Although the compartmentalization of poultry industry components has substantial economic implications, and is therefore a concept with huge significance to poultry industries worldwide, the current requirements for compartment status are generic to all OIE member countries. We examined the consequences for potential outbreaks of highly pathogenic avian influenza in the British poultry industry using a metapopulation modelling framework. This framework was used to assess the effectiveness of compartmentalization relative to zoning control, utilizing empirical data to inform the structure of potential epidemiological contacts within the British poultry industry via network links and spatial proximity. Conditions were identified where, despite the efficient isolation of poultry compartments through the removal of network-mediated links, spatially mediated airborne spread enabled spillover of infection with nearby premises making compartmentalization a more ‘risky’ option than zoning control. However, when zoning control did not effectively inhibit long-distance network links, compartmentalization became a relatively more effective control measure than zoning. With better knowledge of likely distance ranges for airborne spread, our approach could help define an appropriate minimum inter-farm distance to provide more specific guidelines for compartmentalization in Great Britain.

This study assesses the contribution of different sources of human campylobacteriosis in Denmark using two different source-attribution approaches. In total, 794 non-human isolates and 406 isolates from human cases (domestic, travel related, and cases with unknown travel history) were collected. Isolates were characterized by multilocus sequence typing, flaA typing and susceptibility to antibiotics. Both models used indicate that the major burden of human campylobacteriosis in Denmark originates from the domestic broiler chicken reservoir. The second most important reservoir was found to be cattle. The Asymmetric Island model attributed 52% [95% credibility interval (CrI) 37–67] to Danish chicken, 17% (95% CrI 3–33) to imported chicken, and 17% (95% CrI 7–28) to cattle. Similarly, the Campylobacter source-attribution model apportioned 38% (95% CrI 28–47) to Danish chicken, 14% (95% CrI 10–18) to imported chicken, and 16% (95% CrI 7–25) to cattle. The addition of flaA type as an extra discriminatory typing parameter did not change the attribution of cases markedly.

The aim of this study was to describe the incidence and risk factors for respiratory morbidity during the 12-month period following the first respiratory syncytial virus (RSV) season in 242 preterm infants [<33 weeks gestational age (GA)] without bronchopulmonary dysplasia and 201 full-term infants (39–41 weeks GA) from the French CASTOR study cohort. Preterm infants had increased respiratory morbidity during the follow-up period compared to full-terms; they were more likely to have wheezing (21% vs. 11%, P = 0·007) and recurrent wheezing episodes (4% vs. 1%, P = 0·049). The 17 infants (14 preterms, three full-terms) who had been hospitalized for RSV-confirmed bronchiolitis during their first RSV season had significantly more wheezing episodes during the follow-up period than subjects who had not been hospitalized for RSV-confirmed bronchiolitis (odds ratio 4·72, 95% confidence interval 1·71–13·08, P = 0·003). Male gender, birth weight <3330 g and hospitalization for RSV bronchiolitis during the infant's first RSV season were independent risk factors for the development of wheezing episodes during the subsequent 12-month follow-up period.

Between 2007–2008 and 2010–2012, 870 organ samples were collected from wild boars in 16 Transylvanian counties. Anaplasma phagocytophilum DNA was identified using a nested PCR protocol that amplifies a fragment of the 16S rRNA gene. Prevalence was compared between sampling periods and counties using Fisher's exact test. In total, 39 (4·48%) samples tested positive, with significantly higher values recorded in the second period, caused by an increased infection rate in boars from Sibiu county. Positive cases tended to concentrate in the central part of the country. During the second sampling period, A. phagocytophilum was detected in two additional counties, suggesting a spatial spreading of the pathogen. The results confirm that Transylvanian wild boars are naturally infected with A. phagocytophilum, thus raising awarness concerning a potential zoonotic cycle. This is the first study to evaluate spatial and temporal variations of A. phagocytophilum distribution in wild boar populations from Transylvania.

Potential underestimation of the health system burden of pertussis was investigated by linking administrative datasets including pertussis notifications, hospitalizations and emergency department (ED) presentations for 1 304 876 children aged <15 years in NSW, Australia. From 2005 to 2008, 3006 children had a pertussis notification, 455 were hospitalized and 644 had an ED presentation with a coded diagnosis of pertussis. Linking hospital and ED records with pertussis notifications identified 140 hospitalizations and 735 ED presentations which occurred ±7 days from notification but did not have a diagnosis of pertussis recorded. These additional events were more likely to have a diagnosis of bronchiolitis, upper respiratory infection and cough compared to all other admissions and presentations. Including these additional events significantly increased the proportion of notified cases that were hospitalized or visited EDs, particularly for those aged 5 to <15 years. Linked administrative data allowed more comprehensive estimation of the health system burden of pertussis.

