Community-acquired pneumonia (CAP) results in substantial numbers of hospitalisations and deaths in older adults. There are known lifestyle and medical risk factors for pneumococcal disease but the magnitude of the additional risk is not well quantified in Australia. We used a large population-based prospective cohort study of older adults in the state of New South Wales (45 and Up Study) linked to cause-specific hospitalisations, disease notifications and death registrations from 2006 to 2015. We estimated the age-specific incidence of CAP hospitalisation (ICD-10 J12-18), invasive pneumococcal disease (IPD) notification and presumptive non-invasive pneumococcal CAP hospitalisation (J13 + J18.1, excluding IPD), comparing those with at least one risk factor to those with no risk factors. The hospitalised case-fatality rate (CFR) included deaths in a 30-day window after hospitalisation. Among 266 951 participants followed for 1 850 000 person-years there were 8747 first hospitalisations for CAP, 157 IPD notifications and 305 non-invasive pneumococcal CAP hospitalisations. In persons 65–84 years, 54.7% had at least one identified risk factor, increasing to 57.0% in those ⩾85 years. The incidence of CAP hospitalisation in those ⩾65 years with at least one risk factor was twofold higher than in those without risk factors, 1091/100 000 (95% confidence interval (CI) 1060–1122) compared with 522/100 000 (95% CI 501–545) and IPD in equivalent groups was almost threefold higher (18.40/100 000 (95% CI 14.61–22.87) vs. 6.82/100 000 (95% CI 4.56–9.79)). The CFR increased with age but there were limited difference by risk status, except in those aged 45 to 64 years. Adults ⩾65 years with at least one risk factor have much higher rates of CAP and IPD suggesting that additional risk factor-based vaccination strategies may be cost-effective.

Organic carbon (OC) radiocarbon (14C) signatures in marine surface sediments are highly variable and the causes of this heterogeneity remain ambiguous. Here, we present results from a detailed 14C-based investigation of an Arabian Sea sediment, including measurements on organic matter (OM) in bulk sediment, specific grain size fractions, and OC decomposition products from ramped-pyrolysis-oxidation (RPO). Our results show that 14C ages of OM increase with increasing grain size, suggesting that grain size is an important factor controlling the 14C heterogeneity in marine sediments. Analysis of RPO decomposition products from different grain size fractions reveals an overall increase in age of corresponding thermal fractions from finer to coarser fractions. We suggest that hydrodynamic properties of sediment grains exert the important control on the 14C age distribution of OM among grain size fractions. We propose a conceptual model to account for this dimensionality in 14C variability that invokes two predominant modes of OM preservation within different grain size fractions of Arabian Sea sediment: finer (<63 µm) fractions are influenced by OM-mineral grain aggregation processes, giving rise to relatively uniform 14C ages, whereas OM preserved in coarser (>63 µm) fractions includes materials encapsulated within microfossils and/or entrained fossil (14C-depleted) OC hosted in detrital mineral grains. Our findings highlight the value of RPO for assessment of 14C age variability in sedimentary OC, and for assessing mechanisms of OM preservation in aquatic sediments.

Inland water bodies contain significant amounts of carbon in the form of dissolved inorganic carbon (DIC) derived from a mixture of modern atmospheric and pre-aged sources, which needs to be considered in radiocarbon-based dating and natural isotope tracer studies. While reservoir effects in hardwater lakes are generally considered to be constant through time, a comparison of recent and historical DI14C data from 2013 and 1969 for Lake Constance reveals that this is not a valid assumption. We hypothesize that changes in atmospheric carbon contributions to lake water DIC have taken place due to anthropogenically forced eutrophication in the 20th century. A return to more oligotrophic conditions in the lake led to reoxygenation and enhanced terrigenous organic matter remineralization, contributing to lake water DIC. Such comparisons using DI14C measurements from different points in time enable nonlinear changes in lake water DIC source and signature to be disentangled from concurrent anthropogenically induced changes in atmospheric 14C. In the future, coeval changes in lake dynamics due to climate change are expected to further perturb these balances. Depending on the scenario, Lake Constance DI14C is projected to decrease from the 2013 measured value of 0.856 Fm to 0.54–0.62 Fm by the end of the century.

