Infection Ecology and Epidemiology最新文献

{"title":"A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda","authors":"A. Blomström, C. Lalander, A. Komakech, B. Vinnerås, S. Boqvist","doi":"10.3402/iee.v6.32453","DOIUrl":"https://doi.org/10.3402/iee.v6.32453","url":null,"abstract":"Background Vermicomposting is a mesophilic process using earthworms to efficiently and at low cost process large volumes of organic waste. It has been suggested to not only increase soil fertility but also increase biomass of beneficial bacteria while reducing harmful bacteria. The aim of this study was to set up a strategy to investigate and characterise the viral as well as the bacterial composition of a vermicomposting system. Material and methods The vermicomposting unit used in this study was placed at the Makerere University Agricultural Research Institute Kabanyolo on the outskirts of Kampala, Uganda, and was fed with 80% cattle manure and 20% food waste. On Day 172, the compost was terminated and compost samples were collected from three layers of the unit: the top, the middle and the bottom layer. A metagenomic approach was then applied to characterise the viral and bacterial composition of the vermicomposting system. Results and discussion A high abundance and diversity of bacteria were identified. Proteobacteria was the largest phyla in the compost (mainly Alpha-, Gamma- and Betaproteobacteria), constituting almost 65% of the bacterial reads in the data sets. DNA samples from several possible pathogenic bacteria, such as Salmonella spp., Escherichia coli, Enterobacter spp., Enterococcus spp. and Clostridium spp, were detected in the vermicompost, suggesting that there might still be harmful bacteria in the vermicast. Phages constituted the main viral group; apart from phages, mainly insect viruses were identified. The only animal or human virus identified was kobuvirus. In summary, metagenomic analysis was shown to be an efficient technology to characterise the microbial composition of vermicast. The data from this study contribute to a better understanding of the microbes present in this kind of composting system and can help determine measures necessary for safe manure handling.","PeriodicalId":37446,"journal":{"name":"Infection Ecology and Epidemiology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3402/iee.v6.32453","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69759529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anthropogenic antibiotic resistance genes mobilization to the polar regions","authors":"J. Hernández, D. GONZÁLEZ-ACUÑA","doi":"10.3402/iee.v6.32112","DOIUrl":"https://doi.org/10.3402/iee.v6.32112","url":null,"abstract":"Anthropogenic influences in the southern polar region have been rare, but lately microorganisms associated with humans have reached Antarctica, possibly from military bases, fishing boats, scientific expeditions, and/or ship-borne tourism. Studies of seawater in areas of human intervention and proximal to fresh penguin feces revealed the presence of Escherichia coli strains least resistant to antibiotics in penguins, whereas E. coli from seawater elsewhere showed resistance to one or more of the following antibiotics: ampicillin, tetracycline, streptomycin, and trim-sulfa. In seawater samples, bacteria were found carrying extended-spectrum β-lactamase (ESBL)-type CTX-M genes in which multilocus sequencing typing (MLST) showed different sequence types (STs), previously reported in humans. In the Arctic, on the contrary, people have been present for a long time, and the presence of antibiotic resistance genes (ARGs) appears to be much more wide-spread than was previously reported. Studies of E coli from Arctic birds (Bering Strait) revealed reduced susceptibility to antibiotics, but one globally spreading clone of E. coli genotype O25b-ST131, carrying genes of ESBL-type CTX-M, was identified. In the few years between sample collections in the same area, differences in resistance pattern were observed, with E. coli from birds showing resistance to a maximum of five different antibiotics. Presence of resistance-type ESBLs (TEM, SHV, and CTX-M) in E. coli and Klebsiella pneumoniae was also confirmed by specified PCR methods. MLST revealed that those bacteria carried STs that connect them to previously described strains in humans. In conclusion, bacteria previously related to humans could be found in relatively pristine environments, and presently human-associated, antibiotic-resistant bacteria have reached a high global level of distribution that they are now found even in the polar regions.","PeriodicalId":37446,"journal":{"name":"Infection Ecology and Epidemiology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3402/iee.v6.32112","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69758949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Introduction and persistence of tularemia in Bulgaria","authors":"Kerstin Myrtennäs, K. Marinov, A. Johansson, M. Niemcewicz, E. Karlsson, M. Byström, M. Forsman","doi":"10.3402/iee.v6.32838","DOIUrl":"https://doi.org/10.3402/iee.v6.32838","url":null,"abstract":"Introduction Outbreaks of the zoonotic disease tularemia occurred in north-east Bulgaria