False positive congenital cytomegalovirus saliva screening results with an FDA-approved assay at two institutions

BACKGROUND

Congenital cytomegalovirus (CMV) infection is a significant cause of childhood hearing loss and developmental delay. Congenital CMV screening was implemented at two large hospital-affiliated laboratories using the FDA-approved Alethia CMV Assay Test System. In July 2022, an increase in suspected false-positive results was noted, leading to implementation of prospective quality management strategies.

METHODS

The Alethia assay was performed per manufacturer-provided instructions on saliva swab specimens. After discovery of possible elevated false-positive rates, all positive results were confirmed by repeat Alethia testing on the same specimen, orthogonal polymerase chain reaction (PCR) on the same specimen, and/or clinical adjudication. Additionally, root cause analyses were conducted to pinpoint the source of false-positive results.

RESULTS

At Cleveland Clinic (CCF), 696 saliva specimens were tested after initiation of the prospective quality management strategy, of which 36 (5.2%) were positive for CMV. Five of 36 (13.9%) were confirmed CMV positive by repeat Alethia testing and orthogonal PCR. Vanderbilt Medical Center (VUMC) tested 145 specimens, of which 11 (7.6%) were positive. Two of 11 (18.2%) confirmed as positive by orthogonal PCR or clinical adjudication. The remaining specimens (31 from CCF and 9 from VUMC) were negative for CMV by repeat Alethia and/or orthogonal PCR testing.

DISCUSSION

These findings suggest a false positive rate of 4.5-6.2%, higher than the 0.2% reported for this assay in FDA claims. Laboratories using Alethia CMV may consider prospective quality management to evaluate all positive results. False-positive results can lead to unnecessary follow-up care and testing, and decreased confidence in laboratory testing.

Environmental and Anthropogenic Factors Shape the Skin Bacterial Communities of a Semi-Arid Amphibian Species

The amphibian skin microbiome is important in maintaining host health, but is vulnerable to perturbation from changes in biotic and abiotic conditions. Anthropogenic habitat disturbance and emerging infectious diseases are both potential disrupters of the skin microbiome, in addition to being major drivers of amphibian decline globally. We investigated how host environment (hydrology, habitat disturbance), pathogen presence, and host biology (life stage) impact the skin microbiome of wild Dhofar toads (Duttaphrynus dhufarensis) in Oman. We detected ranavirus (but not Batrachochytrium dendrobatidis) across all sampling sites, constituting the first report of this pathogen in Oman, with reduced prevalence in disturbed sites. We show that skin microbiome beta diversity is driven by host life stage, water source, and habitat disturbance, but not ranavirus infection. Finally, although trends in bacterial diversity and differential abundance were evident in disturbed versus undisturbed sites, bacterial co-occurrence patterns determined through network analyses revealed high site specificity. Our results therefore provide support for amphibian skin microbiome diversity and taxa abundance being associated with habitat disturbance, with bacterial co-occurrence (and likely broader aspects of microbial community ecology) being largely site specific.

Narrow pH tolerance found for a microbial fuel cell treating winery wastewater

AIMS

The use of microbial fuel cells (MFC) to treat winery wastewater is promising; however, an initial acidic pH, fluctuating chemical oxygen demand (COD) levels and a lack of natural buffering in these wastewaters make providing a suitable buffer system at an ideal buffer to COD ratio.

METHODS AND RESULTS

A lab scale MFC was designed, inoculated with anaerobic winery sludge and fed with synthetic winery wastewater. It was observed that at pH 6·5, the MFC performed best, the maximum output voltage was 0·63 ± 0·01 V for 60 ± 3 h, and the COD removal efficiency reached 77 ± 7%. The electrogens were affected by pH much more than the bulk COD degrading organisms. Fluorescent in situ hybridization suggested Betaproteobacteria played a significant role in electron transfer.

CONCLUSIONS

A ratio of 1 mmol l^-1 phosphate buffer to 100 mg l^-1 COD was ideal to maintain a stable pH for MFCs treating synthetic winery wastewater.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results find the narrow pH tolerance for MFCs treating winery wastewater and demonstrate the significance of pH and buffer to COD ratio for steady performance of MFCs.

