Complete #Genome Sequence of a Novel Swine Acute Diarrhea Syndrome #Coronavirus, CH/FJWT/2018, Isolated in #Fujian, #China, in 2018 (Microbiol Resour Announc., abstract)

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

Microbiol Resour Announc. 2018 Dec 6;7(22). pii: e01259-18. doi: 10.1128/MRA.01259-18. eCollection 2018 Dec.

Complete Genome Sequence of a Novel Swine Acute Diarrhea Syndrome Coronavirus, CH/FJWT/2018, Isolated in Fujian, China, in 2018.

Li K#1,2, Li H#1,2, Bi Z1,2, Gu J1,2, Gong W1,2, Luo S1,2, Zhang F1,2, Song D1,2, Ye Y1,2, Tang Y1,2.

Author information: 1 Key Laboratory for Animal Health of Jiangxi Province, Nanchang, Jiangxi, China. 2 Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China. # Contributed equally



The full-length genome sequence of a novel swine acute diarrhea syndrome coronavirus (SADS-CoV), CH/FJWT/2018, was determined, which was genetically most closely related to CN/GDWT/2017, recently discovered in Fujian, China. The indel sites of the spike (S) gene of CH/FJWT/2018 were most similar to those of bat-origin SADS-related coronaviruses.

PMID: 30533848 PMCID: PMC6284080 DOI: 10.1128/MRA.01259-18 Free full text

Keywords: Coronavirus; Pigs; SADS-CoV; Fujian; China.



#Pig Movement and #Antimicrobial Use Drive #Transmission of #Livestock-Associated #Staphylococcus aureus CC398 (mBio, abstract)

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

Pig Movement and Antimicrobial Use Drive Transmission of Livestock-Associated Staphylococcus aureus CC398

Tara C. Smith, Meghan F. Davis, Christopher D. Heaney

DOI: 10.1128/mBio.02459-18



The epidemiology of methicillin-resistant Staphylococcus aureus has changed considerably over the last 3 decades, including the recognition of lineages associated with the community and with livestock exposure, in addition to nosocomial strains. A recent study by R. N. Sieber, R. L. Skov, J. Nielsen, J. Schulz, et al. (mBio 9:e02142-18, demonstrates the importance of multisectoral cooperation at the intersection of occupational health, genomics, veterinary medicine practitioners, and farmers in order for us to better understand the epidemiology of antibiotic-resistant organisms.
The views expressed in this article do not necessarily reflect the views of the journal or of ASM.

Keywords: Antibiotics; Drugs Resistance; Pigs; Staphylococcus aureus.


Co-localization of #MERS #Coronavirus and #DPP4 in the #respiratory tract and #lymphoid tissues of #pigs and #llamas (Transbound Emerg Dis., abstract)

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

Transbound Emerg Dis. 2018 Dec 6. doi: 10.1111/tbed.13092. [Epub ahead of print]

Co-localization of Middle East respiratory syndrome coronavirus (MERS-CoV) and dipeptidyl peptidase-4 in the respiratory tract and lymphoid tissues of pigs and llamas.

Te N1, Vergara-Alert J1, Lehmbecker A2, Pérez M1, Haagmans BL3, Baumgärtner W2, Bensaid A1, Segalés J4,5.

Author information: 1 IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. 2 Department of Pathology, University of Veterinary Medicine, Hannover, Germany. 3 Department of Viroscience, Erasmus Medical Center, 3015 CN, Rotterdam, The Netherlands. 4 UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. 5 Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, 08193, Bellaterra, Barcelona, Spain.



