Expressed and cryptic flagellin genes in the H44 and H55 type strains of Escherichia coli

Tominaga, Akira; Kutsukake, Kazuhiro

doi:10.1266/ggs.82.1

Cited by 11 publications

(9 citation statements)

References 49 publications

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“…Molecular serotyping and plasmid sequence comparisons. The molecular serotypes of the STEC/ETEC hybrid strains were determined from the draft genomes by BLASTn analysis utilizing an in-house custom database, including the wzx, wzy, wzm, wzt, fliC, flkA, fllA, flmA, and flnA loci (36)(37)(38)(39)(40)(41)(42). BLASTn analysis that utilized an in-house custom database was also used to identify the allele subtypes of the Shiga toxin genes and the presence of heat-stable enterotoxin-encoding genes.…”

Section: Methodsmentioning

confidence: 99%

Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia sp. Cryptic Lineage 1 Strain 7v Harbors a Hybrid Plasmid

Leonard

Mammel

Rasko

et al. 2016

Appl Environ Microbiol

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Hybrid isolates of Shiga toxin-producing Escherichia coli (STEC) and enterotoxigenic E. coli (ETEC) encoding heat-stable enterotoxin (ST) are being reported with increasing frequency from a variety of sources. However, information regarding the plasmids that these strains harbor is scarce. In this study, we sequence and characterize a plasmid, p7v, from the STEC/ETEC hybrid strain 7v. Whole-genome phylogenetic analyses of STEC/ETEC hybrid strains and prototype E. coli isolates of other pathotypes placed 7v in the Escherichia sp. cryptic lineage 1 (CL1) clade. The complete plasmid, p7v, was determined to be 229,275 bp and encodes putative virulence factors that are typically carried on STEC plasmids as well as those often carried on ETEC plasmids, indicating that the hybrid nature of the strain extends beyond merely encoding the two toxins. Plasmid p7v carries two copies of sta with identical sequences, which were discovered to be divergent from the sta sequences found in the prototype human ETEC strains. Using a nomenclature scheme based on a phylogeny constructed from sta and stb sequences, the sta encoded on p7v is designated STa4. In silico analysis determined that p7v also encodes the K88 fimbria, a colonization factor usually associated with porcine ETEC plasmids. The p7v sequence and the presence of plasmid-encoded virulence factors are compared to those of other STEC/ETEC CL1 hybrid genomes and reveal gene acquisition/loss at the strain level. In addition, the interrogation of 24 STEC/ETEC hybrid genomes for identification of plasmid replicons, colonization factors, Stx and ST subtypes, and other plasmid-encoded virulence genes highlights the diversity of these hybrid strains. IMPORTANCEHybrid Shiga toxin-producing Escherichia coli/enterotoxigenic Escherichia coli (STEC/ETEC) strains, which have been isolated from environmental, animal, and human clinical samples, may represent an emerging threat as food-borne pathogens. Characterization of these strains is important for assessing virulence potential, aiding in the development of pathogen detection methods, and understanding how the hybrid strains evolve to potentially have a greater impact on public health. This study represents, to our knowledge, both the first characterization of a closed plasmid sequence from a STEC/ETEC hybrid strain and the most comprehensive phylogenetic analysis of available STEC/ETEC hybrid genomes to date. The results demonstrate how the mobility of plasmid-associated virulence genes has resulted in the creation of a diverse plasmid repertoire within the STEC/ ETEC hybrid strains. Pathogenic Escherichia coli strains are categorized into pathotypes or pathovars (pathogenic variants) based on virulenceassociated genes whose expression contributes to particular disease symptoms in the human host (1). The virulence-associated genes that are unique to a pathotype have been used as molecular markers to define the pathotype of a given E. coli isolate. Two E. coli pathotypes that cause a significant burden of illness throughout ...

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Section: Methodsmentioning

confidence: 99%

Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia sp. Cryptic Lineage 1 Strain 7v Harbors a Hybrid Plasmid

Leonard

Mammel

Rasko

et al. 2016

Appl Environ Microbiol

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“…PCR detection of fliC alleles has been used for molecular H-typing for some time (Wang et al , 2003). However, some E. coli isolates have an alternative flagellar phase, due to the presence of an additional flagellin gene ( flnaA , fllA , fmlA or flkA ), similar to those found in Salmonella species (Feng et al , 2008; Ratiner, 1998; Ratiner et al , 2010; Tominaga, 2004; Tominaga & Kutsukake, 2007). …”

