David Gordon

The E phylogroup of Escherichia coli is highly diverse and mimics the whole E. coli species population structure

Publisher: Wiley

Date: 09-09-2021

DOI: 10.1111/1462-2920.15742

Abstract: To get a global picture of the population structure of the Escherichia coli phylogroup E, encompassing the O157:H7 EHEC lineage, we analysed the whole genome of 144 strains isolated from various continents, hosts and lifestyles and representative of the phylogroup ersity. The strains possess 4331 to 5440 genes with a core genome of 2771 genes and a pangenome of 33 722 genes. The distribution of these genes among the strains shows an asymmetric U‐shaped distribution. E phylogenetic strains have the largest genomes of the species, partly explained by the presence of mobile genetic elements. Sixty‐eight lineages were delineated, some of them exhibiting extra‐intestinal virulence genes and being virulent in the mouse sepsis model. Except for the EHEC lineages and the reference EPEC, EIEC and ETEC strains, very few strains possess intestinal virulence genes. Most of the strains were devoid of acquired resistance genes, but eight strains possessed extended‐spectrum beta‐lactamase genes. Human strains belong to specific lineages, some of them being virulent and antibiotic‐resistant [sequence type complexes (STcs) 350 and 2064]. The E phylogroup mimics all the features of the species as a whole, a phenomenon already observed at the STc level, arguing for a fractal population structure of E. coli .

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

Publisher: Cold Spring Harbor Laboratory

Date: 13-02-2020

DOI: 10.1101/2020.02.12.945709

Abstract: Escherichia coli is a commensal of birds and mammals, including humans. It can act as an opportunistic pathogen and is also found in water and sediments. Since most population studies have focused on clinical isolates, we studied the phylogeny, genetic ersification, and habitat-association of 1,294 isolates representative of the phylogenetic ersity of more than 5,000, mostly non-clinical, isolates originating from humans, poultry, wild animals and water s led from the Australian continent. These strains represent the species ersity and show large variations in gene repertoires within sequence types. Recent gene transfer is driven by mobile elements and determined by habitat sharing and by phylogroup membership, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. The phylogroups with smallest genomes had the highest rates of gene repertoire ersification and fewer but more erse mobile genetic elements, suggesting that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these small genomes were in freshwater isolates suggesting that some lineages are specifically adapted to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species.

Prevalence, diversity and genetic structure of Escherichia coli isolates from septic tanks.

Publisher: Wiley

Date: 16-12-2022

DOI: 10.1111/1758-2229.13035

Abstract: The present study investigated the ersity and genetic structure of Escherichia coli isolates from 100 septic tanks in the Canberra region, Australia. The physicochemical characteristics of the septic tanks were determined to examine the extent to which environmental factors might influence E. coli prevalence, ersity and population structure. The results of this study indicated that the temperature of the septic tank could explain some of the variation observed in the number of E. coli isolates recovered per septic tank, whereas pH was an important driver of E. coli ersity. Conductivity, pH and household size had a significant impact on E. coli population structure, and household size significantly affected the probability of detecting human-associated E. coli lineages [sequence types (STs) 69, 73, 95 and 131] in septic tanks. Phylogroup A and B1 strains were not randomly distributed among septic tanks, and the strong negative association between them may indicate intraspecific competition. The findings of this study suggest that the combination of environmental factors and intraspecific interactions may influence the distribution and genetic structure of E. coli in the environment.

Molecular and metabolic characteristics of wastewater associated Escherichia coli strains.

Publisher: Wiley

Date: 31-05-2022

DOI: 10.1111/1758-2229.13076

Abstract: We previously characterized the genetic ersity of Escherichia coli strains isolated from septic tanks in the Canberra region, Australia. In this study, we used repetitive element palindromic (REP) PCR fingerprinting to identify dominant REP-types belonging to phylogroups A and B1 strains across septic tanks. Subsequently, 76 E. coli strains were selected for whole-genome sequencing and phenotype microarrays. Comparative genome analysis was performed to compare septic tank E. coli genomes with a collection of 433 E. coli isolates from different hosts and freshwater. Clonal complexes (CCs) 10 (n = 15) and 399 (n = 10) along with sequence type (ST) 401 (n = 9) were the common lineages in septic tanks. CC10 strains have been detected from animal hosts and freshwater, whereas CC399 and ST401 strains appeared to be associated with septic tanks as they were uncommon in isolates from other sources. Comparative genome analysis revealed that CC399 and ST401 were genetically distinct from other isolates and carried an abundance of niche-specific traits involved in environmental adaptation. These strains also showed distinct metabolic characteristics, such as the ability to utilize pectin, which may provide a fitness advantage under nutrient-limited conditions. The results of this study characterized the adaptive mechanisms allowing E. coli to persist in wastewater.

