Emergence of daptomycin non-susceptibility in colonizing vancomycin-resistant Enterococcus faecium isolates during daptomycin therapy

Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin

Multidrug-resistant bacterial pathogens like vancomycin-resistant Enterococcus faecium (VREfm) are a critical threat to human health1. Daptomycin is a last-resort antibiotic for VREfm infections with a novel mode of action2, but for which resistance has been widely reported but is unexplained. Here we show that rifaximin, an unrelated antibiotic used prophylactically to prevent hepatic encephalopathy in patients with liver disease3, causes cross-resistance to daptomycin in VREfm. Amino acid changes arising within the bacterial RNA polymerase in response to rifaximin exposure cause upregulation of a previously uncharacterized operon (prdRAB) that leads to cell membrane remodelling and cross-resistance to daptomycin through reduced binding of the antibiotic. VREfm with these mutations are spread globally, making this a major mechanism of resistance. Rifaximin has been considered 'low risk' for the development of antibiotic resistance. Our study shows that this assumption is flawed and that widespread rifaximin use, particularly in patients with liver cirrhosis, may be compromising the clinical use of daptomycin, a major last-resort intervention for multidrug-resistant pathogens. These findings demonstrate how unanticipated antibiotic cross-resistance can undermine global strategies designed to preserve the clinical use of critical antibiotics.

Persistence of Daptomycin-Resistant and Vancomycin-Resistant Enterococci in Hospitalized Patients with Underlying Malignancies: A 7-Year Follow-Up Study

Vancomycin-resistant enterococci (VRE) commonly colonize the gut of individuals with hematologic malignancies or undergoing hematopoietic cell transplant (HCT) and may cause bacteremia. In 2012, we identified VRE isolates from patients and patients' rooms and showed transmission networks of highly genetically related daptomycin-resistant (DR)-VRE strains. This is a follow-up study performing whole-genome sequencing (WGS) and phylogenetic analyses on 82 clinical VRE strains isolated from stools and blood cultures of patients with leukemia and HCT between 2015 and 2019. Here, we observed transmission of highly genetically related strains between rooms on the same or on different floors, including a DR-VRE strain identified in 2012. Eleven of twenty-eight patients with DR-VRE were never exposed to daptomycin, suggesting horizontal transmission. Fifteen of the twenty-eight patients with DR-VRE died within 30 days of positive blood cultures. Amongst those, one DR-VRE strain belonging to ST1471 had the virulence gene bopD responsible for biofilm formation. Additionally, to our knowledge, this is the first report of a DR-VRE strain belonging to ST323 in the United States. In summary, our study demonstrated the emergence and persistence of VRE strains, especially DR-VRE, in our hospital. Adding WGS to routine infection control measures may timely identify potential horizontal VRE transmission including multi-drug-resistant isolates.

Phylogeny, Virulence, and Antimicrobial Resistance Gene Profiles of Enterococcus faecium Isolated from Australian Feedlot Cattle and Their Significance to Public and Environmental Health

The extent of similarity between E. faecium strains found in healthy feedlot beef cattle and those causing extraintestinal infections in humans is not yet fully understood. This study used whole-genome sequencing to analyse the antimicrobial resistance profile of E. faecium isolated from beef cattle (n = 59) at a single feedlot and compared them to previously reported Australian isolates obtained from pig (n = 60) and meat chicken caecal samples (n = 8), as well as human sepsis cases (n = 302). The E. faecium isolated from beef cattle and other food animal sources neither carried vanA/vanB responsible for vancomycin nor possessed gyrA/parC and liaR/liaS gene mutations associated with high-level fluoroquinolone and daptomycin resistance, respectively. A small proportion (7.6%) of human isolates clustered with beef cattle and pig isolates, including a few isolates belonging to the same sequence types ST22 (one beef cattle, one pig, and two human isolates), ST32 (eight beef cattle and one human isolate), and ST327 (two beef cattle and one human isolate), suggesting common origins. This provides further evidence that these clonal lineages may have broader host range but are unrelated to the typical hospital-adapted human strains belonging to clonal complex 17, significant proportions of which contain vanA/vanB and liaR/liaS. Additionally, none of the human isolates belonging to these STs contained resistance genes to WHO critically important antimicrobials. The results confirm that most E. faecium isolated from beef cattle in this study do not pose a significant risk for resistance to critically important antimicrobials and are not associated with current human septic infections.

Aminopenicillins versus Non-aminopenicillins for Treatment of Enterococcal Lower Urinary Tract Infections

Aminopenicillins achieve urinary concentrations that exceed typical minimum inhibitory concentrations for enterococcal lower urinary tract infection (UTI). Our clinical microbiology laboratory discontinued routine susceptibilities on enterococcal urine isolates and reports "aminopenicillins are predictably reliable for uncomplicated enterococcal UTI". The study objective was to compare outcomes of aminopenicillins (AP) to non-aminopenicillins (NAP) for enterococcal lower UTIs. This was an IRB approved, retrospective cohort of adults hospitalized with symptomatic enterococcal lower UTIs from 2013-2021. Primary endpoint: composite clinical success at 14-days, defined as resolution of symptoms without new symptoms and no repeat culture growth of index organism. A non-inferiority analysis was utilized with a 15% margin, and logistic regression evaluated characteristics associated with 14-day failure. 178 subjects were included: 89 AP, 89 NAP. VRE was identified in 73 (82%) AP and 76 (85%) NAP patients (P=0.54); a total of 34 (38.2%) AP and 66 (74.2%) NAP patients had confirmed E. faecium (P<0.001). Amoxicillin (36, 40.5%) and ampicillin (36, 40.5%) were the most frequent AP utilized; linezolid (41, 46%) and fosfomycin (30, 34%) were the most frequent NAP. 14-day clinical success for AP and NAP was 83.1% and 82.0% (1.1% difference, 97.5%CI, -0.117-0.139). Among the E. faecium subgroup, 14-day clinical success was observed in 27/34 (79.4%) of AP and 53/66 (80.3%) of NAP patients (P=0.916). In logistic regression, APs were not associated with 14-day clinical failure (adjOR 0.84; 95%CI, 0.38-1.86). Aminopenicillins were noninferior to non-aminopenicillins for treating enterococcal lower UTIs and may be considered irrespective of susceptibility results.

