scholarly journals Extensive antimicrobial resistance mobilization via multicopy plasmid encapsidation mediated by temperate phages

2020 ◽  
Vol 75 (11) ◽  
pp. 3173-3180
Author(s):  
Lorena Rodríguez-Rubio ◽  
Carlos Serna ◽  
Manuel Ares-Arroyo ◽  
Bosco R Matamoros ◽  
Jose F Delgado-Blas ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
High Efficiency ◽  
Marker Gene ◽  
Multicopy Plasmid ◽  
Aminoglycoside Resistance ◽  
Plasmid Copy ◽  
Antimicrobial Resistance Genes ◽  
Complete Sequences ◽  
High Level

Abstract Objectives To investigate the relevance of multicopy plasmids in antimicrobial resistance and assess their mobilization mediated by phage particles Methods Several databases with complete sequences of plasmids and annotated genes were analysed. The 16S methyltransferase gene armA conferring high-level aminoglycoside resistance was used as a marker in eight different plasmids, from different incompatibility groups, and with differing sizes and plasmid copy numbers. All plasmids were transformed into Escherichia coli bearing one of four different lysogenic phages. Upon induction, encapsidation of armA in phage particles was evaluated using qRT–PCR and Southern blotting. Results Multicopy plasmids carry a vast set of emerging clinically important antimicrobial resistance genes. However, 60% of these plasmids do not bear mobility (MOB) genes. When carried on these multicopy plasmids, mobilization of a marker gene armA into phage capsids was up to 10000 times more frequent than when it was encoded by a large plasmid with a low copy number. Conclusions Multicopy plasmids and phages, two major mobile genetic elements (MGE) in bacteria, represent a novel high-efficiency transmission route of antimicrobial resistance genes that deserves further investigation.

Multiple-Antibiotic Resistance of Enterococcus faecalis and Enterococcus faecium from Cecal Contents in Broiler Chicken and Turkey Flocks Slaughtered in Canada and Plasmid Colocalization of tetO and ermB Genes

2011 ◽  
Vol 74 (10) ◽  
pp. 1639-1648 ◽  
Author(s):  
CINDY-LOVE TREMBLAY ◽  
ANN LETELLIER ◽  
SYLVAIN QUESSY ◽  
MARTINE BOULIANNE ◽  
DANIELLE DAIGNAULT ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Enterococcus Faecalis ◽  
Resistance Genes ◽  
Enterococcus Faecium ◽  
Broiler Chicken ◽  
Multidrug Resistant ◽  
Poultry Meat ◽  
Antimicrobial Resistance Genes ◽  
High Level ◽  
Level Resistance

This study was conducted to characterize the antimicrobial resistance determinants and investigate plasmid colocalization of tetracycline and macrolide genes in Enterococcus faecalis and Enterococcus faecium from broiler chicken and turkey flocks in Canada. A total of 387 E. faecalis and E. faecium isolates were recovered from poultry cecal contents from five processing plants. The percentages of resistant E. faecalis and E. faecium isolates, respectively, were 88.1 and 94% to bacitracin, 0 and 0.9% to chloramphenicol, 0.7 and 14.5% to ciprofloxacin, 72.6 and 80.3% to erythromycin, 3.7 and 41% to flavomycin, 9.6 and 4.3% (high-level resistance) to gentamicin, 25.2 and 17.1% (high-level resistance) to kanamycin, 100 and 94% to lincomycin, 0 and 0% to linezolid, 2.6 and 20.5% to nitrofurantoin, 3 and 27.4% to penicillin, 98.5 and 89.7% to quinupristin-dalfopristin, 7 and 12.8% to salinomycin, 46.7 and 38.5% (high-level resistance) to streptomycin, 95.6 and 89.7% to tetracycline, 73 and 75.2% to tylosin, and 0 and 0% to vancomycin. One predominant multidrug-resistant phenotypic pattern was identified in both E. faecalis and E. faecium (bacitracin, erythromycin, lincomycin, quinupristin-dalfopristin, tetracycline, and tylosin). These isolates were further examined by PCR and sequencing for the genes encoding their antimicrobial resistance. Various combinations of vatD, vatE, bcrR, bcrA, bcrB, bcrD, ermB, msrC, linB, tetM, and tetO genes were detected, and ermB, tetM, and bcrB were the most common antimicrobial resistance genes identified. For the first time, plasmid extraction and hybridization revealed colocalization of tetO and ermB genes on a ca. 11-kb plasmid in E. faecalis isolates, and filter mating experiments demonstrated its transferability. Results indicate that the intestinal enterococci of healthy poultry, which can contaminate poultry meat at slaughter, could be a reservoir for quinupristin-dalfopristin, bacitracin, tetracycline, and macrolide resistance genes.

