Search Results (473)

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

Background/Objectives: Urinary tract infections (UTIs) caused by extended-spectrum beta-lactamase (ESBL) Enterobacterales have become more frequent. Therefore, strategies for assessing the risks posed by ESBL-producing infections have been developed, creating the need for local validation. The aim of this study was to validate the scoring system designed by Tumbarello et al. to identify ESBL producers in patients with a UTI that require hospital care in a region with a high prevalence of ESBL Escherichia coli. Methods: A retrospective cohort study was conducted in a third-level hospital in Bogotá (Colombia) between 2013 and 2020.The study included 817 patients, who were hospitalized due to pyelonephritis and treated with cefuroxime (the first-line antibiotic according to local guidelines), with an ESBL frequency of 9.68%. Diagnostic performances were estimated for a modified version of Tumbarello’s score (omitting admission from another healthcare facility) evaluating the area under the curve (AUC) for ESBL presence with respect to resistance to second- and third-generation cephalosporins. Results: With an index cut-off of ≥6, the score showed a sensitivity of 18% and a specificity of 83%. The AUC for this cut-off was 0.47. This threshold index could not efficiently predict either third- (AUC = 0.49) or second-generation cephalosporin resistance (AUC = 0.51). Conclusions: In Colombia, a region with a high prevalence of ESBL E. coli producers, as the use of the Tumbarello index would result in excessive utilization of wide-spectrum antibiotics, it is not recommended in this specific scenario for UTIs. Further studies are required in order to develop accurate tools to assess the risk of ESBL producers in high-prevalence settings. Full article

Background: Antimicrobial resistance (AMR) is a major public health concern. Urinary tract infections (UTIs) account for up to 85–90% of community-acquired cases. The COVID-19 pandemic disrupted healthcare access and may have influenced resistance patterns. In this context, we retrospectively evaluated the antibiotic resistance dynamics of various bacterial strains isolated between 2019 and 2023 in a hospital unit; Methods: A total of 8217 clinical specimens (urine, wound secretions, sputum, pharyngeal exudate, nasal exudate, tracheal secretions, vaginal and cervical secretions, puncture fluids, purulent secretions, blood, ear secretions, eye secretions) were processed using standard microbiological techniques. Pathogen identification and susceptibility testing were performed with the VITEK 2 Compact system, following CLSI guidelines. Results: Following the analysis of 8217 clinical samples collected over a five-year period (2019–2023), a total of 2900 microorganisms were isolated and identified. Among these, the most frequently encountered were E. coli strains, with 1204 isolates. Urine cultures represented 71.3% of all processed samples. Out of these 5860 urine cultures, 1530 (26%) were positive. The resistance of E. coli strains to ampicillin (48–55.2%), trimethoprim/sulfamethoxazole (22.9–34%), and ciprofloxacin (21.4–31.5%) remained high throughout the period. ESBL-producing strains peaked at 17.6% in 2020, with multidrug resistance rates ranging from 14% to 22.4%. Conclusions: E. coli strains displayed persistently high resistance to ampicillin, trimethoprim/sulfamethoxazole, and ciprofloxacin, with peaks in ESBL production and multidrug resistance during the COVID-19 pandemic. These trends underscore the importance of continuous surveillance and antibiotic stewardship, with direct implications for empirical UTI therapy and broader strategies to mitigate the public health impact of antimicrobial resistance. Full article

