Interrogation of single nucleotide polymorphisms in gnd provides a novel method for molecular serogrouping of clinically important Shiga toxin producing Escherichia coli (STEC) targeted by regulation in the United States, including the "big six" non-O157 STEC and STEC O157
J. R. Elder, M. Bugarel, H. C. den Bakker, G. H. Loneragan, K. K. Nightingale
Animal and Food Sciences
Escherichia coli O157:H7 has frequently been associated with foodborne infections and is considered an adulterant in raw non-intact beef in the U.S. Shiga toxin-producing E. coli (STEC) belonging to serogroups O26, O45, O103, O111, O121, and O145 (known as the "big six" non-O157) were estimated to cause > 70% of foodborne infections attributed to non-O157 serogroups in the U.S., as a result, these six serogroups have also been targeted by regulation in the U.S. The purpose of this study was to develop a rapid and high-throughput molecular method to group STEC isolates into seven clinically important serogroups (i.e., O157 and the "big six" non-O157 serogroups) targeted by regulation in the U.S. by interrogating single nucleotide polymorphisms (SNPs) in gnd. A collection of 195 STEC isolates, including isolates belonging to O157:H7 (n = 18), O26 (n = 21), O45 (n = 19), O103 (n = 24), O111 (n = 24), O121 (n = 23), O145 (n = 21), and ten other STEC serogroups (n = 45), was assembled and characterized by full gnd sequencing to identify informative SNPs for molecular serogrouping. A multiplex SNP typing assay was developed to interrogate twelve informative gnd SNPs by single base pair extension chemistry and used to characterize the STEC isolate collection assembled here. SNP types were assigned to each isolate by the assay and polymorphisms were confirmed with gnd sequence data. O-serogroup-specific SNP types were identified for each of the seven clinically important STEC serogroups, which allowed the differentiation of these seven STEC serogroups from other non-O157 STEC serogroups. Although serogroups of the "big six" non-O157 STEC and O157:H7 contained multiple SNP types per O-serogroup, there were no overlapping SNP types between serogroups. Our results demonstrate that molecular serogrouping of STEC isolates by interrogation of informative SNPs in gnd represents an alternative to traditional serogrouping by agglutination for rapid and high-throughput identification of clinically important STEC serogroups targeted by regulation for surveillance and epidemiological investigations.
Journal of Microbiological Methods
https://doi.org/10.1016/j.mimet.2016.07.005
Molecular serotyping
Non-O157 STEC
SNP typing
Shiga toxin producing Escherichia coli (STEC)
10.1016/j.mimet.2016.07.005
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Shiga-Toxigenic Escherichia coli Medicine & Life Sciences 100%
Escherichia coli O157 Medicine & Life Sciences 94%
Serogroup Medicine & Life Sciences 67%
Single Nucleotide Polymorphism Medicine & Life Sciences 61%
Red Meat Medicine & Life Sciences 6%
Agglutination Medicine & Life Sciences 6%
Base Pairing Medicine & Life Sciences 5%
Infections Medicine & Life Sciences 5%
Elder, J. R., Bugarel, M., den Bakker, H. C., Loneragan, G. H., & Nightingale, K. K. (2016). Interrogation of single nucleotide polymorphisms in gnd provides a novel method for molecular serogrouping of clinically important Shiga toxin producing Escherichia coli (STEC) targeted by regulation in the United States, including the "big six" non-O157 STEC and STEC O157. Journal of Microbiological Methods, 129, 85-93. https://doi.org/10.1016/j.mimet.2016.07.005
Elder, J. R. ; Bugarel, M. ; den Bakker, H. C. ; Loneragan, G. H. ; Nightingale, K. K. / Interrogation of single nucleotide polymorphisms in gnd provides a novel method for molecular serogrouping of clinically important Shiga toxin producing Escherichia coli (STEC) targeted by regulation in the United States, including the "big six" non-O157 STEC and STEC O157. In: Journal of Microbiological Methods. 2016 ; Vol. 129. pp. 85-93.
