Division of Infectious Diseases, Research Labs

Abstract

Mycobacterium tuberculosis complex (MTBC) species evolve slowly, so isolates from individuals linked in transmission often have identical or nearly identical genomes, making it difficult to reconstruct transmission chains. Finding additional sources of shared MTBC variation could help overcome this problem. Previous studies have reported MTBC diversity within infected individuals; however, whether within-host variation improves transmission inferences remains unclear. Here, we aimed to quantify within-host MTBC variation and assess whether such information improves transmission inferences.We conducted a retrospective genomic epidemiology study in which we reanalysed publicly available sequence data from household transmission studies published in PubMed from database inception until Jan 31, 2024, for which both genomic and epidemiological contact data were available, using household membership as a proxy for transmission linkage. We quantified minority variants (ie, positions with two or more alleles each supported by at least five-fold coverage and with a minor allele frequency of 1% or more) outside of PE and PPE genes, within individual samples and shared across samples. We used receiver operator characteristic (ROC) curves to compare the performance of a general linear model for household membership that included shared minority variants and one that included only fixed genetic differences.We identified three MTBC household transmission studies with publicly available whole-genome sequencing data and epidemiological linkages: a household transmission study in Vitória, Brazil (Colangeli et al), a retrospective population-based study of paediatric tuberculosis in British Columbia, Canada (Guthrie et al), and a retrospective population-based study in Oxfordshire, England (Walker et al). We found moderate levels of minority variation present in MTBC sequence data from cultured isolates that varied significantly across studies: mean 168·6 minority variants (95% CI 151·4-185·9) for the Colangeli et al dataset, 5·8 (1·5-10·2) for Guthrie et al (p<0·0001, Wilcoxon rank sum test, vs Colangeli et al), and 7·1 (2·4-11·9) for Walker et al (p<0·0001, Wilcoxon rank sum test, vs Colangeli et al). Isolates from household pairs shared more minority variants than did randomly selected pairs of isolates: mean 97·7 shared minority variants (79·1-116·3) versus 9·8 (8·6-11·0) in Colangeli et al, 0·8 (0·1-1·5) versus 0·2 (0·1-0·2) in Guthrie et al, and 0·7 (0·1-1·3) versus 0·2 (0·2-0·2) in Walker et al (all p<0·0001, Wilcoxon rank sum test). Shared within-host variation was significantly associated with household membership (odds ratio 1·51 [95% CI 1·30-1·71], p<0·0001), for one standard deviation increase in shared minority variants. Models that included shared within-host variation versus models without within-host variation improved the accuracy of predicting household membership in all three studies: area under the ROC curve 0·95 versus 0·92 for the Colangeli et al study, 0·99 versus 0·95 for the Guthrie et al study, and 0·93 versus 0·91 for the Walker et al study.Within-host MTBC variation persists through culture of sputum and could enhance the resolution of transmission inferences. The substantial differences in minority variation recovered across studies highlight the need to optimise approaches to recover and incorporate within-host variation into automated phylogenetic and transmission inference.National Institutes of Health.

View details for DOI 10.1016/j.lanmic.2024.06.003

View details for PubMedID 39615498

Abstract

Tuberculosis incidence is increasing in Latin America, where the incarcerated population has nearly quadrupled since 1990. We aimed to quantify the impact of historical and future incarceration policies on the tuberculosis epidemic, accounting for effects in and beyond prisons.In this modelling study, we calibrated dynamic compartmental transmission models to historical and contemporary data from Argentina, Brazil, Colombia, El Salvador, Mexico, and Peru, which comprise approximately 80% of the region's incarcerated population and tuberculosis burden. The model was fit independently for each country to incarceration and tuberculosis data from 1990 to 2023 (specific dates were country dependent). The model does not include HIV, drug resistance, gender or sex, or age structure. Using historical counterfactual scenarios, we estimated the transmission population attributable fraction (tPAF) for incarceration and the excess population-level burden attributable to increasing incarceration prevalence since 1990. We additionally projected the effect of alternative incarceration policies on future population tuberculosis incidence.Population tuberculosis incidence in 2019 was 29·4% (95% uncertainty interval [UI] 23·9-36·8) higher than expected without the rise in incarceration since 1990, corresponding to 34 393 (28 295-42 579) excess incident cases across countries. The incarceration tPAF in 2019 was 27·2% (20·9-35·8), exceeding estimates for other risk factors like HIV, alcohol use disorder, and undernutrition. Compared with a scenario where incarceration rates remain stable at current levels, a gradual 50% reduction in prison admissions and duration of incarceration by 2034 would reduce population tuberculosis incidence by over 10% in all countries except Mexico.The historical rise in incarceration in Latin America has resulted in a large excess tuberculosis burden that has been under-recognised to date. International health agencies, ministries of justice, and national tuberculosis programmes should collaborate to address this health crisis with comprehensive strategies, including decarceration.National Institutes of Health.

View details for DOI 10.1016/S2468-2667(24)00192-0

View details for PubMedID 39419058

Abstract

Standardized dosing of anti-tubercular (TB) drugs leads to variable plasma drug levels, which are associated with adverse drug reactions, delayed treatment response, and relapse. Mutations in genes affecting drug metabolism explain considerable interindividual pharmacokinetic variability; however, pharmacogenomic (PGx) assays that predict metabolism of anti-TB drugs have been lacking.To develop a Nanopore sequencing panel and validate its performance in active TB patients to personalize treatment dosing.We developed a Nanopore sequencing panel targeting 15 single nucleotide polymorphisms (SNP) in 5 genes affecting the metabolism of anti-tuberculous drugs. For validation, we sequenced DNA samples (n=48) from the 1000 genomes project and compared variant calling accuracy with Illumina genome sequencing. We then sequenced DNA samples from patients with active TB (n=100) from South Africa on a MinION Mk1C and evaluated the relationship between genotypes and pharmacokinetic parameters for INH and RIF.The PGx panel achieved 100% concordance with Illumina sequencing in variant identification for the samples from the 1000 Genomes Project. In the clinical cohort, coverage was >100x for 1498/1500 (99.8%) amplicons across the 100 samples. One third (33%) of participants were identified as slow, 47% were intermediate and 20% were rapid isoniazid acetylators. Isoniazid clearance was 2.2 times higher among intermediate acetylators and 3.8 times higher among rapid acetylators compared with slow acetylators (p<0.0001).. Rifampin clearance was 17.3% (2.50-29.9) lower in individuals with homozygous AADAC rs1803155 G>A substitutions (p=0.0015).Targeted sequencing can enable detection of polymorphisms influencing TB drug metabolism on a low-cost, portable instrument to personalize dosing for TB treatment or prevention. This article is open access and distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).

