Time to commencement of effective treatment in patients with drug-resistant tuberculosis diagnosed in the Torres Strait-Papua New Guinea cross-border region

INTRODUCTION

Delays between self-reported symptom onset and commencement of effective treatment contribute to ongoing tuberculosis (TB) transmission, which is a particular concern in patients with drug-resistant (DR)-TB. The study authors assessed improvements in time to commencement of effective treatment in patients diagnosed with DR-TB in the Torres Strait-Papua New Guinea cross-border region.

METHODS

All laboratory-confirmed DR-TB cases diagnosed in the Torres Strait between 1 March 2000 and 31 March 2020 were reviewed. Total time from self-reported onset of symptoms to effective treatment commencement in different programmatic time periods was assessed. Pairwise analyses and time to event proportional hazard calculations were used to explore the association between delays in median time to effective treatment, and selected variables. Data were further analysed to examine predictors of excessive treatment delay.

RESULTS

The median number of days from self-reported onset of symptoms to effective treatment commencement was 124 days (interquartile range 51-214) over two decades. Between 2006 and 2012, most (57%) cases exceeded this 'grand median' while the median 'time to treat' in the most recent time period (2016-2020) was significantly reduced to 29 days (p<0.001). Although there was a reduction in the median 'time to treat' with the introduction of Xpert MTB/RIF (135 days pre-Xpert v 67 days post-Xpert) this was not statistically significant (p=0.07). Establishment of the Torres and Cape TB Control Unit on Thursday Island (2016-2020) was significantly associated with reduced treatment delay, compared to the previous TB program period (2000-2005, p<0.04; 2006-2012, p<0.001).

CONCLUSION

Minimising TB treatment delay in remote settings like the Torres Strait-Papua New Guinea cross-border region requires effective decentralised diagnosis and management structures. The results of this study suggest that the establishment of the Torres and Cape TB Control Unit on Thursday Island significantly improved time to commencement of effective TB treatment. Possible contributing factors include better TB education, cross-border communication and patient-centred care.

Phylodynamic inference of bacterial outbreak parameters using nanopore sequencing

Nanopore sequencing and phylodynamic modeling have been used to reconstruct the transmission dynamics of viral epidemics, but their application to bacterial pathogens has remained challenging. Cost-effective bacterial genome sequencing and variant calling on nanopore platforms would greatly enhance surveillance and outbreak response in communities without access to sequencing infrastructure. Here, we adapt random forest models for single nucleotide polymorphism (SNP) polishing developed by Sanderson and colleagues (2020. High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic nanopore sequencing. Genome Res. 30(9):1354–1363) to estimate divergence and effective reproduction numbers (R_e) of two methicillin-resistant Staphylococcus aureus (MRSA) outbreaks from remote communities in Far North Queensland and Papua New Guinea (PNG; n = 159). Successive barcoded panels of S. aureus isolates (2 × 12 per MinION) sequenced at low coverage (>5× to 10×) provided sufficient data to accurately infer genotypes with high recall when compared with Illumina references. Random forest models achieved high resolution on ST93 outbreak sequence types (>90% accuracy and precision) and enabled phylodynamic inference of epidemiological parameters using birth–death skyline models. Our method reproduced phylogenetic topology, origin of the outbreaks, and indications of epidemic growth (R_e > 1). Nextflow pipelines implement SNP polisher training, evaluation, and outbreak alignments, enabling reconstruction of within-lineage transmission dynamics for infection control of bacterial disease outbreaks on portable nanopore platforms. Our study shows that nanopore technology can be used for bacterial outbreak reconstruction at competitive costs, providing opportunities for infection control in hospitals and communities without access to sequencing infrastructure, such as in remote northern Australia and PNG.

Tuberculosis in the Torres Strait: the lady doth test too much

INTRODUCTION

Smear-positive pulmonary tuberculosis (PTB) requires rapid diagnosis and treatment to prevent ongoing transmission. Collection of two sputum specimens is considered the minimum requirement for the diagnosis of PTB but current guidelines in the Torres Strait Islands, Australia, recommend three sputum specimens; this frequently delays treatment initiation.

METHODS

A retrospective study was performed to ascertain the diagnostic yield of sputum specimens collected in the Torres Strait Islands. The study assessed demographics and characteristics of all PTB cases diagnosed between 2000 and 2018, and assessed the diagnostic yield in 143 patients from whom at least three sputum specimens had been collected prior to treatment commencement. Incremental and cumulative yield was calculated for each sputum specimen. Data were further analysed using binary logistic regression to examine the association between selected characteristics and a smear-positive acid-fast bacilli (AFB) result.

RESULTS

Overall, AFB was detected from the first or second sputum specimen in 97 of 101 PTB cases that were sputum smear positive. A smear-positive result was more common (odds ratio 2.84, 95% confidence interval 1.08-7.46) for Papua New Guinea nationals compared to Australian born patients. Of the 429 samples collected, 76 (18%) were of poor quality and the association between poor quality specimens and smear-negative results was significant (p<0.01). Among sputum smear-negative cases, 5/42 (12%) had three consecutive poor quality specimens. The most common collection modality in adults was voluntary expectoration; done in 391/429 (91%) of all specimens collected. Alternative specimen collection methods were mainly used in children; induced sputum 1/429 (0.2%), gastric aspirate 26/429 (6%) and nasopharyngeal aspirate 7/429 (1.6%). Errors with labelling, packaging and transportation occurred in 44 specimens from 15 patients.

