Comorbidity between progressive familial intrahepatic cholestasis and atopic dermatitis in a 19-month-old child.

BMJ Case Rep. 2019 Oct 18;12(10):

Authors: Panasiti I, Briuglia S, Costa S, Caminiti L

Abstract
Atopic dermatitis (AD) is the most common chronic skin disease in children, with an increasing prevalence in the past three decades. Adequate treatment is prescribed for individual patient based on symptoms and disease severity. However, further underlying diagnosis should be researched when therapeutic strategies for symptoms fail and skin lesions and pruritus persist. We reported herein the case of a 19-month-old infant with a history of AD unresponsive to treatment due to the type 2 progressive familial intrahepatic cholestasis (PFIC). A new homozygous mutation of the ABCB11 gene was found. The severe pruritus, the early onset jaundice, poor growth and raised transaminase levels with normal gamma glutamyl transpeptidase have led to the suspicion of PFIC. The presence of severe AD and intrahepatic chronic cholestasis, both pruritus associated, could delay a proper diagnosis. To our knowledge, for the first time, a case of comorbidity between type 2 PFIC and AD-like disease had been described.

PMID: 31630127 [PubMed - in process]

Pro Con Debate - Infection prevention and control in cystic fibrosis: One size fits all The argument against.

Paediatr Respir Rev. 2019 Aug 21;:

Authors: Smyth AR, Smith SJ, Rowbotham NJ

Abstract
As awareness of the risks of cross infection has increased, infection prevention and control measures have become more draconian. Infection control measures can have a profound effect of the organisation and delivery of CF services and on the lives of people with CF outside the hospital. However, the consequences of inadequate infection control measures may be the permanent acquisition of a chronic infection which is virtually untreatable. Recommendations for infection prevention and control therefore must protect patients but should also be evidence-based and proportionate. This article will review the literature, juxtaposing evidence and popular practise.

PMID: 31629644 [PubMed - as supplied by publisher]

Azithromycin is the answer in paediatric respiratory medicine, but what was the question?

Paediatr Respir Rev. 2019 Aug 16;:

Authors: Bush A

Abstract
The first clinical indication of non-antibiotic benefits of macrolides was in the Far East, in adults with diffuse panbronchiolitis. This condition is characterised by chronic airway infection, often with Pseudomonas aeruginosa, airway inflammation, bronchiectasis and a high mortality. Low dose erythromycin, and subsequently other macrolides, led in many cases to complete remission of the condition, and abrogated the neutrophilic airway inflammation characteristic of the disease. This dramatic finding sparked a flurry of interest in the many hundreds of macrolides in nature, especially their anti-inflammatory and immunomodulatory effects. The biggest subsequent trials of azithromycin were in cystic fibrosis, which has obvious similarities to diffuse panbronchiolitis. There were unquestionable improvements in lung function and pulmonary exacerbations, but compared to diffuse panbronchiolitis, the results were disappointing. Case reports, case series and some randomised controlled trials followed in other conditions. Three trials of azithromycin in preschool wheeze gave contradictory results; a trial in pauci-inflammatory adult asthma, and a trial in non-cystic fibrosis bronchiectasis both showed a significant reduction in exacerbations, but none matched the dramatic results in diffuse panbronchiolitis. There is clearly a huge risk of antibacterial resistance if macrolides are used widely and uncritically in the community. In summary, Azithromycin is not the answer to anything in paediatric respiratory medicine; the paediatric respiratory community needs to refocus on the dramatic benefits of macrolides in diffuse panbronchiolitis, use modern - omics technologies to determine the endotypes of inflammatory diseases and discover in nature or synthesise designer macrolides to replicate the diffuse panbronchiolitis results. We must now find out how to do better!

PMID: 31629643 [PubMed - as supplied by publisher]

Orphan Drug Pricing and Costs: A Case Study of Kalydeco and Orkambi.

Healthc Policy. 2019 Aug;15(1):70-80

Authors: Hollis A

Abstract
BACKGROUND: A common narrative is that high prices are necessary for "orphan drugs" because of the fewer patients. In the context of state health insurance systems, the high prices create significant challenges because of limited budgets.
RESULTS: This study carefully examines both costs and revenues of two drugs for cystic fibrosis (ivacaftor and lumacaftor), showing that, for this important example, prices are not high because of fewer patients. The study then explores the justifications usually given for high orphan drug prices, including the need to support research and development for new drugs. Each of these standard justifications is shown to be inadequate; instead, it appears that the exercise of market power in the presence of insurance is the dominant driver of high prices.
INTERPRETATION: Insurers need to re-examine how they address high-priced drugs.

