Prolonged colonisation with Escherichia coli O25:ST131 versus other extended-spectrum beta-lactamase-producing E. coli in a long-term care facility with high endemic level of rectal colonisation, the Netherlands, 2013 to 2014

Longitudinal molecular analysis of clinical and fecal Escherichia coli isolates at a Veterans Affairs Medical Center in Minnesota, USA, 2012-2019

Introduction

Extraintestinal Escherichia coli infections represent a growing public health threat, However, current studies often overlook important factors such as temporal patterns of infection, phylogenetic and clonal background, or the host gut E. coli population, despite their likely significance.

Methods

In this study, we analyzed >7000 clinical E. coli isolates from patients at the Minneapolis Veterans Affairs Health Care System (2012-2019), and concurrent fecal E. coli from uninfected veterans. We assessed phylogenetic group distribution, membership in selected sequence types (STs), and subsets thereof-including the pandemic, resistance-associated ST131-H30R, and ST1193 lineages-and strain type, as defined by pulsed-field gel electrophoresis. We then analyzed these features alongside the temporal patterns of infection in individual hosts.

Results

The H30R lineage emerged as the leading lineage, both overall and among fluoroquinolone-resistant isolates, with ST1193 following among fluoroquinolone-resistant isolates. Recurrences were common, occurring in 31% of subjects and 41% of episodes, and often multiple and delayed/prolonged (up to 23 episodes per subject; up to 2655d post-index). Remarkably, these recurrences typically involved the subject's index strain (63% of recurrences), even when affecting extra-urinary sites. ST131, H30R, ST1193, and fluoroquinolone-resistant strains generally caused significantly more recurrences than did other strains, despite similar recurrence intervals. ST131 strain types shifted significantly over the study period. Infection-causing strains were commonly detectable in host feces at times other than during an infection episode; the likelihood of detection varied with surveillance intensity and proximity to the infection. H30R and ST1193 were prominent causes of fecal-clinical clonal overlap.

Discussion

These findings provide novel insights into the temporal and clonal characteristics of E. coli infections in veterans and support efforts to develop anti-colonization interventions.

Longitudinal carriage of antimicrobial resistant Enterobacterales in healthy individuals in Ireland - Assessing the impact of recreational water use on duration of carriage

The increasing prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales (ESBL-PE) and carbapenemase-producing Enterobacterales (CPE) is a major public health concern worldwide. Despite the associated risk of infection from gut colonisation with a resistant Enterobacterales, the incidence and duration of carriage in healthy individuals is poorly studied. This "persistence study" is the first in Ireland to assess the longitudinal carriage of ESBL-PE and CPE in healthy individuals. A cohort of 45 participants, 22 of whom were colonised with ESBL-PE, was recruited from a recently completed point prevalence study that investigated colonisation in recreational water users (WU) versus controls. Six bi-monthly faecal samples per participant were analysed for CPE and ESBL-PE over one year and the relationship between persistent colonisation and exposure to natural waters was investigated. For 11 of 45 participants (24.4 %) ESBL-E. coli (ESBL-EC) was detected in at least one sample. Genomic analysis revealed that six participants harboured the same ESBL-EC strains as identified in the preceding study. ESBL-EC persisted in the gut for a median duration of 10.3 months (range 4-23 months), consistent with previous research. Five participants (11.1 %) carried ESBL-EC for the entire study year. The carbapenemase gene blaIMI-2 was detected once. Colonisation was higher in water users during the non-bathing season (n = 10, November 2021-April 2022), than during the bathing season (n = 5, May 2022-September 2022) [relative risk 1.99 (95 % CI 0.34-11.71)]. However, overall WU were less likely to be colonised with ESBL-EC than controls (19 % vs 25 % respectively, RR 0.76, CI 0.24-2.34). Further research is warranted to better understand the factors influencing the persistence of gut colonisation with ESBL-EC and CPE and to what extent bathing water quality impacts colonisation for those regularly exposed.

The scope of antimicrobial resistance in residential aged care facilities determined through analysis of Escherichia coli and the total wastewater resistome

IMPORTANCE

Antimicrobial resistance (AMR) is a global threat that imposes a heavy burden on our health and economy. Residential aged care facilities (RACFs), where frequent inappropriate antibiotic use creates a selective environment that promotes the development of bacterial resistance, significantly contribute to this problem. We used wastewater-based epidemiology to provide a holistic whole-facility assessment and comparison of antimicrobial resistance in two RACFs and a retirement village. Resistant Escherichia coli, a common and oftentimes problematic pathogen within RACFs, was isolated from the wastewater, and the phenotypic and genotypic AMR was determined for all isolates. We observed a high prevalence of an international high-risk clone, carrying an extended-spectrum beta-lactamase in one facility. Analysis of the entire resistome also revealed a greater number of mobile resistance genes in this facility. Finally, both facilities displayed high fluoroquinolone resistance rates-a worrying trend seen globally despite measures in place aimed at limiting their use.

Emergence of ST1193 Clone in Maternal and Neonatal ESBL-Producing E. coli Isolates

Objective

The emerging epidemic of extended-spectrum β-lactamase-producing E. coli (ESBL-EC) is a global public health crisis. ESBL-EC infections are increasing worldwide and contribute to morbidity and mortality among newborn infants. However, the antimicrobial resistance characteristics and clonal transmission of maternal and neonatal ESBL-EC isolates need to be further deciphered.

Materials and Methods

We performed phenotypic and genotypic characterization of 33 ESBL-EC isolates from pregnant women and newborn during 2019-2020.

Results

Minimum inhibitory concentrations of 17 antimicrobial agents showed that all isolates were multidrug-resistant (MDR) and had a resistance rate of 100% to ampicillin, and mild resistance to florfenicol, gentamicin, ceftazidime, and amoxicillin-clavulanate. Additionally, imipenem, meropenem, polymyxin, and tigecycline exhibited good activity against the tested ESBL-EC isolates with low MIC50 (0.06-1 μg/mL) and MIC90 (0.06-1 μg/mL). Whole genome sequencing indicated that ESBL-EC isolates contained diverse antimicrobial resistant genes (blaCTX-M, blaTEM, blaSHV, tetA, etc.) and toxin genes (ompA, csg, fimH, hybtA, etc.). blaCTX-M genes were the main ESBL genotype. ST1193 (18.2%) was the second most abundant ST among the ESBL-EC isolates (ST131 was the most common, with 30.3%), and this is the first report of its mother-to-infant colonization transmission in China.

Conclusion

These findings revealed the occurrence of high-risk ST1193 clone among ESBL-EC isolates from pregnant women and newborn colonization in China. Further national or regional multicenter studies are needed to assess the dissemination and evolution of ESBL-EC ST1193 clone as a nosocomial pathogen in China.