Background: The benefit of adjunctive aminoglycosides in the treatment of patients with febrile neutropenia (FN) is controversial. We investigated the incidence of acute kidney injury (AKI) in patients with FN or suspected infection according to empirical amikacin treatment. Methods: This two-centre, retrospective cohort study was conducted at the University Hospitals of Basel (amikacin group) and Bern (non-amikacin group), Switzerland, between 2016 and 2022. Adult patients requiring antibiotic treatment after autologous hematopoietic stem cell transplantation (HSCT) were included. All patients received empiric beta-lactam treatment combined with amikacin in the amikacin group (only University Hospital Basel). The primary endpoint was the incidence of AKI within seven days after the initiation of antibiotic treatment. Results: Overall, 250 patients were included. The majority was male (n = 163, 65.2%) and had a median age of 61 years (interquartile range (IQR) 55 to 67). The median baseline eGFR was similar in both groups (>90 mL/min/1.7 m²). There was no statistically significant difference in the incidence of AKI (4/125 vs. 5/125, p = 1.0). The maximum decline in eGFR from baseline within 7 days was significantly higher in the amikacin group (−4 mL/min/1.7 m² (IQR 8 to −12) vs. −2 mL/min/1.7 m² (IQR −7 to −1), p = 0.001). Two patients suffered from an infection with an extended spectrum beta-lactamase producing (ESBL) pathogen. Conclusions: Amikacin treatment did not significantly impact the incidence of AKI in patients undergoing autologous HSCT. The short-term administration of amikacin in patients with normal to high baseline eGFR is safe regarding renal function. However, in a low-resistance setting, the omission of empirical amikacin treatment should be considered. Full article

CTX-M beta-lactamases have become the predominant extended-spectrum beta-lactamases (ESBLs) globally, contributing to increased patient morbidity, mortality, and healthcare costs. This study investigated the prevalence of biofilm formation and CTX-M genes in Klebsiella pneumoniae strains isolated from Baghdad hospitals, aiming to better understand antimicrobial resistance mechanisms and support the development of targeted interventions. A total of 300 samples were collected from various clinical and hospital sources, and antibiotic susceptibility testing was performed using the Kirby–Bauer disc diffusion method. ESBL production was also confirmed using specifically designed primers. Platanus orientalis Linn extract was evaluated for its antimicrobial and antibiofilm activity against K. pneumoniae isolates. The results showed significant resistance to the majority of antibiotics, including cefotaxime, gentamicin, levofloxacin, ceftazidime, and ceftriaxone. A high prevalence of the CTX-M gene (100%) was detected in the isolates, with the most frequent alleles being blaCTX-M-15 (65.2%) and blaCTX-M-1 (30%). Furthermore, 95.6% of the isolates were capable of forming biofilms. However, when treated with P. orientalis Linn extract, most isolates exhibited reduced biofilm production, becoming weak biofilm producers. Phytochemical analysis of P. orientalis Linn revealed significant amounts of phenolic compounds, tannins, and glycosides, as well as the presence of alkaloids and carbohydrates. Overall, this study demonstrates a correlation between CTX-M production and biofilm-forming ability in K. pneumoniae and highlights the potential role of P. orientalis Linn extract in combating antibiotic-resistant infections. Full article

Antimicrobial resistance (AMR) represents a threat to human, animal, and environmental health. This study evaluated the potential role of birds as AMR dispersers in white storks as a model species investigating dispersal between locations connected by their movements. Throughout a year, 346 samples were collected from two landfills (225 fecal samples) and two wetlands (93 fecal/28 water samples) based on satellite tracking data that confirmed continuous stork movements between foraging (landfill) and nighttime roosting (wetlands) locations. Samples were seeded in selective media with antibiotics for the isolation of antibiotic-resistant bacteria. A total of 313 isolates from 35 different bacterial species were obtained, with an AMR prevalence of 43.1% in fecal samples from landfills, 7.5% in fecal samples from wetlands, and 21.4% in water from wetlands. Multidrug resistant bacteria were only found in fecal samples (19.6% landfills/4.3% wetlands) and extended-spectrum beta-lactamase producing-bacteria were found exclusively in fecal samples from landfills with a marked presence during the fall migration period. Our study reveals marked differences in AMR prevalence and resistance phenotypes between study locations and fecal and water samples throughout the year, thus not supporting a clear role of storks as AMR dispersers. Nevertheless, similar changes in AMR phenotype prevalences during fall migration in stork faecal samples from one of the tested landfills and its paired wetland, and the significant increase in ESBL-producing Enterobacterales prevalence matching the arrival of migratory white storks in fall, underline the need for more in-depth genome-based studies to elucidate the role of white storks as dispersers or sentinels of AMR. Full article

