Arrangements of Mobile Genetic Elements among Virotype E Subpopulation of
            Escherichia coli
            Sequence Type 131 Strains with High Antimicrobial Resistance and Virulence Gene Content

Escherichia coli sequence type 131 (ST131) is a globally dominant multidrug-resistant clone that is commonly associated with extraintestinal infections. Specific sublineages have been shown to have emerged and spread within ST131, highlighting the complex nature of ST131 epidemiology.

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Transmission of NDM-5-Producing and OXA-48-Producing Escherichia coli Sequence Type 648 by International Visitors without Previous Medical Exposure

Microbiology Spectrum ◽

10.1128/spectrum.01827-21 ◽

2021 ◽

Vol 9 (3) ◽

Author(s):

Sohei Harada ◽

Masahiro Suzuki ◽

Toshiharu Sasaki ◽

Aki Sakurai ◽

Masato Inaba ◽

...

Keyword(s):

Escherichia Coli ◽

High Risk ◽

Multidrug Resistant ◽

Sequence Type ◽

Resistant Clone ◽

Content Type ◽

Multidrug Resistant Organisms ◽

History Of ◽

Medical Exposure ◽

International Visitors

Although patients with history of international hospitalization are often subject to screening for multidrug-resistant organisms, it is unclear whether patients who reside in countries where carbapenemase-producing Enterobacterales (CPE) is endemic but have no history of local hospitalization contribute to the transmission of CPE. In this study, NDM-5-producing and OXA-48-producing Escherichia coli sequence type (ST) 648, a recently recognized high-risk, multidrug-resistant clone, were detected from two overseas visitors without previous medical exposure.

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Rapid Emergence, Subsidence, and Molecular Detection of Escherichia coli Sequence Type 1193-fimH64, a New Disseminated Multidrug-Resistant Commensal and Extraintestinal Pathogen

Journal of Clinical Microbiology ◽

10.1128/jcm.01664-18 ◽

2019 ◽

Vol 57 (5) ◽

Cited By ~ 14

Author(s):

James R. Johnson ◽

Brian D. Johnston ◽

Stephen B. Porter ◽

Connie Clabots ◽

Tricia L. Bender ◽

...

Keyword(s):

Escherichia Coli ◽

Medical Center ◽

Virulence Gene ◽

The United States ◽

Multidrug Resistant ◽

Sequence Type ◽

Cross Sectional ◽

Content Type ◽

E Coli ◽

Multiplex Pcr Assay

ABSTRACT Escherichia coli sequence type 1193 (ST1193) is an emerging multidrug-resistant pathogen. We performed longitudinal and cross-sectional surveillance for ST1193 among clinical and fecal E. coli isolates from Minneapolis Veterans Affairs Medical Center (VAMC) patients and their household members, other Minnesota centers, and national VAMCs and compared these ST1193 isolates with archival human and canine ST1193 isolates from Australia (2008). We also developed and extensively validated a novel multiplex PCR assay for ST1193 and its characteristic fimH64 (type 1 fimbrial adhesin) allele. We found that ST1193-H64 (where “H64” refers to a phylogenetic subdivision within ST1193 that is characterized by the fimH64 allele), which was uniformly fluoroquinolone resistant, appeared to emerge in the United States in a geographically staggered fashion beginning around 2011. Its prevalence among clinical and fecal E. coli isolates at the Minneapolis VAMC rose rapidly beginning in 2013, peaked in early 2017, and then plateaued or declined. In comparison with other ST14 complex (STc14) isolates, ST1193-H64 isolates were more extensively multidrug resistant, whereas their virulence genotypes were less extensive but included (uniquely) K1 capsule and fimH64. Pulsed-field gel electrophoresis separated ST1193-H64 isolates from other STc14 isolates and showed genetic commonality between archival Australian versus recent U.S. isolates, fecal versus clinical isolates, and human versus canine isolates. Three main ST1193 pulsotypes differed significantly in resistance profiles and capsular types; emergent pulsotype 2123 was associated with trimethoprim-sulfamethoxazole resistance and K1 (versus K5) capsule. These findings clarify ST1193-H64’s temporal prevalence trends as a fluoroquinolone-resistant pathogen and commensal; document clonal subsets with distinctive geographic, temporal, resistance, and virulence gene associations; and establish a new laboratory tool for rapid and simple detection of ST1193-H64.