scholarly journals Mobilome-driven segregation of the resistome in biological wastewater treatment

2021 ◽  
Author(s):  
Laura de Nies ◽  
Susheel Bhanu Busi ◽  
Benoit Josef Kunath ◽  
Patrick May ◽  
Paul Wilmes
Keyword(s):  
Wastewater Treatment ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Essential Elements ◽  
Biological Wastewater Treatment ◽  
Longitudinal Assessment ◽  
Aminoglycoside Resistance ◽  
Antimicrobial Resistance Genes ◽  
Sulfonamide Resistance ◽  
Sulfonamide Resistance Genes

Biological wastewater treatment plants (BWWTP) are considered to be hotspots of evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization and dissemination of antimicrobial resistance genes (ARGs) and are thereby critical mediators of AMR within the BWWTP microbial community. At present, it is unclear whether specific AMR categories are differentially disseminated via bacteriophages (phages) or plasmids. To understand the segregation of AMR in relation to MGEs, we analyzed meta-omic (metagenomic, metatranscriptomic and metaproteomic) data systematically collected over 1.5 years from a BWWTP. Our results showed a core group of fifteen AMR categories which were found across all timepoints. Some of these AMR categories were disseminated exclusively (bacitracin) or primarily (aminoglycoside, MLS, sulfonamide) via plasmids or phages (fosfomycin and peptide), whereas others were disseminated equally by both MGEs. Subsequent expression- and protein-level analyses further demonstrated that aminoglycoside, bacitracin and sulfonamide resistance genes were expressed more by plasmids, in contrast to fosfomycin and peptide AMR expression by phages, thereby validating our genomic findings. Longitudinal assessment further underlined these findings whereby the log2-fold changes of aminoglycoside, bacitracin and sulfonamide resistance genes were increased in plasmids, while fosfomycin and peptide resistance showed similar trends in phages. In the analyzed communities, the dominant taxon Candidatus Microthrix parvicella was a major contributor to several AMR categories whereby its plasmids primarily mediated aminoglycoside resistance. Importantly, we also found AMR associated with ESKAPEE pathogens within the BWWTP, for which MGEs also contributed differentially to the dissemination of ARGs. Collectively our findings pave the way towards understanding the segmentation of AMR within MGEs, thereby shedding new light on resistome populations and their mediators, essential elements that are of immediate relevance to human health.

scholarly journals Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Robert C. Will ◽  
Thandavarayan Ramamurthy ◽  
Naresh Chand Sharma ◽  
Balaji Veeraraghavan ◽  
Lucky Sangal ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Corynebacterium Diphtheriae ◽  
Core Gene ◽  
Genomic Variation ◽  
Gene Variants ◽  
Antimicrobial Resistance Genes ◽  
Structural Impact ◽  
High Level

AbstractDiphtheria is a respiratory disease caused by the bacterium Corynebacterium diphtheriae. Although the development of a toxin-based vaccine in the 1930s has allowed a high level of control over the disease, cases have increased in recent years. Here, we describe the genomic variation of 502 C. diphtheriae isolates across 16 countries and territories over 122 years. We generate a core gene phylogeny and determine the presence of antimicrobial resistance genes and variation within the tox gene of 291 tox+ isolates. Numerous, highly diverse clusters of C. diphtheriae are observed across the phylogeny, each containing isolates from multiple countries, regions and time of isolation. The number of antimicrobial resistance genes, as well as the breadth of antibiotic resistance, is substantially greater in the last decade than ever before. We identified and analysed 18 tox gene variants, with mutations estimated to be of medium to high structural impact.

