Elevated exopolysaccharide levels in Pseudomonas aeruginosa flagellar mutants have implications for biofilm growth and chronic infections.

Pseudomonas aeruginosa colonizes the airways of cystic fibrosis (CF) patients, causing infections that can last for decades. During the course of these infections, P. aeruginosa undergoes a number of genetic adaptations. One such adaptation is the loss of swimming motility functions. Another involves the formation of the rugose small colony variant (RSCV) phenotype, which is characterized by overproduction of the exopolysaccharides Pel and Psl. Here, we provide evidence that the two adaptations are linked. Using random transposon mutagenesis, we discovered that flagellar mutations are linked to the RSCV phenotype. We found that flagellar mutants overexpressed Pel and Psl in a surface-contact dependent manner. Genetic analyses revealed that flagellar mutants were selected for at high frequencies in biofilms, and that Pel and Psl expression provided the primary fitness benefit in this environment. Suppressor mutagenesis of flagellar RSCVs indicated that Psl overexpression required the mot genes, suggesting that the flagellum stator proteins function in a surface-dependent regulatory pathway for exopolysaccharide biosynthesis. Finally, we identified flagellar mutant RSCVs among CF isolates. The CF environment has long been known to select for flagellar mutants, with the classic interpretation being that the fitness benefit gained relates to an impairment of the host immune system to target a bacterium lacking a flagellum. Our new findings lead us to propose that exopolysaccharide production is a key gain-of-function phenotype that offers a new way to interpret the fitness benefits of these mutations.

Persistence and Progression of Airway Obstruction in Children With Early Onset Scoliosis.

BACKGROUND: Obstructive lung disease occurs in 30% of children with early onset scoliosis (EOS); changes in degree of airway obstruction over time have not been reported. METHODS: Longitudinal patterns of incidental, persistent, and progressive airway obstruction were retrospectively analyzed in a cohort of children with EOS with at least 1 forced expiratory volume in 1 second (FEV1)/forced vital capacity (FVC) value <85% on serial spirometric assessments over a ≥3-year observation period. The prevalence of clinical features and the severity of coronal and sagittal spine deformities for each group at the beginning and end of the study period were compared. RESULTS: Airway obstruction was incidental in 12 (24%) and persistent in 37 (76%) of 49 children with EOS. Twenty of 37 (54%) of those with persistent obstruction developed progressive airway obstruction. The decline in FEV1/FVC over 6±2 years was insignificant in the incidental group (4%±2%) and the persistent nonprogressive group (7%±4%) but significant in the progressive group (13%±4%, t test; P=0.002). In total, 29% of the 49 children at the onset and 57% at the end of the study had airway obstruction. The incidental, persistent nonprogressive, and progressive groups did not differ with regard to age, diagnosis distribution, or sex. The initial coronal curve size, apex, direction of the curve, and degree of kyphosis were statistically similar among the 3 groups. Coronal curve magnitude inversely correlated with FEV1/FVC at the end but not the beginning of the study (r=-0.19, P=0.002). Six of 19 responded to bronchodilator treatment, suggesting concurrent asthma. Airway obstruction did not relate to restrictive pulmonary abnormalities measured by FVC at first or last timepoints [slope=-0.076 (95% confidence interval, -0.99 to 0.038; P=0.19)]. Changes in degrees of airway obstruction and restrictive lung disease over time did not correlate [slope=-0.125 (95% confidence interval, -0.294 to 0.044; P=0.14)]. CONCLUSIONS: Children with EOS and progressive airway obstruction represent an important subgroup which may require new surgical and nonsurgical treatment strategies to prevent loss of lung function over time.

Prevalence and clinical associations of Staphylococcus aureus small-colony variant respiratory infection in children with cystic fibrosis (SCVSA): a multicentre, observational study.

