Tuberculosis (TB) is the leading global infectious cause of death. Understanding TB transmission is critical to creating policies and monitoring the disease with the end goal of TB elimination. To our knowledge, there has been no systematic review of key transmission parameters for TB. We carried out a systematic review of the published literature to identify studies estimating either of the two key TB transmission parameters: the serial interval (SI) and the reproductive number. We identified five publications that estimated the SI and 56 publications that estimated the reproductive number. The SI estimates from four studies were: 0.57, 1.42, 1.44 and 1.65 years; the fifth paper presented age-specific estimates ranging from 20 to 30 years (for infants <1 year old) to <5 years (for adults). The reproductive number estimates ranged from 0.24 in the Netherlands (during 1933–2007) to 4.3 in China in 2012. We found a limited number of publications and many high TB burden settings were not represented. Certain features of TB dynamics, such as slow transmission, complicated parameter estimation, require novel methods. Additional efforts to estimate these parameters for TB are needed so that we can monitor and evaluate interventions designed to achieve TB elimination.

Currently policies enabling cattle herds to regain Official Tuberculosis Free (OTF) status after a bovine tuberculosis (bTB) herd incident vary between individual parts of the British Isles from requiring only one negative single comparative intradermal tuberculin test (SCITT) herd test when bTB infection is not confirmed to needing two consecutively negative SCITT herd tests after disclosure of two or more reactors, irrespective of bTB confirmation. This study used Kaplan–Meier curves and univariable and multivariable Cox Proportional Hazard models to evaluate the effect of the number of SCITT reactors and bTB confirmation on the risk of future bTB herd incident utilising data extracted from the national animal health database in Northern Ireland. Based on multivariable analyses the risk of a future bTB herd incident was positively associated with the number of SCITT reactors identified during the incident period (hazard ratio = 1.861 in incidents >5 SCITT reactors compared to incidents with only one SCITT reactor; P < 0.001), but not with bTB confirmation. These findings suggest that the probability of residual bTB infection in a herd increases with an increasing number of SCITT reactors disclosed during a bTB herd incident. It was concluded that bTB herd incidents with multiple SCITT reactors should be subjected to stricter control measures irrespective of bTB infection confirmation status.

Globally, the prevalence of tuberculosis (TB) disease is higher in males. This study examined the effect of sex and age on Mycobacterium tuberculosis (Mtb) infection. Demographic and exposure data were collected on household contacts of sputum smear-positive pulmonary TB patients in Brazil. Contacts with tuberculin skin test induration ⩾10 mm at baseline or 12 weeks were considered Mtb infected. The study enrolled 917 household contacts from 160 households; 508 (55.4%) were female, median age was 21.0 years (range 0.30–87.0) and 609 (66.4%) had Mtb infection. The proportion infected increased with age from 63.3% in girls <5 years to 75.4% in women ⩾40 years and from 44.9% in boys <5 years to 73.6% in men ⩾40 years. Multivariable modelling showed the odds of infection increased between age 5 and 14 years among female contacts (OR 1.5 per 5-year age increase; 95% CI 1.1–2.2; P = 0.02) and between ages 0–4 and 15–39 years among male contacts (OR 2.7, 95% CI 0.83–8.9 and 1.1, 95% CI 0.99–1.3 per 5-year age increase; P = 0.10, 0.07, respectively). The study suggests that the age at which Mtb infection increases most is different in females compared with males. Studies are needed to explore whether these findings are due to differences in host susceptibility, exposure outside the household or other factors.

Improving access to tuberculosis (TB) care and ensuring early diagnosis are two major aims of the WHO End TB strategy and the Collaborative TB Strategy for England. This study describes risk factors associated with diagnostic delay among TB cases in England. We conducted a retrospective cohort study of TB cases notified to the Enhanced TB Surveillance System in England between 2012 and 2015. Diagnostic delay was defined as more than 4 months between symptom onset and treatment start date. Multivariable logistic regression was used to identify demographic and clinical factors associated with diagnostic delay. Between 2012 and 2015, 22 422 TB cases were notified in England and included in the study. A third (7612) of TB cases had a diagnostic delay of more than 4 months. Being female, aged 45 years and older, residing outside of London and having extra-pulmonary TB disease were significantly associated with a diagnostic delay in the multivariable model (aOR = 1.2, 1.2, 1.2, 1.3, 1.8, respectively). This study identifies demographic and clinical factors associated with diagnostic delay, which will inform targeted interventions to improve access to care and early diagnosis among these groups, with the ultimate aim of helping reduce transmission and improve treatment outcomes for TB cases in England.

