The human Toll-like receptor 2 (TLR2) response during pathogenic Leptospira infection

Background

Human innate immune responses are triggered through the interaction of human pattern recognition receptors and pathogen-associated molecular patterns. The role of toll-like receptor2 (TLR2) in mice innate immune response to leptospirosis is well established, while human studies are limited. The present study aimed to determine the TLR2 response among confirmed cases of leptospirosis.

Methodology/Principle findings

The study has two components. Clinically suspected patients of leptospirosis were confirmed using a previously validated qPCR assay. Total RNA was extracted from patients' RNA-stabilized whole blood samples. Human TLR2 gene expression (RT-qPCR) analysis was carried out using an exon-exon spanning primer pair, using CFX Maestro™ software. The first set of patient samples was used to calculate the Relative Normalized Expression (ΔΔCq value) of the TLR2 gene in comparison to a healthy control sample and normalized by the reference gene GAPDH (Glyceraldehyde-3-phosphate dehydrogenase). Secondly, recruited patient samples were subjected to TLR2 gene expression analysis and compared to healthy controls and normalized by the reference genes Beta-2-microglobulin(B2M), Hypoxanthine phosphoribosyltransferase 1 (HPRT 1).In the initial cohort of 64 confirmed leptospirosis cases, 18 were selected for human TLR2 gene expression analysis based on criteria of leptospiremia and RNA yield. Within this group, one individual exhibited a down-regulation of TLR2 gene (Expression/ΔΔCq=0.01352), whereas the remaining subjects presented no significant change in gene expression. In a subsequent cohort of 23 confirmed cases, 13 were chosen for similar analysis. Among these, three patients demonstrated down-regulation of TLR2 gene expression, with Expression/ΔΔCq values of 0.86574, 0.47200, and 0.28579, respectively. No TLR2 gene expression was noted in the other patients within this second group.

Conclusions

Our investigation into the acute phase of leptospirosis using human clinical samples has revealed a downregulation of TLR2 gene expression. This observation contrasts to the upregulation commonly reported in the majority of in-vitro and in-vivo studies of Leptospira infection. These preliminary findings prompt a need for further research to explore the mechanisms underlying TLR2's role in the pathogenesis of leptospirosis, which may differ in clinical settings compared to laboratory models.

Author Summary

The human immune system employs pattern recognition receptors like toll-like receptor 2 (TLR2) to detect and combat infections such as leptospirosis. While TLR2's role is well-documented in mice, its function in the human response to leptospirosis remains unclear. Our study evaluated TLR2 activity in patients with confirmed leptospirosis. We conducted a genetic analysis of blood samples from these patients, comparing TLR2 gene activity against healthy individuals, with standard reference genes for accuracy. Contrary to expectations and existing laboratory data, we observed a decrease in TLR2 activity in some patients. This suggests that human TLR2 responses in actual infections may diverge from established laboratory models. These findings indicate a need for further study to understand the human immune response to leptospirosis, which may significantly differ from that observed in controlled experimental settings.

Real-time analysis of hospital length of stay in a mixed SARS-CoV-2 Omicron and Delta epidemic in New South Wales, Australia

BACKGROUND

The distribution of the duration that clinical cases of COVID-19 occupy hospital beds (the 'length of stay') is a key factor in determining how incident caseloads translate into health system burden. Robust estimation of length of stay in real-time requires the use of survival methods that can account for right-censoring induced by yet unobserved events in patient progression (e.g. discharge, death). In this study, we estimate in real-time the length of stay distributions of hospitalised COVID-19 cases in New South Wales, Australia, comparing estimates between a period where Delta was the dominant variant and a subsequent period where Omicron was dominant.

METHODS

Using data on the hospital stays of 19,574 individuals who tested positive to COVID-19 prior to admission, we performed a competing-risk survival analysis of COVID-19 clinical progression.

RESULTS

During the mixed Omicron-Delta epidemic, we found that the mean length of stay for individuals who were discharged directly from ward without an ICU stay was, for age groups 0-39, 40-69 and 70 +, respectively, 2.16 (95% CI: 2.12-2.21), 3.93 (95% CI: 3.78-4.07) and 7.61 days (95% CI: 7.31-8.01), compared to 3.60 (95% CI: 3.48-3.81), 5.78 (95% CI: 5.59-5.99) and 12.31 days (95% CI: 11.75-12.95) across the preceding Delta epidemic (1 July 2021-15 December 2021). We also considered data on the stays of individuals within the Hunter New England Local Health District, where it was reported that Omicron was the only circulating variant, and found mean ward-to-discharge length of stays of 2.05 (95% CI: 1.80-2.30), 2.92 (95% CI: 2.50-3.67) and 6.02 days (95% CI: 4.91-7.01) for the same age groups.

