Adverse clinical outcomes associated with infections by Enterobacterales producing ESBL (ESBL-E): a systematic review and meta-analysis

Survey in ruminants from Rwanda revealed high diversity and prevalence of extended-spectrum cephalosporin-resistant Enterobacterales

BACKGROUND

Antimicrobial resistance (AMR) in Enterobacterales constitutes a significant threat to the health of both humans and animals and a socioeconomic problem. Enterobacterales, mainly Escherichia coli, carrying β-lactamases has become one of the main indicators to estimate the burden of AMR in animals within "One Health" approach.

OBJECTIVES

To assess the presence of extended-spectrum cephalosporin-resistant Enterobacterales associated with ruminants (cattle, sheep, goats) habituated in all five provinces of Rwanda and to perform in depth characterization of isolates.

METHODS

We screened 454 rectal swabs from 203 cows, 170 goats, and 81 sheep and selective isolation of extended-spectrum cephalosporin-resistant Enterobacterales was conducted. Isolates were identified as a members of the order Enterobacterales by MALDI-TOF MS and further characterized by susceptibility testing and by whole-genome sequencing.

RESULTS

Out of the 454 samples, 64 extended-spectrum cephalosporin-resistant Enterobacterales were isolated from 58 animals. Isolates belonged to seven bacterial species and were identified as Escherichia coli (n = 54), Enterobacter bugandensis (n = 4), Enterobacter mori (n = 2), Klebsiella pneumoniae (n = 2), Enterobacter dykesii (n = 1), and Citrobacter freundii (n = 1). All isolates displayed an Extended-spectrum β-lactamases (ESBL) phenotype, with exception of Citrobacter freundii isolate displayed both an ESBL and AmpC phenotype. In addition, all Enterobacter isolates were identified as stably de-repressed AmpC-producers. ESBLs genes, blaCTX-M-15 was predominant. Resistance to tetracycline and tet(A) was most frequently observed among non-β-lactam resistance. Forty-eight isolates displayed multidrug-resistance phenotypes. A shiga toxin-producing E. coli and an enterotoxigenic E. coli isolate were observed. Genome comparisons revealed thirty-five E. coli sequence types (ST) (ST10, ST307 being predominate).

CONCLUSIONS

Considering the high proximity between ruminants and humans in Rwanda, the dissemination of antimicrobial drug resistance highlights the public health threats and requires the joint and multisectoral action of human and veterinary medicine, at human-animal-environment interfaces. Therefore, it is important to establish national and global "One Health" surveillance programs of AMR to tackle the antibiotic-resistant crisis in human and veterinary medicine.

Antimicrobial Resistance of Escherichia coli for Uncomplicated Cystitis: Korean Antimicrobial Resistance Monitoring System

Objectives: Uncomplicated cystitis is a leading form of bacterial UTI; the most common causative bacterium worldwide is Escherichia coli. This internet-based, prospective, multicenter, and national observational study aimed to report the antimicrobial resistance of E. coli in patients with uncomplicated cystitis through the use of the Korean Antimicrobial Resistance Monitoring System (KARMS) in 2023. Results: Data for a total of 654 patients were retrieved from the KARMS database. The mean (standard deviation) patient age was 55.9 (18.3) years. The numbers of postmenopausal women and patients with recurrent cystitis were 381 (59.4%) and 78 (11.9%), respectively. Regarding antimicrobial susceptibility, 96.8% were susceptible to fosfomycin, 98.9% to nitrofurantoin, 50.9% to ciprofloxacin, and 82.4% to cefotaxime. Extended-spectrum beta-lactamase positivity was 14.4% (89/616), and was significantly higher in tertiary hospitals (24.6%, p < 0.001) and recurrent cystitis (27.6%, p < 0.001). Fluoroquinolone resistance was significantly higher in tertiary hospitals (57.8%, p < 0.001), postmenopausal women (54.2%, p < 0.001), and recurrent cystitis (70.3%, p < 0.001). In addition, postmenopausal status (95% confidence interval [CI]: 1.44-3.17, odds ratio [OR] 2.13, p < 0.001), recurrent cystitis (95% CI: 1.40-4.66, OR 2.56, p = 0.002) and tertiary hospitals (95% CI: 1.00-2.93, OR 1.71, p = 0.049) were associated with significantly increased fluoroquinolone resistance. Methods: Any female patient diagnosed with clinical uncomplicated cystitis and microbiologically proven E. coli infection in 2023 was eligible for this study. Patient data were obtained from the web-based KARMS database. The antimicrobial susceptibility of E. coli was analyzed according to clinical factors, including hospital region, hospital type, menopause status, and recurrence status. Conclusions: The antimicrobial resistance of E. coli in patients with uncomplicated cystitis in the Republic of Korea has reached a serious level, especially in fluoroquinolone resistance. Therefore, major efforts should be made to reduce antimicrobial resistance.

