Persistent infection with high-risk human papillomavirus (HPV) is the main cause of cervical cancer and the prevalence of HPV types varies depending on the geographic region. Therefore, this study assessed the prevalence of HPV types in women with cervical lesions from Sergipe state, Northeastern Brazil. A cross-sectional study was conducted in women with cervical lesions from March to December 2014. These lesions were investigated by PCR and HPV types were identified by DNA sequencing. 432 patients were included, of which 337 patients tested positive for HPV. Eighteen different HPV types were detected, and high-risk HPV types were detected in 69.2%. HPV 16 (63.4%) was the most prevalent HPV type found, followed by HPV 66 (4.6%), HPV 18 (1.6%) and HPV 45 (1.4%). These results highlight the importance of the high prevalence of HPV 66, which is a possibly carcinogenic virus type not covered by the available vaccines. The prevalence of HPV 16 was high in the studied population, reaffirming the importance of young vaccination. However, the high prevalence of HPV 66 found in this study shows the importance of monitoring the diversity of HPV types in different populations and geographic regions to better understand the impacts of current HPV vaccines.

The aim of this retrospective review was to assess the overall burden and trend in spinal tuberculosis (TB) at tertiary hospitals in the Western Cape Province of South Africa. All spinal TB cases seen at the province's three tertiary hospitals between 2012 and 2015 were identified and clinical records of each case assessed. Cases were subsequently classified as bacteriologically confirmed or clinically diagnosed and reported with accompanying clinical and demographic information. Odds ratios (OR) for severe spinal disease and corrective surgery in child vs. adult cases were calculated. A total of 393 cases were identified (319 adults, 74 children), of which 283 (72%) were bacteriologically confirmed. Adult cases decreased year-on-year (P = 0.04), however there was no clear trend in child cases. Kyphosis was present in 60/74 (81%) children and 243/315 (77%) adults with available imaging. Corrective spinal surgery was performed in 35/74 (47%) children and 80/319 (25%) adults (OR 2.7, 95% confidence interval 1.6–4.5, P = 0.0003). These findings suggest that Western Cape tertiary hospitals have experienced a substantial burden of spinal TB cases in recent years with a high proportion of severe presentation, particularly among children. Spinal TB remains a public health concern with increased vigilance required for earlier diagnosis, especially of child cases.

In North America, the raccoon-associated variant of rabies virus (RRV) is of special concern, given its relatively rapid spread throughout the eastern USA and its potential public health impact due to high raccoon host densities in urban areas. Northward expansion of this epizootic included an outbreak in the Canadian province of Quebec in 2006–2009 due to trans-border spread from the State of Vermont. To inform a more proactive approach to future control efforts, this study uses phylogenetic analyses to explore the role of geography and alternative carnivore hosts in the dynamics of RRV spread within Vermont. Specifically, we sought to examine whether striped skunks, a species frequently infected by RRV, could be part of the maintenance host community. Whole genome sequencing of 160 RRV samples from Vermont and neighbouring US states were used for fine-scale phylogeographic analyses. Results, together with the complete surveillance record of raccoon rabies since its entry into Vermont in 1994, document incursions by two distinct viral lineages and identify topographical features of the landscape which have significantly influenced viral spread, resulting in a complex distribution pattern of viral variants throughout the state. Results of phylogenetic cluster analysis and discrete state reconstruction contained some evidence of skunk-to-skunk and skunk-to-raccoon transmission but overall failed to support a role for skunks as alternative maintenance hosts.

