Mortality following bacteraemic infection caused by extended spectrum beta-lactamase (ESBL) producing E. coli compared to non-ESBL producing E. coli

Tracking antibiotics and antibiotic-resistant E. coli in the aquatic environment linked to agriculture

The application of manure to fertilize agricultural land is associated with the introduction of antibiotic residues and bacteria, including antibiotic-resistant bacteria, which can reach surface water through runoff and drainage and groundwater through leaching from the soil. This was investigated by sampling 50 surface water locations (before and after fertilization) and 50 groundwater wells for the presence of antibiotic residues and the presence of antibiotic-resistant bacteria. For the latter, Escherichia coli and extended-spectrum β-lactamase (ESBL) producing E. coli were used as indicators and profiled for antibiotic resistance. The presence of a wide range of antibiotic residues, though at low concentrations (0.01-10 μg/L), in freshwater ecosystems highlights the extensive spread of these substances. Only 16 % of the samples were consistently free of antibiotic residues throughout both sampling periods. Notably, the frequent occurrence of sulfonamides and lincomycin in surface waters raises concerns as their concentrations occasionally exceed the predicted no-effect levels for antimicrobial resistance selection. Maximum concentrations were reported at 8.83 μg/L and 1.60 μg/L for sulfamethoxazole and lincomycin, respectively. Additionally, resistance patterns in E. coli indicate increased resistance to sulfamethoxazole following the fertilization period, suggesting that the application of manure on fields contributes to a rise in antibiotic resistance from 20 % to 48 %. Although antibiotic contamination in groundwater is less prevalent, antibiotic resistance remains widespread. In particular, ESBL-producing E. coli exhibit heightened resistance levels, not limited to β-lactam antibiotics. The detection of resistance to critical last-resort antibiotics such as carbapenems and colistin further emphasizes the urgency of addressing antibiotic resistance in environmental contexts. This study highlights the need for continued monitoring and the implementation of legislation to reduce antibiotic pollution and tackle resistance in aquatic ecosystems.

Development of a novel risk score for diagnosing urinary tract infections: Integrating Sysmex UF-5000i urine fluorescence flow cytometry with urinalysis

BACKGROUND

Urinary tract infections (UTIs) are common globally, and are developing increased antibiotic resistance. Despite being the diagnostic "gold standard," urine culture is limited by slow results and a high rate of false negative findings, leading to treatment delays, higher costs, and overuse of empirical antibiotics. Our study aims to develop a rapid and reliable model to predict clinical outcomes.

METHODS

From January 1st to October 31st, 2023, we enrolled patients with symptoms suggesting UTI from the Outpatient Department of our hospital. Inclusion criteria were patients aged ≥18, initially diagnosed with UTI, available urinalysis, flow cytometry, and urinary culture. Exclusion criteria included failed sample collection and cultures, and pregnant women. A case-control study was conducted, with UTI cases defined as ≥ 10^5 CFU/ µ L and controls as < 10^5 CFU/ µ L, matched for age and sex in a 1:1 ratio. For validation, retrospective cases from July to December 2022 were selected with matching controls. Using urine culture as the gold standard, the predictive model was developed with backward stepwise logistic regression. Model discrimination was assessed using area under the curve (AUC).

RESULTS

In our discovery cohort, we included 1,335 UTI cases and 1,282 non-UTI controls, with mean ages of 52.9 ± 17.1 years and 51.9 ± 16.4 years, and females of 76.9% and 77.7%. Using 100 cells/uL as a threshold, bacterial counts demonstrated a sensitivity of 91.0% and specificity of 45.7%. Our novel UTIRisk score, developed from urinalysis and flow cytometry parameters, showed strong discrimination for UTI, with a AUC of 0.82 (95% CI: 0.81-0.84). In the validation cohort, the AUC was 0.77 (95% CI: 0.74-0.80). The UTIRisk score exhibited excellent specificity (96.5%) and high positive predictive value (92.6%). The score performed strongly across subgroups, particularly in males and patients aged ≥65.

CONCLUSIONS

Our UTIRisk score can improve diagnosis, reduce unnecessary urine cultures, optimize antibiotic use, and help control antibiotic resistance in LMICs. Multicenter, and intervention-based studies are warranted before clinical implementation.

Optimized methods for the targeted surveillance of extended-spectrum beta-lactamase-producing Escherichia coli in human stool

Understanding transmission pathways of important opportunistic, drug-resistant pathogens, such as extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli, is essential to implementing targeted prevention strategies to interrupt transmission and reduce the number of infections. To link transmission of ESBL-producing E. coli (ESBL-EC) between two sources, single-nucleotide resolution of E. coli strains, as well as E. coli diversity within and between samples, is required. However, the microbiological methods to best track these pathogens are unclear. Here, we compared different steps in the microbiological workflow to determine the impact different pre-enrichment broths, pre-enrichment incubation times, selection in pre-enrichment, selective plating, and DNA extraction methods had on recovering ESBL-EC from human stool samples, with the aim to acquire high-quality DNA for sequencing and genomic epidemiology. We demonstrate that using a 4-h pre-enrichment in Buffered Peptone Water, plating on cefotaxime-supplemented MacConkey agar and extracting DNA using Lucigen MasterPure DNA Purification kit improves the recovery of ESBL-EC from human stool and produced high-quality DNA for whole-genome sequencing. We conclude that our optimized workflow can be applied for single-nucleotide variant analysis of an ESBL-EC from stool.IMPORTANCEDrug-resistant infections are increasingly difficult to treat with antibiotics. Preventing infections is thus highly beneficial. To do this, we need to understand how drug-resistant bacteria spread to take action to stop infection and transmission. This requires us to accurately trace these bacteria between different sources. In this study, we compared different laboratory methods to see which worked best for detecting extended-spectrum beta-lactamase (ESBL)-producing E. coli, a common cause of urinary tract or bloodstream infections, from human stool samples. We found that enriching stool in a nutrient broth for 4 h, then plating the bacterial suspension on antibiotic-selective MacConkey agar, and finally extracting DNA from the bacteria using a specific DNA purification kit resulted in improved recovery of ESBL E. coli and high-quality DNA. Sequencing multiple isolates from stool allowed us to distinguish unambiguously and at high resolution between different variants of ESBL E. coli present in stool.

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.

The role of early use of Carbapenems perioperatively for urolithiasis with ESBL-producing Escherichia coli

BACKGROUND

Urolithiasis combined with ESBL-producing E. coli is often difficult to control and leads to higher postoperative infection-related complications. This study was aim to explore the efficacy and necessity for early use of carbapenem antibiotics perioperatively in urolithiasis patients with urinary tract infections caused by ESBL-producing E. coli.

METHODS

The study included a total of 626 patients who were separated into two groups: Group I (the ESBL-producing E. coli group) and Group II (the non-ESBL-producing E. coli group). Antibiotic susceptibility testing was performed and the two groups induced postoperative infection-related events were recorded. the efficacy of perioperative antibiotics was evaluated.

RESULTS

All strains of E. coli in our research were sensitive to Carbapenems antibiotics. In addition to Carbapenems, the resistance rates of ESBL-producing E. coli to 6 other commonly used antibiotics were higher than those of non-ESBL-producing strains. Based on the preoperative antibiotic susceptibility test for the ESBL-producing E. coli group and the qSOFA score, the Carbapenems were more effective than the β-lactamase inhibitors (p = 0.08), while for the non-ESBL-producing E. coli group, there was no difference in the treatment effects between Carbapenems, β-lactamase inhibitors, Ceftazidime and Quinolones (p = 0.975).

CONCLUSIONS

Carbapenem antibiotics significantly reduced the incidence of postoperative infection-related events compared with other types of antibiotics for ESBL-producing E. coli infections in patient with urolithiasis.

Isolation and characterization of cefotaxime resistant Escherichia coli from household floors in rural Bangladesh

Antimicrobial resistance (AMR) is a rising health concern worldwide. As an indicator organism, E. coli, specifically extended-spectrum β-lactamase (ESBL) producing E. coli, can be used to detect AMR in the environment and estimate the risk of transmitting resistance among humans, animals and the environment. This study focused on detecting cefotaxime resistant E. coli in floor swab samples from 49 households in rural villages in Bangladesh. Following isolation of cefotaxime resistant E. coli, DNA extracted from isolates was subjected to molecular characterization for virulence and resistance genes, determination of resistance to multiple classes of antibiotics to define multidrug resistant (MDR) and extensively drug resistant (XDR) strains, and the biofilm forming capacity of the isolates. Among 49 households, floor swabs from 35 (71 %) households tested positive for cefotaxime resistant E. coli. Notably, all of the 91 representative isolates were ESBL producers, with the majority (84.6 %) containing the bla CTX-M gene, followed by the bla TEM and bla SHV genes detected in 22.0 % and 6.6 % of the isolates, respectively. All isolates were MDR, and one isolate was XDR. In terms of pathogenic strains, 8.8 % of the isolates were diarrheagenic and 5.5 % were extraintestinal pathogenic E. coli (ExPEC). At 25 °C, 45 % of the isolates formed strong biofilm, whereas 43 % and 12 % formed moderate and weak biofilm, respectively. On the other hand, at 37 °C, 1.1 %, 4.4 % and 93.4 % of the isolates were strong, moderate and weak biofilm formers, respectively, and 1.1 % showed no biofilm formation. The study emphasizes the importance of screening and characterizing cefotaxime resistant E. coli from household floors in a developing country setting to understand AMR exposure associated with floors.

Modelling the implementation of narrow versus broader spectrum antibiotics in the empiric treatment of E. coli bacteraemia

The implementation of new antimicrobial resistance stewardship programs is crucial in optimizing antibiotic use. However, prescription choices can be difficult during empiric therapy; clinicians must balance the survival benefits of broader spectrum antibiotics with associated increases in resistance. The aim of this study was to evaluate the overall feasibility of switching to narrow spectrum antibiotics during the empiric treatment of E. coli bacteraemia by quantifying changes in resistance rates, antibiotic usage, and mortality using a deterministic state-transition model. Three unique model scenarios (A, B, and C), each representing a progressively broader spectrum empiric treatment regimen, were used to compare outcomes at 5 years. We show that the empiric use of the narrowest spectrum (first-line) antibiotics can lead to reductions in resistance to second-line antibiotics and the use of third-line antibiotics, but they also lead to increases in resistance to first-line therapy and higher mortality. Crucially, we find that shortening the duration of empiric and overall treatment, as well as reducing the baseline mortality rate, are important for increasing the feasibility of switching to narrow spectrum antibiotics in the empiric treatment of E. coli bacteraemia. We provide a flexible model design to investigate optimal treatment approaches for other bacterial infections.