The present study investigated the co-localization of the Middle East respiratory syndrome coronavirus (MERS-CoV) and its receptor dipeptidyl peptidase-4 (DPP4) across respiratory and lymphoid organs of experimentally MERS-CoV infected pigs and llamas by immunohistochemistry (IHC). Also, scanning electron microscopy (SEM) was performed to assess the ciliary integrity of respiratory epithelial cells in both species. In pigs, on day 2 post-inoculation (p.i.), DPP4-MERS-CoV co-localization was detected in medial turbinate epithelium. On day 4 p.i., the virus/receptor co-localized in frontal and medial turbinate epithelial cells in pigs, and epithelial cells distributed unevenly through the whole nasal cavity and in the cervical lymph node in llamas. MERS-CoV viral nucleocapsid was mainly detected in upper respiratory tract sites on days 2 and 4 p.i. in pigs and day 4 p.i. in llamas. No MERS-CoV was detected on day 24 p.i. in any tissue by IHC. While pigs showed severe ciliary loss in the nasal mucosa both on days 2 and 4 p.i. and moderate loss in the trachea on days 4 and 24 p.i., ciliation of respiratory organs in llamas was not significantly affected. Obtained data confirm the role of DPP4 for MERS-CoV entry in respiratory epithelial cells of llamas. Notably, several nasal epithelial cells in pigs were found to express viral antigen but not DPP4, suggesting the possible existence of other molecule/s facilitating virus entry or down regulation of DPP4 upon infection.

This article is protected by copyright. All rights reserved.

KEYWORDS: Middle East respiratory syndrome coronavirus (MERS-CoV); dipeptidyl peptidase-4 (DPP4); immunohistochemistry; llama; pig; scanning electron microscopy

PMID: 30520548 DOI: 10.1111/tbed.13092

Keywords: MERS-CoV; Pigs; Llamas; Animal models; Viral pathogenesis.


#Origins of the 1918 #Pandemic: Revisiting the #Swine “Mixing Vessel” #Hypothesis (Am J Epidemiol., abstract)

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

Am J Epidemiol. 2018 Dec 1;187(12):2498-2502. doi: 10.1093/aje/kwy150.

Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis.

Nelson MI1, Worobey M2.

Author information: 1 Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland. 2 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona.



How influenza A viruses host-jump from animal reservoir species to humans, which can initiate global pandemics, is a central question in pathogen evolution. The zoonotic and spatial origins of the influenza virus associated with the “Spanish flu” pandemic of 1918 have been debated for decades. Outbreaks of respiratory disease in US swine occurred concurrently with disease in humans, raising the possibility that the 1918 virus originated in pigs. Swine also were proposed as “mixing vessel” intermediary hosts between birds and humans during the 1957 Asian and 1968 Hong Kong pandemics. Swine have presented an attractive explanation for how avian viruses overcome the substantial evolutionary barriers presented by different cellular environments in humans and birds. However, key assumptions underpinning the swine mixing-vessel model of pandemic emergence have been challenged in light of new evidence. Increased surveillance in swine has revealed that human-to-swine transmission actually occurs far more frequently than the reverse, and there is no empirical evidence that swine played a role in the emergence of human influenza in 1918, 1957, or 1968. Swine-to-human transmission occurs periodically and can trigger pandemics, as in 2009. But swine are not necessary to mediate the establishment of avian viruses in humans, which invites new perspectives on the evolutionary processes underlying pandemic emergence.

PMID: 30508193 DOI: 10.1093/aje/kwy150

Keywords: Avian Influenza; Swine Influenza; Influenza A; Pandemic Influenza; H1N1; Spanish Flu; Pigs; Reassortant strain.


#Tissue #tropisms opt for transmissible #reassortants during #avian and #swine #influenza A virus co-infection in swine (PLoS Pathogens, abstract)

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


Tissue tropisms opt for transmissible reassortants during avian and swine influenza A virus co-infection in swine

Xiaojian Zhang , Hailiang Sun , Fred L. Cunningham , Lei Li , Katie Hanson-Dorr, Matthew W. Hopken, Jim Cooley, Li-Ping Long, John A. Baroch, Tao Li, Brandon S. Schmit, Xiaoxu Lin, Alicia K. Olivier,  [ … ], Xiu-Feng Wan

Published: December 3, 2018 / DOI: / This is an uncorrected proof.