Puumala hantavirus (PUUV) causes hemorrhagic fever with renal syndrome in humans, that is an endemic disease in Finland. We estimated the seroprevalence of PUUV in Finland and explored risk factors and disease associations by using unique survey data with health register linkage. A total of 2000 sera from a nationwide health survey from 2011, representative of the adult population, were screened for PUUV IgG by immunofluorescence assay. We performed statistical analysis adjusting for stratified cluster design and taking into account sampling weights. In total, 254 sera among 2000 tested were PUUV-IgG-positive resulting in a weighted seroprevalence of 12.5%, (95% CI 10.9–14.4), mirroring known age and regional variation in reported incidence. No associations between PUUV-seropositivity and chronic diseases including cardiovascular (including hypertension), pulmonary, kidney disease and cancer were observed. Smoking was significantly associated with seropositivity (adjusted OR 1.54; 95% CI 1.16–2.04). In addition, significant dose-response relations were found for the number of cigarettes smoked daily (OR 1.14; 95% CI 1.12–1.28). The results are important for disease burden assessment and guide intervention strategies, highlighting also the role of smoking prevention.

Assessing the relationship between antimicrobial usage (AMU) and antimicrobial resistance (AMR) requires the accurate and precise utilisation of register data. Therefore, validation of register-based data is essential for evaluating the quality and, subsequently, the internal validity of studies based on the data.

In this study, different smoothing methods for Veterinary Medicine Statistic Program database (VetStat)-records were validated by comparing these with farm-records. Comparison between measurements included accuracy as; completeness and correctness, and precision as; a relative difference of the error, correlation with Fisher's z transformation and reliability coefficient. The most valid methods of those examined were then used in re-analyses of the abundance of AMR genes in 10 finisher batches from a previous study.

Improved accuracy was found when detailed smoothing methods were applied. Although the precision also increased, the effect was not as pronounced, as the usage estimate of all smoothing methods deviated moderately compared with the farm-registrations. Applying the most valid methods to the 10 finisher batches increased estimates of statistical model fit for aminoglycosides, lincosamides, tetracyclines and decreased estimates of statistical model fit for macrolides. The estimates of statistical model fit for sulfonamides and broad-spectrum penicillins remained the same.

Through refined data transformation, VetStat-records can be used to calculate a daily amount of AMU per pig reflecting the true usage accurately and moderately precisely, which is the foundation for calculating lifetime AMU.

The Joint Commission Centre for Transforming Healthcare's Web-based Targeted Solutions Tool (TST) for improving hand hygiene was implemented to elucidate contributing factors to low compliance rates of hand hygiene. Monitoring of compliance was done by trained unknown and known observers and rates of hospital-acquired infections were tracked and correlated against the changes in hand hygiene compliance. In total, 5669 of hand hygiene observations were recorded by the secret observers. The compliance rate increased from 75·4% at baseline (May–August 2014) to 88·6% during the intervention (13 months) and the control periods (P < 0·0001). Reductions in healthcare-associated infection rates were recorded for Clostridium difficle infections from 7·95 (CI 0·8937–28·72) to 1·84 (CI 0·02411–10·26) infections per 10 000 patient-days (P = 0·23), central line-associated blood-stream infections from 5·9 (CI 1·194–17·36) to 2·9 (0·7856–7·475) per 1000 device days (P = 0·37) and catheter-associated urinary tract infections from 5·941 (CI 1·194–17·36) to 0 per 1000 device days (P = 0·42). The top contributing factors for non-compliance were: improper use of gloves, hands full of supplies or medications and frequent entry or exit in isolation areas. We conclude that the application of TST allows healthcare organisations to improve hand hygiene compliance and to identify the factors contributing to non-compliance.

