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
Epidemiology

Rapid and Specific Detection of the Escherichia coli Sequence Type 648 Complex within Phylogroup F

James R. Johnson, Brian D. Johnston, David M. Gordon
Daniel J. Diekema, Editor
James R. Johnson
aMinneapolis VA Medical Center, Minneapolis, Minnesota, USA
bUniversity of Minnesota, Minneapolis, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Brian D. Johnston
aMinneapolis VA Medical Center, Minneapolis, Minnesota, USA
bUniversity of Minnesota, Minneapolis, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David M. Gordon
cAustralian National University, Canberra, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daniel J. Diekema
University of Iowa College of Medicine
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/JCM.01949-16
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

ABSTRACT

The Escherichia coli sequence type 648 complex (STc648) is an emerging lineage within phylogroup F—formerly included within phylogroup D—that is associated with multidrug resistance. Here, we designed and validated a novel multiplex PCR-based assay for STc648 that took advantage of (i) four distinctive single-nucleotide polymorphisms in icd allele 96 and gyrB allele 87, two of the multilocus sequence typing alleles that define ST648; and (ii) the typical absence within STc648 of uidA, an E. coli-specific gene encoding β-glucuronidase. Within a diverse 212-strain validation set that included 109 STs other than STc648, from phylogroups A, B1, B2, C, D, E, and F, the assay exhibited 100% sensitivity (95% confidence interval [CI], 82% to 100%) and specificity (95% CI, 98% to 100%). It functioned similarly well in two distant laboratories that used boiled lysates or DNAzol-purified DNA as the template DNA. Thus, this novel multiplex PCR-based assay should enable any laboratory equipped for diagnostic PCR to rapidly, accurately, and economically screen E. coli isolates for membership in STc648.

INTRODUCTION

Escherichia coli, an important cause of extraintestinal infections in humans and animals (1), is highly clonal. Each of its seven recognized phylogenetic groups (phylogroups) comprises numerous individual sequence types (STs), as defined by multilocus sequence typing (MLST) (2). Among thousands of distinct E. coli STs, a dozen or so ST complexes (i.e., groups of closely related STs) account for most human extraintestinal E. coli infections, and so are regarded as extraintestinal pathogenic E. coli (ExPEC) (3, 4); a similarly small proportion account for most antimicrobial-resistant E. coli infections (4–7). Thus, an E. coli isolate's ST can be highly informative regarding its likely pathogenic and resistance capabilities (8, 9).

Phylogroup F is related closely to phylogroup B2, the origin of most human clinical E. coli isolates, and phylogroup D, the origin of most non-B2 ExPEC strains (2, 10). Prior to its recognition as a distinct phylogroup, its members were usually classified under group D, including by a PCR-based phylotyping assay that delineates only four major E. coli phylogroups (11). An updated version of that assay differentiates phylogroup F from phylogroup D (2).

Within phylogroup F, the sequence type 648 complex (STc648) is reported increasingly as an emerging resistance-associated lineage (4). In multiple studies of resistant E. coli from diverse sources and locales, STc648 has been the first, second, or third most prevalent STc, accounting for up to 28% of isolates (12–19). The reported resistance phenotypes for different STc648 strains include fluoroquinolones, extended-spectrum cephalosporins (CTX-M-type enzymes and CMY-2), carbapenems (OXA-48 and NDM and KPC variants), fosfomycin (fosA3), and colistin (mcr-1) (13, 14, 20–30). STc648 is distributed globally and occurs as a pathogen and commensal of humans and animals (whether food producing, companion, or wild) and in the environment (12–39).

Detection of STc648 is relevant now for molecular epidemiological studies, and could prove useful for clonal trend surveillance and patient management (7, 8). However, conventional MLST (e.g., http://mlst.warwick.ac.uk/mlst/dbs/Ecoli ) is expensive and labor-intensive, and whole-genome-based in silico MLST (7) currently has limited availability. Therefore, we sought to develop a multiplex PCR-based assay for STc648 to enable easy and inexpensive screening for STc648 among E. coli isolates.

RESULTS

In silico predictions. A query of the Enterobase database (https://enterobase.warwick.ac.uk/species/index/ecoli ) identified 328 entries (i.e., strains) corresponding with STc648. These represented 61 total STs, including ST648 proper plus 51 single-locus variants and 9 two-locus variants. ST648 proper, with icd96 and gyrB87, accounted for 246 (75%) of the 328 entries. The complex's 60 non-ST648 STs were represented by a single entry each, except for seven multiple-entry STs (with 2, 2, 2, 3, 3, 7, and 10 entries each; 29 entries total). Of the 60 non-ST648 STs, 49 (82%) also contained icd96 and gyrB87, accounting collectively for an additional 71 (22%) of the 328 entries. Thus, 50 STs within STc648 (i.e., ST648 and 49 others) contained icd96 and gyrB87, accounting collectively for 317 (97%) of the total entries. The remaining 10 STs, which accounted collectively for only 11 entries (3.4% of 328), included 3 STs with icd96 but not gyrB87 (3 entries) and 7 with gyrB87 but not icd96 (8 entries). Thus, the combination of icd96 plus gyrB87 was highly sensitive (97%) for STc648, which was represented mainly by ST648 proper.

