We investigated the genetic structure of 120 isolates of serotype 19F Streptococcus pneumoniae from Chinese children with acute respiratory infections collected from 1997 to 2006, and 2010. All strains were susceptible to vancomycin and levofloxacin, and only five strains were not susceptible to penicillin. The non-susceptibility rate to cephalosporins increased from 1997 to 2010. Of 119 erythromycin-resistant strains, 60 carried both ermB and mefA genes. The percentage of clonal complex 271 (CC271) increased from 14·3% in 1997–1998 to 92% in 2010, whereas that of CC983 decreased from 64·3% to 0%. CC271 had a higher non-susceptibility rate to β-lactam antibiotics than CC983 and other CCs. The increased non-susceptibility rate to β-lactam antibiotics in serotype 19F pneumococci was found to be associated with the spread of the international resistant clone CC271 presumably caused by antibiotic pressure. Long-term surveys of serotype 19F S. pneumoniae are required to monitor CC prevalence and trends in antimicrobial resistance.

A cross-sectional serological survey was conducted during January to August 2001 to determine the seroprevalence of Leptospira serovars in five species of livestock in Thailand and to identify associations between seropositivity and sex, age, species and geographical locations. Sera from 14188 livestock (9288 cattle, 1376 buffaloes, 1898 pigs, 1110 sheep, 516 goats) from 36 provinces were tested for antibodies against 24 Leptospira serovars with the microscopic agglutination test (MAT) for which the criterion for a positive result was set at a titre of ⩾1:50. A total of 1635 [11·5%, 95% confidence interval (CI) 11·0–12·0] animals were seropositive and the highest prevalence (30·4%, 95% CI 28·2–32·5) of evidence of infection was recorded in the northeast region followed by the central region (22·2%, 95% CI 20–24·6). Seroprevalences recorded for cattle, buffaloes, pigs, sheep and goats were 9·9% (95% CI 9·3–10·5), 30·5% (95% CI 28·1–32·9), 10·8% (95% CI 9·5–12·3), 4·7% (95% CI 3·6–6·1) and 7·9% (95% CI 5·8–10·5), respectively. Buffaloes were 3·1 (95% CI 2·8–3·4) times more likely than cattle to be seropositive. The most commonly detected antibodies were against L. interrogans serovars Ranarum, Sejroe, and Mini in cattle, Mini, Sejroe, and Bratislava in buffaloes, Ranarum, Pomona, and Bratislava in pigs and Mini, Shermani, and Ranarum in sheep and goats. Seroprevalences in cattle and buffaloes trended upwards with increasing age and there was no difference in the risk of seropositivity between males and females.

We investigated a possible outbreak of H. pylori in a rural Northern Plains community. In a cross-sectional survey, we randomly sampled 244 households from a geocoded emergency medical system database. We used a complex survey design and global positioning system units to locate houses and randomly selected one eligible household member to administer a questionnaire and a 13C-urea breath test for active H. pylori infection (n = 166). In weighted analyses, active H. pylori infection was detected in 55·0% of the sample. Factors associated with infection on multivariate analysis included using a public drinking-water supply [odds ratio (OR) 12·2, 95% confidence interval (CI) 2·9–50·7] and current cigarette smoking (OR 4·1, 95% CI 1·7–9·6). People who lived in houses with more rooms, a possible indicator of decreased crowding in the home, were less likely to have active H. pylori infections (OR 0·7, 95% CI 0·5–0·9 for each additional room).

Both serological and bacteriological investigations revealed a cyclic, seasonal pattern of Yersinia enterocolitica 1B/O8 infections in Poland during the years 2008–2011. A large increase in incidence was observed in the second quarter and a decrease in the third quarter of each year. Such seasonal changes were not seen in the case of infections caused by the other enteropathogenic Yersinia bioserotypes.

This study aimed to confirm that vertical transmission of hepatitis B virus (HBV) can occur via the infected ovum. Specimens studied were obtained from discarded test-tube embryos from mothers with chronic HBV infection who had received in vitro fertilization treatment. Single-cell reverse transcriptase–polymerase chain reaction was used to detect HBV mRNA in the embryos. HBV mRNA was detected in the cleavage embryos of patients with chronic HBV infection, with a detection rate of 13·2% (5/38). The level of serum HBV DNA was not related to the HBV mRNA positivity rates in embryos. In this study, HBV mRNA was detected in test-tube embryos from HBV-infected mothers who had received in vitro fertilization treatment. This confirms the theory of vertical transmission of HBV via the ovum, thereby providing an important theoretical basis for further study on the mechanism of HBV vertical transmission, influencing factors and blocking measures.

