Antibiotic Resistance and Characteristics of Integrons in Escherichia coli Isolated from Penaeus vannamei at a Freshwater Shrimp Farm in Zhejiang Province, China

An update on the prevalence of colistin and carbapenem-resistant Gram-negative bacteria in aquaculture: an emerging threat to public health

Aquaculture has been recognized as a hotspot for the emergence and spread of antimicrobial resistance genes conferring resistance to clinically important antibiotics. This review gives insights into studies investigating the prevalence of colistin and carbapenem resistance (CCR) among Gram-negative bacilli in aquaculture. Overall, a high incidence of CCR has been reported in aquatic farms in several countries, with CCR being more prevalent among opportunistic human pathogens such as Acinetobacter nosocomialis, Shewanella algae, Photobacterium damselae, Vibrio spp., Aeromonas spp., as well as members of Enterobacteriaceae family. A high proportion of isolates in these studies exhibited wide-spectrum profiles of antimicrobial resistance, highlighting their multidrug-resistance properties (MDR). Several mobile colistin resistance genes (including, mcr-1, mcr-1.1, mcr-2, mcr-2.1, mcr-3, mcr-3.1, mcr-4.1, mcr-4.3, mcr-5.1, mcr-6.1, mcr-7.1, mcr-8.1, and mcr-10.1) and carbapenemase encoding genes (including, blaOXA-48, blaOXA-55, blaNDM, blaKPC, blaIMI, blaAIM, blaVIM, and blaIMP) have been detected in aquatic farms in different countries. The majority of these were carried on MDR Incompatibility (Inc) plasmids including IncA/C, and IncX4, which have been associated with a wide host range of different sources. Thus, there is a risk for the possible spread of resistance genes between fish, their environments, and humans. These findings highlight the need to monitor and regulate the usage of antimicrobials in aquaculture. A multisectoral and transdisciplinary (One Health) approach is urgently needed to reduce the spread of resistant bacteria and/or resistance genes originating in aquaculture and avoid their global reach.

Contribution of different class 2 integron elements to fitness costs in multi-drug resistant Escherichia coli and evaluation of their adaptability in “farm-to-table” environments

Integrons play a pivotal role in the dissemination of antimicrobial resistance, because they can capture and express exogenous antimicrobial resistance genes. This study aimed to elucidate the structure and contribution of different elements of class 2 integrons to fitness costs in their host bacteria and evaluate their adaptability to the "farm-to-table" process. We mapped 27 typical class 2 integrons of Escherichia coli isolated from aquatic foods and pork products, each harboring an inactive truncated class 2 integrase gene and the gene cassette (GC) array dfrA1-sat2-aadA1 with strong Pc2A/Pc2B promoters. Notably, the fitness costs associated with class 2 integrons depended on the Pc promoter strength and quantity and content of GCs in the array. Additionally, the costs of integrases were activity-dependent, and a balance was identified between GC capture ability and integron stability, which could explain the inactive truncated integrase identified. Although typical class 2 integrons exhibited low-cost structures in E. coli, the bacteria incurred biological costs, including decreasing growth rates and biofilm formation, in farm-to-table environments, especially under low-nutrient conditions. Nevertheless, sub-inhibitory antibiotic concentrations led to the selection of class 2 integron-carrying bacteria. This study provides important insights into how integrons may travel from preharvest to consumer goods.

Exposure to cadmium induced gut antibiotic resistance genes (ARGs) and microbiota alternations of Babylonia areolata

Cadmium (Cd) is widely distributed in aquatic environments and has multiple adverse effects on aquatic organisms such as the ivory shell (Babylonia areolata). However, its effects on antibiotic resistance genes (ARGs) and gut microbiota of B. areolata remain unclear. In this study, we explored the effects of different concentrations (0, 0.03, 0.18 and 1.08 mg/L) of Cd on intestinal microbial communities and ARGs in B. areolata through 16S rRNA gene sequencing and high-throughput quantitative PCR. The results showed that the structure and diversity of ARGs and microbiota in B. areolata gut were altered upon Cd exposure. Tetracycline, Vancomycin and Macrolide-Lincosamide-Streptogramin B (MLSB) resistance genes were identified as the major ARGs in B. areolata gut. The absolute abundance and alpha diversity of ARGs in B. areolata gut increased with the rise of cadmium concentration. The microbial communities at genus level were enriched in the low and medium Cd concentration groups, while decreased in the high Cd concentration group compared to the control groups. In addition, the influence of microbiota on the ARG profile was more significant than that of Cd concentration and MGEs in B. areolata gut. Null model analysis demonstrated that stochastic processes dominated ARG assembly in the Cd-exposed groups and were enhanced with the increasing Cd concentrations. Four opportunistic bacterial pathogens (Bacteroides, Legionella, Acinetobacter and Escherichia) detected in B. areolata gut maybe the potential hosts of ARGs. Our findings provide references for the hazards assessment of environmental Cd exposure of gut microbiome in aquatic animals.

