This systematic review–meta-analysis appraises and summarizes all the available research (128 papers) on the zoonotic potential of Mycobacterium avium ssp. paratuberculosis. The latter has been debated for a century due to pathogenic and clinical similarities between Johne's disease in ruminants and Crohn's disease (108 studies) in humans and recently for involvement in other human diseases; human immunodeficiency virus (HIV) infection (2), sarcoidosis (3), diabetes mellitus type 1 (T1DM) (7) and type 2 (3), multiple sclerosis (5) and Hashimoto's thyroiditis (2). Meta-analytical results indicated a significant positive association, consistently across different laboratory methods for Crohn's disease [odds ratio (OR) range 4·26–8·44], T1DM (OR range 2·91–9·95) and multiple sclerosis (OR range 6·5–7·99). The latter two and the thyroiditis hypothesis require further investigation to confirm the association. Meta-regression of Crohn's disease studies using DNA detection methods indicated that choice of primers and sampling frame (e.g. general population vs. hospital-based sample) explained a significant proportion of heterogeneity. Other epidemiological studies demonstrated a lack of association between high-risk occupations and development of Crohn's disease. Due to knowledge gaps in understanding the role of M. paratuberculosis in the development or progression of human disease, the evidence at present is not strong enough to inform the potential public health impact of M. paratuberculosis exposure.

There is limited evidence and lack of consensus whether second-hand smoke (SHS) increases risk of tuberculosis (TB), which has substantial implications for unrestricted smoking indoors and TB control policies. We aimed to establish the association between SHS and the risk of acquiring and worsening of TB in non-smokers. We identified 428 articles in the initial search and 12 comparative epidemiological studies met our inclusion criteria. Exposure to SHS was found to have a higher risk of TB infection [risk ratio (RR) 1·19, 95% confidence interval (CI) 0·90–1·57] compared to non-exposure; however, this did not reach statistical significance. There was marked variability (I2 = 74%, P = 0·0008) between studies’ results, which could be explained by the differences in the diagnostic criteria used. Exposure to SHS was found to be statistically significantly associated (RR 1·59, 95% CI 1·11–2·27) with the risk of TB disease. There was significant heterogeneity (I2 = 77%, P = 0·0006) between studies’ results, which was sourced to the internal characteristics of the studies rather than combining different study designs. We did not find any studies for SHS and TB treatment-related outcomes. Thus, we conclude that SHS exposure may increase the risk of acquiring TB infection and progression to TB disease; however, the evidence remains scanty and weak.

Non-tuberculous mycobacteria (NTM) illness is an emerging life-threatening infection, and paediatric features have not been well studied. The objective of our study was to review the NTM isolates of hospitalized paediatric patients identified at our institution and to describe the characteristics of these cases. Our retrospective chart review from 2010 to 2013 identified 45 patients with 46 positive NTM cultures. Fifteen (33%) patients had received haematopoietic cell transplant, 13 (29%) had cystic fibrosis, and six (13%) were previously healthy. Twenty-seven (59%) NTM isolates were Mycobacterium chelonae/abscessus, 14 (30%) were M. avium intracellulare, and four (9%) were M. immunogenum. The majority (65%) of cases were community-acquired, and 20 (43%) patients were treated as infection. This case series identified a predominance of M. chelonae/abscessus, and includes a substantial number of haematopoietic cell transplant patients, which reflects the changing spectrum of NTM disease as molecular diagnostics improve and quaternary care facilities provide for a larger immunocompromised population.

Despite many years of state-sponsored efforts to eradicate the disease from cattle through testing and slaughter, bovine tuberculosis (bTB) is still regarded as the most important and complex of animal health challenges facing the British livestock agricultural industry. This paper provides a historical analysis of the ongoing bTB statutory eradication programme in one part of the UK – Northern Ireland (NI) – which began in 1949 as a voluntary scheme, but between 1959 and 1960 became compulsory for all cattle herd-owners. Tracing bTB back through time sets the eradication efforts of the present day within a deeper context, and provides signposts for what developed in subsequent decades. The findings are based primarily on empirical research using historical published reports of the Ministry of Agriculture and state documents held in the public archives in NI, and they emphasize the need to consider the economic, social and political contexts of disease eradication efforts and their influences on both the past and the present.

