The Journal of Infectious Diseases

People living with human immunodeficiency virus (PLHIV) on antiretroviral therapy (ART) are reported to have three times higher carriage of Streptococcus pneumoniae than their HIV-uninfected counterparts in point prevalence studies. Using a longitudinal cohort study design, we assessed pneumococcal carriage density, shedding and antibiotic resistance profiles, as well as nasal mucosal immunity, in otherwise healthy PLHIV on ART for at least one year, compared to HIV-uninfected participants in Malawi. Pneumococcal carriage density was higher among PLHIV compared to HIV-uninfected participants. Moreover, PLHIV were twice more likely to shed pneumococci than HIV-uninfected participants. In PLHIV, aerosol shed pneumococci were more often multi-drug resistant (MDR) than nasopharyngeal carried isolates recovered from the same individual. Consistent with high shedding, PLHIV exhibited heightened neutrophil-mediated nasal mucosa inflammation. We propose that PLHIV should be considered in intervention strategies, such as vaccination, as they could be an important reservoir for transmission of MDR S. pneumoniae.

BackgroundChronic malaria exposure has been proposed to modulate immune function, but its long-term effects on antibody-mediated responses to unrelated pathogens remain poorly defined. Whether these effects persist beyond periods of active infection, and how early-life exposure shapes humoral immunity over time, is not well understood. MethodsWe leveraged a natural experiment in coastal Kenya - where two regions (Junju and Ngerenya) diverged sharply in malaria transmission from around 2004 - to evaluate the long-term immunological consequences of malaria exposure in childhood. Using a protein microarray platform, we measured IgG responses to vaccine and pathogen antigens in 123 children sampled longitudinally over a 15-year period. Active weekly malaria surveillance enabled precise reconstruction of individual exposure histories. ResultsIgG responses to Plasmodium falciparum apical membrane antigen 1 (AMA1) tracked closely with clinical malaria episodes, confirming the ability of the microarray platform to detect biologically meaningful variation in antigen-specific immunity. Despite comparable vaccination histories, children from the high malaria transmission setting (Junju) exhibited persistently lower measles-specific IgG levels than children from the low-transmission setting (Ngerenya), a pattern validated by ELISA. At 10 years of age, Junju children showed significantly reduced antibody levels to a wide range of unrelated pathogens, including Bordetella pertussis, CMV, rubella, and measles. Within the Ngerenya cohort, children with documented early-life malaria had broadly lower IgG responses at age 10 compared to malaria-naive peers, despite identical geography, vaccines, and follow-up duration. ConclusionsThese findings suggest that malaria exposure during early childhood is linked with durable suppression of antibody responses to unrelated pathogens and vaccines. This effect persists long after infection and may partially explain the overall diminished long-term vaccine effectiveness in malaria-endemic settings.

BackgroundTo characterize interferences between Streptococcus pneumoniae and SARS-CoV-2 we investigated the longitudinal patterns of viral infection and pneumococcal carriage in households infected with SARS-CoV-2. MethodsSARS-CoV-2 and pneumococcus were detected with quantitative molecular methods in saliva from members of eighty participating households. Samples were collected between October 2020 and January 2021 from n=197 adults and n=118 children of which n=176 adults and n=98 children had a complete set of ten samples collected within 42 days since enrolment. Time-dependent Cox models were used to evaluate the associations between SARS-CoV-2 and pneumococcal carriage. ResultsIn the entire cohort, cumulative pneumococcal carriage and SARS-CoV-2 infection rates were 58% and 65%, respectively. Pneumococcal abundances were associated with an increased risk of SARS-CoV-2 infection (HR 1.14, 95% CI, 1.01 - 1.29, P=0.04) and delayed clearance of SARS-CoV-2 infection (HR 0.90, 95% CI, 0.82 - 0.99, P=0.03). Elevated viral loads were observed among pneumococcal carriers and individuals with high overall bacterial 16S abundances, however, there were no longitudinal differences in viral loads in linear mixed-effects models. Individuals with high 16S abundances displayed delayed viral clearance (HR 0.65, 95% CI 0.55 - 0.78, P<0.0001). ConclusionsAlthough we found insufficient evidence for a strong impact of SARS-CoV-2 infection on pneumococcal carriage. Results from the current study suggest that pneumococcal carriers may have an increased risk of SARS-CoV-2 infection and high pneumococcal abundances and 16S abundances may be associated with elevated viral loads and delayed clearance of SARS-CoV-2 infection.

