The objective of this study was to assess the use of statistical algorithms in identifying significant clusters of Salmonella spp. across different sectors of the food chain within an integrated surveillance programme. Three years of weekly Salmonella serotype data from farm animals, meat, and humans were used to create baseline models (first two years) and identify weeks with counts higher than expected using surveillance algorithms in the third (test) year. During the test year, an expert working group identified events of interest reviewing descriptive analyses of same data. The algorithms did not identify Salmonella events presenting as gradual increases or seasonal patterns as identified by the working group. However, the algorithms did identify clusters for further investigation, suggesting they could be a valuable complementary tool within an integrated surveillance system.

We reviewed the first 21 years (1991–2011) of Australia's National Notifiable Diseases Surveillance System (NNDSS). All nationally notified diseases (except HIV/AIDS and Creutzfeldt–Jakob disease) were analysed by disease group (n = 8), jurisdiction (six states and two territories), Indigenous status, age group and notification year. In total, 2 421 134 cases were analysed. The 10 diseases with highest notification incidence (chlamydial infection, campylobacteriosis, varicella zoster, hepatitis C, influenza, pertussis, salmonellosis, hepatitis B, gonococcal infection, and Ross River virus infection) comprised 88% of all notifications. Annual notification incidence was 591 cases/100 000, highest in the Northern Territory (2598/100 000) and in children aged <5 years (698/100 000). A total of 8·4% of cases were Indigenous Australians. Notification incidence increased by 6·4% per year (12% for sexually transmissible infections and 15% for vaccine-preventable diseases). The number of notifiable diseases also increased from 37 to 65. The number and incidence of notifications increased throughout the study period, partly due to addition of diseases to the NNDSS and increasing availability of sensitive diagnostic tests. The most commonly notified diseases require a range of public health responses addressing high-risk sexual and drug-use behaviours, food safety and immunization. Our results highlight populations with higher notification incidence that might require tailored public health interventions.

Staphylococcus aureus is the most important causative agent of subclinical mastitis in cattle resulting in reduced milk production and quality. Methicillin-resistant S. aureus (MRSA) strains has a clear zoonotic relevance, especially in the case of occupational exposure. The aim of the study was to evaluate the prevalence of S. aureus and MRSA in bulk tank milk (BTM) from dairy cattle herds in the Lombardy Region (Northern Italy) and to identify the main MRSA circulating genotypes. MRSA strains were characterized by susceptibility testing, multi-locus sequence typing (MLST), spa typing and SCCmec typing. A total 844 BTM samples were analysed and S. aureus and MRSA were detected in 47·2% and 3·8% of dairy herds, respectively. MLST showed that the majority (28/32) of isolates belonged to the typical livestock-associated lineages: ST398, ST97 and ST1. Interestingly, in this study we report for the first time the new ST3211, a single locus variant of ST(CC)22, with the newly described 462 aroE allele. Our study indicates high diffusion of S. aureus mastitis and low, but not negligible, prevalence of MRSA in the considered area, suggesting the need for planning specific control programmes for bovine mastitis caused by S. aureus, especially when MRSA is implicated.

Seasonal influenza is a significant public health concern globally. While influenza vaccines are the single most effective intervention to reduce influenza morbidity and mortality, there is considerable debate surrounding the merits and consequences of repeated seasonal vaccination. Here, we describe a two-season influenza epidemic contact network model and use it to demonstrate that increasing the level of continuity in vaccination across seasons reduces the burden on public health. We show that revaccination reduces the influenza attack rate not only because it reduces the overall number of susceptible individuals, but also because it better protects highly connected individuals, who would otherwise make a disproportionately large contribution to influenza transmission. We also demonstrate that our results hold on an empirical contact network, in the presence of assortativity in vaccination status, and are robust for a range of vaccine coverage and efficacy levels. Our work contributes a population-level perspective to debates about the merits of repeated influenza vaccination and advocates for public health policy to incorporate individual vaccine histories.

