High-Resolution Two-Locus Clonal Typing of Extraintestinal Pathogenic Escherichia coli

Abstract

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...

Extra-intestinal pathogenic Escherichia coli (ExPEC): Disease, carriage and clones

“…As a consequence, in the setting of an outbreak where phylogenetic information may significantly alter the subsequent management strategy, the delivery of real-time information using WGS is still currently limited in most hospitals. These observations led Weissman et al (25) …”

“…Isolates belonging to the same ST can be genetically distinct and may be associated with variable pathotypic behaviours. In 2012, Weissman et al (25) described a new method, CH typing, which derives its name from fumC and fimH gene analysis. They demonstrated that this approach was able not only to predict the respective MLST-based profile with up to 95% accuracy, but that it also enabled large STs to be split into a number of smaller clonal sub-groups (25).…”

“…In 2012, Weissman et al (25) described a new method, CH typing, which derives its name from fumC and fimH gene analysis. They demonstrated that this approach was able not only to predict the respective MLST-based profile with up to 95% accuracy, but that it also enabled large STs to be split into a number of smaller clonal sub-groups (25). Although CH typing will not replace MLST as a tool for phylogenetic studies, there are clear advantages of this technique, particularly relating to delineation of clones within STs and reduced costs when performing preliminary evaluations on larger clinical specimen collections (25,26).…”

High prevalence of Escherichia coli sequence type 131 among antimicrobial-resistant E. coli isolates from geriatric patients

“…ST131 is a highly successful E. coli clone which has received considerable attention due to its wide geographical distribution, ability to cause a wide range of extra-intestinal infections and association with CTX-M b-lactamases and multidrug resistance (NicolasChanoine et al, 2014). ST131 can be divided into different subclones by other typing methods, of which sequencing the type 1 fimbrial adhesin gene fimH is one widely used approach (Weissman et al, 2012). H30, designated according to the fimH30 variant, is currently the most prevalent subclone of ST131 (Nicolas-Chanoine et al, 2014).…”

Clonal distribution and associated characteristics of Escherichia coli clinical and surveillance isolates from a military medical center

“…Minimum inhibitory concentration (MIC) results were interpreted according to the Clinical Laboratory and Standards Institute criteria (Clinical and Laboratory Standards Institute, 2013). In addition, isolates were assessed molecularly for bla CTX-M-15 , major E. coli phylogenetic group (phylogroup) (Clermont et al, 2013), ST or ST complex (STc; as determined by fumC-fimH typing (Weissman et al, 2012), full or partial MLST (Maiden et al, 1998), or STc-specific PCR assays Johnson et al, 2009;Matsumura et al, 2012)), membership in the ST131-H30 clonal subset or its sublineage ST131-H30Rx (Banerjee et al, 2013), O type (O16 and O25b only) (Johnson et al, 2014), and extended virulence genotype (for 50 markers) (Johnson et al, 2015). Resistance scores were defined as the number of antibiotic classes to which an isolate exhibited resistance.…”