Adv Exp Med Biol. 2021 May 8. doi: 10.1007/5584_2021_641. Online ahead of print.

ABSTRACT

The antibiotic susceptibility of bacterial pathogens is typically determined based on planktonic cells, as recommended by several international guidelines. However, most of chronic infections - such as those established in wounds, cystic fibrosis lung, and onto indwelling devices - are associated to the formation of biofilms, communities of clustered bacteria attached onto a surface, abiotic or biotic, and embedded in an extracellular matrix produced by the bacteria and complexed with molecules from the host. Sessile microorganisms show significantly increased tolerance/resistance to antibiotics compared with planktonic counterparts. Consequently, antibiotic concentrations used in standard antimicrobial susceptibility tests, although effective against planktonic bacteria in vitro, are not predictive of the concentrations required to eradicate biofilm-related infections, thus leading to treatment failure, chronicization and removal of material in patients with indwelling medical devices.Meeting the need for the in vitro evaluation of biofilm susceptibility to antibiotics, here we reviewed several methods proposed in literature highlighting their advantages and limitations to guide scientists towards an appropriate choice.

PMID:33963526 | DOI:10.1007/5584_2021_641

Thorax. 2021 May 7:thoraxjnl-2020-215040. doi: 10.1136/thoraxjnl-2020-215040. Online ahead of print.

ABSTRACT

INTRODUCTION: Early infant diet might influence the risk of subsequent allergic disease.

METHODS: The Merthyr Allergy Prevention Study (MAPS) was a randomised controlled trial in infants at high risk of allergic disease. The trial determined whether a cow's milk exclusion diet for the first 4 months of life decreased the risk of allergic disease including asthma compared with a normal diet. A soya milk preparation was offered to those in the intervention group. A standardised questionnaire for allergic disease was completed at ages 1, 7, 15 and 23 years, with clinical assessment at 1, 7 and 23 years. The effect of the intervention on the risk of atopy, asthma and wheeze at age 23 years was determined.

FINDINGS: 487 subjects entered the study; at age 23 years 299 completed the questionnaire, of which 119 attended clinical assessment. Subjects randomised to the intervention group had a significantly increased risk of atopy (adjusted OR 2.97, 95% CI 1.30 to 6.80; p=0.01) and asthma (OR 2.07, 95%CI 1.09 to 3.91; p=0.03) at age 23 years, but not wheeze (OR 1.43, 95%CI 0.87 to 2.37; p=0.16). Earlier exposure to cow's milk was associated with a decreased risk of wheeze and asthma at age 23 years, while earlier exposure to soya milk was associated with an increased risk of atopy and asthma.

INTERPRETATION: In infants at high risk of allergic disease, either cow's milk exclusion or early soya milk introduction for the first 4 months of life increases the risk of atopy, wheeze and asthma in adulthood.

PMID:33963089 | DOI:10.1136/thoraxjnl-2020-215040

Appl Environ Microbiol. 2021 May 7:AEM.00186-21. doi: 10.1128/AEM.00186-21. Online ahead of print.

ABSTRACT

Lanthipeptides are ribosomally synthesized and post translationally modified peptides, with modifications that are incorporated during biosynthesis by dedicated enzymes. Various modifications of the peptides are possible resulting in a highly diverse group of bioactive peptides that offer a potential reservoir for use in the fight against a plethora of diseases. Their activities range from the antimicrobial properties of lantibiotics, especially against antibiotic-resistant strains, to antiviral activity, immunomodulatory properties, antiallodynic effects and the potential to alleviate cystic fibrosis symptoms. Lanthipeptide biosynthetic genes are widespread within bacterial genomes providing a substantial repository for novel bioactive peptides. Using genome mining tools novel bioactive lanthipeptides can be identified and coupled with rapid screening and heterologous expression technologies the lanthipeptide drug discovery pipeline can be significantly sped up. Lanthipeptides represents a group of bioactive peptides that holds great potential as biotherapeutics, especially at a time when novel and more effective therapies are required.With this review we provide insight into the latest developments made towards the therapeutic applications and production of lanthipeptides, specifically looking at heterologous expression systems.

