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12 pages, 743 KiB  
Article
Genetic Correlates of Synergy Mechanisms of Daptomycin Plus Fosfomycin in Daptomycin-Susceptible and -Resistant Methicillin-Resistant Staphylococcus aureus (MRSA)
by Warren E. Rose, Selvi C. Ersoy, Wessam Abdelhady, Alan R. Dominguez, Jedidiah Ndam Muyah Manna, Jorge N. Artaza, Reetakshi Mishra, Ahmed M. Elsayed, Richard A. Proctor, Sarah L. Baines, Benjamin P. Howden and Nagendra N. Mishra
Microorganisms 2025, 13(7), 1532; https://doi.org/10.3390/microorganisms13071532 - 30 Jun 2025
Viewed by 470
Abstract
This study elucidates potential genetic determinants and mechanisms involved in the synergistic effects of daptomycin (DAP) + fosfomycin (FOF) combination therapy. Among 33 clinically derived DAP-susceptible (S)/DAP-resistant (R) isogenic strain pairs, mutations in the mprF gene occurred in 30/33 DAP-R strains, including polymorphisms [...] Read more.
This study elucidates potential genetic determinants and mechanisms involved in the synergistic effects of daptomycin (DAP) + fosfomycin (FOF) combination therapy. Among 33 clinically derived DAP-susceptible (S)/DAP-resistant (R) isogenic strain pairs, mutations in the mprF gene occurred in 30/33 DAP-R strains, including polymorphisms of L826F (33%) or T345A/L/I (15%). Strain variants of DAP-S CB1483 serially passaged in vitro for 10 days in DAP +/− FOF identified a key non-synonymous mutation in mprF (L826F) only in the DAP monotherapy arm. Interestingly, passage in FOF alone or DAP + FOF prevented the emergence of this mprF mutation following 10-day passage. This L826F mprF polymorphism, associated with a “gain-in-function” phenotype, exhibited increased amounts of lysyl-phosphatidylglycerol (L-PG) in the cell membrane (CM). Transcriptomics revealed a relatively modest number (~10) of distinct genes that were significantly up- or downregulated (≥2 log fold) in both the DAP-S and DAP-R strain pairs upon DAP + FOF exposures (vs. DAP or FOF alone). Of note, DAP + FOF decreased expression of lrgAB and sdrE and increased the expression level of fosB. In a rabbit infective endocarditis (IE) model, the DAP-R CB185 strain treated with DAP +/− FOF showed significantly reduced lrgB expression in vegetations compared with DAP treatment alone. Overall, these findings indicate that DAP + FOF therapy impacts MRSA through multiple specific mechanisms, enhancing bacterial clearance. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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17 pages, 3588 KiB  
Article
Exploring Daptomycin Hypersensitivity in Enterococcus faecium: The Impact of LafB Mutation on Bacterial Virulence
by Pamela I. Huanambal Esquén, Diego A. Leonardo, Livia R. Manzine, Erick Suclupe Farro, Jessica K. Kajfasz, Suelen S. Mello, Mara C. L. Nogueira, João Renato Muniz, Alessandro S. Nascimento, Michael S. Gilmore, Jacqueline Abranches, José A. Lemos and Ilana L. B. C. Camargo
Int. J. Mol. Sci. 2025, 26(13), 5935; https://doi.org/10.3390/ijms26135935 - 20 Jun 2025
Viewed by 453
Abstract
Daptomycin (DAP) is a therapeutic option for vancomycin-resistant Enterococcus faecium (VRE) infections, but DAP resistance may occur during treatment. Previously, we identified a mutation within the E. faecium lafB gene that induces hypersusceptibility to DAP. The lafB gene encodes a glycosyltransferase involved in [...] Read more.
Daptomycin (DAP) is a therapeutic option for vancomycin-resistant Enterococcus faecium (VRE) infections, but DAP resistance may occur during treatment. Previously, we identified a mutation within the E. faecium lafB gene that induces hypersusceptibility to DAP. The lafB gene encodes a glycosyltransferase involved in lipoteichoic acid anchor synthesis, which makes it a promising target for enhancing DAP efficacy. In this study, we characterized E. faecium LafB protein (EfLafB) biophysical properties, used AlphaFold3 to predict LafB in silico three-dimensional structure, and determined lafB gene mutation’s role in virulence, comparing E. faecium HBSJRP18 (DAP-hypersusceptible) and a lafB revertant, HBSJRP18_2.7, and analyzing bacterial growth kinetics, biofilm formation ability, and virulence in a Galleria mellonella model. After gene cloning and expressing and purifying EfLafB, circular dichroism and SEC-MALS assays revealed its monomeric nature under in vitro conditions, with approximately a 40 kDa molecular mass and a melting temperature of 50 °C. In silico prediction indicated that LafB is an αβ-type protein with two domains conforming to the GT-4 family glycosyltransferases. These results are further supported by the highly conserved amino acids (E257, D91, R184, and K185), likely involved in UDP-Glc binding. The studied lafB gene mutation resulted in a significant decrease in bacterial growth and virulence in the invertebrate model. Full article
(This article belongs to the Special Issue Antibacterial Activity against Drug-Resistant Strains, 2nd Edition)
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15 pages, 635 KiB  
Review
Use of Daptomycin to Manage Severe MRSA Infections in Humans
by Marco Fiore, Aniello Alfieri, Daniela Fiore, Pasquale Iuliano, Francesco Giuseppe Spatola, Andrea Limone, Ilaria Pezone and Sebastiano Leone
Antibiotics 2025, 14(6), 617; https://doi.org/10.3390/antibiotics14060617 - 18 Jun 2025
Viewed by 851
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) represents a major therapeutic challenge due to its multidrug-resistance and the associated clinical burden. Daptomycin (DAP), a cyclic lipopeptide antibiotic, has become a key agent for the treatment of severe MRSA infections owing to its rapid bactericidal activity and [...] Read more.