PMID: 31629457 [PubMed - in process]

Basal Serum Cortisol and Testosterone/Cortisol Ratio Are Related to Rate of Na+ Lost During Exercise in Elite Soccer Players.

Int J Sport Nutr Exerc Metab. 2019 Oct 17;:1-6

Authors: Castro-Sepulveda M, Cancino J, Fernández-Verdejo R, Pérez-Luco C, Jannas-Vela S, Ramirez-Campillo R, Del Coso J, Zbinden-Foncea H

Abstract
During exercise, the human body maintains optimal body temperature through thermoregulatory sweating, which implies the loss of water, sodium (Na+), and other electrolytes. Sweat rate and sweat Na+ concentration show high interindividual variability, even in individuals exercising under similar conditions. Testosterone and cortisol may regulate sweat Na+ loss by modifying the expression/activity of the cystic fibrosis transmembrane conductance regulator. This has not been tested. As a first approximation, the authors aimed to determine whether basal serum concentrations of testosterone or cortisol, or the testosterone/cortisol ratio relate to sweat Na+ loss during exercise. A total of 22 male elite soccer players participated in the study. Testosterone and cortisol were measured in blood samples before exercise (basal). Sweat samples were collected during a training session, and sweat Na+ concentration was determined. The basal serum concentrations of testosterone and cortisol and their ratio were (mean [SD]) 13.6 (3.3) pg/ml, 228.9 (41.4) ng/ml, and 0.06 (0.02), respectively. During exercise, the rate of Na+ loss was related to cortisol (r = .43; p < .05) and to the testosterone/cortisol ratio (r = -.46; p < .01), independently of the sweating rate. The results suggest that cortisol and the testosterone/cortisol ratio may influence Na+ loss during exercise. It is unknown whether this regulation depends on the cystic fibrosis transmembrane conductance regulator.

PMID: 31629352 [PubMed - as supplied by publisher]

Evaluation of active neutrophil elastase in sputum of bronchiectasis and cystic fibrosis patients: A comparison among different techniques.

Pulm Pharmacol Ther. 2019 Oct 15;:101856

Authors: Oriano M, Terranova L, Sotgiu G, Saderi L, Bellofiore A, Retucci M, Marotta C, Gramegna A, Miglietta D, Carnini C, Marchisio P, Chalmers JD, Aliberti S, Blasi F

Abstract
Neutrophil elastase (NE) is a crucial marker of neutrophilic inflammation. We aimed to compare different techniques to detect active NE in sputum samples of 50 Bronchiectasis (BE) and 50 Cystic Fibrosis (CF) patients. Three methods including a ProteaseTag® Active NE Immunoassay (ELISA) and two enzymatic digestion assays (chromogenic -CS- and fluorogenic -FS- substrate) were compared. Results of active NE were also correlated with clinical data. The three methods provided statistically different values for NE activity in the same sputum samples in both cohorts. In the BE cohort, the highest correlations between NE activity and Bronchiectasis Severity Index (rho = 0.40, P < 0.0001), sputum purulence (AUC = 0.79), and chronic infections due to any pathogen (AUC = 0.76) and P. aeruginosa (AUC = 0.80) were found when NE was measured through the activity-based immunoassay. In the CF cohort, the highest correlations between NE activity and sputum quantity (rho = 0.71) and FEV1% (rho = 0.42, P = 0.03) were observed when the FS method was used, while similar correlations with chronic P. aeruginosa infection were identified with the FS and ELISA methods. NE activity in sputum correlates with clinical variables in both diseases. However, different methods to evaluate active NE in sputum lead to significantly different results, also in terms of correlation with clinical data.

PMID: 31626976 [PubMed - as supplied by publisher]

Tezacaftor and ivacaftor for the treatment of cystic fibrosis.

