Microbiol Spectr. 2023 Mar 28:e0020923. doi: 10.1128/spectrum.00209-23. Online ahead of print.

ABSTRACT

COVID-19 has significantly affected hospital infection prevention and control (IPC) practices, especially in intensive care units (ICUs). This frequently caused dissemination of multidrug-resistant organisms (MDROs), including carbapenem-resistant Acinetobacter baumannii (CRAB). Here, we report the management of a CRAB outbreak in a large ICU COVID-19 hub Hospital in Italy, together with retrospective genotypic analysis by whole-genome sequencing (WGS). Bacterial strains obtained from severe COVID-19 mechanically ventilated patients diagnosed with CRAB infection or colonization between October 2020 and May 2021 were analyzed by WGS to assess antimicrobial resistance and virulence genes, along with mobile genetic elements. Phylogenetic analysis in combination with epidemiological data was used to identify putative transmission chains. CRAB infections and colonization were diagnosed in 14/40 (35%) and 26/40 (65%) cases, respectively, with isolation within 48 h from admission in 7 cases (17.5%). All CRAB strains belonged to Pasteur sequence type 2 (ST2) and 5 different Oxford STs and presented blaOXA-23 gene-carrying Tn2006 transposons. Phylogenetic analysis revealed the existence of four transmission chains inside and among ICUs, circulating mainly between November and January 2021. A tailored IPC strategy was composed of a 5-point bundle, including ICU modules' temporary conversion to CRAB-ICUs and dynamic reopening, with limited impact on ICU admission rate. After its implementation, no CRAB transmission chains were detected. Our study underlies the potentiality of integrating classical epidemiological studies with genomic investigation to identify transmission routes during outbreaks, which could represent a valuable tool to ensure IPC strategies and prevent the spread of MDROs. IMPORTANCE Infection prevention and control (IPC) practices are of paramount importance for preventing the spread of multidrug-resistant organisms (MDROs) in hospitals, especially in the intensive care unit (ICU). Whole-genome sequencing (WGS) is seen as a promising tool for IPC, but its employment is currently still limited. COVID-19 pandemics have posed dramatic challenges in IPC practices, causing worldwide several outbreaks of MDROs, including carbapenem-resistant Acinetobacter baumannii (CRAB). We present the management of a CRAB outbreak in a large ICU COVID-19 hub hospital in Italy using a tailored IPC strategy that allowed us to contain CRAB transmission while preventing ICU closure during a critical pandemic period. The analysis of clinical and epidemiological data coupled with retrospective genotypic analysis by WGS identified different putative transmission chains and confirmed the effectiveness of the IPC strategy implemented. This could be a promising approach for future IPC strategies.

PMID:36976013 | DOI:10.1128/spectrum.00209-23

Int J Neonatal Screen. 2023 Mar 17;9(1):15. doi: 10.3390/ijns9010015.

ABSTRACT

In 1963, Robert Guthrie's pioneering work developing a bacterial inhibition assay to measure phenylalanine in dried blood spots, provided the means for whole-population screening to detect phenylketonuria in the USA. In the following decades, NBS became firmly established as a part of public health in developed countries. Technological advances allowed for the addition of new disorders into routine programmes and thereby resulted in a paradigm shift. Today, technological advances in immunological methods, tandem mass spectrometry, PCR techniques, DNA sequencing for mutational variant analysis, ultra-high performance liquid chromatography (UPLC), iso-electric focusing, and digital microfluidics are employed in the NBS laboratory to detect more than 60 disorders. In this review, we will provide the current state of methodological advances that have been introduced into NBS. Particularly, 'second-tier' methods have significantly improved both the specificity and sensitivity of testing. We will also present how proteomic and metabolomic techniques can potentially improve screening strategies to reduce the number of false-positive results and improve the prediction of pathogenicity. Additionally, we discuss the application of complex, multiparameter statistical procedures that use large datasets and statistical algorithms to improve the predictive outcomes of tests. Future developments, utilizing genomic techniques, are also likely to play an increasingly important role, possibly combined with artificial intelligence (AI)-driven software. We will consider the balance required to harness the potential of these new advances whilst maintaining the benefits and reducing the risks for harm associated with all screening.