Mobilization of tet (X4) by IS 1 family elements in porcine Esc herichia coli isolates

2021 ◽  
Author(s):  
Runhao Yu ◽  
Zheng Chen ◽  
Stefan Schwarz ◽  
Hong Yao ◽  
Xiang-Dang Du
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Suicide Plasmid ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
High Level

The dissemination mechanism of the high-level tigecycline resistance gene tet (X4) in porcine Escherichia coli was investigated . tet (X4) and other antimicrobial resistance genes were located on the plasmids p1919D3-1 and p1919D62-1 and flanked by two or three copies of IS 1 family elements, which can form one to three translocatable units (TUs). Using a reduced transposition model, IS 1A was experimentally demonstrated to mediate the transposition of tet (X4) from a suicide plasmid into the E. coli chromosome.

scholarly journals Associations between Antimicrobial Resistance Genes in Fecal Generic Escherichia coli Isolates from Cow-Calf Herds in Western Canada

2008 ◽  
Vol 74 (12) ◽  
pp. 3658-3666 ◽  
Author(s):  
Sheryl P. Gow ◽  
Cheryl L. Waldner ◽  
Josee Harel ◽  
Patrick Boerlin
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Gene Selection ◽  
Western Canada ◽  
Genetic Determinants ◽  
Aminoglycoside Resistance ◽  
Antimicrobial Resistance Genes ◽  
Cow Calf ◽  
Aminoglycoside Resistance Genes

ABSTRACT The objective of this study was to examine associations among the genetic determinants of antimicrobial resistance (AMR) in 207 fecal generic Escherichia coli isolates obtained from 77 cow-calf herds in western Canada. Twenty-three resistance genes corresponding to six different antimicrobial families were assessed using DNA hybridization and PCR. The most common resistance genes in the study sample (207 isolates) were sul2 (48.3%), tet(B) (45.4%), and ant(3″)-Ia (aadA1) (19.3%). Several statistically significant associations between the examined resistance genes were detected. The strongest associations observed were those between genes for resistance to chloramphenicol (catI) and trimethoprim (dhfrI) (odds ratio [OR] = 214; P = 0.0001), sulfonamide (sul1) and chloramphenicol (catI) (OR = 96.9; P = 0.0001), streptomycin [ant(3″)-Ia (aadA1)] and trimethoprim (dhfrI) (OR = 96.2; P = 0.0001), sulfonamide (sul1) and streptomycin [ant(3″)-Ia (aadA1)] (OR = 79.3; P = 0.0001), and tetracycline [tet(B)] and sulfonamides (sul2) (OR = 25.7; P = 0.0001). At least one of the resistance genes corresponding to each nonaminoglycoside family of antimicrobials examined in this study was associated with the two aminoglycoside resistance genes ant(3″)-Ia (aadA1) and aph(3′)-Ia. The multiple, strong associations between genes and the diverse nature of the associations described in this study demonstrate the complexity of resistance gene selection in cow-calf herds and should be considered in the planning of AMR control practices for cow-calf operations.

scholarly journals Long-Read Sequencing Reveals Evolution and Acquisition of Antimicrobial Resistance and Virulence Genes in Salmonella enterica

2021 ◽  
Vol 12 ◽  
Author(s):  
Cong Li ◽  
Gregory H. Tyson ◽  
Chih-Hao Hsu ◽  
Lucas Harrison ◽  
Errol Strain ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Heavy Metal Resistance ◽  
Multidrug Resistant ◽  
Metal Resistance ◽  
Virulence Plasmids ◽  
Antimicrobial Resistance Genes ◽  
Long Read ◽  
High Level