Section: Introductionmentioning

confidence: 85%

“…The two exceptions were O57 and O14, as isolates with these O-groups lack any of these genes and harbour only small O-antigen gene clusters, with no known polymerase or flippase genes; and only the housekeeping genes galF , gnd and hisI together with ugd and wzz , which are not sufficient to delineate these O-groups. The EcOH database also includes sequences for all 53 known H-types, allowing for the detection of both fliC and non- fliC flagellin ( flnA , fmlA , flkA and fllA ) genes, and for the identification of isolates that may be able to undergo flagellum phase variation (Tominaga, 2004; Tominaga & Kutsukake, 2007). For the O-groups, the database specifies the 16 O-group clusters containing 37 O-groups as identified by Iguchi et al (2014) where there was >95 % sequence identity.…”

Section: Methodsmentioning

confidence: 99%

In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages

et al. 2016

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The lipopolysaccharide (O) and flagellar (H) surface antigens of Escherichia coli are targets for serotyping that have traditionally been used to identify pathogenic lineages. These surface antigens are important for the survival of E. coli within mammalian hosts. However, traditional serotyping has several limitations, and public health reference laboratories are increasingly moving towards whole genome sequencing (WGS) to characterize bacterial isolates. Here we present a method to rapidly and accurately serotype E. coli isolates from raw, short read WGS data. Our approach bypasses the need for de novo genome assembly by directly screening WGS reads against a curated database of alleles linked to known and novel E. coli O-groups and H-types (the EcOH database) using the software package srst2. We validated the approach by comparing in silico results for 197 enteropathogenic E. coli isolates with those obtained by serological phenotyping in an independent laboratory. We then demonstrated the utility of our method to characterize isolates in public health and clinical settings, and to explore the genetic diversity of >1500 E. coli genomes from multiple sources. Importantly, we showed that transfer of O- and H-antigen loci between E. coli chromosomal backbones is common, with little evidence of constraints by host or pathotype, suggesting that E. coli ‘strain space’ may be virtually unlimited, even within specific pathotypes. Our findings show that serotyping is most useful when used in combination with strain genotyping to characterize microevolution events within an inferred population structure.

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“…The two exceptions were O57 and O14, as isolates with these O-groups lack any of these genes and harbour only small O-antigen gene clusters, with no known polymerase or flippase genes, and only the housekeeping genes galF, gnd and hisI together with ugd and wzz which is not sufficient to delineate these O-groups. The EcOH database also includes sequences for all 53 known H-types, allowing for the detection of both fliC and non-fliC flagellin genes, and for the identification of isolates that may be able to undergo flagellum phase variation (Tominaga, 2004; Tominaga & Kutsukake, 2007).…”

Section: Resultsmentioning

confidence: 99%

“…PCR detection of fliC alleles has been used for molecular H-typing for some time (Wang et al ., 2003). However, some E. coli isolates have an alternative flagellar phase, due to the presence of an additional flagellin gene (flnaA, fllA, fmlA or flkA) , similar to those found in Salmonella species (Feng et al ., 2008; Ratiner, 1998; Ratiner et al ., 2010; Tominaga, 2004; Tominaga & Kutsukake, 2007).…”

Section: Introductionmentioning

confidence: 99%

EcOH:In silicoserotyping ofE. colifrom short read data

Ingle

Valcanis

Kuzevski

et al. 2015

Preprint

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22"! 23"The lipopolysaccharide (O) and flagellar (H) surface antigens of Escherichia coli are targets 24"for serotyping that have traditionally been used to identify pathogenic lineages of E. coli. As 25"serotyping has several limitations, public health reference laboratories are increasingly 26"moving towards whole genome sequencing (WGS) for the rapid characterisation of bacterial 27"isolates. Here we present a method to rapidly and accurately serotype E. coli isolates from 28"raw, short read sequence data, leveraging the known genetic basis for the biosynthesis of O- 29"and H-antigens. Our approach bypasses the need for de novo genome assembly by directly 30"screening WGS reads against a curated database of alleles linked to known E. coli O-groups 31"and H-types (the EcOH database) using the software package SRST2. We validated our 32"approach by comparing in silico results with those obtained via serological phenotyping of 33"197 enteropathogenic (EPEC) isolates. We also demonstrated the utility of our method to 34"characterise enterotoxigenic E. coli (ETEC) and the uropathogenic E. coli (UPEC) epidemic 35"clone ST131, and for in silico serotyping of foodborne outbreak-related isolates in the public 36"GenomeTrakr database.

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Expressed and cryptic flagellin genes in the H44 and H55 type strains of Escherichia coli

Cited by 11 publications

References 49 publications

Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia sp. Cryptic Lineage 1 Strain 7v Harbors a Hybrid Plasmid

Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia sp. Cryptic Lineage 1 Strain 7v Harbors a Hybrid Plasmid

In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages

EcOH:In silicoserotyping ofE. colifrom short read data

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