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Occurrence of blaKPC-2, blaCTX-M, and mcr-1 in Enterobacteriaceae from Well Water in Rural China

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02569-16 ◽

2017 ◽

Vol 61 (4) ◽

Cited By ~ 31

Author(s):

Pan Sun ◽

Zhenwang Bi ◽

Maud Nilsson ◽

Beiwen Zheng ◽

Björn Berglund ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Rural China ◽

Multidrug Resistant ◽

Sequence Type ◽

Well Water ◽

Content Type ◽

Potential Source ◽

Extended Spectrum

ABSTRACT We report on the coexistence of mcr-1 and bla CTX-M in multidrug-resistant, extended-spectrum β-lactamase-producing Escherichia coli belonging to the sequence type 10 complex isolated from well water in rural China. Raoultella ornithinolytica with bla KPC-2 was also detected in well water from the same area. This study shows that genes coding for resistance to last-resort antibiotics are present in wells in rural China, indicating a potential source of antibiotic resistance.

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Genetic Structure and Antimicrobial Resistance of Escherichia coli and Cryptic Clades in Birds with Diverse Human Associations

Applied and Environmental Microbiology ◽

10.1128/aem.00861-15 ◽

2015 ◽

Vol 81 (15) ◽

pp. 5123-5133 ◽

Cited By ~ 24

Author(s):

Michaela D. J. Blyton ◽

Hongfei Pi ◽

Belinda Vangchhia ◽

Sam Abraham ◽

Darren J. Trott ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Multidrug Resistant ◽

Wild Birds ◽

Phylogenetic Groups ◽

Treatment Protocols ◽

Content Type ◽

Backyard Poultry ◽

Wildlife Rehabilitation ◽

Wilderness Areas

ABSTRACTThe manner and extent to which birds associate with humans may influence the genetic attributes and antimicrobial resistance of their commensalEscherichiacommunities through strain transmission and altered selection pressures. In this study, we determined whether the distribution of the differentEscherichia coliphylogenetic groups and cryptic clades, the occurrence of 49 virulence associated genes, and/or the prevalence of resistance to 12 antimicrobials differed between four groups of birds from Australia with contrasting types of human association. We found that birds sampled in suburban and wilderness areas had similarEscherichiacommunities. TheEscherichiacommunities of backyard domestic poultry were phylogenetically distinct from theEscherichiacommunities sourced from all other birds, with a large proportion (46%) of poultry strains belonging to phylogenetic group A and a significant minority (17%) belonging to the cryptic clades. Wild birds sampled from veterinary and wildlife rehabilitation centers (in-care birds) carriedEscherichiaisolates that possessed particular virulence-associated genes more often thanEscherichiaisolates from birds sampled in suburban and wilderness areas. TheEscherichiaisolates from both the backyard poultry and in-care birds were more likely to be multidrug resistant than theEscherichiaisolates from wild birds. We also detected a multidrug-resistantE. colistrain circulating in a wildlife rehabilitation center, reinforcing the importance of adequate hygiene practices when handling and caring for wildlife. We suggest that the relatively high frequency of antimicrobial resistance in the in-care birds and backyard poultry is due primarily to the use of antimicrobials in these animals, and we recommend that the treatment protocols used for these birds be reviewed.

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A Comprehensive Account of Escherichia coli Sequence Type 131 in Wastewater Reveals an Abundance of Fluoroquinolone-Resistant Clade A Strains

Applied and Environmental Microbiology ◽

10.1128/aem.01913-19 ◽

2019 ◽

Vol 86 (4) ◽

Author(s):

Thomas J. Finn ◽

Lena Scriver ◽

Linh Lam ◽

Mai Duong ◽

Gisele Peirano ◽

...

