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Global distribution ofantimicrobial
resistance genes inaquaculture
Yuting Deng1,2, Aiping Tan1*, Fei Zhao1, Feifei Wang1, Hua Gong1, Yingtiao Lai1 and Zhibin Huang1
Abstract
Aquaculture has rapidly developed into one of the most fast-expanding food industries, providing an essential source
of protein for humanity worldwide. The rapid growth of the aquaculture industry is closely associated with the cru-
cial role of antimicrobials in the prevention and treatment of animal diseases. Nevertheless, the irrational utilization
of antimicrobials gives rise to the emergence of pathogen resistance, which poses a potential threat to human health
and environmental sustainability. This issue has garnered considerable attention from international organizations
and has escalated into a global public health crisis that requires urgent intervention. This paper undertakes a review
of the sources of antimicrobial resistance in aquaculture, drawing on data from Microbial Browser for Identification
of Genetic and Genomic Elements (MicroBIGG-E) and related literature. The characteristics and distribution patterns
of drug resistance genes in pathogenic bacteria of diseased aquatic animals and food-borne bacteria of contami-
nated aquatic products were elaborated in detail. The emergence of resistant aquatic bacteria is not solely attribut-
able to the utilization of antimicrobials in aquaculture, but rather is closely related to human social activities. Diverse
antimicrobial resistance genes related to tetracyclines, aminoglycosides, β-lactams, quinolones, sulfonamides,
and amphenicols that coexist in foodborne pathogens might contribute to multidrug resistance in aquaculture. This
review also evaluates the potential risks of antimicrobial resistance in aquaculture with respect to human health,
food safety, and ecological balance. Government entities, research institutions, and private companies are adopting
proactive measures and initiating specific strategies to alleviate the dissemination of antimicrobial resistance, thereby
enhancing human and animal health as well as ecological sustainability.
Keywords Aquaculture, Antimicrobials, Pathogen, Aquatic products, Resistance genes, Distribution
Introduction
Aquaculture represents one of the most promising
sectors within global food production [1]. In 2022,
global aquaculture production increased to 185 mil-
lion tons [2]. However, the global aquaculture indus-
try is encountering sustainability challenges, such as
environmental impacts, disease control, market insta-
bility, and extreme weather events. The transition
from semi-intensive to intensive farming practices,
alongside the application of antimicrobial agents for
disease management, are pivotal factors contributing
to the increase in aquaculture yield. In aquaculture
environments, antimicrobials are frequently present at
concentrations lower than those for therapeutic pur-
poses. This not only enhances the selection pressure
*Correspondence:
Aiping Tan
tap@prfri.ac.cn
1 River Fisheries Research Institute, Chinese Academy of Fishery Sciences,
Food and Agriculture Organization of the United Nations (FAO) Reference
Centre on AMR and Aquaculture Biosecurity, Key Laboratory of Fishery
Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong
Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable
Aquaculture, Guangzhou, Guangdong 510380, China
2 Key Laboratory of Aquatic Product Quality and Safety Control, Ministry
of Agriculture and Rural Affairs, Beijing 100141, China
Page 2 of 14
Dengetal. One Health Advances (2025) 3:6
for resistant bacteria in animals or the environment to
screen out resistant bacteria, but might also facilitate
the transfer of resistance genes among different spe-
cies of bacteria within aquatic ecosystems. It is now
well documented that antimicrobial resistance genes
(ARGs) and antimicrobial-resistant bacteria (ARB)
migrate from aquatic environments to terrestrial eco-
systems, potentially posing risks to human and animal
health [3].
Antimicrobial resistance (AMR) occurs as a result of
natural selection; however, the heavy use of antimicro-
bials and other influencing factors of modern human
life, accelerate the evolution of "silent" or "precur-
sor" resistance genes within bacteria. In addition to
a small number of bacteria with natural resistance to
certain drugs, the majority of bacteria develop resist-
ance mainly through changes in target sites, reduction
of bacterial outer membrane permeability, acquisi-
tion of active efflux systems, and production of inac-
tivated enzymes [4]. These resistance mechanisms do
not exist independently; instead, the level of bacterial
resistance is determined by their combined effects.
Genes that confer resistance spread from environmen-
tal bacteria via mobile genetic elements and are subse-
quently transferred to humans and animals, leading to
increased abundance, diversity, and mobility of resist-
ant bacteria [5].
Recently, the matter of AMR has drawn the atten-
tion of international organizations to jointly tackle the
global public health crisis. The United Nations Envi-
ronment Programme (UNEP) lists ARGs as the first of
six novel environmental pollutants. In 2022, to address
a variety of health threats, the World Health Organi-
zation (WHO), World Organization for Animal Health
(WOAH), Food and Agriculture Organization of the
United Nations (FAO), and UNEP co-issued the "One
Health" Joint Action Plan. It focuses on zoonotic epi-
demics, food safety risks, AMR, and the environment,
with the aims of improving human, animal, plant, and
environmental health while promoting sustainable
development [6]. Within the framework of the "One
Health" notion, the problem of AMR in aquaculture
should also be considered of great importance. In
this review, we aim to present the sources of AMR in
aquaculture, detailing the characteristics and distribu-
tion patterns of ARGs in diseased aquatic animals and
contaminated aquatic products, both domestically and
internationally. We also describe some of the strate-
gies that have been implemented, and offer additional
recommendations to alleviate the emergence of AMR
among aquatic bacterial populations.