Phage Cocktails with Daptomycin and Ampicillin Eradicates Biofilm-Embedded Multidrug-Resistant Enterococcus faecium with Preserved Phage Susceptibility

Multidrug-resistant (MDR) Enterococcus faecium is a challenging nosocomial pathogen known to colonize medical device surfaces and form biofilms. Bacterio (phages) may constitute an emerging anti-infective option for refractory, biofilm-mediated infections. This study evaluates eight MDR E. faecium strains for biofilm production and phage susceptibility against nine phages. Two E. faecium strains isolated from patients with bacteremia and identified to be biofilm producers, R497 (daptomycin (DAP)-resistant) and HOU503 (DAP-susceptible dose-dependent (SDD), in addition to four phages with the broadest host ranges (ATCC 113, NV-497, NV-503-01, NV-503-02) were selected for further experiments. Preliminary phage-antibiotic screening was performed with modified checkerboard minimum biofilm inhibitory concentration (MBIC) assays to efficiently screen for bacterial killing and phage-antibiotic synergy (PAS). Data were compared by one-way ANOVA and Tukey (HSD) tests. Time kill analyses (TKA) were performed against R497 and HOU503 with DAP at 0.5× MBIC, ampicillin (AMP) at free peak = 72 µg/mL, and phage at a multiplicity of infection (MOI) of 0.01. In 24 h TKA against R497, phage-antibiotic combinations (PAC) with DAP, AMP, or DAP + AMP combined with 3- or 4-phage cocktails demonstrated significant killing compared to the most effective double combination (ANOVA range of mean differences 2.998 to 3.102 log10 colony forming units (CFU)/mL; p = 0.011, 2.548 to 2.868 log10 colony forming units (CFU)/mL; p = 0.023, and 2.006 to 2.329 log10 colony forming units (CFU)/mL; p = 0.039, respectively), with preserved phage susceptibility identified in regimens with 3-phage cocktails containing NV-497 and the 4-phage cocktail. Against HOU503, AMP combined with any 3- or 4-phage cocktail and DAP + AMP combined with the 3-phage cocktail ATCC 113 + NV-497 + NV-503-01 demonstrated significant PAS and bactericidal activity (ANOVA range of mean differences 2.251 to 2.466 log10 colony forming units (CFU)/mL; p = 0.044 and 2.119 to 2.350 log10 colony forming units (CFU)/mL; p = 0.028, respectively), however, only PAC with DAP + AMP maintained phage susceptibility at the end of 24 h TKA. R497 and HOU503 exposure to DAP, AMP, or DAP + AMP in the presence of single phage or phage cocktail resulted in antibiotic resistance stabilization (i.e., no antibiotic MBIC elevation compared to baseline) without identified antibiotic MBIC reversion (i.e., lowering of antibiotic MBIC compared to baseline in DAP-resistant and DAP-SDD isolates) at the end of 24 h TKA. In conclusion, against DAP-resistant R497 and DAP-SDD HOU503 E. faecium clinical blood isolates, the use of DAP + AMP combined with 3- and 4-phage cocktails effectively eradicated biofilm-embedded MDR E. faecium without altering antibiotic MBIC or phage susceptibility compared to baseline.

An orally administered drug prevents selection for antibiotic-resistant bacteria in the gut during daptomycin therapy

Background and objectives

Previously, we showed proof-of-concept in a mouse model that oral administration of cholestyramine prevented enrichment of daptomycin-resistant Enterococcus faecium in the gastrointestinal (GI) tract during daptomycin therapy. Cholestyramine binds daptomycin in the gut, which removes daptomycin selection pressure and so prevents the enrichment of resistant clones. Here, we investigated two open questions related to this approach: (i) can cholestyramine prevent the enrichment of diverse daptomycin mutations emerging de novo in the gut? and (ii) how does the timing of cholestyramine administration impact its ability to suppress resistance?

Methodology

Mice with GI E. faecium were treated with daptomycin with or without cholestyramine, and E. faecium was cultured from feces to measure changes in daptomycin susceptibility. A subset of clones was sequenced to investigate the genomic basis of daptomycin resistance.

Results

Cholestyramine prevented the enrichment of diverse resistance mutations that emerged de novo in daptomycin-treated mice. Whole-genome sequencing revealed that resistance emerged through multiple genetic pathways, with most candidate resistance mutations observed in the clsA gene. In addition, we observed that cholestyramine was most effective when administration started prior to the first dose of daptomycin. However, beginning cholestyramine after the first daptomycin dose reduced the frequency of resistant E. faecium compared to not using cholestyramine at all.

Conclusions and implications

Cholestyramine prevented the enrichment of diverse daptomycin-resistance mutations in intestinal E. faecium populations during daptomycin treatment, and it is a promising tool for managing the transmission of daptomycin-resistant E. faecium.

Rapid in vivo development of resistance to daptomycin in vancomycin-resistant Enterococcus faecium due to genomic alterations

Daptomycin is a cyclic lipopeptide used in the treatment of vancomycin-resistant Enterococcus faecium (VREfm). However, the development of daptomycin-resistant VREfm challenges the treatment of nosocomial VREfm infections. Resistance mechanisms of daptomycin are not fully understood. Here we analysed the genomic changes leading to a daptomycin-susceptible VREfm isolate becoming resistant after 50 days of daptomycin and linezolid combination therapy. Seven isogenic VREfm isolates from the same patient (daptomycin-susceptible and daptomycin-resistant) were analysed using Illumina whole genome sequencing, and two isolates were further characterised with Nanopore sequencing. One nonsynonymous SNP in the rpoC gene previously shown to harbour mutations in daptomycin-resistant VREfm was identified in the daptomycin-resistant isolates. Whole genome comparative analysis identified the loss of a 46.5 kb fragment, duplication of a 29.7 kb fragment, and integration of two plasmids upon acquisition of daptomycin resistance. Transmission electron microscopy showed similar alterations in cell morphology and cell wall structure as have previously been described in daptomycin-resistant Enterococcus faecalis.

