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BMC Microbiology Mar 2014Enterococci, ubiquitous colonizers of humans and other animals, play an increasingly important role in health-care associated infections (HAIs). It is believed that the...
BACKGROUND
Enterococci, ubiquitous colonizers of humans and other animals, play an increasingly important role in health-care associated infections (HAIs). It is believed that the recent evolution of two clinically relevant species, Enterococcus faecalis and Enterococcus faecium occurred in a big part in a hospital environment, leading to formation of high-risk enterococcal clonal complexes (HiRECCs), which combine multidrug resistance with increased pathogenicity and epidemicity. The aim of this study was to establish the species composition in wastewater, its marine recipient as well as a river estuary and to investigate the antimicrobial susceptibility of collected isolates. Molecular methods were additionally applied to test the presence of HiRRECC-related E. faecium.
RESULTS
Two wastewater treatment plants (WWTPs), their marine outfalls and Vistula river that influence significantly the quality of waters in Gulf of Gdansk were sampled to investigate the presence of Enterococcus spp. Four-hundred-twenty-eight isolates were obtained, including E. faecium (244 isolates, 57.0%), E. hirae (113 isolates, 26.4%) and E. faecalis (63 isolates, 14.7%); other species (E. gallinarum/casseliflavus, E. durans and E. avium) accounted for 1.9%. Antimicrobial susceptibility testing revealed the presence of isolates resistant to erythromycin, tetracycline, amipicillin, fluoroquinolones and aminoglycosides (high-level resistance), especially among E. faecium, where such isolates were usually characterized by multilocus sequence types associated with nosocomial lineages 17, 18 and 78 of this species representing HiRECC, formerly called CC17. These isolates not only carried several resistance determinants but were also enriched in genes encoding pathogenicity factors (Esp, pili) and genes associated with mobile genetic elements (MGE), a feature also typical for nosocomial HiRECC.
CONCLUSIONS
Our data show that WWTPs constitute an important source of enterococcal strains carrying antimicrobial resistance determinants, often associated with the presence of MGE, for the recipient water environment, thus increasing a pool of such genes for other organisms. The presence of HiRECCs in wastewaters and marine/river environment may indicate that adaptations gained in hospitals may be also beneficial for survival of such clones in other settings. There is an obvious need to monitor the release and spread of such strains in order to elucidate better ways to curb their dissemination.
Topics: Cluster Analysis; DNA, Bacterial; Drug Resistance, Bacterial; Enterococcus faecium; Estuaries; Genotype; Hospitals; Humans; Microbial Sensitivity Tests; Molecular Sequence Data; Multilocus Sequence Typing; Poland; Rivers; Seawater; Virulence Factors; Wastewater
PubMed: 24629030
DOI: 10.1186/1471-2180-14-66 -
Protein Expression and Purification Oct 2023The family of ATP-binding cassette F proteins (ABC-F) is mainly made up of cytosolic proteins involved in regulating protein synthesis, and they are often part of a...
The family of ATP-binding cassette F proteins (ABC-F) is mainly made up of cytosolic proteins involved in regulating protein synthesis, and they are often part of a mechanism that confers resistance to ribosome-targeting antibiotics. The existing literature has emphasized the difficulty of purifying these recombinant proteins because of their very low solubility and stability. Here, we describe a rapid and efficient three-step purification procedure that allows for the production of untagged ABC-F proteins from Enterococcus faecium in the heterologous host Escherichia coli. After four purified ABC-F proteins were produced using this protocol, their biological activities were validated by in vitro experiment. In conclusion, our study provides an invaluable tool for obtaining large amounts of untagged and soluble ABC-F proteins that can then be used for in vitro experiments.
Topics: Enterococcus faecium; ATP-Binding Cassette Transporters; Protein Biosynthesis; Anti-Bacterial Agents; Ribosomes; Escherichia coli
PubMed: 37354924
DOI: 10.1016/j.pep.2023.106325 -
BMC Microbiology Jul 2019Enterococcus species continues to be an important cause of hospital-acquired infection worldwide. This study was designed to determine the antibiotic resistance...
BACKGROUND
Enterococcus species continues to be an important cause of hospital-acquired infection worldwide. This study was designed to determine the antibiotic resistance profiles, virulence genes and molecular characteristics of Enterococcus faecium strains isolated from an Iranian children hospital in a four-years period.
