Host genetic requirements for DNA release of lactococcal phage TP901-1.

The first step in phage infection is the recognition of, and adsorption to, a receptor located on the host cell surface. This reversible host adsorption step is commonly followed by an irreversible event, which involves phage DNA delivery or release into the bacterial cytoplasm. The molecular components that trigger this latter event are unknown for most phages of Gram-positive bacteria. In the current study, we present a comparative genome analysis of three mutants of Lactococcus cremoris 3107, which are resistant to the P335 group phage TP901-1 due to mutations that affect TP901-1 DNA release. Through genetic complementation and phage infection assays, a predicted lactococcal three-component glycosylation system (TGS) was shown to be required for TP901-1 infection. Major cell wall saccharidic components were analysed, but no differences were found. However, heterologous gene expression experiments indicate that this TGS is involved in the glucosylation of a cell envelope-associated component that triggers TP901-1 DNA release. To date, a saccharide modification has not been implicated in the DNA delivery process of a Gram-positive infecting phage.

Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses.

Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018. In total, 3800 submissions were received with a steady increase in swIAV-positive submissions, reaching 56% in 2018. Full-genome sequences were obtained from 129 swIAV-positive samples. Altogether, 17 different circulating genotypes were identified including six novel reassortants harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx (clade 1A.3.3.2) viruses. The results provide essential data for the control of swIAV in pigs and emphasize the importance of contemporary surveillance for discovering novel swIAV strains posing a potential threat to the human population.

European surveillance network for influenza in pigs: surveillance programs, diagnostic tools and Swine influenza virus subtypes identified in 14 European countries from 2010 to 2013.

Swine influenza causes concern for global veterinary and public health officials. In continuing two previous networks that initiated the surveillance of swine influenza viruses (SIVs) circulating in European pigs between 2001 and 2008, a third European Surveillance Network for Influenza in Pigs (ESNIP3, 2010-2013) aimed to expand widely the knowledge of the epidemiology of European SIVs. ESNIP3 stimulated programs of harmonized SIV surveillance in European countries and supported the coordination of appropriate diagnostic tools and subtyping methods. Thus, an extensive virological monitoring, mainly conducted through passive surveillance programs, resulted in the examination of more than 9 000 herds in 17 countries. Influenza A viruses were detected in 31% of herds examined from which 1887 viruses were preliminary characterized. The dominating subtypes were the three European enzootic SIVs: avian-like swine H1N1 (53.6%), human-like reassortant swine H1N2 (13%) and human-like reassortant swine H3N2 (9.1%), as well as pandemic A/H1N1 2009 (H1N1pdm) virus (10.3%). Viruses from these four lineages co-circulated in several countries but with very different relative levels of incidence. For instance, the H3N2 subtype was not detected at all in some geographic areas whereas it was still prevalent in other parts of Europe. Interestingly, H3N2-free areas were those that exhibited highest frequencies of circulating H1N2 viruses. H1N1pdm viruses were isolated at an increasing incidence in some countries from 2010 to 2013, indicating that this subtype has become established in the European pig population. Finally, 13.9% of the viruses represented reassortants between these four lineages, especially between previous enzootic SIVs and H1N1pdm. These novel viruses were detected at the same time in several countries, with increasing prevalence. Some of them might become established in pig herds, causing implications for zoonotic infections.

Influenza a virus with a human-like n2 gene is circulating in pigs.

A novel reassortant influenza A virus, H1avN2hu, has been found in Danish swine. The virus contains an H1 gene similar to the hemagglutinin (HA) gene of H1N1 avian-like swine viruses and an N2 gene most closely related to the neuraminidase (NA) gene of human H3N2 viruses from the mid-1990s.

Surveillance for avian influenza viruses in wild birds in Denmark and Greenland, 2007-10.