Xpert MTB/RIF (Xpert) is the preferred first-line test for all persons with tuberculosis (TB) symptoms in South Africa in line with a diagnostic algorithm. This study evaluates pre- and post-implementation trends in diagnostic practices for drug-sensitive, pulmonary TB in adults in an operational setting, following the introduction of the Xpert-based algorithm. We retrospectively analysed data from the national TB database for Greater Tzaneen sub-district, Limpopo Province. Trends in a number of cases, diagnosis and outcome and characteristics associated with death are reported. A total of 8407 cases were treated from 2008 until 2015, with annual cases registered decreasing by 31·7% over that time period (from 1251 to 855 per year). After implementation of Xpert, 69·9% of cases were diagnosed by Xpert, 29·4% clinically, 0·6% by smear microscopy and 0·1% by culture. Cases with a recorded microbiological test increased from 76·2% to 96·4%. Cases started on treatment without confirmation, but with a negative microbiological test increased from 7·1% to 25·7%. Case fatality decreased from 15·0% to 9·8%, remaining consistently higher in empirically treated groups, regardless of HIV status. Implementation of the algorithm coincided with a reduced number of TB cases treated and improved coverage of microbiological testing; however, a substantial proportion of cases continued to start treatment empirically.

We describe the investigation of two temporally coincident illness clusters involving salmonella and Staphylococcus aureus in two states. Cases were defined as gastrointestinal illness following two meal events. Investigators interviewed ill persons. Stool, food and environmental samples underwent pathogen testing. Alabama: Eighty cases were identified. Median time from meal to illness was 5·8 h. Salmonella Heidelberg was identified from 27 of 28 stool specimens tested, and coagulase-positive S. aureus was isolated from three of 16 ill persons. Environmental investigation indicated that food handling deficiencies occurred. Colorado: Seven cases were identified. Median time from meal to illness was 4·5 h. Five persons were hospitalised, four of whom were admitted to the intensive care unit. Salmonella Heidelberg was identified in six of seven stool specimens and coagulase-positive S. aureus in three of six tested. No single food item was implicated in either outbreak. These two outbreaks were linked to infection with Salmonella Heidelberg, but additional factors, such as dual aetiology that included S. aureus or the dose of salmonella ingested may have contributed to the short incubation periods and high illness severity. The outbreaks underscore the importance of measures to prevent foodborne illness through appropriate washing, handling, preparation and storage of food.

Scale-up of antiretroviral therapy (ART) for human immunodeficiency virus (HIV) infection has reduced the incidence of pulmonary tuberculosis (PTB) in South Africa. Despite the strong association of HIV infection with extrapulmonary tuberculosis (EPTB), the effect of ART on the epidemiology of EPTB remains undocumented. We conducted a retrospective record review of patients initiated on treatment for EPTB in 2009 (ART coverage <5%) and 2013 (ART coverage 41%) at four public hospitals in rural Mopani District, South Africa. Data were obtained from TB registers and patients’ clinical records. There was a 13% decrease in overall number of TB cases, which was similar for cases registered as EPTB (n = 399 in 2009 vs. 336 in 2013; P < 0·01) and for PTB (1031 vs. 896; P < 0·01). Among EPTB cases, the proportion of miliary TB and disseminated TB decreased significantly (both P < 0·01), TB meningitis and TB of bones increased significantly (P < 0·01 and P = 0·02, respectively) and TB pleural effusion and lymphadenopathy remained the same. This study shows a reduction of EPTB cases that is similar to that of PTB in the context of the ART scale-up. The changing profile of EPTB warrants attention of healthcare workers.