RESULTS
A total 189 Enterococcus strains, comprising 108 (57%) E. faecium, 67 (35%) E. faecalis and 14 (7%) isolates of other spp. were isolated during the collection period. More than 92% of E. faecium isolates were resistant to ampicillin (92.5%), ciprofloxacin (96%), erythromycin (100%) and clindamycin (96%). A high frequency of resistance to clindamycin (100%), erythromycin (98.5%) and ciprofloxacin (80.5%) was observed among E. faecalis isolates, while resistance to ampicillin (7%) was less frequent. The prevalence of vanA gene among vancomycin resistant E. faecium and vancomycin resistant E. faecalis was 95 and 50%, respectively. The analysis of 108 E. faecium isolates revealed 34 variable number tandem repeat (VNTR) patterns and 27 Multi Locus VNTR Analysis (MLVA) types (MTs).
CONCLUSIONS
The results show a shift from E. faecalis to E. faecium as the dominant enterococcal species among patients at the children Hospital. Our data revealed that the majority of E. faecium isolates (66%) belonged to three common MTs and these types were isolated from different wards in children hospital.
Topics: Child; Child, Preschool; Drug Resistance, Bacterial; Enterococcus faecalis; Enterococcus faecium; Genes, Bacterial; Gram-Positive Bacterial Infections; Humans; Iran; Virulence; Virulence Factors
PubMed: 31286887
DOI: 10.1186/s12866-019-1539-y -
BMC Genomics Jul 2019As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the... (Comparative Study)
Comparative Study
BACKGROUND
As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolates originated from the natural environments.
RESULTS
In this study, comparative genomic analysis was conducted on 161 isolates originated from human, animal, and naturally fermented dairy products. The results showed that the environment played an important role in shaping the genomes of Enterococcus faecium. The isolates from human had the largest average genome size, while the isolates from dairy products had the smallest average genome size and fewest antibiotic resistance genes. A phylogenetic tree was reconstructed based on the genomes of these isolates, which revealed new insights into the phylogenetic relationships among the dairy isolates and those from hospitals, communities, and animals. Furthermore, 202 environment-specific genes were identified, including 136 dairy-specific, 31 human blood-specific, and 35 human gastrointestinal-specific genes. Interestingly, five dairy-specific genes (namely lacF, lacA/B, lacD, lacG, and lacC) that constituted an integrated lactose metabolism pathway existed in almost all dairy isolates. The pathway conservation demonstrated an active role of the environment in shaping the genomes of Enterococcus faecium.
CONCLUSIONS
This study shows that the Enterococcus faecium species has great genomic plasticity and high versatility to occupy broad ecological roles, dwelling as non-harmful dairy and animal gut commensals as well as significant nosocomial pathogens that disseminate antibiotic resistance genes.
Topics: Adaptation, Physiological; Databases, Genetic; Drug Resistance, Microbial; Enterococcus faecium; Environment; Genes, Bacterial; Genomics; Phylogeny; Virulence Factors
PubMed: 31331270
DOI: 10.1186/s12864-019-5975-8 -
Journal of Animal Science Apr 2018Probiotics, an antibiotic alternative, are widely used as feed additives for performance benefits in cattle and swine production systems. Among bacterial species...
Probiotics, an antibiotic alternative, are widely used as feed additives for performance benefits in cattle and swine production systems. Among bacterial species contained in probiotics, Enterococcus faecium is common. Antimicrobial resistance (AMR), particularly multidrug resistance, is a common trait among enterococci because of their propensity to acquire resistance and horizontally transfer AMR genes. Also, E. faecium is an opportunistic pathogen, and in the United States, it is the second most common nosocomial pathogen. There has been no published study on AMR and virulence potential in E. faecium contained in probiotic products used in cattle and swine in the United States. Therefore, our objectives were to determine phenotypic susceptibilities or resistance to antimicrobials, virulence genes (asa1, gelE, cylA, esp, and hyl) and assess genetic diversity of E. faecium isolated from commercial products. Twenty-two commercially available E. faecium-based probiotic products used in cattle (n = 13) and swine (n = 9) were procured and E. faecium was isolated and species confirmed. Antimicrobial susceptibility testing to determine minimum inhibitory concentrations was done by micro-broth dilution method using National Antimicrobial Resistance Monitoring Systems Gram-positive Sensititre panel plate (CMV3AGPF), and categorization of strains as susceptible or resistant was as per Clinical Laboratory and Standards Institute's guidelines. E. faecium strains from 7 products (3 for swine and 4 for cattle) were pan-susceptible to the 16 antimicrobials tested. Strains from 15 products (6 for swine and 9 for cattle) exhibited resistance to at least one antimicrobial and a high proportion of strains was resistant to lincomycin (10/22), followed by tetracycline (4/22), daptomycin (4/22), ciprofloxacin (4/22), kanamycin (3/22), and penicillin (2/22). Four strains were multidrug resistant, with resistant phenotypes ranging from 3 to 6 antimicrobials or class. None of the E. faecium strains were positive for any of the virulence genes tested. The clonal relationships among the 22 E. faecium strains were determined by pulsed-field gel electrophoresis (PFGE) typing. A total of 10 PFGE patterns were observed with 22 strains and a few of the strains from different probiotic products had identical (100% Dice similarity) PFGE patterns. In conclusion, the E. faecium strains in a few commercial probiotics exhibited AMR to medically-important antimicrobials, but none contained virulence genes.