Keyword(s):

Escherichia Coli ◽

International Health ◽

Multidrug Resistant ◽

Screening Strategy ◽

Sequence Type ◽

High Rate ◽

Dominant Form ◽

Content Type ◽

Comprehensive Account ◽

Tract Infections

ABSTRACT In the ten years since its discovery, the Escherichia coli clone sequence type 131 (ST131) has become a major international health threat, with the multidrug-resistant and extended-spectrum β-lactamase (ESBL)-producing clade C emerging as the globally dominant form. ST131 has previously been isolated from wastewater; however, most of these studies selectively screened for ESBL-producing organisms, thereby missing the majority of remaining ST131 clades. In this study, we used a high-throughput PCR-based screening strategy to comprehensively examine wastewater for the presence of ST131 over a 1-year period. Additional multiplex PCRs were used to differentiate clades and obtain an unbiased account of the total ST131 population structure within the collection. Furthermore, antimicrobial susceptibility profiles of all ST131-positive samples were tested against a range of commonly used antibiotics. From a total of over 3,762 E. coli wastewater samples, 1.86% (n = 70) tested positive for ST131, with the majority being clade A isolates. In total, 63% (n = 44) were clade A, 29% (n = 20) were clade B, 1% (n = 1) were clade C0, 6% (n = 4) were clade C1, and 1% (n = 1) were clade C2. In addition, a very high rate of resistance to commonly used antibiotics among wastewater isolates is reported, with 72.7% (n = 32) of clade A resistant to ciprofloxacin and high rates of resistance to gentamicin, sulfamethoxazole-trimethoprim, and tetracycline in clades that are typically sensitive to antibiotics. IMPORTANCE ST131 is a global pathogen. This clone causes urinary tract infections and is frequently isolated from human sources. However, little is known about ST131 from environmental sources. With the widely reported increase in antibiotic concentrations found in wastewater, there is additional selection pressure for the emergence of antibiotic-resistant ST131 in this niche. The unbiased screening approach reported herein revealed that previously antibiotic-sensitive lineages of ST131 are now resistant to commonly used antibiotics present in wastewater systems and may be capable of surviving UV sterilization. This is the most comprehensive account of ST131 in the wastewater niche to date and an important step in better understanding the ecology of this global pathogen.

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Detection of an Escherichia coli Sequence Type 167 Strain with Two Tandem Copies ofblaNDM-1in the Chromosome

Journal of Clinical Microbiology ◽

10.1128/jcm.01581-16 ◽

2016 ◽

Vol 55 (1) ◽

pp. 199-205 ◽

Cited By ~ 21

Author(s):

Ping Shen ◽

Maoli Yi ◽

Ying Fu ◽

Zhi Ruan ◽

Xiaoxing Du ◽

...

Keyword(s):

Escherichia Coli ◽

Insertion Sequence ◽

Southern Blotting ◽

Multidrug Resistant ◽

Sequence Type ◽

New Delhi ◽

Genomic Context ◽

Content Type ◽

Link Type ◽

Reference Genomes

ABSTRACTNew Delhi metallo-β-lactamase-1 (NDM-1)-producingEnterobacteriaceaehas disseminated rapidly throughout the world and poses an urgent threat to public health. Previous studies confirmed that theblaNDM-1gene is typically carried in plasmids but rarely in chromosome. We discovered a multidrug-resistantEscherichia colistrain Y5, originating from a urine sample and containing theblaNDM-1gene, which did not transfer by either conjugation or electrotransformation. We confirmed the possibility of its chromosome location by S1-pulsed-field gel electrophoresis (PFGE) and XbaI-PFGE, followed by Southern blotting. To determine the genomic background ofblaNDM-1, the genome of Y5 was completely sequenced and compared to other reference genomes. The results of our study revealed that this isolate consists of a 4.8-Mbp chromosome and three plasmids, it is an epidemic clone of sequence type (ST) 167, and it shows 99% identity withEscherichia coli6409 (GenBank accession no.CP010371), which lacks the sameblaNDM-1gene-surrounding structure as Y5. TheblaNDM-1gene is embedded in the chromosome along with two tandem copies of an insertion sequence common region 1 (ISCR1) element (sul1-ARR-3-cat-blaNDM-1-bleo-ISCR1), which appears intact in the plasmid fromProteus mirabilis(GenBank accession no.KP662515). The genomic context indicates that the ISCR1element mediated theblaNDM-1transposition from a single source plasmid to the chromosome. Our study is the first report of anEnterobacteriaceaestrain harboring a chromosomally integratedblaNDM-1, which directly reveals the vertical spreading pattern of the gene. Close surveillance is urgently needed to monitor the emergence and potential spread of ST167 strains that harborblaNDM-1.

