Extended-spectrum β-lactamases producing Enterobacteriaceae (ESBL-PE) prevalence in Nepal: A systematic review and meta-analysis

Construction and validation of an interpretable XGBoost machine learning model to predict ESBL positivity rates based on urinalysis data

BACKGROUND

Microbiological culture and drug susceptibility testing of urine samples have lengthy turnaround times, increasing the risk of extended-spectrum β-lactamase (ESBL)-positive urinary tract infection (UTI) patients progressing to sepsis.

OBJECTIVE

To develop an efficient machine learning model for the identification of ESBL positivity in UTI patients.

METHODS

This retrospective study included 528 samples that had undergone drug susceptibility testing, based on inclusion and exclusion criteria. Variables were screened using Lasso regression, with 70% of the samples used to construct nine machine learning models (XGBClassifier, LogisticRegression, LGBMClassifier, AdaBoostClassifier, SVC, MLPClassifier, ComplementNB, GaussianNB, and GradientBoostingClassifier). Model selection was based on criteria including accuracy, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), F1 score, Kappa score, and Area Under the Curve (AUC). The best model type was identified through ten-fold cross-validation, which was then built using the remaining 30% of the data as a test set. Interpretations of predictive results were provided using the SHAP model, clarifying the impact of each feature on predictions and enhancing model transparency and interpretability.

RESULTS

The variables selected by the Lasso regression model are as follows: gender + urinary protein + urobilinogen + leukocytes + occult blood + age + pH + specific gravity + leukocyte count + erythrocyte count + epithelial cell count + cast count.The XGBoost model outperformed others in ten-fold cross-validation, with scores on the validation set as follows: AUC (95%CI): 0.924 (0.860-0.989); cutoff: 0.664(0.637-0.690); accuracy: 0.862(0.839-0.885); sensitivity: 0.9(0.879-0.920); specificity: 0.725(0.618-0.832); PPV: 0.923(0.896-0.950); NPV: 0.667(0.626-0.707); F1 score: 0.911(0.896-0.925); Kappa: 0.603(0.527-0.679). The final model achieved an AUC of 0.968 and accuracy of 0.943 on the test set.

CONCLUSION

This study developed a rapid and efficient machine learning model capable of identifying ESBL positivity based solely on routine urine test data.

Insight into the Prevalence of Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae in Vegetables: A Systematic Review and Meta-Analysis

The occurrence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in vegetables is an escalating global problem. This study aimed to document the global prevalence of ESBL-producing Enterobacteriaceae in vegetables using a comprehensive meta-analysis. A web-based search of electronic databases such as ScienceDirect, Google Scholar, and PubMed was conducted using studies published between 2014 and 2024. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines were followed for the systematic review and meta-analysis. The Comprehensive Meta-Analysis (CMA) Ver 4.0 software was used to analyse the data. The pooled prevalence estimate (PPE) with a 95% confidence interval (CI) was calculated using the random effects model. After reviewing 1802 articles, 63 studies were carefully analyzed and were part of the comprehensive meta-analysis. The overall PPE of ESBL-producing Enterobacteriaceae (ESBL-E) was 11.9% (95% CI: 0.091-0.155), with high heterogeneity (I2 = 96.8%, p < 0.001) from 2762 isolates. The blaSHV ESBL-encoding gene was the most prevalent, showing a PPE of 42.8% (95% CI: 0.269-0.603), while the PPE of blaampC-beta-lactamase-producing Enterobacteriaceae was 4.3% (95% CI: 0.025-0.71). Spain had a high ESBL-E PPE of 28.4% (0.284; 95% CI: 0.057-0.723, I2 = 98.2%), while China had the lowest PPE at 6.4% (0.064; 95% CI: 0.013-0.259, I2 = 95.6%). Continentally, the PPE of ESBL-E was significantly higher in reports from South America at 19.4% (95% CI: 0.043-0.560). This meta-analysis showed that ESBL-E in vegetables increased by 9.0%, 9.8%, and 15.9% in 2018-2019, 2020-2021, and 2022-2024, respectively. The findings emphasize the potential risks of consuming raw or inadequately cleaned produce and the importance of vegetables as ESBL-E reservoirs. Our work calls for immediate attention to food safety procedures and more thorough surveillance as antibiotic resistance rises to reduce antimicrobial resistance risks in food systems.

