Information on the factors that cause or amplify foodborne illness outbreaks (contributing factors), such as ill workers or cross-contamination of food by workers, is critical to outbreak prevention. However, only about half of foodborne illness outbreaks reported to the United States’ Centers for Disease Control and Prevention (CDC) have an identified contributing factor, and data on outbreak characteristics that promote contributing factor identification are limited. To address these gaps, we analyzed data from 297 single-setting outbreaks reported to CDC's new outbreak surveillance system, which collects data from the environmental health component of outbreak investigations (often called environmental assessments), to identify outbreak characteristics associated with contributing factor identification. These analyses showed that outbreak contributing factors were more often identified when an outbreak etiologic agent had been identified, when the outbreak establishment prepared all meals on location and served more than 150 meals a day, when investigators contacted the establishment to schedule the environmental assessment within a day of the establishment being linked with an outbreak, and when multiple establishment visits were made to complete the environmental assessment. These findings suggest that contributing factor identification is influenced by multiple outbreak characteristics, and that timely and comprehensive environmental assessments are important to contributing factor identification. They also highlight the need for strong environmental health and food safety programs that have the capacity to complete such environmental assessments during outbreak investigations.

Elderly individuals with tuberculosis (TB) are more likely to have a non-specific clinical presentation of TB and high mortality. However, factors associated with mortality in elderly TB patients have not been extensively studied. This retrospective cohort study aimed to identify factors associated with death among elderly Taiwanese with TB. All elderly patients with TB from 2006 to 2014 in Taipei, Taiwan, were included in a study. Multiple logistic regression was used to identify the factors associated with death in elderly TB patients. The mean age of the 5011 patients was 79·7 years; 74·1% were men; 32·7% had mortality during the study follow-up period. After controlling for potential confounders, age ⩾75 years (reference: 65–74 years), male sex, end-stage renal disease (ESRD), malignancy, acid-fast bacilli-smear positivity, TB-culture positivity, pleural effusion on chest radiograph and notification by an ordinary ward or intensive care unit were associated with a higher risk of all-cause death; while high school, and university or higher education, cavity on chest radiograph and directly observed therapy were associated with a lower risk of all-cause death. This study found that the proportion of death among elderly patients with TB in Taipei, Taiwan, was high. To improve TB treatment outcomes, future control programmes should particularly target individuals with comorbidities (e.g. ESRD and malignancy) and those with a lower socio-economic status (e.g. not educated).

The establishment of Aedes albopictus in southern France, a recognized competent vector for several arboviruses, represents a new threat for the local transmission and spread of what were until recently considered as tropical diseases. A preparedness and response plan, based on vigilance of both clinicians and laboratories, has introduced significant changes in guidelines and behaviour regarding patients’ care specifically during the activity period of mosquitoes. In the present study, we report the results of a 1-year activity in arboviral infection diagnosis. A total of 141 patients were included in this retrospective study. The number of suspected imported and autochthonous cases was 69 and 72, respectively. A diagnosis of arboviral infection was confirmed for 15 (21·7%) suspected imported cases, with identification of 13 dengue viruses, one chikungunya virus and one Zika virus. No autochthonous cases were detected. This report illustrates the increase in requests for arboviral infection diagnosis and confirms the challenge with identifying autochthonous arboviral infection cases in many unspecific febrile syndromes.

Since April 2015, whole genome sequencing (WGS) has been the routine test for Salmonella identification, surveillance and outbreak investigation at the national reference laboratory in England and Wales. In May 2015, an outbreak of Salmonella Enteritidis cases was detected using WGS data and investigated. UK cases were interviewed to obtain a food history and links between suppliers were mapped to produce a food chain network for chicken eggs. The association between the food chain network and the phylogeny was explored using a network comparison approach. Food and environmental samples were taken from premises linked to cases and tested for Salmonella. Within the outbreak single nucleotide polymorphism defined cluster, 136 cases were identified in the UK and 18 in Spain. One isolate from a food containing chicken eggs was within the outbreak cluster. There was a significant association between the chicken egg food chain of UK cases and phylogeny of outbreak isolates. This is the first published Salmonella outbreak to be prospectively detected using WGS. This outbreak in the UK was linked with contemporaneous cases in Spain by WGS. We conclude that UK and Spanish cases were exposed to a common source of Salmonella-contaminated chicken eggs.

