardiovascular complications in CAP. This is preceded by an evaluation of the burden of pneumococcal infection in CAP, the clinical features and putative pathogenic mechanisms of the CVE, and concludes with an evaluation of the potential utility of the anti-platelet activity of macrolides and various adjunctive therapies.

Platelets in Sepsis: An Update on Experimental Models and Clinical Data

Beyond their important role in hemostasis, platelets play a crucial role in inflammatory diseases. This becomes apparent during sepsis, where platelet count and activation correlate with disease outcome and survival. Sepsis is caused by a dysregulated host response to infection, leading to organ dysfunction, permanent disabilities, or death. During sepsis, tissue injury results from the concomitant uncontrolled activation of the complement, coagulation, and inflammatory systems as well as platelet dysfunction. The balance between the systemic inflammatory response syndrome (SIRS) and the compensatory anti-inflammatory response (CARS) regulates sepsis outcome. Persistent thrombocytopenia is considered as an independent risk factor of mortality in sepsis, although it is still unclear whether the drop in platelet count is the cause or the consequence of sepsis severity. The role of platelets in sepsis development and progression was addressed in different experimental in vivo models, particularly in mice, that represent various aspects of human sepsis. The immunomodulatory function of platelets depends on the experimental model, time, and type of infection. Understanding the molecular mechanism of platelet regulation in inflammation could bring us one step closer to understand this important aspect of primary hemostasis which drives thrombotic as well as bleeding complications in patients with sterile and infectious inflammation. In this review, we summarize the current understanding of the contribution of platelets to sepsis severity and outcome. We highlight the differences between platelet receptors in mice and humans and discuss the potential and limitations of animal models to study platelet-related functions in sepsis.