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According to the WHO 2009 classification, dengue with warning signs is at the risk of developing severe form of dengue disease. One of the most important warning signs is plasma leakage, which can be a serious complication associated with higher morbidity and mortality. We report that the frequency of CD4+CD8+ double-positive (DP) T cells is significantly increased in patients at risk of developing plasma leakage. Transcriptomic analysis demonstrated that CD4+CD8+ DP cells were distinct from CD4+ Single Positive (SP) T cells but co-clustered with CD8+ SP cells, indicating a largely similar transcriptional profile. Twenty significant differentially expressed (DE) genes were identified between CD4+CD8+ DP and CD8+ SP cells. These genes encode OX40 and CCR4 proteins as well as other molecules associated with cell signaling on the cell surface (NT5E, MXRA8, and PTPRK). While comparing the profile of gene expression in CD4+CD8+ DP cells from patients with and without warning signs of plasma leakage, similar expression profile was observed, implying a role of CD4+CD8+ DP cells in plasma leakage through a quantitative increase rather than functional alteration. This study provided novel insight into the host immune response during the acute febrile phase of DENV infection and the role of CD4+CD8+ DP T cells in the pathogenesis of plasma leakage.

While several lines of evidence suggest a protective role of T cells against disease associated with Dengue virus (DENV) infection, their potential contribution to immunopathology in the acute phase of DENV infection remains controversial, and it has been hypothesized that the more severe form of the disease (dengue hemorrhagic fever, DHF) is associated with altered T cell responses. To address this question, we determined the transcriptomic profiles of DENV-specific CD8+T cells in a cohort of 40 hospitalized DENV donors with either a milder form of the disease (dengue fever, DF) or a more severe disease form (dengue hemorrhagic fever, DHF). We found multiple transcriptomic signatures, one associated with DENV-specific Interferon-gamma responding cells, and two other gene signatures, one specifically associated with the acute phase, and the other with the early convalescent phase. Additionally, we found no differences in quantity and quality of DENV-specific CD8+T cells based on disease severity. Taken together with previous findings that did not detect altered DENV-specific CD4 T cell responses, the current analysis argues against alteration in DENV-specific T cell responses as being a correlate of immunopathology.

Tuberculosis is a significant health problem without an effective vaccine to combat it. A thorough understanding of the immune response and correlates of protection is needed to develop a more efficient vaccine. The immune response against Mycobacterium tuberculosis (Mtb) is complex and involves all aspects of the immune system, however, the optimal protective, non‐pathogenic T cell response against Mtb is still elusive. This review will focus on discussing CD4 T cell immunity against mycobacteria and its importance in Mtb infection with a primary focus on human studies. We will in particular discuss the large heterogeneity of immune cell subsets that have been revealed by recent immunological investigations at an unprecedented level of detail. These studies have identified specific classical CD4 T cell subsets important for immune responses against Mtb in various states of infection. We further discuss the functional attributes that have been linked to the various subsets such as upregulation of activation markers and cytokine production. Another important topic to be considered is the antigenic targets of Mtb‐specific immune responses, and how antigen reactivity is influenced by both disease state and environmental exposure(s). These are key points for both vaccines and immune diagnostics development. Ultimately, these factors are holistically considered in the definition and investigations of what are the correlates on protection and resolution of disease.

Upon Ag encounter, T cells can rapidly divide and form an effector population, which plays an important role in fighting acute infections. In humans, little is known about the molecular markers that distinguish such effector cells from other T cell populations. To address this, we investigated the molecular profile of T cells present in individuals with active tuberculosis (ATB), where we expect Ag encounter and expansion of effector cells to occur at higher frequency in contrast to Mycobacterium tuberculosis–sensitized healthy IGRA+ individuals. We found that the frequency of HLA-DR+ cells was increased in circulating CD4 T cells of ATB patients, and was dominantly expressed in M. tuberculosis Ag–specific CD4 T cells. We tested and confirmed that HLA-DR is a marker of recently divided CD4 T cells upon M. tuberculosis Ag exposure using an in vitro model examining the response of resting memory T cells from healthy IGRA+ to Ags. Thus, HLA-DR marks a CD4 T cell population that can be directly detected ex vivo in human peripheral blood, whose frequency is increased during ATB disease and contains recently divided Ag-specific effector T cells. These findings will facilitate the monitoring and study of disease-specific effector T cell responses in the context of ATB and other infections.

