Thierry Perez

Climate change effects on a miniature ocean: the highly diverse, highly impacted Mediterranean Sea

Little doubt is left that climate change is underway, strongly affecting the Earths biodiversity. Some of the greatest challenges ahead concern the marine realm, but it is unclear to what extent changes will affect marine ecosystems. The Mediterranean Sea could give us some of the answers. Data recovered from its shores and depths have shown that sea temperatures are steadily increasing, extreme climatic events and related disease outbreaks are becoming more frequent, faunas are shifting, and invasive species are spreading. This miniature ocean can serve as a giant mesocosm of the worlds oceans, with various sources of disturbances interacting synergistically and therefore providing an insight into a major unknown: how resilient are marine ecosystems, and how will their current functioning be modified?

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges.

Marine sponges are well known for their associations with highly diverse, yet very specific and often highly similar microbiota. The aim of this study was to identify potential bacterial sub-populations in relation to sponge phylogeny and sampling sites and to define the core bacterial community. 16S ribosomal RNA gene amplicon pyrosequencing was applied to 32 sponge species from eight locations around the worlds oceans, thereby generating 2567 operational taxonomic units (OTUs at the 97% sequence similarity level) in total and up to 364 different OTUs per sponge species. The taxonomic richness detected in this study comprised 25 bacterial phyla with Proteobacteria, Chloroflexi and Poribacteria being most diverse in sponges. Among these phyla were nine candidate phyla, six of them found for the first time in sponges. Similarity comparison of bacterial communities revealed no correlation with host phylogeny but a tropical sub-population in that tropical sponges have more similar bacterial communities to each other than to subtropical sponges. A minimal core bacterial community consisting of very few OTUs (97%, 95% and 90%) was found. These microbes have a global distribution and are probably acquired via environmental transmission. In contrast, a large species-specific bacterial community was detected, which is represented by OTUs present in only a single sponge species. The species-specific bacterial community is probably mainly vertically transmitted. It is proposed that different sponges contain different bacterial species, however, these bacteria are still closely related to each other explaining the observed similarity of bacterial communities in sponges in this and previous studies. This global analysis represents the most comprehensive study of bacterial symbionts in sponges to date and provides novel insights into the complex structure of these unique associations.

Pulmonary Embolism in Patients with Unexplained Exacerbation of Chronic Obstructive Pulmonary Disease: Prevalence and Risk Factors

