scholarly journals Insertion sequences associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteremia.

2021 ◽  
Author(s):  
Zulema Udaondo ◽  
Kaleb Z Abram ◽  
Atul Kothari ◽  
Se-Ran Jun
Keyword(s):  
Antibiotic Resistance ◽  
Transposable Elements ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Insertion Sequences ◽  
Rapid Adaptation ◽  
Resistance Mutations ◽  
New Paradigm ◽  
Novel Association ◽  
Extended Analysis

Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in dissemination and modification of antibiotic resistance phenotype. To that end, we leveraged fully resolved Enterococcus faecium and Enterococcus faecalis genomes of isolates collected over four days from an inpatient with prolonged bacteremia. Isolates from both species harbored similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events, and IS-medicated excision events in plasmids of E. faecium isolates. We also characterize a novel arrangement of the IS in a Tn1546-like transposon in E. faecalis isolates likely implicated in a vancomycin genotype-phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in liaSR genes and a putative composite transposon in E. faecium offering a new paradigm for the study of daptomycin-resistance and novel insights into the route of daptomycin resistance dissemination. In conclusion, our study highlights the role ISs and other transposable elements play in rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.

scholarly journals Chloramphenicol Resistance in Clostridium difficile Is Encoded on Tn4453 Transposons That Are Closely Related to Tn4451 from Clostridium perfringens

1998 ◽  
Vol 42 (7) ◽  
pp. 1563-1567 ◽  
Author(s):  
Dena Lyras ◽  
Christine Storie ◽  
Andrea S. Huggins ◽  
Paul K. Crellin ◽  
Trudi L. Bannam ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Clostridium Difficile ◽  
Transposable Elements ◽  
Clostridium Perfringens ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Nucleotide Sequencing ◽  
Chloramphenicol Resistance ◽  
Circular Form ◽  
And Function

ABSTRACT The chloramphenicol resistance gene catD fromClostridium difficile was shown to be encoded on the transposons Tn4453a and Tn4453b, which were structurally and functionally related to Tn4451 fromClostridium perfringens. Tn4453a and Tn4453b excised precisely from recombinant plasmids, generating a circular form, as is the case for Tn4451. Evidence that this process is mediated by Tn4453-encodedtnpX genes was obtained from experiments which showed that in trans these genes complemented a Tn4451tnpXΔ1 mutation for excision. Nucleotide sequencing showed that the joint of the circular form generated by the excision of Tn4453a and Tn4453b was similar to that from Tn4451. These results suggest that the Tn4453-encoded TnpX proteins bind to similar DNA target sequences and function in a manner comparable to that of TnpX from Tn4451. Furthermore, it has been shown that Tn4453a and Tn4453b can be transferred to suitable recipient cells by RP4 and therefore are mobilizable transposons. It is concluded that, like Tn4451, they must encode a functional tnpZ gene and a targetoriT or RSA site. The finding that related transposable elements are present in C. difficile andC. perfringens has implications for the evolution and dissemination of antibiotic resistance genes and the mobile elements on which they are found within the clostridia.

scholarly journals F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in Human-Associated Commensal Escherichia coli

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Craig Stephens ◽  
Tyler Arismendi ◽  
Megan Wright ◽  
Austin Hartman ◽  
Andres Gonzalez ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Transposable Elements ◽  
Dna Sequencing ◽  
Resistance Genes ◽  
Bacterial Pathogens ◽  
Acquired Resistance ◽  
Antibiotic Resistance Genes ◽  
Content Type ◽  
E Coli

