Using amplicon sequencing of rpoB for identification of inoculant rhizobia from peanut nodules

To improve the nitrogen fixation, legume crops are often inoculated with selected effective rhizobia. However, there is large variation in how well the inoculant strains compete with the indigenous microflora in soil. To assess the success of the inoculant, it is necessary to distinguish it from other, closely related strains. Methods used until now have generally been based either on fingerprinting methods or on the use of reporter genes. Nevertheless, these methods have their shortcomings, either because they do not provide sufficiently specific information on the identity of the inoculant strain, or because they use genetically modified organisms that need prior authorization to be applied in the field or other uncontained environments. Another possibility is to target a gene that is naturally present in the bacterial genomes. Here we have developed a method that is based on amplicon sequencing of the bacterial housekeeping gene rpoB, encoding the beta-subunit of the RNA polymerase, which has been proposed as an alternative to the 16S rRNA gene to study the diversity of rhizobial populations in soils. We evaluated the method under laboratory and field conditions. Peanut seeds were inoculated with various Bradyrhizobium strains. After nodule development, DNA was extracted from selected nodules and the nodulating rhizobia were analysed by amplicon sequencing of the rpoB gene. The analyses of the sequence data showed that the method reliably identified bradyrhizobial strains in nodules, at least at the species level, and could be used to assess the competitiveness of the inoculant compared to other bradyrhizobia.

Risk Assessment for the Transmission of Middle East Respiratory Syndrome Coronavirus (MERS-Cov) on Aircraft: A Systematic Review

Middle East respiratory syndrome coronavirus (MERS-CoV) causes a potentially fatal respiratory disease. Although it is most common in the Arabian Peninsula, it has been exported to 17 countries outside the Middle East, mostly through air travel. The Risk Assessment Guidelines for Infectious Diseases transmitted on Aircraft (RAGIDA) advise authorities on measures to take when an infected individual travelled by air. The aim of this systematic review was to gather all available information on documented MERS-CoV cases that had travelled by air, to update RAGIDA. The databases used were PubMed, Embase, Scopus and Global Index Medicus; Google was searched for grey literature and hand searching was performed on the EU Early Warning and Response System and the WHO Disease Outbreak News. Forty-seven records were identified, describing 21 cases of MERS that had travelled on 31 flights. Contact tracing was performed for 17 cases. Most countries traced passengers sitting in the same row and the two rows in front and behind the case. Only one country decided to trace all passengers and crew. No cases of in-flight transmission were observed; thus, considering the resources it requires, a conservative approach may be appropriate when contact tracing passengers and crew where a case of MERS has travelled by air.

Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care

OBJECTIVES

Hospital-based surveillance of influenza and acute respiratory infections relies on International Classification of Diseases (ICD) codes and hospital laboratory reports (Standard-of-Care). It is unclear how many cases are missed with either method, i.e. remain undiagnosed/coded as influenza and other respiratory virus infections. Various influenza-like illness (ILI) definitions co-exist with little guidance on how to use them. We compared the diagnostic accuracy of standard surveillance methods with a prospective quality management (QM) programme at a Berlin children's hospital with the Robert Koch Institute.

METHODS

Independent from routine care, all patients fulfilling pre-defined ILI-criteria (QM-ILI) participated in the QM programme. A separate QM team conducted standardized clinical assessments and collected nasopharyngeal specimens for blinded real-time quantitative PCR for influenza A/B viruses, respiratory syncytial virus, adenovirus, rhinovirus and human metapneumovirus.

RESULTS

Among 6073 individuals with ILI qualifying for the QM programme, only 8.7% (528/6073) would have undergone virus diagnostics during Standard-of-Care. Surveillance based on ICD codes would have missed 61% (359/587) of influenza diagnoses. Of baseline ICD codes, 53.2% (2811/5282) were non-specific, most commonly J06 ('acute upper respiratory infection'). Comparison of stakeholder case definitions revealed that QM-ILI and the WHO ILI case definition showed the highest overall sensitivities (84%-97% and 45%-68%, respectively) and the CDC ILI definition had the highest sensitivity for influenza infections (36%, 95% CI 31.4-40.8 for influenza A and 48%, 95% CI 40.5-54.7 for influenza B).

