Development of a trash classification system to map potential Aedes aegypti breeding grounds using unmanned aerial vehicle imaging.

Aedes aegypti mosquitos are the primary vector for dengue, chikungunya, and Zika viruses and tend to breed in small containers of water, with a propensity to breed in small piles of trash and abandoned tires. This study piloted the use of aerial imaging to map and classify potential Ae. aegypti breeding sites with a specific focus on trash, including discarded tires. Aerial images of coastal and inland sites in Kenya were obtained using an unmanned aerial vehicle. Aerial images were reviewed for identification of trash and suspected trash mimics, followed by extensive community walk-throughs to identify trash types and mimics by description and ground photography. An expert panel reviewed aerial images and ground photos to develop a classification scheme and evaluate the advantages and disadvantages of aerial imaging versus walk-through trash mapping. A trash classification scheme was created based on trash density, surface area, potential for frequent disturbance, and overall likelihood of being a productive Ae. aegypti breeding site. Aerial imaging offers a novel strategy to characterize, map, and quantify trash at risk of promoting Ae. aegypti proliferation, generating opportunities for further research on trash associations with disease and trash interventions.

Impact of a multicomponent navigation strategy on stigma among people living with HIV and Kaposi's sarcoma in Kenya: a qualitative analysis.

Persons with HIV-associated Kaposi's sarcoma (KS) experience three co-existing stigmatizing health conditions: skin disease, HIV, and cancer, which contribute to a complex experience of stigmatization and to delays in diagnosis and treatment. Despite the importance of stigma among these patients, there are few proven stigma-reduction strategies for HIV-associated malignancies. Using qualitative methods, we explore how people with HIV-associated KS in western Kenya between August 2022 and 2023 describe changes in their stigma experience after participation in a multicomponent navigation strategy, which included 1) physical navigation and care coordination, 2) video-based education with motivational survivor stories, 3) travel stipend, 4) health insurance enrollment assistance, 5) health insurance stipend, and 6) peer mentorship. A purposive sample of persons at different stages of chemotherapy treatment were invited to participate. Participants described how a multicomponent navigation strategy contributed to increased knowledge and awareness, a sense of belonging, hope to survive, encouragement, and social support, which served as stigma mitigators, likely counteracting the major drivers of intersectional stigma in HIV-associated KS.

HIV-associated gut microbial alterations are dependent on host and geographic context.

HIV-associated changes in intestinal microbiota are believed to be important drivers of disease progression. However, the majority of studies have focused on populations in high-income countries rather than in developing regions where HIV burden is greatest. To better understand the impact of HIV on fecal microbiota globally, we compare the fecal microbial community of individuals in the U.S., Uganda, and Botswana. We identify significant bacterial taxa alterations with both treated and untreated HIV infection with a high degree of uniqueness in each cohort. HIV-associated taxa alterations are also significantly different between populations that report men who have sex with men (MSM) behavior and non-MSM populations. Additionally, while we find that HIV infection is consistently associated with higher soluble markers of immune activation, most specific bacterial taxa associated with these markers in each region are not shared and none are shared across all three geographic locations in our study. Our findings demonstrate that HIV-associated changes in fecal microbiota are overall distinct among geographical locations and sexual behavior groups, although a small number of taxa shared between pairs of geographic locations warrant further investigation, highlighting the importance of considering host context to fully assess the impact of the gut microbiome on human health and disease.

Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation.

Environmental enteropathy (EE) is a subclinical condition of the small intestine that is highly prevalent in low- and middle-income countries. It is thought to be a key contributing factor to childhood malnutrition, growth stunting, and diminished oral vaccine responses. Although EE has been shown to be the by-product of a recurrent enteric infection, its full pathophysiology remains unclear. Here, we mapped the cellular and molecular correlates of EE by performing high-throughput, single-cell RNA-sequencing on 33 small intestinal biopsies from 11 adults with EE in Lusaka, Zambia (eight HIV-negative and three HIV-positive), six adults without EE in Boston, United States, and two adults in Durban, South Africa, which we complemented with published data from three additional individuals from the same clinical site. We analyzed previously defined bulk-transcriptomic signatures of reduced villus height and decreased microbial translocation in EE and showed that these signatures may be driven by an increased abundance of surface mucosal cells-a gastric-like subset previously implicated in epithelial repair in the gastrointestinal tract. In addition, we determined cell subsets whose fractional abundances associate with EE severity, small intestinal region, and HIV infection. Furthermore, by comparing duodenal EE samples with those from three control cohorts, we identified dysregulated WNT and MAPK signaling in the EE epithelium and increased proinflammatory cytokine gene expression in a T cell subset highly expressing a transcriptional signature of tissue-resident memory cells in the EE cohort. Together, our work elucidates epithelial and immune correlates of EE and nominates cellular and molecular targets for intervention.

