scholarly journals Genetic Determinants for Metal Tolerance and Antimicrobial Resistance Detected in Bacteria Isolated from Soils of Olive Tree Farms

Antibiotics ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 476
Author(s):  
Nicolás Glibota ◽  
Mª José Grande ◽  
Antonio Galvez ◽  
Elena Ortega
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Metal Tolerance ◽  
Antibiotic Resistance Genes ◽  
Olive Tree ◽  
Bacterial Strains ◽  
Genetic Determinants ◽  
Genetic Traits ◽  
Tree Farms

Copper-derived compounds are often used in olive tree farms. In a previous study, a collection of bacterial strains isolated from olive tree farms were identified and tested for phenotypic antimicrobial resistance and heavy metal tolerance. The aim of this work was to study the genetic determinants of resistance and to evaluate the co-occurrence of metal tolerance and antibiotic resistance genes. Both metal tolerance and antibiotic resistance genes (including beta-lactamase genes) were detected in the bacterial strains from Cu-treated soils. A high percentage of the strains positive for metal tolerance genes also carried antibiotic resistance genes, especially for genes involved in resistances to beta-lactams and tetracycline. Significant associations were detected between genes involved in copper tolerance and genes coding for beta-lactamases or tetracycline resistance mechanisms. A significant association was also detected between zntA (coding for a Zn(II)-translocating P-type ATPase) and tetC genes. In conclusion, bacteria from soils of Cu-treated olive farms may carry both metal tolerance and antibiotic resistance genes. The positive associations detected between metal tolerance genes and antibiotic resistance genes suggests co-selection of such genetic traits by exposure to metals.

scholarly journals Characterization of Genetic Determinants Involved in Antimicrobial Resistance in Aeromonas hydrophila, Escherichia coli and Vibrio cholerae Isolated from Different Aquatic Environments

Proceedings ◽  
2020 ◽  
Vol 45 (1) ◽  
pp. 15
Author(s):  
Iroha I. Romanus ◽  
Ude Ibiam ◽  
Ejikeugwu C. Peter ◽  
Onochie C. Chike
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
16S Rrna ◽  
Resistance Genes ◽  
Aeromonas Hydrophila ◽  
Antibiotic Resistance Genes ◽  
Aquatic Environments ◽  
Genetic Determinants ◽  
Specific Primers

Aeromonas hydrophila, Escherichia coli and Vibrio cholerae are among a myriad of bacteria pathogen commonly found in natural water bodies that cause serious waterborne infection while antibiotic resistance genes are emerging contaminants posing potential worldwide human health risk. This study was designed to determined genetic determinants involved in antimicrobial resistance in bacteria isolates from aquatic environments. A total of 372 water samples, comprising of 111, 144 and 117 ponds, rivers and streams were collected from three local governments areas (Abakaliki, Ebonyi and Ikwo) of Ebonyi State Nigeria over a period of twelve (12) months. Bacteria Isolates obtained from water bodies were identified and characterized by polymerase chain reaction (PCR) analysis using 16S rRNA specific primers. The susceptibility of the isolates to different antibiotics was determined using disc diffusion technique. Total DNA was extracted and sequenced on Genetic Analyzer 3130 xl sequencer and the amplified 16S rRNA gene sequence. The presence of antibiotic resistance genes was determined by PCR using specific primers. Bacteria isolated were Aeromonas hydrophila (103), Escherichia coli (118) and Vibrio cholera (87). The isolates were susceptibility to gentamicin (96.12%), meropenem (94.17%), ciprofloxacin (89.32%) imipenem (85.44%) and chloramphenicol (84.47%) while they showed 94.17%, 93.20%, 90.29%, 89.32%, 88.35%, 86.41% and 83.5% resistance to penicillin, sulphamethoxazole, kanamycin, azithromycin, streptomycin cephalothin and cefuroxime respectively. The isolates were found to harbor the following antibiotic resistance genes, blaCTXM, blaSHV, class 1 Integron Ac, Intl1, blaTEM and TetB. These findings deserve serious attention, as the presence of bacteria coliforms in water harbouring antibiotic resistance genes are potential risk to the health of people. Keywords: aquatic environment resistant genes characterization.

