Related Antimicrobial Resistance Genes Detected in Different Bacterial Species Co-isolated from Swine Fecal Samples

2011 ◽  
Vol 8 (6) ◽  
pp. 663-679 ◽  
Author(s):  
Jonathan G. Frye ◽  
Rebecca L. Lindsey ◽  
Richard J. Meinersmann ◽  
Mark E. Berrang ◽  
Charlene R. Jackson ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Fecal Samples ◽  
Antimicrobial Resistance Genes

scholarly journals Antimicrobial Susceptibility Testing and Tentative Epidemiological Cutoff Values for FiveBacillusSpecies Relevant for Use as Animal Feed Additives or for Plant Protection

2018 ◽  
Vol 84 (19) ◽  
Author(s):  
Yvonne Agersø ◽  
Birgitte Stuer-Lauridsen ◽  
Karin Bjerre ◽  
Michelle Geervliet Jensen ◽  
Eric Johansen ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Animal Feed ◽  
Bacterial Species ◽  
Feed Additives ◽  
Content Type ◽  
Cutoff Values ◽  
Antimicrobial Resistance Genes ◽  
Species Specific

ABSTRACTBacillus megaterium(n= 29),Bacillus velezensis(n= 26),Bacillus amyloliquefaciens(n= 6),Bacillus paralicheniformis(n= 28), andBacillus licheniformis(n= 35) strains from different sources, origins, and time periods were tested for the MICs for nine antimicrobial agents by the CLSI-recommended method (Mueller-Hinton broth, 35°C, for 18 to 20 h), as well as with a modified CLSI method (Iso-Sensitest [IST] broth, 37°C [35°C forB. megaterium], 24 h). This allows a proposal of species-specific epidemiological cutoff values (ECOFFs) for the interpretation of antimicrobial resistance in these species. MICs determined by the modified CLSI method were 2- to 16-fold higher than with the CLSI-recommended method for several antimicrobials. The MIC distributions differed between species for five of the nine antimicrobials. Consequently, use of the modified CLSI method and interpretation of resistance by use of species-specific ECOFFs is recommended. The genome sequences of all strains were determined and used for screening for resistance genes against the ResFinder database and for multilocus sequence typing. A putative chloramphenicol acetyltransferase (cat) gene was found in oneB. megateriumstrain with an elevated chloramphenicol MIC compared to the otherB. megateriumstrains. InB. velezensisandB. amyloliquefaciens, a putative tetracycline efflux gene,tet(L), was found in all strains (n= 27) with reduced tetracycline susceptibility but was absent in susceptible strains. AllB. paralicheniformisand 23% ofB. licheniformisstrains had elevated MICs for erythromycin and harboredermD. The presence of these resistance genes follows taxonomy suggesting they may be intrinsic rather than horizontally acquired. Reduced susceptibility to chloramphenicol, streptomycin, and clindamycin could not be explained in all species.IMPORTANCEWhen commercializing bacterial strains, likeBacillusspp., for feed applications or plant bioprotection, it is required that the strains are free of acquired antimicrobial resistance genes that could potentially spread to pathogenic bacteria, thereby adding to the pool of resistance genes that may cause treatment failures in humans or animals. Conversely, if antimicrobial resistance is intrinsic to a bacterial species, the risk of spreading horizontally to other bacteria is considered very low. Reliable susceptibility test methods and interpretation criteria at the species level are needed to accurately assess antimicrobial resistance levels. In the present study, tentative ECOFFs for fiveBacillusspecies were determined, and the results showed that the variation in MICs followed the respective species. Moreover, putative resistance genes, which were detected by whole-genome sequencing and suggested to be intrinsic rather that acquired, could explain the resistance phenotypes in most cases.

scholarly journals Diverse Bacterial Resistance Genes Detected in Fecal Samples From Clinically Healthy Women and Infants in Australia—A Descriptive Pilot Study