CONCLUSIONS

Disease-burden estimates and surveillance should account for the underreporting of cases in routine care. Future studies should explore the effect of ILI screening and surveillance in various age groups and settings. Diagnostic algorithms should be based on the WHO ILI case definition combined with targeted testing.

Start of the 2014/15 influenza season in Europe: drifted influenza A(H3N2) viruses circulate as dominant subtype

The influenza season 2014/15 started in Europe in week 50 2014 with influenza A(H3N2) viruses predominating. The majority of the A(H3N2) viruses characterised antigenically and/or genetically differ from the northern hemisphere vaccine component which may result in reduced vaccine effectiveness for the season. We therefore anticipate that this season may be more severe than the 2013/14 season. Treating influenza with antivirals in addition to prevention with vaccination will be important.

Human-Dromedary Camel Interactions and the Risk of Acquiring Zoonotic Middle East Respiratory Syndrome Coronavirus Infection

Middle East respiratory syndrome coronavirus (MERS‐CoV) cases without documented contact with another human MERS‐CoV case make up 61% (517/853) of all reported cases. These primary cases are of particular interest for understanding the source(s) and route(s) of transmission and for designing long‐term disease control measures. Dromedary camels are the only animal species for which there is convincing evidence that it is a host species for MERS‐CoV and hence a potential source of human infections. However, only a small proportion of the primary cases have reported contact with camels. Other possible sources and vehicles of infection include food‐borne transmission through consumption of unpasteurized camel milk and raw meat, medicinal use of camel urine and zoonotic transmission from other species. There are critical knowledge gaps around this new disease which can only be closed through traditional field epidemiological investigations and studies designed to test hypothesis regarding sources of infection and risk factors for disease. Since the 1960s, there has been a radical change in dromedary camel farming practices in the Arabian Peninsula with an intensification of the production and a concentration of the production around cities. It is possible that the recent intensification of camel herding in the Arabian Peninsula has increased the virus' reproductive number and attack rate in camel herds while the ‘urbanization’ of camel herding increased the frequency of zoonotic ‘spillover’ infections from camels to humans. It is reasonable to assume, although difficult to measure, that the sensitivity of public health surveillance to detect previously unknown diseases is lower in East Africa than in Saudi Arabia and that sporadic human cases may have gone undetected there.

Comparing introduction to Europe of highly pathogenic avian influenza viruses A(H5N8) in 2014 and A(H5N1) in 2005

Since the beginning of November 2014, nine outbreaks of highly pathogenic avian influenza virus (HPAIV) A(H5N8) in poultry have been detected in four European countries. In this report, similarities and differences between the modes of introduction of HPAIV A(H5N1) and A(H5N8) into Europe are described. Experiences from outbreaks of A(H5N1) in Europe demonstrated that early detection to control HPAIV in poultry has proven pivotal to minimise the risk of zoonotic transmission and prevention of human cases.

Influenza season 2013/14 has started in Europe with influenza A(H1)pdm09 virus being the most prevalent subtype

The 2013/14 influenza season has started in Europe. Four countries have reported medium intensity influenza activity, with children under 15 years being the most affected age group. A growing number of countries see increasing rates of influenza-like illness or acute respiratory infection and increasing proportions of specimens positive for influenza A(H1)pdm09 virus. In previous seasons, this subtype was associated with higher reported numbers of severe and fatal cases. Clinicians should offer influenza vaccination to unvaccinated persons belonging to risk groups.

Influenza-related deaths--available methods for estimating numbers and detecting patterns for seasonal and pandemic influenza in Europe

Two methodologies are used for describing and estimating influenza-related mortality: Individual-based methods, which use death certification and laboratory diagnosis and predominately determine patterns and risk factors for mortality, and population-based methods, which use statistical and modelling techniques to estimate numbers of premature deaths. The total numbers of deaths generated from the two methods cannot be compared. The former are prone to underestimation, especially when identifying influenza-related deaths in older people. The latter are cruder and have to allow for confounding factors, notably other seasonal infections and climate effects. There is no routine system estimating overall European influenza-related premature mortality, apart from a pilot system EuroMOMO. It is not possible at present to estimate the overall influenza mortality due to the 2009 influenza pandemic in Europe, and the totals based on individual deaths are a minimum estimate. However, the pattern of mortality differed considerably between the 2009 pandemic in Europe and the interpandemic period 1970 to 2008, with pandemic deaths in 2009 occurring in younger and healthier persons. Common methods should be agreed to estimate influenza-related mortality at national level in Europe, and individual surveillance should be instituted for influenza-related deaths in key groups such as pregnant women and children.