Xenogenetic evolutionary of integrons promotes the environmental pollution of antibiotic resistance genes - Challenges, progress and prospects

Environmental pollution of antibiotic resistance genes (ARGs) has been a great public concern. Integrons, as mobile genetic elements, with versatile gene acquisition systems facilitate the horizontal gene transfer (HGT) and pollution disseminations of ARGs. However, little is understood about the characteristics of ARGs mediated by integrons, which hampers our monitoring and control of the mobile antimicrobial resistance risks. To address these issues, we reviewed 3,322 publications concerning detection methods and pipeline, ARG diversity and evolutionary progress, environmental and geographical distribution, bacterial hosts, gene cassettes arrangements, and based on which to identify ARGs with high risk levels mediated by integrons. Diverse ARGs of 516 subtypes attributed to 12 types were capable of being carried by integrons, with 62 core ARG subtypes prevalent in pollution source, natural and human-related environments. Hosts of ARG-carrying integrons reached 271 bacterial species, most frequently carried by opportunistic pathogens Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae. Moreover, the observed emergence of ARGs together with their multiple arrangements indicated the accumulation of ARGs mediated by integrons, and thus pose increasing HGT risks under modern selective agents. With the concerns of public health, we urgently call for a better monitoring and control of these high-risk ARGs. Our identified Risk Rank I ARGs (aacA7, blaOXA10, catB3, catB8, dfrA5) with high mobility, reviewed key trends and noteworthy advancements, and proposed future directions could be reference and guidance for standard formulation.

Rapid detection of multiple resistance genes to last-resort antibiotics in Enterobacteriaceae pathogens by recombinase polymerase amplification combined with lateral flow dipstick

The worrying emergence of multiple resistance genes to last-resort antibiotics in food animals and human populations throughout the food chain and relevant environments has been increasingly reported worldwide. Enterobacteriaceae pathogens are considered the most common reservoirs of such antibiotic resistance genes (ARGs). Thus, a rapid, efficient and accurate detection method to simultaneously screen and monitor such ARGs in Enterobacteriaceae pathogens has become an urgent need. Our study developed a recombinase polymerase amplification (RPA) assay combined with a lateral flow dipstick (LFD) for simultaneously detecting predominant resistance genes to last-resort antibiotics of Enterobacteriaceae pathogens, including mcr-1, bla_NDM-1 and tet(X4). It is allowed to complete the entire process, including crude DNA extraction, amplification as well as reading, within 40 min at 37°C, and the detection limit is 10¹ copies/μl for mcr-1, bla_NDM-1 and tet(X4). Sensitivity analysis showed obvious association of color signals with the template concentrations of mcr-1, bla_NDM-1 and tet(X4) genes in Enterobacteriaceae pathogens using a test strip reader (R ² = 0.9881, R ² = 0.9745, and R ² = 0.9807, respectively), allowing for quantitative detection using multiplex RPA-LFD assays. Therefore, the RPA-LFD assay can suitably help to detect multiple resistance genes to last-resort antibiotics in foodborne pathogens and has potential applications in the field.

Migration of antibiotic resistance genes and evolution of flora structure in the Xenopus tropicalis intestinal tract with combined exposure to roxithromycin and oxytetracycline

The intestinal flora is one of the most important environments for antibiotic resistance development, owing to its diverse mix of bacteria. An excellent medicine model organism, Xenopus tropicalis, was selected to investigate the spread of antibiotic resistance genes (ARGs) in the intestinal bacterial community with single or combined exposure to roxithromycin (ROX) and oxytetracycline (OTC). Seventeen resistance genes (tetA, tetB, tetE, tetM, tetO, tetS, tetX, ermF, msrA, mefA, ereA, ereB, mphA, mphB, intI1, intI2, intI3) were detected in the intestines of Xenopus tropicalis living in three testing tanks (ROX tanks, OTC tanks, ROX + OTC tanks) and a blank tank for 20 days. The results showed that the relative abundance of total ARGs increased obviously in the tank with single stress but decreased in the tank with combined stress, and the genes encoding the macrolide antibiotic efflux pump (msrA), phosphatase (mphB) and integron (intI2, intI3) were the most sensitive. With the aid of AFM scanning, DNA was found to be scattered short chain in the blank, became extended or curled and then compacted with the stress from a single antibiotic, and was compacted and then fragmented with combined stress, which might be the reason for the variation of the abundance of ARGs with stress. The ratio of Firmicutes/Bacteroides related to diseases was increased by ROX and OTC. The very significant correlation between intI2 and intI3 with tetS (p ≤ 0.001) hinted at a high risk of ARG transmission in the intestines. Collectively, our results suggested that the relative abundance of intestinal ARGs could be changed depending on the intestinal microbiome and DNA structures upon exposure to antibiotics at environmental concentrations.

