The faecal microbiome of the Australian silver gull contains phylogenetically diverse ExPEC, aEPEC and Escherichia coli carrying the transmissible locus of stress tolerance

Wyrsch, Ethan R.; Hoye, Bethany J.; Sanderson-Smith, Martina; Gorman, Jody; Maute, Kimberly; Cummins, Max L.; Jarocki, Veronica M.; Marenda, Marc S.; Dolejska, Monika; Djordjevic, Steven P.

doi:10.1016/j.scitotenv.2024.170815

Cited by 1 publication

(2 citation statements)

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“…Even though various combinations were present, the F29 allele variant was the most prevalent one occurring in such cases which highlights the importance of proper assignment due to its association with pUTI89-like plasmid. Combinations of other variants were observed in a lower number of cases, none of them corresponding to the most prevalent combinations in our results [18], [19].…”

Section: Figure 5 the Most Common Allele Variants Combinations Obtain...contrasting

confidence: 60%

“…This phenomenon has not been described before except for a few papers where the multiple allele variants appear in the output but are not commented on [18], [19]. It was previously reported in various E. coli STs such as ST10, ST58, ST155, ST963, ST973 and ST1140 as well as in the ST we focused on the most, ST131 [18]. The improper allele assignment in these cases regarded only the FII allele, which was also the most common incorrectly assigned allele in our collections.…”

Section: Figure 5 the Most Common Allele Variants Combinations Obtain...mentioning

confidence: 99%

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Multiple variants of IncF plasmid alleles discovered within single bacterial cells challenge previous assumptions

Ruzickova,

Palkovicova,

Papousek

et al. 2024

Preprint

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IncF plasmids are diverse mobile genetic elements found in bacteria from the Enterobacteriaceae family and often carry critical antibiotic and virulence gene cargo. The classification of IncF plasmids using the plasmid Multi-Locus Sequence Typing (pMLST) tool compares the sequences of IncF alleles against a database to create a plasmid sequence type (ST). Accurate identification of plasmid STs is epidemiologically useful because it enables an assessment of the crucial IncF plasmid lineages associated with pandemic and emerging enterobacterial sequence types, inferring important information about specific bacterial lineages. Our initial observations showed discrepancies in IncF allele variants reported by pMLST in a collection of 898Escherichia coliST131 genomes. To evaluate the limitations of the pMLST tool, we interrogated an in-house and publicly available repository of 70324 E. coli genomes of various STs and other Enterobacterales genomes (n=1247). All short-read genomes and representatives selected for long-read sequencing were used to assess allele variants and to compare the output with the real biological situation. When multiple allele variants occurred in a single bacterial genome, the python and web versions of the tool randomly selected one allele to report, leading to limited and inaccurate ST identification. Discrepancies were detected in 5804 of 72469 genomes (8.01%). Long read sequencing of 27 carefully selected genomes confirmed multiple IncF allele variants present on one plasmid, or two separate IncF plasmids present in a single bacterial cell. The pMLST tool was unable to accurately distinguish allele variants and their location on replicons using short-read nor long-read genome sequences.

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Section: Figure 5 the Most Common Allele Variants Combinations Obtain...contrasting

confidence: 60%

Section: Figure 5 the Most Common Allele Variants Combinations Obtain...mentioning

confidence: 99%

Multiple variants of IncF plasmid alleles discovered within single bacterial cells challenge previous assumptions

Ruzickova,

Palkovicova,

Papousek

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

The faecal microbiome of the Australian silver gull contains phylogenetically diverse ExPEC, aEPEC and Escherichia coli carrying the transmissible locus of stress tolerance

Cited by 1 publication

References 104 publications

Multiple variants of IncF plasmid alleles discovered within single bacterial cells challenge previous assumptions

Multiple variants of IncF plasmid alleles discovered within single bacterial cells challenge previous assumptions

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