BackgroundClassified by the WHO as one of the 19 most dangerous fungal pathogens, Pneumocystis jirovecii has been associated with increasing outbreaks of Pneumocystis pneumonia (PCP) among solid organ transplant (SOT) recipients worldwide. Mycophenolic acid (MPA), an inosine monophosphate dehydrogenase (IMPDH) inhibitor commonly used as an immunosuppressant to prevent organ rejection, is a risk factor for PCP. However, MPA also displays antifungal activity, potentially protecting against PCP, despite not being used to treat it. Therefore the underlying factors driving these outbreaks remain undefined. MethodsIn this international multicenter retrospective observational study, P. jirovecii samples were collected from 96 SOT patients (including 94 from nine separate outbreaks and 84 on MPA therapy) and 67 non-transplant controls (none on MPA), between 1986 and 2020 across six countries in Europe, North America and Asia. All samples underwent extensive targeted sequencing of the P. jirovecii inosine monophosphate dehydrogenase (impdh) gene and multiple genetic markers, with selected samples further analyzed for complete mitogenome and restriction fragment length polymorphisms. Computational modeling was employed to predict the effects of IMPDH mutations on protein structure and MPA binding. ResultsSix impdh mutations (including one previously reported) were identified, with frequencies of 4-21% each in SOT patients and 0-1% in controls. These mutations were strongly associated with prior MPA exposure and showed marked geographic segregation and temporal shifts. Four mutations were each linked to multiple distinct genotype profiles, representing separate P. jirovecii strains. Structure modeling predicted that these four mutations reduced protein stability and binding affinity to MPA. ConclusionsThis study suggests that the widespread use of MPA in SOT recipients has unexpectedly driven the emergence of multiple impdh mutations in P. jirovecii, each presumably arising independently in multiple strains worldwide. These mutations likely confer drug resistance and provide a selective survival advantage to P. jirovecii in SOT recipients exposed to MPA, thereby facilitating transmission and outbreaks. These findings have significant implications for the prevention and clinical management of PCP in SOT recipients, highlighting a rare example of how antimicrobial resistance can emerge through unexpected pathways, transcending conventional antimicrobial use and emphasizing the need for increased vigilance and strategic adaptation in clinical practice.

BackgroundPneumococcus is a diverse pathogen, with >90 serotypes, each of which has a distinct polysaccharide capsule. Pneumococci can switch capsules, evading vaccine pressure. Certain serotype pairs are more likely to switch, but the drivers of these patterns are not well understood.\n\nMethodsWe used the PubMLST and Global Pneumococcal Sequencing (GPS) databases to quantify the number of genetic lineages on which different serotype pairs co-occur. We also quantified the genetic diversity of each serotype. Regression models evaluated the relationship between shared polysaccharide structural components and the frequency of serotype switching and diversity.\n\nResultsA number of serotype pairs co-occurred on the same genetic lineage more commonly than expected. Co-occurrence of between-serogroup pairs was more common when both serotypes had glucose as a component of the capsule (and, potentially, glucuronic acid). Diversity also varied markedly by serotype and was lower for serotypes with glucuronic acid in the capsule and higher for those with galactose in the capsule.\n\nConclusionsCertain pairs of serotypes are more likely to occur on the same genetic background, and these patterns were correlated with shared polysaccharide components. This might indicate adaptation of strains to produce capsules with particular characteristics.