Sources ofAMR inaquaculture
Antimicrobials used inaquaculture
Since the sulfonamides were introduced for disease con-
trol in the 1940s, significant progress has been made in
preventing and treating bacterial diseases in fish [7]. By
the 1950s, other antimicrobial agents in addition to the
sulfonamides, including tetracyclines, quinolones, and
aminoglycosides had become widely utilized for treating
infection and preventing diseases [8]. Despite the use of
oral feeding and immersion as the most effective admin-
istration methods, the researchers estimated that about
70–80% of antimicrobials are not absorbed by fish and
are eventually excreted into aquatic ecosystems via urine
or feces [9–11]. e irrational utilization of antimicrobi-
als will not only have an impact on the microorganisms
within the animal body and the environment, but also
exert huge antibiotic pressure on the microorganisms,
leading to the rapid development and dissemination
of AMR within the bacterial community [12]. Previous
studies have also reported large-scale epidemic infec-
tions caused by pathogens resistant to different classes
of antibiotics [13–15]. e issue of resistance in aquacul-
ture has also drawn the attention of international organi-
zations. In 2006, a joint meeting of WHO, FAO, and
WOAH was held to evaluate the consequences related to
utilitation of antimicrobials agents in aquaculture, high-
lighting the necessity of paying attention to the potential
risk of ARGs spreading from aquatic animals to humans
[16].
Wastewater fromurban rivers
Traditional aquaculture ponds are open water bodies
with nearby rivers as the primary source of water. Con-
sequently, urban rivers are considered as important
reservoirs for ARB and ARGs in aquaculture. With the
acceleration of urbanization and industrialization, large
quantities of wastewater from pharmaceutical factories,
hospitals, and farms are discharged into urban rivers,
which then become the main carrier for the spread of
ARGs and ARB [12, 17–19]. Aiming to evaluate AMR in
China’s Pearl River, Gao etal. [18] utilized metagenom-
ics to analyze global microbiome data, revealing that the
types of ARGs and ARB in the water and sediment of the
Pearl River were more diverse than those in other coun-
tries. Discharge of wastewater from sewage treatment
plants and landfills drives the epidemic of riverine bacte-
rial resistance, and the levels of resistance among bacte-
rial groups are highly correlated with human and animal
sources. Das Manas etal. [19] conducted a metagenomic
analysis of the surface water and sediments of Indian
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Dengetal. One Health Advances (2025) 3:6
rivers. eir results indicated that ARB in the environ-
ment mainly originated from Enterobacteriaceae, which
showed multidrug resistance to fluoroquinolones, sul-
fonamides, β-lactams, tetracyclines, aminoglycosides,
and other drugs. Using isolates from aquatic animals
and aquacultural environments, several studies have also
identified clinically significant genes that confer resist-
ance to various drugs, including extended-spectrum
β-lactamases (ESBLs) [20–22], carbapenem (blaNDM)
[23–25], colistin (mcr) [26, 27], tigecycline (tet[X]) [28,
29], vancomycin (vanA) [30, 31], and linezolid (optrA)
[32, 33]. Although these types of resistance genes are fre-
quently found in patient and hospital wastewater, there
is concern about their potential spread through rivers to
nearby ponds. e aquaculture environment may act as a
reservoir and transmission vector for clinically significant
resistant pathogens, thereby increasing the threat to pub-
lic health.
Sewage fromlivestock andpoultry farms
In addition to the direct administration of antimicro-
bials, integrated fish farming constitutes another criti-
cal source of AMR in aquaculture. From the 1990s to
the beginning of this century, a farming model based
on multi-utilization of livestock, poultry, and aquacul-
ture resources was popular in South China, South and
Southeast Asia, and Africa, with examples including
integrated pig-fish and duck/goose-fish farms [34–37].
Farmers typically constructed pig houses or duck/goose
sheds near ponds, utilizing the waste from the livestock
and poultry as organic fertilizer for fish cultivation [37].
By saving breeding space and feed costs, this produc-
tion mode increased the economic benefits of breeding
and was among the most economically efficient aqua-
culture models in the era of low breeding density and
limited antibiotic use [37]. However, the expansion of
large-scale livestock and poultry farming has gradu-
ally exposed the shortcomings of this model. Livestock
and poultry feces contain antibiotics excreted through
metabolism, as well as ARB carrying various ARGs.
Untreated fecal matter that is discharged directly into
ponds may affect the microbial community of aquatic
animals and aquaculture water bodies, potentially pol-
luting the ecological environment [12]. In a previous
study [38], we found that Aeromonas isolated from live-
stock/poultry-fish integrated farms were exhibited sig-
nificantly higher resistance to 13 antibiotics than those
isolated from non-integrated farms. Furthermore, we
identified class I integrons carrying diverse gene cas-
settes in resistant Aeromonas isolates from livestock-
fish integrated farms, implying that antibiotic usage
in livestock farming contributes to the dissemination
of multidrug resistance in aquaculture [34]. Since the
enactment of China’s most stringent environmental
protection legislation in 2017 [39], small-scale pig farms
in rural areas have been effectively prohibited, and inte-
grated pig-fish farming has gradually decreased. How-
ever, integrated waterfowl-fish farming is still common
in the Pearl River Delta region of Guangdong province.
e potential influence of ARB and resistance gene
pollution caused by this model requires more atten-
tion. e study revealed that total relative abundance
of ARG subtypes in the samples of duck-fish integrated
farms were significantly higher than those of freshwater
single farms, where Enterobacteriaceae was the main
host source of ARG [40–42].
Foodborne pathogen contamination ofaquatic products
Foodborne pathogens can contaminate aquatic prod-
ucts during havesting, transportation, processing, stor-
age, sales and other processes, thereby becoming the
source of the dissemination of various bacterial dis-
eases, and posing a potential threat to human health
and safety [43]. Consuming undercooked aquatic prod-
ucts can readily lead to food-borne poisoning, result-
ing in diarrhea, vomiting and fever. Hence, aquatic
foods are among the products that give rise to food-
borne bacterial diseases worldwide [44]. Bacteria com-
monly present in aquatic food including fresh aquatic
animals and processed products can be classified
into three categories: bacteria that naturally coexist
along with freshwater or marine aquatic animals (e.g.,
Aeromonas spp. and Vibrio spp.); environmental bac-
teria that exist with frozen foods (e.g., Listeria monocy-
togenes); and commensal or opportunistic pathogenic
bacteria that naturally inhabit in intestines of humans
or animals (e.g., Escherichia coli, Salmonella enterica,
Klebsiella pneumoniae, Campylobacter jejuni, and
Staphylococcus aureus) [44]. The occurrence of AMR
foodborne pathogens in aquatic products has steadily
increased worldwide in recent years [32, 43–45]. The
growing prevalence of S. enterica and E. coli strains
exhibiting resistance to “last-resort” antibiotics, such
as imipenem, polymyxin B, and tigecycline, is of great
concern [25, 26, 28, 44, 46].
