Comparing COVID-19-related Morbidity and Mortality Between Patients With and Without Substance Use Disorders: A Retrospective Cohort Study

Objectives:

People with substance use disorders (SUD) are suggested to have higher risk of hospitalization, intubation, or death from coronavirus disease 2019 (COVID-19), although data are mixed. Little is known about other COVID-19-related complications in this group. We compared morbidity and mortality among individuals with and without SUD who were admitted to an urban safety net hospital with COVID-19 early in the pandemic, contemporaneous to other published studies on this subject.

Methods:

We performed a retrospective study of patients ⩾18 years old admitted with COVID-19 from March 16th to April 8th, 2020. SUD included alcohol, opioid, cocaine, amphetamine, and benzodiazepine use disorders and was identified using diagnostic codes, free text clinical documentation, and urine drug screens. The primary outcome was inpatient mortality. Secondary outcomes included clinical complications (eg, secondary infections, venous thromboembolism) and resource utilization (eg, mechanical ventilation, length of stay). We used multivariable regression to assess the relationship between SUD and mortality.

Results:

Of 409 patients, the mean age was 56 years and 13.7% had SUD. Those with SUD were more likely to be male, have experienced homelessness, have pulmonary disease or hepatitis C, or use tobacco or cannabis. After multivariable analysis, SUD was not associated with mortality (aOR 1.03; 95% CI, 0.31-3.10). Secondary outcomes were also similar between groups.

Conclusions:

Our findings suggest that persons with and without SUD have similar COVID-19-related outcomes. Previously reported increased COVID-19 complications may be from medical comorbidities.

Extra-genital Neisseria gonorrhoeae infections with genetic mutations conferring ciprofloxacin resistance among men who have sex with men and transgender women in Lima, Peru

BACKGROUND

The increasing prevalence of drug-resistant Neisseria gonorrhoeae (NG) infections has caused great concern. Ciprofloxacin remains the empiric antimicrobial recommended to treat NG infections in Peru disregarding the susceptibility profile of circulating NG strains. We report the prevalence of individuals infected with NG strains presenting mutations in the gyrA gene that confers ciprofloxacin resistance.

METHODS

We conducted a descriptive study assessing extragenital swab samples collected from a cohort of men who have sex with men and transgender women in Lima, Peru. Anal and pharyngeal NG positive swabs for Aptima Combo 2 assay (Hologic Inc., USA) were used for DNA extraction. We performed TaqMan real time PCR assays to detect a point mutation at codon Ser91 of the gyrase A (gyrA) gene.

RESULTS

From 156 individuals who had at least one positive sample for NG reported by the Aptima assay, 80 individuals had at least one amplified DNA for the gyrA gene. We found that 67 of them (84.0%) were infected with a gyrA-mutated NG strain at the Ser91 codon.

CONCLUSIONS

We report a high prevalence of gyrA mutation conferring ciprofloxacin resistance among individuals with extragenital NG infection. Empirical treatment of NG needs to be urgently updated in Peru in concordance with international guidelines.

SARS-CoV-2 Infection and Testing Experiences in a Nationwide Sample of Transgender and Gender-Diverse Adults, June-December 2021

OBJECTIVES

COVID-19 surveillance data are rarely collected or disaggregated by gender identity in the United States. We quantified COVID-19 testing experiences and SARS-CoV-2 infection history among transgender and gender-diverse (TGD) people to inform testing strategies and public health responses.

METHODS

From June 14 through December 16, 2021, TGD adults enrolled in a US nationwide online survey with optional SARS-CoV-2 antibody testing. We used multinomial regression analyses to identify correlates of suspected and confirmed SARS-CoV-2 infection (vs no known infection). We identified correlates of inability to access COVID-19 testing when needed using generalized linear models for binomial variables.

