The clinical and pathologic characterisation of two fatal cases of tick-borne rickettsiosis in rural (El Valle) and urban (City of Panama) Panama are described. Clinical and autopsy findings were non-specific, but the molecular analysis was used to identify Rickettsia rickettsii in both cases. No ticks were collected in El Valle, while in the urban case, R. rickettsii was detected in Rhipicephalus sanguineus s.l., representing the first molecular finding in this tick in Panama and Central America.

Salmonella Give is a rare serotype across Europe. In October 2016, a national outbreak of S. Give occurred in Malta. We describe the epidemiological, environmental, microbiological and veterinary investigations. Whole-genome sequencing (WGS) was performed on human, food, environmental and veterinary isolates. Thirty-six human cases were reported between October and November 2016, 10 (28%) of whom required hospitalisation. Twenty-six (72%) cases were linked to four restaurants. S. Give was isolated from ready-to-eat antipasti served by three restaurants which were all supplied by the same local food manufacturer. Food-trace-back investigations identified S. Give in packaged bean dips, ham, pork and an asymptomatic food handler at the manufacturer; inspections found inadequate separation between raw and ready-to-eat food during processing. WGS indicated two genetically distinguishable strains of S. Give with two distinct clusters identified; one cluster linked to the local food manufacturer and a second linked to veterinary samples. Epidemiological, environmental and WGS evidence pointed towards cross-contamination of raw and ready-to-eat foods at the local manufacturer as the likely source of one cluster. Severity of illness indicates a high virulence of this specific serotype. To prevent future cases and outbreaks, adherence to food safety practices at manufacturing level need to be reinforced.

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

This study aimed at evaluating the integrated measles and rubella surveillance system (IMRSS) in Apulia region, Italy, from its introduction in 2013 to 30 June 2016. Measles and rubella case reports were extracted from IMRSS. We estimated system sensitivity at the level of case reporting, using the capture–recapture method for three data sources. Data quality was described as the completeness of variables and timeliness of notification as the median-time interval from symptoms onset to initial alert. The proportion of suspected cases with laboratory investigation, the rate of discarded cases and the origin of infection were also computed. A total of 127 measles and four rubella suspected cases were reported to IMRSS and 82 were laboratory confirmed. Focusing our analysis on measles, IMRSS sensitivity was 82% (95% CI: 75–87). Completeness was >98% for mandatory variables and 57% for ‘genotyping’. The median-time interval from symptoms onset to initial alert was 4.5 days, with a timeliness of notification of 33% (41 cases reported ⩽48 h). The proportion of laboratory investigation was 87%. The rate of discarded cases was 0.1 per 100 000 inhabitants per year. The origin of infection was identified for 85% of cases. It is concluded that IMRSS provides good quality data and has good sensitivity; still efforts should be made to improve the completeness of laboratory-related variables, timeliness and to increase the rate of discarded cases.

Tuberculosis (TB) has been known to affect elephants for thousands of years. It was put into spotlight when few circus elephants were diagnosed carrying Mycobacterium (M.) tuberculosis. Because of the zoonotic risk and high susceptibility to M. tuberculosis, periodic testing was enacted since, in captive breeding programmes. Presently, trunk wash is the recommended diagnostic procedure for TB. Trunk wash, however, puts the operator at risk, has low sensitivity, and is prone to contamination. Here, bronchoalveolar lavage is described for the first time for TB diagnosis in elephants. Bronchial, trunk and mouth fluids were investigated using bacterial culture, M. tuberculosis complex (MTC)-specific real-time quantitative PCR (qPCR) and mycobacterial genus-specific qPCR for overall presence of mycobacteria or mycobacterial DNA including bacteria or DNA of closely related genera, respectively, in 14 elephants. Neither bacteria of the MTC nor their DNA were identified in any of the elephants. Yet, 25% of the cultures grew non-tuberculous mycobacteria (NTM) or closely related bacterial species. Furthermore, 85% of the samples contained DNA of NTM or closely related bacterial genera. This finding might explain continued false-positive results from various serological tests. From a zoonotic point of view, bronchoalveolar lavage is safer for the testing personal, has higher probability of capturing MTC and, through PCR, identifies DNA NTM in elephants. Yet, necessary endoscopic equipment, animal sedation and access to a TB reference laboratory might pose challenging requirements in remote conditions in some elephant range countries.

