Spatiotemporal analysis is an important tool to monitor changes of tuberculosis (TB) epidemiology, identify high-risk regions and guide resource allocation. However, there are limited data on the contributing factors of TB incidence. This study aimed to investigate the spatiotemporal pattern of TB incidence and its associated factors in mainland China during 2005–2013. Global Moran's I test, Getis-Ord Gi index and heat maps were used to examine the spatial clustering and seasonal patterns. Generalized Linear Mixed Model was applied to identify factors associated with TB incidence. TB incidence presented high geographical variations with two main hot spots, while a generally consistent seasonal pattern was observed with a peak in late winter. Furthermore, we found province-level TB incidence increased with the proportion of the elderly but decreased with Gross Demographic Product per capita and the male:female ratio. Meteorological factors also influenced TB incidence. TB showed obvious spatial clustering in mainland China and both the demographic and socio-economic factors and meteorological measures were associated with TB incidence. These results provide the related information to identify the high-risk districts and the evidence for the government to develop corresponding control measures.

In 2013–2014, the Public Health Agency of Sweden developed a web-based participatory surveillance system, Hӓlsorapport, based on a random sample of individuals reporting symptoms weekly online, to estimate the community incidence of self-reported acute gastrointestinal (AGI), acute respiratory (ARI) and influenza-like (ILI) illnesses and their severity. We evaluated Hӓlsorapport's acceptability, completeness, representativeness and its data correlation with other surveillance data. We calculated response proportions and Spearman correlation coefficients (r) between (i) incidence of illnesses in Hӓlsorapport and (ii) proportions of specific search terms to medical-advice website and reasons for calling a medical advice hotline. Of 34 748 invitees, 3245 (9·3%) joined the cohort. Participants answered 81% (139 013) of the weekly questionnaires and 90% (16 351) of follow-up questionnaires. AGI incidence correlated with searches on winter-vomiting disease [r = 0·81, 95% confidence interval (CI) 0·69–0·89], and ARI incidence correlated with searches on cough (r = 0·77, 95% CI 0·62–0·86). ILI incidence correlated with the web query-based estimated incidence of ILI patients consulting physicians (r = 0·63, 95% CI 0·42–0·77). The high response to different questionnaires and the correlation with other syndromic surveillance systems suggest that Hӓlsorapport offers a reasonable representation of AGI, ARI and ILI patterns in the community and can complement traditional and syndromic surveillance systems to estimate their burden in the community.

Anaplasmataceae agents comprise obligate intracellular bacteria that can cause disease in humans and animals. Between August 2013 and March 2015, 31 Nasua nasua (coati), 78 Cerdocyon thous (crab-eating fox), seven Leopardus pardalis (ocelot), 110 wild rodents, 30 marsupials, and 42 dogs were sampled in the Pantanal wetland, Brazil. In addition, ectoparasites found parasitizing the animals were collected and identified. The present work aimed to investigate the occurrence of Anaplasmataceae agents in wild mammals, domestic dogs and ectoparasites, by molecular and serological techniques. Overall, 14 (17·9%) C. thous, seven (16·6%) dogs and one (3·2%) N. nasua were seroreactive to Ehrlichia canis. Nine dogs, two C. thous, one N. nasua, eight wild rodents, five marsupials, eight Amblyomma sculptum, four Amblyomma parvum, 13 A. sculptum nymphal pools, two Amblyomma larvae pools and one Polygenis (Polygenis) bohlsi bohlsi flea pool were positive for Ehrlichia spp. closely related to E. canis. Seven N. nasua, two dogs, one C. thous, one L. pardalis, four wild rodents, three marsupials, 15 A. sculptum, two Amblyomma ovale, two A. parvum and one Amblyomma spp. larval pools were positive for Anaplasma spp. closely related to A. phagocytophilum or A. bovis. The present study provided evidence that wild animals from Brazilian Pantanal are exposed to Anaplasmataceae agents.

