The laboratory diagnosis of Lyme disease relies upon serologic testing. A standard or modified two-tiered testing algorithm is used to enhance the accuracy of antibody detection. However, this ...approach suffers from a lack of sensitivity in early Lyme disease. Ongoing efforts to develop more sensitive antibody detection technologies and other diagnostic approaches are dependent upon the availability of quality-assured biospecimens linked to reliable clinical data. In this issue of the
, Horn et al. (E. J. Horn, G. Dempsey, A. M. Schotthoefer, U. L. Prisco, et al., J Clin Microbiol 58:e00032-20, 2020, https://doi.org/10.1128/JCM.00032-20) described the development of the Lyme Disease Biobank. Clinically categorized case patients with early Lyme disease and healthy controls were identified (without laboratory diagnostic testing) from three sites where Lyme disease is endemic. Subjects provided whole blood and urine, which were processed and stored at a central biorepository. Whole blood, serum, and urine aliquots were prepared and are available to investigators developing laboratory diagnostics for Lyme disease. After obtaining samples, extensive laboratory testing was performed, including serologic and nucleic acid amplification testing for
and other tick-borne pathogens. Direct detection methods yielded few positive results. Relative to the findings for another commonly used biorepository cohort, the results of this testing demonstrated a low seropositive rate, as determined by standard two-tiered testing. Additionally, relatively few subjects demonstrated seroconversion with testing of convalescent-phase samples. This clinical and serologically defined cohort of samples from Lyme disease and control cases from areas of Lyme disease endemicity offers an additional valuable resource for novel test development that includes alternate specimen types.
SARS-CoV-2 is a novel positive-sense single-stranded RNA virus that has caused a recent pandemic. Most patients have a mild disease course, while approximately 20% have moderate to severe disease, ...often requiring hospitalization and, in some cases, care in the intensive care unit. By investigating a perceived increased rate of indeterminate QuantiFERON-TB Gold Plus results in hospitalized COVID patients, we demonstrate that severely ill COVID-19 patients have at least a 6-fold reduction of interferon gamma (IFN-γ) levels compared to control patients. What is more, over 60% of these severely ill COVID-19 patients' peripheral T cells were found to be unable to produce measurable IFN-γ when stimulated with phytohemagglutinin (PHA), a potent IFN-γ mitogen, reflected by an indeterminate QuantiFERON-TB Gold Plus result. This defect of IFN-γ production was independent of absolute lymphocyte counts and immunosuppressive therapy. It was associated with increased levels of interleukin-6 (IL-6), which was a predictor of patient outcomes for our cohort when measured early in the course of disease. Finally, in a subset of COVID-19 patients, we found elevated IL-10 levels in addition to IL-6 elevation. In addition to finding a significant limitation of interferon-gamma release assay (IGRA) testing in severely ill COVID-19 patients, these data provide evidence that many of these patients demonstrate a focused Th2 immune response with inhibition of IFN-γ signaling and, in many cases, significant elevations of IL-6.
Predator effects on prey dynamics are conventionally studied by measuring changes in prey abundance attributed to consumption by predators. We revisit four classic examples of predator—prey systems ...often cited in textbooks and incorporate subsequent studies of nonconsumptive effects of predators (NCE), defined as changes in prey traits (e.g., behavior, growth, development) measured on an ecological time scale. Our review revealed that NCE were integral to explaining lynx—hare population dynamics in boreal forests, cascading effects of top predators in Wisconsin lakes, and cascading effects of killer whales and sea otters on kelp forests in nearshore marine habitats. The relatives roles of consumption and NCE of wolves on moose and consequent indirect effects on plant communities of Isle Royale depended on climate oscillations. Nonconsumptive effects have not been explicitly tested to explain the link between planktonic alewives and the size structure of the zooplankton, nor have they been invoked to attribute keystone predator status in intertidal communities or elsewhere. We argue that both consumption and intimidation contribute to the total effects of keystone predators, and that characteristics of keystone consumers may differ from those of predators having predominantly NCE. Nonconsumptive effects are often considered as an afterthought to explain observations inconsistent with consumption-based theory. Consequently, NCE with the same sign as consumptive effects may be overlooked, even though they can affect the magnitude, rate, or scale of a prey response to predation and can have important management or conservation implications. Nonconsumptive effects may underlie other classic paradigms in ecology, such as delayed density dependence and predator-mediated prey coexistence. Revisiting classic studies enriches our understanding of predator—prey dynamics and provides compelling rationale for ramping up efforts to consider how NCE affect traditional predator—prey models based on consumption, and to compare the relative magnitude of consumptive and NCE of predators.
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of ...pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.