PMID:33962984 | DOI:10.1128/AEM.00186-21

Methods Mol Biol. 2021;2242:185-202. doi: 10.1007/978-1-0716-1099-2_12.

ABSTRACT

Predicting host traits from metagenomes presents new challenges that can be difficult to overcome for researchers without a strong background in bioinformatics and/or statistics. Profiling bacterial communities using shotgun metagenomics often leads to the generation of a large amount of data that cannot be used directly for training a model. In this chapter we provide a detailed description of how to build a working machine learning model based on taxonomic and functional features of bacterial communities inhabiting the lungs of cystic fibrosis patients. Models are built in the R environment by using different freely available machine learning algorithms.

PMID:33961225 | DOI:10.1007/978-1-0716-1099-2_12

Monaldi Arch Chest Dis. 2021 May 4. doi: 10.4081/monaldi.2021.1762. Online ahead of print.

ABSTRACT

In February 2020 the first COVID-19 case was reported in Italy and afterwards the virus started spreading rapidly, increasing dramatically the number of infected subjects. To face the pandemic outbreak, hospitals converted wards to assure COVID-19 patients' care and adopted measures to reduce virus diffusion. The aim of this study was to determine how many physiotherapists, in the Lombardy region, worked during pandemic, whether they continued their usual practice or were employed in COVID-19 wards and in which tasks they were involved. The survey was submitted online by the national professional order. The response rate was 11.79%. During the pandemic, 648 (53.9%) respondents interrupted their services. Less than 20% of the physiotherapists that continued working were assigned to COVID-19 wards with the role of physiotherapist. Only a small proportion of respondents had advanced skills in respiratory physiotherapy. Moreover, this study showed a limited involvement of physiotherapists inside the very acute and intense settings. In conclusion, this work revealed that, during COVID-19 pandemic, in the Lombardy region a small percentage of physiotherapists was employed in COVID-19 wards, mainly in post-acute context. Even though the response rate of this survey was very low, this study highlights the need to define and underline the role of physiotherapy in acute setting during emergency.

PMID:33960187 | DOI:10.4081/monaldi.2021.1762

Cureus. 2021 Mar 31;13(3):e14231. doi: 10.7759/cureus.14231.

ABSTRACT

Introduction Bronchiectasis is a chronic respiratory disease that can affect patients of all ages and significantly impact the quality of life (QOL) in patients who suffer from it. In spite of its widespread prevalence, and the significant impact on QOL, data on the quantitative impact of bronchiectasis on QOL is lacking. The Quality of Life-Bronchiectasis (QOL-B) is a self-administered patient-reported outcome measure, that was recently developed as a response to the emergent need for such measurement tools to study the impact of bronchiectasis on QOL. Methods We conducted a single-center cross-sectional study to study the correlation between QOL and various other outcome parameters such as exercise capacity, lung functions, co-morbidities, inflammatory markers, and body mass index (BMI). The secondary outcome was to find out various determinants of quality of life in non-cystic fibrosis bronchiectasis (NCFB). Results Forty-four patients who determined the pre-determined criteria for NCFB were enrolled in this study. This study demonstrated a significant impact on the QOL of NCFB patients based on the QOL-B scoring system. Almost all domains of QOL-B were found to be adversely impacted as measured by one or more of the outcome parameters but the FEV1, age, colonization, extension, dyspnea (FACED) score, bronchiectasis severity index (BSI) score, six-minute walk test (6MWD), and FEV1 showed associations across most scales while the other outcome parameters showed varying associations. Conclusions The QOL is significantly reduced in NCFB and it may be quantified using the QOL-B questionnaire. The impact on QOL in NCFB may be assessed using validated tools such as the FACED and BSI scoring systems, as well as other well-established outcome parameters like 6MWD and FEV1 predicted.

PMID:33959430 | PMC:PMC8093104 | DOI:10.7759/cureus.14231

Tanaffos. 2020 Dec;19(4):385-391.