RESULTS

Participants (N = 2092) reported trans masculine (30.5%), trans feminine (27.3%), and nonbinary (42.2%) gender identities. Ten percent of respondents had a confirmed history of SARS-CoV-2 infection, and 29.8% had a history of suspected SARS-CoV-2 infection. Nonbinary gender (adjusted prevalence ratio [aPR] = 1.68; 95% CI, 1.12-2.53), experiencing homelessness (aPR = 1.65; 95% CI, 1.05-2.60), and food insecurity (aPR = 1.45; 95% CI, 1.03-2.04) were associated with confirmed SARS-CoV-2 infection. Food insecurity (aPR = 1.38; 95% CI, 1.10-1.72), chronic physical health condition (aPR = 1.44; 95% CI, 1.15-1.80), chronic mental health condition (aPR = 3.65; 95% CI, 2.40-5.56), and increased anticipated discrimination scores (aPR = 1.03; 95% CI, 1.01-1.05) were associated with suspected SARS-CoV-2 infection. Thirty-four percent (n = 694 of 2024) of participants reported an inability to access COVID-19 testing when needed, which was associated with Latinx or Hispanic ethnicity, inconsistent telephone access, homelessness, disability, and transportation limitations. The majority (79.4%) reported a complete COVID-19 vaccine course at the time of participation.

CONCLUSIONS

Inclusion of TGD people in public health surveillance and tailored public health strategies to address TGD communities' social and structural vulnerabilities may reduce barriers to COVID-19 testing.

Worsening premature death burden gap from systemic sclerosis in men and black persons: A US nationwide population-based study

Objective

Male sex and black race incur poor prognosis in systemic sclerosis (SSc). There is no nationwide population-based assessment of premature SSc death burden by sex and race.

Methods

This is a population-based study comprising all recorded SSc deaths across the United States. We constructed histograms depicting the number of SSc deaths for each age by sex and race, and calculated the cumulative percent death at each age and the median age of death. We determined the odds ratios for the risk of premature death from SSc by sex and race. We then calculated the percent of total SSc deaths for different age groups by sex and race from 1970 to 2015. We performed chi-square test with Yates's correction and quantified the odds ratio (OR) with 95% confidence interval (CI).

Results

The median age of SSc death was 63 years in males versus 68 years in females, and 57 years in blacks versus 70 years in whites. The odds for SSc death before 65 years age was 1.8 (95% CI, 1.6-2.0) for males compared with females and 5.1 (95% CI, 4.4-6.0) for blacks compared with whites. The higher odds for premature death in males than in females was similar for both races. Differences in the proportions of premature deaths from 1970 to 2015 increased between males and females (-5% to 17%) and between blacks and whites (14% to 36%).

Conclusion

Males and black persons die of SSc at younger ages. The worsening premature death burden gap between the two sexes and races over the last five decades is troublesome.

Enhancing domestic violence advocates' ability to discuss HIV pre-exposure prophylaxis (PrEP): Feasibility and acceptability of an educational intervention

BACKGROUND

Survivors of intimate partner violence are at elevated risk for HIV acquisition, yet there is limited research on the best strategies to optimize biomedical HIV prevention, such as pre-exposure prophylaxis among this population. Domestic violence agencies are critical collaborating partners and function as potential entry points into HIV prevention services for survivors; however, limited knowledge regarding HIV prevention has been an important barrier to advocate-led discussions. This study aimed to develop, implement, and evaluate an HIV prevention intervention for domestic violence advocates.

SETTING

A nonrandomized, group-based intervention with pre-intervention, immediate post-intervention, and 3-month post-intervention periods were conducted with multiple domestic violence agencies in Mississippi.

METHODS

Overall, 25 domestic violence advocates participated in the two-session intervention. Surveys were administered to assess pre-exposure prophylaxis knowledge, self-efficacy, subjective norms, and willingness to provide HIV prevention services to intimate partner violence survivors. Generalized estimating equations were conducted to assess change in behavioral outcomes over time.

RESULTS

Compared to pre-intervention, there were significant increases at immediate and 3-month post-intervention in advocates' intervention acceptability, pre-exposure prophylaxis knowledge, and self-efficacy to provide HIV prevention information, discuss pre-exposure prophylaxis eligibility criteria, assist pre-exposure prophylaxis-engaged clients, and initiate pre-exposure prophylaxis counseling.

CONCLUSION

This group-based intervention enhanced domestic violence advocates' acceptability, pre-exposure prophylaxis knowledge, and self-efficacy to offer HIV care information, discuss pre-exposure prophylaxis eligibility, assist pre-exposure prophylaxis-engaged survivors, and initiate pre-exposure prophylaxis counseling with intimate partner violence survivors. Efforts should focus on training domestic violence advocates in HIV prevention care for survivors and also include these agencies in collaborative strategies to reduce HIV incidence.

Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies

Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.

Child Undernutrition following the Introduction of a Large-Scale Toilet Construction Campaign in India

BACKGROUND

Lack of toilets and the widespread practice of open defecation may contribute to India's large burden of child undernutrition.

OBJECTIVES

We examine whether a large national sanitation campaign launched in 2014, the Swachh Bharat Mission (SBM), precedes a reduction in stunting and wasting among under 5-y-old (u5) children in India.

METHODS

In this observational study, we used district-level data from before (2013-2014) and after (2015-2016) SBM from 3 national surveys to derive, as our outcomes, the percentage of u5 children per district who are stunted and wasted. We defined our exposures as 1) binary indicator of SBM and 2) percentage of households with toilets per district. Our analytic sample comprised nearly all 640 Indian districts (with ∼1200 rural/urban divisions per district per time point). Linear regression analyses controlled for baseline differences in districts, linear time trends by state, and relevant covariates.

RESULTS

Relative to pre-SBM, u5 stunting declines by 0.06% (95% CI: -0.10, -0.01; P = 0.009) with every percentage increase in households with toilets post-SBM. Rural regions and districts with higher pre-SBM toilet availability show greater decline in u5 stunting post-SBM.

CONCLUSIONS

An increase in toilet availability on a national scale, precipitated by the SBM sanitation campaign, is associated with a reduction in undernutrition among u5 children in India over the early phase of the campaign.

The Use and Misuse of Mathematical Modeling for Infectious Disease Policymaking: Lessons for the COVID-19 Pandemic

Mathematical modeling has played a prominent and necessary role in the current coronavirus disease 2019 (COVID-19) pandemic, with an increasing number of models being developed to track and project the spread of the disease, as well as major decisions being made based on the results of these studies. A proliferation of models, often diverging widely in their projections, has been accompanied by criticism of the validity of modeled analyses and uncertainty as to when and to what extent results can be trusted. Drawing on examples from COVID-19 and other infectious diseases of global importance, we review key limitations of mathematical modeling as a tool for interpreting empirical data and informing individual and public decision making. We present several approaches that have been used to strengthen the validity of inferences drawn from these analyses, approaches that will enable better decision making in the current COVID-19 crisis and beyond.

A natural polymorphism of Mycobacterium tuberculosis in the esxH gene disrupts immunodomination by the TB10.4-specific CD8 T cell response

CD8 T cells provide limited protection against Mycobacterium tuberculosis (Mtb) infection in the mouse model. As Mtb causes chronic infection in mice and humans, we hypothesize that Mtb impairs T cell responses as an immune evasion strategy. TB10.4 is an immunodominant antigen in people, nonhuman primates, and mice, which is encoded by the esxH gene. In C57BL/6 mice, 30–50% of pulmonary CD8 T cells recognize the TB10.4₄₋₁₁ epitope. However, TB10.4-specific CD8 T cells fail to recognize Mtb-infected macrophages. We speculate that Mtb elicits immunodominant CD8 T cell responses to antigens that are inefficiently presented by infected cells, thereby focusing CD8 T cells on nonprotective antigens. Here, we leverage naturally occurring polymorphisms in esxH, which frequently occur in lineage 1 strains, to test this “decoy hypothesis”. Using the clinical isolate 667, which contains an EsxH^A10T polymorphism, we observe a drastic change in the hierarchy of CD8 T cells. Using isogenic Erd.EsxH^A10T and Erd.EsxH^WT strains, we prove that this polymorphism alters the hierarchy of immunodominant CD8 T cell responses. Our data are best explained by immunodomination, a mechanism by which competition for APC leads to dominant responses suppressing subdominant responses. These results were surprising as the variant epitope can bind to H2-K^b and is recognized by TB10.4-specific CD8 T cells. The dramatic change in TB10.4-specific CD8 responses resulted from increased proteolytic degradation of A10T variant, which destroyed the TB10.4_4-11epitope. Importantly, this polymorphism affected T cell priming and recognition of infected cells. These data support a model in which nonprotective CD8 T cells become immunodominant and suppress subdominant responses. Thus, polymorphisms between clinical Mtb strains, and BCG or H37Rv sequence-based vaccines could lead to a mismatch between T cells that are primed by vaccines and the epitopes presented by infected cells. Reprograming host immune responses should be considered in the future design of vaccines.