Assay performance.In both study laboratories, when the assay was tested against 212 validation set isolates (including 19 STc648 isolates and 193 non-STc648, from 109 different STs), it was 100% accurate in differentiating STc648 and non-STc648 isolates (Table 1). Therefore, its overall performance characteristics were estimated at 100% for sensitivity, specificity, and positive and negative predictive values, with associated 95% confidence intervals of 82% to 100% for sensitivity and positive predictive value, and 98% to 100% for specificity and negative predictive value (Table 1).

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

Performance characteristics of the Escherichia coli sequence type 648 complex (STc648) PCR assay with 212 validation strains

In laboratory 1, none of the 50 non-STc648 validation isolates yielded a product from either the icd96 or gyrB87 primers. In contrast, in laboratory 2, 14 (10%) of 143 non-STc648 validation isolates yielded products with the icd96 (n = 7) or gyrB87 (n = 7) primers. In 5 strains, this phenomenon corresponded with the presence of authentic icd96 (n = 3) or gyrB87 (n = 2), whereas in 9 strains, it corresponded with an alternate allele of icd (icd52 or icd6) or gyrB (gyrB97 or gyrB180). The presence of binding sites for the gyrB87 primers in these gyrB alleles was confirmed, with the distinctive allele-defining single-nucleotide polymorphisms (SNPs) occurring outside or toward the 5′ end of the primer-binding sites, which likely enabled amplification. In contrast, in the icd alleles, the binding sites for the forward icd96 primer had a SNP at the 3′ end, which likely prevented amplification. Thus, although neither the icd96 nor gyrB87 primers were entirely specific for the targeted alleles, nearly all strains that amplified with a given primer pair contained the targeted allele, and amplification with both primer pairs was limited to STc648 strains.

DISCUSSION

This novel multiplex PCR-based assay for E. coli STc648, which targets four STc648-associated SNPS in icd and gyrB and capitalizes on the uidA-negative status of STc648 strains, proved to be 100% sensitive and specific in distinguishing STc648 from 108 diverse non-STc648 E. coli STs, including many within phylogroup F, the origin of STc648. Only 7% of the 212 non-STc648 isolates provided an amplicon for either icd or gyrB; none provided amplicons for both loci. The assay performed well in two geographically separate laboratories, one using boiled lysates and the other using DNAzol-purified DNA as PCR template. Thus, this novel assay should enable ready and reliable detection of E. coli STc648 in any laboratory equipped for conventional PCR.

The new E. coli STc648-specific assay can be used in conjunction with published assays that detect ST131 and its subsets (40–42), eight other major clonal subsets within phylogroup B2 (43), and three important phylogroup D-derived clonal subsets (ST69, the O15:K52:H1–ST31/ST393 complex, and ST405) (44–46), for an extensive clonal analysis of extraintestinal E. coli isolates. Because several of these lineages are typically multidrug-resistant (4), such clonal typing may help to identify reservoirs of resistance, track epidemiological trends, and guide empirical antimicrobial therapy selection (8).

The typical absence of uidA (β-glucuronidase) in STc648 isolates may spuriously reduce the prevalence of STc648 among E. coli isolates, if isolates are identified as E. coli based in part on their production of β-glucuronidase. We show that this distinctive characteristic of STc648 can be advantageous for distinguishing STc648 from other E. coli lineages, all or nearly all of which are uidA positive.

The limitations of this study include that the validation set was not exhaustive with respect to non-ST648 STs (which is inevitable, given the enormous number of E. coli STs), that the observed predictive values are not generalizable to populations with a different prevalence of STc648, and that minor genetic variation will inevitably lead to some false-positive and false-negative assay results. The strengths of this study include the extensively diverse validation set, the participation of two geographically distant laboratories, and the use of boiled lysates and purified DNA as PCR templates.

Comment.For many bacteria, whole-genome sequence analysis will likely supersede PCR-based typing in the not-too-distant future (7). However, at present, this approach remains unavailable for routine use. Thus, in the near term, PCR-based assays, such as this novel SNP-based multiplex assay for E. coli STc648, will likely remain useful for efforts to understand, prevent, diagnose, and treat extraintestinal E. coli infections, including those caused by emerging multidrug-resistant lineages, such as STc648.

