escherichia coli atcc 25922 type strain  (ATCC)

Journal: bioRxiv

Article Title: A type II Thoeris anti-phage defense enacts growth arrest independent of NAD depletion

doi: 10.64898/2026.01.22.701046

Figure Lengend Snippet: A : Overview of the different types of discovered Thoeris systems. Previously characterized Thoeris systems are grouped into four distinct types, with type I and type II further distinguished into 11 subfamilies. All types have in common one or more TIR-domain containing genes (called thsB in type I and II, thcB in type III and PsTIR in type IV). The categorization is based on the effector domain (highlighted with diagonal bars), which is unique for every type. B : Genome context of the ATCC 25922 type II Thoeris system: An overview of the 5, 132, 219 bp genome of E. coli ATCC 25922, with the locations of known phage-defense systems highlighted. The Thoeris system, highlighted in blue, is located in a part of the genome that is not homologous to other E. coli strains, but is not in proximity to other known phage defense systems. C : Domain annotation: The Thoeris locus, consisting of thsA , thsB2 and thsB1 , with their predicted functional domains annotated. The exact amino acid boundaries are shown on top. ThsB2 is predicted to contain a TIR-like domain (pf08937), similar to other Thoeris systems, while thsB1 is predicted to contain a TIR domain (pf13676). D : Alignment of the predicted structures of the ATCC 25922 ThsB2 protein (red) with the Streptococcus suis ThsB (blue; CYX44050. 1). CYX44050. 1 was chosen as representative of the subgroup 9 of type II Thoeris systems. TM-align of the two structures gave a TM-score of 0. 84431, where 1 would indicate a perfect match and < 0. 2 would correspond to randomly chosen unrelated proteins.

Article Snippet: To determine whether plasmid-based expression of thsAB2 also confers protection in the native host, we introduced the same pthsAB2 expression plasmid into both the wild-type (WT) ATCC 25922 strain and Δ thsAB2B1 mutant.

Techniques: Functional Assay

Journal: bioRxiv

Article Title: A type II Thoeris anti-phage defense enacts growth arrest independent of NAD depletion

doi: 10.64898/2026.01.22.701046

Figure Lengend Snippet: progressiveMAUVE alignment of ATCC 25922 and MG1655 genome sequences. The bottom shows a zoomed in view of the ATCC 25922 genomic region (1, 850, 000 - 2, 150, 000) containing the Thoeris locus, which is highlighted in blue. The height of the bar describes the similarity profile that corresponds to the average conservation between regions, while an empty space indicates a lack of detectable homology. The color of the bars show large regions that are presumably homologous and internally free from genomic rearrangement.

Article Snippet: To determine whether plasmid-based expression of thsAB2 also confers protection in the native host, we introduced the same pthsAB2 expression plasmid into both the wild-type (WT) ATCC 25922 strain and Δ thsAB2B1 mutant.

Techniques:

Journal: bioRxiv

Article Title: A type II Thoeris anti-phage defense enacts growth arrest independent of NAD depletion

doi: 10.64898/2026.01.22.701046

Figure Lengend Snippet: A: E. coli ATCC 25922 is resistant to most of the Basel phage collection, even in the absence of Thoeris. Number of phage plaques forming on the native ATCC 25922 host (WT), with the thsAB2B1 locus knocked out (KO) or on a susceptible host carrying an empty vector plasmid (pET28) or the same vector carrying the thsAB2 locus (pthsAB2). An asterisk highlights the phages showing >100-fold difference between pthsAB2 and pET28. A crossed out square means no plaques detected. Each square represents the average of two biological replicates. EOP: efficiency of plating. B: Susceptibility of E. coli ATCC 25922 to phage T4 infection. The E. coli strain contains the native Thoeris thsAB2B1 locus or expresses the thsAB2 locus from a plasmid, compared to the thsAB2B1 knockout strain and an empty vector control. C: Growth curves of ATCC 25922 WT and thsAB2B1- deletion strains, carrying thsAB2 plasmid, infected by phage T4 at varying MOIs. ATCC 25922 WT carrying an empty vector control is shown as negative control, being susceptible to phage T4. D: Heterologous expression of the thsB1B2A locus, with thsB1 under the control of an arabinose inducible promoter. Growth curves of E. coli MG1655 and ATCC 25922 strains heterologously expressing thsAB2B1 under inducing (+ L-arabinose) or repressing (+ D-glucose) conditions. Lines and shaded regions represent the mean and standard deviation of three independent cultures.

