Infection by Ralstonia species in cystic fibrosis patients: identification of R. pickettii and R. mannitolilytica by polymerase chain reaction

Complexity, temporal stability, and clinical correlates of airway bacterial community composition in primary ciliary dyskinesia

Primary ciliary dyskinesia (PCD) is a genetic disease characterized by abnormalities in ciliary function, leading to compromised airway clearance and chronic bacterial infection of the upper and lower airways. The compositions of these infections and the relationships between their characteristics and disease presentation are poorly defined. We describe here the first systematic culture-independent evaluation of lower airway bacteriology in PCD. Thirty-three airway samples (26 from sputum, 7 from bronchoalveolar lavage [BAL] fluid) were collected from 24 PCD patients aged 4 to 73 years. 16S rRNA quantitative PCR and pyrosequencing were used to determine the bacterial loads and community compositions of the samples. Bacterial loads, which ranged from 1.3 × 10(4) to 5.2 × 10(9) CFU/ml, were positively correlated with age (P = 0.002) but not lung function. An analysis of ∼7,000 16S rRNA sequences per sample identified bacterial species belonging to 128 genera. The concurrently collected paired samples showed high bacterial community similarity. The mean relative abundance of the dominant genera was 64.5% (standard deviation [SD], 24.5), including taxa reported through standard diagnostic microbiology (members of the genera Pseudomonas, Haemophilus, and Streptococcus) and those requiring specific ex vivo growth conditions (members of the genera Prevotella and Porphyromonas). The significant correlations observed included a positive relationship between Pseudomonas aeruginosa relative abundance and age and a negative relationship between P. aeruginosa relative abundance and lung function. Members of the genus Ralstonia were also found to contribute substantially to the bacterial communities in a number of patients. Follow-up samples from a subset of patients revealed high levels of bacterial community temporal stability. The detailed microbiological characterization presented here provides a basis for the reassessment of the clinical management of PCD airway infections.

Microbial community analysis of a coastal hot spring in Kagoshima, Japan, using molecular- and culture-based approaches

Ibusuki hot spring is located on the coastline of Kagoshima Bay, Japan. The hot spring water is characterized by high salinity, high temperature, and neutral pH. The hot spring is covered by the sea during high tide, which leads to severe fluctuations in several environmental variables. A combination of molecular- and culture-based techniques was used to determine the bacterial and archaeal diversity of the hot spring. A total of 48 thermophilic bacterial strains were isolated from two sites (Site 1: 55.6°C; Site 2: 83.1°C) and they were categorized into six groups based on their 16S rRNA gene sequence similarity. Two groups (including 32 isolates) demonstrated low sequence similarity with published species, suggesting that they might represent novel taxa. The 148 clones from the Site 1 bacterial library included 76 operational taxonomy units (OTUs; 97% threshold), while 132 clones from the Site 2 bacterial library included 31 OTUs. Proteobacteria, Bacteroidetes, and Firmicutes were frequently detected in both clone libraries. The clones were related to thermophilic, mesophilic and psychrophilic bacteria. Approximately half of the sequences in bacterial clone libraries shared <92% sequence similarity with their closest sequences in a public database, suggesting that the Ibusuki hot spring may harbor a unique and novel bacterial community. By contrast, 77 clones from the Site 2 archaeal library contained only three OTUs, most of which were affiliated with Thaumarchaeota.

Real-time polymerase chain reaction in the diagnosis of acute postoperative endophthalmitis

PURPOSE

To evaluate the efficacy of quantitative real-time polymerase chain reaction (qPCR) in the diagnosis of postoperative bacterial endophthalmitis among patients who underwent cataract surgery at a tertiary care center.

DESIGN

Prospective experimental study.

METHODS

This was a single-center study of 64 eyes of 64 patients presenting with clinical signs and symptoms of endophthalmitis within 1 year of cataract surgery. Patients with glaucoma filtering or cornea surgery in the past year, postoperative trauma, fungal endophthalmitis, or preoperative inflammatory conditions were excluded. Vitreous samples were obtained during vitreous tap or vitrectomy and sent for both culture and qPCR with sequencing. Vitreous samples obtained from 50 patients undergoing vitrectomy for noninflammatory indications served as controls. The main outcome measures were the sensitivity of qPCR compared to culture and concordance of results of pathogen identification with sequencing vs phenotypic speciation.

RESULTS

qPCR detected 16s bacterial DNA in 37 patients (66%), compared to 19 (34%) with traditional culture. Only 1 patient had a positive result by culture (Nocardia species) but negative result by qPCR. For the 18 samples positive by both qPCR and culture, there was a 100% concordance in pathogen identification between sequencing and phenotypic speciation.

CONCLUSION

In cases of suspected bacterial endophthalmitis, qPCR offers an improved diagnostic yield and may be a useful adjunct to traditional culture. Further large-scale clinical studies are needed to elucidate the full clinical utility of qPCR.

