Cough Swabs Research Articles

Upper airway microbial colonization in patients with neuromuscular disorders.

Inherited neuromuscular disorders (NMD) inevitably result in severe lung volume restriction and cough insufficiency associated with high morbidity and mortality. The aim of this retrospective study was to evaluate whether the airways of patients with NMD are colonized with potential pathogenic microorganisms that might contribute to the pulmonary morbidity in NMD. In this cross-sectional study, cough swabs were obtained and cultured for microbiological analyses from 77 patients with NMD and different degrees of lung volume restriction and cough insufficiency. Upper airway microbial colonization was compared to lung function parameters and cough peak flow values. Upper airway microbial colonization with potential pathogenic pathogens was identified in 39/77 (51%) of the subjects. Upper airway microbial colonization was associated with lower forced vital capacity (% pred.) 26.6 ± 19.7 versus 41.8 ± 20.4, P < 0.001 and cough peak flow (l/min) 125 ± 55 versus 207 ± 100, P < 0.001. In the subgroup colonized with potential pathogenic Gram-negative bacteria or Staphylococcus aureus forced vital capacity and cough peak flow remained significantly lower compared with subjects without upper airway colonization (FVC (% pred.): 22.6 ± 16.5 vs 37.9 ± 21.5, P = 0.003; CPF (l/min): 123 ± 60 vs 179 ± 93, P = 0.013). Severe respiratory compromise in patients with NMD is associated with upper airway microbial airway colonization, which might contribute to respiratory morbidity/insufficiency.

A case of failed eradication of cystic fibrosis-related sinus colonisation by Pseudomonas aeruginosa

BackgroundPseudomonas aeruginosa is a pathogen associated with cystic fibrosis that has potential to decrease lung function and cause respiratory failure. Paranasal sinuses are increasingly recognised as potential reservoirs for intermittent colonisation by P. aeruginosa. This case documents investigation and outcome of P. aeruginosa recurrence in a male paediatric patient over an eight year period.Case presentationA 12 year old Irish male paediatric cystic fibrosis patient experienced intermittent culturing of P. aeruginosa from the oropharyngeal region, indicating chronic infection of the sinuses despite absence of symptoms, retaining good lung function, and normal bronchoscopy and bronchoalveloar lavage. However, P. aeruginosa was isolated from a sinus wash-out and was identified as a unique strain of P. aeruginosa that was also cultured from cough swabs. Despite treatment, successful eradication from the paranasal sinuses was not achieved.ConclusionsFew reports have addressed the paranasal sinuses as a reservoir for lung infection in cystic fibrosis patients despite increased recognition of the need to investigate this niche. In this case, attempts at eradication of P. aeruginosa present in paranasal sinuses including oral and nebulised antimicrobials proved unsuccessful. However, detection of P. aeruginosa in the paranasal sinuses instigated antimicrobial treatment which may have contributed to prevention of migration to the lower airways. Our outcome provides additional insight and may indicate utility of nasal lavage or nasal endoscopy in paediatric cystic fibrosis patients’ annual review clinic visits.

76 Identification of Pseudomonas aeruginosa infection in a paediatric CF population

Objective To analyse the importance of obtaining regular sputum samples in identifying P. aeruginosa infection in a paediatric cystic fibrosis (CF) population. Royal Manchester Children's Hospital provides care to 182 children with CF. Sputum and/or cough swab samples are taken at each clinic visit. Our local practice is to encourage families to also send sputum samples/ cough swabs to us twice a month. Methods Analysis of cough swab and sputum samples of all our CF patients during a 2-year period (October 2012 to September 2014). Children were classified according to the Leeds criteria for P. aeruginosa infection, with an additional category of Results 5973 samples were obtained over the 2-year period from our CF population. Table 1P. aeruginosa statusNumber of children (total = 182)Never infected61 (33%)Free of infection67 (37%)Intermittent infection29 (16%)Chronic infection18 (10%)First growth7 (4%) We then analysed P. aeruginosa status if only samples taken at clinic were used. Table 2. Table 2P. aeruginosa statusNumber of childrenAll samplesClinic samples onlyIntermittent infection2914First growth74 If clinic samples alone were analysed, we would have identified 14/29 children with intermittent infection and 4/7 children with first growth. Conclusion Potentially significant pathogens may not be identified if sputum/cough swab samples are only obtained at clinic visits. In our CF population, 18 children (10%) with P. aeruginosa growth would not have been identified if samples had only been taken at clinic.