Salmonella enterica is a significant and phylogenetically diverse zoonotic pathogen. To understand its genomic heterogeneity and antimicrobial resistance, we performed long-read sequencing on Salmonella isolated from retail meats and food animals. A collection of 134 multidrug-resistant isolates belonging to 33 serotypes were subjected to PacBio sequencing. One major locus of diversity among these isolates was the presence and orientation of Salmonella pathogenic islands (SPI), which varied across different serotypes but were largely conserved within individual serotypes. We also identified insertion of an IncQ resistance plasmid into the chromosome of fourteen strains of serotype I 4,[5],12:i:– and the Salmonella genomic island 1 (SGI-1) in five serotypes. The presence of various SPIs, SGI-1 and integrated plasmids contributed significantly to the genomic variability and resulted in chromosomal resistance in 55.2% (74/134) of the study isolates. A total of 93.3% (125/134) of isolates carried at least one plasmid, with isolates carrying up to seven plasmids. We closed 233 plasmid sequences of thirteen replicon types, along with twelve hybrid plasmids. Some associations between Salmonella isolate source, serotype, and plasmid type were seen. For instance, IncX plasmids were more common in serotype Kentucky from retail chicken. Plasmids IncC and IncHI had on average more than five antimicrobial resistance genes, whereas in IncX, it was less than one per plasmid. Overall, 60% of multidrug resistance (MDR) strains that carried >3 AMR genes also carried >3 heavy metal resistance genes, raising the possibility of co-selection of antimicrobial resistance in the presence of heavy metals. We also found nine isolates representing four serotypes that carried virulence plasmids with the spv operon. Together, these data demonstrate the power of long-read sequencing to reveal genomic arrangements and integrated plasmids with a high level of resolution for tracking and comparing resistant strains from different sources. Additionally, the findings from this study will help expand the reference set of closed Salmonella genomes that can be used to improve genome assembly from short-read data commonly used in One Health antimicrobial resistance surveillance.

scholarly journals Antimicrobial Resistance and Whole-Genome Characterisation of High-Level Ciprofloxacin-Resistant Salmonella Enterica Serovar Kentucky ST 198 Strains Isolated from Human in Poland

2021 ◽  
Vol 22 (17) ◽  
pp. 9381
Author(s):  
Tomasz Wołkowicz ◽  
Katarzyna Zacharczuk ◽  
Rafał Gierczyński ◽  
Magdalena Nowakowska ◽  
Katarzyna Piekarska
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Genomic Island ◽  
Test Methods ◽  
Whole Genome ◽  
Disc Diffusion ◽  
Genome Sequences ◽  
Antimicrobial Resistance Genes ◽  
High Level ◽  
Relationship Of

Background: Salmonella Kentucky belongs to zoonotic serotypes that demonstrate that the high antimicrobial resistance and multidrug resistance (including fluoroquinolones) is an emerging problem. To the best of our knowledge, clinical S. Kentucky strains isolated in Poland remain undescribed. Methods: Eighteen clinical S. Kentucky strains collected in the years 2018–2019 in Poland were investigated. All the strains were tested for susceptibility to 11 antimicrobials using the disc diffusion and E-test methods. Whole genome sequences were analysed for antimicrobial resistance genes, mutations, the presence and structure of SGI1-K (Salmonella Genomic Island and the genetic relationship of the isolates. Results: Sixteen of 18 isolates (88.9%) were assigned as ST198 and were found to be high-level resistant to ampicillin (>256 mg/L) and quinolones (nalidixic acid MIC ≥ 1024 mg/L, ciprofloxacin MIC range 6–16 mg/L). All the 16 strains revealed three mutations in QRDR of GyrA and ParC. The substitutions of Ser83 → Phe and Asp87 → Tyr of the GyrA subunit and Ser80→Ile of the ParC subunit were the most common. One S. Kentucky isolate had qnrS1 in addition to the QRDR mutations. Five of the ST198 strains, grouped in cluster A, had multiple resistant determinants like blaTEM1-B, aac(6′)-Iaa, sul1 or tetA, mostly in SGI1 K. Seven strains, grouped in cluster B, had shorter SGI1-K with deletions of many regions and with few resistance genes detected. Conclusion: The results of this study demonstrated that a significant part of S. Kentucky isolates from humans in Poland belonged to ST198 and were high-level resistant to ampicillin and quinolones.

scholarly journals High-Level Vancomycin-Resistant Staphylococcus aureus Isolates Associated with a Polymicrobial Biofilm

