Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About JCM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Journal of Clinical Microbiology
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About JCM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
Bacteriology

Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans

C. W. Knetsch, N. Kumar, S. C. Forster, T. R. Connor, H. P. Browne, C. Harmanus, I. M. Sanders, S. R. Harris, L. Turner, T. Morris, M. Perry, F. Miyajima, P. Roberts, M. Pirmohamed, J. G. Songer, J. S. Weese, A. Indra, J. Corver, M. Rupnik, B. W. Wren, T. V. Riley, E. J. Kuijper, T. D. Lawley
Brad Fenwick, Editor
C. W. Knetsch
aSection Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
N. Kumar
bHost-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
S. C. Forster
bHost-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
cCentre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
dDepartment of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
T. R. Connor
eCardiff School of Biosciences, Sir Martin Evans Building, Cardiff, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
H. P. Browne
bHost-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
C. Harmanus
aSection Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
I. M. Sanders
aSection Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
S. R. Harris
fPathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
L. Turner
gPublic Health Wales, Microbiology, Wales, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
T. Morris
gPublic Health Wales, Microbiology, Wales, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
M. Perry
gPublic Health Wales, Microbiology, Wales, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
F. Miyajima
hInstitute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
P. Roberts
hInstitute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
M. Pirmohamed
hInstitute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
J. G. Songer
iDepartment of Veterinary Science and Microbiology, The University of Arizona, Tucson, Arizona, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
J. S. Weese
jDepartment of Pathobiology, Canada Veterinary College, University of Guelph, Guelph, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
A. Indra
kInstitute of Medical Microbiology and Hygiene, Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Vienna, Austria
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
J. Corver
aSection Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
M. Rupnik
lFaculty of Medicine, University of Maribor, Maribor, Slovenia
mNational Laboratory for Health, Environment and Food, Maribor, Slovenia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
B. W. Wren
nDepartment of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, University of London, London, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
T. V. Riley
oDepartment of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Western Australia, Australia
pMicrobiology & Immunology, School of Pathology & Laboratory Medicine, The University of Western Australia, Western Australia, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
E. J. Kuijper
aSection Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
T. D. Lawley
bHost-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Brad Fenwick
University of Tennessee at Knoxville
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/JCM.01384-17
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

ABSTRACT

The emergence of Clostridium difficile as a significant human diarrheal pathogen is associated with the production of highly transmissible spores and the acquisition of antimicrobial resistance genes (ARGs) and virulence factors. Unlike the hospital-associated C. difficile RT027 lineage, the community-associated C. difficile RT078 lineage is isolated from both humans and farm animals; however, the geographical population structure and transmission networks remain unknown. Here, we applied whole-genome phylogenetic analysis of 248 C. difficile RT078 strains from 22 countries. Our results demonstrate limited geographical clustering for C. difficile RT078 and extensive coclustering of human and animal strains, thereby revealing a highly linked intercontinental transmission network between humans and animals. Comparative whole-genome analysis reveals indistinguishable accessory genomes between human and animal strains and a variety of antimicrobial resistance genes in the pangenome of C. difficile RT078. Thus, bidirectional spread of C. difficile RT078 between farm animals and humans may represent an unappreciated route disseminating antimicrobial resistance genes between humans and animals. These results highlight the importance of the “One Health” concept to monitor infectious disease emergence and the dissemination of antimicrobial resistance genes.

INTRODUCTION

Over the past decade, Clostridium difficile has emerged as the primary cause of infectious antibiotic-associated diarrhea in hospitalized patients (1). Unlike other common health care-associated pathogens, C. difficile produces resistant spores that facilitate host-to-host transmission and enable long term survival and dispersal in the health care system and the wider environment (2). The emergence of epidemic C. difficile ribotype (RT) 027 (NAP1/ST-1), responsible for many large-scale hospital outbreaks worldwide (3, 4), has been linked to environmental spore contamination and the acquisition of fluoroquinolone resistance (5). Enhanced research focus on C. difficile in the aftermath of the C. difficile RT027 outbreaks has revealed other evolutionarily distinct C. difficile lineages, in particular C. difficile RT078 (NAP07-08/ST-11), that are now emerging for unknown reasons as significant human pathogens (6).