View details for DOI 10.1164/rccm.202309-1583OC

View details for PubMedID 38647526

Abstract

The effectiveness of BCG vaccine for adult pulmonary tuberculosis remains uncertain. In this study, we aimed to evaluate the effect of vaccination with BCG-Denmark to prevent initial and sustained interferon-γ release assay conversion in Brazilian health-care workers.This substudy is a nested randomised controlled trial embedded within the BRACE trial (NCT04327206). Specifically, this substudy enrolled Brazilian health-care workers (aged ≥18 years) from three sites in Brazil (Manaus, Campo Grande, and Rio de Janeiro) irrespective of previously receiving BCG vaccination. Participants were excluded if they had contraindications to BCG vaccination, more than 1 month of treatment with specific tuberculosis treatment drugs, previous adverse reactions to BCG, recent BCG vaccination, or non-compliance with assigned interventions. Those eligible were randomly assigned (1:1) to either the BCG group (0·1 mL intradermal injection of BCG-Denmark [Danish strain 1331; AJ Vaccines, Copenhagen]) or the placebo group (intradermal injection of 0·9% saline) using a web-based randomisation process in variable-length blocks (2, 4, or 6), and were stratified based on the study site, age (<40, ≥40 to <60, ≥60 years), and comorbidity presence (diabetes, chronic respiratory disease, cardiac condition, hypertension). Sealed syringes were used to prevent inadvertent disclosure of group assignments. The QuantiFERON-TB Gold (QFT) Plus test (Qiagen; Hilden, Germany) was used for baseline and 12-month tuberculosis infection assessments. The primary efficacy outcome was QFT Plus conversion (≥0·35 IU/mL) by 12 months following vaccination in participants who had a negative baseline result (<0·35 IU/mL).Between Oct 7, 2020, and April 12, 2021, 1985 (77·3%) of 2568 participants were eligible for QFT Plus assessment at 12 months and were included in this substudy; 996 (50·2%) of 1985 were in the BCG group and 989 (49·8%) were in the placebo group. Overall, 1475 (74·3%) of 1985 participants were women and 510 (25·7%) were men, and the median age was 39 years (IQR 32-47). During the first 12 months, QFT Plus conversion occurred in 66 (3·3%) of 1985 participants, with no significant differences by study site (p=0·897). Specifically, 34 (3·4%) of 996 participants had initial QFT conversion in the BCG group compared with 32 (3·2%) of 989 in the placebo group (risk ratio 1·09 [95% CI 0·67-1·77]; p=0·791).BCG-Denmark vaccination did not reduce initial QFT Plus conversion risk in Brazilian health-care workers. This finding underscores the need to better understand tuberculosis prevention in populations at high risk.Bill & Melinda Gates Foundation, the Minderoo Foundation, Sarah and Lachlan Murdoch, the Royal Children's Hospital Foundation, Health Services Union NSW, the Peter Sowerby Foundation, SA Health, the Insurance Advisernet Foundation, the NAB Foundation, the Calvert-Jones Foundation, the Modara Pines Charitable Foundation, the United Health Group Foundation, Epworth Healthcare, and individual donors.For the Portuguese translation of the abstract see Supplementary Materials section.

View details for DOI 10.1016/S1473-3099(23)00818-6

View details for PubMedID 38423021

Abstract

People who are incarcerated are at high risk of developing tuberculosis. We aimed to estimate the annual global, regional, and national incidence of tuberculosis among incarcerated populations from 2000 to 2019.We collected and aggregated data for tuberculosis incidence and prevalence estimates among incarcerated individuals in published and unpublished literature, annual tuberculosis notifications among incarcerated individuals at the country level, and the annual number of incarcerated individuals at the country level. We developed a joint hierarchical Bayesian meta-regression framework to simultaneously model tuberculosis incidence, notifications, and prevalence from 2000 to 2019. Using this model, we estimated trends in absolute tuberculosis incidence and notifications, the incidence and notification rates, and the case detection ratio by year, country, region, and globally.In 2019, we estimated a total of 125 105 (95% credible interval [CrI] 93 736-165 318) incident tuberculosis cases among incarcerated individuals globally. The estimated incidence rate per 100 000 person-years overall was 1148 (95% CrI 860-1517) but varied greatly by WHO region, from 793 (95% CrI 430-1342) in the Eastern Mediterranean region to 2242 (1515-3216) in the African region. Global incidence per 100 000 person-years between 2000 and 2012 among incarcerated individuals decreased from 1884 (95% CrI 1394-2616) to 1205 (910-1615); however, from 2013 onwards, tuberculosis incidence per 100 000 person-years was stable, from 1183 (95% CrI 876-1596) in 2013 to 1148 (860-1517) in 2019. In 2019, the global case detection ratio was estimated to be 53% (95% CrI 42-64), the lowest over the study period.Our estimates suggest a high tuberculosis incidence rate among incarcerated individuals globally with large gaps in tuberculosis case detection. Tuberculosis in incarcerated populations must be addressed with interventions specifically tailored to improve diagnoses and prevent transmission as a part of the broader global tuberculosis control effort.National Institutes of Health.

View details for DOI 10.1016/S2468-2667(23)00097-X

View details for PubMedID 37393090

Abstract

At this stage in the COVID-19 pandemic, most infections are "breakthrough" infections that occur in individuals with prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure. To refine long-term vaccine strategies against emerging variants, we examined both innate and adaptive immunity in breakthrough infections. We performed single-cell transcriptomic, proteomic, and functional profiling of primary and breakthrough infections to compare immune responses from unvaccinated and vaccinated individuals during the SARS-CoV-2 Delta wave. Breakthrough infections were characterized by a less activated transcriptomic profile in monocytes and natural killer cells, with induction of pathways limiting monocyte migratory potential and natural killer cell proliferation. Furthermore, we observed a female-specific increase in transcriptomic and proteomic activation of multiple innate immune cell subsets during breakthrough infections. These insights suggest that prior SARS-CoV-2 vaccination prevents overactivation of innate immune responses during breakthrough infections with discernible sex-specific patterns and underscore the potential of harnessing vaccines in mitigating pathologic immune responses resulting from overactivation.

View details for DOI 10.1126/scitranslmed.adq1086

View details for PubMedID 39879318

Abstract

Sex differences have been observed in acute coronavirus disease 2019 (COVID-19) and Long Covid (LC) outcomes, with greater disease severity and mortality during acute infection in males and greater proportions of females developing LC. We hypothesized that sex-specific immune dysregulation contributes to LC pathogenesis. To investigate the immunologic underpinnings of LC development and symptom persistence, we performed multiomic analyses on blood samples obtained during acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and 3 and 12 months after infection in a cohort of 45 participants who either developed LC or recovered. Several sex-specific immune pathways were associated with LC. Males who would later develop LC exhibited increases in transforming growth factor-β (TGF-β) signaling during acute infection, whereas females who would go on to develop LC had reduced TGFB1 expression. Females who developed LC demonstrated increased expression of XIST, an RNA gene implicated in autoimmunity, during acute infection compared with females who recovered. Many immune features of LC were also conserved across sexes, such as alterations in monocyte phenotype and activation state. Nuclear factor κB (NF-κB) transcription factors were up-regulated in many cell types at acute and convalescent time points. Those with ongoing LC demonstrated reduced ETS1 expression across lymphocyte subsets and elevated intracellular IL-4 in T cell subsets, suggesting that ETS1 alterations may drive aberrantly elevated T helper cell 2-like responses in LC. Altogether, this study describes multiple innate and adaptive immune correlates of LC, some of which differ by sex, and offers insights toward the pursuit of tailored therapeutics.