New Agents Are Coming, and So Is the Resistance

Antimicrobial resistance is a global threat that requires urgent attention to slow the spread of resistant pathogens. The United States Centers for Disease Control and Prevention (CDC) has emphasized clinician-driven antimicrobial stewardship approaches including the reporting and proper documentation of antimicrobial usage and resistance. Additional efforts have targeted the development of new antimicrobial agents, but narrow profit margins have hindered manufacturers from investing in novel antimicrobials for clinical use and therefore the production of new antibiotics has decreased. In order to combat this, both antimicrobial drug discovery processes and healthcare reimbursement programs must be improved. Without action, this poses a high probability to culminate in a deadly post-antibiotic era. This review will highlight some of the global health challenges faced both today and in the future. Furthermore, the new Infectious Diseases Society of America (IDSA) guidelines for resistant Gram-negative pathogens will be discussed. This includes new antimicrobial agents which have gained or are likely to gain FDA approval. Emphasis will be placed on which human pathogens each of these agents cover, as well as how these new agents could be utilized in clinical practice.

Multidrug-resistance and extended-spectrum beta-lactamase-producing lactose-fermenting enterobacteriaceae in the human-dairy interface in northwest Ethiopia

BACKGROUND

Antimicrobial resistance (AMR) is among the top public health concerns in the globe. Estimating the prevalence of multidrug resistance (MDR), MDR index (MDR-I) and extended-spectrum beta-lactamase (ESBL)-producing lactose fermenting Enterobacteriaceae (LFE) is important in designing strategies to combat AMR. Thus, this study was designed to determine the status of MDR, MDR-I and ESBL-producing LFE isolated from the human-dairy interface in the northwestern part of Ethiopia, where such information is lacking.

METHODOLOGY

A cross-sectional study was conducted from June 2022 to August 2023 by analyzing 362 samples consisting of raw pooled milk (58), milk container swabs (58), milker's hand swabs (58), farm sewage (57), milker's stool (47), and cow's feces (84). The samples were analyzed using standard bacteriological methods. The antimicrobial susceptibility patterns and ESBL production ability of the LFE isolates were screened using the Kirby-Bauer disk diffusion method, and candidate isolates passing the screening criteria were phenotypically confirmed by using cefotaxime (30 μg) and cefotaxime /clavulanic acid (30 μg/10 μg) combined-disk diffusion test. The isolates were further characterized genotypically using multiplex polymerase chain reaction targeting the three ESBL-encoding- genes namely blaTEM, blaSHV, and blaCTX-M.

RESULTS

A total of 375 bacterial isolates were identified and the proportion of MDR and ESBL-producing bacterial isolates were 70.7 and 21.3%, respectively. The MDR-I varied from 0.0 to 0.81 with an average of 0.30. The ESBL production was detected in all sample types. Genotypically, the majority of the isolates (97.5%), which were positive on the phenotypic test, were carrying one or more of the three genes.

CONCLUSION

A high proportion of the bacterial isolates were MDR; had high MDR-I and were positive for ESBL production. The findings provide evidence that the human-dairy interface is one of the important reservoirs of AMR traits. Therefore, the implementation of AMR mitigation strategies is highly needed in the area.

Comparison of methods proposed for monitoring cefotaxime-resistant Escherichia coli in the water environment

Escherichia coli is a promising subject for globally coordinated surveillance of antimicrobial resistance (AMR) in water environments due to its clinical relevance and widespread use as an indicator of fecal contamination. Cefotaxime-resistant E. coli was recently evaluated favorably for this purpose by the World Health Organization TriCycle Protocol, which specifies tryptone bile x-glucuronide (TBX) medium and incubation at 35°C. We assessed comparability with the U.S. Environmental Protection Agency-approved method for E. coli quantification, which uses membrane-thermotolerant E. coli (mTEC) agar and incubation at 44.5°C, in terms of recovery of E. coli and cefotaxime-resistant E. coli from wastewater influent and surface waters. Total E. coli concentrations in wastewater influent were 106-108 CFU/100 mL, while cefotaxime-resistant E. coli were ~100-fold lower. Total E. coli in surface waters were ~102 CFU/100 mL, and cefotaxime-resistant isolates were near the limit of detection (0.4 CFU/100 mL). Total and putative cefotaxime-resistant E. coli concentrations did not differ significantly between media or by incubation method; however, colonies isolated on mTEC were more frequently confirmed to species (97.1%) compared to those from TBX (92.5%). Incubation in a water bath at 44.5°C significantly decreased non-specific background growth and improved confirmation frequency on both media (97.4%) compared to incubation at 35°C (92.3%). This study helps to advance globally coordinated AMR in water environments and suggests that the TriCycle Protocol is adaptable to other standard methods that may be required in different locales, while also offering a means to improve specificity by decreasing the frequency of false-positive identification of cefotaxime-resistant E. coli by modifying incubation conditions.IMPORTANCEAs antibiotic-resistant bacteria in water environments are increasingly recognized as contributors to the global antibiotic resistance crisis, the need for a monitoring subject that captures antibiotic resistance trends on a global scale increases. The World Health Organization TriCycle Protocol proposes the use of cefotaxime-resistant Escherichia coli isolated on tryptone bile x-glucuronide agar. The U.S. Environmental Protection Agency (USEPA) criteria for safe recreational waters also use E. coli as an indicator but specify the use of mTEC agar at a higher incubation temperature (44.5°C vs 35°C). We assessed the comparability of these methods for isolating total and cefotaxime-resistant E. coli, finding overall good agreement and performance, but significantly higher specificity toward E. coli selection with the use of the USEPA incubation protocol and mTEC agar. This study is the first to directly compare these methods and provides evidence that the methods may be used interchangeably for global surveillance of antibiotic resistance in the environment.

Surveillance and Resistance of Community-Onset Extended-Spectrum β-Lactamase-Producing Escherichia coli and Klebsiella pneumonia in Oral and Maxillofacial Surgery Site Infections

Background: The prevalence of community-onset infections of extended spectrum β-lactamase (ESBL)-producing strains has increased globally, yet surveillance and resistance in patients with oral and maxillofacial surgery site infections is less investigated. Patients and Methods: A retrospective cohort study was performed to investigate risk factors and resistance of ESBL-producing Escherichia coli (ESBL-EC) and ESBL-producing Klebsiella pneumonia (ESBL-KP) among community-onset patients with oral and maxillofacial surgery during January 2010 to December 2016. Demographic features, predisposing factors, clinical outcomes, and antibiotic agent costs were analyzed. Antimicrobial susceptibility testing of nine antimicrobial agents against ESBL-KP and ESBL-EC were measured. Results: Among 2,183 cultures from infection sites in patients with oral and maxillofacial surgery site (45 cases [2.06%]) were confirmed with community-onset ESBL-KP (24; 1.10%) or ESBL-EC (21; 0.96%) infection. Multivariable analysis showed the independent risk factors for ESBL-producing bacterial infection were prior history of hospitalization (adjusted odds ratio [aOR], 10.984; 95% confidence interval [CI], 5.965-59.879; p = 0.025) and malignant condition (aOR, 3.373; 95% CI 2.947-7.634; p = 0.024). Based on antimicrobial susceptibility testing, 57.8% ESBL-KP and ESBL-EC were found receiving inappropriate antimicrobial therapy, and antibiotic agent costs were higher than non-ESBL-producing bacterial infections ($493.8 ± $367.3 vs. $304.1 ± $334.7; p = 0.031). Conclusions: Infections caused by ESBL-KP and ESBL-EC among patients in sites with oral and maxillofacial surgery are associated with prior history of hospitalization and malignant conditions. Prompt detection and appropriate antibiotic administration for community-onset infections of ESBLs are necessary for such populations.

A systematic review on the excess health risk of antibiotic-resistant bloodstream infections for six key pathogens in Europe

BACKGROUND

Antimicrobial resistance is a global threat, which requires novel intervention strategies, for which priority pathogens and settings need to be determined.

OBJECTIVES

We evaluated pathogen-specific excess health burden of drug-resistant bloodstream infections (BSIs) in Europe.

METHODS

A systematic review and meta-analysis.

DATA SOURCES

MEDLINE, Embase, and grey literature for the period January 1990 to May 2022.

STUDY ELIGIBILITY CRITERIA

Studies that reported burden data for six key drug-resistant pathogens: carbapenem-resistant (CR) Pseudomonas aeruginosa and Acinetobacter baumannii, third-generation cephalosporin or CR Escherichia coli and Klebsiella pneumoniae, methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium. Excess health outcomes compared with drug-susceptible BSIs or uninfected patients. For MRSA and third-generation cephalosporin E. coli and K. pneumoniae BSIs, five or more European studies were identified. For all others, the search was extended to high-income countries.

PARTICIPANTS

Paediatric and adult patients diagnosed with drug-resistant BSI.

INTERVENTIONS

Not applicable.

ASSESSMENT OF RISK OF BIAS

An adapted version of the Joanna-Briggs Institute assessment tool.

METHODS OF DATA SYNTHESIS

Random-effect models were used to pool pathogen-specific burden estimates.

RESULTS

We screened 7154 titles, 1078 full-texts and found 56 studies on BSIs. Most studies compared outcomes of drug-resistant to drug-susceptible BSIs (46/56, 82.1%), and reported mortality (55/56 studies, 98.6%). The pooled crude estimate for excess all-cause mortality of drug-resistant versus drug-susceptible BSIs ranged from OR 1.31 (95% CI 1.03-1.68) for CR P. aeruginosa to OR 3.44 (95% CI 1.62-7.32) for CR K. pneumoniae. Pooled crude estimates comparing mortality to uninfected patients were available for vancomycin-resistant Enterococcus and MRSA BSIs (OR of 11.19 [95% CI 6.92-18.09] and OR 6.18 [95% CI 2.10-18.17], respectively).

CONCLUSIONS

Drug-resistant BSIs are associated with increased mortality, with the magnitude of the effect influenced by pathogen type and comparator. Future research should address crucial knowledge gaps in pathogen- and infection-specific burdens to guide development of novel interventions.