CONCLUSIONS

Hospital length of stay was substantially reduced across all clinical pathways during a mixed Omicron-Delta epidemic compared to a prior Delta epidemic, contributing to a lessened health system burden despite a greatly increased infection burden. Our results demonstrate the utility of survival analysis in producing real-time estimates of hospital length of stay for assisting in situational assessment and planning of the COVID-19 response.

Estimating the excess burden of pertussis disease in Australia within the first year of life, that might have been prevented through timely vaccination

BACKGROUND

Previous Australian studies have shown that delayed vaccination with each of the three primary doses of diphtheria-tetanus-pertussis-containing vaccines (DTP) is up to 50 % in certain subpopulations. We estimated the excess burden of pertussis that might have been prevented if (i) all primary doses and (ii) each dose was given on time.

METHODS

Perinatal, immunization, pertussis notification and death data were probabilistically linked for 1 412 984 infants born in two Australian states in 2000-12. A DTP dose administered >15 days after the recommended age was considered delayed. We used Poisson regression models to compare pertussis notification rates to 1-year of age in infants with ≥1 dose delayed (Aim 1) or any individual dose delayed (Aim 2) versus a propensity weighted counterfactual on-time cohort.

RESULTS

Of all infants, 42% had ≥1 delayed DTP dose. We estimated that between 39 to 365 days of age, 85 (95% CI: 61-109) cases per 100 000 infants, could have been prevented if all infants with ≥1 delayed dose had received their three doses within the on-time window. Risk of pertussis was higher in the delayed versus the on-time cohort, so crude rates overestimated the excess burden (110 cases per 100 000 infants (95% CI: 95-125)). The estimated dose-specific excess burden per 100 000 infants was 132 for DTP1, 50 for DTP2 and 19 for DTP3.

CONCLUSIONS

We provide robust evidence that improved DTP vaccine timeliness, especially for the first dose, substantially reduces the burden of infant pertussis. Our methodology, using a potential outcomes framework, is applicable to other settings.

472Long-term effectiveness of 3-dose primary course and 4-year booster dose of pertussis vaccine in Australia

Background

Australia’s National Immunisation Program recommended a 3-dose primary Diphtheria-Tetanus-Pertussis (DTP) vaccination course at 2, 4 and 6 months and a booster dose at 4 years during 2003-2015. We examined vaccine effectiveness by time since doses 3 and 4, as studies to date have shown conflicting results.

Methods

Perinatal, immunisation, pertussis notification and death data were linked for 1,086,319 infants born in two Australian states in 2003-2012. Administration of DTP doses 3 and 4 from 5.5-7 months and 47-53 months respectively, was considered age-appropriate. Adjusted Cox proportional hazards models with time-varying vaccination status were used to estimate vaccine effectiveness (VE = 1–hazard ratio) against notified pertussis post age-appropriate doses 3 and 4 compared to unvaccinated children, with additional benefit of dose 4 compared to receipt of primary course alone.

Results

Dose 3 VE declined from 79% (CI 75%-83%) from 0-6 months to 64% (CI 60%-67%) at 6-36 months and 45% (CI 31%-56%) at 36-42 months post-vaccination. Compared to unvaccinated children, VE after dose 4 declined from 83% (CI 80%-86%) at 0-12 months to 67% (CI 60%-72%) and 55% (CI 46%-63%) in the following two 12-month periods post-vaccination. When compared to dose 3, the relative VE for dose 4 was 58% (CI 51%-64%) in 0-18 months post-vaccination.

Conclusion and Key messages

Our study adds to previous Australian evidence for substantial waning of vaccine induced immunity against pertussis over a 3-year period following dose 3. VE was significantly higher in the 18 months following dose 4 compared to receipt of primary course alone.

473Preventable pertussis burden in Australia within the first year of life by improving vaccination timeliness

Background

Previous Australian studies have shown that on-time Diphtheria-Tetanus-Pertussis (DTP) vaccination coverage is 50-60% in certain subpopulations. We estimated the potentially preventable burden of pertussis if, 1) the full primary course and, 2) each dose was given on-time.

Methods

Perinatal, immunisation, pertussis notification, and death data were linked for 1,412,984 infants born in two Australian states in 2000-2012. A DTP dose administered >15 days after the recommended age was categorised as delayed. For aim 1, pertussis rates up to 1-year of age were compared in infants with ≥1 dose delayed versus all doses on-time, using Poisson regression methods. For aim 2, the expected number of cases preventable by each dose was calculated as the product of the number of cases observed during the period of delay and (1 – dose-specific vaccine effectiveness).