Briefly, apart from the use of antimicrobial agents in
aquaculture, AMR of aquatic bacteria is also closely
related to human social activities involving families,
hospitals, pharmaceutical factories, and the farming,
processing, and transportation of livestock and poultry
[12, 47]. Antimicrobial agents are extensively utilized in
human and veterinary medicine, and then introduced
into the environment via human and animal excretion
or inadequately treated pharmaceutical waste [12].
e environment can facilitate the colonization and
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Dengetal. One Health Advances (2025) 3:6
infection of hosts by ARB, contributing to the evolution
and dissemination of both ARB and ARGs [47].
Distribution ofARB andARGs inaquaculture
Current situation
The intricate origins of AMR in aquaculture highlight
the diversity and complexity of ARGs. The majority
of ARGs found in human clinical and terrestrial ani-
mal isolates can also be identified in aquatic animals
and processed (frozen, dried, smoked, etc.) aquatic
products [25, 32]. To achieve a comprehensive under-
standing of the genetic information of human clini-
cal, animal, and foodborne pathogens worldwide,
the National Center for Biotechnology Informa-
tion (NCBI) has developed the Microbial Browser
for Identification of Genetic and Genomic Elements
(MicroBIGG-E) (https:// www. ncbi. nlm. nih. gov/ patho
gens/ micro bigge/) [48]. Featuring all bacterial isolates
and three categories of genes (AMR, stress response,
and virulence), this tool has become essential for uti-
lizing bacterial genomics to explore and compare the
global distribution and origin information of vari-
ous genes, and to comprehend the spread of AMR
worldwide [49]. For this review, we used the follow-
ing terms to search MicroBIGG-E for host sources of
pathogenic bacteria: "fish," "shrimp/prawn," "crab,"
and "shellfish/clam" as keywords, and "AMR" as filter
words. We found that, by 30th December 2024, 23,165
contigs related to drug resistance of aquatic animals
and products from 75 countries and regions had been
uploaded, of which 9689 contigs (1977 isolates) were
from fish, 8923 contigs (1620 isolates) were from
shrimp, 1925 contigs (263 isolates) were from crabs,
and 2448 contigs (519 isolates) were from shellfish.
Distribution ofARB inaquaculture
To examine the different host bacteria carrying ARGs in
various types of aquatic products, records were selected
through keyword searches of MicroBIGG-E. e results
showed that 4379 pathogenetic bacteria covering 58
bacterial taxa were identified in aquatic animals and
products. e predominant bacterial genera carrying
ARGs in different aquatic hosts are shown in Fig. 1.
Overall, the records uploaded to MicroBIGG-E were
mainly associated with Vibrio spp. (1896 isolates, 43.3%)
and Salmonella spp. (1382 isolates, 31.6%). Resistant
isolates of Vibrio spp. were mainly obtained from shell-
fish and shrimp, accounting for 409 isolates (78.8%)
and 855 isolates (52.8%), respectively. e predominant
resistant strains isolated from fish were Salmonella spp.
and Vibrio spp., with 716 isolates (36.2%) and 574 iso-
lates (29.0%), respectively, while those isolated from
crab were Salmonella spp. and Listeria spp., with 71 iso-
lates (27.0%) and 64 isolates (34.3%), respectively. e
higher number of resistance records related to Vibrio
spp. in the database is due to the natural coexistence
of this species with aquatic animals in aquatic environ-
ments, especially sea and brackish water [50]. In con-
trast, Salmonella spp. do not naturally inhabit aquatic
environments. e high detection rate of salmonella in
aquatic products could potentially be ascribed to the
contamination of offshore waters by human domes-
tic sewage and poor sanitary conditions in the aquatic
products market. [44].
Fig. 1 Analysis of the primary hosts of antimicrobial resistance genes (ARGs) across various aquatic animals and products based on data
from Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E)
Page 5 of 14
Dengetal. One Health Advances (2025) 3:6
Occurrence ofARGs inpathogens fromdiseased aquatic
animals
e growing prevalence of resistant bacterial patho-
gens constitutes a significant challenge for aquaculture,
restricting the attempts to control diseases in aquatic
animals [51]. To effectively manage quatic pathogens, it
is vitally important that we understand the occurrence
and distribution of their ARGs. e majority of bacte-
rial infections affecting aquatic animals are attributed to
Vibrio spp., Aeromonas spp., Streptococcus spp., Edwards-
iella piscicida, Photobacterium damselae, and Yersinia
ruckeri [52]. After filtering for "isolation source," we were
able to analyze a total of 3699 isolates of the aforemen-
tioned fish and shrimp pathogens for genotypic resistance
determinants. Although the genomic sequences from
MicroBIGG-E were limited, we found that these patho-
gens had diverse types of ARGs, with the number varying
from 1 to 13 types of ARGs in one strain. Table1presents
examples of ARGs identified in typical aquatic pathogens
from diseased animals. Comparing different pathogenic
species, the majority of strains of Aeromonas spp., Vibrio
parahaemolyticus, and P. damselae were found to carry
more than three classes of ARGs, making them prone to
contributing to multidrug resistance.
It is well documented that the genus Aeromonas dem-
onstrates resistance to several antimicrobials, suggest-
ing that certain drugs might be ineffective in controlling
infections caused by some Aeromonas species [22, 34].
