Impact of microbiological samples in the hospital management of community-acquired, nursing home-acquired and hospital-acquired pneumonia in older patients

The Effects of Immunosuppression on the Lung Microbiome and Metabolites in Rats

Immunosuppressed patients are more likely to suffer from pneumonia, especially Streptococcus and Enterobacter pneumonia. Studies have demonstrated the existence of a complex and dynamic microbiota on the surface of human respiratory epithelial cells, both in healthy and diseased states. However, it is not clear whether the pneumonia in immunosuppressed patients is caused by inhaled oropharyngeal pathogens or abnormal proliferation of pulmonary proteobacteria. In this study, immunosuppressed model was made by intraperitoneal injection of cyclophosphamide and oropharyngeal saliva aspiration was simulated by oral and pharyngeal tracheal instillation of sterilized phosphate buffered saline (PBS). Furthermore, the effects of immunosuppression on the lung microbial community and its metabolism were investigated using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS) metabolomics analysis. The 16S rRNA gene sequencing results showed that immunosuppression alone did not change the composition of pulmonary bacteria. Moreover, although the bacteria brought by sterilized PBS from oropharynx to lower respiratory tract changed the composition of the microflora in healthy and immunosuppressed rats, the change in the latter was more obvious. Metabolomic analysis revealed that the levels of pulmonary metabolites were disturbed in the immunosuppressed rats. The altered lung microbiota, including Streptococcaceae and Enterobacteriaceae, showed significant positive correlations with pulmonary metabolites. Our study suggested that the source of the pathogens of pneumonia in immunosuppressed rats was via inhalation and explored the relationship between lung microbiome and metabolites in immunosuppressed rats. Our results provide the basis for the development of prevention and treatment strategies for pneumonia.

Perspective on the clone library method for infectious diseases

Recently, culture-independent molecular methods, such as DNA sequencing techniques targeting the 16S-ribosomal RNA (rRNA) gene and/or other housekeeping genes with Sanger method-based technologies, next generation sequencing (NGS), and metagenomic analysis, have been developed for detecting microorganisms in the human body; these can provide information on microbiomes of samples from individuals with or without infectious diseases. Determining the bacterial species is crucial in identifying causative bacteria of upper and lower respiratory tract infections, especially for Streptococcus species, but NGS analysis is often not precise enough to identify bacteria at the species level. This review briefly introduces previous observations of the microbiome of samples from various respiratory and other infections assessed using the clone library method with Sanger sequencing of the 16S-rRNA gene. On analysis of 16S-rRNA gene-sequence data of bronchoalveolar lavage fluid obtained from pneumonia lesions in patients with bacterial pneumonia and lung abscess, anaerobes are often detected in non-elderly patients with pneumonia, and the detection rate of Staphylococcus aureus in patients with hospital-acquired pneumonia is lower than that previously reported. Analysis of pleural effusion samples from patients with pleurisy indicated a more important role of anaerobes than previous believed. The other topics reviewed include microbiomes of nontuberculous mycobacteriosis and lower respiratory tract infections in children with permanent tracheostomy due to neuromuscular disorders, in nasal discharge, in bacterial vaginosis, in the intracystic fluid of postoperative maxillary cyst, and in bacterial conjunctivitis; urine microbiota in urethritis; fecal microbiota; and newly detected infectious organisms in the human respiratory tract.

Pneumonia in older adults

PURPOSE OF REVIEW

The purpose of this review is to address the relevant issues surrounding older adults with community-acquired pneumonia (CAP) today.

RECENT FINDINGS

Approximately 1 million people >65 years have CAP in the US per year, which is more than previously reported (or realized). Older adults are vulnerable to the increasing prevalence of viral CAP, as the SARS-CoV-2 pandemic emphasizes, but pneumococcus is still the most common pathogen to cause CAP. Racial disparities continue to need to be addressed in order to improve early and late outcomes of older adults with CAP.

SUMMARY

The epidemiology of CAP, specifically for older adults is changing. More recent pathogen incidence studies have included culture, as well as newer microbiological methods to determine etiology. Current disparities among disadvantaged populations, including African-Americans, result in more comorbidities which predisposes to more severe CAP. However, outcomes in the hospital between races tend to be similar, and outcomes between age groups tends to be worse for older compared to younger adults. Finally, the cost of CAP is significant compared to diabetes mellitus, myocardial infarction and stroke.

