Genetic determinants of antimicrobial resistance in Streptococcus canis in France

Arcobacter spp. are emerging waterborne and foodborne zoonotic pathogens responsible for gastroenteritis in humans. In this work, we evaluated the occurrence and the antimicrobial resistance profile of Arcobacter isolates recovered from different aquatic sources. Besides, we searched for Arcobacter spp. in seaweeds and the corresponding seawater samples. Bacteriological and molecular methods applied to 100 samples led to the isolation of 28 Arcobacter isolates from 27 samples. The highest prevalence was detected in rivers followed by artificial ponds, streams, well waters, and spring waters. Seaweeds contained a higher percentage of Arcobacter than the corresponding seawater samples. The isolates were identified as Arcobacter butzleri (96.4%) and Arcobacter cryaerophilus (3.6%). All the isolates showed a multi-drug resistance profile, being resistant to at least three different classes of antibiotics. Molecular analysis of genetic determinants responsible for tetracycline resistance in nine randomly chosen isolates revealed the presence of tetO and/or tetW. This work confirms the occurrence and the continuous emergence of antibiotic-resistant Arcobacter strains in environmental samples; also, the presence of quinolone-resistant Arcobacter spp. in aquatic sources used for water supply and irrigation represents a potential risk for human health.

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Metagenomics: aid to combat antimicrobial resistance in diarrhea

Gut Pathogens ◽

10.1186/s13099-019-0331-8 ◽

2019 ◽

Vol 11 (1) ◽

Cited By ~ 5

Author(s):

Rituparna De

Keyword(s):

Antimicrobial Resistance ◽

Antimicrobial Agents ◽

Genetic Recombination ◽

Molecular Taxonomy ◽

Ecological Niches ◽

Next Generation ◽

Genetic Determinants ◽

Antimicrobial Resistance Genes ◽

And Function ◽

Generation Sequencing

Abstract Antimicrobial resistance (AMR) has emerged as an obstacle in the supple administration of antimicrobial agents to critical diarrheal patients. Most diarrheal pathogens have developed resistance against the major classes of antibiotics commonly used for assuaging diarrheal symptoms. Antimicrobial resistance develops when pathogens acquire antimicrobial resistance genes (ARGs) through genetic recombination from commensals and pathogens. These are the constituents of the complex microbiota in all ecological niches. The recombination events may occur in the environment or in the gut. Containment of AMR can be achieved through a complete understanding of the complex and diverse structure and function of the microbiota. Its taxonomic entities serve as focal points for the dissemination of antimicrobial resistance genetic determinants. Molecular methods complemented with culture-based diagnostics have been historically implemented to document these natural events. However, the advent of next-generation sequencing has revolutionized the field of molecular epidemiology. It has revolutionized the method of addressing relevant problems like diagnosis and surveillance of infectious diseases and the issue of antimicrobial resistance. Metagenomics is one such next-generation technique that has proved to be a monumental advancement in the area of molecular taxonomy. Current understanding of structure, function and dysbiosis of microbiota associated with antimicrobial resistance was realized due to its conception. This review describes the major milestones achieved due to the advent and implementation of this new technique in the context of antimicrobial resistance. These achievements span a wide panorama from the discovery of novel microorganisms to invention of translational value.

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Changes in Antimicrobial Susceptibility of Native Enterococcus faecium in Chickens Fed Virginiamycin

Applied and Environmental Microbiology ◽

10.1128/aem.71.9.4986-4991.2005 ◽

2005 ◽

Vol 71 (9) ◽

pp. 4986-4991 ◽

Cited By ~ 20

Author(s):

Patrick F. McDermott ◽

Patti Cullen ◽

Susannah K. Hubert ◽

Shawn D. McDermott ◽

Mary Bartholomew ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Enterococcus Faecium ◽

