"Pathogen Eradication" and "Emerging Pathogens": Difficult Definitions in Cystic Fibrosis.

Infection is a common complication of cystic fibrosis (CF) airway disease. Current treatment approaches include early intervention with the intent to eradicate pathogens in the hope of delaying the development of chronic infection and the chronic use of aerosolized antibiotics to suppress infection. The use of molecules that help restore CFTR (cystic fibrosis transmembrane conductance regulator) function, modulate pulmonary inflammation, or improve pulmonary clearance may also influence the microbial communities in the airways. As the pipeline of these new entities continues to expand, it is important to define when key pathogens are eradicated from the lungs of CF patients and, equally important, when new pathogens might emerge as a result of these novel therapies.

Snow angels - the microbiology of freshly fallen snow: implications for immunocompromised patients.

The frequency of seasonal snowfall results in the transient covering of gardens/amenity sites/open public spaces, which encourages recreational interaction mainly with children. No data is available demonstrating the microbiological composition of such fallen snow and therefore a study was undertaken to examine the microbiology of snow from 37 sites, estimating (i) total viable count (TVC), (ii) identification of bacteria, and (iii) the presence of Pseudomonas aeruginosa. Mean TVC count of 8.3 colony-forming units (cfu)/ml snow melt water, 51.7 cfu/ml, 865 cfu/ml and 2,197 cfu/ml, was obtained for public amenity sites, domestic gardens, public open spaces and melting snow from public footpaths, respectively. No bacterial organisms (<10 cfu/ml) were detected in 5/14 (35.7%) open public spaces, 2/5 (40%) amenity sites and in 1/10 (10%) domestic gardens. Pseudomonas aeruginosa was not detected from any snow sample examined. Bacterial diversity consisted of 15 bacterial species (11 Gram-positive/four Gram-negative). The six Gram-positive genera identified from snow were Actinomyces, Bacillus, Brevibacillus, Micrococcus, Staphylococcus and Streptococcus. The four Gram-negative genera identified were Enterobacter, Pantoea, Pseudomonas and Xanthomonas. Bacillus licheniformis was the most commonly isolated organism from snow; it was isolated from every snow type. Snow may contain a diverse range of bacteria, many of which are capable of causing human infections.

Case Report: The Conundrum of What to Pick? Antibiotic Susceptibility Variability in Burkholderia cenocepacia in Cystic Fibrosis: Implications for Antibiotic Susceptibility Testing and Treatment.

Within cystic fibrosis microbiology, there is often mismatch between the antibiotic susceptibility result of an isolated bacterial pathogen and the clinical outcome, when the patient is treated with the same antibiotic. The reasoning for this remains largely elusive. Antibiotic susceptibility to four antibiotics (ceftazidime, meropenem, minocycline and trimethoprim-sulfamethoxazole) was determined in consecutive isolates (n = 11) from an adult cystic fibrosis patient, over a 63 month period. Each isolate displayed its own unique resistotype. The first isolate was sensitive to all four antibiotics, in accordance with Clinical and Laboratory Standards Institute methodology and interpretative criteria. Resistance was first detected at four months, showing resistance to ceftazidime and meropenen and intermediate resistance to minocycline and trimethoprim-sulfamethoxazole. Pan resistance was first detected at 18 months (resistotype IV), with three resistotypes (I, II and III) preceding this complete resistotype. The bacterium continued to display further antibiotic susceptibility heterogeneity for the next 45 months, with the description of an additional seven resistotypes (resistotypes V-XI). The Relative Resistance Index of this bacterium over the 63 month period showed no relationship between the development of antibiotic resistance and time. Adoption of mathematical modelling employing multinomial distribution demonstrated that large numbers of individual colony picks (>40/sputum), would be required to be 78% confident of capturing all 11 resistotypes present. Such a requirement for large numbers of colony picks combined with antibiotic susceptibility-related methodological problems creates a conundrum in biomedical science practice, in providing a robust assay that will capture antibiotic susceptibility variation, be pragmatic and cost-effective to deliver as a pathology service, but have the reliability to help clinicians select appropriate antibiotics for their patients. This study represents an advance in biomedical science as it demonstrates potential variability in antibiotic susceptibility testing with Burkholderia cenocepacia. Respiratory physicians and paediatricians need to be made aware of such variation by biomedical scientists at the bench, so that clinicians can contextualise the significance of the reported susceptibility result, when selecting appropriate antibiotics for their cystic fibrosis patient. Furthermore, consideration needs to be given in providing additional guidance on the laboratory report to highlight this heterogeneity to emphasise the potential for misalignment between susceptibility result and clinical outcome.

