Epidemiology & Infection - Latest issue

Seasonal autoregressive integrated moving average (SARIMA) has been used to model nationwide tuberculosis (TB) incidence in other countries. This study aimed to characterise monthly TB notification rate in China. Monthly TB notification rate from 2005 to 2017 was used. Time-series analysis was based on a SARIMA model and a hybrid model of SARIMA-generalised regression neural network (GRNN) model. A decreasing trend (3.17% per years, P < 0.01) and seasonal variation of TB notification rate were found from 2005 to 2016 in China, with a predominant peak in spring. A SARIMA model of ARIMA (0,1,1) (0,1,1)12 was identified. The mean error rate of the single SARIMA model and the SARIMA–GRNN combination model was 6.07% and 2.56%, and the determination coefficient was 0.73 and 0.94, respectively. The better performance of the SARIMA–GRNN combination model was further confirmed with the forecasting dataset (2017). TB is a seasonal disease in China, with a predominant peak in spring, and the trend of TB decreased by 3.17% per year. The SARIMA–GRNN model was more effective than the widely used SARIMA model at predicting TB incidence.

This research investigates the long-forgotten relationship between diphtheria and tuberculosis. Historical medical reports from the late 19th century are reviewed followed by a statistical regression analysis of the relationship between the two diseases in the early 20th century. Historical medical reports show a consistent association between diphtheria and tuberculosis that can increase the likelihood and severity of either disease in a co-infection. The statistical analysis uses historical weekly public health data on reported cases in five American cities over a period of several years, finding a modest but statistically significant relationship between the two diseases. No current medical theory explains the association between diphtheria and tuberculosis. Alternative explanations are explored with a focus on how the diseases assimilate iron. In a co-infection, the effectiveness of tuberculosis at assimilating extracellular iron may lead to increased production of diphtheria toxin, worsening that disease, which may, in turn, exacerbate tuberculosis. Iron-dependent repressor genes connect both diseases.

The burden of tuberculosis (TB) among adolescents and young adults in endemic settings is poorly characterised. This study aimed to review published and unpublished estimates of the incidence and prevalence of bacteriologically confirmed TB among young people aged 10–24 years. We searched PubMed and World Health Organization archives for publications and unpublished data from population-based epidemiologic studies reporting confirmed pulmonary TB among young people, conducted from January 2000 onwards. We identified 27 publications and unpublished data from two national surveys, representing a total of 26 studies in 19 countries. The prevalence of bacteriologically confirmed TB ranged from 45 to 799 per 100 000 in the Asia-Pacific region and from 160 to 462 per 100 000 in African settings. We did not identify any epidemiologic studies of confirmed TB among adolescents living with human immunodeficiency virus (HIV). Many studies were excluded due to absent or inadequately reported age-specific data. Adolescents and young adults living in many endemic settings appear to be at substantial risk of developing active TB. There is a pressing need to improve the routine reporting of age in epidemiologic studies of TB, and to generate high-quality epidemiologic data regarding TB among adolescents living with HIV.

Studies estimating the human health impact of the foodborne disease often include estimates of the number of gastroenteritis hospitalisations. The aims of this study were to examine the degree to which hospital discharge data underreport hospitalisations due to bacterial gastroenteritis and to estimate the frequency of stool sample submission among patients presenting with gastroenteritis. Using linked laboratory and hospital discharge data from a healthcare organisation and its affiliated hospital, we examined the International Classification of Disease (ICD-9-CM) diagnosis codes assigned to hospitalised adults with culture-confirmed Campylobacter, Salmonella, or Escherichia coli O157 infections and determined the frequency of stool sample submission. Among 138 hospitalised patients with culture-confirmed infections, 43% of Campylobacter patients, 56% of Salmonella patients and 35% of E. coli O157 patients had that pathogen-specific code listed on the discharge record. Among patients without their infection listed as a diagnosis, 65% were assigned a nonspecific gastroenteritis code. Submitting a specimen for culture ⩾3 days before discharge was significantly associated with having the pathogen-specific diagnosis listed. Of 6181 patients assigned a nonspecific gastroenteritis code, 69% had submitted a stool sample for bacterial culture. This study can be used to understand differences and adjust for the underreporting and underdiagnosed of Campylobacter, Salmonella and E. coli O157 in hospital discharge and surveillance data, respectively.

