Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections

Stephens, Craig; Skerker, Jeffrey M.; Sekhon, Manraj S.; Arkin, Adam P.; Riley, Lee W.

doi:10.1128/genomea.01241-15

Cited by 18 publications

(17 citation statements)

References 6 publications

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“…Based on their fimH genotype and antibiotic resistance phenotypes, four ST95 isolates from San Francisco were selected for long-read, single-molecule real-time (SMRT) sequencing (Pacific Biosciences) to develop high-quality, fully assembled reference genomes (15). The complete genomes were from SF-166 ( fimH6 [pansusceptible, as defined in Materials and Methods]), SF-173 ( fimH47 [MDR]), SF-468 ( fimH1 [MDR]), and SF-088 ( fimH9 [MDR]).…”

Section: Resultsmentioning

confidence: 99%

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Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains

Stephens

Adams‐Sapper

Sekhon

et al. 2017

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Antibiotic resistance in bacterial pathogens is a major public health concern. This work was motivated by the observation that only a small proportion of ST95 isolates, a major pandemic lineage of extraintestinal pathogenic E. coli, have acquired antibiotic resistance, in contrast to many other pandemic lineages. Understanding bacterial genetic factors that may prevent acquisition of resistance could contribute to the development of new biological, medical, or public health strategies to reduce antibiotic-resistant infections.

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Section: Resultsmentioning

confidence: 99%

“…Library preparation and sequencing using single-molecule real-time (SMRT) sequencing technology (Pacific Biosciences) have been described elsewhere (15). Analysis of DNA methylation patterns in the SMRT data (19) was done using analysis tools provided by the manufacturer.…”

Section: Methodsmentioning

confidence: 99%

Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains

Stephens

Adams‐Sapper

Sekhon

et al. 2017

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“…Interestingly, two large contigs, of 40.9 kb and 31.9 kb, showed 99% similarity to a 92.7-kb plasmid (pSF-468-2) (GenBank accession no. CP012627) of an extraintestinal pathogenic E. coli (ExPEC) strain isolated from a bloodstream infection (43). Subsequent mapping of the consensus sequence of pSFO157 258/98-2 to the reference sequence of pSF-468-2 demonstrated that pSFO157 258/98-2 covered 92% of the reference plasmid, with an identity of 98% in the overlapping region ( Fig.…”

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Sorbitol-Fermenting Enterohemorrhagic Escherichia coli O157:H ⁻ Isolates from Czech Patients with Novel Plasmid Composition Not Previously Seen in German Isolates

Bauwens

Marejková

Middendorf-Bauchart

et al. 2017

Appl Environ Microbiol

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Sorbitol-fermenting (SF) enterohemorrhagic (EHEC) O157:H strains, first identified in Germany, have emerged as important pathogens throughout Europe. Besides chromosomally encoded Shiga toxin 2a (the major virulence factor), several putative virulence loci, including the ,, and operons, encoding EHEC hemolysin, type II secretion system proteins, and Sfp fimbriae, respectively, are located on the 121-kb plasmid pSFO157 in German strains. Here we report novel SF EHEC O157:H strains isolated from patients in the Czech Republic. These strains share the core genomes and chromosomal virulence loci encoding toxins ( and the -ABC operon) and adhesins (-γ, ,, and ) with German strains but differ essentially in their plasmids. In contrast to all previously detected SF EHEC O157:H strains, the Czech strains carry two plasmids, of 79 kb and 86 kb. The 79-kb plasmid harbors the operon, but neither of the plasmids contains the and operons. Sequence analyses demonstrated that the 79-kb plasmid (pSFO157 258/98-1) evolved from pSFO157 of German strains by deletion of a 41,534-bp region via homologous recombination, resulting in loss of the and operons. The 86-kb plasmid (pSFO157 258/98-2) displays 98% sequence similarity to a 92.7-kb plasmid of an extraintestinal pathogenic bloodstream isolate. Our finding of this novel plasmid composition in SF EHEC O157:H strains extends the evolutionary history of EHEC O157 plasmids. Moreover, the unique molecular plasmid characteristics permit the identification of such strains, thereby facilitating further investigations of their geographic distribution, clinical significance, and epidemiology. Since their first identification in Germany in 1989, sorbitol-fermenting enterohemorrhagic O157:H (nonmotile) strains have emerged as important causes of the life-threatening disease hemolytic-uremic syndrome in Europe. They account for 10 to 20% of sporadic cases of this disease and have caused several large outbreaks. The strains isolated throughout Europe share conserved chromosomal and plasmid characteristics. Here we identified novel sorbitol-fermenting enterohemorrhagic O157:H patient isolates in the Czech Republic which differ from all such strains reported previously by their unique plasmid characteristics, including plasmid number, composition of plasmid-carried virulence genes, and plasmid origins. Our findings contribute substantially to understanding the evolution of O157 strains and their plasmids. In practical terms, they enable the identification of strains with these novel plasmid characteristics in patient stool samples and thus the investigation of their roles as human pathogens in other geographic areas.

