Genome Sequence Analysis and Characterization of Shiga Toxin 2 Production by Escherichia coli O157:H7 Strains Associated With a Laboratory Infection

Abstract

A laboratory-acquired E. coli O157:H7 infection with associated severe sequelae including hemolytic uremic syndrome occurred in an individual working in the laboratory with a mixture of nalidixic acid-resistant (NalR) O157:H7 mutant strains in a soil-biochar blend. The patient was hospitalized and treated with an intravenous combination of metronidazole and levofloxacin. The present study investigated the source of this severe laboratory acquired infection and further examined the influence of the antibiotics used during treatment on the expression and production of Shiga toxin. Genomes of two Stx2a-and eae-positive O157:H7 strains isolated from the patient’s stool were sequenced along with two pairs of the wt strains and their derived NalR mutants used in the laboratory experiments. High-resolution SNP typing determined the strains’ individual genetic relatedness and unambiguously identified the two laboratory-derived NalR mutant strains as the source of the researcher’s life-threatening disease, rather than a conceivable ingestion of unrelated O157:H7 isolates circulating at the same time. It was further confirmed that in sublethal doses, the antibiotics increased toxin expression and production. Our results support a simultaneous co-infection with clinical strains in the laboratory, which were the causative agents of previous O157:H7 outbreaks, and further that the administration of antibiotics may have impacted the outcome of the infection.

Pathogenomes of Shiga Toxin Positive and Negative Escherichia coli O157:H7 Strains TT12A and TT12B: Comprehensive Phylogenomic Analysis Using Closed Genomes

“…Availability of high-resolution closed genomes allowed us to record subtle strain-level sequence and structural polymorphisms with high phylogenetic accuracy, demonstrating an isogenic relationship of these Stx(+/−) TT12A and TT12B isolates. The number of strain-differentiating SNPs is similar to the range reported for clonal O157:H7 outbreak strains [40,106,107,111,195]. However, SNP data on its own are clearly insufficient to infer clonality in microbes without further assessing changes in genome structure and content.…”

“…Whole genome sequence typing has proven to be invaluable for the identification and strain attribution of near clonal E. coli pathogen populations [40,107,193,194]. Availability of high-resolution closed genomes allowed us to record subtle strain-level sequence and structural polymorphisms with high phylogenetic accuracy, demonstrating an isogenic relationship of these Stx(+/−) TT12A and TT12B isolates.…”

“…This toxin is cytopathic for eukaryotic cells and specifically toxigenic to renal cells [29][30][31][32][33][34][35]. Single or multiple ΦStx-prophages can be carried, with the toxin expressed and produced after phage mobilization during the phage lytic cycle [31,[36][37][38][39][40]. Various suballeles of the major stx alleles 1 and 2 have been described [41][42][43][44].…”

Pathogenomes and virulence profiles of representative big six non-O157 serogroup Shiga toxin-producing Escherichia coli

“…The actual disease outcome cannot be predicted from in silico virulence profiling, considering the complex interactions between infective agent, the host microbiota ( Pruimboom-Brees et al, 2000 ; Gamage et al, 2006 ; Nguyen and Sperandio, 2012 ), and the infected patient ( Wong et al, 2000 ; Dundas et al, 2001 ; Gould et al, 2009 ; Foster, 2013 ). Induction efficiency of the Stx-phages is positively correlated to Stx-production ( Muniesa et al, 2004 ; Loś et al, 2009 ; Del Cogliano et al, 2018 ) and thus mobilization of Stx-phages is used as a means to assess the conferred pathogenic potential ( Karch et al, 1999 ; Eppinger et al, 2022 ; Miyata et al, 2023 ). For the panel cultures, we recorded Stx-production traits under non-induced culture growth in LB and under phage mobilizing conditions by adding sublethal doses of MMC to the standard LB medium ( Figure 8 ).…”

“…More specifically, we noted a correlation of Stx-levels to the respective stx status patterns of the strains. The class of ΦStx 2a phages carry a highly potent cytotoxin ( Fuller et al, 2011 ; Hauser et al, 2020 ; Pinto et al, 2021 ) and are known to mobilize upon activation of the SOS-response ( Bonanno et al, 2016 ; Zhang et al, 2019 ; Eppinger et al, 2022 ). In consequence, the Stx titers of the three stx 2a + isolates were all found exacerbated ( Figure 8 ).…”