OBJECTIVES:Increased blood leukocytes are associated with all-cause mortality and death from coronary disease and cancer in the general population. Limited information is available in people with HIV. METHODS:We analyzed blood leukocytes in 1850 participants of the Swiss HIV Cohort Study who died (2000-2023) and 1850 matched controls (median age at death 52 years, 77% male, 77% with suppressed HIV RNA on antiretroviral therapy). We assessed uni-/multivariable odds ratios (OR) for all-cause mortality, considering major clinical and HIV-related mortality risk factors, leukocytes measured >1 year before death (primary analysis) and in the latest available blood sample, and potential confounders for leukocytes. RESULTS:Leukocytes showed a U-shaped association with mortality. At a median of 433 (interquartile range [IQR], 396-495) days before death, multivariable-adjusted OR for death in the highest (leukocytes ≥7730/μL) vs. middle quintile (leukocytes 5290-6260/μL) was 1.56 (95% confidence interval, 1.20-2.02). Multivariable-adjusted OR in the lowest (leukocytes ≤4250/μL) vs. middle leukocyte quintile was 1.51 (1.14-2.01). For comparison, death-OR for hypertension, diabetes and current smoking were 1.27 (1.06-1.53), 1.91 (1.41-2.57), and 2.72 (2.14-3.45), respectively. Leukocytosis was uncommon (cases, 4.4% vs. controls, 2.3%; p = 0.004). The effect size of the highest leukocyte quintile increased in the latest blood sample (median 86 [IQR], 43-152 days before death; OR=1.99 [1.44-2.76]). High leukocytes were associated with death from non-AIDS/non-hepatic cancer, cardiovascular, and respiratory causes. Low leukocytes were associated with liver-related death. CONCLUSIONS:High leukocytes, measured >1 year before death and mostly within the normal range, are independently associated with mortality in people with HIV in Switzerland.

The relatively slow mutation rates of bacterial pathogens impose severe limitations on phylodynamic analysis of bacterial outbreaks. However, whole-genome sequencing may enable accurate inference of bacterial transmission dynamics in health-care settings. We simulated the epidemic dynamics of a Staphylococcus aureus lineage using a stochastic model with a hospital and community compartment connected by patient admission and discharge. We generated synthetic genomic sequences and performed Bayesian phylodynamic inference on a proportion of samples from each simulated outbreak. When samples are obtained from both compartments, hospital transmission rate ([Formula: see text]) and community transmission rate ([Formula: see text]) are accurately estimated, if [Formula: see text] is on the same scale as the discharge rate. If [Formula: see text] is substantially lower than the discharge rate, a robust quantification of within-hospital transmission dynamics is challenging. Excluding samples from the community resulted in a notable underestimation of [Formula: see text] when [Formula: see text]. When transmission was 'community-driven', but sampling was restricted to hospital cases only, estimates are closer to the true [Formula: see text], if hospital sampling proportion is known. Otherwise, [Formula: see text] estimates reflected the transmission dynamics within the community. When using genomic data to estimate bacterial transmission rates in a health-care setting, it is essential to take into account the surrounding community. Many infections related to nosocomial outbreaks will not be observed within the hospital due to fast discharge rates. In the absence of usable genomic data from the community, alternative estimates of community transmission rates from publicly available data should be incorporated. Transmission rate estimates from nosocomial genomes alone need to be interpreted with care.

Pneumocystis jirovecii (PJ) causes pneumonia primarily in immunocompromised individuals. Although direct immunofluorescence (IF) remains widely used in routine diagnostics, PCR assays are increasingly being adopted because they offer higher sensitivity and reduced observer dependency. This study evaluates the ELITe InGenius PJ PCR assay compared with IF for PJ detection in respiratory specimens. Respiratory samples submitted for IF-based PJ testing at the University Hospital Zurich over a 19-month period were retrospectively analyzed using the ELITe InGenius PCR assay. Diagnostic accuracy was assessed using IF as the reference method, and performance was evaluated by receiver operating characteristic (ROC) analysis. A total of 222 samples from 213 patients were included (70 sputum, 152 bronchoalveolar lavage). PCR and IF results were concordant in 175 (78.8