BACKGROUND: Staphylococcus aureus is the bacterium cultured most often from respiratory secretions of people with cystic fibrosis. Both meticillin-susceptible S aureus and meticillin-resistant S aureus (MRSA) can adapt to form slow-growing, antibiotic-resistant isolates known as small-colony variants that are not routinely identified by clinical laboratories. We aimed to determine the prevalence and clinical significance of S aureus small-colony variants and their subtypes among children with cystic fibrosis. METHODS: The Small Colony Variant Staphylococcus aureus (SCVSA) study was a 2-year longitudinal study of children aged 6-16 years at five US cystic fibrosis centres, using culture methods sensitive for small-colony variants. Children were eligible if they had a documented diagnosis of cystic fibrosis and a minimum of two cystic fibrosis clinic visits and two respiratory cultures in the previous 12 months at enrolment. Participants attended clinic visits quarterly, at which respiratory tract samples were taken and measures of lung function (percentage of predicted forced expiratory volume in 1 s [FEV1] and frequency of respiratory exacerbations) were recorded. We determined the prevalence of small-colony variants and their subtypes, and assessed their independent associations with lung function and respiratory exacerbations using linear mixed-effects and generalised estimating equation logistic regression models. Analyses included both univariate models (unadjusted) and multivariate models that adjusted for potential confounders, including age, sex, race, baseline microbiology, treatment with CFTR modulator, and CTFR genotype. FINDINGS: Between July 1, 2014, and May 26, 2015, we enrolled 230 children. Participants were followed-up for 2 years, with a mean of 6·4 visits (SD 1·14) per participant (range 2-9 visits) and a mean interval between visits of 3·94 months (SD 1·77). Across the 2-year period, S aureus small-colony variants were detected in 64 (28%) participants. Most (103 [56%] of 185) of the small-colony variants detected in these participants were thymidine dependent. Children with small-colony variants had significantly lower mean percentage of predicted FEV1 at baseline than did children without small-colony variants (85·5 [SD 19] vs 92·4 [SD 18·6]; p=0·0145). Small-colony variants were associated with significantly lower percentage of predicted FEV1 throughout the study in regression models, both in univariate analyses (regression coefficient -7·07, 95% CI -12·20 to -1·95; p=0·0068) and in multivariate analyses adjusting for potential confounders (-5·50, -10·51 to -0·48; p=0·0316). Small colony variants of the thymidine-dependent subtype had the strongest association with lung function in multivariate regression models (regression coefficient -10·49, -17·25 to -3·73; p=0·0024). Compared with children without small-colony variants, those with small-colony variants had significantly increased odds of respiratory exacerbations in univariate analyses (odds ratio 1·73, 95% CI 1·19 to 2·52; p=0·0045). Children with thymidine-dependent small-colony variants had significantly increased odds of respiratory exacerbations (2·81, 1·69-4·67; p=0·0001), even after adjusting for age, sex, race, genotype, CFTR modulator, P aeruginosa culture status, and baseline percentage of predicted FEV1 (2·17, 1·33-3·57; p=0·0021), whereas those with non-thymidine-dependent small-colony variants did not. In multivariate models including small-colony variants and MRSA status, P aeruginosa was not independently associated with lung function (regression coefficient -4·77, 95% CI -10·36 to 0·83; p=0·10) and was associated with reduced odds of exacerbations (0·54, 0·36 to 0·81; p=0·0028). Only the small-colony variant form of MRSA was associated with reduced lung function (-8·44, -16·15 to -0·72; p=0·0318) and increased odds of exacerbations (2·15, 1·24 to 3·71; p=0·0061). INTERPRETATION: Infection with small-colony variants, and particularly thymidine-dependent small-colony variants, was common in a multicentre paediatric population with cystic fibrosis and associated with reduced lung function and increased risk of respiratory exacerbations. The adoption of small-colony variant identification and subtyping methods by clinical laboratories, and the inclusion of small-colony variant prevalence data in cystic fibrosis registries, should be considered for ongoing surveillance and study. FUNDING: The Cystic Fibrosis Foundation and the National Institutes of Health.

Chronic Azithromycin Use in Cystic Fibrosis and Risk of Treatment-Emergent Respiratory Pathogens.