Table 1 Examples of antimicrobial resistance genes (ARGs) identified in typical aquatic pathogens from diseased animals
Host
(species) Pathogen Genotype Number of
resistance genes
carrying
Isolation source Location Collection year Assembly No.
fish Aeromonas salmo-
nicida
aadA7, ampC,
aph(3’’)-Ib, aph(6)-
Id, blaCMY-2, blaOXA,
cphA, floR, mcr-3,
sul1, sul2, tet(A),
vat
13 sick fish Canada: New
Brunswick
2004 GCA_000786805.1
fish Aeromonas dhak-
ensis
ampC, blaOXA,
cphA, floR3, mcr-3,
qnrS2, sul1, sul2,
dfrA1, tet(A), vat
11 kidney, liver Vietnam 2018 GCA_031915045.1
fish Aeromonas veronii aadA1, blaOXA,
catB3, cphA, dfrB4,
sul1, tet(A), vat
8 kidney, liver Vietnam 2019 GCA_031914865.1
Fish
(Cyprinus carpio)
Aero-
monas hydrophila
blaOXA, cepH,
cphA1, mcr-3,
mph(A), tet(E)
6 liver USA: LA 2019 GCA_021356275.1
Fish
(Tiger grouper)
Vibrio vulnificus varG, catB, tet(35),
tet(34)
4 diseased fish Thailand: Song-
khla
2012 GCA_039833915.1
Fish
(Epinephelus
fuscoguttatus)
Vibrio alginolyticus blaCARB, catC,
tet(35), tet(34)
4 diseased fish Thailand: South-
ern part, Karabi
province
2013 GCA_026962575.1
freshwater fish Vibrio harveyi blaVHH, tet(35),
tet(34)
3 brain USA: Florida 2019 GCA_028991555.1
Shrimp
(Penaeus van-
namei)
Vibrio parahaemo-
lyticus
blaCARB-18, blaCTX-
M-14, catC, sul2,
tet(34), tet(35),
tet(E)
7 hepatopancreas China: Guang-
dong
2022 GCA_027277845.1
Shrimp
(P. vannamei)
V. harveyi blaVHH, tet(35),
tet(34)
3 diseased shrimp
lesion
Mexico 2005 GCA_000259935.1
fish Photobacte-
rium damselae
bla, catA2, qnrS,
aar-3, aadA16,
sul1, sul2, dfrA27,
tet(M), tet(B)
10 / China: Qingdao,
Shandong
2009 GCA_030169025.1
Fish
(Channa spp.)
Edwardsiella.
piscicida
ampC, mph(A),
catA1, catA2, sul1,
drfA12, tet(D)
7 / / 2019 GCA_030340645.1
Fish
(Salmo salar)
Yersinia ruckeri blaYRC 1 / Australia: Tas-
mania
2014 GCA_001883155.1
Fish
(Oreochromis spp.)
Streptococcus
agalactiae
tet(M) 1 fish organ Malaysia: Kuala
Lipis
2009 GCA_041728555.1
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Dengetal. One Health Advances (2025) 3:6
According to the MicroBIGG-E database, over 90% of
Aeromonas isolates from diseased fishes, including Aer-
omonas dhakensis, Aeromonas hydrophila, Aeromonas
veronii, and Aeromonas salmonicida, possess ARGs for
aminoglycosides, β-lactams, tetracyclines, and trimetho-
prim. β-lactam resistance genes with diverse genotypes
and subtypes are highly prevalent in Aeromonas strains,
and include oxa, cmy, aqu, mox, cphA, and ampC; some
of these are regarded as ESBL genes. e production of
ESBLs by aquatic pathogens may represent failed actions
of cephalosporins [53]. Interestingly, we also found that
only Aeromonas strains carried mcr-3, which encodes
a phosphoethanolamine transferase and contributes
to colistin resistance. In a previous study, Guo et al.
reported that the non-mobile colistin resistance (NMCR)
determinants NMCR-3, NMCR-4, and NMCR-5 located
on the chromosomes of Aeromonas are the progenitors of
mcr-3, mcr-5, and mcr-7 [54]. Aeromonas spp. are exten-
sively distributed in freshwater environments and fresh-
water aquatic animals, indicating that aquaculture may
facilitate the emergence and dissemination of novel colis-
tin resistance mechanisms in aquatic and terrestrial ani-
mals, thereby posing a potential threat to public health
and food safety [54, 55].
Another of the most common bacterial diseases that
affect various marine fish, shrimps, and shellfish is vibri-
osis. Several species of the Vibrionaceae, including V.
parahaemolyticus, Vibrio harveyi, Vibrio vulnificus, and
Vibrio alginolyticus,cause this disease [56]. e frequent
identification of resistant Vibrio strains has caused sub-
stantial economic losses to farmers around the world.
Unexpectedly, apart from V. parahaemolyticus, other
species of Vibrio were found to carry only a few geno-
types of ARGs. Tetracycline resistance genes are the
predominant class identified in Vibrio strains, among
which tet(34) and tet(35) are the main genotypes. ese
genes may enhance the activity of efflux pumps, protect
ribosomes and facilitate the inactivation of microbial
enzymes in these microorganisms [57]. e catC gene, a
member of the chloramphenicol acetyltransferase (CAT)
family, is located on the V. parahaemolyticus chromo-
some, where it confers intrinsic resistance to chloram-
phenicol [58]. We found that over 90% of isolates of V.
alginolyticus also harbored catC, which was absent in V.
harveyi and V. vulnificus.
Occurrence ofARGs infoodborne pathogens inaquatic
products
Aquatic products are irreplaceable components of the
human diet. Given the aforementioned sources of AMR
in aquatic products, resistant foodborne pathogens
such as E. coli, S. enterica, C. jejuni, S. aureus, L. mono-
cytogenes, and Clostridum botulinum pose an alarming
global and widespread threat to public health [59]. Over
the past decades, the incidence of resistant foodborne
pathogens has been constantly increasing worldwide [43,
44, 59]. In addition, foodborne pathogens that are resist-
ant to several clinically significant antimicrobials desig-
nated for the treatment of multiple drug resistance, such
as extended-spectrum cephalosporins, fluoroquinolones,
polymyxins B, tigecycline, vancomycin, and linezolid,
have also been identified in aquatic products in several
countries worldwide, which should draw more attention
and concern. [28, 60–62]. Based on MicroBIGG-E data,
the resistant foodborne pathogens from aquatic products
possess diverse types of ARGs, with the number ranging
from 1 to 26 types in a single strain. Table2 details some
of the most frequently detected ARGs alongside their
respective antibiotic classes, including tetracyclines, ami-
noglycosides, β-lactams, quinolones, sulfonamides, and
amphenicols. Strains of the Enterobacteriaceae, including
E. coli, S. enterica and K. pneumoniae, carry more diverse
genotypes compared with other species, suggesting that
Enterobacteriaceae may constitute a major reservoir of
ARGs.
