Altered microbial communities are thought to play an important role in eosinophilic oesophagitis, an allergic inflammatory condition of the oesophagus. Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. However, these data consist of non-negative, highly skewed sequence counts with a large proportion of zeros. In addition, hierarchical study designs are often performed with repeated measurements or multiple samples collected from the same subject, thus requiring approaches to account for within-subject variation, yet only a small number of microbiota studies have applied hierarchical regression models. In this paper, we describe and illustrate the use of a hierarchical regression-based approach to evaluate multiple factors for a small number of organisms individually. More specifically, the zero-inflated negative binomial mixed model with random effects in both the count and zero-inflated parts is applied to evaluate associations with disease state while adjusting for potential confounders for two organisms of interest from a study of human microbiota sequence data in oesophagitis.

The Charlson comorbidity index (CCI) is widely used for control of confounding from comorbidities in epidemiological studies. International Classification of Diseases (ICD)-coded diagnoses from administrative hospital databases is potentially an efficient way of deriving CCI. However, no studies have evaluated its validity in infectious disease research. We aim to compare CCI derived from administrative data and medical record review in predicting mortality in patients with infections. We conducted a cross-sectional study on 199 inpatients. Correlation analyses were used to compare comorbidity scores from ICD-coded administrative databases and medical record review. Multivariable regression models were constructed and compared for discriminatory power for 30-day in-hospital mortality. Overall agreement was fair [weighted kappa 0·33, 95% confidence interval (CI) 0·23–0·43]. Kappa coefficient ranged from 0·17 (95% CI 0·01–0·36) for myocardial infarction to 0·85 (95% CI 0·59–1·00) for connective tissue disease. Administrative data-derived CCI was predictive of CCI ⩾5 from medical record review, controlling for age, gender, resident status, ward class, clinical speciality, illness severity, and infection source (C = 0·773). Using the multivariable model comprising age, gender, resident status, ward class, clinical speciality, illness severity, and infection source to predict 30-day in-hospital mortality, administrative data-derived CCI (C = 0·729) provided a similar C statistic as medical record review (C = 0·717, P = 0·8548). In conclusion, administrative data-derived CCI can be used for assessing comorbidities and confounding control in infectious disease research.

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease that was caused by a novel bunyavirus, SFTSV. The study aimed to disclose the epidemiological and clinical characteristics of SFTSV infection in China so far. An integrated clinical database comprising 1920 SFTS patients was constructed by combining first-hand clinical information collected from SFTS sentinel hospitals (n = 1159) and extracted data (n = 761) from published literature. The considered variables comprised clinical manifestations, routine laboratory tests of acute infection, hospitalization duration and disease outcome. SFTSV-IgG data from 19 119 healthy subjects were extracted from the published papers. The key clinical variables, case-fatality rate (CFR) and seroprevalence were estimated by meta-analysis. The most commonly seen clinical manifestations of SFTSV infection were fever, anorexia, myalgia, chill and lymphadenopathy. The major laboratory findings were elevated lactate dehydrogenase, aminotransferase, followed by thrombocytopenia, lymphocytopenia, elevated alanine transaminase and creatine kinase. A CFR of 12·2% was estimated, significantly higher than that obtained from national reporting data, but showing no geographical difference. In our paper, the mortality rate was about 1·9 parts per million. Older age and longer delay to hospitalization were significantly associated with fatal outcome. A pooled seroprevalence of 3·0% was obtained, which increased with age, while comparable for gender. This study represents a clinical characterization on the largest group of SFTS patients up to now. A higher than expected CFR was obtained. A wider spectrum of clinical index was suggested to be used to identify SFTSV infection, while the useful predictor for fatal outcome was found to be restricted.