RATIONALE: Azithromycin has been shown to improve lung function and reduce the number of pulmonary exacerbations in patients with cystic fibrosis. Concerns remain, however, regarding the potential emergence of treatment-related respiratory pathogens. OBJECTIVES: To determine whether chronic azithromycin use (defined as three-times weekly administration) is associated with increased rates of detection of eight specific respiratory pathogens. METHODS: We performed a new-user, propensity score-matched retrospective cohort study utilizing data from the Cystic Fibrosis Foundation Patient Registry. Incident azithromycin users were propensity score matched 1:1 with contemporaneous nonusers. Kaplan-Meier curves and Cox proportional hazards regression were used to evaluate the association between chronic azithromycin use and incident respiratory pathogen detection. Analyses were performed separately for each pathogen, limited to patients among whom that pathogen had not been isolated in the 2 years before cohort entry. RESULTS: After propensity score matching, the mean age of the cohorts was approximately 12 years. Chronic azithromycin users had a significantly lower risk of detection of new methicillin-resistant Staphylococcus aureus, nontuberculous mycobacteria, and Burkholderia cepacia complex compared with nonusers. The risk of acquiring the remaining five pathogens was not significantly different between users and nonusers. CONCLUSIONS: Using an innovative new-user, propensity score-matched study design to minimize indication and selection biases, we found in a predominantly pediatric cohort that chronic azithromycin users had a lower risk of acquiring several cystic fibrosis-related respiratory pathogens. These results may ease concerns that chronic azithromycin exposure increases the risk of acquiring new respiratory pathogens among pediatric patients with cystic fibrosis.

Maximal Respiratory Muscle Strength and Vital Capacity in Children With Early Onset Scoliosis.

STUDY DESIGN: Descriptive cross-sectional study. OBJECTIVE: To measure respiratory muscle function in children with early onset scoliosis (EOS), determine the frequency of respiratory muscle weakness, and correlate these measures with vital capacity, body mass index, and Cobb angle. SUMMARY OF BACKGROUND DATA: Progressive restrictive respiratory disease is common among children with moderate to severe EOS. Reduced respiratory muscle strength is associated with the loss of lung function in adolescents and adults with scoliosis. We hypothesized that reduced inspiratory and expiratory respiratory muscle strength also occur in children with EOS and correlate with reduced vital capacity, poor nutritional status, and severity of the spine deformity. METHODS: We measured maximum inspiratory pressure (MIP) and maximum expiratory pressure (MEP), forced vital capacity (FVC), body mass index IBMI), and Cobb angle in 49 children with EOS but with no diagnosis of underlying muscle weakness. We measured these indices in 12 children serially over 18 months to see if abnormal respiratory muscle function was sustained. RESULTS: FVC averaged 51% (SD 21) of predicted norms with 26 subjects having an FVC <50% predicted. The mean MIP was 57% (SD 25) and the mean MEP was 53% (SD 23) of predicted norms. Thirteen (27%) of the group had MIP values >2SD below the age and sex-based norms. BMI ranged between 1% and 99% of age-based norms. Cobb angle averaged 59° (SD27). MIP% and MEP% significantly correlated with FVC% (r =0.37, P = 0.01 and r = 0.52, P < 0.001 respectively)) but not with BMI or Cobb angle. Reduced MIP% and MEP% were sustained over 7 to 41 months. CONCLUSION: Respiratory muscle weakness is common and persistent in children with EOS and correlates with reductions in vital capacity. Mechanisms for abnormal respiratory function are unclear but must be determined to develop surgical treatment strategies that preserve respiratory muscle function in children with EOS throughout childhood. LEVEL OF EVIDENCE: 2.

Socioeconomic Status, Smoke Exposure, and Health Outcomes in Young Children With Cystic Fibrosis.