Expanded access to dolutegravir as part of a fixed-dose combination with tenofovir disoproxil fumarate and lamivudine (TLD) has revolutionized global human immunodeficiency virus (HIV) treatment, with more than 25 million people prescribed this regimen in 2024. We reviewed national clinical guidelines for management of virologic failure on first-line TLD in the 50 countries with the highest prevalence of HIV among adults; recent guidelines were not available online for four. Among the remaining 46 country guidelines, we identified four distinct approaches: (1) empiric switch to a protease inhibitor (PI)-based regimen without genotypic resistance testing (GRT) (n = 28; 61%); (2) GRT to guide antiretroviral therapy selection (n = 14; 30%); (3) continuation of TLD without GRT (n = 3; 7%); and (4) empiric switch to a PI-based regimen with concurrent GRT (n = 1; 2%). The diversity of guideline-endorsed approaches underscores the critical need for additional data to inform policy regarding this important clinical scenario.

Abstract Background Vaccination of people with HIV (PWH) on suppressive antiretroviral therapy (ART) represents a novel approach for evaluating candidate broadly neutralizing antibody (bnAb) immunogens for preventive and therapeutic HIV vaccines. Given pre-existing immunity in PWH, the safety of this approach requires careful assessment prior to broader application. Here, we report on the design and safety of the RENEW-SHCS study which evaluates the immunization of PWH with BG505 SOSIP.v4.1-GT1.1, an immunogen engineered to induce precursors of CD4 binding site (CD4bs)- and V2-apex targeting bnAbs. Methods RENEW-SHCS is a phase I, open-label, non-randomized vaccination trial evaluating a single dose of the recombinant germline-targeting envelope trimer BG505 SOSIP.v4.1-GT1.1 (GT1.1), adjuvanted with 3M052-AF and Aluminum hydroxide (alum), in PWH on suppressive ART enrolled from the Swiss HIV Cohort Study. Participants were previously classified as bnAb or non-neutralizing antibody (nnAb) inducers, with a target enrollment of 15 per group, and were monitored for safety and immunogenicity for 24 weeks while continuing standard ART. Due to an out-of-specification stability measurement of adjuvant 3M052-AF the trial was paused after 23 immunizations and subjected to an unscheduled interim safety and reactogenicity assessment comprising protocol defined outcome measures (adverse events, clinical laboratory measurements and HIV-1 viral load). Results Twenty-three participants (10 bnAb and 13 nnAb inducers, median age 59 years, 17 male / 6 female) were vaccinated between March and August 2025 before interruption of the trial. All participants completed follow-up with full protocol adherence. The interim-safety analysis confirmed that no vaccine-related serious adverse events occurred. Solicited local (96%) and systemic (83%) reactions were common, predominantly grade 1–2, transient, and self-limited. Transient laboratory changes occurred but mostly remained within the normal range, with no vaccine-related grade 3 abnormalities. We observed predominantly transient local and systemic reactions, which were similar or milder to the reactogenicity profile reported for immunization of adult people without HIV (PWOH) with GT1.1 adjuvanted with AS01b reported in the IAVI C101 trial. No viral rebound under ART occurred. One participant experienced two viral blips (>50 HIV-1 RNA copies/ml), one before and one 16 weeks after vaccination with subsequent re-suppression. All others maintained viral suppression (<50 copies/ml) throughout follow-up. Conclusion RENEW-SHCS demonstrated a favorable safety and reactogenicity profile of single dose immunization with GT1.1 in PWH, comparable to that observed in PWOH. The findings of this phase I study support the feasibility of vaccinating ART-treated PWH in trials of preventive and therapeutic HIV vaccine strategies. Trial registration SNCTP000006192 | BASEC2024-01623. ClinicalTrials.gov NCT07769983

Background:Studies in Switzerland and other settings have reported minimal pretreatment integrase strand transfer inhibitor (INSTI) resistance, but many were conducted before widespread use of INSTIs or are limited regarding data availability and representativeness. Consequently, many questions remain regarding the transmissibility of INSTI drug resistance mutations (DRMs). Methods:In sequences predating antiretroviral therapy (ART) initiation collected in the Swiss HIV Cohort Study (SHCS) resistance database, we assessed INSTI DRMs using the Stanford HIV database algorithm. We use bayesian regression models to assess INSTI DRM trends, as well as epidemiological clustering. Models are adjusted for age, sex, HIV subtype, and time as a spline, with random effects for the SHCS center of registration and the sequencing laboratory. Results:In total, 3704 SHCS participants had an integrase sequence before ART initiation; 213 (5.8%) had INSTI DRMs, including 11 (0.3%) with major INSTI DRMs. The most common DRMs were the polymorphic accessory INSTI DRMs E157Q, T97A, and L74M. There was no change in the probability of detecting INSTI DRM(s) over the past 3 decades. Epidemiological clustering was similar between individuals with or without pre-ART INSTI DRMs; however, the clusters they formed were smaller, particularly before 2010. Conclusions:This study demonstrates that in Switzerland pre-ART INSTI DRMs are very rare, despite INSTIs being used for more than 10 years. In cases where pre-ART INSTI DRMs are detected, information on the context in which they emerged is rarely available, highlighting the need for continued genetic surveillance, particularly in the face of increasing numbers of individuals with INSTI resistance globally.