ABSTRACT The evolution and propagation of antibiotic resistance by bacterial pathogens are significant threats to global public health. Contemporary DNA sequencing tools were applied here to gain insight into carriage of antibiotic resistance genes in Escherichia coli, a ubiquitous commensal bacterium in the gut microbiome in humans and many animals, and a common pathogen. Draft genome sequences generated for a collection of 101 E. coli strains isolated from healthy undergraduate students showed that horizontally acquired antibiotic resistance genes accounted for most resistance phenotypes, the primary exception being resistance to quinolones due to chromosomal mutations. A subset of 29 diverse isolates carrying acquired resistance genes and 21 control isolates lacking such genes were further subjected to long-read DNA sequencing to enable complete or nearly complete genome assembly. Acquired resistance genes primarily resided on F plasmids (101/153 [67%]), with smaller numbers on chromosomes (30/153 [20%]), IncI complex plasmids (15/153 [10%]), and small mobilizable plasmids (5/153 [3%]). Nearly all resistance genes were found in the context of known transposable elements. Very few structurally conserved plasmids with antibiotic resistance genes were identified, with the exception of an ∼90-kb F plasmid in sequence type 1193 (ST1193) isolates that appears to serve as a platform for resistance genes and may have virulence-related functions as well. Carriage of antibiotic resistance genes on transposable elements and mobile plasmids in commensal E. coli renders the resistome highly dynamic. IMPORTANCE Rising antibiotic resistance in human-associated bacterial pathogens is a serious threat to our ability to treat many infectious diseases. It is critical to understand how acquired resistance genes move in and through bacteria associated with humans, particularly for species such as Escherichia coli that are very common in the human gut but can also be dangerous pathogens. This work combined two distinct DNA sequencing approaches to allow us to explore the genomes of E. coli from college students to show that the antibiotic resistance genes these bacteria have acquired are usually carried on a specific type of plasmid that is naturally transferrable to other E. coli, and likely to other related bacteria.

scholarly journals BacAnt: A Combination Annotation Server for Bacterial DNA Sequences to Identify Antibiotic Resistance Genes, Integrons, and Transposable Elements

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaoting Hua ◽  
Qian Liang ◽  
Min Deng ◽  
Jintao He ◽  
Meixia Wang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Transposable Elements ◽  
Resistance Genes ◽  
Dna Sequences ◽  
Antibiotic Resistance Genes ◽  
Bacterial Dna ◽  
Annotation Server

Graphical AbstractOverall BacAnt’s service workflow. The figure is adapted with permissions from IntegronFinder (Cury et al., 2016).

scholarly journals Class II Transposon-Borne Structure Harboring Metallo-β-Lactamase Gene blaVIM-2 in Pseudomonas putida

2006 ◽  
Vol 50 (8) ◽  
pp. 2889-2891 ◽  
Author(s):  
Laurent Poirel ◽  
Ludovic Cabanne ◽  
Louis Collet ◽  
Patrice Nordmann
Keyword(s):  
Antibiotic Resistance ◽  
Pseudomonas Putida ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Class Ii ◽  
Insertion Sequences ◽  
Carbapenem Resistant ◽  
Lactamase Gene

ABSTRACT A plasmid-encoded class II transposon element was identified in a carbapenem-resistant Pseudomonas putida isolate. Tn1332, closely related to Tn1331, harbored the metallo-β-lactamase gene bla VIM-2 in addition to four other antibiotic resistance genes, aacA4, aadA1, bla OXA-9, and bla TEM-1, and two novel insertion sequences, ISPpu17 and ISPpu18.

scholarly journals A glyphosate-based herbicide cross-selects for antibiotic resistance genes in bacterioplankton communities

2021 ◽  
Author(s):  
Naíla Barbosa da Costa ◽  
Marie-Pier Hébert ◽  
Vincent Fugère ◽  
Yves Terrat ◽  
Gregor Fussmann ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Antibiotic Resistance Genes ◽  
Efflux Pumps ◽  
Cross Resistance ◽  
Resistant Bacteria ◽  
Metagenomic Sequencing ◽  
Resistance Mutations ◽  
Variation Explained

Agrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, Roundup, a widely-used glyphosate-based herbicide (GBH), has the potential to indirectly select for antibiotic resistant bacteria. Such cross-selection could occur, for example, if the same genes (e.g. encoding efflux pumps) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added Roundup to 1,000-L mesocosms filled with water from a pristine lake. Over 57 days, we tracked changes in bacterial communities with shotgun metagenomic sequencing, and annotated metagenome-assembled genomes (MAGs) for the presence of known antibiotic resistance genes (ARGs), plasmids, and resistance mutations in the enzyme targeted by glyphosate (enolpyruvyl-shikimate-3-phosphate synthase; EPSPS). We found that high doses of GBH significantly increased ARG frequency and selected for multidrug efflux pumps in particular. The relative abundance of MAGs after a high dose of GBH was predictable based on the number of ARGs encoded in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS (2% of variation explained). Together, these results indicate that GBHs have the potential to cross-select for antibiotic resistance in natural freshwater bacteria.

scholarly journals The Association between Insertion Sequences and Antibiotic Resistance Genes