Background: The Enterobacteriaceae family is the most heterogeneous group of Gram-negative bacilli, with both environmental and clinical relevance. Although many of these species are part of the normal intestinal microbiota, species such as Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis are among the most common opportunistic pathogens, frequently responsible for nosocomial infections, including urinary tract infections, bacteraemia, and pneumonia. Based on these concerns, these species are increasingly being studied for their ability to develop antimicrobial resistance, often mediated by extended spectrum β-lactamase or carbapenemase production. The present study aims to analyse the antimicrobial resistance profiles of Enterobacteriaceae isolated from a southern Italian hospital focusing on the species of major clinical importance. Methods: A retrospective analysis was carried out on biological samples collected between 2019 and 2023 at the Microbiology Laboratory of the San Pio Hospital, Vasto (Italy). Eight hundred ninety patients were included, with an average age of 73 years. Bacterial identification was carried out using bacterial culture and biochemical methods, while antimicrobial sensitivity was assessed by using the automated Walk Away System. Results: The most frequently isolated species were Escherichia coli (63.2%), Klebsiella spp. (21.9%), and Proteus spp. (8.8%). All isolates showed resistance to at least one antimicrobial and most to more than four. The highest resistance rates were observed for Cefotaxime (16.0%), followed by Ampicillin (15.6%) and Ciprofloxacin (13.2%). Conclusions: The high prevalence of antimicrobial resistance among clinically relevant Enterobacteriaceae species is a growing clinical challenge. The results of this study, which describe the trend of resistance among Enterobacteriaceae in a local hospital, could help to raise awareness highlighting the urgent need for more advanced diagnostic tools and new therapeutic strategies to treat infections caused by multi-resistant microorganisms. Full article

Background: The intestinal tract is a host to a high number of diverse bacteria, and the presence of multidrug-resistant (MDR) Enterobacterales strains acts as a reservoir and a source of infection. The interactions between the intestinal microbiome and colonizer Enterobacterales strains influence long-lasting colonization. Aims: In this narrative review, we summarize available data about the intestinal colonization of MDR Enterobacterales strains and correlations between colonization and the intestinal microbiome. Results: Several endogenous and exogenous factors influence the intestinal colonization of MDR Enterobacterales strains. On the gut microbiome level, the intestinal microbial community is composed of the Lachnospiraceae family (e.g., Lachnoclostridium, Agathobacter, Roseburia, Tyzzerella), which indicates a protective role against colonizer MDR Enterobacterales strains; by contrast, a high abundance of Enterobacterales correlates with the colonization of MDR Enterobacterales strains. In specific patient groups, striking differences in microbiome composition can be detected. Among hematopoietic stem-cell-transplanted patients colonized by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales, a greater abundance of Bifidobacterium, Blautia, Clostridium, Coprococcus, L-Ruminococcus, Mogibacteriaceae, Peptostreptococceae and Oscillospira was observed compared to patients not colonized by ESBL-producing strains, who had a greater abundance of Actinomycetales. In liver transplant patients, a reduction in the alpha-diversity of the intestinal microbiome in fecal samples correlates with the carriage of MDR Enterobacterales. Conclusions: Intestinal colonization with MDR Enterobacterales is a multifactorial process that involves the MDR strain (e.g., its plasmids, fimbria), host and mucosal factors (e.g., IgA and defensin) and exogenous factors (e.g., use of antibiotics, hospitalization). On the gut microbiome level, the Lachnospiraceae family is dominant among intestines not colonized by MDR strains, but a high abundance of Enterobacterales was correlated with colonization with MDR Enterobacterales strains. Full article