People with human immunodeficiency virus (PWH) exhibit accelerated aging and a higher prevalence of aging-related conditions, despite effective antiretroviral therapy. The biological mechanisms involved remain incompletely understood. Integrating genomic and metabolomic profiling may help uncover genes and pathways contributing to aging-related disease in this population. Using a genome-wide association study framework and untargeted metabolomic profiling, we searched for associations between human genetic variants and the plasma concentrations of 1,930 putative metabolites in 1,244 individuals enrolled in the Swiss HIV Cohort Study. We performed an expression quantitative trait locus (eQTL) colocalization analysis to explore biological links between genetic variants and metabolites and used Mendelian randomization to search for causal relationships between metabolites and agingrelated diseases. We identified 27 metabolites significantly associated with 12 genetic loci, including genes encoding the metabolic enzymes NAT8 and FUT2; 10 associations had been previously reported in general-population studies, of which eight were replicated in our analysis. The colocalization analyses provided evidence for a large overlap between genetic regulation of mRNA expression and metabolite levels, while Mendelian randomization suggested several causal effects. Our study uncovered genetic-metabolic associations observed in PWH and explored their biological relevance. These findings highlight the potential of integrated multi-omics profiling to deepen mechanistic understanding and inform future precision approaches to comorbidity management in this population.

BACKGROUND:Integrase mutations associated with dolutegravir resistance have been well characterized, but based on limited data from non-B subtypes. OBJECTIVES:We aim to identify potential integrase mutations not currently classified as integrase strand transfer inhibitor (INSTI) resistance mutations (DRMs) in individuals with viremia on dolutegravir-based regimens. METHODS:We included integrase sequences from DTG RESIST study sites in African countries. These were interpreted using Stanford HIVdb v9.8. We used a viral genome-wide association study-like approach restricted to the integrase region (INT-WAS) to identify mutations not classified as major or accessory INSTI DRMs but occurring more frequently in sequences carrying major INSTI DRMs than in those without major INSTI DRMs. We performed the same INT-WAS analysis with drug-naïve sequences from the Los Alamos HIV-1 database to test whether these identified mutations were enriched among sequences from individuals with viraemia whilst receiving DTG-based treatment. RESULTS:Among 382 sequences, 104 (27.2%) showed at least intermediate dolutegravir resistance. Twelve integrase mutations not classified as major or accessory DRMs (S39R, L45I, I72L, L74I, V79I, I113V, S119R, K156N, I208M, T218M, A265V, and R284G) were significantly associated with predicted DTG resistance. Among them, V79I [adjusted odds ratio (aOR) 167.1, 95% credible interval (CrI) 17.9-2947.6] and I72L (aOR 65.6, 95% CrI 6.6-1273.7) were strongly associated. S39R, L45I, V79I, S119R, and K156N were linked to established INSTI resistance pathways, and I72L, L74I, V79I, K156N, I208M, and R284G were overrepresented in sequences from viraemic individuals on DTG-based treatment relative to drug-naïve sequences. CONCLUSIONS:We identified several amino acid substitutions outside the established DRMs that are strongly associated with predicted dolutegravir resistance. Dolutegravir resistance evolution is complex and likely involves mutations not currently classified as DRMs.

Numerous factors may influence the optimal rollout of new gonococcal antibiotics. We compared 8 rollout strategies using a gonorrhea transmission model and ranked strategies by the number of gonococcal infections and clinically useful antibiotic lifespan. Rankings were most sensitive to the starting ceftriaxone resistance prevalence and screening frequency.