CONCLUSION

Two good quality specimens ensure adequate diagnostic yield for PTB and a third specimen should only be collected from patients with two negative specimens who have persistent symptoms. Ideally, decentralised Xpert Ultra&reg; should be the frontline diagnostic test in remote settings, especially in settings like the Torres Strait Islands with high rates of drug-resistant TB.

Does High Public Trust Amplify Compliance with Stringent COVID-19 Government Health Guidelines? A Multi-country Analysis Using Data from 102,627 Individuals

PURPOSE

To examine how public trust mediates the people's adherence to levels of stringent government health policies and to establish if these effects vary across the political regimes.

METHODS

This study utilizes data from two large-scale surveys: the global behaviors and perceptions at the onset of COVID-19 pandemic and the Oxford COVID-19 Government Response Tracker (OxCGRT). Linear regression models were used to estimate the effects of public trust and strictness of restriction measures on people's compliance level. The model accounted for individual and daily variations in country-level stringency of preventative measures. Differences in the dynamics between public trust, the stringent level of government health guidelines and policy compliance were also examined among countries based on political regimes.

RESULTS

We find strong evidence of the increase in compliance due to the imposition of stricter government restrictions. The examination of heterogeneous effects suggests that high public trust in government and the perception of its truthfulness double the impact of policy restrictions on public compliance. Among political regimes, higher levels of public trust significantly increase the predicted compliance as stringency level rises in authoritarian and democratic countries.

CONCLUSION

This study highlights the importance of public trust in government and its institutions during public health emergencies such as the COVID-19 pandemic. Our results are relevant and help understand why governments need to address the risks of non-compliance among low trusting individuals to achieve the success of the containment policies.

Evaluation of the malaria reporting system supported by the District Health Information System 2 in Solomon Islands

Background

District Health Information Systems 2 (DHIS2) is used for supporting health information management in 67 countries, including Solomon Islands. However, there have been few published evaluations of the performance of DHIS2-enhanced disease reporting systems, in particular for monitoring infectious diseases such as malaria. The aim of this study was to evaluate DHIS2 supported malaria reporting in Solomon Islands and to develop recommendations for improving the system.

Methods

The evaluation was conducted in three administrative areas of Solomon Islands: Honoria City Council, and Malaita and Guadalcanal Provinces. Records of nine malaria indicators including report submission date, total malaria cases, Plasmodium falciparum case record, Plasmodium vivax case record, clinical malaria, malaria diagnosed with microscopy, malaria diagnosed with (rapid diagnostic test) (RDT), record of drug stocks and records of RDT stocks from 1st January to 31st December 2016 were extracted from the DHIS2 database. The indicators permitted assessment in four core areas: availability, completeness, timeliness and reliability. To explore perceptions and point of view of the stakeholders on the performance of the malaria case reporting system, focus group discussions were conducted with health centre nurses, whilst in-depth interviews were conducted with stakeholder representatives from government (province and national) staff and World Health Organization officials who were users of DHIS2.

Results

Data were extracted from nine health centres in Honoria City Council and 64 health centres in Malaita Province. The completeness and timeliness from the two provinces of all nine indicators were 28.2% and 5.1%, respectively. The most reliable indicator in DHIS2 was ‘clinical malaria’ (i.e. numbers of clinically diagnosed malaria cases) with 62.4% reliability. Challenges to completeness were a lack of supervision, limited feedback, high workload, and a lack of training and refresher courses. Health centres located in geographically remote areas, a lack of regular transport, high workload and too many variables in the reporting forms led to delays in timely reporting. Reliability of reports was impacted by a lack of technical professionals such as statisticians and unavailability of tally sheets and reporting forms.

Conclusion

The availability, completeness, timeliness and reliability of nine malaria indicators collected in DHIS2 were variable within the study area, but generally low. Continued onsite support, supervision, feedback and additional enhancements, such as electronic reporting will be required to further improve the malaria reporting system.

Early analysis of the Australian COVID-19 epidemic

As of 1 May 2020, there had been 6808 confirmed cases of COVID-19 in Australia. Of these, 98 had died from the disease. The epidemic had been in decline since mid-March, with 308 cases confirmed nationally since 14 April. This suggests that the collective actions of the Australian public and government authorities in response to COVID-19 were sufficiently early and assiduous to avert a public health crisis - for now. Analysing factors that contribute to individual country experiences of COVID-19, such as the intensity and timing of public health interventions, will assist in the next stage of response planning globally. We describe how the epidemic and public health response unfolded in Australia up to 13 April. We estimate that the effective reproduction number was likely below one in each Australian state since mid-March and forecast that clinical demand would remain below capacity thresholds over the forecast period (from mid-to-late April).

Delaying the COVID-19 epidemic in Australia: evaluating the effectiveness of international travel bans

OBJECTIVE

Following the outbreak of novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), and the disease named COVID-19, in Wuhan, China in late 2019, countries have implemented different interventions such as travel bans to slow the spread of this novel virus. This brief report evaluates the effect of travel bans imposed to prevent COVID-19 importation in the Australian context.

METHODS

We developed a stochastic meta-population model to capture the global dynamics and spread of COVID-19. By adjusting our model to capture the travel bans imposed globally and in Australia, the predicted COVID-19 cases imported to Australia were evaluated in comparison to observed imported cases.