Diagnosis of latent tuberculosis infection (LTBI) is a concern in haemodialysis (HD) patients. Many studies have compared QuantiFERON-TB Gold In-Tube (QFT-GIT) and tuberculin skin test (TST) for detecting LTBI and reported the κ statistic of agreement between QFT-GIT and TST in HD patients. The present study aimed to systematically review this literature and conduct meta-analysis of individual studies that estimated the κ between QFT-GIT with TST among HD patients. All relevant published studies that were available as full-text were obtained by searching Medline (1950), Web of Sciences (1945), Scopus (1973) through May 2016. The κ was re-estimated from the individual studies and pooled using random effect meta-analysis. Subgroup analysis and meta-regression were applied to evaluate the effect of Bacillus Calmette–Guérin (BCG) vaccination, TST cut-off points, quality of studies, sample size and age on variation of κ estimate. Eight studies involving 901 HD patients were included in meta-analysis. The pooled κ estimate was 0·28 (I 2 = 18·4%, P = 0·239, 95% confidence intervals 0·22–0·34). The discordance of TST−/QFT-GIT+ was more than TST+/QFT-GIT−. History of BCG vaccination, TST cut-off points and age are related to variation of κ estimates. TST and QFT-GIT are not comparable in detecting LTBI in HD patients. The higher TST−/QFT-GIT+ ratio compared with TST+/QFT-GIT− ratio, may indicate the superiority of QFT-GIT over TST for detection LTBI in HD patients.

Bovine calf scours reported to be caused by multiple aetiologies resulting in heavy mortality in unweaned calves and huge economic loss to the dairy farmers. Among these, cryptosporidiosis is an emerging waterborne zoonoses and one of the important causes of neonatal calf diarrhoea. Poor immune response coupled with primary cryptosporidial infections predispose neonatal calves to multiple secondary infections resulting in their deaths. In the present study, faecal samples from 100 diarrhoeic calves randomly picked up out of 17 outbreaks of bovine calf diarrhoea in periurban Ludhiana, Punjab in Northern India were subjected to conventional (microscopy, modified Zeihl–Neelsen (mZN) staining) and immunological and molecular techniques (faecal antigen capture ELISA and PCR) for detection of primary Cryptosporidium parvum infection as well as other frequently reported concurrent pathogens, viz. rotavirus and coronavirus, Salmonella spp., Escherichia coli, Clostridium perfringens and Eimeria spp. The faecal antigen capture ELISA and PCR revealed 35% prevalence of C. parvum in contrast to 25% by mZN staining with a relatively higher prevalence (66·7%) in younger (8–14-day-old) calves. The detection rate of the other enteropathogens associated with C. parvum was 45·71% for C. perfringens followed by Salmonella spp (40·0%), rotavirus (36·0%), coronavirus (16·0%), E. coli (12·0%) and Eimeria spp (4·0%) The sensitivity for detection of C. parvum by ELISA and mZN staining in comparison to PCR was 97·14% and 72·72%, respectively. An important finding of the study was that C. parvum alone was found in only 10% of the diarrhoeic faecal samples, whereas, majority of the samples (90%) showed mixed infections ranging from a combination of two to five agents. This is the first documentary proof of C. parvum and associated pathogens responsible for severe periurban outbreaks of bovine calf diarrhoea culminating in heavy mortality from Northern India.

Zoonotic diseases are a significant health threat for humans and animals. To better understand the epidemiology, etiology, and pathology of infectious agents affecting humans and animals combined approaches are needed. Here we describe an epidemiological investigation conducted by physicians and veterinarians after a reported case of psittacosis. Upon admission suffering from respiratory distress syndrome in a hospital and with a history of bird contact, a female patient was serologically diagnosed with psittacosis. After the case notification, veterinarians were able to investigate the source of infection by detecting Chlamydia psittaci in her pet cockatiel. The bird was hospitalized and successfully treated. In addition, the establishment where the pet bird was purchased was traced and through molecular techniques other birds intended to be sold as pets tested positive for C. psittaci. As a result, sanitary measures were applied and the establishment then was closed down. The birds intended for the pet commerce were treated and retested with negative molecular results for C. psittaci, thus avoiding disease propagation. Reliable data about zoonotic diseases can only be generated through the application of multidisciplinary approaches which take into account the epidemiological factors and interactions of humans, animals and their environments as an integrated system.

