Genetic Characterization of Escherichia coli O104 Isolates from Different Sources in the United States

ABSTRACTEscherichia coliO104 isolates collected from different sources in the United States were examined for virulence genes typical of enterohemorrhagicE. coliand those identified in the O104:H4 isolate associated with the 2011 German outbreak. The unexpected presence of virulence markers in these isolates highlights the importance of screening unusual and potentially pathogenic Shiga toxin-producingE. coliserotypes.

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Extraintestinal Pathogenic and Antimicrobial-Resistant Escherichia coli, Including Sequence Type 131 (ST131), from Retail Chicken Breasts in the United States in 2013

Applied and Environmental Microbiology ◽

10.1128/aem.02956-16 ◽

2017 ◽

Vol 83 (6) ◽

Cited By ~ 15

Author(s):

James R. Johnson ◽

Stephen B. Porter ◽

Brian Johnston ◽

Paul Thuras ◽

Sarah Clock ◽

...

Keyword(s):

United States ◽

Escherichia Coli ◽

Virulence Genes ◽

Meat Products ◽

The United States ◽

Sequence Type ◽

The Other ◽

Antibiotic Resistant ◽

Content Type ◽

E Coli

ABSTRACT Chicken meat products are hypothesized to be vehicles for transmitting antimicrobial-resistant and extraintestinal pathogenic Escherichia coli (ExPEC) to consumers. To reassess this hypothesis in the current era of heightened concerns about antimicrobial use in food animals, we analyzed 175 chicken-source E. coli isolates from a 2013 Consumer Reports national survey. Isolates were screened by PCR for ExPEC-defining virulence genes. The 25 ExPEC isolates (12% of 175) and a 2:1 randomly selected set of 50 non-ExPEC isolates were assessed for their phylogenetic/clonal backgrounds and virulence genotypes for comparison with their resistance profiles and the claims on the retail packaging label (“organic,” “no antibiotics,” and “natural”). Compared with the findings for non-ExPEC isolates, the group of ExPEC isolates had a higher prevalence of phylogroup B2 isolates (44% versus 4%; P < 0.001) and a lower prevalence of phylogroup A isolates (4% versus 30%; P = 0.001), a higher prevalence of multiple individual virulence genes, higher virulence scores (median, 11 [range, 4 to 16] versus 8 [range, 1 to 14]; P = 0.001), and higher resistance scores (median, 4 [range, 0 to 8] versus 3 [range, 0 to 10]; P < 0.001). All five isolates of sequence type 131 (ST131) were ExPEC (P = 0.003), were as extensively resistant as the other isolates tested, and had higher virulence scores than the other isolates tested (median, 12 [range, 11 to 13] versus 8 [range, 1 to 16]; P = 0.005). Organic labeling predicted lower resistance scores (median, 2 [range, 0 to 3] versus 4 [range, 0 to 10]; P = 0.008) but no difference in ExPEC status or virulence scores. These findings document a persisting reservoir of extensively antimicrobial-resistant ExPEC isolates, including isolates from ST131, in retail chicken products in the United States, suggesting a potential public health threat. IMPORTANCE We found that among Escherichia coli isolates from retail chicken meat products purchased across the United States in 2013 (many of these isolates being extensively antibiotic resistant), a minority had genetic profiles suggesting an ability to cause extraintestinal infections in humans, such as urinary tract infection, implying a risk of foodborne disease. Although isolates from products labeled “organic” were less extensively antibiotic resistant than other isolates, they did not appear to be less virulent. These findings suggest that retail chicken products in the United States, even if they are labeled “organic,” pose a potential health threat to consumers because they are contaminated with extensively antibiotic-resistant and, presumably, virulent E. coli isolates.