Broiler Chickens ◽

Potential Hazard ◽

Experimental Setting ◽

Genetic Determinants ◽

Fourth Trial ◽

Resistant Population ◽

Feeding Trials ◽

Time Point

ABSTRACT The extent of transfer of antimicrobial resistance from agricultural environments to humans is controversial. To assess the potential hazard posed by streptogramin use in food animals, this study evaluated the effect of virginiamycin exposure on antimicrobial resistance in Enterococcus faecium recovered from treated broilers. Four consecutive broiler feeding trials were conducted using animals raised on common litter. In the first three trials, one group of birds was fed virginiamycin continuously in feed at 20 g/ton, and a second group served as the nontreated control. In the fourth trial, antimicrobial-free feed was given to both groups. Fecal samples were cultured 1 day after chickens hatched and then at 1, 3, 5, and 7 weeks of age. Isolates from each time point were tested for susceptibility to a panel of different antimicrobials. Quinupristin/dalfopristin-resistant E. faecium appeared after 5 weeks of treatment in trial 1 and within 7 days of trials 2 to 4. Following removal of virginiamycin in trial 4, no resistant isolates were detected after 5 weeks. PCR failed to detect vat, vgb, or erm(B) in any of the streptogramin-resistant E. faecium isolates, whereas the msr(C) gene was detected in 97% of resistant isolates. In an experimental setting using broiler chickens, continuous virginiamycin exposure was required to maintain a stable streptogramin-resistant population of E. faecium in the animals. The bases of resistance could not be explained by known genetic determinants.

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Antimicrobial resistance and its genetic determinants in aeromonads isolated in ornamental (koi) carp (Cyprinus carpio koi) and common carp (Cyprinus carpio)

Veterinary Microbiology ◽

10.1016/j.vetmic.2009.10.001 ◽

2010 ◽

Vol 142 (3-4) ◽

pp. 435-439 ◽

Cited By ~ 27

Author(s):

Alois Čížek ◽

Monika Dolejská ◽

Radana Sochorová ◽

Kateřina Strachotová ◽

Veronika Piačková ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Common Carp ◽

Cyprinus Carpio ◽

Genetic Determinants ◽

Koi Carp ◽

Common Carp Cyprinus Carpio ◽

Carp Cyprinus Carpio ◽

Cyprinus Carpio Koi

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Genetic antimicrobial resistance determinants and their prevalence in molecular subtypes of Treponema pallidum subsp. pallidum

Clinical Microbiology and Antimicrobial Chemotherapy ◽

10.36488/cmac.2018.3.216-221 ◽

2018 ◽

Vol 20 (3) ◽

pp. 216-221 ◽

Cited By ~ 1

Author(s):

O.A. Obraztsova ◽

K.A. Aleynikova ◽

A.P. Obukhov ◽

A.A. Kubanov ◽

Dmitry G. Deryabin

Keyword(s):

Antimicrobial Resistance ◽

16S Rrna ◽

Russian Federation ◽

Molecular Subtypes ◽

Treponema Pallidum ◽

Clinical Isolates ◽

23S Rrna ◽

Rrna Gene ◽

Genetic Determinants ◽

The Russian Federation

Objective. To investigate genetic determinants of resistance to antimicrobial agents recommended for the treatment of syphilis and assess their prevalence in molecular subtypes of Treponema pallidum subsp. pallidum in the Russian Federation over the period of 2014-2017. Materials and Methods. A total of 161 clinical isolates of T. pallidum obtained from Tyva, Stavropol, Irkutsk, Kaluga, Novosibirsk and Omsk regions were included in this study. Genetic material of T. pallidum was detected by PCR with primers to polA gene. Determinants of resistance to penicillins (tromp1, tp47), tetracyclines (16S rRNA) and macrolides (23S rRNA) were determined using the gene sequence analysis. Molecular typing was performed by characterizing variable arp, tpr (E, G, J) and tp0548 genes according to the CDC protocol. Results of this study were compared to historical data on antimicrobial resistance of T. pallidum over the period of 2011-2012. Results. Analysis of tromp1 and tp47 gene sequences detected C22G and G208T substitutions, respectively. These polymorphisms were not significant for activity of the corresponding proteins, but differed the studied clinical isolates from the reference strain Nichols, therefore, linking them with epidemic genogroup T. pallidum Street Strain 14. Based on the analysis of G1058C mutation in the 16S rRNA gene, all clinical isolates obtained in 2014-2017 belonged to wild type, whereas this genetic determinant of resistance to tetracyclines was determined in 2 of 190 isolates obtained in 2011-2012. Also, A2059G/C mutation in the 23S rRNA gene was not found, whereas a significant A2058G substitution in this gene was determined in 4 isolates obtained in 2014-2017. Results of this study confirm sporadic resistance to macrolides in the Russian Federation, which was previously (2011-2012) found in 3 of 190 isolates of T. pallidum. A2058G mutation was detected predominantly in minor subtypes of T. pallidum (14 b/f, 14 b/g and 14 d/g) and was unrepresentative for molecular subtype 14 d/f which is a predominant one in the Russian Federation. Conclusions. The long-term use of penicillins for the treatment of syphilis did not result in emergence of T. pallidum resistance to this antibiotic class. An absence of genetic determinants of resistance to tetracyclines confirms them to be second-line drugs. A sporadic prevalence of determinants of resistance to macrolides requires they be used for the treatment of syphilis with caution.

