#Genome #investigations show host #adaptation and #transmission of LA- #MRSA CC398 from #pigs into #Danish #healthcare #institutions (Sci Rep., abstract)

[Source: Scientific Reports, full page: (LINK). Abstract, edited.]

Genome investigations show host adaptation and transmission of LA-MRSA CC398 from pigs into Danish healthcare institutions

Raphael Niklaus Sieber, Anders Rhod Larsen, Tinna Ravnholt Urth, Søren Iversen, Camilla Holten Møller, Robert Leo Skov, Jesper Larsen & Marc Stegger

Scientific Reports, volume 9, Article number: 18655 (2019)



Over the last decade, an increasing number of infections with livestock-associated methicillin-resistant Staphylococcus aureus of clonal complex 398 (LA-MRSA CC398) in persons without contact to livestock has been registered in Denmark. These infections have been suggested to be the result of repeated spillover of random isolates from livestock into the community. However, other studies also found emerging sub-lineages spreading among humans. Based on genome-wide SNPs and genome-wide association studies (GWAS), we assessed the population structure and genomic content of Danish LA-MRSA CC398 isolates from healthcare-associated infections from 2014 to 2016 (n = 73) and compared these to isolates from pigs in Denmark from 2014 (n = 183). Phylogenetic analyses showed that most human isolates were closely related to and scattered among pig isolates showing that the majority of healthcare-associated infections are the result of repeated spillover from pig farms, even though cases of human-to-human transmission also were identified. GWAS revealed frequent loss of antimicrobial resistance genes and acquisition of human-specific virulence genes in the human isolates showing adaptation in response to changes in selective pressures in different host environments, which over time could lead to the emergence of LA-MRSA CC398 lineages more adapted to human colonization and transmission.

Keywords: Antibiotics; Drugs Resistance; Staphylococcus aureus; MRSA; Pigs; Human; Nosocomial outbreaks; Denmark.


A case of #reassortant seasonal #influenza A(#H1N2) virus, #Denmark, April 2019 (Euro Surveill., abstract)

[Source: Eurosurveillance, full page: (LINK). Abstract, edited.]

A case of reassortant seasonal influenza A(H1N2) virus, Denmark, April 2019

Ramona Trebbien1, Anders Koch2, Lene Nielsen3, Dår Kristian Kur4, Pontus Westerström5, Tyra Grove Krause2

Affiliations: 1 National Influenza Center, Statens Serum Institut, Copenhagen, Denmark; 2 Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark; 3 Department of Clinical Microbiology, Herlev Hospital, Copenhagen University, Herlev, Denmark; 4 Department of Clinical Biochemistry, North Zealand Hospital, Hillerød, Denmark; 5 Department of Pulmonary and Infectious Diseases, North Zealand Hospital, Hillerød, Denmark

Correspondence:  Ramona Trebbien

Citation style for this article: Trebbien Ramona, Koch Anders, Nielsen Lene, Kur Dår Kristian, Westerström Pontus, Krause Tyra Grove. A case of reassortant seasonal influenza A(H1N2) virus, Denmark, April 2019. Euro Surveill. 2019;24(27):pii=1900406. https://doi.org/10.2807/1560-7917.ES.2019.24.27.1900406

Received: 21 Jun 2019;   Accepted: 03 Jul 2019



A reassortant influenza A subtype H1N2 virus with gene segments from seasonal A(H1N1)pdm09 virus (HA, MP, NP, NS, PA, PB1 and PB2) and seasonal A(H3N2) virus (NA) was identified in a routine surveillance sample in Denmark. The patient recovered fully. This is the second reassortant influenza A(H1N2) virus identified in Europe in the 2018/19 influenza season, with the first case being detected December 2018 in Sweden.

©  This work is licensed under a Creative Commons Attribution 4.0 International License.

Keywords: Seasonal Influenza; H1N1pdm09; H3N2; H1N2; Reassortant strain; Human; Denmark.


#Age-Dependent Increase in #Incidence of #Staphylococcus aureus #Bacteremia, #Denmark, 2008–2015 (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 5—May 2019 / CME ACTIVITY – Research

Age-Dependent Increase in Incidence of Staphylococcus aureus Bacteremia, Denmark, 2008–2015

Louise Thorlacius-Ussing  , Haakon Sandholdt, Anders Rhod Larsen, Andreas Petersen, and Thomas Benfield

Author affiliations: Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark (L. Thorlacius-Ussing, H. Sandholdt, T. Benfield); Statens Serum Institut, Copenhagen (A. Larsen, A. Petersen)



Staphylococcus aureus bacteremia (SAB) is a major cause of illness and death worldwide. We analyzed temporal trends of SAB incidence and death in Denmark during 2008–2015. SAB incidence increased 48%, from 20.76 to 30.37 per 100,000 person-years, during this period (p<0.001). The largest change in incidence was observed for persons >80 years of age: a 90% increase in the SAB rate (p<0.001). After adjusting for demographic changes, annual rates increased 4.0% (95% CI 3.0–5.0) for persons <80 years of age, 8.4% (95% CI 7.0–11.0) for persons 80–89 years of age, and 13.0% (95% CI 9.0–17.5) for persons >90 years of age. The 30-day case-fatality rate remained stable at 24%; crude population death rates increased by 53% during 2008–2015 (p<0.001). Specific causes and mechanisms for this rapid increase in SAB incidence among the elderly population remain to be clarified.