Results

58% of infants had all primary DTP doses on time. We estimated that 85 (95% CI: 61-109) cases per 100,000 infants, aged 39-days to 1-year, could have been prevented if all infants had been vaccinated on time; 77% of these infants had received ≥1 DTP dose within the first year of life. Estimated preventable burden attributable to delayed DTP1 (58/100,000) was higher than for DTP2 (26/100,000) and DTP3 (15/100,000).

Conclusions and Key messages

Poor vaccine timeliness, especially delayed DTP1, is a key contributor to the residual burden of pertussis. These findings can inform cost-benefit analyses of targeted programs and public health messaging to reduce delays.

Whole of population-based cohort study of recovery time from COVID-19 in New South Wales Australia

Background

COVID-19 results in persisting symptoms but there is little systematically collected data estimating recovery time following infection.

Methods

We followed 94% of all COVID-19 cases diagnosed in the Australian state of New South Wales between January and May 2020 using 3-4 weekly telephone interviews and linkage to hospitalisation and death data to determine if they had recovered from COVID-19 based on symptom resolution. Proportional hazards models with competing risks were used to estimate time to recovery adjusted for age and gender.

Findings

In analyses 2904 cases were followed for recovery (median follow-up time 16 days, range 1-122, IQR 11-24).There were 2572 (88.6%) who reported resolution of symptoms (262/2572 were also hospitalised), 224 (7.8%) had not recovered at last contact (28/224 were also hospitalised), 51 (1.8%) died of COVID-19, and 57 (2.0%) were hospitalised without a documented recovery date. Of those followed, 20% recovered by 10 days, 60% at 20, 80% at 30, 91% at 60, 93% at 90 and 96% at 120 days. Compared to those aged 30-49 years, those 0-29 years were more likely to recover (aHR 1.22, 95%CI 1.10-1.34) while those aged 50-69 and 70+ years were less likely to recover (aHR respectively 0.74, 95%CI 0.67-0.81 and 0.63, 95%CI 0.56-0.71). Men were faster to recover than women (aHR 1.20, 95%CI 1.11-1.29) and those with pre-existing co-morbidities took longer to recover than those without (aHR 0.90, 95%CI 0.83-0.98).

Interpretation

In a setting where most cases of COVID-19 were ascertained and followed, 80% of those with COVID-19 recover within a month, but about 5% will continue to experience symptoms 3 months later.

Funding

NSW Health Emergency Response Priority Research Projects

Modelling the in-host dynamics of Neisseria gonorrhoeae infection

The bacterial species Neisseria gonorrhoeae (NG) has evolved to replicate effectively and exclusively in human epithelia, with its survival dependent on complex interactions between bacteria, host cells and antimicrobial agents. A better understanding of these interactions is needed to inform development of new approaches to gonorrhoea treatment and prevention but empirical studies have proven difficult, suggesting a role for mathematical modelling. Here, we describe an in-host model of progression of untreated male symptomatic urethral infection, including NG growth and interactions with epithelial cells and neutrophils, informed by in vivo and in vitro studies. The model reproduces key observations on bacterial load and clearance and we use multivariate sensitivity analysis to refine plausible ranges for model parameters. Model variants are also shown to describe mouse infection dynamics with altered parameter ranges that correspond to observed differences between human and mouse infection. Our results highlight the importance of NG internalisation, particularly within neutrophils, in sustaining infection in the human model, with ∼80% of the total NG population internalised from day 25 on. This new mechanistic model of in-host NG infection dynamics should also provide a platform for future studies relating to antimicrobial treatment and resistance and infection at other anatomical sites.

ENVirT: inference of ecological characteristics of viruses from metagenomic data

Background

Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databases to first estimate an average genome length of a viral community before being able to estimate other parameters, such as viral richness. Although this approach has been widely used, it can adversely skew results since the majority of viruses are yet to be catalogued in databases.

Results

In this paper, we present ENVirT, a method for estimating the richness of novel viral mixtures, and for the first time we also show that it is possible to simultaneously estimate the average genome length without a priori information. This is shown to be a significant improvement over database-dependent methods, since we can now robustly analyze samples that may include novel viral types under-represented in current databases. We demonstrate that the viral richness estimates produced by ENVirT are several orders of magnitude higher in accuracy than the estimates produced by existing methods named PHACCS and CatchAll when benchmarked against simulated data. We repeated the analysis of 20 metavirome samples using ENVirT, which produced results in close agreement with complementary in virto analyses.

