Time Of Specimen Collection Research Articles

Profiling of SARS-CoV-2 Subgenomic RNAs in Clinical Specimens.

ABSTRACTSARS-CoV-2 transcribes a set of subgenomic RNAs (sgRNAs) essential for the translation of structural and accessory proteins to sustain its life cycle. We applied RNA-seq on 375 respiratory samples from individual COVID-19 patients and revealed that the majority of the sgRNAs were canonical transcripts with N being the most abundant (36.2%), followed by S (11.6%), open reading frame 7a (ORF7a; 10.3%), M (8.4%), ORF3a (7.9%), ORF8 (6.0%), E (4.6%), ORF6 (2.5%), and ORF7b (0.3%); but ORF10 was not detected. The profile of most sgRNAs, except N, showed an independent association with viral load, time of specimen collection after onset, age of the patient, and S-614D/G variant with ORF7b and then ORF6 being the most sensitive to changes in these characteristics. Monitoring of 124 serial samples from 10 patients using sgRNA-specific real-time RT-PCR revealed a potential of adopting sgRNA as a marker of viral activity. Respiratory samples harboring a full set of canonical sgRNAs were mainly collected early within 1 to 2 weeks from onset, and most of the stool samples (90%) were negative for sgRNAs despite testing positive by diagnostic PCR targeting genomic RNA. ORF7b was the first to become undetectable and again being the most sensitive surrogate marker for a full set of canonical sgRNAs in clinical samples. The potential of using sgRNA to monitor viral activity and progression of SARS-CoV-2 infection, and hence as one of the objective indicators to triage patients for isolation and treatment should be considered.IMPORTANCE Attempts to use subgenomic RNAs (sgRNAs) of SARS-CoV-2 to identify active infection of COVID-19 have produced diverse results. In this work, we applied next-generation sequencing and RT-PCR to profile the full spectrum of SARS-CoV-2 sgRNAs in a large cohort of respiratory and stool samples collected throughout infection. Numerous known and novel discontinuous transcription events potentially encoding full-length, deleted and frameshift proteins were observed. In particular, the expression profile of canonical sgRNAs was associated with genomic RNA level and clinical characteristics. Our study found sgRNAs as potential biomarkers for monitoring infectivity and progression of SARS-CoV-2 infection, which provides an alternative target for the management and treatment of COVID-19 patients.

Evaluation of the Diagnostic Accuracy of Nasal Cavity and Nasopharyngeal Swab Specimens for SARS-CoV-2 Detection via Rapid Antigen Test According to Specimen Collection Timing and Viral Load.

The rapid diagnosis of SARS-CoV-2 is an essential aspect in the detection and control of the spread of COVID-19. We evaluated the accuracy of the rapid antigen test (RAT) using samples from the nasal cavity and nasopharynx based on sample collection timing and viral load. We enrolled 175 patients, of which 71 patients and 104 patients had tested positive and negative, respectively, based on real time-PCR. Nasal cavity and nasopharyngeal swab samples were tested using STANDARD Q COVID-19 Ag tests (Q Ag, SD Biosensor, Korea). The sensitivity of the Q Ag test was 77.5% (95% confidence interval [CI], 67.8–87.2%) for the nasal cavity and 81.7% (95% [CI, 72.7–90.7%) for the nasopharyngeal specimens. The RAT results showed a substantial agreement between the nasal cavity and nasopharyngeal specimens (Cohen’s kappa index = 0.78). The sensitivity of the RAT for nasal cavity specimens exceeded 89% for <5 days after symptom onset (DSO) and 86% for Ct of E and RdRp < 25. The Q Ag test performed fairly well, especially in the early DSO when a high viral load was present, and the nasal cavity swab can be considered an alternative site for the rapid diagnosis of COVID-19.

Effect of body refrigeration on the postmortem formation of gamma hydroxybutyrate in whole blood

Gamma hydroxybutyrate (GHB) levels in biological fluids are known to be increased after death. To date, there have been studies on sample storage conditions and preservatives on the postmortem in vitro formation of GHB. However, only few studies explored the effects of body storage conditions on GHB formation after death. In this study, we determined the effect of body refrigeration during body storage in mortuary refrigerators on postmortem formation of GHB in whole blood samples. A total of 41 fatalities were divided into two groups: Group A with a total refrigeration time less than 10 h and Group B with a total body refrigeration time more than 10 h. Femoral blood was collected 3 times: upon arrival at the mortuary, after 4 h of refrigeration, and at autopsy. Rectal temperatures were recorded at the time of specimen collection. Blood GHB concentration was analyzed by LC-MS/MS. The rate of change in GHB levels was calculated. The study revealed that in the later phase of refrigeration, no difference was observed in the blood GHB levels between the two groups despite differences in the postmortem interval (PMI) and refrigeration time. Moreover, the rate of change in the GHB levels was lower in the group with a longer refrigeration time. Hence, we concluded that once the plateau of postmortem GHB formation is reached in a refrigerated body, further formation is not expected even with prolonged PMI. Early body refrigeration can minimize postmortem GHB production, thereby preventing the incorrect interpretation of analytical results.