Dengue is a mosquito-borne disease caused by four closely related dengue virus (genus Flavivirus) serotypes (DENV-1–4). The clinical outcomes vary from mild febrile illness to life-threatening haemorrhagic manifestations. DENVs are endemic in the tropics and subtropics globally and currently no specific treatment or vaccines are available. In Venezuela, the American-Asian genotype of DENV-2 is the most prevalent and has been associated with severe disease outcomes. We aimed to follow-up the molecular epidemiology of DENV-2 in Venezuela to investigate if the evolution of the virus has remained the same throughout time or if the same dynamics documented in Brazil (hyperendemic co-circulation) also occurred. The results show that whereas the epidemiology of DENV in several endemic areas is characterized by serotype replacements through time, in Venezuela the American-Asian genotype DENV-2 has evolved into several genetic lineages and has remained in hyperendemic co-circulation with the other serotypes.

Shiga toxin-producing Escherichia coli (STEC) have led to outbreaks worldwide and are considered emerging pathogens. Infections by STEC in humans have been reported after consumption of mainly beef, but also deer. This study investigated the occurrence of STEC in deer in Germany. The virulence genes eae, e-hlyA and saa, the stx subtypes, pulsed-field gel electrophoresis (PFGE) patterns and serovars were studied. In total, 120 samples of 60 animals were screened by real-time polymerase chain reaction (PCR). The PCR results showed a high detection rate of stx genes (83%). Mainly faecal samples, but also some lymphatic tissue samples, tested stx-positive. All isolates carried stx2, were eae-negative and carried e-hlyA in 38% and saa in 9% of samples. Serovars (O88:[H8], O174:[H8], O146:H28) associated with human diseases were also identified. In some animals, isolates from lymphatic tissue and faecal samples showed undistinguishable PFGE patterns. The examined deer were shown to be relevant reservoirs of STEC with subtype stx2b predominating.

We describe an outbreak of simultaneous Clostridium difficile and norovirus infections in a long-term-care facility. Thirty patients experienced acute gastroenteritis, and four had co-infection with identical C. difficile 027 and genotype II.4 New Orleans norovirus strains. Co-occurring infection requires improved understanding of risk factors, clinical impact, and testing strategies.

This paper shows that control of foodborne disease outbreaks may be challenging even after establishing the source of infection. An outbreak of Salmonella Typhimurium U323 infections occurred in Denmark from March to September 2010, involving 172 cases. Before the detection of human cases, several positive isolates of the outbreak strain had been found in a particular pig slaughterhouse and thus early traceback, investigation and control measures were possible. Several batches of pork and pork products were recalled and the slaughterhouse was closed twice for disinfection. No single common food item was identified as the outbreak source, but repeated isolation of the outbreak strain from the slaughterhouse environment and in pork and products as well as patient interviews strongly suggested different pork products as the source of infection. Furthermore, a matched case-control study identified a specific ready-to-eat spreadable pork sausage (teewurst) as the source of a sub-outbreak (matched odds ratio 17, 95% confidence interval 2·1–130).

In September 2009, an outbreak of Salmonella enterica serovar Enteritidis affected 327 of 1419 inmates at a London prison. We applied a cohort design using aggregated data from the kitchen about portions of food distributed, aligned this with individual food histories from 124 cases (18 confirmed, 106 probable) and deduced the exposures of those remaining well. Results showed that prisoners eating egg cress rolls were 26 times more likely to be ill [risk ratio 25·7, 95% confidence interval (CI) 15·5–42·8, P<0·001]. In a case/non-case multivariable analysis the adjusted odds ratio for egg cress rolls was 41·1 (95% CI 10·3–249·7, P<0·001). The epidemiological investigation was strengthened by environmental and microbiological investigations. This paper outlines an approach to investigations in large complex settings where aggregate data for exposures may be available, and led to the development of guidelines for the management of future gastrointestinal outbreaks in prison settings.