69 The Cystic Fibrosis Sputum Induction Trial (CF-SpIT). Induced sputum in young healthy non-productive children with cystic fibrosis

Objective Young children with CF are often non-productive of sputum even during a chest exacerbation. Effective bacterial surveillance is challenging, but critical as respiratory infection and lung disease begins early in life. CF-SpIT (CF-Sputum Induction Trial: UKCRN 14615) seeks to identify whether using induced sputum (IS) improves bacterial surveillance, in young non-productive children with CF. Methods 86 children from CF-SpIT are included in this analysis. In all cases, a routine cough swab (CS) was followed by IS. Paired samples were compared for microbiology yield. In 20 children, where bronchoscopy was clinically indicated, CS, IS and extensive 6 lobe bronchoalveolar lavage (BAL) were compared for microbiology yield. Results IS was tolerated in 98% of patients, and successful in 81% (n = 69). Tolerability and success did not differ in children below or above 6 years of age, despite more of the younger cohort being naive to hypertonic saline (30%), not spontaneously productive (92%) and unwell at the time (68%). Of the 69 patients, 17% had positive cough swabs, 47% had positive IS samples (χ 2 = 10. P=0.002). IS identified a pathogen not previously isolated in the previous year in 29% of patients. In 20 patients where CS, IS and BAL were taken, 20 pathogens were grown in 16 patients. CS, IS and BAL identified 5, 13 and 14 pathogens respectively. Pathogens were identified on IS but not on BAL in 4 patients. 16S sequencing of culture-negative BAL was positive for the pathogen identified on IS in 3 of 4 cases. Conclusion Induced Sputum is a well tolerated, non-invasive, effective way to sample the lower airway in young non-productive healthy children with CF.

61 Comparison of two chromogenic media for isolation of Staphylococcus aureus from respiratory samples from patients with cystic fibrosis

Objective To evaluate two chromogenic culture media, chromID S. aureus (chromID) and chromID S. aureus Elite (chromID Elite) for isolation of Staphylococcus aureus from respiratory samples from patients with cystic fibrosis (CF). Methods The samples included 123 sputum samples and 108 cough swabs from 171 CF patients. Sputum samples were homogenized with sputasol and 10 µL was cultured onto each medium. The clinical material from cough swabs was dispersed in 2 mL of saline and 10 µL was cultured onto each medium. Media were incubated at 37°C and plates were read after 20 h, 48 h and 72 h. Any colonies showing expected coloration were identified using MALDI-TOF MS. Results S. aureus was isolated from 52 samples (22%). The sensitivity for chromID was 62% after 20 h of incubation rising to 79% after 72 h. chromID Elite showed a sensitivity of 79% after 20 h rising to 92% after 72 h ( P = 0.12). Fewer false positive colonies were encountered on chromID Elite (n = 68) compared with chromID ( n = 146). Conclusion chromID Elite is an effective medium for isolation of S. aureus with challenging clinical samples that may contain auxotrophic isolates of S. aureus (small colony variants) and a diversity of other species, including many with antibiotic resistance. It was notable that after 18 h incubation, chromID Elite showed equivalent performance to chromID that had been incubated for 72 h. A further advantage of chromID Elite was the fact that fewer false positive samples required investigation (P S. aureus from respiratory samples from patients with CF.

