Use of Genomics to Investigate Historical Importation of Shiga Toxin–Producing<i>Escherichia coli</i>Serogroup O26 and Nontoxigenic Variants into New Zealand

Browne, A. Springer; Biggs, Patrick J.; Wilkinson, David A.; Midwinter, Anne C.; Bloomfield, Samuel; Hranac, C. Reed; Rogers, Lynn; Marshall, Jonathan; Benschop, Jackie; Withers, Helen; Hathaway, S.C.; George, Tessy; Jaros, Patricia; Irshad, Hamid; Fong, Yang; Dufour, Muriel; Karki, Naveena; Winkleman, Taylor; French, Nigel P.

doi:10.3201/eid2503.180899

Cited by 9 publications

(6 citation statements)

References 33 publications

(39 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recent literature indicates that the genomic content of STEC is strongly influenced by the isolation location, and E. coli genomic plasticity would allow the evolution of a STEC population in a defined region ( Browne et al, 2019 ). This and the results described above led us to hypothesize that it might be possible to identify molecular markers of STEC isolated in Chile.…”

Section: Discussionmentioning

confidence: 99%

“…Interestingly, all New Zealand isolates clustered together regardless of the Shiga toxin type they carried ( Browne et al, 2019 ). Even when some STEC sequence types are distributed worldwide, this and other evidence using WGS approach suggests that STEC phylogeny is influenced by the origin of the geographic isolate and that there are highly conserved genes linked to local environments where they evolved ( Yu et al, 2018 ; Browne et al, 2019 ). Therefore, there may be STEC molecular markers and distinct genes based on their geographic origin ( Kiel et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Whole-Genome Phylogenetic Analysis Reveals a Wide Diversity of Non-O157 STEC Isolated From Ground Beef and Cattle Feces

et al. 2021

View full text Add to dashboard Cite

Shiga toxin-producing Escherichia coli (STEC) causes foodborne outbreaks that can lead to complications such as hemolytic uremic syndrome. Their main reservoir is cattle, and ground beef has been frequently associated with disease and outbreaks. In this study, we attempted to understand the genetic relationship among STEC isolated in Chile from different sources, their relationship to STEC from the rest of the world, and to identify molecular markers of Chilean STEC. We sequenced 62 STEC isolated in Chile using MiSeq Illumina. In silico typing was determined using tools of the Center Genomic Epidemiology, Denmark University (CGE/DTU). Genomes of our local STEC collection were compared with 113 STEC isolated worldwide through a core genome MLST (cgMLST) approach, and we also searched for distinct genes to be used as molecular markers of Chilean isolates. Genomes in our local collection were grouped based on serogroup and sequence type, and clusters were formed within local STEC. In the worldwide STEC analysis, Chilean STEC did not cluster with genomes of the rest of the world suggesting that they are not phylogenetically related to previously described STEC. The pangenome of our STEC collection was 11,650 genes, but we did not identify distinct molecular markers of local STEC. Our results showed that there may be local emerging STEC with unique features, nevertheless, no molecular markers were detected. Therefore, there might be elements such as a syntenic organization that might explain differential clustering detected between local and worldwide STEC.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Whole-Genome Phylogenetic Analysis Reveals a Wide Diversity of Non-O157 STEC Isolated From Ground Beef and Cattle Feces

et al. 2021

View full text Add to dashboard Cite

show abstract

“…To investigate the prevalence of ICEs in E. coli, BLAST homology searches were conducted against 1032 ICE sequences obtained from ICEberg database 2.0 [15]. In silico E. coli subtyping was performed based on outer membrane lipopolysaccharide (O) and flagellar (H) surface antigens using an in-house ECTyper and EcOH [52,53] to designate isolates as either O or H groups.…”

Section: Whole Genome Sequence Analysesmentioning

confidence: 99%

Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing Escherichia coli along Segments of the One Health Continuum