Methicillin-resistant Staphylococcus aureus (MRSA) represents a major therapeutic challenge due to its multidrug-resistance and the associated clinical burden. Daptomycin (DAP), a cyclic lipopeptide antibiotic, has become a key agent for the treatment of severe MRSA infections owing to its rapid bactericidal activity and favourable safety profile. In this narrative review, we examine studies published between 2010 and April 2025. The data suggest that treatment with high-dose (8–10 mg kg⁻1) DAP shortened the time to blood-culture sterilisation by a median of 2 days compared with standard-dose vancomycin without increasing toxicity when model-informed area-under-the-curve monitoring was employed. Particular attention is given to the synergistic effects of DAP combined with fosfomycin or β-lactams, especially ceftaroline and ceftobiprole, in overcoming persistent and refractory MRSA infections; this approach results in a reduction in microbiological failure relative to monotherapy. Resistance remains uncommon (<2% of isolates), but recurrent mutations in mprF, liaFSR, and walK underscore the need for proactive genomic surveillance. Despite promising preclinical and clinical evidence supporting combination strategies, further randomized controlled trials are necessary to establish their definitive role in clinical practice, as are head-to-head cost-effectiveness evaluations. DAP remains a critical option in the evolving landscape of MRSA management, provided its use is integrated with precision dosing, resistance surveillance, and antimicrobial-stewardship frameworks. Full article
(This article belongs to the Section Antibiotics Use and Antimicrobial Stewardship)
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17 pages, 1028 KiB  
Review
Vancomycin-Resistant E. faecium: Addressing Global and Clinical Challenges
by Daniel E. Radford-Smith and Daniel C. Anthony
Antibiotics 2025, 14(5), 522; https://doi.org/10.3390/antibiotics14050522 - 19 May 2025
Cited by 1 | Viewed by 1547
Abstract
Antimicrobial resistance (AMR) poses a profound threat to modern healthcare, with vancomycin-resistant Enterococcus faecium (VREfm) emerging as a particularly resilient and clinically significant pathogen. This mini-review examines the biological mechanisms underpinning VREfm resistance, including biofilm formation, stress tolerance, and the acquisition of resistance [...] Read more.
Antimicrobial resistance (AMR) poses a profound threat to modern healthcare, with vancomycin-resistant Enterococcus faecium (VREfm) emerging as a particularly resilient and clinically significant pathogen. This mini-review examines the biological mechanisms underpinning VREfm resistance, including biofilm formation, stress tolerance, and the acquisition of resistance genes such as vanA and vanB. It also explores the behavioural, social, and healthcare system factors that facilitate VREfm transmission, highlighting disparities in burden across vulnerable populations and low-resource settings. Prevention strategies are mapped across the disease pathway, spanning primary, secondary, and tertiary levels, with a particular focus on the role and evolving challenges of antimicrobial stewardship programmes (ASP). We highlight emerging threats, such as rifaximin-induced cross-resistance to daptomycin, which challenge conventional stewardship paradigms. Finally, we propose future directions to enhance global surveillance, promote equitable stewardship interventions, and accelerate the development of innovative therapies. Addressing VREfm requires a coordinated, multidisciplinary effort to safeguard the efficacy of existing antimicrobials and protect at-risk patient populations. Full article
(This article belongs to the Section Antibiotics Use and Antimicrobial Stewardship)
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17 pages, 554 KiB  
Article
MRSA Profiles Reveal Age- and Gender-Specificity in a Tertiary Care Hospital: High Burden in ICU Elderly and Emerging Community Patterns in Youth
by Kamaleldin B. Said, Khalid Alshammari, Ruba M. Elsaid Ahmed, Fawwaz Alshammari, Ahmed H. Jadani, Ihab Rakha, Salem A. Almijrad, Anwar E. Almallahi, Bader Alkharisi, Naif M. Altamimi, Tarig Mahmoud, Nada A. Abozaid and Amal D. Alshammari
Microorganisms 2025, 13(5), 1078; https://doi.org/10.3390/microorganisms13051078 - 6 May 2025
Viewed by 866
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a devastating global health concern. Hypervirulent strains are on the rise, causing morbidities and mortalities worldwide. In tertiary care hospitals, critically ill patients, those undergoing invasive procedures, and pediatric and geriatric patients are at risk. It is not [...] Read more.