Two fatal drumming-related inhalational anthrax incidents occurred in 2006 and 2008 in the UK. One individual was a drum maker and drummer from the Scottish Borders, most likely infected whilst playing a goat-skin drum contaminated with Bacillus anthracis spores; the second, a drummer and drum maker from East London, likely became infected whilst working with contaminated animal hides.

We have collated epidemiological and environmental data from these incidents and reviewed them alongside three similar contemporaneous incidents in the USA. Sampling operations recovered the causative agent from drums and drum skins and from residences and communal buildings at low levels. From these data, we have considered the nature of the exposures and the number of other individuals likely to have been exposed, either to the primary infection events or to subsequent prolonged environmental contamination (or both).

Despite many individual exposures to widespread low-level spore contamination in private residences and in work spaces for extended periods of time (at least 1 year in one instance), only one other individual acquired an infection (cutaneous). Whilst recognising the difficulty in making definitive inferences from these incidents to specific residual contamination levels, and by extending the risk to public health, we believe it may be useful to reflect on these findings when considering future incident management risk assessments and decisions in similar incidents that result in low-level indoor contamination.

Anthrax is an important disease caused by the bacterium Bacillus anthracis affecting both domestic and wild animals at the wildlife/livestock interface, defined here as a physical space in which wild and domestic species overlap in range and potentially interact. In endemic regions, sporadic anthrax outbreaks occur, causing significant deaths of both wildlife and livestock and sporadically, humans. However, it may also occur as isolated outbreaks with a few animals affected. Such isolated anthrax outbreaks maybe missed. High seroprevalence among carnivores suggests either regular non-fatal exposure to the pathogen circulating in a given environment, or contact with missed cases through consumption of anthrax carcases. To investigate the relevance of this potential indicator, a cross-sectional study was conducted to determine anthrax seroprevalence in domestic dogs (Canis lupus familiaris) from selected interface and non-interface areas of Zimbabwe with known history of anthrax outbreaks. Based on past anthrax outbreaks in the respective areas, the sites were further classified as high or low risk areas for anthrax outbreaks. Sera were collected from domestic dogs (n = 186) and tested for antibodies against B. anthracis protective antigens (PA) using an ELISA test. The overall seroprevalence was 51.6% (96/186; 95% CI 44.2–59.0). Sites from the non-interface areas recorded a significantly (P < 0.001) higher (72.1%) anthrax seroprevalence compared with those from the wildlife –livestock interface (41.5%). The results demonstrated a strong association (χ2 = 14.3; OR = 3.2, 1.6 < OR < 6.2, P < 0.001) between anthrax seropositivity and interface type. Low-risk sites (42.5%) had a significantly (P = 0.044) lower seroprevalence compared with high-risk sites (58.5%) but still demonstrated high seroprevalence for areas where anthrax was last reported more than 20 years back. Dogs from Tsholotsho South were more than 90-times (OR = 96.5, 13.5 < OR < 690.8) more likely to be seropositive compared with those from Hwange. The study demonstrated the potential to use domestic dogs as indicators of anthrax in the study areas to survey anthrax circulation in supposed low-risk areas and calls for a redefinition of both low and high risk areas for anthrax in Zimbabwe based on an improved surveillance.

Hepatitis E virus genotype 1 (HEV G1) is an important cause of morbidity and mortality in Africa and Asia. HEV G1's natural history, including the incubation period, remains poorly understood, hindering surveillance efforts and effective control. Using individual-level data from 85 travel-related HEV G1 cases in England and Wales, we estimate the incubation period distribution using survival analysis methods, which allow for appropriate inference when only time ranges, rather than exact times are known for the exposure to HEV and symptom onset. We estimated a 29.8-day (95% confidence interval (CI) 24.1–36.0) median incubation period with 5% of people expected to develop symptoms within 14.3 days (95% CI 10.1–21.7) and 95% within 61.9 days (95% CI 47.4–74.4) of exposure. These estimates can help refine clinical case definitions and inform the design of disease burden and intervention studies.

