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Representation of the genetic variation among the 40 Escherichia coli isolates across the four collections. Gene names are displayed with different hypothetical proteins labelled successively, and with any SNP differences between isolates shown along branches. O-antigen cluster genes represent different glycosyltransferases in the O-antigen cluster. Highlighted boxes illustrate genetic differences in genes involved in surface structures (LPS, O-or K-antigen). n: number of isolates.
Source publication
Whole-genome sequencing has enabled detailed studies on bacterial evolution during infection, but there is limited knowledge on intraclonal variation. In this study, we sought to provide a snapshot of the intraclonal diversity of Escherichia coli as both commensal in the faecal environment and pathogen during urinary tract infection, respectively....
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... in the present study would be expected to be even larger for long-term colonisation in the intestine. Analyses of the accessory genome were performed to compare the intraclonal gene content of the four clones; we identified small variation in gene content between the 10 otherwise identical clones for both the faecal and urinary environment (Fig. 1, Table 3, 4, 5 and 6). From these analyses, it is evident that the gene content in each clone varied with between 2-15 genes within each clone (ten isolates sampled). Presence/absence of these are correlated for some of the genes. In many cases a variation was seen across several isolates of the same clone, e.g. Faecal-2, where four genes ...
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... genes within each clone (ten isolates sampled). Presence/absence of these are correlated for some of the genes. In many cases a variation was seen across several isolates of the same clone, e.g. Faecal-2, where four genes located on the same putatively plasmid associated contig were lost across six isolates, indicating partial loss of a plasmid (Fig. 1, Table 4). Despite the small sample size, overall the faecal clones show more diversity compared to the UTI clones and interestingly, the gene content variation was larger among the isolates with the highest SNP diversity and in isolates carrying plasmids (Fig. 1, Table 1). The variation is observed in metabolic-associated genes as well as ...
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... contig were lost across six isolates, indicating partial loss of a plasmid (Fig. 1, Table 4). Despite the small sample size, overall the faecal clones show more diversity compared to the UTI clones and interestingly, the gene content variation was larger among the isolates with the highest SNP diversity and in isolates carrying plasmids (Fig. 1, Table 1). The variation is observed in metabolic-associated genes as well as plasmid-encoded genes and genes encoding surface traits (Table 3, 4, 5 and ...
Citations
... Though clonal stability within E. coli STs has only been described to a limited extent, 47 the criteria we used to identify potential strain-sharing events of % 10 SNPs is comparable to the 9 SNP differences observed in a recurrent outbreak of ST10 clones in a broiler unit 97 and the % 6 SNP differences observed in within-host intra-clonal E. coli isolates from human UTIs and feces. 98 We also report the cut-off of % 100 SNPs often seen in the literature. 99 ll OPEN ACCESS ...
Human and domesticated animal waste infiltrates global freshwater, terrestrial, and marine environments, widely disseminating fecal microbes, antibiotics, and other chemical pollutants. Emerging evidence suggests that guts of wild animals are being invaded by our microbes, including Escherichia coli, which face anthropogenic selective pressures to gain antimicrobial resistance (AMR) and increase virulence. However, wild animal sources remain starkly under-represented among genomic sequence repositories. We sequenced whole genomes of 145 E. coli isolates from 55 wild and 13 domestic animal fecal samples, averaging 2 (ranging 1–7) isolates per sample, on a preserve imbedded in a human-dominated landscape in California Bay Area, USA, to assess AMR, virulence, and pan-genomic diversity. With single nucleotide polymorphism analyses we predict potential transmission routes. We illustrate the usefulness of E. coli to aid our understanding of and ability to surveil the emergence of zoonotic pathogens created by the mixing of human and wild bacteria in the environment.
... Clonal stability within E. coli sequence types has been described but only to a limited extend [12]. The genetic variation observed in the 18-month period is comparable to the 0-6 SNPs difference observed in within-host intraclonal E. coli isolates from human urinary tract infections and feces [13]. ...
The current investigation aimed at characterizing the cause of multiple disease outbreaks in the same broiler production unit during a course of 18 months. The outbreaks had mortality rates of up to 22%. Escherichia coli was diagnosed as the responsible agent. Multiple-locus variable-number tandem-repeat analysis showed that all chicken isolates had identical band patterns. Core genome comparisons demonstrated that the 36 chicken isolates differed with maximum of nine nucleotides indicating that the same E. coli clone was responsible for all seven disease outbreaks despite adherence to the all-in-all production principle and rigorous cleaning and disinfection procedures.