To illustrate the occurrence and distribution of clini-
cally significant ARGs in aquatic products, we utilized
the MicroBIGG-E database and literature searches of
Elsevier’s ScienceDirect, PubMed, and Wiley Online
Library. Table3 outlines the main clinically significant
ARGs that were identified in aquatic products. In 2009,
Indian scientists first reported the identification of the
NDM-1 gene from a patient. is gene encoded a carbap-
enem enzyme that hydrolyzed most β-lactam [63], and
has since been reported worldwide, particularly in Enter-
obacteriaceae from various sources. While more than
60 subtypes of NDM enzymes have been documented,
only NDM-1 and NDM-5 have been detected in aquatic
products (Table3). In addition to Enterobacteriaceae [21,
25, 64], NDM-1 has been reported in Vibrio spp. [65, 66]
and Aeromonas spp. [22, 45], whereas NDM-5 is mainly
identified in E. coli [20, 46] and K. pneumoniae [24, 67]
(Table3). Some reports of aquatic products identified as
carrying blaNDM-1 and sold in supermarkets in Australia
[66], the USA [25], Canada [64], France [23], and Japan
[62] were mainly found to originate from Southeast Asia,
suggesting that this ARG has been widely spread through
global trading.
In 2016, Chinese scientist Liu YY reported a new colis-
tin resistance gene mcr-1, which was located on the plas-
mid in commensal E. coli from food animals [72]. Its
transferability has made it difficult to treat clinical infec-
tions of colistin-resistant E. coli. In the MicroBIGG-E
database and recent literature on colistin-resistant bacte-
ria from aquatic products, mcr-3 was mainly identified in
Aeromonas spp., whereas mcr-1 was mainly reported in
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Dengetal. One Health Advances (2025) 3:6
Table 2 Examples of ARGs identified in typical foodborne pathogens from aquatic products
Host Foodborne-
pathogen Genotype Number of
resistance
genes carrying
Isolation source Location Collection year Assembly No.
fish Escherichia coli aac(3)-IId, aadA1, aadA2,
aadA5, blaEC, blaTEM-1,
cmlA1, sul3, drfA12,
dfrA17, estT, floR, lun(F),
oqxA, oqxB, qnrS1, tet(A),
tet(X4)
18 / China: Guang-
dong 2021 GCA_032285135.1
shrimp E. coli aadA1, aadA2, aph(3’)-Ia,
blaEC, blaSHV, blaTEM-1,
cmlA1, floR, dfrA12,
dfrA17, estT, lnu(F), qnrS1,
sul3, tet(A), tet(M), tet(X4)
17 / China: Guang-
dong 2021 GCA_032286305.1
shellfish E. coli aac(6’)-Ib4, aadA1,
aph(3’’)-Ib, aph(3’)-XV,
aph(6)-Id, blaACC-1, blaEC,
blaSHV-12, blaVIM-1, catB2,
dfrA14, sul1, sul2, mph(A),
qnrS1
15 / Italy 2016 GCA_002776495.1
crab E. coli rmtB1, aadA1, aadA2,
blaCTX-M-55, blaEC, blaTEM-1,
cmlA1, dfrA12, sul3, qnrB7,
tet(A)
11 / India: Cochin 2017 GCA_017813585.1
fish Klebsiella pneu-
moniae
aac(3)-IId, aadA16,
aph(3’)-Ia, aph(3’)-Ib,
aph(6)-Ic, aph(6)-Id,
arr-3, blaCTX-M-3, blaDHA-1,
blaSHV-1, blaTEM-1, ble,
dfrA27, sul1, sul2, floR,
fosA, fosA3, mph(A), oqxA,
oqxB19, qnrB4, qnrB91,
qnrS1, aac(6’)-Ib-cr5,
tet(A)
26 / China: Shandong 2019 GCA_028863925.1
shrimp K. pneumoniae aph(3’)-Ia, aph(3’’)-Ib,
aph(6)-Id, blaLAP-2,
blaSHV-1, floR, fosA, oqxA,
oqxB, qnrS1, sul2, tet(A)
12 / China: Shenzhen 2023 GCA_037198215.1
crab K. pneumoniae aac(6’)-Ib3, aph(3’)-Ia,
blaCTX-M-2, blaKPC-2,
blaOXA-2, blaSHV-11,
catA1, fosA,
mph(A), oqxA, oqxB, sul1
12 / Brazil: Sao Vicente 2017 GCA_013002785.1
shellfish K. pneumoniae blaSHV-60, fosA, oqxA10,
oqxB19
4 / India: Cochin 2019 GCA_017814795.1
fish Salmonella
enterica
aac(3)-IVa, aadA1, aadA2,
aph(3’)-Ia, aph(4’)-Ia,
arr-3, blaOXA-1, bleO, catB3,
cmlA1, dfrA12, sul1, sul2,
sul3, floR, aac(6’)-Ib-cr,
oqxA, oqxB, tet(B)
19 frozen eel fish USA 2015 GCA_005899085.1
shellfish S. enterica aac(3)-IVa, aadA1, aadA2,
aph(3’)-Ia, aph(4)-Ia,
arr-3, blaOXA-1, bleO, catB3,
cmlA1, floR, aac(6’)-Ib-
cr5, oqxA, oqxB, sul1, sul2,
sul3, tet(B)
18 / China: Shanghai 2012 GCA_044318665.1
shrimp S. enterica aadA1, aadA2, aph(3’)-
Ia, blaTEM-1, dfrA12,
sul2, sul3, cmlA1, floR,
qnrB19, tet(A), tet(M)
12 frozen shrimp Ecuador 2022 GCA_024423175.1
Page 8 of 14
Dengetal. One Health Advances (2025) 3:6
E. coli [69, 73], and mcr-9.1 [27] and mcr-10 (GenBank
Accession No. NZ_JADOZA010000047.1) were also
found in enterobacteria (Table3). Studies have revealed
that diverse subtypes of the MCR family might originate
from precursor genes on the chromosomes of bacteria,
such as Moraxella spp. [68], Aeromonas spp. [74], and
Shewanella spp. [75], implying that certain aquatic path-
ogens are intrinsically resistant to colistin and contribute
to the dissemination of colistin resistance through the
aquaculture sector [75, 76].