RESULTS

Our modelling results closely aligned with observed cases in Australia and elsewhere. We observed a 79% reduction in COVID-19 importation and a delay of the COVID-19 outbreak in Australia by approximately one month. Further projection of COVID-19 to May 2020 showed spread patterns depending on the basic reproduction number.

CONCLUSION

Imposing the travel ban was effective in delaying widespread transmission of COVID-19. However, strengthening of the domestic control measures is needed to prevent Australia from becoming another epicentre. Implications for public health: This report has shown the importance of border closure to pandemic control.

Delaying the COVID-19 epidemic in Australia: evaluating the effectiveness of international travel bans

OBJECTIVE

Following the outbreak of novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), and the disease named COVID-19, in Wuhan, China in late 2019, countries have implemented different interventions such as travel bans to slow the spread of this novel virus. This brief report evaluates the effect of travel bans imposed to prevent COVID-19 importation in the Australian context.

METHODS

We developed a stochastic meta-population model to capture the global dynamics and spread of COVID-19. By adjusting our model to capture the travel bans imposed globally and in Australia, the predicted COVID-19 cases imported to Australia were evaluated in comparison to observed imported cases.

RESULTS

Our modelling results closely aligned with observed cases in Australia and elsewhere. We observed a 79% reduction in COVID-19 importation and a delay of the COVID-19 outbreak in Australia by approximately one month. Further projection of COVID-19 to May 2020 showed spread patterns depending on the basic reproduction number.

CONCLUSION

Imposing the travel ban was effective in delaying widespread transmission of COVID-19. However, strengthening of the domestic control measures is needed to prevent Australia from becoming another epicentre. Implications for public health: This report has shown the importance of border closure to pandemic control.

The predominance of seafood allergy in Vietnamese adults: Results from the first population-based questionnaire survey

Background

Food allergy (FA) is a serious, costly and growing health problem worldwide. FA occurs in both children and adults; however, there is a paucity of information on FA prevalence and its clinical features in the adult population, especially in Asia. We sought to assess the prevalence of FAs in Vietnamese adults and the distribution of offending food items among different regions throughout Vietnam.

Methods

A nationwide, cross-sectional, population-based survey was conducted among University students aged 16–50 years. We used a structured, anonymous questionnaire, which was modified from recently published FA epidemiologic studies and based on European Academy of Allergy and Clinical Immunology (EAACI) guidelines, to collect data on FA prevalence, clinical presentations, and implicated food groups. Statistical analysis was performed to generate the prevalence of self-reported and doctor-diagnosed FA and to examine the association of key environmental factors and FA incidence in this population.

Results

Of the 14,500 surveys distributed, a total of 9,039 responses were returned, resulting in a response rate of 62.4%. Among participants who reported food-induced adverse reactions, 48.0% have repeated reactions. 18.0% of the participants perceived FA symptoms, but less than half of them sought medical services for confirmation (37.9%). Stratifying for true FA symptoms, the prevalence of self-reported FA was 11.8% and of doctor-diagnosed FA, 4.6%. The most common doctor-diagnosed FA was to crustacean (3.0%; 95% CI, 2.6–3.3), followed by fish (1.6%; 95% CI, 1.3–1.8), mollusk (1.3%; 95% CI, 1.0–1.5) and beef (1.0%; 95% CI, 0.8–1.2). The prevalence of doctor-diagnosed FA differed among participants living in urban (6.5%) and rural regions (4.9%) (P < 0.001). Atopic family history was the strongest predictor for FA (odds ratio 8.0; 95% CI, 6.2–10.4).

Conclusions

Seafood allergy among adults is predominant in Vietnam, followed by beef, milk, and egg, while peanut, soy, and tree nut allergy are much less common. Populations in rural regions have considerably less FA; however, the protective environmental factors have yet to be identified.

Urbanization: a problem for the rich and the poor?

Urbanization has long been associated with human development and progress, but recent studies have shown that urban settings can also lead to significant inequalities and health problems. This paper is concerned with the adverse impact of urbanization on both developed and developing nations and both wealthy and poor populations within those nations, addressing issues associated with public health problems in urban areas. The discussion in this paper will be of interest to policy makers. The paper advocates policies that improve the socio-economic conditions of the urban poor and promote their better health. Further, this discussion encourages wealthy people and nations to become better informed about the challenges that may arise when urbanization occurs in their regions without the required social supports and infrastructure.

Strategic Planning for Tuberculosis Control in the Republic of Fiji

The tuberculosis (TB) health burden in Fiji has been declining in recent years, although challenges remain in improving control of the diabetes co-epidemic and achieving adequate case detection across the widely dispersed archipelago. We applied a mathematical model of TB transmission to the TB epidemic in Fiji that captured the historical reality over several decades, including age stratification, diabetes, varying disease manifestations, and incorrect diagnoses. Next, we simulated six intervention scenarios that are under consideration by the Fiji National Tuberculosis Program. Our findings show that the interventions were able to achieve only modest improvements in disease burden, with awareness raising being the most effective intervention to reduce TB incidence, and treatment support yielding the highest impact on mortality. These improvements would fall far short of the ambitious targets that have been set by the country, and could easily be derailed by moderate increases in the diabetes burden. Furthermore, the effectiveness of the interventions was limited by the extensive pool of latent TB infection, because the programs were directed at only active cases, and thus were unlikely to achieve the desired reductions in burden. Therefore, it is essential to address the co-epidemic of diabetes and treat people with latent TB infection.