MATERIALS AND METHODS

Assay development.STc648 was defined operationally as including ST648 and its single- and double-locus variants. To develop the STc648-specific assay, we used an approach similar to that we used for developing other STc-specific PCR-based assays (40, 41, 43–45). First, we assessed the STc648-defining alleles at each of the seven Achtman MLST loci for specificity (or quasi-specificity) to STc648. Using the most promising loci, we next identified STc648-specific (or quasi-specific) SNPs by aligning the published alleles using MEGA6 and scrutinizing the alignments. We then assessed the candidate SNPs for their suitability as primer targets on the basis of the characteristics of the immediate flanking sequences and, within a given gene, the distances of different SNPs from one another. The most promising SNP pairs were used to design forward and reverse primer pairs in different genes, with the 3′ end of each primer being one of the selected SNPs. Primer pairs were designed for use in combination, to add specificity and to enable multiplexing.

After empirically optimizing PCR conditions and screening several candidate primer pairs against control strains, the best-performing primer pair combination (Table 2) and PCR conditions (described below) were used in validation experiments. For this, the selected icd96 primers (267-bp product) and gyrB87 primers (143-bp product) were combined with published primers for uidA, the E. coli-specific β-glucuronidase gene (510-bp product) (47), in a single-tube multiplex PCR (Table 2).

View this table:
  • View inline
  • View popup
TABLE 2

Primers used in the Escherichia coli sequence type 648 complex (STc648) multiplex PCR assay

For a 15-μl reaction, the amplification mix included: 0.75 U GoTaq hot start polymerase (Promega), 1× GoTaq Flexi Buffer (Promega), 2.5 mM MgCl2, 0.8 mM deoxynucleoside triphosphates (dNTPs), 9 pmol ST648 primers, 0.6 pmol uidA control primers, 1.2 μl sample DNA, and H2O to 15 μl. The cycling conditions were denaturation at 95°C for 2 min, 30 amplification cycles of 94°C for 20 s and 67°C for 45 s, extension at 72°C for 5 min, and then holding at 4°C.

PCR products were visualized in agarose gels. The presence or absence of the predicted amplicons for each of the primer pairs was inferred from the band size. A positive STc648 result was the presence of both the icd96 and gyrB87 amplicons and the absence of the uidA amplicon, which is uniformly absent within STc648, according to all 244 available STc648 genomes, representing 12 different ST within STc648 (unpublished data) (Table 3). A negative STc648 result was the absence of either the icd96 or the gyrB87 amplicon, or the absence of both amplicons and presence of the uidA amplicon. Other band combinations were considered indeterminate. As the assay yielded categorically positive or negative results when performed with freshly extracted DNA, blinding was not used.

View this table:
  • View inline
  • View popup
TABLE 3

Interpretation algorithm for the Escherichia coli sequence type 648 complex (STc648) multiplex PCR assay

Assay validation.The assay was validated in two different laboratories, one in the United States and one in Australia, using 212 total reference strains that represented, collectively, 108 STs, as determined by full or partial MLST. For partial MLST, allele combinations involving <7 loci that map to only one ST or STc were used to define an isolate's ST or STc. The phylogroups were inferred from the STc or were determined by multiplex PCR (2).

Laboratory 1 used the assay to screen, in duplicates, 60 total isolates, including 10 STc648 isolates and 50 non-STc648 isolates, which represented 50 different STs. The non-STc648 isolates and corresponding STs were from phylogroups (number per phylogroup) A (10), B1 (10), B2 (10), C (3), D (10), E (3), and F (4).

Laboratory 2 used the assay to screen 152 total isolates from phylogroups B2, D, and F, including 9 STc648 isolates and 143 non-STc648 isolates, which represented 68 different STs. The non-STc648 isolates and corresponding STs were distributed by phylogroup as follows: B2 (27 isolates, 27 STs), D (46 isolates, 22 STs), and F (70 isolates, 19 STs).

The ST overlap between the two laboratories included STc648 and nine other STs. PCR templates were boiled lysates in laboratory 1 and DNAzol-purified DNA (Thermo Fisher) in laboratory 2.

Statistical analysis.We calculated assay sensitivity, specificity, and positive and negative predictive values, along with 95% confidence intervals (CIs) (Table 1).

ACKNOWLEDGMENTS

The Minneapolis VA Medical Center clinical microbiology laboratory provided some of the isolates used in the study.

The opinions expressed here are strictly those of the authors and do not necessarily reflect those of the author's respective institutions or the Department of Veterans Affairs.