Topics: Animals; Anti-Infective Agents; Cattle; Cattle Diseases; Drug Resistance, Bacterial; Electrophoresis, Gel, Pulsed-Field; Enterococcus faecium; Genetic Variation; Gram-Positive Bacterial Infections; Microbial Sensitivity Tests; Opportunistic Infections; Phenotype; Probiotics; Swine; Swine Diseases; Virulence
PubMed: 29584914
DOI: 10.1093/jas/sky056 -
Applied and Environmental Microbiology Jan 2014Certain strains of Enterococcus faecium and Enterococcus faecalis contribute beneficially to animal health and food production, while others are associated with...
Certain strains of Enterococcus faecium and Enterococcus faecalis contribute beneficially to animal health and food production, while others are associated with nosocomial infections. To determine whether there are structural and functional genomic features that are distinct between nonclinical (NC) and clinical (CL) strains of those species, we analyzed the genomes of 31 E. faecium and 38 E. faecalis strains. Hierarchical clustering of 7,017 orthologs found in the E. faecium pangenome revealed that NC strains clustered into two clades and are distinct from CL strains. NC E. faecium genomes are significantly smaller than CL genomes, and this difference was partly explained by significantly fewer mobile genetic elements (ME), virulence factors (VF), and antibiotic resistance (AR) genes. E. faecium ortholog comparisons identified 68 and 153 genes that are enriched for NC and CL strains, respectively. Proximity analysis showed that CL-enriched loci, and not NC-enriched loci, are more frequently colocalized on the genome with ME. In CL genomes, AR genes are also colocalized with ME, and VF are more frequently associated with CL-enriched loci. Genes in 23 functional groups are also differentially enriched between NC and CL E. faecium genomes. In contrast, differences were not observed between NC and CL E. faecalis genomes despite their having larger genomes than E. faecium. Our findings show that unlike E. faecalis, NC and CL E. faecium strains are equipped with distinct structural and functional genomic features indicative of adaptation to different environments.
Topics: Adaptation, Biological; Animals; Enterococcus faecalis; Enterococcus faecium; Environmental Microbiology; Genes, Bacterial; Genome, Bacterial; Genomics; Gram-Positive Bacterial Infections; Interspersed Repetitive Sequences; Synteny
PubMed: 24141120
DOI: 10.1128/AEM.03108-13 -
Clinical Microbiology and Infection :... Jun 2010Enterococci are organisms with a remarkable ability to adapt to the environment and acquire antibiotic resistance determinants. The evolution of antimicrobial resistance... (Review)
Review
Enterococci are organisms with a remarkable ability to adapt to the environment and acquire antibiotic resistance determinants. The evolution of antimicrobial resistance in these organisms poses enormous challenges for clinicians when faced with patients affected with severe infections. The increased prevalence and dissemination of multidrug-resistant Enterococcus faecium worldwide has resulted in a major decrease in therapeutic options because the majority of E. faecium isolates are now resistant to ampicillin and vancomycin, and exhibit high-level resistance to aminoglycosides, which are three of the traditionally most useful anti-enterococcal antibiotics. Newer antibiotics such as linezolid, daptomycin and tigecycline have good in vitro activity against enterococcal isolates, although their clinical use may be limited in certain clinical scenarios as a result of reduced rates of success, possible underdosing for enterococci and low serum levels, respectively, and also by the emergence of resistance. The experimental agent oritavancin may offer some hope for the treatment of vancomycin-resistant enterococci but clinical data are still lacking. Thus, optimal therapies for the treatment of multidrug-resistant enterococcal infections continue to be based on empirical observations and extrapolations from in vitro and animal data. Clinical studies evaluating new strategies, including combination therapies, to treat severe vancomycin-resistant E. faecium infections are urgently needed.
Topics: Anti-Bacterial Agents; Cross Infection; Drug Resistance, Multiple, Bacterial; Enterococcus faecium; Gram-Positive Bacterial Infections; Humans
PubMed: 20569266
DOI: 10.1111/j.1469-0691.2010.03214.x -
Journal of Microbiology and... Oct 2019To shed light on the genetic basis of salt tolerance in , , and , we performed comparative genome analysis of 10 , 11 , and three strains. Factors involved in salt... (Comparative Study)
Comparative Study
To shed light on the genetic basis of salt tolerance in , , and , we performed comparative genome analysis of 10 , 11 , and three strains. Factors involved in salt tolerance that could be used to distinguish the species were identified. Overall, contained a greater number of potassium transport and osmoprotectant synthesis genes compared with the other two species. In particular, our findings suggested that may be the only one among the three species capable of synthesizing glycine betaine from choline, cardiolipin from glycerol and proline from citrate. These molecules are well-known osmoprotectants; thus, we propose that these genes confer the salt-tolerance of .
