Factors that impact on the burden of Escherichia coli bacteraemia: multivariable regression analysis of 2011–2015 data from West London

Association of microbiological factors with mortality in Escherichia coli bacteraemia presenting with sepsis/septic shock: a prospective cohort study

OBJECTIVES

This study aimed to determine the association of Escherichia coli microbiological factors with 30-day mortality in patients with bloodstream infection (BSI) presenting with a dysregulated response to infection (i.e. sepsis or septic shock).

METHODS

Whole-genome sequencing was performed on 224 E coli isolates of patients with sepsis/septic shock, from 22 Spanish hospitals. Phylogroup, sequence type, virulence, antibiotic resistance, and pathogenicity islands were assessed. A multivariable model for 30-day mortality including clinical and epidemiological variables was built, to which microbiological variables were hierarchically added. The predictive capacity of the models was estimated by the area under the receiver operating characteristic curve (AUROC) with 95% confidence intervals (CI).

RESULTS

Mortality at day 30 was 31% (69 patients). The clinical model for mortality included (adjusted OR; 95% CI) age (1.04; 1.02-1.07), Charlson index ≥3 (1.78; 0.95-3.32), urinary BSI source (0.30; 0.16-0.57), and active empirical treatment (0.36; 0.11-1.14) with an AUROC of 0.73 (95% CI, 0.67-0.80). Addition of microbiological factors selected clone ST95 (3.64; 0.94-14.04), eilA gene (2.62; 1.14-6.02), and astA gene (2.39; 0.87-6.59) as associated with mortality, with an AUROC of 0.76 (0.69-0.82).

DISCUSSION

Despite having a modest overall contribution, some microbiological factors were associated with increased odds of death and deserve to be studied as potential therapeutic or preventive targets.

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.

Clinical presentation and antimicrobial resistance of invasive Escherichia coli disease in hospitalized older adults: a prospective multinational observational study

BACKGROUND

Clinical data characterizing invasive Escherichia coli disease (IED) are limited. We assessed the clinical presentation of IED and antimicrobial resistance (AMR) patterns of causative E. coli isolates in older adults.

METHODS

EXPECT-2 (NCT04117113) was a prospective, observational, multinational, hospital-based study conducted in patients with IED aged ≥ 60 years. IED was determined by the microbiological confirmation of E. coli from blood; or by the microbiological confirmation of E. coli from urine or an otherwise sterile body site in the presence of requisite criteria of systemic inflammatory response syndrome (SIRS), Sequential Organ Failure Assessment (SOFA), or quick SOFA (qSOFA). The primary outcomes were the clinical presentation of IED and AMR rates of E. coli isolates to clinically relevant antibiotics. Complications and in-hospital mortality were assessed through 28 days following IED diagnosis.

RESULTS

Of 240 enrolled patients, 80.4% had bacteremic and 19.6% had non-bacteremic IED. One-half of infections (50.4%) were community-acquired. The most common source of infection was the urinary tract (62.9%). Of 240 patients, 65.8% fulfilled ≥ 2 SIRS criteria, and 60.4% had a total SOFA score of ≥ 2. Investigator-diagnosed sepsis and septic shock were reported in 72.1% and 10.0% of patients, respectively. The most common complication was kidney dysfunction (12.9%). The overall in-hospital mortality was 4.6%. Of 299 E. coli isolates tested, the resistance rates were: 30.4% for trimethoprim-sulfamethoxazole, 24.1% for ciprofloxacin, 22.1% for levofloxacin, 16.4% for ceftriaxone, 5.7% for cefepime, and 4.3% for ceftazidime.

CONCLUSIONS

The clinical profile of identified IED cases was characterized by high rates of sepsis. IED was associated with high rates of AMR to clinically relevant antibiotics. The identification of IED can be optimized by using a combination of clinical criteria (SIRS, SOFA, or qSOFA) and culture results.

