CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

Alcock, Brian; Huynh, William; Chalil, Romeo; Smith, Keaton W; Raphenya, Amogelang R.; Wlodarski, Mateusz A; Edalatmand, Arman; Petkau, A.; Syed, Sohaib A; Tsang, Kara K.; Baker, Sheridan J C; Dave, Mugdha; McCarthy, Madeline C.; Mukiri, Karyn M; Nasir, Jalees A; Golbon, Bahar; Imtiaz, Hamna; Jiang, Xianzhi; Kaur, Komal; Kwong, Megan; Liang, Zi Cheng; Niu, Keyu C; Shan, Prabakar; Yang, Jasmine Y J; Gray, Kristen L; Hoad, Gemma; Jia, Baofeng; Bhando, Timsy; Carfrae, Lindsey A; Farha, Maya A.; French, Shawn; Gordzevich, Rodion; Rachwalski, Kenneth; Tu, Megan M.; Bordeleau, Emily; Dooley, Damion; Griffiths, Emma; Zubyk, Haley L.; Brown, Eric D.; Maguire, Finlay; Beiko, Robert G.; Hsiao, William W. L.; Brinkman, Fiona S. L.; Domselaar, Gary Van; McArthur, Andrew G.

doi:10.1093/nar/gkac920

Cited by 481 publications

(353 citation statements)

References 24 publications

(33 reference statements)

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“…Gene calling and annotation were performed with the Rapid Annotation using Subsystem Technology (RAST) server ( ) ( Aziz et al., 2008 ) and the SEED viewer framework ( Overbeek et al., 2014 ). In addition, the antibiotic resistance genes of strains are obtained by comparison in the comprehensive antibiotic resistance database ( ) ( Alcock et al., 2022 ). Using the virulence factor database (VFDB, ) ( Liu et al., 2019 ), we identified genome encoded virulence factor (VF) genes.…”

Section: Methodsmentioning

confidence: 99%

“…In addition, the antibiotic resistance genes of strains are obtained by comparison in the comprehensive antibiotic resistance database (https://card. mcmaster.ca/analyze) (Alcock et al, 2022). Using the virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/main.htm) (Liu et al, 2019), we identified genome encoded virulence factor (VF) genes.…”

Section: Whole-genome Sequencing Analysesmentioning

confidence: 99%

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Morphological and genomic characteristics of two novel actinomycetes, Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. isolated from bat faeces (Rousettus leschenaultia and Taphozous perforates)

Huang

Zhang²,

Tao³

et al. 2023

Front. Cell. Infect. Microbiol.

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Four Gram-staining-positive, aerobic, non-motile, circle-shaped bacteria were isolated from the faeces of bats (Rousettus leschenaultia and Taphozous perforates) collected from Guangxi autonomous region (E106°49′20″, N22°20′54″) and Yunnan province (E102°04′39″, N25°09′10″) of South China. Strains HY006T and HY008 shared highly 16S rRNA gene sequence similarity to those of Ornithinimicrobium pratense W204T (99.3%) and O. flavum CPCC 203535T (97.3%), while the strains HY1745 and HY1793T were closest to the type strains O. ciconiae H23M54T (98.7%), O. cavernae CFH 30183T (98.3%), and O. murale 01-Gi-040T (98.1%). Furthermore, when compared to the other members of the genus Ornithinimicrobium, the digital DNA-DNA hybridization and average nucleotide identity values of the four novel strains were within the ranges of 19.6–33.7% and 70.6–87.4%, respectively, both of which were below the respective recommended cutoff values of 70.0% and 95–96%. Significantly, strain HY006T was resistant to chloramphenicol and linezolid whereas strain HY1793T was resistant to erythromycin, clindamycin (intermediately), and levofloxacin (intermediately). The main cellular fatty acids (>20.0%) of our isolates were iso-C15:0 and iso-C16:0. Strains HY006T and HY1793T contained ornithine as the diagnostic diamino acid, also along with the alanine, glycine and glutamic acid in their cell wall. Based on phylogenetic, chemotaxonomic and phenotypic analyses, these four strains could be classified as two novel species of the genus Ornithinimicrobium, for which the names Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. are proposed. The type strains are HY006T (=CGMCC 1.16565T =JCM 33397T) and HY1793T (=CGMCC 1.19143T =JCM 34881T), respectively.

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Section: Methodsmentioning

confidence: 99%

Section: Whole-genome Sequencing Analysesmentioning

confidence: 99%

Morphological and genomic characteristics of two novel actinomycetes, Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. isolated from bat faeces (Rousettus leschenaultia and Taphozous perforates)

Huang

Zhang²,

Tao³

et al. 2023

Front. Cell. Infect. Microbiol.