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Genetic Characterization of Escherichia coli O104 Isolates from Different Sources in the United States

Applied and Environmental Microbiology ◽

10.1128/aem.01878-12 ◽

2012 ◽

Vol 78 (19) ◽

pp. 7170-7170

Author(s):

Lydia V. Rump ◽

Sonya Bodeis-Jones ◽

Jason Abbott ◽

Shaohua Zhao ◽

Julie Kase ◽

...

Keyword(s):

United States ◽

Escherichia Coli ◽

Genetic Characterization ◽

The United States ◽

Different Sources

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PacBio Genome Sequences of Eight Escherichia albertii Strains Isolated from Humans in the United States

Microbiology Resource Announcements ◽

10.1128/mra.01663-18 ◽

2019 ◽

Vol 8 (9) ◽

Cited By ~ 2

Author(s):

Rebecca L. Lindsey ◽

Lori A. Rowe ◽

Dhwani Batra ◽

Peyton Smith ◽

Nancy A. Strockbine

Keyword(s):

United States ◽

Escherichia Coli ◽

Virulence Genes ◽

The United States ◽

Genome Sequences ◽

Emerging Pathogen ◽

Content Type ◽

E Coli

Escherichia albertii is an emerging pathogen that is closely related to Escherichia coli and can carry some of the same virulence genes as E. coli. Here, we report the release of Illumina-corrected PacBio sequences for eight E. albertii genomes.

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Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States

mSphere ◽

10.1128/msphere.00990-20 ◽

2020 ◽

Vol 5 (5) ◽

Author(s):

Shivdeep Singh Hayer ◽

Seunghyun Lim ◽

Samuel Hong ◽

Ehud Elnekave ◽

Timothy Johnson ◽

...

Keyword(s):

United States ◽

Escherichia Coli ◽

High Risk ◽

The United States ◽

Genetic Determinants ◽

Content Type ◽

E Coli ◽

Extended Spectrum ◽

Animal Populations ◽

Swine Population

ABSTRACT Fluoroquinolones and cephalosporins are critically important antimicrobial classes for both human and veterinary medicine. We previously found a drastic increase in enrofloxacin resistance in clinical Escherichia coli isolates collected from diseased pigs from the United States over 10 years (2006 to 2016). However, the genetic determinants responsible for this increase have yet to be determined. The aim of the present study was to identify and characterize the genetic basis of resistance against fluoroquinolones (enrofloxacin) and extended-spectrum cephalosporins (ceftiofur) in swine E. coli isolates using whole-genome sequencing (WGS). blaCMY-2 (carried by IncA/C2, IncI1, and IncI2 plasmids), blaCTX-M (carried by IncF, IncHI2, and IncN plasmids), and blaSHV-12 (carried by IncHI2 plasmids) genes were present in 87 (82.1%), 19 (17.9%), and 3 (2.83%) of the 106 ceftiofur-resistant isolates, respectively. Of the 110 enrofloxacin-resistant isolates, 90 (81.8%) had chromosomal mutations in gyrA, gyrB, parA, and parC genes. Plasmid-mediated quinolone resistance genes [qnrB77, qnrB2, qnrS1, qnrS2, and aac-(6)-lb′-cr] borne on ColE, IncQ2, IncN, IncF, and IncHI2 plasmids were present in 24 (21.8%) of the enrofloxacin-resistant isolates. Virulent IncF plasmids present in swine E. coli isolates were highly similar to epidemic plasmids identified globally. High-risk E. coli clones, such as ST744, ST457, ST131, ST69, ST10, ST73, ST410, ST12, ST127, ST167, ST58, ST88, ST617, ST23, etc., were also found in the U.S. swine population. Additionally, the colistin resistance gene (mcr-9) was present in several isolates. This study adds valuable information regarding resistance to critical antimicrobials with implications for both animal and human health. IMPORTANCE Understanding the genetic mechanisms conferring resistance is critical to design informed control and preventive measures, particularly when involving critically important antimicrobial classes such as extended-spectrum cephalosporins and fluoroquinolones. The genetic determinants of extended-spectrum cephalosporin and fluoroquinolone resistance were highly diverse, with multiple plasmids, insertion sequences, and genes playing key roles in mediating resistance in swine Escherichia coli. Plasmids assembled in this study are known to be disseminated globally in both human and animal populations and environmental samples, and E. coli in pigs might be part of a global reservoir of key antimicrobial resistance (AMR) elements. Virulent plasmids found in this study have been shown to confer fitness advantages to pathogenic E. coli strains. The presence of international, high-risk zoonotic clones provides worrisome evidence that resistance in swine isolates may have indirect public health implications, and the swine population as a reservoir for these high-risk clones should be continuously monitored.

