Analyses of HPAI H5 viruses from poultry outbreaks across a wide Eurasian region since July 2020 including the Russian Federation, Republics of Iraq and Kazakhstan, and recent detections in migratory waterfowl in the Netherlands, revealed undetected maintenance of H5N8, likely in galliform poultry since 2017/18 and both H5N5 and H5N1. All viruses belong to A/H5 clade 2.3.4.4b with closely related HA genes. Heterogeneity in Eurasian H5Nx HPAI emerging variants threatens poultry production, food security and veterinary public health.
A n episode of unusual disease resulting in deaths in different species at a wildlife rehabilitation center in the United Kingdom during late 2020 led to the retrospective detection of infl uenza A virus subtype H5N8 of avian origin in 5 mute swans, a fox, and 3 seals. The wildlife rehabilitation center admits >6,000 animals each year. New arrivals are initially housed in a quarantine facility upon admission. Four juvenile common seals (Phoca vitulina), 1 juvenile gray seal (Halichoerus grypus), and 1 juvenile red fox (Vulpes vulpes) died or were euthanized over a 2-day period. The fox died suddenly after a short period of nonspecifi c malaise and inappetence. The seals exhibited sudden-onset neurologic signs, including seizures before death or euthanasia (Figure 1). This mortality event occurred ≈1 week after the deaths or euthanasia of 5 mute swans (Cygnus olor) held in isolation at the center because of acute-onset malaise and terminal seizures. The 5 swans were submitted for examination and testing under the Avian Infl uenza Wild Bird Surveillance Scheme (undertaken by the United Kingdom's Animal and Plant Health Agency) (1), and they tested positive for highly pathogenic avian infl uenza A(H5N8) virus.The unusual spatiotemporal cluster of unexplained death and neurologic disease in multiple avian and nonavian species warranted further investigation. Infl uenza of avian origin was not suspected in the fox and seals, and none of the other captive birds at the center showed any clinical signs of disease. The linkage between the mortality event in the swans and that observed in the fox and seals was not
The UK and Europe have seen successive outbreaks of highly pathogenic avian influenza across the 2020/21 and 2021/22 autumn/winter seasons. Understanding both the epidemiology and transmission of these viruses in different species is critical to aid mitigating measures where outbreaks cause extensive mortalities in both land- and waterfowl. Infection of different species can result in mild or asymptomatic outcomes, or acute infections that result in high morbidity and mortality levels. Definition of disease outcome in different species is of great importance to understanding the role different species play in the maintenance and transmission of these pathogens. Further, the infection of species that have conservation value is also important to recognise and characterise to understand the impact on what might be limited wild populations. Highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b has been detected in great skuas (Stercorarius skua) across different colonies on islands off the shore of Scotland, Great Britain during summer 2021. A large number of great skuas were observed as developing severe clinical disease and dying during the epizootic and mortalities were estimated to be high where monitored. Of eight skuas submitted for post-mortem examination, seven were confirmed as being infected with this virus using a range of diagnostic assays. Here we overview the outbreak event that occurred in this species, listed as species of conservation concern in Great Britain and outline the importance of this finding with respect to virus transmission and maintenance.