Panton-Valentine leukocidin-positive Staphylococcus aureus in skin and soft tissue infections from primary care patients

OBJECTIVES

To characterize deep skin and soft tissue infections (dSSTI) caused by Panton-Valentine leukocidin (PVL)-positive versus PVL-negative Staphylococcus aureus isolates.

METHODS

We performed a retrospective analysis of patients' records including S. aureus isolates from outpatients with dSSTI. Samples had been submitted by primary care physicians, i.e. general practitioners, surgeons, dermatologists and paediatricians, located in Berlin, Germany, in 2007-2017. Bacterial isolates were identified and tested for antimicrobial susceptibility by VITEK 2; PVL was detected by PCR.

RESULTS

In total, 1199 S. aureus isolates from 1074 patients with dSSTI were identified, and 613 (51.1%) of 1199 samples were PVL⁺. The median age of patients with PVL⁺S. aureus was lower than in patients with PVL- S. aureus (34 years, range 0-88 years, vs. 44 years, range 0-98 years; p < 0.0001). PVL was associated with repeated/multiple samples compared to single sample submission (69/92, 75% vs. 448/982, 45.6%, p < 0.0001; odds ratio (OR), 3.6; 95% confidence interval (CI), 2.2-5.8). Interestingly, the highest PVL positivity rate was found in isolates from gluteal (82/108, 75.9%; OR, 3.6; 95% CI, 2-5) or axillary (76/123, 61.8%; OR, 2; 95% CI, 1.1-3.3) localizations compared to isolates from the arm. The PVL positivity rate did not increase over time. Yet we noticed an increase in the trimethoprim/sulfamethoxazole (SXT) resistance rate in PVL⁺ isolates, mainly methicillin-sensitive S. aureus, when considering SXT resistance rates of 2007-2012 versus 2013-2017 (35/226, 15.5% vs. 74/289, 25.6%; p 0.01).

CONCLUSIONS

In outpatients, gluteal and axillary dSSTI are indicative of PVL⁺S. aureus. Providing SXT as a complementary treatment for dSSTI should be based on susceptibility testing.

Analytical and Workflow Evaluation of the ARIES Sample-to-Result Molecular Assay for Clostridium difficile

We evaluated the analytical and workflow characteristics of the ARIES Clostridium difficile assay, a recently developed qPCR-based test for toxigenic C. difficile ARIES was compared to the illumigene C. difficile assay, a commonly employed, loop-mediated amplification technique with similar sample-to-result capabilities. Following illumigene analysis, 122 positive and 164 negative stool specimens were banked for subsequent ARIES testing. The analytical agreement between the platforms was high: 93.4% positive agreement (89.0-97.8%) and 97.5% negative agreement (95.2-99.9%). For discordant specimens, amplification/bidirectional sequencing of tcdA/tcdB demonstrated toxigenic C. difficile in 2/4 illumigene(-)ARIES(+) and 2/8 illumigene(+)ARIES(-) specimens. In a time-motion study, the ARIES assay required less hands-on time than illumigene, but with greater total testing time. Overall, these findings support the ARIES C. difficile Assay as a new option for laboratories in their diagnostic repertoire.

A computerized data-capture system for animal biosafety level 4 laboratories

The restrictive nature of an Animal Biosafety Level 4 (ABSL4) laboratory complicates even simple clinical evaluation including data capture. Typically, clinical data are recorded on paper during procedures, faxed out of the ABSL4, and subsequently manually entered into a computer. This system has many disadvantages including transcriptional errors. Here, we describe the development of a highly customizable, tablet-PC-based computerized data-capture system, allowing reliable collection of observational and clinical data from experimental animals in a restrictive biocontainment setting. A multidisciplinary team with skills in containment laboratory animal science, database design, and software engineering collaborated on the development of this system. The goals were to design an easy-to-use and flexible user interface on a touch-screen tablet PC with user-supportable processes for recovery, full auditing capabilities, and cost effectiveness. The system simplifies data capture, reduces the necessary time in an ABSL4 environment, offers timely reporting and review of data, facilitates statistical analysis, reduces potential of erroneous data entry, improves quality assurance of animal care, and advances the use and refinement of humane endpoints.