A Q fever outbreak was declared in February 2016 in a company that manufactures hoists and chains and therefore with no apparent occupational-associated risk. Coxiella burnetii infection was diagnosed by serology in eight of the 29 workers of the company; seven of them had fever or flu-like signs and five had pneumonia, one requiring hospitalisation. A further case of C. burnetii pneumonia was diagnosed in a local resident. Real-time PCR (RTi–PCR) showed a widespread distribution of C. burnetii DNA in dust samples collected from the plant facilities, thus confirming the exposure of workers to the infection inside the factory. Epidemiological investigations identified a goat flock with high C. burnetii seroprevalence and active shedding which was owned and managed by one of the workers of the company as possible source of infection. Genotyping by multispacer sequence typing (MST) and a 10-loci single-nucleotide polymorphism (SNP) discrimination using RTi–PCR identified the same genotype (MST18 and SNP type 8, respectively) in the farm and the factory. These results confirmed the link between the goat farm and the outbreak and allowed the identification of the source of infection. The circumstances and possible vehicles for the bacteria entering the factory are discussed.

In August to October 2012, a nationwide outbreak of Salmonella enteritidis phase type (PT) 1B with 53 cases occurred in Finland. Hypothesis generating interviews pointed toward ready-to-eat chicken salad from a Finnish company and at the same time Estonian authorities informed of a S. enteritidis PT 1B outbreak linked to chicken wrap prepared at an Estonian restaurant. We found that chicken salad was associated with the infection (odds ratio (OR) 16·1, 95% confidence interval (CI) 1·7–148·7 for consumption and OR 17·5. 95% CI 4·0–76·0 for purchase). The frozen pre-cooked chicken cubes used in Finnish salad and in Estonian wraps were traced back to a production plant in China. Great Britain made two Rapid Alert Systems for Food and Feed notifications on chicken cubes imported to the UK from the same Chinese production plant. Microbiological investigation confirmed that the patient isolates in Estonia and in Finland were indistinguishable from the strains isolated from chicken cubes in Estonia and in the UK. We recommend that despite certificates for tested Salmonella, food items should be analyzed when Salmonella contamination in outbreak investigations is suspected. In outbreak investigations, electronically implemented case–case study saves time, effort, and money compared with case–control study.

This study assessed the incidence and risk factors for dengue virus (DENV) infection among children in a prospective birth cohort conducted in the city of Recife, a hyperendemic dengue area in Northeast Brazil. Healthy pregnant women (n = 415) residing in Recife who agreed to have their children followed were enrolled. Children were followed during their first 24 months of age (May/2011–June/2014), before the 2015 Zika virus outbreak. DENV infection was detected by reverse-transcriptase polymerase chain reaction and/or serology (anti-DENV IgM/IgG). The incidence rates per 1000 person-years (py) and its association with risk factors by age bands (0–12, >12–30 months) were estimated through Poisson regression models. Forty-nine dengue infections were detected; none progressed to severe forms. The incidence rates were 107·6/1000py (95% CI 76·8–150·6) and 93·3/1000py (95% CI 56·1–154·4) in the first and second years of age, respectively. Male children (risk ratios (RR) = 2·33; 95% CI 1·09–4·98) and those born to DENV-naïve mothers (RR = 2·42; 95% CI 1·01–5·80) were at greater risk of infection in the first year of age. In the second year, children born to Caucasian/Asian descent skin colour mothers had a threefold higher risk of infection (RR = 3·34; 95% CI: 1·08–10·33). These data show the high exposure of children to DENV infection in our setting and highlight the role of biological factors in this population's susceptibility to infection.

