Acinetobacter spp. are important healthcare pathogens, being closely linked to antibiotic resistance and outbreaks worldwide. Although such species are rarely observed in patients with cystic fibrosis (CF), we describe the characteristics of 53 strains of Acinetobacter spp. isolated from the sputum of 39 Brazilian patients with CF. The species distribution was A. baumannii (n = 29), A. pittii (n = 13), A. nosocomialis (n = 8), A. seifertii (n = 1), A. soli (n = 1) and A. variabilis (n = 1) determined by partial rpoB gene sequencing. Sixteen strains (10 A. baumannii, 3 A. pittii and 3 A. nosocomialis) were multidrug-resistant (MDR) by disk diffusion test (30%) and eight MDR carbapenem-resistant A. baumannii strains harboured the blaOXA-23-like oxacillinase gene. Thirty-three sequence types (STs) were identified by multilocus sequence typing of which eight were novel (A. baumannii: 843, 844, 845, 847, 848; A. pitti: 643; A. nosocomialis: 862 and A. seifertii: 846); six STs (2 A. baumannii, 3 A. pittii and 1 A. nosocomialis) were found in more than one patient. Four strains of A. baumannii were assigned to two common clonal complexes (CCs), namely, CC1 (ST1, ST20 and ST160), and CC79 (ST79). This study underlines the extensive species diversity of Acinetobacter spp. strains in CF lung infections which may present difficulties for therapy due to significant antimicrobial resistance.

Persistent infection with one or more highly oncogenic human papillomaviruses (HPVs) or high-risk-HPV (HR-HPV) is necessary but not a sufficient aetiological agent for the development of cervical neoplasia. A number of viral, host, environmental and behavioural factors are suggested to be associated with the progression of cervical disorder. This study aimed to evaluate the impact of environmental and behavioural cofactors on the development of cervical disorders in HR-HPV-infected women in Serbia. A total of 541 women have been tested by PCR for the presence of HPV on the cervix. HPV genotypes were determined by direct DNA sequencing. Women identified as HR-HPV-positive were further classified into four subgroups according to their cytological status. All relevant information about demographical and behavioural factors was obtained by interviewer-based questionnaire. A number of analytical and descriptive statistical methods were used for processing the data. The cofactors found to be of significance for the progression of cervical disease were older age, body mass index >25, lower educational level, long-term smoking, previous genital infections and cervical interventions. On the other hand, condom use was found to have a protective role. Information about these cofactors might be very important for the development of more efficient cancer prevention programmes and promotion of anti-HPV vaccination.

Sex between men is the most frequent mode of HIV transmission in industrialised countries. Monitoring risk behaviours among men who have sex with men (MSM) is crucial, especially to understand the drivers of the epidemic. A cross-sectional survey (PREVAGAY), based on time-location sampling, was conducted in 2015 among MSM attending gay venues in 5 metropolitan cities in France. We applied the generalised weight share method (GWSM) to estimate HIV seroprevalence for the first time in this population, taking into account the frequency of venue attendance (FVA). Our objectives were to describe the implementation of the sampling design and to demonstrate the importance of taking into account sampling weights, including FVA by comparing results obtained by GWSM and by other methods which use sample weights not including FVA or no weight. We found a global prevalence of 14.3% (95% CI (12.0–16.9)) using GWSM and an unweighted prevalence of 16.4% (95% CI (14.9–17.8)). Variance in HIV prevalence estimates in each city was lower when we did not take into account either the sampling weights or the FVA. We also highlighted an association of FVA and serological status in the most of investigated cities.