Associations of dietary polyunsaturated fatty acids with bone mineral density in elderly women

BACKGROUND/OBJECTIVES

Significance of dietary fatty acids on bone health is not clear, and the evidence is controversial. This study aimed to investigate the relationship between dietary polyunsaturated fatty acids (PUFAs) and bone mineral density (BMD) among elderly women.

SUBJECTS/METHODS

Subjects (n=554) were drawn from the Kuopio OSTPRE Fracture Prevention Study. At baseline they filled a 3-day food record and a questionnaire on lifestyle factors, diseases and medications. BMD was measured at lumbar spine (L2-L4), femoral neck and total body by dual energy X-ray absorptiometry at baseline and after 3 years. The associations between dietary fatty acids and BMD were analyzed by a linear mixed model adjusting for potential dietary and non-dietary confounders.

RESULTS

Our findings suggested a positive relationship between the dietary PUFAs and BMD at lumbar spine and in total body but not at femoral neck. Further analyses revealed that these results were due to associations among the women without hormone therapy (HT) at baseline. Among them, the intake of total PUFAs as well the intakes of linoleic and linolenic acids and total n-3 and n-6 fatty acids were significantly associated with BMD at lumbar spine; P for trend over the quartiles ranged between 0.013 and 0.001. Similarly, significant associations were demonstrated for total body BMD and fatty acids with an exception of total PUFA. No significant associations were found among women with HT at baseline.

CONCLUSIONS

Our findings among elderly women without HT support the suggested beneficial effect of dietary PUFAs on bone health.

Initial surveillance of 2009 influenza A(H1N1) pandemic in the European Union and European Economic Area, April-September 2009

European Union (EU) and European Economic Area (EEA) countries reported surveillance data on 2009 pandemic influenza A(H1N1) cases to the European Centre for Disease Prevention and Control (ECDC) through the Early Warning and Response System (EWRS) during the early phase of the 2009 pandemic. We describe the main epidemiological findings and their implications in respect to the second wave of the 2009 influenza pandemic. Two reporting systems were in place (aggregate and case-based) from June to September 2009 to monitor the evolution of the pandemic. The notification rate was assessed through aggregate reports. Individual data were analysed retrospectively to describe the population affected. The reporting peak of the first wave of the 2009 pandemic influenza was reached in the first week of August. Transmission was travel-related in the early stage and community transmission within EU/EEA countries was reported from June 2009. Seventy eight per cent of affected individuals were less than 30 years old. The proportions of cases with complications and underlying conditions were 3% and 7%, respectively. The most frequent underlying medical conditions were chronic lung (37%) and cardio-vascular diseases (15%). Complication and hospitalisation were both associated with underlying conditions regardless of age. The information from the first wave of the pandemic produced a basis to determine risk groups and vaccination strategies before the start of the winter wave. Public health recommendations should be guided by early capture of profiles of affected populations through monitoring of infectious diseases.

A public-private partnership for TB control in Timika, Papua Province, Indonesia

SETTING

A district-level tuberculosis (TB) control programme in Papua Province, Indonesia.

OBJECTIVE

To describe a successful partnership between the District Health Department, a private company and non-governmental health care providers.

METHODS

Routinely collected surveillance data were analysed. A conceptual model was constructed to describe TB control in the district. Data were compared with the National TB Control Programme (NTP) performance indicators.

RESULTS

Funding for the programme's TB clinic is provided by a private company (PT Freeport Indonesia). The NTP provides the policy framework, treatment guidelines and some supplies. TB clinic staff are included in training programmes and the TB laboratory in the provincial quality assurance system. TB clinic staff are responsible for diagnosis, treatment, default tracing, recording and reporting, health education and community mobilisation. The largest proportion of TB patient referrals came from the community hospital (41%). The TB notification rate (311/100000), TB-HIV (human immunodeficiency virus) co-infection (12%) and multidrug-resistant (MDR) TB (2%) are significantly higher in Mimika, but the treatment success rate for smear-positive patients (91%) is similar to Indonesian national figures.