Bacterial Diversity and Antibiotic Susceptibility of Sparus aurata from Aquaculture

In a world where the population continues to increase and the volume of fishing catches stagnates or even falls, the aquaculture sector has great growth potential. This study aimed to contribute to the depth of knowledge of the diversity of bacterial species found in Sparus aurata collected from a fish farm and to understand which profiles of diminished susceptibility to antibiotics would be found in these bacteria that might be disseminated in the environment. One hundred thirty-six bacterial strains were recovered from the S. aurata samples. These strains belonged to Bacillaceae, Bacillales Family XII. Incertae Sedis, Comamonadaceae, Enterobacteriaceae, Enterococcaceae, Erwiniaceae, Micrococcaceae, Pseudomonadaceae and Staphylococcaceae families. Enterobacter sp. was more frequently found in gills, intestine and skin groups than in muscle groups (p ≤ 0.01). Antibiotic susceptibility tests found that non-susceptibility to phenicols was significantly higher in gills, intestine and skin samples (45%) than in muscle samples (24%) (p ≤ 0.01) and was the most frequently found non-susceptibility in both groups of samples. The group of Enterobacteriaceae from muscles presented less decreased susceptibility to florfenicol (44%) than in the group of gills, intestine and skin samples (76%). We found decreased susceptibilities to β-lactams and glycopeptides in the Bacillaceae family, to quinolones and mupirocin in the Staphylococcaceae family, and mostly to β-lactams, phenicols and quinolones in the Enterobacteriaceae and Pseudomonadaceae families. Seven Enterobacter spp. and five Pseudomonas spp. strains showed non-susceptibility to ertapenem and meropenem, respectively, which is of concern because they are antibiotics used as a last resort in serious clinical infections. To our knowledge, this is the first description of species Exiguobacterium acetylicum, Klebsiella michiganensis, Lelliottia sp. and Pantoea vagans associated with S. aurata (excluding cases where these bacteria are used as probiotics) and of plasmid-mediated quinolone resistance qnrB19-producing Leclercia adecarboxylata strain. The non-synonymous G385T and C402A mutations at parC gene (within quinolone resistance-determining regions) were also identified in a Klebsiella pneumoniae, revealing decreased susceptibility to ciprofloxacin. In this study, we found not only bacteria from the natural microbiota of fish but also pathogenic bacteria associated with fish and humans. Several antibiotics for which decreased susceptibility was found here are integrated into the World Health Organization list of "critically important antimicrobials" and "highly important antimicrobials" for human medicine.

Spread of resistance genes from duck manure to fish intestine in simulated fish-duck pond and the promotion of cefotaxime and As

Integrated culture is a widespread culture mode in South China, in which resistance genes (RGs) also spread in the circulation system with nutrients. Accordingly, the aim of the present study was to investigate the spread of RGs in a fish-duck pond and the RGs and bacterial community of fish intestines. Five fish tanks, including a control tank and four experimental tanks (duck manure, duck manure + cefotaxime, duck manure + As, and duck manure + cefotaxime + As), were tested for 100 days. The results showed that duck manure increased both the diversity and relative abundance of RGs in fish intestines, and the addition of stress factors (cefotaxime, As) increased the relative abundance of RGs by one to two orders of magnitude. The stress-inducing effect of cefotaxime was greater than that of As. Tetracycline resistance genes were more sensitive to stress factors and were the predominant RGs in fish intestines. RGs in duck manure preferentially spread from the water to biofilm and then to fish intestines, whereas co-stress of cefotaxime and As obviously promoted the spread of RGs to fish intestines. In comparison to the control tank, duck manure and stress factors significantly changed the bacterial community of fish intestines. Correlation analysis also revealed that arsB, MOX, tetA and sul1 were significantly correlated with intI1 (P < 0.01), which hinted a potentially dissemination risk of RGs in fish intestines. These findings provide a theoretical basis for further investigating the dissemination of RGs in integrated culture systems and for evaluating the ecological risk of antibiotic and As use in aquaculture.