P104 Comparison Of The Upper And Lower Airway Microbiota In Children

Introduction The lower airway microbiota is important in chronic lung disease but young children do not expectorate, making longitudinal studies difficult. Upper airway samples, of uncertain reliability, are used as a surrogate. Whilst throat swabs (TS) have shown differences in the microbiota between healthy and wheezing children [ PLoS One 2012;7(10):e46803], the role of cough swabs (CS) is at present unclear. This study assessed the correlation between upper and lower airway samples as a prelude to a longitudinal study. We hypothesised that upper airway samples reflect the lower airway microbiota. Methods TS and lower airway samples (bronchoalveolar lavage fluid, bronchial brushings or both) were collected from 55 children undergoing a clinically indicated fibre-optic bronchoscopy (FOB), including CS from 35 children. Bacterial DNA was extracted for quantitative PCR (qPCR) and 454 FLX pyrosequencing of the V3-V5 region of the 16S rRNA bacterial gene. Data analysis was performed with Quantitative Insights Into Microbial Ecology (QIIME) and Phyloseq in R. Results FOB indications included: recurrent lower respiratory tract infections (47%); cystic fibrosis (CF) (35%), and Primary Ciliary Dyskinesia (PCD) (11%). Only seven CS amplified successfully. 375,268 high quality 16S rRNA sequences were obtained from 132 upper and lower airway samples. No significant difference was seen in richness (H = 1.352, 2 d.f., p = 0.509), evenness (H = 3.942, 2 d.f, p = 0.139), Shannon’s diversity index (H = 1.38, 2 d.f., p = 0.501), and Inverse Simpson’s diversity index (F (2,91) = 0.547, p = 0.581) between TS and lower airway samples. Beta-diversity (diversity between samples) was significantly different; ≤7.2% of variation in diversity attributed to the sampling method (p = 0.002). Greater variation was observed between underlying pathologies and between patients (≤41.2% and 68.3% respectively, p = 0.001). Conclusions CS are not useful for pyrosequencing. TS are predictive of the lower airway microbiota and can differentiate diseases. TS are therefore potentially useful in studying longitudinal changes in the microbiota in children with chronic lung diseases.

P103 Do Children With Primary Ciliary Dyskinesia Harbour The Same Pathogens In The Upper And Lower Airway?

Background Primary ciliary dyskinesia (PCD) is characterised by chronic nasal discharge and lower respiratory tract infections. We aimed to assess the prevalence and concordance of pathogens present in samples from the upper (UA) and lower airway (LA) of children with PCD. Method Microbiology samples from UA (naso-sinal lavage or nasal swab) and LA (sputum or cough swabs) were taken at the same time from children attending a specialist PCD centre, diagnosed on standard criteria (Eur Respir J 2009:34:1264–1276). Results 70 children (30 male), median age 10.7 yrs (range 1–18), were studied. 36/70 were prescribed long term prophylactic oral antibiotics. 42 (60%) of UA samples were culture positive compared to 21 (30%) positive LA samples. The UA positive group were not statistically different in age or FEV 1 % pred (11.1 vs 10 yrs and 78% vs 75%). 14 patients were culture positive in both UA and LA, 10 of which had matched pathogens and 4 were unmatched. 20 were matched culture negative. The range of pathogens and where they were isolated are shown in the Table, some samples had more than one isolate. Note the Table shows concordance for same pathogens Conclusion In PCD, pathogens are isolated far more commonly from the UA than the LA. The clinical impact of these pathogens in the long term is unknown. 11 (16%) had PA in UA with only 2 of these having PA in their LA. We speculate that the UA may be, at least in some children, the source of LA infection. Clinical trials of eradication therapy after positive nasal cultures are indicated

P106 Sputum Induction Reduces The Need For Bronchoscopy In School-aged Children With Cystic Fibrosis