Chronic hepatitis C virus (HCV) infection is the most common blood-borne infection in the USA. Estimating prevalence is critical for monitoring diagnosis, treatment, and cure and for allocating resources. Surveillance data reported to the New York City (NYC) Health Department, 2000–2015, were used to estimate HCV prevalence in NYC in 2015. The numbers who died, out-migrated or whose last RNA test was negative were removed from the count of people reported with HCV. A simulation model was used to remove estimates of people whose infection spontaneously cleared or was cured and to add an estimate of people unaware of infection. The surveillance-based HCV prevalence in NYC in 2015 overall was 1.4% (95% certainty level (CL) 1.2–1.6%; n ≈ 116 000, 95% CL ≈99 000–135 000) and among adults aged ⩾20 years was 1.8% (95% CL 1.5–2.0%, n ≈ 115 000, 95% CL ≈99 000–134 000), lower than the 2010 estimate among adults aged ⩾20 years of 2.4% (n ≈ 147 000). Contributors to the decrease in HCV prevalence from 2010 to 2015 include both the availability of highly effective treatment and also deaths among an ageing population. The 2015 estimate can be used to set NYC-specific HCV screening and treatment targets and monitor progress towards HCV elimination.

Occurrence of Salmonella spp. in captive wild animal species in India is largely unknown. The purpose of this study was to determine the occurrence of different Salmonella serotypes, antimicrobial resistance patterns and genotypic relatedness of recovered isolates. A total of 370 samples including faecal (n = 314), feed and water (n = 26) and caretakers stool swabs (n = 30) were collected from 40 different wild animal species in captivity, their caretakers, feed and water in four zoological gardens and wildlife enclosures in India. Salmonellae were isolated using conventional culture methods and tested for antimicrobial susceptibility with the Kirby–Bauer disc diffusion method. Salmonella isolates were serotyped and genotyping was performed using enterobacterial repetitive intergenic consensus (ERIC) PCR and 16S rRNA sequencing. Animal faecal samples were also subjected to direct PCR assay. Salmonella was detected in 10 of 314 (3.1%) faecal samples by isolation and 18 of 314 (5.7%) samples by direct PCR assay; one of 26 (3.8%) feed and water samples and five of 30 (16.7%) caretakers stool swabs by isolation. Salmonella was more commonly isolated in faecal samples from golden pheasants (25%; 2/8) and leopard (10%; 2/20). Salmonella enterica serotypes of known public health significance including S. Typhimurium (37.5%; 6/14), S. Kentucky (28.5%; 4/14) and S. Enteritidis (14.3%; 2/14) were identified. While the majority of the Salmonella isolates were pan-susceptible to the commonly used antibiotics. Seven (43.7%; 7/16) of the isolates were resistant to at least one antibiotic and one isolate each among them exhibited penta and tetra multidrug-resistant types. Three S. Kentucky serotype were identified in a same golden pheasants cage, two from the birds and one from the feed. This serotype was also isolated from its caretaker. Similarly, one isolate each of S. Typhimurium were recovered from ostrich and its caretaker. These isolates were found to be clonally related suggesting that wildlife may serve as reservoir for infections to humans and vice versa. These results emphasise the transmission of Salmonella among hosts via environmental contamination of feces to workers, visitors and other wildlife.