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Molecular Characterization of Resistance to Extended-Spectrum Cephalosporins in Clinical Escherichia coli Isolates from Companion Animals in the United States

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00656-11 ◽

2011 ◽

Vol 55 (12) ◽

pp. 5666-5675 ◽

Cited By ~ 60

Author(s):

Bashar W. Shaheen ◽

Rajesh Nayak ◽

Steven L. Foley ◽

Ohgew Kweon ◽

Joanna Deck ◽

...

Keyword(s):

United States ◽

Escherichia Coli ◽

Regulatory Region ◽

Companion Animals ◽

The United States ◽

Conjugative Plasmid ◽

Chromosomal Gene ◽

Content Type ◽

E Coli ◽

Extended Spectrum

ABSTRACTResistance to extended-spectrum cephalosporins (ESC) among members of the familyEnterobacteriaceaeoccurs worldwide; however, little is known about ESC resistance inEscherichia colistrains from companion animals. Clinical isolates ofE. coliwere collected from veterinary diagnostic laboratories throughout the United States from 2008 to 2009.E. coliisolates (n= 54) with reduced susceptibility to ceftazidime or cefotaxime (MIC ≥ 16 μg/ml) and extended-spectrum-β-lactamase (ESBL) phenotypes were analyzed. PCR and sequencing were used to detect mutations in ESBL-encoding genes and the regulatory region of the chromosomal geneampC. Conjugation experiments and plasmid identification were conducted to examine the transferability of resistance to ESCs. All isolates carried theblaCTX-M-1-group β-lactamase genes in addition to one or more of the following β-lactamase genes:blaTEM,blaSHV-3,blaCMY-2,blaCTX-M-14-like, andblaOXA-1.DifferentblaTEMsequence variants were detected in some isolates (n= 40). Three isolates harbored ablaTEM-181gene with a novel mutation resulting in an Ala184Val substitution. Approximately 78% of the isolates had mutations in promoter/attenuator regions of the chromosomal geneampC, one of which was a novel insertion of adenine between bases −28 and −29. Plasmids ranging in size from 11 to 233 kbp were detected in the isolates, with a common plasmid size of 93 kbp identified in 60% of isolates. Plasmid-mediated transfer of β-lactamase genes increased the MICs (≥16-fold) of ESCs for transconjugants. Replicon typing among isolates revealed the predominance of IncI and IncFIA plasmids, followed by IncFIB plasmids. This study shows the emergence of conjugative plasmid-borne ESBLs amongE. colistrains from companion animals in the United States, which may compromise the effective therapeutic use of ESCs in veterinary medicine.

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Genomic Diversity and Virulence Profiles of Historical Escherichia coli O157 Strains Isolated from Clinical and Environmental Sources

Applied and Environmental Microbiology ◽

10.1128/aem.02616-14 ◽

2014 ◽

Vol 81 (2) ◽

pp. 569-577 ◽

Cited By ~ 8

Author(s):

Lydia V. Rump ◽

Narjol Gonzalez-Escalona ◽

Wenting Ju ◽

Fei Wang ◽

Guojie Cao ◽

...