The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications

Until recently, relationships between evidence of colonization or infection by specific microbial species and the development, persistence or exacerbation of pulmonary disease have informed our opinions of airway microbiology. However, recent applications of culture-independent tools for microbiome profiling have revealed a more diverse microbiota than previously recognized in the airways of patients with chronic pulmonary disease. New evidence indicates that the composition of airway microbiota differs in states of health and disease and with severity of symptoms and that the microbiota, as a collective entity, may contribute to pathophysiologic processes associated with chronic airway disease. Here, we review the evolution of airway microbiology studies of chronic pulmonary disease, focusing on asthma, chronic obstructive pulmonary disease and cystic fibrosis. Building on evidence derived from traditional microbiological approaches and more recent culture-independent microbiome studies, we discuss the implications of recent findings on potential microbial determinants of respiratory health or disease.

Genotypic and phenotypic diversity of Ralstonia pickettii and Ralstonia insidiosa isolates from clinical and environmental sources including High-purity Water. Diversity in Ralstonia pickettii

BACKGROUND

Ralstonia pickettii is a nosocomial infectious agent and a significant industrial contaminant. It has been found in many different environments including clinical situations, soil and industrial High Purity Water. This study compares the phenotypic and genotypic diversity of a selection of strains of Ralstonia collected from a variety of sources.

RESULTS

Ralstonia isolates (fifty-nine) from clinical, industrial and environmental origins were compared genotypically using i) Species-specific-PCR, ii) PCR and sequencing of the 16S-23S rRNA Interspatial region (ISR) iii) the fliC gene genes, iv) RAPD and BOX-PCR and v) phenotypically using biochemical testing. The species specific-PCR identified fifteen out of fifty-nine designated R. pickettii isolates as actually being the closely related species R. insidiosa. PCR-ribotyping of the 16S-23S rRNA ISR indicated few major differences between the isolates. Analysis of all isolates demonstrated different banding patterns for both the RAPD and BOX primers however these were found not to vary significantly.

CONCLUSIONS

R. pickettii species isolated from wide geographic and environmental sources appear to be reasonably homogenous based on genotypic and phenotypic characteristics. R. insidiosa can at present only be distinguished from R. pickettii using species specific PCR. R. pickettii and R. insidiosa isolates do not differ significantly phenotypically or genotypically based on environmental or geographical origin.

Specific PCR to identify the heavy-metal-resistant bacterium Cupriavidus metallidurans

The aim of this study is to develop a polymerase chain reaction (PCR) assay for rapid detection of Cupriavidus metallidurans. PCR primers targeting the Signal transduction histidine kinase gene were designed and designated Cm-F1/Cm-R1. Strains of C. metallidurans were positively identified. The size of the PCR products was 437 bp, as expected. This PCR method enables monitoring of industrial, environmental and clinical sources for presence of C. metallidurans.

Detection and accurate identification of new or emerging bacteria in cystic fibrosis patients

Respiratory infections remain a major threat to cystic fibrosis (CF) patients. The detection and correct identification of the bacteria implicated in these infections is critical for the therapeutic management of patients. The traditional methods of culture and phenotypic identification of bacteria lack both sensitivity and specificity because many bacteria can be missed and/or misidentified. Molecular analyses have recently emerged as useful means to resolve these problems, including molecular methods for accurate identification or detection of bacteria and molecular methods for evaluation of microbial diversity. These recent molecular technologies have increased the list of new and/or emerging pathogens and epidemic strains associated with CF patients. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of intact cells has also emerged recently as a powerful and rapid method for the routine identification of bacteria in clinical microbiology laboratories and will certainly represent the method of choice also for the routine identification of bacteria in the context of CF. Finally, recent data derived from molecular culture-independent analyses indicate the presence of a previously underestimated, complex microbial community in sputa from CF patients. Interestingly, full genome sequencing of some bacteria frequently recovered from CF patients has highlighted the fact that the lungs of CF patients are hotspots for lateral gene transfer and the adaptation of these ecosystems to a specific chronic condition.

Clinical significance of microbial infection and adaptation in cystic fibrosis

A select group of microorganisms inhabit the airways of individuals with cystic fibrosis. Once established within the pulmonary environment in these patients, many of these microbes adapt by altering aspects of their structure and physiology. Some of these microbes and adaptations are associated with more rapid deterioration in lung function and overall clinical status, whereas others appear to have little effect. Here we review current evidence supporting or refuting a role for the different microbes and their adaptations in contributing to poor clinical outcomes in cystic fibrosis.

The changing microbial epidemiology in cystic fibrosis

Infection of the airways remains the primary cause of morbidity and mortality in persons with cystic fibrosis (CF). This review describes salient features of the epidemiologies of microbial species that are involved in respiratory tract infection in CF. The apparently expanding spectrum of species causing infection in CF and recent changes in the incidences and prevalences of infection due to specific bacterial, fungal, and viral species are described. The challenges inherent in tracking and interpreting rates of infection in this patient population are discussed.

Fatal infection caused by Cupriavidus gilardii in a child with aplastic anemia

Cupriavidus gilardii is a Gram-negative bacterium that has rarely been associated with human infections. We report a fatal case of sepsis caused by C. gilardii in a previously healthy 12-year-old female.