BackgroundSARS-CoV-2 has caused over 36,000,000 cases and 1,000,000 deaths globally. Comprehensive assessment of the multifaceted anti-viral antibody response is critical for diagnosis, differentiation of severe disease, and characterization of long-term immunity. Initial observations suggest that severe disease is associated with higher antibody levels and greater B cell/plasmablast responses. A multi-antigen immunoassay to define the complex serological landscape and clinical associations is essential. MethodsWe developed a multiplex immunoassay and evaluated serum/plasma from adults with RT-PCR-confirmed SARS-CoV-2 infections during acute illness (N=52) and convalescence (N=69); and pre-pandemic (N=106) and post-pandemic (N=137) healthy adults. We measured IgA, IgG, and/or IgM against SARS-CoV-2 Nucleocapsid (N), Spike domain 1 (S1), receptor binding domain (S1-RBD) and S1-N-terminal domain (S1-NTD). ResultsTo diagnose infection, the combined [IgA+IgG+IgM] or IgG for N, S1, and S1-RBD yielded AUC values -0.90 by ROC curves. From days 6-30 post-symptom onset, the levels of antigen-specific IgG, IgA or [IgA+IgG+IgM] were higher in patients with severe/critical compared to mild/moderate infections. Consistent with excessive concentrations of antibodies, a strong prozone effect was observed in sera from severe/critical patients. Notably, mild/moderate patients displayed a slower rise and lower peak in anti-N and anti-S1 IgG levels compared to severe/critical patients, but anti-RBD IgG and neutralization responses reached similar levels at 2-4 months. ConclusionThis SARS-CoV-2 multiplex immunoassay measures the magnitude, complexity and kinetics of the antibody response against multiple viral antigens. The IgG and combined-isotype SARS-CoV-2 multiplex assay is highly diagnostic of acute and convalescent disease and may prognosticate severity early in illness. One Sentence SummaryIn contrast to patients with moderate infections, those with severe COVID-19 develop prominent, early antibody responses to S1 and N proteins.

Asymptomatic Plasmodium falciparum infection is common among school-aged children in endemic settings, yet its metabolic consequences are poorly defined. We investigated whether subclinical malaria is associated with altered adipocytokine profiles in Nigerian children and whether effects vary with parasite density. In a community-based cross-sectional survey in Ibadan, Nigeria, we enrolled 317 primary-school children and ascertained malaria by rapid test and light microscopy. Plasma adiponectin, leptin, and resistin were quantified using validated enzyme immunoassays, and the leptin-to-adiponectin ratio was derived. Multivariable linear models with clustering by school evaluated associations between asymptomatic malaria and each biomarker, adjusting for age, sex, height-for-age and body-mass-index-for-age z-scores, socioeconomic status, and hemoglobin. Sensitivity analyses restricted exposure to microscopy-confirmed infection and to participants with C-reactive protein [&le;]3 mg/L. Among malaria-positive children, we examined correlations between parasite density and adipocytokines with false discovery rate control. Of 317 children, 102 (32.2%) had asymptomatic parasitemia. Compared with uninfected peers, infected children had higher adiponectin (geometric mean 45.2 vs 32.1 g/mL) and a lower leptin-to-adiponectin ratio. In adjusted analyses, asymptomatic malaria was associated with +42% adiponectin (95% CI 18 to 71) and -31% leptin-to-adiponectin ratio (95% CI, -49 to -7); leptin and resistin were not independently associated with infection status. Among malaria-positive children, higher parasite density correlated with higher adiponectin (Spearman 0.31; 95% CI, 0.12 to 0.47), while correlations with other markers were not significant. Findings were consistent in sensitivity analyses, including after restricting to low C-reactive-protein samples. Asymptomatic malaria in childhood is characterized by elevated adiponectin and a reduced leptin-to-adiponectin ratio, indicating altered metabolic signaling during subclinical infection. The dose-response with parasite density suggests that ostensibly silent infections are metabolically active. These results suggest considering metabolic factors in child-focused malaria control strategies and motivate tests of whether treating asymptomatic infection normalizes metabolic signals and improves longer-term health.

BackgroundInterleukin 17 producing CD4 T cells contribute to the control of Mycobacterium tuberculosis (Mtb) infection in humans; whether infection with Human Immunodeficiency Virus (HIV) disproportionately affects distinct Th17 cell subsets that respond to Mtb is incompletely defined. MethodsWe performed high-definition characterization of circulating Mtb-specific Th17 cells by spectral flow cytometry in people with latent TB and treated HIV (HIV-ART). We also measured kynurenine pathway activity by LC/MS on plasma and tested the hypothesis that tryptophan catabolism influences Th17 cell frequencies in this context. ResultsWe identified two subsets of Th17 cells: subset 1 defined as CD4+V7.2-CD161+CD26+ and subset 2 defined as CD4+V7.2-CCR6+CXCR3- cells of which subset 1 was significantly reduced in LTBI with HIV-ART, yet Mtb-responsive IL17-producing CD4 T cells were preserved; we found that IL17-producing CD4 T cells dominate the response to Mtb antigen but not CMV antigen or staphylococcal enterotoxin B (SEB); and tryptophan catabolism negatively correlates with both subset 1 and subset 2 Th17 cell frequencies. ConclusionsWe found differential effects of ART-suppressed HIV on distinct subsets of Th17 cells, that IL17-producing CD4 T cells dominate responses to Mtb but not CMV antigen or SEB, and that kynurenine pathway activity is associated with decreases of circulating Th17 cells that may contribute to tuberculosis immunity.