Troponin Elevation in Older Patients with Acute Pneumonia: Frequency and Prognostic Value

Cardiovascular (CV) events are particularly frequent after acute pneumonia (AP) in the elderly. We aimed to assess whether cardiac troponin I, a specific biomarker of myocardial injury, independently predicts CV events and death after AP in older inpatients. Among 214 consecutive patients with AP aged ≥75 years admitted to a university hospital, 171 with a cardiac troponin I sample in the 72 h following diagnosis of AP were included, and 71 (42%) were found to have myocardial injury (troponin > 100 ng/L). Patients with and without myocardial injury were similar in terms of age, gender and comorbidities, but those with myocardial injury had more severe clinical presentation (median (interquartile range) Pneumonia Severity Index: 60 (40-95) vs. 45 (30-70), p = 0.003). Myocardial injury was strongly associated with in-hospital myocardial infarction (25% vs. 0%, p < 0.001), CV mortality (11 vs. 1%, p = 0.003) and all-cause mortality (34 vs. 13%, p = 0.002). After adjustment for confounders, myocardial injury remained a strong predictive factor of in-hospital mortality (odds ratio (95% confidence interval): 3.32 (1.42-7.73), p = 0.005) but not one-year mortality (1.61 (0.77-3.35), p = 0.2). Cardiac troponin I elevation, a specific biomarker of myocardial injury, was found in nearly half of an unselected cohort of older inpatients with AP and was associated with a threefold risk of in-hospital death.

Where is Chlamydophila pneumoniae pneumonia?

BACKGROUND

Molecular diagnostic methods have recently gained widespread use, and consequently, the importance of viral pathogens in community-acquired pneumonia (CAP) has undergone re-evaluation. Under these circumstances, the role of Chlamydophila pneumoniae as a pathogen that causes CAP also needs to be reviewed.

METHODS

We reviewed articles that contained data on the frequency of identification of C. pneumoniae pneumonia as a causative pathogen for CAP. The articles were identified by performing a search in PubMed with the keywords "community-acquired pneumonia" and "pathogen".

RESULTS

Sixty-three articles were identified. The reviewed articles demonstrated that the rates of identification of C. pneumoniae as the causative pathogen for CAP were significantly lower in assessments based on polymerase chain reaction (PCR) methods than in those based on serological methods. In some studies, it was possible to compare both serological and PCR methods directly using the same set of samples.

CONCLUSIONS

The use of PCR methods, including multiplex PCR assays, has revealed that C. pneumoniae may play a limited role as a pathogen for CAP.

Prevalence and Etiology of Community-acquired Pneumonia in Immunocompromised Patients

Background

The correct management of immunocompromised patients with pneumonia is debated. We evaluated the prevalence, risk factors, and characteristics of immunocompromised patients coming from the community with pneumonia.

Methods

We conducted a secondary analysis of an international, multicenter study enrolling adult patients coming from the community with pneumonia and hospitalized in 222 hospitals in 54 countries worldwide. Risk factors for immunocompromise included AIDS, aplastic anemia, asplenia, hematological cancer, chemotherapy, neutropenia, biological drug use, lung transplantation, chronic steroid use, and solid tumor.

Results

At least 1 risk factor for immunocompromise was recorded in 18% of the 3702 patients enrolled. The prevalences of risk factors significantly differed across continents and countries, with chronic steroid use (45%), hematological cancer (25%), and chemotherapy (22%) the most common. Among immunocompromised patients, community-acquired pneumonia (CAP) pathogens were the most frequently identified, and prevalences did not differ from those in immunocompetent patients. Risk factors for immunocompromise were independently associated with neither Pseudomonas aeruginosa nor non–community-acquired bacteria. Specific risk factors were independently associated with fungal infections (odds ratio for AIDS and hematological cancer, 15.10 and 4.65, respectively; both P = .001), mycobacterial infections (AIDS; P = .006), and viral infections other than influenza (hematological cancer, 5.49; P < .001).

Conclusions

Our findings could be considered by clinicians in prescribing empiric antibiotic therapy for CAP in immunocompromised patients. Patients with AIDS and hematological cancer admitted with CAP may have higher prevalences of fungi, mycobacteria, and noninfluenza viruses.