Tuberculosis (TB) is the second leading infectious killer after COVID-19 worldwide. Gene expression analysis of whole blood and peripheral blood mononuclear cells (PBMC) from TB infected versus uninfected donors suggests that myeloid cells contribute to the immune signature of TB infection. In this study, we carried out the largest cellular and molecular profiling of the circulating myeloid compartment in the context of Mycobacterium tuberculosis (Mtb) infection to date. Using flow cytometry and RNA sequencing, we isolated and interrogated the transcriptomic profile of myeloid cell subsets isolated from PBMC in a cohort of active TB (ATB) patients with paired sampling at diagnosis and mid-treatment, as well as from Mtb sensitized (IGRA+) and unsensitized (IGRA−) healthy individuals. We identified an increased frequency of CD14+CD16− and CD14+CD16+ myeloid cells in ATB at diagnosis with upregulated expression of interferon signaling genes that significantly overlapped with previously reported blood TB signatures. In CD14+CD16+ cells, there was an additional increased expression of MHC-II related genes, which could be traced down to a subset of pro-inflammatory dendritic cells (DCs), namely CD14+CD163+ DC3. This cell population significantly upregulated CD16 in ATB at diagnosis, thus displaying a CD14+CD16+ phenotype, similarly to intermediate monocytes. This result also suggests CD16 might play an important role in inflammatory DC function in ATB. Thus, our study demonstrates quantitative and qualitative changes in CD14+ myeloid cells that are contributing to blood TB signatures. Additionally, it reveals phenotypic overlaps between subsets of monocytes and DCs in human blood that may hold disease relevance. Supported by a grant from NIH (U19 AI118626)

Our results highlight for the first time that a significant proportion of cell doublets in flow cytometry, previously believed to be the result of technical artifacts and thus ignored in data acquisition and analysis, are the result of biological interaction between immune cells. In particular, we show that cell:cell doublets pairing a T cell and a monocyte can be directly isolated from human blood, and high resolution microscopy shows polarized distribution of LFA1/ICAM1 in many doublets, suggesting in vivo formation. Intriguingly, T cell-monocyte complex frequency and phenotype fluctuate with the onset of immune perturbations such as infection or immunization, reflecting expected polarization of immune responses. Overall these data suggest that cell doublets reflecting T cell-monocyte in vivo immune interactions can be detected in human blood and that the common approach in flow cytometry to avoid studying cell:cell complexes should be re-visited.

Our results highlight for the first time that a significant proportion of cell doublets in flow cytometry, previously believed to be the result of technical artefacts and thus ignored in data acquisition and analysis, are the result of true biological interaction between immune cells. In particular, we show that cell:cell doublets pairing a T cell and a monocyte can be directly isolated from human blood, and high resolution microscopy shows polarized distribution of LFA1/ICAM1 in many doublets, suggesting in vivo formation. Intriguingly, T cell:monocyte complex frequency and phenotype fluctuate with the onset of immune perturbations such as infection or immunization, reflecting expected polarization of immune responses. Overall these data suggest that cell doublets reflecting T cell-monocyte in vivo immune interactions can be detected in human blood and that the common approach in flow cytometry to avoid studying cell:cell complexes should be revisited.

BackgroundSri Lanka experienced the largest ever dengue outbreak in year 2017, which coincided with the shift of the predominant circulating dengue virus (DENV) 1 to DENV2 after 9 years. As it was felt that more patients appeared to develop complications and severe dengue, we compared clinical features of patients with acute dengue, with the previous circulating serotype (DENV1) and also sequenced the new virus, to determine the lineage of the virus.Methodology/Principal findingsWe studied the clinical and laboratory features of 172 adult patients with acute DENV1 (n=79) and DENV2 (n=93) infection. 65 (82.3%) of those with DENV1 and 86 (92.4%) of those with DENV2 were experiencing a secondary infection. The risk of developing dengue haemorrhagic fever (DHF) was significantly higher (=0.005, odds ratio=2.5) in those infected with DENV2 (54.8%) when compared to DENV1(32.9%), even though similar proportions of patients had a secondary dengue infection. Patients with DENV2 infection developed leakage significantly earlier (pWhole genome sequencing showed that these DENV-2 isolates belonged to a cosmopolitan strain and was genetically more distant than the DENV-2 strains that circulated from 1981 to 2004 in Sri Lanka.Conclusions/significanceSince this DENV2 strain appears to cause more severe forms of clinical disease, it would be important to determine variations in the virus genome or other factors that could have contributed to severe disease.Author summarySri Lanka experienced the largest ever dengue outbreak in year 2017, which coincided with the shift of the predominant circulating dengue virus (DENV) 1 to DENV2 after 9 years. We studied the clinical and laboratory features of 172 adult patients with acute DENV1 (n=79) and DENV2 (n=93) infection. The risk of developing dengue haemorrhagic fever was significantly higher (=0.005, odds ratio=2.5) in those infected with DENV2 (54.8%) when compared to DENV1(32.9%), even though similar proportions of patients had a secondary dengue infection. Patients with DENV2 infection developed leakage significantly earlier (p

DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on 714 healthy adult blood bank donors from Colombo, Sri Lanka, to characterize allele frequencies in support of studies on T cell immunity against pathogens, including Dengue virus. Deviations from Hardy Weinberg proportions were not detected at any locus. Several alleles were found in >30% of individuals, including the class II alleles DPB1 * 04:01, DPB1 * 02:01, DQB1 * 06:01 and DRB1 * 07:01, and the class I alleles A * 33:03 and A * 24:02. Genotype data will be available in the Allele Frequencies Net Database.