Mycobacterium bovis causes bovine tuberculosis (bTB) in many mammals including cattle, deer and brushtail possum. The aim of this study was to estimate the strength of association, using model selection (AICc) regression analyses, between the proportion of cattle and farmed deer herds with bTB in New Zealand and annual costs of TB control, namely disease control in livestock, in wildlife or in a combination of the two. There was more support for curved (concave up) than linear models which related the proportion of cattle and farmed deer herds with bTB to the annual control costs. The curved, concave-up, best-fitting relationships showed diminishing returns with no positive asymptote and implied TB eradication is feasible in New Zealand.

This study examined the relationship between body mass index (BMI) and the risk of pneumonia in Aboriginal Australians. A total of 677 adults aged 20–60 years were followed up from the baseline examination during 1992–1995 to June 2012. The pneumonia events were identified through hospital records. Pneumonia incident rates were calculated according to BMI groups. Hazard ratios were computed using Cox regression adjusting for age, smoking and alcohol consumption status. The incident rate of pneumonia was 13·3/1000 person-years, and this rate was significantly higher in females than males (hazard ratio = 1·5). Compared to males with normal BMI (18·5–24·9 kg/m2), the adjusted hazard ratio was 3·5 for males with lowest BMI (P < 0·01). Low BMI was significantly associated with a higher risk of hospitalized pneumonia for Aboriginal males. However, the U-shaped trend of this association indicates that the risk of pneumonia is likely to be associated with both low and high BMI.

This study investigated the carriage of antimicrobial resistant Haemophilus influenzae in 582 healthy children attending kindergarten or elementary school at four intervals over a 9-month period in Seoul, Korea. Diverse colonization patterns and a lower level of long-term persistent carriage by H. influenzae status were evident in this study. Colonizing H. influenzae isolates showed a high rate of resistance to β-lactams including ampicillin (51·9%), cefaclor (52·1%), and amoxicillin/clavulanate (16·3%). Based on the ampicillin resistance mechanism, H. influenzae isolates were categorized as β-lactamase-negative, ampicillin-susceptible (BLNAS) (48·1%), β-lactamase-positive, ampicillin-resistant (BLPAR) (22·6%), β-lactamase-negative, ampicillin-resistant (BLNAR) (22·8%), and β-lactamase-positive, amoxicillin/clavulanate-resistant (BLPACR) strains (6·5%). This study provides the first evidence of a high prevalence (22·8%) of BLNAR strains of H. influenzae nasal carriage in healthy children attending kindergarten or the first 2 years of elementary school in Korea. The high carriage of these resistant strains in overcrowded urban settings may create reservoirs for development of H. influenzae-resistant strains.

In August 2011, we investigated an outbreak of Escherichia coli O157 in Plymouth, England, utilizing a case-control study and food traceback. Nine cases, eight laboratory-confirmed with E. coli O157 phage type 21/28 verocytotoxin 2 and one epidemiologically linked, had onsets from 30 July 2011 to 15 August 2011. We compared cases (n = 8) with controls (n = 28) of similar age and sex (median age 61 vs. 55 years, females 75% vs. 61%). Cases were 58 times more likely to have eaten crab (88% vs. 11%; odds ratio 58, 95% confidence interval 4-2700). Eight cases consumed crab sourced from the same supplier who was not registered with the local authority. This outbreak pointed to crab as a possible vehicle of E. coli O157 infection. We ensured the withdrawal of crab meat sourced from unregistered suppliers from food venues by 25 August 2011. We also emphasized the importance of only using registered suppliers to the food venues. Since then no further associated cases have been reported.

Leptospirosis is the major infectious disease on Reunion Island but little is known about the animal reservoir. We conducted a wide-ranging survey that included samples from 574 animals belonging to 12 species. The seroprevalence and prevalence of renal carriage varied greatly depending on the species, with the highest seroprevalence (79·5%) found in Norway rats, and the lowest (13·2%) in tenrecs. The renal carriage rate ranged from 84·6% in mice to 0% in tenrecs. Our results suggest that rodents are the most important reservoirs of leptospirosis on Reunion Island. The epidemiological role that animals play in human infection is discussed. For the first time, we quantified the renal concentration of leptospires in ten naturally infected mammals. The history of Reunion Island colonization probably explains why the circulating Leptospira serogroups were similar to those found in Europe. Our study provides evidence that will help implement preventive measures against this zoonosis.