in the 1960s. Then came 30 years of epidemiological silence until new outbreaks occurred in west Bulgaria in the 1990s. To investigate how bacterial strains of Francisella tularensis causing tularemia in wildlife and humans in the 1960s and the 1990s were related, we explored their genetic diversity. Material and methods Ten F. tularensis genomes from the 1960s (n=3) and the 1990s (n=7) were sequenced, assigned to canonical single-nucleotide polymorphism (canSNP) clades, and compared to reference genomes. We developed four new canSNP polymerase chain reaction (PCR) assays based on the genome sequence information. Results and discussion The genetic analysis showed that the outbreaks in the 1960s as well as in the 1990s involved multiple clones and new genetic diversity. The smallest genetic difference found between any of the Bulgarian strains was five SNPs between the strains L2 and 81 isolated 43 years apart, indicating that F. tularensis may persist locally over long time periods without causing outbreaks. The existence of genetically highly similar strain-pairs isolated the same year in the same area from different hosts supports a hypothesis of local expansion of clones during outbreaks. Close relationship (two SNPs) was found between one strain isolated 1961 in northeast Bulgaria and one strain isolated 5 years before in USSR. Historical data coinciding with the actual time point describe the introduction of water rats from USSR into the Bulgarian outbreak area, which may explain the close genetic relationship and the origin of the outbreak. Conclusion Genome analysis of strains from two outbreaks in the 1960s and the 1990s provided valuable information on the genetic diversity and persistence of F. tularensis in Bulgaria.","PeriodicalId":37446,"journal":{"name":"Infection Ecology and Epidemiology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3402/iee.v6.32838","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69759774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"One Health research and training and government support for One Health in South Asia","authors":"J. McKenzie, Rojan Dahal, M. Kakkar, N. Debnath, Mahmudur Rahman, Sithar Dorjee, Khalid Naeem, T. Wijayathilaka, B. Sharma, Nasir Maidanwal, A. Halimi, Eunmi Kim, P. Chatterjee, B. Devleesschauwer","doi":"10.3402/iee.v6.33842","DOIUrl":"https://doi.org/10.3402/iee.v6.33842","url":null,"abstract":"Introduction Considerable advocacy, funding, training, and technical support have been provided to South Asian countries to strengthen One Health (OH) collaborative approaches for controlling diseases with global human pandemic potential since the early 2000s. It is essential that the OH approach continues to be strengthened given South Asia is a hot spot for emerging and endemic zoonotic diseases. The objectives of this article are to describe OH research and training and capacity building activities and the important developments in government support for OH in these countries to identify current achievements and gaps. Materials and methods A landscape analysis of OH research, training, and government support in South Asia was generated by searching peer-reviewed and grey literature for OH research publications and reports, a questionnaire survey of people potentially engaged in OH research in South Asia and the authors’ professional networks. Results Only a small proportion of zoonotic disease research conducted in South Asia can be described as truly OH, with a significant lack of OH policy-relevant research. A small number of multisectoral OH research and OH capacity building programmes were conducted in the region. The governments of Bangladesh and Bhutan have established operational OH strategies, with variable progress institutionalising OH in other countries. Identified gaps were a lack of useful scientific information and of a collaborative culture for formulating and implementing integrated zoonotic disease control policies and the need for ongoing support for transdisciplinary OH research and policy-relevant capacity building programmes. Discussion Overall we found a very small number of truly OH research and capacity building programmes in South Asia. Even though significant progress has been made in institutionalising OH in some South Asian countries, further behavioural, attitudinal, and institutional changes are required to strengthen OH research and training and implementation of sustainably effective integrated zoonotic disease control policies.","PeriodicalId":37446,"journal":{"name":"Infection Ecology and Epidemiology","volume":"67 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3402/iee.v6.33842","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69760262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"One Health capacity building in sub-Saharan Africa","authors":"I. Rwego, Olutayo Olajide Babalobi, Protus Musotsi, S. Nzietchueng, Christian K. Tiambo, J. Kabasa, I. Naigaga, G. Kalema‐Zikusoka, K. Pelican","doi":"10.3402/iee.v6.34032","DOIUrl":"https://doi.org/10.3402/iee.v6.34032","url":null,"abstract":"Background Africa of late has been faced with challenges that require a multidisciplinary and multisectoral approach to