PMID:36975853 | DOI:10.3390/ijns9010015

Int J Neonatal Screen. 2023 Feb 21;9(1):10. doi: 10.3390/ijns9010010.

ABSTRACT

Most people with cystic fibrosis (CF) are diagnosed following abnormal newborn screening (NBS), which begins with measurement of immunoreactive trypsinogen (IRT) values. A case report found low concentrations of IRT in an infant with CF exposed to the CF transmembrane conductance regulator (CFTR) modulator, elexacaftor-tezacaftor-ivacaftor (ETI), in utero. However, IRT values in infants born to mothers taking ETI have not been systematically assessed. We hypothesized that ETI-exposed infants have lower IRT values than newborns with CF, CFTR-related metabolic syndrome/CF screen positive, inconclusive diagnosis (CRMS/CFSPID), or CF carriers. IRT values were collected from infants born in Indiana between 1 January 2020, and 2 June 2022, with ≥1 CFTR mutation. IRT values were compared to infants born to mothers with CF taking ETI followed at our institution. Compared to infants identified with CF (n = 51), CRMS/CFSPID (n = 21), and CF carriers (n = 489), ETI-exposed infants (n = 19) had lower IRT values (p < 0.001). Infants with normal NBS results for CF had similar median (interquartile range) IRT values, 22.5 (16.8, 30.6) ng/mL, as ETI-exposed infants, 18.9 (15.2, 26.5). IRT values from ETI-exposed infants were lower than for infants with abnormal NBS for CF. We recommend that NBS programs consider performing CFTR variant analysis for all ETI-exposed infants.

PMID:36975847 | DOI:10.3390/ijns9010010

Nanomedicine (Lond). 2023 Mar 28. doi: 10.2217/nnm-2021-0437. Online ahead of print.

ABSTRACT

Diagnosis and treatment of lung diseases pose serious challenges. Currently, diagnostic as well as therapeutic methods show poor efficacy toward drug-resistant bacterial infections, while chemotherapy causes toxicity and nonspecific delivery of drugs. Advanced treatment methods that cure lung-related diseases, by enabling drug bioavailability via nasal passages during mucosal formation, which interferes with drug penetration to targeted sites, are in demand. Nanotechnology confers several advantages. Currently, different nanoparticles, or their combinations, are being used to enhance targeted drug delivery. Nanomedicine, a combination of nanoparticles and therapeutic agents, that delivers drugs to targeted sites increases the bioavailability of drugs at these sites. Thus, nanotechnology is superior to conventional chemotherapeutic strategies. Here, the authors review the latest advancements in nanomedicine-based drug-delivery methods for managing acute and chronic inflammatory lung diseases.

PMID:36975758 | DOI:10.2217/nnm-2021-0437

Pediatr Allergy Immunol. 2023 Mar;34(3):e13935. doi: 10.1111/pai.13935.

NO ABSTRACT

PMID:36974648 | DOI:10.1111/pai.13935

Am J Respir Crit Care Med. 2023 Mar 27. doi: 10.1164/rccm.202302-0310ST. Online ahead of print.

ABSTRACT

Current American Thoracic Society (ATS) standards promote the use of racial/ethnic-specific reference equations for pulmonary function test (PFT) interpretation. There is rising concern that the use of race/ethnicity in PFT interpretation contributes to a false view of fixed differences between races and may mask the effects of differential exposures. This use of race/ethnicity may contribute to health disparities by norming differences in pulmonary function. In the United States, race serves as a social construct that is based on appearance and reflects social values, structures, and practices. Classification of people into racial/ethnic groups differs geographically and temporally. These considerations challenge the notion that racial/ethnic categories have biological meaning and question the use of race in PFT interpretation. The ATS convened a diverse group of clinicians and investigators for a workshop to evaluate the use of race/ethnicity in PFT interpretation. Review of evidence published since then that challenges current practice and continued discussion concluded with a recommendation to replace race/ethnicity-specific equations with race-neutral average reference equations, which must be accompanied with broader re-evaluation of how PFTs are used to make clinical/employment/insurance decisions. There was also a call to engage key stakeholders not represented in this workshop and a statement of caution regarding the uncertain effects and potential harms of this change. Other recommendations include continued research and education to understand the impact of the change, to improve the evidence for the use of PFTs in general, and to identify modifiable risk factors for reduced pulmonary function.

