Pneumonia—Overview

mtx-COBRA: Subcellular localization prediction for bacterial proteins

BACKGROUND

Bacteria can have beneficial effects on our health and environment; however, many are responsible for serious infectious diseases, warranting the need for vaccines against such pathogens. Bioinformatic and experimental technologies are crucial for the development of vaccines. The vaccine design pipeline requires identification of bacteria-specific antigens that can be recognized and can induce a response by the immune system upon infection. Immune system recognition is influenced by the location of a protein. Methods have been developed to determine the subcellular localization (SCL) of proteins in prokaryotes and eukaryotes. Bioinformatic tools such as PSORTb can be employed to determine SCL of proteins, which would be tedious to perform experimentally. Unfortunately, PSORTb often predicts many proteins as having an "Unknown" SCL, reducing the number of antigens to evaluate as potential vaccine targets.

METHOD

We present a new pipeline called subCellular lOcalization prediction for BacteRiAl Proteins (mtx-COBRA). mtx-COBRA uses Meta's protein language model, Evolutionary Scale Modeling, combined with an Extreme Gradient Boosting machine learning model to identify SCL of bacterial proteins based on amino acid sequence. This pipeline is trained on a curated dataset that combines data from UniProt and the publicly available ePSORTdb dataset.

RESULTS

Using benchmarking analyses, nested 5-fold cross-validation, and leave-one-pathogen-out methods, followed by testing on the held-out dataset, we show that our pipeline predicts the SCL of bacterial proteins more accurately than PSORTb.

CONCLUSIONS

mtx-COBRA provides an accessible pipeline that can more efficiently classify bacterial proteins with currently "Unknown" SCLs than existing bioinformatic and experimental methods.

Comprehensive Physiotherapy Approach for Pneumonia After Angioplasty in an 83-Year-Old Hypertensive Male Patient: A Case Report

Pneumonia is an infection that causes inflammation in the air sacs of the lungs. Coronary artery disease is a condition characterized by the buildup of plaque in the coronary arteries, which supply blood to the heart. This obstruction restricts blood flow, resulting in chest pain (angina) and, in extreme cases, heart attacks. An important part of successfully treating diseases like peripheral artery disease and coronary artery disease is balloon angioplasty, a commonly used medical procedure for treating narrowed or clogged arteries. An 83-year-old man who had pneumonia after angioplasty was the subject of this case study. The patient had pneumonia after angioplasty, which was managed by proper medications and cardio-respiratory physiotherapy. The patient was intubated and referred for cardio-respiratory physiotherapy. Physiotherapy treatments like mild chest vibrations, suctioning, and bed mobility exercises were given initially. After extubation, physiotherapy treatment continued with deep breathing exercises, coughing techniques, relaxation techniques, and mobility exercises for the upper limbs and lower limbs. Effective physical rehabilitation was necessary in order to minimize complications following angioplasty and allow him to resume his daily activities. Several outcome measures, like the ICU mobility scale, CURB-65 score, and chest X-ray grading scores, were used to monitor the patient's progress during rehabilitation. The benefits of pulmonary rehabilitation programs emphasize the need for tailored approaches in addressing individual patient needs for comprehensive recovery.

Rapid Point-of-Care PCR Testing of Drug-Resistant Strains on Endotracheal Aspirate Samples: A Repurposed Effective Tool in the Stepwise Approach of Healthcare-Acquired Pneumonia-A Pilot Study

Healthcare-associated pneumonia (HCAP) is a common nosocomial infection with high morbidity and mortality. Culture-based detection of the etiologic agent and drug susceptibility is time-consuming, potentially leading to the inadequate use of broad-spectrum empirical antibiotic regimens. The aim was to evaluate the diagnostic capabilities of rapid point-of-care multiplex polymerase chain reaction (PCR) assays from the endotracheal aspirate of critically ill patients with HCAP. A consecutive series of 29 intensive care unit (ICU) patients with HCAP and a control group of 28 patients undergoing elective surgical procedures were enrolled in the study. The results of the PCR assays were compared to the culture-based gold standard. The overall accuracy of the PCR assays was 95.12%, with a sensitivity of 92.31% and a specificity of 97.67%. The median time was 90 min for the rapid PCR tests (p < 0.001), while for the first preliminary results of the cultures, it was 48 h (46-72). The overall accuracy for rapid PCR testing in suggesting an adequate antibiotic adjustment was 82.98% (95% CI 69.19-92.35%), with a specificity of 90% (95% CI 55.50-99.75%), a positive predictive value of 96.77% (95% CI 83.30-99.92%), and a negative predictive value of 56.25 (95% CII 29.88-80.25%). This method of rapid point-of-care PCR could effectively guide antimicrobial stewardship in patients with healthcare-acquired pneumonia.