Prevalence of ESBL non-CRE Escherichia coli and Klebsiella pneumoniae among clinical isolates collected by the SMART global surveillance programme from 2015 to 2019

This study aimed to determine the prevalence of extended-spectrum β-lactamase (ESBL) non-carbapenem-resistant Enterobacterales (non-CRE) phenotype among clinical Escherichia coli and Klebsiella pneumoniae isolates collected in 2018–2019 for the SMART global surveillance programme and review trends in prevalence over 5 years (2015–2019). MICs were determined by CLSI reference broth microdilution. ESBL non-CRE phenotypes were defined as non-susceptible to ceftriaxone (MIC ≥ 2 μg/mL) and susceptible to ertapenem (MIC ≤ 0.5 μg/mL). In 2018–2019, ESBL non-CRE phenotypes among E. coli were more common in respiratory tract infection isolates than other infection sources across all global regions; for K. pneumoniae there was wide variation by geographic region in the specimen source most frequently associated with this phenotype. In most regions, ESBL non-CRE phenotype isolates were found more frequently in samples from ICU patients than non-ICU patients and from patients with hospital length of stay at time of specimen collection ≥48 h versus <48 h. ESBL non-CRE phenotypes exceeded 50% of isolates for E. coli from India, Thailand, Vietnam, China, Russia, Mexico, Kenya and Kuwait and for K. pneumoniae from Lithuania and Kuwait. ESBL non-CRE phenotype E. coli increased significantly (P < 0.05) in Asia (excluding China), Australia/New Zealand and Latin America from 2015–2019, while ESBL non-CRE phenotype K. pneumoniae increased significantly in Latin America, USA and Canada. There was marked variability in ESBL rates across countries, over time, and by sample source and ward type. Trending data from 2015–2019 showed ESBL rates are increasing in many regions worldwide.

P250 Clinical validation of a point of care test for fecal calprotectin in distinguishing irritable bowel syndrome from Inflammatory Bowel Disease

Abstract Background Calprotectin is a small calcium-binding protein that when measured in human stool has shown utility in assessing the degree of bowel inflammation in inflammatory bowel disease (IBD) and in distinguishing IBD from irritable bowel syndrome (IBS). However, most fecal calprotectin (FCP) assays are slow and inconvenient. This study examined the analytical agreement and clinical utility of a point of care (POC) assay for FCP. Methods A fast (~5 min.), time-resolved fluorescence resonance energy transfer based immunoassay (Procise FCP™) was developed for the POC measurement of FCP using 15 mg of fecal specimen eluted in collection fluid from the Procise Stool Collection Device™. The analytical agreement between the Procise FCP assay and a commercial ELISA assay: Inova Quanta Lite Calprotectin Extended Range was assessed using 46 leftover deidentified fecal specimens. Clinical performance of the assay was assessed using stored frozen stool specimens from a nested cohort derived from a prospective study of chronic diarrhea patients. Chronic diarrhea was defined as unexplained diarrhea of at least 4 weeks duration. Study subjects were males and females of ages 2 – 70 with no chronic liver disease and were consecutively enrolled. Diagnoses were made by attending physicians, and IBD patients did not necessarily have active disease beyond diarrhea at the time of specimen collection. Primary endpoint: Proportion of patients diagnosed with either IBS or IBD testing positive for FCP. Statistical analysis Method comparison analysis was performed by Deming linear regression. A post hoc analysis of patients from the diarrhea study diagnosed with either IBS or IBD was performed. The significance of the proportion of patients diagnosed with either IBS or IBD testing positive for FCP was calculated using Fisher’s Exact Probability Test. The assay was assessed at cut-offs of 50 µg/g and 120 µg/g. Results Figure 1. Table 1. Table 2. Conclusion The Procise FCP assay shows excellent analytical agreement to another commercial FCP assay and can clinically significantly distinguish between IBD and IBS in chronic diarrhea patients. Thus, the assay can aid in the differentiation of IBD from IBS. Distinguishing IBS from IBD with a convenient POC format test enhances the clinical utility of FCP by enabling faster treatment response

Performance of a Rapid Diagnostic Test for Influenza in a Tertiary Military Hospital, Philippines.