The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans

Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostic, prevention and treatment is still lacking. We used a collection of 912 BSI and 370 commensal E. coli isolates collected in France over a 17-year period (2000-2017). We compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity continuously increased through 1980, 2000, to 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.

Hospital-acquired E. coli bacteraemia at a large UK NHS Trust. A return towards baseline following implementation of a 5-year quality improvement programme

Introduction

Until recently, healthcare-associated E. coli bacteraemia was a neglected area of infection prevention and control (IPC), despite a 30-day mortality of 15-20%. Recently, the UK Department of Health (DH) introduced a target to reduce hospital-acquired E. coli bacteraemias by 50% over a five-year period. Following implementation of multifaceted and multidisciplinary interventions, the aim of this study was to determine its impact on achieving this target.

Methods

From April 2017 to March 2022, consecutive hospital-acquired E. coli bacteraemic inpatients within Barts Health NHS Trust were prospectively studied. Using quality improvement methodology, and implementing the plan, do, study, act (PDSA) cycle at each stage, antibiotic prophylaxis for high-risk procedures were modified and 'good practice' interventions around medical devices introduced. Characteristics of bacteraemic patients were analysed and trends in bacteraemic episodes recorded. Statistical analysis was undertaken in Stata SE (version 16).

Results

There were 770 patients and 797 episodes of hospital-acquired E. coli bacteraemias. Following a baseline of 134 episodes in 2017-18, this peaked at 194 in 2019-20 before dropping to 157 in 2020-21 and 159 in 2021-22. Most hospital-acquired E. coli bacteraemias occurred in those aged > 50, 551 (69.1%), with the highest proportion occurring in those age > 70, 292 (36.6%). Hospital-acquired E. coli bacteraemia occurred more commonly between October to December.Most episodes occurred in either medicine or care of the elderly patients, 345 (43.3%), specialist surgery, 141 (17.7%), haematology/oncology, 127 (15.9%) and patients requiring critical care, 108 (13.6%). The urinary tract, 336 (42.2%), both catheter and non-catheter associated, was the commonest sites of infection. 175 (22.0%) of E. coli bacteraemic isolates were extended spectrum beta lactamase (ESB) producing. Co-amoxiclav resistance was 315 (39.5%), ciprofloxacin resistance 246 (30.9%) and gentamicin resistance 123 (15.4%). At 7 days, 77 patients (9.7%; 95% CI 7.4-12.2%) died and by 30 days this had risen to 129 (16.2%; 95% CI 13.7-19.9%).

Conclusion

Despite implementation of quality improvement (QI) interventions, it was not possible to achieve a 50% reduction from baseline although an 18% reduction was achieved from 2019-20 onwards. Our work highlights the importance of antimicrobial prophylaxis and medical device 'good practice'. Over time, these interventions, if properly implemented, could further reduce healthcare-associated E. coli bacteraemic infection.

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.

Evaluation of an extracorporeal ozone-based bactericide system for the treatment of Escherichia coli sepsis

BACKGROUND

Sepsis is associated with substantial mortality rates. Antibiotic treatment is crucial, but global antibiotic resistance is now classified as one of the top ten global public health risks facing humanity. Ozone (O₃) is an inorganic molecule with no evident function in the body. We investigated the bactericide properties of ozone, using a novel system of extracorporeal ozone blood treatment. We hypothesized that ozone would decrease the concentration of viable Escherichia coli (E. coli) in human whole blood and that the system would be technically feasible and physiologically tolerable in a clinically relevant model of E. coli sepsis in swine.

METHODS

The E. coli strain B09-11822, a clinical isolate from a patient with septic shock was used. The in vitro study treated E. coli infected human whole blood (n = 6) with ozone. The in vivo 3.5-h sepsis model randomized swine to E. coli infusion and ozone treatment (n = 5) or E. coli infusion and no ozone treatment (n = 5). Live E. coli, 5 × 10⁷ colony-forming units (CFU/mL) was infused in a peripheral vein. Ozone treatment was initiated with a duration of 30 min after 1.5 h.