We aimed to quantify the proportion of people receiving care for HIV-infection that are 50 years or older (older HIV patients) in Latin America and the Caribbean between 2000 and 2015 and to estimate the contribution to the growth of this population of people enrolled before (<50yo) and after 50 years old (yo) (⩾50yo). We used a series of repeated, cross-sectional measurements over time in the Caribbean, Central and South American network (CCASAnet) cohort. We estimated the percentage of patients retained in care each year that were older HIV patients. For every calendar year, we divided patients into two groups: those who enrolled before age 50 and after age 50. We used logistic regression models to estimate the change in the proportion of older HIV patients between 2000 and 2015. The percentage of CCASAnet HIV patients over 50 years had a threefold increase (8% to 24%) between 2000 and 2015. Most of the growth of this population can be explained by the increasing proportion of people that enrolled before 50 years and aged in care. These changes will impact needs of care for people living with HIV, due to multiple comorbidities and high risk of disability associated with aging.

Circulating 25-hydroxy vitamin D (25(OH)D) is related to decreased rates of gastrointestinal and ear infections in school-age children. Vitamin D-binding protein (DBP) transports 25(OH)D and exerts immunological functions; however, it is unknown whether DBP is associated with infectious morbidity in children. We quantified plasma DBP concentrations in 540 school-age children at the time of recruitment into a cohort study in Bogotá, Colombia and obtained daily information on infectious morbidity symptoms and doctor visits during the school year. We compared the incidence rates of gastrointestinal and respiratory symptoms across quartiles of DBP concentration by estimating adjusted incidence rate ratios (IRRs) with 95% confidence interval (CI). We also estimated the per cent of the associations between DBP and morbidity that were mediated through 25(OH)D using a counterfactual frame. Mean ± s.d. DBP concentration was 2650 ± 1145 nmol/l. DBP was inversely associated with the rates of diarrhoea with vomiting (IRR for quartiles 2–4 vs. 1 = 0.48; 95% CI 0.25–0.92; P = 0.03) and earache/ear discharge with fever (IRR for quartiles 2–4 vs. 1 = 0.29; 95% CI 0.12–0.71; P = 0.006). The DBP–morbidity associations were not mediated through 25(OH)D. We conclude that plasma DBP predicts lower incidence of gastrointestinal and ear infections in school-age children independent of 25(OH)D.

Mixing matrices quantify how people with similar or different characteristics make contact with each other, creating potential for disease transmission. Little empirical data on mixing patterns among persons who inject drugs (PWID) are available to inform models of blood-borne disease such as HIV and hepatitis C virus. Egocentric drug network data provided by PWID in Baltimore, Maryland between 2005 and 2007 were used to characterise drug equipment-sharing patterns according to age, race and gender. Black PWID and PWID who were single (i.e. no stable sexual partner) self-reported larger equipment-sharing networks than their white and non-single counterparts. We also found evidence of assortative mixing according to age, gender and race, though to a slightly lesser degree in the case of gender. Highly assortative mixing according to race and gender highlights the existence of demographically isolated clusters, for whom generalised treatment interventions may have limited benefits unless targeted directly. These findings provide novel insights into mixing patterns of PWID for which little empirical data are available. The age-specific assortativity we observed is also significant in light of its role as a key driver of transmission for other pathogens such as influenza and tuberculosis.

Using the dengue surveillance program, we prospectively collected data on all the suspected and confirmed cases of dengue in Barbados from 2006 to 2015. Data were analysed for demographic, seasonal and temporal dynamics of this disease in this country. The overall mean annual incidence rate of suspected and confirmed dengue over the study period was 0.49% (range 0.15%–0.99%) and 0.16% (range 0.05%−0.48%), respectively. There was a significant correlation between the mean monthly number of confirmed cases, the mean monthly rainfall and the mean monthly relative humidity percentage. Dengue in this population is predominantly an infection affecting children and young adults. The median age of the patients with both, suspected and confirmed dengue was 25 years and the highest proportion of cases was seen in the age group 0–15 years. The annual incidence rates of both the suspected and the confirmed cases showed an upward trend during the study period and this upward trend was more pronounced among children.