It is important to evaluate the performance of existing rapid influenza diagnostic tests (RIDTs) and the factors that can affect performance especially when the circulation dynamics of influenza strains change such as the displacement and replacement of the circulating seasonal influenza strains. Nasal swabs were collected from patients presenting at V Luna Medical Center, Armed Forces of the Philippines Health Service Command, with influenza-like illness (ILI) with one swab tested using Quickvue (QV) influenza A+B RIDT (Quidel) and the other swab tested using the ABI 7500 (Applied Biosystems) real-time reverse transcriptase-polymerase chain reaction. Sensitivity, specificity, positive predictive value, and negative predictive value were estimated. We identified clinical symptoms predictive of influenza subtype and evaluated the independence of QV sensitivity on (1) Cycle threshold (Ct) value, controlling for timing of collection; (2) timing of collection, controlling for Ct value; and (3) Ct value and timing of collection taken together. Between August 2011 and October 2016, patients presenting with ILI (n = 2333) underwent testing. Quickvue sensitivity across all subtypes was significantly correlated with lower Ct values (higher virus titers) (P <.001) and, except for flu A/H3 (P = .974), was also significantly associated with timing of specimen collection (P <.05). No statistically significant difference was noted in QV sensitivity for Flu A/H3 (P = .130), pandemic H1/N1 (P = .207), Flu A/H3 + pandemic H1/N1 (P = .341), and Flu B (P = .103) across different age groups but sensitivity of QV significantly differed (P <.001) across the different influenza subtypes. Overall specificity of QV was high across all flu subtypes, but overall sensitivity was low (Flu A/pdm H1) to moderate (Flu A/H3 and Flu B). The findings highlight the need to develop more sensitive influenza RDTs to detect circulating influenza strains and the use of the quadrivalent flu vaccine during the annual influenza vaccination.

21-Deoxycortisol is a Key Screening Marker for 21-Hydroxylase Deficiency

To assess whether 21-deoxycortisol (21deoxy) can be used to predict 21-hydroxylase deficiency (21OHD) in newborns and to evaluate the influence of gestational age and the timing of collection on 21deoxy concentrations. 17-hydroxyprogesterone (17OHP) and 21deoxy levels were measured in 906 newborn screening specimens (851 unaffected newborns, 55 confirmed cases of 21OHD) to compare their ability to identify babies with 21OHD. In addition, these 2 steroids were assessed in the unaffected cohort to determine the influence of gestational age (ranging from 23 to 42weeks) and the timing of specimen collection on the measured concentrations. The gestational age of the newborn impacted both 17OHP and 21deoxy concentrations, but the degree of influence was more substantial for 17OHP. Timing of collection did not affect 21deoxy concentration. Moreover, 21deoxy was a better predictor of 21OHD status compared with 17OHP, with little overlap in concentrations between the unaffected population and confirmed cases of 21OHD. A streamlined decision tree using solely 21deoxy (cutoff value, 0.85ng/mL) yielded a 91.7% positive predictive value for 21OHD screening. Our findings demonstrate that 21deoxy is a key disease marker of 21OHD and can be used to improve the accuracy of newborn screening for this disorder.

Bacterial urine profile and optimal urine specimen collection timing in asymptomatic chronically catheterized adults with spinal cord injuries and disorders

Adults with spinal cord injuries and disorders (SCI/D) require chronic indwelling catheterization which is associated with an increased risk of catheter-associated (CA) adverse events. We studied urine samples (culture and urinalysis) from 2 cohorts of chronically catheterized males with SCI/D. Cohort 1 included 28 participants; 3 samples per patient were collected (before, after, and 7 days after catheter change). Cohort 2 included 21 participants; 7 samples per patient were collected (before, immediately after, 30 minutes, 1 hour, 1 day, 2 days, and 7 days after catheter change). A statistically significant decrease in the post catheter change percentage of "significant cultures" was found in both our cohorts (P<.05). Additionally, our second cohort demonstrated a significant decrease in the number of organisms growing at 100.000 cfu/mL (median=-1, mean=-1.5, P=.0006) and in urinalysis bacterial numbers (median=-0.5, mean=-1, P=.006) from pre- to 1-hour post catheter removal. Although there appears to be an improvement of organism burden seen after catheter change, this is only temporary, and its significance in chronically catheterized patients is still unknown. Our second cohort demonstrated an optimal time for sample collection at the 1-hour post-catheter change sample, but further research is required for the extrapolation of these findings.

