The objective of this systematic review and meta-analysis was to estimate the proportion of cases of non-typhoidal salmonellosis (NTS) that develop chronic sequelae, and to investigate factors associated with heterogeneity. Articles published in English prior to July 2011 were identified by searching PubMed, Agricola, CabDirect, and Food Safety and Technology Abstracts. Observational studies reporting the number of NTS cases that developed reactive arthritis (ReA), Reiter's syndrome (RS), haemolytic uraemic syndrome (HUS), irritable bowel syndrome (IBS), inflammatory bowel disease (IBD) or Guillain–Barré syndrome (GBS), Miller–Fisher syndrome (MFS) were included. Meta-analysis was performed using random effects and heterogeneity was assessed using the I2 value. Meta-regression was used to explore the influence of study-level variables on heterogeneity. A total of 32 studies were identified; 25 reported on ReA, five reported on RS, seven reported on IBS, two reported on IBD, two reported on GBS, one reported on MFS, and two reported on HUS. There was insufficient data in the literature to calculate a pooled estimate for RS, HUS, IBD, GBS, or MFS. The pooled estimate of the proportion of cases of NTS that developed ReA and IBS had substantive heterogeneity, limiting the applicability of a single estimate. Thus, these estimates should be interpreted with caution and reasons for the high heterogeneity should be further explored.

We examined multistate outbreaks attributed to raw tomatoes in the United States from 1990 to 2010. We summarized the demographic and epidemiological characteristics of 15 outbreaks resulting in 1959 illnesses, 384 hospitalizations, and three deaths. Most (80%) outbreaks were reported during 2000–2010; 73% occurred May–September. Outbreaks commonly affected adult (median age 34 years) women (median 58% of outbreak cases). All outbreaks were caused by Salmonella [serotypes Newport (n = 6 outbreaks), Braenderup (n = 2), Baildon, Enteritidis, Javiana, Montevideo, Thompson, Typhimurium (n = 1 each); multiple serotypes (n = 1)]. Red, round (69% of outbreaks), Roma (23%), and grape (8%) tomatoes were implicated. Most (93%) outbreaks were associated with tomatoes served predominantly in restaurants. However, traceback investigations suggested that contamination occurred on farms, at packinghouses, or at fresh-cut processing facilities. Government agencies, academia, trade associations, and the fresh tomato industry should consider further efforts to identify interventions to reduce contamination of tomatoes during production and processing.

Shiga toxin-producing Escherichia coli (STEC) infections have been associated with severe illness. Ruminants are seen as the main reservoir and the major transmission route is considered to be foodborne. In The Netherlands, a case-control study was conducted, using data collected during 2008–2012. Patients were interviewed and controls completed a self-administered questionnaire. Patients travelling abroad were excluded from the analyses. STEC O157 and non-O157 were examined separately and differentiated into two age groups (<10 years, ⩾10 years). We included 130 O157 cases, 78 non-O157 cases and 1563 controls. In both age groups of O157 patients, raw spreadable sausage was the main risk factor for infection. For STEC non-O157 cases aged <10 years, contact with farm animals was the main risk factor and in non-O157 cases aged ⩾10 years, consumption of beef was the main risk factor. During 2008–2012, risk factors for STEC infections in the Dutch population differed between age groups and serogroup categories, and were related to eating meat and contact with farm animals. Advising the public about the risks of consuming raw or undercooked meat (products) and hygiene habits in case of contact with farm animals, could help in the prevention of STEC infections.

Laboratory-based surveillance data is essential for monitoring trends in the incidence of enteric disease. Current Canadian human enteric surveillance systems report only confirmed cases of human enteric disease and are often unable to capture the number of negative test results. Data from 9116 hospital stool specimens from the Waterloo Region in Canada, with a mixed urban and rural population of about 500 000 were analysed to investigate the use of stool submission data and its role in reporting bias when determining the incidence of enteric disease. The proportion of stool specimens positive for Campylobacter spp. was highest in the 15–29 years age group, and in the 5–14 years age group for Salmonella spp. and E. coli O157:H7. By contrast, the age-specific incidence rates were highest for all three pathogens in the 0–4 years age group which also had the highest stool submission rate. This suggests that variations in age-specific stool submission rates are influencing current interpretation of surveillance data.