Genetic reassortment between influenza A viruses (IAVs) facilitate emergence of pandemic strains, and swine are proposed as a “mixing vessel” for generating reassortants of avian and mammalian IAVs that could be of risk to mammals, including humans. However, how a transmissible reassortant emerges in swine are not well understood. Genomic analyses of 571 isolates recovered from nasal wash samples and respiratory tract tissues of a group of co-housed pigs (influenza-seronegative, avian H1N1 IAV–infected, and swine H3N2 IAV–infected pigs) identified 30 distinct genotypes of reassortants. Viruses recovered from lower respiratory tract tissues had the largest genomic diversity, and those recovered from turbinates and nasal wash fluids had the least. Reassortants from lower respiratory tracts had the largest variations in growth kinetics in respiratory tract epithelial cells, and the cold temperature in swine nasal cells seemed to select the type of reassortant viruses shed by the pigs. One reassortant in nasal wash samples was consistently identified in upper, middle, and lower respiratory tract tissues, and it was confirmed to be transmitted efficiently between pigs. Study findings suggest that, during mixed infections of avian and swine IAVs, genetic reassortments are likely to occur in the lower respiratory track, and tissue tropism is an important factor selecting for a transmissible reassortant.


Author summary

Genetic reassortments between avian and swine influenza viruses are likely to occur in the swine lower respiratory track, and tissue tropism is an important factor selecting for a transmissible reassortant; determination of tissue tropisms for potential reassortants between contemporary avian and swine influenza viruses would help identify transmissible reassortants with public health risks.


Citation: Zhang X, Sun H, Cunningham FL, Li L, Hanson-Dorr K, Hopken MW, et al. (2018) Tissue tropisms opt for transmissible reassortants during avian and swine influenza A virus co-infection in swine. PLoS Pathog 14(12): e1007417.

Editor: Anice C. Lowen, Emory University School of Medicine, UNITED STATES

Received: July 24, 2018; Accepted: October 18, 2018; Published: December 3, 2018

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Data Availability: The sequence of A/swine/Texas/A01104013/2012 (H3N2) and A/mallard/Wisconsin/A00751454/2009 (H1N1) viruses are available from Genbank under the accession numbers JX280447 to JX280454 and MH879773 to MH879780. All other relevant data are included in the main text of this paper or the Supporting Information files associated with this paper.

Funding: This study was supported by the U.S. Department of Agriculture and the National Institutes of Health (NIH) [grant number R21AI135820]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Avian Influenza; Swine Influenza; Influenza A; H1N1; H3N2 Pigs; Reassortant strain.


Novel #linezolid #resistance #plasmids in #Enterococcus from #food #animals in the #USA (J Antimicrob Chemother., abstract)

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

Novel linezolid resistance plasmids in Enterococcusfrom food animals in the USA

Gregory H Tyson, Jonathan L Sabo, Maria Hoffmann, Chih-Hao Hsu, Sampa Mukherjee, Jacqueline Hernandez, Glenn Tillman, Jamie L Wasilenko, Jovita Haro, Mustafa Simmons, Wanda Wilson Egbe, Patricia L White, Uday Dessai, Patrick F Mcdermott

Journal of Antimicrobial Chemotherapy, dky369,

Published: 01 October 2018




To sequence the genomes and determine the genetic mechanisms for linezolid resistance identified in three strains of Enterococcus isolated from cattle and swine caecal contents as part of the US National Antimicrobial Resistance Monitoring System (NARMS) surveillance programme.


Broth microdilution was used for in vitro antimicrobial susceptibility testing to assess linezolid resistance. Resistance mechanisms and plasmid types were identified from data generated by WGS on Illumina® and PacBio® platforms. Conjugation experiments were performed to determine whether identified mechanisms were transmissible.


Linezolid resistance plasmids containing optrA were identified in two Enterococcus faecalis isolates and one Enterococcus faecium. The E. faecium isolate also carried the linezolid resistance gene cfr on the same plasmid as optrA. The linezolid resistance plasmids had various combinations of additional resistance genes conferring resistance to phenicols (fexA), aminoglycosides [spc and aph(3′)-III] and macrolides [erm(A) and erm(B)]. One of the plasmids was confirmed to be transmissible by conjugation, resulting in linezolid resistance in the transconjugant.


