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.

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.

Yersinia enterocolitica infection is a zoonosis with worldwide distribution, gastroenteritis being by far the most common clinical manifestation of human infection. In Gipuzkoa, northern Spain, human Y. enterocolitica infections increased from the mid-1980s to the beginning of the 21st century (from 7·9 to 23·2 annual episodes per 100 000 population) to decrease to 7·2 annual episodes per 100 000 population in the last years of the study. The hospital admission rate due to yersiniosis during the last 15 years of the study was 7·3%. More than 99% of isolates were serotype O:3. Infection affected mainly children under 5 years of age (average rate: 140 episodes per 100 000 population). The incidence in adults was low but hospitalisation increased with age, exceeding 50% in people over 64 years old.

Shiga toxin-producing Escherichia coli (STEC) is a known food pathogen, which main reservoir is the intestine of ruminants. The abundance of different STEC lineages in nature reflect a heterogeneity that is characterised by the differential expression of certain genotypic characteristics, which in turn are influenced by the environmental conditions to which the microorganism is exposed. Bacterial homeostasis and stress response are under the control of the alarmone guanosine tetraphosphate (ppGpp), which intrinsic levels varies across the E. coli species. In the present study, 50 STEC isolates from healthy sheep were evaluated regarding their ppGpp content, cytotoxicity and other relevant genetic and phenotypic characteristics. We found that the level of ppGpp and cytotoxicity varied considerably among the examined strains. Isolates that harboured the stx2 gene were the least cytotoxic and presented the highest levels of ppGpp. All stx2 isolates belonged to phylogroup A, while strains that carried stx1 or both stx1 and stx2 genes pertained to phylogroup B1. All but two stx2 isolates belonged to the stx2b subtype. Strains that belonged to phylogroup B1 displayed on average low levels of ppGpp and high cytotoxicity. Overall, there was a negative correlation between cytotoxicity and ppGpp.

A total of 45 strains of Vibrio cholerae O1 isolated from 10 different places in India where they were associated with cases of cholera between the years 2007 and 2008 were examined by molecular methods. With the help of phenotypic and genotypic tests the strains were confirmed to be O1 El Tor biotype strains with classical ctxB gene. Polymerase chain reaction (PCR) analysis by double – mismatch amplification mutation assay PCR showed 16 of these strains carried the ctxB-7 allele reported in Haitian strains. Sequencing of the ctxB gene in all the 45 strains revealed that in 16 strains the histidine at the 20th amino acid position had been replaced by asparagine and this single nucleotide polymorphism did not affect cholera toxin production as revealed by beads enzyme-linked immunosorbent assay. This study shows that the new ctxB gene sequence was circulating in different places in India. Seven representatives of these 45 strains analysed by pulsed – field gel electrophoresis showed four distinct Not I digested profiles showing that multiple clones were causing cholera in 2007 and 2008.

In April 2015, Finnish public health authorities alerted European Union member states of a possible multi-country Salmonella enteritidis outbreak linked to an international youth ice-hockey tournament in Latvia. The European Centre for Disease Prevention and Control (ECDC), Finnish and Latvian authorities initiated an outbreak investigation to identify the source. The investigation included a description of the outbreak, retrospective cohort study, microbiological investigation and trace-back. We identified 154 suspected and 96 confirmed cases from seven countries. Consuming Bolognese sauce and salad at a specific event arena significantly increased the risk of illness. Isolates from Finnish, Swedish and Norwegian cases had an identical multiple-locus variable-number of tandem repeats analysis-profile (3-10-6-4-1). Breaches in hygiene and food storing practices in the specific arena's kitchen allowing for cross-contamination were identified. Riga Cup participants were recommended to follow good hand hygiene and consume only freshly cooked foods. This investigation demonstrated that the use of ECDC's Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses platform was essential to progress the investigation by facilitating information exchange between countries. Cross-border data sharing to perform whole genome sequencing gave relevant information regarding the source of the outbreak.

