H9N2 is the most widespread avian influenza virus subtype in poultry worldwide. It infects a broad spectrum of host species including birds and mammals. Infections in poultry and humans vary from silent to fatal. Importantly, all AIV, which are fatal in humans (e.g. H5N1, H7N9) acquired their ‘internal’ gene segments from H9N2 viruses. Although H9N2 is endemic in the Middle East (ME) and North Africa since the late 1990s, little is known about its epidemiology and genetics on a regional level. In this review, we summarised the epidemiological situation of H9N2 in poultry and mammals in Iran, Iraq, Kuwait, Qatar, United Arab Emirates, Oman, Bahrain, Yemen, Saudi Arabia, Jordan, Palestine, Israel, Syria, Lebanon, Turkey, Egypt, Sudan, Libya, Tunisia, Algeria and Morocco. The virus has been isolated from humans in Egypt and serosurveys indicated widespread infection particularly among poultry workers and pigs in some countries. Some isolates replicated well in experimentally inoculated dogs, mice, hamsters and ferrets. Insufficient protection of immunised poultry was frequently reported most likely due to concurrent viral or bacterial infections and antigenic drift of the field viruses from outdated vaccine strains. Genetic analysis indicated several distinct phylogroups including a panzootic genotype in the Asian and African parts of the ME, which may be useful for the development of vaccines. The extensive circulation of H9N2 for about 20 years in this region where the H5N1 virus is also endemic in some countries, poses a serious public health threat. Regional surveillance and control strategy are highly recommended.

In 2014, the Food and Drug Administration approved a new human papillomavirus 9-valent vaccine (9vHPV), targeting nine HPV types: HPV types 6, 11, 16, and 18, which are also targeted by the quadrivalent HPV vaccine (qHPV), plus five additional high cancer risk HPV types (HPV types 31, 33, 45, 52, and 58). The aim of the current study was to systematically retrieve, qualitatively and quantitatively pool, as well as critically appraise all available evidence on 9vHPV from randomized controlled trials (RCTs). We conducted a systematic review of the literature on 9vHPV efficacy, immunogenicity and safety, as well as a systematic search of registered, completed, and ongoing RCTs. We retrieved and screened 227 records for eligibility. A total of 10 publications reported on RCTs’ results on 9vHPV and were included in the review. Sixteen RCTs on 9vHPV have been registered on RCT registries. There is evidence that 9vHPV generated a response to HPV types 6, 11, 16 and 18 that was non-inferior to qHPV. Vaccine efficacy against five additional HPV type-related diseases was directly assessed on females aged 16–26 years (risk reduction against high-grade cervical, vulvar or vaginal disease = 96·7%, 95% CI 80·9%–99·8%). Bridging efficacy was demonstrated for males and females aged 9–15 years and males aged 16–26 years (the lower bound of the 95% CIs of both the geometric mean titer ratio and difference in seroconversion rates meeting the criteria for non-inferiority for all HPV types). Overall, 9vHPV has been proved to be safe and well tolerated. Other RCTs addressed: 9vHPV co-administration with other vaccines, 9vHPV administration in subjects that previously received qHPV and 9vHPV efficacy in regimens containing fewer than three doses. The inclusion of additional HPV types in 9vHPV offers great potential to expand protection against HPV infection. However, the impact of 9vHPV on reducing the global burden of HPV-related disease will greatly depend on vaccine uptake, coverage, availability, and affordability.

Accurate identification of individuals at high risk of surgical site infections (SSIs) or periprosthetic joint infections (PJIs) influences clinical decisions and development of preventive strategies. We aimed to determine progress in the development and validation of risk prediction models for SSI or PJI using a systematic review. We searched for studies that have developed or validated a risk prediction tool for SSI or PJI following joint replacement in MEDLINE, EMBASE, Web of Science and Cochrane databases; trial registers and reference lists of studies up to September 2016. Nine studies describing 16 risk scores for SSI or PJI were identified. The number of component variables in a risk score ranged from 4 to 45. The C-index ranged from 0·56 to 0·74, with only three risk scores reporting a discriminative ability of >0·70. Five risk scores were validated internally. The National Healthcare Safety Network SSIs risk models for hip and knee arthroplasties (HPRO and KPRO) were the only scores to be externally validated. Except for HPRO which shows some promise for use in a clinical setting (based on predictive performance and external validation), none of the identified risk scores can be considered ready for use. Further research is urgently warranted within the field.