e emergence and widespread dissemination of
Tet(X4)-degrading enzymes and a novel efflux pump
have attracted much attention in recent years [28, 70].
e tet(X4) gene, which is located on a plasmid and
confers high levels of tigecycline resistance, was first
detected in animal samples in 2019 [77]. Since then,
Table 2 (continued)
Host Foodborne-
pathogen Genotype Number of
resistance
genes carrying
Isolation source Location Collection year Assembly No.
crab S. enterica aac(3)-IVa, aadA1,
aph(3’)-Ia, aph(4)-Ia,
dfrA14, floR, sul1, tet(A)
8 crab meat jumbo
lump USA 2018 GCA_004224865.1
fish V. parahaemo-
lyticus
aph(3’’)-Ib, aph(6)-Id,
blaCARB-18, catC, sul2,
tet(34), tet(35), tet(59)
8 freshwater food China 2020 GCA_045007075.1
shrimp V. parahaemo-
lyticus
ant(2’’)-Ia, aph(3’)-Ia,
aph(3’’)-Ib, aph(6)-Id,
arr-2, blaCARB-18, blaVEB-1,
catC, floR, dfrA31, ere(A),
qnrVC1, sul2, tet(34),
tet(35), tet(C)
16 / Indonesia 2020 GCA_023313035.1
shellfish V. parahaemo-
lyticus
aph(3’’)-Ib, aph(6)-Id,
blaCARB-18, blaGMA-1,
catC, dfrA46, sul2, floR,
qnrVC6, tet(34), tet(35),
tet(B), tet(M)
13 / China: Liaoning 2015 GCA_028472865.1
crab V. parahaemo-
lyticus
aph(3’’)-Ib, aph(6)-Id,
blaCARB-18, blaCTX-M-15,
catC, dfrA23, dfrA46, sul2,
qnrVC6, tet(34), tet(35),
tet(A)
12 / Germany 2017 GCA_020741135.1
fish Vibrio vulnificus catB, floR, sul2, tet(34),
tet(35), tet(59), varG
7 freshwater fish China: Shanghai 2018 GCA_032050495.1
shrimp Staphylococcus
aureus
aph(2’’)-Ia, ant(6)-Ia,
aph(3’)-IIIa, dfrG, fosB,
mecA, mepA, mph(C),
msr(A), sat4, tet(38)
11 / India: Alappuzha,
Kerala 2019 GCA_024668545.2
crab S. aureus ant(6)-Ia, aph(3’)-IIIa,
fosB, mecA, mecR1, mepA,
mph(C), msr, sat4, tet(38)
10 fresh crab meat USA: MD 2024 GCA_044400285.1
fish S. aureus ant(6)-Ia, aph(3’)-IIIa,
erm(C), fexA, fosY, mepA,
sat4, tet(38), tet(K)
9 / China 2024 GCA_041923585.1
fish Listeria monocy-
togenes
fosX, vga(G), tet(M) 3 smoked fish dip
cajun style USA: Florida 2005 GCA_004572115.1
shellfish L. monocytogenes fosX, vga(G), tet(M) 3 / USA: RI 2014 GCA_004445175.1
crab L. monocytogenes fosX, vga(G), tet(M) 3 jonah crab meat USA: RI 2014 PDT000034733.3
shrimp L. monocytogenes fosX, vga(G) 2 frozen raw shrimp Indonesia 2020 GCA_016434905.1
shrimp Campylobacter
jejuni
aph(3’)-I, blaCMY-65, blaGIL,
catA
4 / USA: MO 2019 GCA_022967615.1
shellfish C. jejuni blaOXA-184, tet(O) 2 / France 2017 GCA_032797205.1
fish Clostridum botu-
linum
bla, catA, cfr, cplR, fosX, lsa 6 retail fish market India: Kerala,
Cochin 2004 GCA_003017225.1
Page 9 of 14
Dengetal. One Health Advances (2025) 3:6
Table 3 Occurrence and distribution of clinically significant ARGs in aquatic animals and products
Classes of ARGs Genotypes Resistant phenotype Pathogen Host Isolation sources Prevalence Collection date Location GenBank No.