Antimicrobial tolerance and its role in the development of resistance: Lessons from enterococci

Bacteria have developed resistance against every antimicrobial in clinical use at an alarming rate. There is a critical need for more effective use of antimicrobials to both extend their shelf life and prevent resistance from arising. Significantly, antimicrobial tolerance, i.e., the ability to survive but not proliferate during antimicrobial exposure, has been shown to precede the development of bona fide antimicrobial resistance (AMR), sparking a renewed and rapidly increasing interest in this field. As a consequence, problematic infections for the first time are now being investigated for antimicrobial tolerance, with increasing reports demonstrating in-host evolution of antimicrobial tolerance. Tolerance has been identified in a wide array of bacterial species to all bactericidal antimicrobials. Of particular interest are enterococci, which contain the opportunistic bacterial pathogens Enterococcus faecalis and Enterococcus faecium. Enterococci are one of the leading causes of hospital-acquired infection and possess intrinsic tolerance to a number of antimicrobial classes. Persistence of these infections in the clinic is of growing concern, particularly for the immunocompromised. Here, we review current known mechanisms of antimicrobial tolerance, and include an in-depth analysis of those identified in enterococci with implications for both the development and prevention of AMR.

Prevalence of ESKAPE pathogens in the environment: Antibiotic resistance status, community-acquired infection and risk to human health

The ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) pathogens are characterised by increased levels of resistance towards multiple classes of first line and last-resort antibiotics. Although these pathogens are frequently isolated from clinical environments and are implicated in a variety of life-threatening, hospital-associated infections; antibiotic resistant ESKAPE strains have been isolated from environmental reservoirs such as surface water, wastewater, food, and soil. Literature on the persistence and subsequent health risks posed by the ESKAPE isolates in extra-hospital settings is however, limited and the current review aims to elucidate the primary reservoirs of these pathogens in the environment, their antibiotic resistance profiles, and the link to community-acquired infections. Additionally, information on the current state of research regarding health-risk assessments linked to exposure of the ESKAPE pathogens in the natural environment, is outlined.

New Mutations in cls Lead to Daptomycin Resistance in a Clinical Vancomycin- and Daptomycin-Resistant Enterococcus faecium Strain

Daptomycin (DAP), a last-resort antibiotic for treating Gram-positive bacterial infection, has been widely used in the treatment of vancomycin-resistant enterococci (VRE). Resistance to both daptomycin and vancomycin leads to difficulties in controlling infections of enterococci. A clinical multidrug-resistant Enterococcus faecium EF332 strain that shows resistance to both daptomycin and vancomycin was identified, for which resistance mechanisms were investigated in this work. Whole-genome sequencing and comparative genomic analysis were performed by third-generation PacBio sequencing, showing that E. faecium EF332 contains four plasmids, including a new multidrug-resistant pEF332-2 plasmid. Two vancomycin resistance-conferring gene clusters vanA and vanM were found on this plasmid, making it the second reported vancomycin-resistant plasmid containing both clusters. New mutations in chromosomal genes cls and gdpD that, respectively, encode cardiolipin synthase and glycerophosphoryl diester phosphodiesterase were identified. Their potential roles in leading to daptomycin resistance were further investigated. Through molecular cloning and phenotypic screening, two-dimensional thin-layer chromatography, fluorescence surface charge test, and analysis of cardiolipin distribution patterns, we found that mutations in cls decrease surface negative charges of the cell membrane (CM) and led to redistribution of lipids of CM. Both events contribute to the DAP resistance of E. faecium EF332. Mutation in gdpD leads to changes in CM phospholipid compositions, but cannot confer DAP resistance. Neither mutation could result in changes in cellular septa. Therefore, we conclude that the daptomycin resistance of E. faecium EF332 is conferred by new cls mutations. This work reports the genetic basis for vancomycin and daptomycin resistance of a multidrug-resistant E. faecium strain, with the finding of new mutations of cls that leads to daptomycin resistance.

Acquisition of Daptomycin Resistance by Enterococcus faecium Confers Collateral Sensitivity to Glycopeptides

Daptomycin is a last-line antibiotic used in the treatment of multidrug-resistant Enterococcus faecium infections. Alarmingly, daptomycin-resistant E. faecium isolates have emerged. In this study, we investigated the evolution and mechanisms of daptomycin resistance in clinical E. faecium isolates and the corresponding acquisition of collateral sensitivity (CS) as an evolutionary trade-off. We evolved daptomycin resistance in six daptomycin-susceptible E. faecium isolates to obtain daptomycin-resistant mutants. The six E. faecium strains successfully acquired high-level resistance to daptomycin in vitro, but this led to fitness costs in terms of growth, in vitro competition, and virulence. Mutations in liaFSR, yycFG, and cls; increased surface positive charge; thicker cell walls; and elevated expression of dltABCD and tagGH were observed in daptomycin-resistant mutants. Surprisingly, we observed the emergence of CS in SC1762 isolates after the induction of daptomycin resistance. Compared with parental strains, the SC1174-D strain (i.e., daptomycin-resistant mutant of SC1174; non-CS) showed significantly upregulated expression of the vanA gene cluster. However, in SC1762-D (i.e., daptomycin-resistant mutant of SC1762), all vanA cluster genes except the vanX gene were obviously downregulated. Further in silico analyses revealed that an IS1216E-based composite transposon was generated in SC1762-D, and it disrupted the vanH gene, likely affecting the structure and expression of the vanA gene cluster and resulting in resensitization to glycopeptides. Overall, this study reports a novel form of CS between daptomycin and glycopeptides in E. faecium. Further, it provides a valuable foundation for developing effective regimens and sequential combinations of daptomycin and glycopeptides against E. faecium.

