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Keywords = antimicrobial susceptibility tests

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38 pages, 1890 KB  
Article
The Potential for Sample Testing at the Pen Level to Inform Prudent Antimicrobial Selection for Bovine Respiratory Disease Treatment: Investigations Using a Feedlot Simulation Tool
by Dana E. Ramsay, Wade McDonald, Sheryl P. Gow, Lianne McLeod, Simon J. G. Otto, Nathaniel D. Osgood and Cheryl L. Waldner
Antibiotics 2025, 14(10), 1009; https://doi.org/10.3390/antibiotics14101009 (registering DOI) - 11 Oct 2025
Abstract
Background: Antimicrobial drugs are used to treat bacterial diseases in livestock production systems, including bovine respiratory disease (BRD) in feedlot cattle. It is recommended that therapeutic antimicrobial use (AMU) in food animals be informed by diagnostic tests to limit the emergence of antimicrobial [...] Read more.
Background: Antimicrobial drugs are used to treat bacterial diseases in livestock production systems, including bovine respiratory disease (BRD) in feedlot cattle. It is recommended that therapeutic antimicrobial use (AMU) in food animals be informed by diagnostic tests to limit the emergence of antimicrobial resistance (AMR) and preserve the effectiveness of available drugs. Recent evidence demonstrates preliminary support for the pen as a prospective target for AMR testing-based interventions in higher-risk cattle. Methods: A previously reported agent-based model (ABM) was modified and then used in this study to investigate the potential for different pen-level sampling and laboratory testing-informed BRD treatment strategies to favorably impact selected antimicrobial stewardship and management outcomes in the western Canadian context. The incorporation of sample testing to guide treatment choice was hypothesized to reduce BRD relapses, subsequent AMU treatments and resultant AMR in sentinel pathogen Mannheimia haemolytica. The ABM was extended to include a discrete event simulation (DES) workflow that models the testing process, including the time at sample collection (0 or 13 days on feed) and the type of AMR diagnostic test (antimicrobial susceptibility testing or long-read metagenomic sequencing). Candidate testing scenarios were simulated for both a test-only control and testing-informed treatment (TI) setting (n = 52 total experiments). Key model outputs were generated for both the pen and feedlot levels and extracted to data repositories. Results: There was no effect of the TI strategy on the stewardship or economic outcomes of interest under baseline ecological and treatment conditions. Changes in the type and number of uses by antimicrobial class were observed when baseline AMR in M. haemolytica was assumed to be higher at feedlot arrival, but there was no corresponding impact on subsequent resistance or morbidity measures. The impacts of sample timing and diagnostic test accuracy on AMR test positivity and other outputs were subsequently explored with a theoretical “extreme” BRD treatment protocol that maximized selection pressure for AMR. Conclusions: The successful implementation of a pen-level sampling and diagnostic strategy would be critically dependent on many interrelated factors, including the BRD treatment protocol, the prevalences of resistance to the treatment classes, the accuracy of available AMR diagnostic tests, and the selected “treatment change” thresholds. This study demonstrates how the hybrid ABM-DES model can be used for future experimentation with interventions proposed to limit AMR risk in the context of BRD management. Full article
18 pages, 1256 KB  
Article
Analysis of Antimicrobial Residues and Resistance Profiles of Escherichia coli and Enterococcus spp. in Lagoon Water from California Dairies
by Siqi Wang, Sharif S. Aly, Essam Abdelfattah, Pius Ekong, David B. Sheedy, Wagdy ElAshmawy, Betsy M. Karle, Randi Black, Deniece R. Williams, Pramod Pandey and Emmanuel Okello
Vet. Sci. 2025, 12(10), 960; https://doi.org/10.3390/vetsci12100960 - 8 Oct 2025
Viewed by 174
Abstract
The widespread use of antimicrobial drugs (AMDs) in livestock production contributes to antimicrobial resistance (AMR), a global One Health concern affecting humans, animals, and the environment. This study analyzed AMD residues and the AMR profiles in Escherichia coli and Enterococcus spp./Streptococcus spp. [...] Read more.