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Genetic determinants of multi-drug resistance in Acinetobacter baumannii at an academic hospital in Pretoria, South Africa

10.1101/809129 ◽

2019 ◽

Author(s):

Noel-David Nogbou ◽

Dikwata Thabiso Phofa ◽

Maphoshane Nchabeleng ◽

Andrew Munyalo Musyoki

Keyword(s):

South Africa ◽

Antimicrobial Resistance ◽

Genetic Relatedness ◽

Efflux Pump ◽

Multi Drug Resistance ◽

Drug Resistant ◽

Genetic Determinants ◽

Pump System ◽

Active Efflux ◽

Almost All

AbstractAntimicrobial resistance is now globally recognised as the greatest threat to human health. Acinetobacter baumanniis’ (A. baumannii) clinical significance has been driven by its ability to obtain and transmit antimicrobial resistance factors. In South Africa, A. baumannii is a leading cause of healthcare associated infections (HAI). In this study, we investigated the genetic determinants of multi-drug resistant A. baumannii (MDRAB) at a teaching hospital in Pretoria, South Africa.One hundred non repetitive isolates of A. baumannii were collected for the study at Dr George Mukhari Tertiary Laboratory (DGMTL). Antimicrobial susceptibility testing was performed using the VITEK2 system (bioMerieux, France). The prevalence of common resistance associated genes and AdeABC efflux pump system associated genes were investigated using conventional PCR. Genetic relatedness of isolates was then determined using rep-PCR.Seventy (70) of 100 isolates collected were confirmed to be multi-drug resistant and were blaOXA51 positive. Phenotypically, the isolates where resistant to almost all tested antibiotics. However, one isolate showed intermediate susceptibility to tigecycline while all were susceptible to colistin. Oxacillinase encoding gene blaOXA-23 was the most detected at 99% and only 1% was positive for blaOXA-40. The PCR results for metallo-betalactamase (MBL) encoding genes showed that MBL blaVIM was the most frequently detected at 86% and blaSIM-1 at 3% was the least detected. Out of 70 isolates, 56 isolates had the required gene combination for an active efflux pump. The most prevalent clone was clone A at 69% of the isolates. Regarding treatment; colistin and tigecycline are the most effective against strains encountered at DGMTL as all tested carbapenems seem to have lost their effectiveness.The major genotypic determinants for drug resistances are oxacillinases: blaOXA-51 (100%) and blaOXA-23 (99%). The study reports for the first time, blaOXA-40 and blaSIM-1 detection in A. baumannii in South Africa.

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Study of antimicrobial resistance for the causative agent of the bovine reproductive system infection by the NGS method

BIO Web of Conferences ◽

10.1051/bioconf/20213606029 ◽

2021 ◽

Vol 36 ◽

pp. 06029

Author(s):

Sergey Zaytsev ◽

Mariya Khizhnyakova ◽

Ekaterina Krasnikova ◽

Olga Larionova ◽

Valentina Feodorova

Keyword(s):

Next Generation Sequencing ◽

Antimicrobial Resistance ◽

Reproductive System ◽

Animal Husbandry ◽

Genetic Determinants ◽

Bacterial Dna ◽

Sequencing Method ◽

Generation Sequencing ◽

Resistant Microorganism ◽

Next Generation Sequencing Method

In the present study, the biomaterial specimen derived from a farm animal with a chronic reproductive system infection was carefully investigated using the Next Generation Sequencing method. The bacterial DNA of the genus Enterobacter was detected. The genetic determinants of resistance to 12 classes of antibiotics were identified in the genome of this microorganism. The data obtained highlight the necessity of strengthening global control over the spread of resistant microorganism strains in agriculture especially in the animal husbandry sector.