Human carriage of ESBL/pAmpC-producing Escherichia coli and Klebsiella pneumoniae in relation to the consumption of raw or undercooked vegetables, fruits, and fresh herbs

We investigated to what extent the consumption of raw or undercooked vegetables, fruits, and fresh herbs influences carriage rates of ESBL/pAmpC-producing Escherichia coli and Klebsiella pneumoniae (ESBL-E/K) in the general population. We assessed long-term carriage and changes in ESBL-E/K prevalence over time, by comparing the results to findings in the same population 5 years earlier. Between July and December 2021, participants sent in two fecal samples and questionnaires, 3 months apart. Food frequency questionnaires were sent on a monthly basis. Fecal samples were cultured and screened for ESBL-E/K, and phenotypically positive isolates were sequenced. Multivariable logistic regression models were established to assess the association between the consumption of fresh produce and ESBL-E/K carriage. The ESBL-E/K prevalence was 7.6% [41/537; 95% confidence interval (CI): 5.7-10.2] in the first sampling round and 7.0% (34/489; 95% CI: 5.0-9.6) in the second. Multivariable models did not result in statistical significance for any of the selected fruit and vegetable types. Trends for increased carriage rates were observed for the consumption of raspberry and blueberry in the summer period. ESBL-E/K prevalence was comparable with the prevalence in the same cohort 5 years earlier (7.5%; 95% CI: 5.6-10.1%). In six persons (1.2%) a genetically highly homologous ESBL-E/K was found. In conclusion, the contribution of the consumption of raw fruits, vegetables, and herbs to ESBL-E/K carriage in humans in the Netherlands is probably low. Despite COVID-19 containment measures (e.g., travel restrictions, social distancing, and hygiene) the ESBL-E/K prevalence was similar to 5 years earlier. Furthermore, indications for long-term carriage were found.IMPORTANCEESBL-producing bacteria are resistant against important classes of antibiotics, including penicillins and cephalosporines, which complicates treatment of infections. Food is one of the main routes of transmission for carriage of these bacteria in the general population. Although fruits, vegetables, and herbs are generally less frequently contaminated with ESBL-producing bacteria compared to meat, exposure might be higher since these products are often eaten raw or undercooked. This research showed that the contribution of the consumption of raw or undercooked fresh produce to ESBL-E/K carriage in the general Dutch population was low. No specific types of fruit or vegetables could be identified that gave a higher risk of carriage. In addition, we demonstrated the presence of genetically highly homologous ESBL-E/K in six persons after a period of 5 years, indicative for long-term carriage.

Association of piperacillin/tazobactam MIC and mortality in a cohort of ceftriaxone-resistant Escherichia coli bloodstream infections treated with piperacillin/tazobactam and carbapenems: a multicentric propensity score-weighted observational cohort study

OBJECTIVES

To assess the impact of piperacillin/tazobactam MICs on in-hospital 30 day mortality in patients with third-generation cephalosporin-resistant Escherichia coli bloodstream infection treated with piperacillin/tazobactam, compared with those treated with carbapenems.

METHODS

A multicentre retrospective cohort study was conducted in three large academic hospitals in Italy between 2018 and 2022. The study population comprised patients with monomicrobial third-generation cephalosporin-resistant E. coli bloodstream infection, who received either piperacillin/tazobactam or carbapenem therapy within 48 h of blood culture collection. The primary outcome was in-hospital 30 day all-cause mortality. A propensity score was used to estimate the likelihood of receiving empirical piperacillin/tazobactam treatment. Cox regression models were performed to ascertain risk factors independently associated with in-hospital 30 day mortality.

RESULTS

Of the 412 consecutive patients included in the study, 51% received empirical therapy with piperacillin/tazobactam, while 49% received carbapenem therapy. In the propensity-adjusted multiple Cox model, the Pitt bacteraemia score [HR 1.38 (95% CI, 0.85-2.16)] and piperacillin/tazobactam MICs of 8 mg/L [HR 2.35 (95% CI, 1.35-3.95)] and ≥16 mg/L [HR 3.69 (95% CI, 1.86-6.91)] were significantly associated with increased in-hospital 30 day mortality, while the empirical use of piperacillin/tazobactam was not found to predict in-hospital 30 day mortality [HR 1.38 (95% CI, 0.85-2.16)].

CONCLUSIONS

Piperacillin/tazobactam use might not be associated with increased mortality in treating third-generation cephalosporin-resistant E. coli bloodstream infections when the MIC is <8 mg/L.

The diagnostic accuracy of the GeneXpert ESBL-ampC prototype assay for rapid PCR-based detection of extended-spectrum beta-lactamase genes directly from urine

IMPORTANCE

Early identification of complicated urinary tract infections caused by ESBL-producing Enterobacterales has the potential to limit the use of carbapenems to those patients without alternative antibiotic options and avoid the empirical use of carbapenems in patients without ESBL-producing bacteria. The purpose for such a test will differ by setting and ESBL prevalence rates. Countries with low ESBL rates and cephalosporins as empiric treatment (e.g., The Netherlands) will need a rule-in test to decide to use carbapenems, while countries with high ESBL rates and empiric carbapenem treatment will need a rule-out test for ESBLs to de-escalate therapy early. Anyway, such as a test would-at least theoretically-improve patient care and reduce selective pressure for the emergence of carbapenem resistance.

Risk Factors for Recurrence of Community-Onset Urinary Tract Infections Caused by Extended-Spectrum Cephalosporin-Resistant Enterobacterales

Background

Extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) are an increasingly important cause of community-onset urinary tract infections (UTIs), including recurrent infections. We evaluated risk factors for recurrence among patients with community-onset ESCrE UTI.

Methods

This retrospective cohort study included adults with community-onset ESCrE UTI in the Duke University Health System from April 2018 through December 2021. ESCrE UTI recurrence by the same species was assessed 14-180 days (ie, 6 months) after completion of antibiotic treatment. We evaluated the relationships between candidate risk factors and time to recurrence using Cox proportional hazards regression models.

Results

Among 1347 patients with community-onset ESCrE UTI, 202 (15.0%) experienced recurrent infection during the 6-month follow-up period. Independent risk factors for recurrence included neurogenic bladder (adjusted hazard ratio [aHR], 1.8 [95% confidence interval {CI}, 1.2-2.6]; P = .005), prior history of UTI (aHR, 2.4 [95% CI, 1.7-3.3]; P < .001), and fluoroquinolone nonsusceptibility of the index UTI (aHR, 1.5 [95% CI, 1.1-2.1]; P = .02). Klebsiella pneumoniae infection was associated with recurrence in univariate analysis (HR, 1.6 [95% CI, 1.1-2.1]; P = .007) but not multivariate analysis (aHR, 1.4 [95% CI, 1.0-1.9]; P = .06). Inappropriate initial or definitive antibiotic therapy was not predictive of ESCrE UTI recurrence.

Conclusions

Recurrence of community-onset ESCrE UTI was common and associated with several patient and pathogen-level risk factors. Future studies should evaluate microbial risk factors for recurrence and improve the management of ESCrE UTI.

Rapid phenotypic testing for detection of carbapenemase- or extended-spectrum ß-lactamase-producing Enterobacterales directly from blood cultures: a systematic review and meta-analysis

BACKGROUND

Early identification of extended-spectrum ß-lactamase (ESBL) and carbapenemase-producing Enterobacterales (CP-CRE) is critical for timely therapy. Rapid phenotypic tests identifying these resistance mechanisms from pure bacterial colonies have been developed.

OBJECTIVES

To determine the operating characteristics of available rapid phenotypic tests when applied directly to positive blood cultures.

METHODS OF DATA SYNTHESIS

Bivariate random effects models were used unless convergence was not achieved where we used separate univariate models for sensitivity and specificity.

DATA SOURCES

MEDLINE, CENTRAL, Embase, BIOSIS, and Scopus from inception to 16 March 2021.

STUDY ELIGIBILITY CRITERIA

Studies using any rapid phenotypic assay for detection of ESBL or CP-CRE directly from blood cultures positive for Enterobacterales, including those utilizing spiked blood cultures. Case reports/series, posters, abstracts, review articles, those with ≤5 resistant isolates, and studies lacking data or without full text were excluded.

PARTICIPANTS

Consecutive patient samples (main analysis) or spiked blood cultures (sensitivity analysis).

TESTS

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assays (MALDI-TOF) and commercially available chromogenic or immunogenic assays.

REFERENCE STANDARD

Conventional laboratory methods and/or polymerase chain reaction (PCR).

ASSESSMENT OF RISK OF BIAS

Quality Assessment of Diagnostic Accuracy Studies Version 2 (QUADAS-2).

RESULTS

For detection of the ESBL phenotype the respective pooled sensitivities and specificities for consecutive clinical samples were as follows: 94% (95% CI 93-99%) and 97% (95% CI 95-100%) for MALDI-TOF/mass spectrometry (n = 1); and 98% (95% CI 92-100%) and 100% (95% CI 96-100%) for chromogenic assays (n = 7). For the CP-CRE phenotype the respective pooled sensitivity and specificities for consecutive clinical samples were as follows: 100% (95% CI 99-100%) and 100% (95% CI 100-100%) for MALDI-TOF (n = 2); 96% (95% CI 77-99%) and 100% (95% CI 81-100%) for chromogenic assays (n = 4); and 98% (95% CI 96-100%) and 100% (95% CI 100-100%) for immunogenic testing (n = 2).

CONCLUSIONS

Rapid phenotypic assays that can be directly applied to positive blood cultures to detect ESBL and carbapenemase production from Enterobacterales exist and, although clinical studies are limited, they appear to have high sensitivity and specificity. Their potential to facilitate patient care through timely identification of bacterial resistance should be further explored.

Extended Spectrum β-Lactamase-Producing Enterobacterales of Shrimp and Salmon Available for Purchase by Consumers in Canada-A Risk Profile Using the Codex Framework

The extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-EB) encompass several important human pathogens and are found on the World Health Organization (WHO) priority pathogens list of antibiotic-resistant bacteria. They are a group of organisms which demonstrate resistance to third-generation cephalosporins (3GC) and their presence has been documented worldwide, including in aquaculture and the aquatic environment. This risk profile was developed following the Codex Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance with the objectives of describing the current state of knowledge of ESBL-EB in relation to retail shrimp and salmon available to consumers in Canada, the primary aquacultured species consumed in Canada. The risk profile found that Enterobacterales and ESBL-EB have been found in multiple aquatic environments, as well as multiple host species and production levels. Although the information available did not permit the conclusion as to whether there is a human health risk related to ESBLs in Enterobacterales in salmon and shrimp available for consumption by Canadians, ESBL-EB in imported seafood available at the retail level in Canada have been found. Surveillance activities to detect ESBL-EB in seafood are needed; salmon and shrimp could be used in initial surveillance activities, representing domestic and imported products.