Background/Objectives: The prevalence of ESBL-producing Escherichia coli (E. coli) has increased significantly, impacting prognoses due to delayed or limited treatment options. We aimed to determine the demographic patterns, risk factors, and clinical outcomes of ESBL-producing E. coli in a top-referral hospital in Indonesia. Methods: This study was observational in design and focused on hospitalized patients with bacteremia due to E. coli during 2022–2024. Results: We identified 224 patients during the study period. The median of length of stay was 7 (3–13) days. Mortality occurred in 149 (66.55%) patients, and there was no difference in the mortality between patients with ESBL E. coli and those with non-ESBL E. coli. The severity of illness, as defined by the Pitt bacteremia score (PBS), was higher in the ESBL E. coli group. Urinary tract infection (UTI), previous antibiotic use, and central venous catheter (CVC) insertion were independent risk factors for bacteremia due to ESBL E. coli bacteremia. Male gender, shorter length of stay (LOS), solid tumor, pneumonia, mechanical ventilation, CVC insertion, inappropriate initial antibiotic therapy (IIAT), and sequential organ failure assessment (SOFA) score were risk factors for mortality in bacteremia caused by E. coli, including both ESBL and non-ESBL producers. Male gender, shorter LOS, CVC usage, and SOFA score were independent risk factors for mortality in bacteremia due to ESBL E. coli. Conclusions: ESBL-producing E. coli increases the severity of bacteremia. Recognizing patients at high risk for ESBL-producing E. coli infections is crucial for initiating appropriate empirical antibiotic treatment targeting ESBL-producing pathogens. Full article

Background/Objectives: Extended-Spectrum Beta-Lactamase-producing Escherichia coli (ESBL-E. coli) are widely circulating in livestock of low- and middle-income countries. However, the drivers of their circulation remain largely unknown. Small-scale farms in Peru exhibit an unusually high prevalence of fecal carriage of ESBL-E. coli in their livestock. The objective of this study was to compare the prevalence of ESBL-E. coli fecal carriage in dairy cows, pigs, and poultry in the Lima and Ica regions of Peru and to identify the drivers associated with the observed prevalence at the farm level. Methods: We compared the prevalence of fecal carriage of ESBL-E. coli isolated from dairy cattle (N = 244 animals; 25 farms), pigs (N = 261; 25), and laying hens (N = 255; 10). We also administrated questionnaires to 59 farmers regarding their socioeconomic status, husbandry practices, animal diseases, and antibiotic use. Results: All but one of the 60 farms sampled had at least one animal carrying ESBL-E. coli. A statistically higher prevalence of ESBL-E. coli was estimated in dairy cows (75%) and pigs (61%) from Lima compared to laying hens from Ica (34%). Our statistical analyses (Poisson generalized linear models) using two variable selection approaches revealed that the prevalence of ESBL-E. coli was lower in farms raising laying hens, when farmers oversaw both animal husbandry and healthcare, and in farms with a lower number of gastrointestinal outbreaks in the last semester. Socio-economic features of farmers and self-reporting antibiotic use varied across farms (i.e., highest antibiotic use over the last semester was reported among pig farmers (96%), followed by laying hen (70%) and dairy cattle farmers (50%)), but these factors were not associated with the prevalence of ESBL-E. coli. Conclusions: Despite a relatively low number of farms sampled, our findings suggest that the widespread circulation of ESBL-E. coli among livestock in Peru could be mainly associated with unknown species-specific drivers, independently of the socioeconomic status of farmers and antibiotic use. Therefore, our study calls for future research to identify the specific drivers promoting the high prevalence of ESBL-E. coli among cattle and pigs in Peru. Full article

