Seasonality of acquisition of respiratory bacterial pathogens in young children with cystic fibrosis

Stenotrophomonas maltophilia in people with Cystic Fibrosis: a systematic review of prevalence, risk factors and management

To summarize the current knowledge of the clinical impact of Stenotrophomonas maltophilia (SM) in cystic fibrosis (CF) patients. A systematic review according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guideline recommendations, was performed through searches in PubMed and EMBASE databases, and CF National and International Registries websites from 2000 to 2022. Overall, 184 articles were initially retrieved, out of which 15 were selected and included in the review. Data form 6 Registries and 9 pertinent articles from the references of the studies selected were also considered, resulting in 30 studies in total. The prevalence of SM in patients with CF is increasing in Europe while it is declining in North America. The role of chronic colonization of SM on lung function and clinical status in CF patients is still under debate. The most recent studies suggested a pathogenic role of SM chronic infections in CF patients with an acceleration in lung function decline, an increase in hospitalization rates and an association with co-infection. Reflecting the uncertainty about the role of SM in CF, little is available about antibiotic therapeutic strategies for both acute exacerbations and chronic infections. Antimicrobial therapy should be performed in the acute exacerbations, while it may be reasonable to attempt eradication when the first colonization is identified. Nevertheless, it is not established which antibiotic regimen should be preferred, and overtreatment could contribute to the selection of antimicrobial-resistant strains. Further studies are warranted in this regard.

Modifier Factors of Cystic Fibrosis Phenotypes: A Focus on Modifier Genes

Although cystic fibrosis (CF) is recognized as a monogenic disease, due to variants within the CFTR (Cystic Fibrosis Transmembrane Regulator) gene, an extreme clinical heterogeneity is described among people with CF (pwCF). Apart from the exocrine pancreatic status, most studies agree that there is little association between CFTR variants and disease phenotypes. Environmental factors have been shown to contribute to this heterogeneity, accounting for almost 50% of the variability of the lung function of pwCF. Nevertheless, pwCF with similar CFTR variants and sharing the same environment (such as in siblings) may have highly variable clinical manifestations not explained by CFTR variants, and only partly explained by environmental factors. It is recognized that genetic variants located outside the CFTR locus, named "modifier genes", influence the clinical expression of the disease. This short review discusses the latest studies that have described modifier factors associated with the various CF phenotypes as well as the response to the recent CFTR modulator therapies.

Multidrug-Resistant Bacteria in Children and Adolescents with Cystic Fibrosis

In patients with cystic fibrosis (CF), multidrug-resistant (MDR) bacteria can predispose to exacerbations, limit the effectiveness of antibiotic treatments and promote the progression of lung disease. The aim of this retrospective study was to compare pulmonary exacerbations (Pex), hospitalizations, lung function and nutritional status in a group of children and adolescents with CF colonized by MDR bacteria and in a noncolonized control group. Overall, 7/54 pediatric patients (12.9%) were colonized by MDR bacteria and enrolled (3 with Achromobacter xyloxidans, 3 with Stenotrophomonas maltophilia and 1 with Burkholderia cepacia). The control group included 14 sex- and age-matched CF patients (8/14 colonized by Staphylococcus aureus, 2/14 by Pseudomonas aeruginosa, 2/14 by both microorganisms and 2/14 germ free). At the time of enrollment and 12 months before the first detection of the MDR microorganism, children colonized by MDR bacteria showed lower body mass index (BMI) and lower FEV₁/FVC compared to the control group. Over the previous year before the first detection, children colonized with MDR had more Pex compared to control group; those colonized by S. maltophilia experienced the highest number of Pex. In the 12 months following the first detection of MDR bacteria, all seven patients colonized by MDR had at least one Pex and patients colonized by S. maltophilia had the highest number (mean ± SD: 6 ± 2.6 vs. 1.7 ± 2.3). Our study suggests that CF pediatric patients infected by MDR bacteria have lower BMI, more obstructive disease and experience more exacerbations than patients without MDR bacteria. These differences are present even before being infected, suggesting that children and adolescents with more severe disease are predisposed to be colonized by MDR bacteria. S. maltophilia appeared to be the most aggressive pathogen. Further studies and the implementation of antimicrobial stewardship programs are necessary to clarify when and how to treat patients with CF and MDR bacteria in order to avoid the improper use of antibiotics and the development of antibiotic resistance.

