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Biology Apr 2022(1) Background: This paper aims to provide a description of non-faecalis non-faecium enterococci isolated from a tertiary care hospital in Romania and to briefly review...
(1) Background: This paper aims to provide a description of non-faecalis non-faecium enterococci isolated from a tertiary care hospital in Romania and to briefly review the existing literature regarding the involvement of Enterococcus raffinosus, Enterococcus durans and Enterococcus avium in human infections and their antimicrobial resistance patterns; (2) Methods: We retrospectively analyzed all Enteroccocus species isolated from the “Prof. Dr. O. Fodor” Regional Institute of Gastroenterology and Hepatology from Cluj-Napoca during one year focusing on non-faecalis non-faecium Enterococci. A brief review of the literature was performed using case reports involving Enterococcus raffinosus, Enterococcus durans and Enterococcus avium; (3) Results: Only 58 out of 658 Enteroccocus isolates were non-faecalis non-faecium and met the inclusion criteria. These species were isolated more often (p < 0.05) from the surgical ward from mixed etiology infections with E. coli. In our review, we included 39 case reports involving E. raffinosus, E. durans and E. avium; (4) Conclusions: Isolation of non-faecalis non-faecium enterococci displays an emerging trend with crucial healthcare consequences. Based on the analysis of the case reports, E. avium seems to be involved more often in neurological infections, E. durans in endocarditis, while E. raffinosus displays a more heterogenous distribution.
PubMed: 35453797
DOI: 10.3390/biology11040598 -
Journal of Global Antimicrobial... Sep 2023Linezolid is an antibiotic used to treat infectious diseases caused by vancomycin-resistant enterococci and methicillin-resistant Staphylococcus aureus. Recently,...
OBJECTIVES
Linezolid is an antibiotic used to treat infectious diseases caused by vancomycin-resistant enterococci and methicillin-resistant Staphylococcus aureus. Recently, Enterococcus Spp.-carrying mobile linezolid resistance genes were reported. Herein, we report the complete genome sequence of Enterococcus raffinosus JARB-HU0741, which was isolated from a bile sample of a patient in Japan on May 5, 2021, and carries a linezolid resistance gene, cfr(B). Nevertheless, this isolate was susceptible to linezolid.
METHODS
Whole-genome sequencing was performed using HiSeq X FIVE (Illumina) and GridION (Oxford Nanopore Technologies). The sequence reads were assembled using Unicycler v0.4.8, and the complete genome was annotated using DFAST v1.2.18. Antimicrobial resistance genes were detected with Abricate v1.0.1, using the ResFinder database. The minimum inhibitory concentrations (MICs) were determined using broth microdilution and interpreted according to the guidelines of the Clinical and Laboratory Standards Institute.
RESULTS
E. raffinosus JARB-HU0741 contained a 3 248 808-bp chromosome and a 1 156 277-bp megaplasmid. cfr(B) was present in the Tn6218-like transposon, which was inserted into a gene encoding a PRD domain-containing protein present in the megaplasmid, but the isolate was susceptible to linezolid (MIC, 0.5 µg/mL). The Tn6218-like transposon was similar to the Tn6218 of Clostridioides difficile Ox3196 and the Tn6218-like transposon of Enterococcus faecium UW11733; however, three genes encoding a topoisomerase, an S-adenosylmethionine-dependent methyltransferase, and a TetR family transcriptional regulator were present in the previous Tn6218- or Tn6218-like transposon.
CONCLUSION
This is the first report of the complete genome sequence of E. raffinosus carrying cfr(B). E. raffinosus carrying cfr(B) without linezolid resistance poses a threat, as it could serve as a reservoir for mobile linezolid resistance genes.
Topics: Humans; Linezolid; Methicillin-Resistant Staphylococcus aureus; Japan; Bile; Enterococcus
PubMed: 37356664
DOI: 10.1016/j.jgar.2023.06.004 -
Gut Pathogens Dec 2021Enterococcus raffinosus is one of the Enterococcus species that often cause nosocomial infections. To date, only one E. raffinosus genome has been completely assembled,...
BACKGROUND
Enterococcus raffinosus is one of the Enterococcus species that often cause nosocomial infections. To date, only one E. raffinosus genome has been completely assembled, and the genomic features have not been characterized. Here, we report the complete genome sequence of the strain CX012922, isolated from the feces of a Crohn's disease patient, and perform a comparative genome analysis to the relevant Enterococcus spp. strains in silico.