BackgroundMycoplasma genitalium (MG) is an emerging sexually transmitted infection (STI) associated with pelvic inflammatory disease and tubal factor infertility. Its relationship with impaired fecundity remains unclear and is rarely examined in the context of co-seropositivity with other STIs. MethodsWe conducted a secondary analysis of the Effects of Aspirin in Gestation and Reproduction (EAGeR) trial, a prospective preconception cohort of women with proven fecundity and prior pregnancy loss. MG serostatus was determined using Western blot-based IgG assays on 1146 stored serum specimens. Chlamydia trachomatis (CT) and other STIs were also measured. Associations between MG seropositivity and measures of impaired fecundity were assessed. Pregnancy loss and live birth were modeled using inverse-probability weighted quasi-Poisson and unweighted log-binomial models to calculate relative risks (RR). Fecundability-odds-ratio (FOR) was estimated using a discrete Cox proportional hazards model accounting for left truncation and right censoring. Propensity score (PS) weighted versions of these models assessed risks associated with CT co-seropositivity. Analyses were adjusted for demographic and reproductive history variables. ResultsOverall, 17.1% (n=210) of participants were MG seropositive, with 27.6% (n=58) co-seropositive with CT. Compared to STI-seronegative women, MG seropositivity was not associated with any outcome, although trends were observed for reduced fecundability (FORadj: 0.87, 95% CI 0.70-1.08) and live birth (RRadj: 0.94, 95% CI 0.79-1.11). Co-seropositivity with CT was associated with lower likelihood of live birth [Relative Risk (RR)PS-weighted: 0.82, 95% CI: 0.70-0.96]. Sensitivity analyses supported the robustness of these findings. ConclusionsBeing co-seropositive for MG and CT preconception may impair fecundity.

BackgroundThe global resurgence of syphilis requires novel prevention strategies. Whole genome sequencing (WGS) of Treponema pallidum (TPA) using different specimen types is essential for vaccine development. MethodsPatients with primary (PS) and secondary (SS) syphilis were recruited in Guangzhou, China. We collected ulcer exudates and blood from PS participants, and skin biopsies and blood from SS participants for TPA polA polymerase chain reaction (PCR); ulcer exudates and blood were also used to isolate TPA strains by rabbit infectivity testing (RIT). TPA WGS was performed on 52 ulcer exudates and biopsy specimens and 25 matched rabbit isolates. ResultsWe enrolled 18 PS and 51 SS participants from December 2019 to March 2022. Among PS participants, TPA DNA was detected in 16 (89%) ulcer exudates and three (17%) blood specimens. Among SS participants, TPA DNA was detected in 50 (98%) skin biopsies and 27 (53%) blood specimens. TPA was isolated from 48 rabbits, with a 71% (12/17) success rate from ulcer exudates and 69% (36/52) from SS bloods. Twenty-three matched SS14 clade genomes were virtually identical, while two Nichols clade pairs had discordant tprK sequences. Forty-two of 52 unique TPA genomes clustered in an SS14 East Asia subgroup, while ten fell into two East Asian Nichols subgroups. ConclusionsOur TPA detection rate was high from PS ulcer exudates and SS skin biopsies and over 50% from SS whole blood, with RIT isolation in over two-thirds of samples. Our results support the use of WGS from rabbit isolates to inform vaccine development. SummaryWe performed Treponema pallidum molecular detection and genome sequencing from multiple specimens collected from early syphilis patients and isolates obtained by rabbit inoculation. Our results support the use of whole genome sequencing from rabbit isolates to inform syphilis vaccine development.