The Microbiology of Non-aeruginosa Pseudomonas Isolated From Adults With Cystic Fibrosis: Criteria to Help Determine the Clinical Significance of Non-aeruginosa Pseudomonas in CF Lung Pathology.

Introduction: There is a paucity of reports on non-aeruginosa Pseudomonas (NAPs) in cystic fibrosis, hence this study wished 1). to examine the diversity/frequency of NAPs in an adult CF population, 2) to compare/contrast the microbiology and genomics of NAPs to P. aeruginosa and 3) to propose clinical and laboratory criteria to help determine their clinical significance in CF lung pathology. Materials and Methods: Microbiological data was examined from 100 adult patients with cystic fibrosis from birth to present (31/12/2021), equating to 2455 patient years. 16S rDNA phylogenetic relatedness of NAPs was determined, as well as bioinformatical comparison of whole genomes of P. aeruginosa against P. fluorescens. Results: Ten species were isolated from this patient cohort during this time period, with three species, i.e., P. fluorescens, P. putida and P. stutzeri, accounting for the majority (87.5%) of non-aeruginosa reports. This is the first report of the isolation of P. fragi, P. nitroreducens, P. oryzihabitans and P. veronii in patients with cystic fibrosis. The mean time to first detection of any non-aeruginosa species was 183 months (15.25 years) [median = 229 months (19.1 years)], with a range from 11 months to 338 months (28.2 years). Several of the NAPs were closely related to P. aeruginosa. Discussion: NAPs were isolated infrequently and were transient colonisers of the CF airways, in those patients with CF in which they were isolated. A set of ten clinical and laboratory criteria are proposed to provide key indicators, as to the clinical importance of the non-aeruginosa species isolated.

Delafloxacin--A novel fluoroquinolone for the treatment of ciprofloxacin-resistant Pseudomonas aeruginosa in patients with cystic fibrosis.

INTRODUCTION: Fluoroquinolone antibiotics, namely ciprofloxacin and levofloxacin, play an important role in treating infection in cystic fibrosis (CF) and ciprofloxacin remains the last widely used and orally available antipseudomonal agent. Recently, a new fluoroquinolone, delafloxacin, has been approved by the FDA for the indication of Acute Bacterial Skin and Skin Structure Infections (ABSSSI). This antibiotic is a novel dual-targeting anionic fluoroquinolone and differs from previous agents in its class, as it lacks a protonatable substituent. To date, there are no reports of its use or activity against Pseudomonas aeruginosa in CF. Alarmingly, fluoroquinolone resistance is increasing among CF P aeruginosa isolates. The aims of the study were to (a) examine in vitro susceptibility of delafloxacin against a population of P. aeruginosa (n = 52) isolated from adult CF patients at our CF centre, (b) to compare delafloxacin and ciprofloxacin in vitro susceptibilities against CF P. aeruginosa and (c) to evaluate where delafloxacin may add benefit in treating CF P aeruginosa. METHODS: In vitro susceptibilities were examined on 52 non-mucoid P. aeruginosa and P. aeruginosa ATCC™ 27853 reference strain, by employing Etest® gradient test strips for delafloxacin (range:0.002 - 32 mg/L) and ciprofloxacin (0.002 - 32 mg/L), as per manufacturer's instructions (Biomerieux). RESULTS: MIC range, MIC50 and MIC90 for delafloxacin were 0.064 â†’ 32 mg/L, 0.56 mg/L and 2.19 mg/L, respectively. For ciprofloxacin, these were 0.047 â†’ 32 mg/L, 1.69 mg/L and 8.0 mg/L, respectively. Overall, isolates were statistically more sensitive to delafloxacin (p = 0.0005) than ciprofloxacin. Of note, 4/12 (33.3%) isolates with intermediate resistance to ciprofloxacin were sensitive to delafloxacin. Similarly, 10/28 (35.7%) isolates resistant to ciprofloxacin were sensitive to delafloxacin, with only 17.9% isolates resistant to ciprofloxacin, resistant to delafloxacin. CONCLUSION: Given similar breakpoints of these fluoroquinolones, these data show that delafloxacin has greater activity than ciprofloxacin. While delafloxacin and ciprofloxacin were equally effective with sensitive isolates, the value of delafloxacin was noted with more resistant isolates to ciprofloxacin. While ciprofloxacin should remain the first line fluoroquinolone for treating CF P aeruginosa, delafloxacin shows potential in treating ciprofloxacin-resistant P aeruginosa.

The virtual CF clinic: Implications for sputum microbiology.