Commensal Fitness Advantage May Contribute to the Global Dissemination of Multidrug-Resistant Lineages of Bacteria-The Case of Uropathogenic E. coli

It is widely accepted that favorable fitness in commensal colonization is one of the prime facilitators of clonal dissemination in bacteria. The question arises as to what kind of fitness advantage may be wielded by uropathogenic strains of the two predominant fluoroquinolone- and multidrug-resistant clonal groups of E. coli-ST131-H30 and ST1193, which has permitted their unprecedented pandemic-like global expansion in the last few decades. The colonization-associated genes' content, carriage of low-cost plasmids, and integrons with weak promoters could certainly contribute to the fitness of the pandemic groups, although those genetic factors are common among other clonal groups as well. Also, ST131-H30 and ST1193 strains harbor fluoroquinolone-resistance conferring mutations targeting serine residues in DNA gyrase (GyrA-S83) and topoisomerase IV (ParC-S80) that, in those clonal backgrounds, might result in a commensal fitness benefit, i.e., beyond the antibiotic resistance per se. This fitness gain might have contributed not only to the widespread dissemination of these major clones in the healthcare setting but also to their long-term colonization of healthy individuals and, thus, circulation in the community, even in a low or no fluoroquinolone use environment. This evolutionary shift affecting commensal E. coli, initiated by mutations co-favorable in both antibiotics-treated patients and healthy individuals warrants more in-depth studies to monitor further changes in the epidemiological situation and develop effective measures to reduce the antibiotic resistance spread.

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

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

Longitudinal Study of Dynamic Epidemiology of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Pigs and Humans Living and/or Working on Pig Farms

Extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales have been increasingly isolated from pigs, highlighting their potential for transmission to humans living and/or working within pig farms. As longitudinal data on the prevalence and the molecular characteristics of such isolates from the high-risk farming population remain scarce, we performed a long-term study on 39 Dutch pig farms. Fecal samples from pigs, farmers, family members, and employees were collected during four sampling occasions with a 6-month period. The presence of ESBL-producing Enterobacterales and their molecular characteristics (ESBL gene, plasmid, and sequence types) were determined by standard methods. Data on personal and farm characteristics were collected using questionnaires. ESBL-producing Escherichia coli was present in pigs at least once for 18 of 39 farms and in 17 of 146 farmers, family members, and/or employees. Among these 417 E. coli isolates, blaCTX-M-1 was the most frequently observed ESBL gene in pigs (n = 261) and humans (n = 25). Despite the great variety in plasmid (sub)types and E. coli sequence types (STs), we observed genetic similarity between human- and pig-derived isolates in (i) ESBL gene, plasmid (sub)type, and ST, suggesting potential clonal transmission in seven farms, and (ii) only ESBL gene and plasmid (sub)type, highlighting the possibility of horizontal transfer in four farms. Five pig farmers carried ESBL producers repeatedly, of whom two carried an identical combination of gene, plasmid (sub)type, and ST over time. Human ESBL carriage was associated with both presence of ESBL producers in pigs and average number of hours working on the pig farm per week, while prolonged human carriage was observed only incidentally. IMPORTANCE Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli represents a public health hazard due to reduced therapeutic options for the treatment of infections. Although direct contact with pigs is considered a risk factor for human ESBL-producing E. coli carriage through occupational exposure, nationwide data regarding the occurrence of such isolates among pigs and humans living and/or working on farms remain scarce. Therefore, we determined (i) the longitudinal dynamics in prevalence and molecular characteristics of ESBL-producing E. coli in Dutch pig farmers and their pigs over time and (ii) the potential transmission events between these reservoirs based on genetic relatedness and epidemiological associations in longitudinal data. Our data suggesting the possibility of clonal and horizontal dissemination of ESBL-producing Escherichia coli between pigs and pig farmers can be used to inform targeted intervention strategies to decrease the within-farm human exposure to ESBL-producing E. coli.

Duration of rectal colonization with extended-spectrum beta-lactamase-producing Escherichia coli: results of an open, dynamic cohort study in Dutch nursing home residents (2013–2019)

Background

In 2016, a study in a Dutch nursing home showed prolonged colonization duration of extended-spectrum β-lactamase-producing (ESBL)-ST131 compared to ESBL-non-ST131. In this study, we assessed the duration of rectal ESBL-producing E. coli (ESBL-EC) colonization in residents in the same nursing home for an extended period of six years. We aimed to estimate the influence of a possible bias when follow up is started during an outbreak.

Methods

Between 2013 and 2019, repetitive point prevalence surveys were performed by culturing rectal or faecal swabs from all residents. Kaplan–Meier survival analysis was performed to calculate the median time to clearance of ESBL-EC with a log-rank analysis to test for differences between ESBL-ST131 and ESBL-non-ST131.

Results

The study showed a median time to clearance of 13.0 months (95% CI 0.0–27.9) for ESBL-ST131 compared to 11.2 months (95% CI 4.8–17.6) for ESBL-non-ST131 (p = 0.044). In the subgroup analysis of residents who were ESBL-EC positive in their first survey, the median time to clearance for ST131 was 59.7 months (95% CI 23.7–95.6) compared to 16.2 months (95% CI 2.1–30.4) for ESBL-non-ST131 (p = 0.036). In the subgroup analysis of residents who acquired ESBL-EC, the median time to clearance for ST131 was 7.2 months (95% CI 2.1–12.2) compared to 7.9 months (95% CI 0.0–18.3) for ESBL-non-ST131 (p = 0.718). The median time to clearance in the ESBL-ST131 group was significantly longer in residents who were ESBL-ST131 colonised upon entering the study than in residents who acquired ESBL-ST131 during the study (p = 0.001).

Conclusion

A prolonged colonization with ESBL-ST131 was only found in the subgroup who was ESBL-EC positive upon entering the study. The prolonged duration with ESBL-ST131 in the previous study was probably biased by factors that occured during (the start of) the outbreak.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-022-01132-9.

The Causes and Control Measures of Extended Spectrum Beta-Lactamase Producing Enterobacteriaceae in Long-Term Care Facilities: A Systematic Review and Meta-Analysis

Background

Due to extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE), infections among residents are increasing in long-term care facilities (LTCFs), resulting in a high rate of morbidity and healthcare costs. A designated infection control team is unavailable to control the disease.

Methods

A systematic review and meta-analysis were conducted to characterize the causes of ESBL-PE and evaluate the infection control strategies within LTCFs. Multiple regression analysis (MRA) was included as supplementary statistical analysis to identify relationships between LTCFs, geographical locations, infection control measures (ICMs), and ESBL-PE. A systematic search was conducted for studies from January 2008 to December 2018. Twenty-two of the 3106 studies met the inclusion criteria.

Results

The pooled prevalence for ESBL-PE among LTCFs residents was a mean difference (MD) of 15.78 (95% CI: 0.04, 31.53). Risk factors included the influence of regional areas was a standardized mean difference (SMD) of 0.61(95% CI: 0.32, 0.91) in Europe, SMD was 14.92 (95% CI: 9.17, 20.68) in Asia, and SMD was 0.51(95% CI: 0.35, 0.67) in other regions (North America and Australia). Nine of 22 studies reported ICMs were MD of 13.59 (95% CI: 5.32, 21.86).

Conclusions

Meta-analysis and MRA revealed a statistically significant association between LTCF and ESBL-PE among residents (p = .05). Strict adherence to infection control measures in LTCFs is needed to address this ESBL-PE prevalence among residents. The potential positive social change is promoting knowledge about vulnerable residents in LTCFs and the community factors responsible for ESBL infection.