Expert Rev Respir Med. 2019 Oct 18;:

Authors: Paterson SL, Barry PJ, Horsley AR

Abstract
Introduction: Cystic fibrosis (CF) is a complex, multi-system, genetic disease affecting over 70,000 people worldwide. The underlying defect is a mutation in the CFTR gene. Dysfunctional CFTR protein results in abnormal anion movement across epithelial membranes in affected organs. There has been a paradigm shift in CF treatment over the last decade with the advent of CFTR modulation, treatments which target this underlying genetic defect and have the potential to change the course of CF clinical disease. Areas covered: Available CFTR modulators in current clinical practice are reviewed in this article, with a direct comparison and summary of relevant pivotal clinical trials. The approval of ivacaftor and subsequent development of lumacaftor and tezacaftor dual combinations represent an exciting development in CF management in recent years. Expert opinion: Tezacaftor/ivacaftor (tez/iva) appears to have a more favourable adverse event and drug-drug interaction profile than lumacaftor/ivacaftor. Tez/iva has been approved, alongside Phe508del, for a large number of 'residual function' CFTR mutations, with some based on response to in vitro culture. Dual therapy with tez/iva has paved the way for triple CFTR modulation currently in clinical trials with an ultimate view to provide modulation therapy to the majority of CF genotypes in the future.

PMID: 31626570 [PubMed - as supplied by publisher]

Targeting Proteases in Cystic Fibrosis Lung Disease: Paradigms, Progress, and Potential.

Am J Respir Crit Care Med. 2019 Oct 18;:

Authors: McKelvey MC, Weldon S, McAuley DF, Mall MA, Taggart CC

Abstract
Cystic fibrosis (CF) is the most common life-limiting hereditary condition of Caucasian populations and is characterised by chronic airways inflammation driving progressive structural lung damage. Despite tremendous advances in the treatment of CF and concomitant increased life expectancy for patients, chronic lung disease remains the main cause of morbidity and mortality among CF patients. While universal restoration of cystic fibrosis transmembrane conductance regulator activity remains a future hope, novel therapies aimed at reducing or preventing chronic airways inflammation and progressive structural lung damage are required. It is well-established that proteolytic enzymes are important in the CF lung beyond the basic turnover of proteins and intracellular degradation of pathogens. When secreted, these enzymes play key roles in extracellular substrate modification implicated in important biological processes such as matrix and airway remodelling, goblet cell metaplasia and mucus hypersecretion, immune cell recruitment and dysregulation of epithelial ion channels. Importantly, the burden of proteases in the CF lung is significantly elevated, overwhelming the endogenous antiprotease shield. Indeed, free protease activity has emerged as a major risk factor of the onset and progression of bronchiectasis and lung function decline in patients with CF. Recent research has highlighted the importance of new players such as cathepsin S and matrix metalloprotease-12, as well as the membrane-associated activity of key proteases such as neutrophil elastase on the surface of neutrophils. Here, we review the current knowledge and emerging concepts of the role of host proteases in the pathogenesis of CF lung disease and their potential as therapeutic targets.

PMID: 31626562 [PubMed - as supplied by publisher]

[Insurability and history of cancer].

Rev Prat. 2019 Apr;69(4):454-460

Authors: Bousquet PJ, Lafay L

Abstract
At the instigation of the Aeras convention -Insuring and borrowing with an aggravated health risk - and the 2014- 2019 Cancer Plan, the Law of 26 January 2016 introduces the « right to be forgotten » for people with cancer. Thus, people wishing to take out an insurance policy for a mortgage or consumer credit do not have to declare their cancer 10 years after the end of the therapeutic protocol, in the absence of relapse. This period is reduced to 5 years for cancers occurring before the age of 18 years. Associated with this right, the « reference grid » identifies situations for which insurance will be granted without surcharge or exclusion of guarantee, or under conditions that are close to standard conditions. This concerns both cancer -breast, thyroid, prostate cancers ...- and noncancer diseases -HIV, hepatitis C, cystic fibrosis ...-. Through his relationship with his patient, the doctor plays a key role in providing the best insight and helping him in his efforts.

PMID: 31626506 [PubMed - in process]

Complete Genome Sequence of Stenotrophomonas Phage Pokken.

Microbiol Resour Announc. 2019 Oct 17;8(42):

Authors: Hayden A, Martinez N, Moreland R, Liu M, Gonzalez CF, Gill JJ, Ramsey J

Abstract
Stenotrophomonas maltophilia is a Gram-negative bacterium associated with multidrug-resistant nosocomial infections, a problem for immunocompromised patients and those with cystic fibrosis. Here, we present the new S. maltophilia-infecting podophage Pokken. Its 76,239-bp genome, with 92 protein-coding genes and 5 tRNA genes predicted, is similar to that of phage N4.

PMID: 31624175 [PubMed]

Antibiotic efficacy varies based on the infection model and treatment regimen for Pseudomonas aeruginosa.