Prediction of Antimicrobial Resistance in Clinical Enterococcus faecium Isolates Using a Rules-Based Analysis of Whole-Genome Sequences.

Enterococcus faecium is a major cause of clinical infections, often due to multidrug-resistant (MDR) strains. Whole-genome sequencing (WGS) is a powerful tool to study MDR bacteria and their antimicrobial resistance (AMR) mechanisms. In this study, we used WGS to characterize E. faecium clinical isolates and test the feasibility of rules-based genotypic prediction of AMR. Clinical isolates were divided into derivation and validation sets. Phenotypic susceptibility testing for ampicillin, vancomycin, high-level gentamicin, ciprofloxacin, levofloxacin, doxycycline, tetracycline, and linezolid was performed using the Vitek 2 automated system, with confirmation and discrepancy resolution by broth microdilution, disk diffusion, or gradient diffusion when needed. WGS was performed to identify isolate lineage and AMR genotype. AMR prediction rules were derived by analyzing the genotypic-phenotypic relationship in the derivation set. Phylogenetic analysis demonstrated that 88% of isolates in the collection belonged to hospital-associated clonal complex 17. Additionally, 12% of isolates had novel sequence types. When applied to the validation set, the derived prediction rules demonstrated an overall positive predictive value of 98% and negative predictive value of 99% compared to standard phenotypic methods. Most errors were falsely resistant predictions for tetracycline and doxycycline. Further analysis of genotypic-phenotypic discrepancies revealed potentially novel pbp5 and tet(M) alleles that provide insight into ampicillin and tetracycline class resistance mechanisms. The prediction rules demonstrated generalizability when tested on an external data set. In conclusion, known AMR genes and mutations can predict E. faecium phenotypic susceptibility with high accuracy for most routinely tested antibiotics, providing opportunities for advancing molecular diagnostics.

Synthetic Cassettes for pH-Mediated Sensing, Counting, and Containment.

As pH is fundamental to all biological processes, pH-responsive bacterial genetic circuits enable precise sensing in any environment. Where the unintentional release of engineered bacteria poses a concern, coupling pH sensing to the expression of a toxin creates an effective bacterial containment system. Here, we present a pH-sensitive kill switch (acidic termination of replicating population [acidTRP]), based on the Escherichia coli asr promoter, with a survival ratio of <1 in 106. We integrate acidTRP with cryodeath to produce a 2-factor containment system with a combined survival ratio of <1 in 1011 while maintaining evolutionary stability. We further develop a pulse-counting circuit with single-cell readout for each administered stimulus pulse. We use this pulse counter to record multiple pH changes and combine it with acidTRP to make a 2-count acid-sensitive kill switch. These results demonstrate the ability to build complex genetic systems for biological containment.

Community-acquired in name only: A cluster of carbapenem-resistant Acinetobacter baumannii in a burn intensive care unit and beyond.

OBJECTIVE: To describe an investigation into 5 clinical cases of carbapenem-resistant Acinetobacter baumannii (CRAB). DESIGN: Epidemiological investigation supplemented by whole-genome sequencing (WGS) of clinical and environmental isolates. SETTING: A tertiary-care academic health center in Boston, Massachusetts. PATIENTS OR PARTICIPANTS: Individuals identified with CRAB clinical infections. METHODS: A detailed review of patient demographic and clinical data was conducted. Clinical isolates underwent phenotypic antimicrobial susceptibility testing and WGS. Infection control practices were evaluated, and CRAB isolates obtained through environmental sampling were assessed by WGS. Genomic relatedness was measured by single-nucleotide polymorphism (SNP) analysis. RESULTS: Four clinical cases spanning 4 months were linked to a single index case; isolates differed by 1-7 SNPs and belonged to a single cluster. The index patient and 3 case patients were admitted to the same room prior to their development of CRAB infection, and 2 case patients were admitted to the same room within 48 hours of admission. A fourth case patient was admitted to a different unit. Environmental sampling identified highly contaminated areas, and WGS of 5 environmental isolates revealed that they were highly related to the clinical cluster. CONCLUSIONS: We report a cluster of highly resistant Acinetobacter baumannii that occurred in a burn ICU over 5 months and then spread to a separate ICU. Two case patients developed infections classified as community acquired under standard epidemiological definitions, but WGS revealed clonality, highlighting the risk of burn patients for early-onset nosocomial infections. An extensive investigation identified the role of environmental reservoirs.