Prevalence, Incidence, and Risk Factors for Intestinal Colonization Due to Fluoroquinolone-Resistant ST131 Escherichia coli: a Longitudinal Study in Highly Dependent, Long-Term Care Facility Residents

Escherichia coli ST131 clade C is an important driver for fluoroquinolone resistance (FQ-R). We conducted a prospective observational study in residents from two long-term care facilities (LTCFs) in Seville, Spain, in 2018. Fecal swabs and environmental samples were obtained. E. coli isolates were screened for clade C, FQ-R ST131 by PCR, and molecular typing by PFGE; representatives from pulsotypes were studied by whole-genome-sequencing (WGS) and assigned to lineages (cgSTs). Prevalence of colonization at each time point, incidence density, and risk factors for acquisition were studied. Seventy-six FQ-R ST131 E. coli isolates belonging to 34 cgSTs were obtained; 24 belonging to subclade C1 (116 isolates, 65.9%) and 10 to C2 (60, 34.1%). C1 lineages showed lower virulence scores than C2 (median [IQR], 19 [18 to 20] versus 21 [20 to 21.5], P = 0.001) and higher number of plasmids (4 [3 to 5] versus 2 [2 to 3], P = 0.01). aac(6')-Ib-cr and blaOXA-1 were less frequent in C1 than C2 (2 [8.3%] versus 6 [60%], P = 0.003 for both); ESBL genes were detected in eight (33.3%) C1 (5 blaCTX-M-27) and three (30%) C2 (all blaCTX-M-15). Of the 82 residents studied, 49 were colonized at some point (59.7%), with a pooled prevalence of 38.6%. Incidence density of new lineage acquisition was 2.22 per 100 resident weeks (1.28 and 0.93 C1 and C2 subclades, respectively). Independent risk factors for acquisitions were having a colonized roommate (HR = 4.21; 95% CI = 1.71 to 10.36; P = 0.002) and urinary or fecal incontinence (HR = 2.82; 95% CI = 1.21 to 6.56; P = 0.01). LTCFs are important reservoirs of clade C ST131 E. coli. The risk factors found suggest that cross-transmission is the most relevant transmission mechanisms. IMPORTANCE We aimed at investigating the microbiological and epidemiological features of clade C fluoroquinolone-resistant ST131 E. coli isolates colonizing highly dependent residents in long-term care facilities (LTCFs) during 40 weeks and the risk factors of acquisition. Isolates from C1 and C2 subclades were characterized in this environment. The clonality of the isolates was characterized and they were assigned to lineages (cgSTs), Resistance genes, virulence factors, and plasmids were also described. This study suggests that cross-transmission is the most relevant transmission mechanisms; however, environmental colonization might also play a role. We believe the data provide useful information to depict the epidemiology of these bacteria by merging detailed microbiological and epidemiological information.

The impact of the ST131 clone on recurrent ESBL-producing E. coli urinary tract infection: a prospective comparative study

The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is of great concern. Almost one third of patients with UTI, develop recurrent UTI (RUTI). We followed 297 patients for one year after their first episode of UTI due to ESBL-E. coli. Our aim was to evaluate the impact of the globally dominant sequence type (ST)131 clone and its clades, on the risk of subsequent recurrences with ESBL-E. coli. Isolates from patients developing RUTI (68/297) were compared with those from patients with sporadic UTI (SUTI, 229/297). No association was found between RUTI and the two most prevalent phylogroups B2 and D, bla_CTX-M genes, or resistance profile. Half of the patients with RUTI were infected with ST131 isolates. Clade C2 were in dominance (50/119) among ST131 isolates. They were more common in patients with RUTI than SUTI (28% vs 13%) and multivariate analysis showed an increased odds-ratio (OR = 2.21, p = 0.033) for recurrences in patients infected with these isolates as compared to non-ST131 isolates. Detecting specific biomarkers, as ST131 clade C2, in ESBL-E. coli UTI isolates may aid in prediction of RUTI and improve diagnostics and care of patients with a risk of ESBL-E. coli recurrences.

Gut colonisation by extended-spectrum β-lactamase-producing Escherichia coli and its association with the gut microbiome and metabolome in Dutch adults: a matched case-control study

BACKGROUND

Gut colonisation by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is a risk factor for developing overt infection. The gut microbiome can provide colonisation resistance against enteropathogens, but it remains unclear whether it confers resistance against ESBL-producing E coli. We aimed to identify a potential role of the microbiome in controlling colonisation by this antibiotic-resistant bacterium.

METHODS

For this matched case-control study, we used faeces from 2751 individuals in a Dutch cross-sectional population study (PIENTER-3) to culture ESBL-producing bacteria. Of these, we selected 49 samples that were positive for an ESBL-producing E coli (ESBL-positive) and negative for several variables known to affect microbiome composition. These samples were matched 1:1 to ESBL-negative samples on the basis of individuals' age, sex, having been abroad or not in the past 6 months, and ethnicity. Shotgun metagenomic sequencing was done and taxonomic species composition and functional annotations (ie, microbial metabolism and carbohydrate-active enzymes) were determined. Targeted quantitative metabolic profiling (proton nuclear magnetic resonance spectroscopy) was done to investigate metabolomic profiles and combinations of univariate (t test and Wilcoxon test), multivariate (principal coordinates analysis, permutational multivariate analysis of variance, and partial least-squares discriminant analysis) and machine-learning approaches (least absolute shrinkage and selection operator and random forests) were used to analyse all the molecular data.

FINDINGS

No differences in diversity parameters or in relative abundance were observed between ESBL-positive and ESBL-negative groups based on bacterial species-level composition. Machine-learning approaches using microbiota composition did not accurately predict ESBL status (area under the receiver operating characteristic curve [AUROC]=0·41) when using either microbiota composition or any of the functional profiles. The metabolome also did not differ between ESBL groups, as assessed by various methods including random forest (AUROC=0·61).

INTERPRETATION

By combining multiomics and machine-learning approaches, we conclude that asymptomatic gut carriage of ESBL-producing E coli is not associated with an altered microbiome composition or function. This finding might suggest that microbiome-mediated colonisation resistance against ESBL-producing E coli is not as relevant as it is against other enteropathogens and antibiotic-resistant bacteria.

FUNDING

None.

Bacteriophage Cocktail and Microcin-Producing Probiotic Escherichia coli Protect Mice Against Gut Colonization With Multidrug-Resistant Escherichia coli Sequence Type 131

Non-antibiotic measures are needed to reduce the rate of infections due to multidrug-resistant organisms (MDROs), including by eliminating the commensal reservoir that underlies such strains’ dissemination and leads to recurrent infections. Here, we tested a cocktail of pre-selected bacteriophages and an engineered microcin C7-producing probiotic Escherichia coli Nissle-1917 strain for their ability to reduce gut colonization by an E. coli strain from sequence type 131 (ST131)-H30R, which is the major clonal group of MDROs among extraintestinal clinical E. coli isolates. Although the bacteriophage cocktail was highly effective against ST131-H30R strains both in vitro and in a murine model of subcutaneous sepsis, it was only weakly and transiently effective against gut colonization by the target ST131-H30R strain (0.5 log₁₀ decrease on d + 1: p < 0.001; no significant effect on d + 4 and beyond). The probiotic strain, while also highly active against ST131-H30R in vitro, was ineffective against ST131-H30R gut colonization despite its abundant presence in feces. Nonetheless, despite failing as decolonizing agents when administered separately, when co-administered the bacteriophage cocktail and probiotic strain exhibited striking synergy against ST131-H30R gut colonization. This combinatory effect was most pronounced on d + 1 (3.3 log₁₀ target strain decrease: p < 0.001), and persisted until d + 7 (0.5 log₁₀ decrease; p < 0.02.). Although by d + 10 the ST131-H30R load was fully restored, these findings provide proof of concept for combined bacteriophage-plus-probiotic administration to reduce or, possibly, to prevent gut colonization with MDROs in high-risk individuals.

