Veronika Tchesnokova

University of Washington Seattle | UW · Department of Microbiology

Background: Community circulating gut microbiota is the main reservoir for uropathogenic Escherichia coli, including those resistant to antibiotics. Ciprofloxacin had been the primary antibiotic prescribed for urinary tract infections, but its broad use has been discouraged and steadily declined since 2015. How this change in prescriptions affecte...

Background: Fluoroquinolone use for urinary tract infections has been steadily declining. Gut microbiota is the main reservoir for uropathogenic Escherichia coli but whether the carriage of fluoroquinolone-resistant E. coli has been changing is unknown. Methods. We determined the frequency of isolation and other characteristics of E. coli nonsucept...

Background: Fluoroquinolone use for urinary tract infections has been steadily declining. Gut microbiota is the main reservoir for uropathogenic Escherichia coli but whether the carriage of fluoroquinolone-resistant E. coli has been changing is unknown. Methods. We determined the frequency of isolation and other characteristics of E. coli nonsucept...

Allosteric proteins transition between ‘inactive’ and ‘active’ states. In general, such proteins assume distinct conformational states at the level of secondary, tertiary and/or quaternary structure. Different conformers of an allosteric protein can be antigenically dissimilar and induce antibodies with a highly distinctive specificities and neutra...

The FimH protein of Escherichia coli is a model two-domain adhesin that is able to mediate an allosteric catch bond mechanism of bacterial cell attachment, where the mannose-binding lectin domain switches from an 'inactive' conformation with fast binding to mannose to an 'active' conformation with slow detachment from mannose. Because mechanical te...

We report that there is a recent global expansion of numerous independent SARS-CoV-2 variants with mutation L452R in the receptor-binding domain (RBD) of the Spike protein. The massive emergence of L452R variants was first linked to lineage B.1.427/B.1.429 (clade 21C) that has been spreading in California since November-December 2020, originally na...

Critical molecular events that control conformational transitions in most allosteric proteins are ill-defined. The mannose-specific FimH protein of Escherichia coli is a prototypic bacterial adhesin that switches from an ‘inactive’ low-affinity state (LAS) to an ‘active’ high-affinity state (HAS) conformation allosterically upon mannose binding and...

The recent rise in mutational variants of SARS-CoV-2, especially with changes in the Spike protein, is of significant concern due to the potential ability for these mutations to increase viral infectivity, virulence and/or ability to escape protective antibodies. Here, we investigated genetic variations in a 414-583 amino acid region of the Spike p...

Bacterial species in the microbiome are often represented by multiple genetically and phenotypically different strains, making insight into subspecies diversity critical to a full understanding of the microbiome, especially with respect to opportunistic pathogens. However, methods allowing efficient high-throughput clonal typing are not currently a...

While microbiome studies have focused on diversity on the species or higher level, bacterial species in microbiomes are represented by different, often multiple strains. These strains could be clonally and phenotypically very different, making assessment of strain content vital to a full understanding of microbiome function. This is especially impo...

We report that fluoroquinolone resistant Escherichia coli are found in feces of 8.8% healthy adult women, with most bacteria belonging to pandemic multi-drug resistant ST131-H30R or ST1193 clonal groups. Moreover, these highly uropathogenic clonal groups demonstrate an especially prolonged gut persistence and high rate of bacteriuria without docume...

Significance Global growth in antibiotic resistance is a major social and health problem. The most common mechanism of high resistance to fluoroquinolones is the sequential acquisition of 3 mutations in 2 DNA topoisomerases, GyrA and ParC. We show that Escherichia coli ST1193 acquired the mutant variants of gyrA and parC not by a conventional stepw...

We describe the rapid and ongoing emergence across multiple US cities of a new multidrug-resistant E. coli clone - ST1193, resistant to fluoroquinolones (100%), trimethoprim/sulfamethoxazole (55%) and tetracycline (53%). ST1193 is associated with younger adults (age < 40 years) and currently comprises a quarter of fluoroquinolone-resistant clinical...

Background: The pandemic spread of antibiotic resistance increases the likelihood of ineffective empirical therapy. The recently emerged fluoroquinolone-resistant Escherichia coli ST131-H30R subclone (H30) is a leading cause of multidrug-resistant urinary tract infection (UTI) and bloodstream infection worldwide. Objective: We studied the relati...

Escherichia coli can cause a variety of extra-intestinal infections, such as urinary tract infection, meningitis, peritonitis and septicemia.….