View details for DOI 10.1126/scitranslmed.adr1032

View details for PubMedID 39536117

Abstract

Inference of cell-cell communication from single-cell RNA sequencing data is a powerful technique to uncover intercellular communication pathways, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell-level information. Here we present Scriabin, a flexible and scalable framework for comparative analysis of cell-cell communication at single-cell resolution that is performed without cell aggregation or downsampling. We use multiple published atlas-scale datasets, genetic perturbation screens and direct experimental validation to show that Scriabin accurately recovers expected cell-cell communication edges and identifies communication networks that can be obscured by agglomerative methods. Additionally, we use spatial transcriptomic data to show that Scriabin can uncover spatial features of interaction from dissociated data alone. Finally, we demonstrate applications to longitudinal datasets to follow communication pathways operating between timepoints. Our approach represents a broadly applicable strategy to reveal the full structure of niche-phenotype relationships in health and disease.

View details for DOI 10.1038/s41587-023-01782-z

View details for PubMedID 37169965

View details for PubMedCentralID 8104132

Abstract

Natural killer (NK) cells are cytotoxic effector cells that target and lyse virally infected cells; many viruses therefore encode mechanisms to escape such NK cell killing. Here, we interrogate the ability of SARS-CoV-2 to modulate NK cell recognition and lysis of infected cells. We find that NK cells exhibit poor cytotoxic responses against SARS-CoV-2-infected targets, preferentially killing uninfected bystander cells. We demonstrate that this escape is driven by downregulation of ligands for the activating receptor NKG2D (NKG2D-L). Indeed, early in viral infection, prior to NKG2D-L downregulation, NK cells are able to target and kill infected cells; however, this ability is lost as viral proteins are expressed. Finally, we find that SARS-CoV-2 non-structural protein 1 (Nsp1) mediates downregulation of NKG2D-L and that Nsp1 alone is sufficient to confer resistance to NK cell killing. Collectively, our work demonstrates that SARS-CoV-2 evades direct NK cell cytotoxicity and describes a mechanism by which this occurs.

View details for DOI 10.1016/j.celrep.2022.111892

View details for PubMedID 36543165

Abstract

Bacteriophage (phage) therapy is a promising therapeutic modality for multidrug-resistant bacterial infections, but its application is mainly limited to personalized therapy due to the narrow host range of individual phages. While phage cocktails targeting all possible bacterial receptors could theoretically confer broad coverage, the extensive diversity of bacteria and the complexity of phage-phage interactions render this approach challenging. Here, using screening protocols for identifying "complementarity groups" of phages using non-redundant receptors, we generate effective, broad-range phage cocktails that prevent the emergence of bacterial resistance. We also discover characteristic interactions between phage complementarity groups and particular antibiotic classes, facilitating the prediction of phage-antibiotic as well as phage-phage interactions. Using this strategy, we create three phage-antibiotic cocktails, each demonstrating efficacy against ≥96% of 153 Pseudomonas aeruginosa clinical isolates, including biofilm cultures, and demonstrate comparable efficacy in an in vivo wound infection model. We similarly develop effective Staphylococcus aureus phage-antibiotic cocktails and demonstrate their utility of combined cocktails against polymicrobial (mixed P. aeruginosa/S. aureus) cultures, highlighting the broad applicability of this approach. These studies establish a blueprint for the development of effective, broad-spectrum phage-antibiotic cocktails, paving the way for off-the-shelf phage-based therapeutics to combat multidrug-resistant bacterial infections.

View details for DOI 10.1038/s41467-024-53994-9

View details for PubMedID 39609398

View details for PubMedCentralID 11153159

Abstract

Bacteriophages, viruses that infect bacteria, have great specificity for their bacterial hosts at the strain and species level. However, the relationship between the phageome and associated bacterial population dynamics is unclear. Here we generated a computational pipeline to identify sequences associated with bacteriophages and their bacterial hosts in cell-free DNA from plasma samples. Analysis of two independent cohorts, including a Stanford Cohort of 61 septic patients and 10 controls and the SeqStudy cohort of 224 septic patients and 167 controls, reveals a circulating phageome in the plasma of all sampled individuals. Moreover, infection is associated with overrepresentation of pathogen-specific phages, allowing for identification of bacterial pathogens. We find that information on phage diversity enables identification of the bacteria that produced these phages, including pathovariant strains of Escherichia coli. Phage sequences can likewise be used to distinguish between closely related bacterial species such as Staphylococcus aureus, a frequent pathogen, and coagulase-negative Staphylococcus, a frequent contaminant. Phage cell-free DNA may have utility in studying bacterial infections.

View details for DOI 10.1038/s41564-023-01406-x

View details for PubMedID 37308590

View details for PubMedCentralID 5594678

Abstract

Chronic wounds infected by Pseudomonas aeruginosa (Pa) are characterized by disease progression and increased mortality. We reveal Pf, a bacteriophage produced by Pa that delays healing of chronically infected wounds in human subjects and animal models of disease. Interestingly, impairment of wound closure by Pf is independent of its effects on Pa pathogenesis. Rather, Pf impedes keratinocyte migration, which is essential for wound healing, through direct inhibition of CXCL1 signaling. In support of these findings, a prospective cohort study of 36 human patients with chronic Pa wound infections reveals that wounds infected with Pf-positive strains of Pa are more likely to progress in size compared with wounds infected with Pf-negative strains. Together, these data implicate Pf phage in the delayed wound healing associated with Pa infection through direct manipulation of mammalian cells. These findings suggest Pf may have potential as a biomarker and therapeutic target in chronic wounds.

View details for DOI 10.1016/j.xcrm.2022.100656

View details for PubMedID 35732145

View details for DOI 10.1126/scitranslmed.aau9748

View details for Web of Science ID 000465116400003

Abstract

Bacteriophage are abundant at sites of bacterial infection, but their effects on mammalian hosts are unclear. We have identified pathogenic roles for filamentous Pf bacteriophage produced by Pseudomonas aeruginosa (Pa) in suppression of immunity against bacterial infection. Pf promote Pa wound infection in mice and are associated with chronic human Pa wound infections. Murine and human leukocytes endocytose Pf, and internalization of this single-stranded DNA virus results in phage RNA production. This triggers Toll-like receptor 3 (TLR3)- and TIR domain-containing adapter-inducing interferon-β (TRIF)-dependent type I interferon production, inhibition of tumor necrosis factor (TNF), and the suppression of phagocytosis. Conversely, immunization of mice against Pf prevents Pa wound infection. Thus, Pf triggers maladaptive innate viral pattern-recognition responses, which impair bacterial clearance. Vaccination against phage virions represents a potential strategy to prevent bacterial infection.