/References
β-lactams blaNDM-1 All β-lactams
with the excep-
tion of aztreonam
and β-inhibitors
E. coli Mastacembelus intestines / 2020.03 Vietnam: Hanoi NZ_AP026939.1
A. veronii Channa striata intestines / 2020.03 Vietnam: Hanoi NZ_AP027937.1
V. fluvialis Solenidae / / 2022.08 China: Shandong NZ_CP126305.1
V. parahaemolyticus a shelled shrimp tail
(imported from Vietnam
to France)
/ / 2016.01 France PETB00000000/ [23]
V. cholerae shrimps (supermarkets) / / 2023 China: Shenzhen NZ_JBBFAW010000010.1
V. alginolyticus shrimps (supermarkets) / 13/1363, 0.95% 2016.12 China: Shenzhen GCA_020223695.1/ [65]
V. alginolyticus cooked prawns
(imported from Thailand)
/ / 2021 Australia: Melbourne GCF_026639325.1/ [24]
Citrobacter braakii, Provi-
dencia rettgeri
frozen retail shrimp
(imported from Vietnam
purchased at a grocery
store in USA)
whole shrimps / 2022 USA: Ohio CP114802, CP114797/ [25]
K. pneumoniae Ruditapes decussatus
(markets)
/ 2/18, 11.1%
(selective media)
2016.03 Tunisia: Gabes [21]
A. sobria, Acinetobacter
baumanii
frozen shrimps
(imported from Asia sold
in supermarkets in USA)
/ 2/948, 0.2% 2019 USA: New York [45]
A. veronii,
A. hydrophila,
Aeromonas enteropelo-
genes
river fish (supermarkets) intestines 7/83, 8.4%
(selective media)
2020.03 Vietnam: Ho Chi Minh [22]
Escherichia cloacae Bivalve mollusks
(retail seafood products
imported from Vietnam)
/ 2/101, 2%
(selective media)
2019–
2014
Canada [64]
E. cloacae Penaeus monodon
(imported from Vietnam)
/ 3/117, 2.6%
(selective media)
2020 Japan BPMY01000001.1/ [62]
blaNDM-5 E. coli Otolithes cuvieri
(retail markets)
/ 1/19, 5.3% 2016 India: Mumbai KJ576638/ [20]
E. coli fish / / 2021 Bangladesh: Dhaka DAQNEZ010000074.1
E. coli, C. freundii Ctenopharyngodon idella
(supermarkets)
intestines 7/196, 3.6%
(selective media)
2019.01 China: Guangzhou NZ_CP054192.1/ [46]
E. coli Procambarus clarkii / / 2020 China NZ_CP084057.1
K. pneumoniae wild- caught fish
(fishmarkets)
a fragment of liver,
kidney and spleen
/ / Djibouti [24]
K. pneumoniae H ypophthalmichthys
molitrix (farms),
Labeo rohita
(farms, markets)
Intestinal swabs 4/18, 22.2%
(selective media)
2020–
2021
India: Uttar Pradesh [67]
Page 10 of 14
Dengetal. One Health Advances (2025) 3:6
Table 3 (continued)
Classes of ARGs Genotypes Resistant phenotype Pathogen Host Isolation sources Prevalence Collection date Location GenBank No.
/References
Colistin mcr-1 Polycolistin B S. enterica serovar Rissen raw mussel
(production area)
/ 1/19, 5.3% 2012–
2016
Spain: Galicia [26]
E. coli Oncorhynchus mykiss
(farms)
intestines 5/5, 100%
(selective media)
2019 Lebanon: Bekaa SAMN14127928/ [68]
E. coli fish (supermarkets) flesh, gills and intestine 4/257, 1.6% 2012–
2016
China: Guangzhou/
Hangzhou/Nanjing
[59]
E. coli intestines 58/63, 92.1%
(selective media)
2019–
2020
Vietnam: Ho Chi Minh/
Can Tho
[69]
mcr-3 E. coli C. striata, C. fuscus
(markets)
intestines 5/63, 7.9%
(selective media)
2019–
2020
Vietnam: Ho Chi Minh/
Can Tho
[69]
mcr-9.1 Enterobacter ludwigii Sparus aurata (a land
tank from a fish multi-
trophic farming)
muscle / 2018.03 Portugal NZ_JABRPH010000155.1/ [27]
S. enterica subsp. enterica
serovar Typhimurium
frozen crawfish whole shrimps / 2011.07 China AAEDLY010000064
mcr-10 Enterobacter hormaechei fish / / 2018 Germany NZ_JADOZA010000047.1
Tetracyclines tet(X4) tigecycline E. coli shrimps (markets) fecal swab 1/29, 3.4%
(selective media)
2023 China: Shenzhen NG_065852.1/ [29]
E. coli, C. freundii fish, shrimps, crabs,
shellfish (markets)
/ 9/73, 12.3%
(selective media)
2021.07–
2022.09
China: Guangzhou SAMN36775957-SAMN36775966/
[28]
tmexCD-
toprJ
A. veronii,
A. hydrophila
fish intestines 7/80, 8.8% 2019.05–
2021.04
China: Zhejiang [70]
tmexC2D2.2-
toprJ2
A. hydrophila fish (markets) muscle 1/45, 2.2%
(selective media)
2021.12 China: Guangzhou [71]
tmexCD2-
toprJ1
Pseudomonas putida shrimp / / 2023.10 China: Huzhou NZ_JBFNXZ010000012
Glycopeptides vanA high level resist-
ance to vancomycin
and teicoplanin
Enterococcus faecium,
Enterococcus faecalis,
Enterococcus durans
S. aurata
(natural marine eco-
system)
faeces 7/118, 5.9%
(selective media)
2007 Portugal [30]
E. faecalis,
E. gallinarum
tilapia, shrimps
(supermarkets)
/ 20/54, 37% 2023.06–
2023.12
Egypt [33]
vanB E. faecalis,
Enterococcus gallinarum
tilapia, shrimps (super-
markets)
/ 17/54, 31.5% 2023.06–2023.12 Egypt [33]
Oxazolidinones optrA linezolid S. agalactiae tilapia (supermarkets) sliced fish / 2015 Singapore DASIHH010000019.1
E. faecalis catfish / / 2020 USA: Los Angeles AAXDOC010000037.1
E. faecium,
E. faecalis, E. durans
fish / / 2022 China NZ_JARPTN010000027.1NZ_JAR-
QEZ010000006.1
S. aureus, Staphylococcus
lentus,
Staphylococcus haemo-
lyticus
Gadidae
(salted and seasoned
seafoods)
fillets (muscle and skin
tissues)
44/311, 14.1% / Italy [32]
Page 11 of 14
Dengetal. One Health Advances (2025) 3:6
tet(X4) has been identified in food-borne Enterobacte-
riaceae from humans and terrestrial animals. Recently,
it was reported in a strain of E. coli isolated from the
intestines of commercial shrimp sold in a local seafood
market in China [29], suggesting that aquatic products
may be contaminated with tigecycline-resistant food-
borne bacteria. In Gram-negative bacteria, resistance
to tigecycline can also be caused by overexpression
of efflux pump genes. In 2020, Chinese scientists first
reported a novel plasmid-mediated efflux pump gene
cluster, namely TMexCD1-TOprJ1, in K. pneumoniae
of chicken-origin [78]. Subsequently, six variants of the
cluster were detected in a variety of important pathogens
of humans, terrestrial animals, food, and sewage [79].
