Relationship between the respiratory microbiome and the severity of airflow limitation, history of exacerbations and circulating eosinophils in COPD patients

Background

The respiratory microbiome is altered in COPD patients but its relationship with core components of the disease, such as the severity of airflow limitation, the frequency of exacerbations or the circulating levels of eosinophils, is unclear.

Methods

Cross-sectional study comprising 72 clinically stable COPD patients (mean age 68 [SD 7.9] years; FEV1 48.7 [SD 20.1]% of reference) who provided spontaneous sputum samples for 16S rRNA gene amplification and sequencing. The microbiome composition was analysed with QIIME.

Results

We observed that: (1) more severe airflow limitation was associated with reduced relative abundance (RA) of Treponema and an increase in Pseudomonas; (2) patients with ≥2 exacerbations the previous year showed a significantly different bacterial community with respect to non-exacerbators (p = 0.014), with changes in 13 genera, including an increase of Pseudomonas, and finally, (3) peripheral eosinophils levels ≥2% were associated with more diverse microbiome [Chao1 224.51 (74.88) vs 277.39 (78.92) p = 0.006; Shannon 3.94 (1.05) vs 4.54 (1.06) p = 0.020], and a significant increase in the RAs of 20 genera.

Conclusion

The respiratory microbiome in clinically stable COPD patients varies significantly according to the severity of airflow limitation, previous history of exacerbations and circulating eosinophils levels.

Electronic supplementary material

The online version of this article (10.1186/s12890-019-0867-x) contains supplementary material, which is available to authorized users.

Discriminatory usefulness of pulsed-field gel electrophoresis and sequence-based typing in Legionella outbreaks

Aim: To compare the discriminatory power of pulsed-field gel electrophoresis (PFGE) and sequence-based typing (SBT) in Legionella outbreaks for determining the infection source. Materials & methods: Twenty-five investigations of Legionnaires’ disease were analyzed by PFGE, SBT and Dresden monoclonal antibody. Results: The results suggested that monoclonal antibody could reduce the number of Legionella isolates to be characterized by molecular methods. The epidemiological concordance PFGE–SBT was 100%, while the molecular concordance was 64%. Adjusted Wallace index (AW) showed that PFGE has better discriminatory power than SBT (AWSBT→PFGE = 0.767; AWPFGE→SBT = 1). The discrepancies appeared mostly in sequence type (ST) 1, a worldwide distributed ST for which PFGE discriminated different profiles. Conclusion: SBT discriminatory power was not sufficient verifying the infection source, especially in worldwide distributed STs, which were classified into different PFGE patterns.

[Proteomics in infectious diseases]

Infectious diseases have a high incidence in the population, causing a major impact on global health. In vitro culture of microorganisms is the first technique applied for infection diagnosis which is laborious and time consuming. In recent decades, efforts have been focused on the applicability of "Omics" sciences, highlighting the progress provided by proteomic techniques in the field of infectious diseases. This review describes the management, processing and analysis of biological samples for proteomic research.

Functional Metagenomics of the Bronchial Microbiome in COPD

The course of chronic obstructive pulmonary disease (COPD) is frequently aggravated by exacerbations, and changes in the composition and activity of the microbiome may be implicated in their appearance. The aim of this study was to analyse the composition and the gene content of the microbial community in bronchial secretions of COPD patients in both stability and exacerbation. Taxonomic data were obtained by 16S rRNA gene amplification and pyrosequencing, and metabolic information through shotgun metagenomics, using the Metagenomics RAST server (MG-RAST), and the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) programme, which predict metagenomes from 16S data. Eight severe COPD patients provided good quality sputum samples, and no significant differences in the relative abundance of any phyla and genera were found between stability and exacerbation. Bacterial biodiversity (Chao1 and Shannon indexes) did not show statistical differences and beta-diversity analysis (Bray-Curtis dissimilarity index) showed a similar microbial composition in the two clinical situations. Four functional categories showed statistically significant differences with MG-RAST at KEGG level 2: in exacerbation, Cell growth and Death and Transport and Catabolism decreased in abundance [1.6 (0.2-2.3) vs 3.6 (3.3-6.9), p = 0.012; and 1.8 (0-3.3) vs 3.6 (1.8-5.1), p = 0.025 respectively], while Cancer and Carbohydrate Metabolism increased [0.8 (0-1.5) vs 0 (0-0.5), p = 0.043; and 7 (6.4-9) vs 5.9 (6.3-6.1), p = 0.012 respectively]. In conclusion, the bronchial microbiome as a whole is not significantly modified when exacerbation symptoms appear in severe COPD patients, but its functional metabolic capabilities show significant changes in several pathways.