Context Pulmonary embolism (PE) is common in patients with chronic obstructive pulmonary disease (COPD) exacerbations, and the 2 conditions present similarly. Content For 45 months, every patient presenting with severe COPD exacerbation of unknown cause received an evaluation for PE that included a spiral computed tomography scan and color Doppler ultrasonography of the legs. Twenty-five percent of 197 patients had PE. Malignant disease, history of thromboembolism, and a decrease in Paco 2 level relative to baseline were the only factors associated with PE. Cautions This was a single-center study. Implications We need additional studies to confirm the high prevalence of PE in unexplained severe exacerbations of COPD and to study the value of routine testing for PE in patients with this clinical presentation. The Editors The management of patients with suspected acute pulmonary embolism (PE) has greatly improved in recent years because of clinical assessment of the probability of PE, pretest probability, ultrasonography, ventilationperfusion scanning, and spiral computed tomography angiography (CTA) (1, 2). However, clinical diagnosis of acute PE is difficult in patients with chronic obstructive pulmonary disease (COPD). Pulmonary embolism resembles COPD exacerbation so closely that these 2 entities are often impossible to distinguish clinically (3). The reported incidence of PE in studies done postmortem of patients with COPD ranges from 28% to 51% (4, 5). Pulmonary embolism is known to increase the rate of death from COPD at 1 year (6), but the clinical probability of PE and the value of noninvasive tests to rule out the diagnosis in patients with COPD have not yet been clearly assessed. To date, 2 studies have evaluated PE in patients with this disorder (3, 7). In the Prospective Investigation of Pulmonary Embolism Diagnosis (PIOPED) study, Lesser and colleagues (3) examined the characteristics of 108 patients with COPD and suspected PE; 21 (19%) received diagnoses of PE by pulmonary angiography. In this population, risk factors, symptoms, and arterial blood gas values were similar in patients with and without PE. The second study (7) showed that the presence of COPD does not affect the diagnostic performance of d-dimer testing, CTA, or pulmonary angiography for PE (7). The true frequency of PE in patients with COPD in whom PE is clinically suspected ranges from 19% to 29% (3, 7-9). Thus, clinical detection of PE in these patients is particularly difficult. In this study, we prospectively evaluated PE in patients with COPD exacerbation of unknown origin and examined factors associated with the presence of PE, including the Geneva score (1). Methods Study Objectives The objectives of our study were to assess the presence of PE in patients with COPD exacerbation of unknown origin and to explore factors associated with the presence of PE, including the Geneva score. Study Group Between April 1999 and December 2002, all consecutive patients with COPD referred to the Lung Department at the 59-bed Lille University Hospital for severe exacerbation of unknown origin were assessed for PE. Chronic obstructive pulmonary disease was diagnosed and its severity was determined according to the criteria of the American Thoracic Society (10). All patients smoked or were former smokers. Patients with asthma were not included in the study. Severe exacerbation was defined as acute deterioration from a stable condition that required hospitalization. The absence of a lower respiratory tract infection (increased sputum volume and/or increased sputum purulence, fever, history of cold, and sore throat); absence of pneumothorax and iatrogenic intervention; presence of parenchymal condensation without fever and chills; or presence of a discrepancy between clinical and radiologic features and hypoxemia severity classified the exacerbation as of unknown origin. Physicians were required to discuss each case of COPD with 1 of the referring physicians. Patients requiring invasive mechanical ventilation were referred to the intensive care unit and were not included in the study. Intervention All patients were examined within 48 hours of admission to the hospital and had spiral CTA of pulmonary circulation and color Doppler and venous lower-limb ultrasonography. These are the first-line diagnostic tests for acute PE at our institution. The decision to perform additional examinations, including d-dimer determination and ventilationperfusion scanning, was left to the discretion of the attending physician. Our local ethics committee approved the study protocol, which did not require informed patient consent. Spiral CTA In 1999, spiral CTA of pulmonary circulation was performed with a Somatom Plus 4A (Siemens Medical Systems, Forchheim, Germany) using a collimation of 3 mm3 mm, a pitch of 2, and a scanning time of 0.75 second per revolution. The results were read during the clinical work-up as previously described (9, 11-13). Because the equipment at our institution was upgraded during this study, spiral CTA of pulmonary circulation between January 2000 and December 2002 was performed with a multislice spiral computed tomography (CT) scanner, using a collimation of 4 mm1 mm, a pitch of 2, and a rotation time of 0.5 second. All patients with negative results on spiral CTA had a 3-month follow-up visit after inclusion in the study to assess critical events that were potentially related to PE. A chest physician reported death, subsequent admission to the hospital, new symptoms, and use of anticoagulant medications. Ultrasonography Venous compression ultrasonography of both legs was done from the common femoral vein and including the calf vein. Lack of compressibility was considered to indicate deep venous thrombosis. Definition Patients were classified as PE positive (positive results on spiral CTA or negative results on spiral CTA and positive results on ultrasonography) or PE negative (negative results on spiral CTA and negative results on ultrasonography or negative results on spiral CTA and no recurrence of PE at follow-up 3 months later). Assessment of the Geneva Score Because the Geneva score (1) was published by the time our study ended in 2001, we evaluated this score a posteriori in our sample before reviewing the data on PE. The probability of PE was expressed as low (a score 4), intermediate (a score of 5 to 8), or high (a score 9) (Table 1) (1). Table 1. The Geneva Score and the Modified Geneva Score Statistical Analysis Statistical analysis was done by using Epi Info software, version 3.3.2 (Centers for Disease Control and Prevention, Atlanta, Georgia), and CIs were calculated with StatExact and Stata, version 7 (Stata Corp., College Station, Texas). We calculated risk ratios and exact CIs for the various risk factors and clinical symptoms and determined P values using the Fisher exact test. A P value less than 0.05 indicated statistical significance. Role of the Funding Source No funding was received for this study. Results Study Group A total of 211 consecutive patients with COPD were referred for severe exacerbation of unknown origin. Fourteen patients were not included in the study because the results of the spiral CTA and ultrasonography were inconclusive (8 patients) or because of iodine intolerance (6 patients). Thus, the study group included 197 patients with COPD and severe exacerbation of unknown origin. There were 165 men and 32 women, and their mean age was 60.5 years (SD, 12.1). A total of 136 patients (69%) were referred from the emergency department, and 61 (31%) were inpatients who developed severe exacerbation while hospitalized. Arterial blood gas values on room air were 61.9 mm Hg (SD, 10.9) for Pao 2 and 42 mm Hg (SD, 9) for Paco 2. The mean number of risk factors for PE per patient was 0.87 (SD, 0.7). In 160 of the 197 study patients, results of a pulmonary function test performed within 3 months of the severe exacerbation were available. The mean FEV1 was 1.56 L (SD, 0.6), 52% (SD, 19%) of the predicted value. The mean FEV1vital capacity ratio was 56.4% (SD, 14.8%). The severity of respiratory disease was assessed according to the criteria of the American Thoracic Society (10): grade I, FEV1 greater than 50% of the predicted value (66 patients [41%]); grade II, FEV1 between 35% and 50% of predicted (67 patients [42%]); and grade III, FEV1 less than 35% of predicted (27 patients [17%]). Forty-nine (25%) patients were receiving long-term oxygen therapy. Pulmonary Embolism All patients had spiral CTA (37 patients had a single-slice CT scan, and 160 had a multislice CT scan), and 180 had venous ultrasonography (Table 2). None of the 197 study patients were thought to have clinical recurrence of PE during the 3 months of follow-up. Forty-three patients had positive results on CT. Twenty-five patients had deep venous thrombosis on ultrasonography; of these patients, 6 had negative results on spiral CTA. Nineteen (44%) of the 43 patients with positive results on spiral CTA also had positive results on ultrasonography. One hundred forty-eight patients did not have PE, on the basis of negative results on CT and ultrasonography and negative findings at 3-month follow-up. Thus, the prevalence of PE in our study group was 49 of 197 patients (25% [95% CI, 19% to 32%]). Table 2. Results of Spiral Computed Tomography Angiography in Patients Initially Referred for Suspected Acute Pulmonary Embolism Clinical Characteristics according to the Presence or Absence of Pulmonary Embolism The 49 patients with COPD who had PE did not differ statistically significantly from the 148 patients with COPD who did not have PE in terms of referral location (data not shown). We performed a bivariate analysis of baseline characteristics (Table 3) and clinical characteristics at admission (Table 4) that were potentially associated with PE. Clinical symptoms, such as change in dyspnea, pleuritic pain, hemoptysis, tachycardia (pulse rate >100 beats/m