Background Pseudomonas aeruginosa is a ubiquitous environmental microorganism and also a common cause of infection. Its ability to survive in many different environments and persistently colonize humans is linked to its presence in biofilms formed on indwelling device surfaces. Biofilm promotes adhesion to, and survival on surfaces, protects from desiccation and the actions of antibiotics and disinfectants. Results We examined the genetic basis for biofilm production on polystyrene at room (22 °C) and body temperature (37 °C) within 280 P. aeruginosa. 193 isolates (69 %) produced more biofilm at 22 °C than at 37 °C. Using GWAS and pan-GWAS, we found a number of accessory genes significantly associated with greater biofilm production at 22 °C. Many of these are present on a 165 kb region containing genes for heavy metal resistance (arsenic, copper, mercury and cadmium), transcriptional regulators and methytransferases. We also discovered multiple core genome SNPs in the A-type flagellin gene and Type II secretion system gene xpsD. Analysis of biofilm production of isolates of the MDR ST111 and ST235 lineages on stainless-steel revealed several accessory genes associated with enhanced biofilm production. These include a putative translocase with homology to a Helicobacter pylori type IV secretion system protein, a TA system II toxin gene and the alginate biosynthesis gene algA, several transcriptional regulators and methytransferases as well as core SNPs in genes involved in quorum sensing and protein translocation. Conclusions Using genetic association approaches we discovered a number of accessory genes and core-genome SNPs that were associated with enhanced early biofilm formation at 22 °C compared to 37 °C. These included a 165 kb genomic island containing multiple heavy metal resistance genes, transcriptional regulators and methyltransferases. We hypothesize that this genomic island may be associated with overall genotypes that are environmentally adapted to survive at lower temperatures. Further work to examine their importance in, for example gene-knockout studies, are required to confirm their relevance. GWAS and pan-GWAS approaches have great potential as a first step in examining the genetic basis of novel bacterial phenotypes.
Background Several outbreaks of highly pathogenic avian influenza (HPAI) caused by influenza A virus of subtype H5N8 have been reported in wild birds and poultry in Europe during autumn 2020. Norway is one of the few countries in Europe that had not previously detected HPAI virus, despite widespread active monitoring of both domestic and wild birds since 2005. Results We report detection of HPAI virus subtype H5N8 in a wild pink-footed goose (Anser brachyrhynchus), and several other geese, ducks and a gull, from south-western Norway in November and December 2020. Despite previous reports of low pathogenic avian influenza (LPAI), this constitutes the first detections of HPAI in Norway. Conclusions The mode of introduction is unclear, but a northward migration of infected geese or gulls from Denmark or the Netherlands during the autumn of 2020 is currently our main hypothesis for the introduction of HPAI to Norway. The presence of HPAI in wild birds constitutes a new, and ongoing, threat to the Norwegian poultry industry, and compliance with the improved biosecurity measures on poultry farms should therefore be ensured. [MK1]Finally, although HPAI of subtype H5N8 has been reported to have very low zoonotic potential, this is a reminder that HPAI with greater zoonotic potential in wild birds may pose a threat in the future. [MK1]Updated with a sentence emphasizing the risk HPAI pose to poultry farms, both in the Abstract and in the Conclusion-section in main text, as suggested by Reviewer 1 (#7).
Phage therapy recently passed a key milestone with success of the first regulated clinical trial using systemic administration. In this single-arm non-comparative safety study, phages were administered intravenously to patients with invasive Staphylococcus aureus infections with no adverse reactions reported. Here, we examined features of 78 lytic S. aureus phages, most of which were propagated using a S. carnosus host modified to be broadly susceptible to staphylococcal phage infection. Use of this host eliminates the threat of contamination with staphylococcal prophage — the main vector of S. aureus horizontal gene transfer. We determined the host range of these phages against an international collection of 185 S. aureus isolates with 56 different multilocus sequence types that included multiple representatives of all epidemic MRSA and MSSA clonal complexes. Forty of our 78 phages were able to infect > 90% of study isolates, 15 were able to infect > 95%, and two could infect all 184 clinical isolates, but not a phage-resistant mutant generated in a previous study. We selected the 10 phages with the widest host range for in vitro characterization by planktonic culture time-kill analysis against four isolates:- modified S. carnosus strain TM300H, methicillin-sensitive isolates D329 and 15981, and MRSA isolate 252. Six of these 10 phages were able to rapidly kill, reducing cell numbers of at least three isolates. The four best-performing phages, in this assay, were further shown to be highly effective in reducing 48 h biofilms on polystyrene formed by eight ST22 and eight ST36 MRSA isolates. Genomes of 22 of the widest host-range phages showed they belonged to the Twortvirinae subfamily of the order Caudovirales in three main groups corresponding to Silviavirus, and two distinct groups of Kayvirus. These genomes assembled as single-linear dsDNAs with an average length of 140 kb and a GC content of c. 30%. Phages that could infect > 96% of S. aureus isolates were found in all three groups, and these have great potential as therapeutic candidates if, in future studies, they can be formulated to maximize their efficacy and eliminate emergence of phage resistance by using appropriate combinations.