RationaleLung mucins are an understudied component of the mucosal immune response and may influence tuberculosis pathogenesis and outcomes. ObjectivesTo assess if variants in lung mucins MUC5B and MUC5AC are associated with Mycobacterium tuberculosis immune responses, susceptibility, and outcomes. MethodsWe characterized four haplotype tagging single nucleotide polymorphisms (SNPs) in MUC5B and MUC5AC for association with log2 TNF concentrations in cerebral spinal fluid (CSF) from TBM patients. SNPs associated with CSF TNF concentrations were carried forward for analyses of pulmonary and meningeal TB susceptibility and TBM mortality. Measurements and Main ResultsMUC5AC SNP rs28737416 T allele was associated with lower CSF concentrations of TNF(p=1.8*10-8) and IFN{gamma}(p=2.3*10-6), and higher TBM, but not pulmonary TB, susceptibility (OR 1.24, 95% confidence interval 1.03, 1.49; p=0.021). Mortality from TBM was higher among participants with the rs28737416 T/T and T/C genotype (35/119, 30.4%) versus the C/C genotype (11/89, 12.4%; log-rank p=0.005) in a Vietnamese cohort (N=211). This finding was confirmed in an independent Vietnamese validation cohort (N=87; 9/87, 19.1% vs 1/20, 2.5%; log-rank p=0.02) and an Indonesian validation cohort (N=468, 127/287, 44.3% vs 65/181, 35.9%, log-rank p=0.06). ConclusionsThe MUC5AC rs28737416 T/T and T/C genotypes were associated with higher susceptibility and mortality from TBM and lower CSF concentrations of TNF and IFN{gamma} compared to the C/C genotype, suggesting that MUC5AC contributes to immune changes that influence TBM outcomes.

BackgroundAfter the global deployment of pneumococcal conjugate vaccines (PCVs), serotype 12F has become the predominant serotype responsible for invasive pneumococcal disease (IPD) worldwide. As PCVs that include serotype 12F are gradually introduced, we aim to characterise the global population structure and genetic diversity of the 12F capsule locus using whole-genome sequencing. Capsule variants with vaccine evasion potential were further investigated by functional experiments. MethodsA global collection of pneumococcal serotype 12F genomes (n=806) from 37 countries across six continents were included in this study. To characterise the serotype 12F population, Global Pneumococcal Sequence Cluster (GPSC), in silico serotype, and antimicrobial resistance profile were inferred from whole-genome data for each isolate. The capsule biosynthesis (cps) locus was analysed for gene content variations that could alter polysaccharide capsule production or structure, thereby influencing recognition by vaccine-induced antibodies. These isolates were further investigated by assessing their capsule production using immunofluorescence assays and its susceptibility to vaccine-elicited antibody killing by opsonophagocytosis assays. FindingsThe global increase in serotype 12F was driven by both distinct pneumococcal lineages across different continents, and a globally-disseminated and multidrug-resistant lineage GPSC26. We identified six capsule variants in nine isolates that had disruptive mutations in cps genes including wze, wcil, wciJ and fnlA. Most (6/9) of the disruptive mutations were a result of strand-slippage mutations. A convergent strand-slippage mutation disrupting the glycosyltransferase gene wciJ was identified in four isolates from distinct lineages and countries. Despite the truncation, three of four isolates with available Quellung typing results still identified them as 12F, indicating the production of the capsule. We then created a genetically engineered lab strain with wciJ knockout and complemented with wciJ containing the strand-slipppage mutation. The knockout strain did not produce any capsule. In contrast, the lab strain with wciJ containing the strand-slippage mutation produced a mixed population of encapsulated and non-encapsulated pneumococci, even within the same chain of pneumococcal cells. This observation indicated encapsulated subpopulation possesses a functional WciJ and rapidly reversible strand-slippage mutation during replication. Opsonophagocytosis assays indicated that the clinical 12F strain with strand-slippage mutation in wciJ exhibited reduced susceptibility to vaccine-elicited serum killing, compared to a genetically closely related 12F clinical strain with an intact wciJ. However, substantial inter-individual antisera variation limits definitive interpretation. InterpretationOur work revealed the global rise of serotype 12F pneumococci has been driven by both regional-specific lineages, and a globally-disseminated and multidrug-resistant lineage GPSC26. We demonstrated that strand-slippage mutation is one of the major drivers of serotype 12F capsule variants and represents a novel mechanism enabling reversible on-off switching of capsule production. The ability to switch off capsule expression in a subpopulation may enable evasion of antibody-mediated killing but increase susceptibility to innate immune clearance. FundingBill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control and Prevention.