An important question for vaccine developers is the relative potency of CD4 vs. CD8 T cells against Mtb, as strategies differ for eliciting these different T cell subsets. Despite robust antigen-specific pulmonary CD8 T cell responses, CD4 T cells mediate more protection than CD8 T cells in the murine model. Most CD8 T cells recognize a single antigen, TB10.4, which is encoded by the esxH gene. Based on finding that TB10.4₄₋₁₁-specific CD8 T cells poorly recognize Mtb-infected macrophages, we hypothesized that Mtb evades detection by CD8 T cells and focuses the CD8 T cell response on non-protective antigen. We termed these antigens “decoy antigens.” To test this hypothesis, we took advantage of a natural variant of the esxH gene, which contains an A10T polymorphism within the TB10.4₄₋₁₁ epitope. This polymorphism drastically alters the hierarchy of CD8 T cell responses elicited by Mtb. These data suggest that immunodomination by the TB10.4 epitope acts to suppress subdominant CD8 T cell responses to other Mtb antigens, impairing the CD8 T cell response to other Mtb antigens, some of which might be presented by Mtb-infected macrophages and be targets of protective immunity. Importantly, this single amino acid polymorphism, which does not significantly alter MHC-binding or T cell recognition, alters the half-life of the epitope and consequently, has a profound effect on CD8 T cell priming and recognition of infected cells. These data also provide a mechanism that could be exploited to manipulate the hierarchy of immunodominant responses.

Knowledge of Good Samaritan Laws and Beliefs About Arrests Among Persons Who Inject Drugs a Year After Policy Change in Baltimore, Maryland

OBJECTIVES

Delivering and receiving prompt medical care during an overdose are imperative to ensure survival. Good Samaritan laws encourage people to call 911 during an overdose by providing immunity from selected drug arrests (eg, low-level possession). However, it is unclear whether persons who inject drugs (PWID) are aware of and understand these laws and their implications. We examined awareness among PWID of the 2015 Good Samaritan law in Maryland and their beliefs about whether they could be arrested for calling 911 or having an overdose.

METHODS

We surveyed 298 PWID in Baltimore, Maryland. We estimated the proportion who knew what the Good Samaritan law addressed and who believed they could be arrested for calling 911 or overdosing. We used a multivariate model to assess the association between harm-reduction services and knowledge of the Good Samaritan law or beliefs about getting arrested for calling 911 or overdosing.

RESULTS

Of PWID, 56 of 298 (18.8%) knew what the Good Samaritan law addressed, 43 of 267 (16.1%) believed they could be arrested for calling 911, and 32 of 272 (11.8%) believed they could be arrested for having an overdose. After adjusting for demographic characteristics, accessing the syringe services program was associated with accurate knowledge and the belief that PWID could be arrested for calling 911; however, training in overdose reversal was not associated.

CONCLUSIONS

Most PWID were unaware of the Good Samaritan law; this lack of awareness is a barrier to preventing overdose deaths. Educating PWID about Good Samaritan laws is essential, and such education should include police to ensure that law enforcement is congruent with Good Samaritan laws and does not perpetuate mistrust between police and PWID.

Select targeting of intracellular Toll-interleukin-1 receptor resistance domains for protection against influenza-induced disease

TLRs are a family of PRRs that respond to PAMPs or host-derived Danger-Associated Molecular Patterns (DAMPs) to initiate host inflammation and immune responses. TLR dimerization and recruitment of adapter molecules is critical for intracellular signaling and is mediated through intracellular Toll-Interleukin 1 Receptor Resistance (TIR) domain interactions. Human TIR domains, including reported structures of TIR1, TIR2, TIR6, TIR10, TIRAP, and MyD88, contain Cysteine (Cys) interactions or modifications that are disproportionally at, or near, reported biological TIR interfaces, or in close proximity to functionally important regions. Therefore, we hypothesized that intracellular TIR Cys regulation may have greater functional importance than previously appreciated. Expression of mutant TLR4-C747S or treatment of TLR4 reporter cells with a small molecule, Cys-binding inhibitor of TLR4, TAK-242, abrogated LPS signaling in vitro . Using TAK-242, mice were protected from lethal influenza challenge as previously reported for extracellular TLR4 antagonists. Molecular modeling and sequence analysis of the region surrounding TLR4-Cys747 indicate conservation of a WxxxE motif identified among bacterial and NAD+-consuming TIRs, as well as within the TIRs domains of surface TLRs 1, 2, 4, 6, and 10. Together, these data support the hypothesis that critical Cys within the TIR domain are essential for TLR4 functionality.