Chitotriosidase, secreted by activated macrophages, is a biomarker of activated macrophages. In this study, we explored whether chitotriosidase could be adopted as a biomarker to evaluate the curative effect on tuberculosis (TB). Five counties were randomly selected out of 122 counties/cities/districts in Hunan Province, China. Our cases were all TB patients who were newly diagnosed or had been receiving treatment at the Centers for Disease Control (CDCs) of these five counties between April and August in 2009. Healthy controls were selected from a community health facility in the Kaifu district of Changsha City after frequency-matching of gender and age with the cases. Chitotriosidase activity was evaluated by a fluorometric assay. Categorical variables were analysed with the χ2 test. Measurement data in multiple groups were tested with analysis of variance and least significant difference (LSD). Correlation between chitotriosidase activity and the degree of radiological extent (DRE) was examined by Spearman's rank correlation test. The average chitotriosidase activity levels of new TB cases, TB cases with different periods of treatment (<3, 3–6, >6 months) and the control group were 54·47, 34·77, 21·54, 12·73 and 10·53 nmol/h.ml, respectively. Chitotriosidase activity in TB patients declined along with the continuity of treatment. The chitotriosidase activity of both smear-positive and the smear-negative pulmonary TB patients decreased after 6 months' treatment to normal levels (P < 0·05). Moreover, chitotriosidase activity was positively correlated with DRE (r = 0·607, P < 0·001). Our results indicate that chitotriosidase might be a marker of TB treatment effects. However, further follow-up study of TB patients is needed in the future.

The incidence of tuberculosis (TB) in native ethnic minorities remains high in developed countries. Arabs, the major ethnic minority in Israel, comprise 21% of its population. This retrospective study compared TB incidence, demographic, clinical, laboratory, genotyping characteristics and treatment outcomes in all Israeli-born citizens diagnosed with TB between 1999 and 2011 by ethnicity, i.e. Israeli-born Arabs (IA) and Jews (IJ). A total of 831 Israeli-born TB patients were reported. Of those, there were 530 (64%) IJ and 301 (36%) IA, with an average annual TB rate of 1·1 and 1·6 cases/100 000 population, respectively, lower than the national average (7·0 cases/100 000 population). TB rates in IA and IJ declined and converged to 1 case/100 000 residents. IA TB patients were more likely to be older, have more pulmonary TB and have lower treatment success rates than IJ. Older age and HIV co-infection, but not ethnicity, were predictive of non-success in TB treatment. Ten mixed IA–IJ clades were detected by spoligotyping and three mixed IA–IJ clusters were identified by MIRU-VNTR typing. Only one IA–IJ couple recalled mutual contact. In conclusion, TB rate in IA was higher than in IJ, but declined and converged in both to 1 case/100 000. Treatment success was high in both groups, and was unrelated to ethnicity.

Portugal, a medium- to low-level endemic country (21·6 cases/100 000 population in 2012), has one of the highest European Union tuberculosis (TB) incidences. Although incidence is declining progressively, the country's heterogeneity in both regional endemics and their evolution suggests the importance of a better understanding of subnational epidemiology to customize TB control efforts. We aimed to update knowledge on municipality-years pulmonary TB incidence clustering, identify areas with different time trends, and show the potential of combining complementary clustering methods in control of infectious diseases. We used national surveillance municipality-level data (mainland Portugal, 2000–2010). Space–time clustering and spatial variation in temporal trends methods were applied. Space–time critical clusters identified (P < 0·001) were still the Lisbon and Oporto regions. The global incidence declined at a 5·81% mean annual percentage change, with high space–time heterogeneity and distinct time trend clusters (P < 0·001). Municipalities with incidences declining more rapidly belonged to critical areas. In particular, the Oporto trend cluster had a consistent −8·98% mean annual percentage change. Large space–time heterogeneities were identified, with critical incidences in the greater Lisbon and Oporto regions, but declining more rapidly in these regions. Oporto showed a consistent, steeper decrease and could represent a good example of local control strategy. Combining results from these approaches gives promise for prospects for infectious disease control and the design of more effective, focused interventions.

