Clonal dissemination of Enterococcus faecalis ST201 and Enterococcus faecium CC17–ST64 containing Tn5382–vanB2 among 16 hospitals in Chile

Genomic insights into antibiotic-resistance and virulence genes of Enterococcus faecium strains from the gut of Apis mellifera

Enterococcus faecium is a lactic acid bacterium that confers beneficial health effects in humans. However, lately, a number of E. faecium strains have been linked to the spread of nosocomial infections in the hospital environment. Therefore, any potential commercial usage of E. faecium isolates should be preceded by an assessment of infection risk. In the current study, the genomes of two novel E. faecium strains Am1 (larval isolate) and Bee9 (adult bee isolate) isolated from the gut of Apis mellifera L. (honeybee) were sequenced to allow evaluation of their safety. In particular, their genomes were screened for antibiotic-resistance and virulence genes. In addition, their potential to spread resistance in the environment was evaluated. The analysis revealed that Am1 and Bee9 possess 2832 and 2844 protein-encoding genes, respectively. In each case, the genome size was 2.7 Mb with a G+C content of 37.9 mol%. Comparative analysis with probiotic, non-pathogenic and pathogenic enterococci revealed that there are variations between the two bee E. faecium isolates and pathogenic genomes. They were, however, closely linked to the probiotic comparison strains. Phenotypically, the Am1 and Bee9 strains were susceptible to most antibiotics tested, but showed intermediate sensitivity towards erythromycin, linezolid and trimethoprim/sulfamethoxazole. Notably, no genes associated with antibiotic resistance in clinical isolates (e.g. vancomycin resistance: vanA, vanB, vanS, vanX and vanY) were present. In addition, the insertion sequences (IS16, ISEfa11 and ISEfa5), acting as molecular pathogenicity markers in clinically relevant E. faecium strains, were also absent. Moreover, the analysis revealed the absence of three key pathogenicity-associated genes (acm, sgrA, ecbA) in the Am1 and Bee9 strains that are found in the prominent clinical isolates DO, V1836, Aus0004 and Aus0085. Overall, the findings of this investigation suggest that the E. faecium isolates from the bee gut have not suffered any recent clinically relevant antibiotic exposure. It also suggests that E. faecium Am1 and Bee9 are safe potential probiotic strains, because they lack the phenotypic and genetic features associated with strains eliciting nosocomial infections.

Antimicrobial Resistance, Biofilm Formation, and Virulence Genes in Enterococcus Species from Small Backyard Chicken Flocks

Backyard birds are small flocks that are more common in developing countries. They are used for poultry meat and egg production. However, they are also implicated in the maintenance and transmission of several zoonotic diseases, including multidrug-resistant bacteria. Enterococci are one of the most common zoonotic bacteria. They colonize numerous body sites and cause a wide range of serious nosocomial infections in humans. Therefore, the objective of the present study was to investigate the diversity in Enterococcus spp. in healthy birds and to determine the occurrence of multidrug resistance (MDR), multi-locus sequence types, and virulence genes and biofilm formation. From March 2019 to December 2020, cloacal swabs were collected from 15 healthy backyard broiler flocks. A total of 90 enterococci strains were recovered and classified according to the 16S rRNA sequence into Enterococcus faecalis (50%); Enterococcus faecium (33.33%), Enterococcus hirae (13.33%), and Enterococcus avium (3.33%). The isolates exhibited high resistance to tetracycline (55.6%), erythromycin (31.1%), and ampicillin (30%). However, all of the isolates were susceptible to linezolid. Multidrug resistance (MDR) was identified in 30 (33.3%) isolates. The enterococci AMR-associated genes ermB, ermA, tetM, tetL, vanA, cat, and pbp5 were identified in 24 (26.6%), 11 (12.2%), 39 (43.3%), 34 (37.7%), 1 (1.1%), 4 (4.4%), and 23 (25.5%) isolates, respectively. Of the 90 enterococci, 21 (23.3%), 27 (30%), and 36 (40%) isolates showed the presence of cylA, gelE, and agg virulence-associated genes, respectively. Seventy-three (81.1%) isolates exhibited biofilm formation. A statistically significant correlation was obtained for biofilm formation versus the MAR index and MDR. Multi-locus sequence typing (MLST) identified eleven and eight different STs for E. faecalis and E. faecium, respectively. Seven different rep-family plasmid genes (rep1–2, rep3, rep5–6, rep9, and rep11) were detected in the MDR enterococci. Two-thirds (20/30; 66.6%) of the enterococci were positive for one or two rep-families. In conclusion, the results show that healthy backyard chickens could act as a reservoir for MDR and virulent Enterococcus spp. Thus, an effective antimicrobial stewardship program and further studies using a One Health approach are required to investigate the role of backyard chickens as vectors for AMR transmission to humans.

