#Circulation of #plasmids harboring #resistance genes to #quinolones and/or extended spectrum #cephalosporins in multiple #Salmonella enterica serotypes from #swine in the #US (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Circulation of plasmids harboring resistance genes to quinolones and/or extended spectrum cephalosporins in multiple Salmonella enterica serotypes from swine in the United States

Ehud Elnekave, Samuel L. Hong, Seunghyun Lim, Shivdeep Singh Hayer, Dave Boxrud, Angela J. Taylor, Victoria Lappi, Noelle Noyes, Timothy J. Johnson, Albert Rovira, Peter Davies,Andres Perez, Julio Alvarez

DOI: 10.1128/AAC.02602-18

 

ABSTRACT

Nontyphoidal Salmonella enterica (NTS) poses a major public-health risk worldwide that is amplified by the existence of antimicrobial resistant strains, especially to quinolones and extended-spectrum cephalosporins (ESC). Little is known on the dissemination of plasmids harboring the acquired genetic determinants that confer resistance to these antimicrobials across NTS serotypes from livestock in the United States.

NTS isolates (n=183) from U.S. swine clinical cases retrieved during 2014-2016 were selected for sequencing based on their phenotypic resistance to enrofloxacin (quinolone) or ceftiofur (3rd-generation cephalosporin). De-novo assemblies were used to identify chromosomal mutations and acquired antimicrobial resistance genes (AARGs). In addition, plasmids harboring AARGs were identified using short-read assemblies and characterized using a multi-step approach that was validated by long-read sequencing.

AARGs to quinolones (qnrB15/qnrB19/qnrB2/qnrD/qnrS1/qnrS2/aac(6′)Ib-cr) and ESC (blaCMY-2/blaCTX-M-1/blaCTX-M-27/blaSHV-12) were distributed across serotypes, and were harbored by several plasmids. In addition, chromosomal mutations associated with resistance to quinolones were identified in the target enzyme and efflux pump regulation genes. The predominant plasmid harboring the prevalent qnrB19 gene was distributed across serotypes. It was identical to a plasmid previously reported in S. Anatum from swine in the U.S. (KY991369.1), and similar to Escherichia coli plasmids from humans in South America (GQ374157.1 and JN979787.1). Our findings suggest that plasmids harboring AARGs to critically important antimicrobials are present in multiple NTS serotypes circulating in swine in the U.S. and can contribute to resistance expansion through horizontal transmission.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Antibiotics; Drugs Resistance; Cephalosporins; Quinolones; Pigs; USA.

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#Bat-Origin #Coronaviruses Expand Their #Host Range to #Pigs (Front Microbiol., abstract)

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

Trends Microbiol. 2018 Jun;26(6):466-470. doi: 10.1016/j.tim.2018.03.001. Epub 2018 Apr 18.

Bat-Origin Coronaviruses Expand Their Host Range to Pigs.

Wang L1, Su S2, Bi Y3, Wong G4, Gao GF5.

Author information: 1 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China. 2 MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China. 3 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen 518112, China. 4 Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen 518112, China. 5 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen 518112, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China. Electronic address: gaof@im.ac.cn.

 

Abstract

Infections with bat-origin coronaviruses have caused severe illness in humans by ‘host jump’. Recently, novel bat-origin coronaviruses were found in pigs. The large number of mutations on the receptor-binding domain allowed the viruses to infect the new host, posing a potential threat to both agriculture and public health.

Copyright © 2018 Elsevier Ltd. All rights reserved.

KEYWORDS: SeACoV; bat-origin; host jump; public health; swine enteric alphacoronaviruses

PMID: 29680361 DOI: 10.1016/j.tim.2018.03.001 [Indexed for MEDLINE]

Keywords: Coronavirus; Bats; Pigs; Alphacoronavirus.

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#Human-Origin #Influenza A(#H3N2) #Reassortant Viruses in #Swine, Southeast #Mexico (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 4—April 2019 / Research

Human-Origin Influenza A(H3N2) Reassortant Viruses in Swine, Southeast Mexico

Martha I. Nelson  , Carine Souza, Nídia S. Trovão, Andres Diaz, Ignacio Mena, Albert Rovira, Amy L. Vincent, Montserrat Torremorell, Douglas Marthaler1, and Marie R. Culhane

Author affiliations: National Institutes of Health, Bethesda, Maryland, USA (M.I. Nelson, N.S. Trovão); National Animal Disease Center, Ames, Iowa, USA (C. Souza, A.L. Vincent); Icahn School of Medicine at Mount Sinai, New York, New York, USA (N.S. Trovão, I. Mena); University of Minnesota, Saint Paul, Minnesota, USA (A. Diaz, A. Rovira, M. Torremorell, D. Marthaler, M.R. Culhane)

 