RESULTS

The single pass in vitro treatment decreased E. coli by 27%, mean 1941 to 1422 CFU/mL, mean of differences - 519.0 (95% CI - 955.0 to - 82.98, P = 0.0281). pO₂ increased (95% CI 31.35 to 48.80, P = 0.0007), pCO₂ decreased (95% CI - 3.203 to - 1.134, P = 0.0069), oxyhemoglobin increased (95% CI 1.010 to 3.669, P = 0.0113). Methemoglobin was not affected. In the sepsis model, 9/10 swine survived. One swine randomized to ozone treatment died from septic shock before initiation of the treatment. Circulatory, respiratory, and metabolic parameters were not affected by the ozone treatment. E. coli in arterial blood, in organs and in aerobic and anaerobic blood cultures did not differ. Hemoglobin, leucocytes, and methemoglobin were not affected by the treatment.

CONCLUSIONS

Ozone decreased the concentration of viable E. coli in human whole blood. The system was technically feasible and physiologically tolerable in porcine sepsis/septic shock and should be considered for further studies towards clinical applications.

Bacterial genotypic and patient risk factors for adverse outcomes in Escherichia coli bloodstream infections: a prospective molecular epidemiological study

OBJECTIVES

Escherichia coli bloodstream infections have shown a sustained increase in England, for reasons that are unknown. Furthermore, the contribution of MDR lineages such as ST131 to overall E. coli disease burden and outcome is undetermined.

METHODS

We genome-sequenced E. coli blood isolates from all patients with E. coli bacteraemia in north-west London from July 2015 to August 2016 and assigned MLST genotypes, virulence factors and AMR genes to all isolates. Isolate STs were then linked to phenotypic antimicrobial susceptibility, patient demographics and clinical outcome data to explore relationships between the E. coli STs, patient factors and outcomes.

RESULTS

A total of 551 E. coli genomes were analysed. Four STs (ST131, 21.2%; ST73, 14.5%; ST69, 9.3%; and ST95, 8.2%) accounted for over half of cases. E. coli genotype ST131-C2 was associated with phenotypic non-susceptibility to quinolones, third-generation cephalosporins, amoxicillin, amoxicillin/clavulanic acid, gentamicin and trimethoprim. Among 300 patients from whom outcome was known, an association between the ST131-C2 lineage and longer length of stay was detected, although multivariable regression modelling did not demonstrate an association between E. coli ST and mortality. Several unexpected associations were identified between gentamicin non-susceptibility, ethnicity, sex and adverse outcomes, requiring further research.

CONCLUSIONS

Although E. coli ST was associated with defined antimicrobial non-susceptibility patterns and prolonged length of stay, E. coli ST was not associated with increased mortality. ST131 has outcompeted other lineages in north-west London. Where ST131 is prevalent, caution is required when devising empiric regimens for suspected Gram-negative sepsis, in particular the pairing of β-lactam agents with gentamicin.

Health Care Costs of Target Attainment for Beta-Lactam Antibiotics in Critically Ill Patients: A Retrospective Analysis of the EXPAT Study

BACKGROUND

Optimizing beta-lactam antibiotic treatment is a promising method to reduce the length of intensive care unit (ICU) stay and therefore reduce ICU costs. We used data from the EXPAT trial to determine whether beta-lactam antibiotic target attainment is a cost determinant in the ICU.

METHODS

Patients included in the EXPAT trial were divided into target attainment and target nonattainment based on serum antibiotic levels. All hospital costs were extracted from the hospital administration system and categorized.

RESULTS

In total, 79 patients were included in the analysis. Target attainment showed a trend toward higher total ICU costs (€44,600 versus €28,200, P = 0.103). This trend disappeared when correcting for ICU length of stay (€2680 versus €2700). Renal replacement therapy was the most important cost driver.

CONCLUSIONS

Target attainment for beta-lactam antibiotics shows a trend toward higher total costs in ICU patients, which can be attributed to the high costs of a long stay in the ICU and renal replacement therapy.