Adator

Walker²,

Narváez‐Bravo

et al. 2020

Microorganisms

View full text Add to dashboard Cite

Antimicrobial resistance (AMR) has important implications for the continued use of antibiotics to control infectious diseases in both beef cattle and humans. AMR along the One Health continuum of the beef production system is largely unknown. Here, whole genomes of presumptive extended-spectrum β-lactamase E. coli (ESBL-EC) from cattle feces (n = 40), feedlot catch basins (n = 42), surrounding streams (n = 21), a beef processing plant (n = 4), municipal sewage (n = 30), and clinical patients (n = 25) are described. ESBL-EC were isolated from ceftriaxone selective plates and subcultured on ampicillin selective plates. Agreement of genotype-phenotype prediction of AMR ranged from 93.2% for ampicillin to 100% for neomycin, trimethoprim/sulfamethoxazole, and enrofloxacin resistance. Overall, β-lactam (100%; blaEC, blaTEM-1, blaSHV, blaOXA, blaCTX-M-), tetracycline (90.1%; tet(A), tet(B)) and folate synthesis (sul2) antimicrobial resistance genes (ARGs) were most prevalent. The ARGs tet(C), tet(M), tet(32), blaCTX-M-1, blaCTX-M-14, blaOXA-1, dfrA18, dfrA19, catB3, and catB4 were exclusive to human sources, while blaTEM-150, blaSHV-11–12, dfrA12, cmlA1, and cmlA5 were exclusive to beef cattle sources. Frequently encountered virulence factors across all sources included adhesion and type II and III secretion systems, while IncFIB(AP001918) and IncFII plasmids were also common. Specificity and prevalence of ARGs between cattle-sourced and human-sourced presumptive ESBL-EC likely reflect differences in antimicrobial use in cattle and humans. Comparative genomics revealed phylogenetically distinct clusters for isolates from human vs. cattle sources, implying that human infections caused by ESBL-EC in this region might not originate from beef production sources.

show abstract

“…The serogroup O145 pangenome of >14,000 genes was open (Fig 4), demonstrating the genetic heterogeneity of this dataset, and is consistent with the identification of distinct phylogenetic lineages. The number of core genes reported for E. coli varies among studies and ranges from 1,472 to 5,173 [43,44,[86][87][88]. Although pangenomes consisting of >13,000 genes have been reported for E. coli [86,88], pangenome analysis of 325 E. coli O26 genome sequences and 239 O145:H28 strains indicated an open pangenome with an accessory genome of only 8,804 genes [88] and 9,342 [44], respectively.…”

Section: Plos Onementioning

confidence: 99%

Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies

et al. 2020

Self Cite

View full text Add to dashboard Cite

Shiga toxin-producing Escherichia coli (STEC) are a leading cause of foodborne outbreaks of human disease, but they reside harmlessly as an asymptomatic commensal in the ruminant gut. STEC serogroup O145 are difficult to isolate as routine diagnostic methods are unable to distinguish non-O157 serogroups due to their heterogeneous metabolic characteristics, resulting in under-reporting which is likely to conceal their true prevalence. In light of these deficiencies, the purpose of this study was a twofold approach to investigate enhanced STEC O145 diagnostic culture-based methods: firstly, to use a genomic epidemiology approach to understand the genetic diversity and population structure of serogroup O145 at both a local (New Zealand) (n = 47) and global scale (n = 75) and, secondly, to identify metabolic characteristics that will help the development of a differential media for this serogroup. Analysis of a subset of E. coli serogroup O145 strains demonstrated considerable diversity in carbon utilisation, which varied in association with eae subtype and sequence type. Several carbon substrates, such as D-serine and D-malic acid, were utilised by the majority of serogroup O145 strains, which, when coupled with current molecular and culture-based methods, could aid in the identification of presumptive E. coli serogroup O145 isolates. These carbon substrates warrant subsequent testing with additional serogroup O145 strains and non-O145 strains. Serogroup O145 strains displayed extensive genetic heterogeneity that was correlated with sequence type and eae subtype, suggesting these genetic markers are good indicators for distinct E. coli phylogenetic lineages. Pangenome analysis identified a core of 3,036 genes and an open pangenome of >14,000 genes, which is consistent with the identification of distinct phylogenetic lineages. Overall, this study highlighted the phenotypic and genotypic heterogeneity within E. coli serogroup O145, suggesting that the development of a differential media targeting this serogroup will be challenging.

show abstract

Use of Genomics to Investigate Historical Importation of Shiga Toxin–ProducingEscherichia coliSerogroup O26 and Nontoxigenic Variants into New Zealand

Cited by 9 publications

References 33 publications

Whole-Genome Phylogenetic Analysis Reveals a Wide Diversity of Non-O157 STEC Isolated From Ground Beef and Cattle Feces

Whole-Genome Phylogenetic Analysis Reveals a Wide Diversity of Non-O157 STEC Isolated From Ground Beef and Cattle Feces

Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing Escherichia coli along Segments of the One Health Continuum

Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies

Contact Info

Product

Resources

About