Published ahead of print on July 13, 2006, doi:10.1164/rccm.200601-074OC
© 2006 American Thoracic Society doi: 10.1164/rccm.200601-074OC
The Bacteriology of Pleural Infection by Genetic and Standard Methods and Its Mortality SignificanceDepartment of Respiratory Medicine, Southmead Hospital, North Bristol NHS Trust, Bristol; Department of Microbiology, Royal Free Hospital, London; Oxford Pleural Unit, Oxford Centre for Respiratory Medicine, Oxford Radcliffe Hospital, Headington, Oxford; and Department of Respiratory Medicine, Royal Berkshire Hospital, Reading, United Kingdom Correspondence and requests for reprints should be addressed to R.J.O. Davies, D.M., F.R.C.P., Reader and Consultant in Respiratory Medicine, Oxford Pleural Unit, Oxford Centre for Respiratory Medicine, Churchill Hospital Site, Oxford Radcliffe Hospital, Headington, Oxford, OX3 7LJ UK. E-mail: robert.davies{at}ndm.ox.ac.uk
Background: Antibiotic choices for pleural infection are uncertain as its bacteriology is poorly described. Methods: Pleural fluid from 434 pleural infections underwent standard culture and a screen for bacteria by amplification and sequencing of bacterial 16S ribosomal RNA gene.
Results: Approximately 50% of community-acquired infections were streptococcal, and 20% included anaerobic bacteria. Approximately 60% of hospital-acquired infections included bacteria frequently resistant to antibiotics (methicillin-resistant Staphylococcus aureus, 25%; Enterobacteriaceae, 18%; Pseudomonas spp., 5%, enterococci, 12%). Mortality was increased in hospital-acquired infection (hospital, 17/36 [47%]; community, 53/304 [17%]; relative risk, 4.24; 95% confidence interval, 2.078.69; p < 0.00001; Conclusion: Pleural infection differs bacteriologically from pneumonia and requires different treatment. Antibiotics for community-acquired infection should treat aerobic and anaerobic bacteria. Hospital-acquired, gram-negative S. aureus and mixed aerobic infections have a high mortality rate.
Key Words: empyema ISRCTN 39138989 MIST1 trial parapneumonic effusion pleural infection Bacterial pleural infection has been a substantial clinical challenge since ancient times. Descriptions of its treatment date from Hippocrates and perhaps ancient Egypt (1, 2). Today, it affects up to 65,000 patients each year in the United Kingdom and United States (3) and has a 12-mo mortality of 22%, with another 15% of patients requiring surgical abscess drainage (4). Appropriate antibiotic choices are important to minimize this morbidity, and these choices are likely to be different from those of pneumonia because small series suggest these syndromes differ bacteriologically (515). However, this difference in antibiotic choice is unclear because these studies were small, biased by case selection, or retrospective (515), and do not take into account the increasing prevalence of antibiotic-resistant pathogens. Antibiotic selection is also problematic because about 40% of patients with convincing pleural infection have no pathogens identified on standard laboratory culture (4). The First Multicenter Intrapleural Sepsis Trial (MIST1) assembled a large, well-characterized patient cohort (4), and this article presents the bacterial microbiology of this cohort, including prognostic significance of different bacterial isolates. The results include a screen for bacterial pathogens from pleural fluid samples by the amplification and sequencing of the bacterial 16S ribosomal RNA gene, which has been shown to improve the identification of pathogens from cases of pleural infection (15). This analysis provides a detailed description of the microbiology of pleural infection using current techniques, describes how this differs from pneumonia, and determines the influence of different bacterial species on prognosis, allowing clinicians to make logical therapeutic choices.