The COVID19 pandemic has shifted the paradigm of how outpatient clinics are delivered within CF care, resulting in a significant reduction of patient visits to CF centres. One consequence of this has been a reduction in the number of sputa/cough swabs that patients submit for routine analysis. This report examines why it is important to maintain optimal sputum microbiology and explores (i). the microbiological efficiency of postal submission of sputum specimens from the community and (ii) the regulatory conditions that must be met through postal submission of respiratory specimens. Virtual clinics have now been established within CF care and it is incumbent on each speciality within the CF MDT to explore ways to nurture and support their individual contribution to the success of the virtual clinic. Within microbiology, adopting innovative approaches to sputum collection in the community and transportation via postal services will allow for continued microbiological vigilance thereby supporting patient safety.

Nebuliser hygiene in cystic fibrosis: evidence-based recommendations.

Nebulised therapies are extensively used in the daily therapeutic management of cystic fibrosis both for mucociliary clearance and for the management of chronic infections. Extensive developments have been made in relation to nebulised drug delivery mechanisms and drug formulations, and guidelines have been prepared that have addressed the appropriate use of such therapies. However, due to these developments, a plethora of nebuliser devices and drug chambers exist, and frequently, the limited guidance provided in relation to nebuliser hygiene is to follow manufacturers' instructions. Such instructions are inconsistent and at times confusing, translating to an increase in the burden associated with nebuliser maintenance. An evidence-based universal guideline relating to nebuliser care and hygiene is urgently required that is applicable to both at-home use and inpatient use. This article reviews the scientific literature in order to propose an evidence-based approach to nebuliser hygiene to ensure optimum drug delivery, and infection prevention and control. EDUCATIONAL AIMS: To understand the reasons why nebuliser hygiene is important.To give an overview of the current nebuliser care instructions that have been described by manufacturers, societies and the scientific literature.To outline the current nebuliser hygiene practices used by persons with cystic fibrosis in the home and hospital settings.To highlight areas that need further evaluation to promote optimum nebuliser care.To establish an evidence-based guideline for nebuliser hygiene in relation to cystic fibrosis.

Steam disinfection of toothbrushes from patients with cystic fibrosis: Evidence-based recommendations.

BACKGROUND: Patients with cystic fibrosis have increased morbidity/mortality due to chronic respiratory infections, which primarily originate from the environment. Infection prevention and control emphasize the importance of cleaning and disinfection of respiratory devices, however, there is a paucity of guidance on toothbrush hygiene, which have been shown to be a source of cystic fibrosis (CF) pathogens. METHODS: This study examined steam disinfection of toothbrushes contaminated with clinically significant CF isolates (n = 80; Gram positive = 33; Gram negative = 32, and non-tuberculous mycobacteria = 6) and yeasts (n = 9), as well as oral streptococci (n = 26) and environmental Pseudomonas aeruginosa (n = 12). RESULTS: Steam disinfection eradicated all organisms tested, as well as all organisms in CF sputum applied to toothbrushes. CONCLUSIONS: Steam disinfection offers a relatively simple, cheap and available method of eliminating non-spore-forming CF pathogens on toothbrushes. Toothbrushes should be thoroughly rinsed after each use before steam disinfection, to remove plaque, epithelial cells, and residual toothpaste. Toothbrushes should be steam disinfected after each use employing a baby bottle steam disinfector, adhering to manufacturers' operating instructions and stored in the disinfector until next used within 12 to 24 hours. Toothbrushes should be replaced every 3 to 4 months, or sooner if the bristles look worn out, as well as every time a pulmonary exacerbation occurs or every time the patient is treated for a pulmonary/throat infection. Steam disinfection of toothbrushes is crucial when the patient is undergoing eradication regimes for P. aeruginosa and methicillin-resistant Staphylococcus aureus, so that the patient does not become reinfected from this source, thereby aiding eradication and enhancing patient safety.

Who's at The Door? - Surface Contamination of Door Frames in a Single-Bedded In-Patient Adult Cystic Fibrosis (CF) Unit.

The Gram-negative bacterium, Pseudomonas aeruginosa, is a major respiratory pathogen in patients with cystic fibrosis (CF), with an associated increase in morbidity and mortality. Consequently, infection prevention and control (IPC) plays an important role within health care in order to minimize the risk of cross-infection of this organism amongst patients and the hospital environment. It was the aim of this study to examine bacterial contamination of the health estate of CF in-patients' single-bedded rooms and related environments (n=40). Twelve bacterial genera were identified, six being Gram-positive (Brevibacterium, Dermacoccus, Micrococcus, Rothia, Staphylococcus and Streptococcus), and six being Gram-negative (Acinetobacter, Citrobacter, Klebsiella, Moraxella, Pantoea and Pseudoxanthomonas). None of the organisms identified were considered of particular clinical significance to CF patients. The CF lung and associated sputa may be important reservoirs of Pseudomonas aeruginosa, with potential for spill-over into the health care estate. In the aftermath of the Pseudomonas neonatal outbreak at Altnagelvin and the Royal Jubilee Maternity Hospitals, where there was heightened IPC awareness regarding the presence of this bacterium, it is encouraging to note its absence from the CF-health care estate examined.

