Detection of a chromosomal truncated cfr gene in a linezolid-susceptible LA-MRSA ST398 isolate of porcine origin, Italy

Fioriti, Simona; Coccitto, Sonia Nina; Morroni, Gianluca; Simoni, Serena; Cinthi, Marzia; Sante, Laura Di; Álvarez-Suárez, José M.; Mingoia, Marina; Giovanetti, Eleonora; Brenciani, Andrea

doi:10.1016/j.jgar.2021.06.008

Cited by 3 publications

(5 citation statements)

References 7 publications

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“…An almost (99.99%) identical cfr gene cluster of MRSA G322 (MW298531), described by Fioriti and colleagues in 2021 [ 18 ], was identified within the transposon harboured on contig 9 of our isolate ID 76669/3 (21276..39515 nt). Both cfr gene clusters differed by only one nucleotide in the fex A gene encoding a phenicol resistance.…”

Section: Resultsmentioning

confidence: 56%

“…From the NCBI database interrogation, we also observed that the same single base-pair deletion (c.381delA) found in the cfr gene of the CC398 LA-MRSA isolate ID 76669/3 was recently described in a cfr gene located in a 18,240 bp chromosomal region ( cfr gene cluster; MW298531) of a CC398 LA-MRSA sample isolated in 2019 from a single pig nasal swab in Central Italy [ 18 ]. Multiple alignment confirmed this deletion by comparing our sequence with the cfr reference sequences of S. sciuri (NG_047631) and S. warneri (AM408573) ( Figure 2 ).…”

Section: Resultsmentioning

confidence: 69%

“…In our isolate, this gene was identical to the fex A1 reference sequence in the ResFinder database (AJ549214) whereas the fex A gene within the cfr gene cluster of isolate MRSA G322 presented a single-point mutation (G to C) at position 1192 (G1192C). MRSA G322 remained phenotypically resistant to chloramphenicol and florfenicol [ 18 ].…”

Section: Resultsmentioning

confidence: 99%

“…This isolate, together with the CC1 isolate ID 55864/23, presented a frameshift mutation caused by a single base-pair deletion in the cfr gene and, consequently, a truncated protein, corroborating their phenotypic susceptibility to linezolid (MIC value = 1 mg/L). Prior to our findings, linezolid-susceptible MSSA and MRSA associated with cfr variants with a single base-pair deletion or mutation were isolated from two human clinical cases (one in Brazil [ 21 ] and one in the Netherlands [ 11 ]), and also from two nasal swabs of porcine origin (one in Italy [ 18 ] and the other in Australia (CP029172)). All of them belonged to CC398.…”

Section: Discussionmentioning

confidence: 98%

“…The presence of mutations of the cfr genes was confirmed, and their genetic environment was investigated by comparing the multiple alignment of the contig-harbouring cfr of isolate ID 76669/3 with publicly available selected sequences harbouring cfr from: (i) S. warneri (AM408573) [ 22 ]; (ii) S. sciuri (NG_047631) [ 51 ]; and (iii) S. aureus G322 (MW29853) [ 18 ]. This was achieved using Geneious Prime 2023.0.1 software.…”

Section: Methodsmentioning

confidence: 99%

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Genomics Insight into cfr-Mediated Linezolid-Resistant LA-MRSA in Italian Pig Holdings

et al. 2023

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The cfr genes encode for a 23S rRNA methyltransferase, conferring a multiresistance phenotype to phenicol, lincosamide, oxazolidinone, pleuromutilin, and streptogramin A antibiotics. These genes have been described in staphylococci, including methicillin-resistant Staphylococcus aureus (MRSA). In this study, we retrospectively performed an in-depth genomic characterisation of three cfr-positive, multidrug-resistant (MDR) livestock-associated (LA) MRSA clonal complexes (CCs) 1 and 398 detected in different Italian pig holdings (2008–2011) during population studies on Italian livestock (2008–2014). We used a combined Illumina and Oxford Nanopore Technologies (ONT) whole genome sequencing (WGS) approach on two isolates (the 2008 CC1 and the 2010 CC398 isolates, but not the 2011 CC1 isolate). Interestingly, the three isolates presented different cfr variants, with only one displaying a linezolid-resistant phenotype. In isolate 2008 CC1, the cfr gene was identified within a Tn558 composite transposon-like structure flanked by IS elements located on a novel 44,826 bp plasmid. This represents the first report of CC1 LA-MRSA harbouring the cfr gene in its functional variant. Differently, cfr was chromosomally located in isolate 2010 CC398. Our findings have significant public health implications, confirm the need for the continuous genomic surveillance of cfr-positive zoonotic LA-MRSA, and backdate cfr presence in LA-MRSA from Italian pigs to at least 2008.