Community-based prevention strategies for seasonal and pandemic influenza are essential to minimize their potential threat to public health. Our aim was to evaluate the efficacy of hand hygiene interventions in reducing influenza transmission in the community and to investigate the possible modifying effects of latitude, temperature and humidity on hand hygiene efficacy. We identified 979 articles in the initial search and 10 randomized controlled trials met our inclusion criteria. The combination of hand hygiene with facemasks was found to have statistically significant efficacy against laboratory-confirmed influenza while hand hygiene alone did not. Our meta-regression model did not identify statistically significant effects of latitude, temperature or humidity on the efficacy of hand hygiene. Our findings highlight the potential importance of interventions that protect against multiple modes of influenza transmission, and the modest efficacy of hand hygiene suggests that additional measures besides hand hygiene may also be important to control influenza.

We report the molecular characterization of methicillin-resistant Staphylococcus aureus (MRSA) with resistance to tigecycline and to daptomycin isolated from intensive-care-unit patients in Brazil over a 6-month period. Thirty-six isolates (25 from infection sites, 11 from nasal sites) recovered from 23 patients who presented with MRSA infection during this period were characterized by pulsed-field gel electrophoresis, multilocus sequence typing, staphylococcal cassette chromosome mec (SCCmec) typing, and antimicrobial susceptibility profiling. Ten isolates from six patients and two isolates from different patients were resistant to tigecycline and daptomycin, respectively. Eight pulsotypes were identified and one, type A, accounted for 21 isolates from 12 patients; type A isolates were SCCmecII as were a further nine isolates of other pulsotypes. All but four of the total isolates were sequence type (ST) 5 or ST105 and classified as clonal complex (CC) 5; the historically prevalent lineage in Brazil, ST239-SCCmecIII, was identified in only three patients. Tigecycline-resistant strains were all ST105-SCCmecII and two patients were nasally colonized by strains of the same pulsotype found in infection sites. Two ST5-SCCmecII were daptomycin resistant after 48 h incubation. The origin and mechanism of these resistant strains remains unknown and further studies are warranted to determine whether such clones are becoming endemic in Brazilian hospitals and to assess their impact on infection control practice.

Drug-resistant paediatric tuberculosis (TB) is an overlooked global problem. In Italy, the epidemiology of TB has recently changed and data regarding drug-resistant forms in the paediatric setting is scanty. The aim of this case series was to report the cases of drug-resistant TB, diagnosed between June 2006 and July 2010 in four Italian tertiary centres for paediatric infectious diseases, in children and adolescents living in Italy. Twenty-two children were enrolled, of these 17 were resistant to one or more drugs and five had multidrug-resistant TB. All but one child were either foreign born or had at least one foreign parent. Twenty-one patients completed their treatment without clinical or radiological signs of activity at the end of treatment, and one patient was lost to follow up. The outcomes were good, with few adverse effects using second-line anti-TB drugs. Although this series is limited, it might already reflect the worrisome increase of drug-resistant TB, even in childhood.

Non-O157 Shiga toxin-producing Escherichia coli (STEC) infections are increasingly detected, but sources are not well established. We summarize outbreaks to 2010 in the USA. Single-aetiology outbreaks were defined as ⩾2 epidemiologically linked culture-confirmed non-O157 STEC infections; multiple-aetiology outbreaks also had laboratory evidence of ⩾2 infections caused by another enteric pathogen. Twenty-six states reported 46 outbreaks with 1727 illnesses and 144 hospitalizations. Of 38 single-aetiology outbreaks, 66% were caused by STEC O111 (n = 14) or O26 (n = 11), and 84% were transmitted through food (n = 17) or person-to-person spread (n = 15); food vehicles included dairy products, produce, and meats; childcare centres were the most common setting for person-to-person spread. Of single-aetiology outbreaks, a greater percentage of persons infected by Shiga toxin 2-positive strains had haemolytic uraemic syndrome compared with persons infected by Shiga toxin 1-only positive strains (7% vs. 0·8%). Compared with single-aetiology outbreaks, multiple-aetiology outbreaks were more frequently transmitted through water or animal contact.