The “One Health” concept, which connects the health of humans to the health of animals and their shared environments, represents a relevant framework for understanding the emergence and spread of pathogens. C. difficile RT078 is commonly isolated from both humans and farm animals (7) and is increasingly recognized as a causative agent of both health care- and community-associated C. difficile infection (CDI) (8). This lineage typically affects a younger population (9) and results in higher mortality than infection by C. difficile RT027 (10). Standard genotyping tools have highlighted genetic similarities between human and animal C. difficile RT078 (11–13) strains, raising the possibility of zoonotic transmission (14). Nevertheless, the exact evolutionary and epidemiological relationships between human and animal C. difficile RT078 strains remain unknown due to the lack of discriminatory power of these typing methods and the clonal nature of C. difficile lineages. Recently, using whole-genome phylogeny, we reported that asymptomatic farmers and their pigs can be colonized with clonal C. difficile RT078 isolates, demonstrating evidence for spread between animals and humans (15).

MATERIALS AND METHODS

Collection of C. difficile strains.C. difficile laboratories worldwide were asked to send a diverse representation of their C. difficile 078 collections to the Lawley Laboratory, hosted at the Wellcome Trust Sanger Institute. Sample shipping was coordinated by the Lawley Laboratory. After receiving all shipped samples, DNA extraction was performed batchwise by one person using the same protocol and reagents to minimize bias. Phenol-chloroform was the preferred method for extraction, since it provides high DNA yield and intact chromosomal DNA. The genomes of 182 strains designated C. difficile RT078 (/NAP07-08/ST-11) by PCR ribotyping (16) were sequenced and combined with our previous collection of 65 strains of C. difficile RT078 (15), making a total of 247 strains analyzed in this study. These 247 strains were collected between 1996 and 2012 and are comprised of representative strains from 4 continents (North America, Europe, Australia, and Asia). Of these strains, 183 were derived from humans, 59 from animals (pigs, cattle, horses, and poultry), 4 from foods and 1 from an environmental sample. Details of all sequenced strains are listed in Table S1 in the supplemental material, including the European Nucleotide Archive (ENA) sample accession numbers. Metadata of the C. difficile RT078 strains has been made freely publicly available through Microreact (https://microreact.org/project/rJs-SYgMe) (17).

Bacterial culture and genomic DNA preparation.C. difficile strains were cultured on blood agar plates (bioMérieux, The Netherlands) for 48 h, inoculated into liquid medium (brain heart infusion [BHI] broth supplemented with yeast extract and cysteine) and grown overnight (ca. 16 h) anaerobically at 37°C. Cells were pelleted and washed with phosphate-buffered saline (PBS), and genomic DNA preparation was performed using a phenol-chloroform extraction as previously described (18).

DNA sequencing, assembly, and annotation.Paired-end multiplex libraries were prepared and sequenced using an Illumina Hi-Seq platform with fragment size of 200 to 300 bp and a read length of 100 bp as previously described (19, 20). An inhouse pipeline developed at the Wellcome Trust Sanger Institute (https://github.com/sanger-pathogens/Bio-AutomatedAnnotation) was used for bacterial assembly and annotation. It consisted of de novo assembly for each sequenced genome using Velvet v. 1.2.10 (21), SSPACE v. 2.0 (22), and GapFiller v. 1.1 (23) followed by annotation using Prokka v. 1.5.1 (24).

Construction and analysis of the pangenome.We used the pangenome pipeline Roary (25) to identify the C. difficile RT078 pangenome. Roary takes annotated draft assemblies in GFF3 format that were produced by Prokka (24). Predicted coding regions were extracted from the input and converted to protein sequences. Partial sequences (>5% nucleotides unknown or sequence length less than 120 nucleotides) were filtered, and the remaining sequences were iteratively clustered with CD-HIT (Cluster Database at High Identity with Tolerance), beginning with a sequence identity of 100% and matching length of 100% and continuing down to a default sequence identity of 98%. One final clustering step was performed again with CD-HIT, with a sequence identity of 100% and leaving one representative sequence for each cluster in a protein FASTA file. This was followed by a comprehensive pairwise comparison with blastp on the reduced sequences, with a default sequence identity percentage of 95% and matching length of 100%. The pangenome embodies the core genome, defined as those genes present in at least 90% of the genomes, and the accessory genome, defined as those genes present in between 10% and 90% of the genomes. Rare variant genes, found in less than 10% of genomes, were discarded.