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Section: Resultsmentioning

confidence: 56%

Section: Resultsmentioning

confidence: 69%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 98%

Section: Methodsmentioning

confidence: 99%

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Genomics Insight into cfr-Mediated Linezolid-Resistant LA-MRSA in Italian Pig Holdings

et al. 2023

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Oxazolidinones: mechanisms of resistance and mobile genetic elements involved

Brenciani

Morroni

Schwarz

et al. 2022

Journal of Antimicrobial Chemotherapy

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The oxazolidinones (linezolid and tedizolid) are last-resort antimicrobial agents used for the treatment of severe infections in humans caused by MDR Gram-positive bacteria. They bind to the peptidyl transferase centre of the bacterial ribosome inhibiting protein synthesis. Even if the majority of Gram-positive bacteria remain susceptible to oxazolidinones, resistant isolates have been reported worldwide. Apart from mutations, affecting mostly the 23S rDNA genes and selected ribosomal proteins, acquisition of resistance genes (cfr and cfr-like, optrA and poxtA), often associated with mobile genetic elements [such as non-conjugative and conjugative plasmids, transposons, integrative and conjugative elements (ICEs), prophages and translocatable units], plays a critical role in oxazolidinone resistance. In this review, we briefly summarize the current knowledge on oxazolidinone resistance mechanisms and provide an overview on the diversity of the mobile genetic elements carrying oxazolidinone resistance genes in Gram-positive and Gram-negative bacteria.

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Occurrence of cfr-Positive Linezolid-Susceptible Staphylococcus aureus and Non-aureus Staphylococcal Isolates from Pig Farms

Lee

Yang

2023

Antibiotics

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The emergence and spread of cfr-mediated resistance to linezolid in staphylococci have become a serious global concern. The acquisition of cfr confers multidrug resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A (PhLOPSA phenotype). However, occurrence of cfr-positive and linezolid-susceptible staphylococci has been identified. To investigate the mechanism underlying linezolid susceptibility in cfr-positive Staphylococcus aureus and non-aureus staphylococci (NAS) isolates from pig farms in Korea. Eleven cfr-positive and linezolid-susceptible staphylococci were analyzed for mutations in domain V of 23S rRNA, ribosomal proteins (L3, L4, and L22), cfr open reading frames (ORFs), and cfr promoter regions. The effect of the cfr mutation (Q148K) on the PhLOPSA phenotype was determined using plasmid constructs expressing either the mutated (cfrQ148K) or nonmutated cfr genes. All 11 (six S. aureus and five NAS) cfr-positive and linezolid-susceptible isolates had a point mutation at position 442 in cfr ORFs (C to A) that resulted in the Q148K mutation. No mutations were detected in 23S rRNA, L3, L4, or L22. The Q148K mutation in Cfr is responsible for phenotypes susceptible to PhLOPSA antimicrobial agents. To our knowledge, this is the first study to report the causal role of a single nucleotide mutation (Q148K) in cfr of S. aureus and NAS isolates in PhLOPSA resistance. Continued nationwide surveillance is necessary to monitor the occurrence and dissemination of mutations in cfr that affect resistance phenotypes in staphylococci of human and animal origin.

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Detection of a chromosomal truncated cfr gene in a linezolid-susceptible LA-MRSA ST398 isolate of porcine origin, Italy

Cited by 3 publications

References 7 publications

Genomics Insight into cfr-Mediated Linezolid-Resistant LA-MRSA in Italian Pig Holdings

Genomics Insight into cfr-Mediated Linezolid-Resistant LA-MRSA in Italian Pig Holdings

Oxazolidinones: mechanisms of resistance and mobile genetic elements involved

Occurrence of cfr-Positive Linezolid-Susceptible Staphylococcus aureus and Non-aureus Staphylococcal Isolates from Pig Farms

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