The widespread use of antimicrobial drugs (AMDs) in livestock production contributes to antimicrobial resistance (AMR), a global One Health concern affecting humans, animals, and the environment. This study analyzed AMD residues and the AMR profiles in Escherichia coli and Enterococcus spp./Streptococcus spp. (ES) isolated from lagoon water samples collected from nine California dairies. Antimicrobial susceptibility testing was performed using the microbroth dilution method, and enzyme-linked immunosorbent assay (ELISA) kits were used to detect AMD residues in lagoon water. Overall, residues of florfenicol and tilmicosin were detected in more than 90% of the samples, while tetracycline was detected in 74.2 ± 4.6% of the samples. In contrast, penicillin and sulfamethazone residues were low, observed in only 3.4 ± 1.9% and 32.3 ± 5.0% of samples, respectively. The very low prevalence of penicillin was likely due to limited use in dairy cattle, given its prolonged withdrawal period. Prevalence estimates for AMR in the lagoon samples showed 100% resistance of E. coli to tiamulin, tilmicosin or tylosin and high prevalence against florfenicol (96.0% ± 2.0) or gamithromycin (92.0% ± 1.9). However, low AMR estimates (less than 10%) were observed against other AMDs tested. Similarly, the prevalence estimates for AMR of ES isolates in the studied lagoon were high against florfenicol (95.1% ± 2.0), tildipirosin (97.6% ± 1.7), or tilmicosin (98.8% ± 1.2), but low against ampicillin (4.9% ± 1.9) and penicillin (8.5% ± 2.4). Despite numerical differences in AMR prevalence by season, region, and sampling point, these variations were not statistically significant. Logistic regression models were applied to explore associations between AMD residues and AMR phenotypes where appropriate. Tilmicosin residues were significantly associated with reduced resistance to danofloxacin, enrofloxacin, and tildipirosin in E. coli isolates, while sulfamethoxazole residues were linked to increased tetracycline resistance in Enterococcus spp. The presence of florfenicol residues, potentially originating from treated calves and heifers, helps explain the high prevalence of resistance to this drug in both bacterial species. However, not all AMD residues were associated with AMR, underscoring the complex ecological and genetic factors involved in the development and maintenance of resistance in dairy environments. These findings underscore the importance of integrating AMR surveillance and prudent AMD use practices across all segments of dairy production systems. Full article
(This article belongs to the Special Issue Advanced Research on Antimicrobial Resistance in Farm Animals)
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10 pages, 5304 KB  
Case Report
Early Detection and Identification of Methylobacterium radiotolerans Bacteremia in an Early T-Cell Precursor Acute Lymphoblastic Leukemia Patient: A Rare Infection and Literature Review
by Jiayu Xiao, Lingli Liu, Xuzhen Qin and Yingchun Xu
Pathogens 2025, 14(10), 1015; https://doi.org/10.3390/pathogens14101015 - 7 Oct 2025
Viewed by 122
Abstract
(1) Background: Methylobacterium radiotolerans (M. radiotolerans) is a fastidious, aerobic, Gram-negative bacillus primarily found in environmental sources such as soil and sewage, with rare clinical isolation. Its identification remains challenging due to poor growth with conventional culture methods. (2) Case presentation: [...] Read more.
(1) Background: Methylobacterium radiotolerans (M. radiotolerans) is a fastidious, aerobic, Gram-negative bacillus primarily found in environmental sources such as soil and sewage, with rare clinical isolation. Its identification remains challenging due to poor growth with conventional culture methods. (2) Case presentation: A 42-year-old male patient with early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) presented with M. radiotolerans bacteremia during hospitalization. The organism was successfully isolated from peripheral blood using the Myco/F Lytic culture vial (Becton, Dickinson and Company, Lincoln, MT, USA). Comparative analysis demonstrated markedly superior growth of M. radiotolerans in Myco/F Lytic culture vials compared with Plus Aerobic/F Lytic and Lytic/10 Anaerobic/F culture vials (Becton, Dickinson and Company, Lincoln, MT, USA). Antimicrobial susceptibility testing, performed with the epsilometer test (E-test) and Bauer–Kirby disk diffusion (BK) method, guided the selection of an appropriate therapeutic regimen. The patient’s infection was ultimately controlled following targeted antimicrobial therapy. (3) Conclusions: M. radiotolerans demonstrates a distinct growth preference for the Myco/F Lytic culture medium. This observation highlights the importance of considering alternative culture media in cases of rare or fastidious bacterial infections that cannot be reliably detected using conventional Plus Aerobic/F Lytic or Lytic/10 Anaerobic/F culture vials, which are typically employed for clinical isolation of aerobic and anaerobic bacteria. Full article
(This article belongs to the Section Bacterial Pathogens)
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14 pages, 279 KB  
Article
Significant Prevalence of Dual KPC/NDM Carbapenemase-Producing Klebsiella pneumoniae in an ICU Cohort in Thessaloniki (2023), Including an ST512 Isolate Co-Harboring blaNDM-1 and blaKPC-3
by Maria Chatzidimitriou, Apostolos Voulgaridis, Pandora Tsolakidou, Fani Chatzopoulou, Ioannis Chonianakis, Eleni Vagdatli, Melania Kachrimanidou and Timoleon-Achilleas Vyzantiadis
Antibiotics 2025, 14(10), 994; https://doi.org/10.3390/antibiotics14100994 - 4 Oct 2025
Viewed by 333
Abstract
Background/Objectives: Carbapenem-resistant Klebsiella pneumoniae (CRKP) threatens Intensive Care Units (ICU), particularly in settings where serine (KPC) and metallo-β-lactamases (NDM) co-circulate. The aim of this study was to assess CRKP susceptibility especially to novel β-lactam/β-lactamase inhibitor combinations, characterize the genetic determinants of resistance, [...] Read more.