View details for PubMedID 30923196

Abstract

Few studies have tracked human CD4+ T cell clones through repeated infections. We used longitudinal single-cell RNA and T cell receptor (TCR) tracking to study the functional stability and memory potential of CD4+ T cell clonotypes during repeated Plasmodium falciparum (Pf) infections in Ugandan children and adults. Nearly all clonotypes displayed a strong preference for one of seven CD4+ subsets. This phenomenon of "clonal fidelity" was influenced by clonal expansion, linking T cell polarization and proliferation in vivo. Using clone tracking, we characterized subset-specific activation trajectories and identified antigen-specific clones. Type 1 regulatory T (TR1) cells accounted for nearly 90% of Pf-specific CD4+ T cells in blood. Tracking these clones longitudinally for hundreds of days, we observed malaria-induced expansion of TR1 effectors, long-term persistence of TR1 memory cells, and high-fidelity recall responses after reinfection. This work establishes clonal fidelity as a natural phenomenon and demonstrates the stable, long-term memory potential of TR1 cells.

View details for DOI 10.1126/sciimmunol.ads2957

View details for PubMedID 40279404

Abstract

Natural killer (NK) cells make important contributions to anti-malarial immunity through antibody-dependent cellular cytotoxicity (ADCC), but the role of different components of this pathway in promoting NK cell activation remains unclear.We compared the functions and phenotypes of NK cells from malaria-exposed and malaria-naive donors, and then varied the erythrocyte genetic background, Plasmodium falciparum strain and opsonising plasma used in ADCC to observe their impacts on NK cell degranulation as measured by CD107a mobilisation.Natural killer cells from malaria-exposed adult Ugandan donors had enhanced ADCC, but an impaired pro-inflammatory response to cytokine stimulation, compared to NK cells obtained from malaria-naive adult North American donors. Cellular phenotypes from malaria-exposed donors reflected this specialisation for ADCC, with a compartment-wide downregulation of the Fc receptor γ-chain and enrichment of highly differentiated CD56dim and CD56neg populations. NK cell degranulation was enhanced in response to opsonised P. falciparum schizonts cultured in sickle cell heterozygous erythrocytes relative to wild-type erythrocytes, and when using opsonising plasma collected from donors living in a high transmission area compared to a lower transmission area despite similar levels of 3D7 schizont-specific IgG levels. However, degranulation was lowered in response to opsonised field isolate P. falciparum schizonts isolated from clinical malaria infections, compared to the 3D7 laboratory strain typically used in these assays.This work highlights important host and parasite factors that contribute to ADCC efficacy that should be considered in the design of ADCC assays.

View details for DOI 10.1002/cti2.70005

View details for PubMedID 39493859

View details for PubMedCentralID PMC11528551

Abstract

The regulation of inflammation is a critical aspect of disease tolerance and naturally acquired clinical immunity to malaria. Here, we demonstrate using RNA sequencing and epigenetic landscape profiling by cytometry by time-of-flight, that the regulation of inflammatory pathways during asymptomatic parasitemia occurs downstream of pathogen sensing-at the epigenetic level. The abundance of certain epigenetic markers (methylation of H3K27 and dimethylation of arginine residues) and decreased prevalence of histone variant H3.3 correlated with suppressed cytokine responses among monocytes of Ugandan children. Such an epigenetic signature was observed across diverse immune cell populations and not only characterized active asymptomatic parasitemia but also correlated with future long-term disease tolerance and clinical immunity when observed in uninfected children. Pseudotime analyses revealed a potential trajectory of epigenetic change that correlated with a child's age and recent parasite exposure and paralleled the acquisition of clinical immunity. Thus, our data support a model whereby exposure to Plasmodium falciparum induces epigenetic changes that regulate excessive inflammation and contribute to naturally acquire clinical immunity to malaria.

View details for DOI 10.1093/pnasnexus/pgae325

View details for PubMedID 39161730

View details for PubMedCentralID PMC11331423

Abstract

Malaria, caused by infection with Plasmodium parasites, drives multiple regulatory responses across the immune landscape. These regulatory responses help to protect against inflammatory disease but may in some situations hamper the acquisition of adaptive immune responses that clear parasites. In addition, the regulatory responses that occur during Plasmodium infection may negatively affect malaria vaccine efficacy in the most at-risk populations. Here, we discuss the specific cellular mechanisms of immunoregulatory networks that develop during malaria, with a focus on knowledge gained from human studies and studies that involve the main malaria parasite to affect humans, Plasmodium falciparum. Leveraging this knowledge may lead to the development of new therapeutic approaches to increase protective immunity to malaria during infection or after vaccination.

View details for DOI 10.1038/s41577-024-01041-5

View details for PubMedID 38862638

View details for PubMedCentralID 8191919

Abstract

Malaria in pregnancy (MIP) causes higher morbidity in primigravid compared to multigravid women; however, the correlates and mechanisms underlying this gravidity-dependent protection remain incompletely understood. We aimed to compare the cellular immune response between primigravid and multigravid women living in a malaria-endemic region and assess for correlates of protection against MIP.We characterised the second trimester cellular immune response among 203 primigravid and multigravid pregnant women enrolled in two clinical trials of chemoprevention in eastern Uganda, utilizing RNA sequencing, flow cytometry, and functional assays. We compared responses across gravidity and determined associations with parasitaemia during pregnancy and placental malaria.Using whole blood RNA sequencing, no significant differentially expressed genes were identified between primigravid (n = 12) and multigravid (n = 11) women overall (log 2(FC) > 2, FDR < 0.1). However, primigravid (n = 49) women had higher percentages of malaria-specific, non-naïve CD4+ T cells that co-expressed IL-10 and IFNγ compared with multigravid (n = 85) women (p = 0.000023), and higher percentages of these CD4+ T cells were associated with greater risks of parasitaemia in pregnancy (Rs = 0.49, p = 0.001) and placental malaria (p = 0.0073). These IL-10 and IFNγ co-producing CD4+ T cells had a genomic signature of Tr1 cells, including expression of transcription factors cMAF and BATF and cell surface makers CTLA4 and LAG-3.Malaria-specific Tr1 cells were highly prevalent in primigravid Ugandan women, and their presence correlated with a higher risk of malaria in pregnancy. Understanding whether suppression of Tr1 cells plays a role in naturally acquired gravidity-dependent immunity may aid the development of new vaccines or treatments for MIP.This work was funded by NIH (PO1 HD059454, U01 AI141308, U19 AI089674, U01 AI155325, U01 AI150741), the March of Dimes (Basil O'Connor award), and the Bill and Melinda Gates Foundation (OPP 1113682).