Background E. coli ST131-H30 is a globally important pathogen implicated in rising rates of multidrug resistance among E. coli causing extraintestinal infections. Previous studies have focused on adults, leaving the epidemiology of H30 among children undefined. Methods We used clinical data and isolates from a case-control study of extended-spectr...

Background: E. coli ST131-H30 is a globally important pathogen implicated in rising rates of multidrug resistance among E. coli causing extraintestinal infections. Previous studies have focused on adults, leaving the epidemiology of H30 among children undefined. Methods: We used clinical data and isolates from a case-control study of extended-spect...

The aim of this study was to construct a valid publicly available method for in silico fimH sub-typing of Escherichia coli particularly suitable for differentiation of fine-resolution subgroups within clonal groups defined by standard multi-locus sequence typing (MLST). FimTyper was constructed as a FASTA database containing all currently known fim...

We analyzed the within-household evolution of two household-associated Escherichia coli strains from pandemic clonal group ST131-H30, using isolates recovered from five individuals within two families, each of which had a distinct strain. Family 1's strain was represented by a urine isolate from the index patient (older sister) with recurrent cysti...

Despite the known clonal distribution of antibiotic resistance in many bacteria, empiric (pre-culture) antibiotic selection still relies heavily on species-level cumulative antibiograms, resulting in overuse of broad-spectrum agents and excessive antibiotic/pathogen mismatch. Urinary tract infections (UTIs), which account for a large share of antib...

Local reference set Table of clonotype-specific antibiograms compiled based on 1,225 E. coli urine isolates obtained from Kaiser Permanente Washington patients. (DOCX)

Escherichia coli isolates from the local reference collection. Following variables are listed: ID (isolate’s name in UW collection), clonotype (septatype), resistance to seven antibiotics (AMP, ampicillin, CZ, cefazolin, CTR, ceftriaxone, T/S, trimethoprim/sulfamethoxazole, CIP, ciprofloxacin, NIT, nitrofurantoin, FOS, fosfomycin). Resistance is gi...

Escherichia coli isolates from the multi-national (non-Seattle) reference collection. Following variables are listed: ID (isolate’s name in UW collection), clonotype (septatype), resistance to six antibiotics (AMP, ampicillin, CZ, cefazolin, CTR, ceftriaxone, T/S, trimethoprim/sulfamethoxazole, CIP, ciprofloxacin, NIT, nitrofurantoin). Resistance i...

Comparison of antibiotic resistance prevalence among study vs. local and multi-national (non-Seattle) reference Escherichia coli isolates for the 10 most frequent study clonotypes. (DOCX)

Correlation between Escherichia coli load in urine (by culture) and time-to-positive for the 7SNP-test. Data are for all test-positive samples (N = 274). Bubble size corresponds to the relative number of samples. According to linear regression the average time required for the test to detect E. coli is shortened by 1.8 min (95% CI 1.5–2.1, P < .001...

Allowed trimethoprim/sulfamethoxazole (T/S) use at different thresholds and different reference sets. As the validation set we used the 220 subjects whose urine was positive for E. coli both by culture and 7-SNP test, and who had an antibiotic prescribed at the index visit or the next day. As the reference set we used either the local reference set...

Samples from prospective clonal diagnostic study. Following variables are listed: study ID (name of the de-identified sample); bacterial load determined by 7-SNP test and bacterial load determined by culture (log10 cfu/ml); clonotype (septatype) determined in 7-SNP test directly from urine sample and clonotype from cultured bacteria; and resistance...

Antimicrobial-resistant Escherichia coli are a concern for military health services. We studied 100 extended-spectrum beta-lactamase (ESBL)-producing and non-producing E. coli clinical and surveillance isolates from military personnel and civilians at Brooke Army Medical Center (2007–2011). Major E. coli lineages, most prominently ST10 (24%), ST131...

Streptococcus pyogenes (Group A Streptococcus or GAS) is a hemolytic human pathogen associated with a wide variety of infections ranging from minor skin and throat infections to life-threatening invasive diseases. The cell wall of GAS consists of peptidoglycan sacculus decorated with a carbohydrate comprising a polyrhamnose backbone with immunodomi...

Background: TheH30 subclone withinEscherichia colisequence type 131 (ST131-H30) has emerged rapidly to become the leading antibiotic-resistantE. colistrain. Hyper-virulence, multi-drug resistance, and opportunism have been proposed as explanations for its epidemic success. Methods: We assessed 1,133 consecutive uniqueE. coliclinical isolates fro...