Molecular Evidence of Drug-Resistant Tuberculosis in the Balimo Region of Papua New Guinea

Papua New Guinea (PNG) has a high burden of tuberculosis (TB), including drug-resistant TB (DR-TB). DR-TB has been identified in patients in Western Province, although there has been limited study outside the provincial capital of Daru. This study focuses on the Balimo region of Western Province, aiming to identify the proportion of DR-TB, and characterise Mycobacterium tuberculosis (MTB) drug resistance-associated gene mutations. Sputum samples were investigated for MTB infection using published molecular methods. DNA from MTB-positive samples was amplified and sequenced, targeting the rpoB and katG genes to identify mutations associated with rifampicin and isoniazid resistance respectively. A total of 240 sputum samples were collected at Balimo District Hospital (BDH). Of these, 86 were classified as positive based on the results of the molecular assays. For samples where rpoB sequencing was successful, 10.0% (5/50, 95% CI 4.4–21.4%) were considered rifampicin-resistant through detection of drug resistance-associated mutations. We have identified high rates of presumptive DR-TB in the Balimo region of Western Province, PNG. These results emphasise the importance of further surveillance, and strengthening of diagnostic and treatment services at BDH and throughout Western Province, to facilitate detection and treatment of DR-TB, and limit transmission in this setting.

Cytokine biomarkers for the diagnosis of tuberculosis infection and disease in adults in a low prevalence setting

OBJECTIVE

Accurate and timely diagnosis of tuberculosis (TB) is essential to control the global pandemic. Currently available immunodiagnostic tests cannot discriminate between latent tuberculosis infection (LTBI) and active tuberculosis. This study aimed to determine whether candidate mycobacterial antigen-stimulated cytokine biomarkers can discriminate between TB-uninfected and TB-infected adults, and additionally between LTBI and active TB disease.

METHODS

193 adults were recruited, and categorised into four unambiguous diagnostic groups: microbiologically-proven active TB, LTBI, sick controls (non-TB lower respiratory tract infections) and healthy controls. Whole blood assays were used to determine mycobacterial antigen (CFP-10, ESAT-6, PPD)-stimulated cytokine (IL-1ra, IL-2, IL-10, IL-13, TNF-α, IFN-γ, IP-10 and MIP-1β) responses, measured by Luminex multiplex immunoassay.

RESULTS

The background-corrected mycobacterial antigen-stimulated cytokine responses of all eight cytokines were significantly higher in TB-infected participants compared with TB-uninfected individuals, with IL-2 showing the best performance characteristics. In addition, mycobacterial antigen-stimulated responses with IL-1ra, IL-10 and TNF-α were higher in participants with active TB compared those with LTBI, reaching statistical significance with PPD stimulation, although there was a degree of overlap between the two groups.

CONCLUSION

Mycobacterial antigen-stimulated cytokine responses may prove useful in future immunodiagnostic tests to discriminate between tuberculosis-infected and tuberculosis-uninfected individual, and potentially between LTBI and active tuberculosis.

Impaired placental autophagy in placental malaria

Background

Placental malaria is a major cause of low birthweight, principally due to impaired fetal growth. Intervillositis, a local inflammatory response to placental malaria, is central to the pathogenesis of poor fetal growth as it impairs transplacental amino acid transport. Given the link between inflammation and autophagy, we investigated whether placental malaria-associated intervillositis increased placental autophagy as a potential mechanism in impaired fetal growth.

Methods

We examined placental biopsies collected after delivery from uninfected women (n = 17) and from women with Plasmodium falciparum infection with (n = 14) and without (n = 7) intervillositis. Western blotting and immunofluorescence staining coupled with advanced image analysis were used to quantify the expression of autophagic markers (LC3-II, LC3-I, Rab7, ATG4B and p62) and the density of autophagosomes (LC3-positive puncta) and lysosomes (LAMP1-positive puncta).

Results

Placental malaria with intervillositis was associated with higher LC3-II:LC3-I ratio, suggesting increased autophagosome formation. We found higher density of autophagosomes and lysosomes in the syncytiotrophoblast of malaria-infected placentas with intervillositis. However, there appear to be no biologically relevant increase in LC3B/LAMP1 colocalization and expression of Rab7, a molecule involved in autophagosome/lysosome fusion, was lower in placental malaria with intervillositis, indicating a block in the later stage of autophagy. ATG4B and p62 expression showed no significant difference across histological groups suggesting normal autophagosome maturation and loading of cargo proteins into autophagosomes. The density of autophagosomes and lysosomes in the syncytiotrophoblast was negatively correlated with placental amino acid uptake.

Conclusions

Placental malaria-associated intervillositis is associated with dysregulated autophagy that may impair transplacental amino acid transport, possibly contributing to poor fetal growth.