Is It Time to Start Worrying? A Comprehensive Report on the Three-Year Prevalence of ESBL-Producing Bacteria and Their Trends in Antibiotic Resistance from the Largest University Hospital in Slovakia

BACKGROUND/OBJECTIVES

Over the past few decades, extended-spectrum β-lactamase (ESBL)-producing bacteria have become a great concern in healthcare systems worldwide, imposing large burdens by increasing antimicrobial resistance and patient morbidity. Given the high mortality rates and emergence of multidrug-resistant (MDR) strains, monitoring ESBL prevalence and resistance patterns is crucial. This study aimed to evaluate ESBL-producing Escherichia coli, Proteus mirabilis, and Klebsiella pneumoniae over three years, focusing on phenotypic distribution and resistance profiles.

METHODS

A total of 1599 ESBL-producing bacterial samples were collected and analysed. A panel of 20 antibiotics was tested to determine resistance traits. Data were recorded on phenotypical distribution, isolation types, changes in antibiotic resistance, and the relation of such changes to antibiotic consumption (defined daily dose) from clinical isolates.

RESULTS

Phenotypical analysis revealed the minimal presence of the Cefotaximase from Munich (CTX-M) phenotype in E. coli and K. pneumoniae, creating a distinct epidemiological profile compared to global patterns. Shifts in isolation trends, particularly in P. mirabilis, suggest an expected increase in associated-mortality-rate in the coming years. While resistance trends were not statistically significant, MDR and extensively drug-resistant (XDR) strains were identified across all three bacteria. Only meropenem showed consistent 100% efficacy against E. coli, with other antibiotics displaying only partial effectiveness.

CONCLUSIONS

These findings highlight the need for ongoing surveillance of ESBL-producing bacteria and underscore challenges in managing antibiotic resistance due to limited efficacy of last-resort treatments. The unique phenotypical distribution observed could impact local resistance management strategies in hospital settings in the coming years.

Prevalence of carbapenem-resistant Enterobacterales (CRE) in Saudi Arabia: A systematic review and meta-analysis

Antimicrobial resistance is a significant public health issue. In addressing the threat of multidrug resistant bacterial infections, carbapenems have been used. The carbapenem-resistant Enterobacterales (CRE) are, however, rapidly expanding worldwide. Since the issue of CRE is also a problem in Saudi Arabia, the current meta-analysis was performed to comprehensively evaluate the resistance rates to the main carbapenem antibiotics and determine the actual prevalence of CRE in the country. Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines was followed. Different web databases including PubMed, Scopus, Web of Science, and ScienceDirect were searched for relevant records. Data were extracted, and summary estimates for resistance to carbapenems were calculated using DerSimonian-Laird method of meta-analysis and the random-effects model. From a total of 787 retrieved records, 69 studies were found fully eligible and were included in the final analyses. More than 50 % of all the studies were conducted after 2010, and the most frequently examined members of the Enterobacterales were Escherichia coli and Klebsiella pneumoniae. The pooled prevalence estimate for imipenem resistance was 6.6 % (95 % CI: 4.7-9.2), 9.1 % (95 % CI: 6.7-12.3) for meropenem, and 18.6 % (95 % CI: 11.9-27.9) for ertapenem. High heterogeneity (I2  > 97 %, p < 0.001) was observed for all the estimates. Compared to other regions of the country, there was higher resistance rates in the Al-Qassim and Al-Jouf provinces. Additionally, resistance to ertapenem was as high as 34.2 % in the most recent study period (2021-2024). Proteus spp was the most prevalent CRE (26.2 %). This review highlights an increasing rate of carbapenem resistance among Enterobacterales, emphasizing the need for collaborative efforts to implement strict infection control and prevention measures. Consistent surveillance is indispensable for safeguarding public health, guiding clinical decisions, and strengthening efforts to tackle the challenges of antibiotic resistance.

Prevalence and clinical significance of the genotypic carriage among ESBL phenotype-negative Escherichia coli and Klebsiella pneumoniae clinical isolates in bacteremia: a study in a Malaysian tertiary center

Background

Antimicrobial resistance (AMR) can lead to fatal consequences. AMR genes carriage by phenotypically susceptible bacteria, such as Extended-Spectrum β-Lactamases (ESBL)s in Enterobacteriaceae, have potential implications for AMR spread and therapeutic outcomes. This phenomenon should be investigated.

