Bacterial cGAS senses a viral RNA to initiate immunity.

Cyclic oligonucleotide-based antiphage signalling systems (CBASS) protect prokaryotes from viral (phage) attack through the production of cyclic oligonucleotides, which activate effector proteins that trigger the death of the infected host1,2. How bacterial cyclases recognize phage infection is not known. Here we show that staphylococcal phages produce a structured RNA transcribed from the terminase subunit genes, termed CBASS-activating bacteriophage RNA (cabRNA), which binds to a positively charged surface of the CdnE03 cyclase and promotes the synthesis of the cyclic dinucleotide cGAMP to activate the CBASS immune response. Phages that escape the CBASS defence harbour mutations that lead to the generation of a longer form of the cabRNA that cannot activate CdnE03. As the mammalian cyclase OAS1 also binds viral double-stranded RNA during the interferon response, our results reveal a conserved mechanism for the activation of innate antiviral defence pathways.

Theoretical considerations and empirical predictions of the pharmaco- and population dynamics of heteroresistance.

Antibiotics are considered one of the most important contributions to clinical medicine in the last century. Due to the use and overuse of these drugs, there have been increasing frequencies of infections with resistant pathogens. One form of resistance, heteroresistance, is particularly problematic; pathogens appear sensitive to a drug by common susceptibility tests. However, upon exposure to the antibiotic, resistance rapidly ascends, and treatment fails. To quantitatively explore the processes contributing to the emergence and ascent of resistance during treatment and the waning of resistance following cessation of treatment, we develop two distinct mathematical and computer-simulation models of heteroresistance. In our analysis of the properties of these models, we consider the factors that determine the response to antibiotic-mediated selection. In one model, heteroresistance is progressive, with each resistant state sequentially generating a higher resistance level. In the other model, heteroresistance is non-progressive, with a susceptible population directly generating populations with different resistance levels. The conditions where resistance will ascend in the progressive model are narrower than those of the non-progressive model. The rates of reversion from the resistant to the sensitive states are critically dependent on the transition rates and the fitness cost of resistance. Our results demonstrate that the standard test used to identify heteroresistance is insufficient. The predictions of our models are consistent with empirical results. Our results demand a reevaluation of the definition and criteria employed to identify heteroresistance. We recommend that the definition of heteroresistance should include a consideration of the rate of return to susceptibility.

The book of Lambda does not tell us that naturally occurring lysogens of Escherichia coli are likely to be resistant as well as immune.

The most significant difference between bacteriophages functionally and ecologically is whether they are purely lytic (virulent) or temperate. Virulent phages can only be transmitted horizontally by infection, most commonly with the death of their hosts. Temperate phages can also be transmitted horizontally, but upon infection of susceptible bacteria, their genomes can be incorporated into that of their host's as a prophage and be transmitted vertically in the course of cell division by their lysogenic hosts. From what we know from studies with the temperate phage Lambda and other temperate phages, in laboratory culture, lysogenic bacteria are protected from killing by the phage coded for by their prophage by immunity; where upon infecting lysogens, the free temperate phage coded by their prophage is lost. Why are lysogens not only resistant but also immune to the phage coded by their prophage since immunity does not confer protection against virulent phages? To address this question, we used a mathematical model and performed experiments with temperate and virulent mutants of the phage Lambda in laboratory culture. Our models predict and experiments confirm that selection would favor the evolution of resistant and immune lysogens, particularly if the environment includes virulent phage that shares the same receptors as the temperate. To explore the validity and generality of this prediction, we examined 10 lysogenic Escherichia coli from natural populations. All 10 were capable of forming immune lysogens, but their original hosts were resistant to the phage coded by their prophage.

Randomized adaptive selection trial of cryotherapy, compression therapy, and placebo to prevent taxane-induced peripheral neuropathy in patients with breast cancer.