The objective of our analysis was to describe the aetiology, clinical features, and socio-demographic background of adults with diarrhoea attending different urban and rural diarrhoeal disease hospitals in Bangladesh. Between January 2010 and December 2011, a total of 5054 adult diarrhoeal patients aged ⩾20 years were enrolled into the Diarrhoeal Disease Surveillance Systems at four different hospitals (two rural and two urban) of Bangladesh. Middle-aged [adjusted odds ratio (aOR) 0·28, 95% confidence interval (CI) 0·23–0·35, P < 0·001] and elderly (aOR 0·15, 95% CI 0·11–0·20, P < 0·001) patients were more likely to present to rural diarrhoeal disease facilities than urban ones. Vibrio cholerae was the most commonly isolated pathogen (16%) of the four pathogens tested followed by rotavirus (5%), enterotoxigenic Escherichia coli (ETEC) (4%), and Shigella (4%). Of these pathogens, V. cholerae (19% vs. 11%, P < 0·001), ETEC (9% vs. 4%, P < 0·001), and rotavirus (5% vs. 3%, P = 0·013) were more commonly detected from patients presenting to urban hospitals than rural hospitals, but Shigella was more frequently isolated from patients presenting to rural hospitals than urban hospitals (7% vs. 2%, P < 0·001). The isolation rate of Shigella was higher in the elderly than in younger adults (8% vs. 3%, P < 0·001). Some or severe dehydration was higher in urban adults than rural adults (P < 0·001). Our findings indicate that despite economic and other progress made, conditions facilitating transmission of V. cholerae and Shigella prevail in adults with diarrhoea in Bangladesh and further efforts are needed to control these infections.

Escherichia coli O157 is a human pathogen carried asymptomatically by cattle and shed in their faeces. Infection can occur from the consumption of contaminated beef or by direct contact. Large variations of E. coli O157 shedding in cattle exist and vary in the number of cattle positive for E. coli O157 and the amount of bacteria (c.f.u./g faeces) shed by positive animals. To investigate E. coli O157 shedding and super-shedding (>104 c.f.u./g) we used daily sampling over two 8-day periods; in January 2013 (n = 12) and February 2013 (n = 21). Samples were tested by direct faecal culture for enumeration and by immunomagnetic separation to detect lower levels of shedding. We identified three patterns of shedding, similar to previously observed descriptions: intermittent, transient and consistent. The most commonly observed pattern was intermittent shedding and variation in the level of shedding could be large. This extreme variation is demonstrated by a heifer from which E. coli O157 could be not detected one day, was super-shedding E. coli O157 the next and was detected as shedding >100 c.f.u./g the following day. Recto-anal mucosal swab testing did not predict super-shedding in this cohort of heifers. The variable individual patterns of shedding suggest that a common mechanism of infection may not operate within such a herd when considering previously described patterns and the inferred mechanisms. The sporadic and intermittent nature of shedding is a challenge to identifying risk factors and potential intervention strategies.

Monitoring infections and risk in people who inject drugs (PWID) is important for informing public health responses. In 2011, a novel hepatitis C antibody (anti-HCV) avidity-testing algorithm to identify samples compatible with recent primary infection was introduced into a national surveillance survey. PWID are recruited annually, through >60 needle-and-syringe programmes and prescribing services. Of the 980 individuals that could have been at risk of HCV infection, there were 20 (2%) samples that were compatible with recent primary infection. These were more common among: those imprisoned ⩾5 times [8/213; adjusted odds ratio (aOR) 8·7, 95% confidence interval (CI) 2·04–37·03]; women (8/230; aOR 3·8, 95% CI 1·41–10·38); and those ever-infected with hepatitis B (5/56; aOR 6·25, 95% CI 2·12–18·43). This study is the first to apply this algorithm and to examine the risk factors associated with recently acquired HCV infection in a national sample of PWID in the UK. These findings highlight underlying risks and suggest targeted interventions are needed.

Using surveillance data, we describe the prevalence and characteristics of individuals in New York City (NYC) co-infected with human immunodeficiency virus (HIV) and hepatitis B virus (HBV) and/or hepatitis C virus (HCV). Surveillance databases including persons reported to the NYC Department of Health and Mental Hygiene with HIV, HBV, and HCV by 31 December 2010 and not known to be dead as of 1 January 2000, were matched with 2000–2011 vital statistics mortality data. Of 140 606 persons reported with HIV, 4% were co-infected with HBV only, 15% were co-infected with HCV only, and 1% were co-infected with HBV and HCV. In all groups, 70–80% were male. The most common race/ethnicity and HIV transmission risk groups were non-Hispanic blacks and men who have sex with men (MSM) for HIV/HBV infection, and non-Hispanic blacks, Hispanics, and injection drug users for HIV/HCV and HIV/HBV/HCV infections. The overall age-adjusted 2000–2011 mortality was higher in co-infected than HIV mono-infected individuals. Use of population-based surveillance data provided a comprehensive characterization of HIV co-infection with HBV and HCV. Our findings emphasize the importance of targeting HIV and viral hepatitis testing and prevention efforts to populations at risk for co-infection, and of integrating HIV and viral hepatitis care and testing services.

