This study was conducted to examine the incidence trend of campylobacteriosis in Michigan over a 10-year period and to investigate risk factors and clinical outcomes associated with infection. Campylobacter case data from 2004 to 2013 was obtained from the Michigan Disease Surveillance System. We conducted statistical and spatial analyses to examine trends and identify factors linked to campylobacteriosis as well as ecological associations using animal density data from the National Agricultural Statistics Service. An increasing trend of Campylobacter incidence and hospitalization was observed, which was linked to specific age groups and rural residence. Cases reporting ruminant contact and well water as the primary drinking source had a higher risk of campylobacteriosis, while higher cattle density was associated with an increased risk at the county level. Additional studies are needed to identify age-specific risk factors and examine prevalence and transmission dynamics in ruminants and the environment to aid in the development of more effective preventive strategies.

Salmonellosis is a disease that represents a major public health concern in both developing and developed countries. The aim of this article is to evaluate the public health burden of Salmonella illness in Lebanon. The current scope of the Salmonella infection problem was assessed in relation to disease incidence and distribution with respect to age, gender and district. Factors that provide a better understanding of the magnitude of the problem were explored and highlighted. Data reported to the Epidemiologic Surveillance Department at the Lebanese Ministry of Public Health between 2001 and 2013 was reviewed. Information obtained was compared to information reported regionally and globally. The estimated true incidence was derived using multipliers from the CDC and Jordan. A literature review of all published data from Lebanon about Salmonella susceptibility/resistance patterns and its serious clinical complications was conducted. The estimated incidence was 13·34 cases/100 000 individuals, most cases occurred in the 20–39 years age group with no significant gender variation. Poor and less developed districts of Lebanon had the highest number of cases and the peak incidence was in summer. Reflecting on the projected incidence derived from the use of multipliers indicates a major discrepancy between what is reported and what is estimated. We conclude that data about Salmonella infection in Lebanon and many Middle Eastern and developing countries lack crucial information and are not necessarily representative of the true incidence, prevalence and burden of illness.

Between December 2010 and July 2011, 252 cases of STEC O157 PT8 stx1 + 2 infection were reported in England, Scotland and Wales. This was the largest outbreak of STEC reported in England and the second largest in the UK to date. Eighty cases were hospitalized, with two cases of haemolytic uraemic syndrome and one death reported. Routine investigative data were used to generate a hypothesis but the subsequent case-control study was inconclusive. A second, more detailed, hypothesis generation exercise identified consumption or handling of vegetables as a potential mode of transmission. A second case-control study demonstrated that cases were more likely than controls to live in households whose members handled or prepared leeks bought unwrapped [odds ratio (OR) 40, 95% confidence interval (CI) 2·08-769·4], and potatoes bought in sacks (OR 13·13, 95% CI 1·19-145·3). This appears to be the first outbreak of STEC O157 infection linked to the handling of leeks.

Shigellosis is endemic in most developing countries and thus a known risk in refugees and internally displaced persons. In 2015, a massive influx of refugees into Greece, due to the political crisis in the Middle East, led to the development of appropriate conditions for outbreaks of communicable diseases as shigellosis. We present a cluster of 16 shigellosis cases in refugees, detected by the implementation of a syndromic notification system in one transit centre in Athens, between 20 August and 7 October 2015. Both Shigella flexneri (n = 8) and S. sonnei (n = 8) were identified, distributed in various serotypes. All tested isolates (n = 13) were multidrug resistant; seven were CTX-M-type extended-spectrum β-lactamase producers. Our results indicate lack of a potential common source, although pulsed-field gel electrophoresis typing results revealed small clusters in isolates of the same serotype indicating possible limited person-to-person transmission without identifying secondary community cases related to the refugees. To prevent the spread of shigellosis, empirical antibiotic treatment as well as environmental hygiene measures were implemented. The detection of multi-drug resistance is important for determining the appropriate empirical antibiotic treatment for the more severe cases, while at the same time real-time typing is useful for epidemiological investigation and control measures.

Decision making on hazard surveillance in livestock product chains is a multi-hazard, multi-stakeholder, and multi-criteria process that includes a variety of decision alternatives. The multi-hazard aspect means that the allocation of the scarce resource for surveillance should be optimized from the point of view of a surveillance portfolio (SP) rather than a single hazard. In this paper, we present a novel conceptual approach for economic optimization of a SP to address the resource allocation problem for a surveillance organization from a theoretical perspective. This approach uses multi-criteria techniques to evaluate the performances of different settings of a SP, taking cost-benefit aspects of surveillance and stakeholders’ preferences into account. The credibility of the approach has also been checked for conceptual validity, data needs and operational validity; the application potentials of the approach are also discussed.