Background/Objectives: Carbapenem-resistant Klebsiella pneumoniae (CRKP) threatens Intensive Care Units (ICU), particularly in settings where serine (KPC) and metallo-β-lactamases (NDM) co-circulate. The aim of this study was to assess CRKP susceptibility especially to novel β-lactam/β-lactamase inhibitor combinations, characterize the genetic determinants of resistance, and contribute to the understanding of local epidemiology in the ICU of our hospital. Methods: We studied 32 non-duplicate CRKP isolates (30 ICU, 2 wards) collected at Hippokration General Hospital, Thessaloniki (May–Oct 2023). Bacterial identification and Antimicrobial susceptibility testing (AST) were performed by VITEK-2; Minimum inhibitory concentrations (MICs) for ceftazidime/avibactam (CAZ/AVI), meropenem/vaborbactam (MER/VAB), and imipenem/relebactam (IMI/REL) were determined by E-tests. Colistin MICs were performed by broth microdilution. Carbapenemases were screened phenotypically and by immunochromatography and confirmed by multiplex PCR. One bronchial isolate co-harboring blaNDM and blaKPC genes underwent WGS. Results: All isolates were carbapenem-resistant and showed extensive resistance to β-lactams and fluoroquinolones. By PCR, 8/32 (25%) carried blaKPC alone, 8/32 (25.0%) blaNDM alone, and 16/32 (50%) co-harbored blaKPC and blaNDM. KPC-only isolates were generally susceptible in vitro to CAZ/AVI, MER/VAB, and IMI/REL, whereas dual KPC-NDM producers were resistant to all three combinations. Tigecycline showed the highest retained activity; colistin remained active in a minority. WGS of one ST512 (CG258) isolate revealed co-harboring blaNDM-1 and blaKPC-3 with additional resistance determinants and plasmid replicons, consistent with high-risk spread. Conclusions: Half of CRKP isolates in this ICU-predominant series co-produced KPC and NDM, severely limiting β-lactam/β-lactamase inhibitor options. These data support routine screening for carbapenemases, strict infection prevention, antimicrobial stewardship, and access to agents active against MBLs. Full article
16 pages, 1191 KB  
Article
First Report of Candida auris Candidemia in Portugal: Genomic Characterisation and Antifungal Resistance-Associated Genes Analysis
by Isabel M. Miranda, Micael F. M. Gonçalves, Dolores Pinheiro, Sandra Hilário, José Artur Paiva, João Tiago Guimarães and Sofia Costa de Oliveira
J. Fungi 2025, 11(10), 716; https://doi.org/10.3390/jof11100716 - 3 Oct 2025
Viewed by 463
Abstract
Candida auris has emerged as a global public health threat due to its high mortality rates, multidrug resistance, and rapid transmission in healthcare settings. This study reports the first documented cases of C. auris candidemia in Portugal, comprising eight isolates from candidemia and [...] Read more.
Candida auris has emerged as a global public health threat due to its high mortality rates, multidrug resistance, and rapid transmission in healthcare settings. This study reports the first documented cases of C. auris candidemia in Portugal, comprising eight isolates from candidemia and colonised patients admitted to a major hospital in northern Portugal in 2023. Whole-genome sequencing (WGS) was performed to determine the phylogenetic relationships of the isolates, which were classified as belonging to Clade I. Genome sequencing also enabled the detection of missense mutations in antifungal resistance genes, which were correlated with antifungal susceptibility profiles determined according to EUCAST (European Committee on Antimicrobial Susceptibility Test) protocols and guidelines. All isolates exhibited resistance to fluconazole and amphotericin B according to the recently established EUCAST epidemiological cut-offs (ECOFFs). Most of the isolates showed a resistant phenotype to anidulafungin and micafungin. All isolates were resistant to caspofungin. Missense mutations identified included Y132F in ERG11, E709D in CDR1, A583S in TAC1b, K52N and E1464K in SNQ2, K74E in CIS2, M192I in ERG4, a novel mutation S237T in CRZ1, and variants in GCN5, a gene involved in chromatin remodelling and stress-response regulation. Identifying known and novel mutations highlights the evolution of antifungal resistance mechanisms in C. auris. These findings underscore the need for further research to understand C. auris resistance pathways and to guide effective clinical management strategies. Full article
(This article belongs to the Collection Invasive Candidiasis)
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19 pages, 2954 KB  
Protocol
A Six-Step Protocol for Monitoring Antimicrobial Resistance Trends Using WHONET and R: Real-World Application and R Code Integration
by Fabio Ingravalle, Antonio Vinci, Marco Ciotti, Carla Fontana, Francesca Pica, Emanuele Sebastiani, Clara Donnoli, Martino Guido Rizzo, Dario Tedesco, Silvia D’Arezzo, Stefania Cicalini, Michele Tancredi Loiudice and Massimo Maurici
Methods Protoc. 2025, 8(5), 115; https://doi.org/10.3390/mps8050115 - 2 Oct 2025
Viewed by 268
Abstract
Antimicrobial resistance is a global health issue, and the WHO has made significant efforts in the development of tools for its monitoring. However, such tools are underutilized, due to limited knowledge, technical capacity, and scarcity of economic resources. AMR surveillance can be conducted [...] Read more.