2021 ◽  
Vol 12 ◽  
Author(s):  
Vanina Guernier-Cambert ◽  
Anthony Chamings ◽  
Fiona Collier ◽  
Soren Alexandersen
Keyword(s):  
Antimicrobial Resistance ◽  
Gut Microbiota ◽  
Resistance Genes ◽  
Bacterial Resistance ◽  
Resistance Pattern ◽  
Shotgun Metagenomics ◽  
Fecal Samples ◽  
South Eastern ◽  
Healthy Humans ◽  
Antimicrobial Resistance Genes

The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs), the so-called “resistome.” In Australia, where antibiotic use is high and resistance rates in some common pathogens are increasing, very little is known about the human resistome. To assess the presence and diversity of ARGs in the gut of Australians from south-eastern Victoria, we investigated fecal samples from clinically healthy infants and pregnant women using non-targeted (shotgun metagenomics sequencing or SMS) and targeted sequencing (two Ion AmpliseqTM panels). All methods detected ARGs in all samples, with the detection overall of 64 unique genes conferring resistance to 12 classes of antibiotics. Predominant ARGs belonged to three classes of antibiotics that are the most frequently prescribed in Australia: tetracycline, β-lactams and MLSB (macrolide, lincosamide, streptogramin B). The three bacterial Orders commonly identified as carrying ARGs were Clostridiales, Bacteroidales, and Enterobacteriales. Our preliminary results indicate that ARGs are ubiquitously present and diverse among the gut microbiota of clinically healthy humans from south-eastern Victoria, Australia. The observed resistance pattern partly overlaps with antimicrobial usage in human medicine in Australia, but ARGs to tetracycline are more common than could be expected. Our current sample is small and limited to south-eastern Victoria, and more data on healthy individuals will be needed to better depict resistance patterns at the population level, which could guide population and/or environmental monitoring and surveillance of antibiotic resistance on various spatio-temporal scales in Australia. For future studies, we recommend using the Ion AmpliseqTM Antimicrobial Resistance Research panel, which is sensitive and user-friendly, or combining several methods to increase the detected diversity.

Co-occurrence of mcr-1, mcr-3, mcr-7 and clinically relevant antimicrobial resistance genes in environmental and fecal samples

2020 ◽  
Vol 202 (7) ◽  
pp. 1795-1800
Author(s):  
Lucas David Rodrigues dos Santos ◽  
João Pedro Rueda Furlan ◽  
Micaela Santana Ramos ◽  
Inara Fernanda Lage Gallo ◽  
Lucas Victor Pereira de Freitas ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Fecal Samples ◽  
Antimicrobial Resistance Genes

scholarly journals Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis

Antibiotics ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 221
Author(s):  
Ashenafi F. Beyi ◽  
Alan Hassall ◽  
Gregory J. Phillips ◽  
Paul J. Plummer
Keyword(s):  
Antimicrobial Resistance ◽  
Microbial Communities ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Tetracycline Resistance ◽  
Digital Dermatitis ◽  
Proximity Ligation ◽  
Tetracycline Resistance Genes ◽  
Complex Microbial Community ◽  
Antimicrobial Resistance Genes

Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with ≥80% complete genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin were identified along with their bacterial hosts. In conclusion, the widespread distribution of genes conferring resistance against tetracycline and other antimicrobials in bacteria of DD lesions is reported for the first time. Use of proximity ligation to identify microorganisms hosting specific ARGs holds promise for tracking ARGs transmission in complex microbial communities.

scholarly journals Antimicrobial resistance genes in raw milk for human consumption

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Adrienn Gréta Tóth ◽  
István Csabai ◽  
Eszter Krikó ◽  
Dóra Tőzsér ◽  
Gergely Maróti ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Raw Milk ◽  
Human Consumption ◽  
Human Populations ◽  
Peptide Antibiotics ◽  
Milk Samples ◽  
Antimicrobial Resistance Genes ◽  
Depth Analysis