Medical Research Council/BTS MIST1 Trial This article reports the bacteriology from the Medical Research Council/ British Thoracic Society (BTS) MIST1 trial of streptokinase in pleural infection (4). This trial showed no treatment effect from streptokinase and so patient outcome is not confounded by this factor. Briefly, the MIST1 trial recruited 454 patients from 52 centers in the United Kingdom. Entry criteria were macroscopically purulent, or bacterial culture, or Gram stainpositive pleural fluid, or a pleural fluid of pH < 7.2, in the presence of clinical evidence of infection. Apart from trial intrapleural streptokinase, patients received standard clinical care. All patients received antibiotics at the discretion of their local managing physician, but antibiotic guidelines were provided in the trial protocol (available in the online supplement). Baseline microbiological information included the results of pleural fluid Gram stain, and aerobic and anaerobic pleural fluid culture, performed in the recruiting center. The trial outcomes included mortality, which is used in the survival analyses presented here. At randomization, pleural fluid was collected and transferred to the coordinating center and frozen at 70°C. Samples were frozen within 48 h of being taken. Culture-negative pleural fluid samples were also gathered from 20 patients with pleural effusions due to noninfectious causes to act as control samples. The trial was approved by the Anglia and Oxford Multicentre Research Ethics Committee (MREC) (ref: 98/5/61), the Oxford Local Research Ethics Committee, and the local research ethics committees for each center. All participants gave informed, written consent.
Nucleic Acid Amplification and Identification
Pleural fluid DNA extraction.
Polymerase chain reaction.
Sequencing.
Cloning.
M13 PCR to analyze transformants.
Bacterial identification.
Data Analysis
Survival analyses in bacterial subgroups.
Survival was also compared between cases acquired in the community and in hospital.
Statistical analysis.
Subjects The clinical and blood culture characteristics of the subjects with pleural infection are shown in Table 1, and elsewhere (4). Of the patients, 82 of 454 (18%) had chronic lung disease. The bacteriology was similar in this group to the whole sample.
Negative control subjects for the molecular microbiology. Twenty age-matched control patients (11 male; mean age, 69 yr [SD, 20 yr]), with pleural effusion believed clinically to be of a noninfectious cause, gave samples to act as negative controls. Seven were transudative effusions (by "Light's criteria" [18]) and 13 had histocytologically proven malignant pleural effusion. These controls were selected on the basis of the security of their diagnosis and negative standard cultures for aerobic and anaerobic bacteria, mycobacteria, and fungi.
Overall Bacteriology Among the 12 of 404 (3%) cases where nucleic acid amplification showed more than one bacterial DNA sequence, cloning suggested the following bacteria to be present. Six samples revealed only one bacterium: Proechimys oris in two cases; and one case each of Staphylococcus intermedius, Streptococcus pneumoniae, Streptococcus pyrogenes, and Filifactor micros. Six samples revealed more than one bacterium: Fusobacterium nucleatum and Peptostreptococcus micros in three cases; and one case each of Bacteriodes fragilis + P. oris; F. nucleatum subsp. vincentii + P. oral clone; Peptostreptococcus micros + Peptostreptococcus oral clone + Fusobacterium oral clone + Bacteroides oral clone. These results were combined with those from nucleic acid amplification. The summary bacteriology derived from both standard culture and nucleic amplification is presented in Table 2. S. intermedius, S. anginosis, and S. constellatus were grouped together as the "S. intermedius group."
Comparison of Community- and Hospital-acquired Infection The bacteriologies of hospital- and community-acquired infection differed substantially (Table 2), and both differ from pneumonia, which is consistent with previous small reports (515). Pleural infections acquired in the community were most frequently due to streptococcal infection (S. pneumoniae, 71/336 [21%]; S. intermedius group, 80/336 [24%]; other streptococcal species, 25/336 [7%]), and infections due to S. aureus and enterococci were more prevalent in the infections acquired in hospital. Fifteen of the 60 (25%) isolates in hospital-acquired infection were due to methicillin-resistant S. aureus.