Escherichia coli O157:H7 is the largest cause of hemolytic uremic syndrome (HUS). Previous studies proposed that HUS risk varies across the E. coli O157:H7 phylogenetic tree (hypervirulent clade 8), but the role of age in the association is unknown. We determined phylogenetic lineage of E. coli O157:H7 isolates from 1160 culture-confirmed E. coli O157:H7 cases reported in Washington State, 2004–2015. Using generalised estimating equations, we tested the association between phylogenetic lineage and HUS. Age was evaluated as an effect modifier. Among 1082 E. coli O157:H7 cases with both phylogenetic lineage and HUS status (HUS n = 76), stratified analysis suggested effect modification by age. Lineages IIa and IIb, relative to Ib, did not appear associated with HUS in children 0–9-years-old. For cases 10–59-years-old, lineages IIa and IIb appeared to confer increased risk of HUS, relative to lineage Ib. The association reversed in ⩾60-year-olds. Results were similar for clade 8. Phylogenetic lineage appears to be associated with HUS risk only among those ⩾10-years-old. Among children <10, the age group most frequently affected, lineage does not explain progression to HUS. However, lineage frequency varied across age groups, suggesting differences in exposure and/or early disease manifestation.

In the absence of perfect reference standard, classical techniques result in biased diagnostic accuracy and prevalence estimates. By statistically defining the true disease status, latent class models (LCM) constitute a promising alternative. However, LCM is a complex method which relies on parametric assumptions, including usually a conditional independence between tests and might suffer from data sparseness. We carefully applied LCMs to assess new campylobacter infection detection tests for which bacteriological culture is an imperfect reference standard. Five diagnostic tests (culture, polymerase chain reaction and three immunoenzymatic tests) of campylobacter infection were collected in 623 patients from Bordeaux and Lyon Hospitals, France. Their diagnostic accuracy were estimated with standard and extended LCMs with a thorough examination of models goodness-of-fit. The model including a residual dependence specific to the immunoenzymatic tests best complied with LCM assumptions. Asymptotic results of goodness-of-fit statistics were substantially impaired by data sparseness and empirical distributions were preferred. Results confirmed moderate sensitivity of the culture and high performances of immunoenzymatic tests. LCMs can be used to estimate diagnostic tests accuracy in the absence of perfect reference standard. However, their implementation and assessment require specific attention due to data sparseness and limitations of existing software.

Records of absenteeism from primary schools are valuable data for infectious diseases surveillance. However, the analysis of the absenteeism is complicated by the data features of clustering at zero, non-independence and overdispersion. This study aimed to generate an appropriate model to handle the absenteeism data collected in a European Commission granted project for infectious disease surveillance in rural China and to evaluate the validity and timeliness of the resulting model for early warnings of infectious disease outbreak. Four steps were taken: (1) building a ‘well-fitting’ model by the zero-inflated Poisson model with random effects (ZIP-RE) using the absenteeism data from the first implementation year; (2) applying the resulting model to predict the ‘expected’ number of absenteeism events in the second implementation year; (3) computing the differences between the observations and the expected values (O–E values) to generate an alternative series of data; (4) evaluating the early warning validity and timeliness of the observational data and model-based O–E values via the EARS-3C algorithms with regard to the detection of real cluster events. The results indicate that ZIP-RE and its corresponding O–E values could improve the detection of aberrations, reduce the false-positive signals and are applicable to the zero-inflated data.

Common childhood infectious diseases have been associated with a reduced risk of following haematopoietic malignancies, but investigations on multiple myeloma (MM) are scarce. Information about 213 MM cases and 1128 healthy controls were obtained from a multicentre population-based Italian case-control study. The association between chickenpox, measles, mumps, pertussis and rubella and the MM risk was estimated by unconditional logistic regression, adjusting for age, gender and residence area. No association was found between MM risk and any considered infectious disease. The number of infections was slightly inversely associated with the risk of MM, but statistical significance was not reached (OR 0.87, 95% CI 0.55–1.4 for 1-2 diseases vs. none and OR 0.68, 95% CI 0.41–1.1 for 3-5 diseases, respectively, P = 0.131). We did not find a clear evidence that common infections during childhood are associated with the subsequent risk of developing MM.