Methods

Positive blood cultures from hospitalized patients in a Malaysian tertiary center between April 2022 and March 2023 were reviewed. A total of 137 clinical isolates of Escherichia coli (E.coli), Klebsiella pneumoniae (K.pneumoniae), and Klebsiella oxytoca were included. The antibiotic susceptibility and ESBL phenotypes were determined by disk diffusion method and the identification of genotypes by multiplex polymerase chain reaction. The clinical characteristics and outcome information were extracted by reviewing patients' medical records to evaluate the clinical significance of the ESBL genotype-positive but phenotype-negative isolates in bacteremia.

Results

All 137 isolates were positive for at least one genotype (bla CTX-M, n = 71, 51.8%; bla SHV, n = 87, 63.5%; bla TEM, n = 95, 69.3%; bla OXA-1, n = 38, 27.7%). While bla CTX-M was proportionately higher in the ESBL phenotype-positive isolates than ESBL phenotype-negative isolates (33/37, 89.2% vs 38/100, 38%; p < 0.001), more than half of those harboring bla CTX-M remained susceptible to third-generation cephalosporins (3GC). The sensitivity (Sen) of bla CTX-M for ESBL phenotypes prediction was 89.19% (95% confidence interval [CI], 74.58 - 96.97%); however, specificity (Sp) was low (46.47%; 95% CI 39.75 - 53.32). The patient characteristics were similar among 98 ESBL phenotype-negative cases, except that the non-bla CTX-M carrier group had significantly more renal impairment (0/37 vs 7/61, p = 0.043) and gastrointestinal sources of bacteremia (9/37 vs 27/61, p = 0.047). No differences were observed in infection severity, in-hospital mortality, and length of stay (LOS) between the bla CTX-M and non-bla CTX-M carrier groups.

Conclusion

The current study provides insight into the gene carriage in E.coli and Klebsiella species clinical isolates, including bla CTX-M genotypes in antibiotic-susceptible strains from a Malaysian hospital. The ESBL encoding genotypes such as bla CTX-M presented substantially beyond one-third of the ESBL phenotype-negative or 3GC susceptible E.coli and K.pneumoniae isolated from bloodstream infection. Although clinical outcomes were not worsened with bla CTX-M genotype-positive but ESBL phenotype-negative isolates in bacteremia, the potential implications for AMR spread deserve further investigation.

Exploring Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli in Food-Producing Animals and Animal-Derived Foods

Antimicrobials serve as crucial treatments in both veterinary and human medicine, aiding in the control and prevention of infectious diseases. However, their misuse or overuse has led to the emergence of antimicrobial resistance, posing a significant threat to public health. This review focuses on extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in animals and their associated food products, which contribute to the proliferation of antimicrobial-resistant strains. Recent research has highlighted the presence of ESBL-producing E. coli in animals and animal-derived foods, with some studies indicating genetic similarities between these isolates and those found in human infections. This underscores the urgent need to address antimicrobial resistance as a pressing public health issue. More comprehensive studies are required to understand the evolving landscape of ESBLs and to develop strategic public health policies grounded in the One Health approach, aiming to control and mitigate their prevalence effectively.

A new in vivo model of intestinal colonization using Zophobas morio larvae: testing hyperepidemic ESBL- and carbapenemase-producing Escherichia coli clones

Finding strategies for decolonizing gut carriers of multidrug-resistant Escherichia coli (MDR-Ec) is a public-health priority. In this context, novel approaches should be validated in preclinical in vivo gut colonization models before being translated to humans. However, the use of mice presents limitations. Here, we used for the first time Zophobas morio larvae to design a new model of intestinal colonization (28-days duration, T28). Three hyperepidemic MDR-Ec producing extended-spectrum β-lactamases (ESBLs) or carbapenemases were administered via contaminated food to larvae for the first 7 days (T7): Ec-4901.28 (ST131, CTX-M-15), Ec-042 (ST410, OXA-181) and Ec-050 (ST167, NDM-5). Growth curve analyses showed that larvae became rapidly colonized with all strains (T7, ~106-7 CFU/mL), but bacterial load remained high after the removal of contaminated food only in Ec-4901.28 and Ec-042 (T28, ~103-4 CFU/mL). Moreover, larvae receiving a force-feeding treatment with INTESTI bacteriophage cocktail (on T7 and T10 via gauge needle) were decolonized by Ec-4901.28 (INTESTI-susceptible); however, Ec-042 and Ec-050 (INTESTI-resistant) did not. Initial microbiota (before administering contaminated food) was very rich of bacterial genera (e.g., Lactococcus, Enterococcus, Spiroplasma), but patterns were heterogeneous (Shannon diversity index: range 1.1-2.7) and diverse to each other (Bray-Curtis dissimilarity index ≥30%). However, when larvae were challenged with the MDR-Ec with or without administering bacteriophages the microbiota showed a non-significant reduction of the diversity during the 28-day experiments. In conclusion, the Z. morio larvae model promises to be a feasible and high-throughput approach to study novel gut decolonization strategies for MDR-Ec reducing the number of subsequent confirmatory mammalian experiments.