Core gene (n = 3,368) alignment, an output from Roary, was used to construct the phylogenetic structure of 248 C. difficile strains. Single nucleotide polymorphisms (SNPs) were extracted from the core gene alignment using SNP-sites (26). A maximum likelihood tree based on SNP alignment was constructed using FastTree with the settings -gamma and -gtr (27), and the tree was visualized with iTOL (28).

Average nucleotide identity (ANI) analysis.Using Roary analysis, C. difficile RT078 strains isolated from humans and animals with identical core genomes were extracted using an inhouse R script. ANI was calculated by performing pairwise comparison of genome assemblies of these C. difficile RT078 strains using MUMmer (29).

Identification of antimicrobial resistance gene sequence.Antimicrobial resistance genes were identified within the C. difficile RT078 genomes through comparison to the CARD database with the ARIBA (Antimicrobial Resistance Identification By Assembly) software (https://github.com/sanger-pathogens/ariba).

Accession number(s).The genomes sequenced in this study were deposited in the ENA under accession numbers ERS005819 to ERS005821, ERS005823, ERS005825 to ERS005827, ERS005829, ERS005830, ERS005834 to ERS005837, ERS005839, ERS005840, ERS005842, ERS005847, ERS138003 to ERS138016, ERS138019 to ERS138025, ERS138057, ERS138067, ERS138068, ERS138087 to ERS138090, ERS138092 to ERS138100, ERS138103 to ERS138105, ERS138107, ERS138115 to ERS138120, ERS138122, ERS138124 to ERS138127, ERS138130, ERS138132 to ERS138149, ERS138151, ERS138152, ERS138154, ERS1645161 to ERS1645168, ERS188478 to ERS188487, ERS188489, ERS188492 to ERS188495, ERS188498, ERS188502 to ERS188504, ERS188534, ERS188555 to ERS188567, ERS188569 to ERS188592, ERS188658 to ERS188667, ERS199743, ERS199744, ERS199746 to ERS199751, ERS199753, ERS199755, ERS199756, ERS199759, ERS199762, ERS199765, ERS199826, and ERS199827 (see Table S1 in the supplemental material).

RESULTS AND DISCUSSION

Here we assess the broad genetic diversity of C. difficile RT078, by performing whole-genome sequence analysis of 247 strains isolated predominantly from humans and animals that were collected from 22 countries across North America, Europe, Australia, and Asia between 1996 and 2012 (https://microreact.org/project/rJs-SYgMe) (Table S1). We explored the phylogenetic structure of C. difficile RT078 by generating a core genome maximum likelihood phylogeny that included the 247 C. difficile RT078 strains and the reference genome of C. difficile M120 (n = 248) (Fig. 1). Superimposing the geographic origin of strains revealed considerable coclustering of European (dark green) and North American (purple) strains across the phylogeny (Fig. 1). Permutation analysis on randomly generated equalized subsets of European (dark green) and North American (purple) genomes confirmed coclustering of geographically diverse strains (see Fig. S1 in the supplemental material). In addition, the absence of a single clade of C. difficile RT078 isolated in Australia (light green) is also suggestive of sporadic transmission between Europe and Australia (Fig. 1). Overall, the observed lack of geographic clustering is characteristic of repeated international transmission.

FIG 1
  • Open in new tab
  • Download powerpoint
FIG 1

Phylogeography of human and animal Clostridium difficile RT078 strains. Maximum likelihood, midpoint-rooted phylogenetic tree of 248 genomes represents strains isolated from human (dark blue), animal (red), food (orange), and environmental (light blue) sources and collected from Europe (dark green), North America (purple), Asia (pink), and Australia (light green). Branches with bootstrap confidence values above 0.7 are shown as solid lines. The phylogeny demonstrates clear mixing of European and North American strains, indicating multiple transmission events between continents, and mixing of human and animal strains, indicating multiple transmissions events between these hosts. Closely related clusters (see Table 1) containing both human and animal isolates are labeled 1 through 6 and highlighted in yellow.