Occurrence of Virulence Factors and Antibiotic and Heavy Metal Resistance in Vibrio parahaemolyticus Isolated from Pacific Mackerel at Markets in Zhejiang, China

ABSTRACT

Vibrio parahaemolyticus is a widespread bacterium in the marine environment and is one of the leading causes of food-derived bacterial poisoning in humans worldwide. The main objective of this study was to determine the prevalence, virulence factors, and antibiotic and heavy metal resistance profiles of V. parahaemolyticus in Pacific mackerel (Pneumatophorus japonicus) from different markets in Zhejiang Province, People's Republic of China. In total, 112 (31.11%) V. parahaemolyticus isolates were identified from 360 Pacific mackerel samples, with an extremely low occurrence of the virulence genes trh (1.79%, 2 of 112) and tdh (0%, 0 of 112). Antibiotic resistance testing revealed that most isolates showed resistance to ampicillin (96.43%, 108 of 112) and streptomycin (90.18%, 101 of 112), whereas all strains were sensitive to kanamycin, florfenicol, cefamandole, and trimethoprim-sulfamethoxazole. Furthermore, 46.43% (52 of 112) of isolates, which had 12 different phenotypes, were classified as multidrug resistant. In addition, the multiple antibiotic resistance index values of isolates were between 0.05 and 0.63, and the maximum multiple antibiotic resistance index was attributed to two isolates that exhibited resistance to 12 antibiotics. Heavy metal resistance patterns were similar among the six different markets. The majority of isolates showed resistance to Cd2+ (78.57%) and Pb2+ (51.79%), and fewer were resistant to Cu2+ (37.50%), Zn2+ (25.00%), Co2+ (9.82%), Ni2+ (6.25%), and Mn2+ (4.46%). No isolates were resistant to Cr3+. In total, 22.32% (25 of 112) of strains were multiheavy metal resistant. Furthermore, multidrug resistance and multiheavy metal resistance were found to be positively correlated in the V. parahaemolyticus strains by using Pearson's correlation analysis (P = 0.008; R = 0.925). This information will contribute to the monitoring of variations in the antibiotic and heavy metal resistance profiles of V. parahaemolyticus strains from seafood and provide insight into the appropriate use of antibiotics and the safe consumption of seafood.

HIGHLIGHTS

Co-occurrence of Antibiotic and Heavy Metal Resistance and Sequence Type Diversity of Vibrio parahaemolyticus Isolated From Penaeus vannamei at Freshwater Farms, Seawater Farms, and Markets in Zhejiang Province, China

Vibrio parahaemolyticus is the leading cause of seafood-borne bacterial poisoning in China and is a threat to human health worldwide. The aim of this study was to assess the antibiotic resistance profiles and distribution of heavy metal resistance of V. parahaemolyticus isolates from Penaeus vannamei from freshwater farms, seawater farms, and their corresponding markets in Zhejiang, China and to assess the relationship between multidrug resistance (MDR) and multi-heavy metal resistance (MHMR). Of the 360 P. vannamei samples that we tested, 90 (25.00%) were V. parahaemolyticus positive, but the occurrence of pathogenic isolates carrying the toxin genes tdh (4.44%) and trh (3.33%) was low. None of the tested isolates harbored both the tdh and trh genes. However, antibiotic resistance profiles varied among different sampling locations, levels of resistance to the antibiotics ampicillin (76.67%) and streptomycin (74.44%) were high overall, and MDR isolates were common (40.00% of all isolates). Heavy metal resistance patterns were similar among the different sampling locations. Overall, the majority of V. parahaemolyticus isolates displayed tolerance to Cd²⁺ (60.00%), and fewer were resistant to Cu²⁺ (40.00%), Zn²⁺ (38.89%), Ni²⁺ (24.44%), Cr³⁺ (14.44%), and Co²⁺ (8.89%). In addition, 34.44% (31/90) of isolates tested in this study were found to be MHMR. Using Pearson's correlation analysis, MDR and MHMR were found to be positively correlated (P = 0.004; R = 0.759). The 18 V. parahaemolyticus isolates that were both MDR and MHMR represented 18 sequence types, of which 12 were novel to the PubMLST database, and displayed a high level of genetic diversity, suggesting that dissemination may be affected by mobile genetic elements via horizontal gene transfer. However, a low percentage of class 1 integrons without gene cassettes and no class 2 or 3 integrons were detected in the 18 MDR and MHMR isolates or in the 90 V. parahaemolyticus isolates overall. Thus, we suggest that future research focus on elucidating the mechanisms that lead to a high prevalence of resistance determinants in V. parahaemolyticus. The results of this study provide data that will support aquatic animal health management and food safety risk assessments in the aquaculture industry.