RESULTS
De novo assembly of the sequencing reads of the strain CX012922 generated a circular genome of 2.83 Mb and a circular megaplasmid of 0.98 Mb. Phylogenomic analysis revealed that the strain CX012922 belonged to the E. raffinosus species. By comparative genome analysis, we found that some strains previously identified as E. raffinosus or E. gilvus should be reclassified as novel species. Genome islands (GIs), virulence factors, and antibiotic genes were found in both the genome and the megaplasmid, although pathogenic genes were mainly encoded in the genome. A large proportion of the genes encoded in the megaplasmid were involved in substrate utilization, such as raffinose metabolism. Giant megaplasmids (~1 Mb) equipped with toxin-antitoxin (TA) systems generally formed symbiosis relationships with the genome of E. raffinosus strains.
CONCLUSIONS
Enterococcus spp. have a higher species-level diversity than is currently appreciated. The pathogenicity of E. raffinosus is mainly determined by the genome-encoded virulence factors, while the megaplasmid broadens the gene function pool. The symbiosis between the genome and the megaplasmids endows E. raffinosus with large genomic sizes as well as versatile gene functions, especially for their colonization, adaptation, virulence, and pathogenesis in the human gut.
PubMed: 34876224
DOI: 10.1186/s13099-021-00468-8 -
Access Microbiology 2023is an understudied member of its genus possessing a characteristic megaplasmid contributing to a large genome size. Although less commonly associated with human...
is an understudied member of its genus possessing a characteristic megaplasmid contributing to a large genome size. Although less commonly associated with human infection compared to other enterococci, this species can cause disease and persist in diverse niches such as the gut, urinary tract, blood and environment. Few complete genome assemblies have been published to date for . In this study, we report the complete assembly of the first clinical urinary strain, Er676, isolated from a postmenopausal woman with history of recurrent urinary tract infection. We additionally completed the assembly of clinical type strain ATCC49464. Comparative genomic analyses reveal inter-species diversity driven by large accessory genomes. The presence of a conserved megaplasmid indicates it is a ubiquitous and vital genetic feature of . We find that the chromosome is enriched for DNA replication and protein biosynthesis genes while the megaplasmid is enriched for transcription and carbohydrate metabolism genes. Prophage analysis suggests that diversity in the chromosome and megaplasmid sequences arises, in part, from horizontal gene transfer. Er676 demonstrated the largest genome size reported to date for and the highest probability of human pathogenicity. Er676 also possesses multiple antimicrobial resistance genes, of which all but one are encoded on the chromosome, and has the most complete prophage sequences. Complete assembly and comparative analyses of the Er676 and ATCC49464 genomes provide important insight into the inter-species diversity of that gives it its ability to colonize and persist in the human body. Investigating genetic factors that contribute to the pathogenicity of this species will provide valuable tools to combat diseases caused by this opportunistic pathogen.
PubMed: 37424546
DOI: 10.1099/acmi.0.000508.v3 -
Antimicrobial Agents and Chemotherapy Jul 1991We reidentified our laboratories' collections of 57 enterococcal isolates previously classified as Enterococcus avium by the API Rapid Strep identification system... (Comparative Study)
Comparative Study
Comparison of Enterococcus raffinosus with Enterococcus avium on the basis of penicillin susceptibility, penicillin-binding protein analysis, and high-level aminoglycoside resistance.
We reidentified our laboratories' collections of 57 enterococcal isolates previously classified as Enterococcus avium by the API Rapid Strep identification system (Analytab Products, Plainview, N.Y.) with the identification criteria recommended by Facklam and Collins (R. R. Facklam and M. D. Collins, J. Clin. Microbiol. 27: 731-734, 1989). Thirty isolates were identified as true E. avium, 25 isolates were identified as E. raffinosus, and 2 isolates were identified as E. pseudoavium. E. raffinosus could be differentiated from E. avium on the basis of penicillin susceptibility, as follows: MIC for 50% of E. raffinosus isolates tested (MIC50), 32 micrograms/ml; MIC90, 64 micrograms/ml (range, 4 to 64 micrograms/ml); E. avium MIC50, 1 microgram/ml; MIC90, 2 micrograms/ml (range, 0.5 to 2 micrograms/ml). No strains produced detectable beta-lactamase. Penicillin-binding protein (PBP) analysis of all E. raffinosus isolates demonstrated the unique pattern reported previously (M. D. Collins, R. R. Facklam, J. A. E. Farrow, and R. Williamson, FEMS Microbiol. Lett. 57:283-288, 1989); however, a number of newly identified PBPs were noted. Of 25 isolates, 13 had an additional PBP of 77 kDa (designated PBP 6*), while all isolates possessed a 52-kDa PBP (PBP 7) and a 46-kDa PBP (PBP 8). The presence or absence of PBP 6* did not correlate with penicillin susceptibility; however, PBP 7 demonstrated many features suggestive of low penicillin-binding affinity and may represent a possible mechanism for the relative resistance of this species to penicillin, although this hypothesis remains speculative since attempts to develop a penicillin-hypersusceptible E. raffinosus mutant were unsuccessful. E. raffinosus isolates were significantly more likely to exhibit high-level resistance to kanamycin than E. avium strains were (P < 0.001; chi-square); however, no strains demonstrated high-level resistance to gentamicin. No trend toward increasing penicillin resistance was noted among this collection of E. avium and E. raffinosus isolates collected over the past 35 and 14 years, respectively. Relative resistance to penicillin may be a helpful differentiating feature between E. avium and E. raffinosus when assessment of raffinose metabolism is not possible or is indeterminant.
