Characterization of Clostridioides difficile Isolates Available through the CDC &amp; FDA Antibiotic Resistance Isolate Bank

Paulick, Ashley; Adamczyk, Michelle; Anderson, Karen; Vlachos, Nick; Machado, María-José; McAllister, Gillian; Korhonen, Lauren; Guh, Alice; Halpin, Alison Laufer; Rasheed, J. Kamile; Karlsson, Maria; Lutgring, Joseph D.; Gargis, Amy S.

doi:10.1128/mra.01011-20

Cited by 7 publications

(7 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The geographic locations from which strains were isolated are specified: for GWAS strains were isolated in United States, Europe and Israel and other locations, as documented; other strains were from Texas Medical Center. Also included were strains reported from the United States Centers for Disease Control and Prevention Emerging Infections Program 66 . B. fragilis 638R/pIP417(strain DSM103646) and DSM2151 were from Leibniz Institute DSMZ; DSM2151 is an antibiotic susceptibility testing control strain.…”

Section: Methodsmentioning

confidence: 99%

Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile

et al. 2023

View full text Add to dashboard Cite

Severe outbreaks and deaths have been linked to the emergence and global spread of fluoroquinolone-resistant Clostridioides difficile over the past two decades. At the same time, metronidazole, a nitro-containing antibiotic, has shown decreasing clinical efficacy in treating C. difficile infection (CDI). Most metronidazole-resistant C. difficile exhibit an unusual resistance phenotype that can only be detected in susceptibility tests using molecularly intact heme. Here, we describe the mechanism underlying this trait. We find that most metronidazole-resistant C. difficile strains carry a T-to-G mutation (which we term PnimBG) in the promoter of gene nimB, resulting in constitutive transcription. Silencing or deleting nimB eliminates metronidazole resistance. NimB is related to Nim proteins that are known to confer resistance to nitroimidazoles. We show that NimB is a heme-dependent flavin enzyme that degrades nitroimidazoles to amines lacking antimicrobial activity. Furthermore, occurrence of the PnimBG mutation is associated with a Thr82Ile substitution in DNA gyrase that confers fluoroquinolone resistance in epidemic strains. Our findings suggest that the pandemic of fluoroquinolone-resistant C. difficile occurring over the past few decades has also been characterized by widespread resistance to metronidazole.

show abstract

Section: Methodsmentioning

confidence: 99%

Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile

et al. 2023

View full text Add to dashboard Cite

show abstract

“…The geographic locations from which strains were isolated are specified: for GWAS strains were isolated in United States, Europe and Israel and other locations, as documented; other strains were from Texas Medical Center. Also included were reported from the United States Centers for Disease Control and Prevention Emerging Infections Program 54 . B. fragilis 638R/pIP417(strain DSM103646) and DSM2151 were from Leibniz Institute DSMZ; DSM2151 is an antibiotic susceptibility testing control strain.…”

Section: Methodsmentioning

confidence: 99%

Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile

Olaitan

Dureja

Youngblom

et al. 2022

Preprint

View full text Add to dashboard Cite

Severe outbreaks and deaths have been linked to the emergence and global spread of fluoroquinolone-resistant Clostridioides difficile over the past two decades. At the same time, metronidazole, a nitro-containing antibiotic, has shown decreasing clinical efficacy in treating C. difficile infection (CDI). Most metronidazole-resistant C. difficile exhibit an unusual resistance phenotype that can only be detected in susceptibility tests utilizing molecularly intact heme. Here we describe the mechanism underlying this trait, which we discovered using molecular genetics, phylogenetics, and population analyses. Most metronidazole-resistant strains evolved a T to G mutation, we term PnimBG, in the -10 regulatory promoter of the 5-nitroimidazole reductase nimB, resulting in the gene being constitutively transcribed. Silencing or deleting nimB eliminated metronidazole resistance. We identified the protein as a heme-dependent nitroreductase that degraded nitro-drugs to an amine lacking antimicrobial activity. We further discovered that the metronidazole-resistant PnimBG mutation was strongly associated with the Thr82Ile substitution conferring fluoroquinolone resistance in epidemic strains. Re-analysis of published genomes from global isolates confirmed that all but one encoding PnimBG also carried the Thr82Ile mutation. Our findings suggest that fluoroquinolone and metronidazole resistance co-mediated the pandemic of healthcare-associated C. difficile that are associated with poorer treatment outcomes in CDI patients receiving metronidazole.

show abstract

“…Both RT 027 and 176 cause severe disease and increased mortality; however, RT is not a clear predictor of infection severity (19). Epidemic clones such as RT 027 have also 18 nt deletions and deletion at position 117 in tcdC gene (20). Deletion at position 117 nt in tcdC gene is associated with recurrent CDI and overall higher mortality rate.…”

Section: Discusionmentioning

confidence: 99%

Use of tcdC gene sequencing to prevent misidentification of Clostridioides difficile ribotype 176 and 027

Havrilova,

Novakova,

Lucansky

et al. 2024

Medicinski Glasnik

View full text Add to dashboard Cite

Aim To compare the sequences of the tcdC gene between Clostridioides difficile (C. difficile) strains identified as PCR ribotype 176 and the reference strain C. difficile PCR ribotype 027 and to evaluate the use of the Xpert C. difficile/Epi assay for their differentiation.&nbsp; Methods A total of 45 strains were grown from storage beads. DNA of sufficient quality and quantity for sequencing was extracted from 9 samples. Single consensus sequences of PCR ribotype 176 strains and PCR ribotype 001, PCR ribotype 070 (a control group) were mapped to a reference genome of strain CDI-01 (PCR ribotype 027).&nbsp; Results Four strains (out of seven; 57%) characterized as PCR ribotype 176 had 100% identity of the tcdC gene with the reference strain. The average length of the tcdC gene in these four strains (PCR ribotype 176) was 643 bp, which is 36 bp shorter than the reference genome. Three strains (PCR ribotype 176) had a percentage identity of the tcdC gene in the range of 99.37-100%. Strains 25 (PCR ribotype 001) and 28 (PCR ribotype 070) had a similarity in the range of 95.39-95.63% as a result of different ribotype to the reference strain.&nbsp; Conclusion PCR ribotype 176 strains have almost the same tcdC gene sequence as PCR ribotype 027, resulting in misidentification of this PCR ribotype by the Xpert C. difficile/Epi assay. Information about presumptive positive results based on deletion in the tcdC gene should be treated with caution or disregarded

show abstract

Characterization of Clostridioides difficile Isolates Available through the CDC & FDA Antibiotic Resistance Isolate Bank

Cited by 7 publications

References 16 publications

Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile

Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile

Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile

Use of tcdC gene sequencing to prevent misidentification of Clostridioides difficile ribotype 176 and 027

Contact Info

Product

Resources

About