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Representing Genetic Determinants in Bacterial GWAS with Compacted De Bruijn Graphs

10.1101/113563 ◽

2017 ◽

Cited By ~ 5

Author(s):

Magali Jaillard ◽

Maud Tournoud ◽

Leandro Lima ◽

Vincent Lacroix ◽

Jean-Baptiste Veyrieras ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Pathogenic Bacteria ◽

Resistance Mechanisms ◽

Health Concern ◽

Genetic Determinants ◽

De Bruijn Graphs ◽

De Bruijn ◽

Marker Discovery ◽

Core Genes

AbstractMotivationAntimicrobial resistance has become a major worldwide public health concern, calling for a better characterization of existing and novel resistance mechanisms. GWAS methods applied to bacterial genomes have shown encouraging results for new genetic marker discovery. Most existing approaches either look at SNPs obtained by sequence alignment or consider sets of kmers, whose presence in the genome is associated with the phenotype of interest. While the former approach can only be performed when genomes are similar enough for an alignment to make sense, the latter can lead to redundant descriptions and to results which are hard to interpret.ResultsWe propose an alignment-free GWAS method detecting haplotypes of variable length associated to resistance, using compacted De Bruijn graphs. Our representation is flexible enough to deal with very plastic genomes subject to gene transfers while drastically reducing the number of features to explore compared to kmers, without loss of information. It accomodates polymorphisms in core genes, accessory genes and noncoding regions. Using our representation in a GWAS leads to the selection of a small number of entities which are easier to visualize and interpret than fixed-length kmers. We illustrate the benefit of our approach by describing known as well as potential novel determinants of antimicrobial resistance in P. aeruginosa, a pathogenic bacteria with a highly plastic genome.Availability and implementationThe code and data used in the experiments will be made available upon acceptance of this [email protected]

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

Applied and Environmental Microbiology ◽

10.1128/aem.02505-07 ◽

2008 ◽

Vol 74 (12) ◽

pp. 3658-3666 ◽

Cited By ~ 52

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.

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PATRIC as a unique resource for studying antimicrobial resistance

Briefings in Bioinformatics ◽

10.1093/bib/bbx083 ◽

2017 ◽

Vol 20 (4) ◽

pp. 1094-1102 ◽

Cited By ~ 28

Author(s):

Dionysios A Antonopoulos ◽

Rida Assaf ◽

Ramy Karam Aziz ◽

Thomas Brettin ◽

Christopher Bun ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Genetic Determinants ◽

Functional Roles ◽

Phenotype Data ◽

Whole Genomes ◽

Public Repositories ◽

Public Archives ◽

Genomic Regions ◽

Omic Data ◽

Design Experiments

AbstractThe Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org) is designed to provide researchers with the tools and services that they need to perform genomic and other ‘omic’ data analyses. In response to mounting concern over antimicrobial resistance (AMR), the PATRIC team has been developing new tools that help researchers understand AMR and its genetic determinants. To support comparative analyses, we have added AMR phenotype data to over 15 000 genomes in the PATRIC database, often assembling genomes from reads in public archives and collecting their associated AMR panel data from the literature to augment the collection. We have also been using this collection of AMR metadata to build machine learning-based classifiers that can predict the AMR phenotypes and the genomic regions associated with resistance for genomes being submitted to the annotation service. Likewise, we have undertaken a large AMR protein annotation effort by manually curating data from the literature and public repositories. This collection of 7370 AMR reference proteins, which contains many protein annotations (functional roles) that are unique to PATRIC and RAST, has been manually curated so that it projects stably across genomes. The collection currently projects to 1 610 744 proteins in the PATRIC database. Finally, the PATRIC Web site has been expanded to enable AMR-based custom page views so that researchers can easily explore AMR data and design experiments based on whole genomes or individual genes.

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