Pneumonia due to either Streptococcus pneumoniae (Sp) or Staphylococcus aureus (Sa) accounts for most mortality after influenza and acute respiratory illness (ARI). Because carriage precedes infection, we estimated Sp and Sa carriage to examine the co-colonization dynamics between Sp, Sa and respiratory viruses in the presence of ARI in the oropharynx. We tested oropharyngeal specimens of community subjects (aged ⩾2 years) with ARI for the presence of influenza A and B, 11 other common respiratory viruses, Sp and Sa, using real-time PCR. A total of 338 participants reported 519 ARI episodes of which 119 (35%) carried Sp, 52 (13%) carried Sa and 25 (7%) carried both. Thirty-five subjects tested positive for influenza, of which 14 (40%) carried Sp and six (17%) carried Sa, significantly more than in the influenza-negative group (P = 0·03 and P = 0·04, respectively). In subjects infected by any virus compared to those with no virus, Sp carriage (39·2% vs. 27·9%, P = 0·03) but not Sa carriage (11·6% vs. 14%, P = 0·6) was more frequent. For children, when Sa was present, Sp carriage tended to be less frequent than expected given the presence of viral infection, but not significantly [observed relative risk 1·14, 95% confidence interval (CI) 0·4–3·1; with a relative excess risk due to interaction of –0·11]. Independent of age, Sp carriers were more likely to return that season with subsequent ARI (odds ratio 2·14, 95% CI 1·1–4·3, P = 0·03). Both Sp and Sa carriage rates in the oropharynx increase during influenza infection in children. However, no negative interaction between Sp and Sa was observed. Sp carriers are more likely to suffer subsequent ARI episodes than non-carriers.

To evaluate measles incidence and its relevant changes over a 14-year period (2000–2014), we analysed data from the regional hospital discharge database on children and adults hospitalized in Tuscany, Italy. A total of 181 paediatric and 413 adult cases were identified. Despite all the efforts towards regional measles elimination, we observed that the overall measles hospitalization rates for children and adults living in Tuscany globally increased from 0·45 to 0·85/100 000 during the study period (P = 0·001) showing fluctuations due to periodic measles outbreaks. Data stratified by age group showed that the hospitalization rate significantly increased in young adults over the study period, confirming an increase in susceptibility to measles in this subpopulation. Conversely, no statistically significant difference was observed in the hospitalization rate in the other age groups. However, children aged <1 year still exhibit the highest hospitalization rate. Pneumonia represented the most common complication in both the adult and children subsets. No death was reported. Measles still represents a public health problem, and national strategies should be implemented, focusing on emergent susceptible subsets, such as infants and young adults.

Molecular epidemiology and clinical impact of human rhinovirus (HRV) are not well documented in tropical regions. This study compared the clinical characteristics of HRV to other common viral infections and investigated the molecular epidemiology of HRV in hospitalized children with acute respiratory infections (ARIs) in Vietnam. From April 2010 to May 2011, 1082 nasopharyngeal swabs were screened for respiratory viruses by PCR. VP4/VP2 sequences of HRV were further characterized. HRV was the most commonly detected virus (30%), in which 70% were diagnosed as either pneumonia or bronchiolitis. Children with single HRV infections presented with significantly higher rate of hypoxia than those infected with respiratory syncytial virus or parainfluenza virus (PIV)-3 (12·4% vs. 3·8% and 0%, respectively, P < 0·05), higher rate of chest retraction than PIV-1 (57·3% vs. 34·5%, P = 0·028), higher rate of wheezing than influenza A (63·2% vs. 42·3%, P = 0·038). HRV-C did not differ to HRV-A clinically. The genetic diversity and changes of types over time were observed and may explain the year-round circulation of HRV. One novel HRV-A type was discovered which circulated locally for several years. In conclusion, HRV showed high genetic diversity and was associated with significant morbidity and severe ARIs in hospitalized children.

Accurate detection of infection with Mycobacterium bovis in live badgers would enable targeted tuberculosis control. Practical challenges in sampling wild badger populations mean that diagnosis of infection at the group (rather than the individual) level is attractive. We modelled data spanning 7 years containing over 2000 sampling events from a population of wild badgers in southwest England to quantify the ability to correctly identify the infection status of badgers at the group level. We explored the effects of variations in: (1) trapping efficiency; (2) prevalence of M. bovis; (3) using three diagnostic tests singly and in combination with one another; and (4) the number of badgers required to test positive in order to classify groups as infected. No single test was able to reliably identify infected badger groups if <90% of the animals were sampled (given an infection prevalence of 20% and group size of 15 badgers). However, the parallel use of two tests enabled an infected group to be correctly identified when only 50% of the animals were tested and a threshold of two positive badgers was used. Levels of trapping efficiency observed in previous field studies appear to be sufficient to usefully employ a combination of two existing diagnostic tests, or others of similar or greater accuracy, to identify infected badger groups without the need to capture all individuals. To improve on this, we suggest that any new diagnostic test for badgers would ideally need to be >80% sensitive, at least 94% specific, and able to be performed rapidly in the field.

