Population dynamics of an Escherichia coli ST131 lineage during recurrent urinary tract infection

Forde, Brian M.; Roberts, Leah W.; Phan, Minh-Duy; Peters, Kate M.; Fleming, Brittany A.; Russell, Colin W.; Lenherr, Sara; Myers, Jeremy B.; Barker, Adam P.; Fisher, Mark A.; Chong, Teik-Min; Yin, Wai‐Fong; Chan, Kok‐Gan; Schembri, Mark A.; Mulvey, Matthew A.; Beatson, Scott A.

doi:10.1038/s41467-019-11571-5

Cited by 83 publications

(62 citation statements)

References 73 publications

(88 reference statements)

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“…Once introduced into the intestine, these strains may establish colonization for some time but then may be replaced later by other E. coli genotypes introduced into the intestine by food. A recent study has shown that ESBL‐producing ST131 strain was detected in the intestine of a 74‐year‐old woman for over 5 years, although repeated exposures to sources containing this genotype could not be ruled out (Forde et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community

Matsui

Rubin

et al. 2020

MicrobiologyOpen

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Community‐acquired urinary tract infections (UTIs) are one of the most common bacterial infections worldwide. Escherichia coli is the most common cause of community‐acquired UTI. In general, UTI results from E. coli in the intestine that enters the bladder via the urethra. However, whether these E. coli strains that cause UTI represent members of the intestinal commensal E. coli or a distinct subgroup of pathogenic E. coli remains unestablished. Here, we analyzed E. coli isolates from fecal samples of healthy volunteers and urine samples of UTI patients obtained from a university‐affiliated health center. The E. coli isolates were genotyped by multilocus sequence typing (MLST). From May to October 2018, we analyzed 89 E. coli isolates from 76 (75%) rectal swabs from 113 unique healthy volunteers. We also analyzed 106 (27%) E. coli isolates from 398 unique urine samples collected between August and October 2018. Fecal and urine E. coli isolates each contained 31 distinct sequence types (STs). Nine STs were shared by fecal and urine E. coli isolates, which accounted for approximately 50% of urine isolates typed by MLST. Among the shared genotypes, ST10 and ST131 were significantly more frequently found in fecal samples, whereas ST95 and ST127 were significantly more frequently recovered from UTI samples. ST73 was found only among urine samples. These E. coli genotypes clustered and fluctuated over time. These observations suggest that E. coli genotypes found to cause UTI transiently colonize the intestine and that their primary reservoir may reside outside of the human intestine.

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Section: Discussionmentioning

confidence: 99%

Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community

Matsui

Rubin

et al. 2020

MicrobiologyOpen

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“…Unfortunately, four patients with UTIs associated with E. coli strains O25: H4 and O75: NM did not respond to the treatment with the autologous BL and the UTIs persisted. Several studies have associated UPEC O25: H4 strains to persistent UTIs due to the formation of intracellular bacterial communities [32].…”

Section: Discussionmentioning

confidence: 99%

Effect and Analysis of Bacterial Lysates for the Treatment of Recurrent Urinary Tract Infections in Adults

et al. 2020

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Urinary tract infection (UTI) is a relevant public health problem, economically and socially affecting the lives of patients. The increase of antimicrobial bacterial resistance significantly hinders the treatment of UTIs, raising the need to search for alternative therapies. Bacterial lysates (BL) obtained from Escherichia coli and other pathogens have been used to treat different infectious diseases with promising results. This work aims to evaluate the effect and composition of an autologous BL for the treatment and control of recurrent UTIs in adults. The results show remission in 70% of the patients within the first three months after the administration of BL, while the infection is maintained under control for 6–12 months. The analysis by liquid chromatography–mass spectrometry (LC-MS) of the BL fractions recognized by the sera of patients shows the presence of cytosolic proteins, fimbriae, OMPs, and LPS. Our study demonstrates that the autologous BL contributed to the treatment and control of recurrent UTIs in adults, and its composition shows that different surface components of E. coli are potential immunogens that could be used to create a polyvalent protective vaccine.

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“…Thirteen of them encode enzymes of metabolic pathways (aes, icd, pabB, trpA, trpB, fumC, mdh, purA, aspC, fadD, uidA, aroE, mtlD); ten belong to replication, repair, or transcription systems (polB, gyrA, recA, dinB, dnaG, mutS, arcA, cyaA, grpE, rpoS), and the remaining four control the production of two symporters (putP, lysP), kinase (adk) and protease (clpX). The sequences of these genes were obtained from 124 E. coli genomes (listed in Supplementary Table S1), including 59 complete genomes, whose phylogroups were previously identified in original papers [45,52,[55][56][57][58][59][60][61][62][63][64][65][66][67][68][69] (shown in bold in Supplementary Table S1). The remaining 65 genomes unassigned to phylogroups and containing orthologs of discriminatory genes were added to increase the resolution of phylogenetic trees.…”

Section: Alignment-based Multilocus Sequence Typing Resulted In Tree mentioning

confidence: 99%

Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

Panyukov

Kiselev

Ozoline

2020

IJMS

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The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker k-mers turned out to be capable of identifying not only species, but also strains of microorganisms with known genomes. Here, we evaluated the ability of genus-specific k-mers to distinguish eight phylogroups of Escherichia coli (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn’s disease. We found that a phylogenetic tree inferred from the pairwise distance matrix for unique 18-mers and 22-mers of 124 genomes was fully consistent with the topology of the tree, obtained with concatenated aligned sequences of orthologous genes. Therefore, we propose strain-specific “barcodes” for rapid phylotyping. Using unique 22-mers for taxonomic analysis, we detected microbes of all groups in human microbiomes; however, their presence in the five samples was significantly different. Pointing to the intraspecies heterogeneity of E. coli in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.

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Population dynamics of an Escherichia coli ST131 lineage during recurrent urinary tract infection

Cited by 83 publications

References 73 publications

Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community

Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community

Effect and Analysis of Bacterial Lysates for the Treatment of Recurrent Urinary Tract Infections in Adults

Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

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