Methicillin-resistant Staphylococcus aureus (MRSA) is a devastating global health concern. Hypervirulent strains are on the rise, causing morbidities and mortalities worldwide. In tertiary care hospitals, critically ill patients, those undergoing invasive procedures, and pediatric and geriatric patients are at risk. It is not fully clear how strains adapt and specialize in humans and emerge despite the well-established commonality of the S. aureus genome from humans and animals. This study investigates the influence of age-, gender-, and source-specific profiles (clinical, intensive care unit (ICU vs. non-ICU)) on the evolution of hospital-associated (HA)-MRSA versus community-associated (CA)-MRSA lineages. A total of 253 non-duplicate S. aureus isolates were obtained from May 2023 to March 2025. The patients were stratified by age and gender in ICUs and non-ICUs. Standard microbiology methods and Clinical and Laboratory Standards Institute (CLSI) guidelines were used for identification and susceptibility testing, with cefoxitin and oxacillin disk diffusions and molecular diagnosis confirming MRSA. Mann–Whitney U and Chi-square tests assessed the demographic distributions, clinical specimen sources, and MRSA/methicillin-sensitive S. aureus (MSSA) prevalence. Of 253, 41.9% originated from ICUs (71% male; 29% female) and 58.1% from non-ICU wards (64% male; 36% female). In both settings, MRSA colonized the two extremes of age (10–29 and 70+) for males and females, with different mid-life peaks or declines by gender. However, the overall demographic distribution did not differ significantly between the ICU and non-ICU groups (p = 0.287). Respiratory specimens constituted 37% and had the highest MRSA rate (42%), followed by blood (24.5%) and wounds (10.3%). In contrast, MSSA dominated wounds (20.3%). Overall, 73.9% were resistant to cefoxitin and cefotaxime, whereas vancomycin, linezolid, daptomycin, and tigecycline remained highly effective. Younger non-ICU patients (10–29) had higher MSSA, whereas older ICU ones showed pronounced HA-MRSA profiles. By the virtue of methicillin resistance, all MRSA were classified as multidrug resistance. Thus, MRSA colonization of the two extremes of life mostly in ICU seniors and the dominance of invasive MSSA and CA-MRSA patterns in non-ICU youth imply early age- and gender-specific adaptations of the three lineages. MRSA colonizes both ICU and non-ICU populations at extremes of age and gender specifically. High β-lactam resistance underscores the importance of robust stewardship and age- and gender-specific targeting in screening. These findings also indicate host- and organ-specificity in the sequalae of MSSA, CA-MRSA, and HA-MRSA evolutionary dynamics, emphasizing the need for continued surveillance to mitigate MRSA transmission and optimize patient outcomes in tertiary care settings. Full article
(This article belongs to the Section Medical Microbiology)
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23 pages, 1575 KiB  
Article
Mutation- and Transcription-Driven Omic Burden of Daptomycin/Dalbavancin-R and Glycopeptide-RS Fitness Costs in High-Risk MRSA: A Nexus in Antimicrobial Resistance Mechanisms—Genome Proneness—Compensatory Adaptations
by Eleonora Chines, Gaia Vertillo Aluisio, Maria Lina Mezzatesta, Maria Santagati and Viviana Cafiso
Antibiotics 2025, 14(5), 465; https://doi.org/10.3390/antibiotics14050465 - 2 May 2025
Viewed by 693
Abstract
Background: In Staphylococcus aureus, antimicrobial resistance (AMR) imposes significant fitness costs (FCs), including reduced growth rate, interbacterial competitiveness, and virulence. However, the FC molecular basis remains poorly understood. This study investigated the FC omic basis and compensatory adaptations in high-risk HA-, LA-, [...] Read more.