We performed a systematic review and meta-analyses of studies assessing tuberculosis (TB) patient-related risk factors for transmission of Mycobacterium tuberculosis infection. Meta-analyses were conducted for sputum smear-positivity, lung cavitation and HIV seropositivity of index patients with both crude and adjusted odds ratios (AORs) pooled using random effect models. Thirty-seven studies were included in the review. We found that demographic characteristics such as age and sex were not significant risk factors, while behaviours such as smoking and alcohol intake were associated with infectiousness although inconsistently. Treatment delay of >28 days was a significant predictor of greater infectiousness. Contacts of sputum smear-positive index patients were found to be more likely to be infected than contacts of sputum smear-negative patients, with a pooled AOR of 2.15 (95% confidence interval (CI) 1.47–3.17, I2 = 38%). Similarly, contacts of patients with the cavitary disease were around twice as likely to be infected as contacts of patients without cavitation (pooled AOR 1.9, 95% CI 1.26–2.84, I2 = 63%). In contrast, HIV seropositive patients were associated with few contact infections than HIV seronegative patients (AOR 0.45, 95% CI 0.26–0.80, I2 = 52%). In conclusion, behavioural and clinical characteristics of TB patients can be used to identify highly infectious patients for targeted interventions.

Swine can act as asymptomatic carriers of some Leptospira serovars. In this study, 1194 sera from 61 farms located in five different Regions of North-West Italy were collected from slaughtered healthy pigs. Presence of antibody against four Leptospira serovars was evaluated. Overall, 52.5% of analysed farms presented at least one positive animal and 34.4% presented at least one positive swine with titre ⩾1:400. A percentage of 16.6% sera was positive and 5.9% samples presented a positive titre ⩾1:400. Tuscany and Lombardy showed the highest percentage of positive farms (64.3% and 54.6%, respectively) and sera (28.5% and 13.3%, respectively), probably due to environmental conditions and potential risk factors, which promote maintenance and spreading of Leptospira in these areas. The main represented serogroups were Australis (21.3% positive farms, 8.2% positive sera) and Pomona (18.0% positive farms, 8.1% positive sera). In swine, these serogroups are the most detected worldwide; however, our results seem to highlight a reemerging of serogroup Pomona in pigs in investigated areas. A low percentage of sera (0.6%) scored positive to Canicola, leaving an open question on the role of pigs in the epidemiology of this serovar. Higher antibody titres were detected for serogroups Australis and Pomona. Swine leptospirosis is probably underestimated in Italy and could represent a potential risk for animal and human health.

Social contact between individuals is believed to be a fundamental cause in the transmission of many respiratory tract infections. Because they have not yet been fully vaccinated, infants are at high risk for contracting whooping cough, influenza and their serious complications. Therefore, determining infant social contact patterns is an important step in protecting them from respiratory tract infection. This study included 1200 healthy infants (<12 months of age). Social contact diaries were used to estimate the frequency and nature of the infants’ social contacts. This survey also gathered information regarding the infants’ respiratory symptoms and their frequency of attendance at crowded places over a period of 1 week. The diary return rate was 83.8% (N = 1006), and there was a total of 4706 contacts reported for these infants. The median daily contact number per capita was 4 (range 1–18). The median number of contacts with adolescents was 0 (range 0–7). Of the infants, 50.3% had contact with non-household individuals. The mothers had the longest contacts with their babies. Contacts with school children, frequency of attendance at crowded places and age were determined to be significant effective factors for reporting respiratory symptoms. Results suggest that school-age siblings and the mothers should be primarily vaccinated, and parents should keep their babies away from crowded places for protecting their infants.