We next examined the phylogenetic distribution of strains isolated from humans (n = 184) and animals (n = 59) to understand the potential for zoonotic spread. This analysis identified examples of human to human and animal to animal spread and strong evidence of bidirectional spread of C. difficile RT078 between animals and humans across the phylogeny. These observations are supported by the extensive coclustering of human (blue lines) and animal strains (red lines) (Fig. 1). Focused analysis of closely related C. difficile RT078 strains identified 6 clusters containing both animal and human isolates with an identical core genome and highly similar whole genomes (ANI, ≥99.73%; Table 1). Surprisingly, Cluster 1 consists of an animal strain from Canada and human strains from the United Kingdom, indicating that zoonotic spread of C. difficile is not confined to a local population of humans and animals, as found previously (15). The existence of highly related human and animal isolates suggests that C. difficile RT078 has frequently spread between animals and humans.

View this table:
  • View inline
  • View popup
TABLE 1

Six highly similar C. difficile RT078 clusters identified as identical through core genome analysisa

Next, a detailed analysis of the accessory genome, including mobile genetic elements, was performed to further explore the genomic similarities between human and animal strains. Of the 6,239 unique genes present across our genome collection, 3,368 genes (54.0%) were assigned to the core genome, leaving 2,871 genes (46.0%) present in the accessory genome (see Fig. S2 in the supplemental material). Considering only the human and animal isolates, 2,859 accessory genes were identified. The vast majority of human- and animal-specific accessory genes were found at low frequencies in the population (Fig. 2A). We observed no statistically significant difference in the number of strains carrying accessory genes exclusive to either the human or the animal population (χ2 test P value, 0.39). Considering only those accessory genes present in at least 10% of isolates (n = 465), 461 (99.1%) were identified in both human and animal isolates. The absence of accessory genes unique to either group either demonstrates that C. difficile has a stable accessory genome that is host-independent or provides further support for the frequent transmission of C. difficile between host populations.

FIG 2
  • Open in new tab
  • Download powerpoint
FIG 2

Indistinguishable accessory genome of C. difficile RT078 harbors a variety of antimicrobial resistance genes. (A) The accessory genes (n = 2,859) categorized according to host origin. The number of accessory genes (x axis) only found in human genomes (dark blue), only found in animal genomes (red), or found in both human and animal genomes (green) is plotted against the number of genomes in which these genes are present (y axis). (B) The frequency of predicted antimicrobial resistance genes (ARGs) within the 243 C. difficile RT078 strains. Human (dark blue) and animal (red) isolation sources are shown by color.

Given the high percentage of mobile elements, including antimicrobial resistance genes harbored by C. difficile genomes (5, 6), we next sought to analyze distribution of different ARGs in the pangenome of human and animal strains. In total, 22 different putative ARGs are present in the 243 C. difficile RT078 genomes (Fig. 2B). The most common ARG was the chromosome-encoded cdeA, a well-known multidrug transporter that was detected in all strains; however, other common genes included those encoding resistance to aminoglycosides, tetracycline, and erythromycin (Fig. 2B). Importantly, no specific ARGs were statistically enriched in the animal isolates; however, the ermB (erythromycin resistance methylase) gene was identified in the human isolates (Fisher's exact test, Q value = 1.25 × 10−07). These results provide further support that a clonal C. difficile RT078 population containing a broad array of ARGs—exclusive of ermB, which has signs of unknown selective pressure in the human isolates—is spreading between humans and farm animals.

C. difficile is an ancient, genetically diverse species that has only emerged as a significant human pathogen over the past 4 decades. It remains to be determined why evolutionarily distinct lineages such as C. difficile RT027 and RT078 (6) are simultaneously emerging to cause disease in the human population. Previously, we have demonstrated that C. difficile RT027 acquired fluoroquinolone resistance during the 1990s in North America and rapidly spread through the global health care system (5). Here, we demonstrated that C. difficile RT078 has spread multiple times between continents, in particular between North America and Europe, highlighting that C. difficile emergence and spread is a global issue. In contrast to the distinct animal- and human-associated populations observed for the multidrug-resistant enteric pathogen Salmonella enterica serovar Typhimurium strain DT104 (30), we demonstrated that C. difficile RT078 is a clonal population moving frequently between livestock and human hosts, with no geographical barriers. Although the original reservoir remains unknown, the reciprocal transmission between humans and farm animals emphasizes the importance of a comprehensive One Health perspective in managing and controlling C. difficile RT078.