In the present study, it is shown that although Escherichia coli CFT073, a human uropathogenic (UPEC) strain, grows in liquid glucose M9 minimal medium, it fails to grow on glucose M9 minimal medium agar plates seeded with ≤1⁰6 CFU. The cells on glucose plates appear to be in a "quiescent" state that can be prevented by various combinations of lysi...

Background. Escherichia coli is a highly clonal pathogen. Extraintestinal isolates belong to a limited number of genetically related groups, which often exhibit characteristic antimicrobial resistance profiles. Methods. We developed a rapid clonotyping method for extraintestinal E coli based on detection of the presence or absence of 7 single nucle...

Minimum bactericidal concentrations (MBCs) for ciprofloxacin were significantly higher among 41 members of the H30 subclone within Escherichia coli sequence type 131 than among 48 other fluoroquinolone-resistant E. coli. This MBC difference - which was not explained by ciprofloxacin MICs, gyrA/parC/parE mutations, presence of aac(6')-Ib-cr, or orga...

To develop and evaluated a rapid multiplex-qPCR to identify fecal carriers of multi-drug resistant extra-intestinal pathogenic E. coli clonal groups. Men presenting for transrectal prostate biopsy (TPB) at the San Diego Veterans Affairs Medical Center underwent rectal culture immediately prior to TPB. Rectal swabs were streaked ciprofloxacin-supple...

Significance The binding pocket of a receptor often switches between two conformations, with the tight “active” conformation binding ligand with higher affinity than the loose “inactive” one. We demonstrate here that in physiologically relevant nonequilibrium conditions, stabilizing the active conformation actually reduces binding. We furthermore s...

The recent expansion of the H30 subclone of Escherichia coli sequence type 131 (ST131), and its CTX-M-15-associated H30Rx subset, remains unexplained. Although ST131-H30 typically exhibits fluoroquinolone resistance, so do multiple other E. coli lineages that have not expanded similarly. To determine whether H30 isolates have more intense fluoroqui...

Author Summary A common approach in the development of selective inhibitors for ligand-receptor interactions is targeting the receptor binding site with the expectation that inhibitors will sterically interfere with ligand binding and thus block receptor function via a competitive (orthosteric) mechanism. However, using monoclonal antibodies specif...

We report observations on the dynamics of bacterial communities in response to methane stimulus in laboratory microcosm incubations prepared with lake sediment samples. We first measured taxonomic compositions of long-term enrichment cultures and determined that, although dominated by Methylococcaceae types, these cultures also contained accompanyi...

Cystic fibrosis (CF) patients suffer from chronic recurrent bacterial airway infections, which eventually lead to reduced life expectancy. Escherichia coli has not been considered as a CF pathogen. A total of 176 patients were observed over 5.6 years on average from 2002 to 2009 in two CF centers in Muenster, Germany. Sputum and throat swab culture...

We designed a study to describe the characteristics of sequence type 131 (ST131) lineages, including the H30-Rx sublineage, among a global collection of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates from 9 countries collected from 2000 to 2011. A total of 240 nonrepeat isolates from Canada, the United States, Brazil, the...

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 mult...

Unlabelled: The Escherichia coli sequence type 131 (ST131) clone is notorious for extraintestinal infections, fluoroquinolone resistance, and extended-spectrum beta-lactamase (ESBL) production, attributable to a CTX-M-15-encoding mobile element. Here, we applied pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing to reconstruct the...

We assessed Escherichia coli ST131 and its H30 and H30-Rx subclones for virulence genes, antimicrobial resistance, and extended-spectrum beta-lactamase (ESBL) type. Although both subclones were associated with ESBL production, H30-Rx isolates had higher resistance scores and were associated specifically with CTX-M-15. Three virulence genes (iha, sa...

Significance Antibodies targeting the receptor-binding pocket of viral and bacterial adhesins are highly protective against infection. However, functional site epitopes in the antigens are not always highly immunogenic, possibly because of the binding epitope-masking effects of natural ligand–receptor interactions. By using the mannose-specific fim...

Background: Escherichia coli sequence type 131 (ST131), typically fluoroquinolone-resistant (FQ-R) and/or extended-spectrum β-lactamase (ESBL)-producing, has emerged globally. We assessed its prevalence and characteristics among US veterans. Methods: In 2011, 595 de-identified E. coli clinical isolates were collected systematically within 3 resi...