Transmission of acute respiratory infections (ARI) and acute gastroenteritis (AGE) often occurs in households. The aim of this study was to assess which proportion of ARI and AGE is introduced and transmitted by children in German households with children attending child care. We recruited families with children aged 0–6 years in Braunschweig (Germany), for a 4 months prospective cohort study in the winter period 2014/2015. Every household member was included in a health diary and used nasal swabs for pathogen identification in case of ARI. We defined a transmission if two persons had overlapping periods with symptoms and used additional definitions for sensitivity analyses. In total, 77 households participated with 282 persons. We observed 277 transmission events for ARI and 23 for AGE. In most cases, the first infected person in a household was a child (ARI: 63%, AGE: 53%), and the risk of within-household transmission was two times higher when the index case was a child. In 26 ARI-transmission events, pathogens were detected for both cases; hereof in 35% (95% confidence interval (17–56%)) the pathogens were different. Thus, symptomatic infections in household members, apparently linked in time, were in 2/3 associated with the same pathogens.

Multiple human immunodeficiency virus (HIV)-1 genotypes in China were first discovered in Yunnan Province before disseminating throughout the country. As the HIV-1 epidemic continues to expand in Yunnan, genetic characteristics and transmitted drug resistance (TDR) should be further investigated among the recently infected population. Among 2828 HIV-positive samples newly reported in the first quarter of 2014, 347 were identified as recent infections with BED-captured enzyme immunoassay (CEIA). Of them, 291 were successfully genotyped and identified as circulating recombinant form (CRF)08_BC (47.4%), unique recombinant forms (URFs) (18.2%), CRF01_AE (15.8%), CRF07_BC (14.4%), subtype C (2.7%), CRF55_01B (0.7%), subtype B (0.3%) and CRF64_BC (0.3%). CRF08_BC and CRF01_AE were the predominant genotypes among heterosexual and homosexual infections, respectively. CRF08_BC, URFs, CRF01_AE and CRF07_BC expanded with higher prevalence in central and eastern Yunnan. The recent common ancestor of CRF01_AE, CRF07_BC and CRF08_BC dated back to 1983.1, 1992.1 and 1989.5, respectively. The effective population sizes (EPS) for CRF01_AE and CRF07_BC increased exponentially during 1991–1999 and 1994–1999, respectively. The EPS for CRF08_BC underwent two exponential growth phases in 1994–1998 and 2001–2002. Lastly, TDR-associated mutations were identified in 1.8% of individuals. These findings not only enhance our understanding of HIV-1 evolution in Yunnan but also have implications for vaccine design and patient management strategies.

The high rate of chronic hepatitis C (CHC) was one of the key issues of global public health concern. Interferon (IFN)-λ relevant genes were in the antiviral treatment pathway, not only influenced hepatitis C virus (HCV) spontaneous clearance, but also affected the IFN-mediated viral clearance. The aim of this study was to identify the association of interleukin 28B (IL28B), myxovirus resistance A (MxA) gene polymorphisms with HCV spontaneous clearance and therapeutic response in Chinese CHC patients. IL28B and MxA gene genotypes were detected among 231 CHC carriers, 428 subjects with HCV spontaneous clearance and 662 CHC patients with pegylated IFN-α and ribavirin (pegIFN-α/RBV) treatment. Patients with MxA rs2071430 TT genotype were more likely to develop HCV infection chronicity (additive model: odds ratio (OR) 1.22, 95% confidence interval (CI) 1.01–1.48, P = 0.042). IL28B rs1298075 variant genotypes (additive model: OR 0.58, 95% CI 0.34–0.98, P = 0.040) and MxA rs17000900 variant genotypes (additive model: OR 0.54, 95% CI 0.30–0.99, P = 0.048) were less likely to achieve a sustained virological response. The life table indicated that patients with IL28B rs1298075 AG genotype were slower to achieve a viral load <500 copies/ml (P = 0.018). During the treatment, the downward trend in viral load was different among each IL28B rs1298075 genotype, especially in subgroup with a baseline HCV-RNA >106 copies/ml (all P < 0.05). This study illustrated that the carriage of IL28B rs12980275 AA had a positive effect on treatment response to pegIFN-α/RBV among Chinese CHC patients.