To identify which medications were most commonly taken by non-pregnancy-related listeriosis patients prior to illness, we compared the medications reported by 512 cases identified via national surveillance in England between 2007 and 2009 with national prescription data, using British National Formulary (BNF) coding. Relative risks and corresponding confidence intervals were calculated, as appropriate, for BNF chapters and sections. Among listeriosis cases, the rates for cytotoxic drugs, drugs affecting the immune response and corticosteroids were significantly higher than for other medications. However, interactions between medications and how medications might confound or be confounded by concurrent medical conditions need to be investigated further. Nevertheless our findings suggest that targeting food-safety advice to prevent this foodborne disease in certain treatment groups is warranted.

This study aimed to determine the seroprevalence of Kaposi's sarcoma-associated herpesvirus (KSHV) and related factors in men who have sex with men (MSM) in China. A total of 208 subjects were recruited from eastern China from 2008 to 2009. Plasma samples were collected and screened for KSHV, HIV and syphilis. Overall, KSHV seroprevalence was 32·7% in the subjects. About 92·7% of subjects reported having ever had anal sex with a man, of whom 67·8% had receptive anal sex and 77·9% had insertive anal sex. About 93·1% of the study participants reported having had oral sex with a man, of whom 76·0% had receptive oral sex and 56·7% had insertive oral sex. KSHV seropositivity was independently associated with receptive anal sex [odds ratio (OR) 2·68, 95% confidence interval (CI) 1·15–6·23], syphilis (OR 3·25, 95% CI 1·56–6·76) and HSV-2 infection (OR 2·40, 95% CI 1·09–5·26). KSHV infection is highly prevalent and is probably sexually transmitted among MSM in eastern China.

We describe nine patients (eight aged <1 year) clinically diagnosed with pertussis yet laboratory-confirmed with Bordetella holmesii infections, a human pathogen normally isolated from blood. Most patients reported cough and cold symptoms. No death was reported. We report B. holmesii isolation in infants with respiratory symptoms in Argentina.

Non-typhoidal Salmonella are an important but poorly characterized cause of paediatric diarrhoea in developing countries. We conducted a hospital-based case-control study in children aged <5 years in Ho Chi Minh City to define the epidemiology and examine risk factors associated with Salmonella diarrhoeal infections. From 1419 diarrhoea cases and 571 controls enrolled between 2009 and 2010, 77 (5·4%) diarrhoea cases were stool culture-positive for non-typhoidal Salmonella. Salmonella patients were more likely to be younger than controls (median age 10 and 12 months, respectively) [odds ratio (OR) 0·97; 95% confidence interval (CI) 0·94–0·99], to report a recent diarrhoeal contact (8·1% cases, 1·8% controls; OR 5·98, 95% CI 1·8–20·4) and to live in a household with >2 children (cases 20·8%, controls 10·2%; OR 2·32, 95% CI 1·2–4·7). Our findings indicate that Salmonella are an important cause of paediatric gastroenteritis in this setting and we suggest that transmission may occur through direct human contact in the home.

In recent years, human leptospirosis has been reported in Jinping and Liping counties, Guizhou province, but the leptospires have never been isolated. To track the source of infection and understand the aetiological characteristics, we performed surveillance for field mice carriage of leptospirosis in 2011. Four strains of leptospire were isolated from Apodemus agrarius. PCR confirmed the four isolates as pathogenic. Multiple-locus variable-number tandem repeat analysis (MLVA) showed that the four strains were closely related to serovar Lai strain 56601 belonging to serogroup Icterohaemorrhagiae, which is consistent with the antibody detection results from local patients. Furthermore, the diversity of leptospiral isolates from different hosts and regions was demonstrated with MLVA. Our results suggest that A. agrarius may be the main carrier of Leptospira in Jinping and Liping counties, and the serogroup Icterohaemorrhagiae serovar may be the epidemic serogroup of Leptospira. This will contribute to the control and prevention of leptospirosis in these localities.