Logically Inferred Tuberculosis Transmission (LITT): A Data Integration Algorithm to Rank Potential Source Cases

Understanding tuberculosis (TB) transmission chains can help public health staff target their resources to prevent further transmission, but currently there are few tools to automate this process. We have developed the Logically Inferred Tuberculosis Transmission (LITT) algorithm to systematize the integration and analysis of whole-genome sequencing, clinical, and epidemiological data. Based on the work typically performed by hand during a cluster investigation, LITT identifies and ranks potential source cases for each case in a TB cluster. We evaluated LITT using a diverse dataset of 534 cases in 56 clusters (size range: 2–69 cases), which were investigated locally in three different U.S. jurisdictions. Investigators and LITT agreed on the most likely source case for 145 (80%) of 181 cases. By reviewing discrepancies, we found that many of the remaining differences resulted from errors in the dataset used for the LITT algorithm. In addition, we developed a graphical user interface, user's manual, and training resources to improve LITT accessibility for frontline staff. While LITT cannot replace thorough field investigation, the algorithm can help investigators systematically analyze and interpret complex data over the course of a TB cluster investigation.Code available at:https://github.com/CDCgov/TB_molecular_epidemiology/tree/1.0; https://zenodo.org/badge/latestdoi/166261171

Earth Virtualization Engines (EVE)

To manage Earth in the Anthropocene, new tools, new institutions, and new forms of international cooperation will be required. Earth Virtualization Engines is proposed as an international federation of centers of excellence to empower all people to respond to the immense and urgent challenges posed by climate change

Aedes aegypti Males as Vehicles for Insecticide Delivery

Aedes aegypti continues to spread globally and remains a challenge to control, in part due to its ‘cryptic behavior’ in that it often deposits eggs (oviposits) in larval habitats that are difficult to find and treat using traditional methods. Auto-dissemination strategies target these cryptic breeding sites by employing mosquitoes to deliver lethal doses of insecticide. This report describes the initial field trials of an application known as Autodissemination Augmented by Males (ADAM), utilizing A. aegypti males dusted with pyriproxyfen (PPF). Findings presented here are drawn from both caged and field trial studies. Together, these trials examined for the ability of A. aegypti males to disseminate PPF and to impact field populations. PPF-dusted males were able to effectively deliver lethal doses of PPF to oviposition sites under the conditions tested. Results from field trials in Florida and California demonstrated reduced A. aegypti populations in treated areas, compared to areas where PPF-treated males were not released. These results indicate that the release of PPF-dusted A. aegypti males can impact A. aegypti populations as measured by both reduced larval survival and lower numbers of adult female A. aegypti. We propose the ADAM approach as an addition to existing mosquito control techniques targeting A. aegypti and other mosquitoes that utilize cryptic larval habitats

Aedes aegypti Males as Vehicles for Insecticide Delivery

Aedes aegypti continues to spread globally and remains a challenge to control, in part due to its 'cryptic behavior' in that it often deposits eggs (oviposits) in larval habitats that are difficult to find and treat using traditional methods. Auto-dissemination strategies target these cryptic breeding sites by employing mosquitoes to deliver lethal doses of insecticide. This report describes the initial field trials of an application known as Autodissemination Augmented by Males (ADAM), utilizing A. aegypti males dusted with pyriproxyfen (PPF). Findings presented here are drawn from both caged and field trial studies. Together, these trials examined for the ability of A. aegypti males to disseminate PPF and to impact field populations. PPF-dusted males were able to effectively deliver lethal doses of PPF to oviposition sites under the conditions tested. Results from field trials in Florida and California demonstrated reduced A. aegypti populations in treated areas, compared to areas where PPF-treated males were not released. These results indicate that the release of PPF-dusted A. aegypti males can impact A. aegypti populations as measured by both reduced larval survival and lower numbers of adult female A. aegypti. We propose the ADAM approach as an addition to existing mosquito control techniques targeting A. aegypti and other mosquitoes that utilize cryptic larval habitats

Bi-allelic variants in CELSR3 are implicated in central nervous system and urinary tract anomalies

CELSR3 codes for a planar cell polarity protein. We describe twelve affected individuals from eleven independent families with bi-allelic variants in CELSR3. Affected individuals presented with an overlapping phenotypic spectrum comprising central nervous system (CNS) anomalies (7/12), combined CNS anomalies and congenital anomalies of the kidneys and urinary tract (CAKUT) (3/12) and CAKUT only (2/12). Computational simulation of the 3D protein structure suggests the position of the identified variants to be implicated in penetrance and phenotype expression. CELSR3 immunolocalization in human embryonic urinary tract and transient suppression and rescue experiments of Celsr3 in fluorescent zebrafish reporter lines further support an embryonic role of CELSR3 in CNS and urinary tract formation

Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome.

Dubowitz syndrome (DubS) is considered a recognizable syndrome characterized by a distinctive facial appearance and deficits in growth and development. There have been over 200 individuals reported with Dubowitz or a "Dubowitz-like" condition, although no single gene has been implicated as responsible for its cause. We have performed exome (ES) or genome sequencing (GS) for 31 individuals clinically diagnosed with DubS. After genome-wide sequencing, rare variant filtering and computational and Mendelian genomic analyses, a presumptive molecular diagnosis was made in 13/27 (48%) families. The molecular diagnoses included biallelic variants in SKIV2L, SLC35C1, BRCA1, NSUN2; de novo variants in ARID1B, ARID1A, CREBBP, POGZ, TAF1, HDAC8, and copy-number variation at1p36.11(ARID1A), 8q22.2(VPS13B), Xp22, and Xq13(HDAC8). Variants of unknown significance in known disease genes, and also in genes of uncertain significance, were observed in 7/27 (26%) additional families. Only one gene, HDAC8, could explain the phenotype in more than one family (N = 2). All but two of the genomic diagnoses were for genes discovered, or for conditions recognized, since the introduction of next-generation sequencing. Overall, the DubS-like clinical phenotype is associated with extensive locus heterogeneity and the molecular diagnoses made are for emerging clinical conditions sharing characteristic features that overlap the DubS phenotype