ACKNOWLEDGMENTS

We acknowledge the Wellcome Trust (grant 098051), the United Kingdom Medical Research Council (grants PF451 to T.D.L., MR/L015080/1 to T.R.C., and MR/K000551/1to F.M., M.P., B.W.W. and T.D.L.), the Australian National Health and Medical Research Council (grant 1091097 to S.C.F.), and the Victorian Government's Operational and Infrastructure Support Program (to S.C.F.) for financial support. C.W.K. was supported by a ZonMw grant (125020004).

We are grateful to A. Neville and the Wellcome Trust Sanger Institute Pathogen Informatics team for their input.

We declare that we have no competing financial interests.

FOOTNOTES

    • Received 29 August 2017.
    • Returned for modification 28 October 2017.
    • Accepted 8 December 2017.
    • Accepted manuscript posted online 13 December 2017.
  • Supplemental material for this article may be found at https://doi.org/10.1128/JCM.01384-17.

  • Copyright © 2018 Knetsch et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Lessa FC,
    2. Winston LG,
    3. McDonald LC
    , Emerging Infections Program CdST. 2015. Burden of Clostridium difficile infection in the United States. N Engl J Med 372:2369–2370. doi:10.1056/NEJMoa1408913.
    OpenUrlCrossRefPubMed
  2. 2.↵
    1. Leffler DA,
    2. Lamont JT
    . 2015. Clostridium difficile Infection. N Engl J Med 372:287–288. doi:10.1056/NEJMc1506004.
    OpenUrlCrossRef
  3. 3.↵
    1. Kuijper EJ,
    2. Coignard B,
    3. Tull P
    ; ESCMID Study Group for Clostridium difficile; EU Member States; European Centre for Disease Prevention and Control. 2006. Emergence of Clostridium difficile-associated disease in North America and Europe. Clin Microbiol Infect 12(Suppl 6):S2–S18. doi:10.1111/j.1469-0691.2006.01580.x.
    OpenUrlCrossRef
  4. 4.↵
    1. Loo VG,
    2. Poirier L,
    3. Miller MA,
    4. Oughton M,
    5. Libman MD,
    6. Michaud S,
    7. Bourgault AM,
    8. Nguyen T,
    9. Frenette C,
    10. Kelly M,
    11. Vibien A,
    12. Brassard P,
    13. Fenn S,
    14. Dewar K,
    15. Hudson TJ,
    16. Horn R,
    17. Rene P,
    18. Monczak Y,
    19. Dascal A
    . 2005. A predominantly clonal multi-institutional outbreak of Clostridium difficile-associated diarrhea with high morbidity and mortality. N Engl J Med 353:2442–2449. doi:10.1056/NEJMoa051639.
    OpenUrlCrossRefPubMedWeb of Science
  5. 5.↵
    1. He M,
    2. Miyajima F,
    3. Roberts P,
    4. Ellison L,
    5. Pickard DJ,
    6. Martin MJ,
    7. Connor TR,
    8. Harris SR,
    9. Fairley D,
    10. Bamford KB,
    11. D'Arc S,
    12. Brazier J,
    13. Brown D,
    14. Coia JE,
    15. Douce G,
    16. Gerding D,
    17. Kim HJ,
    18. Koh TH,
    19. Kato H,
    20. Senoh M,
    21. Louie T,
    22. Michell S,
    23. Butt E,
    24. Peacock SJ,
    25. Brown NM,
    26. Riley T,
    27. Songer G,
    28. Wilcox M,
    29. Pirmohamed M,
    30. Kuijper E,
    31. Hawkey P,
    32. Wren BW,
    33. Dougan G,
    34. Parkhill J,
    35. Lawley TD
    . 2013. Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet 45:109–113. doi:10.1038/ng.2478.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. He M,
    2. Sebaihia M,
    3. Lawley TD,
    4. Stabler RA,
    5. Dawson LF,
    6. Martin MJ,
    7. Holt KE,
    8. Seth-Smith HM,
    9. Quail MA,
    10. Rance R,
    11. Brooks K,
    12. Churcher C,
    13. Harris D,
    14. Bentley SD,
    15. Burrows C,
    16. Clark L,
    17. Corton C,
    18. Murray V,
    19. Rose G,
    20. Thurston S,
    21. van Tonder A,
    22. Walker D,
    23. Wren BW,
    24. Dougan G,
    25. Parkhill J
    . 2010. Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A 107:7527–7532. doi:10.1073/pnas.0914322107.
    OpenUrlAbstract/FREE Full Text
  7. 7.↵
    1. Rupnik M,
    2. Widmer A,
    3. Zimmermann O,
    4. Eckert C,
    5. Barbut F
    . 2008. Clostridium difficile toxinotype V, ribotype 078, in animals and humans. J Clin Microbiol 46:2146. doi:10.1128/JCM.00598-08.