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Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

mBio ◽

10.1128/mbio.02162-15 ◽

2016 ◽

Vol 7 (2) ◽

Cited By ~ 149

Author(s):

Nicole Stoesser ◽

Anna E. Sheppard ◽

Louise Pankhurst ◽

Nicola De Maio ◽

Catrin E. Moore ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Evolutionary History ◽

Mobile Genetic Elements ◽

The United States ◽

Sequence Type ◽

E Coli ◽

Genetic Elements ◽

Extended Spectrum ◽

History Of

ABSTRACT Escherichia coli sequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. This study of the largest worldwide collection ( n = 215) of sequenced ST131 E. coli isolates to date demonstrates that the clonal expansion of two previously recognized antimicrobial-resistant clades, C1/ H 30R and C2/ H 30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/ H 30Rx clade driven by the acquisition of a bla CTX-M-15 -containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids and chromosomal integration of bla CTX-M within subclusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed among ST131, the bla CTX-M-14/14-like group. The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages of E. coli . These data also highlight the global imperative to reduce specific antibiotic selection pressures and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages. IMPORTANCE Escherichia coli , perennially a major bacterial pathogen, is becoming increasingly difficult to manage due to emerging resistance to all preferred antimicrobials. Resistance is concentrated within specific E. coli lineages, such as sequence type 131 (ST131). Clarification of the genetic basis for clonally associated resistance is key to devising intervention strategies. We used high-resolution genomic analysis of a large global collection of ST131 isolates to define the evolutionary history of extended-spectrum beta-lactamase production in ST131. We documented diverse contributory genetic processes, including stable chromosomal integrations of resistance genes, persistence and evolution of mobile resistance elements within sublineages, and sporadic acquisition of different resistance elements. Both global distribution and regional segregation were evident. The diversity of resistance element acquisition and propagation within ST131 indicates a need for control and surveillance strategies that target both bacterial strains and mobile genetic elements.

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Activity of Eravacycline against Escherichia coli Clinical Isolates Collected from U.S. Veterans in 2011 in Relation to Coresistance Phenotype and Sequence Type 131 Genotype

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02403-15 ◽

2015 ◽

Vol 60 (3) ◽

pp. 1888-1891 ◽

Cited By ~ 9

Author(s):

James R. Johnson ◽

Stephen B. Porter ◽

Brian D. Johnston ◽

Paul Thuras

Keyword(s):

Escherichia Coli ◽

Multidrug Resistant ◽

Veterans Affairs ◽

Sequence Type ◽

Clinical Isolates ◽

Gram Negative ◽

Content Type ◽

Medical Centers ◽

Resistant Strains ◽

Veterans Affairs Medical Centers

Eravacycline is a novel broad-spectrum fluorocycline with potent Gram-negative activity, including for multidrug-resistant strains. Among 472Escherichia coliclinical isolates from 24 Veterans Affairs medical centers (in 2011), divided equally as susceptible versus resistant to fluoroquinolones, broth microdilution eravacycline MICs were distributed unimodally, ranging from 0.03 to 1.0 μg/ml (MIC50of 0.125 μg/ml, MIC90of 0.25 μg/ml). Eravacycline MICs were ∼2-fold higher among fluoroquinolone-resistant, gentamicin-resistant, multidrug-resistant, and sequence type 131 (ST131) isolates (P< 0.01 for each comparison).

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Escherichia coliSequence Type 410 Is Causing New International High-Risk Clones

mSphere ◽

10.1128/msphere.00337-18 ◽

2018 ◽

Vol 3 (4) ◽

pp. e00337-18 ◽

Cited By ~ 51

Author(s):

Louise Roer ◽

Søren Overballe-Petersen ◽

Frank Hansen ◽

Kristian Schønning ◽

Mikala Wang ◽

...