After the introduction of conjugate vaccines, a strong rearrangement of pneumococcal serotypes was observed globally. Probably most concerning was the emergence of serotype 19A, which has not only high invasive disease potential, but also high antibiotic resistance. In the current study we focused on the increased prevalence of serotype 19A after the PCV vaccination rate became widely used in Hungary. A total of 2262 children aged 3–6 years were screened for pneumococcus carriage using nasal swabs. Children were divided into two groups according to the vaccination rates, low level (group 1) vs. high level (group 2). While the carriage rate did not change over time (average 32·9%), the serotype distribution differed greatly in the two groups. The prevalence of serotype 19A increased >eightfold. Almost all 19A isolates had high-level macrolide resistance and elevated penicillin minimum inhibitory concentrations. Genotyping methods revealed that these new 19A isolates are different from the previously frequent Hungary19A−6 PMEN clone. Both the carriage rate and the overall penicillin and macrolide resistance remained stable over time, but while several serotypes were represented in group 1, serotype 19A alone was clearly dominant in group 2.

Orthobunyaviruses, tri-segmented, negative-sense RNA viruses, have long been associated with mild to severe human disease in Africa, but not haemorrhagic fever. However, during a Rift Valley fever outbreak in East Africa in 1997–1998, Ngari virus was isolated from two patients and antibody detected in several others with haemorrhagic fever. The isolates were used to identify Ngari virus as a natural Orthobunyavirus reassortant. Despite their potential to reassort and cause severe human disease, characterization of orthobunyaviruses is hampered by paucity of genetic sequences. Our objective was to obtain complete gene sequences of two Bunyamwera virus and three Ngari virus isolates from recent surveys in Kenya and to determine their phylogenetic positioning within the Bunyamwera serogroup. Newly sequenced Kenyan Bunyamwera virus isolates clustered closest to a Bunyamwera virus isolate from the same locality and a Central African Republic isolate indicating that similar strains may be circulating regionally. Recent Kenyan Ngari isolates were closest to the Ngari isolates associated with the 1997–1998 haemorrhagic fever outbreak. We observed a temporal/geographical relationship among Ngari isolates in all three gene segments suggesting a geographical/temporal association with genetic diversity. These sequences in addition to earlier sequences can be used for future analyses of this neglected but potentially deadly group of viruses.

To estimate HCV seroprevalence in subpopulations of women delivering live-born infants in the North Thames region in England in 2012, an unlinked anonymous (UA) cross-sectional survey of neonatal dried blood spot samples was conducted. Data were available from 31467 samples from live-born infants received by the North Thames screening laboratory. Thirty neonatal samples had HCV antibodies, corresponding to a maternal seroprevalence of 0·095% (95% confidence interval 0·067–0·136). Estimated HCV seroprevalences in women born in Eastern Europe, Southern Asia and the UK were 0·366%, 0·162% and 0·019%, respectively. For women born in Eastern Europe seroprevalence was highest in those aged around 27 years, while in women born in the UK and Asia-Pacific region, seroprevalence increased significantly with age. HCV seroprevalence in UK-born women whose infant's father was also UK-born was 0·016%. One of the 30 HCV-seropositive women was HIV-1 seropositive. Estimated HCV seroprevalence for women delivering live-born infants in North Thames in 2012 (0·095%) was significantly lower than that reported in an earlier UA survey in 1997–1998 (0·191%). Data indicate that the cohort of UK-born HCV-seropositive women is ageing and that, in this area of England, most perinatally HCV-exposed infants were born to women themselves born in Southern Asia or Eastern Europe.

Scarce data exist on the relationship between diabetes and extrapulmonary tuberculosis (EPTB). We evaluated whether diabetes impacts site of TB and risk of death in patients with EPTB. We evaluated a cohort of TB cases from the state of Georgia between 2009 and 2012. Patients aged ⩾16 years were classified by diabetes status according to medical records. Site of EPTB was determined by culture and/or state TB classification. Death was defined by all-cause mortality. Of 1325 eligible reported TB cases, 369 (27·8%) had any EPTB including 258 (19·5%) with only EPTB and 111 (8·4%) with pulmonary TB and EPTB. Of all TB cases, 158 had diabetes (11·9%). In multivariable analysis, the odds of any EPTB was similar in patients with and without diabetes [adjusted odds ratio 1·04, 95% confidence interval (CI) 0·70–1·56]. The risk of death was 23·8% in patients with EPTB and diabetes vs. 9·8% in those with no diabetes (P < 0·01); after adjusting for covariates the difference was not significant (aRR 1·19, 95% CI 0·54–2·63). Diabetes was common in patients with EPTB and risk of death was high. Improved understanding of the relationship between diabetes and EPTB is critical to determine the extent that diabetes affects TB diagnosis and clinical management.