Urinary Tract Infections in Pregnant Individuals

SUMMARY

Urinary tract infection (UTI) is one of the more common perinatal complications, affecting approximately 8% of pregnancies (1, 2). These infections represent a spectrum, from asymptomatic bacteriuria, to symptomatic acute cystitis, to the most serious, pyelonephritis. The presence of UTIs has been associated with adverse pregnancy outcomes, including increased rates of preterm delivery and low birth weight. Screening for and treating asymptomatic bacteriuria have been shown in multiple studies to reduce the incidence of pyelonephritis in pregnancy (3-5). Given the frequency at which UTIs are encountered in pregnancy, the ability to recognize, diagnose, and treat them is essential for those providing care to pregnant individuals. This Clinical Consensus document was developed using an established protocol in conjunction with the authors listed.

Comparison of Cefotaxime-Resistant Escherichia coli and sul1 and intI1 by qPCR for Monitoring of Antibiotic Resistance of Wastewater, Surface Water, and Recycled Water

Awareness of the need for surveillance of antimicrobial resistance (AMR) in water environments is growing, but there is uncertainty regarding appropriate monitoring targets. Adapting culture-based fecal indicator monitoring to include antibiotics in the media provides a potentially low-tech and accessible option, while quantitative polymerase chain reaction (qPCR) targeting key genes of interest provides a broad, quantitative measure across the microbial community. The purpose of this study was to compare findings obtained from the culture of cefotaxime-resistant (cefR) Escherichia coli with two qPCR methods for quantification of antibiotic resistance genes across wastewater, recycled water, and surface waters. The culture method was a modification of US EPA Method 1603 for E. coli, in which cefotaxime is included in the medium to capture cefR strains, while qPCR methods quantified sul1 and intI1. A common standard operating procedure for each target was applied to samples collected by six water utilities across the United States and processed by two laboratories. The methods performed consistently, and all three measures reflected the same overarching trends across water types. The qPCR detection of sul1 yielded the widest dynamic range of measurement as an AMR indicator (7-log versus 3.5-log for cefR E. coli), while intI1 was the most frequently detected target (99% versus 96.5% and 50.8% for sul1 and cefR E. coli, respectively). All methods produced comparable measurements between labs (p < 0.05, Kruskal-Wallis). Further study is needed to consider how relevant each measure is to capturing hot spots for the evolution and dissemination of AMR in the environment and as indicators of AMR-associated human health risk.

Escherichia coli ST131 Associated with Increased Mortality in Bloodstream Infections from Urinary Tract Source

Escherichia coli sequence type 131 (ST131) is a globally dominant multidrug-resistant clone, although its clinical impact on patients with bloodstream infection (BSI) is incompletely understood. This study aims to further define the risk factors, clinical outcomes, and bacterial genetics associated with ST131 BSI. A prospectively enrolled cohort study of adult inpatients with E. coli BSI was conducted from 2002 to 2015. Whole-genome sequencing was performed with the E. coli isolates. Of the 227 patients with E. coli BSI in this study, 88 (39%) were infected with ST131. Patients with E. coli ST131 BSI and those with non-ST131 BSI did not differ with respect to in-hospital mortality (17/82 [20%] versus 26/145 [18%]; P = 0.73). However, in patients with BSI from a urinary tract source, ST131 was associated with a numerically higher in-hospital mortality than patients with non-ST131 BSI (8/42 [19%] versus 4/63 [6%]; P = 0.06) and increased mortality in an adjusted analysis (odds ratio of 5.85; 95% confidence interval of 1.44 to 29.49; P = 0.02). Genomic analyses showed that ST131 isolates primarily had an H4:O25 serotype, had a higher number of prophages, and were associated with 11 flexible genomic islands as well as virulence genes involved in adhesion (papA, kpsM, yfcV, and iha), iron acquisition (iucC and iutA), and toxin production (usp and sat). In patients with E. coli BSI from a urinary tract source, ST131 was associated with increased mortality in an adjusted analysis and contained a distinct repertoire of genes influencing pathogenesis. These genes could contribute to the higher mortality observed in patients with ST131 BSI.

Risk Factors for Bloodstream Infections Due to ESBL-Producing Escherichia coli, Klebsiella spp., and Proteus mirabilis

(1) Background: Risk factors for extended-spectrum beta-lactamase (ESBL) infections could vary geographically. The purpose of this study was to identify local risk factors for ESBL production in patients with Gram-negative bacteremia. (2) Methods: This retrospective observational study included adult patients admitted from January 2019 to July 2021 and had positive blood cultures for E. coli, K. pneumoniae, K. oxytoca, and P. mirabilis. Patients with ESBL infection were matched to a non-ESBL-producing infection with the same organism. (3) Results: A total of 150 patients were included: 50 in the ESBL group and 100 in the non-ESBL group. Patients in the ESBL group had a longer length of stay (11 vs. 7 days, p < 0.001), but not increased mortality (14% vs. 15%, p = 0.87) Multivariate analysis identified the receipt of >1 antibiotic in the last 90 days as a risk factor for ESBL infection (OR = 3.448, 95% CI = 1.494-7.957; p = 0.004); (4) Conclusions: Recent antimicrobial use was identified as an independent risk factors for ESBL-producing Enterobacterales infections. Knowledge of this risk may improve empirical therapy and reduce inappropriate use.

Characteristics of Extended-Spectrum β-Lactamase Producing Enterobacterales Isolated from Dogs and Cats, 2011–2021

The rising prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales is a significant threat to animal and human health. This study aims to describe the clinical features, antimicrobial susceptibility patterns, and genotypic features of infections associated with ESBL-producing Enterobacterales in dogs and cats seen at a tertiary referral veterinary teaching hospital. Enterobacterales isolated from dogs and cats that underwent ESBL testing during the study period were identified using a search of the hospital antimicrobial susceptibility test software database. Medical records of confirmed ESBL isolates were reviewed, and the source of infection, clinical findings, and antimicrobial susceptibility were recorded. Genomic DNA from bacterial isolates was evaluated for antimicrobial resistance genes with whole genome sequencing. Thirty ESBL-producing isolates were identified based on phenotypic testing (twenty-nine from dogs, one from a cat); twenty-six were Escherichia coli and the remainder were Klebsiella spp. Bacterial cystitis was the most commonly identified (8/30, 27%) clinical problem associated with infection. Resistance to three or more antimicrobial classes was identified in 90% (27/30) of isolates, and all isolates were susceptible to imipenem. Over 70% of isolates were susceptible to piperacillin-tazobactam, amikacin, and cefoxitin. BlaCTX-M-15 was the most common ESBL gene identified, present in 13/22 (59%) isolate genomes. A wide range of clinical infections were identified. Piperacillin-tazobactam and amikacin may be alternatives to carbapenem therapy. Further, larger-scale studies are needed.

Prevalence, Characterization, and Antimicrobial Resistance of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli from Domestic Free-Range Poultry in Agogo, Ghana

Poultry has been suggested as an important source for extended-spectrum beta-lactamase (ESBL)-producing bacteria that can lead to difficult-to treat infections in humans. Therefore, this study aims to determine the frequency, the genetics, and antimicrobial resistance profiles of ESBL-producing Escherichia coli in domestic free-range poultry in Agogo, Ghana. The study was set up and piloted from January 2019 until June 2019. Between June and December 2019, fecal samples (N = 144) were collected from free-roaming chickens from domestic farms in the regions of Sukuumu, Bontodiase, and Freetown and cultured on ESBL screening agar. Strain identification and antibiotic susceptibility were performed using the VITEK 2 compact system. ESBL-producing E. coli were confirmed using the double disk synergy test. Molecular characterization of ESBL-associated genes (bla_TEM, bla_SHV, and bla_CTX-M) were performed using conventional polymerase chain reaction (PCR) and further sequencing of obtained PCR amplicons. The result showed that 56.2% (n/N = 81/144) of collected fecal samples were positive for ESBL-producing E. coli. Majority of the isolates showed resistance to tetracycline (93.8%, n/N = 76/81) and trimethoprim-sulfamethoxazole (66.7, n/N = 54/81), whereas resistance to carbapenems was not found. The majority of ESBL-producing E. coli carried the bla_CTX-M genes, with bla_CTX-M-15 being the dominant (95.1%, n/N = 77/81) genotype. In this study, we report high frequencies of ESBL-producing E. coli in smallholder free-range poultry representing a potential source of infection, highlighting the need for control of antibiotic use and animal hygiene/sanitation measures, both important from a One Health perspective.

Incidence of Urinary Tract Infection Among Patients: Systematic Review and Meta-Analysis

Healthcare-associated infection is one of the most common and severe threats to patients' health and remains a significant challenge for healthcare providers. Among healthcare-associated infections, urinary tract infection (UTI) is one of the most common infections. This study aimed to determine the global incidence of UTI among patients. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guideline was used to perform this systematic review and meta-analysis. The articles were searched from April 4 to August 5, 2022, from electronic databases (Scopus, PubMed, Web of Science, Google Scholar, DOAJ, and MedNar) using Boolean logic operators, MeSH terms, and keywords. The quality of the study was assessed using the JBI Critical Assessment tool. One thousand nine ninety three articles were retrieved from the electronic databases, of which 38 articles conducted on 981 221 patients were included in the current study. The study found the global pooled incidence of UTI accounted for 1.6%. Based on the subgroup analysis by survey period and WHO region, the highest incidence of UTI was reported in the African Region [3.6%] and among studies conducted between 1996 and 2001 [3.7%]. This study revealed the overall pooled incidence of UTI was 1.6%. The highest incidence of UTI (3.6%) was reported in the African region. This indicates that there is a need to implement safety measures.