Incidence, relevance and response for Ralsfonia respiratory infections

BACKGROUND

Cases of Ralstonia colonization/infection occasionally reported by hospitals has generated increased interest in an organism previously little known to most clinicians. Our goal was to determine the incidence of respiratory colonizations and infections involving Ralstonia and the association of mechanical ventilation (limited to reports on respiratory-related occurrences in the U.S.A.) and propose a decision chart to assist response.

METHODS

We performed a secondary analysis of published clinical reports of Ralstonia to determine the potential risks for respiratory colonization and infection in the USA and if being on mechanical ventilation (MV) had an influence on colonization and conversion to infection (symptomatic).

RESULTS

The odds of developing colonization with Ralstonia were eight times higher and the likelihood of developing infection with Ralstonia was twelve times higher in those mechanically ventilated compared to those not mechanically ventilated.

CONCLUSIONS

Our results suggest that individuals who are currently on mechanical ventilation and are Ralstonia culture-positive have an increased risk for colonization and may have increased propensity to the development of infection (two decision trees for approaching diagnosis and therapy included).

An immunocompetent patient presenting with severe septic arthritis due to Ralstonia pickettii identified by molecular-based assays: a case report

Introduction

Ralstonia pickettii is an infrequent pathogen of invasive infections in healthy individuals. The microorganism is supposed to be of relatively low virulence, but can cause infections, mainly of the respiratory tract, in immunocompromised and cystic fibrosis patients. Ralstonia pickettii has also been associated with hospital outbreaks related to contamination of products used for medical care and laboratory diagnosis.

Case presentation

We report here a case of septic arthritis due to Ralstonia pickettii in a female diabetic patient. The microorganism was identified from the synovial fluid by molecular-based methods, while the conventional synovial and blood cultures proved to be negative. The patient was treated by intravenous ceftazidime with complete remission of her symptoms; she was discharged 3 weeks after admission in a very good health. At follow-up examination 3 weeks later, she was still in good health condition without any sign of arthritis of the right knee and afebrile.

Conclusion

In culture negative serious bacterial infections, as septic arthritis, the use of molecular-based techniques might be of outmost importance as additional and rapid diagnostic tools for the identification of the causative agent allowing a prompt and appropriate antimicrobial therapy and a favourable outcome.

Airway infection with a novel Cupriavidus species in persons with cystic fibrosis

We describe the recovery and identification of a bacterium that represents a new species of the genus Cupriavidus from cultures of respiratory tract specimens from two patients with cystic fibrosis (CF). The elucidation of the role of this species in CF lung disease will require an evaluation of a greater number of cases.

Mucoid Inquilinus limosus in a young adult with cystic fibrosis

Inquilinus limosus is a alpha-proteobacterium that has been recently isolate in the airways of cystic fibrosis (CF) patients. We report the isolation of a mucoid strain of I. limosus from the sputum of a 20-year-old male patient with CF over 1 year that was associated with the clinical, spirometric, and radiographic decline in a previously healthy patient.

Ralstonia pickettii-induced ataxia in immunodeficient mice

We report here the characterization of an asymmetric ataxia syndrome (head tilt and circling, with death in the most severe cases) demonstrated by profoundly immunodeficient mice housed at the Institut Curie SPF facility. The immune system of the affected mice had been genetically modified so that they were deficient in both B and T cells. Extensive bacteriologic, parasitic, serologic, and histopathologic analysis of the affected animals and their healthy controls led us to identify Ralstonia pickettii as the causative agent of the ataxic syndrome. The outbreak was managed through a test-and-cull process. Even though they also carried Ralstonia pickettii, immunocompetent mice that were kept in the same facility, did not show any of the signs that were expressed by their immunodeficient counterparts. This case highlights the difficulty of maintaining immunocompetent and immunodeficient mice in the same microbiologic unit and the importance of enlarging the spectrum of health monitoring to opportunistic agents when investigating clinical cases in populations of immunocompromised rodents.

Pulmonary bacterial pathogens in cystic fibrosis patients and antibiotic therapy: a tool for the health workers

Cystic fibrosis is the most common and best known genetic disease involving a defect in transepithelial Cl- transport by mutations in the CF gene on chromosome 7, which codes for the cystic fibrosis transmembrane conductance regulator protein (CFTR). The most serious symptoms are observed in the lungs, augmenting the risk of bacterial infection. The objective of this review was to describe the bacterial pathogens colonizing patients with cystic fibrosis. A systematic search was conducted using the international bibliographic databanks SCIELO, HIGHWIRE, PUBMED, SCIRUS and LILACS to provide a useful and practical review for healthcare workers to make them aware of these microorganisms. Today, B. cepacia, P. aeruginosa and S. aureus are the most important infectious agents in cystic fibrosis patients. However, healthcare professionals must pay attention to emerging infectious agents in these patients, because they represent a potentially serious future problem. Therefore, these pathogens should be pointed out as a risk to these patients, and hospitals all over the world must be prepared to detect and combat these bacteria.

