Overview
Researchers from Macquarie University and the University of Sydney have identified a novel antibiotic resistance gene, designated mcr-12, in contaminated freshwater sediment in New South Wales. The discovery, published in Nature Communications, represents the first time any member of the mcr gene family has been found in a purely environmental setting outside of clinical, agricultural, or food-production contexts, and the first such discovery anywhere in the Southern Hemisphere. The gene was isolated from the bacterium Pigmentiphaga litoralis and confers resistance to polymyxins, specifically colistin, which is widely regarded as a last-resort antibiotic deployed when all other treatment options have failed.
What makes this finding particularly consequential is not merely the novelty of the gene itself, but the mechanism by which it persists and spreads in the natural environment. The research demonstrates that mcr-12 is carried on a mobile plasmid, designated pPLE30.2, which also encodes resistance to heavy metals including copper, zinc, and lead. This co-location means that heavy metal contamination, an extraordinarily common feature of legacy industrial sites, urban stormwater infrastructure, and mining-affected catchments across Australia, provides the selective pressure needed to maintain and propagate colistin resistance in sediments even in the complete absence of antibiotic exposure. The contaminated freshwater sediment is not a passive recipient of pollution; it is an active evolutionary environment generating clinically dangerous resistance traits.
For environmental professionals advising developers, local councils, industrial landholders, and transaction parties on contaminated land, this research introduces a fundamentally new biological risk pathway that existing assessment frameworks do not currently capture. The consequences reach well beyond regulatory compliance. They touch on public health, ecological risk, remediation cost-benefit analysis, and the scope of duty of care owed by site owners and their consultants.
Key details of the mcr-12 discovery and its mechanisms
The study isolated Pigmentiphaga litoralis from freshwater sediment samples collected at a site in New South Wales characterised by elevated concentrations of heavy metals consistent with industrial and urban stormwater runoff. Whole-genome sequencing revealed the presence of a previously uncharacterised gene within the mcr family, now designated mcr-12. This gene encodes a phosphoethanolamine transferase enzyme that modifies the lipid A component of bacterial lipopolysaccharide, reducing the binding affinity of colistin and rendering the antibiotic ineffective. The researchers confirmed full enzymatic functionality when the gene was expressed in surrogate host organisms, including strains of Escherichia coli and Klebsiella pneumoniae, two of the most clinically significant opportunistic human pathogens globally.
The mobility of mcr-12 is central to the public health significance of this finding. The gene resides on a conjugative plasmid, pPLE30.2, meaning it can be transferred horizontally between bacterial species through direct cell-to-cell contact, without the need for vertical inheritance. This is the same transfer mechanism responsible for the rapid global spread of earlier mcr variants, particularly mcr-1, which emerged in Chinese livestock in 2015 and was subsequently detected across more than 30 countries within two years. The researchers demonstrated successful conjugative transfer of pPLE30.2 from the environmental isolate to clinical pathogen strains under laboratory conditions, with retention of full colistin resistance in the recipient organisms.
Critically, the plasmid pPLE30.2 also carries a suite of heavy metal resistance determinants targeting copper, zinc, and lead. This genetic architecture creates a co-selection dynamic: when bacteria in contaminated sediment are exposed to elevated metal concentrations, any organism carrying pPLE30.2 gains a survival advantage, and the plasmid, along with its colistin resistance cargo, is maintained in the population. This means remediated metal concentrations that fall just within regulatory thresholds may still provide sufficient selective pressure to sustain resistance gene pools in residual contamination. The authors note that copper concentrations as low as those commonly detected in urban stormwater sediments can sustain this co-selection pressure, though the precise minimum effective concentrations require further investigation.
The broader mcr gene family now comprises twelve identified members. Prior to this discovery, all confirmed environmental detections had been linked to agricultural soils with documented histories of antibiotic or manure application, or to food-production supply chains with direct antibiotic use. The identification of mcr-12 in a freshwater sediment matrix with no direct antibiotic exposure history demonstrates for the first time that heavy metal pollution alone is sufficient to select for, and sustain, clinically relevant last-resort antibiotic resistance in the natural environment.
Australian context: NEPM 2013, ANZG 2018, and the gap this discovery exposes
Australian contaminated land assessments are primarily governed by the National Environment Protection (Assessment of Site Contamination) Measure 1999, as amended in 2013 (NEPM 2013). Schedule B1 of the NEPM 2013 provides Health Investigation Levels (HILs) and Ecological Investigation Levels (EILs) for a range of contaminants, including copper, zinc, and lead, expressed in mg/kg for soil and µg/L for groundwater. These thresholds are derived from toxicological endpoints relating to direct human health exposure and ecological toxicity, and do not account for the role those contaminants may play in selecting for or sustaining antimicrobial resistance genes in environmental matrices.
References and related sources
- Primary source: www.the-microbiologist.com
- researchgate.net
- labroots.com
- researchgate.net
- orcid.org
- ANZG Water Quality Guidelines
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This is an iEnvi Machete news summary. Prepared by iEnvi to summarise the source article for contaminated land, groundwater, remediation, approvals and site risk professionals.
Published: 22 Jul 2026
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