PMID:36973004 | DOI:10.1164/rccm.202302-0310ST

J Cyst Fibros. 2023 Mar 25:S1569-1993(23)00072-3. doi: 10.1016/j.jcf.2023.03.009. Online ahead of print.

ABSTRACT

BACKGROUND: Cystic fibrosis (CF) neutrophils fail to eradicate infection despite their massive recruitment into the lung. While studies mostly focus on pathogen clearance by normal density neutrophils in CF, the contribution of low-density neutrophil (LDNs) subpopulations to disease pathogenesis remains unclear.

METHODS: LDNs were isolated from whole blood donations of clinically stable adult CF patients and from healthy donors. LDN proportion and immunophenotype was assessed by flow cytometry. Associations of LDNs with clinical parameters were determined.

RESULTS: LDN proportion was increased in CF patients' circulation compared with healthy donors. LDNs are a heterogeneous population of both mature and immature cells in CF and in healthy individuals. Moreover, a higher proportion of mature LDN correlates with a gradual decline in lung function and repeated pulmonary exacerbations in CF patients.

CONCLUSIONS: Collectively, our observations suggest that low-density neutrophils are linked to CF pathogenesis and underscore the potential clinical relevance of neutrophil subpopulations in CF.

PMID:36973151 | DOI:10.1016/j.jcf.2023.03.009

Microbiol Spectr. 2023 Mar 27:e0225122. doi: 10.1128/spectrum.02251-22. Online ahead of print.

ABSTRACT

Lumacaftor-ivacaftor is a cystic fibrosis transmembrane conductance regulator (CFTR) modulator combination approved for patients with cystic fibrosis (CF) who are homozygous for the F508del allele. This treatment showed significant clinical improvement; however, few studies have addressed the evolution of the airway microbiota-mycobiota and inflammation in patients receiving lumacaftor-ivacaftor treatment. Seventy-five patients with CF aged 12 years or older were enrolled at the initiation of lumacaftor-ivacaftor therapy. Among them, 41 had spontaneously produced sputa collected before and 6 months after treatment initiation. Airway microbiota and mycobiota analyses were performed via high-throughput sequencing. Airway inflammation was assessed by measuring the calprotectin levels in sputum; the microbial biomass was evaluated via quantitative PCR (qPCR). At baseline (n = 75), bacterial alpha-diversity was correlated with pulmonary function. After 6 months of lumacaftor-ivacaftor treatment, a significant improvement in the body mass index and a decreased number of intravenous antibiotic courses were noted. No significant changes in bacterial and fungal alpha- and beta-diversities, pathogen abundances, or calprotectin levels were observed. However, for patients not chronically colonized with Pseudomonas aeruginosa at treatment initiation, calprotectin levels were lower, and a significant increase in bacterial alpha-diversity was observed at 6 months. This study shows that the evolution of the airway microbiota-mycobiota in CF patients depends on the patient's characteristics at lumacaftor-ivacaftor treatment initiation, notably chronic colonization with P. aeruginosa. IMPORTANCE The management of cystic fibrosis has been transformed recently by the advent of CFTR modulators, including lumacaftor-ivacaftor. However, the effects of such therapies on the airway ecosystem, particularly on the microbiota-mycobiota and local inflammation, which are involved in the evolution of pulmonary damage, are unclear. This multicenter study of the evolution of the microbiota under protein therapy supports the notion that CFTR modulators should be started as soon as possible, ideally before the patient is chronically colonized with P. aeruginosa. (This study has been registered at ClinicalTrials.gov under identifier NCT03565692).

PMID:36971560 | DOI:10.1128/spectrum.02251-22

mSphere. 2023 Mar 27:e0008323. doi: 10.1128/msphere.00083-23. Online ahead of print.