Antimicrobial-Resistant Escherichia coli Distribution and Whole-Genome Analysis of Sequence Type 131 Escherichia coli Isolates in Public Restrooms in Taiwan

The threat of antibiotic-resistant bacteria to public health may originate from public restrooms. To better understand the community burden of antimicrobial-resistant Escherichia coli and sequence type complex 131 E. coli (STc131) in the public restroom, we performed a surveillance in public restrooms in southern Taiwan. Swabs were sampled from randomly selected public restrooms in Tainan, Taiwan in 2019. Antimicrobial susceptibility, phylogenetic grouping, and multiplex PCR were performed for the major ST complex in the B2 phylogenetic group. If STc131 isolates were identified, the whole-genome sequencing was performed. A total of 613 collection sites found 132 sites (21.5%) positive for E. coli. The most common phylogenetic group was A (30.9%) followed by B2 (30.3%). Ceftriaxone-resistant E. coli and extended-spectrum β-lactamases–producing E. coli were found in 2.4 and 1.0% of total public restrooms, respectively. The isolates in rural areas had higher ceftriaxone non-susceptibility than those in the city centers (3.9 vs. 1.2%, P = 0.038). Nine STc131 isolates were found in public restrooms, and most (77.8%) belonged to the subtype fimH41, whereas 22.2% belonged to fimH30. With the inclusion of STc131 isolates from human and dog fecal colonization in Taiwan, whole-genome sequencing was performed in 35 isolates. A large cluster of fimH41 in SNP-tree and GrapeTree was found from different sources (human, dog, and environment) and geographical areas. In conclusion, our surveillance of antimicrobial-resistant E. coli showed a higher prevalence of E. coli detected in public restrooms in the rural areas compared to those in city centers. The whole-genome sequence implies that fimH41 STc131 strains are successfully circulated in the community in Taiwan.

Escherichia coli ST131 isolated from urological patients can acquire plasmid-mediated extended spectrum β-lactamase from other bacteria with high frequency

OBJECTIVES

To investigate the prevalence of the clonal group Escherichia coli ST131 in urologic patients, and to clarify the mechanisms underlying the high prevalence of the antimicrobial resistant genes in ST131.

METHODS

We used 65 Escherichia coli strains collected from the Department of Urology, Nagasaki University Hospital, between January 2018 and December 2018. All of them underwent multilocus sequence typing and were analyzed for genes associated with quinolone resistance and extended-spectrum β-lactamases. To compare ST131 and non-ST131 strains, bacterial conjugation experiments and intestinal colonization evaluations were performed.

RESULTS

ST131 was the most dominant among all the strains, along with levofloxacin resistant strains, and extended-spectrum β-lactamases positive strains (32%, 63%, and 73%, respectively). 12 out of 15 extended-spectrum β-lactamases-producing Escherichia coli strains harbored CTX-M-9. In particular, all extended-spectrum β-lactamases-producing ST131 strains possessed CTX-M-9. The proportions of ST131 strains with or without quinolone resistance-determining region mutations were significantly higher and lower, respectively, than that of non-ST131 strains (P = 0.0002 and P < 0.0001, respectively). When Klebsiella pneumoniae was used as a donor, three ST131 strains acquired extended-spectrum β-lactamases a total of 16 times (six, four, and six times each), which was significantly more than that in one of the non-ST131 strains (two times). The amount of bacteria was significantly lower in the ST131 strains than in the non-ST131 strains administered to mice. Both the ST131 and non-ST131 strains increased again after the administration of vancomycin, even after the colony was not detected.

CONCLUSIONS

These results support the mechanisms underlying the prevalence of ST131 strains in hospitals, particularly in urologic patients.

Intestinal Persistence of Colonizing Escherichia coli Strains, Especially ST131-H30, in Relation to Bacterial and Host Factors

BACKGROUND

Superior gut colonization may underlie the pandemic emergence of the resistance-associated H30 subclone of Escherichia coli sequence type 131 (ST131-H30). Little is known about the associated host and bacterial characteristics, or the comparative persistence of non-ST131 intestinal E. coli.

METHODS

Generic and fluoroquinolone-resistant E. coli isolates from volunteers' serial fecal samples underwent clonal analysis and extensive polymerase chain reaction (PCR)-based characterization (phylogroup, selected sequence types, virulence genes). Kaplan-Meier survival analysis and Cox proportional hazards survival analysis using penalized regression (a machine-learning method) were used to identify correlates of strain persistence.

RESULTS

Screening of 2005 subjects at the Minneapolis VA Medical Center identified 222 subjects (117 veterans, 105 human and animal household members) for longitudinal fecal surveillance. Analysis of their 585 unique-by-subject fecal E. coli strains identified multiple epidemiological, ecological, and bacterial correlates of strain persistence. ST131-H30, a strong univariable correlate of persistence, was superseded in multivariable analysis by outpatient status, fluoroquinolone resistance, and diverse (predominantly iron uptake-related) virulence genes.

CONCLUSIONS

ST131-H30 exhibits exceptional intestinal persistence, possibly due to a combination of fluoroquinolone resistance and virulence factors, which may be primarily colonization factors. This identifies both likely contributors to the ST131-H30 pandemic and potential targets for interventions against it.

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.

Conserved FimH mutations in the global Escherichia coli ST131 multi-drug resistant lineage weaken interdomain interactions and alter adhesin function

The binding of the type 1 fimbrial adhesin FimH to mannosylated receptors is allosterically regulated to enhance the fitness of uropathogenic Escherichia coli (UPEC) during urinary tract infection (UTI). Mutations in the two FimH domains (pilin and lectin) located outside the mannose binding pocket have been shown to influence mannose binding affinity, yet the details of the allostery mechanism are not fully elucidated. Here we characterised different FimH conformational states (termed low-affinity tense and high-affinity relaxed conformations) of natural FimH variants using molecular dynamics (MD) simulation techniques and report key structural dynamics differences between them. The clinically dominant FimH30 variant from the pandemic multidrug resistant E. coli ST131 lineage contains an R166H mutation that weakens FimH interdomain interactions and allows enhanced mannose interactions with pre-existing high-affinity relaxed conformations. When expressed in an isogenic ST131 strain background, FimH30 mediated high human cell adhesion and invasion, and enhanced biofilm formation over other variants. Collectively, our computational and experimental findings support a model of FimH protein allostery that is mediated by shifts in the pre-existing conformational equilibrium of FimH, additional to the sequential step-wise process of structural perturbations transmitted from one site to another within the protein. Importantly, it is the first study to shed light into how natural mutations in a clinically dominant FimH variant influence the protein’s conformational landscape optimising its function for ST131 fitness at intestinal and extraintestinal niches.