The microbiome actively influences antimicrobial resistance (AMR) dynamics by shaping both ecological and evolutionary processes. However, the extent of its role in resistance emergence, transmission and persistence remains unclear. Traditional AMR research has mainly focused on genetic mechanisms and pathogen-level dynamics. In contrast, the intersection of AMR and the microbiome, including resistance-gene reservoirs, microbial competition and community-mediated selection, remains poorly represented, especially in a modelling context. Here we present a structured framework for incorporating microbiome-AMR interactions into predictive models. We identify key microbiome-mediated processes shaping AMR across different levels of complexity, describe how these can be quantitatively integrated into models, and identify critical data gaps that limit current approaches. By bridging microbiome ecology, AMR biology and mathematical modelling, we set out research priorities and strategies to improve resistance prediction and guide microbiome-targeted interventions.

OBJECTIVES:To improve estimation of cohort coverage in the Swiss HIV Cohort Study (SHCS) using a data triangulation framework that compares SHCS data with multiple external data sources. DESIGN:Retrospective longitudinal analysis of the SHCS. METHODS:Cohort coverage of HIV diagnoses, AIDS diagnoses, and antiretroviral therapy (ART) uptake was triangulated across SHCS data (1985-2023), national HIV/AIDS surveillance (1985-2023), longitudinal antiretroviral therapy (ART) sales data (2017-2024), and a targeted literature comparison. Temporal trends in cohort coverage were assessed, and demographic representativeness was evaluated by sex, age, HIV acquisition mode, and region. Mean cohort coverage estimates were calculated for three outcomes: HIV and AIDS diagnoses (Step 1) and ART uptake (Step 2). RESULTS:Over 38 years, mean SHCS coverage was 62.4% for HIV diagnoses, 74.0% for AIDS, and 64.9% for ART uptake, consistent with literature-based estimates. Coverage of HIV diagnoses declined in recent years, and geographical heterogeneity was observed. The SHCS remained broadly representative across most subgroups; however, females, older adults, and people with heterosexually acquired HIV or using psychoactive substances were underrepresented, while people on single-tablet and salvage ART regimens were overrepresented. CONCLUSIONS:A data triangulation framework provides a practical approach for monitoring cohort coverage and representativeness. While the SHCS captures a broadly representative sample of diagnosed individuals, tailored strategies are needed to improve inclusion of underrepresented subgroups and maintain cohort coverage. Sustained monitoring is essential to ensure that cohort-based research remains generalizable and continues to inform clinical care and public health responses in Switzerland and beyond.

Microbiota composition influences methicillin-resistant S aureus (MRSA) colonization, yet the contribution of the oral microbiota and the impact of decolonization approaches remain insufficiently explored. In this study, we report microbiota shifts in 3 adults with oral MRSA colonization who underwent decolonization treatment, including povidone-iodine. Relative bacterial abundances fluctuated across oral sites and over time, indicating distinct ecological responses to treatment. These findings improve our understanding of how the oral microbiota may affect MRSA decolonization and highlight the importance of oral microbial dynamics to guide more personalized and effective strategies.

Autoantibodies neutralizing type-I interferons (AAN-I-IFNs) emerge as global, common, and strong determinants of a growing number of severe viral diseases. We report that AAN-I-IFNs+ patients with life-threatening COVID-19 pneumonia harbor circulating type-I IFN-specific B cells indistinguishable from patients bearing T cell tolerance defects of genetic origin. This autoimmune response mobilizes a highly diverse and stable circulating B cell response that is detected prior to severe viral infection and acquires high affinity and neutralization potential to type-I IFNs through extended somatic hypermutation. X-ray crystallography and AlphaFold3 structural analysis of hundreds of patient-derived monoclonal antibodies reveals the extended breadth of this response, targeting three major B cell epitopes covering all facets of type-I IFNs. These findings support a model in which a germinal-center-derived memory B cell response directed against type-I IFNs is established before severe viral infection, providing a core mechanism linking T cell tolerance defect to pathogenic AAN-I-IFNs underlying severe viral diseases.