As part of the Human Immune Project Consortium (HIPC) program, we are aiming to decipher CD4 T cell immune signatures of tuberculosis (TB) in the context of controlled (latent TB) and uncontrolled (active TB) infection. We found commonalities and differences in TB-specific CD4 T cell immune responses of latent TB vs active TB subjects. Both cohorts had higher frequency of peptide-reactive CD4 T cells compared to TB uninfected individuals, and showed strong upregulation of type I and type II interferon genes in response to antigen-specific in vitro stimulation. Conversely, we also detected differences in the transcriptome of CD4 T cells between latent vs active TB subjects that can inform us on TB-specific T cell immune signatures of controlled infection versus disease. In particular, active TB was associated with higher expression of genes associated with inflammation (TNF, IL-1 and TLR signaling) whereas latent TB was enriched for genes associated with metabolism, oxidative phosphorylation and neutrophil-mediated immunity. Looking at inter-individual variability, we also identified that some latent TB infected subjects showed similar expression patterns for a subset of genes to those with active TB, suggesting this molecular pattern might contain mechanistic and prognostic information on the risk of developing active TB. Overall, our approach has identified a plethora of TB-associated T cell immune signatures that allowed us to gain mechanistic insights into the key CD4 T cell components contributing to TB protective immunity. Additionally, our findings have the potential to be translated into new diagnostic and prognostic tools, in particular, identifying latent TB infected individuals at risk of developing active TB.

BACKGROUND Extended-spectrum s-lactamase-producing Enterobacteriaceae (ESBL-PE) are increasingly reported as pathogens in urinary tract infections (UTIs). However, in Sri Lanka, the clinical and molecular epidemiology of ESBL-PE implicated in UTIs has not been well described. MATERIALS AND METHODS We conducted prospective, laboratory-based surveillance from October to December 2013 at a tertiary care hospital in southern Sri Lanka and enrolled patients ≥1 year of age with clinically relevant UTIs due to ESBL-PE. Isolate identity, antimicrobial drug susceptibility, and ESBL production were determined. Presence of s-lactamase genes, bla(SHV), bla(TEM), and bla(CTX-M), was identified by polymerase chain reaction. RESULTS During the study period, Enterobacteriaceae were detected in 184 urine samples, with 74 (40.2%) being ESBL producers. Among 47 patients with ESBL-PE who had medical records available, 38 (80.9%) had clinically significant UTIs. Most UTIs (63.2%) were community acquired and 34.2% were in patients with diabetes. Among 36 cultured ESBL-PE isolates, significant susceptibility (>80%) was only retained to amikacin and the carbapenems. The group 1 bla(CTX-M) gene was present in 90.0% of Escherichia coli isolates and all Klebsiella pneumoniae and Enterobacter cloacae isolates. The bla(SHV) and bla(TEM) genes were more common in K. pneumoniae (75% and 50%) and E. cloacae (50% and 50%) isolates than in E. coli (10% and 20%) isolates, respectively. CONCLUSION The majority of UTIs caused by ESBL-PE were acquired in the community and due to organisms carrying the group 1 CTX-M s-lactamase. Further epidemiologic studies of infections due to ESBL-PE are urgently needed to better prevent and treat these infections in South Asia.

Early diagnosis is important for clinical management of dengue disease. While classic laboratory tests are often tedious and time consuming, point of care devices offer a rapid, cost-effective and user-friendly alternative provided their accuracy is acceptable. This study evaluated the sensitivity, specificity and efficiency of SD BIOLINE Dengue Duo® rapid NS1, IgM and IgG test kit for diagnosis of acute dengue virus infection. Standard laboratory diagnostics, RT-PCR, IgM and IgG capture ELISAs were carried out on 143 suspected dengue patient samples obtained from a Sri Lankan population. Using the results of these standard laboratory tests as reference, the sensitivity and specificity of the SD Dengue Duo® NS1 test was 57% and 87%, respectively, and those of the IgM test was 50% and 84%, respectively. The combined sensitivity and specificity of the SD Dengue Duo® NS1/ IgM test was 72% and 80%, respectively. The SD Dengue Duo® NS1 test detected NS1 for up to 9 days from onset of fever. Primary and secondary dengue cases were classified according to the IgG test, of which the kit identified 88% and 26% of primary and of secondary infection, respectively. Although the SD Dengue Duo® kit was not as accurate as the standard tests, it still can serve the useful reference for initial screening of suspected dengue cases, especially in poor resource hospital settings and aid in clinical disease management of dengue infection.

In 2009, a severe epidemic of dengue disease occurred in Sri Lanka, with higher mortality and morbidity than any previously recorded epidemic in the country. It corresponded to a shift to dengue virus 1 as the major disease-causing serotype in Sri Lanka. Dengue disease reached epidemic levels in the next 3 years. We report phylogenetic evidence that the 2009 epidemic DENV-1 strain continued to circulate within the population and caused severe disease in the epidemic of 2012. Bayesian phylogeographic analyses suggest that the 2009 Sri Lankan epidemic DENV-1 strain may have traveled directly or indirectly from Thailand through China to Sri Lanka, and after spreading within the Sri Lankan population, it traveled to Pakistan and Singapore. Our findings delineate the dissemination route of a virulent DENV-1 strain in Asia. Understanding such routes will be of particular importance to global control efforts.