#Interspecies #Transmission of #Reassortant #Swine #Influenza A Virus Containing #Genes from Swine Influenza A #H1N1pdm09 and A(#H1N2) Viruses (Emerg Infect Dis., abstract)

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

Volume 26, Number 2—February 2020 / Research

Interspecies Transmission of Reassortant Swine Influenza A Virus Containing Genes from Swine Influenza A(H1N1)pdm09 and A(H1N2) Viruses

Helen E. Everett  , Bethany Nash, Brandon Z. Londt1, Michael D. Kelly, Vivien Coward, Alejandro Nunez, Pauline M. van Diemen, Ian H. Brown, and Sharon M. Brookes

Author affiliations: Animal and Plant Health Agency, Weybridge, UK



Influenza A(H1N1)pdm09 (pH1N1) virus has become established in swine in the United Kingdom and currently co-circulates with previously enzootic swine influenza A virus (IAV) strains, including avian-like H1N1 and human-like H1N2 viruses. During 2010, a swine influenza A reassortant virus, H1N2r, which caused mild clinical disease in pigs in the United Kingdom, was isolated. This reassortant virus has a novel gene constellation, incorporating the internal gene cassette of pH1N1-origin viruses and hemagglutinin and neuraminidase genes of swine IAV H1N2 origin. We investigated the pathogenesis and infection dynamics of the H1N2r isolate in pigs (the natural host) and in ferrets, which represent a human model of infection. Clinical and virologic parameters were mild in both species and both intraspecies and interspecies transmission was observed when initiated from either infected pigs or infected ferrets. This novel reassortant virus has zoonotic and reverse zoonotic potential, but no apparent increased virulence or transmissibility, in comparison to pH1N1.

Keywords: Swine Influenza; Influenza A; Reassortant strain; H1N1pdm09; H1N2; Pigs; UK.


Quantifying the #spatial #risk of #Avian #Influenza introduction into #British #poultry by #wildbirds (Sci Rep., abstract)

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

Sci Rep. 2019 Dec 27;9(1):19973. doi: 10.1038/s41598-019-56165-9.

Quantifying the spatial risk of Avian Influenza introduction into British poultry by wild birds.

Hill A1,2, Gillings S3, Berriman A4, Brouwer A4, Breed AC4,5,6, Snow L4, Ashton A4, Byrne C4, Irvine RM4.

Author information: 1 Animal and Plant Health Agency, New Haw, KT15 3NB, United Kingdom. a.a.hill@surrey.ac.uk. 2 University of Surrey, Guildford, UK. a.a.hill@surrey.ac.uk. 3 British Trust for Ornithology, Thetford, IP24 2PU, United Kingdom. 4 Animal and Plant Health Agency, New Haw, KT15 3NB, United Kingdom. 5 School of Veterinary Science, University of Queensland, Brisbane, Australia. 6 Epidemiology and One Health Section, Department of Agriculture, Canberra, Australia.



The transmission of pathogens across the interface between wildlife and livestock presents a challenge to the development of effective surveillance and control measures. Wild birds, especially waterbirds such as the Anseriformes and Charadriiformes are considered to be the natural hosts of Avian Influenza (AI), and are presumed to pose one of the most likely vectors for incursion of AI into European poultry flocks. We have developed a generic quantitative risk map, derived from the classical epidemiological risk equation, to describe the relative, spatial risk of disease incursion into poultry flocks via wild birds. We then assessed the risk for AI incursion into British flocks. The risk map suggests that the majority of AI incursion risk is highly clustered within certain areas of Britain, including in the east, the south west and the coastal north-west of England. The clustering of high risk areas concentrates total risk in a relatively small land area; the top 33% of cells contribute over 80% of total incursion risk. This suggests that targeted risk-based sampling in a relatively small geographical area could be a much more effective and cost-efficient approach than representative sampling. The generic nature of the risk map method, allows rapid updating and application to other diseases transmissible between wild birds and poultry.

PMID: 31882592 DOI: 10.1038/s41598-019-56165-9

Keywords: Avian Influenza; Wild Birds; Poultry; UK.


Post-exposure #prophylaxis with #rVSVZEBOV following exposure to a #patient with #Ebola virus disease relapse in the #UK: an operational, safety and immunogenicity report (Clin Infect Dis., abstract)

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

Clin Infect Dis. 2019 Nov 30. pii: ciz1165. doi: 10.1093/cid/ciz1165. [Epub ahead of print]

Post-exposure prophylaxis with rVSV-ZEBOV following exposure to a patient with Ebola virus disease relapse in the UK: an operational, safety and immunogenicity report.