Abstract

The genetic diversity of influenza A viruses circulating in swine in Mexico complicates control efforts in animals and presents a threat to humans, as shown by influenza A(H1N1)pdm09 virus. To describe evolution of swine influenza A viruses in Mexico and evaluate strains for vaccine development, we sequenced the genomes of 59 viruses and performed antigenic cartography on strains from 5 regions. We found that genetic and antigenic diversity were particularly high in southeast Mexico because of repeated introductions of viruses from humans and swine in other regions in Mexico. We identified novel reassortant H3N2 viruses with genome segments derived from 2 different viruses that were independently introduced from humans into swine: pandemic H1N1 viruses and seasonal H3N2 viruses. The Mexico swine viruses are antigenically distinct from US swine lineages. Protection against these viruses is unlikely to be afforded by US virus vaccines and would require development of new vaccines specifically targeting these diverse strains.

Keywords: Seasonal Influenza; Swine Influenza; Reassortant Strain; Pigs; Human; H1N1pdm09; H3N2; Mexico.

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The #antimicrobial #resistome in relation to antimicrobial use and #biosecurity in #pig #farming, a metagenome-wide association study in nine #European countries (J Antimicrob Chemother., abstract)

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

The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries

Liese Van Gompel, Roosmarijn E C Luiken, Steven Sarrazin, Patrick Munk, Berith E Knudsen, Rasmus B Hansen, Alex Bossers, Frank M Aarestrup, Jeroen Dewulf, Jaap A Wagenaar, Dik J Mevius, Heike Schmitt, Dick J J Heederik, Alejandro Dorado-García, Lidwien A M Smit, EFFORT consortium

Journal of Antimicrobial Chemotherapy, dky518, https://doi.org/10.1093/jac/dky518

Published: 14 January 2019

 

Abstract

Objectives

Previous studies in food-producing animals have shown associations between antimicrobial use (AMU) and resistance (AMR) in specifically isolated bacterial species. Multi-country data are scarce and only describe between-country differences. Here we investigate associations between the pig faecal mobile resistome and characteristics at the farm-level across Europe.

Methods

A cross-sectional study was conducted among 176 conventional pig farms from nine European countries. Twenty-five faecal samples from fattening pigs were pooled per farm and acquired resistomes were determined using shotgun metagenomics and the Resfinder reference database, i.e. the full collection of horizontally acquired AMR genes (ARGs). Normalized fragments resistance genes per kilobase reference per million bacterial fragments (FPKM) were calculated. Specific farm-level data (AMU, biosecurity) were collected. Random-effects meta-analyses were performed by country, relating farm-level data to relative ARG abundances (FPKM).

Results

Total AMU during fattening was positively associated with total ARG (total FPKM). Positive associations were particularly observed between widely used macrolides and tetracyclines, and ARGs corresponding to the respective antimicrobial classes. Significant AMU-ARG associations were not found for β-lactams and only few colistin ARGs were found, despite high use of these antimicrobial classes in younger pigs. Increased internal biosecurity was directly related to higher abundances of ARGs mainly encoding macrolide resistance. These effects of biosecurity were independent of AMU in mutually adjusted models.

Conclusions

Using resistome data in association studies is unprecedented and adds accuracy and new insights to previously observed AMU-AMR associations. Major components of the pig resistome are positively and independently associated with on-farm AMU and biosecurity conditions.

Issue Section: ORIGINAL RESEARCH

© 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; Macrolides; Colistin; Tetracyclines; Pigs; European Region.

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Detection of #mcr-mediated #colistin #resistance in #Escherichia coli isolated from #pigs in small-scale #farms in #Cambodia (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Detection of mcr-mediated colistin resistance in Escherichia coli isolated from pigs in small-scale farms in Cambodia

G Ström Hallenberg, S Börjesson, S Sokerya, T Sothyra, U Magnusson

DOI: 10.1128/AAC.02241-18

 

ABSTRACT

Colistin is today considered a last-line antimicrobial for the treatment of infections in humans caused by multidrug-resistant Enterobacteriaceae [1]. The dissemination of colistin resistance has received increased attention since a mobilized gene conferring resistance to colistin, mcr-1, was described in Enterobacteriaceae from humans and food-producing animals in China in 2015 [2], and additional gene homologs have since been identified [3-15].

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Antibiotics; Drugs Resistance; Colistin; MCR1; Pigs; Cambodia.

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The #Geographic Variation of #Surveillance and #Zoonotic #Spillover Potential of #Influenza Viruses in Domestic #Poultry and #Swine (Open Forum Infect Dis., abstract)

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

Open Forum Infect Dis. 2018 Nov 27;5(12):ofy318. doi: 10.1093/ofid/ofy318. eCollection 2018 Dec.

The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine.

