ABSTRACT
RATIONALE: There has been a sustained interest in chronic cough, defined as 8 to 12 weeks of daily coughing (adults) or 4 weeks (children). The interest was initially driven by discrimination of cough based on etiology and response to therapy, and the proposed diagnosis of refractory chronic cough when other major etiologies have been excluded. Perhaps not coincidentally, the convergence of cough counting as a valid method of assessing response to therapy (necessary and sufficient) with the clinical development of first generation P2X3 inhibitors has led to the emergence of a number of patient-oriented devices that claim to count coughs. The emergence of “COVID cough” and “post COVID cough” have heightened the interest in cough. METHODS: The Strados Labs RESPTM has been validated to count coughs. Presented are three methods to count coughs in a continuous recording, in order of increased automation. Each validated method has been confirmed to be within +/- 10% of the true cough count for the gold standard recordings. Each method is validated using >6 patients (>48 hours) of continuous recordings. Number of coughs are annotated by trained professionals and are then reviewed by clinical professionals. This is the gold standard cough count. Cough Counting Methods:1.Multiple trained labelers listen to the recordings and agree on if a sound is a cough or not. The number of agreed upon coughs are added together to determine a total cough count. 2.A highly sensitive machine learning algorithm highlights samples that have a probable likelihood of a cough. Multiple trained labelers listen to recordings and agree if a cough or not. 3.Fully automated machine learning algorithm. RESULTS: In comparison with the gold standard, the highly sensitive method was (>98% sensitivity, and the fully automated machine learning algorithm is >90% specific and >90% accurate and reports the number of coughs. CONCLUSIONS: The process shown here is both necessary and sufficient to validate cough data collection using the RESP. However, unlike other approaches, the RESP provides significant quantitative and qualitative data beyond counting coughs. The RESP provides spectrograms and chest wall motion as well as archival recordings so that parsing coughs into single, multiple and spasms can be reclassified as the data set and science expand. Cough architecture can be evaluated to differentiate intrathoracic from extra-thoracic cough, cough onset in inspiration versus expiration, and response to therapy in real time and with increased anatomic certainty.
ABSTRACT
INTRODUCTION: The nasal methicillin resistant Staphyloccocus aureus (MRSA) polymerase chain reaction (PCR) screen has important antimicrobial stewardship implications for respiratory infections. The MRSA PCR test has a high negative predictive value for MRSA pulmonary infections. Universal decolonization with mupirocin prior to the assay may reduce the reliability of the screen. Intranasal povidone iodine is an alternative agent used for universal decolonization in the ICU. The impact of the nasal MRSA PCR screen's negative predictive value after the use of intranasal povidone iodine has not been evaluated, so our objective was to evaluate the performance of the nasal MRSA screening test after administration of povidone iodine. METHODS: We conducted a single-center, retrospective study that evaluated the performance of a nasal MRSA screen in critically ill, adult patients undergoing intranasal povidone iodine suppression from January 1st, 2020 to June 1st, 2021. Patients were included if they received intravenous vancomycin for a suspected pulmonary infection and had blood and/or respiratory cultures available. Exclusion criteria were as follows: coinfection from a presumed nonpulmonary source, known MRSA infection in the 30 days prior to the MRSA nasal screen, more than one dose of an anti-MRSA agent (other than vancomycin) prior to the PCR assay, MRSA screen more than 14 days before suspected infection, pregnancy, incarceration, and active severe acute respiratory syndrome coronavirus 2 infection. The primary outcome was the negative predictive value of the nasal MRSA screen. RESULTS: A total of 201 patients were screened for eligibility. 150 patients were excluded leaving 51 patients eligible for analysis. 32 patients received povidone iodine before the MRSA screen, and 19 patients received povidone iodine after the MRSA screen. Notably, none of the included patients had a positive MRSA culture. The negative predictive value of the nasal MRSA screen was 100% in both groups. Furthermore, specificity of the screen was 90.6% and 94.7% in the before and after groups, respectively. CONCLUSIONS: Preliminary data from this project suggests that the MRSA PCR screen may retain its reliability even if conducted after the administration of povidone iodine. Further prospective studies are needed to validate these results.
ABSTRACT
Random mutations and recombinations are the main sources for the genetic diversity in SARS-CoV-2, with mutations in the SARS-CoV-2 spike (S) receptor binding motif (RBM) representing a high potential for the emergence of new putative variants under investigation (VUI) or variants of concern (VOC). It is of importance, to measure the different circulating SARS-CoV-2 lineages in order to establish a regional SARS-CoV-2 surveillance program. We established whole genome sequencing (WGS) of circulating SARS-CoV-2 lineages in order to establish a regional SARS-CoV-2 surveillance program. We established a surveillance program for circulating SARS-CoV-2 lineages by performing whole genome sequencing (WGS) in SARS-CoV-2 isolates. Specimens were collected over a period of 5 months from three different sites. Specimens were collected from both patients suffering from COVID-19 and from outpatients without any clinical signs or symptoms;both in a tertiary university hospital, and two private laboratories within an urban area of eastern part Germany. Viral WGS from the 364 respiratory specimens with positive SARS-CoV-2 RT-PCR comprised 16 different SARS-CoV-2 lineages. The majority of the obtained sequences (252/364=69%) was assigned to the variant of concern (VOC) Alpha (B.1.1.7). This variant first appeared in February in our samples and quickly became the dominant virus variant. All SNP PCR results could be verified using WGS. Other VOCs found in our cohort were Beta (B.1.351, n=2) and Delta (B.1.617.2, n=1). Lineage analysis revealed 16 different virus variants among 364 respiratory samples analyzed by WGS. The number of distinct lineages dramatically decreased over time in leaving only few variants, in particular, the VOC Alpha or B.1.1.7. By closer inspection of point mutations, we found several distinct mutations of the viral spike protein that were reported to increase affinity or enable immune escape. Within a study period of only 5 months, SARS-CoV-2 lineage B.1.1.7 became the dominant lineage in our study population. This study emphasizes the benefit of SARS-CoV-2 testing by WGS. The increasing use of WGS to sequence the entire SARS-CoV-2 genome will reveal additional VUIs and VOCs with the potential to evade the immune system and, thus, will be a promising tool for data mining of relevant information for epidemiological studies. SARS-CoV-2 lineage monitoring using WGS is an important surveillance tool for early detection of upcoming new lineages of concern. © 2021