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Correlation between the genomic o454-nlpD region polymorphisms, virulence gene equipment and phylogenetic group of extraintestinal Escherichia coli (ExPEC) enables pathotyping irrespective of host, disease and source of isolation.

Ewers C, Dematheis F, Singamaneni HD, Nandanwar N, Fruth A, Diehl I, Semmler T, Wieler LH - Gut Pathog (2014)

Bottom Line: A strong association between pattern III and either the Ecor group B2 or the sequence type complexes known to represent the phylogenetic background of highly virulent ExPEC strains (such as STC95, STC73 and STC131) was found as well.The significant association between pattern III and group B2 strains suggested the o454-nlpD region to be of great value in identifying highly virulent strains among the mixed population of E. coli promising to be the basis of a future typing tool for ExPEC and their gut reservoir.These data are most valuable for defining ExPEC pathotype in future in vivo assays.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Hygiene and Infectious Diseases of Animals, Justus-Liebig-Universität Giessen, Frankfurter Str. 85-89, Giessen, 35392, Germany.

ABSTRACT

Background: The mutS-rpoS intergenic region in E. coli displays a mosaic structure which revealed pathotype specific patterns. To assess the importance of this region as a surrogate marker for the identification of highly virulent extraintestinal pathogenic E. coli (ExPEC) strains we aimed to: (i) characterize the genetic diversity of the mutS gene and the o454-nlpD genomic region among 510 E. coli strains from animals and humans; (ii) delineate associations between the polymorphism of this region and features such as phylogenetic background of E. coli, pathotype, host species, clinical condition, serogroup and virulence associated genes (VAG)s; and (iii) identify the most important VAGs for classification of the o454-nlpD region.

Methods: Size variation in the o454-nlpD region was investigated by PCR amplification and sequencing. Phylogenetic relationships were assessed by Ecor- and Multilocus sequence- typing (MLST), and a comparative analysis between mutS gene phylogenetic tree obtained with RAxML and the MLST grouping method was performed. Correlation between o454-nlpD patterns and the features described above were analysed. In addition, the importance of 47 PCR-amplified ExPEC-related VAGs for classification of o454-nlpD patterns was investigated by means of Random Forest algorithm.

Results: Four main structures (patterns I-IV) of the o454-nlpD region among ExPEC and commensal E. coli strains were identified. Statistical analysis showed a positive and exclusive association between pattern III and the ExPEC strains. A strong association between pattern III and either the Ecor group B2 or the sequence type complexes known to represent the phylogenetic background of highly virulent ExPEC strains (such as STC95, STC73 and STC131) was found as well. RF analyses determined five genes (csgA, malX, chuA, sit, and vat) to be suitable to predict pattern III strains.

Conclusion: The significant association between pattern III and group B2 strains suggested the o454-nlpD region to be of great value in identifying highly virulent strains among the mixed population of E. coli promising to be the basis of a future typing tool for ExPEC and their gut reservoir. Furthermore, top-ranked VAGs for classification and prediction of pattern III were identified. These data are most valuable for defining ExPEC pathotype in future in vivo assays.

No MeSH data available.


Related in: MedlinePlus

Physical maps of thefhlA-nlpDintergenic region ofE. colistrains as determined by publicly available sequences (EDL933, GenBank NC_002655; MG1655, U00096; CFT073, AE014075; E2348/69, FM180568), showing positions of ORFs and location ofo454-nlpDpattern sequences and sizes amplified by PCR; the position of oligonucleotide primers (F = forward; R = reverse) are indicated and the length of fragments amplified from different strains and primer combinations are provided in Table1.
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Figure 1: Physical maps of thefhlA-nlpDintergenic region ofE. colistrains as determined by publicly available sequences (EDL933, GenBank NC_002655; MG1655, U00096; CFT073, AE014075; E2348/69, FM180568), showing positions of ORFs and location ofo454-nlpDpattern sequences and sizes amplified by PCR; the position of oligonucleotide primers (F = forward; R = reverse) are indicated and the length of fragments amplified from different strains and primer combinations are provided in Table1.

Mentions: The results of pattern distribution were in agreement with the presence/absence and sizes of other amplicons along the fhlA-nlpD genetic region (Table 1 and Figure 1). For example, fhlA-mutS amplicons (primers F1/R1; Table 1) of 1.673 bp and o454-o347 amplicons (primers F5/R5) of 816 bp in size were exclusively determined in pattern III strains, such as UPEC strain CFT073. A 716-bp o454-yclC (kpdC) amplicon (primers F5/R4) was only detected in pattern IV strains, and a 1318-bp mutS-yclC/kpdC amplicon was only present in pattern I strains.