Antibiotic Susceptibility, Biofilm-Forming Ability, and Incidence of Class 1 Integron of Salmonella spp., Escherichia coli, and Staphylococcus aureus Isolated from Various Foods in a School Canteen in China

In recent years, the food poisoning incidents from school canteens have aroused widespread concern in China. Microbial contamination to the foods is the main factor responsible for these food poisoning events. In this study, identification of microbial pathogens including Salmonella spp., Escherichia coli, and Staphylococcus aureus in samples (frozen pork, fresh pork, fresh chicken, and different fresh vegetables) of a school canteen in China during 2017 to 2018 was performed. The antibiotic susceptibility pattern, class 1 integron, and biofilm formation ability of the isolated pathogens were also investigated. In total, 96 strains were isolated (32 Salmonella spp., 32 E. coli, and 32 S. aureus). The antibiogram study results demonstrated that 61.5% strains were found resistant to at least one type of antibiotics, and 17.7% were resistant to three or more antibiotics. In addition, 31.3% strains possessed class 1 integron. Among the integron-positive isolates, 38.9% Salmonella spp. and 87.5% E. coli contained ∼800 or/and 1500 bp size gene cassette within the integrons. However, four S. aureus strains possessing class 1 integron without gene cassette were found. Although none of the isolated strains were found strong biofilm producer, 44.8% were found to have weak or moderate biofilm formation ability. Despite biofilm formation ability or not, the Salmonella spp. containing positive class 1 integron showed significant resistance to cefazolin and gentamicin. In addition, class 1 integron-positive E. coli isolates having the biofilm formation ability hardly showed sensitive to four antibiotics, such as amikacin, amoxicillin-clavulanate, cefazolin, and gentamicin. Therefore, it is necessary to reduce the prevalence of antibiotic resistance gene cassettes containing antibiotic resistance genes by the prudent use of antibiotics in livestock farms, and the improvement of food processing and storage environment.

Diverse Mobile Genetic Elements and Conjugal Transferability of Sulfonamide Resistance Genes (sul1, sul2, and sul3) in Escherichia coli Isolates From Penaeus vannamei and Pork From Large Markets in Zhejiang, China

High prevalence rates of sulfonamide resistance genes sul1, sul2, and sul3 have been observed in Gram-negative bacteria isolated from humans, domestic animals, and aquaculture species worldwide. We investigated the distribution characteristics, location, conjugative transferability, and genetic environments of sul genes from Escherichia coli isolates collected from Penaeus vannamei and pork samples from three large markets in Zhejiang, China. The prevalence rates of sul genes in sulfonamide-resistant E. coli isolates from P. vannamei and pork samples were 90.0 and 88.6%, respectively, and the prevalence of sul1 and sul2 was significantly higher than that of sul3 (p < 0.05). Twenty-four representative sul-positive E. coli isolates were analyzed in detail. Southern blot hybridization confirmed that sul genes of E. coli isolates were located on plasmids and/or chromosomes. Transfer of resistance through conjugation was observed in all 18 E. coli isolates harboring sul genes on plasmids. Replicon typing identified seven different incompatibility groups and IncF was the dominant replicon type among sul gene-containing plasmids from both sources. PCR walking analysis indicated that 87.5% (35/40) of sul gene-related fragments carried insertion sequences (ISs) belonging to a variety of families in diverse sites, with IS26 occurring most frequently. In addition, the sul1 gene was detected mainly in fragments carrying class 1 integrons. Co-location on the same fragment with resistance genes that may contribute to the persistence and dissemination of sul1 and/or sul2 genes. The diversity of mobile genetic elements and resistance genes adjacent to sul3 was much lower than those adjacent to sul1 and sul2, especially those located in chromosomes, which reduced the transmission potential of the sul3 gene. In conclusion, combined with the results of clonal relatedness analysis by PFGE and MLST of 24 representative E. coli isolates from P. vannamei and pork samples, it showed that a small number of sul genes were vertically transmitted among E. coli from P. vannamei and that horizontal gene transfer was likely the main transmission mechanism of sul genes from both sources. Our results provide important information to better understand the risk of transmission of sul genes from seafood and meat to humans.