Clinical COPD phenotypes: a novel approach using principal component and cluster analyses

Classification of chronic obstructive pulmonary disease (COPD) is usually based on the severity of airflow limitation, which may not reflect phenotypic heterogeneity. Here, we sought to identify COPD phenotypes using multiple clinical variables. COPD subjects recruited in a French multicentre cohort were characterised using a standardised process. Principal component analysis (PCA) was performed using eight variables selected for their relevance to COPD: age, cumulative smoking, forced expiratory volume in 1 s (FEV1) (% predicted), body mass index, exacerbations, dyspnoea (modified Medical Research Council scale), health status (St George’s Respiratory Questionnaire) and depressive symptoms (hospital anxiety and depression scale). Patient classification was performed using cluster analysis based on PCA-transformed data. 322 COPD subjects were analysed: 77% were male; median (interquartile range) age was 65.0 (58.0–73.0) yrs; FEV1 was 48.9 (34.1–66.3)% pred; and 21, 135, 107 and 59 subjects were classified in Global Initiative for Chronic Obstructive Lung Disease (GOLD) stages 1, 2, 3 and 4, respectively. PCA showed that three independent components accounted for 61% of variance. PCA-based cluster analysis resulted in the classification of subjects into four clinical phenotypes that could not be identified using GOLD classification. Importantly, subjects with comparable airflow limitation (FEV1) belonged to different phenotypes and had marked differences in age, symptoms, comorbidities and predicted mortality. These analyses underscore the need for novel multidimensional COPD classification for improving patient care and quality of clinical trials.