Infections caused by extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) have become increasingly prevalent, posing a serious public threat worldwide. It is commonly believed that untreated urinary tract infections (UTI) and asymptomatic bacteriuria (ABU) during pregnancy are associated with poor obstetric outcomes. Currently, there is a paucity of data regarding the outcomes or risk factors of such ESBL-E infections in pregnant women. We conducted a retrospective 1:2 matched case–control study of hospitalised pregnant women with ESBL-E- vs. non-ESBL-producing Enterobacteriaceae-positive urine cultures obtained between 2004 and 2015, and compared risk factors for the development of resistant bacteria, clinical course and outcomes. In total, 87 pregnant women with ESBL-E-positive urine cultures were matched to 174 controls by decade of age, ethnicity and pregnancy trimester. Significant risk factors for acquisition of ESBL-E included prior UTI/ABU episodes (50.6% vs. 26.3%, P < 0.001), previous isolation of ESBL-E in urine cultures (12.6% vs. 0.6%, P < 0.001) and prior antibiotic exposure (71.3% vs. 54%, P = 0.002). Previous hospitalisation, however, was not found to be a risk factor. No significant difference was found in adverse obstetric outcomes. We conclude that prior urinary infections and antibiotic exposure were significant risk factors for the isolation of ESBL-E pathogens from the urine of pregnant women; however, this was not associated with worse obstetric outcomes compared with non-ESBL-E pathogens.

We aimed to verify the effectiveness of real-time reverse transcription (rRT) polymerase chain reaction (PCR) for detecting cases of modified measles (M-Me) and for predicting super-spreader candidates through the experience of a measles outbreak dominated by M-Me in Yamagata, Japan, during March–April 2017. We applied rRT-PCR to specimens from 35 cases of M-Me, nine cases of typical measles (T-Me) and nine cases of prodromal stage of T-Me (P-Me). From rRT-PCR among the M-Me cases, peripheral blood mononuclear cells (PBMC) showed the highest positive rate (80.0%), followed by throat swab (48.6%), urine (33.3%) and serum (3.1%). The negative result of PBMC in M-Me cases was recovered by the result of a throat swab. In specimens of PBMC, throat swab and urine, M-Me group showed the significantly higher cycle of threshold (i.e., lower viral load) in the rRT-PCR than T-Me and P-Me groups, respectively. Furthermore, three super-spreaders in T-Me or P-Me showed an extremely low cycle of threshold in their throat swab specimens. rRT-PCR using PBMC and throat swab might be helpful for clinical management and measles control by certain detection of M-Me cases and by predicting super-spreading events resulting from measles cases with the high viral load.

Foodborne non-typhoidal salmonellosis causes approximately 1 million illnesses annually in the USA. In April 2015, we investigated a multistate outbreak of 65 Salmonella Paratyphi B variant L(+) tartrate(+) infections associated with frozen raw tuna imported from Indonesia, which was consumed raw in sushi. Forty-six (92%) of 50 case-patients interviewed ate sushi during the week before illness onset, and 44 (98%) of 45 who specified ate sushi containing raw tuna. Two outbreak strains were isolated from the samples of frozen raw tuna. Traceback identified a single importer as a common source of tuna consumed by case-patients; this importer issued three voluntary recalls of tuna sourced from one Indonesian processor. Four Salmonella Weltevreden infections were also linked to this outbreak. Whole-genome sequencing was useful in establishing a link between Salmonella isolated from ill people and tuna. This outbreak highlights the continuing foodborne illness risk associated with raw seafood consumption, the importance of processing seafood in a manner that minimises contamination with pathogenic microorganisms and the continuing need to ensure imported foods are safe to eat. People at higher risk for foodborne illness should not consume undercooked animal products, such as raw seafood.