Topics: Bacterial Proteins; Enterococcaceae; Enterococcus faecalis; Enterococcus faecium; Genome, Bacterial; Membrane Transport Proteins; Salt Tolerance; Species Specificity
PubMed: 31546297
DOI: 10.4014/jmb.1908.08015 -
European Journal of Clinical... Feb 2017The objective of this study was to investigate the antimicrobial resistance, Tn1546 transposon variability and plasmid diversity among Polish vancomycin-resistant...
The objective of this study was to investigate the antimicrobial resistance, Tn1546 transposon variability and plasmid diversity among Polish vancomycin-resistant Enterococcus faecium (VREfm) isolates of VanA phenotype in the context of their clonal structure. Two hundred sixteen clinical VREfm isolates collected between 1997 and 2010 were studied by antimicrobial susceptibility testing, MLST, MLVA and detection of IS16, esp , pilA, intA and plasmid-specific genes by PCR. Tn1546 structure was revealed by overlapping PCR and sequencing. Selected isolates were subjected to PFGE-S1 and Southern hybridization analyses. The vast majority of the isolates (95.8 %) belonged to lineages 17/18 (during the whole study period 1997-2010) and 78 (mostly in 2006-2010) of hospital-adapted meroclone of E. faecium. All isolates displayed a multi-drug resistance phenotype. Twenty-eight Tn1546 types (including 26 novel ones) were associated with eight different ISs (IS1216, IS1251, ISEfa4, ISEfa5, ISEfm2, ISEf1, IS3-like, ISEfm1-like). The vanA-determinant was typically located on plasmids, which most commonly carried rep2, rep17, rep18, rep1, ω-ε-ζ and axe-txe genes. VanA isolates from 1997-2005 to 2006-2010 differed in clonal composition, prevalence of gentamicin- and tetracycline-resistance and plasmidome. Our analysis revealed high complexity of Tn1546-type transposons and vanA-plasmids, and suggested that diverse genetic events, such as conjugation transfer, recombination, chromosomal integration and DNA mutations shaped the structure of these elements among Polish VREfm.
Topics: Bacterial Proteins; Carbon-Oxygen Ligases; DNA Transposable Elements; Enterococcus faecium; Evolution, Molecular; Genetic Variation; Genotyping Techniques; Gram-Positive Bacterial Infections; Humans; Microbial Sensitivity Tests; Molecular Typing; Nucleic Acid Hybridization; Plasmids; Poland; Polymerase Chain Reaction; Sequence Analysis, DNA
PubMed: 27752789
DOI: 10.1007/s10096-016-2804-8 -
Scientific Reports Mar 2020For a One-Health investigation of antimicrobial resistance (AMR) in Enterococcus spp., isolates from humans and beef cattle along with abattoirs, manured fields, natural...
For a One-Health investigation of antimicrobial resistance (AMR) in Enterococcus spp., isolates from humans and beef cattle along with abattoirs, manured fields, natural streams, and wastewater from both urban and cattle feedlot sources were collected over two years. Species identification of Enterococcus revealed distinct associations across the continuum. Of the 8430 isolates collected, Enterococcus faecium and Enterococcus faecalis were the main species in urban wastewater (90%) and clinical human isolates (99%); Enterococcus hirae predominated in cattle (92%) and feedlot catch-basins (60%), whereas natural streams harbored environmental Enterococcus spp. Whole-genome sequencing of E. faecalis (n = 366 isolates) and E. faecium (n = 342 isolates), revealed source clustering of isolates, indicative of distinct adaptation to their respective environments. Phenotypic resistance to tetracyclines and macrolides encoded by tet(M) and erm(B) respectively, was prevalent among Enterococcus spp. regardless of source. For E. faecium from cattle, resistance to β-lactams and quinolones was observed among 3% and 8% of isolates respectively, compared to 76% and 70% of human clinical isolates. Clinical vancomycin-resistant E. faecium exhibited high rates of multi-drug resistance, with resistance to all β-lactam, macrolides, and quinolones tested. Differences in the AMR profiles among isolates reflected antimicrobial use practices in each sector of the One-Health continuum.
Topics: Anti-Bacterial Agents; Drug Resistance, Bacterial; Enterococcus; Enterococcus faecalis; Enterococcus faecium; Humans; Macrolides; Phylogeny; Quinolones; Tetracyclines; Virulence; Whole Genome Sequencing; beta-Lactam Resistance
PubMed: 32127598
DOI: 10.1038/s41598-020-61002-5