Background: In Staphylococcus aureus, antimicrobial resistance (AMR) imposes significant fitness costs (FCs), including reduced growth rate, interbacterial competitiveness, and virulence. However, the FC molecular basis remains poorly understood. This study investigated the FC omic basis and compensatory adaptations in high-risk HA-, LA-, and CA-MRSA, acquiring mono- or cross-resistance to second-line daptomycin (DAP) and dalbavancin (DAL), as well as reduced susceptibility (RS) to first-line glycopeptides, i.e., vancomycin and teicoplanin (GLYs, i.e., VAN, TEC), related to the specific mechanism of action (MOA)-related AMR-mechanisms and genomic backgrounds, paying increasing FCs. Methods: The FC omic basis associated with mono- or cross- DAP-/DAL-R and GLY-RS were investigated by integrated omics. This study focused on core-genome essential (EG) and accessory virulence gene (VG) SNPomics and transcriptomics by Illumina MiSeq whole-genome sequencing, RNA-seq, and bioinformatic analysis. Results: Moderate impact nsSNPs were identified in EGs related to vital cellular functions and VGs. Comparative EG transcriptomics revealed differential expressions and key dysregulations—via asRNAs—prevalently affecting the protein synthesis and cell-envelope EG clusters, as well as the VG cluster. Conclusions: Our data, firstly, underlined the EG and VG mutation- and transcription-driven omic-based FC burden and the compensatory adaptations associated with the emergence of mono-DAP-R, cross-DAP-R/hGISA, and DAP-R/DAL-R/GISA, linked to specific MOA-related AMR-mechanisms and genomic backgrounds in high-risk HA-, LA-, and CA-MRSA. Full article
(This article belongs to the Special Issue Molecular Characterization of Multidrug-Resistant Pathogens)
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14 pages, 2464 KiB  
Article
Genomic Characterization of Enterococcus casseliflavus Isolated from Beef Cows and Calves
by Sani-e-Zehra Zaidi, Rahat Zaheer, Athanasios Zovoilis, Jayce Fossen, Gary Van Domselaar, Cheryl Waldner and Tim A. McAllister
Microorganisms 2025, 13(4), 907; https://doi.org/10.3390/microorganisms13040907 - 15 Apr 2025
Cited by 1 | Viewed by 612
Abstract
Enterococcus species are used as One Health indicators of antimicrobial resistance (AMR) in humans, animals, and the environment. A surveillance study in beef cows and calves isolated Enterococcus casseliflavus along with E. faecium, E. faecalis, and E. hirae. Given the [...] Read more.
Enterococcus species are used as One Health indicators of antimicrobial resistance (AMR) in humans, animals, and the environment. A surveillance study in beef cows and calves isolated Enterococcus casseliflavus along with E. faecium, E. faecalis, and E. hirae. Given the high prevalence of E. casseliflavus, we elected to characterize this species to better understand its role in the antimicrobial resistance of enterococci in cows and calves. Almost 12% of E. casseliflavus isolates exhibited multidrug resistance with the majority being resistant to lincomycin (99%), followed by quinupristin–dalfopristin (34%), ciprofloxacin (9.6%), tylosin (4.5%), erythromycin (2.7%), tetracycline (1.8%), tigecycline (1.5%), daptomycin (0.6%), streptomycin (0.3%), and kanamycin (0.3%). All E. casseliflavus were susceptible to chloramphenicol, penicillin, streptomycin, nitrofurantoin, gentamicin, and linezolid. Whole genome antimicrobial resistance gene profiling identified vanC-type intrinsic vancomycin resistance genes in all E. casseliflavus, with the vanC4XYT gene cluster being dominant (67%) followed by vanC2XYT (31%) and vanC3XYT (1.5%). Resistance genes for erythromycin (ermB) and tetracycline (tetM) were rarely identified (2.1% and 1.2%, respectively) within E. casseliflavus genomes. No resistance genes were identified to explain either the quinupristin–dalfopristin or ciprofloxacin resistance in these isolates. A core genome phylogenetic tree revealed two clades that exhibited no distinct association with the age of the host, time of sample collection, or the farm sampled. The open nature of the E. casseliflavus pan-genome highlighted its intraspecies diversity. These findings suggest that E. casseliflavus is likely a low-risk species in terms of contributing to antimicrobial resistance in the cow–calf sector. Full article
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10 pages, 1379 KiB  
Article
Efficacy of Ceftobiprole and Daptomycin at Bone Concentrations Against Methicillin-Resistant Staphylococcus aureus Biofilm: Results of a Dynamic In Vitro PK/PD Model
by Mikel Mancheño-Losa, María Ángeles Meléndez-Carmona, Carlos Lumbreras and Jaime Lora-Tamayo
Antibiotics 2025, 14(4), 386; https://doi.org/10.3390/antibiotics14040386 - 5 Apr 2025
Viewed by 709
Abstract
Background: The presence of biofilms and low antimicrobial concentrations in bone tissue make prosthetic joint infections (PJI) difficult to treat. Ceftobiprole (CTO) has a potential role in MRSA PJI. This study evaluated the efficacy of ceftobiprole and daptomycin (DAP) alone and in [...] Read more.
