A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome.

H37Rv is the most widely used Mycobacterium tuberculosis strain, and its genome is globally used as the M. tuberculosis reference sequence. Here, we present Bact-Builder, a pipeline that uses consensus building to generate complete and accurate bacterial genome sequences and apply it to three independently cultured and sequenced H37Rv aliquots of a single laboratory stock. Two of the 4,417,942 base-pair long H37Rv assemblies are 100% identical, with the third differing by a single nucleotide. Compared to the existing H37Rv reference, the new sequence contains ~6.4 kb additional base pairs, encoding ten new regions that include insertions in PE/PPE genes and new paralogs of esxN and esxJ, which are differentially expressed compared to the reference genes. New sequencing and de novo assemblies with Bact-Builder confirm that all 10 regions, plus small additional polymorphisms, are also present in the commonly used H37Rv strains NR123, TMC102, and H37Rv1998. Thus, Bact-Builder shows promise as an improved method to perform accurate and reproducible de novo assemblies of bacterial genomes, and our work provides important updates to the primary M. tuberculosis reference genome.

The Language We Use: Providers' Perceptions About Families.

Implicitly-held unconscious associations and attitudes may not align with the beliefs we hold outwardly or explicitly but can affect our professional perceptions, decisions, and actions. In a phenomenological study identifying strategies used to support families in vulnerable circumstances, we conducted nine focus groups to examine how early interventionists (EIs) described families and children, the language they used, and how they used it. Thematic qualitative analysis revealed three themes about families: perceptions of parenting, perceptions of capability, and perceptions of priorities. How EIs characterized families and their interactions with families were both reflective of and counter to family-centeredness and, at times, indicative of implicit bias. This study addresses a critical gap in the field, given the lack of empirical research available about implicit bias in early childhood intervention professionals. Implications for personnel preparation and practice change are discussed to begin the necessary work of moving the field toward more culturally sustaining practices.

Mycobacterium tuberculosis progresses through two phases of latent infection in humans.

Little is known about the physiology of latent Mycobacterium tuberculosis infection. We studied the mutational rates of 24 index tuberculosis (TB) cases and their latently infected household contacts who developed active TB up to 5.25 years later, as an indication of bacterial physiological state and possible generation times during latent TB infection in humans. Here we report that the rate of new mutations in the M. tuberculosis genome decline dramatically after two years of latent infection (two-sided p < 0.001, assuming an 18 h generation time equal to log phase M. tuberculosis, with latency period modeled as a continuous variable). Alternatively, assuming a fixed mutation rate, the generation time increases over the latency duration. Mutations indicative of oxidative stress do not increase with increasing latency duration suggesting a lack of host or bacterial derived mutational stress. These results suggest that M. tuberculosis enters a quiescent state during latency, decreasing the risk for mutational drug resistance and increasing generation time, but potentially increasing bacterial tolerance to drugs that target actively growing bacteria.

Use, reuse or discard: quantitatively defined variance in N95 respirator integrity following vaporized hydrogen peroxide decontamination during the COVID-19 pandemic.

BACKGROUND: COVID-19 has stretched the ability of many institutions to supply needed personal protective equipment, especially N95 respirators. N95 decontamination and reuse programs provide one potential solution to this problem. Unfortunately, a comprehensive evaluation of the effects of decontamination on the integrity of various N95 models using a quantitative fit test (QTFT) approach is lacking. AIMS: 1) To investigate the effects of up to eight rounds of vaporized H2O2 (VHP) decontamination on the integrity of N95 respirators currently in use in a hospital setting. 2) To examine if N95 respirators worn by one user can adapt to the face shape of a second user with no compromise of integrity following VHP decontamination. METHODS: The PortaCount Pro+ Respirator Fit Tester Model 8038 was used to quantitatively define the integrity, measured by fit, of N95 respirators following decontamination with VHP. FINDINGS: There was an observable downward trend in the integrity of Halyard Fluidshield 46727 N95 respirators throughout eight cycles of decontamination with VHP. The integrity of 3M 1870 N95 respirators was significantly reduced after the respirator was worn, decontaminated with VHP, and then quantitatively fit tested on a second user. Furthermore, we uncovered inconsistencies between qualitative fit test and QTFT results that may have strong implications on the fit testing method used by institutions. CONCLUSIONS: Our data revealed variability in the integrity of different N95 models after VHP decontamination and exposed potential limitations of N95 decontamination and reuse programs.