Compound-specific radiocarbon analysis (CSRA) of benzene polycarboxylic acids (BPCAs) yields molecular-level, source-specific information necessary to constrain isotopic signatures of pyrogenic carbon. However, the purification of individual BPCAs requires a multistep procedure that typically results in only microgram quantities of the target analyte(s). Such small samples are highly susceptible to contamination by extraneous carbon, which needs to be minimized and carefully accounted for in order to yield accurate results. Here, we undertook comprehensive characterization and quantification of contamination associated with molecular radiocarbon (14C) BPCA analyses through systematic processing of multiple authentic standards with both fossil and modern 14C signatures at various concentrations. Using this approach, we precisely apportion the contribution of extraneous carbon with respect to the four implemented subprocedures. Assuming a constant source and quantity of extraneous carbon we correct and statistically evaluate uncertainties in resulting 14C data. Subsequently, we examine the results of triplicate analyses of reference materials representing four different environmental matrices (sediment, soil, aerosol, riverine natural organic matter) and apportion their BPCA sources in terms of carbon residues derived from biomass or fossil fuel combustion. This comprehensive approach to CSRA facilitates retrieval of robust 14C data, with application in environmental studies of the continuum of pyrogenic carbon.

Introduction of antiretroviral therapy (ART) has dramatically reduced the incidence of infectious ocular diseases in human immunodeficiency virus (HIV)-infected individuals. However, the effects of long-term ART and chronic HIV infection on the eye are ill-defined. This study determined the occurrence and severity of ocular diseases among 342 participants in a rural South African setting: HIV-naïve (n = 105), HIV-infected ART-naïve (n = 16), HIV-infected on ART for <12 months (short-term ART; n = 56) and HIV-infected individuals on ART for >36 months (long-term ART; n = 165). More HIV-infected participants presented with an external eye condition, in particular blepharitis, than HIV-naïve individuals (18% vs. 7%; age-adjusted odds ratio (aOR) = 2·8, P < 0·05). Anterior segment conditions (particularly keratoconjunctivitis sicca and pterygium) were also more common (50% vs. 27%; aOR = 2·4; P < 0·01). Compared with individuals on short-term ART, participants receiving long-term ART were more likely to have clinically detectable cataract (57% vs. 38%; aOR = 2·2, P = 0·01) and posterior segment diseases, especially HIV retinopathy (30% vs. 11%; aOR = 3·4, P < 0·05). Finally, long-term ART was significantly associated with presence of HIV retinopathy (P < 0·01). These data implicate that ocular disease is more common and of more diverse etiology among HIV-infected individuals, especially those on long-term ART and suggest that regular ophthalmological monitoring of HIV-infected individuals on ART is warranted.

Substances enriched with radiocarbon can easily contaminate samples and laboratories used for natural abundance measurements. We have developed a new method using wet chemical oxidation for swabbing laboratories and equipment to test for 14C contamination. Here, we report the findings of 18 months’ work and more than 800 tests covering studies at multiple locations. Evidence of past and current use of enriched 14C was found at all but one location and a program of testing and communication was used to mitigate its effects. Remediation was attempted with mixed success and depended on the complexity and level of the contamination. We describe four cases from different situations.

Studies using carbon isotopes to understand the global carbon cycle are critical to identify and quantify sources, sinks, and processes and how humans may impact them. 13C and 14C are routinely measured individually; however, there is a need to develop instrumentation that can perform concurrent online analyses that can generate rich data sets conveniently and efficiently. To satisfy these requirements, we coupled an elemental analyzer to a stable isotope mass spectrometer and an accelerator mass spectrometer system fitted with a gas ion source. We first tested the system with standard materials and then reanalyzed a sediment core from the Bay of Bengal that had been analyzed for 14C by conventional methods. The system was able to produce %C, 13C, and 14C data that were accurate and precise, and suitable for the purposes of our biogeochemistry group. The system was compact and convenient and is appropriate for use in a range of fields of research.