    OpenUrlFREE Full Text
  8. 8.↵
    1. Bauer MP,
    2. Notermans DW,
    3. van Benthem BH,
    4. Brazier JS,
    5. Wilcox MH,
    6. Rupnik M,
    7. Monnet DL,
    8. van Dissel JT,
    9. Kuijper EJ
    ; ECDIS Study Group. 2011. Clostridium difficile infection in Europe: a hospital-based survey. Lancet 377:63–73. doi:10.1016/S0140-6736(10)61266-4.
    OpenUrlCrossRefPubMedWeb of Science
  9. 9.↵
    1. Goorhuis A,
    2. Bakker D,
    3. Corver J,
    4. Debast SB,
    5. Harmanus C,
    6. Notermans DW,
    7. Bergwerff AA,
    8. Dekker FW,
    9. Kuijper EJ
    . 2008. Emergence of Clostridium difficile infection due to a new hypervirulent strain, polymerase chain reaction ribotype 078. Clin Infect Dis 47:1162–1170. doi:10.1086/592257.
    OpenUrlCrossRefPubMedWeb of Science
  10. 10.↵
    1. Walker AS,
    2. Eyre DW,
    3. Wyllie DH,
    4. Dingle KE,
    5. Griffiths D,
    6. Shine B,
    7. Oakley S,
    8. O'Connor L,
    9. Finney J,
    10. Vaughan A,
    11. Crook DW,
    12. Wilcox MH,
    13. Peto TE
    , Infections in Oxfordshire Research D. 2013. Relationship between bacterial strain type, host biomarkers, and mortality in Clostridium difficile infection. Clin Infect Dis 56:1589–1600. doi:10.1093/cid/cit127.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Bakker D,
    2. Corver J,
    3. Harmanus C,
    4. Goorhuis A,
    5. Keessen EC,
    6. Fawley WN,
    7. Wilcox MH,
    8. Kuijper EJ
    . 2010. Relatedness of human and animal Clostridium difficile PCR ribotype 078 isolates determined on the basis of multilocus variable-number tandem-repeat analysis and tetracycline resistance. J Clin Microbiol 48:3744–3749. doi:10.1128/JCM.01171-10.
    OpenUrlAbstract/FREE Full Text
  12. 12.↵
    1. Keel K,
    2. Brazier JS,
    3. Post KW,
    4. Weese S,
    5. Songer JG
    . 2007. Prevalence of PCR ribotypes among Clostridium difficile isolates from pigs, calves, and other species. J Clin Microbiol 45:1963–1964. doi:10.1128/JCM.00224-07.
    OpenUrlAbstract/FREE Full Text
  13. 13.↵
    1. Keessen EC,
    2. Gaastra W,
    3. Lipman LJ
    . 2011. Clostridium difficile infection in humans and animals, differences and similarities. Vet Microbiol 153:205–217. doi:10.1016/j.vetmic.2011.03.020.
    OpenUrlCrossRefPubMed
  14. 14.↵
    1. Squire MM,
    2. Riley TV
    . 2013. Clostridium difficile infection in humans and piglets: a ‘One Health’ opportunity. Curr Top Microbiol Immunol 365:299–314. doi:10.1007/82_2012_237.
    OpenUrlCrossRef
  15. 15.↵
    1. Knetsch CW,
    2. Connor TR,
    3. Mutreja A,
    4. van Dorp SM,
    5. Sanders IM,
    6. Browne HP,
    7. Harris D,
    8. Lipman L,
    9. Keessen EC,
    10. Corver J,
    11. Kuijper EJ,
    12. Lawley TD
    . 2014. Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011. Euro Surveill 19(45):pii=20954. doi:10.2807/1560-7917.ES2014.19.45.20954.
    OpenUrlCrossRef
  16. 16.↵
    1. Stubbs SL,
    2. Brazier JS,
    3. O'Neill GL,
    4. Duerden BI
    . 1999. PCR targeted to the 16S-23S rRNA gene intergenic spacer region of Clostridium difficile and construction of a library consisting of 116 different PCR ribotypes. J Clin Microbiol 37:461–463.
    OpenUrlAbstract/FREE Full Text
  17. 17.↵
    1. Argimon S,
    2. Abudahab K,
    3. Goater RJ,
    4. Fedosejev A,
    5. Bhai J,
    6. Glasner C,
    7. Feil EJ,
    8. Holden MT,
    9. Yeats CA,
    10. Grundmann H,
    11. Spratt BG,
    12. Aanensen DM
    . 2016. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom 2:e000093. doi:10.1099/mgen.0.000093.
    OpenUrlCrossRefPubMed
  18. 18.↵
    1. Croucher NJ,
    2. Harris SR,
    3. Fraser C,
    4. Quail MA,
    5. Burton J,
    6. van der Linden M,
    7. McGee L,
    8. von Gottberg A,
    9. Song JH,
    10. Ko KS,
    11. Pichon B,
    12. Baker S,
    13. Parry CM,
    14. Lambertsen LM,
    15. Shahinas D,
    16. Pillai DR,
    17. Mitchell TJ,
    18. Dougan G,
    19. Tomasz A,