Berger KA1,2, Pigott DM3, Tomlinson F1, Godding D1, Maurer-Stroh S4,5, Taye B4,6, Sirota FL4, Han A4,5, Lee RTC4, Gunalan V4, Eisenhaber F4,5, Hay SI3, Russell CA7.

Author information: 1 Department of Veterinary Medicine, University of Cambridge, United Kingdom. 2 Agrimetrics Ltd., Harpenden, United Kingdom. 3 Institute for Health Metrics and Evaluation, University of Washington, Seattle. 4 Bioinformatics Institute, ASTAR, Singapore. 5 National University of Singapore. 6 European Molecular Biology Laboratory, Deutsches Elektronen-Synchrotron, Hamburg, Germany. 7 Academic Medical Center, University of Amsterdam, The Netherlands.

 

Abstract

BACKGROUND:

Avian and swine influenza viruses circulate worldwide and pose threats to both animal and human health. The design of global surveillance strategies is hindered by information gaps on the geospatial variation in virus emergence potential and existing surveillance efforts.

METHODS:

We developed a spatial framework to quantify the geographic variation in outbreak emergence potential based on indices of potential for animal-to-human and secondary human-to-human transmission. We then compared our resultant raster model of variation in emergence potential with the global distribution of recent surveillance efforts from 359105 reports of surveillance activities.

RESULTS:

Our framework identified regions of Southeast Asia, Eastern Europe, Central America, and sub-Saharan Africa with high potential for influenza virus spillover. In the last 15 years, however, we found that 78.43% and 49.01% of high-risk areas lacked evidence of influenza virus surveillance in swine and domestic poultry, respectively.

CONCLUSIONS:

Our work highlights priority areas where improved surveillance and outbreak mitigation could enhance pandemic preparedness strategies.

KEYWORDS: avian influenza; outbreak; spillover; surveillance; swine influenza

PMID: 30619908 PMCID: PMC6309522 DOI: 10.1093/ofid/ofy318

Keywords: Avian Influenza; Poultry; Pigs; Pandemic preparedness.

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#Antimicrobial #resistance monitoring in commensal #enterococci from healthy #cattle, #pigs and #chickens across #Europe during 2004–14 (EASSA Study) (J Antimicrob Chemother., abstract)

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

Antimicrobial resistance monitoring in commensal enterococci from healthy cattle, pigs and chickens across Europe during 2004–14 (EASSA Study)

Anno de Jong, Shabbir Simjee, Markus Rose, Hilde Moyaert, Farid El Garch, Myriam Youala, EASSA Study Group

Journal of Antimicrobial Chemotherapy, dky537, https://doi.org/10.1093/jac/dky537

Published: 08 January 2019

 

Abstract

Objectives

The European Antimicrobial Susceptibility Surveillance in Animals (EASSA) programme collects zoonotic and commensal bacteria from healthy food-producing animals at slaughter and tracks their susceptibility to medically important antibiotics. Results for enterococci, collected over three time periods, are presented.

Methods

Intestinal contents from cattle, pigs and chickens were randomly sampled (five or six countries/host; at least four abattoirs/country; one sample/animal/farm) for isolation of enterococci; antimicrobial susceptibilities were centrally assessed by CLSI agar dilution. Clinical breakpoints (CLSI) and epidemiological cut-off values (EUCAST) were applied for data interpretation.

Results

In total, 2435 Enterococcus faecium and 1389 Enterococcus faecalis strains were recovered. Seven E. faecium/faecalis strains were linezolid resistant. One E. faecium strain was non-WT (NWT), with a daptomycin MIC of 8 mg/L. Clinical vancomycin resistance was very low or absent; eight strains had decreased susceptibility (MICs of 8 mg/L). Two strains were clinically resistant to tigecycline. Little resistance to ampicillin or gentamicin was observed. Clinical resistance of E. faecium to quinupristin/dalfopristin was slightly higher (2.2%–33.6%) and 38.5%–83.2% of the strains were classified NWT. Very high resistance to tetracycline (67.4%–79.1%) and erythromycin (27.1%–57.0%) was noted for E. faecium and E. faecalis in pigs and chickens. For both of these compounds, similar NWT results were observed for Enterococcus hirae (n = 935), Enterococcus durans (n = 286) and Enterococcus casseliflavus (n = 154) whereas the percentage of NWT for linezolid, tigecycline and vancomycin was generally zero or low.

Conclusions

In this pan-EU survey of commensal enterococci, antibiotic susceptibility varied widely between antibiotics, animal species, countries and enterococcal species. Clinical resistance to antibiotics that are critically important for human medicine was absent or low, except for erythromycin.

Issue Section: ORIGINAL RESEARCH

© 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; Enterococcus spp.; Pigs; Cattle; Poultry; European Region.

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