ABSTRACT

Regulation of porin expression in bacteria is complex and often involves small-RNA regulators. Several small-RNA regulators have been described for Burkholderia cenocepacia, and this study aimed to characterize the biological role of the conserved small RNA NcS25 and its cognate target, outer membrane protein BCAL3473. The B. cenocepacia genome carries a large number of genes encoding porins with yet-uncharacterized functions. Expression of the porin BCAL3473 is strongly repressed by NcS25 and activated by other factors, such as a LysR-type regulator and nitrogen-depleted growth conditions. The porin is involved in transport of arginine, tyrosine, tyramine, and putrescine across the outer membrane. Porin BCAL3473, with NcS25 as a major regulator, plays an important role in the nitrogen metabolism of B. cenocepacia. IMPORTANCE Burkholderia cenocepacia is a Gram-negative bacterium which causes infections in immunocompromised individuals and in people with cystic fibrosis. A low outer membrane permeability is one of the factors giving it a high level of innate resistance to antibiotics. Porins provide selective permeability for nutrients, and antibiotics can also traverse the outer membrane by this means. Knowing the properties and specificities of porin channels is therefore important for understanding resistance mechanisms and for developing new antibiotics and could help in overcoming permeability issues in antibiotic treatment.

PMID:36971554 | DOI:10.1128/msphere.00083-23

Microbiol Spectr. 2023 Mar 27:e0377422. doi: 10.1128/spectrum.03774-22. Online ahead of print.

ABSTRACT

Pseudomonas aeruginosa commonly infects hospitalized patients and the lungs of individuals with cystic fibrosis. This species is known for forming biofilms, which are communities of bacterial cells held together and encapsulated by a self-produced extracellular matrix. The matrix provides extra protection to the constituent cells, making P. aeruginosa infections challenging to treat. We previously identified a gene, PA14_16550, which encodes a DNA-binding TetR-type repressor and whose deletion reduced biofilm formation. Here, we assessed the transcriptional impact of the 16550 deletion and found six differentially regulated genes. Among them, our results implicated PA14_36820 as a negative regulator of biofilm matrix production, while the remaining 5 had modest effects on swarming motility. We also screened a transposon library in a biofilm-impaired ΔamrZ Δ16550 strain for restoration of matrix production. Surprisingly, we found that disruption or deletion of recA increased biofilm matrix production, both in biofilm-impaired and wild-type strains. Because RecA functions both in recombination and in the DNA damage response, we asked which function of RecA is important with respect to biofilm formation by using point mutations in recA and lexA to specifically disable each function. Our results implied that loss of either function of RecA impacts biofilm formation, suggesting that enhanced biofilm formation may be one physiological response of P. aeruginosa cells to loss of either RecA function. IMPORTANCE Pseudomonas aeruginosa is a notorious human pathogen well known for forming biofilms, communities of bacteria that protect themselves within a self-secreted matrix. Here, we sought to find genetic determinants that impacted biofilm matrix production in P. aeruginosa strains. We identified a largely uncharacterized protein (PA14_36820) and, surprisingly, RecA, a widely conserved bacterial DNA recombination and repair protein, as negatively regulating biofilm matrix production. Because RecA has two main functions, we used specific mutations to isolate each function and found that both functions influenced matrix production. Identifying negative regulators of biofilm production may suggest future strategies to reduce the formation of treatment-resistant biofilms.

PMID:36971546 | DOI:10.1128/spectrum.03774-22

Int J Pharm X. 2023 Mar 11;5:100178. doi: 10.1016/j.ijpx.2023.100178. eCollection 2023 Dec.

ABSTRACT

The potential gain in efficacy of pulmonary administration over IV administration of some antibiotics such as ciprofloxacin (CIP) may be limited by the short residence time of the drug at the site of infection after nebulization. Complexation of CIP with copper reduced its apparent permeability in vitro through a Calu-3 cell monolayer and greatly increased its pulmonary residence time after aerosolisation in healthy rats. Chronic P. aeruginosa lung infections in cystic fibrosis patients result in airway and alveolar inflammation that may increase the permeability of inhaled antibiotics and alter their fate in the lung after inhalation compared to what was seen in healthy conditions. The objective of this study was to compare the pharmacokinetics and efficacy of CIP-Cu2+ complex-loaded microparticles administered by pulmonary route with a CIP solution administered by IV to model rats with chronic lung infection. After a single pulmonary administration of microparticles loaded with CIP-Cu2+ complex, pulmonary exposure to CIP was increased 2077-fold compared to IV administration of CIP solution. This single lung administration significantly reduced the lung burden of P. aeruginosa expressed as CFU/lung measured 24 h after administration by 10-fold while IV administration of the same dose of CIP was ineffective compared to the untreated control. This better efficacy of inhaled microparticles loaded with CIP-Cu2+ complex compared with CIP solution can be attributed to the higher pulmonary exposure to CIP obtained with inhaled CIP-Cu2+ complex-loaded microparticles than that obtained with IV solution.