Sex differences in the incidence of infections may indicate different risk factors and behaviour but have not been analysed across pathogens. Based on 3.96 million records of 33 pathogens in Germany, notified from 2001 to 2013, we applied Poisson regression to generate age-standardised incidence rate ratios and assessed their distribution across age and sex. The following trends became apparent: (a) pathogens with male incidence preponderance at infant and child age (meningococcal disease (incidence rate ratio (IRR) = 1.19, 95% CI 1.03–1.38, age = 0–4); influenza (IRR = 1.09, 95% CI 1.06–1.13, age = 0–4)), (b) pathogens with sex-switch in incidence preponderance at puberty (e.g. norovirus (IRR = 1.10, 95% CI 1.02–1.19 in age = 5–14, IRR = 0.96, 95% CI 0.93–0.99, age ⩾ 60), (c) pathogens with general male incidence preponderance (bacterial/parasitic infections with campylobacter, Yersinia and Giardia), (d) pathogens with male incidence preponderance at juvenile and adult age (sexually transmitted or vector-borne infections (combined-IRR = 2.53, 95% CI 2.36–2.71, age = 15–59), (e) pathogens with male preponderance at older age (tick-borne encephalitis - IRR = 2.75, 95% CI 1.21–6.24, listeriosis - IRR = 2.06, 95% CI 1.38–3.06, age ⩾ 60). Risk factor concepts only partly serve to interpret similarities of grouped infections, i.e. transmission-related explanations and sex-specific exposures not consistently explain the pattern of food-borne infections (b). Sex-specific differences in infectious disease incidence are well acknowledged regarding the sexually transmitted diseases. This has led to designing gender-specific prevention strategies. Our data suggest that for infections with other transmission routes, gender-specific approaches can also be of benefit and importance.

Acute respiratory infections cause significant morbidity and mortality accounting for 5.8 million deaths worldwide. In Australia, influenza-like illness (ILI), defined as cough, fever and fatigue is a common presentation in general practice and results in reduced productivity and lost working days. Little is known about the epidemiology of ILI in working-age adults. Using data from the ASPREN influenza surveillance network in Australia (2010–2013) we found that working-age adults made up 45.2% of all ILI notifications with 55% of samples positive for at least one respiratory virus. Viruses most commonly detected in our study included influenza A (20.6%), rhinovirus (18.6%), influenza B (6.2%), human meta-pneumovirus (3.4%), respiratory syncytial virus (3.1%), para-influenza virus (2.6%) and adenovirus (1.3%). We also demonstrated that influenza A is the predominant virus that increases ILI (by 1.2% per month for every positive influenza A case) in working-age adults during autumn–winter months while other viruses are active throughout the year. Understanding the epidemiology of viral respiratory infections through a year will help clinicians make informed decisions about testing, antibiotic and antiviral prescribing and when the beginning of the ‘flu season’ can be more confidently predicted.

Fever is a common adverse event following measles vaccination, more frequent among older children and those receiving Measles-Mumps-Rubella-Varicella vaccine vs. Measles-Mumps-Rubella vaccine, two factors associated with a better antibody response. However, the role of fever in the immunogenicity of measles-containing vaccines (MCV) is unclear. We performed a post-hoc pooled analysis of data of 5 216 11 to 22 month-old children receiving MCV from 2004 to 2012 in Europe and USA to evaluate the association between post-immunisation fever and antibody response, measured by geometric mean concentrations (GMCs). We further evaluated fever as an effect modifier or a mediator in the associations between the type of MCV or the age at first vaccination and vaccine immunogenicity. After the first dose, fever was associated with 60% higher GMCs (95% CI 1.51–1.68). For children vaccinated at ⩾12 months, the fever did not modify and minimally mediated (2% to 3%) the association between age and antibody response. Fever mediated 18% of the association between type of MCV and GMCs. In a model including fever, age and type of vaccine, fever was the strongest predictor of GMCs. These results suggest that fever is associated with a stronger measles antibody response independently of age and type of MCV.

HIV-positive children are still born in Europe despite low mother-to-child transmission (MTCT) rates. We aimed to clarify the remaining barriers to the prevention of MTCT. By combining the national registers, we identified all women living with HIV delivering at least one child during 1983–2013. Of the 212 women delivering after HIV diagnosis, 46% were diagnosed during the pregnancy. In multivariate analysis, age >30 years (P = 0.001), sexual transmission (P = 0.012), living outside of the metropolitan area (P = 0.001) and Eastern European origin (P = 0.043) were risk factors for missed diagnosis before pregnancy. The proportion of immigrants increased from 18% before 1999 to 75% during 2011–2013 (P < 0.001). They were diagnosed during the pregnancy equally to natives and achieved similar, good treatment results. No MTCT occurred when the mother was diagnosed before the delivery. In addition, 12 women had delivered in 2 years prior their HIV diagnosis, most before implementation of the national screening of pregnant women. Three of these children were infected, the last one in 2000. Our data demonstrate that complete elimination of MTCT is feasible in a high-income, low-prevalence country. This requires ongoing universal screening in early pregnancy and easy access to antiretroviral therapy to all HIV-positive people.