BACKGROUND: Lower socioeconomic status (SES) and environmental tobacco smoke (ETS) exposure are both associated with poorer disease outcomes in cystic fibrosis (CF), and children with low SES are disproportionately exposed to ETS. We analyzed a large cohort of young children with CF to distinguish the impact of SES and ETS on clinical outcomes. METHODS: The Early Pseudomonas Infection Control Observational study enrolled Pseudomonas-negative young children with CF <13 years of age. An enrollment survey assessed SES and ETS exposures. Forced expiratory volume in 1 second (FEV1), crackles and wheezes, and weight-for-age percentile were assessed at each clinical encounter over at least 4 years. Repeated measures analyses estimated the association of SES and ETS exposures with longitudinal clinical outcomes, adjusting for confounders. RESULTS: Of 1797 participants, 1375 were eligible for analysis. Maternal education was high school or less in 28.1%, 26.8% had household income <$40 000, and 43.8% had Medicaid or no insurance. Maternal smoking after birth was present in 24.8%, more prevalent in household with low SES. In separate models, lower SES and ETS exposure were significantly associated with lower FEV1% predicted, presence of crackles or wheezes, and lower weight percentile. In combined models, effect estimates for SES changed minimally after adjustment for ETS exposures, whereas estimates for ETS exposures were attenuated after adjusting for SES. CONCLUSIONS: ETS exposure was disproportionately high in low SES families in this cohort of children with CF. Lower SES and ETS exposure had independent adverse effects on pulmonary and nutritional outcomes. Estimated effect of SES on FEV1 decreased minimally after ETS adjustment, suggesting health disparity risks independent of ETS exposure.

Optimized In Vitro Antibiotic Susceptibility Testing Method for Small-Colony Variant Staphylococcus aureus.

Staphylococcus aureus small-colony variants (SCVs) emerge frequently during chronic infections and are often associated with worse disease outcomes. There are no standardized methods for SCV antibiotic susceptibility testing (AST) due to poor growth and reversion to normal-colony (NC) phenotypes on standard media. We sought to identify reproducible methods for AST of S. aureus SCVs and to determine whether SCV susceptibilities can be predicted on the basis of treatment history, SCV biochemical type (auxotrophy), or the susceptibilities of isogenic NC coisolates. We tested the growth and stability of SCV isolates on 11 agar media, selecting for AST 2 media that yielded optimal SCV growth and the lowest rates of reversion to NC phenotypes. We then performed disk diffusion AST on 86 S. aureus SCVs and 28 isogenic NCs and Etest for a subset of 26 SCVs and 24 isogenic NCs. Growth and reversion were optimal on brain heart infusion agar and Mueller-Hinton agar supplemented with compounds for which most clinical SCVs are auxotrophic: hemin, menadione, and thymidine. SCVs were typically nonsusceptible to either trimethoprim-sulfamethoxazole or aminoglycosides, in accordance with the auxotrophy type. In contrast, SCVs were variably nonsusceptible to fluoroquinolones, macrolides, lincosamides, fusidic acid, and rifampin; mecA-positive SCVs were invariably resistant to cefoxitin. All isolates (both SCVs and NCs) were susceptible to quinupristin-dalfopristin, vancomycin, minocycline, linezolid, chloramphenicol, and tigecycline. Analysis of SCV auxotrophy type, isogenic NC antibiograms, and antibiotic treatment history had limited utility in predicting SCV susceptibilities. With clinical correlation, this AST method and these results may prove useful in directing treatment for SCV infections.

Yoga as a Therapy for Adolescents and Young Adults With Cystic Fibrosis: A Pilot Study.

RATIONALE: Yoga has been shown to improve outcomes in patients with asthma but has not been investigated in cystic fibrosis (CF) patients. METHODS: This was a prospective pilot study to evaluate the safety of a standardized yoga program among CF patients aged 12 to 25 years. Participants engaged in a 50-minute yoga session twice weekly for 8 weeks conducted by a certified yoga instructor using a standardized program designed to be safe for health-compromised individuals. Yoga sessions were individual to avoid transmission of infections. Primary outcome was safety and tolerability. Secondary outcome measures included respiratory symptoms, the Cystic Fibrosis Quality of Life instrument (CFQ-R), lung function, Ease of Breathing Score (measure of exercise tolerance), and weight. RESULTS: Eleven participants were enrolled, and 10 completed the study. Adherence was very good; the mean (SD) number of sessions completed was 14.2 (1.3) out of 16 sessions. Eight patients reported 25 adverse events. The most common was cough, reported in 7. Two events were possibly related to study procedures: calf pain and headache. There were no significant changes in dyspnea or pain scales. The mean (SD) CFQ-R respiratory domain score increased from screening to end of study: 67.9 (11.4) to 82.1 (9.9), P=.04. There were no significant changes in the other outcome measures. CONCLUSIONS: In this pilot study, a standardized 8-week yoga program was safe and well tolerated among adolescent and young adult CF patients with mild to moderate lung disease. This study may be helpful to yoga instructors who are interested in working with CF patients. Larger controlled trials are warranted to determine further benefits.