Deep Learning Model to Predict Serious Infection Among Children With Central Venous Lines.

Objective: Predict the onset of presumed serious infection, defined as a positive blood culture drawn and new antibiotic course of at least 4 days (PSI*), among pediatric patients with Central Venous Lines (CVLs).Design: Retrospective cohort study.Setting: Single academic children's hospital.Patients: All hospital encounters from January 2013 to December 2018, excluding the ones without a CVL or with a length-of-stay shorter than 24 h.Measurements and Main Results: Clinical features including demographics, laboratory results, vital signs, characteristics of the CVLs and medications used were extracted retrospectively from electronic medical records. Data were aggregated across all hospitals within a single pediatric health system and used to train a deep learning model to predict the occurrence of PSI* during the next 48 h of hospitalization. The proposed model prediction was compared to prediction of PSI* by a marker of illness severity (PELOD-2). The baseline prevalence of line infections was 0.34% over all segmented 48-h time windows. Events were identified among cases using onset time. All data from admission till the onset was used for cases and among controls we used all data from admission till discharge. The benchmarks were aggregated over all 48 h time windows [N=748,380 associated with 27,137 patient encounters]. The model achieved an area under the receiver operating characteristic curve of 0.993 (95% CI = [0.990, 0.996]), the enriched positive predictive value (PPV) was 23 times greater than the base prevalence. Conversely, prediction by PELOD-2 achieved a lower PPV of 1.5% [0.9%, 2.1%] which was 5 times the baseline prevalence.Conclusion: A deep learning model that employs common clinical features in the electronic health record can help predict the onset of CLABSI in hospitalized children with central venous line 48 hours prior to the time of specimen collection.

Characterization of the association between cigarette smoking intensity and urinary concentrations of 2-hydroxyethyl mercapturic acid among exclusive cigarette smokers in the National Health and Nutrition Examination Survey (NHANES) 2011–2016

Background 2-Hydroxyethyl mercapturic acid (2HEMA, N-acetyl-S-(2-hydroxyethyl)-L-cysteine) is a urinary metabolite of several volatile organic compounds including acrylonitrile and ethylene oxide, which are found in cigarette smoke. Methods We measured 2HEMA concentrations in urine specimens collected during the National Health and Nutrition Examination Survey (2011–2016) from eligible participants aged >12 years (N = 7,416). We developed two multiple linear regression models to characterize the association between cigarette smoking and 2HEMA concentrations wherein the dependent variable was 2HEMA concentrations among participants who exclusively smoked cigarettes at the time of specimen collection and the independent variables included sex, age, race/ethnicity, creatinine, diet, and either cigarettes smoked per day (CPD) or serum cotinine. Results We detected 2HEMA in 85% of samples tested among exclusive cigarette smokers, and only 40% of specimens from non-smokers. When compared to exclusive cigarette smokers who smoked 1–9 CPD, smoking 10–19 CPD was associated with 36% higher 2HEMA (p < 0.0001) and smoking >19 CPD was associated with 61% higher 2HEMA (p < 0.0001). Additionally, 2HEMA was positively associated with serum cotinine. Conclusions This study demonstrates that cigarette smoking intensity is associated with higher urinary 2HEMA concentrations and is likely a major source of acrylonitrile and/or ethylene oxide exposure.

Asymptomatic bacteriuria and antibiotic resistance profile in children with neurogenic bladder who require clean intermittent catheterization

A retrospective cohort study. To document the prevalence of asymptomatic bacteriuria and to characterize the resistance patterns to antibiotics among children with neurogenic bladder who require clean intermittent catheterization, with an emphasis on multidrug resistance. A national referral pediatric and adolescent rehabilitation facility in Jerusalem, Israel. Routine urine cultures were collected before urodynamic studies in suitable individuals during 2010-2018. None of them had symptoms of urinary tract infection at the time of specimen collection. Cultures were defined as being positive if a single bacterial species was isolated together with a growth of over 105 colony-forming units/ml. Resistance patterns were defined as extended-spectrum beta-lactamase (ESBL) and resistant to 3 antimicrobial groups (multi-drug resistant, MDR). In total, 281 urine cultures were available for 186 participants (median age 7 years, range 0.5-18). Etiologies for CIC included myelomeningocele (n = 137, 74%), spinal cord injury (n = 16, 9%) and caudal regression syndrome (n = 9, 5%). Vesicoureteral reflux was diagnosed in 36 participants (19%), 14 of whom were treated with prophylactic antibiotics. Asymptomatic bacteriuria was present in 217 specimens (77%, 95%CI [0.72-0.82]). The bacteria species were E. coli (71%), Klebsiella (13%), and Proteus (10%). ESBL was found in 11% of the positive cultures and MDR in 9%, yielding a total of 34 (16% of positive cultures) positive for ESBL and/or MDR bacteria. Asymptomatic bacteriuria and resistance to antimicrobials are common in pediatric individuals who require CIC.