Noroviruses (NoVs) are major causal agents of acute gastroenteritis in humans. NoV GII.4 is the predominant genotype globally. However, uncommon and minor types of NoVs are consistently detected and some have been shown to dominate over GII.4. Therefore, the prevalence of dominant and uncommon NoVs makes the identification of these viruses important for the prediction and prevention of pandemics. In this study, the full-genome sequence of a NoV (strain JW) detected in Korea was extensively characterized. The full-length genome was 7510 nucleotides long, and phylogenetic analysis based on the whole-genome sequences, including open reading frame (ORF)1, ORF2, and ORF3, indicated that it belonged to the GII.21 genotype. Strain JW showed maximum identity with strain YO284; however, comparison of the amino acid sequence of ORF2, which functions as an antigen, showed substitutions in several amino acids. GII.21 is not a prevalent epidemiological agent of acute gastroenteritis in humans, but it is consistently found in gastroenteritis patients from several countries. The present study provides the first full-genome sequence analysis of NoV GII.21 isolated from a patient in Korea. Our findings provide not only valuable genome information but also data for epidemiology studies, epidemic prevention, and vaccine development strategies.

Accurate knowledge of pathogen incubation period is essential to inform public health policies and implement interventions that contribute to the reduction of burden of disease. The incubation period distribution of campylobacteriosis is currently unknown with several sources reporting different times. Variation in the distribution could be expected due to host, transmission vehicle, and organism characteristics, however, the extent of this variation and influencing factors are unclear. The authors have undertaken a systematic review of published literature of outbreak studies with well-defined point source exposures and human experimental studies to estimate the distribution of incubation period and also identify and explain the variation in the distribution between studies. We tested for heterogeneity using I2 and Kolmogorov–Smirnov tests, regressed incubation period against possible explanatory factors, and used hierarchical clustering analysis to define subgroups of studies without evidence of heterogeneity. The mean incubation period of subgroups ranged from 2·5 to 4·3 days. We observed variation in the distribution of incubation period between studies that was not due to chance. A significant association between the mean incubation period and age distribution was observed with outbreaks involving only children reporting an incubation of 1·29 days longer when compared with outbreaks involving other age groups.

Information on the factors that cause or amplify foodborne illness outbreaks (contributing factors), such as ill workers or cross-contamination of food by workers, is critical to outbreak prevention. However, only about half of foodborne illness outbreaks reported to the United States’ Centers for Disease Control and Prevention (CDC) have an identified contributing factor, and data on outbreak characteristics that promote contributing factor identification are limited. To address these gaps, we analyzed data from 297 single-setting outbreaks reported to CDC's new outbreak surveillance system, which collects data from the environmental health component of outbreak investigations (often called environmental assessments), to identify outbreak characteristics associated with contributing factor identification. These analyses showed that outbreak contributing factors were more often identified when an outbreak etiologic agent had been identified, when the outbreak establishment prepared all meals on location and served more than 150 meals a day, when investigators contacted the establishment to schedule the environmental assessment within a day of the establishment being linked with an outbreak, and when multiple establishment visits were made to complete the environmental assessment. These findings suggest that contributing factor identification is influenced by multiple outbreak characteristics, and that timely and comprehensive environmental assessments are important to contributing factor identification. They also highlight the need for strong environmental health and food safety programs that have the capacity to complete such environmental assessments during outbreak investigations.

Zoonotic diseases are a significant health threat for humans and animals. To better understand the epidemiology, etiology, and pathology of infectious agents affecting humans and animals combined approaches are needed. Here we describe an epidemiological investigation conducted by physicians and veterinarians after a reported case of psittacosis. Upon admission suffering from respiratory distress syndrome in a hospital and with a history of bird contact, a female patient was serologically diagnosed with psittacosis. After the case notification, veterinarians were able to investigate the source of infection by detecting Chlamydia psittaci in her pet cockatiel. The bird was hospitalized and successfully treated. In addition, the establishment where the pet bird was purchased was traced and through molecular techniques other birds intended to be sold as pets tested positive for C. psittaci. As a result, sanitary measures were applied and the establishment then was closed down. The birds intended for the pet commerce were treated and retested with negative molecular results for C. psittaci, thus avoiding disease propagation. Reliable data about zoonotic diseases can only be generated through the application of multidisciplinary approaches which take into account the epidemiological factors and interactions of humans, animals and their environments as an integrated system.