Early Childhood Risk Factors for Decreased FEV1 at Age Six to Seven Years in Young Children with Cystic Fibrosis.

RATIONALE: There are limited objective measures of the severity of lung disease before children are able to routinely perform spirometry, generally at age 6 years. Identifying risk factors for reduced lung function at age 6 provides opportunities to intervene and slow the progression of cystic fibrosis (CF) lung disease. OBJECTIVES: To evaluate early childhood predictors of lung function at age 6-7 in a large U.S. CF cohort in the current era of widespread early eradication therapy for Pseudomonas aeruginosa (P. aeruginosa). METHODS: Participants were children with CF enrolled before age 4 in the Early Pseudomonas Infection Control (EPIC) Observational Study, a multicenter, longitudinal study that enrolled P. aeruginosa-negative children not exceeding 12 years of age. Linear regression was used to estimate the association between potential early childhood risk factors and the best FEV1% predicted at age 6-7 years. MEASUREMENTS AND MAIN RESULTS: Four hundred and eighty-four children (of 1,797 enrolled in the EPIC Observational Study) met the eligibility criteria for this analysis. Mean (SD) age at enrollment was 2.0 (1.3) years. In a multivariable model adjusted for age at enrollment, the following risk factors were significantly associated with lower mean (95% confidence interval) FEV1% predicted at age 6-7: weight percentile less than 10% during the year of enrollment (-5.3 [-9.1, -1.5]), P. aeruginosa positive during the year of enrollment (-2.8 [-5.7, 0.0]), crackles or wheeze during the year of enrollment (-5.7 [-9.4, -1.9]), mother's education of high school or less (-4.2 [-7.3, -1.2]), and mother smoked during pregnancy (-4.4 [-8.8, 0.1]). CONCLUSIONS: In this large U.S. cohort, we identified several early childhood risk factors for lower FEV1 at age 6-7 years, most of which are modifiable. Clinical trial registered with www.clinicaltrials.gov (NCT00097773).

Risk factors for lung function decline in a large cohort of young cystic fibrosis patients.

OBJECTIVE: To identify novel risk factors and corroborate previously identified risk factors for mean annual decline in FEV1% predicted in a large, contemporary, United States cohort of young cystic fibrosis (CF) patients. METHODS: Retrospective observational study of participants in the EPIC Observational Study, who were Pseudomonas-negative and ≤12 years of age at enrollment in 2004-2006. The associations between potential demographic, clinical, and environmental risk factors evaluated during the baseline year and subsequent mean annual decline in FEV1 percent predicted were evaluated using generalized estimating equations. RESULTS: The 946 participants in the current analysis were followed for a mean of 6.2 (SD 1.3) years. Mean annual decline in FEV1% predicted was 1.01% (95%CI 0.85-1.17%). Children with one or no F508del mutations had a significantly smaller annual decline in FEV1 compared to F508del homozygotes. In a multivariable model, risk factors during the baseline year associated with a larger subsequent mean annual lung function decline included female gender, frequent or productive cough, low BMI (<66th percentile, median in the cohort), ≥1 pulmonary exacerbation, high FEV1 (≥115% predicted, in the top quartile), and respiratory culture positive for methicillin-sensitive Staphylococcus aureus, methicillin-resistant S. aureus, or Stenotrophomonas maltophilia. CONCLUSIONS: We have identified a range of risk factors for FEV1 decline in a large cohort of young, CF patients who were Pa negative at enrollment, including novel as well as previously identified characteristics. These results could inform the design of a clinical trial in which rate of FEV1 decline is the primary endpoint and identify high-risk groups that may benefit from closer monitoring.

Exome Sequencing of Phenotypic Extremes Identifies CAV2 and TMC6 as Interacting Modifiers of Chronic Pseudomonas aeruginosa Infection in Cystic Fibrosis.