Genomic Surveillance of Vancomycin-Resistant Enterococcus faecium Reveals Spread of a Linear Plasmid Conferring a Nutrient Utilization Advantage

Healthcare-associated outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are a worldwide problem with increasing prevalence. The genomic plasticity of this hospital-adapted pathogen contributes to its efficient spread despite infection control measures. Here, we aimed to identify the genomic and phenotypic determinants of health care-associated transmission of VREfm. We assessed the VREfm transmission networks at the tertiary-care University Hospital of Zurich (USZ) between October 2014 and February 2018 and investigated microevolutionary dynamics of this pathogen. We performed whole-genome sequencing for the 69 VREfm isolates collected during this time frame and assessed the population structure and variability of the vancomycin resistance transposon. Phylogenomic analysis allowed us to reconstruct transmission networks and to unveil external or wider transmission networks undetectable by routine surveillance. Notably, it unveiled a persistent clone, sampled 31 times over a 29-month period. Exploring the evolutionary dynamics of this clone and characterizing the phenotypic consequences revealed the spread of a variant with decreased daptomycin susceptibility and the acquired ability to utilize N-acetyl-galactosamine (GalNAc), one of the primary constituents of the human gut mucins. This nutrient utilization advantage was conferred by a novel plasmid, termed pELF_USZ, which exhibited a linear topology. This plasmid, which was harbored by two distinct clones, was transferable by conjugation. Overall, this work highlights the potential of combining epidemiological, functional genomic, and evolutionary perspectives to unveil adaptation strategies of VREfm. IMPORTANCE Sequencing microbial pathogens causing outbreaks has become a common practice to characterize transmission networks. In addition to the signal provided by vertical evolution, bacterial genomes harbor mobile genetic elements shared horizontally between clones. While macroevolutionary studies have revealed an important role of plasmids and genes encoding carbohydrate utilization systems in the adaptation of Enterococcus faecium to the hospital environment, mechanisms of dissemination and the specific function of many of these genetic determinants remain to be elucidated. Here, we characterize a plasmid providing a nutrient utilization advantage and show evidence for its clonal and horizontal spread at a local scale. Further studies integrating epidemiological, functional genomics, and evolutionary perspectives will be critical to identify changes shaping the success of this pathogen.

Evaluation of Bacteriophage-Antibiotic Combination Therapy for Biofilm-Embedded MDR Enterococcus faecium

Multidrug-resistant (MDR) Enterococcus faecium is a challenging pathogen known to cause biofilm-mediated infections with limited effective therapeutic options. Lytic bacteriophages target, infect, and lyse specific bacterial cells and have anti-biofilm activity, making them a possible treatment option. Here, we examine two biofilm-producing clinical E. faecium strains, daptomycin (DAP)-resistant R497 and DAP-susceptible dose-dependent (SDD) HOU503, with initial susceptibility to E. faecium bacteriophage 113 (ATCC 19950-B1). An initial synergy screening was performed with modified checkerboard MIC assays developed by our laboratory to efficiently screen for antibiotic and phage synergy, including at very low phage multiplicity of infection (MOI). The data were compared by one-way ANOVA and Tukey (HSD) tests. In 24 h time kill analyses (TKA), combinations with phage-DAP-ampicillin (AMP), phage-DAP-ceftaroline (CPT), and phage-DAP-ertapenem (ERT) were synergistic and bactericidal compared to any single agent (ANOVA range of mean differences 3.34 to 3.84 log10 CFU/mL; p < 0.001). Furthermore, phage-DAP-AMP and phage-DAP-CPT prevented the emergence of DAP and phage resistance. With HOU503, the combination of phage-DAP-AMP showed the best killing effect, followed closely by phage-DAP-CPT; both showed bactericidal and synergistic effects compared to any single agent (ANOVA range of mean differences 3.99 to 4.08 log10 CFU/mL; p < 0.001).

Development of 1,2,4-Oxadiazole Antimicrobial Agents to Treat Enteric Pathogens within the Gastrointestinal Tract

Colonization of the gastrointestinal (GI) tract with pathogenic bacteria is an important risk factor for the development of certain potentially severe and life-threatening healthcare-associated infections, yet efforts to develop effective decolonization agents have been largely unsuccessful thus far. Herein, we report modification of the 1,2,4-oxadiazole class of antimicrobial compounds with poorly permeable functional groups in order to target bacterial pathogens within the GI tract. We have identified that the quaternary ammonium functionality of analogue 26a results in complete impermeability in Caco-2 cell monolayers while retaining activity against GI pathogens Clostridioides difficile and multidrug-resistant (MDR) Enterococcus faecium. Low compound recovery levels after oral administration in rats were observed, which suggests that the analogues may be susceptible to degradation or metabolism within the gut, highlighting a key area for optimization in future efforts. This study demonstrates that modified analogues of the 1,2,4-oxadiazole class may be potential leads for further development of colon-targeted antimicrobial agents.