The emergence and dissemination of extended-spectrum beta-lactamase (ESBL)-producing bacteria pose a major public health threat, necessitating a One Health approach to addressing this threat. Thus, the diversity, ESBL production, and potential public health implications of Gram-negative bacteria recovered from man-made lakes and surrounding lettuce in Yamoussoukro, Côte d’Ivoire were assessed in this study. Also, the lakes’ physicochemical parameters were assessed and correlated with bacteria community using Pearson correlation. A total of 68 Gram-negative bacterial isolates were recovered from the samples and identified via 16S rDNA gene sequencing. Phylogenetic analysis suggested multiple genus-/species-level variations within the isolates. Escherichia coli was the most prevalent in lake water (39.5%), while Acinetobacter was the dominant genus in lettuce (30%). E. coli isolates showed high resistance to ampicillin (90.9%), cefepime (72.7%), cefotaxime (68.2%), and aztreonam (63.6%). Moreover, ESBL production was confirmed in E. coli isolates (22.05%), predominantly mediated by the bla_CTX-M gene. Multidrug-resistant phenotypes were widespread, yielding similar multiple antibiotic resistance index (MARI) values in water (0.27–0.63) and lettuce (0.27–0.81). These data indicate high environmental contamination, which unfortunately is not being taken into account by lettuce producers according to an interview. Statistical analyses showed a significant relationship between bacterial diversity and lakes’ physicochemical parameters, including dissolved oxygen, pH, and turbidity. The basic education level of farmers, the prevalence of ESBL-producing E. coli, and the high prevalence of MDR Gram-negative bacteria in both environmental and crop sources in Yamoussoukro underscore the need for both integrated surveillance and management strategies to mitigate potential microbial public health risks within a One Health framework. Full article

Klebsiella pneumoniae, due to its capacity to produce numerous virulence factors and form biofilms, is one of the most significant etiological agents of nosocomial infections. The extensive and often unwarranted use of antibiotic therapy has driven the emergence of various mutations, adaptive mechanisms, and horizontal gene transfer among K. pneumoniae strains, resulting in resistance to most beta-lactam antibiotics, carbapenems, and the last-resort drug—colistin. A promising alternative or adjunctive treatment is the application of rotating magnetic fields (RMFs). The present study aimed to evaluate changes in colistin susceptibility among 20 extended-spectrum beta-lactamases (ESBLs) and 20 K. pneumoniae carbapenemase (KPC)-positive K. pneumoniae strains isolated from hospital infections following exposure to RMF at frequencies of 5 and 50 Hz. Exposure to RMF at 5 Hz resulted in decreased colistin minimum inhibitory concentration (MIC) values in over half of the tested (ESBLs) and (KPC)-positive strains. Additionally, RMF at 50 Hz reduced colistin MIC values in 30% of (ESBL)-positive and 40% of (KPC)-positive strains. Therefore, in the future, RMF may be developed as a supportive therapeutic strategy to improve the efficacy of antibiotics in the treatment of infections caused by multidrug-resistant (MDR) pathogens, including colistin-resistant K. pneumoniae. Full article

Kuwait has reported a problematic increase in the prevalence of Antimicrobial Resistance (AMR). However, the absence of studies that analyze AMR from combined human, agricultural (animal), and environmental domains limits our ability to assess the extent of the problem in Kuwait. Therefore, this systematic review provides a comprehensive insight into the AMR status in Kuwait regarding humans, agriculture (animals), and the environment from the perspective of the One Health approach. A systematic search was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to identify the relevant literature on AMR in Kuwait. Multiple online electronic databases, including the Cochrane Library, Google Scholar, Web of Science, PubMed, BioMed Central (BMC), and Scopus, were searched to perform a narrative synthesis and meta-analysis. Twenty-eight studies published between 2009 and 2024 were included in this study. Domain-wise distribution varied, with 11 studies related to clinical settings, 11 to the environment, 4 to agricultural (animal), and 2 to both clinical and community settings. The narrative synthesis indicated a high occurrence of AMR bacteria in human, agriculture (animal), and environmental domains. In human domains, the dominant AMR isolates belonged to four Gram-negative species: E. coli, K. pneumoniae, P. aeruginosa, and Acinetobacter baumannii. In agriculture (animals), Salmonella isolates from poultry display high resistance to cefotaxime, ampicillin, and amoxicillin. Camel milk analyses revealed that 80% of bacterial isolates are resistant to antibiotics such as penicillin, tetracyclines, and carbapenems. An environmental analysis of sewage, seawater, sediment, and aerosol samples documented widespread antibiotic resistance genes (ARGs) with resistance mechanisms such as extended-spectrum beta-lactamase, carbapenemases, and colistin. The cross-domain analysis identified the overlapping of ARGs. Regarding the One Health approach, none of the studies used this approach to interlink these sectors. Meanwhile, the meta-analysis indicated a high resistance rate in humans (34.05%, 95% CI (22.81 to 46.27, p < 0.0001, I² = 98.94%)), agriculture (animals) (67.42%, 95% CI (30.30 to 94.93, p < 0.0001, I² = 97.40%)), and environment (69.86%, 95% CI (48.80 to 87.26, p < 0.0001, I² = 98.78%)). The reported spread of AMR and the overlap of resistance genes among isolates across the domains demonstrate the interconnected nature of AMR in Kuwait. These findings underscore the need to adopt the One Health approach to strengthen surveillance, implement control measures, and enhance public education strategies to address the complexity of AMR challenges in Kuwait. Full article