Impact of suboptimal or inappropriate treatment on healthcare resource use and cost among patients with uncomplicated urinary tract infection: an analysis of integrated delivery network electronic health records

Background

Although uncomplicated urinary tract infections (uUTIs; occurring in female patients without urological abnormalities or history of urological procedures or complicating comorbidities) are one of the most common community infections in the United States (US), limited data are available concerning associations between antibiotic resistance, suboptimal prescribing, and the economic burden of uUTI. We examined the prevalence of suboptimal antibiotic prescribing and antibiotic resistance and its effects on healthcare resource use and costs.

Methods

This retrospective cohort study utilized electronic health record data from a large Mid-Atlantic US integrated delivery network database, collected July 2016–March 2020. Female patients aged ≥ 12 years with a uUTI, who received ≥ 1 oral antibiotic treatment within ± 5 days of index uUTI diagnosis, and had ≥ 1 urine culture with antimicrobial susceptibility test, were eligible for inclusion in the study. The study examined the proportion of antibiotics that were inappropriately or suboptimally prescribed among patients with confirmed uUTI, and total healthcare costs (all-cause and UTI-related) within 6 months after a uUTI, stratified by antibiotic susceptibility and/or inappropriate or suboptimal treatment. Patient outcomes were assessed after 1:1 propensity score matching of patients with antibiotic-susceptible versus not-susceptible isolates and then by other covariates (e.g., demographics and recent healthcare use). A similar propensity score calculation was used to analyze the effect of inappropriate/suboptimal treatment on health outcomes. Costs were adjusted to 2020 US dollars ($).

Results

Among 2565 patients with a uUTI included in the analysis, the most commonly prescribed antibiotics were nitrofurantoin (61%), trimethoprim-sulfamethoxazole (19%), and ciprofloxacin (15%). More than one-third of the sample (40.2%) had isolates that were not-susceptible to ≥ 1 antibiotic indicated for treating patients with uUTI. Two-thirds (66.6%) of study-eligible patients were prescribed appropriate treatment; 29.9% and 11.9% were prescribed suboptimal and/or inappropriate treatment, respectively. Inappropriate or suboptimally prescribed patients had greater all-cause and UTI-related costs compared with appropriately prescribed patients. Differences were most striking among patients with antibiotic not-susceptible isolates.

Conclusions

These findings highlight how the increasing prevalence of antibiotic resistance combined with suboptimal treatment of patients with uUTI increases the burden on healthcare systems. The finding underlines the need for improved prescribing accuracy by better understanding regional resistance rates and developing improved diagnostic tests.

Codex Alimentarius Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance Are Incompatible with Available Surveillance Data

ABSTRACT

Foodborne antimicrobial-resistant (AMR) microorganisms are a global food safety concern. Antimicrobial drug use (AMU) in livestock may increase the risk of resistant foodborne bacterial infections in humans via contaminated animal products. Consequently, countries have implemented different livestock AMU restriction policies, opening the potential for trade disputes. AMR risk equivalence between countries with different AMU policies must be established by using scientifically justified risk assessments. The Codex Alimentarius Commission's Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance (AMR Codex) recommends an approach that requires quantification of detailed information, for which, in many instances, little to no data exist. Using AMR Salmonella exposure from beef consumption as an example, we demonstrate the difficulty of implementing the AMR Codex by comparing key regionally specific parameters within the United States and European Union, two regions with substantial beef production and consumption, robust foodborne pathogen sampling and surveillance systems, and different AMU policies. Currently, neither region fully captures data for key regional variables to populate a detailed risk assessment as outlined in the AMR Codex, nor are they able to adequately link AMU in livestock to AMR infections in humans. Therefore, the AMR Codex guidelines are currently aspirational and not a viable option to assess the impact of livestock AMU reductions on the human health risk of AMR salmonellosis from beef or produce regionally comparable estimates of risk. More flexible risk assessment guidelines that more directly link livestock AMU to human health risk and are amenable to currently available data are needed to allow for country variations and to calculate comparable regional risk estimates, which can be used to guide international trade policy.

HIGHLIGHTS

E. coli bacteraemia and antimicrobial resistance following antimicrobial prescribing for urinary tract infection in the community

Background

Urinary tract infections are one of the most common infections in primary and secondary care, with the majority of antimicrobial therapy initiated empirically before culture results are available. In some cases, however, over 40% of the bacteria that cause UTIs are resistant to some of the antimicrobials used, yet we do not know how the patient outcome is affected in terms of relapse, treatment failure, progression to more serious illness (bacteraemia) requiring hospitalization, and ultimately death. This study analyzed the current patterns of antimicrobial use for UTI in the community in Scotland, and factors for poor outcomes.

Objectives

To explore antimicrobial use for UTI in the community in Scotland, and the relationship with patient characteristics and antimicrobial resistance in E. coli bloodstream infections and subsequent mortality.

Methods

We included all adult patients in Scotland with a positive blood culture with E. coli growth, receiving at least one UTI-related antimicrobial (amoxicillin, amoxicillin/clavulanic acid, ciprofloxacin, trimethoprim, and nitrofurantoin) between 1st January 2009 and 31st December 2012. Univariate and multivariate logistic regression analysis was performed to understand the impact of age, gender, socioeconomic status, previous community antimicrobial exposure (including long-term use), prior treatment failure, and multi-morbidity, on the occurrence of E. coli bacteraemia, trimethoprim and nitrofurantoin resistance, and mortality.

Results

There were 1,093,227 patients aged 16 to 100 years old identified as receiving at least one prescription for the 5 UTI-related antimicrobials during the study period. Antimicrobial use was particularly prevalent in the female elderly population, and 10% study population was on long-term antimicrobials. The greatest predictor for trimethoprim resistance in E. coli bacteraemia was increasing age (OR 7.18, 95% CI 5.70 to 9.04 for the 65 years old and over group), followed by multi-morbidity (OR 5.42, 95% CI 4.82 to 6.09 for Charlson Index 3+). Prior antimicrobial use, along with prior treatment failure, male gender, and higher deprivation were also associated with a greater likelihood of a resistant E. coli bacteraemia. Mortality was significantly associated with both having an E. coli bloodstream infection, and those with resistant growth.

Conclusion

Increasing age, increasing co-morbidity, lower socioeconomic status, and prior community antibiotic exposure were significantly associated with a resistant E. coli bacteraemia, which leads to increased mortality.

Impact of continuous pharmacist intervention for injectable antimicrobials on the treatment of patients with Escherichia coli bacteremia

BACKGROUND

A prospective audit with intervention and feedback (PAF) by pharmacists is important for the appropriate use of antimicrobials. Clinically, Escherichia coli (E. coli) bacteremia is a common condition, but only few researchers have examined the role of PAF in its appropriate use of antimicrobials.

METHODS

We started PAF by pharmacists in 2017 for all injectable antibiotics. This study included cases of E. coli bacteremia that resulted in hospitalization over a 4 year period from 2016 to 2019. Patients were grouped by year (Period 0-3), and clinical outcomes were examined.

RESULTS

The pharmacists had 12 and 54 suggestions in Periods 0 and 3, respectively. The most common suggestion was de-escalation. The median duration of antimicrobial use was 12 (interquartile range: 8-15) days in Periods 0-2. The duration of antimicrobial use was significantly reduced to 9 (7-12) days in Period 3. In Period 3, the duration of antimicrobial use was reduced by 29%, while anti-pseudomonal drug use was reduced by 42% compared with that in period 0. The 30 day mortality rates were not significantly different between the groups.

CONCLUSIONS

PAF by pharmacists promotes the appropriate use of antimicrobials in patients with E. coli bacteremia; it is important to continue the program for several years.

Sheep and goat milk in Jordan is a reservoir of multidrug resistant extended spectrum and AmpC beta-lactamases Escherichia coli

Limited data is available on the prevalence and antimicrobial resistance of extended spectrum (ESBL) and AmpC β-lactamases Escherichia coli in sheep and goats in Jordan. This study determined the molecular prevalence and antimicrobial-resistance of ESBL and AmpC β-lactamases E. coli in 155 sheep and goat flocks across Jordan by testing 948 milk samples. The samples were enriched in MacConkey broth, and then plated on MacConkey agar with cefotaxime. The presence of ESBL and AmpC genes in the E. coli isolates was determined by PCR and the resistance toward critically important antimicrobials was tested by disc diffusion. In total, 1016 E. coli isolates were isolated from the cefotaxime supplemented MacConkey, 382 isolates harbored ESBL genes and 54 harbored bla_CMY. The prevalence of bla_CTX-M, bla_TEM, bla_CMY and bla_SHVE. coli in the milk samples were 33.5 %, 31.7 %, 5.7 %. and 1.1 %, respectively. At the flock level, 30.3 % flocks had β-lactamase E. coli, specifically 25.2 %, 20.7 %, 5.2 % and 2.6 % had bla_CTX-M, bla_TEM, bla_CMY and blaSHV E. coli, respectively. About 52.2 % of the isolates harbored both bla_CTX-M and bla_TEM. A high percentage (>59 %) of ESBL and AmpC β-lactamases E. coli resisted sulfamethoxazole/trimethoprim, tetracycline and nalidixic acid. Overall, 93.5 % and 96.3 % of ESBL and AmpC E. coli were resistant to ≥1 another antimicrobial class and 44.5 % and 44.4 % were resistant to ≥3 another antimicrobial class, respectively. This study shows that sheep and goat milk is a reservoir of multidrug resistant ESBL and AmpC β-lactamases E. coli, thus good hygienic practices and judicious antimicrobials use are important in small ruminants' farming.

Transmission of gram-negative antibiotic-resistant bacteria following differing exposure to antibiotic-resistance reservoirs in a rural community: a modelling study for bloodstream infections

Exposure to community reservoirs of gram-negative antibiotic-resistant bacteria (GN-ARB) genes poses substantial health risks to individuals, complicating potential infections. Transmission networks and population dynamics remain unclear, particularly in resource-poor communities. We use a dynamic compartment model to assess GN-ARB transmission quantitatively, including the susceptible, colonised, infected, and removed populations at the community-hospital interface. We used two side streams to distinguish between individuals at high- and low-risk exposure to community ARB reservoirs. The model was calibrated using data from a cross-sectional cohort study (N = 357) in Chile and supplemented by existing literature. Most individuals acquired ARB from the community reservoirs (98%) rather than the hospital. High exposure to GN-ARB reservoirs was associated with 17% and 16% greater prevalence for GN-ARB carriage in the hospital and community settings, respectively. The higher exposure has led to 16% more infections and attributed mortality. Our results highlight the need for early-stage identification and testing capability of bloodstream infections caused by GN-ARB through a faster response at the community level, where most GN-ARB are likely to be acquired. Increasing treatment rates for individuals colonised or infected by GN-ARB and controlling the exposure to antibiotic consumption and GN-ARB reservoirs, is crucial to curve GN-ABR transmission.