Eur Respir J. 2019 Oct 17;:

Authors: Cigana C, Ranucci S, Rossi A, De Fino I, Melessike M, Bragonzi A

Abstract
Antibiotic discovery and preclinical testing are needed to combat the Pseudomonas aeruginosa health threat. Most frequently, antibiotic efficacy is tested in models of acute respiratory infection, with chronic pneumonia remaining largely unexplored. This approach generates serious concerns about the evaluation of treatment for chronically infected patients, and highlights the need for animal models that mimic the course of human disease. In this study, the efficacy of marketed antibacterials, tobramycin (TOB) and colistin (COL), was tested in murine models of acute and chronic P. aeruginosa pulmonary infection. Different administration routes -intranasal, aerosol or subcutaneous- and treatment schedules -soon or 7 days post-infection- were tested. In the acute infection model, aerosol and subcutaneous administration of TOB reduced the bacterial burden and inflammatory response, while intranasal treatment showed modest efficacy. COL reduced the bacterial burden less effectively but dampened inflammation. Mice treated soon after chronic infection for 7 days with daily aerosol or subcutaneous administration of TOB showed higher and more rapid body weight recovery, and reduced bacterial burden and inflammation than vehicle-treated mice. COL-treated mice showed no improvement in body weight or change in inflammation. Modest bacterial burden reduction was recorded only with aerosol COL administration. When treatment for chronic infection was commenced 7 days after infection, both TOB and COL failed to reduce P. aeruginosa burden and inflammation, or aid in recovery of body weights. Our findings suggest that the animal model and treatment regimen should be carefully chosen based on the type of infection to assess antibiotic efficacy.

PMID: 31624114 [PubMed - as supplied by publisher]

Adapting to the Airways: Metabolic Requirements of Pseudomonas aeruginosa during the Infection of Cystic Fibrosis Patients.

Metabolites. 2019 Oct 16;9(10):

Authors: La Rosa R, Johansen HK, Molin S

Abstract
Pseudomonas aeruginosa is one of the major causes of morbidity and mortality of cystic fibrosis patients. During the infection, the bacteria colonize the nutritional rich lung mucus, which is present in the airway secretions in the patients, and they adapt their phenotype accordingly to the lung environment. In the airways, P. aeruginosa undergoes a broad metabolic rewiring as a consequence of the nutritional and stressful complexity of the lungs. However, the role of such metabolic rewiring on the infection outcome is poorly understood. Here, we review the metabolic evolution of clinical strains of P. aeruginosa during a cystic fibrosis lung infection and the metabolic functions operating in vivo under patho-physiological conditions. Finally, we discuss the perspective of modeling the cystic fibrosis environment using genome scale metabolic models of P. aeruginosa. Understanding the physiological changes occurring during the infection may pave the way to a more effective treatment for P. aeruginosa lung infections.

PMID: 31623245 [PubMed]

Gastroesophageal reflux in cystic fibrosis across the age spectrum.

Transl Gastroenterol Hepatol. 2019;4:69

Authors: Woodley FW, Hayes D, Kopp BT, Moore-Clingenpeel M, Machado RS, Nemastil CJ, Jadcherla S, Di Lorenzo C, Kaul A, Mousa H

Abstract
Background: Scientific advances have improved longevity in cystic fibrosis (CF) patients and many of these patients can expect to experience age-related gastrointestinal co-morbidities. We aimed to assess the extent to which age might impact gastroesophageal reflux (GER) in patients with CF.
Methods: Our esophageal pH-multichannel intraluminal impedance monitoring database was searched for tracings belonging to CF patients ≥2 years old without prior fundoplication and not taking anti-reflux medications immediately prior (within 7 days) and during the study. Tracings were retrospectively analyzed; Impedance and pH variables were evaluated with respect to age and pulmonary function.
Results: Twenty-eight patients were enrolled; 16 children (3.1-17.7 years) and 12 adults (18.2-48.9 years). Among pH probe parameters, correlation analysis showed DeMeester score (P=0.011) and number of acid reflux events lasting >5 minutes (P=0.047) to be significantly correlated with age. Age was not significantly correlated with any of the impedance parameters. Age was negatively correlated with baseline impedance (BI) in the distal esophagus (r=-0.424, P=0.023) and BI was negatively correlated with several pH parameters, including reflux index (r=-0.553, P=0.002), number of total acid reflux events (r=-0.576, P=0.001), number of acid reflux events lasting >5 minutes (r=-0.534, P=0.003), and DeMeester score (r=-0.510, P=0.006). Pulmonary function (percent predicted forced expiratory volume in one minute; ppFEV1) was negatively correlated with age (r=-0.494, P=0.0007). The interaction of age and ppFEV1 and any of the reflux parameters, however, was not significant (P>0.05); the strongest evidence for an interaction was found for the number of acid reflux events reaching the proximal esophagus, but this interaction still did not reach statistical significance (P=0.070).
Conclusions: In a small cohort, we found evidence that age may be associated with increased acid exposure and that both age and increased acid exposure are associated with reduced BI in the distal esophagus. The negative relationship between pulmonary function and age in our cohort is not related to GER. This pilot study supports the need for esophageal assessment and treatment of GER as standard components of clinical care for an aging CF population.