@article{769068077a7247cab9f09488981afcfe,
title = "Interrogation of single nucleotide polymorphisms in gnd provides a novel method for molecular serogrouping of clinically important Shiga toxin producing Escherichia coli (STEC) targeted by regulation in the United States, including the "big six" non-O157 STEC and STEC O157",
abstract = "Escherichia coli O157:H7 has frequently been associated with foodborne infections and is considered an adulterant in raw non-intact beef in the U.S. Shiga toxin-producing E. coli (STEC) belonging to serogroups O26, O45, O103, O111, O121, and O145 (known as the "big six" non-O157) were estimated to cause > 70% of foodborne infections attributed to non-O157 serogroups in the U.S., as a result, these six serogroups have also been targeted by regulation in the U.S. The purpose of this study was to develop a rapid and high-throughput molecular method to group STEC isolates into seven clinically important serogroups (i.e., O157 and the "big six" non-O157 serogroups) targeted by regulation in the U.S. by interrogating single nucleotide polymorphisms (SNPs) in gnd. A collection of 195 STEC isolates, including isolates belonging to O157:H7 (n = 18), O26 (n = 21), O45 (n = 19), O103 (n = 24), O111 (n = 24), O121 (n = 23), O145 (n = 21), and ten other STEC serogroups (n = 45), was assembled and characterized by full gnd sequencing to identify informative SNPs for molecular serogrouping. A multiplex SNP typing assay was developed to interrogate twelve informative gnd SNPs by single base pair extension chemistry and used to characterize the STEC isolate collection assembled here. SNP types were assigned to each isolate by the assay and polymorphisms were confirmed with gnd sequence data. O-serogroup-specific SNP types were identified for each of the seven clinically important STEC serogroups, which allowed the differentiation of these seven STEC serogroups from other non-O157 STEC serogroups. Although serogroups of the "big six" non-O157 STEC and O157:H7 contained multiple SNP types per O-serogroup, there were no overlapping SNP types between serogroups. Our results demonstrate that molecular serogrouping of STEC isolates by interrogation of informative SNPs in gnd represents an alternative to traditional serogrouping by agglutination for rapid and high-throughput identification of clinically important STEC serogroups targeted by regulation for surveillance and epidemiological investigations.",
keywords = "E. coli O157:H7, Molecular serotyping, Non-O157 STEC, SNP typing, Shiga toxin producing Escherichia coli (STEC), gnd",
author = "Elder, {J. R.} and M. Bugarel and {den Bakker}, {H. C.} and Loneragan, {G. H.} and Nightingale, {K. K.}",
note = "Funding Information: This research was supported by the National Integrated Food Safety Initiative of the USDA Cooperative State Research, Education, and Extension Service , grant number no. 51110-04333 . The funding source did not influence the design or outcome of this study. We would like to recognize the contributions of Dr. Chitrita DebRoy of Pennsylvania State University, Dr. Shannon Manning of Michigan State University, Dr. Robert Elder, and Dr. Joseph Bosilevac of USDA Meat Animal Research Center for providing the STEC strains used to develop the molecular serogrouping method in this study. Publisher Copyright: {\textcopyright} 2016",
doi = "10.1016/j.mimet.2016.07.005",
journal = "Journal of Microbiological Methods",
Elder, JR, Bugarel, M, den Bakker, HC, Loneragan, GH & Nightingale, KK 2016, 'Interrogation of single nucleotide polymorphisms in gnd provides a novel method for molecular serogrouping of clinically important Shiga toxin producing Escherichia coli (STEC) targeted by regulation in the United States, including the "big six" non-O157 STEC and STEC O157', Journal of Microbiological Methods, vol. 129, pp. 85-93. https://doi.org/10.1016/j.mimet.2016.07.005
Interrogation of single nucleotide polymorphisms in gnd provides a novel method for molecular serogrouping of clinically important Shiga toxin producing Escherichia coli (STEC) targeted by regulation in the United States, including the "big six" non-O157 STEC and STEC O157. / Elder, J. R.; Bugarel, M.; den Bakker, H. C.; Loneragan, G. H.; Nightingale, K. K.
In: Journal of Microbiological Methods, Vol. 129, 01.10.2016, p. 85-93.
T1 - Interrogation of single nucleotide polymorphisms in gnd provides a novel method for molecular serogrouping of clinically important Shiga toxin producing Escherichia coli (STEC) targeted by regulation in the United States, including the "big six" non-O157 STEC and STEC O157
AU - Elder, J. R.
AU - Bugarel, M.
AU - den Bakker, H. C.
AU - Loneragan, G. H.
AU - Nightingale, K. K.