Keyword(s):

Escherichia Coli ◽

The United States ◽

Genomic Diversity ◽

Severe Illness ◽

Pathogenic Potential ◽

Content Type ◽

E Coli ◽

Virulence Markers ◽

Virulence Potential ◽

Food Borne

ABSTRACTEscherichia coliO157:H7 is, to date, the majorE. coliserotype causing food-borne human disease worldwide. Strains of O157 with other H antigens also have been recovered. We analyzed a collection of historic O157 strains (n= 400) isolated in the late 1980s to early 1990s in the United States. Strains were predominantly serotype O157:H7 (55%), and various O157:non-H7 (41%) serotypes were not previously reported regarding their pathogenic potential. Although lacking Shiga toxin (stx) andeaegenes, serotypes O157:H1, O157:H2, O157:H11, O157:H42, and O157:H43 carried several virulence factors (iha,terD, andhlyA) also found in virulent serotypeE. coliO157:H7. Pulsed-field gel electrophoresis (PFGE) showed the O157 serogroup was diverse, with strains with the same H type clustering together closely. Among non-H7 isolates, serotype O157:H43 was highly prevalent (65%) and carried important enterohemorrhagicE. coli(EHEC) virulence markers (iha,terD,hlyA, andespP). Isolates from two particular H types, H2 and H11, among the most commonly found non-O157 EHEC serotypes (O26:H11, O111:H11, O103:H2/H11, and O45:H2), unexpectedly clustered more closely with O157:H7 than other H types and carried several virulence genes. This suggests an early divergence of the O157 serogroup to clades with different pathogenic potentials. The appearance of important EHEC virulence markers in closely related H types suggests their virulence potential and suggests further monitoring of those serotypes not implicated in severe illness thus far.

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Complete Genome Sequence of a Carbapenem-Resistant Escherichia coli Isolate with blaNDM-5 from a Dog in the United States

Microbiology Resource Announcements ◽

10.1128/mra.00872-19 ◽

2019 ◽

Vol 8 (34) ◽

Cited By ~ 3

Author(s):

Gregory H. Tyson ◽

Cong Li ◽

Olgica Ceric ◽

Renate Reimschuessel ◽

Stephen Cole ◽

...

Keyword(s):

United States ◽

Escherichia Coli ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Carbapenem Resistance ◽

The United States ◽

Multidrug Resistant ◽

Content Type ◽

E Coli

The carbapenem resistance gene bla NDM-5 was identified in an Escherichia coli strain isolated from a dog. We report here the complete genome sequence of this E. coli strain; the bla NDM-5 gene was present on a large IncFII multidrug-resistant plasmid. This is the first bla NDM-5-carrying E. coli strain from an animal in the United States.

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Genetic Characterization of IncI2 Plasmids CarryingblaCTX-M-55Spreading in both Pets and Food Animals in China

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02155-12 ◽

2013 ◽

Vol 57 (6) ◽

pp. 2824-2827 ◽

Cited By ~ 42

Author(s):

Luchao Lv ◽

Sally R. Partridge ◽

Liangying He ◽

Zhenling Zeng ◽

Dandan He ◽

...

Keyword(s):

Escherichia Coli ◽

Genetic Characterization ◽

Content Type ◽

E Coli ◽

Food Animals ◽

Plasmid Backbone

ABSTRACTpHN1122-1 carryingblaCTX-M-55, from anEscherichia coliisolate from a dog, was completely sequenced. pHN1122-1 has an IncI2 replicon and typical IncI2-associated genetic modules, includingmok/hok-finO-yafA/B,nikABC, and two transfer regions,traandpil, as well as a shufflon.blaCTX-M-55is found within a 3.084-kb ISEcp1transposition unit that includes a fragment of IncA/C plasmid backbone. pHN1122-1 and closely related plasmids were identified in otherE. coliisolates from animals in China.