AbstractThe increasing prevalence of antimicrobial resistance (AMR) is a significant threat to global health. More and more multi-drug-resistant bacterial strains cause life-threatening infections and the death of thousands of people each year. Beyond disease control animals are often given antibiotics for growth promotion or increased feed efficiency, which further increase the chance of the development of multi-resistant strains. After the consumption of unprocessed animal products, these strains may meet the human bacteriota. Among the foodborne and the human populations, antimicrobial resistance genes (ARGs) may be shared by horizontal gene transfer. This study aims to test the presence of antimicrobial resistance genes in milk metagenome, investigate their genetic position and their linkage to mobile genetic elements. We have analyzed raw milk samples from public markets sold for human consumption. The milk samples contained genetic material from various bacterial species and the in-depth analysis uncovered the presence of several antimicrobial resistance genes. The samples contained complete ARGs influencing the effectiveness of acridine dye, cephalosporin, cephamycin, fluoroquinolone, penam, peptide antibiotics and tetracycline. One of the ARGs, PC1 beta-lactamase may also be a mobile element that facilitates the transfer of resistance genes to other bacteria, e.g. to the ones living in the human gut.

The Role of Gut Microbiota in Antimicrobial Resistance: A Mini-Review

2020 ◽  
Vol 18 (3) ◽  
pp. 201-206
Author(s):  
Farzaneh Firoozeh ◽  
Mohammad Zibaei
Keyword(s):  
Antimicrobial Resistance ◽  
Gut Microbiota ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Resistant Bacteria ◽  
Human Gut ◽  
Opportunistic Bacteria ◽  
Antimicrobial Resistance Genes ◽  
Opportunistic Pathogenic

In the current world, development and spread of antimicrobial resistance among bacteria have been raised and antimicrobial-resistant bacteria are one of the most important health challenges. The antimicrobial resistance genes can easily move and transfer among diverse bacterial species and strains. The human gut microbiota consists of a dense microbial population including trillions of microorganisms. Recently, studies have shown that the bacteria which make the major part of gut microbiota, harbor a variety of antimicrobial resistance genes which are called gut resistome. The transfer of resistance genes from commensal bacteria to gut-resident opportunistic bacteria may involve in the emergence of multi-drug resistant (MDR) bacteria. Thus, the main aim of the current mini-review was to study the mechanisms of exchange of antimicrobial resistance genes by commensal and opportunistic pathogenic bacteria in the human gut.

scholarly journals Comparison of microbiota, antimicrobial resistance genes and mobile genetic elements in flies and the feces of sympatric animals

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Anil Poudel ◽  
Yuan Kang ◽  
Rabindra K Mandal ◽  
Anwar Kalalah ◽  
Patrick Butaye ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Mobile Genetic Elements ◽  
Fecal Samples ◽  
Bacterial Phyla ◽  
Genetic Elements ◽  
Antimicrobial Resistance Genes ◽  
Microbial Analysis ◽  
Qpcr Array ◽  
Curtis Dissimilarity

ABSTRACT Flies are well-known vectors of bacterial pathogens, but there are little data on their role in spreading microbial community and antimicrobial resistance. In this study, we compared the bacterial community, antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in flies with those in the feces of sympatric animals. A 16S rRNA-based microbial analysis identified 23 bacterial phyla in fecal samples and 25 phyla in flies; all the phyla identified in the fecal samples were also found in the flies. Bray–Curtis dissimilarity analysis showed that the microbiota of the flies were more similar to the microbiota of the feces of their sympatric animals than those of the feces from the three other animal species studied. The qPCR array amplified 276 ARGs/MGEs in fecal samples, and 216 ARGs/MGEs in the flies, while 198 of these genes were identified in both flies and feces. Long-term studies with larger sample numbers from more geospatially distinct populations and infection trials are indicated to further evaluate the possibility of flies as sentinels for antimicrobial resistance.

scholarly journals Comparing BioFire FilmArray BCID2 and BCID panels for direct detection of bacterial pathogens and antimicrobial resistance genes from positive blood cultures