Background Early detection of organisms such as Pseudomonas aeruginosa in CF is essential for successful eradication but is difficult in children, relying largely on non-invasive methods such as cough swabs (C/S) with sub-optimal sensitivity and specificity. Bronchoalvelolar lavage (BAL) remains the gold standard but disadvantages are its invasive nature, high cost and inability to be performed frequently. Sputum induction (SI) has previously been reported as a useful and safe technique in young children with CF, but it is not yet widely used. Hypothesis As part of a quality improvement initiative, we hypothesised that SI would reduce the need for BAL in school-aged CF children with deteriorating lung function and no significant bacterial growth on CS. Methods After CS and bronchodilator, 7% hypertonic saline was nebulised via an ultrasonic Ultraneb (DeVilbiss Healthcare) for 15 min. Spirometry was performed pre, post and at 5 min intervals throughout. Sputum was collected at 5 min intervals, and at the end of the procedure physiotherapy was performed to collect more sputum. If a child was unable to expectorate then a CS or oropharyngeal (OP) suction was performed. Results 39 children (41% male), median age 11 years (range 5–16 years), median FEV 1 85% (range 39–112%) performed SI from June 2102 to July 2014. Significant bronchoconstriction occurred in 11%. 2 adverse events occurred (vomiting and dizziness). The procedure took a mean of 90 min including equipment set up and cleaning. 34/39 (87%) expectorated a sputum sample of which 15 (38.5%) had a positive bacterial culture; only 3 of these patients (20%) grew the same organism on the preceding CS. Five patients avoided planned BAL due to a positive SI result and 2 avoided an admission for intravenous antibiotics. Conclusion SI is well tolerated in the majority of school-aged children with CF. It has a higher rate of positive bacterial culture than same-day CS and, in this cohort, avoided the need for bronchoscopy in a significant proportion. It is a time-consuming procedure, but based on these data, we consider that establishing SI as a clinical procedure will be a priority for our service.

51 The impact of coliforms isolated from cough swabs from infants under the age of one year with cystic fibrosis

51 The impact of coliforms isolated from cough swabs from infants under the age of one year with cystic fibrosis

Paranasal sinus pathogens in children with cystic fibrosis: Do they relate to lower respiratory tract pathogens and is eradication successful?

BackgroundThe study aims were to assess the association of microflora between the paranasal sinus and the lower airways of children attending a regional paediatric cystic fibrosis centre and to determine the performance of an eradication treatment protocol for positive paranasal sinus samples. MethodPaired nasal lavage and lower airway samples (cough swabs or sputum) were taken from 54 children with cystic fibrosis (median age 11years). Positive paranasal sinus samples received eradication treatment, using oral and sinonasal nebulised antibiotics. ResultsA correlation between paranasal sinus and lower airways was detected in 33/54 paired timed samples (p<0.02). Of 4/54 children who reported sinus symptoms, only 2 had paranasal sinus positive samples. 28 positive nasal lavage samples cultured 8 Pseudomonas aeruginosa (PA), 8 Staphylococcus aureus (SA) and 12 other bacterial pathogens. Eradication using sinonasal nebulised antibiotics and oral antibiotics showed a success of 14/21 (67%) treated paranasal sinus positive samples at 1month & 3months after treatment. Success rate was 75% in the PA group and 71% in the SA group. Ongoing monitoring with nasal lavage will continue. ConclusionThere was agreement between pathogens or lack of them found in the paranasal sinus and lower airways. Paranasal infection is often asymptomatic in children with cystic fibrosis. The eradication protocol for paranasal sinus pathogens had a good success rate.

How to use: bacterial cultures in diagnosing lower respiratory tract infections in cystic fibrosis

Respiratory infections are the leading cause of morbidity and mortality in cystic fibrosis. Certain bacteria, such as Pseudomonas aeruginosa, are associated with a worse clinical outcome than others, but can...

Sampling and Decontamination Method for Culture of Nontuberculous Mycobacteria in Respiratory Samples of Cystic Fibrosis Patients

We confirmed that chlorhexidine decontamination yielded more nontuberculous mycobacteria than did the N-acetyl-l-cysteine-NaOH-oxalic acid procedure from respiratory samples of cystic fibrosis patients on solid cultures. However, this improved recovery is mostly balanced if the latter is combined with liquid culture. Furthermore, none of the 145 cough swabs, used to sample young children, cultured positive, suggesting that swabs are low-quality samples.

The efficacy of cough plates in the identification of bacterial pathogens in children with cystic fibrosis

BackgroundIdentification of bacterial pathogens is paramount for prompt and effective treatment of respiratory exacerbations in children with cystic fibrosis (CF). This can be a challenge in non-expectorating patients as reliability...