Salmonella spp. comprise the second most common food-borne pathogens in the European Union (EU). The role of pigs as carriers of Salmonella has been intensively studied both on farm and at slaughter. Salmonella infection in pigs may cause fever, diarrhoea, prostration and mortality. However, most infected pigs remain healthy carriers, and those infected at the end of the fattening period could pose a threat to human health. Contamination of pig carcasses can occur on the slaughter line, and it is linked to cross-contamination from other carcasses and the presence of Salmonella in the environment. Therefore, Salmonella serovars present on pig carcasses can be different from those detected in the same bathes on the farm. In recent years, S. Typhimurium, S. Derby and S. serotype 4,[5],12:i:- (a monophasic variant of S. Typhimurium) have been the most common serovars to be detected in pigs in EU countries, but S. Rissen, S. Infantis, S. Enteritidis and S. Brandenburg have also been reported. In humans, several cases of salmonellosis have been linked to the consumption of raw or undercooked pork and pork products. Among the main serovars of porcine origin detected in confirmed human cases, S. Typhimurium, the monophasic variant S. 4,[5],12:i:- and S. Derby are certainly the most important.

Rising numbers of campylobacteriosis case notifications in Switzerland resulted in an increased attention to acute gastroenteritis (AG) in general. Patients with a laboratory-confirmed Campylobacter infection perceive their disease as severe and around 15% of these patients are hospitalized. This study aimed at estimating healthcare costs due to AG and campylobacteriosis in Switzerland. We used official health statistics, data from different studies and expert opinion for estimating individual treatment costs for patients with different illness severity and for extrapolating overall costs due to AG and campylobacteriosis. We estimated that total Swiss healthcare costs resulting from these diseases amount to €29–45 million annually. Data suggest that patients with AG consulting a physician without a stool diagnostic test account for €9·0–24·2 million, patients with a negative stool test result for Campylobacter spp. for €12·3 million, patients testing positive for Campylobacter spp. for €1·8 million and hospitalized campylobacteriosis patients for €6·5 million/year. Healthcare costs of campylobacteriosis are high and most likely increasing in Switzerland considering that campylobacteriosis case notifications steadily increased in the past decade. Costs and potential cost savings for the healthcare system should be considered when designing sectorial and cross-sectorial interventions to reduce the burden of human campylobacteriosis in Switzerland.

If the world can successfully control all outbreaks of circulating vaccine-derived poliovirus that may occur soon after global oral poliovirus vaccine (OPV) cessation, then immunodeficiency-associated vaccine-derived polioviruses (iVDPVs) from rare and mostly asymptomatic long-term excretors (defined as ⩾6 months of excretion) will become the main source of potential poliovirus outbreaks for as long as iVDPV excretion continues. Using existing models of global iVDPV prevalence and global long-term poliovirus risk management, we explore the implications of uncertainties related to iVDPV risks, including the ability to identify asymptomatic iVDPV excretors to treat with polio antiviral drugs (PAVDs) and the transmissibility of iVDPVs. The expected benefits of expanded screening to identify and treat long-term iVDPV excretors with PAVDs range from US$0.7 to 1.5 billion with the identification of 25–90% of asymptomatic long-term iVDPV excretors, respectively. However, these estimates depend strongly on assumptions about the transmissibility of iVDPVs and model inputs affecting the global iVDPV prevalence. For example, the expected benefits may decrease to as low as US$260 million with the identification of 90% of asymptomatic iVDPV excretors if iVDPVs behave and transmit like partially reverted viruses instead of fully reverted viruses. Comprehensive screening for iVDPVs will reduce uncertainties and maximize the expected benefits of PAVD use.

Since 1978, a series of papers in the literature have claimed to find a significant association between sunspot activity and the timing of influenza pandemics. This paper examines these analyses, and attempts to recreate the three most recent statistical analyses by Ertel (1994), Tapping et al. (2001), and Yeung (2006), which all have purported to find a significant relationship between sunspot numbers and pandemic influenza. As will be discussed, each analysis had errors in the data. In addition, in each analysis arbitrary selections or assumptions were also made, and the authors did not assess the robustness of their analyses to changes in those arbitrary assumptions. Varying the arbitrary assumptions to other, equally valid, assumptions negates the claims of significance. Indeed, an arbitrary selection made in one of the analyses appears to have resulted in almost maximal apparent significance; changing it only slightly yields a null result. This analysis applies statistically rigorous methodology to examine the purported sunspot/pandemic link, using more statistically powerful un-binned analysis methods, rather than relying on arbitrarily binned data. The analyses are repeated using both the Wolf and Group sunspot numbers. In all cases, no statistically significant evidence of any association was found. However, while the focus in this particular analysis was on the purported relationship of influenza pandemics to sunspot activity, the faults found in the past analyses are common pitfalls; inattention to analysis reproducibility and robustness assessment are common problems in the sciences, that are unfortunately not noted often enough in review.

