Most current fluoroquinolone-resistant E. coli clinical isolates, and the largest share of multidrug-resistant isolates, represent a highly clonal subgroup that likely originated from a single rapidly expanded and disseminated ST131 strain. Focused attention to this strain will be required to control the fluoroquinolone and multidrug-resistant E. coli epidemic.

Multilocus sequence typing (MLST) is usually based on the sequencing of 5 to 8 housekeeping loci in the bacterial chromosome and has provided detailed descriptions of the population structure of bacterial species important to human health. However, even strains with identical MLST profiles (known as sequence types or STs) may possess distinct genotypes, which enable different eco-or pathotypic lifestyles. Here we describe a two-locus, sequence-based typing scheme for Escherichia coli that utilizes a 489-nucleotide (nt) internal fragment of fimH (encoding the type 1 fimbrial adhesin) and the 469-nt internal fumC fragment used in standard MLST. Based on sequence typing of 191 model commensal and pathogenic isolates plus 853 freshly isolated clinical E. coli strains, this 2-locus approach-which we call CH (fumC/fimH) typing-consistently yielded more haplotypes than standard 7-locus MLST, splitting large STs into multiple clonal subgroups and often distinguishing different within-ST ecoand pathotypes. Furthermore, specific CH profiles corresponded to specific STs, or ST complexes, with 95% accuracy, allowing excellent prediction of MLST-based profiles. Thus, 2-locus CH typing provides a genotyping tool for molecular epidemiology analysis that is more economical than standard 7-locus MLST but has superior clonal discrimination power and, at the same time, corresponds closely to MLST-based clonal groupings. E scherichia coli infections, which encompass both intestinal syndromes (e.g., diarrhea, dysentery) and extraintestinal syndromes (e.g., urinary tract infection [UTI], septicemia, newborn meningitis), represent a significant public health burden worldwide (17). Most extraintestinal E. coli infections are caused by strains from phylogenetic groups B2 and D, within which are concentrated the horizontally mobile genetic determinants associated with extraintestinal virulence, such as toxins, adhesins, protectins, and iron-scavenging systems (17).Multilocus sequence typing (MLST) is currently the preferred method for characterizing the relatedness of strains within bacterial species (19). Standardized MLST schemes have been established for numerous human pathogens, including E. coli (38). Certain E. coli sequence types (STs, in which MLST profiles are identical) are epidemiologically associated with specific extraintestinal syndromes, e.g., ST127 and ST73 with pyelonephritis (15, 16), while others have been associated with important emerging antimicrobial resistance properties, e.g., ST69 with trimethoprimsulfamethoxazole resistance (20) and ST131 with fluoroquinolone resistance and extended-spectrum beta-lactamase production (22).However, STs are not uniform with regard to genetic properties or ecotypic/pathotypic behaviors. Within ST95, for example, strains from the North American OMP6 clade of serotype O18: K1:H7 encode P fimbriae and hemolysin and are strongly associated with both newborn meningitis and UTI (14), while strains from the European OMP9 clade of O18:K1:H7 encode neither element and are associated only w...

The ability to identify bacterial pathogens at the subspecies level in clinical diagnostics is currently limited. We investigated whether splitting Escherichia coli species into clonal groups (clonotypes) predicts antimicrobial susceptibility or clinical outcome. A total of 1,679 extraintestinal E. coli isolates (collected from 2010 to 2012) were collected from one German and 5 U.S. clinical microbiology laboratories. Clonotype identity was determined by fumC and fimH (CH) sequencing. The associations of clonotype with antimicrobial susceptibility and clinical variables were evaluated. CH typing divided the isolates into >200 CH clonotypes, with 93% of the isolates belonging to clonotypes with >2 isolates. Antimicrobial susceptibility varied substantially among clonotypes but was consistent across different locations. Clonotype-guided antimicrobial selection significantly reduced "drug-bug" mismatch compared to that which occurs with the use of conventional empirical therapy. With trimethoprim-sulfamethoxazole and fluoroquinolones, the drug-bug mismatch was predicted to decrease 62% and 78%, respectively. Recurrent or persistent urinary tract infection and clinical sepsis were significantly correlated with specific clonotypes, especially with CH40-30 (also known as H30), a recently described clonotype within sequence type 131 (ST131). We were able to clonotype directly from patient urine samples within 1 to 3 h of obtaining the specimen. In E. coli, subspecies-level identification by clonotyping can be used to significantly improve empirical predictions of antimicrobial susceptibility and clinical outcomes in a timely manner. Bacterial species identification is essential for the correct diagnosis of disease and to optimize the empirical choice of antimicrobial treatment before the results of culturing and susceptibility testing are available (up to 2 to 3 days) (1, 2). However, even within a single bacterial species, there is substantial strain-tostrain variation in antimicrobial susceptibilities and virulence (3), and the increasing prevalence of antimicrobial-resistant and multidrug-resistant bacterial pathogens is one of the greatest challenges in clinical medicine today (4, 5). Thus, subspecies-, strain-, or clonal group-level identification might provide significant advantages for the diagnosis of bacterial infections.Escherichia coli is a leading extraintestinal (found especially in the urine and blood) pathogen in the United States, causing millions of infections and tens of thousands of deaths each year (6). As a clonal species, E. coli contains a limited number of genetically related lineages (i.e., clonotypes) (10). Although several E. coli clonotypes with distinctive antimicrobial susceptibility patterns have been described (11)(12)(13)(14)(15), the use of clonotyping as a general predictive marker for antimicrobial susceptibility among unselected extraintestinal clinical E. coli isolates has not been reported. Additionally, the two most-commonly used clonal typing methods for E. coli, multilocus sequ...

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The contribution of homologous exchange (recombination) of core genes in the adaptive evolution of bacterial pathogens is not well understood. To investigate this, we analyzed fully assembled genomes of two Escherichia coli strains from sequence type 131 (ST131), a clonal group that is both the leading cause of extraintestinal E. coli infections and the main source of fluoroquinolone-resistant E. coli. Although the sequences of each of the seven multilocus sequence typing genes were identical in the two ST131 isolates, the strains diverged from one another by homologous recombination that affected at least 9% of core genes. This was on a par with the contribution to genomic diversity of horizontal gene transfer and point gene mutation. The genomic positions of recombinant and mobile genetic regions were partially linked, suggesting their concurrent occurrence. One of the genes affected by homologous recombination was fimH, which encodes mannose-specific type 1 fimbrial adhesin, resulting in functionally distinct copies of the gene in ST131 strains. One strain, a uropathogenic isolate, had a pathoadaptive variant of fimH that was acquired by homologous replacement into the commensal strain background. Close examination of FimH structure and function in additional ST131 isolates revealed that recombination led to acquisition of several functionally distinct variants that, upon homologous exchange, were targeted by a variety of pathoadaptive mutations under strong positive selection. Different recombinant fimH strains also showed a strong clonal association with ST131 isolates that had distinct fluoroquinolone resistance profiles. Thus, homologous recombination of core genes plays a significant role in adaptive diversification of bacterial pathogens, especially at the level of clonally related groups of isolates.