101 Microbial communities and interactions in chronic lung infection in cystic fibrosis patients

Introduction and Aims: Although a number of studies have characterized airway microbiota composition in healthy and CF adult populations, limited data is available for the paediatric population. The aim of this study was to define, using culture based methods, the composition of the airway microbiota in age-matched healthy and CF paediatric groups. Methods: Induced sputum samples (CF) and cough swabs (CF, age-matched healthy volunteers) were collected and processed using both aerobic and strict anaerobic bacteriological culture techniques. Bacteria within the samples were detected by plating on selective agars and identified by PCR and sequencing of 16S ribosomal RNA genes. Results: Samples were collected from 21 healthy volunteers (mean (SD) age 11.0 (3.5) yrs; 13M:8F) and from 12 children with CF (mean (SD) age 12.8 (3.2) yrs; 6M:6F) when clinically stable. Bacteria were detected in all samples from CF patients and in 18/21 (86%) healthy volunteers. Aerobic bacteria from genera including Streptococcus, Staphylococcus, Pseudomonas and Haemophilus were detected in both cohorts with Pseudomonas [CF, n = 2/12 (17%); control, n = 1/21 (5%)] and Haemophilus [CF, n = 7/12 (58%); control n = 4/21 (19%)] present in a greater number of CF patients compared to controls. Anaerobic bacteria from genera including Prevotella, Veillonella, and Actinomyces were detected in both cohorts. Conclusion: Aerobic and anaerobic bacteria have been detected by culture in the lungs of children with CF and healthy children. Pseudomonas and Haemophilus, recognised as pathogens in CF patients, were more prevalent in CF patients compared to controls. Funded by US-Ireland Project Partnership Grant.

100 Comparison of airway microbiota composition in healthy children and children with CF

Introduction and Aims: Although a number of studies have characterized airway microbiota composition in healthy and CF adult populations, limited data is available for the paediatric population. The aim of this study was to define, using culture based methods, the composition of the airway microbiota in age-matched healthy and CF paediatric groups. Methods: Induced sputum samples (CF) and cough swabs (CF, age-matched healthy volunteers) were collected and processed using both aerobic and strict anaerobic bacteriological culture techniques. Bacteria within the samples were detected by plating on selective agars and identified by PCR and sequencing of 16S ribosomal RNA genes. Results: Samples were collected from 21 healthy volunteers (mean (SD) age 11.0 (3.5) yrs; 13M:8F) and from 12 children with CF (mean (SD) age 12.8 (3.2) yrs; 6M:6F) when clinically stable. Bacteria were detected in all samples from CF patients and in 18/21 (86%) healthy volunteers. Aerobic bacteria from genera including Streptococcus, Staphylococcus, Pseudomonas and Haemophilus were detected in both cohorts with Pseudomonas [CF, n = 2/12 (17%); control, n = 1/21 (5%)] and Haemophilus [CF, n = 7/12 (58%); control n = 4/21 (19%)] present in a greater number of CF patients compared to controls. Anaerobic bacteria from genera including Prevotella, Veillonella, and Actinomyces were detected in both cohorts. Conclusion: Aerobic and anaerobic bacteria have been detected by culture in the lungs of children with CF and healthy children. Pseudomonas and Haemophilus, recognised as pathogens in CF patients, were more prevalent in CF patients compared to controls. Funded by US-Ireland Project Partnership Grant.

105 Adaptation of Pseudomonas aeruginosa in the CF host: Link between laboratory findings and the clinic?

Objectives: Several highly transmissible and virulent genotypes of Pseudomonas aeruginosa have been recognised in the UK including the Liverpool, Midlands and Manchester genotypes and Clone C. It has been suggested that patients colonised with a transmissible genotype may have a poorer prognosis and increased treatment needs. We describe the clinical features of patients who isolated P. aeruginosa clone C in our paediatric CF centre. Methods: The hospital microbiology database was used to identify the patients. There were five isolations from five patients (four boys, aged 1−12 years, mean 4.4 years). All isolations were new, obtained from cough swabs performed at routine clinics. Four patients had new wet cough, one of whom had reduced lung function. One patient had no new clinical features. Four patients received intravenous antibiotics and one patient oral antibiotics. The organisms were sensitive to standard antipseudomonal antibiotics. The patients were removed from clinic and seen separately until confirmed negative for infection. Four patients remained free of infection in the one year following isolation. Three patients underwent bronchoscopy and BAL was culture negative. One patient had subsequent second isolation in the same year. The frequency of pre and post pseudomonas isolation respiratory exacerbations remains similar. All five are on conventional physiotherapy with no additional requirement of pharmacological treatment of chest disease. Conclusion: P. aeruginosa clone C isolates in our centre are currently sensitive to standard antibiotics. We have found no evidence of increased virulence or that the organism is overtly transmissible.