Prospective comparison of microbial culture and polymerase chain reaction in the diagnosis of corneal ulcer

PURPOSE

To compare polymerase chain reaction (PCR) to microbial culture for the detection and identification of bacterial and fungal pathogens in microbial keratitis.

DESIGN

Prospective cohort study.

METHODS

A total of 108 consecutive corneal ulcers were cultured and analyzed by PCR using pan-bacterial and pan-fungal primers. PCR products were cloned, sequenced, and compared to culture results using standard bioinformatics tools.

RESULTS

Of the 108 samples, 56 were culture-positive, 25 for bacteria and 31 for fungi; 52 were culture-negative. After eliminating false-positive PCR products, 94 of 108 were positive by PCR, 37 for bacteria and 57 for fungi. Nineteen of 25 bacterial culture-positive samples were positive by PCR, and 29 of 31 samples culture-positive for fungi were positive by PCR. The majority of sequenced PCR products matched the positive culture results. Of the 52 culture-negative samples, 46 (88%) yielded pathogen deoxyribonucleic acid (DNA) PCR products, 18 bacterial and 28 fungal. These represented a variety of species, including at least three novel previously uncultured microbes.

CONCLUSIONS

PCR detects microbial DNA in the majority of bacterial and fungal corneal ulcers, and identifies potentially pathogenic organisms in a high proportion of culture-negative cases. Yield and concordance with culture are higher for fungal than bacterial ulcers. Practical use of the technique is limited by artefactual amplification of nonpathogenic organisms. PCR may be used as an adjunct to culture to identify potential pathogens in microbial keratitis.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis patients

The identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis (CF) patients is usually achieved by using phenotype-based techniques and eventually molecular tools. These techniques remain time-consuming, expensive, and technically demanding. We used a method based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) for the identification of these bacteria. A set of reference strains belonging to 58 species of clinically relevant nonfermenting gram-negative bacilli was used. To identify peaks discriminating between these various species, the profile of 10 isolated colonies obtained from 10 different passages was analyzed for each referenced strain. Conserved peaks with a relative intensity greater than 0.1 were retained. The spectra of 559 clinical isolates were then compared to that of each of the 58 reference strains as follows: 400 Pseudomonas aeruginosa, 54 Achromobacter xylosoxidans, 32 Stenotrophomonas maltophilia, 52 Burkholderia cepacia complex (BCC), 1 Burkholderia gladioli, 14 Ralstonia mannitolilytica, 2 Ralstonia pickettii, 1 Bordetella hinzii, 1 Inquilinus limosus, 1 Cupriavidus respiraculi, and 1 Burkholderia thailandensis. Using this database, 549 strains were correctly identified. Nine BCC strains and one R. mannnitolilytica strain were identified as belonging to the appropriate genus but not the correct species. We subsequently engineered BCC- and Ralstonia-specific databases using additional reference strains. Using these databases, correct identification for these species increased from 83 to 98% and from 94 to 100% of cases, respectively. Altogether, these data demonstrate that, in CF patients, MALDI-TOF-MS is a powerful tool for rapid identification of nonfermenting gram-negative bacilli.

Identification of Bordetella spp. in respiratory specimens from individuals with cystic fibrosis

Bordetella spp. are not normally included when considering the opportunistic bacterial species that are typically involved in respiratory tract infections in individuals with cystic fibrosis (CF). By using a combination of bacterial genotyping and 16S rDNA sequencing, Bordetella spp. were identified in cultures obtained from 43 individuals with CF. Most (n = 23) patients were infected with Bordetella bronchiseptica/parapertussis; five were infected with Bordetella hinzii, four with Bordetella petrii, three with Bordetella avium, and eight with unidentified Bordetella spp. Consideration should be given to the presence of these organisms in the evaluation of CF sputum cultures.

Infections in chronic lung diseases

Chronic lung diseases are prevalent worldwide and cause significant mortality and suffering. This article discusses infections that occur in three chronic lung diseases: chronic obstructive pulmonary disease, bronchiectasis, and cystic fibrosis. Rather than discussing the role of infections as etiology of these diseases, this article focuses on infections that occur in the background of established chronic lung disease.

Cystic fibrosis: a polymicrobial infectious disease

Cystic fibrosis (CF) is the most common lethal genetic disease in the Caucasian population, and should be considered an infectious disease because of the basic pathophysiology. Chronic lower airway infections cause a progressive pathologic deterioration of lung tissue, a decline in pulmonary function and, ultimately, respiratory failure and death in 90% of CF patients. Historically, very few bacterial species have been implicated as principal CF pathogens. However, molecular evidence suggests the presence of a diverse mosaic of bacteria in CF lungs, and infections can be defined as polymicrobial. Here we review the work that supports this concept and we discuss the potential significance of the polymicrobial community in lung pathology. Understanding the dynamics of polymicrobial infections, the interplay between pathogen(s), normal oropharyngeal flora and the host immune system may lead to future advances in the therapeutic management of chronic lung infections.