crAssphage is a newly discovered gut bacteriophage. However, its pathogenicity and molecular epidemiology in humans are as yet unclear. In this study, we investigated the association between crAssphage and diarrhoea, as well as the molecular epidemiology of crAssphage in Chinese patients from our hospital. Our results indicated that there were no significant differences in the crAssphage-positive ratio and viral loads in faecal supernatants between adults with diarrhoea and healthy adults. Of infants and children with diarrhoea, 2·8% were found to be crAssphage-positive, including two infants aged <1 month. Markedly, of all confirmed crAssphage-positive strains, 100% had the ORF00039 deletion and 77·8% had low identity of ORF00018 compared to crAssphage (GenBank accession no. NC_024711, designated genotype 1). Thus, crAssphage was not associated with diarrhoea and most strains of crAssphage in Chinese patients (designated genotype 2) were characterized by the ORF00039 deletion and low identity of ORF00018.

To determine the time to appearance of antibody against hepatitis B surface antigen (anti-HBs) after clearance of hepatitis B surface antigen (HBsAg) in chronically infected individuals, we followed up 3963 cases with positive antibody against hepatitis B e antigen (anti-HBe) from 1991 to 2014. Of these, 101 (67 males, 34 females) lost HBsAg. These serocleared cases were checked every 6-month interval regarding HBsAg, anti-HBs, liver function tests, and liver sonography. Hepatitis B virus DNA was assessed at the time of seroclearance or the appearance of anti-HBs. The mean age of these patients at entry to this study was 34·4 ± 13 years. The mean follow-up duration until seroclearance of HBsAg was 6·6 ± 4·3 years. After the mean follow-up of 43·7 ± 45 months, anti-HBs appeared in 64 (63·4%) cases. The cumulative probabilities of anti-HBs appearance for 2, 5 and 10 years were 24·3%, 58% and 78·2%, respectively. The appearance of anti-HBs was associated with age ⩾35 years and seroclearance of HBsAg (hazard ratio 1·96, 95% confidence interval 1·32–3·38, P = 0·016) but not with sex. The results show that anti-HBs may develop in 78·2% of cases within 10 years of HBsAg clearance. Age ⩾35 years at HBsAg loss was associated with earlier development of anti-HBs.

The purpose of this study was to apply a novel statistical method for variable selection and a model-based approach for filling data gaps in mortality rates associated with foodborne diseases using the WHO Vital Registration mortality dataset. Correlation analysis and elastic net regularization methods were applied to drop redundant variables and to select the most meaningful subset of predictors. Whenever predictor data were missing, multiple imputation was used to fill in plausible values. Cluster analysis was applied to identify similar groups of countries based on the values of the predictors. Finally, a Bayesian hierarchical regression model was fit to the final dataset for predicting mortality rates. From 113 potential predictors, 32 were retained after correlation analysis. Out of these 32 predictors, eight with non-zero coefficients were selected using the elastic net regularization method. Based on the values of these variables, four clusters of countries were identified. The uncertainty of predictions was large for countries within clusters lacking mortality rates, and it was low for a cluster that had mortality rate information. Our results demonstrated that, using Bayesian hierarchical regression models, a data-driven clustering of countries and a meaningful subset of predictors can be used to fill data gaps in foodborne disease mortality.

Dengue is the world's most prevalent mosquito-borne disease, with more than 200 million people each year becoming infected. We used a mechanistic virus transmission model to determine whether climate warming would change dengue transmission in Australia. Using two climate models each with two carbon emission scenarios, we calculated future dengue epidemic potential for the period 2046–2064. Using the ECHAM5 model, decreased dengue transmission was predicted under the A2 carbon emission scenario, whereas some increases are likely under the B1 scenario. Dengue epidemic potential may decrease under climate warming due to mosquito breeding sites becoming drier and mosquito survivorship declining. These results contradict most previous studies that use correlative models to show increased dengue transmission under climate warming. Dengue epidemiology is determined by a complex interplay between climatic, human host, and pathogen factors. It is therefore naive to assume a simple relationship between climate and incidence, and incorrect to state that climate warming will uniformly increase dengue transmission, although in general the health impacts of climate change will be negative.

Laboratory tests in adult outpatients with longer lasting coughs to identify a potential causal pathogen are rarely performed, and there is no gold standard for these diagnostic tests. While the diagnostic validity of serological tests for pertussis is well established their potential contribution for diagnosing adenovirus and influenza virus A and B infections is unclear. A sentinel study into the population-based incidence of longer lasting coughs in adults was done in Rostock (former East Germany) and Krefeld (former West Germany). A total of 971 outpatients who consulted general practitioners or internists were included. Inclusion criteria were coughing for ⩾1 week and no chronic respiratory diseases. We evaluated the performance of polymerase chain reaction (PCR) as well as IgG and IgA serology, applying a latent class model for diagnosing infections with adenovirus, B. pertussis, and influenza virus A and B. The adult outpatients first sought medical attention when they had been coughing for a median of 3 weeks. In this situation, direct detection of infectious agents by PCR had a low sensitivity. Modelling showed that additional serological tests equally improved sensitivity and specificity for diagnosis for adenovirus, B. pertussis and influenza virus A and B infections. The combination of serology and PCR may improve the overall performance of diagnostic tests for B. pertussis and also for adenovirus, and influenza virus A and B infections.