Increasing immigration from high tuberculosis (TB) incidence countries is a challenge for surveillance and control in Finland. Here, we describe the epidemiology of TB in immigrants by using national surveillance data. During 1995–2013, 7030 (84·7%) native and 1199 (14·4%) immigrant cases were identified. The proportion of immigrant cases increased from 5·8% in 1995 to 32·1% in 2013, consistent with increasing immigrant population (2·1–5·6%) and decreasing incidence of TB in the native population (from 12·1 to 3·5/100 000). TB cases in immigrants were significantly younger, more often female, and had extrapulmonary TB more often than native cases (P < 0·01 for all comparisons); multidrug resistance was also more common in immigrants than natives (P < 0·01). Immigrant cases were born in 82 different countries; most commonly in Somalia and the former Soviet Union/Russia. During 2008–2013, 433 Mycobacterium tuberculosis isolates from immigrants were submitted for spoligotyping; 10 different clades were identified. Clades were similar to those found in the case's country of birth. Screening immigrants from high-incidence countries and raising awareness of common characteristics and symptoms of TB is important to ensure early diagnosis and to prevent transmission.

Between December 2010 and August 2011 an outbreak of measles occurred in Serbia with 363 reported cases. Sera and/or nose/throat swabs were collected from 193 patients and tested for measles-specific IgM antibodies by ELISA and viral RNA by RT–PCR, respectively. Epidemiological data were obtained from the surveillance database of the Institute of Public Health of Serbia. Of the 363 cases involved in the outbreak, 113 were laboratory confirmed. More than one third of the patients were hospitalized (n = 130, 35·8%) and for 15 (4·1% of the reported outbreak cases) the infection was complicated by pneumonia. Mostly pre-school children aged ⩽4 years (37·8%) and adults aged ⩾30 years (27·3%) were affected. The majority of patients belonged to the Roma population with a preponderance of female cases (57·0%). Nearly 94% of the patients were either unvaccinated or of unknown vaccination status. The main outbreak virus was the D4-Hamburg strain. The outbreak in Serbia occurred after several years of very low measles incidence despite a high routine immunization coverage in the general population, suggesting that special efforts to identify and vaccinate susceptible population groups are required even in countries with apparently good disease control.

Vibrio cholerae O139 emerged as a causative agent of epidemic cholera in 1992 in India and Bangladesh, and was subsequently reported in China in 1993. The genetic relatedness and molecular characteristics of V. cholerae O139 in Guangdong Province, located in the southern coastal area of China, remains undetermined. In this study, we investigated 136 clinical V. cholerae O139 isolates from 1993 to 2013 in Guangdong. By conventional PCR, 123 (90·4%) isolates were positive for ctxB, ace and zot. Sequencing of the positive amplicons indicated 113 (91·7%) isolates possessed the El Tor allele of ctxB (genotype 3); seven carried the classical ctxB type (genotype 1) and three harboured a novel ctxB type (genotype 5). With respect to tcpA, 123 (90·4%) isolates were positive for the El Tor allele. In addition, pulsed-field gel electrophoresis (with NotI digestion) differentiated the isolates into clusters A and B. Cluster A contained seven of the non-toxigenic isolates from 1998 to 2000; another six non-toxigenic isolates (from 1998 and 2007) and all of the toxigenic isolates formed cluster B. Our results suggest that over a 20-year period, the predominant O139 clinical isolates have maintained a relatively tight clonal structure, although some genetic variance and shift has occurred. Our data highlight the persistence of toxigenic V. cholerae O139 in clinical settings in the southern coastal area of China.

Information is lacking on the integrated evaluation of mortality rates in healthcare-associated infections (HAIs). Our aim was to differentiate the risk factors responsible for the incidence from those for the case-fatality rates in association with HAIs. We therefore examined the time trends of both incidence and case-fatality rates over a 20-year period at a tertiary-care teaching medical centre in Taiwan and the mortality rate was expressed as the product of the incidence rate and the case-fatality rate. During the study period the overall mortality rate fell from 0·46 to 0·32 deaths/1000 patient-days and the incidence rate fell from 3·41 to 2·31/1000 patient-days, but the case-fatality rate increased marginally from 13·5% to 14·0%. The independent risk factors associated with incidence of HAIs were age, gender, infection site, admission type, and department of hospitalization. Significant prognostic factors for HAI case-fatality were age, infection site, intensive care, and clinical department. We conclude that the decreasing trend for the HAI mortality rate was accompanied by a significant decline in the incidence rate and this was offset by a slightly increasing trend in the case-fatality rate. This deconstruction approach could provide further insights into the underlying complex causes of mortality for HAIs.

