Predictive Diagnostics for Escherichia coli Infections Based on the Clonal Association of Antimicrobial Resistance and Clinical Outcome

Abstract

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...

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

“…To date, although the O16 ST131 clade has not achieved the same level of clinical prominence as its (mainly H30 subclone) O25b-associated ST131 counterparts, it appears to be second in prevalence within ST131 after H30 (with its CTX-M-15 ESBLassociated H30-Rx subset [Rx, extensively resistant]) (14,31,34), equaling or exceeding the prevalence of the next-most-prevalent ST131 subclone, H22 (14,23,31). Moreover, the clade is sufficiently prevalent and widespread, and it exhibits a sufficiently distinctive resistance profile, as to make its detection potentially useful for clinical management (23).…”

“…Moreover, the clade is sufficiently prevalent and widespread, and it exhibits a sufficiently distinctive resistance profile, as to make its detection potentially useful for clinical management (23). For example, within each of the two studied large clinical collections, the resistance prevalence differences between the three main subsets within ST131 (O16, H30, and others) and non-ST131 isolates were such that depending on the cut point used to determine the suitability of an agent for empirical use, knowledge of an clonal subset identity of an isolate would allow versus disallow the use of certain drugs (Tables 1 and 3).…”

“…Alleles of fumC were determined according to the Achtman MLST website (http://mlst.ucc.ie/mlst/dbs/Ecoli). Combined fumC and fimH alleles were used to infer STs and fimH-based subdivisions thereof, i.e., CH types (22,23). The fimH30 (H30) ST131 subclone also was detected using allele-specific PCR (4).…”

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

“…Two studies involving whole genome sequencing of ST131 isolates collected from multiple countries came to the same conclusion that fluoroquinolone resistance within ST131 was confined almost entirely to the H30 subclone and that CTX-M-15 producers clustered within a nested subclone, designated H30-Rx (Petty et al, 2014;Price et al, 2013 and 16.9 to 66.2 %, respectively, depending on the isolate sources and selection criteria (Banerjee et al, 2013b;Price et al, 2013). The majority of the ST131 isolates that have been tested for the H30 and H30-Rx subclones were collected from North America and Europe; relatively few isolates were from Asia (Banerjee et al, 2013a, b;Colpan et al, 2013;Johnson et al, 2013Johnson et al, , 2014Tchesnokova et al, 2013). Additionally, few studies have assessed the association of host factors with the two ST131 subclones (Banerjee & Johnson, 2014).…”

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

“…standardised between different laboratories and the database can be accessed easily on a net-based computer enabling the global exchanging of molecular typing data (Maiden et al, 1998). Besides the classical MLST scheme, several other MLST classifications have been established targeting fewer genes (Sahl et al, 2012;Tchesnokova et al, 2013;Weissman et al, 2012). The most common STs detected among APEC and AFEC are globally disseminated and have emerged among different species of animals, regardless of pathogenicity, such as ST354 and ST10 Dissanayake et al, 2014;Kim et al, 2011;Maluta et al, 2014;Manges and Johnson, 2012;Mora et al, 2011;Pires-dos-Santos et al, 2013;Schaufler et al, 2015).…”