Joint External Evaluation-Development and Scale-Up of Global Multisectoral Health Capacity Evaluation Process.

The Joint External Evaluation (JEE), a consolidation of the World Health Organization (WHO) International Health Regulations 2005 (IHR 2005) Monitoring and Evaluation Framework and the Global Health Security Agenda country assessment tool, is an objective, voluntary, independent peer-to-peer multisectoral assessment of a country's health security preparedness and response capacity across 19 IHR technical areas. WHO approved the standardized JEE tool in February 2016. The JEE process is wholly transparent; countries request a JEE and are encouraged to make its findings public. Donors (e.g., member states, public and private partners, and other public health institutions) can support countries in addressing identified JEE gaps, and implementing country-led national action plans for health security. Through July 2017, 52 JEEs were completed, and 25 more countries were scheduled across WHO's 6 regions. JEEs facilitate progress toward IHR 2005 implementation, thereby building trust and mutual accountability among countries to detect and respond to public health threats.

Molecular characterization of adenoviruses among finnish military conscripts.

Although adenoviruses were identified as important respiratory pathogens many years ago, little information is available concerning the prevalence of different adenovirus serotypes, which are circulating and causing epidemics in Finnish military training centers. Over a period of five years from 2008 to 2012, 3577 respiratory specimens were collected from military conscripts presenting with symptoms compatible with acute respiratory tract infection. Upon initial testing for certain respiratory viruses by real-time PCR, 837 of these specimens were identified as adenovirus-positive. For 672 of these specimens, the serotype of the adenovirus responsible was successfully determined by DNA sequencing. Serotypes 1, 2, 3, and 4 were detected in 1, 3, 181, and 487 samples, respectively. Adenovirus epidemics were observed during each year of this study. Based on these findings, adenovirus vaccination should be considered for military conscripts in the Finnish Defence Forces.

Generation of a CRISPR database for Yersinia pseudotuberculosis complex and role of CRISPR-based immunity in conjugation.

The clustered regularly interspaced short palindromic repeat - CRISPR-associated genes (CRISPR-Cas) system is used by bacteria and archaea against invading conjugative plasmids or bacteriophages. Central to this immunity system are genomic CRISPR loci that contain fragments of invading DNA. These are maintained as spacers in the CRISPR loci between direct repeats and the spacer composition in any bacterium reflects its evolutionary history. We analysed the CRISPR locus sequences of 335 Yersinia pseudotuberculosis complex strains. Altogether 1902 different spacer sequences were identified and these were used to generate a database for the spacer sequences. Only ∼10% of the spacer sequences found matching sequences. In addition, surprisingly few spacers were shared by Yersinia pestis and Y. pseudotuberculosis strains. Interestingly, 32 different protospacers were present in the conjugative plasmid pYptb32953. The corresponding spacers were identified from 35 different Y. pseudotuberculosis strains indicating that these strains had encountered pYptb32953 earlier. In conjugation experiments, pYptb32953-specific spacers generally prevented conjugation with spacer-positive and spacer-free strains. However, some strains with one to four spacers were invaded by pYptb32953 and some spacer-free strains were fully resistant. Also some spacer-positive strains were intermediate resistant to conjugation. This suggests that one or more other defence systems are determining conjugation efficiency independent of the CRISPR-Cas system.

Vacuum Oven Drying: A Cost-Effective Way of Producing Field-Deployable Reagents for In-house Real-Time PCR Methods.

The polymerase chain reaction (PCR), is a widely used, sensitive and reliable method for detecting pathogens. However, technical limitations may restrict its use outside sophisticated laboratories, e.g. for detecting pathogens at the site of a disease outbreak. In this study, real-time PCR reagents specific to four bacteria (Bacillus anthracis, Yersinia pestis, Francisella tularensis, and Brucella spp.) and to the Influenza A virus were dried using a vacuum oven drying method. The performance of the dried reagents stored at different temperatures, was monitored using both a standard-size and a portable real-time PCR instrument. The vacuum oven dried real-time PCR reagents were stable and retained the sensitivity for at least 14 months when stored in a refrigerator (+ 4 °C). When stored at room temperature, DNA assays remained stable for at least 10 weeks and Influenza A RNA assay for 3 weeks. These results demonstrate the feasibility of vacuum oven dried real-time PCR reagents and a portable thermocycler for the rapid and reliable detection of pathogens. The drying protocol presented here is cost-effective and easy to use, and could be applied to real-time PCR methods specific to other pathogens as well. In addition, this in-house drying protocol reduces reliance on commercial PCR tests during a time of shortage, such as that experienced during the Corovirus disease (COVID-19) crisis.