J.R.J. has received research grants or consultancies from Actavis/Forest, Crucell/Janssen, Merck, and Tetraphase, and has patent applications for tests to identify E. coli strains. The other authors report no conflicts of interest.

This material is based in part on work supported by the Office of Research and Development, Medical Research Service, Department of Veterans Affairs, grant no. 1 I01 CX000920-01 (to J.R.J.).

FOOTNOTES

    • Received 20 September 2016.
    • Returned for modification 16 October 2016.
    • Accepted 13 January 2017.
    • Accepted manuscript posted online 18 January 2017.
  • Copyright © 2017 American Society for Microbiology.

All Rights Reserved .

REFERENCES

  1. 1.↵
    1. Russo TA,
    2. Johnson JR
    . 2003. Medical and economic impact of extraintestinal infections due to Escherichia coli: an overlooked epidemic. Microbes Infect5:449–456. doi:10.1016/S1286-4579(03)00049-2.
    OpenUrlCrossRefPubMedWeb of Science
  2. 2.↵
    1. Clermont O,
    2. Christenson JK,
    3. Denamur E,
    4. Gordon DM
    . 2013. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep5:58–65.
    OpenUrlCrossRefPubMed
  3. 3.↵
    1. Russo TA,
    2. Johnson JR
    . 2000. A proposal for an inclusive designation for extraintestinal pathogenic Escherichia coli: ExPEC. J Infect Dis181:1753–1754. doi:10.1086/315418.
    OpenUrlCrossRefPubMedWeb of Science
  4. 4.↵
    1. Pitout JD
    . 2012. Extraintestinal pathogenic Escherichia coli: a combination of virulence with antibiotic resistance. Front Microbiol3:9. doi:10.3389/fmicb.2012.00009.
    OpenUrlCrossRefPubMed
  5. 5.↵
    1. Adams-Sapper S,
    2. Diep BA,
    3. Perdreau-Remington F,
    4. Riley LW
    . 2013. Clonal composition and community clustering of drug-susceptible and -resistant Escherichia coli isolates from bloodstream infections. Antimicrob Agents Chemother57:490–497. doi:10.1128/AAC.01025-12.
    OpenUrlAbstract/FREE Full Text
  6. 6.↵
    1. Manges AR,
    2. Perdreau-Remington F,
    3. Solberg O,
    4. Riley LW
    . 2006. Multidrug-resistant Escherichia coli clonal groups causing community-acquired bloodstream infections. J Infect5:25–29. doi:10.1016/j.jinf.2005.09.012.
    OpenUrlCrossRef
  7. 7.↵
    1. Salipante SJ,
    2. Roach DJ,
    3. Kitzman J,
    4. Snyder MW,
    5. Stackhouse B,
    6. Butler-Wu S,
    7. Lee C,
    8. Cookson BT,
    9. Shendure J
    . 2015. Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains. Genome Res15:119–128. doi:10.1101/gr.180190.114.
    OpenUrlCrossRef
  8. 8.↵
    1. Tchesnokova V,
    2. Avagyan H,
    3. Billig M,
    4. Chattopadhyay S,
    5. Aprikian P,
    6. Chan D,
    7. Pseunova J,
    8. Rechkina E,
    9. Riddell K,
    10. Scholes D,
    11. Fang F,
    12. Johnson J,
    13. Sokurenko E
    . 2016. A novel 7-single nucleotide polymorphism-based clonotyping test allows rapid prediction of antimicrobial susceptibility of extraintestinal Escherichia coli directly from urine specimens. Open Forum Infect Dis3:fw002. doi:10.1093/ofid/ofw002.
    OpenUrlCrossRef
  9. 9.↵
    1. Johnson J,
    2. Thuras P,
    3. Johnston B,
    4. Weissman SJ,
    5. Limaye AP,
    6. Riddell K,
    7. Scholes D,
    8. Tchesnokova V,
    9. Sokurenko E
    . 2016. The pandemic H30 subclone of Escherichia coli sequence type 131 is associated with persistent infections and adverse outcomes independent from its multidrug resistance and associations with compromised hosts. Clin Infect Dis62:1529–1536. doi:10.1093/cid/ciw193.
    OpenUrlCrossRefPubMed
  10. 10.↵
    1. Vangchhia B,
    2. Abraham S,
    3. Bell J,
    4. Collignon P,
    5. Gibson JS,
    6. Ingram PR,