Evaluation of Oral Amoxicillin/Clavulanate for Urinary Tract Infections Caused by Ceftriaxone Non-Susceptible Enterobacterales

Urinary tract infections (UTIs) are one of the most common infections and are frequently caused by Gram-negative organisms. The rise of resistant isolates has prompted evaluation of alternative therapies, including amoxicillin-clavulanate which has potent activity against Ambler class A enzymes. This study sought to evaluate clinical outcomes of patients with ceftriaxone non-susceptible UTIs receiving amoxicillin-clavulanate or standard of care (SOC). This was a single-center, retrospective, cohort study of adult patients with urinary tract infections caused by a ceftriaxone non-susceptible pathogen who received amoxicillin-clavulanate or SOC. The primary outcome was clinical failure at 90 days. Secondary outcomes included time to failure, isolation of a resistant organism, and hospital length of stay. Fifty-nine patients met study inclusion: 26 received amoxicillin/clavulanate and 33 received SOC. Amoxicillin-clavulanate recipients did not have higher failure rates compared to SOC recipients. For patients requiring hospital admission, hospital length of stay was numerically shorter with amoxicillin-clavulanate. The frequency of amoxicillin-clavulanate and carbapenem-resistant organisms did not differ significantly between groups. Amoxicillin-clavulanate may be a useful alternative therapy for the treatment of ceftriaxone non-susceptible Enterobacterales UTIs.

Real-Time TDM-Guided Optimal Joint PK/PD Target Attainment of Continuous Infusion Piperacillin-Tazobactam Monotherapy Is an Effective Carbapenem-Sparing Strategy for Treating Non-Severe ESBL-Producing Enterobacterales Secondary Bloodstream Infections: Findings from a Prospective Pilot Study

(1) Objectives: To assess the impact of optimal joint pharmacokinetic/pharmacodynamic (PK/PD) target attainment of continuous infusion (CI) piperacillin-tazobactam monotherapy on the microbiological outcome of documented ESBL-producing Enterobacterlaes secondary bloodstream infections (BSIs). (2) Methods: Patients hospitalized in the period January 2022-October 2023, having a documented secondary BSI caused by ESBL-producing Enterobacterales, and being eligible for definitive targeted CI piperacillin-tazobactam monotherapy according to specific pre-defined inclusion criteria (i.e., absence of septic shock at onset; favorable clinical evolution in the first 48 h after starting treatment; low-intermediate risk primary infection source) were prospectively enrolled. A real-time therapeutic drug monitoring (TDM)-guided expert clinical pharmacological advice (ECPA) program was adopted for optimizing (PK/PD) target attainment of CI piperacillin-tazobactam monotherapy. Steady-state plasma concentrations (Css) of both piperacillin and tazobactam were measured, and the free fractions (f) were calculated based on theoretical protein binding. The joint PK/PD target attainment was considered optimal whenever the piperacillin fCss/MIC ratio was >4 and the tazobactam fCss/target concentration (CT) ratio was >1 (quasi-optimal or suboptimal if only one or neither of the two thresholds were achieved, respectively). Univariate analysis was carried out for assessing variables potentially associated with failure in achieving the optimal joint PK/PD target of piperacillin-tazobactam and microbiological eradication. (3) Results: Overall, 35 patients (median age 79 years; male 51.4%) were prospectively included. Secondary BSIs resulted from urinary tract infections as a primary source in 77.2% of cases. The joint PK/PD target attainment was optimal in as many as 97.1% of patients (34/35). Microbiological eradication occurred in 91.4% of cases (32/35). Attaining the quasi-optimal/suboptimal joint PK/PD target of CI piperacillin-tazobactam showed a trend toward a higher risk of microbiological failure (33.3% vs. 0.0%; p = 0.08) (4) Conclusions: Real-time TDM-guided optimal joint PK/PD target attainment of CI piperacillin-tazobactam monotherapy may represent a valuable and effective carbapenem-sparing strategy when dealing with non-severe ESBL-producing Enterobacterales secondary BSIs.