Exacerbations in cystic fibrosis. 1: Epidemiology and pathogenesis

With the improving survival of patients with cystic fibrosis (CF), the clinical spectrum of this complex multisystem disease continues to evolve. One of the most important clinical events for patients with CF in the course of this disease is an acute pulmonary exacerbation. Clinical and microbial epidemiology studies of CF pulmonary exacerbations continue to provide important insight into the course, prognosis and complications of the disease. This review provides a summary of the pathophysiology, clinical epidemiology and microbial epidemiology of a CF pulmonary exacerbation.

Evolving epidemiology of Pseudomonas aeruginosa and the Burkholderia cepacia complex in cystic fibrosis lung infection

The morbidity and mortality of patients with cystic fibrosis (CF) is primarily determined by chronic and debilitating lung infections caused by a surprisingly narrow spectrum of bacterial pathogens. Pseudomonas aeruginosa is by far the most prevalent life-threatening CF pathogen. In the absence of aggressive early therapy, it infects the majority of adult patients and determines long-term survival. The epidemiology of CF pulmonary infections continues to evolve. Amongst the most recent CF pathogens to have emerged are a group of closely related bacteria, known as the Burkholderia cepacia complex. These organisms are a particular challenge due to inherent antibiotic resistance, the potential for patient-to-patient spread, and the risk of ‘cepacia syndrome’, a rapid fulminating pneumonia sometimes accompanied by bacteremia. Strict cross-infection control was prompted by early epidemiological experience of the B. cepacia complex and is essential in the management of all CF pathogens.

Clonal analysis of Inquilinus limosus isolates from six cystic fibrosis patients and specific serum antibody response

Inquilinus limosus is a novel Gram-negative bacterium of the subdivision alpha-Proteobacteria recently found in the airways of patients with cystic fibrosis (CF). Here, the authors report on the clinical courses of six CF patients colonized with I. limosus. Five patients suffered from either an acute respiratory exacerbation or a progressive loss of pulmonary function, whereas one patient was in a stable clinical situation. This study focused on two aims: (i) the clonal analysis of I. limosus isolates by random amplified polymorphic DNA (RAPD)-PCR, and (ii) the clarification of whether the presence of I. limosus in the respiratory tract is associated with a specific serum antibody response. Serum IgG was detected by immunoblotting using I. limosus whole-cell-lysate proteins as antigens. Sera from healthy blood donors (n=10) and from CF patients colonized with Pseudomonas aeruginosa (n=10) were found to be immunoblot negative. All six Inquilinus-positive patients raised serum IgG antibodies against various I. limosus antigens. Surprisingly, in one patient, a specific I. limosus serum antibody response was already detected 1 year prior to Inquilinus-positive sputum cultures. Two prominent antigens were characterized by MALDI-MS: a 23 kDa protein revealed homology to the outer membrane lipoprotein OmlA of Actinobacillus pleuropneumoniae, and an 18 kDa protein to a protein-tyrosine phosphatase of Burkholderia cepacia. In conclusion, detection of I. limosus is accompanied by a specific serum antibody response and may reflect the infectious/pathogenic potential of I. limosus. Moreover, IgG immunoblotting may be useful to detect early infection with I. limosus and may support the selective cultivation of this novel emerging pathogen.

Identification of peptides from human pathogens able to cross-activate an HIV-1-gag-specific CD4+ T cell clone

Antigen recognition by T cells is degenerate both at the MHC and the TCR level. In this study, we analyzed the cross-reactivity of a human HIV-1 gag p24-specific CD4(+) T cell clone obtained from an HIV-1-seronegative donor using a positional scanning synthetic combinatorial peptide library (PS-SCL)-based biometrical analysis. A number of decapeptides able to activate the HIV-1 gag-specific clone were identified and shown to correspond to sequences found in other human pathogens. Two of these peptides activated the T cell clone with the same stimulatory potency as the original HIV-1 gag p24 peptide. These findings show that an HIV-1-specific human T helper clone can react efficiently with peptides from other pathogens and suggest that cellular immune responses identified as being specific for one human pathogen (HIV-1) could arise from exposure to other pathogens.

Superiority of molecular techniques for identification of gram-negative, oxidase-positive rods, including morphologically nontypical Pseudomonas aeruginosa, from patients with cystic fibrosis

Phenotypic identification of gram-negative bacteria from Cystic Fibrosis (CF) patients carries a high risk of misidentification. Therefore, we compared the results of biochemical identification by API 20NE with 16S rRNA gene sequencing in 88 gram-negative, oxidase-positive rods, other than morphologically and biochemically typical P. aeruginosa, from respiratory secretions of CF patients. The API 20NE allowed correct identification of the bacterial species in 15 out of 88 (17%) isolates investigated. Agreement between the API and the 16S rRNA gene sequencing results was high only in isolates with an API result classified as "excellent identification". Even API results classified as "very good identification" or "good identification" showed a high rate of misidentification (67% and 84%). Fifty-two isolates of morphological and biochemical nontypical Pseudomonas aeruginosa, representing 59% of all isolates investigated, were not identifiable or misidentified in the API 20NE. Therefore, rapid molecular diagnostic techniques like real-time PCR and fluorescence in situ hybridization (FISH) were evaluated in this particular group of bacteria for identification of the clinically most relevant pathogen, P. aeruginosa. The LightCycler PCR assay with a P. aeruginosa-specific probe showed a sensitivity and specificity of 98.1% and 100%, respectively. For FISH analysis, a newly designed P. aeruginosa-specific probe had a sensitivity and specificity of 100%. In conclusion, molecular methods are superior over biochemical tests for identification of gram-negative, oxidase-positive rods in CF patients. In addition, real-time PCR and FISH allowed identification of morphologically nontypical isolates of P. aeruginosa within a few hours.