Toxocariasis is a very prevalent zoonotic disease worldwide. Recently, investigators have focused more on Toxocara spp. seroprevalence in humans. Information regarding Toxocara seroprevalence in people from different ethnic backgrounds in China is limited. For this study, blood samples were collected from a total of 802 Han, 520 Korean, 303 Manchu, and 217 Mongol subjects from Jilin and Shandong provinces. The overall Toxocara seroprevalence was 16·07% (14·21% Han, 20·58% Korean, 11·22% Manchu, 18·89% Mongol). Living in suburban or rural areas, having dogs at home, exposure to soil, and consumption of raw/undercooked meat were risk factors for Toxocara infection. Exposure to soil was identified as the major risk factor for Toxocara seropositivity in all of the tested ethnicities. To the best of our knowledge, this is the first report concerning Toxocara infection in Manchus and Mongols in China. The present study provided baseline data for effective prevention strategies of toxocariasis in northeast China and recommends improvements in personal hygiene standards to achieve this goal.

Campylobacter is the leading cause of bacterial diarrhoeal disease worldwide, with raw and undercooked poultry meat and products the primary source of infection. Colonization of broiler chicken flocks with Campylobacter has proved difficult to prevent, even with high levels of biosecurity. Dipteran flies are proven carriers of Campylobacter and their ingress into broiler houses may contribute to its transmission to broiler chickens. However, this has not been investigated in the UK. Campylobacter was cultured from 2195 flies collected from four UK broiler farms. Of flies cultured individually, 0·22% [2/902, 95% confidence interval (CI) 0–0·53] were positive by culture for Campylobacter spp. Additionally, 1293 flies were grouped by family and cultured in 127 batches: 4/127 (3·15%, 95% CI 0·11-6·19) from three broiler farms were positive for Campylobacter. Multilocus sequence typing of isolates demonstrated that the flies were carrying broiler-associated sequence types, responsible for human enteric illness. Malaise traps were used to survey the dipteran species diversity on study farms and also revealed up to 612 flies present around broiler-house ventilation inlets over a 2-h period. Therefore, despite the low prevalence of Campylobacter cultured from flies, the risk of transmission by this route may be high, particularly during summer when fly populations are greatest.

The increase in pertussis cases in Minnesota in the last decade has been mainly attributed to the switch from whole cell to acellular pertussis [as part of the diphtheria, tetanus and acellular pertussis vaccine (DTaP)]. It is unclear, however, to what degree community-level risk factors also contribute. Understanding these factors can help inform public health policy-makers about where else to target resources. We performed an ecological analysis within Minnesota to identify risk factors at the county level using a Bayesian Poisson generalized linear areal model to account for spatial dependence. Univariate analyses suggested an association between increased pertussis rates at the county level and white maternal ethnicity, being US born, urban counties and average household size. In the multivariable analysis, the rate of pertussis was 1·79 times greater for urban vs. rural counties and 4·75 times greater for counties with a one-person larger average household size. Pertussis rates in counties with higher (i.e. 4+DTaP) receipt in children were 0·97 times lower. Examining county-level factors associated with varying levels of pertussis may help identify those counties that would most benefit from targeted interventions and increased resource allocation.

A number of sophisticated modelling approaches are available to investigate potential associations between antimicrobial use (AMU) and resistance (AMR) in animal health settings. All have their advantages and disadvantages, making it unclear as to which model is most appropriate. We used advanced regression modelling to investigate AMU-AMR associations in faecal non-type-specific Escherichia coli (NTSEC) isolates recovered from 275 pens of feedlot cattle. Ten modelling strategies were employed to investigate AMU associations with resistance to chloramphenicol, ampicillin, sulfisoxazole, tetracycline and streptomycin. Goodness-of-fit statistics did not show a consistent advantage for any one model type. Three AMU-AMR associations were significant in all models. Recent parenteral tetracycline use increased the odds of finding tetracycline-resistant NTSEC [odds ratios (OR) 1·1–3·2]; recent parenteral sulfonamide use increased the odds of finding sulfisoxazole-resistant NTSEC (OR 1·4–2·5); and recent parenteral macrolide use decreased the odds of recovering ampicillin-resistant NTSEC (OR 0·03–0·2). Other results varied markedly depending on the modelling approach, emphasizing the importance of exploring and reporting multiple modelling methods based on a balanced consideration of important factors such as study design, mathematical appropriateness, research question and target audience.