Prolonged carriage of ESBL-producing enterobacterales and potential cross-transmission among residents in geriatric long-term care facilities

Previous studies indicated residents in geriatric long-term care facilities (LTCFs) had much higher prevalence of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) carriage than the general population. Most ESBL-E carriers are asymptomatic. The study tested the hypothesis that residents with ESBL-E carriage may accumulate inside geriatric LTCFs through potential cross-transmission after exposure to residents with prolonged ESBL-E carriage. 260 residents from four Japanese LTCFs underwent ESBL-E testing of fecal specimens and were divided into two cohorts: Cohort 1,75 patients with ≥ 2 months residence at study onset; Cohort 2, 185 patients with < 2 months residence at study onset or new admission during the study period. Three analyses were performed: (1) ESBL-E carriage statuses in Cohort 1 and Cohort 2; (2) changes in ESBL-E carriage statuses 3-12 months after the first testing and ≥ 12 months after the second testing; and (3) lengths of positive ESBL-E carriage statuses. Compared with the residents in Cohort 1, a significantly larger proportion of residents in Cohort 2 were positive for ESBL-E carriage (28.0% in Cohort 1 vs 40.0% in Cohort 2). In the subsequent testing results, 18.3% of residents who were negative in the first testing showed positive conversion to ESBL-E carriage in the second testing, while no patients who were negative in the second testing showed positive conversion in the third testing. The maximum length of ESBL-E carriage was 17 months. The findings indicated that some residents acquired ESBL-E through potential cross-transmission inside the LTCFs after short-term residence. However, no residents showed positive conversion after long-term residence, which indicates that residents with ESBL-E carriage may not accumulate inside LTCFs. Practical infection control and prevention measures could improve the ESBL-E prevalence in geriatric LTCFs.

Epidemiology of ESBL-producing Escherichia coli from repeated prevalence studies over 11 years in a long-term-care facility

Background

Escherichia coli sequence type (ST) 131 H30 is an emerging multidrug resistant subclone, known to spread and cause outbreaks in long-term care facilities (LTCFs).

Objectives and methods

From 2010 through 2020, we performed 11 yearly surveillance studies for determining the prevalence of digestive carriage of ESBL-producing E. coli (ESBL-EC) among residents in a university-affiliated LCTF. Sequencing and genotyping of selected isolates were performed to characterize temporal trends in the prevalence and epidemic potential of ESBL-EC subclones, and for evaluating a potential rebound effect following discontinuation of contact precautions for ESBL-EC carriers in January 2019.

Results

This study included 2′403 LTCF residents, with 252 (10.5%) positive for ESBL-EC. Among the 236 ESBL-EC isolates available for typing, 58.0% belonged to the ST131 lineage, including 94/137 (68.6%) ST131 H30 isolates. An increasing yearly prevalence was observed for ESBL-EC (from 4.6 to 9.4%; p = 0.11), but not for the ST131 H30 subclone, which peaked in 2015 and declined thereafter. Multiple previously unnoticed ESBL-EC outbreaks occurred in the LTCF. Since 2018, we noted the clonal expansion of a rare ST131 H89 subclone (O16:H5) harboring CTX-M-14 and CTX-M-24. No rebound effect was observed in ESBL-EC prevalence nor in the different subclones following discontinuation of contact precautions for ESBL-EC carriers since 2019.

Conclusion

Clonal fluctuation was observed for ST131 H30 ESBL-EC with a current decline in prevalence. Surveillance should include the evolution of ST131 non-H30 subclones, which may spread in LTCFs. Our findings suggest that discontinuation of contact precautions for ESBL-EC carriers in LTCFs may be safely implemented, in support of European recommendations to limit ESBL-producing Enterobacteriaceae control measures in endemic settings to non-E. coli.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-021-01013-7.

Molecular Epidemiology and Risk Factors for Extended-Spectrum β-Lactamase-Producing Enterobacterales in Long-Term Care Residents

OBJECTIVES

We aimed to assess the burden of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales in Swiss long-term care facilities (LTCFs) to describe the molecular epidemiology, describe the intrainstitutional and regional clusters of resistant pathogens, and identify independent institution- and resident-level factors associated with colonization.

DESIGN

Cross-sectional study.

SETTING AND PARTICIPANTS

From August to October 2019, we performed a point prevalence study among residents from 16 LTCFs in Western and Eastern Switzerland (8 per region).

METHODS

Residents underwent screening for ESBL-producing Enterobacterales (ESBL-E); whole-genome sequencing (WGS) was performed. We gathered institution-level (eg, number of beds, staff-resident ratio, alcoholic hand rub consumption) and resident-level [eg, anthropometric data, time in facility, dependency, health care exposure, antibiotic treatment, proton-pump inhibitor (PPI) use] characteristics. Factors associated with colonization were identified using a generalized linear model.

RESULTS

Among 1185 eligible residents, 606 (51%) consented to the study. ESBL-E prevalence was 11.6% (70/606), ranging from 1.9% to 33.3% between institutions, with a median of 12.5% in the West and 6.9% in the East (P = .03). Among 59 Escherichia coli (from 58 residents), multilocus sequence type (ST) 131 was most common (n = 43/59, 73%), predominantly its subclone H30R1 (n = 37/43, 86%). WGS data identified multiple intrainstitutional and regional clusters. Independent risk factors for ESBL carriage were previous ESBL colonization [adjusted odds ratio (aOR) 23.5, 95% confidence interval (CI) 6.6-83.8, P < .001), male gender (aOR 2.6, 95% CI 1.5-4.6, P = .002), and use of PPIs (aOR 2.2, 95% CI 1.2-3.8, P = .01).

CONCLUSIONS AND IMPLICATIONS

Overall ESBL-E prevalence in Swiss LTCF residents is low. Yet, we identified several clusters of residents with identical pathogens within the same institution. This implies that particularly affected institutions might benefit from targeted infection control interventions. PPI use was the only modifiable factor associated with carriage of ESBL producers. This study adds to the growing list of adverse outcomes associated with PPIs, calling for action to restrict their use in the long-term care setting.

Fecal Carriage and Epidemiology of Extended-Spectrum Beta-Lactamase/Carbapenemases Producing Enterobacterales Isolates in Bulgarian Hospitals

The gastrointestinal tract is an important reservoir of extended spectrum beta-lactamase (ESBL)/carbapenemase-producing Enterobacterales isolates. This study included patients from two Bulgarian hospitals. Overall, 98 ESBL producers (including 68 Escherichia coli and 20 Klebsiella pneumoniae isolates) were detected among 99 hospitalized patients, 212 patients at admission, and 92 hospital staff in 42.4%, 24.5%, and 4%, respectively. We observed bla_CTX-M-15 in 47% of isolates, bla_CTX-M-3 in 39% and bla_CTX-M-14 in 11%. Three bla_CTX-M-15 positive isolates were also bla_KPC-2 positive. High transferability was detected for bla_CTX-M-3 carrying plasmids (55%) with L/M and I1 replicon plasmids, followed by CTX-M-14 (36.4%) and CTX-M-15 (27.9%) with IncF plasmids. BlaKPC-2 was carried by FIIAs plasmids. Epidemiology typing revealed 8 K. pneumoniae ST types—ST15(8/20), ST17(4/20), ST37(2/20) and 9 E. coli ST types—ST131 (30.9%, 21/68), ST38 (8/68), ST95(7/68) and ST316(7/68). All ST131 isolates but one was from the highly virulent epidemic clone O25bST131. This is the first report in Bulgaria about ESBL/carbapenemase faecal carriage. We observed high ESBL/carbapenemases prevalence. A predominant number of isolates were members of highly epidemic and virulent PanEuropean clones ST15 K. pneumoniae and O25bST131 E. coli. High antibiotics usage during the COVID pandemic will worsen the situation. Routine screenings and strict infection control measures should be widely implemented.