Mortality and length of hospital stay after bloodstream infections caused by ESBL-producing compared to non-ESBL-producing E. coli

OBJECTIVE

To compare mortality and length of hospital stay between patients with ESBL-producing E. coli bloodstream infections (BSIs) and patients with non-ESBL E. coli BSIs. We also aimed at describing risk factors for ESBL-producing E. coli BSIs and time to effective antibiotic treatment for the two groups.

METHODS

A retrospective case-control study among adults admitted between 2014 and 2021 to a Norwegian University Hospital.

RESULTS

A total of 468 E. coli BSI episodes from 441 patients were included (234 BSIs each in the ESBL- and non-ESBL group). Among the ESBL-producing E. coli BSIs, 10.9% (25/230) deaths occurred within 30 days compared to 9.0% (21/234) in the non-ESBL group. The adjusted 30-day mortality OR was 1.6 (95% CI 0.7-3.7, p = 0.248). Effective antibiotic treatment was administered within 24 hours to 55.2% (129/234) in the ESBL-group compared to 86.8% (203/234) in the non-ESBL group. Among BSIs of urinary tract origin (n = 317), the median length of hospital stay increased by two days in the ESBL group (six versus four days, p < 0.001). No significant difference in the length of hospital stay was found for other sources of infection (n = 151), with a median of seven versus six days (p = 0.550) in the ESBL- and non-ESBL groups, respectively.

CONCLUSION

There was no statistically significant difference in 30-day mortality in ESBL-producing E. coli compared to non-ESBL E. coli BSI, despite a delay in the administration of an effective antibiotic in the former group. ESBL-production was associated with an increased length of stay in BSIs of urinary tract origin.

Evaluation of Extended-Spectrum Beta-Lactamase Resistance in Uropathogenic Escherichia coli Isolates from Urinary Tract Infection Patients in Al-Baha, Saudi Arabia

Urinary tract infections (UTIs) caused by extended-spectrum beta-lactamase (ESBL)-producing organisms are prevalent in both outpatient and inpatient settings, representing the most often encountered forms of infection. This research aimed to estimate the prevalence of ESBL-UTIs along with other uropathogens in the adult population and to assess the antibiotic activity against Escherichia coli extended-spectrum beta-lactamase (E. coli ESBL) isolates from patient samples in Al-Baha. A retrospective cross-sectional study included patients who presented to King Fahad Hospital in Al-Baha with clinical suspicion of UTI between 1 January 2019 and 30 September 2022. A total of 4406 urine samples with significant microbial growth were included in the scope of this investigation. A collective count of 1644 incidents of Escherichia coli (E. coli) was observed, wherein E. coli constituted 85% of the cases, while the remaining 15% comprised E. coli ESBL producers. The prevalence of E. coli ESBL was observed to be 64.7% in females and 35.3% in males, with a majority (67%) of the affected individuals being over the age of 50. The incidence of E. coli infections in the outpatient setting was found to be greater than that observed in the inpatient setting. E. coli ESBL were sensitive to colistin, tigecycline, amikacin, meropenem, imipenem, and nitrofurantoin by 100% and 93.3-100%, 95-99.6%, 95-99.06%, and 81-91%, respectively. On the other hand, the most resistant agents for E. coli ESBL were the group of cephalosporins, aztreonam, and ampicillin with 100% resistance, ciprofloxacin with 56-74% resistance, and cotrimoxazole with a 45-53% resistance level. ESBL-resistant E. coli strains are moderately prevalent in community- and hospital-acquired UTIs, especially in females and elderly patients (>50 years).

Performance of CHROMagar ESBL media for the surveillance of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) from rectal swabs in Botswana