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Trends in Susceptibility of Escherichia coli from Intra-Abdominal Infections to Ertapenem and Comparators in the United States According to Data from the SMART Program, 2009 to 2013

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.05186-14 ◽

2015 ◽

Vol 59 (6) ◽

pp. 3606-3610 ◽

Cited By ~ 49

Author(s):

Sibylle H. Lob ◽

Krystyna M. Kazmierczak ◽

Robert E. Badal ◽

Meredith A. Hackel ◽

Samuel K. Bouchillon ◽

...

Keyword(s):

United States ◽

Escherichia Coli ◽

Antimicrobial Resistance ◽

Statistical Significance ◽

The United States ◽

Multidrug Resistant ◽

Content Type ◽

E Coli ◽

Smart Data ◽

Abdominal Infections

ABSTRACTAntimicrobial resistance inEnterobacteriaceae, including resistance to carbapenems, is increasing worldwide. However, using U.S. Study for Monitoring Antimicrobial Resistance Trends (SMART) data for 2009 to 2013, no statistically significant decreasing susceptibility trends were found overall forEscherichia coliisolates from patients with intra-abdominal infections. In the subset of isolates from community-associated infections, susceptibility to levofloxacin decreased significantly and the increasing rate of multidrug-resistantE. coliapproached statistical significance. In 2013, ertapenem, imipenem, and amikacin showed the highest susceptibility rates (≥99%) and fluoroquinolones the lowest (<70%). The 10 non-ertapenem-susceptible isolates (0.3% of allE. coliisolates) encoded one or more carbapenemases, extended-spectrum β-lactamases (ESBLs), AmpC β-lactamases, or non-ESBL β-lactamases.

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Epidemic Emergence in the United States of Escherichia coli Sequence Type 131-H30 (ST131-H30), 2000 to 2009

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00732-17 ◽

2017 ◽

Vol 61 (8) ◽

Cited By ~ 24

Author(s):

James R. Johnson ◽

Stephen Porter ◽

Paul Thuras ◽

Mariana Castanheira

Keyword(s):

United States ◽

Escherichia Coli ◽

Single Agent ◽

Temporal Trends ◽

Virulence Gene ◽

The United States ◽

Sequence Type ◽

Content Type ◽

E Coli ◽

Recent Emergence

ABSTRACT The H30 subclone of Escherichia coli sequence type 131 (ST131-H30) has become the leading antimicrobial resistance E. coli lineage in the United States and often exhibits resistance to one or both of the two key antimicrobial classes for treating Gram-negative infections, extended-spectrum cephalosporins (ESCs) and fluoroquinolones (FQs). However, the timing of and reasons for its recent emergence are inadequately defined. Accordingly, from E. coli clinical isolates collected systematically across the United States by the SENTRY Antimicrobial Surveillance Program in 2000, 2003, 2006, and 2009, 234 isolates were selected randomly, stratified by year, within three resistance categories: (i) ESC-reduced susceptibility, regardless of FQ phenotype (ESC-RS); (ii) FQ resistance, ESC susceptible (FQ-R); and (iii) FQ susceptible, ESC susceptible (FQ-S). Susceptibility profiles, phylogroup, ST, ST131 subclone, and virulence genotypes were determined, and temporal trends and between-variable associations were assessed statistically. From 2000 to 2006, concurrently with the emergence of ESC-RS and FQ-R strains, the prevalence of (virulence-associated) phylogroup B2 among such strains also rose dramatically, due entirely to rapid emergence of ST131, especially H30. By 2009, H30 was the dominant E. coli lineage overall (22%), accounting for a median of 43% of all single-agent and multidrug resistance (68% for ciprofloxacin). H30's emergence increased the net virulence gene content of resistant (especially FQ-R) isolates, giving stable overall virulence gene scores despite an approximately 4-fold expansion of the historically less virulent resistant population. These findings define more precisely the timing and tempo of H30's emergence in the United States, identify possible reasons for it, and suggest potential consequences, including more frequent and/or aggressive antimicrobial-resistant infections.

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