Measuring Transitions in Sexual Risk Among Men Who Have Sex With Men: The Novel Use of Latent Class and Latent Transition Analysis in HIV Sentinel Surveillance

New combination human acquired deficiency (HIV) prevention strategies that include biomedical and primary prevention approaches add complexity to the task of measuring sexual risk. Latent transition models are beneficial for understanding complex phenomena; therefore, we trialed the application of latent class and latent transition models to HIV surveillance data. Our aims were to identify sexual risk states and model individuals' transitions between states. A total of 4,685 HIV-negative men who have sex with men (MSM) completed behavioral questionnaires alongside tests for HIV and sexually transmissible infections at one of 2 Melbourne, Victoria, Australia, general practices (2007-2013). We found 4 distinct classes of sexual risk, which we labeled "monogamous" (n = 1,224), "risk minimizer" (n = 1,443), "risk potential" (n = 1,335), and "risk taker" (n = 683). A positive syphilis, gonorrhea, or chlamydia test was significantly associated with class membership. Among a subset of 516 MSM who had at least 3 clinic visits, there was general stability across risk classes; MSM had on average a 0.70 (i.e., 70%) probability of remaining in the same class between visits 1 and 2 and between visits 2 and 3. Monogamous MSM were one exception; the probability of remaining in the monogamous class was 0.51 between visits 1 and 2. Latent transition analyses identified unobserved risk patterns in surveillance data, characterized high-risk MSM, and quantified transitions over time.

The Potential Impact of a Hepatitis C Vaccine for People Who Inject Drugs: Is a Vaccine Needed in the Age of Direct-Acting Antivirals?

BACKGROUND AND AIMS

The advent of highly effective hepatitis C (HCV) treatments has questioned the need for a vaccine to control HCV amongst people who inject drugs (PWID). However, high treatment costs and ongoing reinfection risk suggest it could still play a role. We compared the impact of HCV vaccination amongst PWID against providing HCV treatment.

METHODS

Dynamic HCV vaccination and treatment models among PWID were used to determine the vaccination and treatment rates required to reduce chronic HCV prevalence or incidence in the UK over 20 or 40 years. Projections considered a low (50% protection for 5 years), moderate (70% protection for 10 years) or high (90% protection for 20 years) efficacy vaccine. Sensitivities to various parameters were examined.

RESULTS

To halve chronic HCV prevalence over 40 years, the low, moderate and high efficacy vaccines required annual vaccination rates (coverage after 20 years) of 162 (72%), 77 (56%) and 44 (38%) per 1000 PWID, respectively. These vaccination rates were 16, 7.6 and 4.4 times greater than corresponding treatment rates. To halve prevalence over 20 years nearly doubled these vaccination rates (moderate and high efficacy vaccines only) and the vaccination-to-treatment ratio increased by 20%. For all scenarios considered, required annual vaccination rates and vaccination-to-treatment ratios were at least a third lower to reduce incidence than prevalence. Baseline HCV prevalence had little effect on the vaccine's impact on prevalence or incidence, but substantially affected the vaccination-to-treatment ratios. Behavioural risk heterogeneity only had an effect if we assumed no transitions between high and low risk states and vaccinations were targeted or if PWID were high risk for their first year.

CONCLUSIONS

Achievable coverage levels of a low efficacy prophylactic HCV vaccine could greatly reduce HCV transmission amongst PWID. Current high treatment costs ensure vaccination could still be an important intervention option.

Modelling the Impact of Condom Distribution on the Incidence and Prevalence of Sexually Transmitted Infections in an Adult Male Prison System

Aims

To determine the effects of 1) a condom distribution program and 2) a condom distribution program combined with opt-out sexually transmitted infection (STI) screening on the transmission and prevalence of STIs in a prison system.

Methods

Using data from an implementation evaluation of a state-wide prison condom program and parameter estimates from available literature, a deterministic model was developed to quantify the incidence and prevalence of sexually transmitted HIV, hepatitis B, chlamydia, syphilis and gonorrhoea across 14 Victorian prisons. The model included individual prison populations (by longer (>2 years) or shorter sentence lengths) and monthly prisoner transfers. For each STI, simulations were compared: without any intervention; with a condom distribution program; and with a combined condom and opt-out STI screening at prison reception intervention program.

Results

Condoms reduced the annual incidence of syphilis by 99% (N = 66 averted cases); gonorrhoea by 98% (N = 113 cases); hepatitis B by 71% (N = 5 cases); chlamydia by 27% (N = 196 cases); and HIV by 50% (N = 2 cases every 10 years). Condom availability changed the in-prison epidemiology of gonorrhoea and syphilis from self-sustaining to levels unlikely to result in infection outbreaks; however, condoms did not reduce chlamydia prevalence below a self-sustaining level due to its high infectiousness, high prevalence and low detection rate. When combined with a screening intervention program, condoms reduced chlamydia prevalence further, but not below a self-sustaining level. The low prevalence of HIV and hepatitis B in Australian prisons meant the effects of condoms were predicted to be small.

Conclusion

Condoms are predicted to effectively reduce the incidence of STIs in prison and are predicted to control syphilis and gonorrhoea transmission, however even combined with a screening on arrival program may be insufficient to reduce chlamydia prevalence below self-sustaining levels. To control chlamydia transmission additional screening of the existing prison population would be required.