PMID:36970713 | PMC:PMC10033950 | DOI:10.1016/j.ijpx.2023.100178

Oncoimmunology. 2023 Mar 21;12(1):2189823. doi: 10.1080/2162402X.2023.2189823. eCollection 2023.

ABSTRACT

Formyl peptide receptor-1 (FPR1) is a pathogen recognition receptor involved in the detection of bacteria, in the control of inflammation, as well as in cancer immunosurveillance. A single nucleotide polymorphism in FPR1, rs867228, provokes a loss-of-function phenotype. In a bioinformatic study performed on The Cancer Genome Atlas (TCGA), we observed that homo-or heterozygosity for rs867228 in FPR1 (which affects approximately one-third of the population across continents) accelerates age at diagnosis of specific carcinomas including luminal B breast cancer by 4.9 years. To validate this finding, we genotyped 215 patients with metastatic luminal B mammary carcinomas from the SNPs To Risk of Metastasis (SToRM) cohort. The first diagnosis of luminal B breast cancer occurred at an age of 49.2 years for individuals bearing the dysfunctional TT or TG alleles (n = 73) and 55.5 years for patients the functional GG alleles (n = 141), meaning that rs867228 accelerated the age of diagnosis by 6.3 years (p=0.0077, Mann & Whitney). These results confirm our original observation in an independent validation cohort. We speculate that it may be useful to include the detection of rs867228 in breast cancer screening campaigns for selectively increasing the frequency and stringency of examinations starting at a relatively young age.

PMID:36970071 | PMC:PMC10038022 | DOI:10.1080/2162402X.2023.2189823

Front Pharmacol. 2023 Mar 9;14:1130374. doi: 10.3389/fphar.2023.1130374. eCollection 2023.

ABSTRACT

Background: Pseudomonas aeruginosa is the most common microorganism found in the sputum culture of Cystic fibrosis (CF) patients causing the pulmonary destruction. Aminoglycosides have a low diffuse rate from lipid membranes, and respiratory system secretions. Regarding the burden of pulmonary exacerbation caused by the pseudomonas aeruginosa in cystic fibrosis patients in the long term and the limited number of clinical trials focused on appropriate treatment strategies, the present study evaluated the concurrent inhaled and intravenous aminoglycoside antibiotics for pulmonary exacerbation caused by the pseudomonas aeruginosa as a safe and effective treatment in children. Method: This study was a blinded, randomized clinical trial phase conducted in a tertiary referral pediatric teaching hospital from May 2021 to May 2022. The patients were randomly allocated to receive intravenously administered ceftazidime and Amikacin alone or with inhaled Amikacin. Forced expiratory volume (FEV1), Amikacin via the level, kidney function tests, audiometry, inflammatory markers (erythrocyte sedimentation rate and C-reactive protein), hospital stay, and bacterial eradication rate were compared in two therapy groups. Results: the average FEV1 has increased by 47% in Neb + group compared to Neb- group following treatment. Hospital stay was lower in Neb + group. No renal toxicity or ototoxicity was observed in both therapy groups. Pseudomonas aeruginosa eradication rate Neb- and Neb + groups were 44% and 69%, respectively (p-value = 0.15). Conclusion: Concurrent inhaled and intravenous Amikacin is safe and effective to treat Pseudomonas aeruginosa exacerbation in CF patients. Moreover, co-delivery antibiotics' route treatment increased the eradication rate. Although not statistically significant, never the less, it is clinically relevant. The intervention reduced the length of hospitalization in this group. Clinical Trial Registration: clinicaltrials.gov, identifier [IRCT20120415009475N10].