Daptomycin Resistance Occurs Predominantly in vanA-Type Vancomycin-Resistant Enterococcus faecium in Australasia and Is Associated With Heterogeneous and Novel Mutations

Healthcare associated infections caused by vancomycin-resistant Enterococcus faecium (VREfm) have a major impact on health outcomes. VREfm is difficult to treat because of intrinsic and acquired resistance to many clinically used antimicrobials, with daptomycin being one of the few last line therapeutic options for treating multidrug-resistant VREfm. The emergence of daptomycin-resistant VREfm is therefore of serious clinical concern. Despite this, the impact that daptomycin-resistant VREfm have on patient health outcomes is not clearly defined and knowledge on the mechanisms and genetic signatures linked with daptomycin resistance in VREfm remains incomplete. To address these knowledge gaps, phenotypic daptomycin susceptibility testing was undertaken on 324 E. faecium isolates from Australia and New Zealand. Approximately 15% of study isolates were phenotypically resistant to daptomycin. Whole genome sequencing revealed a strong association between vanA-VREfm and daptomycin resistance, with 95% of daptomycin-resistant study isolates harbouring vanA. Genomic analyses showed that daptomycin-resistant VREfm isolates were polyclonal and carried several previously characterised mutations in the liaR and liaS genes as well as several novel mutations within the rpoB, rpoC, and dltC genes. Overall, 70% of daptomycin-resistant study isolates were found to carry mutations within the liaR, rpoB, rpoC, or dltC genes. Finally, in a mouse model of VREfm bacteraemia, infection with the locally dominant daptomycin-resistant clone led to reduced daptomycin treatment efficacy in comparison to daptomycin-susceptible E. faecium. These findings have important implications for ongoing VREfm surveillance activities and the treatment of VREfm infections.

Evolution of vancomycin-resistant Enterococcus faecium during colonization and infection in immunocompromised pediatric patients

Immunocompromised patients are at increased risk for multidrug-resistant infections, due to broad-spectrum antibiotic exposure and a host environment with limited innate defenses. This study explored how vancomycin-resistant Enterococcus faecium (VREfm), a pathogen endemic to many hospitals, underwent genomic and phenotypic changes during intestinal colonization and bloodstream infection of immunocompromised pediatric patients. We identified a mutation conferring bacterial growth in alternative sugars that arose de novo in two different patients and was also present in five other patients. We also characterized mutations in surface polysaccharide production associated with better adherence to surfaces and resistance to the innate immune factor lysozyme. These findings suggest that targeting carbohydrate availability and bacterial adherence may be worthwhile strategies to limit VREfm proliferation in immunocompromised hosts.

Patients with hematological malignancies or undergoing hematopoietic stem cell transplantation are vulnerable to colonization and infection with multidrug-resistant organisms, including vancomycin-resistant Enterococcus faecium (VREfm). Over a 10-y period, we collected and sequenced the genomes of 110 VREfm isolates from gastrointestinal and blood cultures of 24 pediatric patients undergoing chemotherapy or hematopoietic stem cell transplantation for hematological malignancy at St. Jude Children’s Research Hospital. We used patient-specific reference genomes to identify variants that arose over time in subsequent gastrointestinal and blood isolates from each patient and analyzed these variants for insight into how VREfm adapted during colonization and bloodstream infection within each patient. Variants were enriched in genes involved in carbohydrate metabolism, and phenotypic analysis identified associated differences in carbohydrate utilization among isolates. In particular, a Y585C mutation in the sorbitol operon transcriptional regulator gutR was associated with increased bacterial growth in the presence of sorbitol. We also found differences in biofilm-formation capability between isolates and observed that increased biofilm formation correlated with mutations in the putative E. faecium capsular polysaccharide (cps) biosynthetic locus, with different mutations arising independently in distinct genetic backgrounds. Isolates with cps mutations showed improved survival following exposure to lysozyme, suggesting a possible reason for the selection of capsule-lacking bacteria. Finally, we observed mutations conferring increased tolerance of linezolid and daptomycin in patients who were treated with these antibiotics. Overall, this study documents known and previously undescribed ways that VREfm evolve during intestinal colonization and subsequent bloodstream infection in immunocompromised pediatric patients.

Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE)

Vancomycin-resistant enterococci (VRE), due to their intrinsic resistance to various commonly used antibiotics and their malleable genome, make the treatment of infections caused by these bacteria less effective. The aims of this work were to characterize isolates of Enterococcus spp. that originated from processed meat, through phenotypic and genotypic techniques, as well as to detect putative antibiotic resistance biomarkers. The 19 VRE identified had high resistance to teicoplanin (89%), tetracycline (94%), and erythromycin (84%) and a low resistance to kanamycin (11%), gentamicin (11%), and streptomycin (5%). Based on a Next-Generation Sequencing NGS technique, most isolates were vanA-positive. The most prevalent resistance genes detected were erm(B) and aac(6')-Ii, conferring resistance to the classes of macrolides and aminoglycosides, respectively. MALDI-TOF mass spectrometry (MS) analysis detected an exclusive peak of the Enterococcus genus at m/z (mass-to-charge-ratio) 4428 ± 3, and a peak at m/z 6048 ± 1 allowed us to distinguish Enterococcus faecium from the other species. Several statistically significant protein masses associated with resistance were detected, such as peaks at m/z 6358.27 and m/z 13237.3 in ciprofloxacin resistance isolates. These results reinforce the relevance of the combined and complementary NGS and MALDI-TOF MS techniques for bacterial characterization.

Daptomycin perioperative prophylaxis for the prevention of vancomycin-resistant Enterococcus infection in colonized liver transplant recipients

BACKGROUND

Vancomycin-resistant Enterococcus (VRE)-colonized liver transplantation (LT) recipients have increased post-LT morbidity, mortality, and higher rates of VRE infections compared with their non-colonized counterparts. Pre-LT screening for VRE colonization and inclusion of daptomycin in the perioperative antibiotic prophylaxis regimen may mitigate this risk.

METHODS

We performed a retrospective chart review of liver transplant recipients aged ≥ 18 years between 2013 and August 2019 to identify pre-LT VRE-colonized recipients and whether they received daptomycin perioperative prophylaxis (DPP). Demographic and clinical characteristics, including risk factors for VRE infection, were collected. Outcomes measured were VRE-related infection and all-cause mortality within 90 days of LT.