A Simulation Study Comparing Epidemic Dynamics on Exponential Random Graph and Edge-Triangle Configuration Type Contact Network Models

We compare two broad types of empirically grounded random network models in terms of their abilities to capture both network features and simulated Susceptible-Infected-Recovered (SIR) epidemic dynamics. The types of network models are exponential random graph models (ERGMs) and extensions of the configuration model. We use three kinds of empirical contact networks, chosen to provide both variety and realistic patterns of human contact: a highly clustered network, a bipartite network and a snowball sampled network of a "hidden population". In the case of the snowball sampled network we present a novel method for fitting an edge-triangle model. In our results, ERGMs consistently capture clustering as well or better than configuration-type models, but the latter models better capture the node degree distribution. Despite the additional computational requirements to fit ERGMs to empirical networks, the use of ERGMs provides only a slight improvement in the ability of the models to recreate epidemic features of the empirical network in simulated SIR epidemics. Generally, SIR epidemic results from using configuration-type models fall between those from a random network model (i.e., an Erdős-Rényi model) and an ERGM. The addition of subgraphs of size four to edge-triangle type models does improve agreement with the empirical network for smaller densities in clustered networks. Additional subgraphs do not make a noticeable difference in our example, although we would expect the ability to model cliques to be helpful for contact networks exhibiting household structure.

Many hepatitis C reinfections that spontaneously clear may be undetected: Markov-chain Monte Carlo analysis of observational study data

Hepatitis C virus (HCV) reinfection rates are probably underestimated due to reinfection episodes occurring between study visits. A Markov model of HCV reinfection and spontaneous clearance was fitted to empirical data. Bayesian post-estimation was used to project reinfection rates, reinfection spontaneous clearance probability and duration of reinfection. Uniform prior probability distributions were assumed for reinfection rate (more than 0), spontaneous clearance probability (0-1) and duration (0.25-6.00 months). Model estimates were 104 per 100 person-years (95% CrI: 21-344), 0.84 (95% CrI: 0.59-0.98) and 1.3 months (95% CrI: 0.3-4.1) for reinfection rate, spontaneous clearance probability and duration, respectively. Simulation studies were used to assess model validity, demonstrating that the Bayesian model estimates provided useful information about the possible sources and magnitude of bias in epidemiological estimates of reinfection rates, probability of reinfection clearance and duration or reinfection. The quality of the Bayesian estimates improved for larger samples and shorter test intervals. Uncertainty in model estimates notwithstanding, findings suggest that HCV reinfections frequently and quickly result in spontaneous clearance, with many reinfection events going unobserved.

The role of a hepatitis C virus vaccine: modelling the benefits alongside direct-acting antiviral treatments

BACKGROUND

Hepatitis C virus (HCV) elimination is being seriously considered globally. Current elimination models require a combination of highly effective HCV treatment and harm reduction, but high treatment costs make such strategies prohibitively expensive. Vaccines should play a key role in elimination but their best use alongside treatments is unclear. For three vaccines with different efficacies we used a mathematical model to estimate the additional reduction in HCV prevalence when vaccinating after treatment; and to identify in which settings vaccines could most effectively reduce the number of treatments required to achieve fixed reductions in HCV prevalence among people who inject drugs (PWID).

METHODS

A deterministic model of HCV transmission among PWID was calibrated for settings with 25, 50 and 75% chronic HCV prevalence among PWID, stratified by high-risk or low-risk PWID. For vaccines with 30, 60 or 90% efficacies, different rates of treatment and vaccination were introduced. We compared prevalence reductions achieved by vaccinating after treatment to prevent reinfection and vaccinating independently of treatment history in the community; and by allocating treatments and vaccinations to specific risk groups and proportionally across risk groups.

RESULTS

Vaccinating after treatment was minimally different to vaccinating independently of treatment history, and allocating treatments and vaccinations to specific risk groups was minimally different to allocating them proportionally across risk groups. Vaccines with 30 or 60% efficacy provided greater additional prevalence reduction per vaccination in a setting with 75% chronic HCV prevalence among PWID than a 90% efficacious vaccine in settings with 25 or 50% chronic HCV prevalence among PWID.

CONCLUSIONS

Vaccinating after treatment is an effective and practical method of administration. In settings with high chronic HCV prevalence among PWID, even modest coverage with a low-efficacy vaccine could provide significant additional prevalence reduction beyond treatment alone, and would likely reduce the cost of achieving prevalence reduction targets.

Urinary Escherichia coli antimicrobial susceptibility profiles and their relationship with community antibiotic use in Tasmania, Australia

This study assessed urinary Escherichia coli antibiotic susceptibility patterns in Tasmania, Australia, and examined their association with community antibiotic use. The susceptibility profiles of all urinary E. coli isolates collected in Tasmania between January 2010 and December 2012 were included. The amount of Pharmaceutical Benefits Scheme (PBS)-subsidised use of amoxicillin, amoxicillin/clavulanic acid (AMC), cefalexin, norfloxacin, ciprofloxacin and trimethoprim was retrieved (at the Tasmanian population level) and the number of defined daily doses per 1000 population per day in Tasmania for these antibiotics was calculated for each month during the study period. Antimicrobial susceptibility data were assessed for changes over time in the 3-year study period. Antimicrobial use and susceptibility data were assessed for seasonal differences and lag in resistance following antibiotic use. Excluding duplicates, 28145 E. coli isolates were included. Resistance levels were low; 35% of isolates were non-susceptible to amoxicillin, 14% were non-susceptible to trimethoprim and <5% were non-susceptible to AMC, cefalexin, gentamicin and norfloxacin. Amoxicillin use increased by 35% during winter/spring compared with summer/autumn, and AMC use increased by 21%. No seasonal variation in quinolone use or resistance was detected. The low levels of antimicrobial resistance identified may relate to Tasmania's isolated geographical location. Significant seasonal variation in amoxicillin and AMC use is likely to be due to increased use of these antibiotics for treatment of respiratory tract infections in winter. Quinolone use is restricted by the PBS in Australia, which is the likely explanation for the low levels of quinolone use and resistance identified.