Antimicrobial resistance is a global health issue, and the WHO has made significant efforts in the development of tools for its monitoring. However, such tools are underutilized, due to limited knowledge, technical capacity, and scarcity of economic resources. AMR surveillance can be conducted using WHOnet and R, two free-of-charge software tools widely adopted in both clinical practice and scientific research. WHOnet is designed for managing laboratory data and antimicrobial susceptibility test results, while R is a programming language dedicated to statistical computing and data visualization. The combined use of these tools enables a reproducible workflow for retrospective AMR trend analysis. This paper provides step-by-step instructions on how to perform such analysis and also provides the respective R code. The described code and software results are shown using real-world data from an Italian hospital as an example. The standardization of the analysis process and the rapid availability of data on antimicrobial resistance are critical for both clinicians and public health professionals. They would allow for empirical decisions on antimicrobial treatment based on the specific epidemiological characteristics of the hospital or community setting. Full article
(This article belongs to the Section Public Health Research)
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14 pages, 279 KB  
Article
Molecular Epidemiology of Different Bacterial Pathogens and Their Antimicrobial Resistance Genes Among Patients Suffering from Surgical Site Infections in Lebanon
by Inass Kawtharani, Ghassan Ghssein, Ola Srour, Abdul Amir Chaaban and Pascale Salameh
Microbiol. Res. 2025, 16(10), 216; https://doi.org/10.3390/microbiolres16100216 - 1 Oct 2025
Viewed by 217
Abstract
Background: Antimicrobial resistance (AMR) is a major global health threat, particularly in surgical site infections (SSIs), where multidrug-resistant (MDR) pathogens complicate treatment. Objective: This study aimed to identify antimicrobial resistance genes and assess their prevalence in bacterial species causing SSIs in Lebanon. Materials [...] Read more.
Background: Antimicrobial resistance (AMR) is a major global health threat, particularly in surgical site infections (SSIs), where multidrug-resistant (MDR) pathogens complicate treatment. Objective: This study aimed to identify antimicrobial resistance genes and assess their prevalence in bacterial species causing SSIs in Lebanon. Materials and Methods: The present research is a multicenter and prospective study that included patients who developed SSIs after surgery in seven hospitals, within the period of January 2024–September 2024. Bacterial isolates from wound swabs or tissue samples were identified using standard microbiological methods. Antimicrobial susceptibility was tested by disk diffusion, and resistance genes were detected by PCR. Data were analyzed using Statistical Package for the Social Sciences (SPSS). Results: Among 6933 surgical patients, 63 developed SSIs (0.91%; 95% CI [0.70–1.15]). Gram-negative bacteria predominated (73%), mainly Escherichia coli and Pseudomonas aeruginosa, while Gram-positive isolates accounted for 27%, mostly Staphylococcus aureus. MDR was observed in 71% of Gram-positive and 61% of Gram-negative isolates. The most frequent genes were mecA in S. aureus (100%) and coagulase-negative staphylococci (83.3%); blaCTX-M in E. coli, Klebsiella pneumoniae, and Enterobacter cloacae (100%); and blaNDM in E. cloacae (100%) and Acinetobacter baumannii (60%). blaKPC was less common, and no isolates carried Imipenemase (IMP), Verona integron-encoded metallo-β-lactamase (VIM), and Oxacillinase-48-like β-lactamase (OXA-48). Conclusions: This study highlights the high prevalence of antibiotic resistance in agents causing SSIs in Lebanese hospitals. Resistance genes, particularly mecA, blaCTX-M, and blaNDM, were highly prevalent in SSI pathogens, underscoring the urgent need for surveillance and judicious antibiotic use in Lebanese hospitals. Full article
19 pages, 2150 KB  
Article
Molecular and Phenotypic Characterization of Prototheca Species Isolates Associated with Bovine Mastitis Cases in Chile
by Jaime Rodriguez, Paulina Sepúlveda-García, Nivia Canales, Matías Goddard, Carlo Cornuy, Álvaro G. Morales, Luis Collado and Armin Mella
Animals 2025, 15(19), 2869; https://doi.org/10.3390/ani15192869 - 30 Sep 2025
Viewed by 266
Abstract
Background: Bovine mastitis caused by Prototheca spp. is the most significant animal disease of algal origin, with an increasing number of cases reported worldwide. Currently, there is no effective treatment, so control requires the culling of infected animals. In Chile, information is limited, [...] Read more.