Genetic structure, antimicrobial resistance and frequency of human associated Escherichia coli sequence types among faecal isolates from healthy dogs and cats living in Canberra, Australia

Publisher: Public Library of Science (PLoS)

Date: 04-03-2019

DOI: 10.1371/JOURNAL.PONE.0212867

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

Publisher: Public Library of Science (PLoS)

Date: 12-06-2020

DOI: 10.1371/JOURNAL.PGEN.1008866

Phenotypic characteristics contributing to the enhanced growth of Escherichia coli bloom strains.

Publisher: Wiley

Date: 10-11-2019

DOI: 10.1111/1758-2229.12801

Abstract: During bloom events, Escherichia coli cell counts increase to between 10,000 and 100,000 cfu/100 ml of water. The strains responsible for bloom events belong to E. coli phylogenetic groups A and B1, and all have acquired a capsule from Klebsiella. A pan-genome comparison of phylogroup A E. coli revealed that the ferric citrate uptake system (fecIRABCDE) was overrepresented in phylogroup A bloom strains compared with non-bloom E. coli. A series of experiments were carried out to investigate if the capsule together with ferric citrate uptake system could confer a growth rate advantage on E. coli. Capsulated strains had a growth rate advantage regardless of the media composition and the presence/absence of the fec operon, and they had a shorter lag phase compared with capsule-negative strains. The results suggest that the Klebsiella capsule may facilitate nutrient uptake or utilization by a strain. This, together with the protective roles played by the capsule and the shorter lag phase of capsule-positive strains, may explain why it is only capsule-positive strains that produce elevated counts in response to nutrient influx.

Diversity and distribution of Klebsiella capsules in Escherichia coli.

Publisher: Wiley

Date: 22-11-2019

DOI: 10.1111/1758-2229.12710

Abstract: E. coli strains responsible for elevated counts (blooms) in freshwater reservoirs in Australia carry a capsule originating from Klebsiella. The occurrence of Klebsiella capsules in E. coli was about 7% overall and 23 different capsule types were detected. Capsules were observed in strains from phylogroups A, B1 and C, but were absent from phylogroup B2, D, E and F strains. In general, few A, B1 or C lineages were capsule-positive, but when a lineage was encapsulated multiple different capsule types were present. All Klebsiella capsule-positive strains were of serogroups O8, O9 and O89. Regardless of the phylogroup, O9 strains were more likely to be capsule-positive than O8 strains. Given the sequence similarity, it appears that both the capsule region and the O-antigen gene region are transferred to E. coli from Klebsiella as a single block via horizontal gene transfer events. Pan genome analysis indicated that there were only modest differences between encapsulated and non-encapsulated strains belonging to phylogroup A. The possession of a Klebsiella capsule, but not the type of capsule, is likely a key determinant of the bloom status of a strain.

Comparative genomics and phenotypic studies to determine site-specificity of Escherichia coli in the lower gastrointestinal tract of humans

Publisher: Informa UK Limited

Date: 20-06-2023

DOI: 10.1080/19490976.2023.2223332

Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential.

Publisher: Wiley

Date: 28-06-2019

DOI: 10.1111/1462-2920.14713

Abstract: The phylogeny of the Escherichia coli species, with the identification of seven phylogroups (A, B1, B2, C, D, E and F), is linked to the lifestyle of the strains. With the accumulation of whole genome sequence data, it became clear that some strains belong to a group intermediate between the F and B2 phylogroups, designated as phylogroup G. Here, we studied the complete sequences of 112 strains representative of the G phylogroup ersity and showed that it is composed of one main sequence type complex (STc)117 and four other STcs (STc657, STc454, STc738 and STc174). STc117, which phylogeny is characterized by very short internal branches, exhibits extensive O ersity, but little H-type and fimH allele ersity, whereas the other STcs are characterized by a main O, H and fimH type. STc117 strains possess many traits associated with extra-intestinal virulence, are virulent in a mouse sepsis model and exhibit multi-drug resistance such as CTX-M production. Epidemiologic data on 4,524 Australian and French strains suggest that STc117 is a poultry-associated lineage that can also establish in humans and cause extra-intestinal diseases. We propose an easy identification method that will help to trace this potentially virulent and resistant phylogroup in epidemiologic studies.

King's College London

Location: United Kingdom of Great Britain and Northern Ireland

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McGill University

Location: Canada

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Australian National University

Location: Australia

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Discovery Projects - Grant ID: DP130100145

Start Date: 2013

End Date: 12-2016

Amount: $535,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP120100327

Start Date: 06-2012

End Date: 06-2015

Amount: $421,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP210103897

Start Date: 10-2021

End Date: 09-2024

Amount: $476,533.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0989589

Start Date: 2009

End Date: 06-2009

Amount: $550,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0664453

Start Date: 2006

End Date: 12-2009

Amount: $259,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP110103852

Start Date: 2011

End Date: 12-2014

Amount: $455,000.00

Funder: Australian Research Council