Phenomenological and mechanistic models are widely used to assist resource planning for pandemics and emerging infections. We conducted a systematic review, to compare methods and outputs of published phenomenological and mechanistic modelling studies pertaining to the 2013–2016 Ebola virus disease (EVD) epidemics in four West African countries – Sierra Leone, Liberia, Guinea and Nigeria. We searched Pubmed, Embase and Scopus databases for relevant English language publications up to December 2015. Of the 874 articles identified, 41 met our inclusion criteria. We evaluated these selected studies based on: the sources of the case data used, and modelling approaches, compartments used, population mixing assumptions, model fitting and calibration approaches, sensitivity analysis used and data bias considerations. We synthesised results of the estimated epidemiological parameters: basic reproductive number (R0), serial interval, latent period, infectious period and case fatality rate, and examined their relationships. The median of the estimated mean R0 values were between 1·30 and 1·84 in Sierra Leone, Liberia and Guinea. Much higher R0 value of 9·01 was described for Nigeria. We investigated several issues with uncertainty around EVD modes of transmission, and unknown observation biases from early reported case data. We found that epidemic models offered R0 mean estimates which are country-specific, but these estimates are not associating with the use of several key disease parameters within the plausible ranges. We find simple models generally yielded similar estimates of R0 compared with more complex models. Models that accounted for data uncertainty issues have offered a higher case forecast compared with actual case observation. Simple model which offers transparency to public health policy makers could play a critical role for advising rapid policy decisions under an epidemic emergency.

This systematic review aimed at estimating chronic hepatitis B (HBV) and C virus (HCV) prevalence in the European Union (EU) and Economic Area (EEA) countries in the general population, blood donors and pregnant women. We searched PubMed©, Embase© and Cochrane Library databases for reports on HBV and HCV prevalence in the general population and pregnant women in EU/EEA countries published between 2005 and 2015. Council of Europe data were used for HBV and HCV blood donor prevalence. HBV general population estimates were available for 13 countries, ranging from 0·1% to 4·4%. HCV general population estimates were available for 13 countries, ranging from 0·1% to 5·9%. Based on general population and blood donor estimates, the overall HBV prevalence in the EU/EEA is estimated to be 0·9% (95% CI 0·7–1·2), corresponding to almost 4·7 million HBsAg-positive cases; and the overall HCV prevalence to be 1·1% (95% CI 0·9–1·4), equalling 5·6 million anti-HCV-positive cases. We found wide variation in HCV and HBV prevalence across EU/EEA countries for which estimates were available, as well as variability between groups often considered a proxy for the general population. Prevalence estimates are essential to inform policymaking and public health practice. Comparing to other regions globally, HBV and HCV prevalence in the EU/EEA is low.

Guidelines for the severity classification and treatment of Clostridium difficile infection (CDI) were published by Infectious Diseases Society of America (IDSA)/Society for Healthcare Epidemiology of America (SHEA) in 2010; however, compliance and efficacy of these guidelines has not been widely investigated. This present study assessed compliance with guidelines and its effect on CDI patient outcomes as compared with before these recommendations. A retrospective study included all adult inpatients with an initial episode of CDI treated in a single academic center from January 2009 to August 2014. Patients after guideline publication were compared with patients treated in 2009–2010. Demographic, clinical, and laboratory data were collected to stratify for disease severity. Outcome measures included compliance with guidelines, mortality, length of stay (LOS), and surgical intervention for CDI. A total of 1021 patients with CDI were included. Based upon the 2010 guidelines, 42 (28·8%) of 146 patients treated in 2009 would have been considered undertreated, and treatment progressively improved over time, as inadequate treatment decreased to 10·0% (15/148 patients) in 2014 (P = 0·0005). Overall, patient outcomes with guideline-adherent treatment decreased CDI attributable mortality twofold (P = 0·006) and CDI-related LOS by 1·9 days (P = 0·0009) when compared with undertreated patients. Compliance with IDSA/SHEA guidelines was associated with a decreased risk of mortality and LOS in hospitalized patients with CDI.

Since the first description of Wohlfahrtiimonas chitiniclastica in 2008, a number of well described case reports demonstrating its pathogenic role in humans have been published. Infections may be closely linked to flies, such as Wohlfahrtia magnifica, Lucilia sericata, Chrysomya megacephala or Musca domestica. These insects are potent vectors for the distribution of W. chitiniclastica causing local or systemic infections originating from wounds infested with fly larvae. However, other potential sources of transmission of W. chitiniclastica have been described such as soil or chicken meat. Infections in humans reported to date comprise wound infections, cellulitis, osteomyelitis and sepsis. This review summarizes all the literature available up to now and gives the current knowledge about this emerging human pathogen. Additionally, four patients with proven W. chitiniclastica infections treated at Dresden University Hospital between 2013 and 2015, are included. Special focus was placed on microbiological identification and antibiotic susceptibility testing of the pathogen.

