Library · Biology & lab methods
What Bacterial Resistance & Antibiotic Assays got wrong, from 18 theses
Summary written by a model from the records below: The records describe experimental and analytical challenges encountered across bacterial culture, susceptibility testing, and resistance characterization. Methodological failures stem from reporter detection limits, solid media artifacts, physical testing vessel constraints, and confusion between transient phenotypic tolerance and true genetic resistance. These records come from graduate theses, 2021 to 2026, each labeled with its degree where the repository states it, and each links to its thesis. They were extracted by language models reading the full text, so treat each as a lead to read, not a verdict.
Plus 8 problems the authors left open, listed at the end.
Failure modes, by theses reporting them
Select a mode to jump to its records.
Optical and fluorescent viability assays fail due to low sensitivity or probe signal artifacts
Spectrophotometric absorbance and colorimetric dyes failed to detect low-biomass cultures or distinguish viability states due to extracellular matrix interference and insufficient cell densities. Fluorescent reporters and aptamer dye systems also failed to produce detectable signals when challenged with antimicrobial agents.
Considered and rejected
Considered and rejected: Rejected relying on optical density (OD600) for bacterial growth quantification because turbidity from EPS inflated absorbance without corresponding to viable cell replication
An Evaluation of Enriched Aerobic Bacterial Communities Capable of Biodegrading TCE Under Different pH and Temperature · Texas State University · Master's
Tried and failed
incorporating viability dyes in optical scatter assays applied to bacterial viability testing. Outcome: worse than baseline. Reason: Viability dye addition caused unexplained reduction in optical scatter distance between viability states.
Probabilistic Methods For Rapid Characterization Of Complex Biological Samples · Georgia Tech · PhD
Tried and failed
optical density and colorimetric viability assays applied to low-biomass liquid microbial cultures. Outcome: no signal. Reason: optical density and resazurin assays lacked sensitivity to detect bacterial concentrations below 10^3 CFU/ml
Pseudomonas aeruginosa in the era of modulator therapies for cystic fibrosis · Imperial · Doctorate
Tried and failed
reactive oxygen species fluorescent reporter assays applied to antibiotic susceptibility testing. Outcome: no signal. Reason: failed to produce discernible fluorescence changes in response to bacteriostatic or bactericidal agents
Probabilistic Methods For Rapid Characterization Of Complex Biological Samples · Georgia Tech · PhD
Tried and failed
low-inoculum fluorogenic assay for antimicrobial resistance detection applied to bacterial resistance phenotypic screening. Outcome: no signal. Reason: insufficient starting cell density prevented detectable enzyme activity and resistance expression under antibiotic pressure
Detection of Antibiotic Resistance in Enterococcus spp. by Growth Kinetics Measurements in the Presence of Vancomycin Using the Detection System from TECTA-PDS · Queen's University · Master's
Considered and rejected
Considered and rejected: Discarded Pepper530 RNA aptamer/HBC dye system due to lack of detectable fluorescence signal in in vivo bacterial trials
A synthetic biology toolbox for electrical control of gene expression · Imperial · PhD
Solid media and agar diffusion assays fail from physical desiccation, matrix binding, or improper inoculum densities
Agar plates suffered from desiccation and fungal contamination during prolonged evolution experiments, while cationic antimicrobial peptides bound to anionic agar components and lost activity. Furthermore, disk diffusion and colony plating failed to form clear inhibition zones or colonies when inoculum levels were inappropriate or formulations lacked diffusion.
Tried and failed
large-scale agar plate gradient assay applied to bacterial lineage tracking and evolution. Outcome: unstable. Reason: Severe microbial and fungal contamination combined with rapid agar desiccation during incubation at 37°C.
Tried and failed
serial dilution colony forming unit plate count applied to bacteriocin sensitive bacterial isolates. Outcome: no signal. Reason: cultures failed to form colonies past early dilutions despite visible turbidity
Isolation, characterization, and potential clinical application of the M1-Pseudomonas aeruginosa pyocin · Texas Tech · Master's
Considered and rejected
Considered and rejected: Rejected agar-based susceptibility testing for streptococcins because interactions between cationic antimicrobial peptides and anionic agar components substantially reduce activity, adopting broth microdilution instead.
Genomic and experimental investigations into pneumococcal bacteriocins and their role in competition · Imperial · PhD
Tried and failed
standard disk diffusion antimicrobial susceptibility testing applied to weak food-grade antimicrobials against bacteria. Outcome: no signal. Reason: standard clinical inoculum density was too high to produce visible zones of inhibition for weak antimicrobials
Tried and failed
agar disk diffusion assay for antimicrobial susceptibility applied to acidic antimicrobial compounds against bacterial strains. Outcome: no signal. Reason: the specific antimicrobial formulations completely failed to produce zones of inhibition on agar plates
Assays conflate transient phenotypic tolerance or persisters with stable genetic resistance
Re-isolation from inhibition zones and baseline tolerance profiling failed to capture heritable resistance because surviving cells exhibited transient tolerance rather than genetic mutations. Standard plate counts and starvation media similarly skewed resistance frequencies by triggering non-genetic persistence and survival responses.