Keywords: Staphylococcus aureus; Bacteremia; Denmark.


#WGS of 1058 #Enterococcus faecium from Copenhagen, #Denmark, reveals rapid clonal expansion of #vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing #plasmid and acquisition of a heterogeneous accessory genome (J Antimicrob Chemother., abstract9

[Source: Journal of Antimicrobial Chemotherapy, full page: (LINK). Abstract, edited.]

WGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome

Mette Pinholt, Sion C Bayliss, Heidi Gumpert, Peder Worning, Veronika V S Jensen, Michael Pedersen, Edward J Feil, Henrik Westh

Journal of Antimicrobial Chemotherapy, dkz118, https://doi.org/10.1093/jac/dkz118

Published: 30 March 2019




From 2012 to 2015, a sudden significant increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. Clonal relatedness of VREfm and vancomycin-susceptible E. faecium(VSEfm) was investigated, transmission events between hospitals were identified and the pan-genome and plasmids from the largest VREfm clonal group were characterized.


WGS of 1058 E. faecium isolates was carried out on the Illumina platform to perform SNP analysis and to identify the pan-genome. One isolate was also sequenced on the PacBio platform to close the genome. Epidemiological data were collected from laboratory information systems.


Phylogeny of 892 VREfm and 166 VSEfm revealed a polyclonal structure, with a single clonal group (ST80) accounting for 40% of the VREfm isolates. VREfm and VSEfm co-occurred within many clonal groups; however, no VSEfm were related to the dominant VREfm group. A similar vanA plasmid was identified in ≥99% of isolates belonging to the dominant group and 69% of the remaining VREfm. Ten plasmids were identified in the completed genome, and ∼29% of this genome consisted of dispensable accessory genes. The size of the pan-genome among isolates in the dominant group was 5905 genes.


Most probably, VREfm emerged owing to importation of a successful VREfm clone which rapidly transmitted to the majority of hospitals in the region whilst simultaneously disseminating a vanA plasmid to pre-existing VSEfm. Acquisition of a heterogeneous accessory genome may account for the success of this clone by facilitating adaptation to new environmental challenges.

Topic: vancomycin – plasmids – heterogeneity – clone cells – denmark – enterococcus  faecium – genes – genome – whole genome sequencing


© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Antibiotics; Drugs Resistance; Vancomycin; Denmark.


Loose Ends in the #Epidemiology of the 1918 #Pandemic: Explaining the Extreme #Mortality #Risk in #Young Adults (Am J Epidemiol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Am J Epidemiol. 2018 Sep 6. doi: 10.1093/aje/kwy148. [Epub ahead of print]

Loose Ends in the Epidemiology of the 1918 Pandemic: Explaining the Extreme Mortality Risk in Young Adults.

van Wijhe M1, Ingholt MM1, Andreasen V1, Simonsen L1.

Author information: 1 Department of Science and Environment, Roskilde University, Roskilde, Denmark.



In the century since the 1918 influenza pandemic, insights have been sought to explain the pandemic’s signature pattern of high death rates in young adults and low death rates in the elderly and infants. Our understanding of the origin and evolution of the pandemic has shifted considerably. We review evidence of the characteristic age-related pattern of death during the 1918 pandemic relative to the “original antigenic sin” hypothesis. We analyze age-stratified mortality data from Copenhagen around 1918 to identify break points associated with unusual death risk. Whereas infants had no meaningful risk elevation, death risk gradually increased, peaking for young adults 20-34 years of age before dropping sharply for adults ages 35-44 years, suggesting break points for birth cohorts around 1908 and 1878. Taken together with data from previous studies, there is strong evidence that those born before 1878 or after 1908 were not at increased risk of dying of 1918 pandemic influenza. Although the peak death risk coincided with the 1889-1892 pandemic, the 1908 and 1878 break points do not correspond with known pandemics. An increasing number of interdisciplinary studies covering fields such as virology, phylogenetics, death, and serology offer exciting insights into patterns and reasons for the unusual extreme 1918 pandemic mortality risk in young adults.

PMID: 30192906 DOI: 10.1093/aje/kwy148

Keywords: Pandemic Influenza; Spanish Flu; H1N1; Denmark.


