Journal: bioRxiv

Article Title: Rapid and Quantitative Phage Susceptibility Test by Ramanome

doi: 10.64898/2026.02.07.704537

Figure Lengend Snippet: ( A ) ROC analysis was applied to Raman spectral fingerprint regions to identify biomarkers distinguishing infected from uninfected bacteria. Raman spectra were collected from three sensitive systems (T1- Escherichia coli ATCC11303, T4- E. coli ATCC11303, T4- E. coli ATCC25922) at six time points (20∼120 min) under MOI = 10. Peaks showing an average area under the ROC curve (AUC) > 0.80 in at least four of six time points across all three systems are considered candidate biomarkers (n = 15). Combined with difference spectrum analysis, only those showing consistent directional changes (either increased or decreased upon infection) across systems are retained, resulting in four universal candidate regions: 658∼663 cm¹ (decreased), 713∼719 cm¹ (decreased), 1430∼1450 cm¹ (increased), and 1589∼1595 cm¹ (increased). ( B ) Temporal dynamics of the four biomarkers are compared between sensitive and resistant systems. In the sensitive T1-ATCC11303 system, 658∼663 cm¹ and 713∼719 cm¹ gradually decrease, whereas 1430∼1450 cm¹ and 1589∼1595 cm¹ continuously increase over time. In contrast, in the resistant T1-DH5α system, the initial decrease of 658∼663 cm¹ and 713∼719 cm¹ (≤ 40 min) is followed by recovery or stabilization, while 1430∼1450 cm¹ and 1589∼1595 cm¹ transiently decrease at early time points (≤ 60 min) and then remain unchanged or slightly decline. ( C ) Temporal dynamics of the four biomarkers in the weakly sensitive system under different MOI conditions. Under MOI = 10, 658∼663 cm¹ and 713∼719 cm¹ consistently decrease, while 1430∼1450 cm¹ and 1589∼1595 cm¹ increase. Under MOI = 1, responses fluctuate: the first two regions decrease at 40 min, increase at 80 min, and sharply drop at 100 min; the latter two increase at 40∼80 min but also decline at 100 min. n.s., not significant; * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: To assess whether RPST can resolve infection dynamics and determine the minimal effective MOI, we established a multidimensional experimental matrix incorporating five MOIs (0, 0.01, 0.1, 1, and 10) and six time points (0∼120 min at 20-min intervals) across three phage-bacterium systems: T1- E. coli ATCC 11303, T4- E. coli ATCC 11303, and T4- E. coli ATCC 25922.

Techniques: Infection, Bacteria

Journal: bioRxiv

Article Title: Rapid and Quantitative Phage Susceptibility Test by Ramanome

doi: 10.64898/2026.02.07.704537

Figure Lengend Snippet: ( A-B ) Performance comparison of six machine learning models integrating four RPST-derived biomarkers, evaluated by 5×5 cross-validation: direct summation, logistic regression, LDA, naïve Bayes, SVM, and RF. Based on ( A ) ROC and ( B ) precision-recall curves, both AUC and PR-AUC follow RF > LDA > SVM > naïve Bayes > logistic regression > direct summation, with RF achieving the best performance (AUC: 0.995 ± 0.003; PR-AUC: 0.993 ± 0.003). ( C-D ) Comparison between single biomarkers and the RF-based CII. Across repeated cross-validation, CII consistently outperforms all individual features in both ( C ) ROC and ( D ) precision–recall analyses. ( E ) RF-derived feature importance averaged across folds: 1430∼1450 cm¹ (0.516 ± 0.010), 1589∼1595 cm¹ (0.244 ± 0.012), 713∼719 cm¹ (0.151 ± 0.018), and 658∼663 cm¹ (0.089 ± 0.014). ( F ) Dual-cutoff framework for CII-based classification. The optimal cutoff (0.6000) maximizing G-mean defines infection status with 99% confidence bounds (lower: 0.5970; upper: 0.6030), categorizing populations as uninfected (CII < lower), infected (CII > upper), or uncertain (between cutoffs). ( G-H ) Temporal dynamics of CII. In T1- E. coli ATCC11303 (susceptible), CII exceeds the cutoff by 20 min (0.73 ± 0.21), stabilizing by 40 min (0.99 ± 0.02). In T1- E. coli DH5α (resistant), both the infected and control groups remain below the cutoff. ( I ) Validation across 25 phage-host systems ( E. coli , P. aeruginosa , Salmonella , K. pneumoniae ). CII-based classification agrees with plaque assays in 24/25 cases (96.0% accuracy).

Article Snippet: To assess whether RPST can resolve infection dynamics and determine the minimal effective MOI, we established a multidimensional experimental matrix incorporating five MOIs (0, 0.01, 0.1, 1, and 10) and six time points (0∼120 min at 20-min intervals) across three phage-bacterium systems: T1- E. coli ATCC 11303, T4- E. coli ATCC 11303, and T4- E. coli ATCC 25922.