View details for DOI 10.1016/j.ebiom.2023.104772

View details for PubMedID 37634385

View details for DOI 10.1001/jamapediatrics.2025.3561

View details for PubMedID 41021249

Abstract

Schistosomiasis is a neglected disease caused by parasitic flatworms of the genus Schistosoma and affects more than 150 million people worldwide. Praziquantel, the drug used in public health control programmes, has minimal activity against juvenile schistosomes (within 6 weeks of infection) and imperfect cure rates. We aimed to model the population-level impact of hypothetical novel drug candidates, targeting both juvenile and adult schistosomes with various efficacies, across a range of baseline epidemiological settings.In this modelling study, we used a stochastic, individual-based mechanistic model of Schistosoma mansoni infection and simulated mass drug administration control programmes in diverse epidemiological environments. These programmes involved the administration, over a 5-year period at 75% coverage, of praziquantel (single-dose or two-dose regimens) or hypothetical novel drugs with various assumed efficacies against adult and juvenile schistosome parasites: novel drug A, with equivalent efficacy to praziquantel against adult schistosomes plus perfect (100%) efficacy against juvenile schistosomes; novel drug B, with higher efficacy than praziquantel against adult schistosomes and no activity against juveniles; and novel drug C, with higher efficacy than praziquantel against adult schistosomes plus perfect efficacy against juveniles. The outcomes were median observed S mansoni infection prevalence and infection intensity over time in simulated populations.In a simulated high-endemicity setting (baseline prevalence of S mansoni infection of 53%), modelled prevalence after a single treatment was 20·8% (uncertainty interval 15·8-23·6) for single-dose praziquantel, 17·8% (15·2-19·8) for two-dose praziquantel, 18·4% (13·4-21·4) for novel drug A, 16·0% (15·0-16·8) for novel drug B, and 13·4% (12·6-14·0) for novel drug C; at year 5, modelled prevalence was 14·6% (12·2-16·4) for single-dose praziquantel, 13·6% (11·6-14·6) for two-dose praziquantel, 11·8% (9·4-13·4) for novel drug A, 12·6% (11·6-13·4) for novel drug B, and 9·6% (9·0-10·4) for novel drug C. In a simulated low-endemicity setting (baseline prevalence 15%), modelled prevalence after a single treatment was 4·8% (3·6-5·8) for single-dose praziquantel, 4·2% (3·6-5·0) for two-dose praziquantel, 4·6% (3·2-5·4) for novel drug A, 4·0% (3·4-4·6) for novel drug B, and 3·6% (3·2-4·2) for novel drug C; at year 5, modelled prevalence was 3·0% (2·2-3·6) for single-dose praziquantel, 2·8% (2·2-3·4) for two-dose praziquantel, 2·6% (1·8-3·2) for novel drug A, 2·7% (2·2-3·2) for novel drug B, and 2·2% (1·8-2·6) for novel drug C.This study provides policy-relevant data that could help to guide the development and selection of novel drugs for schistosomiasis. Novel anthelmintic drugs that can kill both adult and juvenile schistosomes with higher efficacy than praziquantel could have some public health gains in control programmes for schistosomiasis, especially in high-burden settings. Novel drugs with increased efficacy against adult schistosomes are likely to have an initial and larger impact on disease control, whereas targeting juveniles could moderately improve longer-term control outcomes.US National Institutes of Health.

View details for DOI 10.1016/j.lanmic.2024.101065

View details for PubMedID 40412412

Abstract

Widespread childhood vaccination has eliminated many infectious diseases in the US. However, vaccination rates are declining, and there are ongoing policy debates to reduce the childhood vaccine schedule, which may risk reemergence of previously eliminated infectious diseases.To estimate the number of cases and complications in the US under scenarios of declining childhood vaccination for measles, rubella, poliomyelitis, and diphtheria.A simulation model was used to assess the importation and dynamic spread of vaccine-preventable infectious diseases across 50 US states and the District of Columbia. The model was parameterized with data on area-specific estimates for demography, population immunity, and infectious disease importation risk. The model evaluated scenarios with different vaccination rates over a 25-year period. Inputs for current childhood vaccination rates were based on 2004-2023 data.The primary outcomes were estimated cases of measles, rubella, poliomyelitis, and diphtheria in the US. The secondary outcomes were estimated rates of infection-related complications (postmeasles neurological sequelae, congenital rubella syndrome, paralytic poliomyelitis, hospitalization, and death) and the probability and timing for an infection to reestablish endemicity.At current state-level vaccination rates, the simulation model predicts measles may reestablish endemicity (83% of simulations; mean time of 20.9 years) with an estimated 851 300 cases (95% uncertainty interval [UI], 381 300 to 1.3 million cases) over 25 years. Under a scenario with a 10% decline in measles-mumps-rubella (MMR) vaccination, the model estimates 11.1 million (95% UI, 10.1-12.1 million) cases of measles over 25 years, whereas the model estimates only 5800 cases (95% UI, 3100-19 400 cases) with a 5% increase in MMR vaccination. Other vaccine-preventable diseases are unlikely to reestablish endemicity under current levels of vaccination. If routine childhood vaccination declined by 50%, the model predicts 51.2 million (95% UI, 49.7-52.5 million) cases of measles over a 25-year period, 9.9 million (95% UI, 6.4-13.0 million) cases of rubella, 4.3 million cases (95% UI, 4 cases to 21.5 million cases) of poliomyelitis, and 197 cases (95% UI, 1-1000 cases) of diphtheria. Under this scenario, the model predicts 51 200 cases (95% UI, 49 600-52 600 cases) with postmeasles neurological sequelae, 10 700 cases (95% UI, 6700-14 600 cases) of congenital rubella syndrome, 5400 cases (95% UI, 0-26 300 cases) of paralytic poliomyelitis, 10.3 million hospitalizations (95% UI, 9.9-10.5 million hospitalizations), and 159 200 deaths (95% UI, 151 200-164 700 deaths). In this scenario, measles became endemic at 4.9 years (95% UI, 4.3-5.6 years) and rubella became endemic at 18.1 years (95% UI, 17.0-19.6 years), whereas poliovirus returned to endemic levels in about half of simulations (56%) at an estimated 19.6 years (95% UI, 14.0-24.7 years). There was large variation across the US population.Based on estimates from this modeling study, declining childhood vaccination rates will increase the frequency and size of outbreaks of previously eliminated vaccine-preventable infections, eventually leading to their return to endemic levels. The timing and critical threshold for returning to endemicity will differ substantially by disease, with measles likely to be the first to return to endemic levels and may occur even under current vaccination levels without improved vaccine coverage and public health response. These findings support the need to continue routine childhood vaccination at high coverage to prevent resurgence of vaccine-preventable infectious diseases in the US.