In Denmark and Greenland, extensive surveillance of avian influenza (AI) viruses in wild bird populations has been conducted from 2007 through 2010. In Denmark, the surveillance consisted of passive surveillance of wild birds found dead or sick across Denmark and active surveillance of apparently healthy live birds in waterfowl reservoirs and along migratory flyways, birds living in proximity to domestic poultry, and hunted game birds. Dead birds were sampled by oropharyngeal swabbing. Healthy live wild birds were captured with nets, traps, or by hand and were sampled by swabbing of the oropharyngeal and cloacal tracts, or swabs were collected from fresh fecal droppings. Hunted game birds were delivered to game-handling establishments, where each bird was sampled by oropharyngeal and cloacal swabbing. During the 2007-10 period, a total of 11,055 wild birds were sampled in Denmark, of which 396 were birds that were found dead. In Greenland, samples were collected mainly from fecal droppings in breeding areas. Samples from 3555 live and apparently healthy wild birds were tested. All swab samples were tested by pan-influenza reverse transcriptase-PCR (RT-PCR), and the positive samples were further tested by H5/H7 specific RT-PCRs. H5/H7-positive samples were subjected to hemagglutination cleavage site sequencing for pathotyping. In addition, all RT-PCR-positive samples were subjected to virus isolation, and the virus isolates were subsequently subtyped. In Denmark, low pathogenic (LP) H5 viruses were detected throughout the period, in addition to a few LPAI H7 and several other subtypes. In Greenland, very few samples were positive for AI. None of them were found to be of the H5 or H7 subtypes by RT-PCR. Isolation of these viruses in eggs was unsuccessful; thus, they were not subtyped further. The findings did, however, demonstrate the presence of LPAI viruses in Greenland. For several water bird species overwintering in North America and northwest Europe, respectively, Greenland constitutes a common breeding area. This raises the possibility that viruses could be transmitted to North America via Greenland and vice versa. In Denmark, the screenings for AI showed LPAI viruses to be naturally occurring in the wild bird population, particularly in waterfowl. The occurrence of AI viruses in the wild bird population may pose a risk for AI infections in Danish

Prevalence of Escherichia coli O157 and verocytotoxin producing E. coli (VTEC) on Danish beef carcasses.

The prevalence of verocytotoxin producing Escherichia coli (VTEC), E. coli O157, and VTEC O157 in 474 swab samples from Danish beef carcasses was determined. The presence of E. coli O157 was determined by a culture method that included immunomagnetic separation (IMS) followed by real time PCR testing of isolates for verocytotoxin (vtx) genes. E. coli O157 was recovered from 4.2% of the carcass samples and VTEC O157 from 3.4% of the samples. All VTEC O157 contaminated carcasses were from bull calves and the VTEC O157 prevalence on bull calf carcasses was 7.3%. The VTEC O157 contaminated beef carcasses were sampled again after one week of cold storage, and 15 of the 16 carcasses were then VTEC O157 negative. The presence of VTEC was determined by a duplex real time PCR assay for vtx1 and vtx2 in DNA from enrichment cultures of swabs. In total 45.4% of the samples were VTEC positive. VTEC were isolated from 21% of 77 vtx-positive samples that were identified by replication of colonies on hydrophobic grid membrane filters followed by hybridisation with vtx specific DNA probes. Fourteen of the 16 VTEC isolates were non-O157 and these strains were negative for the virulence gene eae. A real time PCR assay for the E. coli O157 specific rfbE gene was developed. In total 22.4% of the enriched samples were positive for the O157 rfbE gene. The combined results of the vtx and rfbE real time PCR screening showed that 17.5% of the carcasses potentially were contaminated with VTEC O157. Screening of carcass swabs was expanded by real time PCR testing for eae in a subset of the samples. Of 244 samples, 25.4% were positive for both vtx and eae. The eae gene was detected in 81% of the vtx-positive samples and in 46% of 67 vtx-negative samples, indicating that bacteria harbouring eae are widespread on bovine carcasses. The present study shows that real time PCR screening of carcass samples for genes encoding virulence or other genetic markers is a reliable method for rapid identification of carcasses that potentially are contaminated with VTEC.