Background: Bovine mastitis caused by Prototheca spp. is the most significant animal disease of algal origin, with an increasing number of cases reported worldwide. Currently, there is no effective treatment, so control requires the culling of infected animals. In Chile, information is limited, and a discrepancy remains in the literature regarding the Prototheca species involved in bovine mastitis. Methods: This study aimed to molecularly type and phenotypically characterize Prototheca isolates associated with bovine mastitis in Chile. Sixty-six Prototheca isolates obtained from individual bovine mastitis milk samples and bulk tank milk samples were analyzed through cytochrome b gene (cytb) sequencing, Random Amplified Polymorphic DNA–Polymerase Chain Reaction (RAPD-PCR) analysis, and phenotypic evaluation (morphology, antimicrobial susceptibility, and biofilm formation). Results: Sixty-five isolates were identified as P. bovis and one as P. ciferrii, marking the first report of the latter in bovine mastitis in Chile. RAPD analysis revealed a high genetic diversity in P. bovis. All strains exhibited resistance to the antibiotics tested from the Fluoroquinolone, β-lactam, and sulfonamide groups; however, 100% of the strains showed susceptibility to aminoglycosides, with gentamicin standing out as a potential therapeutic option. Most P. bovis strains formed weak (81.5%, 53/65) or moderate (15.4%, 10/65) biofilms, which could favor the persistence of infection. Conclusions: These findings provide novel insights into the molecular and phenotypic characteristics of Prototheca spp. in Chile, highlighting the predominance of P. bovis, the emergence of P. ciferri, and the implications for antimicrobial management and disease control. Full article
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19 pages, 1817 KB  
Article
Urinary Tract Infections in a Single-Center Bulgarian Hospital: Trends in Etiology, Antibiotic Resistance, and the Impact of the COVID-19 Pandemic (2017–2022)
by Milena Yancheva Rupcheva, Kostadin Kostadinov, Yordan Kalchev, Petya Gardzheva, Eli Hristozova, Zoya Rachkovska, Gergana Lengerova, Andreana Angelova, Marianna Murdjeva and Michael M. Petrov
Antibiotics 2025, 14(10), 982; https://doi.org/10.3390/antibiotics14100982 - 30 Sep 2025
Viewed by 407
Abstract
Background: Urinary tract infections (UTIs) are among the most common hospital- and community-acquired infections, creating a substantial healthcare burden due to recurrence, complications, and rising antimicrobial resistance. Accurate diagnosis and timely antimicrobial therapy are essential. This study aimed to identify trends in [...] Read more.
Background: Urinary tract infections (UTIs) are among the most common hospital- and community-acquired infections, creating a substantial healthcare burden due to recurrence, complications, and rising antimicrobial resistance. Accurate diagnosis and timely antimicrobial therapy are essential. This study aimed to identify trends in the etiology, treatment, and resistance patterns of UTIs through a retrospective analysis of urine isolates processed at the Laboratory of Microbiology at University Hospital St. George in Plovdiv, the largest tertiary care and reference microbiology center in Bulgaria, between 2017 and 2022. Materials and Methods: A retrospective single-center study was performed at the hospital’s Microbiology Laboratory. During the study period, 74,417 urine samples from 25,087 hospitalized patients were screened with the HB&L UROQUATTRO system. Positive specimens were cultured on blood agar, Eosin-Methylene Blue, and chromogenic media. Identification was performed using biochemical assays, MALDI-TOF MS, and the Vitek 2 Compact system. Antimicrobial susceptibility testing included disk diffusion, MIC determination, broth microdilution (for colistin), and Vitek 2 Compact, interpreted according to EUCAST standards. Descriptive analysis and temporal resistance trends were evaluated with regression models, and interrupted time-series analysis was applied to assess COVID-19-related effects. Results: Out of 10,177 isolates, Gram-negative bacteria predominated (73%), with Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis as the leading pathogens. Among Gram-positives, Enterococcus faecalis was the most frequent. In the post-COVID-19 period, ESBL production increased in E. coli (34–38%), K. pneumoniae (66–77%), and P. mirabilis (13.5–24%). Carbapenem resistance rose in K. pneumoniae (to 40.6%) and P. aeruginosa (to 24%), while none was detected in E. coli. Colistin resistance increased in K. pneumoniae but remained absent in E. coli and P. aeruginosa. High-level aminoglycoside resistance in E. faecalis was stable (~70%), and vancomycin resistance in E. faecium rose from 4.6% to 8.9%. Conclusions: Both community- and hospital-acquired UTIs in Southeastern Bulgaria are increasingly linked to multidrug-resistant pathogens, particularly ESBL-producing and carbapenem-resistant Enterobacterales. Findings from the region’s largest referral center highlight the urgent need for continuous surveillance, rational antibiotic use, and novel therapeutic approaches. Full article
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12 pages, 474 KB  
Article
Emergence of Multidrug-Resistant Escherichia coli Harbouring the CS31A Virulence Factor in Neonatal Calf Diarrhoea in Central France
by Clémence Provost, Hadjila Yanes, Guillaume Mosnier, Tiago Lima, Gabriela Jorge da Silva, Ana Rita Pedro, Maria José Saavedra and Eduarda Silveira
Animals 2025, 15(19), 2844; https://doi.org/10.3390/ani15192844 - 29 Sep 2025
Viewed by 250
Abstract
Escherichia coli is a significant cause of Neonatal Calf Diarrhoea (NCD). Its extensive antigenic diversity, coupled with the ability to acquire antimicrobial resistance determinants, hampers treatment effectiveness and compromises the control measures. This study investigated the link between the presence of multidrug-resistant (MDR) [...] Read more.