Epigeous fruiting bodies of ectomycorrhizal fungi as indicators of soil fertility and associated nitrogen status of boreal forests

Soil fertility and associated nitrogen (N) status was a key ecosystem attribute, and surveys of ectomycorrhizal fungal (EMF) communities via epigeous fruiting bodies could provide an effective biotic indicator of forest soil productivity. We explored the utility of aboveground EMF communities in this regard by surveying sporocarps over a 3-year period from contrasting plant associations of southern old-growth boreal forests of British Columbia (Canada). Cumulative richness ranged from 39 to 89 EMF species per plot (0.15 ha) and followed a skewed parabolic correlation with foliar N concentrations and soil N availability. EMF species composition was consistently distinct in ordinations and strongly correlated to the increasing rates of N mineralization aligned with soil productivity. Approximately 40 EMF species were specialists, as they collectively indicated oligotrophic, mesotrophic, and eutrophic nutrient regimes, while the remaining species were categorized as broadly tolerant (distributed over 100% of the N gradient), partially intolerant (approximately 70%), or satellites (rare). The functional organization of EMF communities reflected by distribution classes could help define the ecological integrity of forests, which was characterized in this boreal landscape by an average allotment of 20 broadly tolerant, 25 partially intolerant, 15 specialist, and ten satellite species per plot. Epigeous fruiting bodies provided a disparate yet complementary view to the belowground assessment of EMF communities that was valuable in identifying indicators for ecosystem monitoring.

Ectomycorrhizal community structure on western hemlock (Tsuga heterophylla) seedlings transplanted from forests into openings

This study tested whether mature-forest ectomycorrhizal (ECM) communities could be maintained in forest openings on seedlings. Naturally regenerated western hemlock (Tsuga heterophylla (Raf.) Sarg.) seedlings were transplanted from mature forests into openings and the ECM fungal community was compared after 2 years with similar seedlings planted back into the forests or seedlings from openings planted back into openings. Fewer ECM morphotypes, lower average richness per seedling, and a steeper, less even species distribution curve were found, all of which suggest that the mature-forest ECM fungal community changed after transplanting forest seedlings into the openings. The increased abundance of pioneer fungi such as Thelephora terresteris suggested that many of the mature-forest ECM fungi were unable to maintain or continue root colonization in openings. Results suggest that many mature-forest ECM fungi require further stand development to maintain enough rooting density and hyphal contact to persist.Key words: ectomycorrhizal succession, disturbance, species-importance curves, multistage and late-stage fungi.

Mutations in the genome of porcine reproductive and respiratory syndrome virus responsible for the attenuation phenotype

 Although live-attenuated vaccines have been used for some time to control clinical symptoms of the porcine reproductive and respiratory syndrome (PRRS), the molecular bases for the attenuated phenotype remain unclear. We had previously determined the genomic sequence of the pathogenic PRRSV 16244B. Limited comparisons of the structural protein coding sequence of an attenuated vaccine strain have shown 98% homology to the pathogenic 16244B. Here we have confirmed the attenuated phenotype and determined the genomic sequence of that attenuated PRRSV vaccine and compared it to its parental VR-2332 and the 16244B strains. The attenuated vaccine sequence was colinear with that of the strain 16244B sequence containing no gaps and 212 substitutions over 15,374 determined nucleotide sequence. We identified nine amino acid changes distributed in Nsp1β, Nsp2, Nsp10, ORF2, ORF3, ORF5 and ORF6. These changes may provide the molecular bases for the observed attenuated phenotype.

In vivo analysis of the domains of yeast Rvs167p suggests Rvs167p function is mediated through multiple protein interactions

Morphological changes during cell division in the yeast Saccharomyces cerevisiae are controlled by cell-cycle regulators. The Pcl-Pho85p kinase complex has been implicated in the regulation of the actin cytoskeleton at least in part through Rvs167p. Rvs167p consists of three domains called BAR, GPA, and SH3. Using a two-hybrid assay, we demonstrated that each region of Rvs167p participates in protein-protein interactions: the BAR domain bound the BAR domain of another Rvs167p protein and that of Rvs161p, the GPA region bound Pcl2p, and the SH3 domain bound Abp1p. We identified Rvs167p as a Las17p/Bee1p-interacting protein in a two-hybrid screen and showed that Las17p/Bee1p bound the SH3 domain of Rvs167p. We tested the extent to which the Rvs167p protein domains rescued phenotypes associated with deletion of RVS167: salt sensitivity, random budding, and endocytosis and sporulation defects. The BAR domain was sufficient for full or partial rescue of all rvs167 mutant phenotypes tested but not required for the sporulation defect for which the SH3 domain was also sufficient. Overexpression of Rvs167p inhibits cell growth. The BAR domain was essential for this inhibition and the SH3 domain had only a minor effect. Rvs167p may link the cell cycle regulator Pcl-Pho85p kinase and the actin cytoskeleton. We propose that Rvs167p is activated by phosphorylation in its GPA region by the Pcl-Pho85p kinase. Upon activation, Rvs167p enters a multiprotein complex, making critical contacts in its BAR domain and redundant or minor contacts with its SH3 domain.