To the best of our knowledge, this is the first identification of linezolid resistance in the USA in bacteria isolated from food animals. The oxazolidinone class of antibiotics is not used in food animals in the USA, but the genes responsible for resistance were identified on plasmids with other resistance markers, indicating that there may be co-selection for these plasmids due to the use of different antimicrobials. The transmissibility of one of the plasmids demonstrated the potential for linezolid resistance to spread horizontally. Additional surveillance is necessary to determine whether similar plasmids are present in human strains of Enterococcus.

Topic: enterococcus – plasmids – cattle – food – genes  – suidae – bacteria – cecum – macrolides – linezolid – antimicrobials – antimicrobial susceptibility test – surveillance, medical – resistance genes – whole genome sequencing


Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy 2018. This work is written by US Government employees and is in the public domain in the US.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (

Keywords: Antibiotics; Drugs Resistance; Linezolid; Enterococcus; Macrolides.


Spatio-temporal #distribution and #evolution of the A #H1N1pdm09 virus in #pigs in #France from 2009 to 2017: identification of a potential swine-specific lineage (J Virol., abstract)

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

Spatio-temporal distribution and evolution of the A/H1N1 2009 pandemic virus in pigs in France from 2009 to 2017: identification of a potential swine-specific lineage

Amélie Chastagner, Séverine Hervé, Emilie Bonin, Stéphane Quéguiner, Edouard Hirchaud, Dinah Henritzi, Véronique Béven, Stéphane Gorin, Nicolas Barbier, Yannick Blanchard,Gaëlle Simon

DOI: 10.1128/JVI.00988-18



The H1N1 influenza virus responsible for the most recent pandemic in 2009 (H1N1pdm) has spread to swine populations worldwide while it replaced the previous seasonal H1N1 virus in humans. In France, surveillance of swine influenza A viruses in pig herds with respiratory outbreaks led to the detection of 44 H1N1pdm strains between 2009 and 2017, regardless of the season, and findings were not correlated to pig density. From these isolates, 17 whole genome sequences were obtained as well as 6 additional HA/NA sequences, in order to perform spatial and temporal analyses of the genetic diversity, and to compare evolutionary patterns of H1N1pdm in pigs to patterns for human strains. Following mutation accumulation and fixation over time, phylogenetic analyses revealed for the first time the divergence of a swine-specific genogroup within the H1N1pdm lineage. The divergence is thought to have occurred around 2011, although this was only demonstrated through strains isolated in 2015-2016 in the southern half of France. To date, these H1N1pdm swine strains have not been related to any increased virulence in swine herds and have not exhibited any antigenic drift as compared to seasonal human strains. However, further monitoring is encouraged as diverging evolutionary patterns in these two species, i.e. swine and humans, may lead to the emergence of viruses with a potentially higher risk for both animal and human health.



Pigs are a ‘mixing vessel’ for influenza A viruses (IAVs) because of their ability to be infected by avian and human IAVs, and their propensity to facilitate viral genomic reassortment events. Also, as IAVs may evolve differently in swine and humans, pigs can become a reservoir for old human strains against which the human population has become immunologically naïve. Thus, viruses from the novel swine-specific H1N1pdm genogroup may continue to diverge from seasonal H1N1pdm strains and/or from other H1N1pdm viruses infecting pigs and lead to the emergence of viruses that would not be covered by human vaccines and/or swine vaccines based on antigens closely related to the original H1N1pdm virus. This discovery confirms the importance of encouraging swine IAV monitoring because H1N1pdm swine viruses could carry an increased risk for both human and swine health in the future, as a whole H1N1pdm or gene provider in subsequent reassortant viruses.

Copyright © 2018 American Society for Microbiology. All Rights Reserved.

Keywords: Seasonal Influenza; Pandemic Influenza; Swine Influenza; H1N1pdm09; Pigs; France.