Mobile genetic elements beyond the VanB-resistance dissemination among hospital-associated enterococci and other Gram-positive bacteria

An increasing resistance to vancomycin among clinically relevant enterococci, such as Enterococcus faecalis and Enterococcus faecium is a cause of a great concern, as it seriously limits treatment options. The vanB operon is one of most common determinants of this type of resistance. Genes constituting the operon are located in conjugative transposons, such as Tn1549-type transposons or, more rarely, in ICEEfaV583-type structures. Such elements show differences in structure and size, and reside in various sites of bacterial chromosome or, in the case of Tn1549-type transposons, are also occasionally associated with plasmids of divergent replicon types. While conjugative transposition contributes to the acquisition of Tn1549-type transposons from anaerobic gut commensals by enterococci, chromosomal recombination and conjugal transfer of plasmids appear to represent main mechanisms responsible for horizontal dissemination of vanB determinants among hospital E. faecalis and E. faecium. This review focuses on diversity of genetic elements harbouring vanB determinants in hospital-associated strains of E. faecium and E. faecalis, the mechanisms beyond vanB spread in populations of these bacteria, and provides an overview of the vanB-MGE distribution among other enterococci and Gram-positive bacteria as potential reservoirs of vanB genes.

Multiomics Substrates of Resistance to Emerging Pathogens? Transcriptome and Proteome Profile of a Vancomycin-Resistant Enterococcus faecalis Clinical Strain

Antibiotic resistance and hospital acquired infections are on the rise worldwide. Vancomycin-resistant enterococci have been reported in clinical settings in recent decades. In this multiomics study, we provide comprehensive proteomic and transcriptomic analyses of a vancomycin-resistant Enterococcus faecalis clinical isolate from a patient with a urinary tract infection. The previous genotypic profile of the strain C2620 indicated the presence of antibiotic resistance genes characteristic of the vanB cluster. To further investigate the transcriptome of this pathogenic strain, we used whole genome sequencing and RNA-sequencing to detect and quantify the genes expressed. In parallel, we used two-dimensional gel electrophoresis followed by MALDI-TOF/MS (Matrix-assisted laser desorption/ionization-Time-of-flight/Mass spectrometry) to identify the proteins in the proteome. We studied the membrane and cytoplasm subproteomes separately. From a total of 207 analysis spots, we identified 118 proteins. The protein list was compared to the results obtained from the full transcriptome assay. Several genes and proteins related to stress and cellular response were identified, as well as some linked to antibiotic and drug responses, which is consistent with the known state of multiresistance. Even though the correlation between transcriptome and proteome data is not yet fully understood, the use of multiomics approaches has proven to be increasingly relevant to achieve deeper insights into the survival ability of pathogenic bacteria found in health care facilities.

Vancomycin-Resistant Enterococci: A Review of Antimicrobial Resistance Mechanisms and Perspectives of Human and Animal Health

Vancomycin-resistant enterococci (VRE) are both of medical and public health importance associated with serious multidrug-resistant infections and persistent colonization. Enterococci are opportunistic environmental inhabitants with a remarkable adaptive capacity to evolve and transmit antimicrobial-resistant determinants. The VRE gene operons show distinct genetic variability and apparently continued evolution leading to a variety of antimicrobial resistance phenotypes and various environmental and livestock reservoirs for the most common van genes. Such complex diversity renders a number of important therapeutic options including "last resort antibiotics" ineffective and poses a particular challenge for clinical management. Enterococci resistance to glycopeptides and multidrug resistance warrants attention and continuous monitoring.

The ribosomal S10 protein is a general target for decreased tigecycline susceptibility

Tigecycline is a translational inhibitor with efficacy against a wide range of pathogens. Using experimental evolution, we adapted Acinetobacter baumannii, Enterococcus faecium, Escherichia coli, and Staphylococcus aureus to growth in elevated tigecycline concentrations. At the end of adaptation, 35 out of 47 replicate populations had clones with a mutation in rpsJ, the gene that encodes the ribosomal S10 protein. To validate the role of mutations in rpsJ in conferring tigecycline resistance, we showed that mutation of rpsJ alone in Enterococcus faecalis was sufficient to increase the tigecycline MIC to the clinical breakpoint of 0.5 μg/ml. Importantly, we also report the first identification of rpsJ mutations associated with decreased tigecycline susceptibility in A. baumannii, E. coli, and S. aureus. The identified S10 mutations across both Gram-positive and -negative species cluster in the vertex of an extended loop that is located near the tigecycline-binding pocket within the 16S rRNA. These data indicate that S10 is a general target of tigecycline adaptation and a relevant marker for detecting reduced susceptibility in both Gram-positive and -negative pathogens.