Impact of Anatomic Site, Specimen Collection Timing, and Patient Symptom Status on Neisseria gonorrhoeae Culture Recovery.

Neisseria gonorrhoeae culture is required for antimicrobial susceptibility testing, but recovering isolates from clinical specimens is challenging. Although many variables influence culture recovery, studies evaluating the impact of culture specimen collection timing and patient symptom status are limited. This study analyzed urogenital and extragenital culture recovery data from Centers for Disease Control and Prevention's Strengthening the US Response to Resistant Gonorrhea (SURRG) program, a multisite project, which enhances local N. gonorrhoeae culture and antimicrobial susceptibility testing capacity. Eight SURRG jurisdictions collected gonococcal cultures from patients with N. gonorrhoeae-positive nucleic acid amplification test (NAAT) results attending sexually transmitted disease and community clinics. Matched NAAT and culture specimens from the same anatomic site were collected, and culture recovery was assessed. Time between NAAT and culture specimen collection was categorized as same day, 1 to 7 days, 8 to 14 days, or ≥15 days, and patient symptoms were matched to the anatomic site where culture specimens were collected. From 2018 to 2019, among persons with N. gonorrhoeae-positive NAAT, urethral infections resulted in the highest culture recovery (5927 of 6515 [91.0%]), followed by endocervical (222 of 363 [61.2%]), vaginal (63 of 133 [47.4%]), rectal (1117 of 2805 [39.8%]), and pharyngeal (1019 of 3678 [27.7%]) infections. Culture recovery was highest when specimens were collected on the same day as NAAT specimens and significantly decreased after 7 days. Symptoms were significantly associated with culture recovery at urethral (P = <0.0001) and rectal (P = <0.0001) sites of infection but not endocervical, vaginal, or pharyngeal sites. Culture specimen collection timing and patient symptomatic status can impact culture recovery. These findings can guide decisions about culture collection protocols to maximize culture recovery and strengthen detection of antimicrobial-resistant infections.

An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern.

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants concerning for enhanced transmission, evasion of immune responses, or associated with severe disease have motivated the global increase in genomic surveillance. In the current study, large-scale whole-genome sequencing was performed between November 2020 and the end of March 2021 to provide a phylodynamic analysis of circulating variants over time. In addition, we compared the viral genomic features of March 2020 and March 2021.MethodsA total of 1600 complete SARS-CoV-2 genomes were analyzed. Genomic analysis was associated with laboratory diagnostic volumes and positivity rates, in addition to an analysis of the association of selected variants of concern/variants of interest with disease severity and outcomes. Our real-time surveillance features a cohort of specimens from patients who tested positive for SARS-CoV-2 after completion of vaccination.ResultsOur data showed genomic diversity over time that was not limited to the spike sequence. A significant increase in the B.1.1.7 lineage (alpha variant) in March 2021 as well as a transient circulation of regional variants that carried both the concerning S: E484K and S: P681H substitutions were noted. Lineage B.1.243 was significantly associated with intensive care unit admission and mortality. Genomes recovered from fully vaccinated individuals represented the predominant lineages circulating at specimen collection time, and people with those infections recovered with no hospitalizations.ConclusionsOur results emphasize the importance of genomic surveillance coupled with laboratory, clinical, and metadata analysis for a better understanding of the dynamics of viral spread and evolution.

Efficiency of the Cancer Care Program’s Checklist in Chulabhorn Royal Academy

Background: The Biorepository Unit was initially established for the storage of specimens from various departments for the main purpose of biomedical research. However, several problems occurred during the management of specimens. Hence, the authors developed the Cancer Care Program&rsquo;s checklist for the standardization of specimen collection. Objective: To analyze the efficiency of Cancer Care Program&rsquo;s checklist. Materials and Methods: Data of 370 participants were collected in the Cancer Care Program. Fisher&rsquo;s Exact and Mann-Whitney U Test were applied to analyze data and processing time of specimen collection, respectively. Results: We obtained higher numbers of informed consent and blood from participants after implementation of the checklist compared with specimen management without the checklist, with a 95% confidence interval. Additionally, the processing time of blood and colorectal tissue collection significantly improved, while other tissues showed no difference after checklist implementation. Conclusion: This is a preliminary study of checklist development for tissue sample management. After implementation of this checklist, we confirmed a higher number of informed consents and blood collection, with lower processing time of blood and colorectal tissue collection. Nonetheless, further study with more sample sizes is recommended to verify the more efficacy of tissue sample management. Keywords: Checklist, Cancer care program, Biorepository unit, Chulabhorn royal academy