Overall mortality was substantially increased in subjects who acquired their infection in hospital compared with those who acquired their infection in the community (hospital mortality, 17/36 [47%]; community, 53/304 [17%]; relative risk, 4.24; 95% confidence interval [CI], 2.078.69; p < 0.00001;
Survival in Different Bacterial Subsets One-year mortality outcome data were available in 438 of 440 (99.5%) subjects in the survival analyses. All the streptococcal subsets showed similar mortalities (S. pneumoniae, 10/59 [17%]; S. intermedius group, 9/55 [16%]; other streptococci, 4/23 [17%]; p = 0.92; 2, 2 df = 0.17; see survival curve in Figure E1 of the online supplement). These groups were combined in later comparisons.
The mortality in the group in whom no pathogen was identified was 9 of 71 (13%), similar to that in streptococcal infection, which was 23 of 137 (17%; relative risk, 1.27; 95% CI, 0.533.06; p = 0.60;
Mortality at 1 yr varied substantially between the culture-positive bacterial groups (p < 0.00001;
Hospital-acquired Infection, Bacterial Class, and Mortality
Comparison of Conventional Culture and Nucleic Acid Amplification In 140 of 404 (35%) cases, the same organism was found by both nucleic acid amplification (or cloning) and standard culture. Of these, using the rules previously described, in 120 of 140 cases, the standard culture and nucleic acid amplification were in agreement; in 9 of these 140, the standard culture was superior; and in 11 of 140 cases, the nucleic acid amplification was superior. In 107 cases, the standard culture was superior to the nucleic acid amplification because it identified a bacterium not identified from the DNA studies. In 54 cases, nucleic acid amplification was superior to standard culture because it identified a bacterium not identified by culture. In 50 cases, the standard culture and the nucleic acid amplification identified different bacteria, and it could not be assessed which method was more informative. The results of conventional culture and nucleic acid amplification are compared in Table 4.
Nucleic Acid Amplification of Culture-negative Pleural Fluid Control Cases In 19 of the 20 culture-negative and presumed uninfected control subjects, no bacterial DNA was identified. In one, a Prevotella spp. was identified (from a patient with malignant pleural mesothelioma). Post hoc review of the case notes showed this patient was febrile at the time of pleural fluid sampling, although this fever had been attributed to the tumor.
This report has clarified the bacteriology of pleural infection and may improve antibiotic choices for the 65,000 people who develop this infection each year in the United Kingdom and the United States, helping minimize the 22% mortality associated with pleural infection (4). It is the first study to examine the standard culture and genetic bacteriology of pleural infection in a large generalizable cohort, and to relate this to patient mortality. These data provide a foundation for clinical trials to define whether better bacterial diagnosis and antibiotic choices improve outcome in pleural infection. The cases studied here were accumulated from 52 centers in the United Kingdom, including both teaching and district hospitals, and so are likely to be representative. This study's results include DNA sequencing and cloning to clarify the bacteriology in detail, a technique that has proved effective in other smaller samples (15). This has reduced the number of cases that are bacteriologically undiagnosed from 42 to 26%, a diagnostic improvement that is likely to be clinically valuable. This analysis confirms smaller studies (515), which suggest the bacteriology of pleural infection differs from that of pneumonia (reviewed in Reference 21), and that these syndromes should be considered separate. Because pleural infection follows bacterial migration from beneath the visceral pleura, it is often termed "complicated parapneumonic effusion," which could be taken to imply a bacteriologic etiology similar to that of pneumonia. This study shows that this is simplistic and antibiotic choices targeted at the typical range of pneumonic pathogens are not ideal for pyogenic pleural infection. The differences in the bacteriology are probably due to the acidic and hypoxic environment of the infected pleural space favoring selected pathogens. Many of the anaerobic bacteria of pleural infection are strictly anaerobic and cannot tolerate the PO2 of lung parenchyma, whereas streptococci of the "intermediusanginosusconstellatus" group characteristically flourish in low pH and PO2 tissue environments and favor these conditions in artificial culture (19). The microbiological differences from pneumonia suggest that future studies should try to define which clinical phenotypes are associated with which pattern of pathogens. For example, preliminary data are beginning to suggest that different radiographic patterns of lung disease are associated with different bacterial pathogens (20). Interestingly, even the genetic bacterial analysis presented here may underestimate the variety of bacteria present in pleural infection. Our limited cloning strategy suggests even greater bacterial diversity than the 16S amplification, and may provide more clinical information in the future.