View details for DOI 10.1001/jama.2025.6495

View details for PubMedID 40272967

Abstract

Early investigation revealed a reduced risk of SARS-CoV-2 infection among social contacts of COVID-19 vaccinated individuals, referred to as indirect protection. However, indirect protection from SARS-CoV-2 infection-acquired immunity and its comparative strength and durability to vaccine-derived indirect protection in the current epidemiologic context of high levels of vaccination, prior infection, and novel variants are not well characterized. Here, we show that both vaccine-derived and infection-acquired immunity independently yield indirect protection to close social contacts with key differences in their strength and waning. Analyzing anonymized SARS-CoV-2 surveillance data from 9,625 residents in California state prisons from December 2021 to December 2022, we find that vaccine-derived indirect protection against Omicron SARS-CoV-2 infection is strongest within three months of COVID-19 vaccination [30% (95% confidence interval: 20-38%)] with subsequent modest protection. Infection-acquired immunity provides 38% (24-50%) indirect protection for 6 months after SARS-CoV-2 infection, with moderate indirect protection persisting for over one year. Variant-targeted vaccines (bivalent formulation including Omicron subvariants BA.4/BA.5) confer strong indirect protection for at least three months [40% (3-63%)]. These results demonstrate that both vaccine-derived and infection-acquired immunity can reduce SARS-CoV-2 transmission which is important for understanding long-term transmission dynamics and can guide public health intervention, especially in high-risk environments such as prisons.

View details for DOI 10.1038/s41467-024-55029-9

View details for PubMedID 39881133

View details for PubMedCentralID 9799368

View details for DOI 10.1016/S1473-3099(24)00678-9

View details for PubMedID 39455239

Abstract

Wastewater surveillance for infectious agents has proved useful in identifying the circulation of viruses within populations. We investigated the presence and concentration of human immunodeficiency virus (HIV)-1 total nucleic acids (including both viral RNA and proviral DNA) in wastewater solids. We retrospectively measured HIV-1 nucleic acids in two samples per week for 26 months at two wastewater treatment plants serving populations with different prevalences of HIV infections in San Francisco and Santa Clara County, California, USA. We detected HIV nucleic acids in a majority of samples with concentrations ranging from non-detect to 3.9 × 105 cp/g (N = 459 samples total). Concentrations of HIV-1 were significantly higher in samples from the wastewater treatment plant serving a population with a higher prevalence of people living with HIV than in the plant serving a population with a lower prevalence. The HIV-1 nucleic acids amplified were primarily DNA and thus represented proviral DNA shedding into wastewater. Additionally, we found that HIV-1 nucleic acid concentrations in wastewater solids were orders of magnitude higher than those in liquid wastewater indicating that the HIV-1 target preferentially sorbs to solids. Whether concentrations of HIV-1 in wastewater solids can be used to identify the number of incident cases remains unknown. Additional work on HIV-1 shedding from individuals with viremia and people living with HIV is needed to translate wastewater measurements into quantitative information on infections. Additional work may also be needed to document non-human sources of HIV-1 nucleic acids in wastewater.Human immunodeficiency virus (HIV)-1 has infected nearly 100 million people since it emerged in the 1980s. Antiretroviral therapy prevents transmission of HIV and also allows infected individuals to live healthy lives with normal life expectancy. Consequently, identifying unrecognized cases of HIV is of paramount importance. Since wastewater represents a composite biological sample from a community, it may provide valuable information on HIV-1 prevalence that can be used to inform HIV testing and outreach.

View details for DOI 10.1128/aem.01477-24

View details for PubMedID 39526804

Abstract

Respiratory syncytial virus (RSV) is a leading cause of respiratory illness and hospitalization, but clinical surveillance detects only a minority of cases. Wastewater surveillance could determine the onset and extent of RSV circulation in the absence of sensitive case detection, but to date, studies of RSV in wastewater are few. We measured RSV RNA concentrations in wastewater solids from 176 sites during the 2022-2023 RSV season and compared those to publicly available RSV infection positivity and hospitalization rates. Concentrations ranged from undetectable to 107 copies per gram. RSV RNA concentration aggregated at state and national levels correlated with infection positivity and hospitalization rates. RSV season onset was determined using both wastewater and clinical positivity rates using independent algorithms for 14 states where both data were available at the start of the RSV season. In 4 of 14 states, wastewater and clinical surveillance identified RSV season onset during the same week; in 3 states, wastewater onset preceded clinical onset, and in 7 states, wastewater onset occurred after clinical onset. Wastewater concentrations generally peaked in the same week as hospitalization rates but after case positivity rates peaked. Differences in onset and peaks in wastewater versus clinical data may reflect inherent differences in the surveillance approaches.

View details for DOI 10.1021/acsestwater.3c00725

View details for PubMedID 38633368

View details for PubMedCentralID PMC11019535

Abstract

BACKGROUND: Standard pediatric growth curves cannot be used to impute missing height or weight measurements in individual children. The Michaelis-Menten equation, used for characterizing substrate-enzyme saturation curves, has been shown to model growth in many organisms including nonhuman vertebrates. We investigated whether this equation could be used to interpolate missing growth data in children in the first three years of life and compared this interpolation to several common interpolation methods and pediatric growth models.METHODS: We developed a modified Michaelis-Menten equation and compared expected to actual growth, first in a local birth cohort (N=97) then in a large, outpatient, pediatric sample (N=14,695).RESULTS: The modified Michaelis-Menten equation showed excellent fit for both infant weight (median RMSE: boys: 0.22kg [IQR:0.19; 90%<0.43]; girls: 0.20kg [IQR:0.17; 90%<0.39]) and height (median RMSE: boys: 0.93cm [IQR:0.53; 90%<1.0]; girls: 0.91cm [IQR:0.50;90%<1.0]). Growth data were modeled accurately with as few as four values from routine well-baby visits in year 1 and seven values in years 1-3; birth weight or length was essential for best fit. Interpolation with this equation had comparable (for weight) or lower (for height) mean RMSE compared to the best performing alternative models.CONCLUSIONS: A modified Michaelis-Menten equation accurately describes growth in healthy babies aged 0-36months, allowing interpolation of missing weight and height values in individual longitudinal measurement series. The growth pattern in healthy babies in resource-rich environments mirrors an enzymatic saturation curve.

