Untreated sewage in Galápagos creates antibiotic-resistant bacteria reservoirs

Scientists arrived at the Galápagos Islands with a mobile laboratory small enough to fit on a boat, and what they found in the water around San Cristóbal was a problem that no one had fully mapped before: untreated sewage was creating breeding grounds for bacteria that no longer respond to antibiotics.

The research team spent two years sampling water at sixteen marine sites, two freshwater locations, and two municipal wastewater treatment facilities. They were looking for evidence of human sewage in an archipelago famous for its isolation and ecological fragility. What they discovered was systematic contamination. A human-specific fecal marker appeared consistently at Punta Carola Pipe, a major sewage outfall on the island. At that same location, and at sites like Laguna and Muelle de Pescadores, they found more than three thousand colony-forming units per milliliter of coliform bacteria—the kind of numbers you see in raw sewage, not in protected marine environments.

But the bacterial counts were only part of the story. When the researchers sequenced the DNA of the microbes they collected, they found something more alarming: the sewage-contaminated sites were reservoirs of antimicrobial resistance genes. These are the genetic instructions that allow bacteria to survive drugs that should kill them. The genes conferring resistance to tetracyclines, beta-lactams, and macrolides were abundant in the wastewater samples. When the team cultured and tested 183 coliform isolates from the environment, between thirty-eight and forty-two percent of them showed resistance to three or more classes of antibiotics—a condition called multidrug resistance.

Among the resistant bacteria were globally distributed, high-risk strains of E. coli that have been associated with serious infections in human populations. The researchers identified lineages designated ST10, ST58, ST69, and ST155. Many of these strains carried their resistance genes on plasmids—small loops of DNA that bacteria can share with one another, spreading resistance like a contagion. The analysis revealed evidence of recent plasmid exchange and genetic recombination, suggesting that resistance was not static but actively spreading and evolving in these coastal waters. Most concerning, three isolates showed resistance to meropenem, a carbapenem antibiotic that is often considered a last resort when other drugs fail.

The Galápagos archipelago is one of the world's most protected marine environments, a UNESCO World Heritage Site. Most of its islands remain uninhabited. But San Cristóbal and Santa Cruz have experienced rapid population growth and a surge in tourism. The islands lack adequate wastewater treatment infrastructure. Sewage flows directly into the ocean, and the currents, weather patterns, and local geography determine where the contamination spreads. Some recreational beaches showed low or sporadic human contamination, while others near the outfalls were heavily polluted.

The researchers used a portable sequencing technology called Oxford Nanopore to conduct their analysis on-site, avoiding the delays and costs of shipping samples to distant laboratories. They combined this with quantitative PCR assays that could detect fecal markers in real time and culture-based testing that revealed which bacteria were actually resistant to which drugs. This multimodal approach—molecular, genomic, and microbiological—gave them a complete picture of what was happening in the water.

The findings raise immediate concerns for both human and environmental health. The bacteria and resistance genes are not confined to the sewage outfalls. They are dispersing through the marine ecosystem, potentially reaching fish and other organisms that people consume. The resistant bacteria could establish themselves in the island's microbial communities, persisting long after the sewage is treated. And for the people living on San Cristóbal, the contaminated water represents a direct exposure risk.

The study demonstrates that portable field laboratories can work in remote, resource-limited settings where traditional surveillance infrastructure does not exist. But it also underscores an urgent need: the Galápagos Islands need functional wastewater treatment systems. Without them, the archipelago will continue to serve as a reservoir and incubator for multidrug-resistant bacteria, a problem that does not respect island boundaries.