Cough and Sputum Production Are Associated With Frequent Exacerbations and Hospitalizations in COPD Subjects

BACKGROUND Epidemiologic studies indicate that chronic cough and sputum production are associated with increased mortality and disease progression in COPD subjects. Our objective was to identify features associated with chronic cough and sputum production in COPD subjects. METHODS Cross-sectional analysis of data were obtained in a multicenter (17 university hospitals in France) cohort of COPD patients. The cohort comprised 433 COPD subjects (65 +/- 11 years; FEV(1), 50 +/- 20% predicted). Subjects with (n = 321) and without (n = 112) chronic cough and sputum production were compared. RESULTS No significant difference was observed between groups for age, FEV(1), body mass index, and comorbidities. Subjects with chronic cough and sputum production had increased total mean numbers of exacerbations per patient per year (2.20 +/- 2.20 vs 0.97 +/- 1.19, respectively; p < 0.0001), moderate exacerbations (1.80 +/- 2.07 vs 0.66 +/- 0.85, respectively; p < 0.0001), and severe exacerbations requiring hospitalizations (0.43 +/- 0.95 vs 0.22 +/- 0.56, respectively; p < 0.02). The total number of exacerbations per patient per year was the only variable independently associated with chronic cough and sputum production. Frequent exacerbations (two or more per patient per year) occurred in 55% vs 22% of subjects, respectively, with and without chronic cough and sputum production (p < 0.0001). Chronic cough and sputum production and decreased FEV(1) were independently associated with an increased risk of frequent exacerbations and frequent hospitalizations. CONCLUSIONS Chronic cough and sputum production are associated with frequent COPD exacerbations, including severe exacerbations requiring hospitalizations.

Pulmonary function tests and high resolution computed tomography of the lungs in patients with rheumatoid arthritis

OBJECTIVE To compare the results of pulmonary function tests (PFTs) and high resolution computed tomography (HRCT) of the lungs in rheumatoid arthritis (RA) patients. METHODS Sixty eight patients (54 women, 14 men) fulfilling the revised criteria for RA were consecutively included in a transversal prospective study. Their mean age was 58.8 years (range: 35–82) and the mean duration of the disease was 12 years (range: 5–16). Rheumatoid factor was positive in 52 patients (76.5%). Fifty two patients (76.5%) were lifelong non-smokers. Detailed medical and drug histories were obtained. PFTs comprised spirometry and gas transfer measurements. Results for PFTs were expressed as percentage of predicted values for each individual adjusted for age, sex, and height. HRCT was undertaken with a Siemens Somatom Plus. RESULTS A significant decrease of FEV1/FVC, FEF25%, FEF50%, FEF75%, FEF25–75%, and TLCO was observed (p<0.05) and 13.2% of the patients had a small airways involvement defined by a decrease of FEF25–75% below 1.64 SD. The most frequent HRCT findings were: bronchiectasis (30.5%), pulmonary nodules (28%), and air trapping (25%). The patients with small airways involvement had a high frequency of recurrent bronchitis (75% v 34%, p=0.05) and bronchiectasis (71% v 23%, p=0.019). The patients with bronchiectasis were characterised by low values of FEV1, FVC, FEF25–75%, and TLCO (p<0.01), a high prevalence of small airways involvement (29% v 5%, p=0.019), and a low prevalence of HLA DQA1 *0501 allele (14% v 33%, p<0.05). CONCLUSION This study suggests a significant association between small airways involvement on PFTs and bronchiectasis on HRCT in unselected RA patients.

