Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria

Schwarz, Štefan; Zhang, Wanjiang; Du, Xiang-Dang; Krüger, Henrike; Feßler, Andrea T.; Ma, Shizhen; Zhu, Yao; Wu, Congming; Shen, Jianzhong; Wang, Yan

doi:10.1128/cmr.00188-20

Cited by 114 publications

(104 citation statements)

References 321 publications

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“… CfrWT used for the starting point for directed evolution is displayed as the top sequence (Cfr) in blue. Cfr(B), Cfr(C), Cfr(D), and Cfr(E) are Cfr homologs that have been functionally characterized, reviewed here ( Schwarz et al, 2021 ). Remaining sequences are Cfr homologs that clade with Cfr or Cfr-like genes as described previously ( Stojković et al, 2019 ).…”

Section: Resultsmentioning

confidence: 99%

“…Interestingly, mutations obtained through directed evolution have been observed in Cfr homologs that share less than 80% sequence identity with Cfr. Methionine (M) at position 26 is observed for the functionally characterized Cfr homologs Cfr(B) ( Deshpande et al, 2015 ; Marín et al, 2015 ; Hansen and Vester, 2015 ) and Cfr(D) ( Pang et al, 2020 ), which have been recovered from human-derived isolates and share 74% and 64% amino acid identity with Cfr, respectively ( Schwarz et al, 2021 ; Figure 4—figure supplement 5 ). We also observe lysine (K) at position 2, methionine (M) at position 26, and glycine (G) at position 39, akin to N2K, I26M, and S39G mutations, for a number of Cfr homologs that clade with functional Cfr or Cfr-like genes ( Stojković et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

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Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

Tsai

Stojković

Noda‐Garcia

et al. 2022

eLife

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Alteration of antibiotic binding sites through modification of ribosomal RNA (rRNA) is a common form of resistance to ribosome-targeting antibiotics. The rRNA-modifying enzyme Cfr methylates an adenosine nucleotide within the peptidyl transferase center, resulting in the C-8 methylation of A2503 (m8A2503). Acquisition of cfr results in resistance to eight classes of ribosome-targeting antibiotics. Despite the prevalence of this resistance mechanism, it is poorly understood whether and how bacteria modulate Cfr methylation to adapt to antibiotic pressure. Moreover, direct evidence for how m8A2503 alters antibiotic binding sites within the ribosome is lacking. In this study, we performed directed evolution of Cfr under antibiotic selection to generate Cfr variants that confer increased resistance by enhancing methylation of A2503 in cells. Increased rRNA methylation is achieved by improved expression and stability of Cfr through transcriptional and post-transcriptional mechanisms, which may be exploited by pathogens under antibiotic stress as suggested by natural isolates. Using a variant that achieves near-stoichiometric methylation of rRNA, we determined a 2.2 Å cryo-electron microscopy structure of the Cfr-modified ribosome. Our structure reveals the molecular basis for broad resistance to antibiotics and will inform the design of new antibiotics that overcome resistance mediated by Cfr.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

Tsai

Stojković

Noda‐Garcia

et al. 2022

eLife

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“…Previously, all of the poxtA genes described in enterococci have been plasmid-borne, suggesting that plasmids play an important role in the dissemination of the poxtA gene among enterococci ( 22 , 23 ). In this study, two mobilizable poxtA -carrying plasmids were identified in E. faecalis and E. lactis , respectively.…”

Section: Introductionmentioning

confidence: 99%

Plasmid Fusion and Recombination Events That Occurred during Conjugation of poxtA -Carrying Plasmids in Enterococci

et al. 2022

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Until now, all the poxtA genes described in enterococci, including E. faecalis , E. faecium , and E. hirae , are plasmid-borne, suggesting that plasmids play an important role in the dissemination of the poxtA gene among enterococci. This study showed that the mobilizable poxtA -carrying plasmid could transfer with the help of conjugative plasmid in enterococci via plasmid fusion, with one generated by homologous recombination in E. faecalis , and another by replicative transposition in E. lactis .

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“…P variant was distributed in Clostridium difficile and Campylobacter jejuni and EYDNDM variants were found in Enterococcus faecalis, Staphylococcus aureus, Staphylococcus sciuri , Enterococcus avium. 12 Given that the relationship between optrA variants and linezolid MIC remains unclear, novel optrA variants in E. faecium is of concern.…”

Section: Discussionmentioning

confidence: 99%

“…[9][10][11] It is mostly reported in Enterococcus but also detected in Staphylococcus sciuri, Streptococcus suis, and other Gram-positive or Gram-negative strains. 12 OptrA is often located on chromosomes or plasmids and can be transmitted by mobile genetic elements such as transposons and insertion sequences. [13][14][15] The most recently reported poxtA gene, mediating resistance to oxazolidinones, tetracyclines, and phenicols, was first described in an MRSA isolate from respiratory secretion of an Italian patient.…”

Section: Introductionmentioning

confidence: 99%

Emergence of optrA-Mediated Linezolid Resistance in Enterococcus faecium: A Molecular Investigation in a Tertiary Hospital of Southwest China from 2014–2018

Miao¹,

Zou²,

Zhao³

et al. 2022

IDR

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Purpose: To investigate the potential mechanism and molecular characteristics of linezolidnon-sensitive Enterococcus faecium from a tertiary hospital in southwest China and characterize the relevant plasmids. Patients and Methods: Linezolid-non-sensitive Enterococcus faecium (LNSEFM) isolates collected from January 2014 to December 2018 were screened for resistant genes 23s rRNA, rplC, rplD, rplV, optrA, cfr, poxtA, by PCR. Molecular epidemiological analysis was performed by multilocus sequence typing (MLST). The optrA-and-poxtA co-harboring strain EFM_7150 was subjected to the whole genome sequencing (WGS) by Illumina HiSeq and Oxford Nanopore MinION. Results: A total of 15 LNSEFM with linezolid MICs ranging from 4 to 16 mg/L were identified. About 66.7% (10/15) of isolates were linezolid-resistant. About 46.7% (7/15) of strains were positive for optrA. Two types of optrA variants (P and EYDNDM) were identified. About 13.3% (2/15) of isolates had poxtA. 1 harbored a L22 protein alteration (Ser77Thr). One isolate coharbored optrA (EYDNDM variant) and poxtA. There was no mutation in the gene that encoded the ribosomal protein L3/L4 or the domain V of 23S rRNA. No cfr gene was detected. Based on WGS data, optrA was associated with Tn558 inserted to radC gene and poxtA was flanked by IS1216E. Conclusion:OptrA is primary mechanism in linezolid-resistant Enterococcus faecium. This is the first report ofoptrA variants P and EYDNDM identified in Enterococcus faecium and optrA-and-poxtA co-harboring Enterococcus faecium clinically in southwest China. Besides, Tn558 and IS1216Es may play an important role in the dissemination of optrA and poxtA, respectively. The findings revealed the potential threat to nosocomial infection by optrA and coexistence of optrA and poxtA in Enterococcus faecium. Thus, clinical surveillance of linezolid-resistant Enterococcus is urgently needed.

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Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria

Cited by 114 publications

References 321 publications

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

Plasmid Fusion and Recombination Events That Occurred during Conjugation of poxtA -Carrying Plasmids in Enterococci

Emergence of optrA-Mediated Linezolid Resistance in Enterococcus faecium: A Molecular Investigation in a Tertiary Hospital of Southwest China from 2014–2018

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