Performance of diagnostic tests to detect respiratory viruses in older adults.

The performance of 4 laboratory methods for diagnosis of viral respiratory tract infections (RTI) in older adults was evaluated. Seventy-four nasopharyngeal (NP) swab specimens were obtained from 60 patients with RTI at a long-term care facility over 2 respiratory seasons. Sixteen specimens were positive for a respiratory virus by at least 1 method. Multiplex reverse transcriptase polymerase chain reaction (RT-PCR) by the Luminex xTAG Respiratory Viral Panel (RVP) detected 16 (100%) of the positive specimens, RVP of 24-h culture supernatant detected 8 (50%), direct fluorescent antibody testing detected 4 (25%), rapid culture detected 2 (12.5%), and rapid antigen testing detected none. For a comparison group, RVP was performed on NP swabs from 20 outpatient children with RTI. The mean fluorescence intensity by RVP was significantly lower for positive adult patients than pediatric patients (P = 0.0373). Our data suggest that older adult patients shed lower titers of viruses, necessitating a highly sensitive assay such as RT-PCR to reliably detect respiratory viral pathogens

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Antibacterial activity of varying UMF-graded Manuka honeys.

Honey has been used as a traditional remedy for skin and soft tissue infections due to its ability to promote wound healing. Manuka honey is recognized for its unusually abundant content of the antibacterial compound, methylglyoxal (MGO). The Unique Manuka Factor (UMF) grading system reflects the MGO concentration in Manuka honey sold commercially. Our objective was to observe if UMF values correlated with the antibacterial activity of Manuka honey against a variety of pathogens purchased over the counter. The antibacterial effect of Manuka honey with UMF values of 5+, 10+, and 15+ from the same manufacturer was assessed by the broth microdilution method. Minimum inhibitory concentration (MIC) values were determined against 128 isolates from wound cultures representing gram-positive, gram-negative, drug-susceptible, and multi-drug resistant (MDR) organisms. Lower MICs were observed with UMF 5+ honey for staphylococci (n = 73, including 25 methicillin-resistant S. aureus) and Pseudomonas aeruginosa (n = 22, including 10 MDR) compared to UMF 10+ honey (p<0.05) and with UMF 10+ compared to UMF 15+ (p = 0.01). For Enterobacteriaceae (n = 33, including 14 MDR), MIC values were significantly lower for UMF 5+ or UMF 10+ compared to UMF 15+ honey (p<0.01). MIC50 for UMF 5+, UMF 10+, and UMF 15+ honey against staphylococci was 6%, 7%, and 15%, and for Enterobacteriaceae was 21%, 21%, and 27%, respectively. For Pseudomonas aeruginosa MIC50 was 21% and MIC90 was 21-27% for all UMFs. Manuka honey exhibited antimicrobial activity against a spectrum of organisms including those with multi-drug resistance, with more potent activity overall against gram-positive than gram-negative bacteria. Manuka honey with lower UMF values, in our limited sampling, paradoxically demonstrated increased antimicrobial activity among the limited samples tested, presumably due to changes in MGO content of honey over time. The UMF value by itself may not be a reliable indicator of antibacterial effect

Direct MALDI-TOF MS and Antimicrobial Susceptibility Testing of Positive Blood Cultures Using the FASTTM System and FAST-PBC Prep Cartridges&mdash;Performance Evaluation in a Clinical Microbiology Laboratory Serving High-Risk Patients

Bloodstream infections are a leading cause of morbidity and mortality. The rapid diagnostic testing of positive blood cultures (PBCs) shortens times to effective therapy and the de-escalation of broad-spectrum empiric therapy. This is the first study examining the Qvella FASTTM System for the rapid (~20 min) purification of microorganisms directly from PBCs using BacT/Alert&reg; FA/FAN bottles in the bioM&eacute;rieux Virtuo instrument. We compared the performance of the FASTTM System Liquid ColonyTM (LC), for immediate downstream ID and phenotypic AST, to standard workflow involving colonies obtained by overnight subculture. The LC yielded a concordant species ID by VITEK MS in 121/138 (87.7%) samples, identifying 32 different Gram-positive and Gram-negative species with 3/123 (2.6%) discordances. Compared to standard workflow, direct AST of the LC using VITEK&reg; 2 yielded 98.4% categorical agreement and 98.0% essential agreement. Very major error, major error, and minor error rates were 1.0%, 0.0%, and 1.8%, respectively, for Gram-negative organisms; and 1.9%, 0.2%, and 1.2%, respectively, for Gram-positive organisms. The median times from positive blood culture flag to results by FASTTM System for ID and AST were 7.8 h and 15.7 h, respectively, versus 22.4 h and 36.6 h for standard workflow, respectively. In conclusion, the FASTTM System provides reliable results for direct ID and AST from PBCs with significantly decreased turnaround times