This study aimed to molecularly survey Bartonella in dogs from Chile. Quantitative real-time PCR (qPCR) for Bartonella spp. based on nuoG gene was performed in 139 blood samples taken from dogs belonging to rural localities of the Valdivia Province, Los Ríos region, southern Chile. nuoG qPCR-positive samples were submitted to conventional PCR assays for ftsZ, gltA, rpoB and nuoG genes and sequencing for speciation and phylogenetic analysis. Based upon qPCR results, Bartonella spp. occurrence in dogs was 4.3% (6/139). Out of six nuoG qPCR-positive samples, six, three, two and none showed positive results in cPCR assays based on gltA, ftsZ, rpoB and nuoG genes, respectively. Consistent sequencing results were obtained only for the ftsZ gene from sample #1532 (GeneBank accession number: MG252491), and gltA gene from samples #1535 (MG252490) and #1532 (148 bp fragment that was not deposited in GenBank). Phylogenetic analysis of ftsZ and gltA genes allowed speciation of two nuoG-positive samples, one as Bartonella vinsonii subsp. berkhoffii and the other as B. henselae. Bartonella vinsonii subsp. berkhoffii and B. henselae are detected for the first time in dogs from Chile, highlighting the importance of the canine population as a source of zoonotic agents and potential infection risk to humans.

Detecting gastrointestinal (GI) infection transmission among men who have sex with men (MSM) in England is complicated by a lack of routine sexual behavioural data. We investigated whether gender distributions might generate signals for increased transmission of GI pathogens among MSM. We examined the percentage male of laboratory-confirmed patient-episodes for patients with no known travel history for 10 GI infections of public health interest in England between 2003 and 2013, stratified by age and region. An adult male excess was observed for Shigella spp. (annual maximum 71% male); most pronounced for those aged 25–49 years and living in London, Brighton and Manchester. An adult male excess was observed every year for Entamoeba histolytica (range 59.8–76.1% male), Giardia (53.1–57.6%) and Campylobacter (52.1–53.5%) and for a minority of years for hepatitis A (max. 69.8%) and typhoidal salmonella (max. 65.7%). This approach generated a signal for excess male episodes for six GI pathogens, including a characterised outbreak of Shigella among MSM. Stratified analyses by geography and age group were consistent with MSM transmission for Shigella. Optimisation and routine application of this technique by public health authorities elsewhere might help identify potential GI infection outbreaks due to sexual transmission among MSM, for further investigation.

The present cross-sectional serosurvey constitutes the first effort to describe the varicella zoster virus (VZV) seroepidemiology in Serbia. An age-stratified serum bank of 3570 residual samples collected between 2015 and 2016 in each of the seven districts of the Vojvodina Province was tested for IgG anti-VZV antibodies with an enzyme immunoassay. Results were standardised into common units according to the European Sero-Epidemiology Network (ESEN2) methodology. Univariable and multivariable analyses were used to examine the relationships between standardised anti-VZV positivity or logarithmically transformed antibody titres and demographic features of study subjects. Seropositivity (85% overall) increased with age, in parallel with geometric mean titres. By the time of school entry, 68% of children were immune. The slower subsequent acquisition of immunity leaves epidemiologically relevant proportions of adolescents (7%), young adults (6%) and especially females of reproductive age (6%) prone to more severe forms of varicella. In the ongoing pre-vaccine era, natural infection provides a high level of collective immunity, with the highest VZV transmission in children of preschool age. The detected gaps in VZV immunity of the Serbian population support the adoption of the official recommendations for varicella immunisation of non-immune adolescents and young adults, including non-pregnant women of childbearing age.