Raw Meat Contaminated with Cephalosporin-Resistant Enterobacterales as a Potential Source of Human Home Exposure to Multidrug-Resistant Bacteria

The prevalence of cephalosporine-resistant (3GC-R) strains among United States community-related research samples ranged from 5.6 to 10.8%, while, in the European countries, it was 1.2% to 10.1%. Several studies suggest that meat of animal origin could be one of the reservoirs of 3GC-R bacteria. Here, 86 raw meat samples (turkey, pork, chicken and beef) were collected randomly and verified for the presence of 3GC-R bacteria. The 3GC-R bacteria were isolated, identified and characterized phenotypically (antibiotic resistance, motility and biofilm) and genotypically (repetitive-sequence-based rep-PCR) to elucidate any correlations with principal component analysis (PCA). From 28 3GC-R positive samples, 41 strains were isolated, from which the majority belonged to Serratia fonticola (39%), followed by Escherichia coli (19.5%), Enterobacter cloacae (17.1%) and Klebsiella pneumoniae (14.6%). The isolates of E. coli and S. fonticola presented diverse profiles in rep-PCR. Generally, 3GC-R strains were more resistant to antibiotics used in veterinary medicine than in human medicine. PCA derived from antibiotic resistance, motility and biofilm formation of S. fonticola and E. coli strains showed that resistance to beta-lactams was separated from the resistance to other antibiotic classes. Moreover, for the S. fonticola, E. coli and En. cloacae, the type of meat can create a specific tendency towards antibiotic resistance and phenotypic characteristics for S. fonticola, while these relationships were not found for other tested species.

Phenotyping and genotyping studies on extended-spectrum β-lactamase-producing Escherichia coli isolates from mastitic cows on dairy farms in Egypt

Background and Aim: Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae have become a serious public health hazard worldwide. This importance is derived from the increase of new variants, particularly blaTEM, blaSHV, and blaCTX-M genes. This study aimed to examine ESBL-producing Escherichia coli isolated from different governorates in Egypt from dairy cows infected with subclinical and clinical mastitis. Materials and Methods: This study examined 207 milk samples for the resistance of isolates against 14 different antibiotics and ran serological identification of ESBL-producing E. coli isolates with complete antibiotic resistance. Genotypic and sequencing analyses of several resistance genes were conducted using a polymerase chain reaction. Results: E. coli was identified in cases with subclinical mastitis (80.5%) and clinical mastitis (85.7%). ESBL-producing E. coli was isolated from 38.2% of subclinical mastitic milk compared to 39.3% in clinical cases, where O26:k60, O125:k70, and O25:k11 were the serotypes with complete resistance to antibiotics. ESBL-producing E. coli isolates were resistant to cefotaxime, amoxicillin, cloxacillin, oxacillin, rifampicin, and penicillin in 100% but susceptible to amoxicillin and clavulanic acid in 82.5% of the cases. Results also revealed that 51.25%, 52.5%, 66.25%, 77.5% and 60% of ESBL-producing E. coli isolates were responsive to ciprofloxacin, ofloxacin, norfloxacin, levofloxacin, and gentamycin, respectively. The detected genes were registered in GenBank as MW345819.1 and MW345820.1 for the E. coli blaTEM gene and MW295407 for the E. coli blaSHV gene. Conclusion: This study found ESBL-producing E. coli in mastitic milk samples from Egyptian dairy farms and confirmed the occurrence and circulation of the main antibiotic genes (blaTEM and blaSHV) in the samples. Regular and thorough surveillance of ESBL-producing E. coli and subsequent preventive actions are essential for preventing the spread of these resistance genes in the future, which could pose serious and catastrophic health risks. Authorities should cling to the concept of One Health to minimize the risk of new varieties.

Pharmacists' Perspectives of Their Roles in Antimicrobial Stewardship: A Qualitative Study among Hospital Pharmacists in Malaysia

Antimicrobial resistance has negatively impacted patient outcomes and increased healthcare costs. Antimicrobial stewardship (AMS) includes all activities and policies to promote the judicious use of antimicrobials. Pharmacists are key players in AMS models worldwide. However, there is a research gap in the role of pharmacists as antimicrobial stewards in Malaysia. This study aimed to explore hospital pharmacists' perspectives on their roles in, and barriers and facilitators to the implementation of AMS strategies. Individual, semi-structured interviews were conducted with 16 hospital pharmacists involved in AMS activities from 13 public hospitals in Kuala Lumpur and Selangor. Audio-taped interviews were transcribed verbatim and imported into NVivo software version 10.0 (QSR). A thematic analysis method was used to identify themes from the qualitative data until theme saturation was reached. Respondents perceived pharmacists as having important roles in the implementation of AMS strategies, in view of the multiple tasks they were entrusted with. They described their functions as antimicrobial advisors, antimicrobial guardians and liaison personnel. The lack of resources in terms of training, manpower and facilities, as well as attitudinal challenges, were some barriers identified by the respondents. Administrative support, commitment and perseverance were found to be facilitators to the role of pharmacists in AMS. In conclusion, pharmacists in public hospitals play important roles in AMS teams. This study has provided insights into the support that AMS pharmacists in public hospitals require to overcome the barriers they face and to enhance their roles in the implementation of AMS strategies.

OUP accepted manuscript

Objectives

The widespread intestinal carriage of ESBL-producing Escherichia coli (ESBL E. coli) among both patients and healthy individuals is alarming. However, the global prevalence and trend of this MDR bacterium in healthcare settings remains undetermined. To address this knowledge gap, we performed a comparative meta-analysis of the prevalence in community and healthcare settings.

Methods

Our systematic review included 133 articles published between 1 January 2000 and 22 April 2021 and indexed in PubMed, EMBASE or Google Scholar. A random-effects meta-analysis was performed to obtain the global pooled prevalence (community and healthcare settings). Subgroup meta-analyses were performed by grouping studies using the WHO regions and 5 year intervals of the study period.

Results

We found that 21.1% (95% CI, 19.1%–23.2%) of inpatients in healthcare settings and 17.6% (95% CI, 15.3%–19.8%) of healthy individuals worldwide carried ESBL E. coli in their intestine. The global carriage rate in healthcare settings increased 3-fold from 7% (95% CI, 3.7%–10.3%) in 2001–05 to 25.7% (95% CI, 19.5%–32.0%) in 2016–20, whereas in community settings it increased 10-fold from 2.6% (95% CI, 1.2%–4.0%) to 26.4% (95% CI, 17.0%–35.9%) over the same period.

Conclusions

The global and regional human intestinal ESBL E. coli carriage is increasing in both community and healthcare settings. Carriage rates were generally higher in healthcare than in community settings. Key relevant health organizations should perform surveillance and implement preventive measures to address the spread of ESBL E. coli in both settings.

Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study

Background

Escherichia coli is a leading cause of bloodstream infections. Developing interventions to reduce E coli infections requires an understanding of the frequency of nosocomial transmission, but the available evidence is scarce. We aimed to detect and characterise transmission of E coli and associated plasmids in a hospital setting.

Methods

In this prospective observational cohort study, patients were admitted to two adult haematology wards at the Cambridge University Hospitals NHS Foundation Trust in England. Patients aged 16 years and older who were treated for haematological malignancies were included. Stool samples were collected from study participants on admission, once per week, and at discharge. We sequenced multiple E coli isolates (both extended spectrum β-lactamase [ESBL]-producing and non-ESBL-producing) from each stool sample. A genetic threshold to infer E coli transmission was defined by maximum within-host single nucleotide polymorphism (SNP) diversity and the probability of drawing observed pairs of between-patient isolates at different SNP thresholds. Putative transmission clusters were identified when sequences were less than the genetic threshold. Epidemiological links for each transmission event were investigated. We sequenced all E coli positive blood samples from the two adult haematology wards.

Findings

We recruited 174 (51%) of 338 adult patients admitted to the wards between May 13 and Nov 13, 2015. We obtained and cultured 376 stool samples from 149 patients, of which 152 samples from 97 (65%) patients grew E coli. Whole-genome sequencing was done on 970 isolates. We identified extensive diversity in the bacterial population (90 sequence types) and mixed E coli sequence type carriage. 24 (26%) patients carried two sequence types, 12 (13%) carried three, and six (6%) patients carried four or more sequence types. Using a 17 SNP cutoff we identified ten clusters in 20 patients. The largest cluster contained seven patients, whereas four patients were included in multiple clusters. Strong epidemiological links were found between patients in seven clusters. 17 (11%) of 149 patients had stool samples positive for ESBL-producing E coli, the most common of which was associated with bla_CTX-M-15 (12 [71%] of 17). Long-read sequencing revealed that bla_CTX-M-15 was often integrated into the chromosome, with little evidence for plasmid transmission. Seven patients developed E coli bloodstream infection, four with identical strains to those in their stool; two of these had documented nosocomial acquisition.

Interpretation

We provide evidence of bacterial transmission and endogenous infection during routine care by integrating genomic and epidemiological data and by determining a genetic cutoff informed by within-host diversity in the studied population. Our findings challenge single colony-based investigations, and the widely accepted notion of plasmid spread.

Funding

UK Department of Health, Wellcome Trust, UK National Institute for Health Research.

Surgical Site Infections and Antimicrobial Resistance After Cesarean Section Delivery in Rural Rwanda

Background:

As the volume of surgical cases in low- and middle-income countries (LMICs) increases, surgical-site infections (SSIs) are becoming more prevalent with anecdotal evidence of antimicrobial resistance (AMR), despite a paucity of data on resistance patterns.

Objectives:

As a primary objective, this prospective study aimed to describe the epidemiology of SSIs and the associated AMR among women who delivered by cesarean at a rural Rwandan hospital. As secondary objectives, this study also assessed patient demographics, pre- and post-operative antibiotic use, and SSI treatment.

Methods:

Women who underwent cesarean deliveries at Kirehe District Hospital between September 23rd, 2019, and March 16th, 2020, were enrolled prospectively. On postoperative day (POD) 11 (+/– 3 days), their wounds were examined. When an SSI was diagnosed, a wound swab was collected and sent to the Rwandan National Reference Laboratory for culturing and antibiotic susceptibility testing.