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“…diarizonae 60:r:z causing diarrhea and sepsis with fatal outcome. A plasmid identical to the 3,904-bp plasmid found in both ST882S and ST931R was originally discovered in an ESBL-positive (IncF bla TEM-1 and IncI1 bla CTX-M-9 ) urinary tract E. coli isolate (52); almost identical plasmids have been found in an E. coli isolate causing septicemia (104) and in an MDR NTS serovar Heidelberg (105) isolate from turkey meat in Canada (as the largest of four small plasmids, along with an MDRIncHI2 plasmid). These matches support the idea that the original ST882S Salmonella isolate had already encountered plasmid-bearing E. coli prior to the acquisition of pESBL931 and the IncI plasmids.…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Sequencing Identifies In Vivo Acquisition of a bla _CTX-M-27 -Carrying IncFII Transmissible Plasmid as the Cause of Ceftriaxone Treatment Failure for an Invasive Salmonella enterica Serovar Typhimurium Infection

McCollister

Kotter

Frank

et al. 2016

Antimicrob Agents Chemother

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bWe report a case of ceftriaxone treatment failure for bacteremia caused by Salmonella enterica subsp. enterica serovar Typhimurium, due to the in vivo acquisition of a bla CTX-M-27 -encoding IncFII group transmissible plasmid. The original ␤-lactamasesusceptible isolate ST882S was replaced by the resistant isolate ST931R during ceftriaxone treatment. After relapse, treatment was changed to ciprofloxacin, and the patient recovered. Isolate ST931R could transfer resistance to Escherichia coli at 37°C. We used whole-genome sequencing of ST882S and ST931R, the E. coli transconjugant, and isolated plasmid DNA to unequivocally show that ST882S and ST931R had identical chromosomes, both having 206 identical single-nucleotide polymorphisms (SNPs) versus S. Typhimurium 14028s. We assembled a complete circular genome for ST931R, to which ST882S reads mapped with no SNPs. ST882S and ST931R were isogenic except for the presence of three additional plasmids in ST931R. ST931R and the E. coli transconjugant were ceftriaxone resistant due to the presence of a 60.5-kb IS26-flanked, bla CTX-M-27 -encoding IncFII plasmid. Compared to 14082s, ST931R has almost identical Gifsy-1, Gifsy-2, and ST64B prophages, lacks Gifsy-3, and instead carries a unique Fels-2 prophage related to that found in LT2. ST882S and ST931R both had a 94-kb virulence plasmid showing >99% identity with pSLT14028s and a cryptic 3,904-bp replicon; ST931R also has cryptic 93-kb IncI1 and 62-kb IncI2 group plasmids. To the best of our knowledge, in vivo acquisition of extended-spectrum ␤-lactamase resistance by S. Typhimurium and bla CTX-M-27 genes in U.S. isolates of Salmonella have not previously been reported. G reater than 1.4 million cases of nontyphoidal salmonellosis are estimated to occur each year in the United States, with approximately 95% of cases resulting from foodborne transmission (1). Although most infections result in mild to moderate gastroenteritis that usually resolves with or without treatment, concurrent bacteremia is observed in approximately 6% of patients and can be associated with serious disease, especially in infants aged Ͻ1 year, the elderly, and those with immunocompromised states such as HIV infection (2-5). Although routine use of antimicrobial therapy is not generally recommended for the treatment of most Salmonella infections, such therapy may be lifesaving in persons with invasive disease.Treatment of invasive salmonellosis has been compromised in recent years due to the emergence of Salmonella isolates with single or multidrug resistance to a number of first-line agents (6, 7). Antimicrobial resistance in strains of nontyphoidal Salmonella (NTS) has been linked to the use of antimicrobial agents in livestock (8-11). Consequently, agents such as fluoroquinolones and third generation cephalosporins, such as ceftriaxone, have become treatment modalities of choice for therapy against severe Salmonella infections. In the United States before 1996, all reported cases of infection with ceftriaxone-resistant NTS isolates were known o...

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Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections

Cited by 18 publications

References 6 publications

Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains

Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains

Sorbitol-Fermenting Enterohemorrhagic Escherichia coli O157:H ⁻ Isolates from Czech Patients with Novel Plasmid Composition Not Previously Seen in German Isolates

Whole-Genome Sequencing Identifies In Vivo Acquisition of a bla _CTX-M-27 -Carrying IncFII Transmissible Plasmid as the Cause of Ceftriaxone Treatment Failure for an Invasive Salmonella enterica Serovar Typhimurium Infection

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Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections

Cited by 18 publications

References 6 publications

Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains

Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains

Sorbitol-Fermenting Enterohemorrhagic Escherichia coli O157:H − Isolates from Czech Patients with Novel Plasmid Composition Not Previously Seen in German Isolates

Whole-Genome Sequencing Identifies In Vivo Acquisition of a bla CTX-M-27 -Carrying IncFII Transmissible Plasmid as the Cause of Ceftriaxone Treatment Failure for an Invasive Salmonella enterica Serovar Typhimurium Infection

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Sorbitol-Fermenting Enterohemorrhagic Escherichia coli O157:H ⁻ Isolates from Czech Patients with Novel Plasmid Composition Not Previously Seen in German Isolates

Whole-Genome Sequencing Identifies In Vivo Acquisition of a bla _CTX-M-27 -Carrying IncFII Transmissible Plasmid as the Cause of Ceftriaxone Treatment Failure for an Invasive Salmonella enterica Serovar Typhimurium Infection