🦠 microbiology

Genomic Evidence of Multidrug-Resistant Salmonella in Wild Waterbirds from High-Andean Lakes of Ecuador

This study reveals that wild waterbirds in Ecuador's high-Andean lakes serve as reservoirs and potential dispersers of multidrug-resistant *Salmonella* strains, specifically *S. Infantis* and *S. Newport*, which likely originated from poultry production systems and pose significant public health risks under a One Health framework.

Original authors: Reyes, N., Vinueza-Burgos, C., Medina-Santana, J., Ishida, M. L., Sauders, B. D., Anchatuna, D., Luzuriaga-Neira, N.

Published 2026-04-11

📖 4 min read☕ Coffee break read

CC BY 4.0

Original authors: Reyes, N., Vinueza-Burgos, C., Medina-Santana, J., Ishida, M. L., Sauders, B. D., Anchatuna, D., Luzuriaga-Neira, N.

Original paper licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). ⚕️ This is an AI-generated explanation of a preprint that has not been peer-reviewed. It is not medical advice. Do not make health decisions based on this content. Read full disclaimer

🌊 The Big Picture: A "One Health" Mystery

Imagine the world as a giant, interconnected neighborhood. In this neighborhood, humans, farm animals (like chickens), and wild animals (like birds) all share the same water, air, and food sources. This study is like a neighborhood watch report that discovered a hidden danger: super-bugs (bacteria that can't be killed by normal medicine) are moving freely between our farms and the wild.

The researchers looked at wild waterbirds living in three high-altitude lakes in the Ecuadorian Andes. They wanted to see if these birds were carrying Salmonella (the bacteria that causes food poisoning) and, more importantly, if that bacteria was "super-resistant" to antibiotics.

🔍 The Investigation: Catching the Culprits

The team went to three lakes: Yahuarcocha, Yambo, and Colta.

The Trap: They didn't hurt the birds. Instead, they used flashlights at night to gently catch them, took a tiny sample of their droppings (poop), and let them go immediately.
The Result: Out of 134 birds they checked, only 5 were carrying Salmonella.
The Location: Interestingly, all 5 positive birds were found at Lake Yahuarcocha. This lake is the most "stressed" of the three; it's surrounded by cities, farms, and tourists, making the water nutrient-rich but also dirty. The other two lakes, which are more remote, had zero positive cases.

The Analogy: Think of the birds as canaries in a coal mine. Just as miners used canaries to detect toxic gas, these birds are acting as early warning signs. The fact that they found the bacteria in the most polluted lake suggests the environment there is contaminated.

🦠 The Suspects: The "Super-Bugs"

The bacteria found were mostly Salmonella Infantis.

The Bad News: Three of the five birds carried a version of this bacteria that is Multidrug-Resistant (MDR).
What does that mean? Imagine the bacteria has a super-shield. If you try to attack it with a standard antibiotic (like a sword), the shield blocks it. These specific bacteria were resistant to nine different types of antibiotics, including the heavy-duty ones used in hospitals.
The Weapon: The bacteria carried a special "backpack" called a plasmid (specifically a pESI-like plasmid). This backpack is like a Swiss Army Knife of resistance, holding all the tools needed to survive different antibiotic attacks.

🔗 The Connection: How Did They Get There?

This is the most critical part of the study. The researchers didn't just look at the birds; they compared the bird bacteria to bacteria found in chickens, pigs, humans, and supermarket environments.

The DNA Match: They used a high-tech genetic scanner (like a fingerprint reader) to compare the bird bacteria with others.
The Discovery: The bacteria in the wild birds were genetically almost identical to the bacteria found in poultry farms (chickens). They were so similar that they differed by only a tiny number of genetic "typos" (SNPs).
The Conclusion: The wild birds didn't catch this from nature. They caught it from us.

The Analogy: Imagine the bacteria as a famous celebrity. The study found that the "celebrity" hanging out in the wild lake (the bird) is wearing the exact same outfit and has the same DNA as the "celebrity" working at the local chicken farm. It's clear the bird didn't just meet the celebrity by chance; the celebrity traveled from the farm to the lake, likely through contaminated water or food.

🚨 Why Should We Care?

The Spillover Effect: The study proves that bacteria from our industrial farms are "spilling over" into the wild. The birds are acting as messengers, carrying these super-bugs from the farm to the lake, and potentially to other animals or humans who visit the lake.
The One Health Framework: You can't separate human health, animal health, and environmental health. If we overuse antibiotics on farms, we create super-bugs. These bugs don't stay on the farm; they swim, fly, and walk into the wild, making the whole ecosystem dangerous.
The Lake as a Mirror: Lake Yahuarcocha is a mirror reflecting our impact. The more we pollute and farm nearby, the more we see these dangerous bacteria in the wildlife.

💡 The Takeaway

This paper is a wake-up call. It shows that wild birds are not just innocent bystanders; they are active participants in the spread of antibiotic resistance. They are picking up "super-bugs" from our farms and carrying them into nature.

To stop this, we need to treat human, animal, and environmental health as one single team. If we don't fix how we use antibiotics on farms, we risk creating a world where common infections become untreatable, and our wild neighbors are the ones carrying the warning signs.