scholarly journals Extreme genome selection towards complete antimicrobial resistance in a nosocomial strain of Stenotrophomonas maltophilia complex

2019 ◽  
Author(s):  
Sanjeet Kumar ◽  
Kanika Bansal ◽  
Prashant P. Patil ◽  
Amandeep Kaur ◽  
Satinder Kaur ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Stenotrophomonas Maltophilia ◽  
Antibiotic Resistance Genes ◽  
Chromosomal Origin ◽  
Extreme Drug Resistance

ABSTRACTWe report first complete genome sequence and analysis of an extreme drug resistance (XDR) nosocomial Stenotrophomonas maltophilia that is resistant to the mainstream drugs i.e. trimethoprim/sulfamethoxazole (TMP/SXT) and levofloxacin. Taxonogenomic analysis revealed it to be a novel genomospecies of the Stenotrophomonas maltophilia complex (Smc). Comprehensive genomic investigation revealed fourteen dynamic regions (DRs) exclusive to SM866, consisting of diverse antibiotic resistance genes, efflux pumps, heavy metal resistance, various transcriptional regulators etc. Further, resistome analysis of Smc clearly depicted SM866 to be an enriched strain, having diversified resistome consisting of sul1 and sul2 genes. Interestingly, SM866 does not have any plasmid but it harbors two diverse super-integrons of chromosomal origin. Apart from genes for sulfonamide resistance (sul1 and sul2), both of these integrons harbor an array of antibiotic resistance genes linked to ISCR (IS91-like elements common regions) elements. These integrons also harbor genes encoding resistance to commonly used disinfectants like quaternary ammonium compounds and heavy metals like mercury. Hence, isolation of a novel strain belonging to a novel sequence type (ST) and genomospecies with diverse array of resistance from a tertiary care unit of India indicates extent and nature of selection pressure driving XDRs in hospital settings. There is an urgent need to employ complete genome based investigation using emerging technologies for tracking emergence of XDR at the global level and designing strategies of sanitization and antibiotic regime.Impact StatementThe hospital settings in India have one of the highest usage of antimicrobials and heavy patient load. Our finding of a novel clinical isolate of S. maltophilia complex with two super-integrons harbouring array of antibiotic resistance genes along with antimicrobials resistance genes indicates the extent and the nature of selection pressures in action. Further, the presence of ISCR type of transposable elements on both integrons not only indicates its propensity to transfer resistome but also their chromosomal origin suggests possibilities for further genomic/phenotypic complexities. Such complex cassettes and strain are potential threat to global health care. Hence, there is an urgent need to employ cost-effective long read technologies to keep vigilance on novel and extreme antimicrobial resistance pathogens in populous countries. There is also need for surveillance for usage of antimicrobials for hygiene and linked/rapid co-evolution of extreme drug resistance in nosocomial pathogens. Our finding of the chromosomal encoding XDR will shed a light on the need of hour to understand the evolution of an opportunistic nosocomial pathogen belonging to S. maltophilia.RepositoriesComplete genome sequence of Stenotrophomonas maltophilia SM866: CP031058

scholarly journals Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania

2019 ◽  
Vol 74 (6) ◽  
pp. 1484-1493 ◽  
Author(s):  
Happiness H Kumburu ◽  
Tolbert Sonda ◽  
Marco van Zwetselaar ◽  
Pimlapas Leekitcharoenphon ◽  
Oksana Lukjancenko ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes

scholarly journals Antibiotic Resistance Characteristics of Environmental Bacteria from an Oxytetracycline Production Wastewater Treatment Plant and the Receiving River