Waterborne disease outbreaks (WBDO) of acute gastrointestinal illness (AGI) are a public health concern in France. Their occurrence is probably underestimated due to the lack of a specific surveillance system. The French health insurance database provides an interesting opportunity to improve the detection of these events. A specific algorithm to identify AGI cases from drug payment reimbursement data in the health insurance database has been previously developed. The purpose of our comparative study was to retrospectively assess the ability of the health insurance data to describe WBDO. Data from the health insurance database was compared with the data from cohort studies conducted in two WBDO in 2010 and 2012. The temporal distribution of cases, the day of the peak and the duration of the epidemic, as measured using the health insurance data, were similar to the data from one of the two cohort studies. However, health insurance data accounted for 54 cases compared to the estimated 252 cases accounted for in the cohort study. The accuracy of using health insurance data to describe WBDO depends on the medical consultation rate in the impacted population. As this is never the case, data analysis underestimates the total number of AGI cases. However this data source can be considered for the development of a detection system of a WBDO in France, given its ability to describe an epidemic signal.

In June 2014 Public Health England confirmed a case of Legionnaires' disease (LD) in a neonate following birth at home in a hired birthing pool incorporating a heater and a recirculation pump which had been filled in advance of labour. The case triggered a public health investigation and a microbiological survey of an additional ten heated birthing pools hired or recently hired to the general public across England. The birthing pool used by the parent of the confirmed case was identified as the source of the neonate's infection following detection of Legionella pneumophila ST48 in both patient and environmental samples. Legionella species were detected by quantitative polymerase chain reaction but not culture in a further three pools together with other opportunistic pathogens identified by culture and matrix-assisted laser desorption ionization–time of flight (MALDI–ToF) mass spectrometry. A Patient Safety Alert from NHS England and Public Health England was issued stating that heated birthing pools filled in advance of labour should not be used for home births. This recommendation remains in place. This investigation in conjunction with other recent reports has highlighted a lack of awareness regarding the microbiological safety of heated birthing pools and their potential to be a source of LD and other opportunistic infections. Furthermore, the investigation raised important considerations with regards to microbiological sampling and testing in such incidents. Public health authorities and clinicians should consider LD in the differential diagnosis of severe respiratory infection in neonates within 14 days of a water birth.

The community burden of enterovirus is often monitored through syndromic monitoring systems based on reported cases of enterovirus-related infection (EVI) diagnoses. The extent to which this is affected by under- and over-diagnosis has not been reported. In Taiwan, children often make more than one healthcare visit during an episode of infection. We used change of diagnosis within an episode of infection as a guide of diagnostic uncertainty in a nationally representative cohort of Taiwanese children (n = 13 284) followed from birth to the 9th birthday through electronic health records. We conducted a nested case-control analysis and estimated cross-diagnosis ratios (CDRs) as the observed proportion of acute respiratory infection (ARI) diagnoses following an EVI diagnosis in excess of background ARI burdens. With 19 357 EVI diagnoses in this cohort, the CDR within 7 days was 1·51 (95% confidence interval 1·45–1·57), confirming a significant excess of ARI diagnoses within the week following an EVI diagnosis. We used age-specific CDRs to calibrate the weekly EVI burden in children aged 3–5 years in 2008, and the difference between observed and calibrated weekly EVI burdens was small. Therefore, there was evidence suggesting a small uncertainty in EVI diagnosis, but the observed EVI burdens through syndromic monitoring were not substantially affected by the small uncertainty.

In the near future, the inactivated enterovirus 71 (EV71) vaccine is expected to become available on the market in China. Since EV71 is a major cause of hand, foot and mouth disease (HFMD), the vaccine is expected to significantly reduce the number of cases, as well as the detrimental economic effect of the disease. However, for a national vaccination strategy to be developed, policy-makers need more information on the socioeconomic burden of EV71 HFMD infection. Based on the 2011 population data, we estimated the clinical and economic effect of EV71 HFMD infection in children aged 0–9 years in Shanghai, China. The annual cost related to HFMD is >US$7.66 million for a population of 1·42 million children aged 0–9 years with an average cost of US$208.2/case. The extrapolated cost for EV71 HFMD infection was US$3.53 million, comprising 46·1% of the overall cost associated with HFMD. Around 97% of all of the HFMD-related expenses were paid for by the families creating a considerable economic burden. Our findings could provide the necessary recommendations on the most effective national EV71 vaccine implementation, as well as a baseline data for assessing the cost-effectiveness of the vaccine in China.

