Abrupt Emergence of a Single Dominant Multidrug-Resistant Strain of Escherichia coli

Johnson, James R.; Tchesnokova, Veronika; Johnston, Brian; Clabots, Connie; Roberts, Pacita L.; Billig, Mariya; Riddell, Kim; Rogers, Peggy; Qin, Xuan; Butler-Wu, Susan M.; Price, Lance B.; Aziz, Maliha; Nicolas-Chanoine, M.-H.; DebRoy, Chitrita; Robicsek, Ari; Hansen, Gary L.; Urban, Carl; Platell, Joanne L.; Trott, Darren J.; Zhanel, George G.; Weissman, Scott J.; Cookson, Brad T.; Fang, Ferric C.; Limaye, Ajit P.; Scholes, Delia; Chattopadhyay, Sujay; Hooper, David C.; Sokurenko, Evgeni V.

doi:10.1093/infdis/jis933

Cited by 245 publications

(276 citation statements)

References 22 publications

(36 reference statements)

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“…Although ST131 was recognized only in 2008, it is clear that it had already been circulating for several years prior, perhaps initially as a susceptible organism, but then it accumulated resistance. Its spread accounts for much of the rise in multidrug-resistant E. coli seen in the last decade (23).…”

Section: Discussionmentioning

confidence: 99%

Rapid Identification of Major Escherichia coli Sequence Types Causing Urinary Tract and Bloodstream Infections

et al. 2015

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dEscherichia coli sequence types (STs) 69, 73, 95, and 131 are collectively responsible for a large proportion of E. coli urinary tract and bloodstream infections, and they differ markedly in their antibiotic susceptibilities. Here, we describe a novel PCR method to rapidly detect and distinguish these lineages. Three hundred eighteen published E. coli genomes were compared in order to identify signature sequences unique to each of the four major STs. The specificities of these sequences were assessed in silico by seeking them in an additional 98 genomes. A PCR assay was designed to amplify size-distinguishable fragments unique to the four lineages and was validated using 515 E. coli isolates of known STs. Genome comparisons identified 22 regions ranging in size from 335 bp to 26.5 kb that are unique to one or more of the four predominant E. coli STs, with two to 10 specific regions per ST. These regions predominantly harbor genes encoding hypothetical proteins and are within or adjacent to prophage sequences. Most (13/22) were highly conserved (>96.5% identity) in the genomes of their respective ST. The new assay correctly identified all 142 representatives of the four major STs in the validation set (n ‫؍‬ 515), with only two ST12 isolates misidentified as ST95. Compared with MLST, the assay has 100% sensitivity and 99.5% specificity. The rapid identification of major extraintestinal E. coli STs will benefit future epidemiological studies and could be developed to tailor antibiotic therapy to the different susceptibilities of these dominant lineages. Extraintestinal pathogenic Escherichia coli (ExPEC) strains are frequent pathogens, causing infections spanning a great range of severity (1, 2). They are responsible for 70 to 90% of acute community-acquired uncomplicated urinary infections, 85% of asymptomatic bacteriuria cases, and Ͼ60% of recurrent cystitis infections (3). E. coli is also one of the major pathogens of bloodstream infections, with mortality rates of 10 to 30%; in the United Kingdom, it has been the most common cause of bacteremia in most years since 1990, showing year-on year increases and now accounting for almost one-third of all bacteremias (see www.hpa .org.uk) (4). Successful treatment has been complicated by a rise in the prevalence of antibiotic-resistant strains.DNA profiling, e.g., by multilocus sequence typing (MLST), has advanced our understanding of ExPEC lineages, and several international studies have reported the predominance of sequence types (STs) 69, 73, 95, and 131 among large collections of ExPEC from human infections (5-8). In the United Kingdom, recent regional studies reported the consistent prevalences of these four STs among ExPEC from urinary and bloodstream infections. Collectively, they comprised 45% of the ExPEC strains from community and hospital urine samples recovered in 2007 to 2009 and 2007 to 2008 in Northwest (NW) England and the East Midlands, respectively, as well as 58% of those from bacteremias in northern England in 2010 to 2012 (9-11). The antibiotic ...