address them, and academic and non-academic institutions have played a key role in training and conducting research that would promote the One Health approach. Objectives The objective of this review was to document networks and organizations conducting One Health training, research, and outreach in Africa, as one of a series of articles around the world. Methods Data for this review were collected from organizations through key contacts of the authors and their knowledge of networks they have worked with. Web searches were conducted using One Health, training, and research as key words for work done in Africa. Results Africa has major networks involved in One Health training, research, and outreach, with participation of both academic and non-academic institutions. This review highlights an effort in Africa to form networks to conduct multidisciplinary training and research. The main networks include Afrique One, Southern African Centre for Infectious Disease Surveillance (SACIDS), and One Health Central and Eastern Africa (OHCEA). Conclusions Both academic and non-academic institutions and organizations have shown an interest to conduct multidisciplinary training and research in Africa for managing challenges that Africa is facing currently, especially the outbreak of infectious diseases.","PeriodicalId":37446,"journal":{"name":"Infection Ecology and Epidemiology","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3402/iee.v6.34032","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69761135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"One Health research and training in Australia and New Zealand","authors":"S. Reid, J. McKenzie, S. Woldeyohannes","doi":"10.3402/iee.v6.33799","DOIUrl":"https://doi.org/10.3402/iee.v6.33799","url":null,"abstract":"Purpose of the review This review was performed to create a repository of information on One Health research and training in Australia and New Zealand (ANZ). The review sought to determine 1) how many training activities there are in ANZ, 2) how much research on zoonotic diseases is undertaken by multidisciplinary teams, and 3) how collaborative and integrated they are. Recent findings There are few opportunities for training in One Health in ANZ. The majority require enrolment in a postgraduate degree programme, and there is only one postgraduate level course that is also available for continuing professional development (CPD). Of the broad range of One Health research performed in ANZ, the majority is performed by teams with limited disciplinary diversity, although diversity is improving. Summary Progress has been made in building collaboration between human, animal, and environmental health professions. However, the lack of clearly defined competencies and agreed purpose for One Health may be impeding collaboration.","PeriodicalId":37446,"journal":{"name":"Infection Ecology and Epidemiology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3402/iee.v6.33799","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69760563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Campylobacter growth rates in four different matrices: broiler caecal material, live birds, Bolton broth, and brain heart infusion broth","authors":"Tara Battersby, D. Walsh, P. Whyte, D. Bolton","doi":"10.3402/iee.v6.31217","DOIUrl":"https://doi.org/10.3402/iee.v6.31217","url":null,"abstract":"Background The objective of this study was to characterise Campylobacter growth in enrichment broths (Bolton broth, brain heart infusion broth), caecal material (in vitro), and in the naturally infected live broilers (in vivo) in terms of mean lag periods and generation times as well as maximum growth rates and population (cell concentration) achieved. Methods Bolton and brain heart infusion broths and recovered caecal material were inoculated with 10 poultry strains of Campylobacter (eight Campylobacter jejuni and two Campylobacter coli), incubated under microaerobic conditions, and Campylobacter concentrations determined periodically using the ISO 10272:2006 method. Caeca from 10 flocks, infected at first thinning, were used to characterise Campylobacter growth in the live birds. Mean generation times (G) (early lag to exponential phase) were calculated using the formula: G=t/3.3 logb/B. Mean lag times and µmax were calculated using the Micro Fit© Software (Version 1.0, Institute of Food Research). Statistical comparison was performed using GENSTAT ver. 14.1 (VSN International Ltd., Hemel, Hempstead, UK). Results The mean lag periods in Bolton broth, brain heart infusion broth, caecal material, and in the live bird were estimated to be 6.6, 6.7, 12.6, and 31.3 h, respectively. The corresponding mean generation times were 2.1, 2.2, 3.1, and 6.7 h, respectively; maximum growth rates were 0.7, 0.8, 0.4, and 2 generations h−1 and the maximum populations obtained in each matrix were 9.6, 9.9, 7.8, and 7.4 log10 CFU/g, respectively. Conclusion This study provides data on the growth of Campylobacter in a range of laboratory media, caecal contents, and in broilers which may be used to develop predictive models and/or inform science-based control strategies such as the maximum time between flock testing and slaughter, logistical