Conclusions

These insights were previously not captured by existing computational methods. As such, ENVirT is shown to be an essential tool for enhancing our understanding of novel viral populations.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2398-5) contains supplementary material, which is available to authorized users.

Modelling the decline and future of hepatitis A transmission in Australia

Hepatitis A incidence has declined in most countries through a combination of prevention measures, augmented through the use of a highly effective vaccine. In Australia, the proportion of the population susceptible to hepatitis A infection has declined over time due to high rates of opportunistic vaccination as well as the sustained inflow of seropositive immigrants from high-endemicity countries. These factors have contributed to a rapid decline in incidence. An age-structured hepatitis A transmission model incorporating demographic changes was fitted to seroprevalence and disease notification data and used to project incidence trends and transmission potential for hepatitis A in the general population. Robustness of findings was assessed through worst-case scenarios regarding vaccine uptake, migration and the duration of immunity. The decline in age-specific seroprevalence until the introduction of hepatitis A vaccine in 1994 was well explained through a declining basic reproduction number (R₀ ) that remained >1. Accounting for existing immunity, we estimated that the effective reproduction number (R_eff ) <1 in the general population of Australia since the early 1990s, declining more rapidly after the introduction of the hepatitis A vaccine. Future projections under a variety of scenarios support R_eff remaining <1 with continued low incidence in the general population. In conclusion, our results suggest that sustained endemic transmission in the general Australian population is no longer possible although risks of sporadic outbreaks remain. This suggests potential for local elimination of hepatitis A infection in Australia, provided that elimination criteria can be defined and satisfied in risk groups. The methodology used here to investigate elimination potential can easily be replicated in settings such as in the USA where sequential seroprevalence studies are supported by routine notification data.

Assessing Species Diversity Using Metavirome Data: Methods and Challenges

Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods. In this review, existing bioinformatics methods for measuring species diversity using metavirome data are categorised broadly as either sequence similarity-dependent methods or sequence similarity-independent methods. The former includes a comparison of DNA fragments or assemblies generated in the experiment against reference databases for quantifying species diversity, whereas estimates from the latter are independent of the knowledge of existing sequence data. Current methods and tools are discussed in detail, including their applications and limitations. Drawbacks of the state-of-the-art method are demonstrated through results from a simulation. In addition, alternative approaches are proposed to overcome the challenges in estimating species diversity measures using metavirome data.

Quantifying the population effects of vaccination and migration on hepatitis A seroepidemiology in Australia

Since licensure of hepatitis A vaccine in Australia in 1994, infection rates have declined to record lows. Cross-sectional serosurveys conducted over this period meanwhile have shown rising population immunity, particularly in young to middle-aged Australians. In this study, we performed a retrospective birth cohort analysis to estimate the contributions of infection, migration and vaccination towards increased levels of age specific hepatitis A seroprevalence in Australia. When aggregated across age, we find that two-thirds of the increase in population seropositivity (67.04%) between 1994 and 2008 was due to vaccination, just under one-third due to migration, with a negligible contribution from infection (<1%). Comparisons with other data sources reflecting vaccine uptake suggest the magnitude of this effect is realistic. We suggest that these results primarily relate to opportunistic vaccination and indicate the level of population immunity achievable through opportunistic programs providing further evidence for policy considerations around universal hepatitis A vaccine recommendations.

Accurate reconstruction of viral quasispecies spectra through improved estimation of strain richness

BACKGROUND

Estimating the number of different species (richness) in a mixed microbial population has been a main focus in metagenomic research. Existing methods of species richness estimation ride on the assumption that the reads in each assembled contig correspond to only one of the microbial genomes in the population. This assumption and the underlying probabilistic formulations of existing methods are not useful for quasispecies populations where the strains are highly genetically related.

RESULTS

On benchmark data sets, our estimation method provided accurate richness estimates (< 0.2 median estimation error) and improved the precision of ViQuaS by 2%-13% and F-score by 1%-9% without compromising the recall rates. We also demonstrate that our estimation method can be used to improve the precision and F-score of ShoRAH by 0%-7% and 0%-5% respectively.

CONCLUSIONS

The proposed probabilistic estimation method can be used to estimate the richness of viral populations with a quasispecies behavior and to improve the accuracy of the quasispecies spectra reconstructed by the existing methods ViQuaS and ShoRAH in the presence of a moderate level of technical sequencing errors.

AVAILABILITY

http://sourceforge.net/projects/viquas/.