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Section: Discussionmentioning

confidence: 99%

Rapid Identification of Major Escherichia coli Sequence Types Causing Urinary Tract and Bloodstream Infections

et al. 2015

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“…Seven distinct fimH-based putative clonal lineages (H15, H22, H27, H30, H35, H41, and H49) were found among 352 historical and recent ST131 isolates obtained primarily from the United States (42). The H22 subclone was dominant (73%) among the historical isolates (those from 1967 to 1999), whereas the H30 subclone was the most prevalent (75%) among the current clinical isolates (those from 2000 to 2011) and accounted for nearly all fluoroquinolone-resistant isolates.…”

Section: Discussionmentioning

confidence: 99%

Four Main Virotypes among Extended-Spectrum-β-Lactamase-Producing Isolates of Escherichia coli O25b:H4-B2-ST131: Bacterial, Epidemiological, and Clinical Characteristics

et al. 2013

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“…The O16 rfb variant was detected by O-typespecific PCR (21). Alleles of the type-1 fimbrial adhesin gene fimH and the genes encoding DNA gyrase (gyrA) and topoisomerase (parC) were determined by sequence analysis and comparison with private sequence libraries (14,22). Alleles of fumC were determined according to the Achtman MLST website (http://mlst.ucc.ie/mlst/dbs/Ecoli).…”

Section: Methodsmentioning

confidence: 99%

Rapid and Specific Detection, Molecular Epidemiology, and Experimental Virulence of the O16 Subgroup within Escherichia coli Sequence Type 131

et al. 2014

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f Escherichia coli sequence type 131 (ST131), a widely disseminated multidrug-resistant extraintestinal pathogen, typically exhibits serotype O25b:H4. However, certain ST131 isolates exhibit serotype O16:H5 and derive from a phylogenetic clade that is distinct from the classic O25b:H4 ST131 clade. Both clades are assigned to ST131 by the Achtman multilocus sequence typing (MLST) system and a screening PCR assay that targets ST131-specific sequence polymorphisms in the mdh and gyrB genes. However, they are classified as separate STs by the Pasteur Institute MLST system, and an ST131 PCR method that targets the O25b rfb region and an ST131-specific polymorphism in pabB detects only the O25b-associated clade. Here, we describe a novel PCRbased method that allows for rapid and specific detection of the O16-associated ST131 clade. The clade members uniformly contained allele 41 of fimH (type 1 fimbrial adhesin) and a narrow range of alleles of gyrA and parC (fluoroquinolone target genes). The virulence genotypes of the clade members resembled those of classic O25b:H4 ST131 isolates; representative isolates were variably lethal in a mouse subcutaneous sepsis model. Several pulsotypes spanned multiple sources (adults, children, pets, and human fecal samples) and locales. An analysis of recent clinical E. coli collections showed that the O16 ST131 clade is globally distributed, accounts for 1 to 5% of E. coli isolates overall, and, when compared with other ST131 isolates, it is associated with resistance to ampicillin, gentamicin, and trimethoprim-sulfamethoxazole and with susceptibility to fluoroquinolones and extended-spectrum cephalosporins. Attention to this O16-associated ST131 clade, which is facilitated by our novel PCR-based assay, is warranted in future epidemiological studies of ST131 and, conceivably, in clinical applications. E scherichia coli sequence type 131 (ST131), designated according to the Achtman multilocus sequence typing (MLST) system, has emerged dramatically over the past decade to become the single most prevalent human extraintestinal E. coli strain in many regions, especially among isolates resistant to fluoroquinolones and/or extended-spectrum cephalosporins (1-6). Although ST131 classically exhibits serotype O25b:H4, multiple studies have documented a minor subset of ST131 isolates with serotype O16:H5 or O-type O16 (7-12). This O16 subset within ST131 remains poorly characterized.Among the extended-spectrum ␤-lactamase (ESBL)-producing E. coli isolates from Japan, the O16 ST131 subset was recently shown to represent a different Pasteur Institute sequence type (PST506) than classic O25b ST131 isolates (PST43) and to constitute a distinct phylogenetic clade (10, 11). Additionally, compared with classic O25b ST131 clade members, the studied O16 ST131 clade members exhibited a relatively greater prevalence of CTX-M-14 over (ST131-associated) CTX-M-15, were less commonly fluoroquinolone resistant but more commonly trimethoprimsulfamethoxazole resistant, and escaped detection by a widely used PCR...

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Abrupt Emergence of a Single Dominant Multidrug-Resistant Strain of Escherichia coli

Cited by 245 publications

References 22 publications

Rapid Identification of Major Escherichia coli Sequence Types Causing Urinary Tract and Bloodstream Infections

Rapid Identification of Major Escherichia coli Sequence Types Causing Urinary Tract and Bloodstream Infections

Four Main Virotypes among Extended-Spectrum-β-Lactamase-Producing Isolates of Escherichia coli O25b:H4-B2-ST131: Bacterial, Epidemiological, and Clinical Characteristics

Rapid and Specific Detection, Molecular Epidemiology, and Experimental Virulence of the O16 Subgroup within Escherichia coli Sequence Type 131

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