As influenza vaccination is now widely recommended, randomized clinical trials are no longer ethical in many populations. Therefore, observational studies on patients seeking medical care for acute respiratory illnesses (ARIs) are a popular option for estimating influenza vaccine effectiveness (VE). We developed a probability model for evaluating and comparing bias and precision of estimates of VE against symptomatic influenza from two commonly used case-control study designs: the test-negative design and the traditional case-control design. We show that when vaccination does not affect the probability of developing non-influenza ARI then VE estimates from test-negative design studies are unbiased even if vaccinees and non-vaccinees have different probabilities of seeking medical care against ARI, as long as the ratio of these probabilities is the same for illnesses resulting from influenza and non-influenza infections. Our numerical results suggest that in general, estimates from the test-negative design have smaller bias compared to estimates from the traditional case-control design as long as the probability of non-influenza ARI is similar among vaccinated and unvaccinated individuals. We did not find consistent differences between the standard errors of the estimates from the two study designs.

In recent years, several types of human adenovirus (HAdV) have arisen from the recombination between two or more previously known HAdV types, but their epidemiology is poorly understood. In this study, we investigated the circulation of HAdV-58, a recently described HAdV isolated from an HIV-positive patient in Córdoba city, Argentina. For this purpose, a 30-month survey was conducted to study the presence of this type of adenovirus in sewage samples collected at the inlet from a wastewater treatment plant in Córdoba city, Argentina. Complementarily, the virus was sought in stools of HIV-positive patients. Although HAdVs were detected in human stool samples and in a high percentage of sewage samples, no evidence of HAdV-58 circulation was detected. We suggest that there is no endemic circulation of HAdV-58 in the geographical local area. The trend is that the number of identified HAdVs increases over time. In this context, understanding the current circulating HAdVs may be biologically relevant.

Intra-home and kindergarten transmissions were the reported major modes of hand, foot, and mouth disease (HFMD) transmission in preschool children. However, infection at home is not common and 65–80% of cases do not attend preschool. We conducted a matched case-control study to explore the role of public playgrounds in the transmission of HFMD in addition to direct and indirect exposure to HFMD patients. We used 156 hospital source cases and 156 community source controls. Univariate analysis was followed by conditional logistic regression with attributable fraction computed. Adjusted odds ratios were 11·70 [95% confidence interval (CI) 1·26–109·40] for having HFMD cases in the same class, 14·19 (95% CI 3·55–56·74) for having HFMD cases within the 20 nearest neighbourhoods, 6·03 (95% CI 2·84–12·80) for exposure to public playgrounds, 2·13 (95% CI 1·05–4·32) for finger sucking and 0·29 (95% CI 0·11–0·78) for hand washing with soap before meals. The attributable fractions for the first four risk factors were 6·4%, 20·9%, 57·2% and 27·5%, respectively, while the population prevented fraction for hand washing with soap before meals was 18·7%. Based on our findings, hand washing with soap should be advocated. Health education could include topics which underline the precautions which need to be taken and the advice given regarding avoiding the use of public playgrounds during epidemic periods, especially when children have been getting sick.

Alcohol consumption is a possible co-factor of high-risk human papillomavirus (HR-HPV) persistence, a major step in cervical carcinogenesis, but the association between alcohol and continuous HPV infection remains unclear. This prospective study identified the association between alcohol consumption and HR-HPV persistence. Overall, 9230 women who underwent screening during 2002–2011 at the National Cancer Center, Korea were analysed in multivariate logistic regression. Current drinkers [odds ratio (OR) 2·49, 95% confidence interval (CI) 1·32–4·71] and drinkers for ⩾5 years (OR 2·33, 95% CI 1·17–4·63) had a higher risk of 2-year HR-HPV persistence (HPV positivity for 3 consecutive years) than non-drinkers and drinkers for <5 years, respectively (vs. HPV negativity for 3 consecutive years). A high drinking frequency (⩾twice/week) and a high beer intake (⩾3 glasses/occasion) had higher risks of 1-year (OR 1·80, 95% CI 1·01–3·36) HPV positivity for 2 consecutive years) and 2-year HR-HPV persistence (OR 3·62, 95% CI 1·35–9·75) than non-drinkers. Of the HPV-positive subjects enrolled, drinking habit (OR 2·68, 95% CI 1·10–6·51) and high consumption of beer or soju (⩾2 glasses/occasion; OR 2·90, 95% CI 1·06–7·98) increased the risk of 2-year consecutive or alternate HR-HPV positivity (vs. consecutive HPV negativity). These findings suggest that alcohol consumption might increase the risk of cervical HR-HPV persistence in Korean women.