Article Snippet: To determine whether plasmid-based expression of thsAB2 also confers protection in the native host, we introduced the same pthsAB2 expression plasmid into both the wild-type (WT) ATCC 25922 strain and Δ thsAB2B1 mutant.

Techniques: Plasmid Preparation, Infection, Knock-Out, Control, Negative Control, Expressing, Standard Deviation

Journal: Microbiology Spectrum

Article Title: Effect of pH on antimicrobial activity of delafloxacin against Escherichia coli isogenic strains carrying diverse chromosomal and plasmid-mediated fluoroquinolone resistance mechanisms

doi: 10.1128/spectrum.02338-25

Figure Lengend Snippet: Impact of pH on bacteriostatic activity of ciprofloxacin and delafloxacin against E. coli strains with different resistance mechanisms. ( A ) MIC distribution across different chromosomic mutations and plasmid-mediated resistance mechanisms at pH 5.0, 6.0, and 7.3 for ciprofloxacin and delafloxacin. ( B ) Clinical categories (susceptible, intermediate, resistant) based on EUCAST breakpoints for the same resistance mechanisms and conditions. ( C ) Resistance ratio calculated as log2 of the ratio: (MIC_ciprofloxacin_mutant/MIC_ciprofloxacin_wild-type_pH7.3)/(MIC_delafloxacin_mutant/MIC_delafloxacin_wild-type_pH7.3), with red indicating preferential resistance to delafloxacin and blue indicating preferential resistance to ciprofloxacin. Mutations: S83L and S80R in gyrA, D87N in gyrB, and ∆marR (marR deletion). Plasmid-mediated resistance genes tested include qnr variants and aac(6')-Ib-cr. S: susceptible; ATU: area of technical uncertainty; R: resistant.

Article Snippet: A total of 81 isogenic E. coli strains derived from the wild-type (WT) strain E. coli ATCC 25922 were used ( ).

Techniques: Activity Assay, Plasmid Preparation, Mutagenesis

Journal: Microbiology Spectrum

Article Title: Effect of pH on antimicrobial activity of delafloxacin against Escherichia coli isogenic strains carrying diverse chromosomal and plasmid-mediated fluoroquinolone resistance mechanisms

doi: 10.1128/spectrum.02338-25

Figure Lengend Snippet: Time-kill assays of ciprofloxacin and delafloxacin against three E. coli strains at pH 7.3 and 5.0. Individual data points represent colony-forming unit (CFU) counts from independent experiments, with filled circles indicating values above the limit of detection and triangles indicating values below the limit of detection. Solid lines represent mean values for each concentration. The horizontal dashed line indicates the limit of detection (2 log₁₀ CFU/mL). Color coding represents different antibiotic concentrations relative to each strain’s MIC (0× to 8× MIC).

Article Snippet: A total of 81 isogenic E. coli strains derived from the wild-type (WT) strain E. coli ATCC 25922 were used ( ).

Techniques: Concentration Assay

Journal: Microbiology Spectrum

Article Title: Effect of pH on antimicrobial activity of delafloxacin against Escherichia coli isogenic strains carrying diverse chromosomal and plasmid-mediated fluoroquinolone resistance mechanisms

doi: 10.1128/spectrum.02338-25

Figure Lengend Snippet: Predicted bacterial population dynamics under ciprofloxacin and delafloxacin exposure at pH 7.3 and 5.0. Predicted total bacterial populations (CFU/mL ± 90% CI) following simulated clinical dosing of ciprofloxacin (400 mg q12h IV) and delafloxacin (350 mg q12h IV) against three E. coli strains under physiological (pH 7.3, blue lines) and acidic (pH 5.0, orange lines) conditions over 120 h. ATCC 25922 (WT strain), EC02 ( gyrA -S83L chromosomal mutant), and EC11 ( qnrB1 PMQR-carrying strain). Solid lines represent median predictions from the semi-mechanistic pharmacokinetic-pharmacodynamic model, while shaded areas indicate 90% CI derived from Monte Carlo simulations ( n = 10,000).

Article Snippet: A total of 81 isogenic E. coli strains derived from the wild-type (WT) strain E. coli ATCC 25922 were used ( ).

Techniques: Mutagenesis, Derivative Assay