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“…In addition, phage genomes were blasted on the GenBank database, and the life cycle of the closest phage homolog was identified. The presence of antibiotic resistance genes and bacterial virulence factor encoding gene in phage genomes was evaluated using CARD [ 29 ] and the VF analyzer on the Virulence Factor Database [ 30 ], respectively. The absence of prophage, from the production strain, was verified in silico using Phaster [ 31 , 32 ] and the absence of temperate phage expression arising from a prophage lacking the replicase gene was assessed by qPCR in the phage preparation.…”

Section: Methodsmentioning

confidence: 99%

Administration of Bacteriophages via Nebulization during Mechanical Ventilation: In Vitro Study and Lung Deposition in Macaques

Guellec

Pardessus

Bodier-Montagutelli

et al. 2023

Viruses

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Bacteriophages have been identified as a potential treatment option to treat lung infection in the context of antibiotic resistance. We performed a preclinical study to predict the efficacy of delivery of bacteriophages against Pseudomonas aeruginosa (PA) when administered via nebulization during mechanical ventilation (MV). We selected a mix of four anti-PA phages containing two Podoviridae and two Myoviridae, with a coverage of 87.8% (36/41) on an international PA reference panel. When administered via nebulization, a loss of 0.30–0.65 log of infective phage titers was measured. No difference between jet, ultrasonic and mesh nebulizers was observed in terms of loss of phage viability, but a higher output was measured with the mesh nebulizer. Interestingly, Myoviridae are significantly more sensitive to nebulization than Podoviridae since their long tail is much more prone to damage. Phage nebulization has been measured as compatible with humidified ventilation. Based on in vitro measurement, the lung deposition prediction of viable phage particles ranges from 6% to 26% of the phages loaded in the nebulizer. Further, 8% to 15% of lung deposition was measured by scintigraphy in three macaques. A phage dose of 1 × 109 PFU/mL nebulized by the mesh nebulizer during MV predicts an efficient dose in the lung against PA, comparable with the dose chosen to define the susceptibility of the strain.

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“…Furthermore, all intact prophage sequence were screened for antibiotic resistance genes using the RGI tool v.5.2.1, which uses CARD [ 44 ], exploring perfect, strict, and loose hits, and virulence factors via the Virulence Factor Database (VFDB) [ 45 ]. RGI was installed locally using conda, and the CARD database (v.3.1.4) was downloaded.…”

Section: Methodsmentioning

confidence: 99%

Coliphages of the human urinary microbiota

Crum

Merchant²,

Ene³

et al. 2023

PLoS ONE

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Due to its frequent association with urinary tract infections (UTIs), Escherichia coli is the best characterized constituent of the urinary microbiota (urobiome). However, uropathogenic E. coli is just one member of the urobiome. In addition to bacterial constituents, the urobiome of both healthy and symptomatic individuals is home to a diverse population of bacterial viruses (bacteriophages). A prior investigation found that most bacterial species in the urobiome are lysogens, harboring one or more phages integrated into their genome (prophages). Many of these prophages are temperate phages, capable of entering the lytic cycle and thus lysing their bacterial host. This transition from the lysogenic to lytic life cycle can impact the bacterial diversity of the urobiome. While many phages that infect E. coli (coliphages) have been studied for decades in the laboratory setting, the coliphages within the urobiome have yet to be cataloged. Here, we investigated the diversity of urinary coliphages by first identifying prophages in all publicly available urinary E. coli genomes. We detected 3,038 intact prophage sequences, representative of 1,542 unique phages. These phages include both novel species as well as species also found within the gut microbiota. Ten temperate phages were isolated from urinary E. coli strains included in our analysis, and we assessed their ability to infect and lyse urinary E. coli strains. We also included in these host range assays other urinary coliphages and laboratory coliphages. The temperate phages and other urinary coliphages were successful in lysing urinary E. coli strains. We also observed that coliphages from non-urinary sources were most efficient in killing urinary E. coli strains. The two phages, T2 and N4, were capable of lysing 83.5% (n = 86) of strains isolated from females with UTI symptoms. In conclusion, our study finds a diverse community of coliphages in the urobiome, many of which are predicted to be temperate phages, ten of which were confirmed here. Their ability to infect and lyse urinary E. coli strains suggests that urinary coliphages may play a role in modulating the E. coli strain diversity of the urobiome.

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CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

Cited by 481 publications

References 24 publications

Morphological and genomic characteristics of two novel actinomycetes, Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. isolated from bat faeces (Rousettus leschenaultia and Taphozous perforates)

Morphological and genomic characteristics of two novel actinomycetes, Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. isolated from bat faeces (Rousettus leschenaultia and Taphozous perforates)

Administration of Bacteriophages via Nebulization during Mechanical Ventilation: In Vitro Study and Lung Deposition in Macaques

Coliphages of the human urinary microbiota

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