    20. Klugman KP,
    21. Parkhill J,
    22. Hanage WP,
    23. Bentley SD
    . 2011. Rapid pneumococcal evolution in response to clinical interventions. Science 331:430–434. doi:10.1126/science.1198545.
    OpenUrlAbstract/FREE Full Text
  19. 19.↵
    1. Harris SR,
    2. Feil EJ,
    3. Holden MT,
    4. Quail MA,
    5. Nickerson EK,
    6. Chantratita N,
    7. Gardete S,
    8. Tavares A,
    9. Day N,
    10. Lindsay JA,
    11. Edgeworth JD,
    12. de Lencastre H,
    13. Parkhill J,
    14. Peacock SJ,
    15. Bentley SD
    . 2010. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327:469–474. doi:10.1126/science.1182395.
    OpenUrlAbstract/FREE Full Text
  20. 20.↵
    1. Quail MA,
    2. Kozarewa I,
    3. Smith F,
    4. Scally A,
    5. Stephens PJ,
    6. Durbin R,
    7. Swerdlow H,
    8. Turner DJ
    . 2008. A large genome center's improvements to the Illumina sequencing system. Nat Methods 5:1005–1010. doi:10.1038/nmeth.1270.
    OpenUrlCrossRefPubMedWeb of Science
  21. 21.↵
    1. Zerbino DR,
    2. Birney E
    . 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. doi:10.1101/gr.074492.107.
    OpenUrlAbstract/FREE Full Text
  22. 22.↵
    1. Boetzer M,
    2. Henkel CV,
    3. Jansen HJ,
    4. Butler D,
    5. Pirovano W
    . 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578–579. doi:10.1093/bioinformatics/btq683.
    OpenUrlCrossRefPubMedWeb of Science
  23. 23.↵
    1. Boetzer M,
    2. Pirovano W
    . 2012. Toward almost closed genomes with GapFiller. Genome Biol 13:R56. doi:10.1186/gb-2012-13-6-r56.
    OpenUrlCrossRefPubMed
  24. 24.↵
    1. Seemann T
    . 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi:10.1093/bioinformatics/btu153.
    OpenUrlCrossRefPubMedWeb of Science
  25. 25.↵
    1. Page AJ,
    2. Cummins CA,
    3. Hunt M,
    4. Wong VK,
    5. Reuter S,
    6. Holden MT,
    7. Fookes M,
    8. Falush D,
    9. Keane JA,
    10. Parkhill J
    . 2015. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691–3693. doi:10.1093/bioinformatics/btv421.
    OpenUrlCrossRefPubMed
  26. 26.↵
    1. Page AJ,
    2. Taylor B,
    3. Delaney AJ,
    4. Soares J,
    5. Seemann T,
    6. Keane JA,
    7. Harris SR
    . 2016. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microbial Genomics 2:e000056. doi:10.1099/mgen.0.000056.
    OpenUrlCrossRefPubMed
  27. 27.↵
    1. Price MN,
    2. Dehal PS,
    3. Arkin AP
    . 2009. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650. doi:10.1093/molbev/msp077.
    OpenUrlCrossRefPubMedWeb of Science
  28. 28.↵
    1. Letunic I,
    2. Bork P
    . 2011. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39:W475–W478. doi:10.1093/nar/gkr201.
    OpenUrlCrossRefPubMedWeb of Science
  29. 29.↵
    1. Delcher AL,
    2. Phillippy A,
    3. Carlton J,
    4. Salzberg SL
    . 2002. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 30:2478–2483. doi:10.1093/nar/30.11.2478.
    OpenUrlCrossRefPubMedWeb of Science
  30. 30.↵
    1. Mather AE,
    2. Reid SW,
    3. Maskell DJ,
    4. Parkhill J,
    5. Fookes MC,
    6. Harris SR,
    7. Brown DJ,
    8. Coia JE,
    9. Mulvey MR,
    10. Gilmour MW,
    11. Petrovska L,
    12. de Pinna E,
    13. Kuroda M,
    14. Akiba M,
    15. Izumiya H,
    16. Connor TR,
    17. Suchard MA,
    18. Lemey P,
    19. Mellor DJ,
    20. Haydon DT,
    21. Thomson NR
    . 2013. Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science 341:1514–1517. doi:10.1126/science.1240578.
    OpenUrlAbstract/FREE Full Text
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans
C. W. Knetsch, N. Kumar, S. C. Forster, T. R. Connor, H. P. Browne, C. Harmanus, I. M. Sanders, S. R. Harris, L. Turner, T. Morris, M. Perry, F. Miyajima, P. Roberts, M. Pirmohamed, J. G. Songer, J. S. Weese, A. Indra, J. Corver, M. Rupnik, B. W. Wren, T. V. Riley, E. J. Kuijper, T. D. Lawley
Journal of Clinical Microbiology Feb 2018, 56 (3) e01384-17; DOI: 10.1128/JCM.01384-17