Introduction. Lack of laboratory capacity hampers consistent national antimicrobial resistance (AMR) surveillance. Chromogenic media may provide a practical screening tool for detection of individuals colonized by extended-spectrum beta-lactamase (ESBL)-producing organisms.Hypothesis. CHROMagar ESBL media represent an adequate screening method for the detection of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE), isolated from rectal swabs.Aim. To evaluate the performance of CHROMagar ESBL media to accurately identify ESCrE isolates from rectal swab samples attained from hospitalized and community participants.Methodology. All participants provided informed consent prior to enrolment. Rectal swabs from 2469 hospital and community participants were inoculated onto CHROMagar ESBL. The performance of CHROMagar ESBL to differentiate Escherichia coli and Klebsiella spp., Enterobacter spp. and Citrobacter spp. (KEC spp.) as well as select for extended-spectrum cephalosporin resistance were compared to matrix-assisted laser desorption/ionization-time-of-flight MS (MALDI-TOF-MS) and VITEK-2 automated susceptibility testing.Results. CHROMagar ESBL had a positive and negative agreement of 91.2 % (95 % CI, 88.4-93.3) and 86.8 % (95 % CI, 82.0-90.7) for E. coli and 88.1 % (95 % CI 83.2-92.1) and 87.6 % (95 % CI 84.7-90.2) for KEC spp. differentiation, respectively, when compared to species ID by MALDI-TOF-MS. When evaluated for phenotypic susceptibilities (VITEK-2), 88.1 % (714/810) of the isolates recovered on the selective agar exhibited resistance to third-generation cephalosporins.Conclusion. The performance characteristics of CHROMagar ESBL media suggest that they may be a viable screening tool for the identification of ESCrE from hospitalized and community participants and could be used to inform infection prevention and control practices in Botswana and potentially other low-and middle-income countries (LMICs). Further studies are required to analyse the costs and the impact on time-to-result of the media in comparison with available laboratory methods for ESCrE surveillance in the country.

Extended-Spectrum β-Lactamases (ESBL): Challenges and Opportunities

The rise of antimicrobial resistance, particularly from extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E), poses a significant global health challenge as it frequently causes the failure of empirical antibiotic therapy, leading to morbidity and mortality. The E. coli- and K. pneumoniae-derived CTX-M genotype is one of the major types of ESBL. Mobile genetic elements (MGEs) are involved in spreading ESBL genes among the bacterial population. Due to the rapidly evolving nature of ESBL-E, there is a lack of specific standard examination methods. Carbapenem has been considered the drug of first choice against ESBL-E. However, carbapenem-sparing strategies and alternative treatment options are needed due to the emergence of carbapenem resistance. In South Asian countries, the irrational use of antibiotics might have played a significant role in aggravating the problem of ESBL-induced AMR. Superbugs showing resistance to last-resort antibiotics carbapenem and colistin have been reported in South Asian regions, indicating a future bleak picture if no urgent action is taken. To counteract the crisis, we need rapid diagnostic tools along with efficient treatment options. Detailed studies on ESBL and the implementation of the One Health approach including systematic surveillance across the public and animal health sectors are strongly recommended. This review provides an overview of the background, associated risk factors, transmission, and therapy of ESBL with a focus on the current situation and future threat in the developing countries of the South Asian region and beyond.

Detection of blaCTX-M and blaDHA genes in stool samples of healthy people: comparison of culture- and shotgun metagenomic-based approaches

We implemented culture- and shotgun metagenomic sequencing (SMS)-based methods to assess the gut colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESC-R-Ent) in 42 volunteers. Both methods were performed using native and pre-enriched (broth supplemented with cefuroxime) stools. Native culture screening on CHROMID® ESBL plates resulted in 17 positive samples, whereas the pre-enriched culture (gold-standard) identified 23 carriers. Overall, 26 ESC-R-Ent strains (24 Escherichia coli) were identified: 25 CTX-M and 3 DHA-1 producers (2 co-producing CTX-Ms). Using the SMS on native stool ("native SMS") with thresholds ≥60% for both identity and coverage, only 7 of the 23 pre-enriched culture-positive samples resulted positive for blaCTX-M/blaDHA genes (native SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 59.0%; specificity 100%). Moreover, an average of 31.5 and 24.6 antimicrobial resistance genes (ARGs) were detected in the 23 pre-enriched culture-positive and the 19 negative samples, respectively. When the pre-enriched SMS was implemented, more blaCTX-M/blaDHA genes were detected than in the native assay, including in stools that were pre-enriched culture-negative (pre-enriched SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 78.3%; specificity 75.0%). In addition, the pre-enriched SMS identified on average 38.6 ARGs/sample, whereas for the corresponding native SMS it was 29.4 ARGs/sample. Notably, stools resulting false-negative by using the native SMS had lower concentrations of ESC-R-Ent (average: ~105 vs. ~107 CFU/g) and E. coli classified reads (average: 193,959 vs. 1.45 million) than those of native SMS positive samples. Finally, the detection of blaCTX-M/blaDHA genes was compared with two well-established bioinformatic tools. In conclusion, only the pre-enriched SMS assured detection of most carriers of ESC-R-Ent. However, its performance was not comparable to the pre-enriched culture-based approach.