Micro-organisms are abundant in nature and can also be found in hospital settings, causing high rates of infections. This study aimed to identify bacteria isolated from a veterinary hospital, as well as to perform antimicrobial susceptibility testing using the disk diffusion method (Kirby–Bauer), biofilm production tests using 96-well polystyrene microtiter plates and crystal violet dye, and genetic analysis of the ica operon of Staphylococcus isolates. Three collections were made from eleven surfaces and objects in the hospital’s non-critical areas (general areas) and critical areas (surgical center), totaling thirty-three samples. A total of 66 different bacterial isolates were obtained, with 77% (51/66) Gram-positive and 23% (29/66) Gram-negative. Resistance profiles were found for multidrug-resistance (MDR), methicillin-resistant Staphylococcus aureus (MRSA), methicillin-resistant Staphylococcus epidermidis (MRSE), and other unidentified species of methicillin-resistant coagulase-negative (MRCNS) and extended-spectrum beta-lactamase (ESBL), as well as biofilm production rates of 57% (38/66) of the isolates. Analysis of the operon genes for Staphylococcus sp. showed divergence in some samples when compared to the phenotypic test performed. In summary, there is a high presence of micro-organisms with resistance and virulence factors spread throughout the various areas of the veterinary hospital. Full article

An outbreak characterized by clinical signs of diarrhea and paralysis, occasionally progressing to fatal outcomes, occurred at an ostrich breeding facility. Conventional antibiotic treatments proved ineffective. To investigate the etiology of the disease, brain and liver specimens were collected for diagnostic analysis. An Escherichia coli (E. coli) isolate, designated strain HZDC01, was obtained from cerebral tissues, and whole-genome sequencing was performed for genomic characterization. Genomic analysis revealed that the chromosomal DNA harbors numerous resistance genes, conferring multidrug resistance through complex mechanisms. Furthermore, a p0111-type plasmid carrying the bla_CTX-M-55 gene and an IncX1-type plasmid harboring rmtB, sul1, APH(6)-Id, tet(A), AAC(3)-IIc, aadA2, bla_TEM-1B, and floR genes were identified. These plasmids carry numerous mobile genetic elements that can disseminate via horizontal gene transfer, thereby amplifying the risk of resistance-gene spread within bacterial populations. Additionally, the ibeB and ibeC genes, which encode proteins involved in the invasion of brain microvascular endothelial cells, were identified. These genes may facilitate E. coli penetration of the blood–brain barrier, potentially leading to meningitis and posing a life-threatening risk to the host. This is the first report of the isolation and characterization of extended-spectrum beta-lactamase E. coli from the brain of an ostrich with paralysis. The findings provide valuable genomic insights into the antimicrobial resistance profiles and pathogenic mechanisms of ostrich-derived E. coli isolates. Full article