BACKGROUND: Chemotherapy-induced peripheral neuropathy (CIPN) is a common and debilitating adverse effect of taxane therapy. Small non-randomized studies in patients with early-stage breast cancer (ESBC) suggest both cryotherapy and compression therapy may prevent CIPN. It is unknown which is more effective. METHODS: We conducted a randomized phase IIB adaptive sequential selection trial of cryotherapy vs. compression therapy vs. placebo ("loose" gloves/socks) during taxane chemotherapy. Participants were randomized in triplets. Garments were worn for 90-120 min, beginning 15 min prior and continuing for 15 min following the infusion. The primary goal was to select the best intervention based on a Levin-Robbins-Leu sequential selection procedure. The primary endpoint was a < 5-point decrease in the Functional Assessment of Cancer Therapy Neurotoxicity (FACT-NTX) at 12 weeks. An arm was eliminated if it had four or more fewer successes than the currently leading arm. Secondary endpoints included intervention adherence and patient-reported comfort/satisfaction. RESULTS: Between April 2019 and April 2021, 63 patients were randomized (cryotherapy (20); compression (22); placebo (21)). Most patients (60.3%) were treated with docetaxel. The stopping criterion was met after the 17th triplet (n = 51) was evaluated; success at 12 weeks occurred in 11 (64.7%) on compression therapy, 7 (41.1%) on cryotherapy, and 7 (41.1%) on placebo. Adherence to the intervention was lowest with cryotherapy (35.0%) compared to compression (72.7%) and placebo (76.2%). CONCLUSION: Compression therapy was the most effective intervention in this phase IIB selection trial to prevent CIPN and was well tolerated. Compression therapy for the prevention of CIPN should be evaluated in a phase III study. CLINICAL TRIAL REGISTRATION: ClinicaTrials.gov Identifier: NCT03873272.

Evaluating the potential efficacy and limitations of a phage for joint antibiotic and phage therapy of Staphylococcus aureus infections.

In response to increasing frequencies of antibiotic-resistant pathogens, there has been a resurrection of interest in the use of bacteriophage to treat bacterial infections: phage therapy. Here we explore the potential of a seemingly ideal phage, PYOSa, for combination phage and antibiotic treatment of Staphylococcus aureus infections. This K-like phage has a broad host range; all 83 tested clinical isolates of S.aureus tested were susceptible to PYOSa Because of the mode of action of PYOSa, S. aureus is unlikely to generate classical receptor-site mutants resistant to PYOSa; none were observed in the 13 clinical isolates tested. PYOSa kills S. aureus at high rates. On the downside, the results of our experiments and tests of the joint action of PYOSa and antibiotics raise issues that must be addressed before PYOSa is employed clinically. Despite the maintenance of the phage, PYOSa does not clear populations of S. aureus Due to the ascent of a phenotyically diverse array of small-colony variants following an initial demise, the bacterial populations return to densities similar to that of phage-free controls. Using a combination of mathematical modeling and in vitro experiments, we postulate and present evidence for a mechanism to account for the demise-resurrection dynamics of PYOSa and S. aureus Critically for phage therapy, our experimental results suggest that treatment with PYOSa followed by bactericidal antibiotics can clear populations of S. aureus more effectively than the antibiotics alone.

It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements.

Articles on CRISPR commonly open with some variant of the phrase "these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements." There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical-computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.

Exploring perceptions of implementation practice capacity in community-based behavioral health organizations.

Community-based organizations (CBOs) must have the capacity to adopt, implement, and sustain evidence-based practices (EBPs). However, limited research exists examining CBOs' ability/capacity to implement EBPs. The purpose of this preliminary study was to investigate how staff of CBOs perceive implementation practice capacity, determine factors needed for adequate capacity for implementing EBPs, and examine which perspectives of capacity are shared across organizational levels. Ninety-seven administrators and practitioners of CBOs were surveyed using the Implementation Capacity Survey, which examines perceived importance, presence, and organizational capacity of the CBO in nine implementation practice areas (IPAs) (e.g., leadership). Results revealed participants rated IPAs on the importance scale higher than IPAs on the present scale. Presence and organizational capacity scales were strongly correlated, and results showed significant differences between administrators and practitioners on ratings of presence and organizational capacity. Implications for future research aimed at examining/building implementation practice capacity in community settings will be discussed.

Leaky resistance and the conditions for the existence of lytic bacteriophage.

In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIR is maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIR in these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility-a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria-their "existence conditions."

Faith leaders' perceptions of needle exchange programs in the rural Illinois Delta Region: Religion as a social determinant of health.

BACKGROUND AND OBJECTIVES: Despite increasing drug use in rural communities, potentially life-saving harm reduction interventions, such as needle exchange programs (NEPs), remain underutilized. Religion is an integral component of the rural culture that has been shown to influence health, yet no studies to date have explored rural faith leaders' perceptions of harm reduction strategies. METHODS: An online cross-sectional survey was conducted among rural faith leaders (n = 133) in the rural Illinois Delta Region. RESULTS: While most of the respondents felt that drug abuse was an issue in their communities, support was mixed regarding whether they were in favor of NEPs with the majority of respondents having never heard of an NEP before this survey. While the majority believed that NEPs would help decrease bloodborne disease transmission, it was also perceived that NEPs would increase drug use. Significant differences in perceptions based on race, marital status, and political party also exist. CONCLUSION AND SCIENTIFIC SIGNIFICANCE: Congruent with previous harm reduction literature, many rural faith leaders have varied perceptions of NEPs. Rural faith leaders could benefit from education about NEPs, including the possible positive and negative impacts they can have on the community. Future studies should explore contextual differences among rural faith leaders. To date, no studies have examined faith-based organizations' perceptions of NEPs. The findings have the potential to increase the current body of knowledge and provide data to support recommendations for engaging faith-based organizations in behavioral health service delivery.