Keyword(s):

Escherichia Coli ◽

High Risk ◽

Antimicrobial Resistance ◽

Sequence Type ◽

Recurrent Infections ◽

Content Type ◽

E Coli ◽

The Past ◽

Carbapenemase Gene ◽

Globally Distributed

ABSTRACTEscherichia colisequence type 410 (ST410) has been reported worldwide as an extraintestinal pathogen associated with resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems. In the present study, we investigated national epidemiology of ST410E. coliisolates from Danish patients. Furthermore,E. coliST410 was investigated in a global context to provide further insight into the acquisition of the carbapenemase genesblaOXA-181andblaNDM-5of this successful lineage. From 127 whole-genome-sequenced isolates, we reconstructed an evolutionary framework ofE. coliST410 which portrays the antimicrobial-resistant clades B2/H24R, B3/H24Rx, and B4/H24RxC. The B2/H24R and B3/H24Rx clades emerged around 1987, concurrently with the C1/H30R and C2/H30Rx clades inE. coliST131. B3/H24Rx appears to have evolved by the acquisition of the extended-spectrum β-lactamase (ESBL)-encoding geneblaCTX-M-15and an IncFII plasmid, encoding IncFIA and IncFIB. Around 2003, the carbapenem-resistant clade B4/H24RxC emerged when ST410 acquired an IncX3 plasmid carrying ablaOXA-181carbapenemase gene. Around 2014, the clade B4/H24RxC acquired a second carbapenemase gene,blaNDM-5, on a conserved IncFII plasmid. From an epidemiological investigation of 49E. coliST410 isolates from Danish patients, we identified five possible regional outbreaks, of which one outbreak involved nine patients withblaOXA-181- andblaNDM-5-carrying B4/H24RxC isolates. The accumulated multidrug resistance inE. coliST410 over the past two decades, together with its proven potential of transmission between patients, poses a high risk in clinical settings, and thus,E. coliST410 should be considered a lineage with emerging “high-risk” clones, which should be monitored closely in the future.IMPORTANCEExtraintestinal pathogenicEscherichia coli(ExPEC) is the main cause of urinary tract infections and septicemia. Significant attention has been given to the ExPEC sequence type ST131, which has been categorized as a “high-risk” clone. High-risk clones are globally distributed clones associated with various antimicrobial resistance determinants, ease of transmission, persistence in hosts, and effective transmission between hosts. The high-risk clones have enhanced pathogenicity and cause severe and/or recurrent infections. We show that clones of theE. coliST410 lineage persist and/or cause recurrent infections in humans, including bloodstream infections. We found evidence of ST410 being a highly resistant globally distributed lineage, capable of patient-to-patient transmission causing hospital outbreaks. Our analysis suggests that the ST410 lineage should be classified with the potential to cause new high-risk clones. Thus, with the clonal expansion over the past decades and increased antimicrobial resistance to last-resort treatment options, ST410 needs to be monitored prospectively.

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Draft Genome Sequences of Two Multidrug-Resistant Sequence Type 405 Escherichia coli Isolates without Clinical Infection

Microbiology Resource Announcements ◽

10.1128/mra.00508-21 ◽

2021 ◽

Vol 10 (31) ◽

Author(s):

Amanda Chamieh ◽

Rita Zgheib ◽

Sabah El-Sawalhi ◽

Eid Azar ◽

Jean-Marc Rolain

Keyword(s):

Escherichia Coli ◽

Draft Genome ◽

Multidrug Resistant ◽

Sequence Type ◽

Clinical Isolates ◽

Clinical Infection ◽

Genome Sequences ◽

Content Type

We present the genome sequences of two carbapenemase-producing sequence type 405 Escherichia coli clinical isolates, strains Marseille-Q1950 and Marseille-Q1951. The isolates were obtained 1 month apart during the patient’s hospitalization in Lebanon, in May (Marseille-Q1950) and June (Marseille-Q1951) 2019. The genome sizes of strains Marseille-Q1950 and Marseille-Q1951 were 5,181,515 bp and 5,213,451 bp, respectively.

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