Discovery of rare or low frequency variants in exome or genome data that are associated with complex traits often will require use of very large sample sizes to achieve adequate statistical power. For a fixed sample size, sequencing of individuals sampled from the tails of a phenotype distribution (i.e., extreme phenotypes design) maximizes power and this approach was recently validated empirically with the discovery of variants in DCTN4 that influence the natural history of P. aeruginosa airway infection in persons with cystic fibrosis (CF; MIM219700). The increasing availability of large exome/genome sequence datasets that serve as proxies for population-based controls affords the opportunity to test an alternative, potentially more powerful and generalizable strategy, in which the frequency of rare variants in a single extreme phenotypic group is compared to a control group (i.e., extreme phenotype vs. control population design). As proof-of-principle, we applied this approach to search for variants associated with risk for age-of-onset of chronic P. aeruginosa airway infection among individuals with CF and identified variants in CAV2 and TMC6 that were significantly associated with group status. These results were validated using a large, prospective, longitudinal CF cohort and confirmed a significant association of a variant in CAV2 with increased age-of-onset of P. aeruginosa airway infection (hazard ratio = 0.48, 95% CI=[0.32, 0.88]) and variants in TMC6 with diminished age-of-onset of P. aeruginosa airway infection (HR = 5.4, 95% CI=[2.2, 13.5]) A strong interaction between CAV2 and TMC6 variants was observed (HR=12.1, 95% CI=[3.8, 39]) for children with the deleterious TMC6 variant and without the CAV2 protective variant. Neither gene showed a significant association using an extreme phenotypes design, and conditions for which the power of an extreme phenotype vs. control population design was greater than that for the extreme phenotypes design were explored.

Impact of Sustained Eradication of New Pseudomonas aeruginosa Infection on Long-term Outcomes in Cystic Fibrosis.

BACKGROUND: Pseudomonas aeruginosa (Pa) is the most important pathogen infecting the airways in individuals with cystic fibrosis. A key question is whether children with newly acquired Pa infection who are able to achieve sustained eradication after early antipseudomonal therapy demonstrate improved long-term health outcomes compared with those who are unable to achieve a sustained microbiologic response. METHODS: This cohort study utilized observational follow-up data on children participating in the Early Pseudomonas Infection Control trial who received standardized therapy for newly acquired Pa. Sustained eradicators were defined as those who maintained Pa-negative cultures for 12 months after initial antipseudomonal therapy. Associations between eradication status and outcomes were assessed. RESULTS: Of the 249 trial participants included in the study, 172 (69%) achieved sustained eradication of Pa during the trial (sustained eradicators). Over the median 5-year follow-up, sustained eradicators had a 74% reduced risk of developing chronic Pa (hazard ratio [HR], 0.26; 95% confidence interval [CI], .17-.40) and a 57% reduced risk of mucoidy (HR, 0.43; 95% CI, .25-.73) compared with nonsustained eradicators. Sustained eradicators had significantly less anti-Pa antibiotic usage during follow-up compared with nonsustained eradicators. There was no association between eradication status and clinical outcomes including rate of exacerbation and lung function decline. CONCLUSIONS: This is the first study to quantify the long-term durability of microbiological response associated with early antipseudomonal therapy, demonstrating the critical importance of optimizing antipseudomonal therapies during early Pa infection. The clinical impact of failure to achieve sustained Pa eradication remains unclear, however, and may be confounded by anti-Pa antibiotic usage. CLINICAL TRIALS REGISTRATION: NCT00097773.

Clinical outcomes after initial pseudomonas acquisition in cystic fibrosis.