Mycobacterium marinum, a bacterium found in freshwater and saltwater, can infect persons with direct exposure to fish or aquariums. During December 2013, the New York City Department of Health and Mental Hygiene learned of four suspected or confirmed M. marinum skin or soft tissue infections (SSTIs) among persons who purchased whole fish from Chinese markets. Ninety-eight case-patients with non-tuberculous mycobacteria (NTM) SSTIs were identified with onset June 2013–March 2014. Of these, 77 (79%) were female. The median age was 62 years (range 30–91). Whole genome sequencing of clinical isolates revealed two main clusters and marked genetic diversity. Environmental samples from distributors yielded NTM though not M. marinum. We compared 56 case-patients with 185 control subjects who shopped in Chinese markets, frequency-matched by age group and sex. Risk factors for infection included skin injury to the finger or hand (odds ratio [OR]: 15·5; 95% confidence interval [CI]: 6·9–37·3), hand injury while preparing fish or seafood (OR 8·3; 95% CI 3·8–19·1), and purchasing tilapia (OR 3·6; 95% CI 1·1–13·9) or whiting (OR 2·7; 95% CI 1·1–6·6). A definitive environmental outbreak source was not identified.

Occasional cases of classical bovine spongiform encephalopathy (BSE) still continue to occur within the European Union (EU) for animals born after reinforced feed bans (BARBs), which should in theory have eliminated all risk of infection. The study aimed to determine (i) whether a common rate of decline of BSE infection was evident across EU member states, i.e. to determine whether control measures have been equally effective in all member states, (ii) whether there was any evidence of spontaneous occurrence of BSE in the data and (iii) the expected date for the last BSE case in UK. It was found that there was no significant difference in the rate of decline of BSE prevalence between member states, with a common rate of decline of 33·9% per annum (95% CI 30·9–37%) in successive annual birth cohorts. Trend analysis indicated an ultimate decline to 0 prevalence, suggesting that spontaneous occurrence does not explain the majority of cases. Projecting forward the trends from the back-calculation model indicated that there was approximately a 50% probability of further cases in the UK, and should the current rate of decline continue, there remains the possibility of further occasional cases up until 2026.

The house mouse (Mus musculus) and the black rat (Rattus rattus) are reservoir hosts for zoonotic pathogens, several of which cause neglected tropical diseases (NTDs). Studies of the prevalence of these NTD-causing zoonotic pathogens, in house mice and black rats from tropical residential areas are scarce. Three hundred and two house mice and 161 black rats were trapped in 2013 from two urban neighbourhoods and a rural village in Yucatan, Mexico, and subsequently tested for Trypanosoma cruzi, Hymenolepis diminuta and Leptospira interrogans. Using the polymerase chain reaction we detected T. cruzi DNA in the hearts of 4·9% (8/165) and 6·2% (7/113) of house mice and black rats, respectively. We applied the sedimentation technique to detect eggs of H. diminuta in 0·5% (1/182) and 14·2% (15/106) of house mice and black rats, respectively. Through the immunofluorescent imprint method, L. interrogans was identified in 0·9% (1/106) of rat kidney impressions. Our results suggest that the black rat could be an important reservoir for T. cruzi and H. diminuta in the studied sites. Further studies examining seasonal and geographical patterns could increase our knowledge on the epidemiology of these pathogens in Mexico and the risk to public health posed by rodents.

The role of the protozoan parasite Toxoplasma gondii in the pathogenesis of liver disease has recently gained much interest. The aim of this study was to determine the prevalence and risk factors associated with T. gondii infection in patients with liver disease from three cities in Shandong and Henan provinces, China. A case–control study was conducted from December 2014 to November 2015 and included 1142 patients with liver disease and 1142 healthy controls. Serum samples were collected from all individuals and were examined with enzyme-linked immunosorbent assay for the presence of anti-T. gondii IgG and IgM antibodies. Information on the demographics, clinical, and lifestyle characteristics of the participants was collected from the medical records and by the use of a questionnaire. The prevalence of anti-T. gondii IgG was 19·7% in patients with liver disease compared with 12·17% in the controls. Only 13 patients had anti-T. gondii IgM antibodies compared with 12 control individuals (1·14% vs. 1·05%, respectively). The highest seroprevalence was detected in patients with liver cancer (22·13%), followed by hepatitis patients (20·86%), liver cirrhosis patients (20·42%), and steatosis patients (20%). Multivariate logistic regression analysis indicated that consumption of raw meat (odds ratio (OR) = 1·32; 95% confidence interval (CI) 1·01–1·71; P = 0·03) and source of drinking water from wells (OR = 1·56; 95% CI 1·08–2·27; P = 0·01) were independent risk factors for T. gondii infection in liver disease patients. These findings indicate that T. gondii infection is more likely to be present in patients with liver disease. Therefore, efforts should be directed toward health education of populations at high risk of T. gondii infection and measures should be taken to protect vulnerable patients with liver disease.

