scholarly journals Antibiotic Resistance Genes and Bacterial Communities of Farmed Rainbow Trout Fillets (Oncorhynchus mykiss)

2020 ◽  
Vol 11 ◽  
Author(s):  
Nicolas Helsens ◽  
Ségolène Calvez ◽  
Hervé Prevost ◽  
Agnès Bouju-Albert ◽  
Aurélien Maillet ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Rainbow Trout ◽  
Bacterial Community ◽  
16S Rrna ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Antibiotic Resistance Genes ◽  
Rrna Gene ◽  
Antibiotic Residues ◽  
The 16S Rrna Gene

The rise of antibiotic resistance is not only a challenge for human and animal health treatments, but is also posing the risk of spreading among bacterial populations in foodstuffs. Farmed fish-related foodstuffs, the food of animal origin most consumed worldwide, are suspected to be a reservoir of antibiotic resistance genes and resistant bacterial hazards. However, scant research has been devoted to the possible sources of diversity in fresh fillet bacterial ecosystems (farm environment including rivers and practices, and factory environment). In this study bacterial communities and the antibiotic resistance genes of fresh rainbow trout fillet were described using amplicon sequencing of the V3-V4 region of the 16S rRNA gene and high-throughput qPCR assay. The antibiotic residues were quantified using liquid chromatography/mass spectrometry methods. A total of 56 fillets (composed of muscle and skin tissue) from fish raised on two farms on the same river were collected and processed under either factory or laboratory sterile filleting conditions. We observed a core-bacterial community profile on the fresh rainbow trout fillets, but the processing conditions of the fillets has a great influence on their mean bacterial load (3.38 ± 1.01 log CFU/g vs 2.29 ± 0.72 log CFU/g) and on the inter-individual diversity of the bacterial community. The bacterial communities were dominated by Gamma- and Alpha-proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The most prevalent genera were Pseudomonas, Escherichia-Shigella, Chryseobacterium, and Carnobacterium. Of the 73 antibiotic residues searched, only oxytetracycline residues were detected in 13/56 fillets, all below the European Union maximum residue limit (6.40–40.20 μg/kg). Of the 248 antibiotic resistance genes searched, 11 were found to be present in at least 20% of the fish population (tetracycline resistance genes tetM and tetV, β-lactam resistance genes blaDHA and blaACC, macrolide resistance gene mphA, vancomycin resistance genes vanTG and vanWG and multidrug-resistance genes mdtE, mexF, vgaB and msrA) at relatively low abundances calculated proportionally to the 16S rRNA gene.

scholarly journals Effects of Antibiotics on the Bacterial Community, Metabolic Functions and Antibiotic Resistance Genes in Mariculture Sediments during Enrichment Culturing

2020 ◽  
Vol 8 (8) ◽  
pp. 604
Author(s):  
Meng-Qi Ye ◽  
Guan-Jun Chen ◽  
Zong-Jun Du
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Antibiotic Resistance Genes ◽  
Control Group ◽  
Rrna Gene ◽  
Metabolic Functions ◽  
Culture Dependent

The effect of antibiotics on the diversity and functioning of indigenous microorganisms in the environment has attracted much attention. In this study, effects of exposure to six different antibiotics on the bacterial community, metabolic functions and antibiotic resistance genes (ARGs) in marine sediments during enrichment culturing were investigated. Classical culture-dependent method and high-throughput 16S rRNA gene sequencing method were both applied. In the culture-dependent analysis, the obtained 1549 isolates belonged to four phyla (Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria) and 155 genera. Proteobacteria and Firmicutes were the dominant phyla. The diversity and abundance of obtained bacteria after antibiotic processing exhibited different degrees of decrease. Enrichment culturing for different time could also affect the bacterial community composition. Some genera of bacteria were not isolated in the control group, but they could be isolated in the antibiotic-treated groups. In high-throughput 16S rRNA gene amplicon sequencing analyses, all the effective reads were clustered into 2822 OTUs at 97% similarity cutoff; they were annotated to 49 phyla, 103 class, 220 orders, 347 families, 624 genera and 1122 species. An alpha diversity analysis indicated that the community diversity and richness decreased under antibiotic exposure. The changes at the genus level were much more obvious. Only 48 genera of 129 genera were shared by all the samples. A total of 29 genera which were not detected in the initial control sample could be detected in at least one antibiotic-treated group. SIMPER analysis showed that OTU2543 and OTU1450 were the most common taxa to the dissimilarity of bacterial community between antibiotic-treated groups and the control group. OTU2034 and OUT2543 were the most contributive taxa to dissimilarity of groups incubating for different time. Metabolism was the predominant bacterial function. A total of 30 ARGs were detected in the samples. This study mainly focused on the changes of microbiota under the selective pressure of antibiotics for different time and the results demonstrated that the antibiotic could affect the bacterial diversity and richness in the marine ecosystem.