Use of PCR analyses to define the distribution of Ralstonia species recovered from patients with cystic fibrosis

Two new PCR assays (for Ralstonia species and Ralstonia respiraculi), together with previously published PCR assays, were used to assess Ralstonia isolates recovered from 111 cystic fibrosis patients. Ralstonia mannitolilytica accounted for 46% of isolates, while R. respiraculi and Ralstonia pickettii accounted for 19% and 18%, respectively. Ralstonia basilensis and Ralstonia metallidurans, species not previously recovered from human samples, were also identified.

Ostéite du trapèze à Ralstonia pickettii : à propos d'un cas et revue de la littérature

An immunocompromised 29-year-old man presented with a Ralstonia pickettii osteomyelitis affecting the trapezium bone. The patient underwent two surgical debridement stages, including trapezectomy and long-term drainage. The type of the contaminant organism and the trapezium localization make this observation atypical.

Inquilinus limosus in patients with cystic fibrosis, Germany

We identified Inquilinus limosus, a recently described ?-proteobacterium, in sputum of 2 patients with cystic fibrosis whose respiratory tracts were persistently colonized for >9 months. We present data on the epidemiology, antimicrobial susceptibility, and molecular characteristics of I. limosus.

Characterization of clinically isolated Ralstonia mannitolilytica strains using random amplification of polymorphic DNA (RAPD) typing and antimicrobial sensitivity, and comparison of the classification efficacy of phenotypic and genotypic assays

Ralstonia mannitolilytica strains isolated between February 2002 and March 2004 from 30 episodes of infection in 26 patients at Vienna University Hospital were characterized. Twenty-four of the episodes occurred within a 7 month period, suggesting they were outbreak-related, although no common source of infection was identified. The isolates were assayed using PCR to confirm species identification. Random amplification of polymorphic DNA (RAPD) typing classified the R. mannitolilytica isolates into four distinct genotypes: A/I, B/II, C/III and D/IV (15, 13, 1 and 1 isolates, respectively). API 20NE, VITEK Gram-negative Identification Card plus (GNI+) and VITEK Gram Negative Bacillus Identification (GNB) yielded negative or no acceptable biochemical profile for 4, 11 and 11 isolates, respectively. None of the isolates acidified D-arabitol or mannitol. Two isolates (7 %) were positive for nitrate reduction. All 30 R. mannitolilytica isolates were resistant to desferrioxamine, and 29 were able to grow on BCSA. The most active compounds in vitro were ciprofloxacin and cefepime, whilst only the genotype D/IV isolate was sensitive to gentamicin and amikacin (the remaining 29 isolates being resistant to both).

Antimicrobial susceptibility of uncommonly isolated non-enteric Gram-negative bacilli

The frequency of occurrence and antimicrobial susceptibility patterns of 3059 non-enteric Gram-negative bacilli (NGB), other than Pseudomonas aeruginosa and Acinetobacter spp., consecutively collected as part of the SENTRY Antimicrobial Surveillance Program (1997-2003) were reviewed. During this period, a total of 221,084 bacterial isolates were collected from several clinical specimens worldwide, including 25,305 (11.5%) NGB. Acinetobacter spp. and P. aeruginosa accounted for 82.7% of the NGB isolates and have been excluded from this analysis. The antimicrobial susceptibility results of 3509 strains from 13 species/genera have been analysed in this review. The isolates were tested by reference broth microdilution methods in three central laboratories using common reagents and procedures. More than 30 antimicrobial agents were tested and the results for the 18 most active compounds are reported here. Stenotrophomonas maltophilia (2076 strains; 59.2%) was the most frequently isolated pathogen in this group, followed by Aeromonas spp. (385 strain; 11.0%), Burkholderia cepacia (269 strains; 7.7%), Pseudomonas fluorescens/putida (253 strains; 7.2%) and Alcaligenes spp. (236 strains; 6.7%). All other species/genera accounted for less than 3% of the isolates analysed. The antimicrobial agents with the most consistent activity against the NGB evaluated in the present study were the newer fluoroquinolones gatifloxacin and levofloxacin with 84.1 and 84.9% susceptibility overall. Trimethoprim/sulphamethoxazole was active against 85.3% of the isolates tested, but showed reduced activity against P. fluorescens/putida (22.1% susceptibility). Antimicrobial susceptibility varied significantly between species/genera and the geographical regions evaluated. Thus, proper identification and quantitative susceptibility testing will be required for the treatment of NGB infections. Extensive worldwide surveillance programmes remain extremely important to guide empirical antimicrobial therapy for rarely isolated pathogens and also for pathogens that are not routinely tested due to the lack of standardised susceptibility testing methods.

characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16s ribosomal DNA terminal restriction fragment length polymorphism profiling

Progressive loss of lung function resulting from the inflammatory response to bacterial colonization is the leading cause of mortality in cystic fibrosis (CF) patients. A greater understanding of these bacterial infections is needed to improve lung disease management. As culture-based diagnoses are associated with fundamental drawbacks, we used terminal restriction fragment (T-RF) length polymorphism profiling and 16S rRNA clone data to characterize, without prior cultivation, the bacterial community in 71 sputa from 34 adult CF patients. Nineteen species from 15 genera were identified in 53 16S rRNA clones from three patients. Of these, 15 species have not previously been reported in CF lung infections and many were species requiring strict anaerobic conditions for growth. The species richness and evenness were determined from the T-RF length and volume for the 71 profiles. Species richness was on average 13.3 +/- 7.9 per sample and 13.4 +/- 6.7 per patient. On average, the T-RF bands of the lowest and highest volumes represented 0.6 and 59.2% of the total volume in each profile, respectively. The second through fifth most dominant T-RF bands represented 15.3, 7.5, 4.7, and 2.8% of the total profile volume, respectively. On average, the remaining T-RF bands represented 10.2% of the total profile volume. The T-RF band corresponding to Pseudomonas aeruginosa had the highest volume in 61.1% of the samples. However, 18 other T-RF band lengths were dominant in at least one sample. In conclusion, this reveals the enormous complexity of bacteria within the CF lung. Although their significance is yet to be determined, these findings alter our perception of CF lung infections.

PCR-based assay for differentiation of Pseudomonas aeruginosa from other Pseudomonas species recovered from cystic fibrosis patients

Pseudomonas aeruginosa is the major opportunistic bacterial pathogen in persons with cystic fibrosis (CF); pulmonary infection occurs in approximately 80% of adult CF patients. Much of CF patient management depends on accurate identification of P. aeruginosa from sputum culture. However, identification of this species may be problematic due to the marked phenotypic variability demonstrated by CF sputum isolates and the presence of other closely related species. To facilitate species identification, we used 16S ribosomal DNA (rDNA) sequence data to design PCR assays intended to provide genus- or species-level identification. Both assays yielded DNA fragments of the predicted size. We tested 42 culture collection strains (including 14 P. aeruginosa strains and 28 strains representing 16 other closely related Pseudomonas species) and 43 strains that had been previously identified as belonging to 28 nonpseudomonal species also recovered from CF patient sputum. Based on these 85 strains, the specificity and sensitivity of both assays were 100%. To further assess the utility of the PCR assays, we tested 66 recent CF sputum isolates. The results indicated that preliminary phenotypic testing had misidentified several isolates. The 16S rDNA sequence was determined for 38 isolates, and in all cases it confirmed the results of the PCR assays. Thus, we have designed two PCR assays: one is specific for the genus Pseudomonas, while the other is specific for P. aeruginosa. Both assays show 100% sensitivity and specificity.

Pathophysiology and management of pulmonary infections in cystic fibrosis

This comprehensive State of the Art review summarizes the current published knowledge base regarding the pathophysiology and microbiology of pulmonary disease in cystic fibrosis (CF). The molecular basis of CF lung disease including the impact of defective cystic fibrosis transmembrane regulator (CFTR) protein function on airway physiology, mucociliary clearance, and establishment of Pseudomonas aeruginosa infection is described. An extensive review of the microbiology of CF lung disease with particular reference to infection with P. aeruginosa is provided. Other pathogens commonly associated with CF lung disease including Staphylococcal aureus, Burkholderia cepacia, Stenotrophomonas maltophilia, Achromobacter xylosoxidans and atypical mycobacteria are also described. Clinical presentation and assessment of CF lung disease including diagnostic microbiology and other measures of pulmonary health are reviewed. Current recommendations for management of CF lung disease are provided. An extensive review of antipseudomonal therapies in the settings of treatment for early P. aeruginosa infection, maintenance for patients with chronic P. aeruginosa infection, and treatment of exacerbation in pulmonary symptoms, as well as antibiotic therapies for other CF respiratory pathogens, are included. In addition, the article discusses infection control policies, therapies to optimize airway clearance and reduce inflammation, and potential future therapies.