... Third, from all isolated E. coli strains, a single colony was used for SNP analysis. There could be some variation within the host or the existence of different E. coli clones [39] which may lead to an underestimation of species diversity. ...
Introduction:
Recurrent urinary tract infections (rUTI) largely contribute to antibiotic use in older adults. Understanding the genetic characteristics of Escherichia coli (E.coli) is needed to identify patients at risk for recurrence. The aim of this study was to obtain a greater understanding of the genetics of E. coli rUTI in nursing home residents.
Methods:
This is a secondary analysis of a multicenter Dutch nursing home study (PROGRESS). E. coli strains from residents with a suspected UTI and positive urine culture were analyzed using antimicrobial susceptibility testing and whole-genome sequencing (WGS). Same-strain recurrences were identified by single-nucleotide polymorphism (SNP) analysis.
Result:
In total, 121 E. coli strains were analyzed using WGS, of which 54 belonged to a rUTI episode. One third of E. coli rUTI episodes were caused by the same strain (n = 18, 33.3%). Same-strain recurrence occurred anywhere between 30 and 434 days after the index UTI, caused by sequence types (ST): ST12, ST23, ST73, ST131, ST453, ST538 and ST2522, in seven nursing home residents. In both single UTI and rUTI, antimicrobial resistance rates were low.
Conclusion:
Recurrent UTI in nursing home residents are caused by same-strain E. coli as well as due to different E. coli strains or other uropathogens. Same-strain recurrence can occur over 400 days after the index UTI, suggesting that some strains have the ability to colonize the bladder or gut for longer periods.
... This study documented the horizontal transfer of bla CTX-M-1 -harboring plasmids within a single individual. Stegger et al. (2020) analysed 20 E. coli isolates from each of nine urine samples collected from nine women who presented with UTI at a general practice in Zealand, Denmark, from which a single clone was detected in eight out of the nine samples. The authors then selected a total of 40 isolates belonging to the same clone: 10 each from two urine samples and two rectal swabs isolates from two healthy individuals (collected in a previous study; Nielsen et al. 2014) and investigated the intraclonal diversity of E. coli among the commensal and uropathogenic strains. ...
Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing fifty-four individuals and causing approximately 4 000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonisers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 136 since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
... It is possible that the observed variation between the isolate pairs was already present at the first time of sampling. However, we have previously described intraclonal variation in both fecal and urinary environment to be sparse [32], and the transition from the fecal environment to the urinary tract has also been shown to include only minor adaptation [14]. The isolates were collected from a limited area of Sweden, which could be a possible limitation, however, the phylogenetic diversity of the isolates in this study is large and represents a broad range of clones from six different phylotypes. ...
Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses of recurrent and non-recurrent Escherichia coli isolates from general practice. From whole-genome sequencing data, phylogenetic clustering and genomic traits were studied on a collection of isolates which caused recurrent infection compared to non-recurrent isolates. In addition, genomic variation between the 1st and following infection was studied on a subset of the isolates. Evidence of limited adaptation between the recurrent infections based on single nucleotide polymorphism analyses with a range of 0–13 non-synonymous single nucleotide polymorphisms (SNPs) between the paired isolates. This included an overrepresentation of SNPs in metabolism genes. We identified several genes which were more common in rUTI isolates, including nine fimbrial genes, however, not significantly after false-discovery rate. Finally, the results show that recurrent isolates of the present dataset are not distinctive by variation in the core genome, and thus, did not cluster distinct from non-rUTI isolates in a SNP phylogeny.
Little is known about the genomic diversity of Escherichia coli in healthy children from sub-Saharan Africa, even though this is pertinent to understanding bacterial evolution and ecology and their role in infection. We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). We identified 56 genotypes, with an average of 2.7 genotypes per host. These were spread over 37 seven-allele sequence types and the E. coli phylogroups A, B1, B2, C, D, E, F and Escherichia cryptic clade I. Immigration events accounted for three-quarters of the diversity within our study population, while one-quarter of variants appeared to have arisen from within-host evolution. Several isolates encode putative virulence factors commonly found in Enteropathogenic and Enteroaggregative E. coli, and 53% of the isolates encode resistance to three or more classes of antimicrobials. Thus, resident E. coli in these children may constitute reservoirs of virulence- and resistance-associated genes. Moreover, several study strains were closely related to isolates that caused disease in humans or originated from livestock. Our results suggest that within-host evolution plays a minor role in the generation of diversity compared to independent immigration and the establishment of strains among our study population. Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species.