ABSTRACT

BACKGROUND: The six-minute walk test (6MWT) is a suitable tool for the assessment of functional capacity in patients with chronic pulmonary diseases. This study aimed to assess the clinical determinants of the six-minute walk distance (6MWD), exercise-induced desaturation (EID), and pretest saturation of arterial oxygen (SataO2) in patients with diffuse non-cystic fibrosis (CF) bronchiectasis.

MATERIALS AND METHODS: In this cross-sectional study, a total of 57 clinically stable patients with diffuse non-CF bronchiectasis were enrolled. Anthropometric measurements (body mass index [BMI], mid-arm muscle circumference [MAMC], and triceps skinfold thickness [TSF]), spirometric indices (forced expiratory volume in one second [FEV1], forced vital capacity [FVC], and FEV1/FVC ratio), imaging assessment (CT scan), and bacteriological sputum studies were performed, and then, 6MWT was carried out.

RESULTS: The mean 6MWD was measured to be 447.11±94.59 m. The average walked distance in patients with severe, moderate, and mild bronchiectasis was 427.73±92.07, 439.63±102.65, and 485.87±80.47 m, respectively, with no significant difference. The pretest SataO2 was 88.92±5.59%, 93.75±3.36%, and 94.87±2.88% in the severe, moderate, and mild bronchiectasis groups (P<0.001). A significant inverse correlation was observed between the distance walked and BMI (r=-0.434, P=0.001).

CONCLUSION: The predictors of 6MWD in stable non-CF bronchiectasis patients were FVC, SataO2 at rest, BMI, and MAMC. The FEV1, FEV1/FVC, and BMI were independent predictors of SataO2 at rest. The extension of bronchiectasis was the only predictor of EID during the test.

PMID:33959177 | PMC:PMC8088139

Nat Med. 2021 May 6. doi: 10.1038/s41591-021-01332-7. Online ahead of print.

ABSTRACT

Cystic fibrosis (CF) is a lethal autosomal recessive disorder that afflicts more than 70,000 people. People with CF experience multi-organ dysfunction resulting from aberrant electrolyte transport across polarized epithelia due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CF-related lung disease is by far the most important determinant of morbidity and mortality. Here we report results from a multi-institute consortium in which single-cell transcriptomics were applied to define disease-related changes by comparing the proximal airway of CF donors (n = 19) undergoing transplantation for end-stage lung disease with that of previously healthy lung donors (n = 19). Disease-dependent differences observed include an overabundance of epithelial cells transitioning to specialized ciliated and secretory cell subsets coupled with an unexpected decrease in cycling basal cells. Our study yields a molecular atlas of the proximal airway epithelium that will provide insights for the development of new targeted therapies for CF airway disease.

PMID:33958799 | DOI:10.1038/s41591-021-01332-7

Eur Respir J. 2021 May 6:2000507. doi: 10.1183/13993003.00507-2020. Online ahead of print.

ABSTRACT

Acute pulmonary Exacerbations (AE) are episodes of clinical worsening in cystic fibrosis (CF), often precipitated by infection. Timely detection is critical to minimise morbidity and lung function declines associated with acute inflammation during AE. Based on our previous observations that airway protein Short Palate Lung Nasal epithelium Clone 1 (SPLUNC1) is regulated by inflammatory signals, we investigated the use of SPLUNC1 fluctuations to diagnose and predict AE in CF.We enrolled CF participants from two independent cohorts to measure AE markers of inflammation in sputum and recorded clinical outcomes for a 1-year follow-up period.SPLUNC1 levels were high in healthy controls (n=9, 10.7 μg mL-1), and significantly decreased in CF participants without AE (n=30, 5.7 μg mL-1, p=0.016). SPLUNC1 levels were 71.9% lower during AE (n=14, 1.6 μg mL-1, p=0.0034) regardless of age, sex, CF-causing mutation, or microbiology findings. Cytokines Il-1β and TNFα were also increased in AE, whereas lung function did not consistently decrease. Stable CF participants with lower SPLUNC1 levels were much more likely to have an AE at 60 days (HR: 11.49, Standard Error: 0.83, p=0.0033). Low-SPLUNC1 stable participants remained at higher AE risk even one year after sputum collection (HR: 3.21, Standard Error: 0.47, p=0.0125). SPLUNC1 was downregulated by inflammatory cytokines and proteases increased in sputum during AE.In acute CF care, low SPLUNC1 levels could support a decision to increase airway clearance or to initiate pharmacological interventions. In asymptomatic, stable patients, low SPLUNC1 levels could inform changes in clinical management to improve long-term disease control and clinical outcomes in CF.