Pertussis is a worldwide acute respiratory disease caused by the bacterium Bordetella pertussis. Despite high vaccine coverage, the bacterium continues to circulate in populations and is still one of the most common vaccine-preventable diseases. In Brazil, pertussis incidence has presented a significant decrease since 1990 but since 2011 a sudden increase in incidence has been observed. Thus, the aim of this study was to perform a molecular epidemiological characterization of B. pertussis strains isolated in the Central-Western region (specifically in Distrito Federal) of Brazil from August 2012 to August 2014. During this period, 92 B. pertussis strains were isolated from the outbreaks. All strains were characterized by serotyping and XbaI pulsed-field gel electrophoresis profiles. From August to December 2012, the most prevalent serotype observed was 1,3 (13/17). During 2013 the prevalence of serotype 1,3 decreased (13/30) and from January 2014 to August 2014 the most prevalent serotype was 1,2 (33/45). Fourteen PFGE profiles were identified. Of these, BP-XbaI0039 prevalence increased from 3/17 in 2012 to 10/30 in 2013, and 35/45 in 2014. These results evidence the selection of a specific genetic profile during this period, suggesting the occurrence of a bacterial genomic profile with high circulation potential.

The diagnosis and control of Mycobacterium bovis infection (bovine tuberculosis: TB) continues to present huge challenges to the British cattle industry. A clearer understanding of the magnitude and duration of immune response to M. bovis infection in the European badger (Meles meles) – a wildlife maintenance host – may assist with the future development of diagnostic tests, and vaccination and disease management strategies. Here, we analyse 5280 diagnostic test results from 550 live wild badgers from a naturally-infected population to investigate whether one diagnostic test (a gamma interferon release [IFNγ] assay, n = 550 tests) could be used to predict future positive results on two other tests for the same disease (a serological test [n = 2342 tests] and mycobacterial culture [n = 2388 tests]) and hence act as an indicator of likely bacterial excretion or disease progression. Badgers with the highest IFNγ optical density (OD) values were most likely to subsequently test positive on both serological and culture tests, and this effect was detectable for up to 24 months after the IFNγ test. Furthermore, the higher the original IFNγ OD value, the greater the chance that a badger would subsequently test positive using serology. Relationships between IFNγ titres and mycobacterial culture results from different types of clinical sample suggest that the route of infection may affect the magnitude of immune response in badgers. These findings identify further value in the IFNγ test as a useful research tool, as it may help us to target studies at animals and groups that are most likely to succumb to more progressive disease.

Mycobacterium marinum, a bacterium found in freshwater and saltwater, can infect persons with direct exposure to fish or aquariums. During December 2013, the New York City Department of Health and Mental Hygiene learned of four suspected or confirmed M. marinum skin or soft tissue infections (SSTIs) among persons who purchased whole fish from Chinese markets. Ninety-eight case-patients with non-tuberculous mycobacteria (NTM) SSTIs were identified with onset June 2013–March 2014. Of these, 77 (79%) were female. The median age was 62 years (range 30–91). Whole genome sequencing of clinical isolates revealed two main clusters and marked genetic diversity. Environmental samples from distributors yielded NTM though not M. marinum. We compared 56 case-patients with 185 control subjects who shopped in Chinese markets, frequency-matched by age group and sex. Risk factors for infection included skin injury to the finger or hand (odds ratio [OR]: 15·5; 95% confidence interval [CI]: 6·9–37·3), hand injury while preparing fish or seafood (OR 8·3; 95% CI 3·8–19·1), and purchasing tilapia (OR 3·6; 95% CI 1·1–13·9) or whiting (OR 2·7; 95% CI 1·1–6·6). A definitive environmental outbreak source was not identified.

Faecal specimens collected from outbreak (n = 253) and sporadic (n = 147) cases of acute gastroenteritis that occurred in western India between 2006 and 2014 were tested for group C rotavirus (GCR) using partial VP6 gene-based RT–PCR. All specimens were tested previously for the presence of other viral and bacterial aetiological agents by conventional methods. The rate of GCR detection was 8·6% and 0·7% in outbreak and sporadic cases, respectively. GCR infections prevailed in outbreaks reported from rural areas (10·9%) compared to urban areas (1·6%). Clinical severity score of the patients with GCR infection (n = 23) indicated severe disease in the majority (70%) of cases. The age distribution analysis indicated 52·1% of GCR infections in children aged <10 years. The male:female ratio in GCR-positive patients was 2·3:1. Of the 23 GCR-positive cases, 17 (73·9%) had a sole GCR infection and six had mixed infections with other viral and/or bacterial agents. Phylogenetic analysis of nucleotide sequences classified GCR strains of the study in to I2 genotype of the VP6 gene. This is the first study to show the occurrence of GCR in gastroenteritis outbreaks in India.