The purpose of the present study was to reconstruct the phylogeny of dengue virus serotype 4 (DENV-4) that was circulating in Espírito Santo state, Brazil, in 2013 and 2014, and to discuss the epidemiological implications associated with this evolutionary hypothesis. Partial envelope gene of eight DENV-4 samples from Espírito Santo state were sequenced and aligned with 72 worldwide DENV-4 reference sequences from GenBank. A phylogenetic tree was reconstructed through Bayesian Inference and the Time of the Most Recent Common Ancestor was estimated. The study detected the circulation of DENV-4 genotype II in Espírito Santo state, which was closely related to strains from the states of Mato Grosso collected in 2012 and of São Paulo sampled in 2015. This cluster emerged around 2011, approximately 4 years after the entry of the genotype II in Brazil through its northern states, possibly imported from Venezuela and Colombia. This is so far the first phylogenetic study of the DENV-4 circulating in Espírito Santo state and shows the importance of an internal route of dengue viral circulation in Brazil to the introduction of the virus into this state.

In the absence of perfect reference standard, classical techniques result in biased diagnostic accuracy and prevalence estimates. By statistically defining the true disease status, latent class models (LCM) constitute a promising alternative. However, LCM is a complex method which relies on parametric assumptions, including usually a conditional independence between tests and might suffer from data sparseness. We carefully applied LCMs to assess new campylobacter infection detection tests for which bacteriological culture is an imperfect reference standard. Five diagnostic tests (culture, polymerase chain reaction and three immunoenzymatic tests) of campylobacter infection were collected in 623 patients from Bordeaux and Lyon Hospitals, France. Their diagnostic accuracy were estimated with standard and extended LCMs with a thorough examination of models goodness-of-fit. The model including a residual dependence specific to the immunoenzymatic tests best complied with LCM assumptions. Asymptotic results of goodness-of-fit statistics were substantially impaired by data sparseness and empirical distributions were preferred. Results confirmed moderate sensitivity of the culture and high performances of immunoenzymatic tests. LCMs can be used to estimate diagnostic tests accuracy in the absence of perfect reference standard. However, their implementation and assessment require specific attention due to data sparseness and limitations of existing software.

Hemorrhagic fever with renal syndrome (HFRS) caused by hantaviruses is a serious public health problem in China, accounting for 90% of HFRS cases reported globally. In this study, we applied geographical information system (GIS), spatial autocorrelation analyses and a seasonal autoregressive-integrated moving average (SARIMA) model to describe and predict HFRS epidemic with the objective of monitoring and forecasting HFRS in mainland China. Chinese HFRS data from 2004 to 2016 were obtained from National Infectious Diseases Reporting System (NIDRS) database and Chinese Centre for Disease Control and Prevention (CDC). GIS maps were produced to detect the spatial distribution of HFRS cases. The Moran's I was adopted in spatial global autocorrelation analysis to identify the integral spatiotemporal pattern of HFRS outbreaks, while the local Moran's Ii was performed to identify ‘hotspot’ regions of HFRS at province level. A fittest SARIMA model was developed to forecast HFRS incidence in the year 2016, which was selected by Akaike information criterion and Ljung–Box test. During 2004–2015, a total of 165 710 HFRS cases were reported with the average annual incidence at province level ranged from 0 to 13.05 per 100 000 persons. Global Moran's I analysis showed that the HFRS outbreaks presented spatially clustered distribution, with the degree of cluster gradually decreasing from 2004 to 2009, then turned out to be randomly distributed and reached lowest point in 2012. Local Moran's Ii identified that four provinces in northeast China contributed to a ‘high–high’ cluster as a traditional epidemic centre, and Shaanxi became another HFRS ‘hotspot’ region since 2011. The monthly incidence of HFRS decreased sharply from 2004 to 2009 in mainland China, then increased markedly from 2010 to 2012, and decreased again since 2013, with obvious seasonal fluctuations. The SARIMA ((0,1,3) × (1,0,1)12) model was the most fittest forecasting model for the dataset of HFRS in mainland China. The spatiotemporal distribution of HFRS in mainland China varied in recent years; together with the SARIMA forecasting model, this study provided several potential decision supportive tools for the control and risk-management plan of HFRS in China.