Intestinal colonization with multidrug-resistant Enterobacterales: screening, epidemiology, clinical impact, and strategies to decolonize carriers

The clinical impact of infections due to extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing Enterobacterales (Ent) has reached dramatic levels worldwide. Infections due to these multidrug-resistant (MDR) pathogens-especially Escherichia coli and Klebsiella pneumoniae-may originate from a prior asymptomatic intestinal colonization that could also favor transmission to other subjects. It is therefore desirable that gut carriers are rapidly identified to try preventing both the occurrence of serious endogenous infections and potential transmission. Together with the infection prevention and control countermeasures, any strategy capable of effectively eradicating the MDR-Ent from the intestinal tract would be desirable. In this narrative review, we present a summary of the different aspects linked to the intestinal colonization due to MDR-Ent. In particular, culture- and molecular-based screening techniques to identify carriers, data on prevalence and risk factors in different populations, clinical impact, length of colonization, and contribution to transmission in various settings will be overviewed. We will also discuss the standard strategies (selective digestive decontamination, fecal microbiota transplant) and those still in development (bacteriophages, probiotics, microcins, and CRISPR-Cas-based) that might be used to decolonize MDR-Ent carriers.

Empirical treatment and mortality in bacteremia due to extended spectrum β-lactamase producing Enterobacterales (ESβL-E), a retrospective cross-sectional study in a tertiary referral hospital from Colombia

BACKGROUND

Infections caused by extended spectrum β-lactamase (ESβL) producing bacteria are common and problematic. When they cause bloodstream infections, they are associated with significant morbidity and mortality.

METHODS

A retrospective cross-sectional observational study was conducted in a single center in Pereira, Colombia. It included people hospitalized with bacteremia due to gram-negative bacilli with the extended-spectrum β-lactamase producing phenotype. A logistic regression analysis was constructed. Clinical characteristics and risk factors for death from sepsis were established.

RESULTS

The prevalence of bacteremia due to Enterobacterales with extended-spectrum β-lactamase producing phenotype was 17%. 110 patients were analyzed. Most patients were men (62%) with a median age of 58 years, hospital mortality was 38%. Admission to intensive care was 45%. The following risk factors for mortality were established: shock requiring vasoactive support, Pitt score > 3 points, and not having an infectious disease consultation (IDC).

CONCLUSIONS

bacteremia due to Enterobacterales with extended-spectrum β-lactamase producing phenotype have a high mortality. Early recognition of sepsis, identification of risk factors for antimicrobial resistance, and prompt initiation of appropriate empiric antibiotic treatment are important. An infectious disease consultation may help improve outcomes.

Impact of Inappropriate Empirical Antibiotic on Outcomes in Community-acquired Third Generation Cephalosporin Resistant Enterobacterales Bacteremia

BACKGROUND

Currently, third generation cephalosporin resistant Enterobacterales (3GCRE) are becoming more common in community-acquired infection, leading to increasing consumption of carbapenems. Because community-acquired 3GCRE infections are generally less severe and of lower pathogenicity, the impact of inappropriate empirical antibiotics among patients with community-acquired 3GCRE bacteremia remains unknown.

MATERIALS AND METHODS

This prospective cohort study included adult patients with 3GCRE bacteremia from April 2018 to December 2021. Participants were followed for 30 days to measure the primary outcome of mortality. Propensity score analysis was performed to adjust for treatment selection bias.

RESULTS

A total of 155 patients met the eligible criteria (42 participants in the appropriate antibiotics group, and 113 participants in the inappropriate antibiotics group). Eight participants in the inappropriate antibiotics group never received appropriate antibiotics, three of whom died before microbiological results were made available. The most common clinical syndromes were urinary tract infection (56.8%) and biliary tract infection (22.6%). The overall 30-day mortality rate was 12.9%, 14.3% in the appropriate empirical antibiotics group and 12.4% in the inappropriate empirical antibiotics group. After propensity score weighted adjustment, the 30-day mortality rate in the inappropriate group was non-inferior to the appropriate group (mean difference 1.9%; 95% confidence interval: -10.1 - 14.0). From the multivariate analysis, acute respiratory failure and primary bacteremia were associated with 30-day mortality.

CONCLUSION

Among patients with community-acquired 3GCRE bacteremia, inappropriate empirical treatment given within 24 hours after the onset of bacteremia was non-inferior to appropriate antibiotics. In the setting of a high prevalence of 3GCRE carriage in community, adjustment to carbapenem might be tolerable among patients with community-acquired infections.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT03765749.