However, the cluster was found to be less prevalent in
aquatic animals than in, with current reports limited to
Aeromonas isolated from fish [70, 71] and Pseudomonas
putida isolated from shrimp (GenBank Accession No.
NZ_JBFNXZ010000012) (Table2).
Vancomycin and linezolid are typically employed in
clinical settings to treat severe infections caused by mul-
tidrug-resistant Gram-positive bacteria. To date, nine
genotypes of the vancomycin resistance gene (van) fam-
ily have been identified in Enterococcus from different
sources [80]. Among them, vanA and vanB are preva-
lent in Enterococcus isolated from the intestinal tract of
aquatic animals [33] (Table3).
Linezolid belongs to the oxazolidinone class, which was
first introduced to China in 2007 and is regarded as the
last resort for treating serious infections [81]. In 2015,
Wang etal. [82] first reported the optrA gene in Entero-
coccus isolated from animals and humans in China. is
gene belongs to the adenosine triphosphate-binding box
transporter superfamily effector system and mediates
multiple drug resistance. In our search of the Micro-
BIGG-E database, optrA was detected in 10 strains of
Streptococcus agalactiae from tilapia fillets sold in Sin-
gapore supermarkets in 2015 (GenBank Accession No.
DASIHH010000019.1). is gene has also been detected
in Enterococcus and Staphylococcus isolated from aquatic
products worldwide in recent years [32, 33].
With the extensive application of antibiotics, the
aforementioned clinically significant ARGs are car-
ried by pathogen-infected patients, but can also be
detected in food animals and the natural environment,
suggesting that these ARGs have been widely dissemi-
nated. Although the detection rate of these newly dis-
covered ARGs remains low in food animals and the
environment, most could be easily transferred to other
microorganisms via plasmids, and possibly through
the food chain, thereby increasing the threat to human
health [53, 75, 83, 84]. Further research concerning the
possible carriage of such ARGs by aquatic animals is
necessary, and should emphasize the genomic related-
ness of aquatic foodborne pathogens and the factors
influencing bacterial contamination of aquatic envi-
ronments and products.
Solutions andstrategies tomitigate resistance
inaquaculture
AMR poses a public health challenge for populations
worldwide. Government entities, scientific research insti-
tutions, and private enterprises have started moving for-
ward with plans to mitigate the risks of AMR to crucial
aquaculture industries and to protect human and animal
health. Below, we outline three main approaches that
have been taken in China specifically.
1) In terms of government actions, legislative measures,
such as the regulation of antibiotics and the develop-
ment of guidelines for their rational use in aquacul-
ture, have been initiated to strengthen the supervi-
sion of antibiotic management. National surveillance
to monitor the prevalence of AMR of aquatic path-
ogens has been carried out since 2015, covering 16
provinces. Activities to enhance public awareness of
AMR and promote the rational use of antimicrobi-
als have also been undertaken through publicity and
educational campaigns.
2) In scientific research institutes and universities, the
prevalence, mechanisms, and transmission of AMR
in aquaculture have been studied, aiming to com-
prehend the epidemiological characteristics and
trends of AMR in different regions. Novel, rapid,
and precise diagnostic technologies have been
employed for the prevention and control of animal
diseases. In addition, to reduce the usage of anti-
biotics, research is underway to develop multiple
green and safe alternatives to antimicrobials, such
as vaccines, Chinese herbal medicines, microeco-
logical preparations, bacteriophages, and enzyme
preparations. Furthermore, it is crucial that we
create effective technologies to alleviate the selec-
tive pressure on bacteria to develop antimicrobial
resistance (including ARGs), within both living
organisms and environmental cultures.
3) Regarding aquaculture enterprises, good aquaculture
and biosecurity practices are needed for safe, high-
quality aquatic products. Regular, strict hygienic
practices are also indispensable for reducing con-
tamination and transmission of pathogens. Further-
more, enhanced water quality health management
is crucial for increasing aquaculture production and
profitability.
Page 12 of 14
Dengetal. One Health Advances (2025) 3:6
Conclusions
is review focused on the sources of AMR and the
occurrence and distribution of ARGs from diseased
aquatic animals and contaminated aquatic products.
Antimicrobial use and other human activities have con-
tributed to the development and spread of ARB and
ARGs. Following increased understanding and awareness
of AMR in aquaculture, government entities, research
institutions, private enterprises, farmers, and other stake-
holders are taking action to mitigate the transmission of
AMR, thereby enhancing human and animal health as
well as ecological sustainability.
Acknowledgements
We express our sincere gratitude to Jianhua Liu (South China Agriculture
University) for her insightful comments and constructive suggestions, which
significantly contributed to the improvement of this manuscript.
Authors’ contributions
Y.D. and A.T. contributed to the conception and design of the work. Y.D.
drafted the manuscript. F.Z., F.W., H.G., Y.L., and Z.H. substantively revised the
manuscript. All authors read and approved the final version of the manuscript.
Funding
This study was funded by Guangzhou Science and Technology Planning
Project (Grant No. 2023B03J1305) and the Central Public-interest Scientific
Institution Basal Research Fund, CAFS (2023TD48 and 2022GH04).
Data availability
All of the data supporting the conclusions of this article are included within
the article.
Declarations
Ethics approval and consent to participate
Not applicable.
Consent for publication
Not applicable.
Competing interests
The authors declare that they have no competing interests.
Received: 28 October 2024 Revised: 14 January 2025 Accepted: 19 Janu-
ary 2025
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