Trends in Molecular Diagnosis of Nosocomial Pneumonia Classic PCR vs. Point-of-Care PCR: A Narrative Review

Nosocomial pneumonia is one of the most frequent hospital-acquired infections. One of the types of nosocomial pneumonia is ventilator-associated pneumonia, which occurs in endotracheally intubated patients in intensive care units (ICU). Ventilator-associated pneumonia may be caused by multidrug-resistant pathogens, which increase the risk of complications due to the difficulty in treating them. Pneumonia is a respiratory disease that requires targeted antimicrobial treatment initiated as early as possible to have a good outcome. For the therapy to be as specific and started sooner, diagnostic methods have evolved rapidly, becoming quicker and simpler to perform. Polymerase chain reaction (PCR) is a rapid diagnostic technique with numerous advantages compared to classic plate culture-based techniques. Researchers continue to improve diagnostic methods; thus, the newest types of PCR can be performed at the bedside, in the ICU, so-called point of care testing-PCR (POC-PCR). The purpose of this review is to highlight the benefits and drawbacks of PCR-based techniques in managing nosocomial pneumonia.

Serostatus and Epidemiological Characteristics for Atypical Pneumonia Causative Bacteria among Healthy Individuals in Medina, Saudi Arabia, a Retrospective Study

Background: Community-acquired atypical pneumonia is generally a mild and self-limiting infection. Still, it may lead to hospitalization and progressive clinical complications in some cases, particularly among the elderly and individuals with chronic diseases. Chlamydia pneumoniae, Legionella pneumophila, and Mycoplasma pneumoniae are the community’s main causative agents of atypical pneumonia. However, most published studies evaluated their incidence in the hospital setting, and little is known about their prevalence among healthy individuals. This work aims to assess the seroprevalence of these bacteria among healthy people to determine the status of immunity against these bacteria in the community. Methodology: Two hundred and eighty-three serum samples from a multicenter in Medina, Saudi Arabia, were collected in this study. Serum samples were subjected to indirect enzyme-linked immunosorbent assays (ELISAs) to detect IgG antibodies against C. pneumoniae, L. pneumophila, and M. pneumoniae to investigate the seroprevalence of these bacteria and their distribution among different genders and age groups of healthy people. Results: IgG seropositivity for at least one of the three atypical pneumonia-causative bacteria occurred in 85.8% (n= 243/283) of the sample population. IgG seropositivity for C. pneumoniae occurred in 80.6% (228/283) of the population, followed by 37.5% for L. pneumophila and 23% for M. pneumoniae (66/283). In addition, the IgG seropositivity rates for the three bacteria were observed predominantly among male participants. Furthermore, no significant difference in IgG seropositivity distribution occurred between different age groups of healthy people for C. pneumoniae, L. pneumophila and M. pneumoniae. Conclusions: The current study found that C. pneumoniae, L. pneumophila, and M. pneumoniae tended to be highly prevalent among healthy people and more common among males than females. Additionally, their pattern of distribution among healthy individuals seemed to be predominant among young adults (aged 20−40 years), which differs from their predominant distribution among elderly patients in hospital settings (>50 years).

The Association Between Antihypertensive Drug Use and Hospitalization for Pneumonia in the General Population: A Case-Crossover Study Using the National Health Insurance Database of Korea

BACKGROUND

Previous studies have reported an association between pneumonia risk and the use of certain drugs. We investigated the relationship between antihypertensive drugs and pneumonia in the general population.

METHODS

This case-crossover study utilized the nationwide data of South Korea. We included participants who were hospitalized for pneumonia. A single case period was defined as 30 days before pneumonia onset, and two control periods were established (90-120 and 150-180 days before pneumonia onset). Further, we performed sensitivity and subgroup analyses (according to the presence of diabetes, documented disability, and whether participants were aged ≥ 70 years). We used conditional logistic regression models adjusted for covariates, such as angiotensin-converting-enzyme (ACE) inhibitors, angiotensin receptor blockers (ARBs), other antihypertensives, statins, antipsychotics, benzodiazepine, and the number of outpatient visits.

RESULTS

In total, 15,463 subjects were included in this study. ACE inhibitors (adjusted odds ratio [aOR], 0.660; 95% confidence interval [CI], 0.558-0.781), ARBs (aOR, 0.702; 95% CI, 0.640-0.770), and other antihypertensive drugs (aOR, 0.737; 95% CI, 0.665-0.816) were significantly associated with reduced pneumonia risk. Subgroup analyses according to the presence of diabetes mellitus, documented disability, and whether participants were aged ≥ 70 years consistently showed the association of antihypertensives with a reduced risk of hospitalization for pneumonia.

CONCLUSION

All antihypertensive drug types were related to a lower risk of hospitalization for pneumonia in the general population. Our results implied that frequent medical service usage and protective immunity were primarily related to a reduced risk of pneumonia in the general population of South Korea.

Plant-Derived Natural Products as Lead Agents against Common Respiratory Diseases

Never has the world been more challenged by respiratory diseases (RDs) than it has witnessed in the last few decades. This is evident in the plethora of acute and chronic respiratory conditions, ranging from asthma and chronic obstructive pulmonary disease (COPD) to multidrug-resistant tuberculosis, pneumonia, influenza, and more recently, the novel coronavirus (COVID-19) disease. Unfortunately, the emergence of drug-resistant strains of pathogens, drug toxicity and side effects are drawbacks to effective chemotherapeutic management of RDs; hence, our focus on natural sources because of their unique chemical diversities and novel therapeutic applications. This review provides a summary on some common RDs, their management strategies, and the prospect of plant-derived natural products in the search for new drugs against common respiratory diseases.