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print

Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Journal of Clinical Microbiology article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans
(Your Name) has forwarded a page to you from Journal of Clinical Microbiology
(Your Name) thought you would be interested in this article in Journal of Clinical Microbiology.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans
C. W. Knetsch, N. Kumar, S. C. Forster, T. R. Connor, H. P. Browne, C. Harmanus, I. M. Sanders, S. R. Harris, L. Turner, T. Morris, M. Perry, F. Miyajima, P. Roberts, M. Pirmohamed, J. G. Songer, J. S. Weese, A. Indra, J. Corver, M. Rupnik, B. W. Wren, T. V. Riley, E. J. Kuijper, T. D. Lawley
Journal of Clinical Microbiology Feb 2018, 56 (3) e01384-17; DOI: 10.1128/JCM.01384-17
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • INTRODUCTION
    • MATERIALS AND METHODS
    • RESULTS AND DISCUSSION
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

KEYWORDS

Clostridium difficile
RT078
intercontinental transmission
interhost transmission
accessory genome
One Health concept
antibiotic resistance

Related Articles

Cited By...

About

  • About JCM
  • Editor in Chief
  • Board of Editors
  • Editor Conflicts of Interest
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Resources for Clinical Microbiologists
  • Ethics
  • Contact Us

Follow #JClinMicro

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

 

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Print ISSN: 0095-1137; Online ISSN: 1098-660X