Characterization of the NLRP1 inflammasome response in bovine species

Inflammasomes act as sensors of infection or damage to initiate immune responses. While extensively studied in rodents, understanding of livestock inflammasomes is limited. The NLRP1 inflammasome sensor in rodents is activated by Toxoplasma gondii, Bacillus anthracis lethal toxin (LT), and potentially other zoonotic pathogens. LT activates NLRP1 by N-terminal proteolysis, inducing macrophage pyroptosis and a pro-inflammatory cytokine response. In contrast, NLRP1 in macrophages from humans and certain rodent strains is resistant to LT cleavage, and pyroptosis is not induced. Evolution of NLRP1 sequences towards those leading to pyroptosis is of interest in understanding innate immune responses in different hosts. We characterized NLRP1 in cattle (Bos taurus) and American bison (Bison bison). Bovine NLRP1 is not cleaved by LT, and cattle and bison macrophages do not undergo toxin-induced pyroptosis. Additionally, we found a predicted Nlrp1 splicing isoform in cattle macrophages lacking the N-terminal domain. Resistance to LT in bovine and human NLRP1 correlates with evolutionary sequence similarity to rodents. Consistent with LT-resistant rodents, bovine macrophages undergo a slower non-pyroptotic death in the presence of LPS and LT. Overall, our findings support the model that NLRP1 activation by LT requires N-terminal cleavage, and provide novel information on mechanisms underlying immune response diversity.

Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli

Diverse enteropathogen exposures associate with childhood malnutrition. To elucidate mechanistic pathways whereby enteric microbes interact during malnutrition, we used protein deficiency in mice to develop a new model of co-enteropathogen enteropathy. Focusing on common enteropathogens in malnourished children, Giardia lamblia and enteroaggregative Escherichia coli (EAEC), we provide new insights into intersecting pathogen-specific mechanisms that enhance malnutrition. We show for the first time that during protein malnutrition, the intestinal microbiota permits persistent Giardia colonization and simultaneously contributes to growth impairment. Despite signals of intestinal injury, such as IL1α, Giardia-infected mice lack pro-inflammatory intestinal responses, similar to endemic pediatric Giardia infections. Rather, Giardia perturbs microbial host co-metabolites of proteolysis during growth impairment, whereas host nicotinamide utilization adaptations that correspond with growth recovery increase. EAEC promotes intestinal inflammation and markers of myeloid cell activation. During co-infection, intestinal inflammatory signaling and cellular recruitment responses to EAEC are preserved together with a Giardia-mediated diminishment in myeloid cell activation. Conversely, EAEC extinguishes markers of host energy expenditure regulatory responses to Giardia, as host metabolic adaptations appear exhausted. Integrating immunologic and metabolic profiles during co-pathogen infection and malnutrition, we develop a working mechanistic model of how cumulative diet-induced and pathogen-triggered microbial perturbations result in an increasingly wasted host.

Malnourished children are exposed to multiple sequential, and oftentimes, persistent enteropathogens. Intestinal microbial disruption and inflammation are known to contribute to the pathogenesis of malnutrition, but how co-pathogens interact with each other, with the resident microbiota, or with the host to alter these pathways is unknown. Using a new model of enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli in mice fed a protein deficient diet, we identify host growth and intestinal immune responses that are differentially mediated by pathogen-microbe interactions, including parasite-mediated changes in intestinal microbial host co-metabolism, and altered immune responses during co-infection. Our data model how early life cumulative enteropathogen exposures progressively disrupt intestinal immunity and host metabolism during crucial developmental periods. Furthermore, studies in this co-infection model reveal new insights into environmental and microbial determinants of pathogenicity for presently common, but poorly understood enteropathogens like Giardia lamblia, that may not conform to existing paradigms of microbial pathogenesis based on single pathogen-designed models.