Davis C1, Tipton T2, Sabir S1, Aitken C3, Bennett S3, Becker S4, Evans T5, Fehling SK4, Gunson R3, Hall Y2, Jackson C3,5, Johanssen I6, Kieny MP7, McMenamin J8, Spence E5, Strecker T4, Sykes C5, Templeton K6, Thorburn F5, Peters E5, Henao Restrepo AM9, White B10, Zambon M11, Carroll MW2, Thomson EC12.

Author information: 1 MRC-University of Glasgow Centre for Virus Research, Glasgow, UK. 2 Porton Down, National Infection Service, Public Health England, Salisbury, UK. 3 West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow, UK. 4 Institute of Virology, Philipps University Marburg, Germany. 5 Department of Infectious Diseases, Queen Elizabeth University Hospital, Glasgow. 6 Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK. 7 World Health Organisation World Health Organization, Geneva, Switzerland & Inserm, Paris, France. 8 Health Protection Scotland, Glasgow, UK. 9 World Health Organisation, Geneva, Switzerland & Inserm, Paris, France. 10 Department of Infectious Diseases, Queen Elizabeth University Hospital, Glasgow, UK. 11 Public Health England Colindale, London, UK. 12 MRC-University of Glasgow Centre for Virus Research, Glasgow, UK & Department of Infectious Diseases, Queen Elizabeth University Hospital, Glasgow, UK.




In October 2015, 65 people came into direct contact with a healthcare worker presenting with a late reactivation of Ebola virus disease (EVD) in the UK. Vaccination was offered to 45 individuals with an initial assessment of high exposure risk.


Approval for rapid expanded access to the recombinant vesicular stomatitis virus-Zaire Ebola virus vaccine (rVSV-ZEBOV) as an unlicensed emergency medicine was obtained from the relevant authorities. An observational follow-up study was carried out for 1 year following vaccination.


26/45 individuals elected to receive vaccination between October 10th and 11th 2015 following written informed consent. By day 14, 39% had seroconverted, rising to 87% by day 28 and 100% by 3 months, although these responses were not always sustained. Neutralising antibody responses were detectable in 36% by day 14 and 73% at 12 months. Common side effects included fatigue, myalgia, headache, arthralgia and fever. These were positively associated with glycoprotein (GP)-specific T-cell but not IgM or IgG antibody responses. No severe vaccine-related adverse events were reported. No-one exposed to the virus became infected.


This paper reports the use of the rVSV-ZEBOV vaccine given as an emergency intervention to individuals exposed to a patient presenting with a late reactivation of EVD. The vaccine was relatively well tolerated but a high percentage developed a fever ≥37.5oC necessitating urgent screening for Ebola virus and a small number developed persistent arthralgia.

© The Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America.

KEYWORDS: Ebola virus; T cell; rVSV-ZEBOV; vaccine

PMID: 31784751 DOI: 10.1093/cid/ciz1165

Keywords: Ebola; Vaccines; Drugs safety; UK.


#ESBL-producing #Escherichia coli in #human-derived and #foodchain-derived #samples from #England, #Wales, and #Scotland: an epidemiological surveillance and typing study (Lancet Infect Dis., abstract)

[Source: The Lancet Infectious Diseases, full page: (LINK). Abstract, edited.]

Extended-spectrum β-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and Scotland: an epidemiological surveillance and typing study

Michaela J Day, PhD, Katie L Hopkins, PhD, David W Wareham, PhD, Mark A Toleman, PhD, Nicola Elviss, PhD, Luke Randall, PhD, Christopher Teale, MSc, Paul Cleary, MSc, Camilla Wiuff, PhD *, Michel Doumith, PhD †, Matthew J Ellington, PhD, Neil Woodford, PhD, Prof David M Livermore, PhD

Open Access / Published: October 22, 2019 / DOI: https://doi.org/10.1016/S1473-3099(19)30273-7




Extended-spectrum β-lactamase-producing Escherichia coli isolates (ESBL-E coli) cause more than 5000 cases of bacteraemias annually in the UK. The contribution of the food chain to these infections is debated. We aimed to identify the most important reservoirs of ESBL-E coli that colonise and infect humans to identify strategic intervention points.


Sampling for ESBL-E coli was done between Aug 1, 2013, and Dec 15, 2014. We used selective media to seek ESBL-E coli in routinely submitted samples from human faeces, and prospectively collected samples from sewage, farm slurry, and retail foodstuffs in London, East Anglia, northwest England, Scotland, and Wales. We sequenced recovered isolates and compared these isolates with 293 bloodstream and 83 veterinary surveillance ESBL-E coli isolates from the same regions.