Antimicrobial Resistance and Molecular Epidemiology of Escherichia coli From Bloodstream Infection in Shanghai, China, 2016-2019

Background: Bloodstream infections are recognized as important nosocomial infections. Escherichia coli (E. coli) is the most prevalent Gram-negative bacillary pathogen causing bloodstream infections (BSIs). This retrospective study investigated drug susceptibility and molecular epidemiology of E. coli isolated from patients with BSI in Shanghai, China.

Methods: We collected E. coli isolated from the blood cultures of patients with BSI between January 2016 and December 2019. We randomly selected 20 strains each year to investigate antimicrobial resistance, resistance genes, and molecular epidemiological characteristics. Antimicrobial susceptibility testing was performed by the disk diffusion method. PCR was performed to detect extended-spectrum β-lactamases (ESBLs), carbapenemase genes, and housekeeping genes, and phyloviz was applied to analyze multilocus sequence typing (MLST).

Results: Penicillins, first- and second-generation cephalosporins and fluoroquinolones have high resistance rates (>60%). Among the 80 randomly selected strains, 47 (58.8%) produced ESBLs, and one produced carbapenemase. Sequencing of resistance genes identified bla_CTX−M−14 (34%, 16/47), bla_CTX−M−15 (23.4%, 11/47) and bla_CTX−M−27 (14.8%, 7/47) as the most prevalent genotypes of ESBLs. ST131 (14/80) was the most prevalent sequence type (ST), followed by ST1193 (10/80), ST648 (7/80).

Conclusions: Our findings suggest that amikacin, carbapenems, and piperacillin-tazobactam have relatively low resistance rates and may be the preferred antibiotic regimens for empiric therapy. ST131 and bla_CTX−M−14 are still the main prevalent in Shanghai with a rapid increase in the occurrence of ST1193 is rapidly increasing and more diverse bla_CTX genes.

Exploring temporal trends and risk factors for resistance in Escherichia coli-causing bacteraemia in England between 2013 and 2018: an ecological study

BACKGROUND

Escherichia coli are Gram-negative bacteria associated with an increasing burden of antimicrobial resistance (AMR) in England.

OBJECTIVES

To create a comprehensive epidemiological picture of E. coli bacteraemia resistance trends and risk factors in England by linking national microbiology data sources and performing a longitudinal analysis of rates.

METHODS

A retrospective observational study was conducted on all national records for antimicrobial susceptibility testing on E. coli bacteraemia in England from 1 January 2013 to 31 December 2018 from the UK Health Security Agency (UKHSA) and the BSAC Resistance Surveillance Programme (BSAC-RSP). Trends in AMR and MDR were estimated using iterative sequential regression. Logistic regression analyses were performed on UKHSA data to estimate the relationship between risk factors and AMR or MDR in E. coli bacteraemia isolates.

RESULTS

An increase in resistance rates was observed in community- and hospital-onset bacteraemia for third-generation cephalosporins, co-amoxiclav, gentamicin and ciprofloxacin. Among community-acquired cases, and after adjustment for other factors, patients aged >65 years were more likely to be infected by E. coli isolates resistant to at least one of 11 antibiotics than those aged 18-64 years (OR: 1.21, 95% CI: 1.18-1.25; P < 0.05). In hospital-onset cases, E. coli isolates from those aged 1-17 years were more likely to be resistant than those aged 18-64 years (OR: 1.33, 95% CI: 1.02-1.73; P < 0.05).

CONCLUSIONS

Antibiotic resistance rates in E. coli-causing bacteraemia increased between 2013 and 2018 in England for key antimicrobial agents. Findings of this study have implications for guiding future policies on a prescribing of antimicrobial agents, for specific patient populations in particular.