[Botulinum toxin as a biological weapon]. / Botulinumtoksiini biouhka-agenssina.

Botulism is caused by botulinum neurotoxin produced by the bacterium Clostridium botulinum. It is a flaccid paralysis in which consciousness and nociception are preserved. Natural botulism typically results from ingestion of inadequately heated or unheated vacuum-packed foods. In addition, botulinum toxin is one of the most feared biological weapons. In the diagnosis and treatment of botulism early suspicion is essential. Several coinciding or local clusters without a typical connecting source, or an uncommon type of toxin may indicate an intentionally caused epidemic.

[New challenges in the biological weapons convention]. / Biologisten aseiden kieltosopimuksen uudet haasteet.

Microbes and their toxins are biological weapons that can cause disease in humans, animals or plants, and which can be used with hostile intent in warfare and terrorism. Biological agents can be used as weapons of mass destruction and therefore, immense human and social and major economical damage can be caused. Rapid development of life sciences and technologies during the recent decades has posed new challenges to the Biological Weapons Convention. The Convention states that the States Parties to the BWC strive to ensure that the Convention remains relevant and effective, despite changes in science, technology or politics.

[Safe from biothreats? Legislation protects you and society]. / Biouhilta turvassa?--Säädökset suojaavat työntekijää ja yhteiskuntaa.

The 9/11 terror attacks, followed by mailing of letters containing anthrax spores, changed our comprehension on threats towards modern society. Finland is committed by international treaties to develop biosafety and biosecurity legislation, and general awareness of the legislation. However, the rapidly developing field of biosciences cannot be extensively regulated by legislation. Awareness of the risks and challenges involved in handling of biological agents is an important tool in threat prevention. Despite active efforts to update the legislation by government authorities, currently the sustenance and development of biosecurity are primarily in the hands of individual researchers and the scientific community.

Confidence in biopreparedness authorities among Finnish conscripts.

A large sample of Finnish military conscripts of the armored brigade were questioned on the extent to which they trusted the information given biopreparedness authorities (such as the police, military, health care, and public health institutions) and how confident they were in the authority's ability to protect the public during a potential infectious disease outbreak, from either natural or deliberate causes. Participants answered a written questionnaire during their initial health inspection in July 2007. From a total of 1,000 conscripts, 953 male conscripts returned the questionnaire. The mean sum scores for confidence in the information given to biopreparedness authorities and the media on natural and bioterrorism-related outbreaks (range = 0-30) were 20.14 (SD = 7.79) and 20.12 (SD = 7.69), respectively. Mean sum scores for the respondents' confidence in the ability of the biopreparedness authorities to protect the public during natural and bioterrorism-related outbreaks (range 0-25) were 16.04 (SD = 5.78) and 16.17 (SD = 5.89). Most respondents indicated that during a natural outbreak, they would have confidence in information provided by a health care institution such as central hospitals and primary health care centers, whereas in the case of bioterrorism, the respondents indicated that they would have confidence in the defense forces and central hospitals.

The value proposition of the Global Health Security Index.

Infectious disease outbreaks pose major threats to human health and security. Countries with robust capacities for preventing, detecting and responding to outbreaks can avert many of the social, political, economic and health system costs of such crises. The Global Health Security Index (GHS Index)-the first comprehensive assessment and benchmarking of health security and related capabilities across 195 countries-recently found that no country is sufficiently prepared for epidemics or pandemics. The GHS Index can help health security stakeholders identify areas of weakness, as well as opportunities to collaborate across sectors, collectively strengthen health systems and achieve shared public health goals. Some scholars have recently offered constructive critiques of the GHS Index's approach to scoring and ranking countries; its weighting of select indicators; its emphasis on transparency; its focus on biosecurity and biosafety capacities; and divergence between select country scores and corresponding COVID-19-associated caseloads, morbidity, and mortality. Here, we (1) describe the practical value of the GHS Index; (2) present potential use cases to help policymakers and practitioners maximise the utility of the tool; (3) discuss the importance of scoring and ranking; (4) describe the robust methodology underpinning country scores and ranks; (5) highlight the GHS Index's emphasis on transparency and (6) articulate caveats for users wishing to use GHS Index data in health security research, policymaking and practice.

Recent establishment of tick-borne encephalitis foci with distinct viral lineages in the Helsinki area, Finland.