RationaleDisruption of respiratory bacterial communities predicts poor clinical outcomes in critical illness; however, the role of respiratory fungal communities (mycobiome) is poorly understood. ObjectivesWe investigated whether mycobiota variation in the respiratory tract is associated with host-response and clinical outcomes in critically ill patients. MethodsTo characterize the upper and lower respiratory tract mycobiota, we performed rRNA gene sequencing (internal transcribed spacer) of oral swabs and endotracheal aspirates (ETA) from 316 mechanically-ventilated patients. We examined associations of mycobiome profiles (diversity and composition) with clinical variables, host-response biomarkers, and outcomes. Measurements and Main ResultsETA samples with >50% relative abundance for C. albicans (51%) were associated with elevated plasma IL-8 and pentraxin-3 (p=0.05), longer time-to-liberation from mechanical ventilation (p=0.04) and worse 30-day survival (adjusted hazards ratio (adjHR): 1.96 [1.04-3.81], p=0.05). Using unsupervised clustering, we derived two clusters in ETA samples, with Cluster 2 (39%) showing lower alpha diversity (p<0.001) and higher abundance of C. albicans (p<0.001). Cluster 2 was significantly associated with the prognostically adverse hyperinflammatory subphenotype (odds ratio 2.07 [1.03-4.18], p=0.04) and predicted worse survival (adjHR: 1.81 [1.03-3.19], p=0.03). C. albicans abundance in oral swabs was also associated with the hyper-inflammatory subphenotype and mortality. ConclusionsVariation in respiratory mycobiota was significantly associated with systemic inflammation and clinical outcomes. C. albicans abundance emerged as a negative predictor in both the upper and lower respiratory tract. The lung mycobiome may play an important role in the biological and clinical heterogeneity among critically ill patients and represent a potential therapeutic target for lung injury in critical illness.

BackgroundProgression of chronic lung disease often leads to the requirement for a lung transplant (LTX). Despite improvements in short-term survival after LTX, chronic lung allograft dysfunction (CLAD) remains a critical challenge for long-term survival. This study investigates the relationship between the metabolome of bronchoalveolar lavage fluid (BALF) from subjects post-LTX with underlying lung disease and CLAD severity. MethodsUntargeted LC-MS/MS metabolomics was performed on 960 BALF samples collected over 10 years from LTX recipients with alpha-1-antitrypsin disease (AATD, n=22), cystic fibrosis (CF, n=46), chronic obstructive pulmonary disease (COPD, n = 79) or pulmonary fibrosis (PF, n=47). Datasets were analyzed using machine learning and multivariate statistics for associations with underlying disease and final CLAD severity. ResultsBALF metabolomes varied by underlying disease state, with AATD LT recipients being particularly distinctive (PERMANOVA, p=0.001). We also found a significant association with the final CLAD severity score (PERMANOVA, p=0.001), especially those with underlying CF. Association with CLAD severity was driven by changes in phosphoethanolamine (PE) and phosphocholine lipids that increased and decreased, respectively, and metabolites from the bacterial pathogen Pseudomonas aeruginosa. P. aeruginosa siderophores, quorum-sensing quinolones, and phenazines were detected in BALF, and 4-hydroxy-2-heptylquinoline (HHQ) was predictive of the final CLAD stage in samples from CF patients (R=0.34; p[&le;]0.01). Relationships between CLAD stage and P. aeruginosa metabolites were especially strong in those with CF, where 61% of subjects had at least one of these metabolites in their first BALF sample after transplant. ConclusionsBALF metabolomes after LTX are distinctive based on the underlying disease and reflect final CLAD stage. In those with more severe outcomes, there is a lipid transition from PC to predominantly PE phospholipids. The association of P. aeruginosa metabolites with CLAD stages in LTX recipients with CF indicates this bacterium and its metabolites may be drivers of allograft dysfunction. Key messagesDespite the high prevalence of CLAD among LTX recipients, its pathology is not well understood, and no single molecular indicator is known to predict disease onset. Our machine learning metabolomic-based approach allowed us to identify patterns associated with a shift in the lipid metabolism and bacterial metabolites predicting CLAD onset in CF. This study provides a better understanding about the progression of allograft dysfunction through the molecular transitions within the transplanted lung from the host and bacterial pathogens.