A nationwide population-based study of Escherichia coli bloodstream infections: incidence, antimicrobial resistance and mortality

OBJECTIVES

Escherichia coli is the leading cause of bloodstream infection (BSI). The incidence of E. coli BSI caused by antibiotic-resistant strains is increasing. We aimed to describe the nationwide incidence and resistance profile of E. coli BSI in Israel and its impact on mortality, to compare E. coli BSI mortality to all-cause mortality, and community-onset to hospital-onset E. coli BSI.

METHODS

We used mandatory BSI surveillance reports submitted by all Israeli hospitals to the Ministry of Health and the national death registry. All E. coli BSI from January 1, 2018, to December 31, 2019 in patients ages 18 and over were included.

RESULTS

A total of 11 113 E. coli BSI occurred in 10 218 patients; 85% (9012/10 583) were community onset. Median age was 76 (IQR 65-85), and 57% (6304/11 113) of cases occurred in women. The annual incidence was 92.5 per 100,000 population. Antibiotic resistance was frequent and significantly more common in hospital-onset than in community-onset BSI; 65% (1021/1571) vs 45% (4049/9012) were multidrug-resistant (MDR) (p<0.001). The case-fatality rate (CFR) was higher following hospital-onset BSI than community-onset: 23% (276/1214) vs 12% (926/7620) at 14 days, 31% (378/1214) vs 16% (1244/7620) at 30 days, and 55% (418/766) vs 34% (1645/4903) at 1 year (p<0.001 for all comparisons). The 1-year-CFR was 47% (1258/2707) for MDR vs 28% (928/3281) for non-MDR (p<0.001). The annual mortality rate was 31.0 per 100,000 population, comprising 4.2% (31.0/734.8) of all causes of deaths.

CONCLUSIONS

E. coli BSI carries a high burden, with a large proportion of MDR isolates, which are associated with increased incidence and CFR.

Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom

Antimicrobial resistance in enteric or urinary Escherichia coli is a risk factor for invasive E. coli infections. Due to widespread trimethoprim resistance amongst urinary E. coli and increased bacteraemia incidence, a national recommendation to prescribe nitrofurantoin for uncomplicated urinary tract infection was made in 2014. Nitrofurantoin resistance is reported in <6% urinary E. coli isolates in the UK, however, mechanisms underpinning nitrofurantoin resistance in these isolates remain unknown. This study aimed to identify the genetic basis of nitrofurantoin resistance in urinary E. coli isolates collected from north west London and then elucidate resistance-associated genetic alterations in available UK E. coli genomes. As a result, an algorithm was developed to predict nitrofurantoin susceptibility. Deleterious mutations and gene-inactivating insertion sequences in chromosomal nitroreductase genes nfsA and/or nfsB were identified in genomes of nine confirmed nitrofurantoin-resistant urinary E. coli isolates and additional 11 E. coli isolates that were highlighted by the prediction algorithm and subsequently validated to be nitrofurantoin-resistant. Eight categories of allelic changes in nfsA, nfsB, and the associated gene ribE were detected in 12412 E. coli genomes from the UK. Evolutionary analysis of these three genes revealed homoplasic mutations and explained the previously reported order of stepwise mutations. The mobile gene complex oqxAB, which is associated with reduced nitrofurantoin susceptibility, was identified in only one of the 12412 genomes. In conclusion, mutations and insertion sequences in nfsA and nfsB were leading causes of nitrofurantoin resistance in UK E. coli. As nitrofurantoin exposure increases in human populations, the prevalence of nitrofurantoin resistance in carriage E. coli isolates and those from urinary and bloodstream infections should be monitored.

Clinical Characteristics of Patients and Whole Genome Sequencing-Based Surveillance of Escherichia coli Community-Onset Bloodstream Infections at a Non-tertiary Hospital in CHINA

Background:Escherichia coli is the most common pathogens in patients with community-onset blood stream infections (COBSI). Knowledge of the epidemiology of this disease is crucial to improve allocation of health resources, formulate isolation strategies that prevent transmission, and guide empirical antibiotic therapy.

