Rapid Detection of DNA and RNA Shrimp Viruses Using CRISPR-Based Diagnostics.

Timely detection of persistent and emerging pathogens is critical to controlling disease spread, particularly in high-density populations with increased contact between individuals and limited-to-no ability to quarantine. Standard molecular diagnostic tests for surveying pathogenic microbes have provided the sensitivity needed for early detection, but lag in time-to-result leading to delayed action. On-site diagnostics alleviate this lag, but current technologies are less sensitive and adaptable than lab-based molecular methods. Towards the development of improved on-site diagnostics, we demonstrated the adaptability of a loop-mediated isothermal amplification-CRISPR coupled technology for detecting DNA and RNA viruses that have greatly impacted shrimp populations worldwide; White Spot Syndrome Virus and Taura Syndrome Virus. Both CRISPR-based fluorescent assays we developed showed similar sensitivity and accuracy for viral detection and load quantification to real-time PCR. Additionally, both assays specifically targeted their respective virus with no false positives detected in animals infected with other common pathogens or in certified specific pathogen-free animals. IMPORTANCE The Pacific white shrimp (Penaeus vannamei) is one of the most valuable aquaculture species in the world but has suffered major economic losses from outbreaks of White Spot Syndrome Virus and Taura Syndrome Virus. Rapid detection of these viruses can improve aquaculture practices by enabling more timely action to be taken to combat disease outbreaks. Highly sensitive, specific, and robust CRISPR-based diagnostic assays such as those developed here have the potential to revolutionize disease management in agriculture and aquaculture helping to promote global food security.

Bone marrow mesenchymal stem cells provide an antibiotic-protective niche for persistent viable Mycobacterium tuberculosis that survive antibiotic treatment.

During tuberculosis (TB), some Mycobacterium tuberculosis bacilli persist in the presence of an active immunity and antibiotics that are used to treat the disease. Herein, by using the Cornell model of TB persistence, we further explored our recent finding that suggested that M. tuberculosis can escape therapy by residing in the bone marrow (BM) mesenchymal stem cells. We initially showed that M. tuberculosis rapidly disseminates to the mouse BM after aerosol exposure and maintained a stable burden for at least 220 days. In contrast, in the lungs, the M. tuberculosis burden peaked at 28 days and subsequently declined approximately 10-fold. More important, treatment of the mice with the antibiotics rifampicin and isoniazid, as expected, resulted in effective clearance of M. tuberculosis from the lungs and spleen. In contrast, M. tuberculosis persisted, albeit at low numbers, in the BM of antibiotic-treated mice. Moreover, most viable M. tuberculosis was recovered from the bone marrow CD271(+)CD45(-)-enriched cell fraction, and only few viable bacteria could be isolated from the CD271(-)CD45(+) cell fraction. These results clearly show that BM mesenchymal stem cells provide an antibiotic-protective niche for M. tuberculosis and suggest that unraveling the mechanisms underlying this phenomenon will enhance our understanding of M. tuberculosis persistence in treated TB patients.

Genetically diverse mice are novel and valuable models of age-associated susceptibility to Mycobacterium tuberculosis.

BACKGROUND: Tuberculosis, the disease due to Mycobacterium tuberculosis, is an important cause of morbidity and mortality in the elderly. Use of mouse models may accelerate insight into the disease and tests of therapies since mice age thirty times faster than humans. However, the majority of TB research relies on inbred mouse strains, and these results might not extrapolate well to the genetically diverse human population. We report here the first tests of M. tuberculosis infection in genetically heterogeneous aging mice, testing if old mice benefit from rapamycin. FINDINGS: We find that genetically diverse aging mice are much more susceptible than young mice to M. tuberculosis, as are aging human beings. We also find that rapamycin boosts immune responses during primary infection but fails to increase survival. CONCLUSIONS: Genetically diverse mouse models provide a valuable resource to study how age influences responses and susceptibility to pathogens and to test interventions. Additionally, surrogate markers such as immune measures may not predict whether interventions improve survival.

Pregnant sows immunized with Cryptosporidium parvum significantly reduced infection in newborn piglets challenged with C. parvum but not with C. hominis.

BACKGROUND: The piglet is the only model to investigate the immunogenic relationship between Cryptosporidium hominis and C. parvum, the species responsible for diarrhea in humans. Despite being indistinguishable antigenically, and high genetic homology between them, they are only moderately cross protective after an active infection. METHODOLOGY/PRINCIPAL FINDINGS: Here we examined the degree of passive protection conferred to piglets suckling sows immunized during pregnancy with C. parvum. After birth suckling piglets were challenged orally with either C. parvum or C. hominis at age 5 days. Animals challenged with C. parvum had significant reduction of infection rate, while piglets challenged with C. hominis showed no reduction despite high C. parvum serum and colostrum IgG and IgA antibody. CONCLUSIONS/SIGNIFICANCE: We add these data to earlier studies where we described that infection derived immunity provides partial cross-protection. Together, it appears that for full protection, vaccines against human cryptosporidiosis must contain antigenic elements derived from both species.