A Preclinical Candidate Targeting Mycobacterium tuberculosis KasA.

Published Mycobacterium tuberculosis ß-ketoacyl-ACP synthase KasA inhibitors lack sufficient potency and/or pharmacokinetic properties. A structure-based approach was used to optimize existing KasA inhibitor DG167. This afforded indazole JSF-3285 with a 30-fold increase in mouse plasma exposure. Biochemical, genetic, and X-ray studies confirmed JSF-3285 targets KasA. JSF-3285 offers substantial activity in an acute mouse model of infection and in the corresponding chronic infection model, with efficacious reductions in colony-forming units at doses as low as 5 mg/kg once daily orally and improvement of the efficacy of front-line drugs isoniazid or rifampicin. JSF-3285 is a promising preclinical candidate for tuberculosis.

Antitubercular Triazines: Optimization and Intrabacterial Metabolism.

The triazine antitubercular JSF-2019 was of interest due to its in vitro efficacy and the nitro group shared with the clinically relevant delamanid and pretomanid. JSF-2019 undergoes activation requiring F420H2 and one or more nitroreductases in addition to Ddn. An intrabacterial drug metabolism (IBDM) platform was leveraged to demonstrate the system kinetics, evidencing formation of NO⋅ and a des-nitro metabolite. Structure-activity relationship studies focused on improving the solubility and mouse pharmacokinetic profile of JSF-2019 and culminated in JSF-2513, relying on the key introduction of a morpholine. Mechanistic studies with JSF-2019, JSF-2513, and other triazines stressed the significance of achieving potent in vitro efficacy via release of intrabacterial NO⋅ along with inhibition of InhA and, more generally, the FAS-II pathway. This study highlights the importance of probing IBDM and its potential to clarify mechanism of action, which in this case is a combination of NO⋅ release and InhA inhibition.

Adverse childhood experiences and preschool suspension expulsion: A population study.

BACKGROUND: Preschool suspension and expulsion rates are typically based on teacher reports, and don't simultaneously account for adverse childhood experiences (ACEs). OBJECTIVE: To examine estimates in the United States of parent-reported preschool suspension and expulsion rates, in the context of ACEs. PARTICIPANTS AND SETTING: Parents of children aged 3-5 years old (N = 6,100) in the 2016 National Survey of Children's Health dataset. METHOD: We reported the prevalence estimates of preschool suspension and expulsion, and estimated the unique variance of ACEs as risk factors using weighted sequential logistic regression. RESULTS: An estimated 174,309 preschoolers (2.0%) were suspended, and 17,248 (0.2%) children were expelled annually. If divided by 36 school weeks, the instances of weekly suspension and expulsion were at least 4,842 and 479 respectively. Controlling for previous risk factors (i.e., age, gender, race, ethnicity), the odds ratio increased by 80% for every unit of ACEs increment. Children were more likely to be suspended or expelled if they had domestic violence (OR = 10.6, p <  .001), living with mental illness (OR = 9.8, p <  .001), adult substance abuse (OR = 4.8, p <  .001), and victim of violence (OR = 4.5, p =  .004), living in high poverty (OR = 3.9, p =  .001), divorced parents (OR = 3.3, p =  .001), and parent incarceration (OR = 3.0, p =  .009). CONCLUSION: The alarming suspension and expulsion rates call for more comprehensive outreach prevention and response efforts in preschool settings. Cross system collaboration and family support are essential to this work.

Kinetics of viral load and erythrocytic inclusion body formation in Pacific herring artificially infected with erythrocytic necrosis virus.

Viral erythrocytic necrosis (VEN) is a condition that affects marine and anadromous fish species, including herrings and salmonids, in the Atlantic and Pacific oceans. Infection is frequently associated with severe anemia and causes episodic mortality among wild and hatchery fish when accompanied by additional stressors; VEN can be presumptively diagnosed by (1) light microscopic identification of a single characteristic-a round, magenta-colored, 0.8-µm-diameter inclusion body (IB) within the cytoplasm of erythrocytes and their precursors on Giemsa-stained blood films; or (2) observation (via transmission electron microscopy [TEM]) of the causative iridovirus, erythrocytic necrosis virus (ENV), within erythrocytes or their precursors. To better understand the kinetics of VEN, specific-pathogen-free Pacific herring Clupea pallasii were infected with ENV by intraperitoneal injection. At 1, 4, 7, 10, 14, 21, and 28 d postexposure, samples of blood, spleen, and kidney were collected and assessed (1) via light microscopy for the number of intracytoplasmic IBs in blood smears and (2) via TEM for the number of virions within erythrocytes. The mean prevalence of intracytoplasmic IBs in the blood cells increased from 0% at 0-4 d postexposure to 94% at 28 d postexposure. Viral load within circulating red blood cells peaked at 7 d postexposure, fell slightly, and then reached a plateau. However, blood cells observed within the kidney and spleen tissues demonstrated high levels of ENV between 14 and 28 d postexposure. The results indicate that the viral load within erythrocytes does not correlate well with IB prevalence and that the virus can persist in infected fish for more than 28 d.