Number of tick-borne encephalitis (TBE) cases has increased and new foci have emerged in Finland during the last decade. We evaluated risk for locally acquired TBE in the capital region inhabited by 1.2 million people. We screened ticks and small mammals from probable places of TBE virus (TBEV) transmission and places without reported circulation. The TBEV positive samples were sequenced and subjected to phylogenetic analysis. Within the study period 2007-2017, there was a clear increase of both all TBE cases and locally acquired cases in the Helsinki area. The surveillance of ticks and small mammals for TBEV confirmed four distinct TBEV foci in the Helsinki area. All detected TBEV strains were of the European subtype. TBEV genome sequences indicated that distinct TBEV lineages circulate in each focus. Molecular clock analysis suggested that the virus lineages were introduced to these foci decades ago. In conclusion, TBE has emerged in the mainland of Helsinki area during the last decade, with at least four distinct virus lineages independently introduced into the region previously. Although the overall annual TBE incidence is below the threshold for recommending general vaccinations, the situation requires further surveillance to detect and prevent possible further emergence of local TBE clusters.

Accelerating Action in Global Health Security: Global Biosecurity Dialogue as a Model for Advancing the Global Health Security Agenda.

Biosecurity and biosafety measures are designed to mitigate intentional and accidental biological risks that pose potentially catastrophic consequences to a country's health system, security, and political and economic stability. Unfortunately, biosecurity and biosafety are often under-prioritized nationally, regionally, and globally. Security leaders often deemphasize accidental and deliberate biological threats relative to other challenges to peace and security. Given emerging biological risks, including those associated with rapid technological advances and terrorist and state interest in weapons of mass destruction, biosecurity deserves stronger emphasis in health and security fora. The Global Biosecurity Dialogue (GBD) was initiated to align national and regional donor initiatives toward a common set of measurable targets. The GBD was launched by the Nuclear Threat Initiative (NTI), with support from Global Affairs Canada's Weapons Threat Reduction Program and the Open Philanthropy Project, and in coordination with the government of The Netherlands as the 2018-19 Chair of the Global Health Security Agenda (GHSA) Action Package Prevent-3 (APP3) on Biosafety and Biosecurity. The GBD provides a multisectoral forum for sharing models, enabling new actions to achieve biosecurity-related targets, and promoting biosecurity as an integral component of health security. The GBD has contributed to new national and continent-wide actions, including the African Union and Africa Centres for Disease Control and Prevention's new regional Initiative to Strengthen Biosafety and Biosecurity in Africa. Here we present the GBD as a model for catalyzing action within APP3. We describe how the benefits of this approach could expand to other GHSA Action Packages and international health security initiatives.

Developing a multisectoral National Action Plan for Health Security (NAPHS) to implement the International Health Regulations (IHR 2005) in Tanzania.

The Ebola outbreak in West Africa precipitated a renewed momentum to ensure global health security through the expedited and full implementation of the International Health Regulations (IHR) (2005) in all WHO member states. The updated IHR (2005) Monitoring and Evaluation Framework was shared with Member States in 2015 with one mandatory component, that is, States Parties annual reporting to the World Health Assembly (WHA) on compliance and three voluntary components: Joint External Evaluation (JEE), After Action Reviews and Simulation Exercises. In February 2016, Tanzania, was the first country globally to volunteer to do a JEE and the first to use the recommendations for priority actions from the JEE to develop a National Action Plan for Health Security (NAPHS) by February 2017. The JEE demonstrated that within the majority of the 47 indicators within the 19 technical areas, Tanzania had either 'limited capacity' or 'developed capacity'. None had 'sustainable capacity'. With JEE recommendations for priority actions, recommendations from other relevant assessments and complementary objectives, Tanzania developed the NAPHS through a nationwide consultative and participatory process. The 5-year cost estimate came out to approximately US$86.6 million (22 million for prevent, 50 million for detect, 4.8 million for respond and 9.2 million for other IHR hazards and points of entry). However, with the inclusion of vaccines for zoonotic diseases in animals increases the cost sevenfold. The importance of strong country ownership and committed leadership were identified as instrumental for the development of operationally focused NAPHS that are aligned with broader national plans across multiple sectors. Key lessons learnt by Tanzania can help guide and encourage other countries to translate their JEE priority actions into a realistic costed NAPHS for funding and implementation for IHR (2005).

The dynamics of bacteria in the middle ear during the course of acute otitis media with tympanostomy tube otorrhea.