    7. Johnson JR,
    8. Kennedy K,
    9. Trott DJ,
    10. Turnidge JD,
    11. Gordon DM
    . 2016. Phylogenetic diversity, antimicrobial susceptibility and virulence characteristics of phylogroup F Escherichia coli in Australia. Microbiology162:1904–1912. doi:10.1099/mic.0.000367.
    OpenUrlCrossRef
  11. 11.↵
    1. Clermont O,
    2. Bonacorsi S,
    3. Bingen E
    . 2000. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol66:4555–4558. doi:10.1128/AEM.66.10.4555-4558.2000.
    OpenUrlAbstract/FREE Full Text
  12. 12.↵
    1. Cao X,
    2. Zhang Z,
    3. Shen H,
    4. Ning M,
    5. Chen J,
    6. Wei H,
    7. Zhang K
    . 2014. Genotypic characteristics of multidrug-resistant Escherichia coli isolates associated with urinary tract infections. APMIS122:1088–1095. doi:10.1111/apm.12260.
    OpenUrlCrossRef
  13. 13.↵
    1. Sato T,
    2. Yokota S,
    3. Okubo T,
    4. Usui M,
    5. Fujii N,
    6. Tamura Y
    . 2014. Phylogenetic association of fluoroquinolone and cephalosporin resistance of D-O1-ST648 Escherichia coli carrying blaCMY-2 from faecal samples of dogs in Japan. J Med Microbiol63:263–270. doi:10.1099/jmm.0.054676-0.
    OpenUrlCrossRefPubMed
  14. 14.↵
    1. Liu X,
    2. Thungrat K,
    3. Boothe DM
    . 2016. Occurrence of OXA-48 carbapenemase and other β-lactamase genes in ESBL-producing multidrug resistant Escherichia coli from dogs and cats in the United States, 2009–2013. Front Microbiol7:1057. doi:10.3389/fmicb.2016.01057.
    OpenUrlCrossRef
  15. 15.↵
    1. Sherchan JB,
    2. Hayakawa K,
    3. Miyoshi-Akiyama T,
    4. Ohmagari N,
    5. Kirikae T,
    6. Nagamatsu M,
    7. Tojo M,
    8. Ohara H,
    9. Sherchand JB,
    10. Tandukar S
    . 2015. Clinical epidemiology and molecular analysis of extended-spectrum-β-lactamase-producing Escherichia coli in Nepal: characteristics of sequence types 131 and 648. Antimicrob Agents Chemother59:3424–3432. doi:10.1128/AAC.00270-15.
    OpenUrlAbstract/FREE Full Text
  16. 16.↵
    1. Zhao S,
    2. Wang Y,
    3. Xiao S,
    4. Jiang X,
    5. Guo X,
    6. Ni Y,
    7. Han L
    . 2015. Drug susceptibility and molecular epidemiology of Escherichia coli in bloodstream infections in Shanghai, China, 2011–2013. Infect Dis (Lond)47:310–318. doi:10.3109/00365548.2014.990509.
    OpenUrlCrossRef
  17. 17.↵
    1. Xia S,
    2. Fan X,
    3. Huang Z,
    4. Xia L,
    5. Xiao M,
    6. Chen R,
    7. Xu Y,
    8. Zhuo C
    . 2014. Dominance of CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from patients with community-onset and hospital-onset infection in China. PLoS One9:e100707. doi:10.1371/journal.pone.0100707.
    OpenUrlCrossRefPubMed
  18. 18.↵
    1. Kang CI,
    2. Cha MK,
    3. Kim SH,
    4. Ko KS,
    5. Wi YM,
    6. Chung DR,
    7. Peck KR,
    8. Lee NY,
    9. Song JH
    . 2013. Clinical and molecular epidemiology of community-onset bacteremia caused by extended-spectrum β-lactamase-producing Escherichia coli over a 6-year period. J Korean Med Sci28:998–1004. doi:10.3346/jkms.2013.28.7.998.
    OpenUrlCrossRefPubMed
  19. 19.↵
    1. Mushtaq S,
    2. Irfan S,
    3. Sarma J,
    4. Doumith M,
    5. Pike R,
    6. Pitout J,
    7. Livermore D,
    8. Woodford N
    . 2011. Phylogenetic diversity of Escherichia coli strains producing NDM-type carbapenemases. J Antimicrob Chemother66:2002–2005. doi:10.1093/jac/dkr226.
    OpenUrlCrossRefPubMedWeb of Science
  20. 20.↵
    1. Guo S,
    2. Wakeham D,
    3. Brouwers HJ,
    4. Cobbold RN,
    5. Abraham S,
    6. Mollinger JL,
    7. Johnson JR,
    8. Chapman TA,
    9. Gordon DM,
    10. Barrs VR,
    11. Trott DJ
