Genome wide characterization of enterotoxigenic Escherichia coli serogroup O6 isolates from multiple outbreaks and sporadic infections from 1975-2016

Abstract

Enterotoxigenic Escherichia coli (ETEC) are an important cause of diarrhea globally, particularly among children under the age of five in developing countries. ETEC O6 is the most common ETEC serogroup, yet the genome wide population structure of isolates of this serogroup is yet to be determined. In this study, we have characterized 40 ETEC O6 isolates collected between 1975–2016 by whole genome sequencing (WGS) and by phenotypic antimicrobial susceptibility testing. To determine the relatedness of isolates, we evaluated two methods—whole genome high-quality single nucleotide polymorphism (whole genome-hqSNP) and core genome SNP analyses using Lyve-SET and Parsnp respectively. All isolates were tested for antimicrobial susceptibility using a panel of 14 antibiotics. ResFinder 2.1 and a custom quinolone resistance determinants workflow were used for resistance determinant detection. VirulenceFinder 1.5 was used for prediction of the virulence genes. Thirty-seven isolates clustered into three major clades (I, II, III) by whole genome-hqSNP and core genome SNP analyses, while three isolates included in the whole genome-hqSNP analysis only did not cluster with clades I-III by both analyses and formed a distantly related outgroup, designated clade IV. Median number of pairwise whole genome-hqSNPs in clonal ETEC O6 outbreaks ranged from 0 to 5. Of the 40 isolates tested for antimicrobial susceptibility, 18 isolates were pansusceptible. Twenty-two isolates were resistant to at least one antibiotic, nine of which were multidrug resistant. Phenotypic antimicrobial resistance (AR) correlated with AR determinants in 22 isolates. Thirty-two isolates harbored both enterotoxin virulence genes while the remaining 8 isolates had only one of the two virulence genes. In summary, whole genome-hqSNP and core genome SNP analyses from this study revealed similar evolutionary relationships and an overall diversity of ETEC O6 isolates independent of time of isolation. Less than 5 pairwise hqSNPs between ETEC O6 isolates is circumstantially indicative of an outbreak cluster. Findings from this study will be a basis for quicker outbreak detection and control by efficient subtyping by WGS.

Relationship of attitudes toward uncertainty and preventive health behaviors with breast cancer screening participation

“…Smoking and alcohol consumption are risk factors for various cancers, including breast cancer [ 48 ]. Past research has shown a positive association between high breast cancer knowledge and breast cancer screening participation, and suggested individuals might be more likely to undergo breast cancer screening if they are knowledgeable about breast cancer, including its risk factors, the usefulness of mammography, and causes [ 16 , 18 , 49 ].…”

Comparative genomic analysis and molecular examination of the diversity of enterotoxigenic Escherichia coli isolates from Chile

“…The representative ETEC isolates selected for genome completion by PacBio sequencing in the current study were from the major ETEC phylogroups (B1 and A), as well as containing the ST toxin genes, and they complement the complete genomes of the ETEC prototypes [11, 12] and recent isolates [16, 17, 31, 43]. Interestingly, the three phylogroup A isolates selected for complete genome sequencing were very closely related based on the phylogeny (Fig 1), and each isolate has the same plasmid profile, and a very similar virulence factor profile (Table 1).…”

“…[21] and Sahl et al . [13] as well as others [16, 17, 31] have greatly expanded the genomic knowledge of ETEC as a pathovar, by including ETEC from various global geographic locations and clinical presentations. While there have been a number of molecular studies of the ETEC in Chile [24, 32–36], only a limited number of genomes of Chilean ETEC isolates have been examined [21].…”

Genomic Profiling of Antibiotic-Resistant Escherichia coli Isolates from Surface Water of Agricultural Drainage in North-Western Mexico: Detection of the International High-Risk Lineages ST410 and ST617

“…Based on the investigation of virulence factors, a low abundance of VAGs was predicted in the high-risk clones ADD147 (ST410) and ADD167 (ST617). Alternatively, strain ADD183 (O6:H16) belongs to the ETEC O6 group, the most common ETEC serogroup involved in multiple outbreaks and sporadic infections internationally, and typically carries both enterotoxins [ 64 , 65 , 66 ]. In contrast to what was reported in ETEC O6 strains [ 65 , 67 ], E. coli ADD183 harbored additional nonclassical virulence factors found in ETEC ( eatA ) and ExPEC ( iss , kpsE , and kpsM_K15 ) strains, implying the potential of E. coli ADD183 to cause both intestinal and extraintestinal diseases.…”