Helicobacter pylori (H. pylori) is present in the stomach of half of the world's population. The force of infection describes the rate at which susceptibles acquire infection. In this article, we estimated the age-specific force of infection of H. pylori in Mexico. Data came from a national H. pylori seroepidemiology survey collected in Mexico in 1987–88. We modelled the number of individuals with H. pylori at a given age as a binomial random variable. We assumed that the cumulative risk of infection by a given age follows a modified exponential catalytic model, allowing some fraction of the population to remain uninfected. The cumulative risk of infection was modelled for each state in Mexico and were shrunk towards the overall national cumulative risk curve using Bayesian hierarchical models. The proportion of the population that can be infected (i.e. susceptible population) is 85.9% (95% credible interval (CR) 84.3%–87.5%). The constant rate of infection per year of age among the susceptible population is 0.092 (95% CR 0.084–0.100). The estimated force of infection was highest at birth 0.079 (95% CR 0.071–0.087) decreasing to zero as age increases. This Bayesian hierarchical model allows stable estimation of state-specific force of infection by pooling information between the states, resulting in more realistic estimates.

An emerging recombinant norovirus GII.P16/GII.4 Sydney 2012 strain caused a gastroenteritis outbreak amongst attendees at a large health function in regional New South Wales, Australia. This was the third outbreak caused by the recombinant GII.P16/GII.4 Sydney 2012 strain in this region in 2017, which appears to be emerging as a common strain in the Hunter New England region.

Campylobacter is the primary agent of human bacterial gastroenteritis worldwide. In contrast to temperate zones, weather effects on Campylobacter prevalence in broilers under tropical conditions are under-researched. We examined the association between weather and Campylobacter prevalence in slaughtered broilers in Sri Lanka, a tropical country with weather variations led by monsoons. Each month (October 2009–July 2011), 20–30 broiler batches referring to two semi-automated slaughterhouses from five Sri Lankan provinces were tested for Campylobacter contamination and analysed in relation to temperature, humidity and rainfall. Overall prevalence was 63.8% (95% CI 59.6–67.9%, n = 542), peaking in September–November. Each 1 °C increase in monthly mean temperature up to 26 °C increased Campylobacter-positive batches by 16.4% (95% CI 0.4–35.1%). For each 10 mm increase in monthly total rainfall up to 300 mm, Campylobacter-positive batches increased significantly by 0.8% (0.1–1.5%) at 1-month lag. For each 1% increase in relative humidity up to 80% at 1- and 2-month lags, Campylobacter-positive batches increased of respectively 4.2% (1.9–6.7%) and 4.0% (1.5–6.5), and decreased by 3.6% (2.6–4.6%) and 4.0% (2.6–5.4%) for unit increases above 80%. These results suggest that even in tropical countries without marked seasons, there are weather effects possibly reflecting Campylobacter potential to colonise its preferred host and/or survive in the environment.

French Guiana, a tropical country, is characterised by a young and multi-ethnic population. Difficulties in accessing safe water sources lead to outbreaks of gastroenteritis. The objectives of this study were (1) to describe the microbiological profile of shigella strains isolated in western French Guiana, including antimicrobial susceptibility and the distribution of strains in terms of species and serotypes and (2) to estimate the incidence of shigellosis in children under 5 years old. A retrospective observational study was conducted of 213 cases of shigellosis diagnosed in the biology department of the hospital centre for western French Guiana between 2000 and 2012 in children under 5 years old. The serogroups (formerly known as species) that predominates in French Guiana was Shigella flexneri. No resistance was observed to fluoroquinolones or to third-generation cephalosporins. The average incidence of shigellosis in children under 5 years old in western French Guiana was estimated at 189.6 cases per 100 000 inhabitants per year. Shigellosis is a public health problem in western French Guiana. These infections suggest the difficulties in accessing safe water sources and the lack of public sanitation. A quadrivalent vaccine containing Shigella sonnei and three serotypes of S. flexneri (S. flexneri 2a, 3a and 6) could provide broad coverage against shigella infections.