The annual incidence of listeriosis in Italy is lower (0·19–0·27 per 100 000 inhabitants per year) than in Europe (0·34–0·52 per 100 000 inhabitants per year). Since the observed incidence of listeriosis may be biased downward for underdiagnosis or under-reporting, this work aims to estimate the real incidence of listeriosis during a 9-year period in the Lombardy region, Italy. Data on listeriosis cases were collected from national mandatory notification system (MAINF) and Laboratory-based Surveillance System (LabSS). The two sources were cross-matched and capture–recapture method was applied to estimate the number of undetected cases and the real incidence of invasive listeriosis. Five hundred and eighty invasive listeriosis cases were detected by the two sources between 2006 and 2014: 50·2% were identified only via MAINF, 16·7% were recorded only via LabSS, overlaps occurred in 192 cases (33·1%). The mean annual incidence detected only by MAINF was 0·56 per 100 000 inhabitants, which rose to 0·67 per 100 000 considering also the cases detected by LabSS. The capture–recapture method allowed to estimate an incidence of 0·84 per 100 000. The high incidence of listeriosis may be due to improved sensitivity of the surveillance system, but also reflect a real increase, associated with an increased population at risk.

Computer models can be useful in planning interventions against novel strains of influenza. However such models sometimes make unsubstantiated assumptions about the relative infectivity of asymptomatic and symptomatic cases, or conversely assume there is no impact at all. Using household-level data from known-index studies of virologically confirmed influenza A infection, the relationship between an individual's infectiousness and their symptoms was quantified using a discrete-generation transmission model and Bayesian Markov chain Monte Carlo methods. It was found that the presence of particular respiratory symptoms in an index case does not influence transmission probabilities, with the exception of child-to-child transmission where the donor has phlegm or a phlegmy cough.

Ireland reports the highest incidence of verotoxigenic Escherichia coli (VTEC) infection in Europe. This study investigated potential risk factors for confirmed sporadic and outbreak primary VTEC infections during 2008–2013. Overall, 989 VTEC infections including 521 serogroup O157 and 233 serogroup O26 were geo-referenced to 931 of 18 488 census enumeration areas. The geographical distribution of human population, livestock, unregulated groundwater sources, domestic wastewater treatment systems (DWWTS) and a deprivation index were examined relative to notification of VTEC events in 524 of 6242 rural areas. Multivariate modelling identified three spatially derived variables associated with VTEC notification: private well usage [odds ratio (OR) 6·896, P < 0·001], cattle density (OR 1·002, P < 0·001) and DWWTS density (OR 0·978, P = 0·002). Private well usage (OR 18·727, P < 0·001) and cattle density (OR 1·001, P = 0·007) were both associated with VTEC O157 infection, while DWWTS density (OR 0·987, P = 0·028) was significant within the VTEC O26 model. Findings indicate that VTEC infection in the Republic of Ireland is particularly associated with rural areas, which are associated with a ubiquity of pathogen sources (cattle) and pathways (unregulated groundwater supplies).