In 2013, the Guinean health authority had to reorganise and run a national response against malaria as a priority. The review of the National Strategic Plan to fight malaria in Guinea was carried out and one of its critical components was the prevention and rapid management of fever (RMF) attributable to malaria in children. The study reports on the demographic and health determinants of this rapid management in children under 5. The participants were 4786 children from 2874 representative households. RMF was defined in terms of recourse to primary care. The recourse was defined by child's reference for the treatment of fever which led or not to treatment of malaria. We found that 1491 children (31.2%) had a bout of fever within the 2 weeks that preceded the survey. The prevalence of malaria was 45.4% among those children who have a bout of fever. The recourse to traditional healers was estimated at 9.6% and the use of health facilities was estimated at 71.5%. Overall, 74.9% of children with fever received treatment within the recommended timeliness (24 h), with regional disparity in this rapid response. The high proportion of recourse to traditional healers is still a matter of concern. New control and prevention strategies should be extended to traditional healers for their training and involvement in directing febrile children to health facilities.

The Belgian strategic plan to eliminate measles contains several vaccination strategies including routine immunisation programmes and catch-up campaigns. A new expanded programme on immunisation-based survey (2016) assessed the uptake of the recommended measles–mumps–rubella (MMR) vaccine in three different cohorts: toddlers, adolescents and parents of toddlers. A two-stage cluster sampling technique was used to select 875 toddlers (age 18–24 months) and 1250 adolescents (born in 2000) from 107 municipalities in Flanders. After consent of the parent(s), 746 (85.2%) families of toddlers and 1012 (81.0%) families of adolescents were interviewed at home. Measles vaccination coverage was high at 18–24 months (96.2%) and 81.5% were vaccinated at recommended age. Toddlers who had two siblings or a non-working mother or changed vaccinator were more at risk for not being vaccinated. Coverage of the teenager dose reached 93.5% and was lower in adolescents with educational underachievement or whose mother was part-time working or with a non-Belgian background. Only 56.0% of mothers and 48.3% of fathers remembered having received at least one measles-containing vaccine. Although measles vaccination coverage in toddlers meets the required standards for elimination, administration of the teenager dose of MMR vaccine and parent compliance to the recent measles catch-up campaign in Flanders leave room for improvement.

Legionella pneumophila genotyping is important for epidemiological investigation of nosocomial and community-acquired outbreaks of legionellosis. The prevalence of legionellosis in pneumonia patients in the West Bank was monitored for the first time, and the sequence types (STs) from respiratory samples were compared with STs of environmental samples from different wards of the hospital. Sputum (n = 121) and bronchoalveolar lavage (BAL) (n = 74) specimens were cultured for L. pneumophila; genomic DNA was tested by 16S rRNA polymerase chain reaction (PCR) amplification. Nested PCR sequence-based typing (NPSBT) was implemented on DNA of the respiratory and environmental PCR-positive samples. Only one respiratory specimen was positive for L. pneumophila by culture. BAL gave a higher percentage of L. pneumophila-positive samples, 35% (26/74) than sputum, 15% (18/121) by PCR. NPSBT revealed the following STs: ST 1 (29%, 7/24), ST 461 (21%, 5/24), ST 1037 (4%, 1/24) from respiratory samples, STs from environmental samples: ST 1 (28.5%, 4/14), ST 187 (21.4%, 3/14) and ST 2070, ST 461, ST 1482 (7.1%, 1/14) each. This study emphasises the advantage of PCR over culture for the detection of L. pneumophila in countries where antibiotics are indiscriminately used prior to hospital admission. ST 1 was the predominant ST in both respiratory and environmental samples.