PMID: 31620651 [PubMed]

Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics.

J Proteome Res. 2019 Oct 17;:

Authors: Zang X, Monge ME, Gaul DA, McCarty NA, Stecenko A, Fernandez FM

Abstract
The most common cause of death in cystic fibrosis (CF) patients is progressive lung function decline, which is punctuated by acute pulmonary exacerbations (APEs). A major challenge is to discover biomarkers for detecting an oncoming APE and allow for preemptive clinical interventions. Metabolic profiling of exhaled breath condensate (EBC) samples collected from CF patients before, during and after APEs and under stable conditions (n=210) was performed using ultraperformance liquid chromatography (UPLC) coupled to Orbitrap mass spectrometry (MS). Negative ion mode MS data showed that classification between metabolic profiles from "pre-APE" (pending APE before the CF patient had any signs of illness) and stable CF samples was possible with good sensitivities (85.7% and 89.5%), specificities (88.4% and 84.1%), and accuracies (87.7% and 85.7%) for pediatric and adult patients, respectively. Improved classification performance was achieved by combining positive with negative ion mode data. Discriminant metabolites included two potential biomarkers identified in a previous pilot study: lactic acid and 4-hydroxycyclohexylcarboxylic acid. Some of the discriminant metabolites had microbial origins, indicating a possible role of bacterial metabolism in APE progression. The results show promise for detecting an oncoming APE using EBC metabolites, thus permitting early intervention to abort such event.

PMID: 31621328 [PubMed - as supplied by publisher]

Renal involvement in cystic fibrosis: is it a contraindication to transplant?

Minerva Pediatr. 2019 Oct 11;:

Authors: Pedoto D, De Gregorio F, Tosco A, Pecoraro C, D'armiento M, Raia V

Abstract

PMID: 31621279 [PubMed - as supplied by publisher]

Long-term non-invasive ventilation in cystic fibrosis: A bridge too far?

Respirology. 2019 Oct 16;:

Authors: Wilson J, Young A

PMID: 31621151 [PubMed - as supplied by publisher]

Dispersion of endoplasmic reticulum-associated compartments by 4-phenyl butyric acid in yeast cells.

Cell Struct Funct. 2019 Oct 17;:

Authors: Mai TC, Ishiwata-Kimata Y, Le QG, Kido H, Kimata Y

Abstract
In yeast Saccharomyces cerevisiae cells, some aberrant multimembrane-spanning proteins are not transported to the cell surface but form and are accumulated in endoplasmic reticulum (ER)-derived subcompartments, known as the ER-associated compartments (ERACs), which are observed as puncta under fluorescence microscopy. Here we show that a mutant of the cell surface protein Pma1, Pma1-2308, was accumulated in the ERACs, as well as the heterologously expressed mammalian cystic fibrosis transmembrane conductance regulator (CFTR), in yeast cells. Pma1-2308 and CFTR were located on the same ERACs. We also note that treatment of cells with 4-phenyl butyric acid (4-PBA) compromised the ERAC formation by Pma1-2308 and CFTR, suggesting that 4-PBA exerts a chaperone-like function in yeast cells. Intriguingly, unlike ER stress induced by the canonical ER stressor tunicamycin, ER stress that was induced by Pma1-2308 was aggravated by 4-PBA. We assume that this observation demonstrates a beneficial aspect of ERACs, and thus propose that the ERACs are formed through aggregation of aberrant transmembrane proteins and work as the accumulation sites of multiple ERAC-forming proteins for their sequestration. Key words: protein aggregation, organelle, unfolded protein response, ER stress, 4-PBA.

PMID: 31619600 [PubMed - as supplied by publisher]

Pseudomonas aeruginosa colonization in the upper and lower airways of a child with cystic fibrosis: a father's meticulous approach to successful eradication.

J Bras Pneumol. 2019 Oct 14;45(6):e20190191

Authors: Mainz JG, Baier M, Jaudszus A, Tabori H, Ribeiro JD, Lorenz M

PMID: 31618301 [PubMed - in process]

Tedizolid is a promising antimicrobial option for the treatment of Staphylococcus aureus infections in cystic fibrosis patients.