ObjectivePrior genomewide association studies have identified variation in MHC Class I alleles and CCR5{Delta}32 as genetic predictors of viral control, especially in "elite" controllers, individuals who remain virally suppressed in the absence of therapy. DesignCross-sectional genomewide association study. MethodsWe analyzed custom whole exome sequencing and direct HLA typing from 202 ART-suppressed HIV+ non-controllers in relation to four measures of the peripheral CD4+ T cell reservoir: HIV intact DNA, total (t)DNA, unspliced (us)RNA, and RNA/DNA. Linear mixed models were adjusted for potential covariates including age, sex, nadir CD4+ T cell count, pre-ART HIV RNA, timing of ART initiation, and duration of ART suppression. ResultsPreviously reported "protective" host genetic mutations related to viral setpoint (e.g., among elite controllers) were found to predict smaller HIV reservoir size. The HLA "protective" B*57:01 was associated with significantly lower HIV usRNA (q=3.3x10-3), and among the largest subgroup, European ancestry individuals, the CCR5{Delta}32 deletion was associated with smaller HIV tDNA (p=4.3x10-3) and usRNA (p=8.7x10-3). In addition, genomewide analysis identified several SNPs in MX1 (an interferon stimulated gene) that were significantly associated with HIV tDNA (q=0.02), and the direction of these associations paralleled MX1 gene eQTL expression. ConclusionsWe observed a significant association between previously reported "protective" MHC class I alleles and CCR5{Delta}32 with the HIV reservoir size in non-controllers. We also found a novel association between MX1 and HIV total DNA (in addition to other interferon signaling relevant genes, PPP1CB, DDX3X). These findings warrant further investigation in future validation studies.

RationaleThe advent of culture-independent, next-generation DNA sequencing has led to discovery of distinct lung bacterial communities. Studies of lung microbiome taxonomy often reveal only subtle differences between health and disease, but microbial host response may distinguish members of similar communities in different populations. ObjectivesMagnetic-activated cell sorting (MACS) has been applied to the gut microbiome to identify numbers and types of bacteria eliciting a humoral response. We adapted this technique to examine populations of immunoglobulin-bound bacteria and investigate the lung microbiota in HIV as a representative disease. Methods42 people living with HIV (PLWH) and 22 HIV-uninfected individuals underwent bronchoalveolar lavage (BAL). We separated immunoglobulin G-bound bacteria using MACS and sequenced the 16S rRNA gene on the Illumina MiSeq platform. We analyzed sequences and quantified BAL cytokines and bacterial rRNA copy numbers. Measurements and Main ResultsImmunoglobulin G-bound bacteria were detectable in the healthy lung microbiota. Comparison of raw BAL by HIV status showed no significant taxonomic differences, but the immunoglobulin-bound lung microbiota differed by HIV status with greater abundance of Pseudomonas in PLWH. BAL cytokine levels were also higher in PLWH, which correlated with increased quantity of immunoglobulin G-bound bacteria. ConclusionsWe report a novel application of magnetic-activated cell sorting to identify immunoglobulin G-bound bacteria in the lung. This technique identified distinct bacterial communities which differed in composition from raw BAL, revealing differences in health and disease not detected by traditional analyses. Cytokine response was also associated with differential immunoglobulin binding of lung bacteria, suggesting functional importance of these communities.

Due to the proliferation of new SARS-CoV-2 variants, most COVID-19 cases are now caused by post-vaccine infections and a substantial proportion are reinfections. While prior research on correlates of protection has focused on the role of anti-spike antibodies, the results of the corresponding antibody assays may not accurately predict the risk of infection with new SARS-CoV-2 variants. In this study, we investigated the association between live virus neutralising antibody activity and SARS-CoV-2 infection risk using self-administered capillary microsample blood tests from VirusWatch participants. The study was conducted during the transition between the dominance of the B.1.617.2 (Delta) and B.1.1.529 (Omicron BA.1) SARS-CoV-2 variants, enabling us to investigate the association between variant-specific virus inhibition and subsequent infections within each dominance period. Greater inhibition of Omicron BA.1 live virus was associated with a reduction in infection risk during both the Delta and Omicron BA.1 dominance periods. Delta virus inhibition was associated with infection risk reduction during the Delta dominance period, but we found no association between Delta inhibition and protection against infection during the Omicron BA.1 dominance period. Our results are consistent with earlier findings and suggest that variant-specific serosurveillance of immunity and protection against SARS-CoV-2 infection at the population level could inform public health policy in near-real time using inexpensive and accessible home-based testing.