The number of dengue epidemics in Brazil has increased dramatically in the last 15 years. In this study, we analysed the seasonal patterns in the incidence of hospitalisations due to dengue across the different states of Brazil and compared these with the corresponding climatic patterns. We discovered that the seasonality of dengue hospitalisations in Brazil has a clear zonal gradient, characterised by the progression of primary peaks from West to East during the first half of the year, which may be associated with the increased vapour pressure and rainfall during this period, leading to increased mosquito abundance and activity. We also found that the proportion of children among hospitalised individuals was especially high during the peak outbreaks in 2007/2008 and 2010. This may be due to the emergence and spread of the new DENV-2 Southeast Asian genotype lineage II from 2007, which has probably arrived from the Caribbean and may have caused an increase in incidence and severity of the disease, particularly among children. Our findings may allow health systems to improve control interventions and contribute to reducing dengue morbidity and mortality by using integrated vector control in conjunction with early diagnosis and prompt supportive care.

Otitis externa is the inflammation of the external auditory canal. The disease is common and shows a seasonal variation with a greater incidence in warmer months. Pseudomonas aeruginosa is a common pathogen in otitis externa and in this retrospective study, we show a corresponding seasonal variation in the proportional incidence of P. aeruginosa isolates from otitis externa in South East England. In total 7770 patients were diagnosed with otitis externa over a period of 9 years from January 2008 to December 2016. P. aeruginosa was isolated from 2802 patients (proportional incidence of 36%). Incidence was higher in the months of August, September and October and in patients between 5 and 15 years of age. We postulate a combination of increased contact with water during warm weather in the holiday season and increased rainfall in the preceding season as a putative mechanism for the seasonal trends.

The following paper investigates the prevalence and characteristics of asymptomatic norovirus infection in the population living around oyster farm sites. Two consecutive surveys were conducted from January 2014 to December 2014 and 4549 stool samples were screened during the same time period. The total asymptomatic infection rate was 4.04% (184/4549). Norovirus infection rate was 5.20% in oyster farming population which was significantly higher compared with non-farming population where the infection rate was 3.65% (χ2 = 5.49, P < 0.05). A total of 184 NoV positive samples were identified by real time-quantitative polymerase chain reaction (RT-qPCR) and semi-nested RT-PCR and 136 sequences were obtained. The sequences were clustered into 14 genotypes. GI strains were clustered into six genotypes, including GI.2, GI.3, GI.5, GI.6, GI.8 and GI.9; while GII strains were clustered into GII.2, GII.3, GII.4, GII.5, GII.6, GII.8 and GII.13. GI.9 and GII.17 were the predominant and most prevalent genotypes, respectively. The GII.17 genotype replaced GII.4 becoming the dominant genotype in the oyster farming area in 2014. To sum up, long-term monitoring of asymptomatic infection is crucial for the detection of new variant strains and for identifying outbreaks during the early stage.

This study assessed smallholder finances and their attitudes towards the Foot and Mouth Disease (FMD) vaccination programme, when 1 620 000 vaccine doses were provided for strategic administration in large ruminants in FMD ‘high-risk’ areas in Laos between 2012 and 2016. Farmers (n = 168) in the provinces of Xayyabouli (XYL), Xiengkhoung (XK) and Huaphan (HP), were interviewed. Over 91% of the farmers responded that their livestock were vaccinated for FMD, with over 86% ranking FMD vaccination as a good or very good intervention. No FMD cases were reported from the vaccinated provinces after May 2013. Examination of the total income per household in XYL, XK and HP indicated earnings of US$5060(±650), US$4260(±294) and US$1691(±676), respectively (P = 0.001), with 23%, 28% and 68% of the total incomes from annual sales of large ruminant, respectively. Of the farmers in XYL, XK and HP, 83%, 93% and 70% (P = 0.009) said their annual income increased compared with 2012, and 47%, 64% and 41%, respectively (P = 0.005), indicated this increase was from additional large ruminant sales. The study indicated that this large FMD vaccination programme was well regarded by participating farmers and may have provided satisfactory suppression of the disease in Laos, despite not achieving the preferred vaccination coverage. Continuation of the vaccination programme in FMD high-risk areas is suggested as desirable.