J Antimicrob Chemother. 2019 Oct 16;:

Authors: Roch M, Varela MC, Taglialegna A, Rosato AE

Abstract
BACKGROUND: Tedizolid is a protein synthesis inhibitor in clinical use for the treatment of Gram-positive infections. Pulmonary MRSA infections are a growing problem in patients with cystic fibrosis (CF) and the efficacy of tedizolid-based therapy in CF pulmonary infections is unknown.
OBJECTIVES: To evaluate the in vitro and in vivo activity of tedizolid and predict the likelihood of tedizolid resistance selection in CF-background Staphylococcus aureus strains.
METHODS: A collection of 330 S. aureus strains (from adult and paediatric patients), either of normal or small colony variant (SCV) phenotypes, gathered at three CF centres in the USA was used. Tedizolid activity was assessed by broth microdilution, Etest and time-kill analysis. In vivo tedizolid efficacy was tested in a murine pneumonia model. Tedizolid in vitro mutants were obtained by 40 days of exposure and progressive passages. Whole genome sequencing of clinical S. aureus strains with reduced susceptibility to tedizolid was performed.
RESULTS: MRSA strain MIC90s were tedizolid 0.12-0.25 mg/L and linezolid 1-2 mg/L; for MSSA strains, MIC90s were tedizolid 0.12 mg/L and linezolid 1-2 mg/L. Two strains, WIS 441 and Seattle 106, with tedizolid MICs of 2 mg/L and 1 mg/L, respectively, had MICs above the FDA tedizolid breakpoint (0.5 mg/L). Tedizolid at free serum concentrations exhibited a bacteriostatic effect. Mean bacterial burdens in lungs (log10 cfu/g) for WIS 423-infected mice were: control, 11.2 ± 0.5; tedizolid-treated (10 mg/kg), 3.40 ± 1.87; linezolid-treated (40 mg/kg), 4.51 ± 2.1; and vancomycin-treated (30 mg/kg), 5.21 ± 1.93. For WIS 441-infected mice the (log10 cfu/g) values were: control, 9.66 ± 0.8; tedizolid-treated, 3.18 ± 1.35; linezolid-treated 5.94 ± 2.19; and vancomycin-treated, 4.35 ± 1.7.
CONCLUSIONS: These results suggest that tedizolid represents a promising therapeutic option for the treatment of CF-associated MRSA/MSSA infections, having potent in vivo activity and low resistance potential.

PMID: 31617901 [PubMed - as supplied by publisher]

Quantitative real-time PCR assay for the rapid identification of the intrinsically multidrug-resistant bacterial pathogen Stenotrophomonas maltophilia.

Microb Genom. 2019 Oct 16;:

Authors: Fraser TA, Bell MG, Harris PNA, Bell SC, Bergh H, Nguyen TK, Kidd TJ, Nimmo GR, Sarovich DS, Price EP

Abstract
Stenotrophomonas maltophilia is emerging as an important cause of disease in nosocomial and community-acquired settings, including bloodstream, wound and catheter-associated infections. Cystic fibrosis (CF) airways also provide optimal growth conditions for various opportunistic pathogens with high antibiotic tolerance, including S. maltophilia. Currently, there is no rapid, cost-effective and accurate molecular method for detecting this potentially life-threatening pathogen, particularly in polymicrobial specimens, suggesting that its true prevalence is underestimated. Here, we used large-scale comparative genomics to identify a specific genetic target for S. maltophilia, with subsequent development and validation of a real-time PCR assay for its detection. Analysis of 167 Stenotrophomonas spp. genomes identified a conserved 4 kb region in S. maltophilia, which was targeted for Black Hole Quencher assay design. Our assay yielded the positive detection of 89 of 89 (100%) clinical S. maltophilia strains, and no amplification of 23 non-S. maltophilia clinical isolates. S. maltophilia was detected in 10 of 16 CF sputa, demonstrating the assay's utility for direct detection in respiratory specimens. The assay demonstrated good sensitivity, with limits of detection and quantitation on pure culture of ~10 and ~100 genome equivalents, respectively. Our assay provides a highly specific, sensitive and cost-effective method for the accurate identification of S. maltophilia, and will improve the diagnosis and treatment of this under-recognized pathogen by enabling its accurate and rapid detection from polymicrobial clinical and environmental samples.

PMID: 31617838 [PubMed - as supplied by publisher]