CONCLUSIONS

For true progress in attaining the United Nations Millennium Development Goals for TB in Indonesia, innovative local solutions utilising public-private partnerships are essential. The Mimika model is one such solution that should be tested elsewhere.

Clinical and pharmacological determinants of the therapeutic response to dihydroartemisinin-piperaquine for drug-resistant malaria

Dihydroartemisinin-piperaquine (DHP) is an important new treatment for drug-resistant malaria, although pharmacokinetic studies on the combination are limited. In Papua, Indonesia, we assessed determinants of the therapeutic efficacy of DHP for uncomplicated malaria. Plasma piperaquine concentrations were measured on day 7 and day 28, and the cumulative risk of parasitological failure at day 42 was calculated using survival analysis. Of the 598 patients in the evaluable population 342 had infections with Plasmodium falciparum, 83 with Plasmodium vivax, and 173 with a mixture of both species. The unadjusted cumulative risks of recurrence were 7.0% (95% confidence interval [CI]: 4.6 to 9.4%) for P. falciparum and 8.9% (95% CI: 6.0 to 12%) for P. vivax. After correcting for reinfections the risk of recrudescence with P. falciparum was 1.1% (95% CI: 0.1 to 2.1%). The major determinant of parasitological failure was the plasma piperaquine concentration. A concentration below 30 ng/ml on day 7 was observed in 38% (21/56) of children less than 15 years old and 22% (31/140) of adults (P = 0.04), even though the overall dose (mg per kg of body weight) in children was 9% higher than that in adults (P < 0.001). Patients with piperaquine levels below 30 ng/ml were more likely to have a recurrence with P. falciparum (hazard ratio [HR] = 6.6 [95% CI: 1.9 to 23]; P = 0.003) or P. vivax (HR = 9.0 [95% CI: 2.3 to 35]; P = 0.001). The plasma concentration of piperaquine on day 7 was the major determinant of the therapeutic response to DHP. Lower plasma piperaquine concentrations and higher failure rates in children suggest that dose revision may be warranted in this age group.

A case-cohort study to investigate concomitant waterborne outbreaks of Campylobacter and gastroenteritis in Söderhamn, Sweden, 2002-3

Increased domestic, laboratory confirmed, Campylobacter notifications were reported in Siderhamn municipality, December 2002 and January 2003. Concurrently, during preliminary investigations a large outbreak of acute gastroenteritis was detected. Simultaneously, two studies were completed to identify risk factors for infection with Campylobacter and acute gastrointestinal infection (AGI): (1) a case-cohort study using Campylobacter cases (N = 101) with a large random sample from the municipal population as referents (N = 1000) and (2) a retrospective cohort study for the outcome AGI using the same sample. A postal questionnaire was used to collect demographic, clinical, water and food consumption data. Measures of association (risk ratio (RR), odds ratio (OR)) and 95% confidence intervals (CI) were calculated. Stool, environmental and water samples were tested by standard methods at Gävle Hospital and SMI laboratories respectively. In the case-cohort study, Camplylobacter cases were more likely than referents to consume communal water (OR = 12.6 (95% CI 1.7-92.3)). In the cohort study, risk of gastroenteritis was 2.3 times higher in those who consumed water (AR = 27.3%) than others (AR = 12%). Risk of illness was associated with the amount of water consumed in both studies. Campylobacter was detected in stools and Escherichia coli (E. coli) from routine communal water (CW) samples. Results suggest both Söderhamn outbreaks of Campylobacter and AGI were associated with consumption of CW. The method used strengthened epidemiological evidence and was efficient in the use of time and resources.

'Did you have flu last week?’ A telephone survey to estimate a point prevalence of influenza in the Swedish population

Sentinel surveillance usually underestimates the true burden of influenza in a population, as individuals must present to medical establishments to be included in the surveillance system. We carried out a telephone survey to estimate the national burden of influenza in the Swedish population for one week during the 2004/05 influenza season. Fixed-line telephone numbers were randomly sampled and households interviewed concerning influenza illness between 14-20 February 2005 (Week 7 of 2005). Questions regarding seasonal influenza vaccination status, symptoms and the impact of illness on daily life were also included. A self-defined influenza prevalence of 7.7% in week 7 of 2005 was estimated. On applying a case definition of ‘cough and fever and muscle pain’ for influenza like illness, the prevalence decreased to 3.6%. The survey provided insight into the burden of illness in the population further to that estimated through the sentinel surveillance system.