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Mohammad Razavi ◽  
Erik Kristiansson ◽  
Carl-Fredrik Flach ◽  
D. G. Joakim Larsson
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Infections ◽  
Antibiotic Resistance Genes ◽  
Mobile Genetic Elements ◽  
Insertion Sequences ◽  
Negative Consequences ◽  
Bacterial Genomes ◽  
Genetic Elements ◽  
Empirical Approaches

ABSTRACT Insertion sequences (ISs) are abundant mobile genetic elements on bacterial genomes, responsible for mobilization of many genes, including antibiotic resistance genes (ARGs). As ARGs often occur in similar genetic contexts, understanding which ISs tend to be associated with known ARGs could be a first step toward discovering novel ARGs through predictive or experimental strategies. This could be valuable, as early identification of ARGs in pathogens could facilitate surveillance, confinement actions, molecular diagnostics, and drug development. Here, we present a comprehensive analysis of the association of specific ISs with known ARGs. A large collection of bacterial genomes was used to characterize the immediate context of 2,437 known ARGs and 3,768 ISs. While many ARGs were consistently found close to specific ISs, the contexts around all ISs were more variable. Nevertheless, a subset of individual ISs, as well as tentative composite transposons, showed significant associations with ARGs. These included, e.g., insertion sequences classified as IS6, Tn3, IS4, and IS1 that were not only strongly associated with diverse ARGs but also highly abundant in pathogens. Therefore, we conclude that the context of this subset of ISs and tentative composite transposons would be particularly valuable to discover novel ARGs through modeling or empirical approaches. A set of 1,891 metagenomes were analyzed to identify environments where those ISs commonly associated with ARGs were particularly abundant. The associations found in metagenomes were similar to those found in genomes. IMPORTANCE The emergence and spread of antibiotic resistance genes (ARGs) among pathogens threaten the prevention and treatment of bacterial infections as well as our food production chains. Early knowledge about mobile ARGs that are present in pathogens or that have the potential to become clinically relevant could help mitigate potential negative consequences. Recently, exploring integron gene cassettes was shown to be successful for identifying novel mobilized ARGs, some of which were already circulating in pathogens. Still, only a subset of ARGs is mobilized by integrons, and the contexts of other mobile genetic elements associated with ARGs remain unexplored. This includes insertion sequences (ISs) responsible for the mobilization of many ARGs. Our analyses identified ISs, species, and environments where ARG-IS relationships are particularly strong. This could be a first step to guide the discovery of novel ARGs, while also providing insights into mechanisms involved in the mobilization and transfer of ARGs.

Quintuplex PCR to Detect Antibiotic Resistance Genes in Streptococcus pneumoniae

2016 ◽  
Vol 1 (2) ◽  
pp. 22 ◽  
Author(s):  
Navindra Kumari Palanisamy ◽  
Parasakthi Navaratnam ◽  
Shamala Devi Sekaran
Keyword(s):  
Antibiotic Resistance ◽  
Streptococcus Pneumoniae ◽  
Resistance Genes ◽  
Bacterial Pathogen ◽  
Antibiotic Resistance Genes ◽  
Pcr Amplification ◽  
Penicillin Resistance ◽  
Penicillin Binding Proteins ◽  
Efflux Mechanism ◽  
Mic Value

Introduction: Streptococcus pneumoniae is an important bacterial pathogen, causing respiratory infection. Penicillin resistance in S. pneumoniae is associated with alterations in the penicillin binding proteins, while resistance to macrolides is conferred either by the modification of the ribosomal target site or efflux mechanism. This study aimed to characterize S. pneumoniae and its antibiotic resistance genes using 2 sets of multiplex PCRs. Methods: A quintuplex and triplex PCR was used to characterize the pbp1A, ermB, gyrA, ply, and the mefE genes. Fifty-eight penicillin sensitive strains (PSSP), 36 penicillin intermediate strains (PISP) and 26 penicillin resistance strains (PRSP) were used. Results: Alteration in pbp1A was only observed in PISP and PRSP strains, while PCR amplification of the ermB or mefE was observed only in strains with reduced susceptibility to erythromycin. The assay was found to be sensitive as simulated blood cultures showed the lowest level of detection to be 10cfu. Conclusions: As predicted, the assay was able to differentiate penicillin susceptible from the non-susceptible strains based on the detection of the pbp1A gene, which correlated with the MIC value of the strains.

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