Background: The presence of biofilms and low antimicrobial concentrations in bone tissue make prosthetic joint infections (PJI) difficult to treat. Ceftobiprole (CTO) has a potential role in MRSA PJI. This study evaluated the efficacy of ceftobiprole and daptomycin (DAP) alone and in combination against MRSA biofilms at expected bone tissue concentrations. We assessed whether CTO-DAP outperformed DAP combined with a non-anti-MRSA beta-lactam (cefazolin [CZO]). Methods: A dynamic in vitro PK/PD biofilm model (CDC biofilm reactor) was used to simulate concentrations expected in cortical bone at a standard dosing of DAP (10 mg/kg/24 h), CTO (500 mg/8 h), and CZO (2 g/8 h), and assess performance against a 48-h MRSA biofilm from two clinical isolates that cause PJI (MRSA-1811 and MRSA-1733). Time–kill curves using the log change method (Δlog10 CFU/cm2) assessed antimicrobial efficacy over 56 h. Resistance emergence was monitored. Results: Although both monotherapies were active, neither reached bactericidal levels nor was one superior to the other (Δlog10 CFU/cm2 CTO vs. DAP: −1.44 ± 0.25 vs. −1.50 ± 0.01 [p = 0.686] and −1.55 ± 0.74 vs. −0.56 ± 0.36 [p = 0.108] for MRSA-1811 and MRSA-1733, respectively). Only in the MRSA-1811 isolate did the CTO-DAP combination improve the activity of each monotherapy, without achieving a synergistic effect (Δlog10 CFU/cm2: CTO-DAP −2.087 ± 0.048 vs. CTO −1.436 ± 0.249 [p = 0.013] and vs. DAP −1.503 ± 0.011 [p = 0.006]). No combination therapy (CTO-DAP vs. DAP-CZO) outperformed the other in either strain. No resistant bacterial subpopulations appeared with any antibiotic regimen. Conclusions: At clinically relevant concentrations, ceftobiprole and daptomycin showed similar activity against MRSA biofilms. The CTO-DAP combination showed comparable efficacy to DAP-CZO. Full article
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14 pages, 381 KiB  
Article
Unfavorable Outcomes and Their Risk Factors in Hospitalized Patients with Staphylococcus aureus Bacteremia in the US: A Multicenter Retrospective Cohort Study, 2020–2022
by Marya D. Zilberberg, Brian H. Nathanson, Rolf Wagenaar, Jan Posthumus and Andrew F. Shorr
Antibiotics 2025, 14(3), 326; https://doi.org/10.3390/antibiotics14030326 - 20 Mar 2025
Cited by 1 | Viewed by 577
Abstract
Background: In the US, 120,000 cases of Staphylococcus aureus bacteremia (SAB) occur annually. Apart from mortality, little is known about other unfavorable outcomes (UOs). We developed a multifaceted definition for UOs in SAB and examined their incidence and predictors. Methods: We [...] Read more.
Background: In the US, 120,000 cases of Staphylococcus aureus bacteremia (SAB) occur annually. Apart from mortality, little is known about other unfavorable outcomes (UOs). We developed a multifaceted definition for UOs in SAB and examined their incidence and predictors. Methods: We conducted a multicenter (~300 hospitals) retrospective cohort study between 2020 and 2022 of adult hospitalized patients with at least one blood culture (BC) positive for S. aureus. UOs were any of the following: hospital mortality, antibiotic escalation, persistently positive BCs, prolonged post-infection length of stay (LOS), 30-day readmission, and disease worsening. We compared the group with UOs to favorable outcomes (FOs). Regression models identified predictors of UOs. Results: Among 4080 patients with SAB, 2427 (59.5%) experienced a UO, most commonly 30-day readmission (42.0%) and antibiotic escalation (37.7%). Those with UOs more frequently had septic shock at admission (5.7% vs. 1.2%), requiring the ICU (18.8% vs. 14.7%) and dialysis (4.4% vs. 1.9%) prior to SAB onset. Community-onset SAB predominated in both groups, with more complicated SAB in the UO group (39.8% vs. 22.3%). Vancomycin use was similar, while daptomycin was more common in the UO group (8.5% vs. 3.0%). Variables with the highest odds ratios predicting a UO were septic shock on admission (3.498, 95% CI 2.145, 5.704), empiric daptomycin (2.723, 95% CI 1.943, 3.821), and complicated SAB (2.476, 95% CI 2.047, 2.994). Conclusions: UOs occur frequently in the setting of SAB. A broader perspective exploring issues other than mortality demonstrates the substantial implications of SAB both for patients and healthcare systems. Select clinical variables are associated with UOs, some of which may not be modifiable. Full article
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24 pages, 2248 KiB  
Article
Whole-Genome Sequencing of Linezolid-Resistant and Linezolid-Intermediate-Susceptibility Enterococcus faecalis Clinical Isolates in a Mexican Tertiary Care University Hospital
by Pedro Martínez-Ayala, Leonardo Perales-Guerrero, Adolfo Gómez-Quiroz, Brenda Berenice Avila-Cardenas, Karen Gómez-Portilla, Edson Alberto Rea-Márquez, Violeta Cassandra Vera-Cuevas, Crisoforo Alejandro Gómez-Quiroz, Jaime Briseno-Ramírez and Judith Carolina De Arcos-Jiménez
Microorganisms 2025, 13(3), 684; https://doi.org/10.3390/microorganisms13030684 - 19 Mar 2025
Viewed by 1148
Abstract
Linezolid-non-susceptible Enterococcus faecalis (LNSEf) has emerged as a critical clinical concern worldwide, yet data from Latin American settings remain scarce. This study aimed to investigate the molecular epidemiology and mechanisms underlying LNSEf in a Mexican tertiary care university hospital, focusing on clinical correlates [...] Read more.