'Did you have flu last week?' A telephone survey to estimate a point prevalence of influenza in the Swedish population

Sentinel surveillance usually underestimates the true burden of influenza in a population, as individuals must present to medical establishments to be included in the surveillance system. We carried out a telephone survey to estimate the national burden of influenza in the Swedish population for one week during the 2004/05 influenza season. Fixed-line telephone numbers were randomly sampled and households interviewed concerning influenza illness between 14-20 February 2005 (Week 7 of 2005). Questions regarding seasonal influenza vaccination status, symptoms and the impact of illness on daily life were also included. A self-defined influenza prevalence of 7.7% in week 7 of 2005 was estimated. On applying a case definition of 'cough and fever and muscle pain' for influenza like illness, the prevalence decreased to 3.6%. The survey provided insight into the burden of illness in the population further to that estimated through the sentinel surveillance system.

An outbreak of mumps in Sweden, February-April 2004

Between 24 February and 26 April 2004, Västra Götaland county in Sweden reported 42 cases of suspected mumps. A descriptive study of the cases was undertaken. A questionnaire was administered by telephone and vaccine effectiveness was calculated using the screening method. Seventy four per cent (31/42) of the suspected cases were interviewed by telephone. Eight out of the 42 serum samples were positive or equivocal for mumps IgM by ELISA. Mumps virus genome was identified in 21/42 (50%) saliva samples. Eleven were selected for sequencing and all were confirmed to be mumps virus. Cases were predominantly from 2 small towns. Eighteen out of 19 cases that developed bilateral swelling could be linked to one small town. The median age of interviewed cases was 43 years (range 5 to 88). Six cases were admitted to hospital, 5 of which were older than 30 years. The highest incidence occurred in the 35 to 44 years age group. Vaccine effectiveness was estimated to be 65% for 1 dose and 91% for 2 doses. This descriptive study shows the increasing age of mumps cases with increasing vaccine coverage. Vaccine effectiveness was particularly high for 2 doses. Second-dose uptake must be ensured, as primary vaccine failure is well documented in mumps. Stronger precautions must be taken to avoid pools of susceptible older individuals accumulating due to the increased risk of complications.

An outbreak of mumps in Sweden, February-April 2004

Between 24 February and 26 April 2004, Västra Götaland county in Sweden reported 42 cases of suspected mumps. A descriptive study of the cases was undertaken. A questionnaire was administered by telephone and vaccine effectiveness was calculated using the screening method. Seventy four per cent (31/42) of the suspected cases were interviewed by telephone. Eight out of the 42 serum samples were positive or equivocal for mumps IgM by ELISA. Mumps virus genome was identified in 21/42 (50%) saliva samples. Eleven were selected for sequencing and all were confirmed to be mumps virus. Cases were predominantly from 2 small towns. Eighteen out of 19 cases that developed bilateral swelling could be linked to one small town. The median age of interviewed cases was 43 years (range 5 to 88). Six cases were admitted to hospital, 5 of which were older than 30 years. The highest incidence occurred in the 35 to 44 years age group. Vaccine effectiveness was estimated to be 65% for 1 dose and 91% for 2 doses. This descriptive study shows the increasing age of mumps cases with increasing vaccine coverage. Vaccine effectiveness was particularly high for 2 doses. Second-dose uptake must be ensured, as primary vaccine failure is well documented in mumps. Stronger precautions must be taken to avoid pools of susceptible older individuals accumulating due to the increased risk of complications.