Prevalence and Risk Factors for Multidrug-Resistant Organisms Colonization in Long-Term Care Facilities Around the World: A Review

Elderly people confined to chronic care facilities face an increased risk of acquiring infections by multidrug-resistant organisms (MDROs). This review presents the current knowledge of the prevalence and risk factors for colonization by MDROs in long-term care facilities (LTCF), thereby providing a useful reference to establish objectives for implementing successful antimicrobial stewardship programs (ASPs). We searched in PubMed and Scopus for studies examining the prevalence of MDROs and/or risk factors for the acquisition of MDROs in LTCF. One hundred and thirty-four studies published from 1987 to 2020 were included. The prevalence of MDROs in LTCF varies between the different continents, where Asia reported the highest prevalence of extended-spectrum ß-lactamase (ESBL) Enterobacterales (71.6%), carbapenem resistant (CR) Enterobacterales (6.9%) and methicillin-resistant Staphylococcus aureus (MRSA) (25.6%) and North America the highest prevalence to MDR Pseudomonas aeruginosa (5.4%), MDR Acinetobacter baumannii (15.0%), vancomycin-resistant Enterococcus spp. (VRE) (4.0%), and Clostridioides difficile (26.1%). Furthermore, MDRO prevalence has experienced changes over time, with increases in MDR P. aeruginosa and extended spectrum ß-lactamase producing Enterobacterales observed starting in 2015 and decreases of CR Enterobacterales, MDR A. baumannii, VRE, MRSA and C. difficile. Several risk factors have been found, such as male sex, chronic wounds, the use of medical devices, and previous antibiotic use. The last of these aspects represents one of the most important modifiable factors for reducing colonization with MDROs through implementing ASPs in LTCF.

Large Fecal Reservoir of Escherichia coli Sequence Type 131-H30 Subclone Strains That Are Shared Within Households and Resemble Clinical ST131-H30 Isolates

BACKGROUND

Emerging antimicrobial-resistant Escherichia coli represent mainly the nested (fluoroquinolone-resistant [FQR]) H30R and H30Rx subclones within sequence type 131 (ST131). Intestinal colonization and within-household transmission may underlie H30R's emergence.

METHODS

We screened fecal samples from 741 volunteers (383 veterans, 358 household members, including pets) for ST131 and FQR E. coli (FQREC) and used molecular profiling to resolve unique strains. Selected strains underwent PCR-based detection of phylogroups, sequence types (STs), H30, H30Rx, and 53 virulence genes (VGs). Within-household strain sharing was compared with household, host, and bacterial characteristics. Fecal isolates were compared with clinical isolates.

RESULTS

Colonization prevalence was 5.1% for H30R, 8% for ST131 (67% FQREC), and 10% for FQREC (52% ST131). ST131 isolates exhibited more VGs than non-ST131 isolates. Strain sharing (27% of multisubject households, 18% of corresponding subjects) was associated with the elderly, FQREC, H30R, H30Rx, ST73, and specific VGs. Fecal ST131 and FQREC isolates resembled contemporaneous and historical clinical isolates according to all studied traits.

CONCLUSIONS

Veterans and their human household members commonly carry and extensively share FQREC, predominantly H30R, thereby likely facilitating the ST131 pandemic. Strain sharing corresponds with multiple bacterial characteristics, including FQ resistance and specific VGs, which may promote intestinal colonization and/or host-to-host transmission.

Bloodstream Infections Caused by Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Patients with Liver Cirrhosis

Background: This study aimed to investigate the frequency of sequence type (ST) 131 strains and outcome of cirrhotic patients with bloodstream infections (BSIs) caused by extended-spectrum beta-lactamase-producing Escherichiacoli (ESBLEC) and non-extended-spectrum beta-lactamase-producing Escherichiacoli (NESBLEC). Methods: The incidence of ST 131 strains, hospital stay, and 30-day re-admission/mortality were compared between 51 ESBLEC and 51 NESBLEC bacteremic patients with cirrhosis. Results: ST 131 strains were found in 35.3% of the ESBLEC group and 0% of the NESBLEC group (p < 0.001). Mean hospital stay was 26.5 days in the ESBLEC group and 17.1 days in the NESBLEC group (p = 0.006). Thirty-day re-admission rates were 11.8% in the ESBLEC group and 5.9% in the NESBLEC group (p = 0.5). ST 131 strains were associated with 30-day re-admission (odds ratio: 4.5, 95% confidence interval: 1.1–18.9). Thirty-day mortality rate was 31.4% in the ESBLEC group and 23.5% in the NESBLEC group (p = 0.4). Conclusion: In patients with cirrhosis, the ESBLEC BSIs group had a higher frequency of ST 131 strains and longer hospital stay than the NESBLEC BSIs group with similar 30-day re-admission/mortality. ST 131 strains were associated with 30-day re-admission.

Dynamics of Intestinal Carriage of Extended-Spectrum Beta-lactamase-Producing Enterobacteriaceae in the Dutch General Population, 2014-2016

BACKGROUND

In the Netherlands, the prevalence of intestinal extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) carriage in community-dwelling subjects is ~5%. Little is known about the dynamics of ESBL-E carriage.

METHODS

In a nationwide, population-based study (2014-2016) with 4177 community-dwelling subjects, fecal samples from 656 subjects were collected after 1 (time point [T] = 1) and 6 (T = 2) months. The growth of ESBL-E was quantified and a whole-genome sequence analysis was performed. Subjects were categorized as either an incidental, short-term, or long-term carrier or as a noncarrier. Risk factors were determined by random forest models and logistic regression. The transmissibility and duration of ESBL-E carriage was quantified using a transmission model, which also incorporated previous study data.

RESULTS

Out of 656 participants, 96 were ESBL-E carriers at T = 0. Of these, 66 (10.1%) subjects were incidental carriers, 22 (3.3%) were short-term carriers, and 38 (5.8%) were long-term carriers; the remaining 530 (80.8%) were noncarriers. The risk factors for long-term carriage were travelling to Asia, swimming in a sea/ocean, and not changing the kitchen towel daily. The log-transformed colony forming units ratio at T = 0 was predictive for ESBL-E carriage at T = 1 (odds ratio [OR], 1.3; 95% confidence interval [CI], 1.2-1.6) and T = 2 (OR, 1.2; 95% CI, 1.1-1.4). Model simulations revealed a median decolonization rate of 2.83/year, an average duration of carriage of 0.35 years, and an acquisition rate of 0.34/year. The trend of the acquisition rate during the study period was close to 0.

CONCLUSIONS

The risk factors for long-term ESBL-E carriage were travel- and hygiene-related. The dynamics of ESBL-E carriage in the general Dutch population are characterized by balancing decolonization and acquisition rates.