N1 - Funding Information: This research was supported by the National Integrated Food Safety Initiative of the USDA Cooperative State Research, Education, and Extension Service , grant number no. 51110-04333 . The funding source did not influence the design or outcome of this study. We would like to recognize the contributions of Dr. Chitrita DebRoy of Pennsylvania State University, Dr. Shannon Manning of Michigan State University, Dr. Robert Elder, and Dr. Joseph Bosilevac of USDA Meat Animal Research Center for providing the STEC strains used to develop the molecular serogrouping method in this study. Publisher Copyright: © 2016
N2 - Escherichia coli O157:H7 has frequently been associated with foodborne infections and is considered an adulterant in raw non-intact beef in the U.S. Shiga toxin-producing E. coli (STEC) belonging to serogroups O26, O45, O103, O111, O121, and O145 (known as the "big six" non-O157) were estimated to cause > 70% of foodborne infections attributed to non-O157 serogroups in the U.S., as a result, these six serogroups have also been targeted by regulation in the U.S. The purpose of this study was to develop a rapid and high-throughput molecular method to group STEC isolates into seven clinically important serogroups (i.e., O157 and the "big six" non-O157 serogroups) targeted by regulation in the U.S. by interrogating single nucleotide polymorphisms (SNPs) in gnd. A collection of 195 STEC isolates, including isolates belonging to O157:H7 (n = 18), O26 (n = 21), O45 (n = 19), O103 (n = 24), O111 (n = 24), O121 (n = 23), O145 (n = 21), and ten other STEC serogroups (n = 45), was assembled and characterized by full gnd sequencing to identify informative SNPs for molecular serogrouping. A multiplex SNP typing assay was developed to interrogate twelve informative gnd SNPs by single base pair extension chemistry and used to characterize the STEC isolate collection assembled here. SNP types were assigned to each isolate by the assay and polymorphisms were confirmed with gnd sequence data. O-serogroup-specific SNP types were identified for each of the seven clinically important STEC serogroups, which allowed the differentiation of these seven STEC serogroups from other non-O157 STEC serogroups. Although serogroups of the "big six" non-O157 STEC and O157:H7 contained multiple SNP types per O-serogroup, there were no overlapping SNP types between serogroups. Our results demonstrate that molecular serogrouping of STEC isolates by interrogation of informative SNPs in gnd represents an alternative to traditional serogrouping by agglutination for rapid and high-throughput identification of clinically important STEC serogroups targeted by regulation for surveillance and epidemiological investigations.
AB - Escherichia coli O157:H7 has frequently been associated with foodborne infections and is considered an adulterant in raw non-intact beef in the U.S. Shiga toxin-producing E. coli (STEC) belonging to serogroups O26, O45, O103, O111, O121, and O145 (known as the "big six" non-O157) were estimated to cause > 70% of foodborne infections attributed to non-O157 serogroups in the U.S., as a result, these six serogroups have also been targeted by regulation in the U.S. The purpose of this study was to develop a rapid and high-throughput molecular method to group STEC isolates into seven clinically important serogroups (i.e., O157 and the "big six" non-O157 serogroups) targeted by regulation in the U.S. by interrogating single nucleotide polymorphisms (SNPs) in gnd. A collection of 195 STEC isolates, including isolates belonging to O157:H7 (n = 18), O26 (n = 21), O45 (n = 19), O103 (n = 24), O111 (n = 24), O121 (n = 23), O145 (n = 21), and ten other STEC serogroups (n = 45), was assembled and characterized by full gnd sequencing to identify informative SNPs for molecular serogrouping. A multiplex SNP typing assay was developed to interrogate twelve informative gnd SNPs by single base pair extension chemistry and used to characterize the STEC isolate collection assembled here. SNP types were assigned to each isolate by the assay and polymorphisms were confirmed with gnd sequence data. O-serogroup-specific SNP types were identified for each of the seven clinically important STEC serogroups, which allowed the differentiation of these seven STEC serogroups from other non-O157 STEC serogroups. Although serogroups of the "big six" non-O157 STEC and O157:H7 contained multiple SNP types per O-serogroup, there were no overlapping SNP types between serogroups. Our results demonstrate that molecular serogrouping of STEC isolates by interrogation of informative SNPs in gnd represents an alternative to traditional serogrouping by agglutination for rapid and high-throughput identification of clinically important STEC serogroups targeted by regulation for surveillance and epidemiological investigations.
KW - E. coli O157:H7
KW - Molecular serotyping
KW - Non-O157 STEC
KW - SNP typing
KW - Shiga toxin producing Escherichia coli (STEC)
KW - gnd
U2 - 10.1016/j.mimet.2016.07.005
DO - 10.1016/j.mimet.2016.07.005
JO - Journal of Microbiological Methods
JF - Journal of Microbiological Methods
Elder JR, Bugarel M, den Bakker HC, Loneragan GH, Nightingale KK. Interrogation of single nucleotide polymorphisms in gnd provides a novel method for molecular serogrouping of clinically important Shiga toxin producing Escherichia coli (STEC) targeted by regulation in the United States, including the "big six" non-O157 STEC and STEC O157. Journal of Microbiological Methods. 2016 Oct 1;129:85-93. https://doi.org/10.1016/j.mimet.2016.07.005