PMID:33958427 | DOI:10.1183/13993003.00507-2020

Immunohorizons. 2021 May 6;5(5):273-283. doi: 10.4049/immunohorizons.2000095.

ABSTRACT

Cystic fibrosis is associated with chronic Pseudomonas aeruginosa colonization and inflammation. The role of MyD88, the shared adapter protein of the proinflammatory TLR and IL-1R families, in chronic P. aeruginosa biofilm lung infection is unknown. We report that chronic lung infection with the clinical P. aeruginosa RP73 strain is associated with uncontrolled lung infection in complete MyD88-deficient mice with epithelial damage, inflammation, and rapid death. Then, we investigated whether alveolar or myeloid cells contribute to heightened sensitivity to infection. Using cell-specific, MyD88-deficient mice, we uncover that the MyD88 pathway in myeloid or alveolar epithelial cells is dispensable, suggesting that other cell types may control the high sensitivity of MyD88-deficient mice. By contrast, IL-1R1-deficient mice control chronic P. aeruginosa RP73 infection and IL-1β Ab blockade did not reduce host resistance. Therefore, the IL-1R1/MyD88 pathway is not involved, but other IL-1R or TLR family members need to be investigated. Our data strongly suggest that IL-1 targeted neutralizing therapies used to treat inflammatory diseases in patients unlikely reduce host resistance to chronic P. aeruginosa infection.

PMID:33958388 | DOI:10.4049/immunohorizons.2000095

J Cyst Fibros. 2021 May 3:S1569-1993(21)00117-X. doi: 10.1016/j.jcf.2021.04.007. Online ahead of print.

ABSTRACT

BACKGROUND: Pseudomonas aeruginosa (Pa) and Aspergillus species (Asp) are the most common bacterial and fungal organisms respectively in CF airways. Our aim was to examine impacts of Asp infection and Pa/Asp co-infection.

METHODS: Patients on the UK CF Registry in 2016 were grouped into: absent (Pa-), intermittent (Pai) or chronic Pa (Pac), each with Asp positive (Asp+) or negative (Asp-). Primary outcome was best percentage predicted FEV1 (ppFEV1) that year. Secondary outcomes were intravenous (IV) antibiotic courses, growth (height, weight, BMI) and additional disease complications. Associations between outcomes and infection-status were assessed using regression models adjusting for significant confounders (age, sex, Phe508del homozygosity and CF-related diabetes (CFRD)).

RESULTS: 9,270 patients were included (median age 19 [IQR 9-30] years, 54% male, 50% Phe508del/F508del). 4,142 patients (45%) isolated Pa, 1,460 (16%) Asp. Pa-/Asp+ subjects had an adjusted ppFEV1 that was 5.9% lower than Pa-/Asp- (p < 0.0001). In patients with Pai or Pac, there was no additional impact of Asp on ppFEV1. However, there was a higher probability that Pac/Asp+ patients had required IV antibiotics than Pac/Asp- group (OR 1.23 [1.03-1.48]). Low BMI, ABPA, CF-liver disease and CFRD were all more frequent with Asp alone than Pa-/Asp-, though not more common in Pac/Asp+ than Pac/Asp-.

CONCLUSIONS: Co-infection with Pa and Asp was not associated with reduced lung function compared with Pa alone, but was associated with additional use of IV antibiotics. Asp infection itself is associated with several important indicators of disease severity. Longitudinal analyses should explore the impact of co-infection on disease progression.

PMID:33958279 | DOI:10.1016/j.jcf.2021.04.007

J Cyst Fibros. 2021 May 3:S1569-1993(21)00111-9. doi: 10.1016/j.jcf.2021.04.001. Online ahead of print.