Escherichia coli is a significant cause of Neonatal Calf Diarrhoea (NCD). Its extensive antigenic diversity, coupled with the ability to acquire antimicrobial resistance determinants, hampers treatment effectiveness and compromises the control measures. This study investigated the link between the presence of multidrug-resistant (MDR) E. coli and virulence factors (VFs) in NCD from central France (Departments of Cantal, Haute-Loire, Loire, and Puy-de-Dôme), between 2016 and 2022. E. coli was identified at TERANA Laboratories, France, using API 20E (BioMérieux®) and MALDI-TOF Mass Spectrometry. Virulence factors, namely adhesins, were assessed with the slide agglutination method, and antimicrobial susceptibility testing was conducted across various antimicrobial classes. Out of 2367 E. coli strains isolated from cases of NCD, a high percentage were resistant to aminopenicillins (88.8%), aminoglycosides (89.1%), tetracyclines (79.7%), quinolones (48.4%), and sulphonamides (42.4%). More than half (58.6%) carried VFs, and 84.9% exhibited MDR profile, of which 61.34% (1233/2010) also harboured VFs. The adhesin CS31A-producing E. coli was the most prevalent, followed by the fimbrial adhesins F5 and F17 (60.8%, 20.0%, and 8.3%, respectively), all of which were associated with a high prevalence of MDR strains (79.1–93.9%). The highest occurrence of MDR profiles was observed in E. coli strains carrying CS31A and in those lacking VFs, both groups showing co-resistance to aminopenicillins, aminoglycosides, and tetracyclines or sulphonamides. The calf production sector may act as a reservoir for MDR E. coli strains, regardless of the presence of VFs, posing a major threat to public health and safety. Full article
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31 pages, 1838 KB  
Review
Emerging Technologies for the Diagnosis of Urinary Tract Infections: Advances in Molecular Detection and Resistance Profiling
by Baiken Baimakhanova, Amankeldi Sadanov, Vladimir Berezin, Gul Baimakhanova, Lyudmila Trenozhnikova, Saltanat Orasymbet, Gulnaz Seitimova, Sundetgali Kalmakhanov, Gulzakira Xetayeva, Zhanserik Shynykul, Aizat Seidakhmetova and Aknur Turgumbayeva
Diagnostics 2025, 15(19), 2469; https://doi.org/10.3390/diagnostics15192469 - 26 Sep 2025
Viewed by 608
Abstract
Background/Objectives: Urinary tract infections (UTIs) represent a considerable challenge within the field of clinical medicine, as they are responsible for significant morbidity and intensify the operational pressures encountered by healthcare systems. Conventional diagnostic approaches, which include symptom evaluation, dipstick urinalysis, and standard [...] Read more.
Background/Objectives: Urinary tract infections (UTIs) represent a considerable challenge within the field of clinical medicine, as they are responsible for significant morbidity and intensify the operational pressures encountered by healthcare systems. Conventional diagnostic approaches, which include symptom evaluation, dipstick urinalysis, and standard urine culture, often demonstrate inadequacies in identifying atypical clinical manifestations, infections with low bacterial counts, or pathogens that show growth difficulties under typical laboratory conditions. These limitations undermine diagnostic accuracy and hinder timely therapeutic measures. Methods: The present manuscript is a systematic review conducted in accordance with PRISMA guidelines. A structured search was performed in PubMed, Scopus, and Google Scholar, yielding 573 records, of which 107 studies were included for qualitative synthesis. The primary aim of this systematic review is to evaluate both conventional and emerging diagnostic methods for UTIs, with specific objectives of assessing their clinical applicability, limitations, and potential to improve patient outcomes. Results: Recent progress in diagnostic technologies offers promising alternatives. Molecular-based assays, such as multiplex polymerase chain reaction, matrix-assisted laser desorption ionization mass spectrometry, and next-generation sequencing, have substantially improved both the precision and efficiency of pathogen identification. Furthermore, contemporary techniques for evaluating antimicrobial susceptibility, including microfluidic systems and real-time phenotypic resistance assays, enable clinicians to execute targeted therapeutic strategies with enhanced efficacy. Results of this synthesis indicate that while conventional diagnostics remain the cornerstone for uncomplicated cases, innovative molecular and phenotypic approaches demonstrate superior performance in detecting low-count bacteriuria, atypical pathogens, and resistance determinants, particularly in complicated and recurrent infections. These innovations support antimicrobial stewardship by reducing dependence on empirical antibiotic treatment and lessening the risk of resistance emergence. Conclusions: Nonetheless, the incorporation of these technologies into clinical practice requires careful consideration of implementation costs, standardization protocols, and the necessary training of healthcare professionals. In conclusion, this systematic review highlights that emerging molecular diagnostics and resistance-profiling tools offer substantial promise in complementing or enhancing traditional methods, but their widespread adoption will depend on robust validation, cost-effectiveness, and integration into clinical workflows. Full article
(This article belongs to the Special Issue Urinary Tract Infections: Advances in Diagnosis and Management)
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13 pages, 1926 KB  
Article
Iodobacter fluviatilis, a New Potential Opportunistic Pathogen Associated with Skin Lesions, First Report in Hypophthalmichthys nobilis in China
by Kai Chen, Nannan Shen, Ting Qin, Liushen Lu, Dongpo Xu, Bingwen Xi and Jun Xie
Pathogens 2025, 14(10), 978; https://doi.org/10.3390/pathogens14100978 - 26 Sep 2025
Viewed by 324
Abstract
In the spring of 2023, a disease outbreak occurred in Lake Taihu in China, which caused a large number of deaths of H. nobilis. In order to investigate the cause of morbidity and mortality of the H. nobilis, the diseased fish [...] Read more.
