Antibiotic Resistance Gene Spread After Non-Antimicrobial Household Cleaning

Problem Statement

This experiment tests whether cleaning common household surfaces with non-antimicrobial products alters the abundance of antibiotic resistance genes (ARGs) or markers associated with horizontal gene transfer in surface-associated bacterial communities. The experiment measures gene prevalence only and does not assess pathogens, infection risk, or health outcomes.

Hidden Assumption Being Tested

Routine household cleaning using non-antimicrobial products does not meaningfully change the distribution or abundance of antibiotic resistance genes on surfaces.

Sampling Plan

  • Select three frequently touched household surfaces (e.g., kitchen countertop, bathroom sink, refrigerator handle).
  • For each surface, collect two samples:
    • T0 (Baseline): immediately before cleaning
    • T1 (Post-cleaning): 24 hours after cleaning
  • Clean surfaces once using a standard non-antimicrobial household detergent, following manufacturer instructions.
  • Swab a consistent 10 cm × 10 cm area using sterile pre-moistened swabs.
  • Preserve swabs on ice during transport and store at −20 °C until DNA extraction.

qPCR Targets

  • Antibiotic resistance genes: tetA, blaCTX-M, sul1
  • Horizontal transfer marker: intI1 (class 1 integron integrase)
  • Normalization gene: 16S rRNA
  • Published, validated primer sets must be used for all targets.
  • All reactions performed in triplicate with absolute quantification using standard curves.

Data Processing

  • Extract total DNA using a kit suitable for environmental surface samples.
  • Calculate normalized abundance for each gene:
    (gene copies) / (16S rRNA gene copies)
  • For each gene and surface, compute change:
    Δ = log10(T1 / T0)

Binary Signal Change Threshold

  • Negative Result: All genes on all surfaces change by less than ±0.5 log10 (no significant shift).
  • Positive Result: Any gene on any surface changes by ±0.5 log10 or more (≈ threefold change).

Explicit Non-Claims

  • No identification of pathogens or infectious organisms
  • No assessment of clinical infection risk or health outcomes
  • No measurement of microbial load or surface sterility
  • No determination of gene transfer mechanisms or causality
  • Results apply only to gene abundance and transfer-associated markers

Why This Matters

This experiment directly tests whether everyday cleaning practices can shift the genetic composition of surface-associated microbial communities in ways not captured by conventional cleanliness metrics. Any detected change challenges assumptions about the neutrality of routine cleaning with respect to resistance gene ecology.

Below the Edge: Connectivity-Controlled Persistence

Frozen Assumption

All regions of the system contribute to genetic persistence in proportion to their average properties, with no spatially connected subset able to disproportionately reweight antibiotic resistance gene abundance regardless of size or response rate.

Structural Decomposition

Persistence of antibiotic resistance genes on cleaned surfaces is governed by a heterogeneous distribution of local survival, recolonization, and horizontal gene transfer timescales. These timescales are spatially and functionally correlated through shared microenvironments, contact patterns, and surface topology. Local fast-response regions—ARG-bearing organisms or mobile genetic elements—may survive disturbance and dominate recolonization despite low overall abundance. System behavior is dictated not by mean biomass reduction, but by the weight and connectivity of the fastest persisting genetic tail.

Regime Boundary

The assumption holds only if fast-response ARG-bearing regions remain below the percolation threshold for system-spanning influence:

(fraction of fast-response ARG reservoirs) × (spatial or functional correlation length) < (percolation threshold)

Crossing this boundary enables a connected network of resistance gene persistence to dominate post-cleaning genetic composition, independent of total microbial reduction.

Failure Signature

A categorical shift in normalized ARG or integron marker abundance following a single non-antimicrobial cleaning event—observable as a ≥0.5 log10 change on any surface—indicating dominance of a connected fast-response genetic subset rather than proportional disturbance.

Disentitlements

  • ARG persistence can no longer be assumed to scale with total microbial load.
  • Non-antimicrobial cleaning cannot be treated as ecologically neutral with respect to resistance gene distribution.
  • Mean cleanliness metrics are invalid predictors of resistance gene dynamics.
  • Resistance enrichment can no longer be attributed solely to antimicrobial exposure.

Corrected Interpretation

System-scale persistence of antibiotic resistance genes following routine cleaning is controlled by the presence or absence of a percolating network of fast-response genetic reservoirs. When such regions survive and reconnect, these rare but connected domains—not average microbial reduction—govern post-disturbance genetic outcomes.