Genomic analysis of the zoonotic ST73 lineage containing avian and human extraintestinal pathogenic Escherichia coli (ExPEC)

Saidenberg, André Becker Simões; Vliet, Arnoud H. M. van; Stegger, Marc; Johannesen, Thor Bech; Semmler, Torsten; Cunha, Marcos Paulo Vieira; Silveira, Alessandro Conrado de Oliveira; Anzai, Eleine Kuroki; Scaletsky, Isabel C. A.; Dalsgaard, Anders; Ragione, Roberto M. La; Knöbl, Terezinha

doi:10.1016/j.vetmic.2022.109372

Cited by 8 publications

(4 citation statements)

References 34 publications

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“…ST73 was previously described as a human-specific ExPEC lineage [86,87]. However, recent studies have shown that ST73 is prominent in cats [55,88,89], dogs [52,54,90], killer whales [91] and some avian populations [92]. Consistent with previous studies, our phylogenetic analysis showed ST73 as diverse [53,93], and that animal-sourced isolates tended to cluster together [54,55].…”

Section: Discussionsupporting

confidence: 89%

Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids

Elankumaran

Kudinha

et al. 2023

Microbial Genomics

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Extraintestinal pathogenic Escherichia coli (ExPEC) are the most frequent cause of urinary tract infections (UTIs) globally. Most studies of clinical E. coli isolates are selected based on their antimicrobial resistance (AMR) phenotypes; however, this selection bias may not provide an accurate portrayal of which sequence types (STs) cause the most disease. Here, whole genome sequencing (WGS) was performed on 320 E. coli isolates from urine samples sourced from a regional hospital in Australia in 2006. Most isolates (91%) were sourced from patients with UTIs and were not selected based on any AMR phenotypes. No significant differences were observed in AMR and virulence genes profiles across age sex, and uro-clinical syndromes. While 88 STs were identified, ST73, ST95, ST127 and ST131 dominated. F virulence plasmids carrying senB-cjrABC (126/231; 55%) virulence genes were a feature of this collection. These senB-cjrABC+ plasmids were split into two categories: pUTI89-like (F29:A-:B10 and/or >95 % identity to pUTI89) (n=73) and non-pUTI89-like (n=53). Compared to all other plasmid replicons, isolates with pUTI89-like plasmids carried fewer antibiotic resistance genes (ARGs), whilst isolates with senB-cjrABC+/non-pUTI89 plasmids had a significantly higher load of ARGs and class 1 integrons. F plasmids were not detected in 89 genomes, predominantly ST73. Our phylogenomic analyses identified closely related isolates from the same patient associated with different pathologies and evidence of strain-sharing events involving isolates sourced from companion and wild animals.

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Section: Discussionsupporting

confidence: 89%

Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids

Elankumaran

Kudinha

et al. 2023

Microbial Genomics

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“…The MagNA Pure 96 DNA Multi-Sample Kit (Life Technologies, Carlsbad, CA, USA, 4413021) was used to extract genomic DNA according to instructions provided by the manufacturers. The Qubit 1X dsDNA HS Assay Kit (Thermo Fisher Scientific, Scoresby, VIC, Australia) was used for DNA quantification, while Sequencing libraries were prepared using the Illumina Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, USA, FC-131-1096) and sequenced on the NextSeq 500 platform (Illumina, San Diego, CA, USA) using a 300-cycle kit to obtained paired-end 150 bp reads, as previously described (Saidenberg et al, 2022).…”

Section: Whole Genome Sequencingmentioning

confidence: 99%

Clonal relatedness of coagulase-positive staphylococci among healthy dogs and dog-owners in Spain. Detection of multidrug-resistant-MSSA-CC398 and novel linezolid-resistant-MRSA-CC5