Bacteriology and Antibiotic Sensitivity Patterns of Urine in Urology Patients with Indwelling Urinary Catheters at the University Teaching Hospital in Lusaka, Zambia

Introduction: Catheter-associated urinary tract infection (CAUTI) is the most common nosocomial infection in hospitals worldwide, and the incidence has been reported to be up to 35%. The growing antibiotic resistance amongst the uropathogens isolated from CAUTI makes it challenging to manage. In Zambia, prolonged catheter use is a burden, particularly in patients awaiting definitive surgery, the elderly and the socioeconomically challenged. Bacterial colonisation following catheterisation is inevitable, with reports estimating the risk to be around 5-10% per day. By day 10, virtually all patients with urinary tract instrumentation have healthcare-associated UTI, with the duration of catheterisation the most important factor. Methodology: The study was a descriptive cross-sectional study conducted at UTH over a period of 10 months from July 2015 to May 2016. The cases were inpatients and outpatients with indwelling catheters in situ for not less than three calendar days. Simple random sampling was used to select candidates who were inpatients awaiting definitive surgery and outpatients in the same category as they attended clinics. Data collection and collection of specimens were done by the principal investigator, which was analysed by the microbiologist based at the UTH microbiology laboratory. The patients were recruited at one point, and the data collection exercise employed a questionnaire to collect socioeconomic demography and clinical information. The variables were collected using the data collection sheet for each participant. The data was then entered into SPSS software to clean and analyse data. The categorical variables were presented as proportions. The main concerns arising during specimen collection were the duration between the time of specimen collection and transfer to and processing at the main laboratory, which was kept within one hour. Specimens received within two hours of the collection were accepted. Results: A total of 228 patients were enrolled from both outpatient and inpatient departments. Approximately 75% yielded growth of bacteria, and 25.0% were negative. The pure growth yielded Klebsiella Pneumoniae 28.0% and E. coli 25.2%, as the most isolated pathogens. The antibiotic susceptibility testing revealed the highest resistance of the above isolates to ampicillin, nalidixic acid, norfloxacin, ciprofloxacin, levofloxacin, and borderline with cotrimoxazole. The organisms were least resistant to amikacin, imipenem, nitrofurantoin, and gentamycin. Acetinobacter and Citrobacter species were also highly resistant to the above drugs with nitrofurantoin in addition but least resistant to ampicillin. Conclusion: The study revealed a high prevalence of CAUTI in the urology section of the UTH, and practices such as poor hand hygiene, open catheter drainage, non-aseptic methods of catheter insertion and poor catheter care are possible contributing factors. There is an association between the insertion of indwelling catheters and subsequent development of CAUTI, and the strongest factors noted are the size of the catheters used and the patient's level of education. High resistance to antibiotics to many organisms of concern was noted.

"A Rapid Review on the sensitivity of SARS-CoV-2 RT-PCR done on different clinical specimens "

Background: RT-PCR using respiratory tract specimens, most commonly nasopharyngeal swab (NPS), has been used to confirm the diagnosis of COVID-19. NPS is a relatively invasive procedure that causes patient discomfort and risks viral transmission. Other specimens are therefore being investigated for the detection of SARS-CoV-2 RNA. Objective: To determine the sensitivity of non-respiratory tract specimens in detecting SARS-CoV-2 RNA in patients with COVID-19. Methodology: This review summarized the results of eight studies obtained from a literature search done in May 2020 in PubMed MEDLINE, Cochrane Library and MedRxiv. Two independent investigators reviewed and appraised the studies that were included, and pooled estimates of sensitivity for each specimen were determined using Stata’s Metaprop function. Results: The sensitivity in detecting SARS-CoV-2 RNA in non-respiratory tract specimens of diagnosed COVID-19 patients are as follows: Saliva 77% (95% CI 71-83%), stool/rectal swab/anal swab 22% (95% CI 22-37%), blood/serum/plasma 2% (95% CI 1-3%), and urine 22% (95% CI 18-25%). Conclusion: SARS-CoV-2 RNA is detected in saliva, stool/rectal swab/anal swab, blood/serum/plasma and urine. Among these, saliva has the highest estimated sensitivity. However, more studies are needed to correct the heterogeneity brought about by factors such as timing of specimen collection, disease severity and treatment.