The timing and origin of Zika virus (ZIKV) introduction in Brazil has been the subject of controversy. Initially, it was assumed that the virus was introduced during the FIFA World Cup in June–July 2014. Then, it was speculated that ZIKV may have been introduced by athletes from French Polynesia (FP) who competed in a canoe race in Rio de Janeiro in August 2014. We attempted to apply mathematical models to determine the most likely time window of ZIKV introduction in Brazil. Given that the timing and origin of ZIKV introduction in Brazil may be a politically sensitive issue, its determination (or the provision of a plausible hypothesis) may help to prevent undeserved blame. We used a simple mathematical model to estimate the force of infection and the corresponding individual probability of being infected with ZIKV in FP. Taking into account the air travel volume from FP to Brazil between October 2013 and March 2014, we estimated the expected number of infected travellers arriving at Brazilian airports during that period. During the period between December 2013 and February 2014, 51 individuals travelled from FP airports to 11 Brazilian cities. Basing on the calculated force of ZIKV infection (the per capita rate of new infections per time unit) and risk of infection (probability of at least one new infection), we estimated that 18 (95% CI 12–22) individuals who arrived in seven of the evaluated cities were infected. When basic ZIKV reproduction numbers greater than one were assumed in the seven evaluated cities, ZIKV could have been introduced in any one of the cities. Based on the force of infection in FP, basic reproduction ZIKV number in selected Brazilian cities, and estimated travel volume, we concluded that ZIKV was most likely introduced and established in Brazil by infected travellers arriving from FP in the period between October 2013 and March 2014, which was prior to the two aforementioned sporting events.

Early prediction of the final size of any epidemic and in particular for Zika disease outbreaks can be useful for health authorities in order to plan the response to the outbreak. The Richards model is often been used to estimate epidemiological parameters for arboviral diseases based on the reported cumulative cases in single- and multi-wave outbreaks. However, other non-linear models can also fit the data as well. Typically, one follows the so called post selection estimation procedure, i.e., selects the best fitting model out of the set of candidate models and ignores the model uncertainty in both estimation and inference since these procedures are based on a single model. In this paper we focus on the estimation of the final size and the turning point of the epidemic and conduct a real-time prediction for the final size of the outbreak using several non-linear models in which these parameters are estimated via model averaging. The proposed method is applied to Zika outbreak data in four cities from Colombia, during the outbreak ocurred in 2015–2016.

Routine, passive surveillance systems tend to underestimate the burden of communicable diseases such as dengue. When empirical methods are unavailable, complimentary opinion-based or extrapolative methods have been employed. Here, an expert Delphi panel estimated the proportion of dengue captured by the Indonesian surveillance system, and associated health system parameters. Following presentation of medical and epidemiological data and subsequent discussions, the panel made iterative estimates from which expansion factors (EF), the ratio of total:reported cases, were calculated. Panelists estimated that of all symptomatic Indonesian dengue episodes, 57·8% (95% confidence interval (CI) 46·6–59·8) enter healthcare facilities to seek treatment; 39·3% (95% CI 32·8–42·0) are diagnosed as dengue; and 20·3% (95% CI 16·1–24·3) are subsequently reported in the surveillance system. They estimated most hospitalizations occur in the public sector, while ~55% of ambulatory episodes are seen privately. These estimates gave an overall EF of 5·00; hospitalized EF of 1·66; and ambulatory EF of 34·01 which, when combined with passive surveillance data, equates to an annual average (2006–2015) of 612 005 dengue cases, and 183 297 hospitalizations. These estimates are lower than those published elsewhere, perhaps due to case definitions, local clinical perceptions and treatment-seeking behavior. These findings complement global burden estimates, support health economic analyses, and can be used to inform decision-making.