Are Older Adults Unique? Examining Presenting Issues and Changes in Therapy Across the Life Span.

With the urgent need to increase and improve mental health care of the growing population of older adults in the United States, clinical research is warranted to further the knowledge and improve the relevant training for mental health professionals working with older adults. This study drew from two diverse clinical samples of adults ages 18 years to 80 years to examine whether and how initial clinical presentations and changes over time in individual, family-of-origin, and relational measures differed across the life span. Results indicated a variety of linear and curvilinear associations between individual, family-of-origin, and relational measures at intake and age, with some moderation by gender. There were no significant results between the amount of change on those measures and age, indicating that older adults may change in similar fashion to middle-aged and younger adults in psychotherapy. Relevant clinical implications are provided.

Ultra-sensitive and rapid detection of nucleic acids and microorganisms in body fluids using single-molecule tethering.

Detection of microbial nucleic acids in body fluids has become the preferred method for rapid diagnosis of many infectious diseases. However, culture-based diagnostics that are time-consuming remain the gold standard approach in certain cases, such as sepsis. New culture-free methods are urgently needed. Here, we describe Single MOLecule Tethering or SMOLT, an amplification-free and purification-free molecular assay that can detect microorganisms in body fluids with high sensitivity without the need of culturing. The signal of SMOLT is generated by the displacement of micron-size beads tethered by DNA probes that are between 1 and 7 microns long. The molecular extension of thousands of DNA probes is determined with sub-micron precision using a robust and rapid optical approach. We demonstrate that SMOLT can detect nucleic acids directly in blood, urine and sputum at sub-femtomolar concentrations, and microorganisms in blood at 1 CFU mL-1 (colony forming unit per milliliter) threefold faster, with higher multiplexing capacity and with a more straight-forward protocol than amplified methodologies. SMOLT's clinical utility is further demonstrated by developing a multiplex assay for simultaneous detection of sepsis-causing Candida species directly in whole blood.

Draft Genome Sequences of Cloacibacterium normanense IMET F, a Microalgal Growth-Promoting Bacterium, and Aeromonas jandaei IMET J, a Microalgal Growth-Inhibiting Bacterium.

We report here the whole-genome sequencing results of two bacterial isolates, Aeromonas jandaei IMET J and Cloacibacterium normanense IMET F, that inhibit (possibly due to denitrifying gene clusters) and promote (possibly due to an ammonification system), respectively, the growth of the microalgal strains Scenedesmus HTB1 and Chlorella vulgaris 1807.

Lung necrosis and neutrophils reflect common pathways of susceptibility to Mycobacterium tuberculosis in genetically diverse, immune-competent mice.

Pulmonary tuberculosis (TB) is caused by Mycobacterium tuberculosis in susceptible humans. Here, we infected Diversity Outbred (DO) mice with ∼100 bacilli by aerosol to model responses in a highly heterogeneous population. Following infection, 'supersusceptible', 'susceptible' and 'resistant' phenotypes emerged. TB disease (reduced survival, weight loss, high bacterial load) correlated strongly with neutrophils, neutrophil chemokines, tumor necrosis factor (TNF) and cell death. By contrast, immune cytokines were weak correlates of disease. We next applied statistical and machine learning approaches to our dataset of cytokines and chemokines from lungs and blood. Six molecules from the lung: TNF, CXCL1, CXCL2, CXCL5, interferon-γ (IFN-γ), interleukin 12 (IL-12); and two molecules from blood - IL-2 and TNF - were identified as being important by applying both statistical and machine learning methods. Using molecular features to generate tree classifiers, CXCL1, CXCL2 and CXCL5 distinguished four classes (supersusceptible, susceptible, resistant and non-infected) from each other with approximately 77% accuracy using completely independent experimental data. By contrast, models based on other molecules were less accurate. Low to no IFN-γ, IL-12, IL-2 and IL-10 successfully discriminated non-infected mice from infected mice but failed to discriminate disease status amongst supersusceptible, susceptible and resistant M.-tuberculosis-infected DO mice. Additional analyses identified CXCL1 as a promising peripheral biomarker of disease and of CXCL1 production in the lungs. From these results, we conclude that: (1) DO mice respond variably to M. tuberculosis infection and will be useful to identify pathways involving necrosis and neutrophils; (2) data from DO mice is suited for machine learning methods to build, validate and test models with independent data based solely on molecular biomarkers; (3) low levels of immunological cytokines best indicate a lack of exposure to M. tuberculosis but cannot distinguish infection from disease.