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

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

Nursing Home-Associated Pneumonia, Part II: Etiology and Treatment

This is the second of 2 parts of a narrative review of nursing home-associated pneumonia (NHAP) that deals with etiology and treatment in the nursing home. In the 1980s and 1990s, the etiology of NHAP was considered to be similar to community-acquired pneumonia (CAP). This belief was reflected in CAP guidelines until 2005 when the designation healthcare-associated pneumonia or HCAP was introduced and nursing home residents were included in the HCAP category. Patients in the HCAP group were thought to be at high risk for pneumonia because of multidrug resistant organisms and required empiric broad-spectrum antibiotic therapy much like people with hospital-acquired infection. Subsequent studies of the etiology of NHAP using sophisticated diagnostic testing found limited evidence of resistant organisms such as methicillin-resistant Staphylococcus aureus or resistant gram-negative organisms or atypical organisms. In terms of management of NHAP in the nursing home there are several considerations that are discussed: hospitalization decision, initial oral or parenteral therapy, timing of switch to an oral regimen if parenteral therapy is initially prescribed, duration of therapy with an emphasis on shorter courses, and follow-up during therapy including the use of the "antibiotic time out" protocol. The oral and parenteral antibiotic regimens recommended for treatment of NHAP in this report are based on limited information because there are no randomized controlled trials to define the optimum regimen. In conclusion, most residents with pneumonia can be treated successfully in the nursing home. However, there is an urgent need for a specific NHAP diagnosis and treatment guideline that will give providers guidance in the management of this infection in the nursing home.

Comparing the yield of oropharyngeal swabs and sputum for detection of 11 common pathogens in hospitalized children with lower respiratory tract infection

Background

Advances in molecular laboratory techniques are changing the prospects for the diagnosis of viral infectious diseases. Multiplex polymerase chain reaction assay (multiplex-PCR) can detect dozens of pathogens simultaneously, greatly reducing turnaround time (TAT) and improving detection sensitivity. But as a double-edged sword, due to the high sensitivity of PCR, the type of respiratory specimens is critical to diagnosis. In this work, we performed a head-to-head comparison to evaluate the multiplex-PCR yields between two samples, sputum and flocked oropharyngeal swabs (OPS).

Methods

Eleven common respiratory pathogens were tested in hospitalized children< 13 years of age who met the criteria for lower respiratory tract infection by GeXP-based multiplex-PCR of paired OPS and sputum.

Results

From January to June 2018, 440 children with paired OPS and sputum were tested. The positive rate was 84% (369/440) for OPS and 88% (386/440) for sputum (p = .007). The frequency of detection of HRV, RSV, Influenza A virus, HMPV, parainfluenza virus, adenovirus, M. pneumoniae, coronavirus, bocavirus and C. pneumoniae in sputa was higher than that of OPSs (all p < .001). Both types of specimens had similarly very good kappa values for most of pathogens, except for Mycoplasma pneumonia (κ = 0.61) and Chlamydia pneumoniae (κ = 0.24). Additionally, 79.3% (349/440) of cases showed consistent results between the two types of samples, and they were significantly younger than patients with inconsistent results (p = .002).

Conclusions

Flocked oropharyngeal swabs and sputum performed similarly for the detection of common respiratory pathogens in hospitalized children by multiplex-PCR, except for Mycoplasma pneumoniae and Chlamydia pneumoniae. Young patients are likely to have consistent results between the two specimens.

Electronic supplementary material

The online version of this article (10.1186/s12985-019-1177-x) contains supplementary material, which is available to authorized users.

Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study

OBJECTIVES

We aimed to assess the accuracy of PCR detection of viruses and bacteria on nasopharyngeal and oropharyngeal swabs (NPS) for the diagnosis of pneumonia in elderly individuals.

METHODS

We included consecutive hospitalized elderly individuals suspected of having pneumonia. At inclusion, NPS were collected from all participants and tested by PCR for the presence of viral and bacterial respiratory pathogens (index test, defined as comprehensive molecular testing). Routine diagnostic tests (blood and sputum culture, urine antigen detection) were also performed. The reference standard was the presence of pneumonia on a low-dose CT scan as assessed by two independent expert radiologists.

