Genetic counseling access and service delivery in New York State is variable for parents of infants with complex CFTR genotypes conferring uncertain phenotypes.

BACKGROUND: New York State (NYS) utilizes a three-tiered cystic fibrosis newborn screening (CFNBS) algorithm that includes cystic fibrosis transmembrane conductance regulator (CFTR) gene sequencing. Infants with >1 CFTR variant of potential clinical relevance, including variants of uncertain significance or varying clinical consequence are referred for diagnostic evaluation at NYS cystic fibrosis (CF) Specialty Care Centers (SCCs). AIMS: As part of ongoing quality improvement efforts, demographic, screening, diagnostic, and clinical data were evaluated for 289 CFNBS-positive infants identified in NYS between December 2017 and November 2020 who did not meet diagnostic criteria for CF and were classified as either: CFTR-related metabolic syndrome/CF screen positive, inconclusive diagnosis (CRMS/CFSPID) or CF carriers. RESULTS: Overall, 194/289 (67.1%) had CFTR phasing to confirm whether the infant's CFTR variants were in cis or in trans. Eighteen complex alleles were identified in cis; known haplotypes (p.R117H+5T, p.F508del+p.L467F, and p.R74W+p.D1270N) were the most common identified. Thirty-two infants (16.5%) with all variants in cis were reclassified as CF carriers rather than CRMS/CFSPID. Among 263 infants evaluated at an NYS SCC, 70.3% were reported as having received genetic counseling about their results by any provider, with 96/263 (36.5%) counseled by a certified genetic counselor. CONCLUSION: Given the particularly complex genetic interpretation of results generated by CFNBS algorithms including sequencing analysis, additional efforts are needed to ensure families of infants with a positive CFNBS result have CFTR phasing when needed to distinguish carriers from infants with CRMS/CFSPID, and access to genetic counseling to address implications of CFNBS results.

Risk of aspiration pneumonia in paediatric patients with dysphagia who were found to have laryngeal penetration on the instrumental swallow evaluation: a systematic review protocol.

INTRODUCTION: Dysphagia affects several children in USA and around the globe. Videofluoroscopic Swallow Study (VFSS) and Fiberoptic Endoscopic Evaluation of Swallowing (FEES) are the most objective studies to define swallowing function. The presence of tracheal aspiration during VFSS or FEES in children with dysphagia is associated with an increased risk of aspiration pneumonia. However, the association of laryngeal penetration with aspiration pneumonia remains unclear. This systematic review aims to assess the risk of aspiration pneumonia in children with dysphagia with laryngeal penetration on VFSS/FEES and compare it with children with tracheal aspiration and children with neither tracheal aspiration nor laryngeal penetration. METHODS AND ANALYSIS: This study will be a systematic review and meta-analysis. Systematic electronic searches will be conducted on PubMed, EMBASE, Web of Science, CINHAL, Scopus, Cochrane CENTRAL, LILACS and WHO Global Index Medicus. We will include studies published through 6 October 2021. Primary outcome will be the incidence of aspiration pneumonia. Secondary outcomes will be incidence of hospitalisation, paediatric intensive care unit admission, enteral tube requirement, growth, symptoms improvement and mortality. The Cochrane Risk of Bias In Non-Randomised Studies of Interventions tool will be used to assess the risk of bias. Meta-analysis will be used to pool the studies. We will pool dichotomous outcomes to obtain an odd ratio (OR) and report with 95% CI. Continuous outcomes will be pooled to obtain mean difference and reported with 95% CI. Overall grade of evidence will be assessed using Grading of Recommendations Assessment, Development and Evaluation (GRADE) criteria, and findings will be presented in a summary of findings table. ETHICS AND DISSEMINATION: This study is a systematic review without contact with patients. Therefore, IRB approval is not required. Authors consent to publishing this review. Data will be kept for review by editors and peer reviewers. Data will be available to general public on request. PROSPERO REGISTRATION NUMBER: CRD42020222145.

High-Level Antibiotic Tolerance of a Clinically Isolated Enterococcus faecalis Strain.

Bacteria can survive antibiotic treatment both by acquiring antibiotic resistance genes and through mechanisms of tolerance that are based on phenotypic changes and the formation of metabolically inactive cells. Here, we report an Enterococcus faecalis strain (E. faecalis UM001B) that was isolated from a cystic fibrosis patient and had no increase in resistance but extremely high-level tolerance to ampicillin, vancomycin, and tetracycline. Specifically, the percentages of cells that survived 3.5-h antibiotic treatment (at 100 µg · ml-1) were 25.4% ± 4.3% and 51.9% ± 4.0% for ampicillin and tetracycline, respectively; vancomycin did not exhibit any significant killing. Consistent with the changes in antibiotic susceptibility, UM001B was found to have reduced penetration of ampicillin and vancomycin and accumulation of tetracycline compared to the reference strain ATCC 29212. Based on whole-genome sequencing, four amino acid substitutions were identified in one of the tetracycline efflux pump repressors (TetRs), compared to ATCC 29212. Results of molecular simulations and experimental assays revealed that these mutations could lead to higher levels of tetracycline efflux activity. Consistently, replicating these mutations in Escherichia coli MG1655 increased its tolerance to tetracycline. Overall, these findings provide new insights into the development of multidrug tolerance in E. faecalis, which can facilitate future studies to better control enterococcal infections.IMPORTANCEEnterococcus faecalis represents a major group of pathogens causing nosocomial infections that are resistant to multiple classes of antibiotics. An important challenge associated with E. faecalis infection is the emergence of multidrug-tolerant strains, which have normal MICs but do not respond to antibiotic treatment. Here, we report a strain of E. faecalis that was isolated from a cystic fibrosis patient and demonstrated high-level tolerance to ampicillin, vancomycin, and tetracycline. Whole-genome sequencing revealed critical substitutions in one of the tetracycline efflux pump repressors that are consistent with the increased tolerance of E. faecalis UM001B to tetracycline. These findings provide new information about bacterial antibiotic tolerance and may help develop more effective therapeutics.

Sweat chloride testing in infants identified as heterozygote carriers by newborn screening.

The reference ranges for sweat [C1(-)] were reevaluated in 300 infants referred to our Center as carriers of at least 1 cystic fibrosis mutation identified through newborn screening. The recommended borderline range of 30 to 59 mmol/L failed to identify all individuals who were compound heterozygotes. Our data support using a borderline range of 24 to 59 mmol/L.