Topics: Aminoglycosides; Anti-Bacterial Agents; Bacterial Proteins; Carrier Proteins; Electrophoresis, Polyacrylamide Gel; Hexosyltransferases; Microbial Sensitivity Tests; Muramoylpentapeptide Carboxypeptidase; Penicillin Resistance; Penicillin-Binding Proteins; Penicillins; Peptidyl Transferases; Streptococcus
PubMed: 1929301
DOI: 10.1128/AAC.35.7.1408 -
Le Infezioni in Medicina Mar 2009Enterococcus raffinosus, a non-faecalis and non-faecium enterococcus, rarely causes infections in humans. We describe the first reported case of primary bacterial... (Review)
Review
Enterococcus raffinosus, a non-faecalis and non-faecium enterococcus, rarely causes infections in humans. We describe the first reported case of primary bacterial endocarditis caused by E. raffinosus, with a review of the literature.
Topics: Adenoma; Aged; Aged, 80 and over; Bacteremia; Colonic Neoplasms; Colonoscopy; Cross Infection; Disease Susceptibility; Drug Resistance, Multiple, Bacterial; Endocarditis, Bacterial; Enterococcus; Female; Gram-Positive Bacterial Infections; Humans; Male; Middle Aged; Prospective Studies; Ultrasonography
PubMed: 19359819
DOI: No ID Found -
Journal of Clinical Microbiology Nov 1991A prospective study identified 9 (32%) of 28 ampicillin-resistant (MIC greater than or equal to 16 micrograms/ml) enterococcus isolates as Enterococcus raffinosus. A...
A prospective study identified 9 (32%) of 28 ampicillin-resistant (MIC greater than or equal to 16 micrograms/ml) enterococcus isolates as Enterococcus raffinosus. A case-control study found no significant differences with respect to underlying diseases, catheterization, or surgery between patients with ampicillin-resistant E. raffinosus and those with ampicillin-susceptible Enterococcus spp. Prior treatment with antibiotics and prolonged hospitalization were more frequent among patients with ampicillin-resistant E. raffinosus. Patients with the same strain (determined by plasmid analysis) were frequently hospitalized concurrently.
Topics: Aged; Aged, 80 and over; Ampicillin Resistance; California; Case-Control Studies; Cross Infection; Enterococcus; Female; Gram-Positive Bacterial Infections; Hospitals, Veterans; Humans; Male; Middle Aged
PubMed: 1774284
DOI: 10.1128/jcm.29.11.2663-2665.1991 -
Journal of Clinical Microbiology Apr 2002Light yellow-pigmented (strain PQ1) and yellow-pigmented (strain PQ2), gram-positive, non-spore-forming, nonmotile bacteria consisting of pairs or chains of cocci were...