Tried and failed
predicting evolutionary tolerance from baseline phenotypic classification applied to bacterial minimum inhibitory concentration evolution. Outcome: no signal. Reason: Baseline tolerance categories showed no significant association with parent, passaged, or adapted resistance levels
Considered and rejected
Considered and rejected: Standard practice of counting all colonies growing on antibiotic-supplemented agar plates as true resistant mutants, rejected because it conflates transient persisters with genetic mutants and skews resistance frequencies higher
UNDERSTANDING RESISTANCE AND PERSISTENCE OF MYCOBACTERIUM ABCESSUS TO COMMON CLINICAL DRUGS TO PROPOSE AN OPTIMIZED TREATMENT REGIMENT · Johns Hopkins · Master's
Considered and rejected
Considered and rejected: Rejected using PBS for competitive survival assays because 2-hour incubation in minimal media induced robust starvation-mediated antibiotic tolerance in both strains.
THE CONTRIBUTIONS OF THE OMPF AND OSMB GENES IN PROMOTING YERSINIA PSEUDOTUBERCULOSIS SURVIVAL DURING DOXYCYCLINE EXPOSURE · Johns Hopkins · Master's
Genotypic resistance profiling and fixed critical thresholds fail to predict phenotypic susceptibility
Unsupervised clustering models failed to generalize across sequence populations, and bacterial isolates carrying complete resistance genes still displayed phenotypic susceptibility in vitro. Fixed critical concentration breakpoints in automated liquid cultures also missed low-level resistance driven by non-standard target mutations.
Tried and failed
density-based clustering with dimensionality reduction applied to bacterial genomic sequence resistance prediction. Outcome: did not generalise. Reason: failed out-of-population generalisation and achieved consistently lower accuracy than supervised baselines
Evaluation of machine learning algorithms for predictive modelling of antibiotic resistance using genomic and spatiotemporal data · Imperial · PhD
Tried and failed
genotypic prediction of antimicrobial resistance phenotype applied to bacterial pathogen susceptibility testing. Outcome: no signal. Reason: isolate carried a full resistance gene on its chromosome but exhibited phenotypic susceptibility in vitro
Antimicrobial resistance in the microbiome of feedlot watering bowls and bovine respiratory disease associated pathogens. · Saskatchewan · Master's
Tried and failed
automated liquid culture phenotypic susceptibility testing applied to detecting bacterial antibiotic resistance mutations. Outcome: did not generalise. Reason: critical concentration thresholds fail to detect low-level resistance conferred by specific non-standard target mutations
Improving diagnostic approaches in extensively and multidrug resistant tuberculosis: new diagnostic tools and repurposing drugs against X/MDRTB · Imperial · PhD
Assay vessels and biological sample matrices interfere with bacterial growth and dynamic antibiotic exposure
Testing directly in undiluted biological fluids such as pure urine lowered susceptibility testing accuracy compared to diluted media conditions. Additionally, physical apparatus such as Transwell inserts and standard microtiter plates directly inhibited cell growth or prevented the dynamic media exchange required for persistence assays.
Lost to a baseline
Pure urine inoculation at 10^8 CFU/mL resulted in lower AST accuracy across all antibiotics/dyes than 10^7 CFU/mL in 10% urine with 90% media.
DEVELOPMENT OF LOW-COST, MICRO-VOLUME ANTIMICROBIAL RESISTANCE ASSAYS FOR PATHOGENIC BACTERIA · Cornell · PhD
Considered and rejected
Considered and rejected: Rejected using Transwell membrane inserts during bacterial efficacy assays because inserts alone inhibited bacterial growth and interfered with efficacy readings
NANOMEDICINES FOR TREATMENT OF OTITIS MEDIA · Cornell · PhD
Considered and rejected
Considered and rejected: Rejected 96-well micro-well titer plates for persistence screening due to non-adherence of bacteria and the inability to dynamically exchange media during antibiotic treatment and washout
Left open by the authors
Problems the authors named and did not get to.