Radiocarbon measurements in tree rings can be used to estimate atmospheric 14C concentration and thereby used to create a 14C calibration curve. When wood is discovered in construction sites, rivers, buildings, and lake sediments, it is unclear if the wood could fill gaps in the 14C calibration curve or if the wood is of historical interest until the age is determined by dendrochronology or 14C dating. However, dendrochronological dating is subjected to many requirements and 14C dating is costly and time consuming, both of which can be frivolous endeavors if the samples are not in the age range of interest. A simplified 14C dating technique, called Speed Dating, was thus developed. It can be used to quickly obtain 14C ages as wood samples are neither chemically treated nor graphitized. Instead, wood is combusted in an elemental analyzer (EA) and the CO2 produced is carried into an accelerator mass spectrometer (AMS) with a gas ion source. Within a day, 75 samples can be measured with uncertainties between 0.5–2% depending on the age, preservation, and contaminants on the material and Speed Dating costs about one-third of conventional AMS dates.

South Africa's paediatric antiretroviral therapy (ART) programme is managed using a monitoring and evaluation tool known as TIER.Net. This electronic system has several advantages over paper-based systems, allowing profiling of the paediatric ART programme over time. We analysed anonymized TIER.Net data for HIV-infected children aged <15 years who had initiated ART in a rural district of South Africa between 2005 and 2014. We performed Kaplan–Meier survival analysis to assess outcomes over time. Records of 5461 children were available for analysis; 3593 (66%) children were retained in care. Losses from the programme were higher in children initiated on treatment in more recent years (P < 0·0001) and in children aged ≤1 year at treatment initiation (P < 0·0001). For children aged <3 years, abacavir was associated with a significantly higher rate of loss from the programme compared to stavudine (hazard ratio 1·9, P < 0·001). Viral load was suppressed in 48–52% of the cohort, with no significant change over the years (P = 0·398). Analysis of TIER.Net data over time provides enhanced insights into the performance of the paediatric ART programme and highlights interventions to improve programme performance.

Gas-accepting ion sources for radiocarbon accelerator mass spectrometry (AMS) have permitted the direct analysis of CO2 gas, eliminating the need to graphitize samples. As a result, a variety of analytical instruments can be interfaced to an AMS system, processing time is decreased, and smaller samples can be analyzed (albeit with lower precision). We have coupled a gas chromatograph to a compact 14C AMS system fitted with a microwave ion source for real-time compound-specific 14C analysis. As an initial test of the system, we have analyzed a sample of fatty acid methyl esters and biodiesel. Peak shape and memory was better then existing systems fitted with a hybrid ion source while precision was comparable. 14C/12C ratios of individual components at natural abundance levels were consistent with those determined by conventional methods. Continuing refinements to the ion source are expected to improve the performance and scope of the instrument.

A new and unique radiocarbon accelerator mass spectrometry (AMS) facility has been constructed at the Woods Hole Oceanographic Institution. The defining characteristic of the new system is its large-gap optical elements that provide a larger-than-standard beam acceptance. Such a system is ideally suited for high-throughput, high-precision measurements of 14C. Details and performance of the new system are presented.

The radiocarbon content of dissolved organic carbon (DOC) in rivers, lakes, and other non-saline waters can provide valuable information on carbon cycling dynamics in the environment. DOC is typically prepared for 14C analysis by accelerator mass spectrometry (AMS) either by ultraviolet (UV) oxidation or by freeze-drying and sealed tube combustion. We present here a new method for the rapid analysis of 14C of DOC using wet chemical oxidation (WCO) and automated headspace sampling of CO2. The approach is an adaption of recently developed methods using aqueous persulfate oxidant to determine the δ13C of DOC in non-saline water samples and the 14C content of volatile organic acids. One advantage of the current method over UV oxidation is higher throughput: 22 samples and 10 processing standards can be prepared in one day and analyzed in a second day, allowing a full suite of 14C processing standards and blanks to be run in conjunction with samples. A second advantage is that there is less potential for cross-contamination between samples.