scholarly journals Seasonal changes in bacterial communities associated with healthy and diseasedPoritescoral in southern Taiwan

2016 ◽  
Vol 62 (12) ◽  
pp. 1021-1033 ◽  
Author(s):  
Chorng-Horng Lin ◽  
Chih-Hsiang Chuang ◽  
Wen-Hung Twan ◽  
Shu-Fen Chiou ◽  
Tit-Yee Wong ◽  
...  
Keyword(s):  
Health Status ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Southern Taiwan ◽  
The 16S Rrna Gene

We compared the bacterial communities associated with healthy scleractinian coral Porites sp. with those associated with coral infected with pink spot syndrome harvested during summer and winter from waters off the coast of southern Taiwan. Members of the bacterial community associated with the coral were characterized by means of denaturing gradient gel electrophoresis (DGGE) of a short region of the 16S rRNA gene and clone library analysis. Of 5 different areas of the 16S rRNA gene, we demonstrated that the V3 hypervariable region is most suited to represent the coral-associated bacterial community. The DNA sequences of 26 distinct bands extracted from DGGE gels and 269 sequences of the 16S rRNA gene from clone libraries were determined. We found that the communities present in diseased coral were more heterogeneous than the bacterial communities of uninfected coral. In addition, bacterial communities associated with coral harvested in the summer were more diverse than those associated with coral collected in winter, regardless of the health status of the coral. Our study suggested that the compositions of coral-associated bacteria communities are complex, and the population of bacteria varies greatly between seasons and in coral of differing health status.

scholarly journals Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
YiMing Li ◽  
WeiWei Cao ◽  
ShuLi Liang ◽  
Shinji Yamasaki ◽  
Xun Chen ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Community ◽  
Resistance Genes ◽  
Southern China ◽  
Variation Partitioning ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Food Samples ◽  
Rrna Gene

Abstract Ready-to-eat (RTE) foods have been considered to be reservoirs of antibiotic resistance bacteria, which constitute direct threat to human health, but the potential microbiological risks of RTE foods remain largely unexplored. In this study, the metagenomic approach was employed to characterize the comprehensive profiles of bacterial community and antibiotic resistance gene (ARG) in 18 RTE food samples (8 RTE meat, 7 RTE vegetables and 3 RTE fruit) in southern China. In total, the most abundant phyla in RTE foods were Proteobacteria, Firmicutes, Cyanobacteria, Bacteroidetes and Actinobacteria. 204 ARG subtypes belonging to 18 ARG types were detected with an abundance range between 2.81 × 10−5 and 7.7 × 10−1 copy of ARG per copy of 16S rRNA gene. Multidrug-resistant genes were the most predominant ARG type in the RTE foods. Chloramphenicol, macrolide-lincosamide-streptogramin, multidrug resistance, aminoglycoside, bacitracin, tetracycline and β-lactam resistance genes were dominant, which were also associated with antibiotics used extensively in human medicine or veterinary medicine/promoters. Variation partitioning analysis indicated that the join effect of bacterial community and mobile genetic elements (MGEs) played an important role in the resistome alteration. This study further deepens the comprehensive understanding of antibiotic resistome and the correlations among the antibiotic resistome, microbiota, and MGEs in the RTE foods.

scholarly journals Fate of Antibiotic Resistance Genes in Abandoned Swine Feedlots in China: Seasonal Variation

2021 ◽  
Author(s):  
Na Li ◽  
Jianguo Chen ◽  
Chong Liu ◽  
Binxu Li ◽  
Changxiong Zhu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Seasonal Variation ◽  
Bacterial Community ◽  
Community Composition ◽  
Resistance Genes ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Antibiotic Resistance Genes ◽  
Rrna Gene ◽  
Variation Patterns