Temporal change in deep-sea benthic ecosystems: a review of the evidence from recent time-series studies

Societal concerns over the potential impacts of recent global change have prompted renewed interest in the long-term ecological monitoring of large ecosystems. The deep sea is the largest ecosystem on the planet, the least accessible, and perhaps the least understood. Nevertheless, deep-sea data collected over the last few decades are now being synthesised with a view to both measuring global change and predicting the future impacts of further rises in atmospheric carbon dioxide concentrations. For many years, it was assumed by many that the deep sea is a stable habitat, buffered from short-term changes in the atmosphere or upper ocean. However, recent studies suggest that deep-seafloor ecosystems may respond relatively quickly to seasonal, inter-annual and decadal-scale shifts in upper-ocean variables. In this review, we assess the evidence for these long-term (i.e. inter-annual to decadal-scale) changes both in biologically driven, sedimented, deep-sea ecosystems (e.g. abyssal plains) and in chemosynthetic ecosystems that are partially geologically driven, such as hydrothermal vents and cold seeps. We have identified 11 deep-sea sedimented ecosystems for which published analyses of long-term biological data exist. At three of these, we have found evidence for a progressive trend that could be potentially linked to recent climate change, although the evidence is not conclusive. At the other sites, we have concluded that the changes were either not significant, or were stochastically variable without being clearly linked to climate change or climate variability indices. For chemosynthetic ecosystems, we have identified 14 sites for which there are some published long-term data. Data for temporal changes at chemosynthetic ecosystems are scarce, with few sites being subjected to repeated visits. However, the limited evidence from hydrothermal vents suggests that at fast-spreading centres such as the East Pacific Rise, vent communities are impacted on decadal scales by stochastic events such as volcanic eruptions, with associated fauna showing complex patterns of community succession. For the slow-spreading centres such as the Mid-Atlantic Ridge, vent sites appear to be stable over the time periods measured, with no discernable long-term trend. At cold seeps, inferences based on spatial studies in the Gulf of Mexico, and data on organism longevity, suggest that these sites are stable over many hundreds of years. However, at the Haakon Mosby mud volcano, a large, well-studied seep in the Barents Sea, periodic mud slides associated with gas and fluid venting may disrupt benthic communities, leading to successional sequences over time. For chemosynthetic ecosystems of biogenic origin (e.g. whale-falls), it is likely that the longevity of the habitat depends mainly on the size of the carcass and the ecological setting, with large remains persisting as a distinct seafloor habitat for up to 100 years. Studies of shallow-water analogs of deep-sea ecosystems such as marine caves may also yield insights into temporal processes. Although it is obvious from the geological record that past climate change has impacted deep-sea faunas, the evidence that recent climate change or climate variability has altered deep-sea benthic communities is extremely limited. This mainly reflects the lack of remote sensing of this vast seafloor habitat. Current and future advances in deep-ocean benthic science involve new remote observing technologies that combine a high temporal resolution (e.g. cabled observatories) with spatial capabilities (e.g. autonomous vehicles undertaking image surveys of the seabed).

Sponge Systematics Facing New Challenges

Systematics is nowadays facing new challenges with the introduction of new concepts and new techniques. Compared to most other phyla, phylogenetic relationships among sponges are still largely unresolved. In the past 10 years, the classical taxonomy has been completely overturned and a review of the state of the art appears necessary. The field of taxonomy remains a prominent discipline of sponge research and studies related to sponge systematics were in greater number in the Eighth World Sponge Conference (Girona, Spain, September 2010) than in any previous world sponge conferences. To understand the state of this rapidly growing field, this chapter proposes to review studies, mainly from the past decade, in sponge taxonomy, nomenclature and phylogeny. In a first part, we analyse the reasons of the current success of this field. In a second part, we establish the current sponge systematics theoretical framework, with the use of (1) cladistics, (2) different codes of nomenclature (PhyloCode vs. Linnaean system) and (3) integrative taxonomy. Sponges are infamous for their lack of characters. However, by listing and discussing in a third part all characters available to taxonomists, we show how diverse characters are and that new ones are being used and tested, while old ones should be revisited. We then review the systematics of the four main classes of sponges (Hexactinellida, Calcispongiae, Homoscleromorpha and Demospongiae), each time focusing on current issues and case studies. We present a review of the taxonomic changes since the publication of the Systema Porifera (2002), and point to problems a sponge taxonomist is still faced with nowadays. To conclude, we make a series of proposals for the future of sponge systematics. In the light of recent studies, we establish a series of taxonomic changes that the sponge community may be ready to accept. We also propose a series of sponge new names and definitions following the PhyloCode. The issue of phantom species (potential new species revealed by molecular studies) is raised, and we show how they could be dealt with. Finally, we present a general strategy to help us succeed in building a Porifera tree along with the corresponding revised Porifera classification.