Prevalence and molecular characterization of ESBL-producing Enterobacteriaceae in Egypt: a systematic review and meta-analysis of hospital and community-acquired infections

BACKGROUND

ESBL-producing Enterobacteriaceae (ESBL-PE) represent a significant global health threat. In response to this growing concern and the lack of a surveillance system for ESBL-PE infections in Egypt, we conducted this meta-analysis. In this study, we aimed to quantify the prevalence of ESBL-PE based on the source of infection and characterize their molecular dissemination. Additionally, we sought to uncover temporal trends to assess the spread of ESBL-PE over time.

METHODS

A comprehensive literature search was conducted in PubMed, Scopus, Google Scholar, Web of Science, and the Egyptian Knowledge Bank to identify studies that: (1) report the prevalence of ESBL-PE in Egypt; (2) use valid detection methods; (3) involve clinical specimens; and (4) were published between 2010 and 2024. The quality of the included studies was evaluated using the "Joanna Briggs Institute Critical Appraisal Checklist". Meta-analysis was performed using the R meta package, reporting pooled prevalence with 95% confidence intervals (CI) via a random effects model.

RESULTS

This meta-analysis included 34 studies with 4,528 isolates, spanning 2007 to 2023. The overall prevalence of ESBL-PE in Egypt was 60% (95% CI: 54-65). The leave-one-out meta-analysis demonstrated the absence of influential outliers and Egger's test indicated no evidence of publication bias (P = 0.25). The prevalence of ESBL-PE was 62% (95% CI: 55-68) in nosocomial infections and 65% (95% CI: 52-75) in community-acquired infections, with no statistically significant difference (P = 0.68). The prevalence of ESBL producers in E. coli (64%) and K. pneumoniae (63%) is higher than in Proteus mirabilis (46%) (P = 0.06). Temporal analysis showed a stable ESBL prevalence over time. Moreover, in phenotypically confirmed ESBL-producing, E. coli harboring blaCTX-M was most prevalent (73%), followed by blaTEM (60%) and blaSHV (22%), with significant differences (P < 0.01). Subsequent analysis identified blaCTX-M-15 as the predominant variant of the blaCTX-M gene.

CONCLUSIONS

The prevalence of ESBL-PE in Egypt is alarmingly high at 60%. The observed high rates in both hospital and community-acquired infections underscore the need for public health strategies targeting both settings. One limitation of this study is the high heterogeneity, which partly attributed to regional and institutional variations in antibiotic use and stewardship practices.

Extended-spectrum β-lactamase-producing Escherichia coli from poultry: A review

Extended-spectrum β-lactamases (ESBLs) are β-lactamase enzymes produced by Gram-negative bacterial pathogens that harbor the ESBL genes. In addition, most ESBL genes are plasmid-mediated and usually encode a broader spectrum of antimicrobial resistance, especially to penicillins, first-generation, second-generation, and third-generation cephalosporins, as well as monobactam, such as aztreonam. Escherichia coli has become an opportunistic pathogen, especially in poultry, and has been implicated in zoonotic diseases that can be transmitted to humans, resulting in public health problems. Poultry can act as carriers of ESBL-producing E. coli (ESBL-EC) bacteria to humans through poultry meat that is contaminated by waste products, feces, and excretions. The ESBL gene CTX-M type was identified as the main cause of infection in humans and was detected in poultry as a cause of infection accompanied by clinical symptoms. Several studies have also shown a link between E. coli and ESBL gene transfer from birds to humans. Controlling the spread of ESBL-EC involves maintaining the cleanliness of poultry products, especially meat, and eliminating contaminant sources from poultry. Likewise, maintaining the environmental cleanliness of poultry slaughterhouses and poultry farms must be taken as a precautionary measure to curtail the increasing spread of ESBL-EC into the environment. This review aimed to explain the spread of ESBL-producing E. coli in poultry.

Exploring of spectrum beta lactamase producing multidrug-resistant Salmonella enterica serovars in goat meat markets of Bangladesh