Techniques: Comparison, Derivative Assay, Biomarker Discovery, Infection, Control

Journal: bioRxiv

Article Title: Rapid and Quantitative Phage Susceptibility Test by Ramanome

doi: 10.64898/2026.02.07.704537

Figure Lengend Snippet: ( A-B ) Effect of multiplicity of infection (MOI) on the composite infection index (CII) in the Ecp54- E. coli DH5α system. ( A ) Boxplots show progressive CII elevation with increasing MOI after 40 min co-incubation. ( B ) Density plots at 40 min reveal a gradual rise in the proportion of infected cells, exceeding uninfected populations at MOI = 0.1 and approaching complete infection at MOI = 10. ( C-D ) Evaluation of phage Pap12 against three P. aeruginosa strains. ( C ) RPST-based CII distributions show MOI-dependent increases for susceptible strains Pae1 and Pae307, surpassing the infection cutoff at MOI = 0.01 and 1, respectively, while the resistant strain Pae5 remains below the cutoff even at MOI = 10. ( D ) Plaque-based relative infection efficiency (RIE) assays yield RIE = 1 (Pae1), 0.01 (Pae307), and 0 (Pae5). ( E-F ) Evaluation of phage Kpap4 against three K. pneumoniae strains. ( E ) RIE assays show values of 1, 0.1, and 0 for Kpn25, Kpn30, and Kpn6, respectively. ( F ) Corresponding RPST-based CII distributions demonstrate cutoff crossing at MOI = 0.1 for Kpn25, persistent sub-cutoff levels for Kpn6 even at MOI = 10, and gradual but incomplete increases for Kpn30 (RIE > 0). ( G ) Comparative analysis of twelve E. coli phages (MOI = 10, 40 min). Nine elevated population CII above the cutoff, with Ecp9 showing the highest CII. Density plots exhibit unimodal distributions for infective phages, while three noninfective ones display bimodal patterns with population CII remaining below the cutoff.

Article Snippet: To assess whether RPST can resolve infection dynamics and determine the minimal effective MOI, we established a multidimensional experimental matrix incorporating five MOIs (0, 0.01, 0.1, 1, and 10) and six time points (0∼120 min at 20-min intervals) across three phage-bacterium systems: T1- E. coli ATCC 11303, T4- E. coli ATCC 11303, and T4- E. coli ATCC 25922.

Techniques: Infection, Incubation

Journal: bioRxiv

Article Title: Rapid and Quantitative Phage Susceptibility Test by Ramanome

doi: 10.64898/2026.02.07.704537

Figure Lengend Snippet: ( A-C ) MOI- and time-resolved trajectories of CII in three phage-host systems. Populations were monitored under five MOIs (0, 0.01, 0.1, 1, and 10) across seven timepoints (0∼120 min, 20-min intervals). ( A ) In the T1- E. coli ATCC11303 system, populations at MOI = 0 remain below the infection cutoff throughout the experiment, whereas those at MOI = 10 cross the threshold within 20 min. Intermediate MOIs (0.01, 0.1, 1) exhibit delayed but complete transitions into the infected state within 60 min. ( B ) In the T4- E. coli ATCC11303 system, populations cross the infection cutoff within ≤ 20 min at MOI = 10, 60 min at MOI = 1, 80 min at MOI = 0.1, and 120 min at MOI = 0.01, while remaining uninfected at MOI = 0. (C) In the T4- E. coli ATCC25922 system, only MOI = 10 leads to a transition to the infected state. At lower MOIs, CII values rise transiently but subsequently decline, and population-level CII never exceeds the infection cutoff.

Article Snippet: To assess whether RPST can resolve infection dynamics and determine the minimal effective MOI, we established a multidimensional experimental matrix incorporating five MOIs (0, 0.01, 0.1, 1, and 10) and six time points (0∼120 min at 20-min intervals) across three phage-bacterium systems: T1- E. coli ATCC 11303, T4- E. coli ATCC 11303, and T4- E. coli ATCC 25922.

Techniques: Infection

Journal: BMC Complementary Medicine and Therapies

Article Title: Zingiber officinale -mediated zinc oxide nanoparticles: antimicrobial activity against multidrug-resistant bacteria

doi: 10.1186/s12906-026-05281-x

Figure Lengend Snippet: Antimicrobial effects of Z. officinale ethanolic extract, Z. officinale -ZnO NPs and ZnO NPs (unloaded) were assessed by disc diffusion method. Data represented as mean ± SEM

Article Snippet: Furthermore, the antimicrobial activities of zinc oxide nanoparticles, Z. officinale extract, and Z. officinale –mediated ZnO NPs were evaluated against pathogenic microorganisms, including Bacillus cereus ATCC 7064, methicillin-resistant Staphylococcus aureus (MRSA), Enterococcus faecalis ATCC 29212, Listeria monocytogenes Scott A ATCC 49594, Uropathogenic Escherichia coli UTI89, Pseudomonas aeruginosa ATCC 27853, and carbapenem-resistant Klebsiella pneumoniae strains CRKP-239, CRKP-682, and CRKP-692.

Techniques: Diffusion-based Assay, Inhibition

Journal: bioRxiv

Article Title: RSM01, an extended half-life RSV monoclonal antibody with a high barrier to resistance

doi: 10.64898/2026.02.04.703721

Figure Lengend Snippet: Growth kinetics of parental TPP RSV-A2 and B1 and the derived MARMs. HEp-2 cells were inoculated at an MOI of 0.01 TCID 50 /cell. The cultured supernatant was sampled twice daily for four days and viral growth was assessed using a TCID 50 assay. RSV-A2 MARMs ( A-C ) and RSV-B1 MARMs ( D-F ) show similar growth to their parental TPP strains, with the exception of RSM-3 ( D ), which shows delayed and lower titre growth. MARMs, monoclonal antibody resistant mutants; MOI, multiplicity of infection; RSV, respiratory syncytial virus; TCID 50 , half-maximum tissue culture infective dose.

Article Snippet: Master stocks of RSV-A2 (ATCC VR-1540) and RSV-B1 (B WV/14617/85, VR-1400) were triple plaque purified in HEp-2 cells and propagated for a total of 5 and 8 passages, respectively, before use as parental strains.

Techniques: Derivative Assay, Cell Culture, Infection, Virus