Surgical site infection (SSI) following cardiovascular surgery has been well documented, possibly owing to its highly invasive nature, but SSI following surgery on the thoracic aorta has not. This study aimed to describe the epidemiology and assess risk factors associated with the latter in Japan using a national database for SSI. Data on surgery on thoracic aorta performed between 2012 and 2014 were extracted from the Japan Nosocomial Infections Surveillance (JANIS) database. Risk factors were assessed initially by univariate analysis, and then entered into a logistic regression model for final evaluation. The cumulative incidence of SSI was 4.1% (146/3538) and staphylococci were the most frequent pathogens isolated. Factors such as the duration of operation, emergency surgery and male gender were significantly associated with SSI. These findings differ from previous studies on open heart and coronary artery bypass surgery, in which the American Society of Anesthesiologists (ASA) score was significantly associated with SSI, but gender was not. This study suggests that risk stratification in the JANIS system might be improved by incorporating additionally identified factors for risk adjustment, when comparing the incidence of SSI between hospitals.

The aims of this study were to determine the prevalence and associated risk factors of bovine herpes virus type-4 (BoHV-4) infection and describe the genetic characteristics and predominant genotypes of the virus in Yolo and Tulare counties, California. A cross-sectional study involving multi-stage sampling technique was used. One hundred and forty-eight post-partum cows were enrolled from 11 dairy farms. Uterine/vaginal samples were collected and tested for BoHV-4 and other co-infecting viruses using real-time PCR. Data were analysed using multilevel logistic mixed-effect model. Phylogenetic analysis of 10 BoHV-4 isolates was conducted by targeting three open reading frames (ORF3, ORF8 and ORF 22) of the viral genome. The prevalence of BoHV-4 infection was 22.3% (33/148), while post-partum metritis was 33.8% (48/142). Strong association was found between BoHV-4 infection and lactation number, lactation stage and post-partum metritis. The odds of being positive for BoHV-4 infection were 6.47 times (95% CI 1.17–35.92; P < 0.05) and 6.79 times (95% CI 1.19–38.55; P < 0.05) higher for cows in the fourth and fifth lactation, respectively, compared with cows in the first lactation. BoHV-4 was 8.27 times more likely (95% CI 1.43–47.94; P < 0.05) among cows in the early stage of lactation (0–120 days) compared with those in late lactation (>240 days). Cows with post-partum metritis were 4.51 times (95% CI 1.27–16.02; P < 0.05) more likely to test positive for BoHV-4 infection compared with those without post-partum metritis. Phylogenetic analysis of BoHV-4 based on sequencing of glycoprotein and thymidine kinase (TK) genes revealed genetic variability of the virus with glycoprotein B genotype 1 and TK genotype 2 as being dominant genotypes. The reported high genetic variability of BoHV-4 indicates the possibility of co-infection with multiple genotypes.

Prevalence of skin sores and scabies in remote Australian Aboriginal communities remains unacceptably high, with Group A Streptococcus (GAS) the dominant pathogen. We aim to better understand the drivers of GAS transmission using mathematical models. To estimate the force of infection, we quantified the age of first skin sores and scabies infection by pooling historical data from three studies conducted across five remote Aboriginal communities for children born between 2001 and 2005. We estimated the age of the first infection using the Kaplan–Meier estimator; parametric exponential mixture model; and Cox proportional hazards. For skin sores, the mean age of the first infection was approximately 10 months and the median was 7 months, with some heterogeneity in median observed by the community. For scabies, the mean age of the first infection was approximately 9 months and the median was 8 months, with significant heterogeneity by the community and an enhanced risk for children born between October and December. The young age of the first infection with skin sores and scabies reflects the high disease burden in these communities.