Socio-Structural and Neighborhood Predictors of Incident Criminal Justice Involvement in a Population-Based Cohort of Young Black MSM and Transgender Women.

Black men who have sex with men (MSM) and transgender women are disproportionately affected by criminal justice involvement (CJI) and HIV. This study recruited 618 young Black MSM and transgender women in Chicago, IL, using respondent-driven sampling between 2013 and 2014. Random effects logistic regression evaluated predictors of incident CJI over 18 months of follow-up. Controlling for respondent age, gender and sexual identity, spirituality (aOR 0.56, 95% CI 0.33-0.96), and presence of a mother figure (aOR 0.41, 95% CI 0.19-0.89) were protective against CJI. Economic hardship (financial or residential instability vs. neither aOR 2.23, 95% CI 1.10-4.51), two or more past episodes of CJI vs. none (aOR 2.66, 95% CI 1.40-5.66), and substance use (marijuana use vs. none aOR 2.79, 95% CI 1.23-6.34; other drug use vs. none aOR 4.49, 95% CI 1.66-12.16) were associated with CJI during follow-up. Research to identify and leverage resilience factors that can buffer the effects of socioeconomic marginalization may increase the effectiveness of interventions to address the socio-structural factors that increase the risk for CJI among Black MSM and transgender women. Given the intersection of incarceration, HIV and other STIs, and socio-structural stressors, criminal justice settings are important venues for interventions to reduce health inequities in these populations.

The potential of online social networking data for augmenting the study of high-risk personal networks among young men who have sex with men at-risk for HIV.

Capturing dynamics in high-risk personal networks is essential for preventing HIV transmission. Online social networking data offer incentive to augment traditional selfreported approaches for network enumeration. To explore what online networks reveal about dynamics among high-risk associates, we examine the relationship between egocentric confidant and sex networks and personal Facebook friendship networks of a cohort of young Black men who have sex with men. Although overlap exists between self-reported and Facebook associates, the stabilities of each were unrelated. Confidants who were also Facebook friends with a respondent were, however, more likely to be retained. Thus, Facebook networks contain stable confidants.

Preexposure Prophylaxis Initiation and Retention in Care Over 5 Years, 2012-2017: Are Quarterly Visits Too Much?

Retention in preexposure prophylaxis (PrEP) care is critical to elimination of human immunodeficiency virus. We reviewed all Howard Brown Health patients receiving PrEP (n = 5583) from 2012 to 2017. Among those with 12 months of follow-up, 43% remained in care, yet only 15% had all 4 quarters with a PrEP visit. Insurance status and comorbid conditions were drivers of retention in care.

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered Lakes.

Northern lakes are ice-covered for a large part of the year, yet our understanding of microbial diversity and activity during winter lags behind that of the ice-free period. In this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 16S rRNA sequencing, metagenomics and metatranscriptomics. Verrucomicrobia, particularly the V1, V3 and V4 subdivisions, were abundant during ice-covered periods. A diversity of Verrucomicrobia genomes were reconstructed from Quebec lake metagenomes. Several genomes were associated with the ice-covered period and were represented in winter metatranscriptomes, supporting the notion that Verrucomicrobia are metabolically active under ice. Verrucomicrobia transcriptome analysis revealed a range of metabolisms potentially occurring under ice, including carbohydrate degradation, glycolate utilization, scavenging of chlorophyll degradation products, and urea use. Genes for aerobic sulfur and hydrogen oxidation were expressed, suggesting chemolithotrophy may be an adaptation to conditions where labile carbon may be limited. The expression of genes for flagella biosynthesis and chemotaxis was detected, suggesting Verrucomicrobia may be actively sensing and responding to winter nutrient pulses, such as phytoplankton blooms. These results increase our understanding on the diversity and metabolic processes occurring under ice in northern lakes ecosystems.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Metaproteomics of aquatic microbial communities in a deep and stratified estuary.

Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle-rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific "nepheloid" taxa that may contribute significantly to coastal ocean nutrient cycling.

A multiyear time series (2004-2012) of bacterial and archaeal community dynamics in a changing Arctic Ocean.