ABSTRACT Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) is a major antimicrobial resistance concern spreading across human, animal, and environmental domains. To assess between-source transitions, we analyzed 762 ESBL-E. coli genomes collected from wastewater (used as a community shedding indicator), clinical settings, cattle, and wildlife across Switzerland (2021–2023). ST131 was the most prevalent sequence type (ST), and 76% of isolates carried resistance to at least two antibiotic classes in addition to β-lactams. Phylogenetic analysis showed isolates were interspersed across sources, yet genetically similar strains were more common within compartments. Clonal isolates (0 SNPs) were rarely shared (n = 2) between wastewater and corresponding clinics. Ancestral state reconstruction revealed compartmentalization of isolates between wastewater and clinics across the whole phylogeny. However, this pattern disappears within human-associated ST131, ST69, and ST1193, highlighting exchange between clinics and communities. These findings show that wastewater surveillance captures community circulation of ESBL-E. coli, which overlaps with circulating clinically relevant strains.IMPORTANCEExtended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) is a major antimicrobial resistance concern globally, with ready transmission between people, animals, and the environment. Understanding transmission patterns among reservoirs can help inform risks and inform intervention strategies. To date, surveillance is heavily reliant on aggregation of clinical data, resulting in limited insights on ESBL-E. coli circulation in the population. Wastewater-based surveillance has emerged as a powerful tool to understand epidemiology of antimicrobial resistance circulating in communities, thereby complementing clinical surveillance approaches. Here, we demonstrate integrated surveillance of ESBL-E. coli isolates across sectors using whole genome sequencing, providing an opportunity to understand exchange of bacterial isolates between clinics, communities, livestock, and wildlife.

Background:People with human immunodeficiency virus type 1 (HIV-1; PWH) on antiretroviral therapy (ART) and suppressed viremia usually experience a decrease in HIV DNA over time, but about 25% experience an increase. Some also experience intermittent viremia. The reasons for and potential clinical implications of increases in the HIV reservoir remain unclear and a major concern. Methods:In this study, we longitudinally characterized the proviral landscape in 4 distinct groups of PWH (n = 40) successfully treated with ART over 10.4 years without any viral failure, presenting either an increase or decrease of total HIV DNA levels and experiencing or not experiencing intermittent viremia, by intact proviral DNA assay and near-full-length HIV proviral sequencing in bulk and on the single proviral level. Results:A decrease in intact proviruses was observed in all groups, independent of total HIV DNA level dynamics and viral load kinetics by both intact proviral DNA assay and single proviral sequencing. Genetic distances and diversities of individuals' proviral sequences did not increase over time in any group. Although new drug resistance mutations were occasionally observed in proviral DNA, numbers did not differ significantly between the groups. Conclusions:Our results show that the increase in HIV DNA levels is driven by an increase in defective proviruses, also in PWH experiencing intermittent viremia. Furthermore, we did not see evidence of evolution of the HIV reservoir, regardless of HIV reservoir size dynamics and viral load kinetics over a follow-up period of 10 years with ART. Nevertheless, PWH with intermittent viremia should be monitored frequently.

Large language models (LLMs) are emerging as tools to support clinical decision making. HIV management is a compelling use case due to its complexity and dynamic nature, involving diverse treatment options, comorbidities, and adherence challenges. However, integrating LLMs into clinical practice raises concerns about accuracy, safety, and clinician acceptance. Despite growing interest, their performance in HIV care remains poorly studied, and benchmarking is lacking. We developed HIVMedQA, a clinician-curated benchmark of HIV-related open-ended medical question-answer pairs spanning basic knowledge, clinical reasoning, complex patient vignettes, and bias-modified scenarios. We evaluated seven general-purpose and three medical LLMs. Performance was assessed using lexical similarity and an extended medical LLM-as-a-judge framework capturing key clinical dimensions, including question comprehension, reasoning, knowledge recall, bias, potential harm, and factual accuracy, to better capture nuances relevant to the medical domain, with additional evaluation by HIV-experienced physicians. Performance varies substantially across models and task complexity. Gemini 2.5 Pro achieves the highest overall scores, followed by Claude 3.5 Sonnet and MedGemma-27B. Knowledge recall is generally stronger than question comprehension or clinical reasoning. Medical LLMs do not consistently outperform general-purpose models, and model size alone does not predict performance. Several models are sensitive to cognitive bias prompts. LLM-as-a-judge scoring aligns better with clinician assessment than lexical metrics. HIVMedQA provides a structured benchmark for evaluating LLMs in HIV clinical decision support. Current LLMs show promise, but limitations in reasoning, bias robustness, and safety indicate that careful validation, domain-specific evaluation, and clinician oversight remain essential before clinical deployment. Large language models are increasingly being explored to support clinical decision-making, particularly where specialist access is limited. HIV care is complex, requiring integration of evolving therapies, diagnostic data, and patient history. We evaluated multiple AI models using a set of realistic HIV-related questions, assessing accuracy, safety, and clinical usefulness against expert judgment. While several models performed well on simpler tasks, only a few remained reliable for more complex scenarios, with many showing weaknesses in reasoning and susceptibility to misleading information. These results suggest that, although promising, current AI tools are not yet ready for routine clinical use and require further refinement and rigorous evaluation for safe deployment. Cardenal-Antolin et al., develop HIVMedQA, a clinician-curated benchmark of HIV-related open-ended question-answer pairs, and use it to evaluate general-purpose and medical large language models across knowledge, reasoning, bias, safety and accuracy dimensions. Gemini 2.5 Pro performs best overall, reasoning and bias robustness remain limited, and clinician-aligned LLM-as-a-judge assessment more accurately reflects model performance than lexical metrics alone.

