AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

Feldgarden, Michael; Brover, Vyacheslav; González-Escalona, Narjol; Frye, Jonathan G.; Haendiges, Julie; Haft, Daniel H.; Hoffmann, Maria; Pettengill, James B.; Prasad, Arjun B.; Tillman, Glenn E.; Tyson, Gregory H.; Klimke, William

doi:10.1038/s41598-021-91456-0

Cited by 662 publications

(501 citation statements)

References 35 publications

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“…To identify antibiotic resistance genes, genomes were analyzed using NCBI's AMRFinderPlus (Feldgarden et al, 2021 ) where coding sequences (CDS) were predicted, and antimicrobial resistance (AMR) genes were annotated through a combination of HMMER (Eddy, 1998 ) and BLASTP (Altschul et al, 1990 ) searches. AMRFinderPlus searches against a curated database of AMR genes and protein profile HMMs.…”

Section: Methodsmentioning

confidence: 99%

Comparison of CRISPR–Cas Immune Systems in Healthcare-Related Pathogens

Mortensen

Lam

2021

Front. Microbiol.

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The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and Clostridium difficile have been identified as the leading global cause of multidrug-resistant bacterial infections in hospitals. CRISPR–Cas systems are bacterial immune systems, empowering the bacteria with defense against invasive mobile genetic elements that may carry the antimicrobial resistance (AMR) genes, among others. On the other hand, the CRISPR–Cas systems are themselves mobile. In this study, we annotated and compared the CRISPR–Cas systems in these pathogens, utilizing their publicly available large numbers of sequenced genomes (e.g., there are more than 12 thousands of S. aureus genomes). The presence of CRISPR–Cas systems showed a very broad spectrum in these pathogens: S. aureus has the least tendency of obtaining the CRISPR–Cas systems with only 0.55% of its isolates containing CRISPR–Cas systems, whereas isolates of C. difficile we analyzed have CRISPR–Cas systems each having multiple CRISPRs. Statistical tests show that CRISPR–Cas containing isolates tend to have more AMRs for four of the pathogens (A. baumannii, E. faecium, P. aeruginosa, and S. aureus). We made available all the annotated CRISPR–Cas systems in these pathogens with visualization at a website (https://omics.informatics.indiana.edu/CRISPRone/pathogen), which we believe will be an important resource for studying the pathogens and their arms-race with invaders mediated through the CRISPR–Cas systems, and for developing potential clinical applications of the CRISPR–Cas systems for battles against the antibiotic resistant pathogens.

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Section: Methodsmentioning

confidence: 99%

Comparison of CRISPR–Cas Immune Systems in Healthcare-Related Pathogens

Mortensen

Lam

2021

Front. Microbiol.

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“…For phylogenetic reconstruction, we align the core-genome using Parsnp ( Treangen et al, 2014 ), and we build a tree based on core-genome alignment using IQ-TREE. The presence of resistance genes was extracted from the metadata available from the NCBI, a database that annotates the genomes using AMRFinderPlus ( Feldgarden et al, 2021 ). Finally, the visualization of the CPCoA analyzes was used BIC ( http://www.ehbio.com/Cloud_Platform/front/# ).…”

Section: Why Should Insertion Sequences Be An Epidemiological Descriptor?mentioning

confidence: 99%

Beyond to the Stable: Role of the Insertion Sequences as Epidemiological Descriptors in Corynebacterium striatum

Leyton-Carcaman

Abanto

2022

Front. Microbiol.

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In recent years, epidemiological studies of infectious agents have focused mainly on the pathogen and stable components of its genome. The use of these stable components makes it possible to know the evolutionary or epidemiological relationships of the isolates of a particular pathogen. Under this approach, focused on the pathogen, the identification of resistance genes is a complementary stage of a bacterial characterization process or an appendix of its epidemiological characterization, neglecting its genetic components’ acquisition or dispersal mechanisms. Today we know that a large part of antibiotic resistance is associated with mobile elements. Corynebacterium striatum, a bacterium from the normal skin microbiota, is also an opportunistic pathogen. In recent years, reports of infections and nosocomial outbreaks caused by antimicrobial multidrug-resistant C. striatum strains have been increasing worldwide. Despite the different existing mobile genomic elements, there is evidence that acquired resistance genes are coupled to insertion sequences in C. striatum. This perspective article reviews the insertion sequences linked to resistance genes, their relationship to evolutionary lineages, epidemiological characteristics, and the niches the strains inhabit. Finally, we evaluate the potential of the insertion sequences for their application as a descriptor of epidemiological scenarios, allowing us to anticipate the emergence of multidrug-resistant lineages.

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“…Fasta_shift ( https://github.com/b-brankovics/fasta_tools ) was used to set the start position of the polished assembly according to that of S. Typhi CT18 (GenBank accession number GCF_000195995.1 ) and Ty2 ( GCF_000007545.1 ). The complete genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) ( 30 ), and its predicted serotype and antimicrobial resistance profiles were computed using SeqSero2 v1.2.1 ( 31 ) and AMRFinderPlus v3.10.5 ( 32 ), respectively ( Table 1 ). Default options were used unless otherwise indicated.…”

Section: Announcementmentioning

confidence: 99%