The objective was to compare the performance of the updated Charlson comorbidity index (uCCI) and classical CCI (cCCI) in predicting 30-day mortality in patients with Staphylococcus aureus bacteraemia (SAB). All cases of SAB in patients aged ⩾14 years identified at the Microbiology Unit were included prospectively and followed. Comorbidity was evaluated using the cCCI and uCCI. Relevant variables associated with SAB-related mortality, along with cCCI or uCCI scores, were entered into multivariate logistic regression models. Global model fit, model calibration and predictive validity of each model were evaluated and compared. In total, 257 episodes of SAB in 239 patients were included (mean age 74 years; 65% were male). The mean cCCI and uCCI scores were 3.6 (standard deviation, 2.4) and 2.9 (2.3), respectively; 161 (63%) cases had cCCI score ⩾3 and 89 (35%) cases had uCCI score ⩾4. Sixty-five (25%) patients died within 30 days. The cCCI score was not related to mortality in any model, but uCCI score ⩾4 was an independent factor of 30-day mortality (odds ratio, 1.98; 95% confidence interval, 1.05–3.74). The uCCI is a more up-to-date, refined and parsimonious prognostic mortality score than the cCCI; it may thus serve better than the latter in the identification of patients with SAB with worse prognoses.

Outpatient parenteral antimicrobial therapy (OPAT) programmes facilitate hospital discharge, but patients remain at risk of complications and consequent healthcare utilisation (HCU). Here we elucidated the incidence of and risk factors associated with HCU in OPAT patients. This was a retrospective, single-centre, case–control study of adult patients discharged on OPAT. Cases (n = 63) and controls (n = 126) were patients that did or did not utilise the healthcare system within 60 days. Characteristics associated with HCU in bivariate analysis (P ≤ 0.2) were included in a multivariable logistic regression model. Variables were retained in the final model if they were independently (P < 0.05) associated with 60-day HCU. Among all study patients, the mean age was 55 ± 16, 65% were men, and wound infection (22%) and cellulitis (14%) were common diagnoses. The cumulative incidence of 60-day unplanned HCU was 27% with a disproportionately higher incidence in the first 30 days (21%). A statin at discharge (adjusted odds ratios (aOR) 0.23, 95% confidence intervals (CIs) 0.09–0.57), number of prior admissions in past 12 months (aOR 1.48, 95% CIs 1.05–2.10), and a sepsis diagnosis (aOR 4.62, 95% CIs 1.23–17.3) were independently associated with HCU. HCU was most commonly due to non-infection related complications (44%) and worsening primary infection (31%). There are multiple risk factors for HCU in OPAT patients, and formal OPAT clinics may help to risk stratify and target the highest risk groups.

The adenovirus vaccine and benzathine penicillin G (BPG) have been used by the US military to prevent acute respiratory diseases (ARD) in trainees, though these interventions have had documented manufacturing problems. We fit Poisson regression and random forest models (RF) to 26 years of weekly ARD incidence data to explore the impact of the adenovirus vaccine and BPG prophylaxis on respiratory disease burden. Adenovirus vaccine availability was among the most important predictors of ARD in the RF, while BPG was the ninth most important. BPG was a significant protective factor against ARD (incidence rate ratio (IRR) = 0.68; 95% confidence interval (CI) 0.67–0.70), but less so than either the old or new adenovirus vaccine (IRR = 0.39, 95% CI 0.38–0.39 and IRR = 0.11, 95% CI 0.11–0.11), respectively. These results suggest that BPG is moderately predictive of, and significantly protective against ARD, though to a lesser extent than either the old or new adenovirus vaccine.

The incidence of urinary tract infections (UTIs) is seasonal, and this seasonality may be explained by changes in weather, specifically, temperature. Using data from the Nationwide Inpatient Sample, we identified the geographic location for 581 813 hospital admissions with the primary diagnosis of a UTI and 56 630 773 non-UTI hospitalisations in the United States. Next, we used data from the National Climatic Data Center to estimate the monthly average temperature for each location. Using a case–control design, we modelled the odds of a hospital admission having a primary diagnosis of UTI as a function of demographics, payer, location, patient severity, admission month, year and the average temperature for the admission month. We found, after controlling for patient factors and month of admission, the odds of a UTI diagnosis increased with higher temperatures in a dose-dependent manner. For example, relative to months with average temperatures of 5–7.5 °C, an admission in a month with an average temperature of 27.5–30 °C has 20% higher odds of a primary diagnosis of UTI. However, in months with extremely high average temperatures (above 30 °C), the odds of a UTI admissions decrease, perhaps due to changes in behaviour. Thus, at a population level, UTI-related hospitalisations are associated with warmer weather.