Predicting risk-adjusted incidence rates of methicillin-resistant Staphylococcus Aureus and Pseudomonas Aeruginosa in cystic fibrosis programs in the United States

BACKGROUND

Healthcare-associated transmission of methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa occurs for people with cystic fibrosis (CF), but CF programs lack a process to monitor incidence rates (IRs). We assessed predictors of incident infections and created a model to determine risk-adjusted IRs for CF programs.

METHODS

Using the CF Foundation Patient Registry data for all patients from 2012 to 2015, coefficients for variables that predicted IRs were estimated. Hazard functions were then used to predict IRs of MRSA and P. aeruginosa for CF programs based on their patient and program characteristics. Predicted IRs were compared with observed IRs over multiple time intervals.

RESULTS

Multiple patient and program characteristics were identified as predictors of observed IRs. Our model's predicted IRs closely aligned with observed IRs for most CF programs. Alarm values (defined as observed IR > 95% confidence interval of predicted IR) were found at 5.9%, 5.9%, 6.0% (adult, pediatric, affiliate) of programs for MRSA and 3.0%, 1.7%, 0.0% (adult, pediatric, affiliate) of programs for P. aeruginosa.

CONCLUSIONS

We found patient and program characteristics that predicted MRSA and P. aeruginosa IRs. Our model accurately predicted risk-adjusted IRs of MRSA and P. aeruginosa. CF programs could use our model to monitor their IRs and potentially improve infection prevention and control.

Confounding Effect of Undergraduate Semester-Driven "Academic" Internet Searches on the Ability to Detect True Disease Seasonality in Google Trends Data: Fourier Filter Method Development and Demonstration

Background

Internet search volume for medical information, as tracked by Google Trends, has been used to demonstrate unexpected seasonality in the symptom burden of a variety of medical conditions. However, when more technical medical language is used (eg, diagnoses), we believe that this technique is confounded by the cyclic, school year-driven internet search patterns of health care students.

Objective

This study aimed to (1) demonstrate that artificial "academic cycling" of Google Trends' search volume is present in many health care terms, (2) demonstrate how signal processing techniques can be used to filter academic cycling out of Google Trends data, and (3) apply this filtering technique to some clinically relevant examples.

Methods

We obtained the Google Trends search volume data for a variety of academic terms demonstrating strong academic cycling and used a Fourier analysis technique to (1) identify the frequency domain fingerprint of this modulating pattern in one particularly strong example, and (2) filter that pattern out of the original data. After this illustrative example, we then applied the same filtering technique to internet searches for information on 3 medical conditions believed to have true seasonal modulation (myocardial infarction, hypertension, and depression), and all bacterial genus terms within a common medical microbiology textbook.

Results

Academic cycling explains much of the seasonal variation in internet search volume for many technically oriented search terms, including the bacterial genus term ["Staphylococcus"], for which academic cycling explained 73.8% of the variability in search volume (using the squared Spearman rank correlation coefficient, P<.001). Of the 56 bacterial genus terms examined, 6 displayed sufficiently strong seasonality to warrant further examination post filtering. This included (1) ["Aeromonas" + "Plesiomonas"] (nosocomial infections that were searched for more frequently during the summer), (2) ["Ehrlichia"] (a tick-borne pathogen that was searched for more frequently during late spring), (3) ["Moraxella"] and ["Haemophilus"] (respiratory infections that were searched for more frequently during late winter), (4) ["Legionella"] (searched for more frequently during midsummer), and (5) ["Vibrio"] (which spiked for 2 months during midsummer). The terms ["myocardial infarction"] and ["hypertension"] lacked any obvious seasonal cycling after filtering, whereas ["depression"] maintained an annual cycling pattern.

Conclusions

Although it is reasonable to search for seasonal modulation of medical conditions using Google Trends' internet search volume and lay-appropriate search terms, the variation in more technical search terms may be driven by health care students whose search frequency varies with the academic school year. When this is the case, using Fourier analysis to filter out academic cycling is a potential means to establish whether additional seasonality is present.

Advances in the Microbiology of Stenotrophomonas maltophilia

Stenotrophomonas maltophilia is an opportunistic pathogen of significant concern to susceptible patient populations. This pathogen can cause nosocomial and community-acquired respiratory and bloodstream infections and various other infections in humans. Sources include water, plant rhizospheres, animals, and foods. Studies of the genetic heterogeneity of S. maltophilia strains have identified several new genogroups and suggested adaptation of this pathogen to its habitats. The mechanisms used by S. maltophilia during pathogenesis continue to be uncovered and explored. S. maltophilia virulence factors include use of motility, biofilm formation, iron acquisition mechanisms, outer membrane components, protein secretion systems, extracellular enzymes, and antimicrobial resistance mechanisms. S. maltophilia is intrinsically drug resistant to an array of different antibiotics and uses a broad arsenal to protect itself against antimicrobials. Surveillance studies have recorded increases in drug resistance for S. maltophilia, prompting new strategies to be developed against this opportunist. The interactions of this environmental bacterium with other microorganisms are being elucidated. S. maltophilia and its products have applications in biotechnology, including agriculture, biocontrol, and bioremediation.