Effect of bronchial colonisation on airway and systemic inflammation in stable COPD

The recovery of potentially pathogenic microorganisms (PPMs) from bronchial secretions is associated with a local inflammatory response in COPD patients. The objective of this study was to determine the relationships between bronchial colonisation and both bronchial and systemic inflammation in stable COPD. In COPD patients recruited on first admission for an exacerbation, bacterial sputum cultures, interleukin (IL)-1β, IL-6 and IL-8 levels, and blood C-reactive protein (CRP) were measured in stable condition. Bronchial colonisation was found in 39 of the 133 (29%) patients and was significantly related to higher sputum IL-1β (median [percentile 25-75]; 462 [121-993] vs. 154 [41-477] pg/ml, p = 0.002), IL-6 (147 [71-424] vs. 109 [50-197] pg/ml, p = 0.047) and IL-8 values (15 [9-19] vs. 8 [3-15] (×10³) pg/ml, p = 0.002). Patients with positive cultures also showed significantly elevated levels of serum CRP (6.5 [2.5-8.5] vs. 3.5 [1.7-5.4] mg/l, p = 0.016). Bronchial colonisation by Haemophilus influenzae was associated with higher levels of IL-1β and IL-8 and clinically significant worse scores on the activity and impact domains of the St. George's Respiratory Questionnaire. In conclusion, bronchial colonisation is associated with bronchial inflammation and high blood CRP levels in stable COPD patients, being Haemophilus influenzae related to a more severe inflammatory response and impairment in health-related quality of life.

[Low mortality rate in an outbreak of Legionnaires' disease: correlation with the cytopathogenity study]

BACKGROUND

In 2001 an outbreak of Legionnaires' diseases occurred in Murcia, Spain, with one of the lowest known rates of associated mortality. We describe the clinical data of a subgroup of patients, and present the results from molecular and virulence studies to correlate the lower mortality of the overall series with the strain virulence.

PATIENTS AND METHODS

A subgroup of 86 patients from the outbreak of Legionnaires'disease was prospectively included. Demographic, risk factors and clinical evolution data were obtained. Moreover, we performed a pulsed field gel electrophoresis and cytopathogenicity assay of the Murcia outbreak that were compared with other unrelated Legionella isolates.

RESULTS

Sixty-nine (77.9%) patients were males. The mean age of the patients was 58.2 years (range: 32-87). Smoking was the most frequent risk factor in 62 patients (71.7%) and 61 patients (70.2%) had underlying diseases. Clinical, laboratory and radiological manifestations were compatible with the atypical pneumonia syndrome. The mortality rate was 3.2%. All the clinical L. pneumophila isolates analyzed by PFGE showed the same subtype. When analyzing theses strains together with other Legionella strains, they were included in the group with lower virulence in the cytopathogenicity study.

CONCLUSIONS

The most outstanding data in this subgroup of patients were: male-sex, smoking, atypical clinical manifestations and low mortality. The low virulence of this molecular genotype of L. pneumophila may be responsible, in part, for the low mortality observed in the outbreak in Murcia.

Impact of Copper and Silver Ionization on Fungal Colonization of the Water Supply in Health Care Centers: Implications for Immunocompromised Patients

Copper and silver ionization is a well-recognized disinfection method to control Legionella species in water distribution systems in hospitals. These systems may also serve as a potential indoor reservoir for fungi. The prevalence of fungi was significantly lower in ionized than in nonionized water samples from health care facilities. The clinical consequences of this finding require further investigation.

Streptococcus pneumoniae and Legionella pneumophila pneumonia in HIV-infected patients

We compared the epidemiological data, clinical features and mortality of community-acquired pneumonia (CAP) by Streptococcus pneumoniae and Legionella in HIV-infected patients and determined discriminative features. An observational, comparative study was performed (January 1994 to December 2004) in 15 HIV patients with CAP by Legionella and 46 by S. pneumoniae. No significant differences were observed in delay until initiation of appropriate antibiotic therapy. Smoking, cancer and chemotherapy were more frequent in patients with Legionella pneumonia (p=0.03, p=0.00009 and p=0.01). Patients with Legionella pneumonia had a higher mean CD4 count (p=0.04), undetectable viral load (p=0.01) and received highly active antiretroviral therapy more frequently (p=0.004). AIDS was more frequent in patients with S. pneumoniae pneumonia (p=0.03). Legionella pneumonia was more severe (p=0.007). Extrarespiratory symptoms, hyponatraemia and increased creatine phosphokinase were more frequent in Legionella pneumonia (p=0.02, p=0.002 and p=0.006). Respiratory failure, need for ventilation and bilateral chest X-ray involvement were of note in the Legionella group (p=0.003, p=0.002 and p=0.002). Mortality tended to be higher in the Legionella group (6.7 vs 2.2%). In conclusion, CAP by Legionella has a higher morbimortality than CAP by S. pneumoniae in HIV-infected patients. Detailed analysis of CAP presentation features allows suspicion of Legionnaires' disease in this subset.