We report herein the investigation of a leptospirosis outbreak occurring in triathlon competitors on Réunion Island, Indian Ocean. All participants were contacted by phone or email and answered a questionnaire. Detection and molecular characterization of pathogenic Leptospira was conducted in inpatients and in rodents trapped at the vicinity of the event. Of the 160 athletes competing, 101 (63·1%) agreed to participate in the study. Leptospirosis was biologically confirmed for 9/10 suspected cases either by real-time PCR or serological tests (MAT or ELISA). The total attack rate, children's attack rate, swimmers’ attack rate, and the attack rate in adult swimmers were respectively estimated at 8·1% [95% confidence interval (CI) 4·3–14·7], 0%, 12·7% (95% CI 6·8–22·4) and 23·1% (95% CI 12·6–33·8). Leptospirosis cases reported significantly more wounds [risk ratio (RR) 4·5, 95% CI 1·6–13], wore complete neoprene suits less often (RR 4·3, 95% CI 1·3–14·5) and were most frequently unlicensed (RR 6·6, 95% CI 2·9–14·8). The epidemiological investigation supported that some measures such as the use of neoprene suits proved efficient in protecting swimmers against infection. PCR detection in rats revealed high Leptospira infection rates. Partial sequencing of the 16S gene and serology on both human and animal samples strongly suggests that rats were the main contaminators and were likely at the origin of the infection in humans.

The recent appearance of methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a concern for both veterinary and human healthcare. MRSP clonal lineages with sequence type (ST) 71-spa t02-staphylococcal cassette chromosome mec (SCCmec) II–III and ST68-spa t06-SCCmec V have spread throughout Europe and North America, respectively. The current study compared the molecular characteristics of 43 MRSP isolates from dogs in Japan with those of MRSP from previous reports using multilocus sequence typing based on seven housekeeping genes, SCCmec typing, and detection of antimicrobial resistance genes. Three related clonal lineages, ST71, ST169, and the newly registered ST354, were observed in SCCmec II–III isolates from Japan, despite MRSP SCCmec II–III isolates being thought to belong to a single clonal lineage. The majority of SCCmec II–III isolates belonging to ST169 (9/11) and ST354 (3/3), but not ST71 (0/11), harboured tetM. Four STs were observed for the SCCmec V isolates; however, neither ST68 nor related STs were found in the Japanese MRSP isolates. In conclusion, MRSP SCCmec II–III isolates from Japan belonged to ST71 and related STs (ST169 and ST354). A variety of MRSP SCCmec V clones, including some novel clones, were identified.

Balamuthia mandrillaris is an opportunistic free-living amoeba that has been reported to cause cutaneous lesions and Balamuthia amoebic encephalitis. The biology and environmental distribution of B. mandrillaris is still poorly understood and isolation of this pathogen from the environment is a rare event. Previous studies have reported that the presence of B. mandrillaris in the environment in Iran may be common. However, no clinical cases have been reported so far in this country. In the present study, a survey was conducted in order to evaluate the presence of B. mandrillaris in hot-spring samples of northern Iran. A total of 66 water samples were analysed using morphological and molecular tools. Positive samples by microscopy were confirmed by performing PCR amplification of the 16S rRNA gene of B. mandrillaris. Sequencing of the positive amplicons was also performed to confirm morphological data. Two of the 66 collected water samples were positive for B. mandrillaris after morphological and molecular identification. Interestingly, both positive hot springs had low pH values and temperatures ranging from 32 °C to 42 °C. Many locals and tourists use both hot springs due to their medicinal properties and thus contact with water bodies containing the organism increases the likelihood of infection. To the best of our knowledge, this is the first report on the isolation of B. mandrillaris from hot-spring sources related to human activity. Therefore, B. mandrillaris should be considered as a possible causative agent if cases of encephalitis are suspected following immersion in hot springs in addition to Acanthamoeba and Naegleria.