Induction of anti-viral genes during acute infection with Viral hemorrhagic septicemia virus (VHSV) genogroup IVa in Pacific herring (Clupea pallasii).

Infection with the aquatic rhabdovirus Viral hemorrhagic septicemia virus (VHSV) genogroup IVa results in high mortality in Pacific herring (Clupea pallasii) and is hypothesized to be a potential limiting factor for herring recovery. To investigate anti-viral immunity in the Pacific herring, four immune response genes were identified: the myxovirus resistance (Clpa-Mx), a major histocompatibility complex IB (named Clpa-UAA.001), the inducible immunoproteosome subunit 9 (Clpa-PSMB9) and the neutrophil chemotactic factor (Clpa-LECT2). Reverse transcriptase quantitative PCR (RT-qPCR) assays were developed based on these gene sequences to investigate the host immune response to acute VHSV infection following both injection and immersion challenge. Virus levels were measured by both plaque assay and RT-qPCR and peaked at day 6 during the 10-day exposure period for both groups of fish. The interferon stimulated genes (Clpa-Mx, -UAA.001, and -PSMB9) were significantly up-regulated in response to VHSV infection at both 6 and 10 days post-infection in both spleen and fin. Results from this study indicate that Pacific herring mount a robust, early antiviral response in both fin and spleen tissues. The immunological tools developed in this study will be useful for future studies to investigate antiviral immunity in Pacific herring.

Effects of Environmental Temperature on the Dynamics of Ichthyophoniasis in Juvenile Pacific Herring (Clupea pallasii).

The effects of temperature and infection by Ichthyophonus were examined in juvenile Pacific herring (Clupea pallasii) maintained under simulated overwinter fasting conditions. In addition to defining parameters for a herring bioenergetics model (discussed in Vollenweider et al. this issue), these experiments provided new insights into factors influencing the infectivity and virulence of the parasite Ichthyophonus. In groups of fish with established disease, temperature variation had little effect on disease outcome. Ichthyophonus mortality outpaced that resulting from starvation alone. In newly infected fish, temperature variation significantly changed the mortality patterns related to disease. Both elevated and lowered temperatures suppressed disease-related mortality relative to ambient treatments. When parasite exposure dose decreased, an inverse relationship between infection prevalence and temperature was detected. These findings suggest interplay between temperature optima for parasite growth and host immune function and have implications for our understanding of how Ichthyophonus infections are established in wild fish populations.

Larval and juvenile Pacific herring Clupea pallasii are not susceptible to infectious hematopoietic necrosis under laboratory conditions.

Infectious hematopoietic necrosis (IHN) leads to periodic epidemics among certain wild and farmed fish species of the Northeast (NE) Pacific. The source of the IHN virus (IHNV) that initiates these outbreaks remains unknown; however, a leading hypothesis involves viral persistence in marine host species such as Pacific herring Clupea pallasii. Under laboratory conditions we exposed specific pathogen-free (SPF) larval and juvenile Pacific herring to 10(3) to 10(4) plaque-forming units (pfu) of IHNV ml(-1) by waterborne immersion. Cumulative mortalities among exposed groups were not significantly different from those of negative control groups. After waterborne exposure, IHNV was transiently recovered from the tissues of larvae but absent in tissues of juveniles. Additionally, no evidence of viral shedding was detected in the tank water containing exposed juveniles. After intraperitoneal (IP) injection of IHNV in juvenile herring with 10(3) pfu, IHNV was recovered from the tissues of sub-sampled individuals for only the first 5 d post-exposure. The lack of susceptibility to overt disease and transient levels of IHNV in the tissues of exposed fish indicate that Pacific herring do not likely serve a major epizootiological role in perpetuation of IHNV among free-ranging sockeye salmon Oncorhynchus nerka and farmed Atlantic salmon Salmo salar in the NE Pacific.