Airway inflammation and infection in congenital bilateral absence of the vas deferens

In cystic fibrosis (CF), airway disease begins early in life. Bacteria and elevated levels of neutrophils and inflammatory mediators have been detected in bronchoalveolar lavage (BAL) fluid from infants with CF. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) are common in men with congenital bilateral absence of the vas deferens (CBAVD) and it has been suggested that this syndrome represents a mild form of CF. We hypothesized that men with CBAVD also have subclinical pulmonary disease. Bronchoscopy with BAL, viral and quantitative bacterial cultures, and analyses of total and differential cell count, cytokines, and free neutrophil elastase was performed in eight men with CBAVD, who had mutations in the CFTR and intermediate or elevated sweat chloride levels, and in four healthy control subjects. There was light growth of Staphylococcus aureus in one of eight men with CBAVD, and small numbers of opportunistic gram-negative bacteria in six of eight men with CBAVD and in one control subject. BAL cell counts and neutrophil elastase were within the normal range. Interleukin-8 and tumor necrosis factor-alpha levels were higher for men with CBAVD than for control subjects. These data suggest that mutations in the CFTR in men with CBAVD, in addition to causing infertility, lead to subclinical bacterial pulmonary infection and inflammation consistent with mild CF.

Ralstonia respiraculi sp. nov., isolated from the respiratory tract of cystic fibrosis patients

Five isolates recovered from the respiratory tract of cystic fibrosis patients were included in a polyphasic taxonomic study that employed 16S rDNA sequence analysis, cellular protein and fatty acid analysis and biochemical characterization. Four isolates were classified as a novel Ralstonia species, for which the name Ralstonia respiraculi sp. nov. is proposed; the other isolate was phylogenetically closely related to R. respiraculi, but is likely to represent another novel Ralstonia species. The type strain of R. respiraculi is AU3313(T) (=LMG 21510(T)=CCUG 46809(T)).

Use of amplified ribosomal DNA restriction analysis for identification of Ralstonia and Pandoraea species: interest in determination of the respiratory bacterial flora in patients with cystic fibrosis

The recovery of Ralstonia and Pandoraea species from respiratory tract cultures of patients with cystic fibrosis has recently been reported. These species are difficult to identify, and especially to differentiate from Burkholderia cepacia complex organisms, with classical methods. The discriminatory power of amplified ribosomal DNA restriction analysis (ARDRA) within the two genera was assessed by comparing the restriction profiles of reference strains of each species by using a panel of six enzymes already proven suitable for the identification of Burkholderia species. ARDRA provided differentiation of all the Ralstonia species tested and of Pandoraea norimbergensis. Pandoraea species P. pnomenusa, P. sputorum, P. pulmonicola, and P. apista were not discriminated to the species level. This method allowed the identification of five clinical isolates recovered from French cystic fibrosis patients as Ralstonia mannitolilytica.

Classification of Ralstonia pickettii-like isolates from the environment and clinical samples as Ralstonia insidiosa sp. nov

Thirteen Ralstonia pickettii-like isolates from the environment (water, soil and activated sludge) and human clinical samples (including respiratory secretions of cystic fibrosis patients) were investigated in a polyphasic taxonomic study that employed 16S rDNA sequence analysis, DNA-DNA hybridization, determination of DNA base composition, whole-cell protein analysis, biochemical characterization and PCR-based assays. All isolates were classified as a novel Ralstonia species, for which the name Ralstonia insidiosa sp. nov. is proposed. The type strain, LMG 21421T (= CCUG 46789T), was isolated from the sputum of a patient with acute lymphoblastic leukaemia. R. insidiosa can be differentiated from other species of the genus Ralstonia and phenotypically similar species (including the Burkholderia cepacia complex and Achromobacter xylosoxidans) by a variety of biochemical tests, whole-cell protein analysis and several PCR-based assays. Some outstanding issues in the taxonomy of the genus Ralstonia are also discussed.

Energy-generating enzymes of Burkholderia cepacia and their interactions with macrophages

We previously demonstrated that several clinical and environmental isolates of Burkholderia cepacia secreted ATP-utilizing enzymes to the medium; the secretion of these enzymes by cystic fibrosis lung isolate strain 38 was shown to be greatly enhanced in the presence of alpha(2)-macroglobulin. Fractionation of the growth medium of cystic fibrosis isolate strain 71 belonging to genomovar I demonstrated the presence of two additional proteins, homologues of Pseudomonas aeruginosa azurin and cytochrome c(551), which are normally involved in electron transfer during denitrification. A Q-Sepharose column flowthrough fraction of the growth medium of B. cepacia strain 71 enriched with the azurin and cytochrome c(551) homologues triggered apoptosis in macrophages and mast cells, leading to their death. Incubation of the Q-Sepharose column flowthrough fraction with antiazurin and anti-cytochrome c(551) antibodies greatly reduced cell death. We cloned and hyperexpressed a gene from B. cepacia strain 71 that encodes the homologue of P. aeruginosa azurin. Such azurin homologues were detected in the growth medium of several strains belonging to genomovars I, III, and VI but not in the growth medium of strains belonging to other genomovars. The growth medium of the strains that elaborated the azurin homologue had high cytotoxicity towards macrophages. Purified azurin homologue was shown to induce apoptosis in macrophages in a caspase-dependent manner and was localized in both the cytosol and nucleus when incubated with or microinjected into macrophages. This is an interesting example of the interaction of a bacterial protein normally involved in cellular energetics with macrophages to effect their cell death.