In the spring of 2023, a disease outbreak occurred in Lake Taihu in China, which caused a large number of deaths of H. nobilis. In order to investigate the cause of morbidity and mortality of the H. nobilis, the diseased fish were collected for histopathological and etiological studies. Histopathological observation revealed that substantial inflammatory cell infiltration was observed around skin lesion in diseased fish, extensive degeneration and necrosis were observed in the hepatic parenchymal cells, the spleen exhibited congestion, and the kidney showed congestion. A bacterial strain, C1, isolated from diseased H. nobilis was identified as Iodobacter fluviatilis through 16S rRNA gene sequencing and biochemical phenotypic characterization. Experimental infection of the fish via intramuscular injection induced a localized abscess in a subset of fish. Antimicrobial susceptibility testing revealed that the isolate was susceptible to aminoglycosides, tetracyclines, quinolones and amphenicols, but resistant to sulfonamides commonly used in aquaculture. Here, we describe an association between I. fluviatilis and skin lesions in H. nobilis. Furthermore, we report the biochemical characteristics and drug resistance profile of the isolated bacteria. These findings also facilitate further investigations into the role of I. fluviatilis associated with skin diseases of H. nobilis and other freshwater fish. Full article
(This article belongs to the Special Issue Infectious Diseases in Aquatic Animals)
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11 pages, 392 KB  
Article
In Vitro Activity of Delafloxacin Against Corynebacterium spp.
by Montserrat Muñoz-Rosa, Cristina Elías-López, Rosa Pedraza, Cristina Riazzo, Cristina Arjona-Torres, Isabel Machuca, Rocio Tejero-García, Julian Torre-Cisneros and Luis Martínez-Martínez
Antibiotics 2025, 14(10), 973; https://doi.org/10.3390/antibiotics14100973 - 26 Sep 2025
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Abstract
Background/Objectives: The susceptibility of Corynebacterium spp. to antimicrobial agents is species-related, with increasing levels of resistance to fluoroquinolones in several species related to their continued use in clinical practice. The objectives were to determine the in vitro activity of delafloxacin in comparison with [...] Read more.
Background/Objectives: The susceptibility of Corynebacterium spp. to antimicrobial agents is species-related, with increasing levels of resistance to fluoroquinolones in several species related to their continued use in clinical practice. The objectives were to determine the in vitro activity of delafloxacin in comparison with other fluoroquinolones against clinical isolates of Corynebacterium spp., to compare MICs of delafloxacin obtained with gradient strips and with reference microdilution, and to investigate the mechanisms related to fluoroquinolone resistance in the tested strains. Methods: Fifty-three clinical isolates, assigned to five species of Corynebacterium spp., were evaluated using reference microdilution for delafloxacin, ciprofloxacin, levofloxacin, and moxifloxacin (with and without reserpine or phenylalanine-arginine β-naphthylamide), and gradient strips for delafloxacin. The QRDR of the gyrA gene was amplified using primers specific to the different species, and mutations were defined after aligning against the corresponding reference sequences. Results: Delafloxacin was the most active compound with MIC50/MIC90 values of 0.5/8 mg/L. Single mutations at the QRDR were observed in isolates, with MICs of delafloxacin ranging from 0.016 to 4 mg/L, while double mutations occurred in isolates, with MICs ranging from 0.125 to 16 mg/L. The delafloxacin gradient strips showed an essential agreement of 88.7%, bias of −5%, and a Kappa index of 0.848. Conclusions: Increased MICs of delafloxacin against Corynebacterium spp. are related to the presence of non-conservative mutations in the QRDR of gyrA. Delafloxacin gradient strips could be a reasonable alternative for use in the clinical routine of the microbiology laboratory. Delafloxacin could represent an alternative for treating infections due to some species of Corynebacterium. Full article
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17 pages, 1454 KB  
Article
Machine Learning Model for Predicting Multidrug Resistance in Clinical Escherichia coli Isolates: A Retrospective General Surgery Study
by Hüseyin Kerem Tolan, İrfan Aydın, Handan Tanyildizi-Kokkulunk, Mehmet Karakuş, Yüksel Akkaya, Osman Kaya and Ferruh Kemal İşman
Antibiotics 2025, 14(10), 969; https://doi.org/10.3390/antibiotics14100969 - 26 Sep 2025
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Abstract
Background/Objectives: Escherichia coli is one of the leading causes of surgical site infections (SSIs) and poses a growing public health concern due to its increasing antimicrobial resistance. High rates of extended-spectrum beta-lactamase (ESBL) production among E. coli strains complicate treatment outcomes and [...] Read more.