Identifying HIV-1 envelope (Env) traits associated with neutralization cross-reactivity is crucial for vaccine design. Variable loops 1 and 2 (V1V2), positioned at the Env trimer apex, are key regions linked to neutralization. We describe non-canonical cysteine (Cys) residues in V1 that are enriched in individuals with elite neutralization breadth. Analyzing over 65,000 V1 sequences from the CATNAP database, AMP trials, and longitudinal HIV-1 cohorts (SHCS, ZPHI, and CAPRISA), we found that Env variants with extra V1 Cys are present at low levels and fluctuate over time. Extra V1 Cys associate with elite plasma neutralization, and two additional Cys are preferred, suggesting stabilization through disulfide bonds. Among 34 broadly neutralizing antibody (bnAb)-inducer Envs, 17.6% had elongated V1 regions with extra Cys. These extra Cys moderately increased neutralization resistance and altered bnAb epitope accessibility. Collectively, altering epitope exposure alongside Env stabilization renders the V1 twin Cys motif a promising feature for HIV-1 bnAb immunogens.

Introduction: Drug resistance testing may improve the management of people living with HIV (PLWH) in several scenarios in low- and middle-income countries (LMICs). To guide assay development, the WHO published a target product profile (TPP) outlining two priority use cases (scenarios) for genotypic resistance testing: (1) PLWH with confirmed virological failure (VF) on an integrase strand transfer inhibitor (INSTI)-based regimen, such as tenofovir (TFV) disoproxil fumarate, lamivudine (3TC), and dolutegravir (DTG) and (2) heavily treated PLWH, including infants and young children, with confirmed VF after receiving multiple regimens including a boosted protease inhibitor (PI). An additional potential scenario includes PLWH testing positive for HIV-1 while on pre-exposure prophylaxis (PrEP). Methods: To identify drug-resistance mutations (DRMs) most likely to influence clinical management of PLWH in each WHO TPP scenarios and to inform development of assays that detect individual DRMs and the interpretation of sequence-based assays, we reviewed prevalence and in vitro susceptibility data on HIV-1 DRMs in the Stanford HIV Drug Resistance Database associated with the nucleoside RT inhibitor (NRTI), nonnucleoside RT inhibitor (NNRTI), PI, and INSTI classes and the capsid inhibitor lenacapavir. Results: In the first scenario, the most informative NRTI DRMs were K65R and M184V/I; and the most informative INSTI DRMs were G118R, N155H, Q148H/K/R, and R263K. In the second scenario, a broader spectrum of DRMs is likely to be clinically relevant, including additional NRTI DRMs, the PI DRMs associated with reduced susceptibility to darunavir, and the NNRTI DRMs associated with reduced susceptibility to etravirine and doravirine. In PLWH testing positive for HIV-1 despite PrEP, the most informative NRTI and INSTI DRMs overlap with those in the first scenario, together with the capsid DRMs reported in persons experiencing VF while receiving lenacapavir. Conclusions: As global ART programs increasingly rely on INSTI-based regimens, and as the number of heavily treated individuals and difficult-to-treat pediatric cases grows, many LMICs have begun introducing HIV drug resistance testing for patient management. Although sequence-based assays provide the most comprehensive information for managing individual PLWH, assays that detect individual DRMs are also likely to be highly useful in the three WHO TPP scenarios.