Coinfection with human immunodeficiency virus (HIV) and viral hepatitis is associated with high morbidity and mortality in the absence of clinical management, making identification of these cases crucial. We examined characteristics of HIV and viral hepatitis coinfections by using surveillance data from 15 US states and two cities. Each jurisdiction used an automated deterministic matching method to link surveillance data for persons with reported acute and chronic hepatitis B virus (HBV) or hepatitis C virus (HCV) infections, to persons reported with HIV infection. Of the 504 398 persons living with diagnosed HIV infection at the end of 2014, 2.0% were coinfected with HBV and 6.7% were coinfected with HCV. Of the 269 884 persons ever reported with HBV, 5.2% were reported with HIV. Of the 1 093 050 persons ever reported with HCV, 4.3% were reported with HIV. A greater proportion of persons coinfected with HIV and HBV were males and blacks/African Americans, compared with those with HIV monoinfection. Persons who inject drugs represented a greater proportion of those coinfected with HIV and HCV, compared with those with HIV monoinfection. Matching HIV and viral hepatitis surveillance data highlights epidemiological characteristics of persons coinfected and can be used to routinely monitor health status and guide state and national public health interventions.

Prior studies have demonstrated that both bacterial vaginosis (BV) and sexually transmitted infections (STIs) are strong independent risk factors for subsequent STI. In observational studies of this biological enhancement (BE) hypothesis, it is important to adjust for the risk of STI exposure so that the independent effect of BE can be assessed. We sought to model if two markers of local sexual network (partner concurrency and cumulative number of STIs) represented residual confounding in the models of risk for subsequent infection in a study that screened 3620 women for STIs every 3 months for a year. Mixed-effects logistic regression was used to calculate the odds ratios for an incident diagnosis of Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis and BV following a diagnosis of any of these four at the prior visit, controlling for the cumulative number of STIs and partner concurrency variables. We found that partner concurrency and cumulative number of STIs were each associated with incident infection, and in general, controlling for these variables reduced the strength of the association between prior and incident infections. We conclude that the frequently found association between prior and incident STIs is associated with both BE and sexual network structure.

The purpose of the study was to weigh the community burden of chikungunya determinants on Reunion island. Risk factors were investigated within a subset of 2101 adult persons from a population-based cross-sectional serosurvey, using Poisson regression models for dichotomous outcomes. Design-based risk ratios and population attributable fractions (PAF) were generated distinguishing individual and contextual (i.e. that affect individuals collectively) determinants. The disease burden attributable to contextual determinants was twice that of individual determinants (overall PAF value 89.5% vs. 44.1%). In a model regrouping both categories of determinants, the independent risk factors were by decreasing PAF values: an interaction term between the reporting of a chikungunya history in the neighbourhood and individual house (PAF 45.9%), a maximal temperature of the month preceding the infection higher than 28.5 °C (PAF 25.7%), a socio-economically disadvantaged neighbourhood (PAF 19.0%), altitude of dwelling (PAF 13.1%), cumulated rainfalls of the month preceding the infection higher than 65 mm (PAF 12.6%), occupational inactivity (PAF 11.6%), poor knowledge on chikungunya transmission (PAF 7.3%) and obesity/overweight (PAF 5.2%). Taken together, these covariates and their underlying causative factors uncovered 80.8% of chikungunya at population level. Our findings lend support to a major role of contextual risk factors in chikungunya virus outbreaks.