scholarly journals Seasonal and spatial variability of antibiotic resistance genes and Class I integrons in the rivers of the Mekong delta, Vietnam

2021 ◽  
Author(s):  
Thi Thu Hang Pham ◽  
Khoa Dinh Hoang Dang ◽  
Emmanuelle Rohrbach ◽  
Florian Breider ◽  
Pierre Rossi
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Rainy Season ◽  
Large Scale ◽  
River Sediments ◽  
Mekong Delta ◽  
Antibiotic Resistance Genes ◽  
Dry Season ◽  
Class I ◽  
Economic Losses

Aquaculture activities are steadily expanding in Vietnam, covering an estimated 700,000 ha, with 89% of these culture ponds located in the Mekong Delta. Since 2009, large-scale bacterial epidemics have spread in response to this intensive cultivation. Antibiotics, even those considered as a last resort, have only partially mitigated this problem. In turn, the side effects of the massive use of these chemicals include the appearance of mobile genetic elements associated with antibiotic resistance genes (ARGs). The large-scale emergence of a diverse bacterial resistome, along with severe economic losses, has posed significant health risks to local residents. In this study, the seasonal and spatial distributions of the class I integrase (CL1) intl1 and the ARGs sul2 (sulfonamide), BLA-oxa1 (β-lactams), and ermB (erythromycin) were quantified from water and sediment samples collected during two consecutive seasons along the Vam Co River and its tributary (Long An province, Vietnam). The results showed that CL1 was present in all river compartments, reaching 2.98×104 copies/mL and 1.07×106 copies/g of sediment, respectively. The highest relative copy abundances to the 16S rDNA gene were measured in water samples, with up to 3.02% for BLA-oxa1, followed by sul2 (1.16%) and ermB (0.46%). Strong seasonal (dry season vs. rainy season) and spatial patterns were recorded for all resistance genes. Higher amounts of ARGs in river water could be associated with higher antibiotic use during the rainy season. In contrast, higher amounts of ARGs were recorded in river sediments during the dry season, making this habitat a potential reservoir of transient genes. Finally, the observations made in this study allowed us to clarify the environmental and anthropogenic influences that may favor the dispersal and persistence of ARGS in this riverine ecosystem.

scholarly journals Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Yu Pan ◽  
Jiaxiong Zeng ◽  
Liguan Li ◽  
Jintao Yang ◽  
Ziyun Tang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Virulence Factors ◽  
Resistance Genes ◽  
Large Scale ◽  
Antibiotic Resistance Genes ◽  
Comprehensive Analysis ◽  
Health Concern ◽  
Human Pathogens ◽  
Bacterial Genomes ◽  
Gene Acquisition

ABSTRACT Widespread use of antibiotics has enhanced the evolution of highly resilient pathogens and poses a severe risk to human health via coselection of antibiotic resistance genes (ARGs) and virulence factors (VFs). In this study, we rigorously evaluate the abundance relationship and physical linkage between ARGs and VFs by performing a comprehensive analysis of 9,070 bacterial genomes isolated from multiple species and hosts. The coexistence of ARGs and VFs was observed in bacteria across distinct phyla, pathogenicities, and habitats, especially among human-associated pathogens. The coexistence patterns of gene elements in different habitats and pathogenicity groups were similar, presumably due to frequent gene transfer. A shorter intergenic distance between mobile genetic elements and ARGs/VFs was detected in human/animal-associated bacteria, indicating a higher transfer potential. Increased accumulation of exogenous ARGs/VFs in human pathogens highlights the importance of gene acquisition in the evolution of human commensal bacteria. Overall, the findings provide insights into the genic features of combinations of ARG-VF and expand our understanding of ARG-VF coexistence in bacteria. IMPORTANCE Antibiotic resistance has become a serious global health concern. Despite numerous case studies, a comprehensive analysis of ARG and VF coexistence in bacteria is lacking. In this study, we explore the coexistence profiles of ARGs and VFs in diverse categories of bacteria by using a high-resolution bioinformatics approach. We also provide compelling evidence of unique ARG-VF gene pairs coexisting in specific bacterial genomes and reveal the potential risk associated with the coexistence of ARGs and VFs in organisms in both clinical settings and environments.

scholarly journals Occurrence and Distribution Characteristics of Antibiotic Resistance Genes in Sediments Between Urban and Rural of the Liaohe River Basin, China

2021 ◽  
Author(s):  
Guangshui Na ◽  
Keyu Zhang ◽  
Hui Gao ◽  
Ruijing Li ◽  
Shuaichen Jin ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
River Basin ◽  
Resistance Genes ◽  
Rural Areas ◽  
Human Activities ◽  
Rapid Development ◽  
River Sediments ◽  
Antibiotic Resistance Genes ◽  
Liaohe River ◽  
Liaohe River Basin