Sweden reports large and variable numbers of human tularemia cases, but the high-risk regions are anecdotally defined and factors explaining annual variations are poorly understood. Here, high-risk regions were identified by spatial cluster analysis on disease surveillance data for 1984–2012. Negative binomial regression with five previously validated predictors (including predicted mosquito abundance and predictors based on local weather data) was used to model the annual number of tularemia cases within the high-risk regions. Seven high-risk regions were identified with annual incidences of 3·8–44 cases/100 000 inhabitants, accounting for 56·4% of the tularemia cases but only 9·3% of Sweden's population. For all high-risk regions, most cases occurred between July and September. The regression models explained the annual variation of tularemia cases within most high-risk regions and discriminated between years with and without outbreaks. In conclusion, tularemia in Sweden is concentrated in a few high-risk regions and shows high annual and seasonal variations. We present reproducible methods for identifying tularemia high-risk regions and modelling tularemia cases within these regions. The results may help health authorities to target populations at risk and lay the foundation for developing an early warning system for outbreaks.

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.

We investigated the relationship between epidemics and soil radiation through an exploratory study using sentinel surveillance data (individuals aged <20 years) during the last three epidemic seasons of influenza and norovirus in Japan. We used a spatial analysis method of a geographical information system (GIS). We mapped the epidemic spreading patterns from sentinel incidence rates. We calculated the average soil radiation [dm (μGy/h)] for each sentinel site using data on uranium, thorium, and potassium oxide in the soil and examined the incidence rate in units of 0·01 μGy/h. The correlations between the incidence rate and the average soil radiation were assessed. Epidemic clusters of influenza and norovirus infections were observed in areas with relatively high radiation exposure. A positive correlation was detected between the average incidence rate and radiation dose, at r = 0·61–0·84 (P < 0·01) for influenza infections and r = 0·61–0·72 (P < 0·01) for norovirus infections. An increase in the incidence rate was found between areas with radiation exposure of 0 < dm < 0·01 and 0·15 ⩽ dm < 0·16, at 1·80 [95% confidence interval (CI) 1·47–2·12] times higher for influenza infection and 2·07 (95% CI 1·53–2·61) times higher for norovirus infection. Our results suggest a potential association between decreased immunity and irradiation because of soil radiation. Further studies on immunity in these epidemic-prone areas are desirable.

Vitamin D could modulate pathways leading to dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). We examined the associations of serum total 25-hydroxy vitamin D [25(OH)D] and vitamin D binding protein (VDBP) concentrations in patients with uncomplicated dengue fever (DF) with risk of progression to DHF/DSS. In a case–control study nested in a cohort of DF patients who were followed during the acute episode in Bucaramanga, Colombia, we compared 25(OH)D and VDBP at onset of fever between 110 cases who progressed to DHF/DSS and 235 DF controls who did not progress. 25(OH)D concentrations were also compared between the acute sample and a sample collected >1 year post-convalescence in a subgroup. Compared with 25(OH)D ⩾75 nmol/l, adjusted odds ratios (95% CI) for progression were 0·44 (0·22–0·88) and 0·13 (0·02–1·05) for 50 to 75 nmol/l (vitamin D insufficiency) and <50 nmol/l (vitamin D deficiency), respectively (P, trend = 0·003). Mean 25(OH)D concentrations were much lower post-convalescence compared with the acute episode, regardless of case status. Compared with controls, mean VDBP was non-significantly lower in cases. We conclude that low serum 25(OH)D concentrations in DF patients predict decreased odds of progression to DHF/DSS.

The intensity of annual Spanish influenza activity is currently estimated from historical data of the Spanish Influenza Sentinel Surveillance System (SISSS) using qualitative indicators from the European Influenza Surveillance Network. However, these indicators are subjective, based on qualitative comparison with historical data of influenza-like illness rates. This pilot study assesses the implementation of Moving Epidemic Method (MEM) intensity levels during the 2014–2015 influenza season within the 17 sentinel networks covered by SISSS, comparing them to historically reported indicators. Intensity levels reported and those obtained with MEM at the epidemic peak of the influenza wave, and at national and regional levels did not show statistical difference (P = 0·74, Wilcoxon signed-rank test), suggesting that the implementation of MEM would have limited disrupting effects on the dynamic of notification within the surveillance system. MEM allows objective influenza surveillance monitoring and standardization of criteria for comparing the intensity of influenza epidemics in regions in Spain. Following this pilot study, MEM has been adopted to harmonize the reporting of intensity levels of influenza activity in Spain, starting in the 2015–2016 season.

Norovirus is detected in one in five diarrhoea episodes in children, yet little is known about environmental risk factors associated with this disease, especially in low-income settings. The objective of this study was to examine environmental risk factors, and spatial and seasonal patterns of norovirus diarrhoea episodes in children in León, Nicaragua. We followed a population-based cohort of children under age 5 years for norovirus diarrhoea over a 1-year period. At baseline, characteristics of each household were recorded. Households were geocoded and spatial locations of garbage dumps, rivers, and markets were collected. In bivariate analysis we observed younger children and those with animals in their households were more likely to have experienced norovirus episodes. In adjusted models, younger children remained at higher risk for norovirus episodes, but only modest associations were observed with family and environmental characteristics. We next identified symptomatic children living in the same household and within 500 m buffer zones around the household of another child infected with the same genotype. Norovirus diarrhoea episodes peaked early in the rainy season. These findings contribute to our understanding of environmental factors and norovirus infection.

