RESUMEN
Highly pathogenic avian influenza (HPAI) has caused widespread mortality in both wild and domestic birds in Europe 2020-2023. In July 2023, HPAI A(H5N1) was detected on 27 fur farms in Finland. In total, infections in silver and blue foxes, American minks and raccoon dogs were confirmed by RT-PCR. The pathological findings in the animals include widespread inflammatory lesions in the lungs, brain and liver, indicating efficient systemic dissemination of the virus. Phylogenetic analysis of Finnish A(H5N1) strains from fur animals and wild birds has identified three clusters (Finland I-III), and molecular analyses revealed emergence of mutations known to facilitate viral adaptation to mammals in the PB2 and NA proteins. Findings of avian influenza in fur animals were spatially and temporally connected with mass mortalities in wild birds. The mechanisms of virus transmission within and between farms have not been conclusively identified, but several different routes relating to limited biosecurity on the farms are implicated. The outbreak was managed in close collaboration between animal and human health authorities to mitigate and monitor the impact for both animal and human health.
Asunto(s)
Animales Salvajes , Charadriiformes , Brotes de Enfermedades , Subtipo H5N1 del Virus de la Influenza A , Gripe Aviar , Filogenia , Animales , Gripe Aviar/virología , Gripe Aviar/epidemiología , Finlandia/epidemiología , Subtipo H5N1 del Virus de la Influenza A/genética , Subtipo H5N1 del Virus de la Influenza A/patogenicidad , Subtipo H5N1 del Virus de la Influenza A/aislamiento & purificación , Animales Salvajes/virología , Charadriiformes/virología , Brotes de Enfermedades/veterinaria , Granjas , Infecciones por Orthomyxoviridae/veterinaria , Infecciones por Orthomyxoviridae/virología , Infecciones por Orthomyxoviridae/mortalidad , Infecciones por Orthomyxoviridae/epidemiología , Zorros/virología , Aves/virología , Visón/virologíaRESUMEN
BACKGROUND: In collaboration with six European public health agencies as part of the PANDEM-2 consortium, we have developed and validated a self-assessment tool that captures the workforce capacities and capabilities needed at the institutional level within National Public Health Institutes (NPHIs) to deal with public health emergencies. METHODS: The work carried out in this study included (i) a review of existing tools for workforce assessment, (ii) focus group discussions and interviews to map the experiences and needs of NPHI's, (iii) the development of a tool for NPHI's to assess their workforce capacity and capabilities in public health emergency preparedness (PHEP) and (iv) refinement of the assessment tool via a Delphi study. RESULTS: Capacity markers were identified to assess the workforce required for PHEP functions and the availability of surge capacity during a public health emergency. The tool also enables NPHIs to analyze gaps in PHEP staff competencies. The assessment scores can assist NPHI pandemic preparedness by identifying and prioritizing training and recruitment needs. CONCLUSIONS: In line with EU Regulation 2022/2371 on serious cross-border threats to health, article 11 Training of healthcare staff and public health staff, Member States (MS) are tasked with assessing current workforce capacity and capability gaps. The PANDEM-2 workforce self-assessment tool aligns with this requirement and will support effective planning and development to strengthen the public health workforce capacity in EU MS.
Asunto(s)
Defensa Civil , Planificación en Desastres , Salud Pública , Autoevaluación (Psicología) , Humanos , Técnica Delphi , Europa (Continente) , Grupos Focales , COVID-19 , Fuerza Laboral en SaludRESUMEN
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.
RESUMEN
Since mid-July 2023, an outbreak caused by highly pathogenic avian influenza A(H5N1) virus clade 2.3.4.4b genotype BB is ongoing among farmed animals in South and Central Ostrobothnia, Finland. Infections in foxes, American minks and raccoon dogs have been confirmed on 20 farms. Genetic analysis suggests introductions from wild birds scavenging for food in farm areas. Investigations point to direct transmission between animals. While no human infections have been detected, control measures are being implemented to limit spread and human exposure.
Asunto(s)
Subtipo H5N1 del Virus de la Influenza A , Virus de la Influenza A , Gripe Aviar , Animales , Granjas , Finlandia/epidemiología , Subtipo H5N1 del Virus de la Influenza A/genética , Gripe Aviar/epidemiología , Visón , FilogeniaRESUMEN
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.
Asunto(s)
Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , Infecciones por Yersinia pseudotuberculosis/microbiología , Yersinia pseudotuberculosis/clasificación , Yersinia pseudotuberculosis/genética , Animales , Biblioteca de Genes , Humanos , Filogenia , Secuenciación Completa del GenomaRESUMEN
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.
Asunto(s)
Arvicolinae/microbiología , Bacterias/genética , Bacterias/aislamiento & purificación , Genoma Bacteriano , Metagenómica , Animales , Bacterias/clasificación , FinlandiaRESUMEN
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.
Asunto(s)
Bacillus thuringiensis/aislamiento & purificación , ADN Bacteriano/aislamiento & purificación , Juego de Reactivos para Diagnóstico , Esporas Bacterianas/aislamiento & purificación , Límite de Detección , Polvos/químicaRESUMEN
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 â¼10% 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.
Asunto(s)
Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/inmunología , Conjugación Genética/inmunología , Bases de Datos de Ácidos Nucleicos , Plásmidos/inmunología , Yersinia pseudotuberculosis/genética , Bacteriófagos/inmunología , Secuencia de Bases , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , Genómica , Datos de Secuencia Molecular , Plásmidos/genética , Yersinia pestis/genética , Yersinia pseudotuberculosis/clasificaciónRESUMEN
The bacteriophage vB_YecM-ÏR1-37 (ÏR1-37) is a lytic yersiniophage that can propagate naturally in different Yersinia species carrying the correct lipopolysaccharide receptor. This large-tailed phage has deoxyuridine (dU) instead of thymidine in its DNA. In this study, we determined the genomic sequence of phage ÏR1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. The 262,391-bp genome of ÏR1-37 is one of the largest sequenced phage genomes, and it contains 367 putative open reading frames (ORFs) and 5 tRNA genes. Mass-spectrometric analysis identified 69 phage particle structural proteins with the genes scattered throughout the genome. A total of 269 of the ORFs (73%) lack homologues in sequence databases. Based on terminator and promoter sequences identified from the intergenic regions, the phage genome was predicted to consist of 40 to 60 transcriptional units. Image reconstruction revealed that the ÏR1-37 capsid consists of hexameric capsomers arranged on a T=27 lattice similar to the bacteriophage ÏKZ. The tail of ÏR1-37 has a contractile sheath. We conclude that phage ÏR1-37 is a representative of a novel phage type that carries the dU-containing genome in a ÏKZ-like head.