Background:The clonal distribution of E. coli across an unselected population in the current era of widespread antimicrobial resistance is incompletely defined.Methods:We used a newly described clonal typing strategy based on sequencing of fumC and fimH (i.e., CH typing) to infer multi-locus sequence types (STs) for 299 consecutive, non-duplicate e...

Background:Sub-species identification of bacterial pathogens in clinical diagnostics is currently limited. We investigated whether splitting the Escherichia coli species into clonal groups (clonotypes) predicts antimicrobial susceptibility or clinical outcome.Method:Total of 1679 extraintestinal E. coli isolates (2010-2012) were collected from five...

The protein FimH is expressed by the majority of commensal and uropathogenic strains of Escherichia coli on the tips of type 1 fimbriae and mediates adhesion via a catch bond to its ligand mannose. Crystal structures of FimH show an allosteric conformational change, but it remains unclear whether all of the observed structural differences are part...

Unlabelled: Salmonella and Escherichia coli mannose-binding type 1 fimbriae exhibit highly similar receptor specificities, morphologies, and mechanisms of assembly but are nonorthologous in nature, i.e., not closely related evolutionarily. Their operons differ in chromosomal location, gene arrangement, and regulatory components. In the current stu...

List of Escherichia coli strains used in this study.

BLAST analysis of fimA in different enterobacteria.

List of Salmonella enterica strains used in this study.

CfaE, the tip adhesin of enterotoxigenic Escherichia coli colonization factor antigen I fimbriae, initiates binding of this enteropathogen to the small intestine. It comprises stacked β-sandwich adhesin and pilin domains with the putative receptor-binding pocket at one pole and an equatorial interdomain interface. CfaE binding to erythrocytes is en...

Background: Fluoroquinolone-resistant Escherichia coli are increasingly prevalent. Their clonal origins--potentially critical for control efforts--remain undefined. Methods: Antimicrobial resistance profiles and fine clonal structure were determined for 236 diverse-source historical (1967-2009) E. coli isolates representing sequence type ST131 a...

Abstract The Escherichia coli sequence type 131 (ST131) clone is notorious for extraintestinal infections, fluoroquinolone resistance, and extended-spectrum beta-lactamase (ESBL) production, attributable to a CTX-M-15-encoding mobile element. Here, we applied pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing to reconstruct the evo...

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 ST131 - a clonal group that is both the leading cause of extra-intestinal E. coli infections and the main source of f...

Background: Most studies of the population structure of extraintestinal E. coli have focused on antimicrobial-resistant isolates or those from select patient groups. The clonal structure of extraintestinal E. coliacross an unselected population is not well described. Methods: Using a newly described clonal typing strategy based on sequencing...

Static adhesion of representative wild-type and recombinant S. enterica to mannose-containing substrates. Binding of wild-type (A) and recombinant (B) S. enterica strains to Man1 (yeast mannan, red), Man5 (RNaseB, blue) and anti-FimHSE antibody (grey). Attached bacteria were stained with crystal violet and the adhesion was quantified by measuring a...

Man1/Man5 binding ratio calculated for representative wild-type and recombinant strains of S. enterica. Data are the means ± SD of triplicates from one representative experiment of three performed. The strain tags of systemically non-invasive serovars are in black and the invasive serovars in red. ND, not determined. (TIF)

Bacterial accumulation on Man1-coated surfaces in the parallel plate flow chamber. Bacterial binding to Man-BSA under different shear conditions was recorded for 4 min. Data are the means of two independent experiments. (TIF)

Effects of point mutations on binding phenotype of S. enterica FimH. Static adhesion of 3H-labeled bacteria to Man1 (Man-BSA, red), Man5 (RNaseB, blue) and anti-FimHSE antibody (grey). Data are the means ± SD of triplicates from one representative experiment of three performed. (TIF)

Static adhesion of S. Typhimurium LBH4 expressing different variants of FimH to mannose-containing substrates. Binding of 3H-labled bacteria to Man1 (Man-BSA) and Man5 (RNaseB) was determined as described in ‘Materials and Methods’. Data are the means ± SD of triplicates from one representative experiment of three experiments that were performed. (...

List of primers. (RTF)

List of plasmids. (RTF)

Whereas the majority of pathogenic Salmonella serovars are capable of infecting many different animal species, typically producing a self-limited gastroenteritis, serovars with narrow host-specificity exhibit increased virulence and their infections frequently result in fatal systemic diseases. In our study, a genetic and functional analysis of the...