Climate change is profoundly impacting the Arctic, leading to a loss of multiyear sea ice and a warmer, fresher upper Arctic Ocean. The response of microbial communities to these climate-mediated changes is largely unknown. Here, we document the interannual variation in bacterial and archaeal communities across a 9-year time series of the Canada Basin that includes two historic sea ice minima (2007 and 2012). We report an overall loss of bacterial and archaeal community richness and significant shifts in community composition. The magnitude and period of most rapid change differed between the stratified water layers. The most pronounced changes in the upper water layers (surface mixed layer and upper Arctic water) occurred earlier in the time series, while changes in the lower layer (Pacific-origin water) occurred later. Shifts in taxonomic composition across time were subtle, but a decrease in Bacteroidota taxa and increase in Thaumarchaeota and Euryarchaeota taxa were the clearest signatures of change. This time series provides a rare glimpse into the potential influence of climate change on Arctic microbial communities; extension to the present day should contribute to deeper insights into the trajectory of Arctic marine ecosystems in response to warming and freshening.

A Novel Freshwater to Marine Evolutionary Transition Revealed within Methylophilaceae Bacteria from the Arctic Ocean.

Bacteria inhabiting polar oceans, particularly the Arctic Ocean, are less studied than those at lower latitudes. Discovering bacterial adaptations to Arctic Ocean conditions is essential for understanding responses to the accelerated environmental changes occurring in the North. The Methylophilaceae are emerging as a model for investigating the genomic basis of habitat adaptation, because related lineages are widely distributed across both freshwater and marine ecosystems. Here, we investigated Methylophilaceae diversity in the salinity-stratified surface waters of the Canada Basin, Arctic Ocean. In addition to a diversity of marine OM43 lineages, we report on the genomic characteristics and evolution of a previously undescribed Methylophilaceae clade (BS01) common to polar surface waters yet related to freshwater sediment Methylotenera species. BS01 is restricted to the lower-salinity surface waters, while OM43 is found throughout the halocline. An acidic proteome supports a marine lifestyle for BS01, but gene content shows increased metabolic versatility compared to OM43 and evidence for ongoing genome-streamlining. Phylogenetic reconstruction shows that BS01 colonized the pelagic ocean independently of OM43 via convergent evolution. Salinity adaptation and differences in one-carbon and nitrogen metabolism may play a role in niche differentiation between BS01 and OM43. In particular, urea utilization by BS01 is predicted to provide an ecological advantage over OM43 given the limited amount of inorganic nitrogen in the Canada Basin. These observations provide further evidence that the Arctic Ocean is inhabited by distinct bacterial groups and that at least one group (BS01) evolved via a freshwater to marine environmental transition. IMPORTANCE Global warming is profoundly influencing the Arctic Ocean. Rapid ice melt and increased freshwater input is increasing ocean stratification, driving shifts in nutrient availability and the primary production that supports marine food webs. Determining bacterial responses to Arctic Ocean change is challenging because of limited knowledge on the specific adaptations of Arctic Ocean bacteria. In this study, we investigated the diversity and genomic adaptations of a globally distributed group of marine bacteria, the Methylophilaceae, in the surface waters of the Arctic Ocean. We discovered a novel lineage of marine Methylophilaceae inhabiting the Arctic Ocean whose evolutionary origin involved a freshwater to marine environmental transition. Crossing the salinity barrier is thought to rarely occur in bacterial evolution. However, given the ongoing freshening of the Arctic Ocean, our results suggest that these relative newcomers to the ocean microbiome increase in abundance and, therefore, ecological significance in a near-future Arctic Ocean.

A Pragmatic Randomized Controlled Trial to Increase PrEP Uptake for HIV Prevention: 55-Week Results From PrEPChicago.

