Sequencing and analysis of the Escherichia coli serogroup O117, O126, and O146 O-antigen gene clusters and development of PCR assays targeting serogroup O117-, O126-, and O146-specific DNA sequences

The O-antigen gene clusters of Escherichia coli serogroups O2 and O28ac were sequenced, and PCR assays were developed to identify strains belonging to these 2 serogroups. Sixteen and 8 open reading frames were mapped to these loci in E. coli O2:H4 U 9-41 and E. coli O28ac:H25 96-3286, respectively. The wzx (O-antigen flippase) and wzy (O-antigen polymerase) genes in the E. coli O2 and O28ac O-antigen gene clusters were selected as targets for PCR assays for their identification. PCR assays targeting the wzx and wzy genes were specific for these serogroups, with one exception. Escherichia coli serogroup O42 strains gave positive results with wzx and wzy PCR assays targeting E. coli O28ac, and antiserum raised against O42 cross-reacted with serogroup O28ac strains. The O-antigen gene cluster of a strain of E. coli serogroup O42 was sequenced, and there were only 3 nt differences between the O-antigen gene clusters of the O28ac and O42 strains. Multiplex PCR assays targeting the O2 wzx gene, the stx1, stx2, hly, eae, and saa genes, and the O28ac wzx, ial, ipaC, and ipaH genes were developed for detecting Shiga toxin-producing E. coli O2 strains and enteroinvasive E. coli O28ac strains, respectively. The O2 and O28ac wzx and wzy genes can be used as diagnostic markers in PCR assays for rapid identification of these serogroups as an alternative to serotyping, and the multiplex PCR assays targeting serogroup-specific genes in combination with virulence genes can be used to identify and to detect pathogenic serogroup O2 and O28ac strains.

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Development of PCR Assays Targeting Genes in O-Antigen Gene Clusters for Detection and Identification of Escherichia coli O45 and O55 Serogroups

Applied and Environmental Microbiology ◽

10.1128/aem.71.8.4919-4924.2005 ◽

2005 ◽

Vol 71 (8) ◽

pp. 4919-4924 ◽

Cited By ~ 50

Author(s):

Chitrita DebRoy ◽

Pina M. Fratamico ◽

Elisabeth Roberts ◽

Michael A. Davis ◽

Yanhong Liu

Keyword(s):

Escherichia Coli ◽

Multiplex Pcr ◽

Gene Cluster ◽

Real Time Pcr ◽

Gene Clusters ◽

E Coli ◽

Antigen Gene ◽

O Antigen ◽

Detection And Identification ◽

Pcr Assays

ABSTRACT The Escherichia coli O45 O-antigen gene cluster of strain O45:H2 96-3285 was sequenced, and conventional (singleplex), multiplex, and real-time PCR assays were designed to amplify regions in the wzx (O-antigen flippase) and wzy (O-antigen polymerase) genes. In addition, PCR assays targeting the E. coli O55 wzx and wzy genes were designed based on previously published sequences. PCR assays targeting E. coli O45 showed 100% specificity for this serogroup, whereas by PCR assays specific for E. coli O55, 97/102 strains serotyped as E. coli O55 were positive for wzx and 98/102 for wzy. Multiplex PCR assays targeting the E. coli O45 and the E. coli O55 wzx and wzy genes were used to detect the organisms in fecal samples spiked at levels of 106 and 108 CFU/0.2 g feces. Thus, the PCR assays can be used to detect and identify E. coli serogroups O45 and O55.