To assess the prevalence and risk factors for colonization with Staphylococcus aureus in inmates entering two maximum-security prisons in New York State, USA, inmates (N = 830) were interviewed and anterior nares and oropharyngeal samples collected. Isolates were characterized using spa typing. Overall, 50·5% of women and 58·3% of men were colonized with S. aureus and 10·6% of women and 5·9% of men were colonized with MRSA at either or both body sites. Of MSSA isolates, the major subtypes were spa type 008 and 002. Overall, risk factors for S. aureus colonization varied by gender and were only found in women and included younger age, fair/poor self-reported general health, and longer length of prior incarceration. Prevalence of MRSA colonization was 8·2%, nearly 10 times greater than in the general population. Control of epidemic S. aureus in prisons should consider the constant introduction of strains by new inmates.

Hepatitis B virus (HBV) can be eliminated by effective universal vaccination. In Belgium, a free-of-charge HBV vaccination programme in infants with catch-up in adolescents was introduced in 1999. To evaluate the effects in <20-year-olds, seroprotection (anti-HBs >11 mIU/ml, according to the assay) and markers of infection (anti-HBc, HBsAg) were assessed in 2443 residual sera collected 7–8 years after implementation of the programme. The maximal prevalence of a solely anti-HBs seroprotective (‘vaccinated’) serostatus was 82·9% at age 1 year and 60·5% at age 13 years. A clear increase was found in age cohorts targeted by the campaign after a similar serosurvey conducted 4 years earlier. The prevalence of HBV infection remained unchanged at a low level (1·8% in 2006) similar to pre-vaccination data (1993–1994). We conclude that universal HBV vaccination has achieved overall high levels of vaccine-induced immunity, despite regional variations, which may give rise to pockets of susceptible young adults in the future.

Recent discovery of genetically distinct hantaviruses in shrews and moles (order Soricomorpha, family Soricidae and Talpidae) has challenged the conventional view that rodents serve as the principal reservoir hosts. Nova virus (NVAV), previously identified in archival liver tissue of a single European mole (Talpa europaea) from Hungary, represents one of the most highly divergent hantaviruses identified to date. To ascertain the spatial distribution and genetic diversity of NVAV, we employed RT–PCR to analyse lungs from 94 moles, captured in two locations in France, during October 2012 to March 2013. NVAV was detected in more than 60% of moles at each location, suggesting efficient enzootic virus transmission and confirming that this mole species serves as the reservoir host. Although the pathogenic potential of NVAV is unknown, the widespread geographical distribution of the European mole might pose a hantavirus exposure risk for humans.

The role of Campylobacter jejuni as the triggering agent of Guillain–Barré syndrome (GBS) has not been reassessed since the end of the 1990s in France. We report that the number of C. jejuni-related GBS cases increased continuously between 1996 and 2007 in the Paris region (mean annual increment: 7%, P = 0·007).

Weekly data from 7 years (2004–2010) of primary-care counts of acute respiratory illnesses (ARIs) and local weather readings were used to adjust a multivariate time-series vector error correction model with covariates (VECMX). Weather variables were included through a partial least squares index that consisted of weekly minimum temperature (coefficient = − 0·26), weekly median of relative humidity (coefficient = 0·22) and weekly accumulated rainfall (coefficient = 0·5). The VECMX long-term test reported significance for trend (0·01, P = 0·00) and weather index (1·69, P = 0·00). Short-term relationship was influenced by seasonality. The model accounted for 76% of the variability in the series (adj. R 2 = 0·76), and the co-integration diagnostics confirmed its appropriateness. The procedure is easily reproducible by researchers in all climates, can be used to identify relevant weather fluctuations affecting the incidence of ARIs, and could help clarify the influence of contact rates on the spread of these diseases.

Influenza causes significant morbidity and mortality in children. This study's objectives were to describe influenza A(H1N1)pdm09 during the pandemic, to compare it with circulating influenza in 2010/2011, and to identify risk factors for severe influenza defined as requiring admission to a paediatric intensive care unit (PICU). Children hospitalized with influenza during the pandemic were older, and more likely to have received antiviral therapy than children hospitalized during the 2010/2011 season. In 2010/2011, only one child admitted to a PICU with underlying medical conditions had been vaccinated. The risk of severe illness in the pandemic was higher in females and those with underlying conditions. In 2010/2011, infection with influenza A(H1N1)pdm09 compared to other influenza viruses was a significant risk factor for severe disease. An incremental relationship was found between the number of underlying conditions and PICU admission. These findings highlight the importance of improving low vaccination uptake and increasing the use of antivirals in vulnerable children.