1. Problem Statement

Public Health Context: Salmonella spp. is a leading cause of foodborne illness globally. While agricultural animals are primary reservoirs, wild birds in anthropogenically impacted ecosystems can act as reservoirs and dispersers of Salmonella and antimicrobial resistance genes (ARGs).
Knowledge Gap: There is limited understanding of the prevalence, genomic characteristics, and transmission dynamics of multidrug-resistant (MDR) Salmonella in wild aquatic birds within high-altitude Andean ecosystems in South America, particularly in relation to local poultry production systems.
Objective: To evaluate the occurrence of Salmonella in wild aquatic birds across three high-Andean lakes in Ecuador and to characterize the isolates phenotypically and genomically to determine sources and transmission pathways.

2. Methodology

Study Sites: Three high-Andean lakes in Ecuador: Yahuarcocha (2,210 m), Yambo (2,560 m), and Colta (3,310 m). Yahuarcocha was noted for significant eutrophication due to urban and agricultural runoff.
Sampling:
- Period: October 2017 and March 2018.
- Subjects: 134 fecal samples collected from 10 species of resident and migratory waterbirds (e.g., Andean Coot, Neotropical Cormorant).
- Technique: Night capture using spotlight distraction; samples collected from birds held in ornithological bags.
Laboratory Analysis:
- Isolation: Salmonella isolation following ISO 6579-1:2017.
- Phenotyping: Antimicrobial susceptibility testing (AST) via Kirby-Bauer disk diffusion against 12 antibiotic classes (including beta-lactams, aminoglycosides, quinolones, etc.).
- Genomics:
  - Whole-genome sequencing (WGS).
  - Bioinformatics: Quality control and assembly via EnteroBase; Multi-Locus Sequence Typing (MLST) and core-genome MLST (cgMLST); SNP-based phylogenetic analysis.
  - Resistance/Virulence: Identification of ARGs using AMRfinderPlus and ResFinder; virulence factors via VFDB; plasmid identification via Platon and BLAST.
  - Statistical Analysis: Principal Component Analysis (PCA) and phylogenetic tree construction (SNP-based) to assess genetic relatedness with isolates from poultry, humans, and other environmental sources.

3. Key Results

Prevalence:
- Overall prevalence was 3.73% (5/134 samples).
- 100% of positive samples originated from Yahuarcocha Lake (the most eutrophic site).
- Positive species: Fulica ardesiaca (Andean Coot, n=4) and Phalacrocorax brasilianus (Neotropical Cormorant, n=1).
Serotyping and Genotyping:
- Serovars: Salmonella Infantis (n=4) and Salmonella Newport (n=1).
- Sequence Types (ST): S. Infantis belonged to ST32; S. Newport to ST45.
Antimicrobial Resistance (AMR):
- Phenotype: Three S. Infantis isolates were Multidrug-Resistant (MDR), resistant to $\ge$ 3 classes (beta-lactams, aminoglycosides, tetracyclines, sulfonamides, trimethoprim, fosfomycin, chloramphenicol, and nitrofurans). S. Newport was susceptible to most drugs except gentamicin and nitrofurantoin.
- Genotype: The MDR S. Infantis isolates harbored a pESI-like plasmid (Accession CP092302.1) carrying a comprehensive resistance gene cluster:
  - blaCTX-M-65 (extended-spectrum beta-lactamase).
  - tet(A), floR, sul1, dfrA14, fosA3, and various aminoglycoside-modifying enzymes.
  - Mutations in nfsA and nfsB genes conferred nitrofurantoin resistance.
Genomic Epidemiology:
- PCA & Phylogeny: Wild bird isolates clustered tightly with poultry-associated strains (broilers, layers, feed, and farm environments).
- Genetic Distance: Pairwise SNP analysis showed low divergence ( $\le$ 10 SNPs) between wild bird isolates and poultry/human isolates, indicating a shared transmission network.
- Source Attribution: The data suggests a "spillover" event from intensive poultry production systems into the wild bird population, likely mediated by contaminated water or food resources in Yahuarcocha Lake.

4. Key Contributions

First Genomic Characterization: Provides the first genomic evidence of MDR Salmonella (specifically the pESI-like plasmid) in wild aquatic birds in the Ecuadorian Andes.
One Health Evidence: Demonstrates a clear genetic link between agricultural (poultry) reservoirs and wild wildlife, confirming that environmental contamination drives the dissemination of resistance genes into natural ecosystems.
Plasmid Tracking: Identifies the pESI-like plasmid (IncI1 group) as the vector for MDR in these isolates, highlighting its role in the global success of S. Infantis.
Ecological Sentinel Validation: Confirms wild aquatic birds as effective bio-indicators of environmental health and anthropogenic pollution (specifically antibiotic resistance) in high-altitude wetlands.

5. Significance

Public Health Risk: The presence of MDR Salmonella in wild birds poses a risk for the re-introduction of resistant pathogens into human and domestic animal populations, creating a cyclical transmission loop.
Environmental Impact: Highlights the role of eutrophication and agricultural runoff in Yahuarcocha Lake as a catalyst for pathogen transmission at the wildlife-livestock-human interface.
Policy Implications: Supports the need for a One Health approach to monitor and control antimicrobial use in agriculture to prevent the environmental spread of resistance genes. It underscores the necessity of integrating wildlife surveillance into national AMR monitoring programs.

Conclusion: The study concludes that wild aquatic birds in Ecuador are not merely passive carriers but active participants in the transmission network of MDR Salmonella, likely acquiring these strains from nearby poultry operations and disseminating them across interconnected ecosystems.