In September 2016, an imported case of measles in Edinburgh in a university student resulted in a further 17 confirmed cases during October and November 2016. All cases were genotype D8 and were associated with a virus strain most commonly seen in South East Asia. Twelve of the 18 cases were staff or students at a university in Edinburgh and 17 cases had incomplete or unknown measles mumps rubella (MMR) vaccination status. The public health response included mass follow-up of all identified contacts, widespread communications throughout universities in Edinburgh and prompt vaccination clinics at affected campuses. Imported cases of measles pose a significant risk to university student cohorts who may be undervaccinated, include a large number of international students and have a highly mobile population. Public health departments should work closely with universities to promote MMR uptake and put in place mass vaccination plans to prevent rapidly spreading measles outbreaks in higher educational settings in future.

Jamestown Canyon and snowshoe hare viruses are two emerging human pathogens associated with cases of neuroinvasive disease in North America. This study aimed to identify environmental and individual risk factors for seropositivity to these arboviruses in humans and pet dogs from Québec, Canada, 2012–2014. In humans, areas with moderate densities of white-tailed deer (Odocoileus virginianus) were associated with higher odds of seropositivity compared with areas with low densities of white-tailed deer (OR 2.50, P = 0.009) and odds of seropositivity were higher in males than in females (OR 2.03, P = 0.016). Among humans reporting more than 10 mosquito bites weekly, the odds of being seropositive were 4.44 times higher (P = 0.004) for people living in hardwood forested areas. Exposure to areas with coniferous forests was identified as the main environmental risk factor for seroconversion in dogs (OR 2.39, P = 0.04). These findings may help target further public health research, diagnostic and surveillance efforts in Canada.

Commercial point-of-care (POC) diagnostic tests for Group A Streptococcus, Streptococcus pneumoniae, and influenza virus have large potential diagnostic and financial impact. Many published reports on test performance, often funded by diagnostics companies, are prone to bias. The Standards for Reporting of Diagnostic Accuracy (STARD 2015) are a protocol to encourage accurate, transparent reporting. The Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool evaluates risk of bias and transportability of results. We used these tools to evaluate diagnostic test accuracy studies of POC studies for three respiratory pathogens. For the 96 studies analysed, compliance was <25% for 14/34 STARD 2015 standards, and 3/7 QUADAS-2 domains showed a high risk of bias. All reports lacked reporting of at least one criterion. These biases should be considered in the interpretation of study results.

In May 2016 a Norovirus (NoV) gastroenteritis outbreak involved a high school class visiting a seaside resort near Taormina (Mascali, Sicily). Twenty-four students and a teacher were affected and 17 of them showed symptoms on the second day of the journey, while the others got ill within the following 2 days. Symptoms included vomiting, diarrhoea and fever, and 12 students required hospitalisation. Stool samples tested positive for NoV genome by Real-Time polymerase chain reaction assay in all 25 symptomatic subjects. The GII.P2/GII.2 NoV genotype was linked to the outbreak by ORF1/ORF2 sequence analysis. The epidemiological features of the outbreak were consistent with food/waterborne followed by person-to-person and/or vomit transmission. Food consumed at a shared lunch on the first day of the trip was associated to illness and drinking un-bottled tap water was also considered as a risk factor. The analysis of water samples revealed the presence of bacterial indicators of faecal contamination in the water used in the resort as well as in other areas of the municipal water network, linking the NoV gastroenteritis outbreak to tap water pollution from sewage leakage. From a single water sample, an amplicon whose sequence corresponded to the capsid genotype recovered from patients could be obtained.