BackgroundNK cells are major innate and adaptive responders to malaria, with multiple roles in protection. Function of NK cells is heterogeneous, underpinned by expression of a diversity of receptors. One driver of NK cell heterogeneity is latent CMV infection, which drives the expansion of memory-like NK cells. We have recently reported that latent CMV infection can negatively impact the adaptive immune response to malaria, but whether CMV-mediated changes to the NK cell compartment also impact innate responses to malaria is unknown. MethodsWe investigated the impact of latent CMV infection on NK cell response to the malaria parasite Plasmodium falciparum in vitro, and in CMV seronegative and seropositive individuals during controlled human malaria infection. We analysed NK cell activation, cytotoxicity and NK cell receptor expression. Additionally, we investigated the impact of CMV serostatus on cytokine production in response to TLR stimulation in the myeloid cell compartment. The impact of CMV and NK cell responses on parasite control and malaria symptoms was investigated. ResultsNK cells from CMV seropositive individuals had reduced responsiveness to P. falciparum parasites in vitro and had reduced activation during controlled human infection. Reduced activation was not restricted to NK subsets modulated by CMV but occurred across the entire NK cell compartment. Consistent with global NK cell attenuation, IL-12 production from myeloid cells, a response that supports NK cell activation on exposure to P. falciparum parasites, was lower in CMV infected individuals. Linking NK cell activation to clinical outcomes, NK cells expressing perforin were associated with parasite control in CMV seronegative individuals. ConclusionCMV infection modulates NK cell responses during malaria by disruption of IL-12, leading to reduced parasite control.

BackgroundCryptosporidium is one of the top causes of diarrhea in Bangladesh infants. Cryptosporidium infections lead to the production of antibody immune responses, which were associated with a decrease in parasite burden and decreased disease severity in subsequent infections. MethodsWe conducted a longitudinal study of cryptosporidiosis from birth to five years of age in an urban slum of Dhaka Bangladesh. We then retrospectively tested the concentration of anti-Cryptosporidium Cp17 or Cp23 IgA in surveillance stool samples collected from 54 children during their first 3 years of life by enzyme-linked immunosorbent assay (ELISA). We also assessed the concentration of both IgA and IgG antibodies specific to Cryptosporidium Cp17 and Cp23 in the concentration of anti-Cryptosporidium Cp17 or Cp23 IgA and IgG antibodies in the childrens plasma (1-5 years). ResultsThe seroprevalence of both anti-Cp23 and Cp17 antibodies was high at [&le;] one year of age and reflected the exposure of these children in this community to cryptosporidiosis. In Bangladesh, the prevalence of cryptosporidiosis is high during the rainy season (June to October) but decreases during the dry season. In younger infants plasma anti-Cp17 and Cp23 IgG and anti-Cp17 IgA levels were markedly increased during the rainy season in line with the higher initial exposure to the parasite at this time. Both anti-Cp17, anti-Cp23 fecal IgA and the parasite burden declined during repeat infections. ConclusionsWe found that anti-Cryptosporidium plasma and fecal antibody levels in children could contribute to the decrease in new infections in this study population.

AimStreptococcus pneumoniae (Spn) acquires genes for macrolide resistance, MEGA or ermB, in the human host. These genes are carried either in the chromosome, or on integrative conjugative elements (ICEs). Here, we investigated molecular determinants of the acquisition of macrolide resistance. Methods and ResultsWhole genome analysis was conducted for 128 macrolide-resistant pneumococcal isolates to identify the presence of MEGA (44.5%, 57/128) or ermB (100%), and recombination events in Tn916-related elements or in the locus comCDE encoding competence genes. Confocal and electron microscopy studies demonstrated that, during the acquisition of macrolide resistance, pneumococcal strains formed clusters of varying size, with the largest aggregates having a median size of [~]1600 {micro}m2. Remarkably, these pneumococcal aggregates comprise both encapsulated and nonencapsulated pneumococci, exhibited physical interaction, and spanned extracellular and intracellular compartments. We assessed the recombination frequency (rF) for the acquisition of macrolide resistance by a recipient D39 strain, from pneumococcal strains carrying MEGA ([~]5.4 kb) in the chromone, or in large ICEs (>23 kb). Notably, the rF for the acquisition of MEGA, whether in the chromosome or carried on an ICE was similar. However, the rF adjusted to the acquisition of the full-length ICE ([~]52 kb), compared to that of the capsule locus ([~]23 kb) that is acquired by transformation, was three orders of magnitude higher. Finally, metabolomics studies revealed a link between the acquisition of ICE and the metabolic pathways involving nicotinic acid and sucrose. ConclusionsExtracellular and intracellular pneumococcal clusters facilitate the acquisition of full-length ICE at a rF higher than that of typical transformation events, involving distinct metabolic changes that present potential targets for interventions.