    . 2015. Human-associated fluoroquinolone-resistant Escherichia coli clonal lineages, including ST354, isolated from canine feces and extraintestinal infections in Australia. Microbes Infect17:266–274. doi:10.1016/j.micinf.2014.12.016.
    OpenUrlCrossRefPubMed
  21. 21.↵
    1. Gonçalves LF,
    2. de Oliveira Martins-Júnior P,
    3. de Melo AB,
    4. da Silva RC,
    5. de Paulo Martins V,
    6. Pitondo-Silva A,
    7. de Campos TA
    . 2016. Multidrug resistance dissemination by extended-spectrum β-lactamase-producing Escherichia coli causing community-acquired urinary tract infection in the Central-Western Region, Brazil. J Glob Antimicrob Resist6:1–4. doi:10.1016/j.jgar.2016.02.003.
    OpenUrlCrossRef
  22. 22.↵
    1. Nakane K,
    2. Kawamura K,
    3. Goto K,
    4. Arakawa Y
    . 2016. Long-term colonization by bla(CTX-M)-harboring Escherichia coli in healthy Japanese people engaged in food handling. Appl Environ Microbiol82:1818–1827. doi:10.1128/AEM.02929-15.
    OpenUrlAbstract/FREE Full Text
  23. 23.↵
    1. Wailan AM,
    2. Paterson DL,
    3. Caffery M,
    4. Sowden D,
    5. Sidjabat HE
    . 2015. Draft genome sequence of NDM-5-producing Escherichia coli sequence type 648 and genetic context of blaNDM-5 in Australia. Genome Announc3:pii=e00194-15. doi:10.1128/genomeA.00194-15.
    OpenUrlCrossRef
  24. 24.↵
    1. Mizuno Y,
    2. Yamaguchi T,
    3. Matsumoto T
    . 2014. A first case of New Delhi metallo-β-lactamase-7 in an Escherichia coli ST648 isolate in Japan. J Infect Chemother20:814–816. doi:10.1016/j.jiac.2014.08.009.
    OpenUrlCrossRefPubMed
  25. 25.↵
    1. Hornsey M,
    2. Phee L,
    3. Wareham D
    . 2011. A novel variant, NDM-5, of the New Delhi metallo-β-lactamase in a multidrug-resistant Escherichia coli ST648 isolate recovered from a patient in the United Kingdom. Antimicrob Agents Chemother55:5952–5954. doi:10.1128/AAC.05108-11.
    OpenUrlAbstract/FREE Full Text
  26. 26.↵
    1. Xu G,
    2. Jiang Y,
    3. An W,
    4. Wang H,
    5. Zhang X
    . 2015. Emergence of KPC-2-producing Escherichia coli isolates in an urban river in Harbin, China. World J Microbiol Biotechnol31:1443–1450. doi:10.1007/s11274-015-1897-z.
    OpenUrlCrossRefPubMed
  27. 27.↵
    1. Cai JC,
    2. Zhang R,
    3. Hu YY,
    4. Zhou HW,
    5. Chen GX
    . 2014. Emergence of Escherichia coli sequence type 131 isolates producing KPC-2 carbapenemase in China. Antimicrob Agents Chemother58:1146–1152. doi:10.1128/AAC.00912-13.
    OpenUrlAbstract/FREE Full Text
  28. 28.↵
    1. Ho PL,
    2. Chan J,
    3. Lo WU,
    4. Lai EL,
    5. Cheung YY,
    6. Lau TC,
    7. Chow KH
    . 2013. Prevalence and molecular epidemiology of plasmid-mediated fosfomycin resistance genes among blood and urinary Escherichia coli isolates. J Med Microbiol62:1707–1713. doi:10.1099/jmm.0.062653-0.
    OpenUrlCrossRefPubMed
  29. 29.↵
    1. Sonnevend Á Ghazawi A
    , Alqahtani M, Shibl A, Jamal W, Hashmey R, Pal T. 2016. Plasmid-mediated colistin resistance in Escherichia coli from the Arabian Peninsula. Int J Infect Dis50:85–90. doi:10.1016/j.ijid.2016.07.007.
    OpenUrlCrossRef
  30. 30.↵
    1. Zhang H,
    2. Seward CH,
    3. Wu Z,
    4. Ye H,
    5. Feng Y
    . 2016. Genomic insights into the ESBL and MCR-1-producing ST648 Escherichia coli with multi-drug resistance. Sci Bull (Beijing)61:875–878. doi:10.1007/s11434-016-1086-y.
    OpenUrlCrossRefPubMed
  31. 31.↵
    1. Hasan B,
    2. Laurell K,
    3. Rakib M,
    4. Ahlstedt E,
    5. Hernandez J,
    6. Caceres M,
    7. Järhult J