Antimicrobial resistance is a limiting factor for the success of the treatment of infectious diseases and is associated with increased morbidity and cost. The present study aims to evaluate prescribing patterns of antimicrobials and quantify progress in relation to targets for quality improvement in the prescription of antimicrobials in Northern Ireland's secondary care sector using three repetitive point prevalence surveys (PPS) over a 6-year period: the European Surveillance of Antimicrobial Consumption (ESAC-PPS) in 2009 and 2011 and the Global-PPS on Antimicrobial Consumption and Resistance in 2015. Out of 3605 patients surveyed over the three time points, 1239 (34.4%) were treated with an antibiotic, the most frequently prescribed antibiotic groups were a combination of penicillins, including β-lactamase inhibitors. Compliance with hospital antibiotic policies in 2009, 2011 and 2015 were 54.5%, 71.5% and 79.9%, respectively. Likewise, an indication for treatment was recorded in patient notes 88.5%, 87.7% and 90.6% in 2009, 2011 and 2015, respectively, and surgical prophylactic antibiotic prescriptions for >24 h was 3.9%, 3.2% and 0.7% in 2009, 2011 and 2015, respectively. Treatment based on biomarker data was used in 61.5% of cases. In conclusion, a general trend in the improvement of key antimicrobial-related quality indicators was noted. The PPS tool provided a convenient, inexpensive surveillance system of antimicrobial consumption and should be considered an essential component to establish and maintain informed antibiotic stewardship in hospitals.

Antimicrobials play a critical role in treating cases of invasive non-typhoidal salmonellosis (iNTS) and other diseases, but efficacy is hindered by resistant pathogens. Selection for phenotypical resistance may occur via several mechanisms. The current study aims to identify correlations that would allow indirect selection of increased resistance to ceftriaxone, ciprofloxacin and azithromycin to improve antimicrobial stewardship. These are medically important antibiotics for treating iNTS, but these resistances persist in non-Typhi Salmonella serotypes even though they are not licensed for use in US food animals. A set of 2875 Salmonella enterica isolates collected from animal sources by the National Antimicrobial Resistance Monitoring System were stratified in to 10 subpopulations based on serotype and host species. Collateral resistances in each subpopulation were estimated as network models of minimum inhibitory concentration partial correlations. Ceftriaxone sensitivity was correlated with other β-lactam resistances, and less commonly resistances to tetracycline, trimethoprim-sulfamethoxazole or kanamycin. Azithromycin resistance was frequently correlated with chloramphenicol resistance. Indirect selection for ciprofloxacin resistance via collateral selection appears unlikely. Density of the ACSSuT subgraph resistance aligned well with the phenotypical frequency. The current study identifies several important resistances in iNTS serotypes and further research is needed to identify the causative genetic correlations.

Antimicrobial use in pig farming is influenced by a range of risk factors, including herd characteristics, biosecurity level, farm performance, occurrence of clinical signs and vaccination scheme, as well as farmers’ attitudes and habits towards antimicrobial use. So far, the effect of these risk factors has been explored separately. Using an innovative method called multiblock partial least-squares regression, this study aimed to investigate, in a sample of 207 farrow-to-finish farms from Belgium, France, Germany and Sweden, the relative importance of the six above mentioned categories or ‘blocks’ of risk factors for antimicrobial use in pig production. Four country separate models were developed; they showed that all six blocks provided useful contribution to explaining antimicrobial use in at least one country. The occurrence of clinical signs, especially of respiratory and nervous diseases in fatteners, was one of the largest contributing blocks in all four countries, whereas the effect of the other blocks differed between countries. In terms of risk management, it suggests that a holistic and country-specific mitigation strategy is likely to be more effective. However, further research is needed to validate our findings in larger and more representative samples, as well as in other countries.