NO ABSTRACT

PMID:33958278 | DOI:10.1016/j.jcf.2021.04.001

Am J Otolaryngol. 2021 Apr 20;42(6):103067. doi: 10.1016/j.amjoto.2021.103067. Online ahead of print.

ABSTRACT

PURPOSE: Recent data have challenged the historical paradigm that cystic fibrosis (CF) protects against otitis media (OM). These findings raised questions about the pathogenesis of this ostensible change. In this study our aim is to characterize acute OM (AOM) risk based on CF genotype.

METHODS: A retrospective chart review was completed at a tertiary care pediatric hospital. Charts of 159 CF patients seen at our facility from 2010 to 2019 were reviewed. Data collected included demographics, AOM infections, cystic fibrosis transmembrane conductance regulator (CFTR) allele mutations, pulmonary exacerbations (PE), and pancreatic insufficiency (PI) status. Mutation alleles were divided into five classes based on CF guidelines, which were further classified as severe (classes I-III) or mild (classes IV-V).

RESULTS: 54% of patients had at least one episode of AOM with a mean of 1.5 episodes of AOM (standard deviation = 2.3). 86% of patients had severe/severe (S/S) alleles and 14% had severe/mild (S/M). S/S patients had significantly more PE (p = .004) and increased rates of PI (p < .001). Of the 131 patients with S/S mutations, 57% had an episode of AOM while only 46% the 22 S/M patients had an AOM episode (p = .357).

CONCLUSIONS: To our knowledge this is the first report showing a clinical trend towards increased middle ear disease in patients with severe CFTR mutations. Future prospective studies will be powered to demonstrate whether this trend is statistically significant. Patients with S/S mutations not only have more severe clinical phenotypes but may have additional unexpected complications such as middle ear disease.

PMID:33957545 | DOI:10.1016/j.amjoto.2021.103067

Eur J Cardiothorac Surg. 2021 May 6:ezab164. doi: 10.1093/ejcts/ezab164. Online ahead of print.

ABSTRACT

OBJECTIVES: A combined lung and liver transplant in patients with cystic fibrosis (CF) is an uncommon procedure. The goal of this study was to compare long-term outcomes between patients with CF who underwent either a combined lung-liver or a lung-only transplant.

METHODS: This is a retrospective single-centre study of patients with CF who underwent a lung transplant between January 2005 and May 2020. Since 2006, our preference for a combined lung-liver transplant was to transplant the liver first and then the lung. Outcomes were compared using the Kaplan-Meier analysis and the log-rank test. Median follow-up was 53 (23-97) months.

RESULTS: During the study period, among 357 patients with CF who underwent a lung transplant, 14 (4%) required a lung-liver transplant whereas 343 (96%) had a lung-only transplant. Lung cold ischaemic time was longer in the lung-liver transplant group, but no patient in this group showed primary graft dysfunction at 72 h after the transplant. Prevalence of anti-human leucocyte antigen donor-specific antibodies was 7.1% vs 13.7% in the lung-liver versus the lung-only transplant group (P = 0.42). At 5 years, lung graft survival (78% vs 69%) and freedom from chronic lung allograft dysfunction (79% vs 62%) did not differ between the lung-liver versus the lung-only groups (P = 0.45 and P = 0.55, respectively). Freedom from lung biopsy-confirmed rejection was significantly higher in patients undergoing a lung-liver transplant (91% vs 50%; P = 0.027).

CONCLUSIONS: A lung-liver transplant did not impair lung graft function. The lower prevalence of donor-specific antibodies and the better freedom from lung biopsy-confirmed rejection suggest tolerogenic effects of the liver graft.

PMID:33956976 | DOI:10.1093/ejcts/ezab164

Genetics. 2020 Dec 1;216(4):905-930. doi: 10.1534/genetics.120.303596.