The prevalence and spatial distribution of Escherichia coli serogroups O26, O103, O111 and O145 in calves <7 days old in New Zealand and their relationship with serum IgG, weight and sex was determined by collecting recto-anal mucosal swabs (RAMS) (n = 299) and blood samples (n = 299) from two slaughter plants in the North Island. Real-time PCR of RAMS enrichment cultures revealed that 134/299 samples were positive for O26, 68/299 for O103 and 47/299 for O145, but none were positive for O111. Processing of positive enrichment cultures resulted in 49 O26, four O103 and five O145 isolates. Using multiplex PCR 25/49 (51%) O26 isolates were positive for stx1, eae, ehxA, 17/49 (34·7%) for eae, ehxA and 7/49 (14·2%) for eae only. All O103 and O145 isolates were positive for eae, ehxA only. O26 isolates were grouped into four clusters (>70% similarity) using pulsed field gel electrophoresis. Mapping of the farms showed the presence of farms positive for O26, O103 and O145 in three important dairy producing regions of the North Island. Calves positive for O103 were more likely to be positive for O26 and vice versa (P = 0·04). Similarly, calves positive for O145 were more likely to be positive for O103 and vice versa (P = 0·03). This study demonstrates that non-O157 E. coli serogroups of public health and economic importance containing clinically relevant virulence factors are present in calves in the North Island of New Zealand.

This study assessed the seroprevalence of brucellosis and its risk factors in migratory nomads in the Fars province of Iran. Active brucellosis was defined as the combination of clinical symptoms, including fever, chills, night sweats, headache, low back pain, arthralgia, or myalgia, and positive laboratory testing, including either a serum agglutination test (SAT) ⩾1:80 with a 2-mercaptoethanol (2-ME) test ⩾1:40, or a SAT <1:80 combined with a positive Coombs Wright test (CWT) at a titre of at least threefold higher than SAT titre results. For the 536 participants, the female (316, 59%) to male (220, 41%) ratio was 1·4 and the participants' mean age was 32·4 ± 18·9 (range 1–96) years. Of all participants, 325 (60·6%) showed clinical symptoms; in symptomatic participants, the Rose Bengal plate test was positive in 33 (6·1%) cases, the SAT was positive in 18 (3·3%) cases, and the 2-ME test was positive in 30 (5·5%) cases. Positive SAT and 2-ME results were seen in 18 (3·3%) cases, but a negative SAT and a positive CWT were found in 36 (6·7%) cases. As a result, active brucellosis was detected in 54 cases, indicating a prevalence of 10% (95% confidence interval 8–12). In conclusion, we determined that brucellosis is a prevalent yet neglected disease in this nomadic population. Brucellosis control is not possible as long as these high-risk populations remain neglected.

Antiretroviral therapy (ART) is increasingly being used as an HIV-prevention tool, administered to uninfected people with ongoing HIV exposure as pre-exposure prophylaxis (PrEP) and to infected people to reduce their infectiousness. We used a modelling approach to determine the optimal population-level combination of ART and PrEP allocations required in South Africa to maximize programme effectiveness for four outcome measures: new infections, infection-years, death and cost. We considered two different strategies for allocating treatment, one that selectively allocates drugs to sex workers and one that does not. We found that for low treatment availability, prevention through PrEP to the general population or PrEP and ART to sex workers is key to maximizing effectiveness, while for higher drug availability, ART to the general population is optimal. At South Africa's current level of treatment availability, using prevention is most effective at reducing new infections, infection-years, and cost, while using the treatment as ART to the general population best reduces deaths. At treatment levels that meet the UNAIDS's ambitious new 90–90–90 target, using all or almost all treatment as ART to the general population best reduces all four outcome measures considered.

In individuals with latent tuberculosis (TB) infection, those living with human immunodeficiency virus (HIV) had a 20–37 times higher risk of developing active TB compared to those without HIV infection. Systematic testing and treatment of latent TB infection are priorities in HIV-infected persons. In China, the prevalence of HIV infection in men who have sex with men (MSM) has gradually increased in the past decade. However, the prevalence of TB infection has been studied sparsely in HIV-infected MSM. Hence, we conducted a pilot study in MSM living with HIV infection in Xi'an city to evaluate TB infection status by means of interferon-γ release assay (IGRA). A total of 182 HIV-infected MSM were included in this study, the prevalence of IGRA positivity was observed to be 8·79% (16/182). IGRA quantitative results were not statistically influenced by the CD4 cell counts of the study participants. However, IGRA positivity was found to be lower than our previously reported data from the general population. This suggests that immunological deficiency might decrease the sensitivity of IGRA and thus increase the number of false negatives. Our primary results, suggesting systematic testing and treatment of latent TB infection together with active case-finding, were equally important for TB control in persons living with HIV infection.