View details for DOI 10.1186/s12874-024-02145-1

View details for PubMedID 38302887

View details for DOI 10.31478/202310a

View details for PubMedID 38784640

View details for PubMedCentralID PMC11114596

Abstract

Although oral temperature is commonly assessed in medical examinations, the range of usual or "normal" temperature is poorly defined.To determine normal oral temperature ranges by age, sex, height, weight, and time of day.This cross-sectional study used clinical visit information from the divisions of Internal Medicine and Family Medicine in a single large medical care system. All adult outpatient encounters that included temperature measurements from April 28, 2008, through June 4, 2017, were eligible for inclusion. The LIMIT (Laboratory Information Mining for Individualized Thresholds) filtering algorithm was applied to iteratively remove encounters with primary diagnoses overrepresented in the tails of the temperature distribution, leaving only those diagnoses unrelated to temperature. Mixed-effects modeling was applied to the remaining temperature measurements to identify independent factors associated with normal oral temperature and to generate individualized normal temperature ranges. Data were analyzed from July 5, 2017, to June 23, 2023.Primary diagnoses and medications, age, sex, height, weight, time of day, and month, abstracted from each outpatient encounter.Normal temperature ranges by age, sex, height, weight, and time of day.Of 618 306 patient encounters, 35.92% were removed by LIMIT because they included diagnoses or medications that fell disproportionately in the tails of the temperature distribution. The encounters removed due to overrepresentation in the upper tail were primarily linked to infectious diseases (76.81% of all removed encounters); type 2 diabetes was the only diagnosis removed for overrepresentation in the lower tail (15.71% of all removed encounters). The 396 195 encounters included in the analysis set consisted of 126 705 patients (57.35% women; mean [SD] age, 52.7 [15.9] years). Prior to running LIMIT, the mean (SD) overall oral temperature was 36.71 °C (0.43 °C); following LIMIT, the mean (SD) temperature was 36.64 °C (0.35 °C). Using mixed-effects modeling, age, sex, height, weight, and time of day accounted for 6.86% (overall) and up to 25.52% (per patient) of the observed variability in temperature. Mean normal oral temperature did not reach 37 °C for any subgroup; the upper 99th percentile ranged from 36.81 °C (a tall man with underweight aged 80 years at 8:00 am) to 37.88 °C (a short woman with obesity aged 20 years at 2:00 pm).The findings of this cross-sectional study suggest that normal oral temperature varies in an expected manner based on sex, age, height, weight, and time of day, allowing individualized normal temperature ranges to be established. The clinical significance of a value outside of the usual range is an area for future study.

View details for DOI 10.1001/jamainternmed.2023.4291

View details for PubMedID 37669046

Abstract

Understanding the relationship between antibiotic use and the evolution of antimicrobial resistance is vital for effective antibiotic stewardship. Yet, animal models and in vitro experiments poorly replicate real-world conditions1. To explain how resistance evolves in vivo, we exposed 60 human participants to ciprofloxacin and used longitudinal stool samples and a new computational method to assemble the genomes of 5,665 populations of commensal bacterial species within participants. Analysis of 2.3 million polymorphic sequence variants revealed 513 populations that underwent selective sweeps. We found convergent evolution focused on DNA gyrase and evidence of dispersed selective pressure at other genomic loci. Roughly 10% of susceptible bacterial populations evolved towards resistance through sweeps that involved substitutions at a specific amino acid in gyrase. The evolution of gyrase was associated with large populations that decreased in relative abundance during exposure. Sweeps persisted for more than 10 weeks in most cases and were not projected to revert within a year. Targeted amplification showed that gyrase mutations arose de novo within the participants and exhibited no measurable fitness cost. These findings revealed that brief ciprofloxacin exposure drives the evolution of resistance in gut commensals, with mutations persisting long after exposure. This study underscores the capacity of the human gut to promote the evolution of resistance and identifies key genomic and ecological factors that shape bacterial adaptation in vivo.

View details for DOI 10.1038/s41586-025-08781-x

View details for PubMedID 40269166

View details for PubMedCentralID 2730242

Abstract

We evaluated large language model (LLM)-based agents integrated with the electronic medical record to assess blood culture appropriateness. While sensitivity was high, specificity remained low. Performance was shaped by prompt phrasing, sycophantic behavior, and semantic triggers, reflecting both the potential and limitations of LLMs in real-world clinical decision support.

View details for DOI 10.1017/ice.2025.10349

View details for PubMedID 41216923

View details for DOI 10.1017/ash.2025.10077

View details for Web of Science ID 001554694400001

Abstract

To evaluate the effectiveness and acceptability of ventilation interventions in naturally ventilated hospitals in Liberia.Difference-in-differences analysis of pre- and post-air changes per hour of intervention and control spaces.Hospitals in Bong and Montserrado Counties, Liberia.Seventy patient care spaces were evaluated at baseline. Six spaces underwent physical intervention modifications, while 2 spaces were assessed for indirect effects and 2 others used as controls. Healthcare workers were interviewed to assess ventilation knowledge and acceptability.Ventilation interventions included the installation of window screens, louvered doors and windows, and wind turbines.We measured carbon dioxide levels with portable meters and documented persons per room to estimate per-person ventilation rates in both L/s/person for the initial assessment and air changes per hour (ACH) in the intervention. Measurements were taken in patient care spaces in 7 hospitals in Liberia. Healthcare worker acceptability was evaluated via structured interviews.Two-thirds (46/70) of patient care spaces were below the WHO-recommended ventilation threshold of 60 L/s/person. Six spaces underwent ventilation interventions, including placement of window screens (3), wind turbines (2), and louvered doors and windows (1), with 2 additional spaces being indirectly affected by these interventions and 2 more spaces serving as controls. Ventilation improved by an average of 2 ACH in the spaces with wind turbines and louvered doors and windows. Overall acceptability of the interventions was high.Implementing interventions to improve ventilation in naturally ventilated healthcare facilities is efficacious, feasible, and acceptable, though longer-term evaluations should assess sustainability.

View details for DOI 10.1017/ash.2025.10077

View details for PubMedID 40893129

View details for PubMedCentralID PMC12394025

Abstract

We analyzed the diagnostic yield of repeat urine cultures in a retrospective study of adult inpatients. Most urine cultures repeated at less than 6 days provided redundant information. This was true whether the index culture was positive or negative, and whether the threshold for positivity was 10,000 or 100,000 CFU/mL.

View details for DOI 10.1017/ice.2025.10248

View details for PubMedID 40833079

Abstract

We investigated the accuracy and completeness of four large language model (LLM) artificial intelligence tools. Most LLMs provided acceptable answers to commonly asked infection prevention questions (accuracy 98.9%, completeness 94.6%). The use of LLMs to supplement infection prevention consults should be further explored.

View details for DOI 10.1017/ice.2024.205

View details for PubMedID 39664019

Abstract

Antimicrobial resistance poses a significant threat to the sustainability of effective treatments against the three most prevalent infectious diseases: malaria, human immunodeficiency virus (HIV) infection and tuberculosis. Therefore, there is an urgent need to develop novel drugs and treatment protocols capable of reducing the emergence of resistance and combating it when it does occur. In this Review, we present an overview of the status and underlying molecular mechanisms of drug resistance in these three diseases. We also discuss current strategies to address resistance during the research and development of next-generation therapies. These strategies vary depending on the infectious agent and the array of resistance mechanisms involved. Furthermore, we explore the potential for cross-fertilization of knowledge and technology among these diseases to create innovative approaches for minimizing drug resistance and advancing the discovery and development of new anti-infective treatments. In conclusion, we advocate for the implementation of well-defined strategies to effectively mitigate and manage resistance in all interventions against infectious diseases.