Concordance of HER2+ status by IHC/ISH and ERBB2 status by NGS in a real-world clinicogenomic database and analysis of outcomes in patients (pts) with metastatic breast cancer (mBC).

1036 Background: HER2 overexpression/amplification measured by IHC or ISH is a predictive biomarker for HER2-targeted therapies. Next-generation sequencing (NGS) can identify ERBB2 amplification (amp) and mutations. We examined clinical characteristics, NGS testing patterns, and outcomes of pts treated with 1L HER2 therapy with HER2+ mBC based on ERBB2 amp status using a real-world (RW) clinico-genomic database (CGDB). Methods: Pts with mBC (HER2+ by IHC and/or ISH) treated with 1L HER2 therapy who had undergone NGS and were treated within the Flatiron Health (FH) network were eligible. Clinical characteristics and HER2 testing results were obtained via technology-enabled abstraction of clinician notes and radiology/pathology reports and linked to genomic data from Foundation Medicine (FMI) in the nationwide (US-based), de-identified FH-FMI CGDB. Demographic, clinical and genomic characteristics were summarized and stratified by concordance between HER2+ (IHC 3+ or ISH amp+) and ERBB2amp+ status [copy number (CN) ≥ 5]. NGS testing patterns and 1L HER2 therapy were characterized and stratified by concordance status. Concordance was assessed based on contemporaneous timing of paired test specimen collection dates (FMI NGS ≤ 30 days of HER2+ status). RW overall survival (rwOS) stratified by HER2+/ ERBB2 amp concordance was estimated with Kaplan-Meier analysis and adjusted Cox proportional hazards models. Results: Among 268 eligible pts, HER2+/ ERBB2amp+ concordance was 66% (176/268); concordance among contemporaneous paired specimens was 73% (106/145). Demographic and clinical features were overall well-balanced with most pts treated at community sites [94%, (252/268)]; the discordant (HER2+/ ERBB2amp-) group (95/268) had more pts with hormone receptor positive disease (73% vs 62%). Concordance by assay type varied; IHC+ only, IHC+/ISH+, and ISH+ only agreement was 72% (95/132), 76% (26/34) and 52% (50/96), respectively. A higher proportion of discordance (35% vs 19%) was seen in pts treated at community vs. academic sites. Median rwOS was 32.9 months (IQR 25.9-38.9) among concordant (HER2+/ ERBB2amp+) and 15.5 months (IQR 8.9-30.1) among discordant (HER2+/ ERBB2amp-) pts, aHR = 0.71 [95% CI: 0.48-1.03; p = 0.073]. Conclusions: Among RW pts with HER2+ mBC receiving 1L HER2 therapy, discordance between ERBB2amp and IHC/ISH HER2 testing methods was observed. Pts with tumors HER2+ by IHC and/or ISH but negative for ERBB2amp had a trend towards worse rwOS following receipt of HER2 therapy compared to concordant cases. Contemporaneous timing of specimen collection was associated with greater concordance. Future analyses on the additive value of ERBB2 CN as a predictive marker, and assessing factors that may affect discordance such as intratumor HER2 heterogeneity, tumor content, and biopsy site are warranted.

Discrepancies in the clinical and radiological profiles of COVID-19: A case-based discussion and review of literature.