Left open
Investigate the biological mechanisms causing pure-culture skim milk broth growth parameters to overestimate bacterial spoilage rates in HTST fluid milk. Blocker: Requires wet lab microbiological experiments and biological assays to determine mechanistic causes of growth differences
STRATEGIES TO IMPROVE THE SHELF LIFE OF FLUID MILK FROM BUSINESS IMPACTS TO SUSTAINABILITY · Cornell · PhD
Left open
Integrate cell counts, cellular activity measurements, and antimicrobial resistance gene analysis in drinking water distribution system biofilms. Blocker: Requires physical wet-lab biofilm reactor experimentation and microbiological assays
Investigating the impacts of sub-inhibitory concentrations of ciprofloxacin on microbial abundance and diversity in a multi-species groundwater sourced drinking water biofilm · Queen's University · Master's
Left open
Monitor conjugative plasmid spread across multispecies biofilm communities under sub-inhibitory antibiotic exposure. Blocker: Requires a microbiological wet lab, bioreactor setup, and live multispecies biofilm communities.
Effect of sub-inhibitory antibiotic exposure on antimicrobial resistance of river biofilm microbial communities · Saskatchewan · Doctorate
Left open
Resolve the discrepancy with the Carballido-López group regarding MreB filament velocity changes across varying nutrient conditions. Blocker: Requires wet lab experiments with TIRF microscopy imaging of bacterial strains under different nutrient conditions.
Regulation of Cell Wall Synthesis and Role of Surface Sensing in Bacillus Subtilis · Harvard · PhD
Left open
Investigate why M1-sensitive Pseudomonas aeruginosa strains CF710 and CF753 fail to grow properly during serial dilution plate counts. Blocker: Requires a wet lab, bacterial cultures (CF710, CF753), and microbiological assay experiments
Isolation, characterization, and potential clinical application of the M1-Pseudomonas aeruginosa pyocin · Texas Tech · Master's
Left open
Measure dynamic contact angle and range expansion changes in bacterial colonies under varying nutrient levels and surface properties. Blocker: Requires a wet lab and white light interferometry equipment to culture and image live bacterial biofilms under dynamic conditions.
Biophysical basis of bacterial colony growth · Georgia Tech · PhD
Left open
Investigate the effects of DO, pH, ions, and TOC on nanoparticle combination disinfection efficacy using wet-lab batch testing. Blocker: Requires a microbiological wet lab, bacterial cultures (E. coli), water quality instrumentation, and nanoparticle handling facilities.
Impact of Low-Levels of Silver, Zinc and Copper Nanoparticles on Bacterial Removal and Potential Synergy for Point-of-Use Water Treatment Solutions · Carleton University · Master's
Left open
Apply Kirby-Bauer disk diffusion assays using antimicrobial interventions to Salmonella, Listeria monocytogenes, and bacterial cocktail mixtures. Blocker: Requires wet-lab microbiology facilities, bacterial strains (Salmonella, Listeria), and antimicrobial testing reagents.
Who has worked on this
Authors of the public theses cited on this page, most-cited first.
- Ellen Mary Margaret Robinson · Texas Tech · PhD · 2026
The Response of six non-O157 Pathogenic E coli Serotypes compared with E. coli O157:H7 treated with three different commonly used antimicrobial interventions used in Meat and Poultry using the Kirby B - Joseph Clayton Richardson · Georgia Tech · PhD · 2022
Probabilistic Methods For Rapid Characterization Of Complex Biological Samples - Chad Evans · Texas Tech · Master's · 2022
Isolation, characterization, and potential clinical application of the M1-Pseudomonas aeruginosa pyocin - John Andrew King · Imperial · Doctorate · 2025
Pseudomonas aeruginosa in the era of modulator therapies for cystic fibrosis - Matthew Seibel · Johns Hopkins · Master's · 2025
UNDERSTANDING RESISTANCE AND PERSISTENCE OF MYCOBACTERIUM ABCESSUS TO COMMON CLINICAL DRUGS TO PROPOSE AN OPTIMIZED TREATMENT REGIMENT - Xiaojing Ma · Cornell · PhD · 2024
NANOMEDICINES FOR TREATMENT OF OTITIS MEDIA - Aawaz Raj Pokhrel · Georgia Tech · PhD · 2024
Biophysical basis of bacterial colony growth - Samantha Bolten · Cornell · PhD · 2024
Enhancing Understanding of Bacterial Pathogens in Fresh Produce and Dairy Supply Chains: Insights into Population Dynamics, Sanitizer Tolerance, Persistence, and Transmission - Alicia Climent Catala · Imperial · PhD · 2024
A synthetic biology toolbox for electrical control of gene expression - Joseph Ball · Texas State University · Master's · 2024
An Evaluation of Enriched Aerobic Bacterial Communities Capable of Biodegrading TCE Under Different pH and Temperature - Sylvia Katherine Hurlimann · Harvard · PhD · 2023
Regulation of Cell Wall Synthesis and Role of Surface Sensing in Bacillus Subtilis - Benjamin Jeffrey · Imperial · PhD · 2023
Evaluation of machine learning algorithms for predictive modelling of antibiotic resistance using genomic and spatiotemporal data
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