Risk populations for HIV infections tend to neglect condom use, making alternative preventive approaches necessary. Accordingly, we modelled the risk of sexual HIV transmission for condom use vs. use of rapid diagnostic test (RDT) systems with subsequent exclusion of potential sexual partners with a correctly or falsely positive test from unprotected sex with and without the use of HIV pre-exposure prophylaxis (PrEP) in a bio-statistical approach. We combined a previously described model of transmission risk for HIV-exposed individuals with a newly suggested model of risk of HIV exposure for sexually active HIV-negative individuals. The model was adapted for several stages of infection and different strategies of HIV infection prevention.

HIV prevention with RDTs can reduce the transmission risk by up to 97% compared with having sex without any prevention and up to 80% compared with condom use. Nevertheless, RDT-based prevention strategies demonstrate a lack of protection in several stages of infection; in particular, RNA-based RDT systems may fail under treatment. RDT-based pre-screening of potential sex partners prior to unprotected sexual contacts substantially reduces HIV transmission risk. Combination of different prevention strategies is advisable for high-risk groups.

UK guidelines recommend routine HIV testing in high prevalence emergency departments (ED) and targeted testing for HBV and HCV. The ‘Going Viral’ campaign implemented opt-out blood-borne virus (BBV) testing in adults in a high prevalence ED, to assess seroprevalence, uptake, linkage to care (LTC) rates and staff time taken to achieve LTC. Diagnosis status (new/known/unknown), current engagement in care, and severity of disease was established. LTC was defined as patient informed plus ⩾1 clinic visit. A total of 6211/24 981 ED attendees were tested (uptake 25%); 257 (4.1%) were BBV positive (15 co-infected), 84 (33%) required LTC. 100/147 (68%) HCV positives were viraemic; 44 (30%) required LTC (13 new, 16 disengaged). 26/54 (48%) HBV required LTC (seven new, 11 disengaged). 16/71 (23%) HIV required LTC (10 new, five disengaged). 26/84 (31%) patients requiring LTC had advanced disease (CD4 <350, APRI (AST-to-Platelet Ratio Index) >1, Fibroscan F3/F4 or liver cancer), including five with AIDS-defining conditions and three hepatocellular carcinomas. There were five BBV-related deaths. BBV prevalence was high (4.1%); most were HCV (2.4%). HIV patients were more successfully and quickly LTC than HBV or HCV patients. ED testing was valuable as one-third of those requiring LTC (new, disengaged or unknown status patients) had advanced disease.

Respondent-driven sampling (RDS) is widely used to estimate HIV prevalence in men who have sex with men (MSM). Mathematical models that are calibrated to these data may be compromised if they fail to account for selection biases in RDS surveys. To quantify the potential extent of this bias, an agent-based model of HIV in South Africa was calibrated to HIV prevalence and sexual behaviour data from South African studies of MSM, first reweighting the modelled MSM population to match the younger age profile of the RDS surveys (age-adjusted analysis) and then without reweighting (unadjusted analysis). The model estimated a median HIV prevalence in South African MSM in 2015 of 34.6% (inter-quartile range (IQR): 31.4–37.2%) in the age-adjusted analysis, compared with 26.1% (IQR: 24.1–28.4%) in the unadjusted analysis. The median lifetime risk of acquiring HIV in exclusively homosexual men was 88% (IQR: 82–92%) in the age-adjusted analysis, compared with 76% (IQR: 64–85%) in the unadjusted analysis. These results suggest that RDS studies may under-estimate the exceptionally high HIV prevalence rates in South African MSM because of over-sampling of younger MSM. Mathematical models that are calibrated to these data need to control for likely over-sampling of younger MSM.