The current gold standard for the diagnosis of coronavirus disease-19 (COVID-19) is a positive reverse transcriptase polymerase chain reaction (RT-PCR) test, on the background of clinical suspicion. However, RT-PCR has its limitations; this includes issues of low sensitivity, sampling errors and appropriate timing of specimen collection. As pulmonary involvement is the most common manifestation of severe COVID-19, early and appropriate lung imaging is important to aid diagnosis. However, gross discrepancies can occur between the clinical and imaging findings in patients with COVID-19, which can mislead clinicians in their decision making. Although chest X-ray (CXR) has a low sensitivity for the diagnosis of COVID-19 associated lung disease, especially in the earlier stages, a positive CXR increases the pre-test probability of COVID-19. CXR scoring systems have shown to be useful, such as the COVID-19 opacification rating score which helps to predict the need of tracheal intubation. Furthermore, artificial intelligence-based algorithms have also shown promise in differentiating COVID-19 pneumonia on CXR from other lung diseases. Although costlier than CXR, unenhanced computed tomographic (CT) chest scans have a higher sensitivity, but lesser specificity compared to RT-PCR for the diagnosis of COVID-19 pneumonia. A semi-quantitative CT scoring system has been shown to predict short-term mortality. The routine use of CT pulmonary angiography as a first-line imaging modality in patients with suspected COVID-19 is not justifiable due to the risk of contrast nephropathy. Scoring systems similar to those pioneered in CXR and CT can be used to effectively plan and manage hospital resources such as ventilators. Lung ultrasound is useful in the assessment of critically ill COVID-19 patients in the hands of an experienced operator. Moreover, it is a convenient tool to monitor disease progression, as it is cheap, non-invasive, easily accessible and easy to sterilise. Newer lung imaging modalities such as magnetic resonance imaging (MRI) for safe imaging among children, adolescents and pregnant women are rapidly evolving. Imaging modalities are also essential for evaluating the extra-pulmonary manifestations of COVID-19: these include cranial imaging with CT or MRI; cardiac imaging with ultrasonography (US), CT and MRI; and abdominal imaging with US or CT. This review critically analyses the utility of each imaging modality to empower clinicians to use them appropriately in the management of patients with COVID-19 infection.

The impact of creatinine reference value: Normalization of urinary drug concentrations.

Many illicit drug users attempt to manipulate urine drug testing; dilution is one of the methods. In screening tests, false-negative results below the cut-off values can create positive results after creatinine normalization. This study aimed to evaluate the impact of a creatinine reference value on the normalization of the drug concentration in diluted urine. The study focused on 25630 cases and the following information: gender, age, urine collection time, drug screening test results, creatinine concentration (CR), and confirmation analysis result. Mean CR value was 143.71±83.68mg/dl. There was a significant difference between CR and gender (p=0.03). The mean CR for women was lower than that for men. The correlation between age and CR was not significant (r=-0.08, p=0.00). However, after grouping the sample into age groups of 10years, there was a significant difference between age groups and mean CR (p=0.00). The mean CR was significantly lower in the 0-9year age group (n=34) than in the 20-29year age group (n=10943). According to the urine specimen collection time, CR levels during the early hours of the day (06:00-06:59) were lower than those during the remaining hours (p=0.00). The highest converted drug-negative to drug-positive results were obtained from 153.23mg/dl CR reference value. Reference CR values were evaluated according to gender, age, and urine collection time. Different rates of positive results were obtained for each reference value. There is no published local creatinine value for spot urine samples in many countries, including Turkey. This will be useful to develop appropriate normalization models when reporting drug test results.

Evaluation of the timing of MRSA PCR nasal screening: How long can a negative assay be used to rule out MRSA-positive respiratory cultures?

Previous studies indicate that the polymerase chain reaction (PCR) nasal assay for methicillin-resistant Staphylococcus aureus (MRSA) has a consistently high (>95%) negative predictive value (NPV) in ruling out MRSA pneumonia; however, optimal timing of PCR assay specimen and respiratory culture collection is unclear. A study including 736 patients from a community hospital system was conducted. Patients were included if they had undergone MRSA nasal screening with a PCR assay and had documented positive respiratory culture results. In the full cohort, the MRSA PCR nasal screen assay was demonstrated to have an NPV of 94.9% (95% confidence interval [CI], 92.8%-96.5%) in ruling out MRSA-positive respiratory cultures. When evaluating the NPV by level of care (ie, where the MRSA PCR nasal assay sample was collected), no significant difference between values for samples collected in an intensive care unit vs medical/surgical units was identified (NPV [95%CI], 94.9% [92.7%-96.6%] vs 95.3% [88.4%-98.7%]). Additionally, NPV remained high with use of both invasive (NPV [95%CI], 96.8% [92.7%-99.0%]) and noninvasive (NPV [95%CI], 94.5% [91.7%-96.2%]) respiratory sampling methods. Finally, when evaluating the effect of time between MRSA PCR nasal screening and respiratory sample collection, we found high NPVs for all evaluated timeframes: within 24 hours, 93.8% (90.1%-96.4%); within 25 to 48 hours, 98.6% (92.7%-100.0%); within 49 hours to 7 days, 95.7% (91.4%-98.3%); within 8 to 14 days, 92.9% (85.1%-97.3%); and after more than 14 days, 95.5% (84.5%-99.4%). We report high NPVs for up to 2 weeks between specimen collections, which allows clinicians to use a negative MRSA PCR nasal screen assay to rule out MRSA pneumonia, potentially leading to decreased exposure to MRSA-active antibiotics.