Bacterial "Virulence" Traits and Host Demographics Predict Escherichia coli Colonization Behaviors Within Households

Background

Although intestinal colonization precedes most extraintestinal Escherichia coli infections, colonization-promoting factors are incompletely understood. We compared within-household E. coli colonization patterns with host and bacterial traits.

Methods

Twenty-two veterans with a clinical E. coli isolate and their 46 human and animal household members underwent longitudinal fecal sampling. Distinct E. coli strains were characterized for phylogenetic background, virulence genes, antibiotic resistance, and colonization behaviors. Host and bacterial traits were assessed statistically as predictors of colonization behaviors.

Results

Among the 139 unique-by-household fecal E. coli strains, univariable predictors of colonization behavior included (i) host demographics, (ii) matching the index clinical isolate, and (iii) bacterial characteristics (2 phylogroups, 5 clonal lineages, 18 virulence genes, and molecular extraintestinal pathogenic E. coli status). Multivariable predictors of colonization behavior included veteran host, spouse host, matching the index clinical isolate, phylogroup F, ST73, hlyD (alpha hemolysin), hlyF (variant hemolysin), H7 fliC (flagellar variant), vat (vacuolating toxin), and iha (adhesin-siderophore).

Conclusions

Host demographics, multiple bacterial “virulence” traits, and matching the index clinical isolate predicted E. coli fecal colonization behaviors. Thus, certain bacterial characteristics may promote both colonization and pathogenicity. Future interventions directed toward such traits might prevent E. coli infections both directly and by disrupting antecedent colonization.

High prevalence of multidrug resistant Enterobacteriaceae among residents of long term care facilities in Amsterdam, the Netherlands

Introduction

The aim of this study was to determine the rate of asymptomatic carriage and spread of multidrug-resistant micro-organisms (MDRO) and to identify risk factors for extended spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) carriage in 12 long term care facilities (LTCFs) in Amsterdam, the Netherlands.

Materials and methods

From November 2014 to august 2015, feces and nasal swabs from residents from LTCFs in Amsterdam, the Netherlands were collected and analyzed for presence of multidrug-resistant Gram-negative bacteria (MDRGN), including ESBL-E, carbapenemase-producing Enterobacteriaceae (CPE), colistin-resistant Enterobacteriaceae and methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Logistic regression analysis was performed to assess associations between variables and ESBL-carriage.

Results

In total, 385 residents from 12 LTCFs (range 15–48 residents per LTCF) were enrolled. The prevalence of carriage of MDRGN was 18.2% (range among LTCFs 0–47%) and the prevalence of ESBL-E alone was 14.5% (range among LTCFs: 0–34%). Of 63 MDRGN positive residents, 50 (79%) were ESBL-E positive of which 43 (86%) produced CTX-M. Among 44 residents with ESBL-E positive fecal samples of whom data on contact precautions were available at the time of sampling, only 9 (20%) were already known as ESBL-E carriers. The prevalence for carriage of MRSA was 0.8% (range per LTCF: 0–7%) and VRE 0%. One CPE colonized resident was found. All fecal samples tested negative for presence of plasmid mediated resistance for colistin (MCR-1). Typing of isolates by Amplified Fragment Length Polymorphism (AFLP) showed five MDRGN clusters, of which one was found in multiple LTCFs and four were found in single LTCFs, suggesting transmission within and between LTCFs. In multivariate analysis only the presence of MDRO in the preceding year remained a risk factor for ESBL-E carriage.

Conclusions

The ESBL-carriage rate of residents in LTCFs is nearly two times higher than in the general population but varies considerably among LTCFs in Amsterdam, whereas carriage of MRSA and VRE is low. The majority (80%) of ESBL-E positive residents had not been detected by routine culture of clinical specimens at time of sampling. Current infection control practices in LTCFs in Amsterdam do not prevent transmission. Both improvement of basic hygiene, and funding for laboratory screening, should allow LTCFs in Amsterdam to develop standards of care to prevent transmission of ESBL-E.

Risk factors associated with prolonged intestinal colonization of ESBL-producing Enterobacteriaceae - a prospective cohort study

Background

Extended spectrum β-lactamase-producing Enterobacteriaceae (EPE) are responsible for a major part of the widespread antimicrobial resistance (AMR). Increased understanding of risk factors associated with intestinal colonization of EPE is crucial to implement adequate actions against AMR. The aim of this study was to define potential risk factors for prolonged intestinal colonization with EPE. A secondary aim was to analyze if patients were adequately informed about being infected or colonized by antibiotic-resistant bacteria.

Methods

Patients with a positive clinical EPE culture from urine, blood or feces were recruited in a region in the south of Sweden. Selective EPE fecal cultures were obtained at least three months after the initial positive culture. Prolonged intestinal colonization was defined as the prevalence of any EPE in the follow-up fecal sample. Risk factors for prolonged intestinal colonization were evaluated by using a questionnaire and by retrospective review of medical records. A univariate model and a multivariate regression analysis were performed to identify possible risk factors for intestinal EPE colonization.

Results

Out of 143 patients included in the study, 57% remained positive for EPE at the second sampling. In a multivariate regression model, urological intervention, history of EPE infection and travel to Africa and/or Asia within 2 years were found to be significantly associated with prolonged intestinal colonization of EPE. Before being approached by us, 50% of patients displayed inadequate knowledge of EPE infection or colonization.

Conclusion

In this prospective cohort study, urological intervention within 6 months and a history of EPE infection are independently associated with prolonged intestinal colonization with EPE. In contrast, travel to Africa and/or Asia within 2 years is associated with a decreased risk of prolonged intestinal colonization with EPE. There is room for improvement when it comes to patient information regarding EPE to decrease of spread.

Evaluation of an in vitro model with a novel statistical approach to measure differences in bacterial survival of extended-spectrum β-lactamase-producing Escherichia coli on an inanimate surface

Background

The role of environmental contamination in the transmission of Enterobacteriaceae is increasingly recognized. However, factors influencing the duration of survival in the environment have not yet been extensively studied. In this study, we developed and evaluated an in vitro model with a novel statistical approach to accurately measure differences in bacterial survival, that can be used to model the effects of multiple factors/conditions in future experiments.

Methods

Two extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) isolates were used for this in vitro experiment: a CTX-M-15-producing E. coli sequence type (ST) 131 and a CTX-M-1-producing E. coli ST10 isolate. Each strain was 1:1 diluted in sterile water, sterile saline or sheep blood. Cover glasses (18 × 18 mm) were inoculated with the dilution and subsequently kept at room temperature. Bacterial survival on the glasses was determined hourly during the first day, once daily during the following 6 days, and from day 7 on, once weekly up to 100 days. The experiment was repeated six times for each strain, per suspension fluid.

Results

Viable bacteria could be detected up to 70 days. A biphasic survival curve for all suspension fluids was observed, whereby there was a rapid decrease in the number of viable bacteria in the first 7 h, followed by a much slower decrease in the subsequent days.

Conclusions

We found a difference in survival probability between E. coli ST10 and ST131, with a higher proportion of viable bacteria remaining after 7 h for ST131, particularly in sheep blood.