Linezolid-non-susceptible Enterococcus faecalis (LNSEf) has emerged as a critical clinical concern worldwide, yet data from Latin American settings remain scarce. This study aimed to investigate the molecular epidemiology and mechanisms underlying LNSEf in a Mexican tertiary care university hospital, focusing on clinical correlates and clonal relationships. A total of 392 non-duplicated E. faecalis isolates were collected over 12 months, of which 24 with minimum inhibitory concentrations ≥4 µg/mL underwent whole-genome sequencing to identify specific resistance determinants (optrA, cfrA, 23S rRNA mutations) and to perform multilocus sequence typing (MLST) and phylogenetic analyses. Of the 392 isolates, 6.12% showed linezolid non-susceptibility, predominantly linked to plasmid- or chromosomally encoded optrA; only two isolates carried cfrA. No mutations were detected in 23S rRNA domain V or ribosomal proteins L3/L4. Clinically, LNSEf strains were associated with immunosuppression, previous surgical interventions, and prolonged hospital stays. Although most LNSEf isolates retained susceptibility to ampicillin, vancomycin, and daptomycin, they exhibited high rates of resistance to other antibiotic classes, particularly aminoglycosides and fluoroquinolones. These findings underscore the emergence of LNSEf in this region, highlighting the need for robust genomic surveillance, strict infection control, and judicious antimicrobial stewardship to curb further dissemination. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Antimicrobial Resistance)
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18 pages, 2471 KiB  
Article
Kinetic Patterns of Antibiotic Consumption in German Acute Care Hospitals from 2017 to 2023
by Birgitta Schweickert, Niklas Willrich, Marcel Feig, Marc Schneider, Michael Behnke, Luis Alberto Peña Diaz, Christine Geffers, Imke Wieters, Karin Gröschner, Doreen Richter, Alexandra Hoffmann, Tim Eckmanns and Muna Abu Sin
Antibiotics 2025, 14(3), 316; https://doi.org/10.3390/antibiotics14030316 - 18 Mar 2025
Viewed by 637
Abstract
Background: Antimicrobial consumption (AMC) patterns, besides prescribing behaviors, reflect the changing epidemiology of infectious diseases. Routine surveillance data have been used to investigate the development of AMC from 2017 to 2023 and the impact of COVID-19 within the context of the framing time [...] Read more.
Background: Antimicrobial consumption (AMC) patterns, besides prescribing behaviors, reflect the changing epidemiology of infectious diseases. Routine surveillance data have been used to investigate the development of AMC from 2017 to 2023 and the impact of COVID-19 within the context of the framing time periods. Methods: Data from 112 hospitals, continuously participating from 2017 to 2023 in the national surveillance system of hospital antimicrobial consumption based at the Robert Koch Institute, were analyzed according to the WHO ATC (Anatomical Therapeutic Chemical)/DDD (Defined Daily Dose) method and categorized according to the WHO AWaRe-classification. AMC was quantified by consumption density (CD) expressed in DDD/100 patient days (PD) and DDD/100 admissions (AD). The time period was subdivided into three phases: pre-pandemic phase (2017–2019), main pandemic phase (2020–2021) and transition phase (2022–2023). Linear regression models have been used to determine the presence of an overall trend, the change in intra-phasic trends and phase-specific mean consumption levels over time. Results: From 2017 to 2023 total antibiotic consumption decreased by 7% from 57.1 to 52.9 DDD/100 PD. Four main kinetic patterns emerged across different antibiotic classes: Pattern 1 displays a decreasing pre-pandemic trend, which slowed down throughout the pandemic and transition phase and was exhibited by second-generation cephalosporins and fluoroquinolones. Pattern 2 reveals a rising pre-pandemic trend, which decelerated in the pandemic phase and accelerated again in the transition phase and was expressed by aminopenicillins/beta-lactamase inhibitors, beta-lactamase sensitive pencillins, azithromycin and first-generation cephalosporins. Pattern 3 shows elevated mean consumption levels in the pandemic phase exhibited by carbapenems, glycopeptides, linezolid and third-generation cephalosporins. Pattern 4 reveals a rising trend throughout the pre-pandemic and pandemic phase, which reversed in the transition phase without achieving pre-pandemic levels and was expressed by beta-lactamase resistant penicillins, daptomycin, fosfomycin (parenteral) and ceftazidime/avibactam. Conclusions: Kinetic consumption patterns across different antibiotic classes might reflect COVID-19-related effects and associated changes in the epidemiology of co-circulating pathogens and health care supply. Broad-spectrum antibiotics with persisting elevated consumption levels throughout the transition phase require special attention and focused antimicrobial stewardship activities. Full article
(This article belongs to the Section Antibiotics Use and Antimicrobial Stewardship)
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19 pages, 1580 KiB  
Article
Fitness Burden for the Stepwise Acquisition of First- and Second-Line Antimicrobial Reduced-Susceptibility in High-Risk ESKAPE MRSA Superbugs
by Eleonora Chines, Gaia Vertillo Aluisio, Maria Santagati, Maria Lina Mezzatesta and Viviana Cafiso
Antibiotics 2025, 14(3), 244; https://doi.org/10.3390/antibiotics14030244 - 28 Feb 2025
Cited by 1 | Viewed by 2838
Abstract
Background: The fitness costs (FCs) of antimicrobial resistance (AMR) are crucial issues in antimicrobial resistance (AMR) onset, spread, and, consequently, public health. In Staphylococcus aureus, AMR can induce significant FCs due to slow growth, low competitiveness, and virulence. Here, we investigated the [...] Read more.