Methods: This retrospective observational study examined patients with E. coli COBSI (EC-COBSI) at a non-tertiary hospital in China. Whole-genome sequencing and analysis of the isolates was performed. The relationships of clinical variables with antimicrobial resistance and the genetic background of the isolates were examined.

Results: There were 148 isolates in patients with EC-COBSI. All isolates were susceptible to ceftazidime/avibactam, carbapenems, and tigecycline; 35.1% were positive for extended spectrum β-lactamase (ESBL+); and bla_CTX–M–14 was the most common ESBL gene. Patients with ESBL- isolates were more likely to receive appropriate empiric treatment than those with ESBL+ isolates (61.5% vs. 91.4%, p < 0.001), but these two groups had similar mortality rates. The overall 30-day mortality rate was 9.5%. Phylogenetic analysis showed that the isolates were diverse, and that the main sequence types (STs) were ST95, ST131, and ST69. Intra-abdominal infection was the primary source of disease, and isolates from these patients had lower frequencies of virulence genes.

Conclusion: The mortality rate of patients with EC-COBSI was unrelated to ESBL status of the isolates. Most isolates had low resistance to most of the tested antimicrobial agents. The isolates were diverse, and multiple strains were related. Prevention and control of EC-COBSI should target prevention of patient colonization and the living environment.

Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK

Background

The incidence of Gram-negative bloodstream infections (BSIs), predominantly caused by Escherichia coli and Klebsiella species, continues to increase; however, the causes of this are unclear and effective interventions are therefore hard to design.

Methods

In this study, we sequenced 3468 unselected isolates over a decade in Oxfordshire (UK) and linked this data to routinely collected electronic healthcare records and mandatory surveillance reports. We annotated genomes for clinically relevant genes, contrasting the distribution of these within and between species, and compared incidence trends over time using stacked negative binomial regression.

Results

We demonstrate that the observed increases in E. coli incidence were not driven by the success of one or more sequence types (STs); instead, four STs continue to dominate a stable population structure, with no evidence of adaptation to hospital/community settings. Conversely in Klebsiella spp., most infections are caused by sporadic STs with the exception of a local drug-resistant outbreak strain (ST490). Virulence elements are highly structured by ST in E. coli but not Klebsiella spp. where they occur in a diverse spectrum of STs and equally across healthcare and community settings. Most clinically hypervirulent (i.e. community-onset) Klebsiella BSIs have no known acquired virulence loci. Finally, we demonstrate a diverse but largely genus-restricted mobilome with close associations between antimicrobial resistance (AMR) genes and insertion sequences but not typically specific plasmid replicon types, consistent with the dissemination of AMR genes being highly contingent on smaller mobile genetic elements (MGEs).

Conclusions

Our large genomic study highlights distinct differences in the molecular epidemiology of E. coli and Klebsiella BSIs and suggests that no single specific pathogen genetic factors (e.g. AMR/virulence genes/sequence type) are likely contributing to the increasing incidence of BSI overall, that association with AMR genes in E. coli is a contributor to the increasing number of E. coli BSIs, and that more attention should be given to AMR gene associations with non-plasmid MGEs to try and understand horizontal gene transfer networks.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-021-00947-2.

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.

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.

National database study of trends in bacteraemia aetiology among children and adults in Japan: a longitudinal observational study

OBJECTIVES

Domestic epidemiological studies are needed to ascertain the disease burden of bacteraemia in individual countries. This study aimed to evaluate the domestic trends in paediatric and adult bacteraemia in Japan.

SETTING

Laboratory-based surveillance was used to obtain data from 592 hospitals located throughout Japan.

PARTICIPANTS

The study was conducted using the results of 827 780 and 3 512 524 blood culture tests obtained from children and adults, respectively, between January 2010 and December 2016.

OUTCOME MEASURES

We analysed the temporal trends in specific bacterial species (Staphylococcus aureus, Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus agalactiae, Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Haemophilus influenzae, Listeria monocytogenes and Neisseria meningitidis) detected from the blood cultures of children and adults. For children aged ≤2 years, the data were analysed for each year of age. The proportions of bacteraemia-positive results among the patients were also evaluated.