Sporadic and epidemic community legionellosis: two faces of the same illness

The present study compares the risk factors, presentation and outcome of community-acquired Legionella pneumophila pneumonia in 138 sporadic-case patients (1994-2004) and 113 outbreak-case patients (2002) treated in two hospitals in Catalonia (Spain) since urinary antigen assays were adopted. Univariate and multivariate analysis were performed to compare epidemiological and clinical features, blood chemistry values, radiological findings and outcome of sporadic and epidemic legionnaires' disease. Univariate analysis showed that male sex, chronic lung disease, HIV infection and immunosuppressive therapy prevailed in sporadic cases. Presentation with respiratory symptoms, confusion and blood chemistry alterations, such as hyponatraemia, aspartate aminotransferase and blood urea nitrogen elevation, and partial pressure of oxygen P(O)(2) <7.98 KPa (60 mmHg) were also more frequent in sporadic cases, while headache prevailed in outbreak cases. Sporadic cases had a greater delay in treatment, were more severe and had a worse outcome than epidemic cases. Multivariate analysis showed significant differences in sex, chronic lung disease, HIV infection and headache. The clinical and outcome differences between the two groups may be explained by the detection of milder forms of legionnaires' disease, the earlier treatment and the lower severity of underlying disease in the outbreak cases.

Choque térmico como medida de control de un brote de legionelosis hospitalaria

BACKGROUND AND OBJECTIVE

Superheat-and-flush is one of the methods of disinfection used against Legionella in hospital water distribution systems. An outbreak of nosocomial legionellosis (NL) was detected in the hospital Germans Trias i Pujol in January 1996. The aim of this study was to evaluate the impact of this disinfection technique at an environmental and clinical level.

MATERIAL AND METHOD

Water samples were collected daily from central and tap water points 3 days prior to 15 days after superheating and flushing. Clinical surveillance of NL was performed 30 consecutive days following disinfection.

RESULTS

After superheat-and-flush, the inoculum of Legionella pneumophila decreased in the central points but increased after day 11, achieving maximum values at 15 days. On the other hand, L. pneumophila was not detected in tap water points after 4 days but recolonization was observed after day 7, achieving 66% at day 9. No clinical cases of NL were detected during the study period.

CONCLUSIONS

Superheat-and-flush is an effective albeit transitory method of rapid disinfection in outbreaks of NL.

Legionnaires disease and HIV infection

STUDY OBJECTIVES

To compare the outcome of Legionnaires disease (LD) in patients with and without HIV infection.

DESIGN

Retrospective review of clinical charts.

SETTING

Six hundred-bed university hospital.

PATIENTS

We studied the clinical findings of 64 patients without HIV and 15 patients with HIV. Patients with a serologic diagnosis only were not included. Patients with previous immunosuppressive therapy or transplant recipients were excluded from the former group. In the HIV group, the mean CD4 cell count was 347.5/ microL, plasma viral load was undetectable in 50% of the patients, and only one patient (7%) was receiving cotrimoxazole as prophylaxis against Pneumocystis carinii at the time of pneumonia. No differences were observed in the two groups with respect to community or nosocomial acquisition, delay in the initiation of appropriate treatment, the use of macrolides or fluoroquinolones, and Fine score in cases of community-acquired LD.

RESULTS

Univariate analysis showed that time to apyrexia was longer, and respiratory symptoms, bilateral infiltrates in chest radiograph, hyponatremia, increase in aspartate aminotransferase and creatine phosphokinase (CK), and respiratory failure were more frequent in the HIV group. Mortality was greater in patients with HIV, achieving a statistically significant value of 20%; however, multivariate analysis only confirmed these differences with respect to the increase in CK.

CONCLUSIONS

LD has a more severe clinical presentation and worse evolution in patients with HIV.

Factors related to persistence of Legionella urinary antigen excretion in patients with legionnaires' disease

The aim of this prospective study was to compare patient characteristics, clinical data, and evolution of Legionella pneumophila pneumonia according to the duration of Legionella urinary antigen excretion. Urine samples from 61 patients with Legionella pneumonia diagnosed by detection of urinary antigen were obtained periodically until urinary antigen could no longer be detected. Cases were divided into two groups based on the duration of urinary antigen excretion: group I (46 patients, <60 days) and group II (15 patients, >or=60 days). Groups were compared for patient characteristics, clinical data, and evolution of pneumonia. Antigen excretion >or=60 days was observed significantly more frequently in immunosuppressed patients ( P=0.001) in whom the time to apyrexia was >72 h ( P=0.002), although only the time to apyrexia remained significant on multivariate analysis ( P=0.006). In conclusion, the duration of Legionella urinary antigen excretion was <60 days in most patients but was longer in immunosuppressed patients with a longer time to defervescence of fever.