2157 (11%) of 20 243 human faeces samples contained ESBL-E coli, including 678 (17%) of 3995 in London. ESBL-E coli also were frequent in sewage and retail chicken (104 [65%] of 159 meat samples), but were rare in other meats and absent from plant-based foods (0 of 400 fruit and vegetable samples). Sequence type (ST) 131 dominated among ESBL-E coli from human blood (188 [64%] of 293 isolates), faeces (128 [36%] of 360), and sewage (14 [22%] of 65) with STs 38 and 648 also widespread; CTX-M-15 was the predominant ESBL in these lineages (319 [77%] of 416). By contrast, STs 602, 23, and 117—mostly with CTX-M-1 ESBL—dominated among food and veterinary isolates (68 [31%] of 218), with only two ST131 organisms recovered. ST10 occurred in both animals and humans, being frequent in surveillance bovines (11 [22%] of 51 cattle) and representing 15 (4%) of 360 human faecal isolates (but only three [1%] of 293 from bacteraemias); however, both human and animal ST10 isolates were diverse in serotype.


Most human bacteraemias with ESBL-E coli in the UK involve internationally prevalent human-associated STs, particularly ST131; non-human reservoirs made little contribution to invasive human disease. Any interventions that seek to target food or livestock can affect the numbers of human infections caused by ESBL-E coli; prevention of the spread of resistant lineages among humans is more vital.


NIHR Policy Research.

Keywords: Antibiotics; Drugs Resistance; Beta-lactams; Food Safety; UK.


#Pneumococcal #serotype #trends, #surveillance and #risk factors in #UK adult #pneumonia, 2013–18 (Thorax, abstract)

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

Pneumococcal serotype trends, surveillance and risk factors in UK adult pneumonia, 2013–18

Harry Pick1,2, Priya Daniel3, Chamira Rodrigo4, Thomas Bewick3, Deborah Ashton4, Hannah Lawrence5,6, Vadsala Baskaran1,6, Rochelle C Edwards-Pritchard2, Carmen Sheppard7, Seyi D Eletu7, Samuel Rose7, David Litt7, Norman K Fry8, Shamez Ladhani8, Meera Chand9, Caroline Trotter10, Tricia M McKeever6, Wei Shen Lim1

Author affiliations: 1 Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK; 2 Division of Respiratory Medicine, University of Nottingham, Nottingham, UK; 3 Respiratory Medicine, University Hospitals of Derby and Burton NHS Foundation Trust, Derby, UK; 4 Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK; 5 Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK; 6 Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK; 7 Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England Colindale, London, UK; 8 Immunisation and Countermeasures Division, Public Health England Colindale, London, UK; 9 Tuberculosis, Acute Respiratory, Gastrointestinal, Emerging/Zoonotic Infections, Travel and Migrant Health Service (TARGET), Public Health England Colindale, London, UK; 10 Disease Dynamic Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK

Correspondence to Dr Harry Pick, Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK; harry.pick@nhs.net




Changes over the last 5 years (2013–18) in the serotypes implicated in adult pneumococcal pneumonia and the patient groups associated with vaccine-type disease are largely unknown.


We conducted a population-based prospective cohort study of adults admitted to two large university hospitals with community-acquired pneumonia (CAP) between September 2013 and August 2018. Pneumococcal serotypes were identified using a novel 24-valent urinary monoclonal antibody assay and from blood cultures. Trends in incidence rates were compared against national invasive pneumococcal disease (IPD) data. Persons at risk of vaccine-type pneumonia (pneumococcal conjugate vaccine (PCV)13 and pneumococcal polysaccharide vaccine (PPV)23) were determined from multivariate analyses.


Of 2934 adults hospitalised with CAP, 1075 (36.6%) had pneumococcal pneumonia. The annual incidence of pneumococcal pneumonia increased from 32.2 to 48.2 per 100 000 population (2013–18), predominantly due to increases in PCV13non7-serotype and non-vaccine type (NVT)-serotype pneumonia (annual incidence rate ratio 1.12, 95% CI 1.04 to 1.21 and 1.19, 95% CI 1.10 to 1.28, respectively). Incidence trends were broadly similar to IPD data. PCV13non7 (56.9% serotype 3) and PPV23non13 (44.1% serotype 8) serotypes were identified in 349 (32.5%) and 431 (40.1%) patients with pneumococcal pneumonia, respectively. PCV13-serotype pneumonia (dominated by serotype 3) was more likely in patients in the UK pneumococcal vaccination clinical risk group (adjusted OR (aOR) 1.73, 95% CI 1.31 to 2.28) while PPV23-serotype pneumonia was more likely in patients outside the clinical risk group (aOR 1.54, 95% CI 1.13 to 2.10).


The incidence of pneumococcal CAP is increasing, predominantly due to NVT serotypes and serotype 3. PPV23-serotype pneumonia is more likely in adults outside currently identified clinical risk groups.