ABSTRACT

The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well-annotated genome, wealth of genetic resources, and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost-effective, informative, and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole-genome sequencing. Here, we describe the content and performance of a new iteration of the Mouse Universal Genotyping Array (MUGA), MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: (1) chromosomal sex determination, (2) discrimination between substrains from multiple commercial vendors, (3) diagnostic SNPs for popular laboratory strains, (4) detection of constructs used in genetically engineered mice, and (5) an easy-to-interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA, we genotyped 6899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays, both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived, and recombinant inbred lines. Here, we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, new markers that expand the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. We provide preliminary evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the relevant main stock. We conclude that MiniMUGA is a valuable platform for genetic QC, and an important new tool to increase the rigor and reproducibility of mouse research.

PMID:33954773 | DOI:10.1534/genetics.120.303596

Immunol Lett. 2021 May 2:S0165-2478(21)00068-7. doi: 10.1016/j.imlet.2021.04.010. Online ahead of print.

ABSTRACT

The number and function of T cells are abnormal as observed in cystic fibrosis (CF) patients and CF mouse models, and our previous work shows that the CFTR mutant leads to deficiency of primitive and definitive hematopoietic in zebrafish. However, the functions and underlying mechanisms of CFTR in T cell development during early embryogenesis have not been explored. Here, we report that the genetic ablation of CFTR in zebrafish resulted in abrogated embryonic T lymphopoiesis, which was ascribed to impaired thymic homing and expansion of hematopoietic stem cells (HSCs). Transcriptome analysis of isolated HSCs in zebrafish embryos at 48 hpf showed a significant alteration of key factors essential for T cell development and Wnt signaling, consistent with our previous work on CFTR regulating hematopoiesis. In brief, we uncovered the function of CFTR in embryonic T cell development and suggest that the immune deficiency of CF patients may originate from an early embryonic stage.

PMID:33951474 | DOI:10.1016/j.imlet.2021.04.010

Am J Respir Crit Care Med. 2021 May 5. doi: 10.1164/rccm.202103-0796LE. Online ahead of print.

NO ABSTRACT

PMID:33951399 | DOI:10.1164/rccm.202103-0796LE

MMW Fortschr Med. 2021 Mar;163(Suppl 1):74-81. doi: 10.1007/s15006-021-9804-z.

NO ABSTRACT

PMID:33950452 | DOI:10.1007/s15006-021-9804-z

J Bras Pneumol. 2021 Apr 30;47(2):e20210140. doi: 10.36416/1806-3756/e20210140.

NO ABSTRACT

PMID:33950101 | DOI:10.36416/1806-3756/e20210140

Am J Physiol Gastrointest Liver Physiol. 2021 May 5. doi: 10.1152/ajpgi.00095.2021. Online ahead of print.

ABSTRACT

Cystic fibrosis is a deadly multi-organ disorder caused by loss of function mutations in the gene that encodes for the cystic fibrosis transmembrane conductance regulator (CFTR) chloride/bicarbonate ion channel. More than 1700 CFTR genetic variants exist that can cause CF, and, majority of these are extremely rare. Due to genetic and environmental influences, CF patients exhibit large phenotypic variation. These factors make clinical trials difficult and largely impractical due to limited and heterogenous patient pools. Also, the benefit of approved small-molecule CF modulators in a large number of rare mutation patients remain unknown. The goal of this study is to perform a comprehensive bench-side study using in vitro patient enteroids and in vivo mice implanted Human Intestinal Organoids (HIOs) to test CF modulator-Ivacaftor response for a rare CF mutation patient. Based on the positive Ivacaftor response in the enteroids, the patient was enrolled in N=1 clinical trial and showed improved clinical outcomes upon Ivacaftor treatment. HIO implantation model allowed in vivo modulator dosing and provided an elegant human organ-based demonstration of bench-to-bedside testing of modulator effects. Additionally, using the CF HIO model the role of CFTR function in the maturation of human intestine was reported for the first time. In all, we demonstrate that these models effectively serve to translate data from the lab to the clinic and back so that patient specific therapies could be easily identified and disease-relevant developmental abnormalities in CF organs could be studied and addressed.

PMID:33949881 | DOI:10.1152/ajpgi.00095.2021