scholarly journals Co-Carriage of Metal and Antibiotic Resistance Genes in Sewage Associated Staphylococci

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1473
Author(s):  
Atena Amirsoleimani ◽  
Gail Brion ◽  
Patrice Francois
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Metal Resistance ◽  
Aquatic Systems ◽  
Genomic Sequences ◽  
Staphylococcus Warneri ◽  
Gene Acquisition ◽  
Blastn Analysis

Controlling spread of resistance genes from wastewater to aquatic systems requires more knowledge on how resistance genes are acquired and transmitted. Whole genomic sequences from sewage-associated staphylococcus isolates (20 S. aureus, 2 Staphylococcus warneri, and 2 Staphylococcus delphini) were analyzed for the presence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). Plasmid sequences were identified in each isolate to investigate co-carriage of ARGs and MRGs within. BLASTN analysis showed that 67% of the isolates carried more than one ARG. The carriage of multiple plasmids was observed more in CC5 than CC8 S. aureus strains. Plasmid exchange was observed in all staphylococcus species except the two S. delphini isolates that carried multiple MRGs, no ARGs, and no plasmids. 85% of S. aureus isolates carried the blaZ gene, 76% co-carried blaZ with cadD and cadX, with 62% of these isolates carrying blaZ, cadD, and cadX on the same plasmid. The co-carriage of ARGs and MRGs in S. warneri isolates, and carriage of MRGs in S. delphini, without plasmids suggests non-conjugative transmission routes for gene acquisition. More studies are required that focus on the transduction and transformation routes of transmission to prevent interspecies exchange of ARGs and MRGs in sewage-associated systems.

Coexistence between antibiotic resistance genes and metal resistance genes in manure-fertilized soils

Geoderma ◽  
2021 ◽  
Vol 382 ◽  
pp. 114760
Author(s):  
Na Zhang ◽  
Philippe Juneau ◽  
Ruilin Huang ◽  
Zhili He ◽  
Bo Sun ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Metal Resistance

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 Diversity analysis and metagenomic insights into the Antibiotic Resistance and Metal Resistances among Hot Spring Bacteriobiome-insinuating inherent environmental baseline levels of Antibiotic and Metal tolerance

2019 ◽  
Author(s):  
Ishfaq Nabi Najar ◽  
Mingma Thundu Sherpa ◽  
Sayak Das ◽  
Nagendra Thakur
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Hot Springs ◽  
Metal Tolerance ◽  
Hot Spring ◽  
Thermophilic Bacteria ◽  
Antibiotic Resistance Genes ◽  
Metal Resistance ◽  
Culture Independent ◽  
Maximum Similarity

AbstractMechanisms of occurrence and expressions of antibiotic resistance genes (ARGs) in thermophilic bacteria are still unknown owing to limited research and data. The evolution and proliferation of ARGs in the thermophilic bacteria is unclear and needs a comprehensive study. In this research, comparative profiling of antibiotic resistance genes and metal tolerance genes among the thermophilic bacteria has been done by culture-independent functional metagenomic methods. Metagenomic analysis showed the dominance of Proteobacteria, Actinobacteria. Firmicutes and Bacteroidetes in these hot springs. ARG analysis through shotgun gene sequencing was found to be negative in case of thermophilic bacteria. However, few of genes were detected but they were showing maximum similarity with mesophilic bacteria. Concurrently, metal resistance genes were also detected in the metagenome sequence of hot springs. Detection of metal resistance gene and absence of ARG’s investigated by whole genome sequencing, in the reference genome sequence of thermophilic Geobacillus also conveyed the same message. This evolutionary selection of metal resistance over antibiotic genes may have been necessary to survive in the geological craters which are full of different metals from earth sediments rather than antibiotics. Furthermore, the selection could be environment driven depending on the susceptibility of ARG’s in thermophilic environment as it reduces the chances of horizontal gene transfer. With these findings this article highlights many theories and culminates different scopes to study these aspects in thermophiles.