BACKGROUND: Dynamics of bacteria during acute otitis media (AOM) has not been thoroughly studied because it requires repeated tympanocentesis. AOM with tympanostomy tube otorrhea provides a unique opportunity to study the appearance and disappearance of pathogens during the course of the disease without stressing the child. METHODS: Middle ear fluid (MEF) samples were taken before treatment (amoxicillin clavulanate or placebo) and then daily during follow-up from 75 children having AOM with otorrhea through a tympanostomy tube. Bacteria were identified by culture, and typical AOM pathogens also by polymerase chain reaction. RESULTS: Bacteria were initially shown in 67 (89%) children. New bacteria appeared in MEF more often in placebo than in amoxicillin clavulanate recipients [9 of 38 (24%) versus 2 of 37 (5%); P = 0.032]. During the follow-up, new occurrences of Moraxella catarrhalis were detected in MEF more frequently than those of Streptococcus pneumoniae or Haemophilus influenzae. Of the 28 patients with bilateral otorrhea, 11 (39%) had disparate bacteria at study entry and/or during the follow-up. CONCLUSIONS: Changes in bacterial findings during the course of AOM are common in patients not receiving treatment, and even possible despite adequate treatment. In bilateral otorrhea, disparate bacterial findings are common.

Phylogeographic separation and formation of sexually discrete lineages in a global population of Yersinia pseudotuberculosis.

Yersinia pseudotuberculosis is a Gram-negative intestinal pathogen of humans and has been responsible for several nationwide gastrointestinal outbreaks. Large-scale population genomic studies have been performed on the other human pathogenic species of the genus Yersinia, Yersinia pestis and Yersinia enterocolitica allowing a high-resolution understanding of the ecology, evolution and dissemination of these pathogens. However, to date no purpose-designed large-scale global population genomic analysis of Y. pseudotuberculosis has been performed. Here we present analyses of the genomes of 134 strains of Y. pseudotuberculosis isolated from around the world, from multiple ecosystems since the 1960s. Our data display a phylogeographic split within the population, with an Asian ancestry and subsequent dispersal of successful clonal lineages into Europe and the rest of the world. These lineages can be differentiated by CRISPR cluster arrays, and we show that the lineages are limited with respect to inter-lineage genetic exchange. This restriction of genetic exchange maintains the discrete lineage structure in the population despite co-existence of lineages for thousands of years in multiple countries. Our data highlights how CRISPR can be informative of the evolutionary trajectory of bacterial lineages, and merits further study across bacteria.

Metagenomic Evaluation of Bacteria from Voles.

Voles (Arvicolinae, Rodentia) are known carriers of zoonotic bacteria such as Bartonella spp. and Francisella tularensis. However, apart from F. tularensis, the bacterial microbiome of voles has not previously been determined in Finland and rarely elsewhere. Therefore, we studied liver samples from 61 voles using 16S ribosomal RNA gene PCR analysis, followed by Sanger sequencing. Twenty-three of these samples were also studied with tag-encoded pyrosequencing. The samples originated from 21 field voles (Microtus agrestis), 37 tundra voles (Microtus oeconomus), and 3 bank voles (Myodes glareolus). With the more conventional 16S rDNA PCR analysis, 90 (33%) of the recovered 269 sequence types could be identified to genus level, including Bartonella, Francisella, Mycoplasma, Anaplasma, and Acinetobacter in 31, 15, 9, 9, and 9 sequences, respectively. Seventy-five (28%) matched best with sequences of uncultured bacteria, of which 40/75 could be classified to the order Clostridiales and, more specifically, to families Lachnospiraceae and Ruminococcaceae. Pyrosequencing from 23 samples revealed comparable and similar results: clinically relevant bacterial families such as Mycoplasmataceae, Bartonellaceae, Anaplasmataceae, and Francisellaceae were recognized. These analyses revealed significant bacterial diversity in vole livers, consisting of distinct and constant sequence patterns reflecting bacteria found in the intestinal gut, but including some known zoonotic pathogens as well. The molecular bacterial sequence types determined with the two different techniques shared major similarities and verified remarkable congruency between the methods.

Contamination by Norovirus and Adenovirus on Environmental Surfaces and in Hands of Conscripts in Two Finnish Garrisons.