Basic Surveillance Network, a European database for surveillance data on infectious diseases

The Basic Surveillance Network was started in 2000 and is one of the networks on infectious diseases funded by the European Commission. The network collects and makes readily available basic surveillance data on infectious diseases from all the 'old' (pre-2004) European Union member states. The aim is to provide easy access to descriptive data that already exist in national databases, so that it is possible to monitor and compare incidence trends for infectious diseases in the EU member states. The list of diseases covered by the network has recently been expanded from 10 initial 'pilot' diseases to over 40 diseases listed by the EU to be under surveillance. In the near future, the new member states will be invited to participate in the network. Data are case-based and comprise date of onset of disease, age and sex. Only a very short list of disease specific additional variables, such as country of infection or immunisation status, is collected. Classification of cases (possible, probable, confirmed) is specified according to EU case definitions. The participants of the network have access to an internal web site were all the data is presented in tables and graphs. An open website is available for the public at https://www.eubsn.org./BSN/

Basic Surveillance Network, a European database for surveillance data on infectious diseases

The Basic Surveillance Network was started in 2000 and is one of the networks on infectious diseases funded by the European Commission. The network collects and makes readily available basic surveillance data on infectious diseases from all the 'old' (pre-2004) European Union member states. The aim is to provide easy access to descriptive data that already exist in national databases, so that it is possible to monitor and compare incidence trends for infectious diseases in the EU member states. The list of diseases covered by the network has recently been expanded from 10 initial 'pilot' diseases to over 40 diseases listed by the EU to be under surveillance. In the near future, the new member states will be invited to participate in the network. Data are case-based and comprise date of onset of disease, age and sex. Only a very short list of disease specific additional variables, such as country of infection or immunisation status, is collected. Classification of cases ( possible, probable, confirmed) is specified according to EU case definitions. The participants of the network have access to an internal web site were all the data is presented in tables and graphs. An open website is available for the public at https://www.eubsn.org./BSN/

Number concentration and size of particles in urban air: effects on spirometric lung function in adult asthmatic subjects

Daily variations in ambient particulate air pollution are associated with variations in respiratory lung function. It has been suggested that the effects of particulate matter may be due to particles in the ultrafine (0.01-0.1 microm) size range. Because previous studies on ultrafine particles only used self-monitored peak expiratory flow rate (PEFR), we assessed the associations between particle mass and number concentrations in several size ranges measured at a central site and measured (biweekly) spirometric lung function among a group of 54 adult asthmatics (n = 495 measurements). We also compared results to daily morning, afternoon, and evening PEFR measurements done at home (n = 7,672-8,110 measurements). The median (maximum) 24 hr number concentrations were 14,500/cm(3) (46,500/cm(3)) ultrafine particles and 800/cm(3) (2,800/cm(3)) accumulation mode (0.1-1 microm) particles. The median (maximum) mass concentration of PM(2.5) (particulate matter < 2.5 microm) and PM(10) (particulate matter < 10 microm in aerodynamic diameter) were 8.4 microg/m(3) (38.3 microg/m(3)) and 13.5 microg/m(3) (73.7 microg/m(3)), respectively. The number of accumulation mode particles was consistently inversely associated with PEFR in spirometry. Inverse, but nonsignificant, associations were observed with ultrafine particles, and no associations were observed with large particles (PM(10)). Compared to the effect estimates for self-monitored PEFR, the effect estimates for spirometric PEFR tended to be larger. The standard errors were also larger, probably due to the lower number of spirometric measurements. The present results support the need to monitor the particle number and size distributions in urban air in addition to mass.

Ultrafine particles in urban air and respiratory health among adult asthmatics

Airborne particles are associated with adverse health effects and contribute to excess mortality in epidemiological studies. A recent hypothesis proposes that the high numbers of ultrafine (<0.1 microm diameter) particles in ambient air might provoke alveolar inflammation and subsequently cause exacerbations in pre-existing cardiopulmonary diseases. To test the hypothesis adult asthmatics were followed with daily peak expiratory flow (PEF) measurements and symptom and medication diaries for six months, while simultaneously monitoring particulate pollution in ambient air. The associations between daily health endpoints of 57 asthmatics and indicators of air pollution were examined by multivariate regression models. Daily mean number concentration of particles, but not particle mass (PM10 (particle mass <10 microm), PM2.5-10, PM2.5, PM1), was negatively associated with daily PEF deviations. The strongest effects were seen for particles in the ultrafine range. However, the effect of ultrafine particles could not definitely be separated from other traffic generated pollutants, namely nitric oxide, nitrogen dioxide and carbon monoxide. No associations were observed with respiratory symptoms or medication use. Particle mass measurements can be strongly influenced by mechanically produced, soil-derived particles, which may not be associated with adverse health effects. Therefore, air quality monitoring should include particle number concentrations, which mainly reflect ultrafine particles.