RESULTS

Of the 27 VRE-colonized liver transplant recipients within the study period, 25 received DPP. All recipients were admitted to the intensive care unit postoperatively, six (24%) required reoperation, fifteen (60%) required renal replacement therapy, and eight (32%) experienced postoperative hemorrhage within 90 days post-transplant. Two recipients (8%) experienced acute cellular rejection, but no primary graft failure was seen within 90 days. Among those who received DPP, no infections related to VRE or death was seen within 90 days of LT. The two VRE-colonized recipients who did not receive DPP both developed VRE bacteremia in the early post-LT period.

CONCLUSION

Despite having multiple risk factors for post-LT VRE infection, VRE-colonized recipients who received DPP did not develop VRE-related infections in the first 90 days post-LT. Our experience demonstrates that pre-LT VRE screening and DPP may be associated with a reduction in VRE infection in the early post-LT period, but this strategy warrants further evaluation in prospective studies.

Antibiotic Resistance and Molecular Epidemiology of Vancomycin-Resistant Enterococci in a Tertiary Care Hospital in Turkey

PURPOSE

Vancomycin-resistant enterococci (VRE) have become a global health threat in the last two decades. In this study, we aimed to determine antibiotic resistance using phenotypic and genotypic methods in VRE strains obtained from inpatients and to investigate clonal relatedness among strains.

METHODS

Identification and antibiotic susceptibility of 47 VRE strains obtained from inpatients at Karabuk University Hospital from 2014 to 2015 were determined using the BD Phoenix™ automated microbiology system. Vancomycin resistance genes (Van A and B) were detected by polymerase chain reaction. Clonal relatedness among the strains was evaluated by pulsed-field gel electrophoresis (PFGE).

RESULTS

All 47 VRE strains obtained from rectal (n=35), blood (n=7), and urine (n=5) samples were confirmed as Enterococcus faecium; they were resistant to ampicillin, gentamicin, vancomycin, and teicoplanin. One E. faecium isolate was intermediately resistant to linezolid. No strain was resistant to quinupristin-dalfopristin or daptomycin. Only vanA was detected among strains. According to the PFGE results, 31 of 47 strains were clonally related with a clustering rate of 66%. No common clone was detected.

CONCLUSION

VRE infections are associated with high mortality, morbidity, and healthcare expenditures. Increasing resistance to last-line drugs, such as linezolid and daptomycin, among VRE strains is a great concern. Therefore, comprehensive measures should be performed to reduce VRE colonization. Although there was no common clone VRE outbreak, polyclonal spread was observed in our hospital. The high clustering rate indicated cross-contamination. Thus, a more effective infection control program should be implemented.

Association of daptomycin dosing regimen and mortality in patients with VRE bacteraemia: a review

VRE are associated with ∼1300 deaths per year in the USA. Recent literature suggests that daptomycin, a cyclic lipopeptide antibiotic with concentration-dependent bactericidal activity, is the preferred treatment option for VRE bacteraemia, yet the optimal dosing strategy for this indication has not been established. In vitro evidence suggests that higher-than-labelled doses of daptomycin are required to optimally treat VRE bacteraemia and to inhibit the development of resistance. However, concern of dose-dependent toxicities, notably increases in creatine phosphokinase and the development of rhabdomyolysis, are a barrier to initiating high-dose schemes in clinical practice. Thus, the effectiveness and safety of high-dose daptomycin regimens in clinical practice have remained unclear. While early studies failed to identify differences in mortality, newer, larger investigations suggest high-dose (≥9 mg/kg) daptomycin is associated with reduced mortality in patients with VRE bacteraemia compared with standard (6 mg/kg) dosing regimens. Additionally, the high-dose regimens appear to be safe and may be associated with improved microbiological outcomes. The purpose of this review is to examine the published evidence on the effectiveness and safety of high-dose daptomycin compared with standard dosing regimens for VRE bacteraemia.

Utilizing genomic analyses to investigate the first outbreak of vanA vancomycin-resistant Enterococcus in Australia with emergence of daptomycin non-susceptibility

INTRODUCTION

The majority of vancomycin-resistant Enterococcus faecium (VREfm) in Australia is of the vanB genotype. An outbreak of vanA VREfm emerged in our haematology/oncology unit between November 2014 and May 2015. The first case of daptomycin non-susceptible E. faecium (DNSEfm) detected was a patient with vanA VREfm bacteraemia who showed clinical failure of daptomycin therapy, prompting microbiologic testing confirming daptomycin non-susceptibility.

OBJECTIVES

To describe the patient profiles, antibiotic susceptibility and genetic relatedness of vanA VREfm isolates in the outbreak.

METHODS

Chart review of vanA VREfm colonized and infected patients was undertaken to describe the demographics, clinical features and outcomes of therapy. Whole genome sequencing of vanA VREfm isolates involved in the outbreak was conducted to assess clonality.

RESULTS

In total, 29 samples from 24 patients tested positive for vanA VREfm (21 screening swabs and 8 clinical isolates). Five isolates were DNSEfm (four patients colonized, one patient with bacteraemia), with only one patient exposed to daptomycin previously. In silico multi-locus sequence typing of the isolates identified 25/26 as ST203, and 1/26 as ST796. Comparative genomic analysis revealed limited core genome diversity amongst the ST203 isolates, consistent with an outbreak of a single clone of vanA VREfm.

CONCLUSIONS

Here we describe an outbreak of vanA VREfm in a haematology/oncology unit. Genomic analysis supports transmission of an ST203 vanA VRE clone within this unit. Daptomycin non-susceptibility in 5/24 patients left linezolid as the only treatment option. Daptomycin susceptibility cannot be assumed in vanA VREfm isolates and confirmatory testing is recommended.