Predators can affect prey populations through changes in traits that reduce predation risk. These trait changes (nonconsumptive effects, NCEs) can be energetically costly and cause reduced prey ...activity, growth, fecundity, and survival. The strength of nonconsumptive effects may vary with two functional characteristics of predators: hunting mode (actively hunting, sit-and-pursue, sit-and-wait) and habitat domain (the ability to pursue prey via relocation in space; can be narrow or broad). Specifically, cues from fairly stationary sit-and-wait and sit-and-pursue predators should be more indicative of imminent predation risk, and thereby evoke stronger NCEs, compared to cues from widely ranging actively hunting predators. Using a meta-analysis of 193 published papers, we found that cues from sit-and-pursue predators evoked stronger NCEs than cues from actively hunting predators. Predator habitat domain was less indicative of NCE strength, perhaps because habitat domain provides less reliable information regarding imminent risk to prey than does predator hunting mode. Given the importance of NCEs in determining the dynamics of prey communities, our findings suggest that predator characteristics may be used to predict how changing predator communities translate into changes in prey. Such knowledge may prove particularly useful given rates of local predator change due to habitat fragmentation and the introduction of novel predators.
High-resolution human leukocyte antigen (HLA) matching reduces graft- versus -host disease and improves overall patient survival after hematopoietic stem cell transplant. Sanger sequencing has been ...the gold standard for HLA typing since 1996. However, given the increasing number of new HLA alleles identified and the complexity of the HLA genes, clinical HLA typing by Sanger sequencing requires several rounds of additional testing to provide allele-level resolution. Although next-generation sequencing (NGS) is routinely used in molecular genetics, few clinical HLA laboratories use the technology. The performance characteristics of NGS HLA typing using TruSight HLA were determined using Sanger sequencing as the reference method. In total, 211 samples were analyzed with an overall accuracy of 99.8% (2954/2961) and 46 samples were analyzed for precision with 100% (368/368) reproducibility. Most discordant alleles were because of technical error rather than assay performance. More important, the ambiguity rate was 3.5% (103/2961). Seventy-four percentage of the ambiguities were within the DRB1 and DRB4 loci. HLA typing by NGS saves approximately $6000 per run when compared to Sanger sequencing. Thus, TruSight HLA assay enables high-throughput HLA typing with an accuracy, precision, ambiguity rate, and cost savings that should facilitate adoption of NGS technology in clinical HLA laboratories.
Histocompatibility testing is essential for donor identification and risk assessment in solid organ and hematopoietic stem cell transplant. Additionally, it is useful for identifying donor specific ...alleles for monitoring donor specific antibodies in post-transplant patients. Next-generation sequence (NGS) based human leukocyte antigen (HLA) typing has improved many aspects of histocompatibility testing in hematopoietic stem cell and solid organ transplant. HLA disease association testing and research has also benefited from the advent of NGS technologies. In this review we discuss the current impact and future applications of NGS typing on clinical histocompatibility testing for transplant and non-transplant purposes.
Delayed treatment of Rocky Mountain spotted fever is associated with increased morbidity and mortality. Because the diagnosis cannot be established from a single serological test, guidelines ...recommend empirical antibiotic initiation in suspect patients. We evaluated a policy used by UNC Health of paging clinicians when acute testing for Rickettsia returned with a titer ≥1:256. Our objective was to assess the potential effect of paging on routine treatment practices. Notably, we found that a high proportion of cases (N = 28, 40%) were not prescribed antibiotics until the results were available. The vast majority of these cases did not have evidence of compatible symptoms or disease progression. These findings suggest that paging may have prompted unnecessary treatment. Overall, the policy, which has now been discontinued, appears to have had limited benefit. Efforts are urgently needed to improve adherence to testing and treatment guidelines.
The analytical performance of the AIX1000 system, a fully automated and recently FDA-cleared rapid plasma reagin (RPR) system, was evaluated by comparison to a manual RPR test in a traditional ...syphilis testing algorithm. A total of 1,028 consecutive serum samples submitted for syphilis testing to the University of North Carolina Hospitals Clinical Immunology Laboratory were tested per each manufacturer's instructions. Among those samples, 996 were nonreactive and 20 were reactive using both the ASI RPR card system and the AIX1000 system. Of the 12 discrepant specimens, 11 were AIX1000 reactive and ASI card nonreactive whereas 1 specimen was ASI card reactive and AIX1000 nonreactive. The sensitivity and specificity of the manual ASI card were 76.0% and 99.8%, respectively, while the sensitivity and specificity of the AIX100 were 100.0% and 99.4%, respectively (sensitivity
= 0.03). Among the 20 concordant reactive specimens, 68.4% of the titers agreed within ±1 dilution between methods. Reproducibility testing of the AIX1000 system demonstrated qualitative and semiquantitative (within ±1 dilution) agreement between specimens tested on different days of 96.0% and 76.0%, respectively, and 100.0% agreement between replicates within the same run. One of 24 samples analyzed under other disease conditions was reactive on both the AIX1000 system and the ASI card. Overall, the fully automated AIX1000 system demonstrated significantly enhanced sensitivity and specificity similar to that of the manual ASI RPR card test, making the AIX1000 system suitable for the laboratory diagnosis of syphilis in a clinical laboratory setting.
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