Emergence and characterisation of vanB vancomycin-resistant Enterococcus faecalis in Rio de Janeiro, Brazil

Here we describe the detection and characterisation of three isolates of vancomycin-resistant VanB-type Enterococcus faecalis. Sequence analysis suggested that these isolates harboured the vanB1 gene. The isolates were susceptible to the majority of antimicrobial agents tested, with the exception of chloramphenicol, erythromycin and vancomycin, and showed distinct profiles of high-level resistance to aminoglycosides. Analysis of the clonal relatedness of the vanB E. faecalis isolates showed similar pulsed-field gel electrophoresis profiles. To our knowledge, this is the first report of the occurrence of enterococcal strains carrying vanB genes in Brazil.

Diversity of clones and genotypes among vancomycin-resistant clinical Enterococcus isolates recovered in a Spanish hospital

Forty-three vancomycin-resistant enterococci (VRE) from different patients were recovered in a Spanish Hospital (2003-2010), representing 0.4% of the total of enterococci recovered. Mechanisms detected were vanA (five Enterococcus faecium, two E. faecalis), vanB2 (seven E. faecium, five E. faecalis), vanB1 (one E. faecalis), and vanC1/2 (22 E. gallinarum, 1 E. casseliflavus). Four different Tn1546 structures were found among the seven vanA strains, three of them with insertions (ISEf1 or IS1542) or deletions. Most of the VRE presented a multiresistance phenotype and harbored different resistance genes [erm(B), tet(M), tet(L), ant(6)-Ia, aac(6')-aph(2''), aph(3')-IIIa, and catA]. Sixteen unrelated pulsotypes were detected among the 20 vanA/vanB E. faecalis and E. faecium isolates by pulsed-field-gel-electrophoresis and 11 unrelated pulsotypes among the 22 E. gallinarum isolates. Six different sequence types (ST) were demonstrated among the 12 vancomycin-resistant E. faecium strains (one of them new), and 5 were included into the clonal-complex (CC) CC17. Five different ST were detected among the eight E. faecalis strains. The esp gene was detected in 58% and 25% of E. faecium and E. faecalis strains, respectively, and the hyl gene in 78% and 89%, respectively. A high diversity of clones and genotypes of VRE were detected in this hospital.

Vancomycin-resistant vanB-type Enterococcus faecium isolates expressing varying levels of vancomycin resistance and being highly prevalent among neonatal patients in a single ICU

BACKGROUND

Vancomycin-resistant isolates of E. faecalis and E. faecium are of special concern and patients at risk of acquiring a VRE colonization/infection include also intensively-cared neonates. We describe here an ongoing high prevalence of VanB type E. faecium in a neonatal ICU hardly to identify by routine diagnostics.

METHODS

During a 10 months' key period 71 E. faecium isolates including 67 vanB-type isolates from 61 patients were collected non-selectively. Vancomycin resistance was determined by different MIC methods (broth microdilution, Vitek® 2) including two Etest® protocols (McFarland 0.5/2.0. on Mueller-Hinton/Brain Heart Infusion agars). Performance of three chromogenic VRE agars to identify the vanB type outbreak VRE was evaluated (BrillianceTM VRE agar, chromIDTM VRE agar, CHROMagarTM VRE). Isolates were genotyped by SmaI- and CeuI-macrorestriction analysis in PFGE, plasmid profiling, vanB Southern hybridisations as well as MLST typing.

RESULTS

Majority of vanB isolates (n = 56, 79%) belonged to a single ST192 outbreak strain type showing an identical PFGE pattern and analyzed representative isolates revealed a chromosomal localization of a vanB2-Tn5382 cluster type. Vancomycin MICs in cation-adjusted MH broth revealed a susceptible value of ≤4 mg/L for 31 (55%) of the 56 outbreak VRE isolates. Etest® vancomycin on MH and BHI agars revealed only two vanB VRE isolates with a susceptible result; in general Etest® MIC results were about 1 to 2 doubling dilutions higher than MICs assessed in broth and values after the 48 h readout were 0.5 to 1 doubling dilutions higher for vanB VRE. Of all vanB type VRE only three, three and two isolates did not grow on BrillianceTM VRE agar, chromIDTM VRE agar and CHROMagarTM VRE, respectively. Permanent cross contamination via the patients' surrounding appeared as a possible risk factor for permanent VRE colonization/infection.

CONCLUSIONS

Low level expression of vanB resistance may complicate a proper routine diagnostics of vanB VRE and mask an ongoing high VRE prevalence. A high inoculum and growth on rich solid media showed the highest sensitivity in identifying vanB type resistance.