Antibiotic Choices in Pleural Infection By contrast, hospital-acquired infection includes more staphylococcal infection (more than 70% of which is due to methicillin-resistant S. aureus) and Enterobacteriaceae, organisms that are often multiple-drug resistant. This may contribute to the poor prognosis in these patients. Here, empiric antibiotic therapy should be effective against these multidrug-resistant organisms. The differences in the bacteriology and the prognosis between hospital- and community-acquired empyema are sufficiently marked that these syndromes should probably be considered separate clinical entities. Mycoplasma spp., and Legionella spp. are respiratory pathogens that are difficult to isolate using routine culture methods. The molecular bacterial techniques found no evidence of either of these species, which suggests that these pathogens are not likely causes of pleural infection and that empiric antibiotic regimes targeted at them are probably not required. By contrast, molecular diagnostics increased the yield of anaerobic bacteria in comparison to routine culture methods, which is expected given the difficulties of isolating these fastidious organisms in a clinical microbiological laboratory. Therefore, empiric antibiotics targeted at anaerobic infection should be usual. An exception to this is where routine culture has identified S. pneumoniae (because we found no evidence of any coincidental anaerobic infection in these cases, either by standard culture or nucleic acid amplification). Here, specific pneumococcal therapy would be appropriate provided the prevalence of pneumococcal penicillin resistance is low.
Survival in Different Bacterial Subgroups Most previous reports of the bacteriology of pleural infection have suggested that infections including anaerobic bacteria have a particularly high mortality (7, 8, 11). The data reported here contradict this view, showing that infections including anaerobic bacteria have an 80% survival, which is similar to streptococcal infections (Figure 1). The groups with the highest mortality were those patients with staphylococcal, enterobacterial, and mixed aerobic infections: about 45% at 1 yr (Figure 1). Because standard clinical care (with chest tube drainage and antibiotics) is associated with such a high mortality in this group, rapid, aggressive empyema drainage (e.g., with early surgical intervention) should be considered for these patients.
Standard Culture and Nucleic Acid Amplification/Cloning The substantial increase in the number of bacteria identified by nucleic acid amplification when compared with normal culture in this study is similar to the advantage seen when this strategy was applied to a small sample of pediatric empyema fluids (15), strengthening the case for its use.
This study presents the largest comprehensive description of the bacteriology of pleural infection using conventional and molecular methods. The results confirm pleural infection is bacteriologically significantly different from pneumonia, and that hospital-acquired pleural infection is a subentity with a high mortality. Over 40% of hospital-acquired infections were due to multiantibiotic-resistant pathogens. Three bacterial subgroups were associated with a substantially increased mortality and should probably be targeted for early surgical abscess drainage. In contrast to previous reports, we found that infections including anaerobic bacteria do not have a poor outcome. This improved description of the bacteriology of this disease allows better antibiotic and therapeutic strategies to reduce the high morbidity and mortality associated with this disease.