Although measles incidence has reached historic lows in many parts of the world, the disease still causes substantial morbidity globally. Even where control programs have succeeded in driving measles locally extinct, unless vaccination coverage is maintained at extremely high levels, susceptible numbers may increase sufficiently to spark large outbreaks. Human mobility will drive potentially infectious contacts and interact with the landscape of susceptibility to determine the pattern of measles outbreaks. These interactions have proved difficult to characterise empirically. We explore the degree to which new sources of data combined with existing public health data can be used to evaluate the landscape of immunity and the role of spatial movement for measles introductions by retrospectively evaluating our ability to predict measles outbreaks in vaccinated populations. Using inferred spatial patterns of accumulation of susceptible individuals and travel data, we predicted the timing of epidemics in each district of Pakistan during a large measles outbreak in 2012–2013 with over 30 000 reported cases. We combined these data with mobility data extracted from over 40 million mobile phone subscribers during the same time frame in the country to quantify the role of connectivity in the spread of measles. We investigate how different approaches could contribute to targeting vaccination efforts to reach districts before outbreaks started. While some prediction was possible, accuracy was low and we discuss key uncertainties linked to existing data streams that impede such inference and detail what data might be necessary to robustly infer timing of epidemics.

Fever is a common adverse event following measles vaccination, more frequent among older children and those receiving Measles-Mumps-Rubella-Varicella vaccine vs. Measles-Mumps-Rubella vaccine, two factors associated with a better antibody response. However, the role of fever in the immunogenicity of measles-containing vaccines (MCV) is unclear. We performed a post-hoc pooled analysis of data of 5 216 11 to 22 month-old children receiving MCV from 2004 to 2012 in Europe and USA to evaluate the association between post-immunisation fever and antibody response, measured by geometric mean concentrations (GMCs). We further evaluated fever as an effect modifier or a mediator in the associations between the type of MCV or the age at first vaccination and vaccine immunogenicity. After the first dose, fever was associated with 60% higher GMCs (95% CI 1.51–1.68). For children vaccinated at ⩾12 months, the fever did not modify and minimally mediated (2% to 3%) the association between age and antibody response. Fever mediated 18% of the association between type of MCV and GMCs. In a model including fever, age and type of vaccine, fever was the strongest predictor of GMCs. These results suggest that fever is associated with a stronger measles antibody response independently of age and type of MCV.

The present cross-sectional serosurvey constitutes the first effort to describe the varicella zoster virus (VZV) seroepidemiology in Serbia. An age-stratified serum bank of 3570 residual samples collected between 2015 and 2016 in each of the seven districts of the Vojvodina Province was tested for IgG anti-VZV antibodies with an enzyme immunoassay. Results were standardised into common units according to the European Sero-Epidemiology Network (ESEN2) methodology. Univariable and multivariable analyses were used to examine the relationships between standardised anti-VZV positivity or logarithmically transformed antibody titres and demographic features of study subjects. Seropositivity (85% overall) increased with age, in parallel with geometric mean titres. By the time of school entry, 68% of children were immune. The slower subsequent acquisition of immunity leaves epidemiologically relevant proportions of adolescents (7%), young adults (6%) and especially females of reproductive age (6%) prone to more severe forms of varicella. In the ongoing pre-vaccine era, natural infection provides a high level of collective immunity, with the highest VZV transmission in children of preschool age. The detected gaps in VZV immunity of the Serbian population support the adoption of the official recommendations for varicella immunisation of non-immune adolescents and young adults, including non-pregnant women of childbearing age.

The environmental bacterium, Burkholderia pseudomallei, is responsible for the potentially fatal disease melioidosis. Factors responsible for the temporospatial distribution of cases are incompletely understood, although a combination of rainfall, groundwater levels and the physicochemical properties of soil are important. The distribution of culture-positive cases of melioidosis from 1996 to 2016 in Far North Queensland, Australia, was investigated to determine the association with different soil types and landforms in Cairns, the region's largest city. Cases were clustered on alluvial fan landforms of strongly bleached gradational textured and yellow massive gradational textured soils indicating these soils are more suitable for B. pseudomallei and risk of melioidosis infection is higher in these areas, cases were less frequent on other soil types on alluvial fan landforms (despite comparable population density) and beach ridges. This indicates that the combination of these soils might be more suitable for B. pseudomallei, increasing the risk of disease in these locations. Sociodemographic characterisics of the population in cluster locations were considered. Knowledge of local soil characteristics may help predict cases of melioidosis and inform public health strategies to prevent the disease. Because melioidosis case clusters were identified, testing for the presence of B. pseudomallei across the study area is a useful target of future research.