The Belgian strategic plan to eliminate measles contains several vaccination strategies including routine immunisation programmes and catch-up campaigns. A new expanded programme on immunisation-based survey (2016) assessed the uptake of the recommended measles–mumps–rubella (MMR) vaccine in three different cohorts: toddlers, adolescents and parents of toddlers. A two-stage cluster sampling technique was used to select 875 toddlers (age 18–24 months) and 1250 adolescents (born in 2000) from 107 municipalities in Flanders. After consent of the parent(s), 746 (85.2%) families of toddlers and 1012 (81.0%) families of adolescents were interviewed at home. Measles vaccination coverage was high at 18–24 months (96.2%) and 81.5% were vaccinated at recommended age. Toddlers who had two siblings or a non-working mother or changed vaccinator were more at risk for not being vaccinated. Coverage of the teenager dose reached 93.5% and was lower in adolescents with educational underachievement or whose mother was part-time working or with a non-Belgian background. Only 56.0% of mothers and 48.3% of fathers remembered having received at least one measles-containing vaccine. Although measles vaccination coverage in toddlers meets the required standards for elimination, administration of the teenager dose of MMR vaccine and parent compliance to the recent measles catch-up campaign in Flanders leave room for improvement.

Using the dengue surveillance program, we prospectively collected data on all the suspected and confirmed cases of dengue in Barbados from 2006 to 2015. Data were analysed for demographic, seasonal and temporal dynamics of this disease in this country. The overall mean annual incidence rate of suspected and confirmed dengue over the study period was 0.49% (range 0.15%–0.99%) and 0.16% (range 0.05%−0.48%), respectively. There was a significant correlation between the mean monthly number of confirmed cases, the mean monthly rainfall and the mean monthly relative humidity percentage. Dengue in this population is predominantly an infection affecting children and young adults. The median age of the patients with both, suspected and confirmed dengue was 25 years and the highest proportion of cases was seen in the age group 0–15 years. The annual incidence rates of both the suspected and the confirmed cases showed an upward trend during the study period and this upward trend was more pronounced among children.

The purpose of the study was to weigh the community burden of chikungunya determinants on Reunion island. Risk factors were investigated within a subset of 2101 adult persons from a population-based cross-sectional serosurvey, using Poisson regression models for dichotomous outcomes. Design-based risk ratios and population attributable fractions (PAF) were generated distinguishing individual and contextual (i.e. that affect individuals collectively) determinants. The disease burden attributable to contextual determinants was twice that of individual determinants (overall PAF value 89.5% vs. 44.1%). In a model regrouping both categories of determinants, the independent risk factors were by decreasing PAF values: an interaction term between the reporting of a chikungunya history in the neighbourhood and individual house (PAF 45.9%), a maximal temperature of the month preceding the infection higher than 28.5 °C (PAF 25.7%), a socio-economically disadvantaged neighbourhood (PAF 19.0%), altitude of dwelling (PAF 13.1%), cumulated rainfalls of the month preceding the infection higher than 65 mm (PAF 12.6%), occupational inactivity (PAF 11.6%), poor knowledge on chikungunya transmission (PAF 7.3%) and obesity/overweight (PAF 5.2%). Taken together, these covariates and their underlying causative factors uncovered 80.8% of chikungunya at population level. Our findings lend support to a major role of contextual risk factors in chikungunya virus outbreaks.

The definition of severe acute respiratory infection (SARI) – a respiratory illness with fever and cough, occurring within the past 10 days and requiring hospital admission – has not been evaluated for critically ill patients. Using integrated electronic health records data, we developed an automated search algorithm to identify SARI cases in a large cohort of critical care patients and evaluate patient outcomes. We conducted a retrospective cohort study of all admissions to a medical intensive care unit from August 2009 through March 2016. Subsets were randomly selected for deriving and validating a search algorithm, which was compared with temporal trends in laboratory-confirmed influenza to ensure that SARI was correlated with influenza. The algorithm was applied to the cohort to identify clinical differences for patients with and without SARI. For identifying SARI, the algorithm (sensitivity, 86.9%; specificity, 95.6%) outperformed billing-based searching (sensitivity, 73.8%; specificity, 78.8%). Automated searching correlated with peaks in laboratory-confirmed influenza. Adjusted for severity of illness, SARI was associated with more hospital, intensive care unit and ventilator days but not with death or dismissal to home. The search algorithm accurately identified SARI for epidemiologic study and surveillance.