Detection of drug resistant Mycobacterium tuberculosis by high-throughput sequencing of DNA isolated from acid fast bacilli smears

BACKGROUND: Drug susceptibility testing for Mycobacterium tuberculosis (MTB) is difficult to perform in resource-limited settings where Acid Fast Bacilli (AFB) smears are commonly used for disease diagnosis and monitoring. We developed a simple method for extraction of MTB DNA from AFB smears for sequencing-based detection of mutations associated with resistance to all first and several second-line anti-tuberculosis drugs. METHODS: We isolated MTB DNA by boiling smear content in a Chelex solution, followed by column purification. We sequenced PCR-amplified segments of the rpoB, katG, embB, gyrA, gyrB, rpsL, and rrs genes, the inhA, eis, and pncA promoters and the entire pncA gene. RESULTS: We tested our assay on 1,208 clinically obtained AFB smears from Ghana (n = 379), Kenya (n = 517), Uganda (n = 262), and Zambia (n = 50). Coverage depth varied by target and slide smear grade, ranging from 300X to 12000X on average. Coverage of ≥20X was obtained for all targets in 870 (72%) slides overall. Mono-resistance (5.9%), multi-drug resistance (1.8%), and poly-resistance (2.4%) mutation profiles were detected in 10% of slides overall, and in over 32% of retreatment and follow-up cases. CONCLUSION: This rapid AFB smear DNA-based method for determining drug resistance may be useful for the diagnosis and surveillance of drug-resistant tuberculosis

Understanding care coordination for Veterans with complex care needs: protocol of a multiple-methods study to build evidence for an effectiveness and implementation study

Background For patients with complex health and social needs, care coordination is crucial for improving their access to care, clinical outcomes, care experiences, and controlling their healthcare costs. However, evidence is inconsistent regarding the core elements of care coordination interventions, and lack of standardized processes for assessing patients’ needs has made it challenging for providers to optimize care coordination based on patient needs and preferences. Further, ensuring providers have reliable and timely means of communicating about care plans, patients’ full spectrum of needs, and transitions in care is important for overcoming potential care fragmentation. In the Veterans Health Administration (VA), several initiatives are underway to implement care coordination processes and services. In this paper, we describe our study underway in the VA aimed at building evidence for designing and implementing care coordination practices that enhance care integration and improve health and care outcomes for Veterans with complex care needs. Methods In a prospective observational multiple methods study, for Aim 1 we will use existing data to identify Veterans with complex care needs who have and have not received care coordination services. We will examine the relationship between receipt of care coordination services and their health outcomes. In Aim 2, we will adapt the Patient Perceptions of Integrated Veteran Care questionnaire to survey a sample of Veterans about their experiences regarding coordination, integration, and the extent to which their care needs are being met. For Aim 3, we will interview providers and care teams about their perceptions of the innovation attributes of current care coordination needs assessment tools and processes, including their improvement over other approaches (relative advantage), fit with current practices (compatibility and innovation fit), complexity, and ability to visualize how the steps proceed to impact the right care at the right time (observability). The provider interviews will inform design and deployment of a widescale provider survey. Discussion Taken together, our study will inform development of an enhanced care coordination intervention that seeks to improve care and outcomes for Veterans with complex care needs

State-Level Variability in Veteran Reliance on Veterans Health Administration and Potentially Preventable Hospitalizations: A Geospatial Analysis

Most Veterans who use the Veterans Health Administration (VHA) also utilize private-sector health care providers. To better inform local and regional health care planning, we assessed the association between reliance on VHA ambulatory care and total and system-specific preventable hospitalization rates (PHRs) at the state level. We conducted a retrospective dynamic cohort study using Veterans with diabetes mellitus, aged 66 years or older, and dually enrolled in VHA and Medicare parts A and B from 2004 to 2010. While controlling for median age and proportion of males, we measured the association between reliance on VHA ambulatory care and PHRs at the state level using multivariable ordinary least square regression, geographically weighted regression, and generalized additive models. We measured geospatial patterns in PHRs using global Moran’s I and univariate local indicator spatial analysis. Approximately 30% of hospitalized Veterans experienced a preventable hospitalization. Reliance on VHA ambulatory care at the state level ranged from 13.92% to 67.78% and was generally not associated with PHRs. Geospatial analysis consistently identified a cluster of western states with low PHRs from 2006 to 2010. Given the generally low reliance on VHA ambulatory care and lack of association between this reliance and PHRs, policy changes to improve Veterans’ health care outcomes should address private-sector care in addition to VHA care

State-Level Variability in Veteran Reliance on Veterans Health Administration and Potentially Preventable Hospitalizations: A Geospatial Analysis