This study investigated the presence of norovirus and adenovirus, especially enteric adenovirus, on the environmental surfaces (n = 481) and military conscripts' hands (n = 109) in two Finnish garrisons (A and B) in 2013 and 2014. A questionnaire study was conducted to reveal possible correlations between viral findings on the conscripts' hands and their acute gastroenteritis symptoms. In addition to the swab samples, 14 fecal samples were obtained for viral analysis. In total, norovirus was present in 9.0 % of the surface swabs in 2013, whereas enteric adenovirus was present in 0.0 % and non-enteric adenovirus in 9.4 %. In the same year, 2.6 % of the hand swabs contained norovirus, 2.6 % enteric adenovirus, and 40.3 % non-enteric adenovirus. Norovirus GI.6 was continually detected on the surfaces of garrison A, and identical virus was detected in some of the fecal samples. In garrison B, two slightly different norovirus GII.4 strains were present on the surfaces. The questionnaires revealed no recent acute gastroenteritis cases in garrison A, but in garrison B, where the norovirus-positive hand swabs were collected, 30.6 % of the conscripts reported of recent symptoms. In 2014, norovirus was rarely detected, but adenovirus was again frequently present, both on the surfaces and hands. Taken together, our results suggest that gastroenteritis outbreaks occurred in 2013, but not in 2014. Due to the low number of hand swabs positive for enteric viruses, no conclusions about associations between viral findings and gastroenteritis symptoms could be drawn. This study increased our understanding of the possible transmission of viruses via contaminated environment and hands.

Microbiology of acute otitis media in children with tympanostomy tubes: prevalences of bacteria and viruses.

BACKGROUND: Bacteria are found in 50%-90% of cases of acute otitis media (AOM) with or without otorrhea, and viruses are found in 20%-49% of cases. However, for at least 15% of patients with AOM, the microbiological etiology is never determined. Our aim was to specify the full etiology of acute middle ear infection by using modern microbiological methods concomitantly for bacterial and viral detection. METHODS: The subjects were 79 young children having AOM with new onset (<48 h) of otorrhea through a tympanostomy tube. Middle ear fluid samples were suctioned from the middle ear through the tympanostomy tube. Bacteria were sought by culture and polymerase chain reaction; viruses were analyzed by culture, antigen detection, and polymerase chain reaction. RESULTS: At least 1 respiratory tract pathogen was noted in 76 children (96%). Bacteria were found in 73 cases (92%), and viruses were found in 55 (70%). In 52 patients (66%), both bacteria and viruses were found. Bacteria typical of AOM were detected in 86% of patients. Picornaviruses accounted for 60% of all viral findings. CONCLUSIONS: In the great majority of children, AOM is a coinfection with bacteria and viruses. The patent tympanostomy tube does not change the spectrum of causative agents in AOM. A microbiological etiology can be established in practically all cases.

Comparison of four commercial DNA extraction kits for the recovery of Bacillus spp. spore DNA from spiked powder samples.

Bacillus spp. include human pathogens such as Bacillus anthracis, the causative agent of anthrax and a biothreat agent. Bacillus spp. form spores that are physically highly resistant and may remain active over sample handling. We tested four commercial DNA extraction kits (QIAamp DNA Mini Kit, RTP Pathogen Kit, ZR Fungal/Bacterial DNA MiniPrep, and genesig Easy DNA/RNA Extraction kit) for sample inactivation and DNA recovery from two powders (icing sugar and potato flour) spiked with Bacillus thuringiensis spores. The DNA was analysed using a B. thuringiensis-specific real-time PCR assay. The detection limit was 3×10(1)CFU of spiked B. thuringiensis spores with the QIAamp DNA Mini, RTP Pathogen, and genesig Easy DNA/RNA Extraction kits, and 3×10(3)CFU with the ZR Fungal/Bacterial DNA MiniPrep kit. The results showed that manual extraction kits are effective and safe for fast and easy DNA extraction from powder samples even in field conditions. Adding a DNA filtration step to the extraction protocol ensures the removal of Bacillus spp. spores from DNA samples without affecting sensitivity.

Identification of Cardiobacterium hominis by broad-range bacterial polymerase chain reaction analysis in a case of culture-negative endocarditis.

Culture-negative bacterial endocarditis may be attributed to fastidious microorganisms, prior institution of antibiotic treatment, or both. We describe a case of culture-negative endocarditis in which a modified Steiner stain revealed bacterial structures in the resected heart valve material. Prompted by this finding, broad-range polymerase chain reaction (PCR) amplification of small-subunit ribosomal DNA (16S rDNA) was performed, and Cardiobacterium hominis sequences were detected. This case demonstrates the usefulness of both the Steiner stain and broad-range direct molecular amplification as supplemental diagnostic tools in identification of otherwise unexplained infections.