The Bactericidal Activity and Spore Inhibition Effect of Manuka Honey against Clostridioides Difficile

Clostridioides difficile colitis overgrowth occurs when the normal gut microbiome becomes disrupted, often due to antibiotics. Effective treatment remains elusive, due partly to the persistence of its spores in the gut. Natural substances like manuka honey offer an alternative antimicrobial mechanism of action to conventional antibiotics. We investigated the antibiotic activity of manuka honey against 20 C. difficile isolates. The minimum inhibitory concentrations (MICs) and minimal bactericidal concentrations (MBC) of manuka honeys of methylglyoxal (MGO) grades 30+, 100+, 250+, and 400+ were determined based on broth microdilution. Sporicidal activity was assessed in a range of honey concentrations by enumerating total viable cell and spore counts at 0&ndash;96 h after organism inoculation. The MICs of C. difficile ranged from 4% to &gt;30% (w/v). MIC50 for the four MGO grades were similar at 10&ndash;14%. MBC results for the majority of isolates were distributed bimodally at MBC/MIC ratios &le;4 or MBC &gt;30%. Growth kinetics in honey showed total viable cell counts remaining &gt;105 colony-forming units (CFU)/mL at all time points, whereas spore counts remained within 1-log of baseline (102 CFU/mL) in honey but steadily increased in the drug-free control to &gt;105 CFU/mL by 96 h. Manuka honey demonstrated variable inhibitory and bactericidal activity against C. difficile. MGO grade had no noticeable impact on overall MIC distributions or bactericidal activity. Although manuka honey could inhibit spore proliferation, it did not eradicate spores completely

Evaluation of Helicobacter pylori Immunoglobulin G (IgG), IgA, and IgM Serologic Testing Compared to Stool Antigen Testing▿

The utility of Helicobacter pylori serology was evaluated in 4,722 specimens and compared to stool antigen detection. Immunoglobulin M (IgM) sensitivity (6.8%) was unacceptably low. Key performance differences were observed in IgG specificity, IgA sensitivity, and specificity between adults and children that may warrant differentiating optimal serologic cutoff values by age

Clostridioides difficile Toxin B PCR Cycle Threshold as a Predictor of Toxin Testing in Stool Specimens from Hospitalized Adults

Rapid, accurate detection of Clostridioides difficile toxin may potentially be predicted by toxin B PCR cycle threshold (tcdB Ct). We investigated the validity of this approach in an inpatient adult population. Patients who tested positive by C. difficile PCR (Cepheid GeneXpert) from December 2016 to October 2020 (n = 368) at a tertiary medical center were included. All stool samples were further tested by rapid glutamate dehydrogenase (GDH)/toxin B EIA and cell cytotoxin neutralization assay (CCNA). Receiver operating characteristic curves were analyzed. The area under the curve for tcdB Ct predicting toxin result by EIA was 0.795 (95% confidence interval (CI) 0.747&ndash;0.843) and by CCNA was 0.771 (95% CI 0.720&ndash;0.822). The Youden Ct cutoff for CCNA was &le;27.8 cycles (sensitivity 65.0%, specificity 77.2%). For specimens with Ct &le; 25.0 cycles (n = 115), CCNA toxin was positive in &gt;90%. The negative predictive value of tcdB Ct for CCNA was no greater than 80% regardless of cutoff chosen. In summary, very low Ct values (&le;25.0) could have limited value as a rapid indicator of positive toxin status by CCNA in our patient population. A broad distribution of Ct values for toxin-negative and toxin-positive specimens precluded more robust prediction. Additional data are needed before broader application of Ct values from qualitatively designed assays to clinical laboratory reporting