Psittacosis is a zoonotic infectious disease caused by the transmission of the bacterium Chlamydia psittaci from birds to humans. Infections in humans mainly present as community-acquired pneumonia (CAP). However, most cases of CAP are treated without diagnostic testing, and the importance of C. psittaci infection as a cause of CAP is therefore unclear. In this meta-analysis of published CAP-aetiological studies, we estimate the proportion of CAP caused by C. psittaci infection. The databases MEDLINE and Embase were systematically searched for relevant studies published from 1986 onwards. Only studies that consisted of 100 patients or more were included. In total, 57 studies were selected for the meta-analysis. C. psittaci was the causative pathogen in 1·03% (95% CI 0·79–1·30) of all CAP cases from the included studies combined, with a range between studies from 0 to 6·7%. For burden of disease estimates, it is a reasonable assumption that 1% of incident cases of CAP are caused by psittacosis.

Whole apples have not been previously implicated in outbreaks of foodborne bacterial illness. We investigated a nationwide listeriosis outbreak associated with caramel apples. We defined an outbreak-associated case as an infection with one or both of two outbreak strains of Listeria monocytogenes highly related by whole-genome multilocus sequence typing (wgMLST) from 1 October 2014 to 1 February 2015. Single-interviewer open-ended interviews identified the source. Outbreak-associated cases were compared with non-outbreak-associated cases and traceback and environmental investigations were performed. We identified 35 outbreak-associated cases in 12 states; 34 (97%) were hospitalized and seven (20%) died. Outbreak-associated ill persons were more likely to have eaten commercially produced, prepackaged caramel apples (odds ratio 326·7, 95% confidence interval 32·2–3314). Environmental samples from the grower's packing facility and distribution-chain whole apples yielded isolates highly related to outbreak isolates by wgMLST. This outbreak highlights the importance of minimizing produce contamination with L. monocytogenes. Investigators should perform single-interviewer open-ended interviews when a food is not readily identified.

Polio cases due to wild virus are reported by only three countries in the world. Poliovirus type 2 has been globally eradicated and the last detection of poliovirus type 3 dates to November 2012. Poliovirus type 1 remains the only circulating wild strain; between January and September 2016 it caused 26 cases (nine in Afghanistan, 14 in Pakistan, three in Nigeria). The use of oral polio vaccine (OPV) has been the key to success in the eradication effort. However, paradoxically, moving towards global polio eradication, the burden caused by vaccine-derived polioviruses (VDPVs) becomes increasingly important. In this paper circulation of both wild virus and VDPVs is reviewed and implications for the polio eradication endgame are discussed. Between April and May 2016 OPV2 cessation has been implemented globally, in a coordinated switch from trivalent OPV to bivalent OPV. In order to decrease the risk for cVDPV2 re-emergence inactivated polio vaccine (IPV) has been introduced in the routine vaccine schedule of all countries. The likelihood of re-emergence of cVDPVs should markedly decrease with time after OPV cessation, but silent circulation of polioviruses cannot be ruled out even a long time after cessation. For this reason, immunity levels against polioviruses should be kept as high as possible in the population by the use of IPV, and both clinical and environmental surveillance should be maintained at a high level.

Since 2010, human hepatitis E infections have increased in England and Wales. Most cases are locally acquired and caused by hepatitis E virus genotype 3 (HEV G3). HEV G3 is linked to the consumption of pork products. The increase is associated with the emergence of a new phylotype, HEV G3-group 2 (G3-2, also known as G3abcdhij). Sixty individuals with confirmed hepatitis E infection and no history of travel outside the UK were recruited: 19 were infected with HEV G3-group 1 (G3-1 or G3efg) and 41 with G3-2. Epidemiological data relating to usual shopping habits and consumption of ham and sausages were analysed together with typing data to identify any associations with HEV phylotype. Study participants who purchased ham and/or sausage from a major supermarket were more likely to have HEV G3-2 infection (Relative risks 1·85, P = 0·06, CI 0·97–3·53). The HEV G3-2 phylotype has not been detected in indigenous UK pigs and it is suggested that human infections could be the result of consumption of products made from pork originating outside the UK. This does not infer blame on the supermarket but the epidemiology of HEV is dynamic and reflects complex animal husbandry practices which need to be explored further.