#Molecular #epidemiology of #human #adenovirus #infections in #Denmark, 2011-2016 (J Clin Virol., abstract)

[Source: Journal of Clinical Virology, full page: (LINK). Abstract, edited.]

Molecular epidemiology of human adenovirus infections in Denmark, 2011-2016

Céline Barnadas, Dennis Jelsbak Schmidt, Thea K. Fischer, Jannik Fonager

DOI: https://doi.org/10.1016/j.jcv.2018.04.012

Publication History: Published online: April 20, 2018 – Accepted: April 17, 2018 – Received in revised form: April 9, 2018 – Received:January 3, 2018



  • We developed new primers to improve genotyping of HAdV D.
  • Six out of seven HAdV species from at least 13 HAdV types were identified.
  • Young children (<5 years old) were more likely to be positive for HAdV.
  • Co-infections with other gastrointestinal or respiratory viruses were common.
  • A HAdV surveillance system is required to monitor circulating species and types.




Human adenoviruses (HAdVs) can cause respiratory tract infections, conjunctivitis, diarrhoea and outbreaks have been reported. However, little is known about the disease burden and the molecular epidemiology of HAdV.


To retrospectively perform a molecular characterization of HAdV positive samples received at Statens Serum Institut during the period 2011-2016 and to compare this with demographic information, geographic location, sample collection date and type and co-infection with other viral pathogens.

Study design

152 HAdV positive samples were genotyped by Sanger sequencing of a fragment of the hexon gene using published primers along with a newly developed primer set for enhanced genotyping of HAdV D. Phylogenetic analysis was used for genotyping and genotypes were compared with epidemiological information. In addition, HAdV burden and co-infection was evaluated for samples tested in laboratory analysis packages.


Six out of seven HAdV species were identified and represented by 13 types. Young children (<5 years old) were more likely to be positive for HAdV and co-infections with other gastrointestinal or respiratory viruses were common. Possible outbreaks of ocular infections due to HAdV D could not be confirmed.


A diverse set of HAdV species were circulating in Denmark in the study period and although possible transmission clusters were identified, this could not be verified with current genotyping methods Young children were commonly affected by HAdV infection and co-infections with other viral pathogens were frequent suggesting a possible underestimation of the real HAdV burden.

Keywords: Human adenovirus, Molecular epidemiology, Phylogeny, Respiratory virus, Gastroenteritis virus

© 2018 Elsevier B.V. All rights reserved.

Keywords: Adenovirus; Denmark.


In #utero #exposure to the 1918 #pandemic #influenza in #Denmark and risk of #dementia (Influenza Other Respir Viruses, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Influenza Other Respir Viruses. 2018 Jan 22. doi: 10.1111/irv.12542. [Epub ahead of print]

In utero exposure to the 1918 pandemic influenza in Denmark and risk of dementia.

Cocoros NM1, Ording AG2, Horváth-Puhó E2, Henderson VW2,3, Sørensen HT2,3.

Author information: 1 Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA. 2 Department of Clinical Epidemiology, Aarhus University, Aarhus, Denmark. 3 Departments of Health Research & Policy and Neurology & Neurological Sciences, Stanford University, Stanford, CA.




Substantial but inconclusive evidence suggests in utero exposure to influenza infection may be linked with Alzheimer’s disease.


We examined whether individuals exposed in utero to the 1918 influenza pandemic are at increased risk of dementia.


In this cohort study, surveillance data were used to identify months when influenza activity was at its peak during the pandemic. Using birth dates, exposed and unexposed individuals were identified based on whether they were in utero during ≥1 of the peak months. The outcome, any type of dementia, was identified in population-based medical registries. Time and age at risk was restricted so exposed and unexposed had equal time at risk; diagnoses for dementia were assessed between ages 62 and 92, with a maximum of 30 years at risk. Poisson regression was used to estimate sex-adjusted incidence rate ratios (IRR).


We identified 106,479 exposed and 177,918 unexposed persons. Using the cumulative risk function, there were similar proportions of exposed and unexposed with a dementia diagnosis at 11.9% and 11.7%, respectively. Across all ages, the IRR for the association between in utero influenza exposure and any dementia was 1.01 (95% CI 0.99-1.04); for Alzheimer’s disease it was 0.97 (0.93-1.01). When stratified by age and sex, and when dementia type was examined, estimates of association were also null or close to null.


Our study suggests there is likely not an association between in utero exposure to the 1918 influenza pandemic and dementia among those 62 and older.

This article is protected by copyright. All rights reserved.

KEYWORDS: 1918-1919; alzheimer’s disease; dementia; human; influenza; influenza pandemic

PMID: 29356338 DOI: 10.1111/irv.12542

Keyworsd: Pandemic Influenza; Neurology; Denmark.