2010 ◽  
Vol 76 (11) ◽  
pp. 3444-3451 ◽  
Author(s):  
Dong Li ◽  
Tao Yu ◽  
Yu Zhang ◽  
Min Yang ◽  
Zhen Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
River Water ◽  
Resistance Genes ◽  
Treatment Plant ◽  
Antibiotic Resistance Genes ◽  
Tetracycline Resistance ◽  
Production Plant ◽  
Bacterial Strains ◽  
High Concentration ◽  
Receiving River

ABSTRACT We characterized the bacterial populations in surface water receiving effluent from an oxytetracycline (OTC) production plant. Additional sampling sites included the receiving river water 5 km upstream and 20 km downstream from the discharge point. High levels of OTC were found in the wastewater (WW), and the antibiotic was still detectable in river water downstream (RWD), with undetectable levels in river water upstream (RWU). A total of 341 bacterial strains were isolated using nonselective media, with the majority being identified as Gammaproteobacteria. The MICs were determined for 10 antibiotics representing seven different classes of antibiotics, and the corresponding values were significantly higher for the WW and RWD isolates than for the RWU isolates. Almost all bacteria (97%) from the WW and RWD samples demonstrated multidrug-resistant (MDR) phenotypes, while in RWU samples, these were less frequent (28%). The WW and RWD isolates were analyzed for the presence of 23 tetracycline (tet) resistance genes. The majority of isolates (94.2% and 95.4% in WW and RWD, respectively) harbored the corresponding genes, with tet(A) being the most common (67.0%), followed by tet(W), tet(C), tet(J), tet(L), tet(D), tet(Y), and tet(K) (in the range between 21.0% and 40.6%). Class I integrons were detected in the majority of WW and RWD isolates (97.4% and 86.2%, respectively) but were not associated with the tet genes. We hypothesize that the strong selective pressure imposed by a high concentration of OTC contributes to the wide dissemination of tetracycline resistance genes and other antibiotic resistance genes, possibly through mobile genetic elements.

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.

scholarly journals ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

2013 ◽  
Vol 58 (1) ◽  
pp. 212-220 ◽  
Author(s):  
Sushim Kumar Gupta ◽  
Babu Roshan Padmanabhan ◽  
Seydina M. Diene ◽  
Rafael Lopez-Rojas ◽  
Marie Kempf ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Gene Sequence ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Genetic Determinants ◽  
Bacterial Genomes ◽  
Content Type ◽  
A Genome ◽  
Bioinformatic Tool

ABSTRACTARG-ANNOT (Antibiotic Resistance Gene-ANNOTation) is a new bioinformatic tool that was created to detect existing and putative new antibiotic resistance (AR) genes in bacterial genomes. ARG-ANNOT uses a local BLAST program in Bio-Edit software that allows the user to analyze sequences without a Web interface. All AR genetic determinants were collected from published works and online resources; nucleotide and protein sequences were retrieved from the NCBI GenBank database. After building a database that includes 1,689 antibiotic resistance genes, the software was tested in a blind manner using 100 random sequences selected from the database to verify that the sensitivity and specificity were at 100% even when partial sequences were queried. Notably, BLAST analysis results obtained using thermtFgene sequence (a new aminoglycoside-modifying enzyme gene sequence that is not included in the database) as a query revealed that the tool was able to link this sequence to short sequences (17 to 40 bp) found in other genes of thermtfamily with significant E values. Finally, the analysis of 178Acinetobacter baumanniiand 20Staphylococcus aureusgenomes allowed the detection of a significantly higher number of AR genes than the Resfinder gene analyzer and 11 point mutations in target genes known to be associated with AR. The average time for the analysis of a genome was 3.35 ± 0.13 min. We have created a concise database for BLAST using a Bio-Edit interface that can detect AR genetic determinants in bacterial genomes and can rapidly and easily discover putative new AR genetic determinants.

scholarly journals Uropathogenic Escherichia coli in the Urine Samples of Iranian Dogs: Antimicrobial Resistance Pattern and Distribution of Antibiotic Resistance Genes