Incidence and predictors of Escherichia coli producing extended-spectrum beta-lactamase (ESBL-Ec) in Queensland, Australia from 2010 to 2019: a population-based spatial analysis

The dissemination of Escherichia coli producing extended-spectrum beta-lactamase (ESBL-Ec) is evident in the community. A population-based spatial analysis is necessary to investigate community risk factors for ESBL-Ec occurrence. The study population was defined as individuals with ESBL-Ec isolated in Queensland, Australia, from 2010 to 2019. Choropleth maps, global Moran's index and Getis-Ord Gi* were used to describe ESBL-Ec distribution and identify hot spots. Multivariable Poisson regression models with or without spatially structured random effects were performed. A total of 12 786 individuals with ESBL-Ec isolate were identified. The crude incidence rate increased annually from 9.1 per 100 000 residents in 2010 to 49.8 per 100 000 residents in 2019. The geographical distribution of ESBL-Ec changed from random to clustered after 2014, suggesting presence of community-specific factors that can enhance occurrence. Hot spots were more frequently identified in Outback and Far North Queensland, future public health measures to reduce transmission should prioritise these communities. Communities with higher socioeconomic status (RR = 0.66, 95% CI 0.55-0.79, per 100 units increase) and higher proportion of residents employed in the agricultural industry (RR = 0.79, 95% CI 0.67-0.95, per 10% increase) had lower ESBL-Ec incidence. Risk factors for occurrence appear differential between remote and city settings and this should be further investigated.

Pragmatic Comparison of Piperacillin/Tazobactam versus Carbapenems in Treating Patients with Nosocomial Pneumonia Caused by Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae

The effectiveness of piperacillin/tazobactam for managing nosocomial pneumonia caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is unknown. To answer this question, we conducted a retrospective cohort study in two tertiary teaching hospitals of patients admitted between January 2018 and July 2021 with a diagnosis of nosocomial pneumonia caused by ESBL-producing K. pneumoniae receiving either piperacillin/tazobactam or carbapenems within 24 h from the onset of pneumonia for at least 72 h. Clinical outcomes, including 28-day mortality and 14-day clinical and microbiological cure, were analyzed. Of the 136 total patients, 64 received piperacillin/tazobactam and 72 received carbapenems. The overall 28-day mortality was 19.1% (26/136). In the inverse probability of treatment weighted cohort, piperacillin/tazobactam therapy was not associated with worse clinical outcomes, as the 28-day mortality (OR, 0.82, 95% CI, 0.23–2.87, p = 0.748), clinical cure (OR, 0.94, 95% CI, 0.38–2.35, p = 0.894), and microbiological cure (OR, 1.10, 95% CI, 0.53–2.30, p = 0.798) were comparable to those of carbapenems. Subgroup analyses also did not demonstrate any statistical differences. In conclusion, piperacillin/tazobactam could be an effective alternative to carbapenems for treating nosocomial pneumonia due to ESBL-producing K. pneumoniae when the MICs are ≤8 mg/L.

Carriage Duration and Household Transmission of Enterobacterales Producing Extended-Spectrum Beta-Lactamase in the Community: A Systematic Review and Meta-Analysis

An attributing factor to Enterobacterales producing extended-spectrum beta-lactamase (ESBL-E) community spread is human-to-human transmission. This systematic review and meta-analysis aimed to estimate the duration of ESBL-E carriage in the community and the rate of household transmission. Literature search was performed on PubMed, EMBASE, and Scopus. Dose-response meta-analysis was planned to model the proportion of ESBL-E carriers and household transmission over time. Twenty-six studies (n = 2,505 participants) were included. The median carriage duration was 2 months. Approximately 22% (95% confidence interval: 16-28) had persistent carriage after 12 months. Travelers had significantly shorter carriage (median 1-2 months) than discharged hospital patients (median 6 months) at all measured time points. There were insufficient data to robustly meta-analyze household transmission. Nonetheless, five longitudinal studies reported 18.4% to 35.2% of contacts acquired ESBL-E within 4 to 36 months from hospital discharge of index case. Transmission events from travelers to their contacts appeared lower. Travelers with travel-acquired ESBL-E had significantly faster decolonization rate than discharged patients, suggesting that travel-associated import of multidrug-resistant pathogen may have limited contribution to community transmission of ESBL-E. The substantial prevalence of persistent carriers warrant consideration for additional measures to mitigate exposure risk of ESBL-E from discharged patients in the community and from readmitting patients in the hospital.