HIV Care Coordination promotes care re-engagement and viral suppression among people who have been out of HIV medical care: an observational effectiveness study using a surveillance-based contemporaneous comparison group.

BACKGROUND: Medical care re-engagement is critical to suppressing viral load and preventing HIV transmission, morbidity and mortality, yet few rigorous intervention studies address this outcome. We assessed the effectiveness of a Ryan White Part A-funded HIV Care Coordination Program relative to 'usual care,' for short-term care re-engagement and viral suppression among people without recent HIV medical care. METHODS: The Care Coordination Program was launched in 2009 at 28 hospitals, health centers, and community-based organizations in New York City. Designed for people with HIV (PWH) experiencing or at risk for poor HIV outcomes, the Care Coordination Program provides long-term, comprehensive medical case management utilizing interdisciplinary teams, structured health education and patient navigation. The intervention was implemented as a safety-net services program, without a designated comparison group. To evaluate it retrospectively, we created an observational, matched cohort of clients and controls. Using the HIV surveillance registry, we identified individuals meeting program eligibility criteria from December 1, 2009 to March 31, 2013 and excluded those dying prior to 12 months of follow-up. We then matched clients to controls on baseline status (lacking evidence of viral suppression, consistently suppressed, inconsistently suppressed, or newly diagnosed in the past 12 months), start of follow-up and propensity score. For this analysis, we limited to those out of care at baseline (defined as having no viral load test in the 12 months pre-enrollment) and still residing within jurisdiction (defined as having a viral load or CD4 test reported to local surveillance and dated within the 12-month follow-up period). Using a GEE model with binary error distribution and logit link, we compared odds of care re-engagement (defined as having ≥ 2 laboratory events ≥ 90 days apart) and viral suppression (defined as having HIV RNA ≤ 200 copies/mL on the most recent viral load test) at 12-month follow-up. RESULTS: Among 326 individuals out of care at baseline, 87.2% of clients and 48.2% of controls achieved care re-engagement (Odds Ratio: 4.53; 95%CI 2.66, 7.71); 58.3% of clients and 49.3% of controls achieved viral suppression (Odds Ratio: 2.05; 95%CI 1.30, 3.23). CONCLUSIONS: HIV Care Coordination shows evidence of effectiveness for care and treatment re-engagement.

Post-earthquake Self-Reported Depressive Symptoms and Post-Traumatic Stress Disorder and their Correlates among College-Youths in Kathmandu, Nepal.

Exposure to earthquake has previously been associated with adverse mental health outcomes, however, evidence is limited among youth in resource-limited settings. This study explored the association of retrospective extent of exposure on current day depressive symptoms and post-traumatic stress disorder (PTSD) symptoms among 125 youth attending a college in Kathmandu, Nepal. A self-administered survey including socio-demographic variables, scale for earthquake exposure and Nepali language validated standardized scales for depressive and PTSD symptoms was used. Prevalence estimates for depressive symptoms was 43.2% and PTSD symptoms was 19.2%. For each increasing unit of the extent of earthquake exposure, the odds of having depressive symptoms increased by a factor of 1.26 (p = 0.001) and PTSD symptoms increased by a factor of 1.26 (p = 0.002). Being in a complicated romantic relationship increased the odds of both depressive symptoms and PTSD symptoms. Exposure to earthquake is an important factor to consider while assessing depressive and PTSD symptoms among youth earthquake survivors in Kathmandu. It is important that programs or policies aimed at youth mental health concurrently address disaster exposures.

Deoxynucleoside Therapy for Thymidine Kinase 2-Deficient Myopathy.