Despite the rising challenge of antibiotic resistance, current approaches to eradicate nasal pathobionts Staphylococcus aureus and Streptococcus pneumoniae rely on antibacterials. An alternative is the artificial inoculation of commensal bacteria, i.e., probiotic treatment, supported by the increasing evidence for commensal-mediated inhibition of pathogens. To systematically investigate the potential of this approach, we developed a quantitative framework simulating the nasal microbiome dynamics by combining mathematical modeling with longitudinal microbiota data. By inferring community parameters using 16S ribosomal RNA (rRNA) amplicon sequencing data and simulating the nasal microbial dynamics of patients colonized with S. aureus, we compared the decolonization performance of probiotic and antibiotic treatments under different assumptions on patients' community composition and susceptibility profile. To further compare the robustness of these treatments, we simulated an S. aureus challenge and quantified the recolonization probability. Through in vitro experiments using nasal swabs of adults colonized with S. aureus, we confirmed that after antibiotic treatment, recolonization of S. aureus was inhibited in samples treated with a probiotic mixture compared to the nontreated control. Our results suggest that probiotic treatment outperforms antibiotics in terms of decolonization performance, recolonization robustness, and leads to less collateral reduction in the microbiome diversity. Thus, probiotic treatment may provide a promising alternative to combat antibiotic resistance, with the additional advantage of personalized treatment options via using the patient's own metagenomic data. The combination of an in silico framework with in vitro experiments using clinical samples reported in this work is an important step forward to further investigate this alternative in clinical trials.

BACKGROUND:Long-acting injectable cabotegravir and rilpivirine (LAI cabotegravir and rilpivirine) is recommended as maintenance therapy for people living with HIV who achieved viral suppression on oral antiretroviral therapy (ART). However, its effect on drug resistance evolution in resource-limited settings remains uncertain. We aimed to assess this effect under different roll-out strategies and explore key factors for resistance. METHODS:We extended the Modelling Antiretroviral Drug Resistance In South Africa (MARISA) model to assess the effect of introducing LAI cabotegravir and rilpivirine in South Africa from 2025 to 2045. The HIV transmission rate was recalibrated using incidence estimates from the Thembisa model. We considered three strategies: dolutegravir-based ART as per current guidelines; LAI cabotegravir and rilpivirine as a switching option for those with viral suppression; and LAI cabotegravir and rilpivirine for both switching and ART initiation. We assumed faster development of integrase strand transfer inhibitor (INSTI) resistance in individuals with viraemia (≥1000 copies/mL) on LAI cabotegravir and rilpivirine than those with viraemia on dolutegravir-based ART. We evaluated their effect on pre-treatment drug resistance (PDR) and transmitted drug resistance (TDR) for INSTI and rilpivirine, explored resistance mitigation strategies, and identified key uncertainties through one-at-a-time local and global sensitivity analyses. FINDINGS:By 2045, using LAI cabotegravir and rilpivirine for both switching and ART initiation was estimated to lead to higher INSTI resistance levels, with 30·6% INSTI PDR and 11·3% INSTI TDR at 30% LAI cabotegravir and rilpivirine coverage, compared with 14·0% INSTI PDR and 6·9% INSTI TDR with continued oral dolutegravir-based ART. Rilpivirine resistance under the LAI cabotegravir and rilpivirine initiation and switch strategy was estimated to increase to 41·0% PDR and 30·0% TDR, compared with 6·7% and 4·5% with oral dolutegravir-based ART. Resistance levels were similar for LAI cabotegravir and rilpivirine as a switching option for those with viral suppression. A course of oral ART after LAI cabotegravir and rilpivirine interruption (oral bridging) decreased the risk of drug resistance due to the long pharmacokinetic tail, resulting in 22·3% INSTI PDR and 26·0% rilpivirine PDR when using LAI cabotegravir and rilpivirine for both switching and ART initiation. Key factors influencing resistance levels were care disengagement rates, LAI cabotegravir and rilpivirine coverage, and INSTI mutation reversion rates. INTERPRETATION:LAI cabotegravir and rilpivirine roll-out in South Africa should be cautious and targeted. Resistance risks may be mitigated through pre-treatment resistance testing, close monitoring of treatment outcomes, and efforts to increase retention in care. FUNDING:US National Institutes of Health National Institute of Allergy and Infectious Diseases and the Swiss National Science Foundation.