Findings:

Nine hundred thirty women were enrolled, of whom 795 (85.5%) returned for the POD 11 clinic visit. 45 (5.7%) of the 795 were diagnosed with SSI and swabs were collected from 44 of these 45 women. From these 44 swabs, 57 potential pathogens were isolated. The most prevalent bacteria were coagulase-negative staphylococci (n = 12/57, 20.3% of all isolates), and Acinetobacter baumannii complex (n = 9/57, 15.2%). 68.4% (n = 39) of isolates were gram negative; 86.7% if excluding coagulase-negative staphylococci. No gram-negative pathogens isolated were susceptible to ampicillin, and the vast majority demonstrated intermediate susceptibility or resistance to ceftriaxone (92.1%) and cefepime (84.6%).

Conclusions:

Bacterial isolates from SSI swab cultures in rural Rwanda predominantly consisted of gram-negative pathogens and were largely resistant to commonly used antibiotics. This raises concerns about the effectiveness of antibiotics currently used for surgical prophylaxis and treatment and may guide the appropriate selection of treatment of SSIs in rural Rwanda and comparable settings.

Escherichia coli bloodstream infections in the western interior of British Columbia, Canada: a population-based cohort study

Our population-based study objectives were to describe characteristics and outcomes of Escherichia coli bloodstream infections (BSIs), and to evaluate factors associated with outcomes. We included incident E. coli BSIs from western interior residents (British Columbia, Canada; 04/2010–03/2020). We obtained data including patient demographics, location of onset, infection focus, Charlson comorbidity index (CCI), antimicrobial resistance, 30-day all-cause mortality and length of hospital stay (LOS). Using multivariable logistic regression models fitted with generalised estimating equations, we estimated factors associated with 30-day mortality and long post-infection LOS (>75th percentile). We identified 1080 incident E. coli BSIs in 1009 patients. The crude incidence and 30-day mortality rates were 59.1 BSIs and 6.8 deaths/100 000 person-years, respectively. The 30-day case fatality risk was 11.5%. Compared to community-acquired E. coli BSIs, either healthcare-associated or nosocomial cases had higher odds of 30-day mortality. Older cases, non-urogenital BSI foci and CCI ⩾ 3 had higher odds of 30-day mortality compared to younger cases, urogenital foci and CCI < 3. In patients that survived to discharge, those with extended-spectrum β-lactamase (ESBL)-producing E. coli BSIs, nosocomial BSIs, and CCI ⩾ 3 had higher odds of long post-infection LOS compared to those with non-ESBL-producing, community-acquired and healthcare-associated, and CCI < 3. There is a substantial disease burden from E. coli BSIs.

Prevalence and Impact of Biofilms on Bloodstream and Urinary Tract Infections: A Systematic Review and Meta-Analysis

This study sought to assess the prevalence and impact of biofilms on two commonly biofilm-related infections, bloodstream and urinary tract infections (BSI and UTI). Separated systematic reviews and meta-analyses of observational studies were carried out in PubMed and Web of Sciences databases from January 2005 to May 2020, following PRISMA protocols. Studies were selected according to specific and defined inclusion/exclusion criteria. The obtained outcomes were grouped into biofilm production (BFP) prevalence, BFP in resistant vs. susceptible strains, persistent vs. non-persistent BSI, survivor vs. non-survivor patients with BSI, and catheter-associated UTI (CAUTI) vs. non-CAUTI. Single-arm and two-arm analyses were conducted for data analysis. In vitro BFP in BSI was highly related to resistant strains (odds ratio-OR: 2.68; 95% confidence intervals-CI: 1.60–4.47; p < 0.01), especially for methicillin-resistant Staphylococci. BFP was also highly linked to BSI persistence (OR: 2.65; 95% CI: 1.28–5.48; p < 0.01) and even to mortality (OR: 2.05; 95% CI: 1.53–2.74; p < 0.01). Candida spp. was the microorganism group where the highest associations were observed. Biofilms seem to impact Candida BSI independently from clinical differences, including treatment interventions. Regarding UTI, multi-drug resistant and extended-spectrum β-lactamase-producing strains of Escherichia coli, were linked to a great BFP prevalence (OR: 2.92; 95% CI: 1.30–6.54; p < 0.01 and OR: 2.80; 95% CI: 1.33–5.86; p < 0.01). More in vitro BFP was shown in CAUTI compared to non-CAUTI, but with less statistical confidence (OR: 2.61; 95% CI: 0.67–10.17; p < 0.17). This study highlights that biofilms must be recognized as a BSI and UTI resistance factor as well as a BSI virulence factor.

Mortality in Escherichia coli bloodstream infections: a multinational population-based cohort study

Background

Escherichia coli is the most common cause of bloodstream infections (BSIs) and mortality is an important aspect of burden of disease. Using a multinational population-based cohort of E. coli BSIs, our objectives were to evaluate 30-day case fatality risk and mortality rate, and determine factors associated with each.

Methods

During 2014–2018, we identified 30-day deaths from all incident E. coli BSIs from surveillance nationally in Finland, and regionally in Sweden (Skaraborg) and Canada (Calgary, Sherbrooke, western interior). We used a multivariable logistic regression model to estimate factors associated with 30-day case fatality risk. The explanatory variables considered for inclusion were year (2014–2018), region (five areas), age (< 70-years-old, ≥70-years-old), sex (female, male), third-generation cephalosporin (3GC) resistance (susceptible, resistant), and location of onset (community-onset, hospital-onset). The European Union 28-country 2018 population was used to directly age and sex standardize mortality rates. We used a multivariable Poisson model to estimate factors associated with mortality rate, and year, region, age and sex were considered for inclusion.

Results

From 38.7 million person-years of surveillance, we identified 2961 30-day deaths in 30,923 incident E. coli BSIs. The overall 30-day case fatality risk was 9.6% (2961/30923). Calgary, Skaraborg, and western interior had significantly increased odds of 30-day mortality compared to Finland. Hospital-onset and 3GC-resistant E. coli BSIs had significantly increased odds of mortality compared to community-onset and 3GC-susceptible. The significant association between age and odds of mortality varied with sex, and contrasts were used to interpret this interaction relationship. The overall standardized 30-day mortality rate was 8.5 deaths/100,000 person-years. Sherbrooke had a significantly lower 30-day mortality rate compared to Finland. Patients that were either ≥70-years-old or male both experienced significantly higher mortality rates than those < 70-years-old or female.

Conclusions

In our study populations, region, age, and sex were significantly associated with both 30-day case fatality risk and mortality rate. Additionally, 3GC resistance and location of onset were significantly associated with 30-day case fatality risk. Escherichia coli BSIs caused a considerable burden of disease from 30-day mortality. When analyzing population-based mortality data, it is important to explore mortality through two lenses, mortality rate and case fatality risk.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06326-x.

A prospective study of Escherichia coli bloodstream infection among adolescents and adults in northern Tanzania

Background

Characterization of the epidemiology of Escherichia coli bloodstream infection (BSI) in sub-Saharan Africa is lacking. We studied patients with E. coli BSI in northern Tanzania to describe host risk factors for infection and to describe the antimicrobial susceptibility of isolates.

Methods

Within 24 h of admission, patients presenting with a fever at two hospitals in Moshi, Tanzania, were screened and enrolled. Cases were patients with at least one blood culture yielding E. coli and controls were those without E. coli isolated from any blood culture. Logistic regression was used to identify host risk factors for E. coli BSI.

Results

We analyzed data from 33 cases and 1615 controls enrolled from 2007 through 2018. The median (IQR) age of cases was 47 (34–57) y and 24 (72.7%) were female. E. coli BSI was associated with (adjusted OR [aOR], 95% CI) increasing years of age (1.03, 1.01 to 1.05), female gender (2.20, 1.01 to 4.80), abdominal tenderness (2.24, 1.06 to 4.72) and urinary tract infection as a discharge diagnosis (3.71, 1.61 to 8.52). Of 31 isolates with antimicrobial susceptibility results, the prevalence of resistance was ampicillin 29 (93.6%), ceftriaxone three (9.7%), ciprofloxacin five (16.1%), gentamicin seven (22.6%) and trimethoprim-sulfamethoxazole 31 (100.0%).

Conclusions

In Tanzania, host risk factors for E. coli BSI were similar to those reported in high-resource settings and resistance to key antimicrobials was common.

The global prevalence and trend of human intestinal carriage of ESBL-producing Escherichia coli in the community

OBJECTIVES

Intestinal colonization by ESBL Escherichia coli and its association with community-acquired MDR infections is of great concern. This review determined the worldwide prevalence of human faecal ESBL E. coli carriage and its trend in the community over the past two decades.

METHODS

A systematic literature search was conducted using PubMed, EMBASE and Google Scholar to retrieve articles published between 1 January 2000 and 13 February 2020 that contained data on the prevalence of faecal carriage of ESBL E. coli among healthy individuals. A cumulative (for the whole period) meta-analysis was used to estimate the global and regional pooled prevalence rates. Articles were grouped into study periods of 3 years, and subgroup meta-analyses were undertaken to examine the global pooled prevalence over time.

RESULTS

Sixty-two articles covering 29 872 healthy persons were included in this meta-analysis. The cumulative (2003-18) global pooled prevalence of ESBL E. coli intestinal carriage in the community was 16.5% (95% CI 14.3%-18.7%; P  <  0.001). The pooled prevalence showed an upward trend, increasing from 2.6% (95% CI 1.6%-4.0%) in 2003-05 to 21.1% (95% CI 15.8%-27.0%) in 2015-18. Over the whole period, the highest carriage rate was observed in South-East Asia (27%; 95% CI 2.9%-51.3%), while the lowest occurred in Europe (6.0%; 95% CI 4.6%-7.5%).

CONCLUSIONS

Globally, an 8-fold increase in the intestinal carriage rate of ESBL E. coli in the community has occurred over the past two decades. Prevention of its spread may require new therapeutic and public health strategies.