Abstract Background: Environmental hygiene concerns are needed to be settled before the reuse of abandoned swine feedlot sites. However, few researchers have focused on the fate of antibiotic resistance genes (ARGs) in soil microbiota around abandoned swine feedlots. In this study, we examined the seasonal alterations of ARGs and bacterial community composition in soil using quantitative PCR and high-throughput sequencing of 16S rRNA gene. Results: The seasonal variation patterns were different for different ARG subtypes and soil sampling sites. The bacterial community composition at the genus level generally showed no significant alteration from winter to summer. Moreover, the co-occurrence network suggested that the bacterial genera host range of ARGs was broader in the summer than in the winter. Conclusion: This study offers further data on ARG transfer risk in soil, emphasizing the necessity of continuous concern before reuse of abandoned feedlots.

scholarly journals Anaerobic Digestion and Removal of Sulfamethoxazole, Enrofloxacin, Ciprofloxacin and Their Antibiotic Resistance Genes in a Full-Scale Biogas Plant

Antibiotics ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 502
Author(s):  
Andrea Visca ◽  
Anna Barra Caracciolo ◽  
Paola Grenni ◽  
Luisa Patrolecco ◽  
Jasmin Rauseo ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Anaerobic Digestion ◽  
Resistance Genes ◽  
Emerging Contaminants ◽  
Antibiotic Resistance Genes ◽  
Animal Manure ◽  
Full Scale ◽  
Antibiotic Residues ◽  
Anaerobic Digesters ◽  
One Year

Anaerobic digestion is one of the best ways to re-use animal manure and agricultural residues, through the production of combustible biogas and digestate. However, the use of antibiotics for preventing and treating animal diseases and, consequently, their residual concentrations in manure, could introduce them into anaerobic digesters. If the digestate is applied as a soil fertilizer, antibiotic residues and/or their corresponding antibiotic resistance genes (ARGs) could reach soil ecosystems. This work investigated three common soil emerging contaminants, i.e., sulfamethoxazole (SMX), ciprofloxacin (CIP), enrofloxacin (ENR), their ARGs sul1, sul2, qnrS, qepA, aac-(6′)-Ib-cr and the mobile genetic element intI1, for one year in a full scale anaerobic plant. Six samplings were performed in line with the 45-day hydraulic retention time (HRT) of the anaerobic plant, by collecting input and output samples. The overall results show both antibiotics and ARGs decreased during the anaerobic digestion process. In particular, SMX was degraded by up to 100%, ENR up to 84% and CIP up to 92%, depending on the sampling time. In a similar way, all ARGs declined significantly (up to 80%) in the digestate samples. This work shows how anaerobic digestion can be a promising practice for lowering antibiotic residues and ARGs in soil.

scholarly journals Citrobacter tructae sp. nov. Isolated from Kidney of Diseased Rainbow Trout (Oncorhynchus mykiss)

2021 ◽  
Vol 9 (2) ◽  
pp. 275
Author(s):  
Won Joon Jung ◽  
Hyoun Joong Kim ◽  
Sib Sankar Giri ◽  
Sang Guen Kim ◽  
Sang Wha Kim ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
Biochemical Characterization ◽  
Antibiotic Resistance Genes ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Bacterial Identification ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
The 16S Rrna Gene ◽  
Genome Distance

A novel Citrobacter species was isolated from the kidney of diseased rainbow trout (Oncorhynchus mykiss) reared on a trout farm. Biochemical characterization and phylogenetic analysis were performed for bacterial identification. Sequencing of the 16S rRNA gene and five housekeeping genes indicated that the strain belongs to the Citrobacter genus. However, multilocus sequence analysis, a comparison of average nucleotide identity, and genome-to-genome distance values revealed that strain SNU WT2 is distinct and forms a separate clade from other Citrobacter species. Additionally, the phenotype characteristics of the strain differed from those of other Citrobacter species. Quinone analysis indicated that the predominant isoprenoid quinone is Q-10. Furthermore, strain virulence was determined by a rainbow trout challenge trial, and the strain showed resistance to diverse antibiotics including β-lactams, quinolone, and aminoglycosides. The complete genome of strain SNU WT2 is 4,840,504 bp with a DNA G + C content of 51.94% and 106,068-bp plasmid. Genome analysis revealed that the strain carries virulence factors on its chromosome and antibiotic resistance genes on its plasmid. This strain represents a novel species in the genus Citrobacter for which the name C. tructae has been proposed, with SNU WT2 (=KCTC 72517 = JCM 33612) as the type strain.

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