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The DNA Sequence of the Escherichia coli O22 O-Antigen Gene Cluster and Detection of Pathogenic Strains Belonging to E. coli Serogroups O22 and O91 by Multiplex PCR Assays Targeting Virulence Genes and Genes in the Respective O-Antigen Gene Clusters

Food Analytical Methods ◽

10.1007/s12161-008-9046-z ◽

2008 ◽

Vol 2 (3) ◽

pp. 169-179 ◽

Cited By ~ 10

Author(s):

Pina M. Fratamico ◽

Chitrita DebRoy ◽

Yanhong Liu

Keyword(s):

Escherichia Coli ◽

Multiplex Pcr ◽

Gene Cluster ◽

Dna Sequence ◽

Virulence Genes ◽

Gene Clusters ◽

E Coli ◽

Antigen Gene ◽

O Antigen ◽

Pcr Assays

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Escherichia coli O-Antigen Gene Clusters of Serogroups O62, O68, O131, O140, O142, and O163: DNA Sequences and Similarity between O62 and O68, and PCR-Based Serogrouping

Biosensors ◽

10.3390/bios5010051 ◽

2015 ◽

Vol 5 (1) ◽

pp. 51-68 ◽

Cited By ~ 6

Author(s):

Yanhong Liu ◽

Xianghe Yan ◽

Chitrita DebRoy ◽

Pina Fratamico ◽

David Needleman ◽

...

Keyword(s):

Escherichia Coli ◽

Dna Sequences ◽

Gene Clusters ◽

Antigen Gene ◽

O Antigen

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Sequence-based typing of genetic targets encoded outside of the O-antigen gene cluster is indicative of Shiga toxin-producing Escherichia coli serogroup lineages

Journal of Medical Microbiology ◽

10.1099/jmm.0.47053-0 ◽

2007 ◽

Vol 56 (5) ◽

pp. 620-628 ◽

Cited By ~ 23

Author(s):

Matthew W. Gilmour ◽

Adam B. Olson ◽

Ashleigh K. Andrysiak ◽

Lai-King Ng ◽

Linda Chui

Keyword(s):

Escherichia Coli ◽

Gene Cluster ◽

Dna Sequences ◽

Shiga Toxin ◽

Clinical Isolates ◽

Comparative Analyses ◽

Antigen Gene ◽

O Antigen ◽

Additional Support ◽

H Serotypes

Serogroup classifications based upon the O-somatic antigen of Shiga toxin-producing Escherichia coli (STEC) provide significant epidemiological information on clinical isolates. Each O-antigen determinant is encoded by a unique cluster of genes present between the gnd and galF chromosomal genes. Alternatively, serogroup-specific polymorphisms might be encoded in loci that are encoded outside of the O-antigen gene cluster. Segments of the core bacterial loci mdh, gnd, gcl, ppk, metA, ftsZ, relA and metG for 30 O26 STEC strains have previously been sequenced, and comparative analyses to O157 distinguished these two serogroups. To screen these loci for serogroup-specific traits within a broader range of clinically significant serogroups, DNA sequences were obtained for 19 strains of 10 additional STEC serogroups. Unique alleles were observed at the gnd locus for each examined STEC serogroup, and this correlation persisted when comparative analyses were extended to 144 gnd sequences from 26 O-serogroups (comprising 42 O : H-serotypes). These included O157, O121, O103, O26, O5 : non-motile (NM), O145 : NM, O113 : H21, O111 : NM and O117 : H7 STEC; and furthermore, non-toxin encoding O157, O26, O55, O6 and O117 strains encoded distinct gnd alleles compared to STEC strains of the same serogroup. DNA sequencing of a 643 bp region of gnd was, therefore, sufficient to minimally determine the O-antigen of STEC through molecular means, and the location of gnd next to the O-antigen gene cluster offered additional support for the co-inheritance of these determinants. The gnd DNA sequence-based serogrouping method could improve the typing capabilities for STEC in clinical laboratories, and was used successfully to characterize O121 : H19, O26 : H11 and O177 : NM clinical isolates prior to serological confirmation during outbreak investigations.

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Structure and genetics of Escherichia coli O antigens

FEMS Microbiology Reviews ◽

10.1093/femsre/fuz028 ◽

2019 ◽

Vol 44 (6) ◽

pp. 655-683 ◽

Cited By ~ 7

Author(s):

Bin Liu ◽

Axel Furevi ◽

Andrei V Perepelov ◽

Xi Guo ◽

Hengchun Cao ◽

...