The impact of injecting networks on hepatitis C transmission and treatment in people who inject drugs

With the development of new highly efficacious direct-acting antiviral (DAA) treatments for hepatitis C virus (HCV), the concept of treatment as prevention is gaining credence. To date, the majority of mathematical models assume perfect mixing, with injectors having equal contact with all other injectors. This article explores how using a networks-based approach to treat people who inject drugs (PWID) with DAAs affects HCV prevalence. Using observational data, we parameterized an exponential random graph model containing 524 nodes. We simulated transmission of HCV through this network using a discrete time, stochastic transmission model. The effect of five treatment strategies on the prevalence of HCV was investigated; two of these strategies were (1) treat randomly selected nodes and (2) "treat your friends," where an individual is chosen at random for treatment and all their infected neighbors are treated. As treatment coverage increases, HCV prevalence at 10 years reduces for both the high- and low-efficacy treatment. Within each set of parameters, the treat your friends strategy performed better than the random strategy being most marked for higher-efficacy treatment. For example, over 10 years of treating 25 per 1,000 PWID, the prevalence drops from 50% to 40% for the random strategy and to 33% for the treat your friends strategy (6.5% difference; 95% confidence interval: 5.1-8.1).

CONCLUSION

Treat your friends is a feasible means of utilizing network strategies to improve treatment efficiency. In an era of highly efficacious and highly tolerable treatment, such an approach will benefit not just the individual, but also the community more broadly by reducing the prevalence of HCV among PWID.

The role of Staphylococcus aureus carriage in the pathogenesis of bloodstream infection

Background

Staphylococcus aureus (SA) colonisation is associated with development of bloodstream infection (BSI), with the majority of colonising and infecting strains identical by pulsed-field gel electrophoresis (PFGE). We examined SA colonisation in patients with SABSI to delineate better the relationship between the two.

Methods

Patients with SABSI were swabbed in the nose, throat, groin, axilla and rectum. Isolates were typed using PFGE. Logistic regression was performed to determine factors associated with positive swabs.

Results

79 patients with SABSI had swabs taken. 46 (58%) had ≥ 1 screening swab positive for S. aureus; of these 37 (80%) were in the nose, 11 (24%) in the throat, 12 (26%) in the groin, 11 (24%) in the axilla and 8 (17%) in the rectum. On multivariate analysis, days from blood culture to screening swabs (OR 0.5, 95% CI 0.32-0.78, P = 0.003) and methicillin resistance (OR 9.5, 95% CI 1.07-84.73, P = 0.04) were associated with having positive swabs. Of 46 participants who had a blood sample and 1 other sample subtyped, 33 (72%, 95% CI 57-84%) had all identical subtypes, 1 (2%) had subtypes varying by 1–3 bands and 12 (26%) had subtypes ≥ 3 bands different. 30/36 (83%) blood-nose pairs were identical.

Conclusion

Overall, 58% of patients with SABSI had positive screening swabs. Of these, only 80% had a positive nose swab ie less than half (37/79, 47%) of all SABSI patients were nasally colonised. This may explain why nasal mupirocin alone has not been effective in preventing SA infection. Measures to eradicate non-nasal carriage should also be included.

Multiple site surveillance cultures as a predictor of methicillin-resistant Staphylococcus aureus infections

OBJECTIVE

To determine the relationship between methicillin-resistant Staphylococcus aureus (MRSA) colonization density, colonization site, and probability of infection in a frequently screened cohort of intensive care unit (ICU) patients.

METHODS

Patients had swab samples tested for MRSA at admission to the ICU, discharge from the ICU, and twice weekly during their ICU stay, and they were followed up for development of MRSA infection. Swab test results were analyzed to determine the proportion of patients colonized and the proportion colonized at each screening site. Hazard of MRSA infection (rate of infection per day at risk) was calculated using a Cox proportional hazards analysis, and risk factors for MRSA infection, including presence of MRSA, degree of colonization, and pattern of colonization were determined.

RESULTS

Among the 4,194 patient episodes, 238 (5.7%) had screening results that were positive for MRSA, and there were 34 cases of MRSA infection. The hazard ratio (HR) for developing an infection increased as more sites were colonized (HR, 3.4 for being colonized at more than 1 site compared with colonization at 1 site [95% confidence interval, 1.2-9.9]). Colonization site was predictive of developing infection (HR for nose or throat colonization compared with no colonization, 168 [95% confidence interval, 69-407]).

CONCLUSION

This study demonstrated that the hazard of developing an infection was higher when more sites were colonized and that certain sites were more predictive of infection than others. These results may be useful for predicting infection in ICU patients and may influence treatment.

Do active surveillance and contact precautions reduce MRSA acquisition? A prospective interrupted time series

Background

Consensus for methicillin-resistant Staphylococcus aureus (MRSA) control has still not been reached. We hypothesised that use of rapid MRSA detection followed by contact precautions and single room isolation would reduce MRSA acquisition.

Methods

This study was a pre-planned prospective interrupted time series comparing rapid PCR detection and use of long sleeved gowns and gloves (contact precautions) plus single room isolation or cohorting of MRSA colonised patients with a control group. The study took place in a medical-surgical intensive care unit of a tertiary adult hospital between May 21^st 2007 and September 21^st 2009. The primary outcome was the rate of MRSA acquisition. A segmented regression analysis was performed to determine the trend in MRSA acquisition rates before and after the intervention.