The phylogenetic and epidemiological relationships of 102 Burkholderia pseudomallei clinical isolates from different geographical and population sources in China were investigated by multilocus sequence typing (MLST). The MLST data were analysed using the e-BURST algorithm, and an unweighted pair-group method with arithmetic mean dendrogram was constructed based on the pair-wise differences in the allelic profiles of the strains. Forty-one sequence types (STs) were identified, of which eight were novel (ST1341, ST1345, ST1346, ST1347, ST1348, ST1349, ST1350, ST1351). No geographical-specific or host population-specific phylogenetic lineages were identified. ST46, ST50, ST55, ST58, ST70 and ST1095 predominated, but ~44% of isolates were assigned to 45 STs illustrating high genetic diversity in the strain collection. Additionally, the phylogenetic relationships of the dominant STs in China showed significant linkeage with B. pseudomallei isolates from Thailand. Analysis of the gmhD allele suggests high genetic variation in B. pseudomallei in China.

Young age, adverse environmental conditions and infectious agents are established risk factors of lower respiratory tract infection (LRTI), whereas pneumococcal conjugate vaccines may be protective. To explore their relative role as predictors of hospitalizations under the continental climate prevailing in the province of Quebec, Canada, an ecological study was performed. Records with a main diagnosis of LRTI in children born during 2007–2010 and observed up to their second-year anniversary were extracted from the provincial hospital administrative database. Respiratory virus surveillance data and statistics on ambient air temperature were obtained. Vaccine use in different birth cohorts was derived from the Quebec City Immunization Registry. Additive and multiplicative Poisson regression models were applied to estimate attributable fractions. Age, month of birth, ambient temperature, and respiratory syncytial virus (RSV), human metapneumovirus (hMPV) and influenza-positive test proportions were significant predictors of LRTI hospitalizations. No substantial differences were observed in cohorts exposed to the 7-valent or 10-valent pneumococcal conjugate vaccines. In the additive model, the fraction of hospitalizations explained by temperature variation was 37%, whereas RSV circulation explained 28%, hMPV 4% and influenza 1%. Complex interplay between biological, environmental and social mechanisms may explain the important role of ambient air temperature in predicting LRTI hospitalization risk in young children.

In Sweden, acute gastrointestinal illness (AGI) incidence, severity, impact on productivity, related healthcare usage and associated costs are not ascertained. We measured these in 2013–2014 using a population-based cohort reporting weekly. We defined AGI as ⩾3 episodes of loose stools or vomiting/24 h; or loose stools or vomiting with ⩾2 other gastrointestinal symptoms. After each AGI episode, we collected information about perceived severity, healthcare use and absenteeism. We calculated incidence rates, AGI absenteeism and costs comprising direct healthcare costs and productivity loss due to work/school absenteeism. A total of 3241 participants reported 1696 AGI episodes [incidence 360/1000 person-years, 95% confidence interval (CI) 326–395; highest in the <5 years age group]. In the <5 years age group, 31% of episodes were perceived as mild, 61% as moderate and 8% as severe; 9·4% led to primary-care consultations, and 1·4% to hospital admissions. In the ⩾5 years age group, 18% of episodes were perceived as mild, 64% as moderate and 18% as severe; 6·4% led to primary-care consultations, and 1·9% to hospital admissions. AGI caused 8 891 000 days of absenteeism (95% CI 6 009 000–12 780 000). AGI cost €1 005 885 000 (95% CI 754 309 000–1 257 195 000) nationally for the year. In Sweden, a minority of cases perceive AGI as a mild illness. AGI is a burden on the healthcare system and causes productivity loss, with high costs. Countries may consider these estimates when prioritizing health interventions.

West Nile virus (WNV) is a mosquito-borne neurotropic viral pathogen maintained in an enzootic cycle between mosquitoes (vectors) and birds (natural hosts) with equids, humans, and other vertebrates acting as dead-end hosts. WNV activity in Mexico has been reported in several domestic and wild fauna and in humans, and the virus has been isolated from birds, mosquitoes, and humans. However, no serological studies have been conducted in monkeys, and only two in a limited number of crocodiles (Crocodylus moreletii). Here we present data on the prevalence of neutralizing antibodies against WNV in 53 healthy wild monkeys (49 Ateles geoffroyi and four Alouatta pigra), and 80 semi-captive healthy crocodiles (60 C. acutus and 20 C. acutus–C. moreletti hybrids) sampled during 2012. None of the monkey sera neutralized WNV, whereas 55% of the crocodile sera presented neutralizing antibodies against WNV. These results can contribute to the design of surveillance programmes in Mexico.