PMID:36969859 | PMC:PMC10034196 | DOI:10.3389/fphar.2023.1130374

Front Pharmacol. 2023 Mar 8;14:1125853. doi: 10.3389/fphar.2023.1125853. eCollection 2023.

ABSTRACT

Since the introduction of CFTR modulator therapies, longitudinal real-life data of lung clearance index (LCI) during treatment is scarce. In this single-centre, post-approval setting, we report data of 51 patients with different stages of lung disease, age 2-52 years with repeated measurements of forced expiratory volume as a percentage of the predicted value (ppFEV₁) and LCI after 2, 4, and 16 weeks of CFTR modulator treatment and at baseline. In 25 patients during elexacaftor/tezacaftor/ivacaftor (ELX/TEZ/IVA) treatment, significant improvements of LCI (median -1.4) and ppFEV₁ (median +8.3%) were observed after only 2 weeks, and were maintained after 4 and 16 weeks of treatment (LCI: -2.0, -2.2; ppFEV₁: +7.2%, +11.8%). We observed a significant correlation between LCI improvement at week 16 and lower baseline LCI. In 26 younger and healthier patients receiving lumacaftor/ivacaftor (LUM/IVA) treatment, no significant changes of LCI and ppFEV₁ occured. With ELX/TEZ/IVA, our data shows rapid, significant improvements of LCI and ppFEV₁ already after 2 weeks. Early LCI measurements can help to assess the patient's response to this high-cost therapy.

PMID:36969845 | PMC:PMC10030732 | DOI:10.3389/fphar.2023.1125853

Front Physiol. 2023 Mar 10;14:1111647. doi: 10.3389/fphys.2023.1111647. eCollection 2023.

ABSTRACT

Across the globe, millions of people are affected by muco-obstructive pulmonary diseases like cystic fibrosis, asthma, and chronic obstructive pulmonary disease. In MOPDs, the airway mucus becomes hyperconcentrated, increasing viscoelasticity and impairing mucus clearance. Research focused on treatment of MOPDs requires relevant sources of airway mucus both as a control sample type and as a basis for manipulation to study the effects of additional hyperconcentration, inflammatory milieu, and biofilm growth on the biochemical and biophysical properties of mucus. Endotracheal tube mucus has been identified as a prospective source of native airway mucus given its several advantages over sputum and airway cell culture mucus such as ease of access and in vivo production that includes surface airway and submucosal gland secretions. Still, many ETT samples suffer from altered tonicity and composition from either dehydration, salivary dilution, or other contamination. Herein, the biochemical compositions of ETT mucus from healthy human subjects were determined. Samples were characterized in terms of tonicity, pooled, and restored to normal tonicity. Salt-normalized ETT mucus exhibited similar concentration-dependent rheologic properties as originally isotonic mucus. This rheology agreed across spatial scales and with previous reports of the biophysics of ETT mucus. This work affirms previous reports of the importance of salt concentration on mucus rheology and presents methodology to increase yield native airway mucus samples for laboratory use and manipulation.

PMID:36969580 | PMC:PMC10036356 | DOI:10.3389/fphys.2023.1111647

Front Pediatr. 2023 Mar 9;11:1127659. doi: 10.3389/fped.2023.1127659. eCollection 2023.

ABSTRACT

BACKGROUND: Some infants undergoing newborn screening (NBS) tests have inconclusive sweat chloride test (SCT) results that lead to the designation of Cystic Fibrosis Screen Positive, Inconclusive Diagnosis/CFTR-related metabolic syndrome (CFSPID/CRMS). Some proportion of them transition to a CF diagnosis, but no predictive markers can stratify which are at risk for this transition. We report single-center outcomes of children with CRMS.

METHODS: We retrospectively identified all infants born in Alabama from 2008 through 2020 referred to our CF Center with an elevated immunoreactive trypsinogen level (IRT) associated with a cystic fibrosis transmembrane conductance regulator (CFTR) mutation (IRT+/DNA+) who had at least one SCT result documented. Infants were classified per established guidelines as Carrier, CRMS, or CF based on the IRT+/DNA+ and SCT results. The electronic health record was reviewed for follow-up visits until the children received a definitive diagnosis (to carrier or CF) according to current diagnostic guidelines for CF, or through the end of the 2020 year.