Circulation of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli of Pandemic Sequence Types 131, 648, and 410 Among Hospitalized Patients, Caregivers, and the Community in Rwanda

Multi-drug resistant (MDR), gram-negative Enterobacteriaceae, such as Escherichia coli (E. coli) limit therapeutic options and increase morbidity, mortality, and treatment costs worldwide. They pose a serious burden on healthcare systems, especially in developing countries like Rwanda. Several studies have shown the effects caused by the global spread of extended-spectrum beta-lactamase (ESBL)-producing E. coli. However, limited data is available on transmission dynamics of these pathogens and the mobile elements they carry in the context of clinical and community locations in Sub-Saharan Africa. Here, we examined 120 ESBL-producing E. coli strains from patients hospitalized in the University Teaching Hospital of Butare (Rwanda), their attending caregivers as well as associated community members and livestock. Based on whole-genome analysis, the genetic diversification and phylogenetics were assessed. Moreover, the content of carried plasmids was characterized and investigated for putative transmission among strains, and for their potential role as drivers for the spread of antibiotic resistance. We show that among the 30 different sequence types (ST) detected were the pandemic clonal lineages ST131, ST648 and ST410, which combine high-level antimicrobial resistance with virulence. In addition to the frequently found resistance genes bla_CTX–M–15, tet(34), and aph(6)-Id, we identified csg genes, which are required for curli fiber synthesis and thus biofilm formation. Numerous strains harbored multiple virulence-associated genes (VAGs) including pap (P fimbriae adhesion cluster), fim (type I fimbriae) and chu (Chu heme uptake system). Furthermore, we found phylogenetic relationships among strains from patients and their caregivers or related community members and animals, which indicates transmission of pathogens. Also, we demonstrated the presence and potential transfer of identical/similar ESBL-plasmids in different strains from the Rwandan setting and when compared to an external plasmid. This study highlights the circulation of clinically relevant, pathogenic ESBL-producing E. coli among patients, caregivers and the community in Rwanda. Combining antimicrobial resistance with virulence in addition to the putative exchange of mobile genetic elements among bacterial pathogens poses a significant risk around the world.

Molecular characterization of ESBL- producing uropathogenic Escherichia coli recovered from urine samples of patients attending a University Teaching hospital in Nigeria

Infection of the urinary tract ranks as one of the most common infections affecting people worldwide and its treatment is made complicated by the rising incidence of antibiotic resistance. This study aimed to detect extended spectrum beta-lactamase (ESBL) genes and antibiotic resistance profile of uropathogenic Escherichia coli (E. coli) recovered from patients attending a University Teaching hospital in Nigeria. Uropathogenic E. coli isolates were obtained from the culture collection of Department of Microbiology and Parasitology of the University Teaching hospital for a period of four months (October 2019-January, 2020). Antibiotic susceptibility testing was done using the disc diffusion method while phenotypic ESBL production was detected using double disc synergy test (DDST). Detection of β-lactamase genes was done using Real-Time PCR. Forty-nine E. coli isolates were recovered from 120 urine samples, with 24 (49%) being ESBL positive. The resistance to antibiotics in the ESBL producers was: ciprofloxacin (100%), cefotaxime (100%), cefpodoxime (100%), tetracycline (95.7%), ceftazidime (56.7%), amoxicillin-clavulanate (50%), gentamicin (33.3%), and imipenem (0%). All the ESBL producers carried blaTEM, blaCTX-M-1 and blaCTX-M-9, 75% (18/24) carried blaSHV, while blaCTX-M-2, blaCTX-M-8 and blaCTX-M-25 groups were detected in 20.8% (5/24) of the isolates. There was co-occurrence of CTX-M, SHV and TEM β-lactamases in 79.2% (19/24) isolates, while five isolates (20.8%) co-harbored blaCTX-M and blaTEM. This study showed a high level of multidrug resistance and ESBL gene carriage in uropathogenic E. coli obtained in this study, suggesting a likely review of therapeutic options in the treatment of UTI to clamp down on the rising cases of antibiotic resistance.

Antimicrobial Surveillance for Bacterial Uropathogens in Ha'il, Saudi Arabia: A Five-Year Multicenter Retrospective Study

Objective

Urinary tract infections (UTIs) are among the most common infections that require antibiotic intervention. Antibiotic surveillance programs are crucial to assess resistance patterns of microorganisms associated with UTIs and to tailor antibiotic therapy accordingly. Therefore, the aim of the current study is to investigate the prevalence of uropathogens and their antimicrobial susceptibility patterns in Ha’il region.

Methods

We conducted a retrospective study in two main hospitals in Ha’il over a 5-year period (January 2015 to December 2019). Laboratory reports and clinical data of patients with a positive urine culture (≥10⁵ CFU/mL) were included in the study.

Results

A total of 428 patients were included in this study. The majority of positive cultures belonged to female patients (94.4%), adults (76.9%) and outpatients (74.3%). Generally, Escherichia coli was the most common pathogen (45%), followed by Klebsiella pneumoniae (17%) and Staphylococcus aureus (12%). Extended-spectrum β-lactamase (ESBL) strains of E. coli (15.7%) and K. pneumoniae (19.7%) showed resistance to most tested antibiotics, while almost all Gram-negative uropathogens including ESBL strains presented low resistance to cefoxitin, imipenem and meropenem. Most strains of Staphylococcus aureus and Enterococcus faecalis were resistant to trimethoprim/sulfamethoxazole including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecalis (VRE), whereas the activity of linezolid was monitored against almost all different strains of Gram-positive uropathogens.

Conclusion

This surveillance study which was conducted over a 5-year period in the Ha’il region revealed that the most common UTI-associated pathogen was E. coli. Based on the current sensitivity profiles obtained from this surveillance, carbapenems and linezolid can be considered as a first therapeutic choice treating UTIs in Ha’il caused by Gram-negative and positive uropathogens, respectively. Frequent targeted surveillance programs for antibiotic-resistant pathogens and their susceptibility profiles are crucial to enable tailored empirical treatment for patients.

Impact of ceftriaxone and temocillin on fecal abundance of extended-spectrum β-lactamase producing Escherichia coli in a mouse model

BACKGROUND

Gut colonization by ESBL-producing Enterobacteriaceae (ESBL-PE) is widespread and is promoted by antibiotic exposure. Higher fecal abundance of ESBL-PE promotes the dissemination of the bacteria in the environment and is associated with increased risk of infection. Ceftriaxone and temocillin are commonly used antibiotics with a different activity on gut flora. Their impact on fecal abundance of ESBL-producing Enterobacteriaceae has not been studied. The objective of this study was to compare the propensity of ceftriaxone and temocillin to modify the abundance of ESBL-producing Escherichia coli in feces of colonized mice.

METHODS

Mice received broad-spectrum antibiotics in order to disrupt their normal gut flora. A CTX-M-type ESBL-producing E. coli clinical isolate was then administered orally, leading to durable colonization. Thirty days later, mice received either temocillin or ceftriaxone with drinking water at a concentration simulating human intestinal exposure. Third-generation-cephalosporin resistant (3GCR) E. coli were enumerated in feces on selective medium before, 2 days and 10 days after the end of antibiotic exposure. The experiment was performed with two E. coli isolates with different temocillin minimum inhibitory concentrations.

RESULTS

Exposure to ceftriaxone induced an increase in the fecal abundance of 3GCR E. coli. In contrast, temocillin had no effect or transiently decreased the number of 3GCR E. coli. Results obtained with the two strains were similar.

CONCLUSION

Contrary to ceftriaxone, temocillin does not promote expansion of ESBL-producing E. coli in feces of colonized mice. Thus temocillin may be a therapeutic of choice when a temocillin-susceptible strain infection is suspected or proven to prevent the expansion of ESBL-PE in a previously colonized patient.

Measures used to assess the burden of ESBL-producing Escherichia coli infections in humans: a scoping review

BACKGROUND

ESBL-producing bacteria pose a serious challenge to both clinical care and public health. There is no standard measure of the burden of illness (BOI) of ESBL-producing Escherichia coli (ESBL-EC) in the published literature, indicating a need to synthesize available BOI data to provide an overall understanding of the impact of ESBL-EC infections on human health.

OBJECTIVES

To summarize the characteristics of BOI reporting in the ESBL-EC literature to (i) describe how BOI associated with antimicrobial resistance (AMR) is measured and reported; (ii) summarize differences in other aspects of reporting between studies; and (iii) highlight the common themes in research objectives and their relation to ESBL-EC BOI.

METHODS AND RESULTS

Two literature searches, run in 2013 and 2018, were conducted to capture published studies evaluating the BOI associated with ESBL-EC infections in humans. These searches identified 1723 potentially relevant titles and abstracts. After relevance screening of titles and abstracts and review of full texts, 27 studies were included for qualitative data synthesis. This review identified variability in the reporting and use of BOI measures, study characteristics, definitions and laboratory methods for identifying ESBL-EC infections.

CONCLUSIONS

Decision makers often require BOI data to make science-based decisions for the implementation of surveillance activities or risk reduction policies. Similarly, AMR BOI measures are important components of risk analyses and economic evaluations of AMR. This review highlights many limitations to current ESBL-EC BOI reporting, which, if improved upon, will ensure data accessibility and usefulness for ESBL-EC BOI researchers, decision makers and clinicians.

Impact of an Antibiotic Stewardship Program on the Incidence of Resistant Escherichia coli: A Quasi-Experimental Study

Infections caused by multidrug-resistant Gram-negative bacteria increase hospitalizations and mortality rates; antibiotic pressure increases resistance rates. We evaluated the impact of the antibiotics stewardship program (ASP) on Escherichia coli resistance rates, evaluating all antibiotic use and patients with positive cultures hospitalized between 2011 and 2018. Data on antibiotics were collected quarterly as the defined daily dose (DDD)/100 days hospitalization. In 2014, an intervention was introduced, targeting the reduction of overall antibiotic use as well as specifically targeting quinolones and other broad-spectrum antibiotics. Using interrupted time series analysis (ITS), we compared the rates and trends of antibiotic use and resistant E. coli. We included 6001 patients, 3182 pre-ASP and 2819 post-ASP. We observed significant changes in absolute numbers as well as in trends for use of DDD/100 days of all antibiotics by 31% from 76 to 52, and by 52% from 10.4 to 4.9 for quinolones. ITS demonstrated that before the ASP intervention, there was a slope pattern for increased E. coli resistance to antibiotics. This slope was reversed following the intervention for quinolones −1.52, aminoglycosides −2.04, and amoxicillin clavulanate (amox/clav) −1.76; the effect of the intervention was observed as early as three months after the intervention and continued to decrease over time until the end of the study, at 48 months. We conclude that the ASP can positively impact the resistance rate of Gram-negative infections over time, regardless of the targeted combination of antibiotics, if the overall use is reduced.