Genotypic and Phenotypic Characterization of Salmonella Isolated from Fresh Ground Meats Obtained from Retail Grocery Stores in the Brookings, South Dakota, Area

2018 ◽  
Vol 81 (9) ◽  
pp. 1526-1534 ◽  
Author(s):  
ALAN K. ERICKSON ◽  
DEBRA L. MURRAY ◽  
LAURA A. RUESCH ◽  
MILTON THOMAS ◽  
ZACHARY LAU ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
South Dakota ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Genomic Sequences ◽  
Phenotypic Characterization ◽  
Grocery Stores ◽  
Ground Meat ◽  
Veterinary Antibiotics ◽  
Ground Pork

ABSTRACT Salmonella is one of the most common foodborne pathogens found in retail fresh meat products. The purpose of this study was to characterize the Salmonella that is found in common types of fresh ground meats available to consumers in grocery stores in the Brookings, South Dakota, area. Salmonella serotypes were detected in 50 (19%) of 261 retail fresh ground meat samples, with 2 (2%) of 115 ground turkey samples, 6 (14%) of 42 chicken samples, and 42 (40%) of 104 ground pork samples testing positive for Salmonella. The Salmonella isolates were sequenced using an Illumina MiSeq genome sequencer. The resulting genomic sequences were analyzed to determine the serotypes of the isolates and to detect the presence of virulence and antibiotic resistance genes. The Salmonella isolated from the ground meats belonged to 23 different serotypes. The predominant serotype isolated from ground chicken was Enteriditis (5 of 6, 83%). Among the ground pork isolates, the most common serotypes were the potential monophasic variant of Typhimurium (5 of 42, 12%), Uganda (5 of 42, 12%), Anatum (4 of 42, 10%), Derby (3 of 42, 7%), Infantis (3 of 42, 7%), and London (3 of 42, 7%). Among the 45 Salmonella isolates tested to determine their resistance to common veterinary antibiotics, 25 (56%) were found to be susceptible to all 14 antibiotics tested, 11 (24%) were resistant to 1 antibiotic, 4 (9%) were resistant to 2 antibiotics, 1 (2%) was resistant to 3 antibiotics, 2 (4%) were resistant to 4 antibiotics, 1 (2%) was resistant to 8 antibiotics, and 1 (2%) was resistant to 10 antibiotics. The most common antibiotic resistances observed in this study were to streptomycin (15 of 45, 33%), tetracycline (11 of 45, 24%), and sulfisoxazole (7 of 45, 16%). The results of phenotypic evaluation of antibiotic resistance profiles of Salmonella isolates correlated well with the antibiotic resistance genes detected in the genomic sequences of the isolates.

scholarly journals NanoARG: A web service for identification of antimicrobial resistance elements from nanopore-derived environmental metagenomes

2018 ◽  
Author(s):  
G. A. Arango-Argoty ◽  
D. Dai ◽  
A. Pruden ◽  
P. Vikesland ◽  
L. S. Heath ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Sequence Data ◽  
Antibiotic Resistance Genes ◽  
Metal Resistance ◽  
Direct Selection ◽  
Human Pathogens ◽  
Next Generation Sequencing Technology ◽  
Monitoring Tools ◽  
Long Reads

ABSTRACTDirect selection pressures imposed by antibiotics, indirect pressures by co-selective agents, and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effective environmental monitoring tools should ideally capture not only antibiotic resistance genes (ARGs), but also mobile genetic elements (MGEs) and indicators of co-selective forces, such as metal resistance genes (MRGs). Further, a major challenge towards characterizing potential human risk is the ability to identify bacterial host organisms, especially human pathogens. Historically, short reads yielded by next-generation sequencing technology has hampered confidence in assemblies for achieving these purposes. Here we introduce NanoARG, an online computational resource that takes advantage of long reads produced by MinION nanopore sequencing. Specifically, long nanopore reads enable identification of ARGs in the context of relevant neighboring genes, providing relevant insight into mobility, co-selection, and pathogenicity. NanoARG allows users to upload sequence data online and provides various means to analyze and visualize the data, including quantitative and simultaneous profiling of ARG, MRG, MGE, and pathogens. NanoARG is publicly available and freely accessible at http://bench.cs.vt.edu/nanoARG.

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