A peptide library was used to screen for regions containing potential linear B-cell epitope sites in the glycoproteins and nucleoprotein of Crimean-Congo haemorrhagic fever virus (CCHFV) in an enzyme-linked immunosorbent assay (ELISA). The library consisted of 156 peptides, spanning the nucleoprotein and mature GN and GC proteins in a 19-mer with 9-mer overlap format. Using pooled serum samples from convalescent patients to screen the library, six peptides were identified as potential epitope sites. Further testing of these six peptides with individual patient sera identified two of these peptides as probable epitope sites, with peptide G1451–1469 reacting to 13/15 and peptide G1613–1631 to 14/15 human sera. These peptides are situated on the GC protein at amino acid positions 1451–1469 (relative to CCHFV isolate SPU103/97) (TCTGCYACSSGISCKVRIH) and 1613–1631 (FMFGWRILFCFKCCRRTRG). Identified peptides may have application in ELISA for diagnostic or serosurveillance purposes.

Measles vaccination is estimated to have averted 13·8 million deaths between 2000 and 2012. Persisting heterogeneity in coverage is a major contributor to continued measles mortality, and a barrier to measles elimination and introduction of rubella-containing vaccine. Our objective is to identify determinants of inequities in coverage, and how vaccine delivery must change to achieve elimination goals, which is a focus of the WHO Decade of Vaccines. We combined estimates of travel time to the nearest urban centre (⩾50 000 people) with vaccination data from Demographic Health Surveys to assess how remoteness affects coverage in 26 African countries. Building on a statistical mapping of coverage against age and geographical isolation, we quantified how modifying the rate and age range of vaccine delivery affects national coverage. Our scenario analysis considers increasing the rate of delivery of routine vaccination, increasing the target age range of routine vaccination, and enhanced delivery to remote areas. Geographical isolation plays a key role in defining vaccine inequity, with greater inequity in countries with lower measles vaccine coverage. Eliminating geographical inequities alone will not achieve thresholds for herd immunity, indicating that changes in delivery rate or age range of routine vaccination will be required. Measles vaccine coverage remains far below targets for herd immunity in many countries on the African continent and is likely to be inadequate for achieving rubella elimination. The impact of strategies such as increasing the upper age range eligible for routine vaccination should be considered.

In Australia, varicella vaccine was universally funded in late 2005 as a single dose at 18 months. A school-based catch-up programme for children aged 10–13 years without a history of infection or vaccination was funded until 2015, when those eligible for universal infant vaccination would have reached the age of high school entry. This study projects the impact of discontinuing catch-up vaccination on varicella and zoster incidence and morbidity using a transmission dynamic model, in comparison with alternative policy options, including two-dose strategies. At current vaccine coverage (83% at 2 years and 90% at 5 years), ceasing the adolescent catch-up programme in 2015 was projected to increase varicella-associated morbidity between 2035 and 2050 by 39%. Although two-dose infant programmes had the lowest estimated varicella morbidity, the incremental benefit from the second dose fell by 70% if first dose coverage increased from 83% to 95% by age 24 months. Overall zoster morbidity was predicted to rise after vaccination, but differences between strategies were small. Our results suggest that feasibility of one-dose coverage approaching 95% is an important consideration in estimating incremental benefit from a second dose of varicella vaccine.

There exists an urgent need to develop iterative risk assessment strategies of zoonotic diseases. The aim of this study is to develop a method of prioritizing 98 zoonoses derived from animal pathogens in Japan and to involve four major groups of stakeholders: researchers, physicians, public health officials, and citizens. We used a combination of risk profiling and analytic hierarchy process (AHP). Profiling risk was accomplished with semi-quantitative analysis of existing public health data. AHP data collection was performed by administering questionnaires to the four stakeholder groups. Results showed that researchers and public health officials focused on case fatality as the chief important factor, while physicians and citizens placed more weight on diagnosis and prevention, respectively. Most of the six top-ranked diseases were similar among all stakeholders. Transmissible spongiform encephalopathy, severe acute respiratory syndrome, and Ebola fever were ranked first, second, and third, respectively.