The emergence of Salmonella enterica serovars that produce extended-spectrum beta-lactamase and exhibit multi-drug resistance (MDR) poses a substantial global threat, contributing to widespread foodborne illnesses and presenting an alarming issue for public health. This study specifically concentrated on the isolation and identification of ESBL-resistant genes (bla TEM, bla SHV, bla CTX-M1, bla CTX-M2, bla CTX-M9, MultiCase ACC, MultiCase MOX, MultiCase DHA, bla OXA) and the antibiogram profiling of Salmonella enterica serovars found in goat meat samples procured from retail outlets in Bangladesh. During the research in the Sylhet district of Bangladesh, researchers gathered a total of 210 samples of goat meat from 13 different Upazilas. Primarily, cultural and biochemical methods were used for isolation of bacteria from the selected samples. Salmonella enterica serovars Typhimurium and Enteritidis, along with three ESBL-resistant genes, were identified through polymerase chain reactions (PCRs). The disk diffusion test was used to determine antimicrobial susceptibilities. Out of 210 samples analysed, Salmonella spp. was detected in 18.10 % (38 out of 210), with S. Enteritidis and S. Typhimurium found in 9.05 % (19 out of 210) and 5.24 % (11 out of 210) of the samples, respectively. A total of 72.73 % (8/11) of S. Enteritidis and 100 % (19/19) of S. Typhimurium isolates were positive by Multidrug-resistant patterns. The positive outcomes were found of S. Typhimurium tested 63.16 % (12 out of 19) for the bla TEM gene and 21.05 % (4/19) for the bla SHV, gene. The study proposes that the retail goat meat market channel could be a prominent transmission way of ESBL-producing MDR Salmonella enterica serovars, representing a significant public health hazard.

Extended-spectrum β-lactamase-producing bacteria and their resistance determinants in different wastewaters and rivers in Nepal

Wastewaters serve as significant reservoirs of antibiotic resistant bacteria. Despite the evidence of antimicrobial resistance in wastewaters and river water in Kathmandu, direct linkage between them is not discussed yet. This study investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing bacteria and associated resistance genes in wastewaters and river water. Out of 246 bacteria from wastewaters, 57.72% were ESBL producers and 77.64% of them were multidrug resistant (MDR). ESBL producing E. coli was dominant in municipal and hospital wastewaters (HWW) as well as in river water while K. pneumoniae was common in pharmaceutical wastewater. The blaSHV and blaTEM genes were prevalent and commonly co-occurred with aac(6')-Ib-cr in K. pneumoniae isolated pharmaceutical wastewater. blaCTX-M carrying E. coli from hospital co-harbored aac(6')-Ib-cr while that from municipal influent and river water co-harbored qnrS. Whole genome sequencing data revealed the presence of diverse ARGs in bacterial isolates against multiple antibiotics. In average, an E. coli and a K. pneumoniae isolate contained 55.75 ± 0.96 and 40.2 ± 5.36 ARGs, respectively. Multi-locus sequence typing showed the presence of globally high-risk clones with wider host range such as E. coli ST10, and K. pneumoniae ST15 and ST307 in HWW and river indicating frequent dissemination of antimicrobial resistance in wastewater of Kathmandu. Whole genome sequence data aligned with phenotypic antibiograms and resistance genes detected by PCR in selected isolates. The presence of significant plasmid replicons (IncF, IncY) and mobile genetic elements (IS903, IS26) indicate high frequency of spreading antibiotic resistance. These findings indicate burden and dissemination of antimicrobial resistance in the environment and highlight the need for effective strategies to mitigate the antibiotic resistance.

Evaluation of three protocols for direct susceptibility testing for gram negative-Enterobacteriaceae from patient samples in Uganda with SMS reporting

In Uganda, the challenge of generating and timely reporting essential antimicrobial resistance (AMR) data has led to overreliance on empirical antibiotic therapy, exacerbating the AMR crisis. To address this issue, this study aimed to adapt a one-step AMR testing protocol alongside an SMS (Short Message Service) result relay system (SRRS), with the potential to reduce the turnaround time for AMR testing and result communication from 4 days or more to 1 day in Ugandan clinical microbiology laboratories. Out of the 377 samples examined, 54 isolates were obtained. Notably, E. coli (61%) and K. pneumoniae (33%) were the most frequently identified, majority testing positive for ESBL. Evaluation of three AMR testing protocols revealed varying sensitivity and specificity, with Protocol A (ChromID ESBL-based) demonstrating high sensitivity (100%) but no calculable specificity, Protocol B (ceftazidime-based) showing high sensitivity (100%) and relatively low specificity (7.1%), and Protocol C (cefotaxime-based) exhibiting high sensitivity (97.8%) but no calculable specificity. ESBL positivity strongly correlated with resistance to specific antibiotics, including cefotaxime, ampicillin, and aztreonam (100%), cefuroxime (96%), ceftriaxone (93%), and trimethoprim sulfamethoxazole (87%). The potential of integrating an SRRS underscored the crucial role this could have in enabling efficient healthcare communication in AMR management. This study underscores the substantial potential of the tested protocols for accurately detecting ESBL production in clinical samples, potentially, providing a critical foundation for predicting and reporting AMR patterns. Although considerations related to specificity warrant careful assessment before widespread clinical adoption.