Enteric pathogens are commonly known to be transmitted through food or water; however, contact with animals is another important transmission route. This study estimated the annual burden of illness attributable to animal contact for eight enteric pathogens in Canada. Using data from a Canadian expert elicitation on transmission routes, the proportion of enteric illnesses attributable to animal contact was estimated for each pathogen to estimate the annual number of illnesses, hospitalizations and deaths in Canada. For each estimate, a mean and probability intervals were generated. Of all illnesses caused by these eight pathogens, 16% were estimated attributable to animal contact. This estimate translates to 86 000 (31 000–166 000) illnesses, 488 (186–890) hospitalizations and 12 (2–28) deaths annually for the eight pathogens combined. Campylobacter spp. is the leading cause of illnesses annually, with an estimated 38 000 (14 000–71 000) illnesses occurring each year, followed by non-typhoidal Salmonella spp. (17 000, 6000–32 000). The majority of hospitalizations were attributable to non-typhoidal Salmonella spp. (36%) and Campylobacter spp. (31%). Non-typhoidal Salmonella spp. (28%) and Listeria monocytogenes (31%) were responsible for the majority of the estimated deaths. These results identify farm animal and pet/pet food exposure as key pathways of transmission for several pathogens. The estimated burden of illness associated with animal contact is substantial.

During May 2015, an increase in Salmonella Agona cases was reported from western Sydney, Australia. We examine the public health actions used to investigate and control this increase. A descriptive case-series investigation was conducted. Six outbreak cases were identified; all had consumed cooked tuna sushi rolls purchased within a western Sydney shopping complex. Onset of illness for outbreak cases occurred between 7 April and 24 May 2015. Salmonella was isolated from food samples collected from the implicated premise and a prohibition order issued. No further cases were identified following this action. Whole genome sequence (WGS) analysis was performed on isolates recovered during this investigation, with additional S. Agona isolates from sporadic-clinical cases and routine food sampling in New South Wales, January to July 2015. Clinical isolates of outbreak cases were indistinguishable from food isolates collected from the implicated sushi outlet. Five additional clinical isolates not originally considered to be linked to the outbreak were genomically similar to outbreak isolates, indicating the point-source contamination may have started before routine surveillance identified an increase. This investigation demonstrated the value of genomics-guided public health action, where near real-time WGS enhanced the resolution of the epidemiological investigation.

Leptospirosis is the most widespread zoonosis in humans worldwide. In the United States, widespread detection of antibodies to leptospirosis have been identified in feral swine (Sus scrofa) with the highest detection of serovars, Bratislava, Icterohaemorrhagiae, and Pomona. Over the past few years, feral swine populations have expanded their geographical range and distribution in the United States with reports in at least 39 of 50 states. Since feral swine serve as reservoirs for serovars that can infect humans, it is important to understand the risk of transmission. In order to learn more about the probability that feral swine shed infectious leptospires, we collected kidneys and paired serum when possible from 677 feral swine in 124 counties of 29 states. These counties had previously been identified as antibody positive for Leptospira interrogans serovars Bratislava, Canicola, Grippotyphosa, Hardjo, Icterohaemorrhagiae or Pomona. Although exposure to these same six serovars of leptospirosis continued to be high (53% overall) in the counties we sampled, we detected leptospiral DNA in only 3·4% of feral swine kidneys tested. Based on these results, it appears that although feral swine can serve as a source of infection to humans, especially in those who are more likely to encounter them directly such as wildlife biologists, veterinarians, and hunters, the risk may be relatively low. However, further studies to examine the relationship between leptospiral shedding in the urine and kidneys in addition to culturing the organism are recommended in order to better understand the risk associated with feral swine.