RESULTS

The number of bacteraemia-positive samples over the study period was 47,125/827,855 (5.7%) in children and 959,765/3,513,885 (27.3%) in adults. S. pneumoniae was the most frequent cause of bacteraemia in children in 2010. However, after 2011, S. aureus bacteraemia was the most frequent, followed by S. pneumoniae and E. coli. E. coli bacteraemia showed significant increases in both children and adults. In children, S. pneumoniae and H. influenzae bacteraemia decreased from 2010 to 2013. However, S. pneumoniae bacteraemia case numbers stabilised from 2013, whereas H. influenzae bacteraemia cases continued to decrease until 2016.

CONCLUSION

The results suggest that the introduction of the 13-valent pneumococcal conjugate vaccine did not substantially affect disease occurrence. In contrast to the decreasing trends in H. influenzae and S. pneumoniae bacteraemia, S. aureus, E. coli and S. agalactiae bacteraemia showed increasing trends. These findings shed light on recent temporal trends in bacteraemia in both children and adults in Japan.

Risk factors and diagnostic markers for Escherichia coli bloodstream infection in older patients

OBJECTIVE

To investigate risk factors for Escherichia coli (E. coli) bloodstream infection (BSI) in older patients and the diagnostic accuracy of laboratory parameters.

METHODS

The electronic medical records of patients aged 60 years and above who were admitted with a serious condition were extracted. Propensity score matching (PSM) was used to ensure that the included patients had similar baseline clinical features. Multiple regression analysis was used to identify risk factors for E. coli BSI and extended-spectrum β-lactamase (ESBL)-producing E. coli BSI. Receiver operating characteristic (ROC) curve analysis was performed to determine the diagnostic utility of relevant laboratory indicators.

RESULTS

After PSM, 508 patients were included: 254 patients with E. coli BSI and 254 control patients. Bile duct stone (adjusted odds ratio [aOR] 5.131), kidney stone (aOR 3.678), and urinary system infection (aOR 3.173) were independent risk factors for E. coli BSI. Prior exposure to cephems (aOR 3.782) and drainage tube placement (aOR 2.572) were independent risk factors for ESBL-producing E. coli BSI. Serum procalcitonin (PCT) yielded the highest area under the curve (0.783) and the best cut-off value (1.3 ng/ml).

CONCLUSION

Bile duct stone, kidney stone, and urinary system infection must be detected and treated early, in order to prevent E. coli BSI in older patients. Further, administration of cephems and invasive procedures must be undertaken with caution, in order to reduce the risk of BSI with ESBL-producing E. coli. Finally, serum PCT level has potential as diagnostic marker for E. coli BSI in older individuals.

Extended-Spectrum-β-Lactamase- and Plasmid AmpC-Producing Escherichia coli Causing Community-Onset Bloodstream Infection: Association of Bacterial Clones and Virulence Genes with Septic Shock, Source of Infection, and Recurrence

Invasive infections due to extended-spectrum-β-lactamase- and pAmpC-producing Escherichia coli (ESBL/pAmpC-EC) are an important cause of morbidity, often caused by the high-risk clone sequence type (ST131) and isolates classified as extraintestinal pathogenic E. coli (ExPEC). The relative influence of host immunocompetence versus microbiological virulence factors in the acquisition and outcome of bloodstream infections (BSI) is poorly understood. Herein, we used whole-genome sequencing on 278 blood culture isolates of ESBL/pAmpC-EC from 260 patients with community-onset BSI collected from 2012 to 2015 in Stockholm to study the association of virulence genes, sequence types, and antimicrobial resistance with severity of disease, infection source, ESBL/pAmpC-EC BSI low-risk patients, and patients with repeated episodes. ST131 subclade C2 comprised 29% of all patients. Factors associated with septic shock in multivariable analysis were patient host factors (hematologic cancer or transplantation and reduced daily living activity), presence of the E. coli virulence factor iss (increased serum survival), absence of phenotypic multidrug resistance, and absence of the genes pap and hsp Adhesins, particularly pap, were associated with urinary tract infection (UTI) source, while isolates from post-prostate biopsy sepsis had a low overall number of virulence operons, including adhesins, and commonly belonged to ST131 clades A, B, and subclade C1, ST1193, and ST648. ST131 was associated with recurrent episodes. In conclusion, the most interesting finding is the association of iss with septic shock. Adhesins are important for UTI pathogenesis, while otherwise low-pathogenic isolates from the microbiota can cause post-prostate biopsy sepsis.