    . 2016. Fecal carriage of extended-spectrum β-lactamases in healthy humans, poultry, and wild birds in León, Nicaragua—a shared pool of blaCTX-M genes and possible interspecies clonal spread of extended-spectrum β-lactamases-producing Escherichia coli. Microb Drug Resist22:682–687. doi:10.1089/mdr.2015.0323.
    OpenUrlCrossRefPubMed
  32. 32.↵
    1. Müller A,
    2. Stephan R,
    3. Nüesch-Inderbinen M
    . 2016. Distribution of virulence factors in ESBL-producing Escherichia coli isolated from the environment, livestock, food and humans. Sci Total Environ541:667–672. doi:10.1016/j.scitotenv.2015.09.135.
    OpenUrlCrossRef
  33. 33.↵
    1. Rodrigues C,
    2. Machado E,
    3. Pires J,
    4. Ramos H,
    5. Novais Â,
    6. Peixe L
    . 2015. Increase of widespread A, B1 and D Escherichia coli clones producing a high diversity of CTX-M-types in a Portuguese hospital. Future Microbiol10:1125–1131. doi:10.2217/fmb.15.38.
    OpenUrlCrossRefPubMed
  34. 34.↵
    1. Brolund A,
    2. Edquist PJ,
    3. Mäkitalo B,
    4. Olsson-Liljequist B,
    5. Söderblom T,
    6. Wisell KT,
    7. Giske CG
    . 2014. Epidemiology of extended-spectrum β-lactamase-producing Escherichia coli in Sweden 2007–2011. Clin Microbiol Infect20:O344–O352. doi:10.1111/1469-0691.12413.
    OpenUrlCrossRef
  35. 35.↵
    1. Chen Y,
    2. Chen X,
    3. Zheng S,
    4. Yu F,
    5. Kong H,
    6. Yang Q,
    7. Cui D,
    8. Cui D,
    9. Chen N,
    10. Lou B,
    11. Li X,
    12. Tian L,
    13. Yang X,
    14. Xie G,
    15. Dong Y,
    16. Qin Z,
    17. Han D,
    18. Wang Y,
    19. Zhang W,
    20. Tang YW,
    21. Li L
    . 2014. Serotypes, genotypes and antimicrobial resistance patterns of human diarrhoeagenic Escherichia coli isolates circulating in southeastern China. Clin Microbiol Infect20:52–58. doi:10.1111/1469-0691.12188.
    OpenUrlCrossRefPubMed
  36. 36.↵
    1. Huber H,
    2. Zweifel C,
    3. Wittenbrink M,
    4. Stephan R
    . 2013. ESBL-producing uropathogenic Escherichia coli isolated from dogs and cats in Switzerland. Vet Microbiol162:992–996. doi:10.1016/j.vetmic.2012.10.029.
    OpenUrlCrossRefPubMed
  37. 37.↵
    1. Pires-dos-Santos T,
    2. Bisgaard M,
    3. Christensen H
    . 2013. Genetic diversity and virulence profiles of Escherichia coli causing salpingitis and peritonitis in broiler breeders. Vet Microbiol162:873–880. doi:10.1016/j.vetmic.2012.11.008.
    OpenUrlCrossRef
  38. 38.↵
    1. Mshana SE,
    2. Imirzalioglu C,
    3. Hain T,
    4. Domann E,
    5. Lyamuya EF,
    6. Chakraborty T
    . 2011. Multiple ST clonal complexes, with a predominance of ST131, of Escherichia coli harbouring blaCTX-M-15 in a tertiary hospital in Tanzania. Clin Microbiol Infect17:1279–1282. doi:10.1111/j.1469-0691.2011.03518.x.
    OpenUrlCrossRefPubMed
  39. 39.↵
    1. van der Bij AK,
    2. Peirano G,
    3. Goessens WH,
    4. van der Vorm ER,
    5. van Westreenen M,
    6. Pitout JD
    . 2011. Clinical and molecular characteristics of extended-spectrum-beta-lactamase-producing Escherichia coli causing bacteremia in the Rotterdam Area, Netherlands. Antimicrob Agents Chemother55:3576–3578. doi:10.1128/AAC.00074-11.
    OpenUrlAbstract/FREE Full Text
  40. 40.↵
    1. Johnson JR,
    2. Menard M,
    3. Johnston B,
    4. Kuskowski MA,
    5. Nichol K,
    6. Zhanel GG
    . 2009. Epidemic clonal groups of Escherichia coli as a cause of antimicrobial-resistant urinary tract infections in Canada, 2002 to 2004. Antimicrob Agents Chemother53:2733–2739. doi:10.1128/AAC.00297-09.
    OpenUrlAbstract/FREE Full Text
  41. 41.↵
    1. Johnson JR,
    2. Clermont O,
    3. Johnston B,
    4. Clabots C,
    5. Tchesnokova V,
    6. Sokurenko E,
    7. Junka AF,
    8. Maczynska B,
    9. Denamur E