Functional analysis of a 38 kilobase region on chromosome XVI in Saccharomyces cerevisiae

In this report we assess the functional importance of 16 open reading frames (ORFs) contained within a 38 780 base-pair region immediately adjacent to the centromere on the right arm of chromosome XVI in Saccharomyces cerevisiae. This analysis involved replacing one copy of each ORF in a diploid strain with a cassette encoding the green fluorescent protein from the jellyfish Aequorea victoria and HIS3. Each replacement cassette was generated by PCR using oligonucleotide pairs with 45-base extensions complementary to sequences immediately upstream and downstream of the target gene's coding region. After replacement of the targeted genes, each gene-replacement strain was subjected to a series of genetic and phenotypic tests to assess the functional importance of the deleted gene. This analysis showed that two ORFs were essential, one for spores to germinate and another for vegetative growth. A third gene encoded a copper-fist-like transcription factor that was required for proper bud-site selection. One of the 16 ORFs was duplicated, a situation not observed in the strain used to sequence the yeast genome (S288C). RNA analysis showed 11 of the 16 ORFs in this region expressed steady-state poly(A+) RNA levels that were greater than or equal to 2% of the level expressed from the yeast actin gene, ACT1.

Histone H1 in Saccharomyces cerevisiae

The existence of histone H1 in the yeast, Saccharomyces cerevisiae, has long been debated. In this report we describe the presence of histone H1 in yeast. YPL127c, a gene encoding a protein with a high degree of similarity to histone H1 from other species was sequenced as part of the contribution of the Montreal Yeast Genome Sequencing Group to chromosome XVI. To reflect this similarity, the gene designation has been changed HHO1 (Histone H One). The HHO1 gene is highly expressed as poly A+ RNA in yeast. Although deletion of this gene had no detectable effect on cell growth, viability or mating, it significantly altered the expression of beta-galactosidase from a CYC1-lacZ reporter. Fluorescence observed in cells expressing a histone H1-GFP protein fusion indicated that histone H1 is localized to the nucleus.

Salt-resistant hypertension in mice lacking the guanylyl cyclase-A receptor for atrial natriuretic peptide

Around half of all humans with essential hypertension are resistant to salt (blood pressure does not change by more than 5 mm Hg when salt intake is high), and although various inbred strains of rats display salt-insensitive elevated blood pressure, a gene defect to account for the phenotype has not been described. Atrial natriuretic peptide (ANP) is released from the heart in response to atrial stretch and is thought to mediate its natriuretic and vaso-relaxant effects through the guanylyl cyclase-A receptor (GC-A). Here we report that disruption of the GC-A gene results in chronic elevations of blood pressure in mice on a normal salt diet. Unexpectedly, the blood pressure remains elevated and unchanged in response to either minimal or high salt diets. Aldosterone and ANP concentrations are not affected by the genotype. Therefore, mutations in the GC-A gene could explain some salt-resistant forms of essential hypertension and, coupled with previous work, further suggest that the GC-A signaling pathway dominates at the level of peripheral resistance, where it can operate independently of ANP.