Legionnaires’ disease (LD) is a globally distributed systemic infectious disease. The burden of LD in many regions is still unclear, especially in Asian countries including China. A survey of Legionella infection using real-time PCR and nested sequence-based typing (SBT) was performed in two hospitals in Shanghai, China. A total of 265 bronchoalveolar lavage fluid (BALF) specimens were collected from hospital A between January 2012 and December 2013, and 359 sputum specimens were collected from hospital B throughout 2012. A total of 71 specimens were positive for Legionella according to real-time PCR focusing on the 5S rRNA gene. Seventy of these specimens were identified as Legionella pneumophila as a result of real-time PCR amplification of the dotA gene. Results of nested SBT revealed high genetic polymorphism in these L. pneumophila and ST1 was the predominant sequence type. These data revealed that the burden of LD in China is much greater than that recognized previously, and real-time PCR may be a suitable monitoring technology for LD in large sample surveys in regions lacking the economic and technical resources to perform other methods, such as urinary antigen tests and culture methods.

Immunoglobulin A (IgA)-based tests have been evaluated in different studies for their utility in diagnosing dengue infections. In most of the studies, the results were inconclusive because of a small sample size. Hence, a meta-analysis involving nine studies with 2096 samples was performed to assess the diagnostic accuracy of IgA-based tests in diagnosing dengue infections. The analysis was conducted using Meta-Disc software. The results revealed that IgA-based tests had an overall sensitivity, specificity, diagnostic odds ratio, and positive and negative likelihood ratios of 73·9%, 95·2%, 66·7, 22·0 and 0·25, respectively. Significant heterogeneity was observed between the studies. The type of test, infection status and day of sample collection influenced the diagnostic accuracy. The IgA-based diagnostic tests showed a greater accuracy when the samples were collected 4 days after onset of symptoms and for secondary infections. The results suggested that IgA-based tests had a moderate level of accuracy and are diagnostic of the disease. However, negative results cannot be used alone for dengue diagnosis. More prospective studies comparing the diagnostic accuracy of combinations of antigen-based tests with either IgA or IgM are needed and might be useful for suggesting the best strategy for dengue diagnosis.

Differences in the seroprevalence and unique pattern of parvovirus B19 (B19V) acute infections have been documented around the world. This study was conducted to estimate the seroprevalence of anti-parvovirus B19V IgG antibodies in the Israeli population and to assess the pattern of acute infection based on data from two laboratories in Israel. The overall IgG prevalence in the 1008 representative sera samples was 61·4% and the age-adjusted prevalence rate was 58·2%. Seropositivity was significantly associated with age, ranging from 25·7% in children aged <10 years to 70% in people aged >20 years. While no significant differences in seropositivity were detected between sexes and population groups, significantly lower seroprevalence was observed in older Jews born in Africa or Asia. Acute infection rates of 4·1% (234 cases) were found based on the positive IgM results identified in samples from 5663 individuals collected between 2008 and 2013. Annual peaks of infection were observed in 2008 and 2011–2012 and major seasonal peak of B19V IgM positivity was identified in June each year. The number of requests for B19V serology was significantly higher for women aged 20–39 years while the majority IgM-positive cases were identified in young children. With more than 30% of the adult population being susceptible to B19V infection, monitoring B19V status should be considered in specific risk groups such as pregnant women.

Population seroprevalence can be estimated from serosurveys by classifying quantitative measurements into positives (past infection/vaccinated) or negatives (susceptible) according to a fixed assay cut-off. The choice of assay cut-offs has a direct impact on seroprevalence estimates. A time-resolved fluorescence immunoassay (TRFIA) was used to test exposure to human parvovirus 4 (HP4). Seroprevalence estimates were obtained after applying the diagnostic assay cut-off under different scenarios using simulations. Alternative methods for estimating assay cut-offs were proposed based on mixture modelling with component distributions for the past infection/vaccinated and susceptible populations. Seroprevalence estimates were compared to those obtained directly from the data using mixture models. Simulation results showed that when there was good distinction between the underlying populations all methods gave seroprevalence estimates close to the true one. For high overlap between the underlying components, the diagnostic assay cut-off generally gave the most biased estimates. However, the mixture model methods also gave biased estimates which were a result of poor model fit. In conclusion, fixed cut-offs often produce biased estimates but they also have advantages compared to other methods such as mixture models. The bias can be reduced by using assay cut-offs estimated specifically for seroprevalence studies.