OBJECTIVE: Thymidine kinase 2, encoded by the nuclear gene TK2, is required for mitochondrial DNA maintenance. Autosomal recessive TK2 mutations cause depletion and multiple deletions of mtDNA that manifest predominantly as a myopathy usually beginning in childhood and progressing relentlessly. We investigated the safety and efficacy of deoxynucleoside monophosphate and deoxynucleoside therapies. METHODS: We administered deoxynucleoside monophosphates and deoxynucleoside to 16 TK2-deficient patients under a compassionate use program. RESULTS: In 5 patients with early onset and severe disease, survival and motor functions were better than historically untreated patients. In 11 childhood and adult onset patients, clinical measures stabilized or improved. Three of 8 patients who were nonambulatory at baseline gained the ability to walk on therapy; 4 of 5 patients who required enteric nutrition were able to discontinue feeding tube use; and 1 of 9 patients who required mechanical ventilation became able to breathe independently. In motor functional scales, improvements were observed in the 6-minute walk test performance in 7 of 8 subjects, Egen Klassifikation in 2 of 3, and North Star Ambulatory Assessment in all 5 tested. Baseline elevated serum growth differentiation factor 15 levels decreased with treatment in all 7 patients tested. A side effect observed in 8 of the 16 patients was dose-dependent diarrhea, which did not require withdrawal of treatment. Among 12 other TK2 patients treated with deoxynucleoside, 2 adults developed elevated liver enzymes that normalized following discontinuation of therapy. INTERPRETATION: This open-label study indicates favorable side effect profiles and clinical efficacy of deoxynucleoside monophosphate and deoxynucleoside therapies for TK2 deficiency. ANN NEUROL 2019;86:293-303.

Impact of an HIV Care Coordination Program on the Timeliness of Viral Suppression and Immune Recovery Among Clients Newly Diagnosed with HIV.

We compared the time to immune recovery and viral suppression (VS) among people newly diagnosed with HIV who enrolled in the HIV Care Coordination Program (CCP), a comprehensive medical case management program, with a propensity matched group of newly diagnosed people who did not enroll. CCP enrollees had more rapid VS (≤ 200 copies/mL) [hazards ratio (HR) 1.17; 95% confidence interval 1.02-1.34] but no more rapid immune recovery (≥ two successive CD4 counts > 500 cells/mm3) (HR 0.98; 0.84-1.13). Relative to usual care, the CCP may expedite VS (though not immune recovery) for newly diagnosed HIV patients and therefore lower forward transmission risk.

Antibiotic Killing of Diversely Generated Populations of Nonreplicating Bacteria.

Nonreplicating bacteria are known to be (or at least commonly thought to be) refractory to antibiotics to which they are genetically susceptible. Here, we explore the sensitivity to killing by bactericidal antibiotics of three classes of nonreplicating populations of planktonic bacteria: (i) stationary phase, when the concentration of resources and/or nutrients are too low to allow for population growth; (ii) persisters, minority subpopulations of susceptible bacteria surviving exposure to bactericidal antibiotics; and (iii) antibiotic-static cells, bacteria exposed to antibiotics that prevent their replication but kill them slowly if at all, the so-called bacteriostatic drugs. Using experimental populations of Staphylococcus aureus Newman and Escherichia coli K-12 (MG1655) and, respectively, nine and seven different bactericidal antibiotics, we estimated the rates at which these drugs kill these different types of nonreplicating bacteria. In contrast to the common belief that bacteria that are nonreplicating are refractory to antibiotic-mediated killing, all three types of nonreplicating populations of these Gram-positive and Gram-negative bacteria are consistently killed by aminoglycosides and the peptide antibiotics daptomycin and colistin, respectively. This result indicates that nonreplicating cells, irrespectively of why they do not replicate, have an almost identical response to bactericidal antibiotics. We discuss the implications of these results to our understanding of the mechanisms of action of antibiotics and the possibility of adding a short-course of aminoglycosides or peptide antibiotics to conventional therapy of bacterial infections.

Retrospective natural history of thymidine kinase 2 deficiency.

BACKGROUND: Thymine kinase 2 (TK2) is a mitochondrial matrix protein encoded in nuclear DNA and phosphorylates the pyrimidine nucleosides: thymidine and deoxycytidine. Autosomal recessive TK2 mutations cause a spectrum of disease from infantile onset to adult onset manifesting primarily as myopathy. OBJECTIVE: To perform a retrospective natural history study of a large cohort of patients with TK2 deficiency. METHODS: The study was conducted by 42 investigators across 31 academic medical centres. RESULTS: We identified 92 patients with genetically confirmed diagnoses of TK2 deficiency: 67 from literature review and 25 unreported cases. Based on clinical and molecular genetics findings, we recognised three phenotypes with divergent survival: (1) infantile-onset myopathy (42.4%) with severe mitochondrial DNA (mtDNA) depletion, frequent neurological involvement and rapid progression to early mortality (median post-onset survival (POS) 1.00, CI 0.58 to 2.33 years); (2) childhood-onset myopathy (40.2%) with mtDNA depletion, moderate-to-severe progression of generalised weakness and median POS at least 13 years; and (3) late-onset myopathy (17.4%) with mild limb weakness at onset and slow progression to respiratory insufficiency with median POS of 23 years. Ophthalmoparesis and facial weakness are frequent in adults. Muscle biopsies show multiple mtDNA deletions often with mtDNA depletion. CONCLUSIONS: In TK2 deficiency, age at onset, rate of weakness progression and POS are important variables that define three clinical subtypes. Nervous system involvement often complicates the clinical course of the infantile-onset form while extraocular muscle and facial involvement are characteristic of the late-onset form. Our observations provide essential information for planning future clinical trials in this disorder.