OBJECTIVES: We tested preliminary efficacy of a peer change agent type I network intervention to increase pre-exposure prophylaxis (PrEP) linkage to care among network members connected to young Black men who have sex with men. DESIGN: Parent study is a pragmatic randomized controlled trial with 110 weeks of total follow-up. Interim midpoint analyses are performed here using participant data before crossover assignment at 55 weeks. METHODS: We randomly assigned 423 participants in Chicago to receive the network intervention, an opinion leader workshop with telephonic booster sessions, versus a time-matched control from 2016 to 2018. The consolidated surrogate outcome was PrEP referral and linkage to clinical care among network members connected to study participants and was collected from independent administrative data. RESULTS: Each study participant in the trial (n = 423) had on average 1822 network contacts who could be eligible for PrEP referral and linkage. During the 55-week observation period, PrEP referral was most likely to occur within 3 days of an intervention session compared to control [odds ratio (OR) 0.07 (0.02-0.013); P = 0.007] resulting in 1-2 referrals of network members per session. Network members with referral or linkage were more likely to be connected to study participants in the intervention arm than the control condition [aOR 1.50 (1.09-2.06); P = 0.012]. CONCLUSIONS: A peer change agent type I network intervention is preliminarily effective at diffusing PrEP through a network of individuals highly susceptible to HIV over 55 weeks. This low-intensity intervention demonstrated network-level impact among populations that have experienced limited PrEP care engagement in the United States.

Embedding a Linkage to Preexposure Prophylaxis Care Intervention in Social Network Strategy and Partner Notification Services: Results From a Pilot Randomized Controlled Trial.

BACKGROUND: Increased preexposure prophylaxis (PrEP) uptake among black men who have sex with men and black transgender women (BMSM/TW) is needed to end the HIV epidemic. Embedding a brief intervention in network services that engage individuals in HIV transmission networks for HIV/ sexually transmitted infections testing may be an important strategy to accelerate PrEP uptake. SETTING: Partner Services PrEP study is a pilot, randomized, control trial to improve linkage to PrEP care among BMSM/TW presenting for network services in Chicago, IL, from 2015 to 2017. METHODS: BMSM/TW (N = 146) aged 18-40 years were recruited from network services (partners services and social network strategy services). Intervention participants developed an individualized linkage plan based on the information-motivation-behavioral skills model and received minibooster sessions. Control participants received treatment as usual. Sociodemographic, behavioral, and clinical factors were examined at baseline and 3- and 12-month postintervention. Intent-to-treat analyses examined linkage to PrEP care within 3-month postintervention (primary outcome). Secondary outcomes were PrEP initiation, time to linkage to PrEP care, and time to PrEP initiation. RESULTS: Compared with control participants, a significantly greater proportion of the intervention participants were linked to PrEP care within 3 months (24% vs. 11%; P = 0.04) and initiated PrEP (24% vs. 11%; P = 0.05). Among those linked to PrEP care within the study period, intervention participants were linked significantly sooner than control participants [median (interquartile range) days, 26.5 (6.0-141.8) vs. 191.5 (21.5-297.0); P = 0.05]. CONCLUSION: Study results support the preliminary efficacy of Partner Services PrEP to improve linkage to PrEP care and PrEP initiation among BMSM/TW.

Diversity and biogeography of SAR11 bacteria from the Arctic Ocean.

The Arctic Ocean is relatively isolated from other oceans and consists of strongly stratified water masses with distinct histories, nutrient, temperature, and salinity characteristics, therefore providing an optimal environment to investigate local adaptation. The globally distributed SAR11 bacterial group consists of multiple ecotypes that are associated with particular marine environments, yet relatively little is known about Arctic SAR11 diversity. Here, we examined SAR11 diversity using ITS analysis and metagenome-assembled genomes (MAGs). Arctic SAR11 assemblages were comprised of the S1a, S1b, S2, and S3 clades, and structured by water mass and depth. The fresher surface layer was dominated by an ecotype (S3-derived P3.2) previously associated with Arctic and brackish water. In contrast, deeper waters of Pacific origin were dominated by the P2.3 ecotype of the S2 clade, within which we identified a novel subdivision (P2.3s1) that was rare outside the Arctic Ocean. Arctic S2-derived SAR11 MAGs were restricted to high latitudes and included MAGs related to the recently defined S2b subclade, a finding consistent with bi-polar ecotypes and Arctic endemism. These results place the stratified Arctic Ocean into the SAR11 global biogeography and have identified SAR11 lineages for future investigation of adaptive evolution in the Arctic Ocean.

Predictive Analytics for Retention in Care in an Urban HIV Clinic.