The authors thank Prof. John Macfarlane, City Hospital, Nottingham; Dr. Robert Miller, University College, London; and Prof. Tim Peto, Oxford University, Oxford, for their advice on the manuscript. The samples were provided by the Medical Research Council/BTS MIST1 trial group comprising the following members: O.A. Afolabi (North Tyneside General Hospital); N. Ali (Kingsmill Hospital, Mansfield); M. Allen (North Staffordshire Hospital); A. G. Arnold (Castle Hill Hospital, Cottingham); D. Baldwin (City Hospital, Nottingham); J. R. Bateman (Derby City General Hospital); J. Bennett (Derby Royal Hospital); A. Bentley (North Manchester Hospital); D. Boldy (Pilgrim Hospital, Boston); M. Bone (South Tyneside District Hospital); M. Britton (St. Peters Hospital, Surrey); S. Burge (Birmingham Heartlands Hospital); R. Butland (Gloucester Royal Hospital); I. Campbell (Llandough Hospital, Cardiff); J. Congleton (Worthing Hospital); D. C. Currie (Dewsbury & District Hospital); R. J. O. Davies (Oxford Radcliffe Hospital); C. W. H. Davies (The Royal Berkshire Hospital, Reading); A. G. Davison (Southend Hospital); O. Dempsey (Aberdeen Royal Infirmary); R. G. Dent (QEII, Welwyn Garden City); A. P. Greening (Western General Hospital, Edinburgh); J. Hadfield (Chesterfield & Derbyshire Royal Hospital); B. D. W. Harrison (Norfolk and Norwich Hospital); J. Harvey (Southmead Hospital, Bristol); M. Hetzel (Bristol Royal Infirmary); H. Hosker (Airedale General Hospital, Keighley); P. Hughes (Derriford Hospital, Plymouth); A. M. Hunter (York District Hospital); M. Jackson (Brighton General Hospital); W. J. M. Kinnear (Queens Medical Centre, Nottingham); C. Laroche (West Suffolk Hospital, Bury St. Edmonds); C. Laroche (Papworth Hospital, Cambridge); A. Leonard (Great Western Hospital, Swindon); M. C. I. Lipman (Royal Free Hospital, London); D. Lomas (Addenbrookes Hospital, Cambridge); A. Malin (Royal United Hospital, Bath); D. McLeod (Sandwell General Hospital, West Bromwich); M. L. D. Morgan (Glenfield Hospital, Leicester); M. F. Muers (The Leeds General Infirmary); N. C. Munro (University Hospital of North Durham); E. Neville (St. Mary's Hospital, Portsmouth); D. J. Newbury (Ashford Hospital); D. Peckham (St. James University Hospital, Leeds); M. Pond (Bridlington & District Hospital); S. Saboor (Chase Farm Hospital, Enfield); D. Seaton (Ipswich Hospital); R. Smith (Horton General Hospital, Banbury); S. Spiro (The Middlesex Hospital, London); B. Stack (West Glasgow Hospital); D. Thickett (Queen Elizabeth Hospital, Birmingham); C. Wathen (Wycombe General Hospital); J. H. Winter (Nine Wells Hospital, Dundee); N. Withers (Royal Devon & Exeter Hospital); M. Woodhead (Manchester Royal Infirmary); F. Zaman (Pendle Community Hospital, Burnley).
Supported by a Medical Research Council grant (G9721289). This article has an online supplement, which is accessible from this issue's table of contents at www.atsjournals.org Originally Published in Press as DOI: 10.1164/rccm.200601-074OC on July 13, 2006 Conflict of Interest Statement: N.A.M. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. S.B. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. E.L.H. does not have a financial relationship with a commercial entity that has an interest in the subject of this manuscript. C.W.H.D. has received payments for speaking at meetings from Leopharma, AstraSeneca, GlaxoSmithKline, and Pfizer regarding topics on pulmonary embolism, chronic obstructive pulmonary disease, and asthma. C.W.H.D. is also on the Medical Advisory Board for Swiss Medical (PoAEx). S.H.G. is in receipt of a $75,000 grant from Wyeth to support development of molecular diagnostic tests. R.J.O.D., the principal investigator for this study, has received drug and matched placebo for the MISTI trial from which the data for this trial were gathered from Aventis UK. The funding source (Medical Research Council) had no role or influence on the study execution. Received in original form January 17, 2006; accepted in final form July 10, 2006
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