Follow-up blood cultures in Gram-negative bacilli bacteremia: are they needed for critically ill patients?

BACKGROUND

Gram-negative bacilli bacteremias (GNB-Bs) represent a major cause of morbidity and mortality in Intensive Care Unit (ICU) patients. Aim of this study was to investigate the role of follow-up blood cultures (FUBCs) and the clinical significance of persistent bacteremia (PB) in these settings.

METHODS

We retrospectively analyzed clinical data and outcome of GNB-Bs that occurred in ICU patients over a span of 1 year. In particular we sought information on development and clinical details of PB, defined as repeatedly positive FUBCs after ≥96 hours of appropriate antibiotic treatment and ≥48 hours after removal of endovascular devices.

RESULTS

Among 307 ICU patients, 69 (22.4%) developed 107 GNB-Bs. Of these, 78 (73%) could be eventually analyzed: 50 of 78 (64.1%) were non-PBs from 26 patients and 28 of 78 (35.9%) were PBs from 23 patients. Duration of fever and bacteremia, time to procalcitonin normalization and weaning from vasopressors were longer in episodes of PBs than non-PBs (P=0.04, P<0.001, P=0.02 and P=0.004, respectively). Primary bacteremia was more frequent in non-PBs than in PBs (29 of 50, 58% vs. 3/28, 10.7%, P=0.0001), whereas septic thrombus infection (STI) was the source of infection in 14 of 28 (50%). Finally, clinical features and 30-day mortality did not differ between patients with PB and those who developed only non-PB episodes.

CONCLUSIONS

Among our ICU patients, more than one third of GNB-Bs for which FUBCs were performed resulted PB. This condition is often associated with the presence of STI; therefore, FUBCs seem useful for the optimal management of GNB in this clinical setting.

Burden of bacterial bloodstream infection-a brief update on epidemiology and significance of multidrug-resistant pathogens

BACKGROUND

Bloodstream infections comprise a wide variety of pathogens and clinical syndromes with considerable overlap with similar syndromes of non-bacteraemic infections and diverse risk factors, therapeutic implications and outcomes. Yet, this heterogeneous 'entity' has the advantage to be pathogen-defined compared with the broad and even more heterogeneous entity 'sepsis', and so has become helpful for clinicians and epidemiologists for research and surveillance purposes. The increasing availability of population-based and large multicentre well-defined cohort studies should allow us to assess with much confidence and in detail its burden, the significance of antimicrobial resistance, and areas of uncertainty regarding further epidemiological evolution and optimized treatment regimens.

AIM

To review key aspects of bloodstream infection epidemiology and burden, and summarize recent news and questions concerning critical developments.

SOURCES

Peer-reviewed articles based on the search terms 'bloodstream infection' and 'bacteremia' combined with the terms 'epidemiology' and 'burden'. The emphasis was on new information from studies in adult patients and on the added burden due to pathogen resistance to first- and second-line antimicrobial agents.

CONTENT

Topics covered include recent developments in the epidemiology of bloodstream infection due to key pathogens and published information about the relevance of resistance for patient outcomes.

IMPLICATIONS

Despite the availability of population-based studies and an increasing number of large well-defined multicentre cohort studies, more surveillance and systematic data on bloodstream infection epidemiology at regional level and in resource-limited settings may be needed to better design new methods for prevention and define the need for and further develop optimized therapeutic strategies.