slaughter, and single-stage depopulation of broiler units.","PeriodicalId":37446,"journal":{"name":"Infection Ecology and Epidemiology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3402/iee.v6.31217","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69758693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular detection and characterization of Brucella species in raw informally marketed milk from Uganda","authors":"T. Hoffman, K. Rock, D. Mugizi, S. Muradrasoli, Elisabeth Lindahl-Rajala, J. Erume, U. Magnusson, Å. Lundkvist, S. Boqvist","doi":"10.3402/iee.v6.32442","DOIUrl":"https://doi.org/10.3402/iee.v6.32442","url":null,"abstract":"This study identified and characterized Brucella species in the informal milk chain in Uganda. A total of 324 cattle bulk milk samples were screened for the genus Brucella by real-time PCR with primers targeting the bcsp31 gene and further characterized by the omp25 gene. Of the samples tested, 6.5% were positive for Brucella species. In the omp25 phylogeny, the study sequences were found to form a separate clade within the branch containing B. abortus sequences. The study shows that informally marketed cattle milk in Uganda is a likely risk factor for human brucellosis and confirms that B. abortus is present in the cattle population. This information is important for potential future control measures, such as vaccination of cattle.","PeriodicalId":37446,"journal":{"name":"Infection Ecology and Epidemiology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3402/iee.v6.32442","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69759334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"WHO reform: bring back GOARN and Task Force ‘Scorpio’","authors":"J. Woodall","doi":"10.3402/iee.v6.30237","DOIUrl":"https://doi.org/10.3402/iee.v6.30237","url":null,"abstract":"WHO’s Director-General recently put the socalled failure of WHO to respond rapidly and adequately to the Ebola epidemic squarely on the shoulders of the member states, who year after year have restricted WHO’s budget options and never contributed to the emergency fund that was called for after the H1N1 influenza scare in 2009. (Published: 8 February 2016) Citation: Infection Ecology and Epidemiology 2016, 6: 30237 - http://dx.doi.org/10.3402/iee.v6.30237","PeriodicalId":37446,"journal":{"name":"Infection Ecology and Epidemiology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3402/iee.v6.30237","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69757871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seroepidemiology of toxoplasmosis in rural and urban communities from Los Rios Region, Chile","authors":"C. Munoz-Zanzi, C. Campbell, Sergey S. Berg","doi":"10.3402/iee.v6.30597","DOIUrl":"https://doi.org/10.3402/iee.v6.30597","url":null,"abstract":"Background Toxoplasmosis is a prevalent protozoan infection with a complex lifecycle and wide profile of risk factors. The impact of congenital infection is well documented; however, there is increasing evidence of a much broader range of potential health outcomes and the need to improve our understanding of the transmission patterns and infection sources in the overall population. This study examined the epidemiology of toxoplasmosis in distinct community types from a highly endemic area of Chile. Methods A cross-sectional serosurvey was carried out in households from urban slums, rural villages, and farms which included collection of blood samples, as well as data on sociodemographic, behavioral, and spatial variables. Blood samples were analyzed for the presence of T. gondii-specific IgG antibodies. Avidity index was obtained for IgG-positive samples. Mixed-effects regression modeling was used to identify associations with relevant risk factors. Results Crude seroprevalence was 55.9% (95% CI: 52.6–59.1%) with no difference by community type. Results are indicative of early exposure to the parasite, including 40% of 13- to 17-year olds who were already seropositive. Sociodemographic factors associated with seropositivity included age, occupations, and income. However, sex modified the effect of occupation as well as of income. Practices associated with increased seropositivity were consumption of sheep and locally produced vegetables as well as cleaning household barns or sheds. Boiling water for household use was a protective factor. Living on a sloped terrain without vegetation was a protective factor, while living in an area with high flow accumulation index was a risk factor. Conclusions Seroprevalence of infection was high in both rural and urban slum communities with unique risk factor profiles for each community type. Findings highlight the role of the household and the community environment as influential factors in the epidemiology of the infection. Increasing awareness is needed at the health care and public health levels to establish disease burden and options for suitable control programs.","PeriodicalId":37446,"journal":{"name":"Infection Ecology and Epidemiology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3402/iee.v6.30597","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69758070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}