Influences of environmental exposures on individuals living with cystic fibrosis

INTRODUCTION

Natural, social, and constructed environments play a critical role in the development and exacerbation of respiratory diseases. However, less is known regarding the influence of these environmental/community risk factors on the health of individuals living with cystic fibrosis (CF), compared to other pulmonary disorders.

AREAS COVERED

Here, we review current knowledge of environmental exposures related to CF, which suggests that environmental/community risk factors do interact with the respiratory tract to affect outcomes. Studies discussed in this review were identified in PubMed between March 2019 and March 2020. Although the limited data available do not suggest that avoiding potentially detrimental exposures other than secondhand smoke could improve outcomes, additional research incorporating novel markers of environmental exposures and community characteristics obtained at localized levels is needed.

EXPERT OPINION

As we outline, some environmental exposures and community characteristics are modifiable; if not by the individual, then by policy. We recommend a variety of strategies to advance understanding of environmental influences on CF disease progression.

Respiratory viral infections in Western Australians with cystic fibrosis

BACKGROUND

Viral respiratory infections (VRI) in people living with Cystic fibrosis (CF) is less well understood than respiratory bacterial infections, particularly adults with CF and few studies have compared children with adults. This study evaluated the frequency of respiratory viruses in patients with cystic fibrosis (CF) in Western Australia (WA). We determined the VRI in CF and compared them with non-CF patients. Further, we compared CF patients that were hospitalised with those that were not.

PATIENTS/METHODS

Nucleic acid from sputum of 157 CF and 348 non-CF patients was analysed for influenzavirus A (Flu A) and B, (Flu B), respiratory syncytial virus (RSV), human metapneumovirus (hMPV), human rhinovirus (RV), and parainfluenza viruses (PIV 1-3) by RT-PCR, during the 2016 winter respiratory season.

RESULTS

No significant difference in the frequency of respiratory virus detection between CF and non-CF patients was found. RV was the most frequently detected virus in CF patients, and in hospitalised CF. RSV and hMPV were found less frequently in CF patients and RSV was not found in any hospitalised CF patient. A trend for fewer influenzavirus detections in adult CF patients was observed, however the trend was opposite for paediatric patients. RV and Flu A were the most common viruses detected in hospitalised CF patients.

CONCLUSION

There was no significant difference in VRI between CF and non-CF patients. RV and influenza A were most commonly found in hospitalised CF patients, suggesting that infection with these viruses may contribute to hospitalisation for CF respiratory exacerbations.

Achromobacter spp. healthcare associated infections in the French West Indies: a longitudinal study from 2006 to 2016

Background

Bacteria of the Achromobacter genus, more particularly xylosoxidans species, are responsible for various healthcare associated infections (HAI) which are increasingly described since the last decade. Cystic fibrosis (CF) patients are considered as potential reservoirs in hospitals. We performed a retrospective study to estimate the frequencies of Achromobacter spp. HAI among patients from French West Indies, to determine characteristics of infected patients and establish a possible link between CF and infections.

Methods

All adults with at least one Achromobacter spp. positive sample and infection criteria in accordance with European official definitions of HAI, hospitalized in University Hospital of Martinique from 2006 to 2016 for more than 48 h, were included. Patient clinical features, immune status and underlying diseases were obtained from medical files. A list of CF patients was given by clinicians.

Antibiotic-susceptibility profiles of the strains were determined using an automated method.

Results

Mean incidence density was 0.038/1000 days of hospitalization. Achromobacter spp. HAI evolved as an endemic situation with a low but pretty much stable incidence rate over the 11-year observation period. An epidemic peak was noticed in 2013. Among the 66 included patients, 56.1% were immunocompetent and no one had CF. Pneumonia and bacteraemia were the two main HAI. Among the 79 isolated strains, 92.4% were resistant to at least 1 major antibiotic and 16.4% met the definition of multidrug-resistant bacteria.

Conclusions

This microorganism, little known in our country because of the scarcity of CF patients, represents a threat for both immunosuppressed and immunocompetent patients and a therapeutic challenge because of its high resistance.