The depopulation of Pacific islands during the 16th to 19th centuries is a striking example of historical mass mortality due to infectious disease. Pacific Island populations have not been subject to such cataclysmic infectious disease mortality since. Here we explore the processes which could have given rise to this shift in infectious disease mortality patterns. We show, using mathematical models, that the population dynamics exhibited by Pacific Island populations are unlikely to be the result of Darwinian evolution. We propose that extreme mortality during first-contact epidemics is a function of epidemiological isolation, not a lack of previous selection. If, as pathogens become established in populations, extreme mortality is rapidly suppressed by herd immunity, Pacific Island population mortality patterns can be explained with no need to invoke genetic change. We discuss the mechanisms by which this could occur, including (i) a link between the proportion of the population transmitting infectious agents and case-fatality rates, and (ii) the course of infection with pathogens such as measles and smallpox being more severe in adults than in children. Overall, we consider the present-day risk of mass mortality from newly emerging infectious diseases is unlikely to be greater on Pacific islands than in other geographical areas.

A latent tuberculosis infection (LTBI) prevalence survey was conducted using tuberculin skin test (TST) and Quantiferon test (QFT) in 1218 healthcare workers (HCWs) in Medellín, Colombia. In order to improve the prevalence estimates, a latent class model was built using a Bayesian approach with informative priors on the sensitivity and specificity of the TST. The proportion of concordant results (TST+,QFT+) was 41% and the discordant results contributed 27%. The marginal estimate of the prevalence P(LTBI+) was 62·1% [95% credible interval (CrI) 53·0–68·2]. The probability of LTBI+ given positive results for both tests was 99·6% (95% CrI 98·1–99·9). Sensitivity was 88·5 for TST and 74·3 for QFT, and specificity was 87·8 for TST and 97·6 for QFT. A high LTBI prevalence was found in HCWs with time-accumulated exposure in hospitals that lack control plans. In a context of intermediate tuberculosis (TB) incidence it is recommended to use only one test (either QFT or TST) in prevalence surveys or as pre-employment tests. Results will be useful to help implement TB infection control plans in hospitals where HCWs may be repeatedly exposed to unnoticed TB patients, and to inform the design of TB control policies.

Information on morbidity burden of seasonal influenza in China is limited. A multiplier model was used to estimate the incidence and number of outpatient visits for seasonal influenza by age group for the 2015–2016 season in Beijing, the capital of China, based on reported numbers of influenza-like illness consultations and proportions of positive cases from influenza surveillance systems in Beijing, general consultation rates and other parameters from previous studies, surveys and surveillance systems. An estimated total of 1 190 200 (95% confidence interval (CI) 830 400–1 549 900) cases of influenza virus infections occurred in Beijing, 2015–2016 season, with an attack rate of 5·5% (95% CI 3·9–7·2%). These infections resulted in an estimated 468 280 (95% CI 70 700–606 800) outpatient visits, with an attack rate of 2·2% (95% CI 0·3–2·8%). The attack rate of influenza virus infections was highest among children aged 0–4 years (31·9% (95% CI 21·9–41·9%)), followed by children aged 5–14 years (18·7% (95% CI 12·9–24·5%)). Our study demonstrated a substantial influenza-related morbidity in Beijing, China, especially among the preschool- and school-aged children. This suggests that development or modification of seasonal influenza targeted vaccination strategies need to recognize that incidence is highest in children.

We investigated the first presence of qnrA among Shigella sonnei clinical isolates in Jiangsu Province, China. The qnrA-positive isolates coexisted with the mutation in gyrA at codon 83, these isolates were resistant to nalidixic acid and 22·2% (2 of 9) of them were resistant to norfloxacin.

Clinical manifestations of acute bronchiolitis (AB) vary from minimal disease to severe respiratory failure. The response to respiratory viral infections is possibly influenced by genetic polymorphisms linked to the regulation of the inflammatory response. In the present study, we investigated whether interleukin-8 (IL-8) and interleukin-17 (IL-17) genetic variants are associated with the severity of AB. A group of Brazilian infants hospitalized with AB and a control group (infants with no or mild AB, without hospitalization) were genotyped for four IL-8/IL-17 variations. For replication, we studied an Argentinean population sample of infants with mild and severe AB. IL-8 polymorphism (rs 2227543) and IL-17 (rs2275913) variants showed significant associations with the severity of AB. The effect of the IL-8 variation could be replicated in the Argentinean sample. This finding suggests that IL-8 variations may influence the severity of AB in young infants. Further genetic association studies in low- or middle-income populations are necessary with the aim of expanding knowledge in this area.