Light yellow-pigmented (strain PQ1) and yellow-pigmented (strain PQ2), gram-positive, non-spore-forming, nonmotile bacteria consisting of pairs or chains of cocci were isolated from the bile of a patient with cholecystitis (PQ1) and the peritoneal dialysate of another patient with peritonitis (PQ2). Morphologically and biochemically, the organisms phenotypically belonged to the genus Eterococcus. Whole-cell protein (WCP) analysis and sequence analysis of a segment of the 16S rRNA gene suggested that they are new species within the genus Enterococcus. PQ1 and PQ2 displayed less than 70% identities to other enterococcal species by WCP analysis. Sequence analysis showed that PQ1 shared the highest level of sequence similarity with Enterococcus raffinosus and E. malodoratus (sequence similarities of 99.8% to these two species). Sequence analysis of PQ2 showed that it had the highest degrees of sequence identity with the group I enterococci E. malodoratus (98.7%), E. raffinosus (98.6%), E. avium (98.6%), and E. pseudoavium (98.6%). PQ1 and PQ2 can be differentiated from the other Enterococcus spp. in groups II, III, IV, and V by their phenotypic characteristics: PQ1 and PQ2 produce acid from mannitol and sorbose and do not hydrolyze arginine, placing them in group I. The yellow pigmentation differentiates these strains from the other group I enterococci. PQ1 and PQ2 can be differentiated from each other since PQ1 does not produce acid from arabinose, whereas PQ2 does. Also, PQ1 is Enterococcus Accuprobe assay positive and pyrrolidonyl-beta-naphthylamide hydrolysis positive, whereas PQ2 is negative by these assays. The name Enterococcus gilvus sp. nov. is proposed for strain PQ1, and the name Enterococcus pallens sp. nov. is proposed for strain PQ2. Type strains have been deposited in culture collections as E. gilvus ATCC BAA-350 (CCUG 45553) and E. pallens ATCC BAA-351 (CCUG 45554).
Topics: Bacterial Proteins; Bacterial Typing Techniques; Bile; Cholecystitis; DNA, Ribosomal; Enterococcus; Fatty Acids; Gram-Positive Bacterial Infections; Humans; Molecular Sequence Data; Peritonitis; Pigments, Biological; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 11923322
DOI: 10.1128/JCM.40.4.1140-1145.2002 -
Antimicrobial Agents and Chemotherapy May 1996Enterococcus hirae, E. avium, and E. raffinosus isolated in Romania, Tunisia, and Portugal harbored plasmids pICC8, pIP1700, and pIP1701, respectively, encoding...
Enterococcus hirae, E. avium, and E. raffinosus isolated in Romania, Tunisia, and Portugal harbored plasmids pICC8, pIP1700, and pIP1701, respectively, encoding resistance to high levels of gentamicin (Gmr). The Gmr marker was carried on pIP1700 by a Tn4001-like element and on pICC8 and pIP1701 by Tn4001-truncated structures. pICC8 carried, in addition to Gmr, chloramphenicol, erythromycin, and tetracycline-minocycline (TetM) resistance determinants. The gene tetM of pICC8 was carried on a Tn916-like element.
Topics: Drug Resistance, Microbial; Enterococcus; Genes, Bacterial; Genetic Markers; Gentamicins; Humans; Microbial Sensitivity Tests; Nucleic Acid Hybridization; Plasmids; Portugal; Romania; Tunisia
PubMed: 8723479
DOI: 10.1128/AAC.40.5.1263 -
Clinical Microbiology and Infection :... Sep 2007A mixed outbreak caused by vancomycin-resistant Enterococcus raffinosus and Enterococcus faecium carrying the vanA gene was analysed. The outbreak occurred in a large...
A mixed outbreak caused by vancomycin-resistant Enterococcus raffinosus and Enterococcus faecium carrying the vanA gene was analysed. The outbreak occurred in a large hospital in Poland and affected 27 patients, most of whom were colonised, in three wards, including the haematology unit. The E. raffinosus isolates had a high-level multiresistant phenotype and were initially misidentified as Enterococcus avium; their unambiguous identification was provided by multilocus sequence analysis. The molecular investigation demonstrated the clonal character of the E. raffinosus outbreak and the polyclonal structure of the E. faecium isolates. All of the isolates carried the same Tn1546-like element containing an IS1251-like insertion sequence, located on a c. 50-kb conjugative plasmid. One of the E. faecium clones, found previously to be endemic in the hospital, was probably the source of the plasmid. The results of the study suggest that difficulties in identification may have led to an underestimate of the importance of E. raffinosus in vancomycin-resistant enterococci (VRE) control strategies.
Topics: Bacterial Proteins; Cross Infection; DNA Transposable Elements; Disease Outbreaks; Electrophoresis, Gel, Pulsed-Field; Enterococcus; Enterococcus faecium; Gram-Positive Bacterial Infections; Hospitals; Humans; Protein Kinases; Transcription Factors; Vancomycin Resistance
PubMed: 17617184
DOI: 10.1111/j.1469-0691.2007.01774.x