    . 2014. Rapid and specific detection, molecular epidemiology, and experimental virulence of the O16 subgroup within Escherichia coli sequence type 131. J Clin Microbiol52:1358–1365. doi:10.1128/JCM.03502-13.
    OpenUrlAbstract/FREE Full Text
  42. 42.↵
    1. Banerjee R,
    2. Robicsek A,
    3. Kuskowski MA,
    4. Porter S,
    5. Johnston BD,
    6. Sokurenko E,
    7. Tchesnokova V,
    8. Price LB,
    9. Johnson JR
    . 2013. Molecular epidemiology of Escherichia coli sequence type ST131 and its H30 and H30-Rx subclones among extended-spectrum beta-lactamase-positive and -negative E. coli clinical isolates from the Chicago region, 2007 to 2010. Antimicrob Agents Chemother57:6385–6388. doi:10.1128/AAC.01604-13.
    OpenUrlAbstract/FREE Full Text
  43. 43.↵
    1. Clermont O,
    2. Christenson JK,
    3. Daubie AS,
    4. Gordon DM,
    5. Denamur E
    . 2014. Development of an allele-specific PCR for Escherichia coli B2 sub-typing, a rapid and easy to perform substitute of multilocus sequence typing. J Microbiol Methods101:24–27. doi:10.1016/j.mimet.2014.03.008.
    OpenUrlCrossRefPubMed
  44. 44.↵
    1. Johnson JR,
    2. Owens K,
    3. Manges AR,
    4. Riley LW
    . 2004. Rapid and specific detection of Escherichia coli clonal group A by gene-specific PCR. J Clin Microbiol42:2618–2622. doi:10.1128/JCM.42.6.2618-2622.2004.
    OpenUrlAbstract/FREE Full Text
  45. 45.↵
    1. Johnson JR,
    2. Owens K,
    3. Sabate M,
    4. Prats G
    . 2004. Rapid and specific detection of the O15:K52:H1 clonal group of Escherichia coli by gene-specific PCR. J Clin Microbiol42:3841–3843. doi:10.1128/JCM.42.8.3841-3843.2004.
    OpenUrlAbstract/FREE Full Text
  46. 46.↵
    1. Matsumura Y,
    2. Yamamoto M,
    3. Nagao M,
    4. Hotta G,
    5. Matsushima A,
    6. Ito Y,
    7. Takakura S,
    8. Ichiyama S,
    9. Kyoto-Shiga Clinical Microbiology Study Group
    . 2012. Emergence and spread of B2-ST131-O25b, B2-ST131-O16 and D-ST405 clonal groups among extended-spectrum-β-lactamase-producing Escherichia coli in Japan. J Antimicrob Chemother67:2612–2620. doi:10.1093/jac/dks278.
    OpenUrlCrossRefPubMedWeb of Science
  47. 47.↵
    1. Walk ST,
    2. Alm EW,
    3. Gordon DM,
    4. Ram JL,
    5. Toranzos GA,
    6. Tiedje JM,
    7. Whittam TS
    . 2009. Cryptic lineages of the genus Escherichia. Appl Environ Microbiol75:6534–6544. doi:10.1128/AEM.01262-09.
    OpenUrlAbstract/FREE Full Text
PreviousNext
Back to top
Download PDF
Citation Tools
Rapid and Specific Detection of the Escherichia coli Sequence Type 648 Complex within Phylogroup F
James R. Johnson, Brian D. Johnston, David M. Gordon
Journal of Clinical Microbiology Mar 2017, 55 (4) 1116-1121; DOI: 10.1128/JCM.01949-16

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.
Rapid and Specific Detection of the Escherichia coli Sequence Type 648 Complex within Phylogroup F
(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
Rapid and Specific Detection of the Escherichia coli Sequence Type 648 Complex within Phylogroup F
James R. Johnson, Brian D. Johnston, David M. Gordon
Journal of Clinical Microbiology Mar 2017, 55 (4) 1116-1121; DOI: 10.1128/JCM.01949-16
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • INTRODUCTION
    • RESULTS
    • DISCUSSION
    • MATERIALS AND METHODS
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

KEYWORDS

Escherichia coli
Escherichia coli Infections
genotype
Molecular Diagnostic Techniques
Multiplex Polymerase Chain Reaction
Escherichia coli
antimicrobial resistance
diagnostics
molecular epidemiology
polymerase chain reaction
sequence type
strain typing

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