Our study aimed to evaluate changes in the epidemiology of pathogens causing surgical site infections (SSIs) in England between 2000 and 2013 in the context of intensified national interventions to reduce healthcare-associated infections introduced since 2006. National prospective surveillance data on target surgical procedures were used for this study. Data on causative organism were available for 72% of inpatient-detected SSIs meeting the standard case definitions for superficial, deep and organ-space infections (9767/13 531) which were analysed for trends. A multivariable logistic linear mixed model with hospital random effects was fitted to evaluate trends by pathogen. Staphylococcus aureus was the predominant cause of SSI between 2000 (41%) and 2009 (24%), decreasing from 2006 onwards reaching 16% in 2013. Data for 2005–2013 showed that the odds of SSI caused by S. aureus decreased significantly by 14% per year [adjusted odds ratio (aOR) 0·86, 95% confidence interval (CI) 0·83–0·89] driven by significant decreases in methicillin-resistant S. aureus (MRSA) (aOR 0·71, 95% CI 0·68–0·75). However a small significant increase in methicillin-sensitive S. aureus was identified (aOR 1·06, 95% CI 1·02–1·10). Enterobacteriaceae were stable during 2000–2007 (12% of cases overall), increasing from 2008 (18%) onwards, being present in 25% of cases in 2013; the model supported these increasing trends during 2007–2013 (aOR 1·12, 95% CI 1·07–1·18). The decreasing trends in S. aureus SSIs from 2006 and the increases in Enterobacteriaceae SSIs from 2008 may be related to intensified national efforts targeted at reducing MRSA bacteraemia combined with changes in antibiotic use aimed at controlling C. difficile infections.

Norovirus causes viral gastroenteritis, which is a major problem in health care. The disease causes death in elderly and seriously ill patients, and results in significant health costs each year. Proton pump inhibitors (PPIs) reduce gastric acidity, which is an important protection against microorganisms. We hypothesised that treatment with PPIs increases the risk of contracting norovirus infection. This has not previously been studied. The study was a retrospective case–control study, in which 192 hospitalised patients positive for norovirus in Örebro County, Sweden, were identified as cases. For each case, a hospitalised patient who did not have the infection was selected as a control, and matched with respect to ward, gender, admission date and age. Details of exposure, i.e. treatment with PPIs, were retrieved from the patient records. Odds ratio (OR) with confidence intervals (CIs) and P-values were calculated using McNemar's test. There was a significantly increased risk of norovirus infection in patients treated with PPIs compared with patients without PPI treatment (OR 1·73, 95% CI 1·07–2·81; P = 0·02). PPIs appear to be a risk factor for norovirus infection, and our results motivate future studies to further examine this association.

HBsAg reappearance may constitute not only a risk for liver disease but also an infectious source. We aimed to determine whether HBsAg may reappear after spontaneous HBsAg seroclearance. A cohort of 2999 HBsAg-positive subjects aged 30–55 years was recruited in Guangxi, China in 2004. HBsAg was tested every 6 months from July 2004 to June 2007, then, one more time in December 2013. The results showed that spontaneous HBsAg seroclearance occurred in 41 subjects in the first 3 years, giving a 0·54% annual seroclearance rate. Thirteen of the 41 subjects were randomly tested for HBsAg in 2013. Four subjects became HBsAg positive. S gene sequences of HBV were analysed from serum collected before seroclearance and after reappearance, respectively, for subject QS840 (11 and 12 clones), subject TN98 (13 and 13 clones) and subject WX227 (10 and 8 clones). Serotype, subgenotype and amino-acid substitution pattern in each sample collected after reappearance was observed in the sample collected before HBsAg seroclearance. Nucleotide similarity between the two sequences from each subject was >99% and five sequences from subject TN98 were the same. In conclusion, following reactivation, HBsAg may reappear in individuals with spontaneous HBsAg seroclearance many years previously.