Little is known about cause-specific long-term mortality beyond 30 days in pneumonia. We aimed to compare the mortality of patients with hospitalized pneumonia compared to age- and sex-matched controls beyond 30 days. Participants were drawn from the European Prospective Investigation into Cancer (EPIC)-Norfolk prospective population study. Hospitalized pneumonia cases were identified from record linkage (ICD-10: J12-J18). For this study we excluded people with hospitalized pneumonia who died within 30 days. Each case identified was matched to four controls and followed up until the end June 2012 (total 15 074 person-years, mean 6·1 years, range 0·08–15·2 years). Cox regression models were constructed to examine the all-cause, respiratory and cardiovascular mortality using date of pneumonia onset as baseline with binary pneumonia status as exposure. A total of 2465 men and women (503 cases, 1962 controls) [mean age (s.d.) 64·5 (8·3) years] were included in the study. Between a 30-day to 1-year period, hazard ratios (HRs) of all-cause and cardiovascular mortality were 7·3 [95% confidence interval (CI) 5·4–9·9] and 5·9 (95% CI 3·5–9·7), respectively (with very few respiratory deaths within the same period) in cases compared to controls after adjusting for age, sex, asthma, smoking status, pack years, systolic and diastolic blood pressure, diabetes, physical activity, waist-to-hip ratio, prevalent cardiovascular and respiratory diseases. All outcomes assessed also showed increased risk of death in cases compared to controls after 1 year; respiratory cause of death being the most significant during that period (HR 16·4, 95% CI 8·9–30·1). Hospitalized pneumonia was associated with increased all-cause and specific-cause mortality beyond 30 days.

Among the most prevalent Mycobacterium tuberculosis (Mtb) strains worldwide is the Beijing genotype, which has caused large outbreaks of tuberculosis (TB). Characteristics facilitating the dissemination of Beijing family strains remain unknown, but they are presumed to have been acquired through evolution of the lineage. To explore the genetic diversity of the Beijing family Mtb and explore the discriminatory ability of mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) loci in several regions of East Asia, a cross-sectional study was conducted with a total of 163 Beijing strains collected from registered TB patients between 1 June 2009 and 31 November 2010 in Funing County, China. The isolated strains were analysed by 15-MIRU-VNTR loci typing and compared with published MIRU-VNTR profiles of Beijing strains. Synonymous single nucleotide polymorphisms at 10 chromosomal positions were also analysed. The combination of SNP and MIRU-VNTR typing may be used to assess Mtb genotypes in areas dominated by Beijing strains. The modern subfamily in Shanghai overlapped with strains from other countries, whereas the ancient subfamily was genetically differentiated across several countries. Modern subfamilies, especially ST10, were prevalent. Qub11b and four other loci (MIRU 26, Mtub21, Qub26, Mtub04) could be used to discriminate Beijing strains.

For influenza surveillance and diagnosis typical clinical symptoms are traditionally used to discriminate influenza virus infections from infections by other pathogens. During the 2013 influenza season we performed a multiplex assay for 16 different viruses in 665 swabs from patients with acute respiratory infections (ARIs) to display the variety of different pathogens causing ARI and to test the diagnostic value of both the commonly used case definitions [ARI, and influenza like illness (ILI)] as well as the clinical judgement of physicians, respectively, to achieve a laboratory-confirmed influenza diagnosis. Fourteen different viruses were identified as causing ARI/ILI. Influenza diagnosis based on clinical signs overestimated the number of laboratory-confirmed influenza cases and misclassified cases. Furthermore, ILI case definition and physicians agreed in only 287/651 (44%) cases with laboratory confirmation. Influenza case management has to be supported by laboratory confirmation to allow evidence-based decisions. Epidemiological syndromic surveillance data should be supported by laboratory confirmation for reasonable interpretation.

In 2013, an unusual increase of paratyphoid fever cases in travellers returning from Cambodia was reported in Japan. From December 2012 to September 2013, 18 cases of Salmonella Paratyphi A infection were identified. Microbiological analyses revealed that most isolates had the same clonal identity, although the epidemiological link between these cases remains unclear. It was inferred that the outbreak was caused by a common and persistent source in Cambodia that was likely to have continued during 2014. The information of surveillance and laboratory data from cases arising in travellers from countries with limited surveillance systems should be timely shared with the country of origin.