Evolution and mutations predisposing to daptomycin resistance in vancomycin-resistant Enterococcus faecium ST736 strains

We recently identified a novel vancomycin-resistant Enterococcus faecium (VREfm) clone ST736 with reduced daptomycin susceptibility. The objectives of this study were to assess the population dynamics of local VREfm strains and genetic alterations predisposing to daptomycin resistance in VREfm ST736 strains. Multilocus sequence typing and single nucleotide variant data were derived from whole-genome sequencing of 250 E. faecium isolates from 1994–1995 (n = 43), 2009–2012 (n = 115) and 2013 (n = 92). A remarkable change was noticed in the clonality and antimicrobial resistance profiles of E. faecium strains between 1994–1995 and 2013. VREfm sequence type 17 (ST17), the prototype strain of clade A1, was the dominant clone (76.7%) recognized in 1994–1995. By contrast, clone ST736 accounted for 46.7% of VREfm isolates, followed by ST18 (26.1%) and ST412 (20.7%) in 2013. Bayesian evolutionary analysis suggested that clone ST736 emerged between 1996 and 2009. Co-mutations (liaR.W73C and liaS.T120A) of the liaFSR system were identified in all ST736 isolates (n = 111, 100%) examined. Thirty-eight (34.2%) ST736 isolates exhibited daptomycin-resistant phenotype, of which 13 isolates had mutations in both the liaFSR and cardiolipin synthase (cls) genes and showed high level of resistance with a daptomycin MIC₅₀ of 32 μg/mL. The emergence of ST736 strains with mutations predisposing to daptomycin resistance and subsequent clonal spread among inpatients contributed to the observed high occurrence of daptomycin resistance in VREfm at our institution. The expanding geographic distribution of ST736 strains in other states and countries raises concerns about its global dissemination.

Prediction of Bloodstream Infection Due to Vancomycin-Resistant Enterococcus in Patients Undergoing Leukemia Induction or Hematopoietic Stem-Cell Transplantation

Background.

Bloodstream infection (BSI) to due vancomycin-resistant Enterococcus (VRE) is an important complication of hematologic malignancy. Determining when to use empiric anti-VRE antibiotic therapy in this population remains a clinical challenge.

Methods.

A single-center cohort representing 664 admissions for induction or hematopoietic stem-cell transplant (HSCT) from 2006 to 2014 was selected. We derived a prediction score using risk factors for VRE BSI and evaluated the model's predictive performance by calculating it for each of 16232 BSI at-risk inpatient days.

Results.

VRE BSI incidence was 6.5% of admissions (2.7 VRE BSI per 1000 BSI at-risk days). Adjusted 1-year mortality and length of stay were significantly higher in patients with VRE BSI. VRE colonization (adjusted odds ratio [aOR] = 8.4; 95% confidence interval [CI] = 3.4-20.6; P < .0001), renal insufficiency (aOR = 2.4; 95% CI = 1.0-5.8; P = .046), aminoglycoside use (aOR = 4.7; 95% CI = 2.2-9.8; P < .0001), and antianaerobic antibiotic use (aOR = 2.8; 95% CI = 1.3-5.8; P = .007) correlated most closely with VRE BSI. A prediction model with optimal performance included these factors plus gastrointestinal disturbance, severe neutropenia, and prior beta-lactam antibiotic use. The score effectively risk-stratified patients (area under the receiver operating curve = 0.84; 95% CI = 0.79-0.89). At a threshold of ≥5 points, per day probability of VRE BSI was increased nearly 4-fold.

Conclusions.

This novel predictive score is based on risk factors reflecting a plausible pathophysiological model for VRE BSI in patients with hematological malignancy. Integrating VRE colonization status with risk factors for developing BSI is a promising method of guiding rational use of empiric anti-VRE antimicrobial therapy in patients with hematological malignancy. Validation of this novel predictive score is needed to confirm clinical utility.

Institution-wide and Within-Patient Evolution of Daptomycin Susceptibility in Vancomycin-Resistant Enterococcus faecium Bloodstream Infections

We report daptomycin minimum inhibitory concentrations (MICs) for vancomycin-resistant Enterococcus faecium isolated from bloodstream infections over a 4-year period. The daptomycin MIC increased over time hospital-wide for initial isolates and increased over time within patients, culminating in 40% of patients having daptomycin-nonsusceptible isolates in the final year of the study. Infect Control Hosp Epidemiol 2018;39:226-228.

Association of daptomycin use with resistance development in Enterococcus faecium bacteraemia-a 7-year individual and population-based analysis

OBJECTIVE

In this study we aimed to analyse the association between use of daptomycin and MICs of daptomycin in Enterococcus faecium bacteraemia.

METHODS

We prospectively enrolled patients aged ≥18 years with E. faecium bacteraemia hospitalized at the University Hospital Basel from 2008 to 2014. We determined daptomycin MICs by Etests and used pulsed field gel electrophoresis to determine clonal relatedness. We recorded the defined daily dosages of daptomycin (DDDs) per 100 patient-days and clinical data from charts. We correlated daptomycin MIC with use of daptomycin in patients with recurrence/persistence.

RESULTS

In 195 E. faecium bacteraemias originating from 162 patients the median MIC for daptomycin was 2 mg/L (IQR 2-3); 30% (15.4%) isolates had a MIC ≥4 mg/L and 6 (3.1%) were resistant (MIC >4 mg/L) according to CLSI criteria. The usage of daptomycin increased more than four-fold from 0.36 DDDs/100 patient-days in 2008 to 1.6 in 2014. In 13 of 28 (42.9%) patients with a relapsing or persisting bacteraemia, the daptomycin MIC of the second isolate increased from a median of 2.0 to 2.5 mg/L (p 0.010); 3/13 (23.1%) developed resistance. All patients with the same clone in the first and second episode and an increase of daptomycin MIC had been treated with daptomycin (6/6 versus 1/7 p 0.005).