Using Registry Data to Construct a Comparison Group for Programmatic Effectiveness Evaluation: The New York City HIV Care Coordination Program.

Many nonrandomized interventions rely upon a pre-post design to evaluate effectiveness. Such designs cannot account for events external to the intervention that may produce the outcome. We describe a method to construct a surveillance registry-based comparison group, which allows for estimating the effectiveness of the intervention while controlling for secular trends in the outcome of interest. Using data from the population-based, human immunodeficiency virus Surveillance Registry in New York City, we created a contemporaneous comparison group for persons enrolled in the New York City human immunodeficiency virus Care Coordination Program (CCP) from December 2009 to March 2013. Inclusion in the Registry-based (non-CCP) comparison group required meeting CCP eligibility criteria. To control for secular trends in the outcome, we randomly assigned persons in the non-CCP, Registry-based comparison group a pseudoenrollment date such that the distribution of pseudoenrollment dates matched the distribution of enrollment dates among CCP enrollees. We then matched CCP to non-CCP persons on propensity for enrollment in the CCP, enrollment dates, and baseline viral load. Registry-based comparison group estimates were attenuated relative to pre-post estimates of program effectiveness. These methods have broad applicability for observational intervention effectiveness studies and programmatic evaluations for conditions with surveillance registries.

Evolution, human-microbe interactions, and life history plasticity.

A bacterium was once a component of the ancestor of all eukaryotic cells, and much of the human genome originated in microorganisms. Today, all vertebrates harbour large communities of microorganisms (microbiota), particularly in the gut, and at least 20% of the small molecules in human blood are products of the microbiota. Changing human lifestyles and medical practices are disturbing the content and diversity of the microbiota, while simultaneously reducing our exposures to the so-called old infections and to organisms from the natural environment with which human beings co-evolved. Meanwhile, population growth is increasing the exposure of human beings to novel pathogens, particularly the crowd infections that were not part of our evolutionary history. Thus some microbes have co-evolved with human beings and play crucial roles in our physiology and metabolism, whereas others are entirely intrusive. Human metabolism is therefore a tug-of-war between managing beneficial microbes, excluding detrimental ones, and channelling as much energy as is available into other essential functions (eg, growth, maintenance, reproduction). This tug-of-war shapes the passage of each individual through life history decision nodes (eg, how fast to grow, when to mature, and how long to live).

Development of macrolide resistance in Bordetella bronchiseptica is associated with the loss of virulence.

Background: Why resistance to specific antibiotics emerges and spreads rapidly in some bacteria confronting these drugs but not others remains a mystery. Resistance to erythromycin in the respiratory pathogens Staphylococcus aureus and Streptococcus pneumoniae emerged rapidly and increased problematically. However, resistance is uncommon amongst the classic Bordetella species despite infections being treated with this macrolide for decades. Objectives: We examined whether the apparent progenitor of the classic Bordetella spp., Bordetella bronchiseptica, is able to rapidly generate de novo resistance to antibiotics and, if so, why such resistance might not persist and propagate. Methods: Independent strains of B. bronchiseptica resistant to erythromycin were generated in vitro by successively passaging them in increasing subinhibitory concentrations of this macrolide. Resistant mutants obtained were evaluated for their capacity to infect mice, and for other virulence properties including adherence, cytotoxicity and induction of cytokines. Results: B. bronchiseptica rapidly developed stable and persistent antibiotic resistance de novo. Unlike the previously reported trade-off in fitness, multiple independent resistant mutants were not defective in their rates of growth in vitro but were consistently defective in colonizing mice and lost a variety of virulence phenotypes. These changes rendered them avirulent but phenotypically similar to the previously described growth phase associated with the ability to survive in soil, water and/or other extra-mammalian environments. Conclusions: These observations raise the possibility that antibiotic resistance in some organisms results in trade-offs that are not quantifiable in routine measures of general fitness such as growth in vitro, but are pronounced in various aspects of infection in the natural host.