RESULTS: Of the 1,346 infants with IRT+ and at least 1 CFTR mutation identified (IRT+/DNA+), 63 (4.7%) were designated as CRMS. Of these infants, 12 (19.1%) transitioned to Carrier status (CRMS-Carrier), 40 (63.5%) of them remained CRMS status (CRMS-Persistent) and 11 (17.5%) of them transitioned to a diagnosis of CF (CRMS-CF). Of the 11 children in the CRMS-CF group, 4 (36%) had an initial SCT 30-39 mmol/L, 4 (36%) had an initial SCT 40-49 mmol/L and 3 (27%) had an initial SCT 50-59 mmol/L. These children also had higher initial sweat tests and greater yearly increases in sweat chloride values than others with CRMS. We found that in comparison to children in the CRMS-P group, a greater proportion of children in the CRMS-CF group cultured bacteria like methicillin-resistant Staphylococcus aureus, Stenotrophomonas maltophilia, and Pseudomonas aeruginosa, had smaller weight-for-height percentiles and remained smaller over time despite slightly greater growth.

CONCLUSION: Infants with an inconclusive diagnosis of CF should continue to receive annual care and management given their potential risk of transition to CF. Further research is needed to assess whether certain phenotypic patterns, clinical symptoms, diagnostic tests or biomarkers could better stratify these children.

PMID:36969284 | PMC:PMC10034052 | DOI:10.3389/fped.2023.1127659

ACS Cent Sci. 2023 Mar 1;9(3):540-550. doi: 10.1021/acscentsci.2c01487. eCollection 2023 Mar 22.

ABSTRACT

The Burkholderia cepacia complex (Bcc) is a group of bacteria including opportunistic human pathogens. Immunocompromised individuals and cystic fibrosis patients are especially vulnerable to serious infections by these bacteria, motivating the search for compounds with antimicrobial activity against the Bcc. Ubonodin is a lasso peptide with promising activity against Bcc species, working by inhibiting RNA polymerase in susceptible bacteria. We constructed a library of over 90 000 ubonodin variants with 2 amino acid substitutions and used a high-throughput screen and next-generation sequencing to examine the fitness of the entire library, generating the most comprehensive data set on lasso peptide activity so far. This screen revealed information regarding the structure-activity relationship of ubonodin over a large sequence space. Remarkably, the screen identified one variant with not only improved activity compared to wild-type ubonodin but also a submicromolar minimum inhibitory concentration (MIC) against a clinical isolate of the Bcc member Burkholderia cenocepacia. Ubonodin and several of the variants identified in this study had lower MICs against certain Bcc strains than those of many clinically approved antibiotics. Finally, the large library size enabled us to develop DeepLasso, a deep learning model that can predict the RNAP inhibitory activity of an ubonodin variant.

PMID:36968541 | PMC:PMC10037499 | DOI:10.1021/acscentsci.2c01487

Front Cell Infect Microbiol. 2023 Mar 9;13:1144210. doi: 10.3389/fcimb.2023.1144210. eCollection 2023.

ABSTRACT

Mycobacterium abscessus (Mab), an emerging opportunistic pathogen, predominantly infects individuals with underlying pulmonary diseases such as cystic fibrosis (CF). Current treatment outcomes for Mab infections are poor due to Mab's inherent antibiotic resistance and unique host interactions that promote phenotypic tolerance and hinder drug access. The hypoxic, mucus-laden airways in the CF lung and antimicrobial phagosome within macrophages represent hostile niches Mab must overcome via alterations in gene expression for survival. Regulatory mechanisms important for the adaptation and long-term persistence of Mab within the host are poorly understood, warranting further genetic and transcriptomics study of this emerging pathogen. DosRS Mab , a two-component signaling system (TCS), is one proposed mechanism utilized to subvert host defenses and counteract environmental stress such as hypoxia. The homologous TCS of Mycobacterium tuberculosis (Mtb), DosRS Mtb , is known to induce a ~50 gene regulon in response to hypoxia, carbon monoxide (CO) and nitric oxide (NO) in vitro and in vivo. Previously, a small DosR Mab regulon was predicted using bioinformatics based on DosR Mtb motifs however, the role and regulon of DosRS Mab in Mab pathogenesis have yet to be characterized in depth. To address this knowledge gap, our lab generated a Mab dosRS knockout strain (MabΔdosRS) to investigate differential gene expression, and phenotype in an in vitro hypoxia model of dormancy. qRT-PCR and lux reporter assays demonstrate Mab_dosR and 6 predicted downstream genes are induced in hypoxia. In addition, RNAseq revealed induction of a much larger hypoxia response comprised of >1000 genes, including 127 differentially expressed genes in a dosRS mutant strain. Deletion of DosRS Mab led to attenuated growth under low oxygen conditions, a shift in morphotype from smooth to rough, and down-regulation of 216 genes. This study provides the first look at the global transcriptomic response of Mab to low oxygen conditions encountered in the airways of CF patients and within macrophage phagosomes. Our data also demonstrate the importance of DosRS Mab for adaptation of Mab to hypoxia, highlighting a distinct regulon (compared to Mtb) that is significantly larger than previously described, including both genes conserved across mycobacteria as well as Mab-specific genes.