In Chile, while dog rabies has decreased markedly over the last 30 years, bat rabies is still reported frequently. In order to shed new light on the spatiotemporal trends of these reports, we analysed active and passive data from years 1985 and 2012, which included 61 076 samples from 289 counties of Chile. We found that from 1994 to 2012, more than 15 000 bat samples were submitted for diagnostics through passive surveillance, 9·5% of which tested positive for rabies. By contrast, the prevalence of infection was only ~0·4% among the nearly 12 000 bat samples submitted through active surveillance. We found that the prevalence of dog rabies dropped steadily over the same period, with just a single confirmed case since 1998. None of the 928 samples from wild animals, other than bats, were positive for rabies. Although there has been only one confirmed case of human rabies in Chile since 1985, and a single confirmed case in a dog since 1998, bats remain a reservoir for rabies viruses. While active surveillance indicates that rabies prevalence is low in bat colonies, the high proportion of positive bats submitted through passive surveillance is a concern. To prevent human rabies, local public health agencies should increase research on the basic ecology of bats and the role of stray dogs and cats as potential rabies amplifiers.

There is little known regarding the transmissibility of human papillomavirus (HPV) between different sites in men who have sex with men (MSM) and heterosexual individuals. We conducted a retrospective analysis investigating all new patients attending the Melbourne Sexual Health Centre in Australia between 2002 and 2013. We describe the prevalence and ratio of the first episode of anogenital warts in MSM and heterosexual males and females. The proportion of new MSM clients with anal and penile warts was 4·0% (362/8978) and 1·6% (141/8978), respectively; which gave an anal-to-penile wart ratio of 1:2·6. About 13·7% (1656/12112) of heterosexual males had penile warts and 10·0% (1121/11166) of females had vulval warts, which yielded a penile-to-vulval wart ratio of 1:0·7. Penile–anal transmission has a higher ratio than penile–vulval transmission, suggesting that the anal epithelium may be more susceptible to HPV infection than the vulval epithelium in females; these ratios are important in modelling the control of HPV in MSM.

Patterns of sexual mixing are major determinants of sexually transmitted infection (STI) transmission, in particular the extent to which high-risk populations mix with low-risk populations. However, patterns of mixing in the general population are poorly understood. We analysed data from a national probability sample survey of households, the Health Survey for England 2010. A total of 943 heterosexual couples living together, where at least one partner was aged between 16–44 years, were included. We used correlation coefficients to measure the strength of similarities between partners with respect to demographic characteristics, general health, health behaviours and sexual history. Males were on average 2 years older than their female partners, although this age difference ranged from a median of 0 years in men aged 16–24 years to a median of 2 years in men aged 35–44 years. A positive correlation between partners was found for all demographic characteristics. With respect to general health and health behaviours, a strongly positive correlation was found between men and women in reporting alcohol consumption at ⩾3 days a week and smoking. Men typically reported greater numbers of sexual partners than their female partner, although men and women with more partners were more likely to mix with each other. We have been able to elucidate the patterns of sexual mixing between men and women living together in England. Mixing based on demographic characteristics was more assortative than sexual characteristics. These data can better inform mathematical models of STI transmission.

The objectives of this study were to characterize methicillin-resistant Staphylococcus aureus (MRSA) blood culture isolates and to determine their relative importance in both nosocomial and community-acquired infections. A total of 535 MRSA blood culture isolates were analysed. In vitro susceptibility to 14 agents was determined. The genes nuc, mecA and coding for PVL toxin were identified by PCR. All isolates were characterized by PFGE or spa typing to assess their genomic relationships. Most MRSA isolates were retrieved from nosocomial bloodstream infections (474, 89%) and were of the CMRSA2 genotype. Healthcare-associated (HA)-MRSA bloodstream infections were associated with older age (70–89 years, P = 0·002) and most often secondary to central line infections (P = 0·005). Among MRSA strains associated with community-acquired (CA)-MRSA, 28·8% were isolated in intravenous drug users. CA-MRSA genotypes were more frequently found in young adults (20–39 years, P < 0·0001) with skin/soft tissue as the primary sources of infection (P = 0·006). CMRSA10 genotype was the predominant CA-MRSA strain. All MRSA isolates were susceptible to doxycycline, tigecycline, trimethoprim/sulfamethoxazole and vancomycin. Both the presence of the genes coding for PVL toxin (89·8%) and susceptibility to clindamycin (86·5%) were predictive of CA-MRSA genotypes. Whereas in the USA, HA-MRSA have been replaced by USA300 (CMRSA10) clone as the predominant MRSA strain type in positive blood cultures from hospitalized patients, this phenomenon has not been observed in the province of Quebec.