RESULTS

The diagnosis of pneumonia was confirmed in 127 of 199 (64%) included patients (mean age 83 years, community-acquired pneumonia in 105 (83%)). A pathogen was identified by comprehensive molecular testing in 114 patients (57%) and by routine methods in 22 (11%). Comprehensive molecular testing was positive for viruses in 62 patients (31%) and for bacteria in 73 (37%). The sensitivity and specificity were 61% (95% CI 53%-69%) and 50% (95% CI 39%-61%) for comprehensive molecular testing, and 14% (95% CI 82%-21%) and 94% (95% CI 86%-98%) for routine testing, respectively. Positive likelihood ratio was 2.55 for routine methods and 1.23 for comprehensive molecular testing.

CONCLUSION

Comprehensive molecular testing of NPS increases the number of pathogens detected compared with routine methods, but results are poorly predictive of the presence of pneumonia. Hence, comprehensive molecular testing is unlikely to impact clinical decision-making (NCT02467192).

CLINICAL TRIALS REGISTRATION

NCT02467192.

Infectious Diseases in Older Adults of Long-Term Care Facilities: Update on Approach to Diagnosis and Management

The diagnosis, treatment, and prevention of infectious diseases in older adults in long-term care facilities (LTCFs), particularly nursing facilities, remains a challenge for all health providers who care for this population. This review provides updated information on the currently most important challenges of infectious diseases in LTCFs. With the increasing prescribing of antibiotics in older adults, particularly in LTCFs, the topic of antibiotic stewardship is presented in this review. Following this discussion, salient points on clinical relevance, clinical presentation, diagnostic approach, therapy, and prevention are discussed for skin and soft tissue infections, infectious diarrhea (Clostridium difficile and norovirus infections), bacterial pneumonia, and urinary tract infection, as well as some of the newer approaches to preventive interventions in the LTCF setting.

A New Prognosis Score to Predict Mortality After Acute Pneumonia in Very Elderly Patients

OBJECTIVES

Acute pneumonia (AP) induces an excess of mortality among the elderly. We evaluated the value of a new predictive biomarker index compared to usual prognosis scores for predicting in-hospital and 1-year mortalities in elderly inpatients with AP.

DESIGN

Retrospective study in 6 clinical departments of a university hospital.

SETTING

Burgundy university hospital (France).

PARTICIPANTS

All patients aged 75 and over with AP and hospitalized between January 1 and June 30, 2013, in the departments of medicine (5) and intensive care (1) of our university hospital.

MEASUREMENTS

A new index, which we named UBMo, was created by multiplying the uremia (U in the formula) by the N-terminal-pro-brain natriuretic peptide (NT-proBNP) plasmatic rate (B), divided by the monocyte count (Mo).

RESULTS

Among the 217 patients included, there were 138 community-acquired pneumonia, 56 nursing home-acquired pneumonia, and 23 hospital-acquired pneumonia. In-hospital and 1-year mortality rates were respectively 19.8% and 43.8%. In multivariate analysis, Pneumonia Severity Index (PSI), unlike CURB-65 (confusion, urea >7 mmol/L, respiratory rate ≥30 breaths/min, blood pressure <90 mmHg systolic or ≤60 mmHg diastolic, age ≥65) score, was associated with in-hospital and 1-year mortalities. UBMo index performed better than PSI and CURB-65 scores in predicting both in-hospital and 1-year mortalities. For in-hospital mortality, the areas under the receiver operating characteristic curves (AUCs) were 0.89 (95% CI = 0.84-0.94), 0.72 (95% CI = 0.65-0.80), and 0.63 (95% CI = 0.54-0.72), respectively, for the 3 scores. For 1-year mortality, the AUCs were 0.93 (95% CI = 0.89-0.98), 0.66 (95% CI = 0.59-0.74), and 0.58 (95% CI = 0.50-0.66), respectively, for the 3 scores. The cut point for the UBMo index of 20,000 × 10^-9 ng·mmol/L had a sensitivity of 93.1% and 80.9% and a specificity of 76.3% and 95.8%, respectively, for in-hospital and 1-year mortalities.

CONCLUSION

If confirmed by prospective studies, the UBMo index appears very efficient in identifying patients at high risk of in-hospital and 1-year mortalities after an AP.