PMID:36968107 | PMC:PMC10034137 | DOI:10.3389/fcimb.2023.1144210

Heliyon. 2023 Mar 14;9(3):e14568. doi: 10.1016/j.heliyon.2023.e14568. eCollection 2023 Mar.

ABSTRACT

Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), the Cl-/HCO3 - channel implicated in Cystic Fibrosis, is critical to the pathophysiology of many gastrointestinal diseases. Defects in CFTR lead to intestinal dysfunction, malabsorption, obstruction, infection, inflammation, and cancer that increases morbidity and reduces quality of life. This review will focus on CFTR in the intestine and the implications of the subpopulation of CFTR High Expresser Cells (CHEs) in Cystic Fibrosis (CF), intestinal physiology and pathophysiology of intestinal diseases.

PMID:36967909 | PMC:PMC10031467 | DOI:10.1016/j.heliyon.2023.e14568

Transplant Cell Ther. 2023 Mar 24:S2666-6367(23)01198-3. doi: 10.1016/j.jtct.2023.03.022. Online ahead of print.

ABSTRACT

BACKGROUND: Chimeric antigen receptor (CAR) T-cell therapy is a promising approach to improve survival for children and adults with relapsed/refractory (r/r) B-ALL, but these clinical trials may not be equally accessible to patients with low socioeconomic status or to patients from racial or ethnic minority groups.

OBJECTIVE: We sought to describe the sociodemographic characteristics of pediatric and AYA patients enrolled in CAR T-cell clinical trials and to compare these characteristics to other patients with r/r B-ALL.

STUDY DESIGN: We conducted a multicenter retrospective cohort study at five pediatric consortium sites to compare the sociodemographic characteristics of patients treated and enrolled in CAR T-cell trials at their home institution, other patients with r/r B-ALL treated at these sites, and patients referred from an external hospital for CAR T-cell trials. Patients were age 0-27 years with r/r B-ALL treated at one of the consortium sites between 2012-2018. Clinical and demographic data were collected from the electronic health record. We calculated distance from home to treating institution and assigned socioeconomic status scores based on census tract.

RESULTS: Among 337 patients treated for r/r B-ALL, 112 were referred from an external hospital to a consortium site and enrolled in a CAR T-cell trial; 225 were treated primarily at a consortium site, with 34% enrolled in a CAR T-cell trial. Patients treated primarily at a consortium site had similar characteristics, regardless of trial enrollment. A lower proportion of Hispanic patients (37% vs. 56%, p=0.03), patients whose preferred language was Spanish (8% vs. 22%, p=0.006), and publicly insured patients (38% vs. 65%, p=0.001) were referred from an external hospital compared to patients treated primarily at a consortium site and enrolled in a CAR T-cell trial.

CONCLUSIONS: Patients who are Hispanic, Spanish-speaking, or publicly insured are underrepresented in referrals from external hospitals to CAR T-cell centers. External provider implicit bias may also influence referral of these patients. Establishing partnerships between CAR T-cell centers and external hospital sites may improve provider familiarity, patient referral, and patient access to CAR T-cell clinical trials.

PMID:36966871 | DOI:10.1016/j.jtct.2023.03.022