Public Health Bacteriology of Commercially Composted Domestic Food and Garden Waste by the 11 Councils in Northern Ireland - Persistence Of Clostridium perfringens and Implications for Local Food Safety.

BACKGROUND: New legislation has been introduced in Northern Ireland from April 2017, requiring domestic households to recycle all domestic food waste items. The purpose of this study was to examine the bacteriology of compost derived from this source which is supplied free-of-charge to the public for horticultural use. METHODS: Municipal compost samples were compared microbiologically with commercial garden compost samples, examining total viable count and diversity of bacteria cultivated. RESULTS: The municipal compost had a mean Total Viable Count (TVC) of 1.53 × 108 colony forming units (cfu)/ g compost, whereas the commercial garden compost had a mean TVC of 4.5 × 107 cfu/g compost. Campylobacter, Salmonella and Listeria were not isolated from any compost. Twenty-three bacterial genera were represented amongst the 46 organisms recovered. Of these, Pseudomonas aeruginosa and Clostridium perfringens were the most clinically significant. DISCUSSION: The application of municipal compost to cultivate non-food plants, such as roses and flowers presents minimal risk, provided safe handling practices are adopted and hands are thoroughly washed and dried afterwards. However, if applied to soil growing food produce, it is important that municipal compost does not enter the food chain without an effective critical control point which would prevent germination of spores of Clostridium perfringens. Risk may be increased in products such as marinades, home canning, home bottling and associated products. These methods of food preparation are common in ethnic Eastern European populations in Northern Ireland, where awareness of risk needs to be increased.

Lung function and disease severity in cystic fibrosis patients heterozygous for p.Arg117His.

Expression of p.Arg117His cystic fibrosis (CF) transmembrane conductance regulator is influenced by a polythymidine (poly-T) tract and a thymidine-guanine (TG) repeat on intron 9, which vary in length and affect exon 10 skipping. We compared clinical characteristics and the rate of progression of lung disease of CF patients carrying the p.Arg117His mutation with different intron 9 varying sequences (poly-T) and mutation classes in trans. Data were collected from patients in Northern Ireland, UK, including diagnostic features, sweat chloride, nutritional status, sputum microbiology, CF-related complications and lung function. Poly-T and TG repeats were determined by PCR. Forced expiratory volume in 1 s (FEV1) decline was determined from linear regression of FEV1 measurements of patients over time. We identified 62 patients with p.Arg117His, 55 with a class I/II mutation in trans and six with p.Arg117His/p.Gly551Asp. 42 patients had 5T and 13 had 7T. All patients had 12 TG repeats. Patients with p.Arg117His-5T had greater lung function decline, sweat chloride concentrations, pancreatic insufficiency and prevalence of Pseudomonas aeruginosa infection compared with patients with p.Arg117His-7T. Lung function decline and disease severity in p.Arg117His is determined by the poly-T tract length and identity of the mutation in trans. Patients with p.Arg117His-5T and a second class I/II mutation have a severity similar to p.Phe508del homozygous patients, although lung function decline is delayed to an older age. There may be linkage disequilibrium between p.Arg117His and 12 TG repeats.

MRSA eradication of newly acquired lower respiratory tract infection in cystic fibrosis.

UK cystic fibrosis (CF) guidelines recommend eradication of methicillin-resistant Staphylococcus aureus (MRSA) when cultured from respiratory samples. As there is no clear consensus as to which eradication regimen is most effective, we determined the efficacy of eradication regimens used in our CF centre and long-term clinical outcome. All new MRSA positive sputum cultures (n=37) that occurred between 2000 and 2014 were reviewed. Eradication regimen characteristics and clinical, microbiological and long-term outcome data were collected. Rifampicin plus fusidic acid was the most frequently used regimen (24 (65%) out of 37 patients), with an overall success rate of 79% (19 out of 24 patients). Eradication failure was more likely in patients with an additional MRSA-positive peripheral screening swab (p=0.03) and was associated with worse survival (p=0.04). Our results demonstrate the feasibility and clinical benefits of MRSA eradication. As peripheral colonisation was associated with lower eradication success, strategies combining systemic and topical treatments should be considered to optimise outcomes in CF patients.