et al. 2023

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IntroductionNasal carriage of coagulase-positive staphylococci (CoPS) in healthy dogs could indicate increased risks of colonization for in-contact people or vice versa. This study determined the nasal carriage rate of CoPS among healthy dogs and in-contact people, their genotypic characteristics and phylogenetic relatedness.MethodsNasal samples were collected from 27 households (34 dogs and 41 humans) in Spain. Staphylococci were identified by MALDI-TOF-MS, their antimicrobial resistance (AMR) genes and spa-types were tested by PCR/sequencing. The relatedness of CoPS from the same households was assessed by core genome single nucleotide polymorphisms (SNPs) analyses.ResultsStaphylococcus aureus carriage was found in 34.1% of humans (including one methicillin-resistant S. aureus MRSA-CC5-t2220-SCCmec type-IV2B) and 5.9% of dogs; Staphylococcus pseudintermedius in 2.4% of humans and 32.4% of dogs; while Staphylococcus coagulans was only detected in dogs (5.4%). Remarkably, one human co-carried S. aureus/S. pseudintermedius, while a dog co-carried the three CoPS species. Household density was significantly associated with S. pseudintermedius carriage in households with > than 1 dog and >than 1 human (OR = 18.10, 95% CI: 1.24–260.93, p = 0.034). Closely related (<15 SNPs) S. aureus or S. pseudintermedius were found in humans or dogs in three households. About 56.3% S. aureus carriers (dog or human) harboured diverse within-host spa-types or AMR genotypes. Ten clonal complexes (CCs) were detected among the S. aureus, of which methicillin-susceptible S. aureus-CC398-IEC-type C (t1451 and t571) was the most frequent, but exclusive to humans. S. aureus and S. pseudintermedius isolates harboured resistance genes or mutations associated to 9 classes of antimicrobials including linezolid (G2261A & T1584A point mutations in 23S rDNA). The S. coagulans isolates were susceptible to all antimicrobials. Most of the S. pseudintermedius carried lukS/F-I, siet, and sient genes, and all S. aureus were negative for lukS/F-PV, tst-1, eta and etb genes.DiscussionClonally related human-to-human MSSA and dog-to-human MSSP were found. The detection of the MSSA-CC398 clade highlights the need for its continuous surveillance from One Health perspective.

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“…Concern Pathotypes of E. coli, they divided in to two main groups: Extraintestinal pathogenic E. coli (ExPEC) and intestinal pathogenic E. coli (InPEC). ExPEC cause range of infections for Human being outside intestine like meningitides as in neonatal meningitis E. coli (NMEC), urinary tract infection as in uropathogenic E. coli (UPEC) and sepsis-associated E. coli (SEPEC) [1][2][3]. InPEC includes 8 Pathotypes of diarrheagenic E. coli (DEC) including: enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC), diffusely adherent E. coli (DAEC), enteroinvasive E. coli (EIEC), enterohemorrhagic E. coli (EHEC) (also known as Shiga-toxin-producing E. coli (STEC) or, verotoxin-producing E. coli (VTEC), necrotoxic E. coli (NTEC) and adherent-invasive E. coli (AIEC) [4][5][6].…”

Section: Introductionmentioning

confidence: 99%

Phylotypes and Pathotypes of DiarrheagenicEscherichia coliof Gastroenteritis

Abdulabbas¹,

Al-Khafaji²,

Abed³

et al. 2023

Escherichia ColiInfections - An Update [Working Title]

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Escherichia coli responsible for wide range of common bacterial infections, the frequent one is gastroenteritis. Bacterial gastroenteritis mainly attributed to diarrheagenic E. coli and accompanied by diarrhea and vomiting. Actually pathogenic E. coli can be classified according to the site of infection whether it be within intestine (called intestinal pathogenic E. coli InPEC) or cause infection outside intestine (called extraintestinal pathogenic E. coli ExPEC). They are assigned to 4 main phylogenetic groups: InPEC include A and B1 while ExPEC have B2 and D groups. Seven Pathotypes have been assigned: Enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enterohemorrhagic (Shiga-toxin producing E. coli (EHEC/STEC), enteroaggregative E. coli (EAEC), diffusely adherent E. coli (DAEC), enteroinvasive E. coli (EIEC) and adherent invasive E. coli (AIEC). The patho-phylotyping of diarrheagenic E. coli interaction along with antibiotic resistance and biofilm formation capacity may be valuable insight to know real threat of this pathogen and this is tried to be covered with this chapter. The results revealed that the among DEC, EPEC and ETEC were assigned in high rate to B1 followed by A, B2, D, E, C and F while EAEC show different assignment: D followed by B2, A, B1, C, E and F. The other DEC pathotypes showed different styles.

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Genomic analysis of the zoonotic ST73 lineage containing avian and human extraintestinal pathogenic Escherichia coli (ExPEC)

Cited by 8 publications

References 34 publications

Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids

Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids

Clonal relatedness of coagulase-positive staphylococci among healthy dogs and dog-owners in Spain. Detection of multidrug-resistant-MSSA-CC398 and novel linezolid-resistant-MRSA-CC5

Phylotypes and Pathotypes of DiarrheagenicEscherichia coliof Gastroenteritis

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