Background: The fitness costs (FCs) of antimicrobial resistance (AMR) are crucial issues in antimicrobial resistance (AMR) onset, spread, and, consequently, public health. In Staphylococcus aureus, AMR can induce significant FCs due to slow growth, low competitiveness, and virulence. Here, we investigated the genomics and FCs emerging for progressively acquiring daptomycin (DAP) and glycopeptide (GLY) reduced susceptibility in MRSA. Methods: Genomics was carried out using Illumina-MiSeq Whole-genome sequencing and bioinformatics. The biological FCs of isogenic MRSA strain pairs progressively acquiring DAP and GLY-reduced susceptibility, under DAP/GLY mono or combined therapy, were performed by in-vitro independent and competitive mixed growth, phenotypic in-vitro virulence analysis, and in-vivo G. mellonella larvae killing. Results: Genomics evidenced four different extremely resistant high-risk clones, i.e., ST-5 N315 HA-MRSA, ST-398 LA-MRSA, ST-22 USA-100 HA-EMRSA-15, and ST-1 MW2 CA-MRSA. In-vitro fitness assays revealed slow growth, lower competitiveness, and reduced virulence, predominantly in Galleria mellonella killing ability, in DAP-S hGISA, DAP-R GSSA, DAP-R hGISA, and DAP-R GISA strains. Conclusions: The occurrence of glycopeptide and daptomycin reduced susceptibility conferred increasing FCs, paid as a gradual reduction in virulence, competitiveness, and slow growth performance. Full article
(This article belongs to the Special Issue Spread of Multidrug-Resistant Microorganisms, 2nd Edition)
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18 pages, 1525 KiB  
Article
High-Risk VREfm Clones and Resistance Determinants in a Thai Hospital
by Peechanika Chopjitt, Rada Kansaen, Sumontha Chaisaeng, Sawarod Phongchaiwasin, Parichart Boueroy, Piroon Jenjaroenpun, Thidathip Wongsurawat, Anusak Kerdsin and Nuchsupha Sunthamala
Antibiotics 2025, 14(3), 229; https://doi.org/10.3390/antibiotics14030229 - 24 Feb 2025
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Abstract
Background/Objective: Vancomycin-resistant enterococci (VRE), particularly Enterococcus faecium (VREfm), are significant healthcare-associated infections, especially bloodstream infections (BSIs). Method: This study explored the genotypic and phenotypic characteristics of 29 VREfm isolates causing BSIs in Thailand. Bacterial species, sequence types (STs), virulence genes, and vancomycin antimicrobial-resistance [...] Read more.
Background/Objective: Vancomycin-resistant enterococci (VRE), particularly Enterococcus faecium (VREfm), are significant healthcare-associated infections, especially bloodstream infections (BSIs). Method: This study explored the genotypic and phenotypic characteristics of 29 VREfm isolates causing BSIs in Thailand. Bacterial species, sequence types (STs), virulence genes, and vancomycin antimicrobial-resistance genes were identified by multiplex PCR, multilocus sequence typing, and whole-genome sequencing (WGS). Antibiotic susceptibility was determined by disk diffusion, while an E-test or broth microdilution were used for daptomycin, teicoplanin, linezolid, and tigecycline. Biofilm formation was assessed using a microtiter plate assay. Results: All isolates harbored the vanA gene and exhibited resistance to ampicillin, erythromycin, norfloxacin, vancomycin, and rifampin. Resistance to ciprofloxacin, tigecycline, and nitrofurantoin was widespread as well. All isolates remained susceptible to chloramphenicol and linezolid. The majority of isolates belonged to clonal complex 17, with ST17 being predominant (21/29, 72.4%), followed by ST80 (6/29, 20.7%), ST761 (1/29, 3.4%), and ST117 (1/29, 3.4%). WGS analysis confirmed the presence of various antimicrobial resistance genes, including aac(6′)-Ii, ant-Ia, erm(B), and vanA. Additionally, virulence genes such as acm (collagen adhesin) and esp (enterococcal surface protein), which are involved in biofilm formation, were detected. Conclusion: This study provides insights into the genomic characteristics and clonal dissemination of invasive VREfm in Thailand, which is crucial for infection control and public health surveillance. Full article
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42 pages, 3164 KiB  
Review
A Comprehensive Overview of Antibacterial Agents for Combating Multidrug-Resistant Bacteria: The Current Landscape, Development, Future Opportunities, and Challenges
by Ina Gajic, Nina Tomic, Bojana Lukovic, Milos Jovicevic, Dusan Kekic, Milos Petrovic, Marko Jankovic, Anika Trudic, Dragana Mitic Culafic, Marina Milenkovic and Natasa Opavski
Antibiotics 2025, 14(3), 221; https://doi.org/10.3390/antibiotics14030221 - 21 Feb 2025
Cited by 6 | Viewed by 4939
Abstract
Background/Objectives: Antimicrobial resistance poses a major public health challenge. The World Health Organization has identified 15 priority pathogens that require prompt development of new antibiotics. This review systematically evaluates the antibacterial resistance of the most significant bacterial pathogens, currently available treatment options, as [...] Read more.