Characterization of a bacteriophage that carries the genes for production of Shiga-like toxin 1 in Escherichia coli

The Shiga-like toxin 1-converting bacteriophage H-19B was recently shown to carry the structural genes for the toxin and was shown to have DNA sequence homology with phage lambda. We present evidence that the linear genome of bacteriophage H-19B has cohesive termini which become covalently associated during prophage integration. Integration occurs through a site on a 4-kilobase-pair EcoRI fragment located near the center of the bacteriophage chromosome. The relationship between bacteriophages H-19B and lambda was examined by Southern hybridization. Homologous regions were mapped on the respective chromosomes which corresponded to the regions of the J gene, the int-xis area, and the O and P genes of phage lambda. The H-19B tox genes were mapped to the right of the O and P gene homology, which was far away from the phage attachment site. We concluded that H-19B is a lambdoid bacteriophage. Unlike other toxin-converting bacteriophages, the toxin genes were not located adjacent to the phage attachment site. It appeared that the Shiga-like toxin 1 genes were not picked up by a simple imprecise prophage excision. H-19B could, however, have acquired chromosomally located toxin genes by a series of events involving deletion and duplication followed by aberrant excision.

Nucleotide sequence and promoter mapping of the Escherichia coli Shiga-like toxin operon of bacteriophage H-19B

We determined the nucleotide sequence of the Shiga-like toxin-1 (SLT-1) genes carried by the toxin-converting bacteriophage H-19B. Two open reading frames were identified; these were separated by 12 base pairs and encoded proteins of 315 (A subunit) and 89 (B subunit) amino acids. The predicted protein subunits had N-terminal hydrophobic signal sequences of 22 and 20 amino acids, respectively. The predicted amino acid sequence of the B subunit was identical to that of the B subunit of Shiga toxin. The A chain of ricin was found to be significantly related to the predicted A1 fragment of the SLT-1 A subunit. S1 nuclease protection experiments showed that the two cistrons formed a single transcriptional unit, with the A subunit being proximal to the promoter. A probable promoter was identified by primer extension, and transcription was found to increase dramatically under conditions of iron starvation. A 21-base-pair sequence with dyad symmetry was found in the region of the SLT-1 -10 sequence, which was found to be 68% homologous to a region of dyad symmetry found in the -35 region of the promoter of the iucA gene on plasmid ColV-K30, which specifies the 74,000-dalton ferric-aerobactin receptor protein. Betley et al. (M. Betley, V. Miller, and J. Mekalanos, Annu. Rev. Microbiol. 40:577-605, 1986) have recently summarized evidence suggesting that the slt operon is under the control of the fur regulatory system. The area of dyad symmetry found in both promoters may represent a regulatory site. A rho-independent terminator sequence was found 230 base pairs downstream from the B cistron stop codon.

Cloning and expression of the genes specifying Shiga-like toxin production in Escherichia coli H19

Some strains of Escherichia coli produce a protein which is cytotoxic for Vero cell and HeLa cell monolayers. This toxin is very similar to the toxin of Shigella dysenteriae 1 and has been named verotoxin or E. coli Shiga-like toxin. It has been shown that toxin conversion is due to a group of bacteriophages, one of which has been designated H-19B. In this study we report hybridization experiments showing that part of the H-19B genome is homologous to phage lambda. We have cloned a 1.7-kilobase BalI-BglII fragment from the genome of H-19B into pUC18. The recombinant plasmid confers the ability to produce high levels of Shiga-like toxin on transformed E. coli cells. We demonstrate using an in vitro transcription/translation system that the cloned fragment specifies the two verotoxin subunit peptides which have masses of 31 and 5.5 kilodaltons. The identity of peptides was confirmed by immunoprecipitation with verotoxin antiserum and protein A-Sepharose beads.

A RADIOCHEMICAL TECHNIQUE FOR STUDYING RANGE–ENERGY RELATIONSHIPS FOR HEAVY IONS OF KEV ENERGIES IN ALUMINUM

A rapid technique has been developed for dissolving successive thin layers of metal from the surface of an aluminum foil: viz. electrochemical oxidation at constant voltage in aqueous ammonium citrate, followed by removal of the oxide film in a phosphoric acid – chromic oxide solution. Due to the highly protective nature of the aluminum oxide film, this two-step process enables very uniform surface layers of metal as thin as 1 μ/cm2 to be removed. The total weight of aluminum dissolved increases with the applied anodic voltage at a rate of 0.30 μg cm−1 volt−1 (approximately 11 Å per volt) over the range 0–150 volts. The technique should be sufficiently sensitive to study the depth of penetration in aluminum of radioactive ions with kinetic energies as low as a few kiloelectron volts.An approximate value for the range of Na24 recoil atoms from the Al27 (n,α) reaction was obtained. A more extensive application to range studies is given in the next paper.