F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses

Abstract

E. coli ST95 is one of five dominant ExPEC lineages globally and noted for causing urinary tract and bloodstream infections and neonatal meningitis in humans and colibacillosis in poultry. Using high-resolution phylogenomics, we show that F replicon sequence type is linked to ST95 clade structure and zoonotic potential.

Genomic and Temporal Trends in Canine ExPEC Reflect Those of Human ExPEC

“…pUTI89-like plasmids were confined to phylogroups B2 and D and were most common in ST963 (8/9, 89%), ST95 (3/6, 66.7%), and ST131 (5/8, 62.5%) sequences. Their presence in these STs is indicative of sublineage partitioning, as has been recently described for ST131 and ST95 ( 22 , 23 ).…”

“…The major human ExPEC STs, particularly ST95 ( 22 ), ST131 ( 23 , 26 ), and ST73 ( 45 ), comprise sublineages that are often discernible by serotype and fimH allele variation. Lineage subdivision is also often accompanied by carriage of different F plasmid replicon sequence types belonging to ColV (various replicon types) and pUTI89-like (ColIa + /F29:A-:B10) genotypes ( 22 , 25 , 26 ). In the canine collection, 56 isolates (14.9%) carried a ColV plasmid and these sequences were identified across all phylogroups.…”

“…Despite its vast commensal and pathogenic range, deciphering the zoonotic and zooanthroponotic potential of E. coli remains a challenge ( 20 , 21 ). Addressing this issue requires a deep understanding of genomic epidemiology of the dominant ExPEC sequence types (STs) as well as emerging ExPEC STs in both humans and animals ( 7 , 22 – 26 ). There are more than 11,000 E. coli sequence types, but the top 20 ExPEC sequence types are responsible for more than 85% of ExPEC infections in humans ( 13 ).…”

“…Despite the variety of plasmids that are found in E. coli , F plasmids dominate among a proportion of major and emerging ExPEC STs. For example, carriage of F plasmids is very common in ST131, ST95, ST58, and ST127, with separate plasmid lineages found to be characteristic of ST sublineages ( 7 , 22 , 23 , 25 ). F plasmids can be categorized genotypically by their accessory gene content, and plasmid lineages within those genotypes can be approximated by their F replicon sequence types (RSTs).…”

Genomic Analysis of an I1 Plasmid Hosting a sul3-Class 1 Integron and blaSHV-12 within an Unusual Escherichia coli ST297 from Urban Wildlife

“…The sul3 gene has been reported globally and often in association with E. coli sourced from intensive animal production but also frequently in humans [ 34 ]. sul3 has also been linked with pandemic lineages of E. coli including ST95, encompassing various lineages renown for causing extraintestinal human (urinary tract infection, sepsis and meningitis) and poultry disease [ 20 , 35 , 36 ]. Its association with CRRs on ColV virulence plasmids, such as pCERC3 [ 37 ] in commensal E. coli from healthy humans [ 38 ], is concerning.…”