Eosinophilic airway inflammation in nasal polyposis

BACKGROUND Asthma and asymptomatic bronchial hyperresponsiveness (BHR) are frequent findings in patients with nasal polyposis (NP). OBJECTIVE To elucidate mechanisms responsible for the development of BHR, we initiated a prospective study of bronchial inflammation as assessed by bronchial lavage (BL) and bronchial biopsy specimens in 35 patients with noninfectious NP. METHODS BHR was determined with methacholine provocation testing. Differential cell count, ECP, and histamine and tryptase levels were determined in BLs. Pathologic examination of bronchial biopsy specimens was performed with May-Grünwald-Giemsa stain to assess the number of lymphocytes. Indirect immunoenzymatic methods were used to identify eosinophils and mast cells. RESULTS Fourteen patients did not exhibit BHR (group A); 7 patients had asymptomatic BHR (group B); and 14 patients had BHR associated with asthma (group C). Patients of group C tended to have a longer duration of nasal symptoms than those of groups A and B. FEV1 (L) was significantly lower in group C than in groups A and B. The number and percentage of eosinophils were significantly higher in BLs in groups B and C than in group A (P <. 05). Patients of groups B and C had a significantly higher number of eosinophils in bronchial submucosa (14.0 +/- 1.5/mm2 and 19.0 +/- 1. 9/mm2, respectively) than patients of group A (0.1 +/- 0.1/mm2). The number of lymphocytes was also higher in groups B and C than in group A. FEV1 (percent of predicted value) and eosinophil number within bronchial mucosa correlated negatively. CONCLUSION Our results demonstrate that patients with NP and asymptomatic BHR had an eosinophilic bronchial inflammation similar to that observed in asthmatic patients with NP, whereas patients with NP without BHR do not feature eosinophilic lower airways inflammation. The clinical relevance of these results requires careful follow-up to determine whether eosinophilic inflammation in these patients precedes and is responsible for the development of obvious asthma.

Impact of chronic airflow obstruction in a working population

Data on the individual and collective impact of chronic airflow obstruction at a population level are scarce. In a nationwide survey, dyspnoea, quality of life and missed working days were compared between subjects with and without spirometrically diagnosed chronic airflow obstruction. Subjects aged ≥45 yrs were recruited in French health prevention centres (n = 5,008). Results of pre-bronchodilator spirometry and questionnaires (European Community Respiratory Health Survey-derived questionnaire and European quality of life five-dimension questionnaire) were collected. Adequate datasets were available for 4,764 subjects aged 60±10 yrs (only 2% were aged ≥80 yrs). The prevalence of airflow obstruction (forced expiratory volume in one second/forced vital capacity of <0.70) was 7.5%. The vast majority (93.9%) of cases had not been diagnosed previously. Health status was significantly influenced by dyspnoea. Both were associated with the number of missed working days. Despite mild-to-moderate severity, subjects with chronic airflow obstruction exhibited more dyspnoea, poorer quality of life and higher numbers of missed working days (mean 6.71 versus 1.45 days·patient−1·yr−1 in patients without airflow obstruction, for the population with no known heart or lung disease). In conclusion, even mild-to-moderate airflow obstruction is associated with an impaired health status, which represents an additional argument in favour of early detection in chronic obstructive pulmonary disease.