This cross-sectional study aimed to examine and compare prevalence and correlates of whole blood Epstein–Barr virus (EBV) DNA between HIV-positive and HIV-negative men who have sex with men (MSM). Five hundred and four HIV-positive MSM and 504 age-matched HIV-negative MSM were recruited from an HIV counseling and testing clinic in Shanghai, China from November 2014 to November 2015 and were administered with a face-to-face questionnaire interview. Whole blood EBV DNA was tested by nested polymerase chain reaction assays on EBNA-1, EBNA-2, and LMP-1 genes. The prevalence of whole blood EBV DNA was 56·0% (95% CI 51·7–60·3%) among HIV-positive MSM and 26·0% (95% CI 22·4–30·0%) among HIV-negative MSM. Whole blood EBV DNA positivity was significantly associated with HIV infection (adjusted odds ratio (aOR) 3·43, 95% CI 2·58–4·57) and frequent intake of pickled, smoked, or salty food (aOR 1·71, 95% CI 1·02–2·86) in the whole sample, and with <200 cells/μl CD4 cell counts (aOR 1·79, 95% CI 1·05–3·05) and pickled, smoked, or salty food intake (aOR 3·14, 95% CI 1·39–7·08) in HIV-positive group. HIV-infected MSM are at higher risk of active EBV replication than HIV-uninfected MSM, underscoring needs of surveillance and research on EBV-related carcinogenesis in this population.

Ureaplasma urealyticum and U. parvum have been associated with genital infections. The purpose of this study was to detect the presence of ureaplasmas and other sexually transmitted infections in sexually active women from Brazil and relate these data to demographic and sexual health, and cytokines IL-6 and IL-1β. Samples of cervical swab of 302 women were examined at the Family Health Units in Vitória da Conquista. The frequency of detection by conventional PCR was 76·2% for Mollicutes. In qPCR, the frequency found was 16·6% for U. urealyticum and 60·6% U. parvum and the bacterial load of these microorganisms was not significantly associated with signs and symptoms of genital infection. The frequency found for Trichomonas vaginalis, Neisseria gonorrhoeae, Gardnerella vaginalis and Chlamydia trachomatis was 3·0%, 21·5%, 42·4% and 1·7%, respectively. Higher levels of IL-1β were associated with control women colonized by U. urealyticum and U. parvum. Increased levels of IL-6 were associated with women who exhibited U. parvum. Sexually active women, with more than one sexual partner in the last 3 months, living in a rural area were associated with increased odds of certain U. parvum serovar infection.

We estimated the number of people unaware of their human immunodeficiency virus (HIV) infection in our province, Pavia (population 540 000) in Lombardy, Italy, by means of anonymous unlinked testing of 10 044 serum/plasma samples residual from clinical analyses at the outpatient clinic of Policlinico San Matteo in 2014 and 2015. Ethical and legal approval was obtained prior to study start. Samples were irreversibly anonymised, only retaining gender and 5-year age class. Five sample pools were tested for HIV using LIAISON® XL MUREX HIV Ab/Ag (DiaSorin, Saluggia, Italy). If the pool tested positive, individual samples underwent confirmatory tests, Innotest HIV Antigen mAb (Fujirebio Europe, Gent, Belgium) and HIV BLOT 2·2 (MP Diagnostics, Singapore). Among the 10 044 samples processed, eight were confirmed positive (0·08%, 95% confidence interval 0·03–0·16%), all were males and age was >50 in 3 (37·5%). If projected to the entire population of the Pavia province, this would result in approximately 1000 people unaware of their HIV infection, with age older than expected. In Italy, HIV testing is voluntary, universally free-of-charge and (upon request) anonymous. Nevertheless, this study demonstrates that it is suboptimally employed, and that new strategies and population-level actions will be needed to achieve better implementation of HIV testing and HIV control in our province.