In October 2012, an outbreak of gentamicin-resistant, ciprofloxacin non-susceptible extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae occurred in a neonatal intensive care unit in Ireland. In order to determine whether the outbreak strain was more widely dispersed in the country, 137 isolates of K. pneumoniae with this resistance phenotype collected from 17 hospitals throughout Ireland between January 2011 and July 2013 were examined. ESBL production was confirmed phenotypically and all isolates were screened for susceptibility to 19 antimicrobial agents and for the presence of genes encoding blaTEM, blaSHV, blaOXA, and blaCTX-M; 22 isolates were also screened for blaKPC, blaNDM, blaVIM, blaIMP and blaOXA-48 genes. All isolates harboured blaSHV and blaCTX-M and were resistant to ciprofloxacin, gentamicin, nalidixic acid, amoxicillin-clavulanate, and cefpodoxime; 15 were resistant to ertapenem, seven to meropenem and five isolates were confirmed as carbapenemase producers. Pulsed-field gel electrophoresis of all isolates identified 16 major clusters, with two clusters comprising 61% of the entire collection. Multilocus sequence typing of a subset of these isolates identified a novel type, ST1236, a single locus variant of ST48. Data suggest that two major clonal groups, ST1236/ST48 (CG43) and ST15/ST14 (CG15) have been circulating in Ireland since at least January 2011.

In 2005, the Norwegian Institute of Public Health established a web-based outbreak rapid alert system called Vesuv. The system is used for mandatory outbreak alerts from municipal medical officers, healthcare institutions, and food safety authorities. As of 2013, 1426 outbreaks have been reported, involving 32913 cases. More than half of the outbreaks occurred in healthcare institutions (759 outbreaks, 53·2%). A total of 474 (33·2%) outbreaks were associated with food or drinking water. The web-based rapid alert system has proved to be a helpful tool by enhancing reporting and enabling rapid and efficient information sharing between different authorities at both the local and national levels. It is also an important tool for event-based reporting, as required by the International Health Regulations (IHR) 2005. Collecting information from all the outbreak alerts and reports in a national database is also useful for analysing trends, such as occurrence of certain microorganisms, places or sources of infection, or route of transmission. This can facilitate the identification of specific areas where more general preventive measures are needed.

The objective of this study was to assess the effectiveness of a catheter-related bloodstream infection (CR BSI) reduction programme and healthcare workers' compliance with recommendations. A 3-year surveillance programme of CR BSIs in all hospital settings was implemented. As part of the programme, there was a direct observation of insertion and maintenance of central venous catheters (CVCs) to determine performance. A total of 38 education courses were held over the study period and feedback reports with the results of surveillance and recommendations were delivered to healthcare workers every 6 months. A total of 6722 short-term CVCs were inserted in 4982 patients for 58 763 catheter-days. Improvements of compliance with hand hygiene was verified at the insertion (87·1–100%, P < 0·001) and maintenance (51·1–72·1%, P = 0·029) of CVCs; and the use of chlorhexidine for skin disinfection was implemented at insertion (35·7–65·4%, P < 0·001) and maintenance (33·3–45·9%, P < 0·197) of CVCs. There were 266 CR BSI incidents recorded with an annual incidence density of 5·75/1000 catheter-days in the first year, 4·38 in the second year [rate ratio (RR) 0·76, 95% confidence interval (CI) 0·57–1·01] and 3·46 in the third year (RR 0·60, 95% CI 0·44–0·81). The education programme clearly improved compliance with recommendations for CVC handling, and was effective in reducing the burden of CR BSIs.