A tuberculosis (TB) case was reported May 2008 in Kelowna, British Columbia, leading to a multi-year outbreak in homeless persons. The epidemiological characteristics and social networks of cases are described. Outbreak-related cases were identified from epidemiological information in medical records and from genotyping of TB isolates. Social network information from case interviews were used to identify potential locations of TB transmission, where symptom screening and tuberculin skin testing was conducted. Fifty-two cases that were predominantly male (47/52), Canadian-born (44/50), and were homeless or associated with homeless individuals (42/52) were reported from May 2008 to May 2014. Many isolates (40/49) had partial resistance to isoniazid. Transmission primarily occurred at two homeless shelters, with potential further transmission at sites visited by the general population. TB outbreaks in homeless populations can occur in small, low-incidence cities. Social network information helped prioritize sites for TB screening, thereby improving detection of persons with TB disease or latent infection for treatment.

On 23 May 2011, CDC identified a multistate cluster of Salmonella Heidelberg infections and two multidrug-resistant (MDR) isolates from ground turkey retail samples with indistinguishable pulsed-field gel electrophoresis patterns. We defined cases as isolation of outbreak strains in persons with illness onset between 27 February 2011 and 10 November 2011. Investigators collected hypothesis-generating questionnaires and shopper-card information. Food samples from homes and retail outlets were collected and cultured. We identified 136 cases of S. Heidelberg infection in 34 states. Shopper-card information, leftover ground turkey from a patient's home containing the outbreak strain and identical antimicrobial resistance profiles of clinical and retail samples pointed to plant A as the source. On 3 August, plant A recalled 36 million pounds of ground turkey. This outbreak increased consumer interest in MDR Salmonella infections acquired through United States-produced poultry and played a vital role in strengthening food safety policies related to Salmonella and raw ground poultry.

Over the past two decades Clostridium difficile infection (CDI) has appeared as a major public health threat. We performed a retrospective study based on the records of patients hospitalized for CDI at the University Hospital in Krakow, Poland, between 2008 and 2014. In the study period, CDI occurred in 1009 individuals. There were 790 (78%) individuals who developed infection only once, whereas 219 (22%) developed infection more than once. The percentage of deaths within 14 days of CDI confirmation was 2·4%, with a mean age of 74·2 ± 15·9 years. Crude mortality was 12·9% in medical wards, 5·6% for surgical wards and 27·7% in the ICU setting. The time span between diagnosis and death was 5·1 days on average. Between 2008 and 2012 a 6·5-fold increase of CDI frequency with a posterior stabilization and even reduction in 2013 and 2014 was observed. According to the data analysed, 2/3 patients in our population developed CDI during their hospitalization even though they were admitted for different reasons. Medical wards pose a significantly higher risk of CDI than the surgical ones. Age is a risk factor for CDI recurrence. In the case of patients who died, death occurred shortly after diagnosis. The first CDI episode poses much higher risk of mortality than the consecutive ones.

This study aims to describe in detail the temporal dynamics of E. coli O157 shedding and risk factors for shedding in a grass-fed beef herd. During a 9-month period, 23 beef cows were sampled twice a week (58 sampling points) and E. coli O157 was enumerated from faecal samples. Isolates were screened by PCR for presence of rfbE, stx1 and stx2. The prevalence per sampling day ranged from 0% to 57%. This study demonstrates that many members of the herd were concurrently shedding E. coli O157. Occurrence of rainfall (P < 0·01), feeding silage (P < 0·01) and lactating (P < 0·01) were found to be predictors of shedding. Moving cattle to a new paddock had a negative effect on shedding. This approach, based on short-interval sampling, confirms the known variability of shedding within a herd and highlights that high shedding events are rare.

Although cattle movement and commingling play an important role in the inter-herd transmission of pathogens, little is known about the effect of commingling of heifers at raising operations. The objective of this study was to compare the resistance of E. coli and prevalence of Salmonella from pooled faecal pats of heifers raised off-farm at multi-source raisers (MULTI) that raised heifers from at least two farms compared with on-farm raisers (HOME), with heifers from only that farm. MULTI faecal pat samples were collected from pens with animals that had arrived at the farm within the previous 2 months (AP) and from animals that would be departing the heifer raiser in 2–3 months (DP). Corresponding age sampling was conducted at HOME raisers. Odds of ampicillin resistance were 3·0 times greater in E. coli collected from MULTI compared to HOME raisers. E. coli from AP pens had significantly (P < 0·05) higher odds of resistance to ampicillin, neomycin, streptomycin, and tetracycline compared to DP pens. Salmonella recovery was not significantly different between heifer-raising systems (P = 0·3). Heifer-raising system did not have a major overall impact on selection of resistant E. coli, which was strongly affected by the age of the animals sampled.