The aim of this study was to evaluate the presence of influenza virus co-infections in humans and changes in the genetic variability of A(H3N2) virus strains in southern Italy from 1999 to 2009. A partial sequence of the haemagglutinin (HA) gene by human influenza H3N2 strains identified in oropharyngeal swabs from patients with influenza-like illness was analysed by DNA sequencing and a phylogenetic analysis was performed. During the seasons 1999–2000, 2002–2003, 2004–2005 and 2008–2009, the influenza viruses circulating belonged to subtype H3N2. However, A(H1N1) subtype virus and B type were respectively prevalent during the 2000–2001, 2006–2007, 2007–2008 and 2001–2002, 2003–2004, 2005–2006 seasons. The HA sequences appeared to be closely related to the sequence of the influenza A vaccine strain. Only the 2002–2003 season was characterized by co-circulation of two viral lineages: A/New York/55/01(H3N2)-like virus of the previous season and A/Fujian/411/02(H3N2)-like virus, a new H3 variant. In this study, over the decade analysed, no significant change was seen in the sequences of the HA gene of H3 viruses isolated.

M. fortuitum is a rapidly growing mycobacterium associated with community-acquired and nosocomial wound, soft tissue, and pulmonary infections. It has been postulated that water has been the source of infection especially in the hospital setting. The aim of this study was to determine if municipal water may be the source of community-acquired or nosocomial infections in the Brisbane area. Between 2007 and 2009, 20 strains of M. fortuitum were recovered from municipal water and 53 patients’ isolates were submitted to the reference laboratory. A wide variation in strain types was identified using repetitive element sequence-based PCR, with 13 clusters of ⩾2 indistinguishable isolates, and 28 patterns consisting of individual isolates. The clusters could be grouped into seven similar groups (>95% similarity). Municipal water and clinical isolates collected during the same time period and from the same geographical area consisted of different strain types, making municipal water an unlikely source of sporadic human infection.

Serum samples collected during the National Health and Nutrition survey (ENSANUT 2006) were obtained from subjects aged 1–95 years (January–October 2010) and analysed to assess the seroprevalence of Bordetella pertussis (BP) in Mexico. Subjects' gender, age, geographical region and socioeconomic status were extracted from the survey and compiled into a subset database. A total of 3344 subjects (median age 29 years, range 1–95 years) were included in the analysis. Overall, BP seroprevalence was 47·4%. BP seroprevalence was significantly higher in males (53·4%, P = 0·0007) and highest in children (59·3%) decreasing with advancing age (P = 0·0008). BP seroprevalence was not significantly different between regions (P = 0·1918) and between subjects of socioeconomic status (P = 0·0808). Women, adolescents and young adults were identified as potential sources of infection to infants. Booster vaccination for adolescents and primary contacts (including mothers) for newborns and infants may provide an important public health intervention to reduce the disease burden.

In March 2012, there was an unusual increase of gastroenteritis cases in a district with 37 264 inhabitants in central Greece. It was estimated that more than 3600 people developed symptoms. A 1:1 case-control study showed that consumption of tap water was a risk factor for acquiring infection [odds ratio (OR) 2·18, 95% confidence interval (CI) 1·11–4·28]. Descriptive data, low gastroenteritis incidence in adjacent areas with different water supply systems, and water-quality data further supported the hypothesis of a waterborne outbreak. Thirty-eight stool samples were positive for rotavirus. Bacterial indicators of recent faecal contamination were detected in samples from the water source and ice cubes from a local production enterprise. Molecular epidemiology of rotavirus strains, apart from the common strain, G3[P8], identified the unusual G/P combination G2P[8]. Water sanitation measures contributed to the control of the outbreak. This outbreak demonstrated the need for the cooperation of laboratories with different expertise and the importance of early notification of waterborne gastroenteritis outbreaks.

The major evolutionary stresses on Streptococcus pneumoniae are thought to be the widespread use of antibiotics and the deployment of effective vaccines against the capsular polysaccharides. Our current knowledge of genetic lineages among pneumococcal isolates comes largely from investigations just before and after the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) introduced in 2000. We examined 66 serogroup 6 isolates from the 1970s, long before the introduction of PCV7 and before widespread penicillin resistance was common in Birmingham, Alabama, to look for ancestors of the clones that came into play around the introduction of the PCV7 vaccine. The hypothesis was that some clonal complexes, if not individual clones, would be stable enough to persist over this period of time. We compared the 1970s isolates with 122 isolates from the 1990s in US and worldwide collections. Genotyping with pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) revealed that while some clones were probably localized to our area, others have persisted within groups that have expanded or diminished over the years.