Abstract Antibiotic Resistance Genes (ARGs) are considered to be emerging pollutants related to human activities. The rapid development of global urbanization has expanded human activities, thereby exacerbating the global human health risks caused by antibiotic resistance genes. The effects of urban and rural environments are multifarious, which makes the source and distribution of ARGs in the environment diversification. Understanding the distribution and spread of ARGs is essential for studying the environmental behavior of ARGs. In this study, the occurrence 296 genes were detected by the high-throughput qPCR technology, and FC value was used to analyze the diversity of ARGs and Mobile Genetic Elements (MGEs) in sediments between urban and rural areas of the Liaohe River Basin, China. The co-occurrence of MGEs and ARGs was analyzed using network to decipher core genes. A total of 187 ARGs and 10 MGEs were detected in all sediment samples. The average number of genes detected in urban sites is 89 higher than that in rural sites. The high abundance and various types of ARGs and MGEs detected in urban river sediments indicates that the occurrence of urban ARGs is more complex. MGEs were detected high levels and were significantly correlated with the abundance and diversity of ARGs in river sediments providing evidence that MGEs were related to the occurrence and distribution of ARGs and tnpA(tnpA-07, tnpA-01 and tnpA-03) gene were at the key position of co-occurrence of various types of ARGs.

scholarly journals IS26-Mediated Formation of Transposons Carrying Antibiotic Resistance Genes

mSphere ◽  
2016 ◽  
Vol 1 (2) ◽  
Author(s):  
Christopher J. Harmer ◽  
Ruth M. Hall
Keyword(s):  
Antibiotic Resistance ◽  
Homologous Recombination ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Class I ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Content Type ◽  
Movement Mechanism

ABSTRACT In Gram-negative bacteria, IS26 recruits antibiotic resistance genes into the mobile gene pool by forming transposons carrying many different resistance genes. In addition to replicative transposition, IS26 was recently shown to use a novel conservative movement mechanism in which an incoming IS26 targets a preexisting one. Here, we have demonstrated how IS26-bounded class I transposons can be produced from translocatable units (TUs) containing only an IS26 and a resistance gene via the conservative reaction. TUs were incorporated next to an existing IS26, creating a class I transposon, and if the targeted IS26 is in a transposon, the product resembles two transposons sharing a central IS26, a configuration observed in some resistance regions and when a transposon is tandemly duplicated. Though homologous recombination could also incorporate a TU, Tnp26 is far more efficient. This provides insight into how IS26 builds transposons and brings additional transposons into resistance regions. The IS26 transposase, Tnp26, catalyzes IS26 movement to a new site and deletion or inversion of adjacent DNA via a replicative route. The intramolecular deletion reaction produces a circular molecule consisting of a DNA segment and a single IS26, which we call a translocatable unit or TU. Recently, Tnp26 was shown to catalyze an additional intermolecular, conservative reaction between two preexisting copies of IS26 in different plasmids. Here, we have investigated the relative contributions of homologous recombination and Tnp26-catalyzed reactions to the generation of a transposon from a TU. Circular TUs containing the aphA1a kanamycin and neomycin resistance gene or the tet(D) tetracycline resistance determinant were generated in vitro and transformed into Escherichia coli recA cells carrying R388::IS26. The TU incorporated next to the IS26 in R388::IS26 forms a transposon with the insertion sequence (IS) in direct orientation. Introduction of a second TU produced regions containing both the aphA1a gene and the tet(D) determinant in either order but with only three copies of IS26. The integration reaction, which required a preexisting IS26, was precise and conservative and was 50-fold more efficient when both IS26 copies could produce an active Tnp26. When both ISs were inactivated by a frameshift in tnp26, TU incorporation was not detected in E. coli recA cells, but it did occur in E. coli recA + cells. However, the Tnp-catalyzed reaction was 100-fold more efficient than RecA-dependent homologous recombination. The ability of Tnp26 to function in either a replicative or conservative mode is likely to explain the prominence of IS26-bounded transposons in the resistance regions found in Gram-negative bacteria. IMPORTANCE In Gram-negative bacteria, IS26 recruits antibiotic resistance genes into the mobile gene pool by forming transposons carrying many different resistance genes. In addition to replicative transposition, IS26 was recently shown to use a novel conservative movement mechanism in which an incoming IS26 targets a preexisting one. Here, we have demonstrated how IS26-bounded class I transposons can be produced from translocatable units (TUs) containing only an IS26 and a resistance gene via the conservative reaction. TUs were incorporated next to an existing IS26, creating a class I transposon, and if the targeted IS26 is in a transposon, the product resembles two transposons sharing a central IS26, a configuration observed in some resistance regions and when a transposon is tandemly duplicated. Though homologous recombination could also incorporate a TU, Tnp26 is far more efficient. This provides insight into how IS26 builds transposons and brings additional transposons into resistance regions.

Decay of elevated antibiotic resistance genes in natural river sediments after sedimentation of wastewater particles

2020 ◽  
Vol 705 ◽  
pp. 135861 ◽  
Author(s):  
Philip C. Brown ◽  
Ewa Borowska ◽  
Rafael Peschke ◽  
Thomas Schwartz ◽  
Harald Horn
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
River Sediments ◽  
Antibiotic Resistance Genes
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