Background/Objectives: Antimicrobial resistance poses a major public health challenge. The World Health Organization has identified 15 priority pathogens that require prompt development of new antibiotics. This review systematically evaluates the antibacterial resistance of the most significant bacterial pathogens, currently available treatment options, as well as complementary approaches for the management of infections caused by the most challenging multidrug-resistant (MDR) bacteria. For carbapenem-resistant Gram-negative bacteria, treatment options include combinations of beta-lactam antibiotics and beta-lactamase inhibitors, a novel siderophore cephalosporin, known as cefiderocol, as well as older antibiotics like polymixins and tigecycline. Treatment options for Gram-positive bacteria are vancomycin, daptomycin, linezolid, etc. Although the development of new antibiotics has stagnated, various agents with antibacterial properties are currently in clinical and preclinical trials. Non-antibiotic strategies encompass antibiotic potentiators, bacteriophage therapy, antivirulence therapeutics, antimicrobial peptides, antibacterial nanomaterials, host-directed therapy, vaccines, antibodies, plant-based products, repurposed drugs, as well as their combinations, including those used alongside antibiotics. Significant challenges exist in developing new antimicrobials, particularly related to scientific and technical issues, along with policy and economic factors. Currently, most of the alternative options are not part of routine treatment protocols. Conclusions and Future Directions: There is an urgent need to expedite the development of new strategies for treating infections caused by MDR bacteria. This requires a multidisciplinary approach that involves collaboration across research, healthcare, and regulatory bodies. Suggested approaches are crucial for addressing this challenge and should be backed by rational antibiotic use, enhanced infection control practices, and improved surveillance systems for emerging pathogens. Full article
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14 pages, 983 KiB  
Article
Could a Reduced Dose of 8 g of Continuous Infusion Fosfomycin Be Considered as Effective as and Safer than a Standard 16 g Dose When Combined with High-Dose Daptomycin in the Treatment of Staphylococcal osteoarticular Infections?
by Pier Giorgio Cojutti, Sara Tedeschi, Eleonora Zamparini, Giacomo Fornaro, Manuel Zagarrigo, Massimiliano De Paolis, Pierluigi Viale and Federico Pea
Antibiotics 2025, 14(2), 139; https://doi.org/10.3390/antibiotics14020139 - 1 Feb 2025
Cited by 2 | Viewed by 1070
Abstract
Background: Daptomycin plus fosfomycin combination therapy is a valuable strategy for treating staphylococcal osteoarticular infections (OIs), but hypernatremia and hypokalemia due to sodium overload are important issues. The aim of this study was to assess the likelihood of attaining a pharmacokinetic/pharmacodynamic (PK/PD) [...] Read more.
Background: Daptomycin plus fosfomycin combination therapy is a valuable strategy for treating staphylococcal osteoarticular infections (OIs), but hypernatremia and hypokalemia due to sodium overload are important issues. The aim of this study was to assess the likelihood of attaining a pharmacokinetic/pharmacodynamic (PK/PD) target of AUC/MIC > 66.6 and/or of 70%t > MIC with continuous infusion (CI) fosfomycin at the recommended vs. reduced dose in patients with OIs receiving combination therapy with high-dose daptomycin. Adverse events were also evaluated. Methods: Patients with OIs treated with 8–10 mg/kg daily daptomycin plus CI fosfomycin, and who had a ≥1 TDM assessment of CI fosfomycin, were retrospectively included in the high-dose (16 g daily) or reduced-dose (<16 g daily) groups. The attainment of the PK/PD targets of 70%t > MIC and AUC/MIC > 66.6 up to an MIC of 32 mg/L was calculated. A CART analysis was used to identify a cut-off of fosfomycin AUC that indicated occurrence of hypernatremia and/or hypokalemia. Results: A total of 44 and 39 patients were included in the high- and reduced-dose groups, respectively. The two groups did not differ in terms of demographic characteristics, underlying infectious diseases and microbiological isolates. No differences between groups in attaining both PK/PD targets up to an MIC of 32 mg/L and in C-reactive protein reduction at the end of treatment were observed. Fosfomycin AUC > 8245 mg × h/L and >8326 mg × h/L were associated with hypernatremia and hypokalemia, respectively. Conclusions: CI fosfomycin at 8 g daily may reach optimal PK/PD target attainment with better safety than the recommended 16 g daily dose in patients with preserved renal function. Targeting fosfomycin AUC at 2131–8326 mg × h/L or steady-state concentration at 88.8–347 mg/L may be adequate for optimizing drug pharmacodynamics up to an MIC of 32 mg/L and minimizing the risk of hypernatremia and hypokalemia. Full article
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