The study characterizes a collection of 67 neonatal septicaemic Escherichia coli isolates on the basis of phylogroup, serotype, virulence, antibiotic resistance and also the association of CTX-M-producing E. coli and the ST131 clone in a developing country. Phylogroups B2 and D were predominant (33% and 19%, respectively). The most prevalent virulence factors (VFs) were traT (69%) and iucC (68%) and most VFs were concentrated in the B2 isolates. High levels of resistance (⩾70%) to cefotaxime, ciprofloxacin and trimethoprim/sulfamethoxazole was recorded but meropenem remained the most active antimicrobial. Six (9%) of the study isolates belonged to the ST131 clone, five of which were from the same hospital, and were either indistinguishable or closely related by pulsed-field gel electrophoresis. Although the prevalence of CTX-M-15-producing isolates was high (81%), the ST131 clone was relatively infrequent (11%) in extended spectrum β-lactamase (ESBL)-producers. The ST131 clone was characterized by the presence of blaCTX-M-15, qnrS, aac(6′)-Ib-cr, IncF plasmids and virulence determinants such as iucC, papC, traT, usp, hlyA, iroNE.coli, cnf, and sat. We conclude that clonal spread of ST131 did not contribute directly to the high prevalence of CTX-M-15 in our settings.

Giardia spp. is a common gastrointestinal (GI) parasite of multiple host species, including dogs and humans, with the potential for zoonotic transmission. The risk of GI parasitism in dogs (including Giardia spp.) may increase with park use in urban areas. This study aimed to (1) determine whether park attendance is a risk factor for Giardia spp. infection in dogs and (2) characterize the behavioural and demographic risk factors for Giardia spp. infection in park-attending and non-park-attending dogs. From August to September 2012, a total of 1293 dog owners completed a survey and 860 corresponding dog faecal samples were collected. Dog faeces were screened for Giardia spp. using a direct immunofluorescence assay and associations assessed among behaviours, demographics, and Giardia spp. infection. Main results included off-leash and swimming frequencies within parks as significantly positively associated with Giardia spp. infection in dogs. Dog-owner age was negatively associated with off-leash and swimming frequencies in parks. The results suggest some recreational behaviours in parks and certain demographics are risk factors for parasitism in pet dogs.

Norovirus (NV) is an important cause of acute gastroenteritis in children, but is also frequently detected in asymptomatic children, which complicates the interpretation of NV detection results in both the clinical setting and population prevalence studies. A total of 807 faecal samples from children aged <5 years hospitalized for acute gastroenteritis were collected in Thai Binh, Vietnam, from January 2011 to September 2012. Real-time RT–PCR was used to detect and quantify NV-RNA in clinical samples. A bimodal distribution of cycle threshold (Ct) values was observed in which the lower peak was assumed to represent cases for which NV was the causal agent of diarrhoea, whereas the higher peak was assumed to represent cases involving an alternative pathogen other than NV. Under these assumptions, we applied finite-mixture modelling to estimate a threshold of Ct <21·36 (95% confidence interval 20·29–22·46) to distinguish NV-positive patients for which NV was the likely cause of diarrhoea. We evaluated the validity of the threshold through comparisons with NV antigen ELISA results, and comparisons of Ct values in patients co-infected with rotavirus. We conclude that the use of an appropriate cut-off value in the interpretation of NV real-time RT–PCR results may improve differential diagnosis of enteric infections, and could contribute to improved estimates of the burden of NV disease.

Few countries routinely collect comprehensive encephalitis data, yet understanding the epidemiology of this condition has value for clinical management, detecting novel and emerging pathogens, and guiding timely public health interventions. When this study was conducted there was no standardized diagnostic algorithm to aid identification of encephalitis or systematic surveillance for adult encephalitis. In July 2012 we tested three pragmatic surveillance options aimed at identifying possible adult encephalitis cases admitted to a major Australian hospital: hospital admissions searches, clinician notifications and laboratory test alerts (CSF herpes simplex virus requests). Eligible cases underwent structured laboratory investigation and a specialist panel arbitrated on the final diagnosis. One hundred and thirteen patients were initially recruited into the 10-month study; 20/113 (18%) met the study case definition, seven were diagnosed with infectious or immune-mediated encephalitis and the remainder were assigned alternative diagnoses. The laboratory alert identified 90% (102/113) of recruited cases including six of the seven cases of confirmed encephalitis suggesting that this may be a practical data source for case ascertainment. The application of a standardized diagnostic algorithm and specialist review by an expert clinical panel aided diagnosis of patients with encephalitis.