WS1.4 Significant bacterial infection missed using cough swabs compared to bronchoalveolar lavage in 1-year old newborn screened CF infants

WS1.4 Significant bacterial infection missed using cough swabs compared to bronchoalveolar lavage in 1-year old newborn screened CF infants

104 Clinical profile of Pseudomonas aeruginosa clone C infection in CF children

Objectives: Several highly transmissible and virulent genotypes of Pseudomonas aeruginosa have been recognised in the UK including the Liverpool, Midlands and Manchester genotypes and Clone C. It has been suggested that patients colonised with a transmissible genotype may have a poorer prognosis and increased treatment needs. We describe the clinical features of patients who isolated P. aeruginosa clone C in our paediatric CF centre. Methods: The hospital microbiology database was used to identify the patients. There were five isolations from five patients (four boys, aged 1−12 years, mean 4.4 years). All isolations were new, obtained from cough swabs performed at routine clinics. Four patients had new wet cough, one of whom had reduced lung function. One patient had no new clinical features. Four patients received intravenous antibiotics and one patient oral antibiotics. The organisms were sensitive to standard antipseudomonal antibiotics. The patients were removed from clinic and seen separately until confirmed negative for infection. Four patients remained free of infection in the one year following isolation. Three patients underwent bronchoscopy and BAL was culture negative. One patient had subsequent second isolation in the same year. The frequency of pre and post pseudomonas isolation respiratory exacerbations remains similar. All five are on conventional physiotherapy with no additional requirement of pharmacological treatment of chest disease. Conclusion: P. aeruginosa clone C isolates in our centre are currently sensitive to standard antibiotics. We have found no evidence of increased virulence or that the organism is overtly transmissible.

Importance of bacteriology in upper airways of patients with Cystic Fibrosis

Recently the influence of the upper airways (UAW) on the general health of a patient with Cystic Fibrosis (CF) has been acknowledged. Surprisingly the microbiology of the upper compartment of the airways receives barely any attention in the treatment of CF. The aim of the present study was to investigate the microbiology of the upper airways in adult patients with CF, to correlate these findings with cultures from the lower airways (LAW) and with clinical characteristics. In this cross-sectional study bacteriological and clinical data were gathered from 104 adult patients with CF. UAW samples for culture were collected by nasal lavage and middle meatal swabs; LAW cultures were performed on expectorated sputum or cough swabs. Each patient performed the Rhinosinusitis Outcome Measure (RSOM-31). In 72 patients (69.2%) UAW cultures yielded microorganisms other than normal nasal flora and in 50 patients (48.1%) Pseudomonas aeruginosa grew from the UAW cultures. Similarity between UAW and LAW cultures was determined in 50.0% of these 72 patients. In 3 patients P. aeruginosa was cultured from the UAW after successful eradication of P. aeruginosa from the LAW. P. aeruginosa in the UAW did not influence symptoms of sinonasal disease compared to other microorganisms. Comparison of UAW and LAW cultures in adult patients with CF showed one or more concordant microorganism in 50.0% of the patients. P. aeruginosa was most frequently cultured from the UAW. P. aeruginosa can be cultured from the UAW after eradication therapy which may suggest persistence of P. aeruginosa in the UAW. We feel this is may be a motive to include the UAW in eradication therapy in Cystic Fibrosis.

Cough swabs should not be used to isolate non-tuberculous mycobacteria in children with cystic fibrosis

Non-tuberculous mycobacterium (NTM) account for 13% of cystic fibrosis (CF)-related respiratory infections and present a major therapeutic challenge.1 There is increasing evidence to suggest an adverse prognostic significance of NTM,...