Viral respiratory tract infections in young children with cystic fibrosis: a prospective full-year seasonal study

Background

Viral respiratory tract infections are common during early childhood. How they impact cystic fibrosis lung disease history in young children is poorly known. The principal aim of our study was to determinate respiratory tract infections frequency in this cystic fibrosis young population. Secondary outcomes were nature of viral agents recovered and impact of such infections.

Methods

We conducted a prospective cohort study of 25 children affected by cystic fibrosis and aged less than 2 years. Nasal samplings were taken systematically monthly or bimonthly with additional samples taken during respiratory tract infections episodes. Ten pathogens were tested by a combination of five duplex RT-PCRs or PCRs: influenza A and B, respiratory syncytial virus (RSV), metapneumovirus (MPV), rhinovirus/enterovirus (RV/EV)), coronavirus (HKU1, NL63, 229E and OC43), parainfluenza virus (1–4), adenovirus and bocavirus (Respiratory Multi-Well System MWS r-gene®, BioMérieux, Marcy l’Étoile, France). Cycle thresholds (CTs) were reported for all positive samples and considered positive for values below 40. Quantitative variables were compared using a nonparametric statistical test (Wilcoxon signed rank for paired comparisons). Pearson’s correlation coefficient (r) was used to assess relationships between two variables. Statistical analyses were performed using SAS v9.4 (SAS Institute, Cary, NC, USA) or GraphPad Prism V6.00 (GraphPad Software, La Jolla, CA, USA). The significance level was set at 0.05.

Results

The mean age at inclusion was 9.6 ± 6.7 months. The patients had 3.4 ± 1.7 respiratory tract infections episodes per child per year. Forty-four respiratory tract infections (69%) were associated with virus: rhinovirus and enterovirus (RV/EV) were implied in 61% of them and respiratory syncytial virus (RSV) in 14%. Only one patient required hospitalization for lower respiratory tract infections. 86% of the patients were treated by antibiotics for a mean of 13.8 ± 6.2 days. RSV infections (n = 6) were usually of mild severity.

Conclusions

Respiratory tract infections in young children with cystic fibrosis were of mild severity, rarely requiring hospitalization. Unsurprisingly, RV/EV were the most frequent agents. RSV-related morbidity seems low in this population. This raises the question of the usefulness of RSV preventive medication in this young population.

Pathogen acquisition in patients with cystic fibrosis receiving ivacaftor or lumacaftor/ivacaftor

BACKGROUND

The cystic fibrosis transmembrane conductance regulator (CFTR) modulators ivacaftor and lumacaftor/ivacaftor improve the status of existing infections in patients with cystic fibrosis (CF). It is unknown how well these drugs protect patients against incident infections. We hypothesized that CFTR modulator treatment would decrease new infections with Pseudomonas aeruginosa or Staphylococcus aureus.

METHODS

We retrospectively studied a single-center cohort of patients with CF during two time periods (2008-2011, Era 1) and (2012-2015, Era 2) based on the January 2012 approval of ivacaftor. Using Kaplan-Meier analysis, we compared the time to any new infection with P. aeruginosa, methicillin-resistant S. aureus (MRSA), or methicillin-sensitive S. aureus (MSSA) that was absent during a 2-year baseline. We stratified the analysis based on whether patients received ivacaftor or lumacaftor/ivacaftor during Era 2. We used the log-rank test and considered P < 0.05 statistically significant.

RESULTS

For patients receiving ivacaftor or lumacaftor/ivacaftor in Era 2, there was a statistically significant delay in the time to new bacterial acquisition in Era 2 vs. Era 1 ( P = 0.008). For patients who did not receive CFTR modulators, there was a trend toward slower acquisition of new bacterial infections in Era 2 compared to Era 1, but this was not statistically significant ( P = 0.10).

CONCLUSIONS

Patients receiving ivacaftor or lumacaftor/ivacaftor for CF had significantly delayed acquisition of P. aeruginosa and S. aureus after these drugs were released. This method for analyzing incident infections may be useful for future studies of CFTR modulators and bacterial acquisition in CF registry cohorts.