OBJECTIVES: To evaluate clinical outcomes associated with initial isolation of Pseudomonas aeruginosa (Pa) in a large U.S. cystic fibrosis (CF) cohort in the current era of widespread early Pa eradication therapy. METHODS: Participants were children with CF enrolled in the Early Pseudomonas Infection Control (EPIC) Observational Study who had no isolation of Pa from respiratory cultures prior to enrollment. Population-averaged regression models using generalized estimating equation methods were used to estimate the effect of Pa acquisition on endpoints including lung function, growth, pulmonary exacerbation rate, respiratory signs and symptoms, and respiratory cultures. RESULTS: Eight hundred thirty-eight subjects were observed for a mean 4.6 (SD 1.2) years during which 431 (51%) acquired Pa. There was no statistically significant effect of Pa acquisition on the slopes of FEV1 % predicted or growth parameters. Pulmonary exacerbation rate was statistically significantly greater after Pa acquisition (incident rate ratio 1.40, 95% CI 1.07, 1.84) as were odds of crackles or wheeze on physical exam (OR 1.23, 95% CI 1.00, 1.52). Odds of isolation of MRSA (OR 1.86, 95% CI 1.38, 2.49) and S. maltophilia (OR 2.11, 95% CI 1.49, 2.98) increased after Pa acquisition, while the odds of H. influenzae (OR 0.54, 95% CI 0.46, 0.64) decreased. CONCLUSIONS: In this large U.S. cohort, we did not detect an association between acquisition of Pa and deterioration in lung function or nutrition. Pa acquisition was associated with significantly increased pulmonary exacerbation rate and odds of crackles or wheeze. Pa infection may be the cause of these outcomes or a marker of more severe disease.

A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics.

In their 2012 report, the President's Council of Advisors on Science and Technology advocated "replacing standard science laboratory courses with discovery-based research courses"-a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates.

Serology as a diagnostic tool for predicting initialPseudomonas aeruginosa acquisition in children with cystic fibrosis.

RATIONALE: Pseudomonas aeruginosa (Pa) serology could potentially be a useful adjunct to respiratory culture methods for the detection of initial or early Pa infection in patients with cystic fibrosis (CF). OBJECTIVE: To evaluate the utility of Pa serology to predict Pa isolation from respiratory (generally oropharyngeal) cultures in the subsequent 6 or 12 months among young children with CF from whom Pa had never been previously cultured. Pa serology was also evaluated in a group of healthy controls. METHODS: Children ≤ 12 years of age without prior isolation of Pa from respiratory cultures participating in the Early Pseudomonal Infection Control EPIC Observational Study (EPIC OBS) had annual serum samples for measurement of antibodies against alkaline protease, elastase and exotoxin A using a commercial kit; controls had a single serum sample. Logistic regression with generalized estimating equations was used to characterize associations between log10 serum antibody titers and first isolation of Pa from a respiratory culture within the subsequent 6 or 12 months, with adjustment for sex and age. Receiver operating characteristic curves were used to optimize antibody titer cutpoints by age group. The diagnostic properties of each antibody were estimated using these optimized cutpoints. RESULTS: Pa serology was evaluated in 582 children with CF (2084 serum samples) and 94 healthy controls. There was substantial overlap between serum antibody titers among controls, CF patients who did not acquire Pa (N = 261) and CF patients who did acquire Pa (N = 321). The maximum positive predictive value for first Pa positive culture within the ensuing 6 months was 76.2% and maximum negative predictive value was 72.1% for any antigen or combination of antigens; values were similar for 12 months. CONCLUSIONS: Pa serology does not appear useful for predicting first Pa positive oropharyngeal culture among young CF patients.

A course-based research experience: how benefits change with increased investment in instructional time.

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

Home Self-Collection of Nasal Swabs for Diagnosis of Acute Respiratory Virus Infections in Children With Cystic Fibrosis.

BACKGROUND: Understanding the importance of respiratory viruses in children with cystic fibrosis (CF) has been limited because of challenges using clinic- or hospital-based diagnostic testing. We conducted a pilot study to assess feasibility of home self- (or parent-) collection of nasal swabs (NS). METHODS: Cystic fibrosis patients aged 6-18 years with new respiratory illness participated. In clinic, a deep nasal flocked swab was collected by research staff and compared with an anterior foam NS obtained after instillation of saline spray. At home, up to 2 self-collections of paired foam NS (with and without saline) were collected and mailed for real-time polymerase chain reaction (PCR) testing. RESULTS: Paired swabs were collected from 28 patients: 18 sets in clinic (deep nasal vs saline foam NS) and 43 sets at home (saline vs dry foam NS) with 9 (50%) and 35 (81%) virus detections, respectively. Home-collected NS were obtained closer to illness onset, with a mean difference in symptom days of -2.3 between home and clinic collections (95% confidence interval [CI] -3.5, -1.2; P < .001). Rhinovirus comprised 73% of virus detections; the difference in mean PCR cycle threshold values for rhinovirus between swabs collected at home versus clinic was -3.8 (95% CI -6.8, -0.9; P = .014), indicating significantly higher viral load for home-collected swabs. CONCLUSIONS: Home-collected foam NS had a higher positivity rate compared with clinic-collected swabs, likely because collection was closer to illness onset. Home self-collection is feasible and well tolerated for timely respiratory virus diagnosis and provides a novel approach for clinical diagnostics and surveillance of respiratory virus infections among CF patients.