Most Veterans who use the Veterans Health Administration (VHA) also utilize private-sector health care providers. To better inform local and regional health care planning, we assessed the association between reliance on VHA ambulatory care and total and system-specific preventable hospitalization rates (PHRs) at the state level. We conducted a retrospective dynamic cohort study using Veterans with diabetes mellitus, aged 66 years or older, and dually enrolled in VHA and Medicare parts A and B from 2004 to 2010. While controlling for median age and proportion of males, we measured the association between reliance on VHA ambulatory care and PHRs at the state level using multivariable ordinary least square regression, geographically weighted regression, and generalized additive models. We measured geospatial patterns in PHRs using global Moran’s I and univariate local indicator spatial analysis. Approximately 30% of hospitalized Veterans experienced a preventable hospitalization. Reliance on VHA ambulatory care at the state level ranged from 13.92% to 67.78% and was generally not associated with PHRs. Geospatial analysis consistently identified a cluster of western states with low PHRs from 2006 to 2010. Given the generally low reliance on VHA ambulatory care and lack of association between this reliance and PHRs, policy changes to improve Veterans’ health care outcomes should address private-sector care in addition to VHA care

State-Level Variability in Veteran Reliance on Veterans Health Administration and Potentially Preventable Hospitalizations: A Geospatial Analysis

Most Veterans who use the Veterans Health Administration (VHA) also utilize private-sector health care providers. To better inform local and regional health care planning, we assessed the association between reliance on VHA ambulatory care and total and system-specific preventable hospitalization rates (PHRs) at the state level. We conducted a retrospective dynamic cohort study using Veterans with diabetes mellitus, aged 66 years or older, and dually enrolled in VHA and Medicare parts A and B from 2004 to 2010. While controlling for median age and proportion of males, we measured the association between reliance on VHA ambulatory care and PHRs at the state level using multivariable ordinary least square regression, geographically weighted regression, and generalized additive models. We measured geospatial patterns in PHRs using global Moran’s I and univariate local indicator spatial analysis. Approximately 30% of hospitalized Veterans experienced a preventable hospitalization. Reliance on VHA ambulatory care at the state level ranged from 13.92% to 67.78% and was generally not associated with PHRs. Geospatial analysis consistently identified a cluster of western states with low PHRs from 2006 to 2010. Given the generally low reliance on VHA ambulatory care and lack of association between this reliance and PHRs, policy changes to improve Veterans’ health care outcomes should address private-sector care in addition to VHA care

Effectiveness of COVID-19 Treatment With Nirmatrelvir-Ritonavir or Molnupiravir Among U.S. Veterans: Target Trial Emulation Studies With One-Month and Six-Month Outcomes.

BackgroundInformation about the effectiveness of oral antivirals in preventing short- and long-term COVID-19-related outcomes in the setting of Omicron variant transmission and COVID-19 vaccination is limited.ObjectiveTo measure the effectiveness of nirmatrelvir-ritonavir and molnupiravir for outpatient treatment of COVID-19.DesignThree retrospective target trial emulation studies comparing matched cohorts of nirmatrelvir-ritonavir versus no treatment, molnupiravir versus no treatment, and nirmatrelvir-ritonavir versus molnupiravir.SettingVeterans Health Administration (VHA).ParticipantsNonhospitalized veterans in VHA care who were at risk for severe COVID-19 and tested positive for SARS-CoV-2 during January through July 2022.InterventionNirmatrelvir-ritonavir or molnupiravir pharmacotherapy.MeasurementsIncidence of any hospitalization or all-cause mortality at 30 days and from 31 to 180 days.ResultsEighty-seven percent of participants were male; the median age was 66 years, and 18% were unvaccinated. Compared with matched untreated control participants, those treated with nirmatrelvir-ritonavir (n = 9607) had lower 30-day risk for hospitalization (22.07 vs. 30.32 per 1000 participants; risk difference [RD], -8.25 [95% CI, -12.27 to -4.23] per 1000 participants) and death (1.25 vs. 5.47 per 1000 participants; RD, -4.22 [CI, -5.45 to -3.00] per 1000 participants). Among persons alive at day 31, reductions were seen in 31- to 180-day incidence of death (hazard ratio, 0.66 [CI, 0.49 to 0.89]) but not hospitalization (subhazard ratio, 0.90 [CI, 0.79 to 1.02]). Molnupiravir-treated participants (n = 3504) had lower 30-day and 31- to 180-day risks for death (3.14 vs. 13.56 per 1000 participants at 30 days; RD, -10.42 [CI, -13.49 to -7.35] per 1000 participants; hazard ratio at 31 to 180 days, 0.67 [CI, 0.48 to 0.95]) but not hospitalization. A difference in 30-day or 31- to 180-day risk for hospitalization or death was not observed between matched nirmatrelvir- or molnupiravir-treated participants.LimitationThe date of COVID-19 symptom onset for most veterans was unknown.ConclusionNirmatrelvir-ritonavir was effective in reducing 30-day hospitalization and death. Molnupiravir was associated with a benefit for 30-day mortality but not hospitalization. Further reductions in mortality from 31 to 180 days were observed with both antivirals.Primary funding sourceU.S. Department of Veterans Affairs