Reporting of percutaneous injuries (PIs) to the Chinese Exposure Prevention Information Network (EPINet) became mandatory for all public and tertiary referral hospitals in Taiwan in 2011. We have estimated the number of microbially contaminated PIs and the national PI incidence using a retrospective secondary data analysis approach to analyse 2011 data from the Chinese EPINet to determine the types of PI, mechanisms of occurrence and associated risks. The results revealed a national estimate of PIs between 6710 and 8319 in 2011. The most common incidents for physicians were disposable syringes, suture needles, and disposable scalpels; while for nurses they were disposable syringes, intravenous catheters, and lancets. About 13·0% of the source patients were seropositive for hepatitis B virus (HBV) surface antigen, 13·8% were seropositive for hepatitis C virus (HCV), and 1·1% seropositive for human immunodeficiency virus (HIV). From these results we estimate that annually 970 full-time healthcare workers (HCWs) would be exposed to HBV, 1094 to HCV, and 99 to HIV. This study improves our understanding of the mechanisms and risks of PIs and informs the development of more efficient preventive measures to protect HCWs from such injuries.

Ruminants are considered the main reservoir for transmission of Coxiella burnetii (Cb) to humans. The implementation of effective control measures against Cb in ruminants requires knowledge about potential risk factors. The objectives of this study were (i) to describe the spatial distribution of Q fever-infected dairy cattle herds in Sweden, (ii) to quantify the respective contributions of wind and animal movements on the risk of infection, while accounting for other sources of variation, and (iii) to investigate the possible protective effect of precipitation. A total of 1537 bulk milk samples were collected and tested for presence of Cb antibodies. The prevalence of test-positive herds was higher in the south of Sweden. For herds located in areas with high wind speed, open landscape, high animal densities and high temperature, the risk of being infected reached very high values. Because these factors are difficult to control, vaccination could be an appropriate control measure in these areas. Finally, the cumulated precipitation over 1 year was identified as a protective factor.

Mycoplasma infections are most frequently associated with disease in the urogenital or respiratory tracts and, in most cases, mycoplasmas infect the host persistently. In HIV-infected individuals the prevalence and role of genital mycoplasmas has not been well studied. To investigate the six species of Mycoplasma and the risk factors for infection in Jiangsu province, first-void urine and venous blood samples were collected and epidemiological questionnaires were administered after informed consent. A total of 1541 HIV/AIDS patients were recruited in this study. The overall infection rates of six Mycoplasma species were: Ureaplasma urealyticum (26·7%), Mycoplasma hominis (25·3%), M. fermentans (5·1%), M. genitalium (20·1%), M. penetrans (1·6%) and M. pirum (15·4%). The Mycoplasma infection rate in the unmarried group was lower than that of the married, divorced and widowed groups [adjusted odds ratio (aOR) 1·432, 95% confidence interval (CI) 1·077–1·904, P < 0·05]. The patients who refused highly active antiretroviral therapy (HAART) had a much higher risk of Mucoplasma infection (aOR 1·357, 95% CI 1·097–1·679, P < 0·05). Otherwise, a high CD4+ T cell count was a protective factor against Mycoplasma infection (aOR 0·576, 95% CI 0·460–0·719, P < 0·05). Further research will be required to confirm a causal relationship and to identify risk factors for Mycoplasma infection in HIV/AIDS populations.

The goal of this study was to determine the reduction in risk of infection by viruses with the use of an alcohol-based hand sanitizer, used in addition to routine hand washing, in family members in households. A quantitative microbial risk model was used to determine the probability of infection from the concentration of virus on the hands. The model incorporated variation in hand size, frequency of touching orifices (nose, mouth, eyes), and percent transfer to the site of infection, as well as, dose-response for each virus. Data on the occurrence of virus on household members' hands from an intervention study using MS-2 coliphage was used to determine the reduction of viruses on the hands pre- and post-intervention. It was found that the risk of rhinovirus, rotavirus or norovirus infection after the intervention was reduced by 47–98% depending upon the initial concentration of virus on the hands.