Correlation between the genomic o454-nlpD region polymorphisms, virulence gene equipment and phylogenetic group of extraintestinal Escherichia coli (ExPEC) enables pathotyping irrespective of host, disease and source of isolation.

Ewers C, Dematheis F, Singamaneni HD, Nandanwar N, Fruth A, Diehl I, Semmler T, Wieler LH - Gut Pathog (2014)

Physical maps of thefhlA-nlpDintergenic region ofE. colistrains as determined by publicly available sequences (EDL933, GenBank NC_002655; MG1655, U00096; CFT073, AE014075; E2348/69, FM180568), showing positions of ORFs and location ofo454-nlpDpattern sequences and sizes amplified by PCR; the position of oligonucleotide primers (F = forward; R = reverse) are indicated and the length of fragments amplified from different strains and primer combinations are provided in Table1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4209514&req=5

Figure 1: Physical maps of thefhlA-nlpDintergenic region ofE. colistrains as determined by publicly available sequences (EDL933, GenBank NC_002655; MG1655, U00096; CFT073, AE014075; E2348/69, FM180568), showing positions of ORFs and location ofo454-nlpDpattern sequences and sizes amplified by PCR; the position of oligonucleotide primers (F = forward; R = reverse) are indicated and the length of fragments amplified from different strains and primer combinations are provided in Table1.
Mentions: The results of pattern distribution were in agreement with the presence/absence and sizes of other amplicons along the fhlA-nlpD genetic region (Table 1 and Figure 1). For example, fhlA-mutS amplicons (primers F1/R1; Table 1) of 1.673 bp and o454-o347 amplicons (primers F5/R5) of 816 bp in size were exclusively determined in pattern III strains, such as UPEC strain CFT073. A 716-bp o454-yclC (kpdC) amplicon (primers F5/R4) was only detected in pattern IV strains, and a 1318-bp mutS-yclC/kpdC amplicon was only present in pattern I strains.

Bottom Line: A strong association between pattern III and either the Ecor group B2 or the sequence type complexes known to represent the phylogenetic background of highly virulent ExPEC strains (such as STC95, STC73 and STC131) was found as well.The significant association between pattern III and group B2 strains suggested the o454-nlpD region to be of great value in identifying highly virulent strains among the mixed population of E. coli promising to be the basis of a future typing tool for ExPEC and their gut reservoir.These data are most valuable for defining ExPEC pathotype in future in vivo assays.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Hygiene and Infectious Diseases of Animals, Justus-Liebig-Universität Giessen, Frankfurter Str. 85-89, Giessen, 35392, Germany.

ABSTRACT

Background: The mutS-rpoS intergenic region in E. coli displays a mosaic structure which revealed pathotype specific patterns. To assess the importance of this region as a surrogate marker for the identification of highly virulent extraintestinal pathogenic E. coli (ExPEC) strains we aimed to: (i) characterize the genetic diversity of the mutS gene and the o454-nlpD genomic region among 510 E. coli strains from animals and humans; (ii) delineate associations between the polymorphism of this region and features such as phylogenetic background of E. coli, pathotype, host species, clinical condition, serogroup and virulence associated genes (VAG)s; and (iii) identify the most important VAGs for classification of the o454-nlpD region.

Methods: Size variation in the o454-nlpD region was investigated by PCR amplification and sequencing. Phylogenetic relationships were assessed by Ecor- and Multilocus sequence- typing (MLST), and a comparative analysis between mutS gene phylogenetic tree obtained with RAxML and the MLST grouping method was performed. Correlation between o454-nlpD patterns and the features described above were analysed. In addition, the importance of 47 PCR-amplified ExPEC-related VAGs for classification of o454-nlpD patterns was investigated by means of Random Forest algorithm.

Results: Four main structures (patterns I-IV) of the o454-nlpD region among ExPEC and commensal E. coli strains were identified. Statistical analysis showed a positive and exclusive association between pattern III and the ExPEC strains. A strong association between pattern III and either the Ecor group B2 or the sequence type complexes known to represent the phylogenetic background of highly virulent ExPEC strains (such as STC95, STC73 and STC131) was found as well. RF analyses determined five genes (csgA, malX, chuA, sit, and vat) to be suitable to predict pattern III strains.

Conclusion: The significant association between pattern III and group B2 strains suggested the o454-nlpD region to be of great value in identifying highly virulent strains among the mixed population of E. coli promising to be the basis of a future typing tool for ExPEC and their gut reservoir. Furthermore, top-ranked VAGs for classification and prediction of pattern III were identified. These data are most valuable for defining ExPEC pathotype in future in vivo assays.

No MeSH data available.


Related in: MedlinePlus