Europe has experienced extensive outbreaks of highly pathogenic avian influenza (HPAI) during the autumn/winter 2020/21 season. These avian influenza A viruses are highly transmissible and have infected over 1000 commercial and backyard poultry premises in Europe in this period causing high mortality. The impact on wild bird populations has also been significant, with over 400 detections in at least 47 different species reported across Europe as being positive with the H5N8 virus. Although different H5Nx combinations within the H5 clade 2.3.4.4b have been detected, the H5N8 subtype has predominated both in wild birds and domestic poultry outbreaks. In the UK there have been 22 outbreaks of H5N8 in domestic poultry and captive birds and more than 300 wild bird detections involving H5N8 over the autumn/winter 2020/21 period to April 2021. Here we detail the series of events surrounding the detection of an H5N8 influenza A virus of avian origin in five swans, a fox and three seals in a wildlife rehabilitation centre.
13Pseudomonas aeruginosa is a ubiquitous environmental microorganism that is also a 14 common cause of nosocomial infections that vary in severity from chronic wound infections 15 to pneumonia, bloodstream infections and sepsis. Its ability to survive in many different 16 environments and persistently colonize human tissue is linked to its presence within biofilms 17 that form on indwelling device surfaces such as plastics and stainless steel. Biofilm promotes 18 bacterial adhesion and survival on surfaces, reduces susceptibility to desiccation, and the 19 actions of antibiotics and disinfectants. Recent genome sequencing studies demonstrate 20 that P. aeruginosa is a highly diverse species with a very large pan-genome consistent with 21 its adaptability to differing environments. However, most MDR infections are caused by a 22 small number of "high-risk" clones or lineages that recently emerged and spread globally. 24In our 2017 study of the resistome of P. aeruginosa we confirmed the power of genome-25 wide association (GWAS) techniques to explore the genetic basis of several antibiotic 26 resistance phenotypes and discovered 46 novel putative resistance polymorphisms. In this 27 study we sought to examine genetic associations within a subset of these isolates with 28 simple biofilm phenotypes. We examined the genetic basis for biofilm production on 29 polystyrene at room temperature (22°C) and body temperature (37°C) within a total of 280 30 isolates. 69% of isolates (n=193) produced more biofilm mass at 22°C, whilst those 31 producing more biofilm at 37°C had reduced optical density 540 variation. We found 32 statistically significant associations with lpxO and other genes associated with arsenic 33 resistance to be significantly associated with this trait. lpxO which encodes a lipid A 34 hydroxylase and arsenic reduction genes have previously been found to be associated with 35 biofilm production in this species. We analyzed 260 ST111 and ST235 genomes and found 36 considerable genetic variation between isolates in their content of genes previously found 37 associated with biofilm production. This is indicative of a highly variable and flexible 38 population within these clades with frequent emergence of successful sub-lineages. Analysis 39 2 of 48 of these isolates' ability to form biofilm on stainless steel surfaces showed that a 40 'good' biofilm-forming phenotype had significant intra-clone variation, independent of core 41 genome phylogeny with pan-genome analysis, suggesting a possible association and 42 involvement of components of the type IV secretion system. However, GWAS and pan-43 GWAS analyses yielded weaker statistical significance. This study confirms GWAS and pan- 44GWAS trait associations can be performed for biofilm phenotype and produce data in 45 agreement with each other. This panel of 280 study isolates, matched to genomic data has 46 potential for the investigation of other phenotypes in P. aeruginosa perhaps as part of a 47 growing database / collection. A representative, curated, gen...
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