DOI: http://dx.doi.org/10.1136/thoraxjnl-2019-213725




HJP, CS and WSL were responsible for study conception and design. HJP, PD, CR, TB, DA, HL, VB, RCE-P, CS and SE were responsible for data acquisition. HJP, TMM and CT were responsible for the statistical analysis. HJP and WSL drafted the initial versions of the Article. All authors contributed to data interpretation and read, commented on and approved the final version of the article.


This study is independent research supported by the Nottingham National Institute for Health Research Biomedical Research Centre (NIHR BRC) and arising from an unrestricted investigator-initiated research grant from Pfizer. The study concept was developed and agreed by the authors with no input from the funding bodies; Pfizer had no part in the design or execution of the study, the analysis and interpretation of the results, the writing of this manuscript or the decision to submit for publication. The data are the sole responsibility of the authors and the sponsor for the study was Nottingham University Hospitals NHS Trust.


The views expressed in this publication are those of the authors and not necessarily those of the NHS, the NIHR or PHE.

Competing interests 

None declared.

Patient consent for publication 

Not required.

Ethics approval 

Study procedures were approved by the Nottingham Research Ethics Committee (REC reference 08/H0403/80).

Provenance and peer review 

Not commissioned; externally peer reviewed.

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Keywords: Streptococcus pneumoniae; Vaccines; UK; Pneumonia; IPD.


Effect of #Pediatric #Influenza #Vaccination on #Antibiotic #Resistance, #England and #Wales (Emerg Infect Dis., abstract)

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

Volume 26, Number 1—January 2020 / Dispatch

Effect of Pediatric Influenza Vaccination on Antibiotic Resistance, England and Wales

Chungman Chae1, Nicholas G. Davies1  , Mark Jit, and Katherine E. Atkins

Author affiliations: London School of Hygiene and Tropical Medicine, London, UK (C. Chae, N.G. Davies, M. Jit, K.E. Atkins); Public Health England, London (M. Jit); University of Edinburgh, Scotland, UK (K.E. Atkins).



Vaccines against viral infections have been proposed to reduce prescribing of antibiotics and thereby help control resistant bacterial infections. However, by combining published data sources, we predict that pediatric live attenuated influenza vaccination in England and Wales will not substantially reduce antibiotic consumption or adverse health outcomes associated with antibiotic resistance.

Keywords: Seasonal Influenza; Vaccines; Antibiotics; Drugs Resistance; UK.


Characterization of #cefotaxime #resistant #urinary #Escherichia coli from primary care in South-West #England 2017–18 (J Antimicrob Chemother., abstract)

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

Characterization of cefotaxime-resistant urinary Escherichia coli from primary care in South-West England 2017–18

Jacqueline Findlay, Virginia C Gould, Paul North, Karen E Bowker, Martin O Williams, Alasdair P MacGowan, Matthew B Avison

Journal of Antimicrobial Chemotherapy, dkz397, https://doi.org/10.1093/jac/dkz397

Published: 20 September 2019




Third-generation cephalosporin-resistant Escherichia coli from community-acquired urinary tract infections are increasingly reported worldwide. We sought to determine and characterize the mechanisms of cefotaxime resistance employed by urinary E. coli obtained from primary care, over 12 months, in Bristol and surrounding counties in South-West England.


Cefalexin-resistant E. coli isolates were identified from GP-referred urine samples using disc susceptibility testing. Cefotaxime resistance was determined by subsequent plating onto MIC breakpoint plates. β-Lactamase genes were detected by PCR. WGS was performed on 225 isolates and analyses were performed using the Center for Genomic Epidemiology platform. Patient information provided by the referring general practices was reviewed.


Cefalexin-resistant E. coli (n = 900) isolates were obtained from urines from 146 general practices. Following deduplication by patient approximately 69% (576/836) of isolates were cefotaxime resistant. WGS of 225 isolates identified that the most common cefotaxime-resistance mechanism was blaCTX-M carriage (185/225), followed by plasmid-mediated AmpCs (pAmpCs) (17/225), AmpC hyperproduction (13/225), ESBL blaSHV variants (6/225) or a combination of both blaCTX-M and pAmpC (4/225). Forty-four STs were identified, with ST131 representing 101/225 isolates, within which clade C2 was dominant (54/101). Ciprofloxacin resistance was observed in 128/225 (56.9%) of sequenced isolates, predominantly associated with fluoroquinolone-resistant clones ST131 and ST1193.


Most cefalexin-resistant E. coli isolates were cefotaxime resistant, predominantly caused by blaCTX-M carriage. The correlation between cefotaxime resistance and ciprofloxacin resistance was largely attributable to the high-risk pandemic clones ST131 and ST1193. Localized epidemiological data provide greater resolution than regional data and can be valuable for informing treatment choices in the primary care setting.


© 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; Cephalosporins; Fluoroquinolones; E. Coli; UTI; Cefalexin; Cefotaxime; UK; England.