Background/Objectives: Escherichia coli is one of the leading causes of surgical site infections (SSIs) and poses a growing public health concern due to its increasing antimicrobial resistance. High rates of extended-spectrum beta-lactamase (ESBL) production among E. coli strains complicate treatment outcomes and emphasize the need for effective surveillance and control strategies. Methods: A total of 691 E. coli isolates from general surgery clinics (2020–2025) were identified using MALDI-TOF MS. Antibiotic susceptibility data and patient variables were cleaned, encoded, and used to predict resistance using the Random Forest, CatBoost, and Naive Bayes algorithms. SMOTE addressed class imbalance, and model performance was assessed through various validation methods. Results: Among the three machine learning models tested, Random Forest (RF) showed the best performance in predicting antibiotic resistance of E. coli, achieving median accuracy, precision, recall, and F1-scores of 0.90 and AUC values up to 0.99 for key antibiotics. CatBoost performed similarly but was less stable with imbalanced data, while Naive Bayes showed lower accuracy. Feature importance analysis highlighted strong inter-antibiotic resistance links, especially among β-lactams, and some influence of demographic factors. Conclusions: This study highlights the potential of simple, high-performing models using structured clinical data to predict antimicrobial resistance, especially in resource-limited clinical settings. By incorporating machine learning into antimicrobial resistance (AMR) surveillance systems, our goal is to support the advancement of rapid diagnostics and targeted antimicrobial stewardship approaches, which are essential in addressing the growing challenge of multidrug resistance. Full article
(This article belongs to the Section Antibiotics Use and Antimicrobial Stewardship)
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11 pages, 1198 KB  
Article
Evaluation of a Novel Rapid Phenotypic Antimicrobial Susceptibility Testing System
by Yuan-Chao Xue, Filipe Cerqueira, Natalie Williams-Bouyer and Ping Ren
Antibiotics 2025, 14(10), 962; https://doi.org/10.3390/antibiotics14100962 - 25 Sep 2025
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Abstract
Background/Objectives: Phenotypic antimicrobial susceptibility testing (AST) is essential for guiding timely and effective antibiotic therapy. Rapid and accurate reporting of AST results enables earlier optimization of treatment and supports antimicrobial stewardship by minimizing unnecessary use of broad-spectrum antibiotics. This study aimed to evaluate [...] Read more.
Background/Objectives: Phenotypic antimicrobial susceptibility testing (AST) is essential for guiding timely and effective antibiotic therapy. Rapid and accurate reporting of AST results enables earlier optimization of treatment and supports antimicrobial stewardship by minimizing unnecessary use of broad-spectrum antibiotics. This study aimed to evaluate the performance of the Selux DX Next-Generation Phenotyping AST system in comparison with the standard-of-care MicroScan WalkAway Plus system and broth microdilution reference results. Methods: A total of 332 clinical isolates and 97 Antimicrobial Resistance (AR) Bank reference isolates were tested using the Selux DX and MicroScan systems. Performance was assessed by categorical agreement (CA), error rates [very major errors (VMEs), major errors (MEs), minor errors (mEs)], and turnaround time. Results: The Selux DX system demonstrated ≥90% CA for most drug–organism combinations, consistent with Clinical and Laboratory Standards Institute (CLSI) acceptance thresholds, although elevated error rates were noted for erythromycin, aztreonam, cefazolin, minocycline, and ampicillin/sulbactam. Across 5124 drug–bug combinations, 55 VMEs (1.1%), 42 MEs (0.8%), and 203 mEs (4.0%) were identified. The Selux DX system achieved a markedly shorter average turnaround time of 5.5 h compared with 16 h for the MicroScan system, though at the cost of a longer setup time. Conclusions: The Selux DX system provides rapid and reliable phenotypic AST results, supporting earlier clinical decision-making and antimicrobial stewardship. However, discrepancies with certain antimicrobial agents, particularly among highly resistant reference isolates, highlight the need for further validation in larger, multicenter studies. Full article
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