Clustering of polyclonal VanB-type vancomycin-resistant Enterococcus faecium in a low-endemic area was associated with CC17-genogroup strains harbouring transferable vanB2-Tn5382 and pRUM-like repA containing plasmids with axe-txe plasmid addiction systems

VanB-type vancomycin-resistant Enterococcus faecium isolates (n = 17) from 15 patients at the Örebro University hospital in Sweden during a span of 18 months was characterized. All patients had underlying disorders and received broad-spectrum antimicrobial therapy. Pulsed-field gel electrophoresis (PFGE) grouped 14 isolates in three PFGE types and three isolates in unique PFGE patterns. All isolates had multi-locus sequence types [ST17 (n = 5); ST18 (n = 3); ST125 (n = 7); ST262 (n = 1); ST460 (n = 1)] belonging to the successful hospital-adapted clonal complex 17 (CC17), harboured CC17-associated virulence genes, were vanB2-positive and expressed diverse vancomycin minimum inhibitory concentration (MICs; 8 to > 256 mg/L). Isolate 1 had a unique PFGE type and a chromosomal transferable vanB2-Tn5382 element. Interestingly, the other five PFGE types had Tn5382 located on plasmids containing pRUM-like repA and a plasmid addiction system (axe-txe) shown by co-hybridization analysis of PFGE-separated S1-nuclease digested total DNA. The resistance plasmids were mainly of 120-kb and supported intraspecies vanB transfer. Two strains were isolated from patient 6 and we observed a possible transfer of the vanB2-resistance genes from PFGE type III ST460 to a more successful PFGE type I ST125. This latter PFGE type I ST125 became the predominant type afterwards. Our observations support the notion that vanB-type vancomycin-resistant Enterococcus faecium can persist in a low-endemic area through successful clones and plasmids with stability functions in hospital patients with known risk factors.

Mobile genetic elements and their contribution to the emergence of antimicrobial resistant Enterococcus faecalis and Enterococcus faecium

Mobile genetic elements (MGEs) including plasmids and transposons are pivotal in the dissemination and persistence of antimicrobial resistance in Enterococcus faecalis and Enterococcus faecium. Enterococcal MGEs have also been shown to be able to transfer resistance determinants to more pathogenic bacteria such as Staphylococcus aureus. Despite their importance, we have a limited knowledge about the prevalence, distribution and genetic content of specific MGEs in enterococcal populations. Molecular epidemiological studies of enterococcal MGEs have been hampered by the lack of standardized molecular typing methods and relevant genome information. This review focuses on recent developments in the detection of MGEs and their contribution to the spread of antimicrobial resistance in clinically relevant enterococci.

Molecular epidemiology of vancomycin-resistant Enterococcus faecium: a prospective, multicenter study in South American hospitals

Enterococcus faecium has emerged as an important nosocomial pathogen worldwide, and this trend has been associated with the dissemination of a genetic lineage designated clonal cluster 17 (CC17). Enterococcal isolates were collected prospectively (2006 to 2008) from 32 hospitals in Colombia, Ecuador, Perú, and Venezuela and subjected to antimicrobial susceptibility testing. Genotyping was performed with all vancomycin-resistant E. faecium (VREfm) isolates by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. All VREfm isolates were evaluated for the presence of 16 putative virulence genes (14 fms genes, the esp gene of E. faecium [espEfm], and the hyl gene of E. faecium [hylEfm]) and plasmids carrying the fms20-fms21 (pilA), hylEfm, and vanA genes. Of 723 enterococcal isolates recovered, E. faecalis was the most common (78%). Vancomycin resistance was detected in 6% of the isolates (74% of which were E. faecium). Eleven distinct PFGE types were found among the VREfm isolates, with most belonging to sequence types 412 and 18. The ebpAEfm-ebpBEfm-ebpCEfm (pilB) and fms11-fms19-fms16 clusters were detected in all VREfm isolates from the region, whereas espEfm and hylEfm were detected in 69% and 23% of the isolates, respectively. The fms20-fms21 (pilA) cluster, which encodes a putative pilus-like protein, was found on plasmids from almost all VREfm isolates and was sometimes found to coexist with hylEfm and the vanA gene cluster. The population genetics of VREfm in South America appear to resemble those of such strains in the United States in the early years of the CC17 epidemic. The overwhelming presence of plasmids encoding putative virulence factors and vanA genes suggests that E. faecium from the CC17 genogroup may disseminate in the region in the coming years.

Transition of Enterococcus faecium from commensal organism to nosocomial pathogen

The Gram-positive species Enterococcus faecium has long been thought of as a harmless commensal of the mammalian GI tract. In the last two decades, however, E. faecium has become an important cause of nosocomial bacteremias. These infections are often difficult to treat owing to the resistance of E. faecium to a large number of antibiotics. In this article, we review the recent transition of E. faecium from commensal to nosocomial pathogen. We focus on population biology-based studies, which suggest that several clonal populations of E. faecium are mostly responsible for causing infections. We also discuss the role of the accessory genome of E. faecium in contributing to the infectious phenotype and examine the role that surface proteins of E. faecium may have in colonization and infection.