CONCLUSIONS

Daptomycin MICs and Daptomycin usage increased over time. On an individual patient level daptomycin exposure was associated with an increased MIC in subsequent bacteraemia episodes. Diversity did not indicate a clonal origin and argues for a de novo development of resistance.

Sequential steps of daptomycin resistance in Enterococcus faecium and reversion to hypersusceptibility through IS-mediated inactivation of the liaFSR operon

OBJECTIVES

To improve understanding of mechanisms of daptomycin resistance and to dissect the genetic basis of reversion to daptomycin hypersusceptibility in Enterococcus faecium.

METHODS

Daptomycin-resistant mutants (Mut4, Mut8, Mut16, Mut32, Mut64 and Mut128 with MICs from 4 to 128 mg/L) were obtained in vitro from E. faecium strain Aus0004 (MIC at 2 mg/L). The entire genome sequences of Mut64 and Mut128 were determined as well as those of liaFSR and cls genes for other mutants and corresponding revertants (named Rev4 to Rev128). The study of daptomycin resistance stability was performed without any selective pressure. The expression of liaF, liaS and liaR genes was quantified by quantitative RT-PCR.

RESULTS

By comparative genomic analysis, substitutions Asn13Ser in cls and Gly92Asp in liaS were identified in Mut64 and Mut128. Only the liaS mutation was found in Mut16 and Mut32 while Mut4 and Mut8 were devoid of any mutation. After 15 days, all mutants except Mut4 reverted to daptomycin hypersusceptibility (MICs from 0.12 to 0.25 mg/L). In all revertants (except Rev4 and Rev8), an IS was found in the liaFSR operon with a dramatic decrease of its expression: IS66 in the promoter region of liaF (Rev16 and Rev64), IS30 in liaR (Rev32) and IS982 in liaF (Rev128).

CONCLUSIONS

We demonstrated the stepwise and sequential acquisition of mutations in liaS and in cls leading to daptomycin resistance in E. faecium, and the instability of daptomycin resistance as well as the role of liaFSR inactivation in reversion to daptomycin hypersusceptibility.

Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones?

Enterococci are Gram-positive bacteria that are found in plants, soil and as commensals of the gastrointestinal tract of humans, mammals, and insects. Despite their commensal nature, they have also become globally important nosocomial pathogens. Within the genus Enterococcus, Enterococcus faecium, and Enterococcus faecalis are clinically most relevant. In this review, we will discuss how E. faecium and E. faecalis have evolved to become a globally disseminated nosocomial pathogen. E. faecium has a defined sub-population that is associated with hospitalized patients and is rarely encountered in community settings. These hospital-associated clones are characterized by the acquisition of adaptive genetic elements, including genes involved in metabolism, biofilm formation, and antibiotic resistance. In contrast to E. faecium, clones of E. faecalis isolated from hospitalized patients, including strains causing clinical infections, are not exclusively found in hospitals but are also present in healthy individuals and animals. This observation suggests that the division between commensals and hospital-adapted lineages is less clear for E. faecalis than for E. faecium. In addition, genes that are reported to be associated with virulence of E. faecalis are often not unique to clinical isolates, but are also found in strains that originate from commensal niches. As a reflection of more ancient association of E. faecalis with different hosts, these determinants Thus, they may not represent genuine virulence genes but may act as host-adaptive functions that are useful in a variety of intestinal environments. The scope of the review is to summarize recent trends in the emergence of antibiotic resistance and explore recent developments in the molecular epidemiology, population structure and mechanisms of adaptation of E. faecium and E. faecalis.

Enterococci and Their Interactions with the Intestinal Microbiome

The Enterococcus genus comprises over 50 species that live as commensal bacteria in the gastrointestinal (GI) tracts of insects, birds, reptiles, and mammals. Named "entero" to emphasize their intestinal habitat, Enterococcus faecalis and Enterococcus faecium were first isolated in the early 1900s and are the most abundant species of this genus found in the human fecal microbiota. In the past 3 decades, enterococci have developed increased resistance to several classes of antibiotics and emerged as a prevalent causative agent of health care-related infections. In U.S. hospitals, antibiotic use has increased the transmission of multidrug-resistant enterococci. Antibiotic treatment depletes broad communities of commensal microbes from the GI tract, allowing resistant enterococci to densely colonize the gut. The reestablishment of a diverse intestinal microbiota is an emerging approach to combat infections caused by antibiotic-resistant bacteria in the GI tract. Because enterococci exist as commensals, modifying the intestinal microbiome to eliminate enterococcal clinical pathogens poses a challenge. To better understand how enterococci exist as both commensals and pathogens, in this article we discuss their clinical importance, antibiotic resistance, diversity in genomic composition and habitats, and interaction with the intestinal microbiome that may be used to prevent clinical infection.

Enterococci and Their Interactions with the Intestinal Microbiome

The Enterococcus genus comprises over 50 species that live as commensal bacteria in the gastrointestinal (GI) tracts of insects, birds, reptiles, and mammals. Named "entero" to emphasize their intestinal habitat, Enterococcus faecalis and Enterococcus faecium were first isolated in the early 1900s and are the most abundant species of this genus found in the human fecal microbiota. In the past 3 decades, enterococci have developed increased resistance to several classes of antibiotics and emerged as a prevalent causative agent of health care-related infections. In U.S. hospitals, antibiotic use has increased the transmission of multidrug-resistant enterococci. Antibiotic treatment depletes broad communities of commensal microbes from the GI tract, allowing resistant enterococci to densely colonize the gut. The reestablishment of a diverse intestinal microbiota is an emerging approach to combat infections caused by antibiotic-resistant bacteria in the GI tract. Because enterococci exist as commensals, modifying the intestinal microbiome to eliminate enterococcal clinical pathogens poses a challenge. To better understand how enterococci exist as both commensals and pathogens, in this article we discuss their clinical importance, antibiotic resistance, diversity in genomic composition and habitats, and interaction with the intestinal microbiome that may be used to prevent clinical infection.