Mycobacterium avium sp. avium (MAA), M. avium sp. hominissuis (MAH), and M. avium sp. paratuberculosis (MAP) are the main members of the M. avium complex (MAC) causing diseases in several hosts. The aim of this study was to describe the genetic diversity of MAC isolated from different hosts. Twenty-six MAH and 61 MAP isolates were recovered from humans and cattle, respectively. GenoType CM® and IS1311-PCR were used to identify Mycobacterium species. The IS901-PCR was used to differentiate between MAH and MAA, while IS900-PCR was used to identify MAP. Genotyping was performed using a mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) scheme (loci: 292, X3, 25, 47, 3, 7, 10, 32) and patterns (INMV) were assigned according to the MAC-INMV database (http://mac-inmv.tours.inra.fr/). Twenty-two (22/26, 84·6%) MAH isolates were genotyped and 16 were grouped into the following, INMV 92, INMV 121, INMV 97, INMV 103, INMV 50, and INMV 40. The loci X3 and 25 showed the largest diversity (D: 0·5844), and the global discriminatory index (Hunter and Gaston discriminatory index, HGDI) was 0·9300. MAP (100%) isolates were grouped into INMV 1, INMV 2, INMV 11, INMV 8, and INMV 5. The HGDI was 0·6984 and loci 292 and 7 had the largest D (0·6980 and 0·5050). MAH presented a higher D when compared with MAP. The MIRU-VNTR was a useful tool to describe the genetic diversity of both MAH and MAP as well as to identify six new MAH patterns that were conveniently reported to the MAC-INMV database. It was also demonstrated that, in the geographical region studied, human MAC cases were produced by MAH as there was no MAA found among the human clinical samples.

A subtyping methodology for Campylobacter, Comparative Genomic Fingerprinting (CGF40), has been described recently. The objective of this study was to assess the utility of CGF40 as a tool to enhance routine public health surveillance of campylobacteriosis. Isolates of Campylobacter from across the province were requested and sent for CGF40 subtyping. Epidemiological data from cases reported to public health officials in Nova Scotia, Canada, from January 2012 to March 2015 were linked with blinded CGF40 subtyping results. CGF40 was epidemiologically valid; subtyping discerned known epidemiologically related isolates and augmented case-finding. Predominant sources and locations of subtype detection from the national reference database showed some study subtypes were rare and even novel to the database, while others were more commonly identified over multiple years and with exposures locally and internationally. A case-case study design was applied to examine risk factors for the most common CGF40 subtypes detected. Differences in the epidemiology of different CGF40 subtypes were observed. Statistically significant associations were noted for specific subtypes with rural residence, local exposure, contact with a pet dog or cat, contact with chickens, and drinking unpasteurized milk. With prospective use, CGF40 could potentially identify unrecognized outbreaks and contribute to epidemiological investigations of case clusters.

In 2011 the Incidence Assay Critical Path Working Group reviewed the current state of HIV incidence assays and helped to determine a critical path to the introduction of an HIV incidence assay. At that time the Consortium for Evaluation and Performance of HIV Incidence Assays (CEPHIA) was formed to spur progress and raise standards among assay developers, scientists and laboratories involved in HIV incidence measurement and to structure and conduct a direct independent comparative evaluation of the performance of 10 existing HIV incidence assays, to be considered singly and in combinations as recent infection test algorithms. In this paper we report on a new framework for HIV incidence assay evaluation that has emerged from this effort over the past 5 years, which includes a preliminary target product profile for an incidence assay, a consensus around key performance metrics along with analytical tools and deployment of a standardized approach for incidence assay evaluation. The specimen panels for this evaluation have been collected in large volumes, characterized using a novel approach for infection dating rules and assembled into panels designed to assess the impact of important sources of measurement error with incidence assays such as viral subtype, elite host control of viraemia and antiretroviral treatment. We present the specific rationale for several of these innovations, and discuss important resources for assay developers and researchers that have recently become available. Finally, we summarize the key remaining steps on the path to development and implementation of reliable assays for monitoring HIV incidence at a population level.

Campylobacteriosis, the most frequent bacterial enteric disease, shows a clear yet unexplained seasonality. The study purpose was to explore the influence of seasonal fluctuation in the contamination of and in the behaviour exposures to two important sources of Campylobacter on the seasonality of campylobacteriosis. Time series analyses were applied to data collected through an integrated surveillance system in Canada in 2005–2010. Data included sporadic, domestically-acquired cases of Campylobacter jejuni infection, contamination of retail chicken meat and of surface water by C. jejuni, and exposure to each source through barbequing and swimming in natural waters. Seasonal patterns were evident for all variables with a peak in summer for human cases and for both exposures, in fall for chicken meat contamination, and in late fall for water contamination. Time series analyses showed that the observed campylobacteriosis summer peak could only be significantly linked to behaviour exposures rather than sources contamination (swimming rather than water contamination and barbequing rather than chicken meat contamination). The results indicate that the observed summer increase in human cases may be more the result of amplification through more frequent risky exposures rather than the result of an increase of the Campylobacter source contamination.