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Amirhossein Yousefi ◽  
Saam Torkan
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Urine Samples ◽  
Disk Diffusion ◽  
Resistance Pattern ◽  
E Coli ◽  
Tract Infections

Resistant uropathogenic Escherichia coli is the most common cause of urinary tract infections in dogs. The present research was done to study the prevalence rate and antimicrobial resistance properties of UPEC strains isolated from healthy dogs and those which suffered from UTIs. Four-hundred and fifty urine samples were collected and cultured. E. coli-positive strains were subjected to disk diffusion and PCR methods. Two-hundred out of 450 urine samples (44.4%) were positive for E. coli. Prevalence of E. coli in healthy and infected dogs was 28% and 65%, respectively. Female had the higher prevalence of E. coli (P=0.039). Marked seasonality was also observed (P=0.024). UPEC strains had the highest levels of resistance against gentamicin (95%), ampicillin (85%), amikacin (70%), amoxicillin (65%), and sulfamethoxazole-trimethoprim (65%). We found that 21.50% of UPEC strains had simultaneously resistance against more than 10 antibiotics. Aac(3)-IV (77%), CITM (52.5%), tetA (46.5%), and sul1 (40%) were the most commonly detected antibiotic resistance genes. Findings showed considerable levels of antimicrobial resistance among UPEC strains of Iranian dogs. Rapid identification of infected dogs and their treatment based on the results of disk diffusion can control the risk of UPEC strains.

scholarly journals Detection and prevalence of antimicrobial resistance genes in Campylobacter spp. isolated from chickens and humans

2017 ◽  
Vol 84 (1) ◽  
Author(s):  
Samantha Reddy ◽  
Oliver T. Zishiri
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Antibiotic Resistance Genes ◽  
Quinolone Resistance ◽  
Campylobacter Coli ◽  
Antimicrobial Resistance Genes ◽  
Campylobacter Spp ◽  
Clinical Cases

Campylobacter spp. are common pathogenic bacteria in both veterinary and human medicine. Infections caused by Campylobacter spp. are usually treated using antibiotics. However, the injudicious use of antibiotics has been proven to spearhead the emergence of antibiotic resistance. The purpose of this study was to detect the prevalence of antibiotic resistance genes in Campylobacter spp. isolated from chickens and human clinical cases in South Africa. One hundred and sixty one isolates of Campylobacter jejuni and Campylobacter coli were collected from chickens and human clinical cases and then screened for the presence of antimicrobial resistance genes. We observed a wide distribution of the tetO gene, which confers resistance to tetracycline. The gyrA genes that are responsible quinolone resistance were also detected. Finally, our study also detected the presence of the blaOXA-61, which is associated with ampicillin resistance. There was a higher (p < 0.05) prevalence of the studied antimicrobial resistance genes in chicken faeces compared with human clinical isolates. The tetO gene was the most prevalent gene detected, which was isolated at 64% and 68% from human and chicken isolates, respectively. The presence of gyrA genes was significantly (p < 0.05) associated with quinolone resistance. In conclusion, this study demonstrated the presence of gyrA (235 bp), gyrA (270 bp), blaOXA-61 and tetO antimicrobial resistance genes in C. jejuni and C. coli isolated from chickens and human clinical cases. This indicates that Campylobacter spp. have the potential of resistance to a number of antibiotic classes.

scholarly journals Putative mobilized colistin resistance genes in the human gut microbiome

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Bruno G. N. Andrade ◽  
Tobias Goris ◽  
Haithem Afli ◽  
Felipe H. Coutinho ◽  
Alberto M. R. Dávila ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Antibiotic Resistance Genes ◽  
Future Research ◽  
Human Populations ◽  
Bacterial Strains ◽  
Colistin Resistance ◽  
Human Gut ◽  
Human Gut Microbiome

Abstract Background The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes. Results A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings. Conclusion This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.

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