Decoding risk of antibiotic resistance in Nha Trang waters

Fish cage farming areas (A) and groupers (B) sampled for antibiotic resistance research in Nha Trang waters

Antibiotic-resistant bacteria have become a global medical challenge, not limited to hospitals or residential communities. Increasing evidence shows that resistance genes are also prevalent in natural environments, particularly coastal areas affected by aquaculture, urbanisation, and waste discharge. As a prominent coastal region with both thriving tourism and active aquaculture, Nha Trang Bay is a critical site for assessing the presence and distribution of antibiotic-resistant bacteria in Vietnam’s marine environment.

Since 2021, USTH scientists, in collaboration with CNRS, have implemented the project “Distribution of antibiotic resistance genes in marine bacteria and fish gut microbiota in Nha Trang Bay” (Code: QTFR01.01/21-22), led on the Vietnamese side by Dr. Nguyen Quang Huy (USTH).

Dr. Nguyen Quang Huy with Vietnamese colleagues and Dr. Jean-Christophe Auguet (MARBEC – CNRS), the French lead investigator, during a field sampling mission

According to Dr. Nguyen Quang Huy, Nha Trang Bay was chosen for its rich marine ecosystem and increasing pressure from coastal economic activities. With over 2,000 aquaculture farms and a population of half a million, the area records high antibiotic usage, including drugs classified by the World Health Organization (WHO) as “important” and “critically important”. Results show that Gram-positive bacteria resisted up to 60% of tested antibiotics, particularly rifampicin (93%) and tetracycline (80.7%). Alarmingly, Gram-negative bacteria resisted up to 80% of antibiotics, with resistance to piperacillin reaching 93.3%.

These figures reflect the real risk of antibiotic resistance in the marine environment and the urgent need for effective monitoring and control measures. The research team hopes the findings will provide a vital scientific basis for developing policies to manage antibiotic use in the fisheries sector and protect the health of coastal communities.

Map of sampling sites in Nha Trang Bay

Control area (R1–R4); Urban area (U1–U4); Aquaculture area (F1–F4)

Another significant finding was the antibiotic resistance of common bacterial species such as Escherichia coli, Klebsiella pneumoniae, Aromonas spp., and Vibrio spp. These strains showed high resistance to major antibiotic groups such as beta-lactams and tetracyclines, commonly used in both human healthcare and livestock farming.

The results of bacterial isolation on selective media (A), antibiotic susceptibility testing (B), and resistance patterns of pathogenic Enterobacteriaceae strains (C)

Dr. Nguyen Quang Huy further noted that the multi-antibiotic resistance (MAR) index of isolated strains exceeded the global average, especially in the dry season, when environmental factors like salinity, temperature, and waste discharge more strongly affect microbial populations.

The team also detected numerous antibiotic resistance genes in seawater, including those typically found in hospital pathogens – a sign that resistance genes from medical or agricultural sources are indeed spreading into natural environments. The researchers successfully developed a real-time multiplex PCR protocol to rapidly detect common resistance genes, enhancing environmental monitoring and providing early warnings of resistant bacteria spread.

Quantification of resistance genes by sample type and sediment (A), heatmap showing resistance gene distribution (B), and comparative analysis by sampling site and sample type (C)

The project supported the training of three bachelor’s degree graduates and one PhD candidate scheduled for defence in November 2025. It also strengthened collaboration between VAST institutes such as the Institute of Oceanography and the Institute of Biology and leading French research institutions including IRD and CNRS.

The results have been published in Regional Studies in Marine Science (SCIE, Q2), detailing the presence of multidrug-resistant Enterobacteriaceae strains and antibiotic resistance genes found in Nha Trang Bay. Another paper, published in the Vietnam Journal of Science and Technology (SCOPUS), introduced the initial multiplex PCR protocol – a potential tool for rapid monitoring of environmental resistance genes. Findings were also presented at the 2024 National Biotechnology Conference and shared in the VAST2 journal to reach the domestic scientific community.

Bui Duc Thinh, a student representative of the research team, presents project results at the 2024 National Biotechnology Conference in Hue City

This research not only recorded a diverse presence of bacterial strains but also offered deeper insights into the spread and potential dispersal of resistance genes in coastal ecosystems. It provides an important scientific basis for formulating policies and regulations to better control the spread of resistant agents in the marine environment, thereby safeguarding biosecurity and promoting the sustainable development of Vietnam’s fisheries sector.

Building on this foundation, the team aims to conduct deeper metagenomic analyses, clarify the transmission chain of resistant bacteria between environment–animals–humans in aquaculture, and expand domestic and international cooperation to develop early-warning models and effective resistance monitoring systems – for a safe, sustainable, and resilient marine ecosystem in the face of global challenges.

Translated by Phuong Huyen
Link to Vietnamese version