2021 ◽  
Author(s):  
Venere Cortazzo ◽  
Tiziana D’Inzeo ◽  
Liliana Giordano ◽  
Giulia Menchinelli ◽  
Flora Marzia Liotti ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Yeast Species ◽  
Bacterial Species ◽  
Blood Cultures ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
Antimicrobial Resistance Genes

Among molecular assays currently developed for detection and identification of pathogens (and their antimicrobial resistance genes) in positive blood cultures (BCs) (1), the BioFire FilmArray blood culture identification (BCID) panel (bioMérieux, Marcy l’Étoile, France)—a multiplex PCR assay with less than 2 minutes of hands-on time and a ∼1-hour turnaround time—allows syndromic diagnosis of bloodstream infection (BSI) (2, 3). Previously, the panel could identify 24 etiological agents of BSI (11 Gram-negative bacteria, 8 Gram-positive bacteria, and 5 yeast species), as well as three antimicrobial resistance genes (mecA, vanA/B, and blaKPC, which encodes Klebsiella pneumoniae carbapenemase). Now, the BioFire FilmArray BCID2 panel encompasses 43 molecular targets associated with BSI, including 15 Gram-negative bacteria, 11 Gram-positive bacteria, 7 yeast species, and 10 antimicrobial resistance genes (https://www.biomerieux-diagnostics.com/biofire-bcid-panel). The last targets include genes encoding for carbapenemases (IMP, KPC, OXA-48-like, NDM, and VIM), colistin resistance (mcr-1), ESBL (CTX-M), methicillin-resistance (mecA/C and, specifically for methicillin-resistant Staphylococcus aureus [MRSA], mecA/C and MREJ [mec right-extremity junction]), or vancomycin resistance (vanA/B). Unlike BCID, no published studies to date reported on the BCID2 performance. This study evaluated and compared the accuracy of BCID2 with that of BCID to identify bacterial species and relative antimicrobial resistance genes directly from positive BCs.

Clin-mNGS: Automated Pipeline for Pathogen Detection from Clinical Metagenomic Data

2020 ◽  
Vol 15 ◽  
Author(s):  
Akshatha Prasanna ◽  
Vidya Niranjan
Keyword(s):  
Antimicrobial Resistance ◽  
High Performance ◽  
Pathogen Detection ◽  
Bacterial Species ◽  
Workflow Management ◽  
Metagenomic Data ◽  
Antimicrobial Resistance Genes ◽  
Culture Independent ◽  
Automated Pipeline ◽  
User Friendly

Background: Since bacteria are the earliest known organisms, there has been significant interest in their variety and biology, most certainly concerning human health. Recent advances in Metagenomics sequencing (mNGS), a culture-independent sequencing technology have facilitated an accelerated development in clinical microbiology and our understanding of pathogens. Objective: For the implementation of mNGS in routine clinical practice to become feasible, a practical and scalable strategy for the study of mNGS data is essential. This study presents a robust automated pipeline to analyze clinical metagenomic data for pathogen identification and classification. Method: The proposed Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible, and user-friendly framework scripted using the Snakemake workflow management software. The implementation avoids the hassle of manual installation and configuration of the multiple command-line tools and dependencies. The approach directly screens pathogens from clinical raw reads and generates consolidated reports for each sample. Results: The pipeline is demonstrated using publicly available data and is tested on a desktop Linux system and a High-performance cluster. The study compares variability in results from different tools and versions. The versions of the tools are made user modifiable. The pipeline results in quality check, filtered reads, host subtraction, assembled contigs, assembly metrics, relative abundances of bacterial species, antimicrobial resistance genes, plasmid finding, and virulence factors identification. The results obtained from the pipeline are evaluated based on sensitivity and positive predictive value. Conclusion: Clin-mNGS is an automated Snakemake pipeline validated for the analysis of microbial clinical metagenomics reads to perform taxonomic classification and antimicrobial resistance prediction.

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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