View details for DOI 10.1038/s41573-024-00933-4

View details for PubMedID 38750260

View details for PubMedCentralID 9490302

Abstract

Dolutegravir (DTG) is a cornerstone of global antiretroviral (ARV) therapy (ART) due to its high efficacy and favorable tolerability. However, limited data exist regarding the risk of emergent integrase strand transfer inhibitor (INSTI) drug-resistance mutations (DRMs) in individuals receiving DTG-containing ART.We performed a PubMed search using the term "Dolutegravir", last updated 18 December 2023, to estimate the prevalence of VF with emergent INSTI DRMs in people living with HIV (PLWH) without previous VF on an INSTI who received DTG-containing ART.Of 2131 retrieved records, 43 clinical trials, 39 cohorts, and 6 cross-sectional studies provided data across 6 clinical scenarios based on ART history, virological status, and co-administered ARVs: (1) ART-naïve PLWH receiving DTG plus two NRTIs; (2) ART-naïve PLWH receiving DTG plus lamivudine; (3) ART-experienced PLWH with VF on a previous regimen receiving DTG plus two NRTIs; (4) ART-experienced PLWH with virological suppression receiving DTG plus two NRTIs; (5) ART-experienced PLWH with virological suppression receiving DTG and a second ARV; and (6) ART-experienced PLWH with virological suppression receiving DTG monotherapy. The median proportion of PLWH in clinical trials with emergent INSTI DRMs was 1.5% for scenario 3 and 3.4% for scenario 6. In the remaining four trial scenarios, VF prevalence with emergent INSTI DRMs was ≤0.1%. Data from cohort studies minimally influenced prevalence estimates from clinical trials, whereas cross-sectional studies yielded prevalence data lacking denominator details.In clinical trials, the prevalence of VF with emergent INSTI DRMs in PLWH receiving DTG-containing regimens has been low. Novel approaches are required to assess VF prevalence with emergent INSTI DRMs in PLWH receiving DTG in real-world settings.

View details for DOI 10.3390/v16030399

View details for PubMedID 38543764

View details for PubMedCentralID PMC10975848

Abstract

Author summary Human immunodeficiency virus (HIV) drug resistance has implications for antiretroviral treatment strategies and for containing the HIV pandemic because the development of HIV drug resistance leads to the requirement for antiretroviral drugs that may be less effective, less well-tolerated, and more expensive than those used in first-line regimens. HIV drug resistance studies are designed to determine which HIV mutations are selected by antiretroviral drugs and, in turn, how these mutations affect antiretroviral drug susceptibility and response to future antiretroviral treatment regimens. Such studies collectively form a vital knowledge base essential for monitoring global HIV drug resistance trends, interpreting HIV genotypic tests, and updating HIV treatment guidelines. Although HIV drug resistance data are collected in many studies, such data are often not publicly shared, prompting the need to recommend best practices to encourage and standardize HIV drug resistance data sharing. In contrast to other viruses, sharing HIV sequences from phylogenetic studies of transmission dynamics requires additional precautions as HIV transmission is criminalized in many countries and regions. Our recommendations are designed to ensure that the data that contribute to HIV drug resistance knowledge will be available without undue hardship to those publishing HIV drug resistance studies and without risk to people living with HIV.

View details for DOI 10.1371/journal.pmed.1004293

View details for PubMedID 37738247

Abstract

Background: Dolutegravir (DTG)-based antiretroviral therapy (ART) rarely leads to virological failure (VF) and drug resistance in integrase strand transfer inhibitor (INSTI)-naïve persons living with HIV (PLWH). As a result, limited data are available on INSTI-associated drug resistance mutations (DRMs) selected by DTG-containing ART regimens. Methods: We reviewed studies published through July 2023 to identify those reporting emergent major INSTI-associated DRMs in INSTI-naïve PLWH receiving DTG and those containing in vitro DTG susceptibility results using a standardized assay. Results: We identified 36 publications reporting 99 PLWH in whom major nonpolymorphic INSTI-associated DRMs developed on a DTG-containing regimen and 21 publications containing 269 in vitro DTG susceptibility results. DTG-selected DRMs clustered into four largely non-overlapping mutational pathways characterized by mutations at four signature positions: R263K, G118R, N155H, and Q148H/R/K. Eighty-two (82.8%) viruses contained just one signature DRM, including R263K (n = 40), G118R (n = 24), N155H (n = 9), and Q148H/R/K (n = 9). Nine (9.1%) contained ≥1 signature DRM, and eight (8.1%) contained just other DRMs. R263K and G118R were negatively associated with one another and with N155H and Q148H/K/R. R263K alone conferred a median 2.0-fold (IQR: 1.8-2.2) reduction in DTG susceptibility. G118R alone conferred a median 18.8-fold (IQR:14.2-23.4) reduction in DTG susceptibility. N155H alone conferred a median 1.4-fold (IQR: 1.2-1.6) reduction in DTG susceptibility. Q148H/R/K alone conferred a median 0.8-fold (IQR: 0.7-1.1) reduction in DTG susceptibility. Considerably higher levels of reduced susceptibility often occurred when signature DRMs occurred with additional INSTI-associated DRMs. Conclusions: Among INSTI-naïve PLWH with VF and treatment emergent INSTI-associated DRMs, most developed one of four signature DRMs, most commonly R263K or G118R. G118R was associated with a much greater reduction in DTG susceptibility than R263K.

View details for DOI 10.3390/v15091932

View details for PubMedID 37766338

View details for PubMedCentralID PMC10536831

Abstract

HIV-1 DNA exists in nonintegrated linear and circular episomal forms and as integrated proviruses. In patients with plasma viremia, most peripheral blood mononuclear cell (PBMC) HIV-1 DNA consists of recently produced nonintegrated virus DNA while in patients with prolonged virological suppression (VS) on antiretroviral therapy (ART), most PBMC HIV-1 DNA consists of proviral DNA produced months to years earlier. Drug-resistance mutations (DRMs) in PBMCs are more likely to coexist with ancestral wild-type virus populations than they are in plasma, explaining why next-generation sequencing is particularly useful for the detection of PBMC-associated DRMs. In patients with ongoing high levels of active virus replication, the DRMs detected in PBMCs and in plasma are usually highly concordant. However, in patients with lower levels of virus replication, it may take several months for plasma virus DRMs to reach detectable levels in PBMCs. This time lag explains why, in patients with VS, PBMC genotypic resistance testing (GRT) is less sensitive than historical plasma virus GRT, if previous episodes of virological failure and emergent DRMs were either not prolonged or not associated with high levels of plasma viremia. Despite the increasing use of PBMC GRT in patients with VS, few studies have examined the predictive value of DRMs on the response to a simplified ART regimen. In this review, we summarize what is known about PBMC HIV-1 DNA dynamics, particularly in patients with suppressed plasma viremia, the methods used for PBMC HIV-1 GRT, and the scenarios in which PBMC GRT has been used clinically.

View details for DOI 10.1128/cmr.00052-22

View details for PubMedID 36102816