Standard care versus protocol based therapy for new onset Pseudomonas aeruginosa in cystic fibrosis.

RATIONALE: The Early Pseudomonal Infection Control (EPIC) randomized trial rigorously evaluated the efficacy of different antibiotic regimens for eradication of newly identified Pseudomonas (Pa) in children with cystic fibrosis (CF). Protocol based therapy in the trial was provided based on culture positivity independent of symptoms. It is unclear whether outcomes observed in the clinical trial were different than those that would have been observed with historical standard of care driven more heavily by respiratory symptoms than culture positivity alone. We hypothesized that the incidence of Pa recurrence and hospitalizations would be significantly reduced among trial participants as compared to historical controls whose standard of care preceded the widespread adoption of tobramycin inhalation solution (TIS) as initial eradication therapy at the time of new isolation of Pa. METHODS: Eligibility criteria from the trial were used to derive historical controls from the Epidemiologic Study of CF (ESCF) who received standard of care treatment from 1995 to 1998, before widespread availability of TIS. Pa recurrence and hospitalization outcomes were assessed over a 15-month time period. RESULTS: As compared to 100% of the 304 trial participants, only 296/608 (49%) historical controls received antibiotics within an average of 20 weeks after new onset Pa. Pa recurrence occurred among 104/298 (35%) of the trial participants as compared to 295/549 (54%) of historical controls (19% difference, 95% CI: 12%, 26%, P < 0.001). No significant differences in the incidence of hospitalization were observed between cohorts. CONCLUSIONS: Protocol-based antimicrobial therapy for newly acquired Pa resulted in a lower rate of Pa recurrence but comparable hospitalization rates as compared to a historical control cohort less aggressively treated with antibiotics for new onset Pa.

Staphylococcus aureus small-colony variants are independently associated with worse lung disease in children with cystic fibrosis.

BACKGROUND: Cystic fibrosis (CF) lung disease is associated with diverse bacteria chronically infecting the airways. Slow-growing, antibiotic-resistant mutants of Staphylococcus aureus known as small-colony variants (SCVs) have been isolated from respiratory secretions from European adults and children with CF lung disease using specific but infrequently used culture techniques. Staphylococcus aureus SCVs can be selected either by exposure to specific antibiotics or by growth with another CF pathogen, Pseudomonas aeruginosa. We sought to determine the prevalence, clinical significance, and likely mechanisms of selection of S. aureus SCVs among a US cohort of children with CF. METHODS: We performed a 2-year study of 100 children with CF using culture techniques sensitive for S. aureus SCVs, and evaluated associations with clinical characteristics using multivariable regression models. RESULTS: Staphylococcus aureus SCV infection was detected among 24% of participants and was significantly associated with a greater drop in lung function during the study (P = .007, adjusted for age and lung function at enrollment). This association persisted after adjusting for infection with other known CF pathogens, including P. aeruginosa and methicillin-resistant S. aureus. Evidence indicated that S. aureus SCVs were likely selected in vivo by treatment with the antibiotic trimethoprim-sulfamethoxazole and possibly by coinfection with P. aeruginosa. CONCLUSIONS: Infection with SCV S. aureus was independently associated with worse CF respiratory outcomes in this pediatric cohort. As many clinical microbiology laboratories do not specifically detect S. aureus SCVs, validation and extension of these findings would require widespread changes in the usual laboratory and clinical approaches to these bacteria.