Biology and management of methicillin resistant Staphylococcus aureus in cystic fibrosis

Staphylococcus aureus is one of the earliest bacteria isolated from the respiratory tract in people with cystic fibrosis (CF). Its methicillin resistant form, MRSA, has gained attention due to the rapid increase in the last decades and worse outcomes with chronic infection. In the United States, prevalence of MRSA in CF is around 27%, but is much lower (3-18%) in most other countries. Methicillin is typically genetically encoded by the mecA gene, which encodes for an alternative penicillin binding protein (PRBa). This PRBa has low affinity to β-lactams, thereby enabling growth of S. aureus in the presence of penicillinase resistant penicillins and most other β-lactams. Non-mecA positive strains of MRSA, so-called borderline resistant (BORSA) have also been described. In addition to production of toxins, the virulence of S. aureus is conferred by its adaptability allowing persistence in face of antibiotic therapies and host defense. These adaptive growth mechanisms include small colony variants, biofilms, and growth under anaerobic conditions. Several reports have described successful eradication of MRSA, yet only two randomized trials of eradication during early infection have been conducted. A list of MRSA specific antibiotics with dosing relevant to CF patients is presented here. Many of these require special dosing in people with CF. Novel antibiotics are in trials for skin and soft tissue infections and it is unclear if and when those might be available for lung infections. Thus the best strategies for MRSA would be primary prevention.

Seasonal fluctuation of lung function in cystic fibrosis: A national register-based study in two northern European populations

Background

Many risk factors for lung disease in cystic fibrosis (CF) display a seasonal pattern yet it is unclear whether this is reflected in seasonal fluctuations in lung function.

Methods

We conducted a longitudinal study using CF registries in Denmark and the UK. 471 individuals with a median of 104 FEV₁ measurements per person and 7586 individuals with a median of nine FEV₁ measures per person were included from Denmark and the UK respectively. We estimated the effect of seasonality on percent predicted FEV₁ trajectories using mixed effects models whilst adjusting for clinically important covariates.

Results

We found no significant cyclical seasonal variation in lung function in either country. The maximum variation in percent predicted FEV₁ around the yearly average was estimated to be 0.1 percentage points (95%CI 0 to 0.21) and 0.14 percentage points (95%CI 0 to 0.29) in Denmark and the UK, respectively. When considering possible step-like changes between the four seasons, we found that lung function was higher in spring compared to winter in the UK (0.34 percentage points, 95%CI 0.1 to 0.59) though the difference was not of clinical significance.

Conclusion

In both the UK and Denmark there may be small seasonal changes in lung function but this effect is not of clinical importance.

•

It is not well understood how the four seasons affect lung function in CF.

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We performed a longitudinal analysis in the UK and Danish CF populations.

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Forty years of data were included in a comprehensive mixed effects models.

•

The seasonal variation was small and not clinically important.

Fatigue in Chronic Respiratory Diseases: Theoretical Framework and Implications For Real-Life Performance and Rehabilitation

Fatigue is a primary disabling symptom in chronic respiratory diseases (CRD) with major clinical implications. However, fatigue is not yet sufficiently explored and is still poorly understood in CRD, making this symptom underdiagnosed and undertreated in these populations. Fatigue is a dynamic phenomenon, particularly in such evolving diseases punctuated by acute events which can, alone or in combination, modulate the degree of fatigue experienced by the patients. This review supports a comprehensive inter-disciplinary approach of CRD-related fatigue and emphasizes the need to consider both its performance and perceived components. Most studies in CRD evaluated perceived fatigue as a trait characteristic using multidimensional scales, providing precious information about its prevalence and clinical impact. However, these scales are not adapted to understand the complex dynamics of fatigue in real-life settings and should be augmented with ecological assessment of fatigue. The state level of fatigue must also be considered during physical tasks as severe fatigue can emerge rapidly during exercise. CRD patients exhibit alterations in both peripheral and central nervous systems and these abnormalities can be exacerbated during exercise. Laboratory tests are necessary to provide mechanistic insights into how and why fatigue develops during exercise in CRD. A better knowledge of the neurophysiological mechanisms underlying perceived and performance fatigability and their influence on real-life performance will enable the development of new individualized countermeasures. This review aims first to shed light on the terminology of fatigue and then critically considers the contemporary models of fatigue and their relevance in the particular context of CRD. This article then briefly reports the prevalence and clinical consequences of fatigue in CRD and discusses the strengths and weaknesses of various fatigue scales. This review also provides several arguments to select the ideal test of performance fatigability in CRD and to translate the mechanistic laboratory findings into the clinical practice and real-world performance. Finally, this article discusses the dose-response relationship to training and the feasibility and validity of using the fatigue produced during exercise training sessions in CRD to optimize exercise training efficiency. Methodological concerns, examples of applications in selected diseases and avenues for future research are also provided.