Consistent medical care among people living with HIV is essential for both individual and public health. HIV-positive individuals who are 'retained in care' are more likely to be prescribed antiretroviral medication and achieve HIV viral suppression, effectively eliminating the risk of transmitting HIV to others. However, in the United States, less than half of HIV-positive individuals are retained in care. Interventions to improve retention in care are resource intensive, and there is currently no systematic way to identify patients at risk for falling out of care who would benefit from these interventions. We developed a machine learning model to identify patients at risk for dropping out of care in an urban HIV care clinic using electronic medical records and geospatial data. The machine learning model has a mean positive predictive value of 34.6% [SD: 0.15] for flagging the top 10% highest risk patients as needing interventions, performing better than the previous state-of-the-art logistic regression model (PPV of 17% [SD: 0.06]) and the baseline rate of 11.1% [SD: 0.02]. Machine learning methods can improve the prediction ability in HIV care clinics to proactively identify patients at risk for not returning to medical care.

Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy.

The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development.

A modeling framework to inform preexposure prophylaxis initiation and retention scale-up in the context of 'Getting to Zero' initiatives.

OBJECTIVE(S): 'Getting to Zero' (GTZ) initiatives aim to eliminate new HIV infections over a projected time frame. Increased preexposure prophylaxis (PrEP) uptake among populations with the highest HIV incidence, such as young Black MSM, is necessary to accomplish this aim. Agent-based network models (ABNMs) can help guide policymakers on strategies to increase PrEP uptake. DESIGN: Effective PrEP implementation requires a model that incorporates the dynamics of interventions and dynamic feedbacks across multiple levels including virus, host, behavior, networks, and population. ABNMs are a powerful tool to incorporate these processes. METHODS: An ABNM, designed for and parameterized using data for young Black MSM in Illinois, was used to compare the impact of PrEP initiation and retention interventions on HIV incidence after 10 years, consistent with GTZ timelines. Initiation interventions selected individuals in serodiscordant partnerships, or in critical sexual network positions, and compared with a controlled setting where PrEP initiators were randomly selected. Retention interventions increased the mean duration of PrEP use. A combination intervention modeled concurrent increases in PrEP initiation and retention. RESULTS: Selecting HIV-negative individuals for PrEP initiation in serodiscordant partnerships resulted in the largest HIV incidence declines, relative to other interventions. For a given PrEP uptake level, distributing effort between increasing PrEP initiation and retention in combination was approximately as effective as increasing only one exclusively. CONCLUSION: Simulation results indicate that expanded PrEP interventions alone may not accomplish GTZ goals within a decade, and integrated scale-up of PrEP, antiretroviral therapy, and other interventions might be necessary.

Investigation of XoxF methanol dehydrogenases reveals new methylotrophic bacteria in pelagic marine and freshwater ecosystems.

The diversity and distribution of methylotrophic bacteria have been investigated in the oceans and lakes using the methanol dehydrogenase mxaF gene as a functional marker. However, pelagic marine (OM43) and freshwater (LD28 and PRD01a001B) methylotrophs within the Betaproteobacteria lack mxaF, instead possessing a related xoxF4-encoded methanol dehydrogenase. Here, we developed and employed xoxF4 as a complementary functional gene marker to mxaF for studying methylotrophs in aquatic environment. Using xoxF4, we detected OM43-related and LD28-related methylotrophs in the ocean and freshwaters of North America, respectively, and showed the coexistence of these two lineages in a large estuarine system (St Lawrence Estuary). Gene expression patterns of xoxF4 supported a positive relationship between xoxF4-containing methylotroph activity and spring time productivity, suggesting phytoplankton blooms are a source of methylotrophic substrates. Further investigation of methanol dehydrogenase diversity in pelagic ecosystems using comparative metagenomics provided strong support for a widespread distribution of xoxF4 (as well as several distinct xoxF5) containing methylotrophs in marine and freshwater surface waters. In total, these results demonstrate a geographical distribution of OM43/LD28-related methylotrophs that includes marine and freshwaters and suggest that methylotrophy occurring in the water column is an important component of lake and estuary carbon cycling and biogeochemistry.