Keyword(s):

Escherichia Coli ◽

Genetic Basis ◽

Structural Diversity ◽

Gene Clusters ◽

Current Standard ◽

E Coli ◽

Antigen Gene ◽

O Antigen ◽

Or Groups ◽

O Antigens

ABSTRACT Escherichia coli includes clonal groups of both commensal and pathogenic strains, with some of the latter causing serious infectious diseases. O antigen variation is current standard in defining strains for taxonomy and epidemiology, providing the basis for many serotyping schemes for Gram-negative bacteria. This review covers the diversity in E. coli O antigen structures and gene clusters, and the genetic basis for the structural diversity. Of the 187 formally defined O antigens, six (O31, O47, O67, O72, O94 and O122) have since been removed and three (O34, O89 and O144) strains do not produce any O antigen. Therefore, structures are presented for 176 of the 181 E. coli O antigens, some of which include subgroups. Most (93%) of these O antigens are synthesized via the Wzx/Wzy pathway, 11 via the ABC transporter pathway, with O20, O57 and O60 still uncharacterized due to failure to find their O antigen gene clusters. Biosynthetic pathways are given for 38 of the 49 sugars found in E. coli O antigens, and several pairs or groups of the E. coli antigens that have related structures show close relationships of the O antigen gene clusters within clades, thereby highlighting the genetic basis of the evolution of diversity.

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The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2017.00030 ◽

2017 ◽

Vol 7 ◽

Cited By ~ 7

Author(s):

Sabine Delannoy ◽

Lothar Beutin ◽

Patricia Mariani-Kurkdjian ◽

Aubin Fleiss ◽

Stéphane Bonacorsi ◽

...

Keyword(s):

Escherichia Coli ◽

Gene Clusters ◽

Antigen Gene ◽

O Antigen

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The O-Antigen Gene Cluster of Escherichia coli O55:H7 and Identification of a New UDP-GlcNAc C4 Epimerase Gene

Journal of Bacteriology ◽

10.1128/jb.184.10.2620-2625.2002 ◽

2002 ◽

Vol 184 (10) ◽

pp. 2620-2625 ◽

Cited By ~ 70

Author(s):

Lei Wang ◽

Sandy Huskic ◽

Adam Cisterne ◽

Deborah Rothemund ◽

Peter R. Reeves

Keyword(s):

Escherichia Coli ◽

Pseudomonas Aeruginosa ◽

Gene Cluster ◽

Gene Clusters ◽

The Other ◽

Recombination Site ◽

E Coli ◽

Antigen Gene ◽

O Antigen ◽

Usual Location

ABSTRACT Escherichia coli O55 is an important antigen which is often associated with enteropathogenic E. coli clones. We sequenced the genes responsible for its synthesis and identified genes for O-antigen polymerase, O-antigen flippase, four enzymes involved in GDP-colitose synthesis, and three glycosyltransferases, all by comparison with known genes. Upstream of the normal O-antigen region there is a gne gene, which encodes a UDP-GlcNAc epimerase for converting UDP-GlcNAc to UDP-GalNAc and is essential for O55 antigen synthesis. The O55 gne product has only 20 and 26% identity to the gne genes of Pseudomonas aeruginosa and E. coli O113, respectively. We also found evidence for the O55 gene cluster's having evolved from another gene cluster by gain and loss of genes. Only three of the GDP-colitose pathway genes are in the usual location, the other two being separated, although nearby. It is thought that the E. coli O157:H7 clone evolved from the O55:H7 clone in part by transfer of the O157 gene cluster into an O55 lineage. Comparison of genes flanking the O-antigen gene clusters of the O55:H7 and O157:H7 clones revealed one recombination site within the galF gene and located the other between the hisG and amn genes. Genes outside the recombination sites are 99.6 to 100% identical in the two clones, while most genes thought to have transferred with the O157 gene cluster are 95 to 98% identical.

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