2006 ◽  
Vol 51 (1) ◽  
pp. 231-238 ◽  
Author(s):  
Linda M. Weigel ◽  
Rodney M. Donlan ◽  
Dong Hyeon Shin ◽  
Bette Jensen ◽  
Nancye C. Clark ◽  
...  
Keyword(s):  
New York ◽  
Staphylococcus Aureus ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Tetracycline Resistance ◽  
Aminoglycoside Resistance ◽  
Antimicrobial Resistance Genes ◽  
Vancomycin Mics ◽  
Vancomycin Resistant ◽  
High Level

ABSTRACT Glycopeptides such as vancomycin are the treatment of choice for infections due to methicillin-resistant Staphylococcus aureus. This study describes the identification of high-level vancomycin-resistant S. aureus (VRSA) isolates in a polymicrobial biofilm within an indwelling nephrostomy tube in a patient in New York. S. aureus, Enterococcus faecalis, Enterococcus faecium, Micrococcus species, Morganella morganii, and Pseudomonas aeruginosa were isolated from the biofilm. For VRSA isolates, vancomycin MICs ranged from 32 to >128 μg/ml. VRSA isolates were also resistant to aminoglycosides, fluoroquinolones, macrolides, penicillin, and tetracycline but remained susceptible to chloramphenicol, linezolid, rifampin, and trimethoprim-sulfamethoxazole. The vanA gene was localized to a plasmid of ∼100 kb in VRSA and E. faecium isolates from the biofilm. Plasmid analysis revealed that the VRSA isolate acquired the 100-kb E. faecium plasmid, which was then maintained without integration into the MRSA plasmid. The tetracycline resistance genes tet(U) and tet(S), not previously detected in S. aureus isolates, were identified in the VRSA isolates. Additional resistance elements in the VRSA isolate included a multiresistance gene cluster, ermB-aadE-sat4-aphA-3, msrA (macrolide efflux), and the bifunctional aminoglycoside resistance gene aac(6′)-aph(2")-Ia. Multiple combinations of resistance genes among the various isolates of staphylococci and enterococci, including vanA, tet(S), and tet(U), illustrate the dynamic nature of gene acquisition and loss within and between bacterial species throughout the course of infection. The potential for interspecies transfer of antimicrobial resistance genes, including resistance to vancomycin, may be enhanced by the microenvironment of a biofilm.

scholarly journals Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections

2021 ◽  
Vol 9 (4) ◽  
pp. 707
Author(s):  
J. Christopher Noone ◽  
Fabienne Antunes Ferreira ◽  
Hege Vangstein Aamot
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Virulence Gene ◽  
Orthopaedic Implant ◽  
Metagenomic Sequencing ◽  
Gene Detection ◽  
Shotgun Metagenomic Sequencing ◽  
Antimicrobial Resistance Genes ◽  
Culture Independent

Our culture-independent nanopore shotgun metagenomic sequencing protocol on biopsies has the potential for same-day diagnostics of orthopaedic implant-associated infections (OIAI). As OIAI are frequently caused by Staphylococcus aureus, we included S. aureus genotyping and virulence gene detection to exploit the protocol to its fullest. The aim was to evaluate S. aureus genotyping, virulence and antimicrobial resistance genes detection using the shotgun metagenomic sequencing protocol. This proof of concept study included six patients with S. aureus-associated OIAI at Akershus University Hospital, Norway. Five tissue biopsies from each patient were divided in two: (1) conventional microbiological diagnostics and genotyping, and whole genome sequencing (WGS) of S. aureus isolates; (2) shotgun metagenomic sequencing of DNA from the biopsies. Consensus sequences were analysed using spaTyper, MLST, VirulenceFinder, and ResFinder from the Center for Genomic Epidemiology (CGE). MLST was also compared using krocus. All spa-types, one CGE and four krocus MLST results matched Sanger sequencing results. Virulence gene detection matched between WGS and shotgun metagenomic sequencing. ResFinder results corresponded to resistance phenotype. S. aureus spa-typing, and identification of virulence and antimicrobial resistance genes are possible using our shotgun metagenomics protocol. MLST requires further optimization. The protocol has potential application to other species and infection types.

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