Findings

The rate of MRSA acquisition was 18.5 per 1000 at risk patient days in the control phase and 7.9 per 1000 at-risk patient days in the intervention phase, with an adjusted hazard ratio 0.39 (95% CI 0.24 to 0.62). Segmented regression analysis showed a decline in MRSA acquisition of 7% per month in the intervention phase, (95%CI 1.9% to 12.8% reduction) which was a significant change in slope compared with the control phase. Secondary analysis found prior exposure to anaerobically active antibiotics and colonization pressure were associated with increased acquisition risk.

Conclusion

Contact precautions with single room isolation or cohorting were associated with a 60% reduction in MRSA acquisition. While this study was a quasi-experimental design, many measures were taken to strengthen the study, such as accounting for differences in colonisation pressure, hand hygiene compliance and individual risk factors across the groups, and confining the study to one centre to reduce variation in transmission. Use of two research nurses may limit its generalisability to units in which this level of support is available.

Pandemic (H1N1) 2009 risk for frontline health care workers

To determine whether frontline health care workers (HCWs) are at greater risk for contracting pandemic (H1N1) 2009 than nonclinical staff, we conducted a study of 231 HCWs and 215 controls. Overall, 79 (17.7%) of 446 had a positive antibody titer by hemagglutination inhibition, with 46 (19.9%) of 231 HCWs and 33 (15.3%) of 215 controls positive (OR 1.37, 95% confidence interval 0.84–2.22). Of 87 participants who provided a second serum sample, 1 showed a 4-fold rise in antibody titer; of 45 patients who had a nose swab sample taken during a respiratory illness, 7 had positive results. Higher numbers of children in a participant’s family and working in an intensive care unit were risk factors for infection; increasing age, working at hospital 2, and wearing gloves were protective factors. This highly exposed group of frontline HCWs was no more likely to contract pandemic (H1N1) 2009 influenza infection than nonclinical staff, which suggests that personal protective measures were adequate in preventing transmission.

Daily hazard of acquisition of methicillin-resistant Staphylococcus aureus infection in the intensive care unit

OBJECTIVE

Increasing length of hospital stay is associated with methicillin-resistant Staphylococcus aureus (MRSA) acquisition. The exact risk of becoming colonized with MRSA on a given day has not been clearly elucidated. We determined the hazard of MRSA acquisition in relation to the length of time spent in an intensive care unit in which only standard precautions were used for MRSA-colonized and MRSA-infected patients.

METHODS

This study took place at a tertiary referral hospital intensive care unit in which patients were screened for MRSA at hospital admission, at hospital discharge, and twice weekly during intensive care unit stay. We analyzed the hazard of MRSA acquisition by using a statistical smoothing kernel for hazard with a width of 5 days. Patients were stratified according to age, sex, medical unit, and length of hospital stay.

RESULTS

Of the patients who were at risk of colonization or infection, 12.8% acquired MRSA. The mean length of stay in the intensive care unit was 7.2 days. The daily hazard of acquiring MRSA was less than 1% at admission to the intensive care unit and increased linearly to more than 2% risk per day by day 12, followed by a leveling out of risk.

CONCLUSIONS

The daily hazard of acquiring MRSA is not constant. This has implications for studies that assume a constant hazard in their analysis and should be considered.

An alternative scoring system to predict risk for surgical site infection complicating coronary artery bypass graft surgery

OBJECTIVE

To analyze the risk factors for surgical site infection (SSI) complicating coronary artery bypass graft (CABG) surgery and to create an alternative SSI risk score based on the results of multivariate analysis.

METHODS

A prospective cohort study involving inpatient and laboratory-based surveillance of patients who underwent CABG surgery over a 27-month period from January 1, 2003 through March 31, 2005. Data were obtained from 6 acute care hospitals in Victoria, Australia, that contributed surveillance data for SSI complicating CABG surgery to the Victorian Hospital Acquired Infection Surveillance System Coordinating Centre and the Australasian Society of Cardiac and Thoracic Surgeons, also in Victoria.

RESULTS

A total of 4,633 (93%) of the 4,987 patients who underwent CABG surgery during this period were matched in the 2 systems databases. There were 286 SSIs and 62 deep or organ space sternal SSIs (deep or organ space sternal SSI rate, 1.33%). Univariate analysis revealed that diabetes mellitus, body mass index (BMI) greater than 35, and receipt of blood transfusion were risk factors for all types of SSI complicating CABG surgery. Six multivariate analysis models were created to examine either preoperative factors alone or preoperative factors combined with operative factors. All models revealed diabetes and BMI of 30 or greater as risk factors for SSI complicating CABG surgery. A new preoperative scoring system was devised to predict sternal SSI, which assigned 1 point for diabetes, 1 point for BMI of 30 or greater but less than 35, and 2 points for BMI of 35 or greater. Each point in the scoring system represented approximately a doubling of risk of SSI. The new scoring system performed better than the National Nosocomial Infections Surveillance System (NNIS) risk index at predicting SSI.

CONCLUSION

A new weighted scoring system based on preoperative risk factors was created to predict sternal SSI risk following CABG surgery. The new scoring system outperformed the NNIS risk index. Future studies are needed to validate this scoring system.