Risk Factors for Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae Carriage in Patients Admitted to Intensive Care Unit in a Tertiary Care Hospital in Thailand

Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) are important causes of serious infections in intensive care unit (ICU). This study aimed to investigate the risk factors for intestinal carriage of ESBL-PE among patients admitted to ICU, subsequent ESBL-PE infections, and outcomes of these patients. This study prospectively collected rectal swabs from 215 ICU patients in Northern Thailand and ESBL-PE were isolated. A high prevalence of ESBL-PE carriage (134/215, 62.3%) at ICU admission was observed, with Escherichia coli representing the predominant organism (67.5%) followed by Klebsiella pneumoniae (19.4%). Multivariate logistic regression analysis identified chronic renal disease as the independent risk factor for ESBL-PE carriage (p = 0.009; adjusted odds ratio = 4.369; 95% confidence interval = 1.455-13.119). Among colonized patients, 2.2% (3/134) developed ESBL-PE infections during ICU stay. Phylogenetic analysis of E. coli (n = 108) showed that the predominant group was group A (38.0%), followed by groups B1 (17.6%), D (15.7%), B2 (14.8%), C (7.4%), and F (6.5%). Multilocus sequence typing analysis of the pathogenic groups B2, D, and F revealed 11 different sequence types (STs), with ST131 (n = 13) as the most prevalent, followed by ST648 (n = 5), ST38 (n = 4), ST393 (n = 3), and ST1193 (n = 3). These results are of concern since ESBL-PE may be a prerequisite for endogenous infections and potentially disseminate within the hospital. This is the first study describing ESBL-PE carriage among patients at ICU admission and subsequent ESBL-PE infections in Thailand.

Spread of ESBL-producing Escherichia coli in nursing home residents in Ireland and the Netherlands may reflect infrastructural differences

A prevalence study in two nursing homes (one each in the Netherlands and Ireland) found four (11%) Dutch and six (9%) Irish residents colonized with 11 extended-spectrum beta-lactamase-producing Escherichia coli, 10 of which contained CTX-M-15. Four Dutch isolates, from three residents of the same ward, belonged to E. coli O25:H4, sequence type (ST) 131 and were part of the same cluster type by whole-genome sequencing. Four Irish residents on three different wards were colonized with an identical E. coli O89:H9, ST131, complex type 1478. Cross-transmission between three Irish wards may reflect differences in nursing home infrastructure, specifically communal areas and multi-bedded resident rooms.

Rapid Emergence, Subsidence, and Molecular Detection of Escherichia coli Sequence Type 1193-fimH64, a New Disseminated Multidrug-Resistant Commensal and Extraintestinal Pathogen

Escherichia coli sequence type 1193 (ST1193) is an emerging multidrug-resistant pathogen. We performed longitudinal and cross-sectional surveillance for ST1193 among clinical and fecal E. coli isolates from Minneapolis Veterans Affairs Medical Center (VAMC) patients and their household members, other Minnesota centers, and national VAMCs and compared these ST1193 isolates with archival human and canine ST1193 isolates from Australia (2008). We also developed and extensively validated a novel multiplex PCR assay for ST1193 and its characteristic fimH64 (type 1 fimbrial adhesin) allele. We found that ST1193-H64 (where "H64" refers to a phylogenetic subdivision within ST1193 that is characterized by the fimH64 allele), which was uniformly fluoroquinolone resistant, appeared to emerge in the United States in a geographically staggered fashion beginning around 2011. Its prevalence among clinical and fecal E. coli isolates at the Minneapolis VAMC rose rapidly beginning in 2013, peaked in early 2017, and then plateaued or declined. In comparison with other ST14 complex (STc14) isolates, ST1193-H64 isolates were more extensively multidrug resistant, whereas their virulence genotypes were less extensive but included (uniquely) K1 capsule and fimH64 Pulsed-field gel electrophoresis separated ST1193-H64 isolates from other STc14 isolates and showed genetic commonality between archival Australian versus recent U.S. isolates, fecal versus clinical isolates, and human versus canine isolates. Three main ST1193 pulsotypes differed significantly in resistance profiles and capsular types; emergent pulsotype 2123 was associated with trimethoprim-sulfamethoxazole resistance and K1 (versus K5) capsule. These findings clarify ST1193-H64's temporal prevalence trends as a fluoroquinolone-resistant pathogen and commensal; document clonal subsets with distinctive geographic, temporal, resistance, and virulence gene associations; and establish a new laboratory tool for rapid and simple detection of ST1193-H64.

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection

Escherichia coli is a major cause of bloodstream and urinary tract infections globally. The wide dissemination of multidrug-resistant (MDR) strains of extraintestinal pathogenic E. coli (ExPEC) poses a rapidly increasing public health burden due to narrowed treatment options and increased risk of failure to clear an infection. Here, we present a detailed population genomic analysis of the ExPEC ST131 clone, in which we seek explanations for its success as an emerging pathogenic strain beyond the acquisition of antimicrobial resistance (AMR) genes. We show evidence for evolution toward separate ecological niches for the main clades of ST131 and differential evolution of anaerobic metabolism, key colonization, and virulence factors. We further demonstrate that negative frequency-dependent selection acting across accessory loci is a major mechanism that has shaped the population evolution of this pathogen.IMPORTANCE Infections with multidrug-resistant (MDR) strains of Escherichia coli are a significant global public health concern. To combat these pathogens, we need a deeper understanding of how they evolved from their background populations. By understanding the processes that underpin their emergence, we can design new strategies to limit evolution of new clones and combat existing clones. By combining population genomics with modelling approaches, we show that dominant MDR clones of E. coli are under the influence of negative frequency-dependent selection, preventing them from rising to fixation in a population. Furthermore, we show that this selection acts on genes involved in anaerobic metabolism, suggesting that this key trait, and the ability to colonize human intestinal tracts, is a key step in the evolution of MDR clones of E. coli.

Whole-genome sequences of multidrug-resistant Escherichia coli in South-Kivu Province, Democratic Republic of Congo: characterization of phylogenomic changes, virulence and resistance genes

Background

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are responsible for severe infections worldwide. Whereas their genotypic and pathogenic characteristics are not documented in Democratic Republic of Congo (DRC), recent studies conducted at the Bukavu General Hospital in the South Kivu province highlighted their high prevalence in extra-intestinal infections. Here we provide data on molecular characterization of ESBL producing-Escherichia coli isolates from patients with extra-intestinal infections at this provincial hospital.

Methods

Whole-genome sequencing was carried out on 21 of these ESBL-producing Extra-intestinal Pathogenic Escherichia coli (ExPEC) for analysis of phylogenomic evolution, virulence factor and antimicrobial resistance (AMR) genes. Data were compared to phylogenetically close genomes using Multi-Locus Sequence Typing and Single Nucleotide Polymorphism-based phylogenetic approaches.

Results

The distribution of E. coli sequence types (ST) was as follows: ST 131 (n = 7), ST405 (n = 4), ST410 (n = 2), and other STs (ST10, ST58, ST95, ST393, ST443, S617, ST648, and ST2450). All ST131 belonged to the O25b-ST131 pandemic clone. Unexpectedly, they harbored more virulence genes than their GenBank counterparts. IncF plasmid replicons included novel FIB 69, FII 105 and FII 107 alleles. ESBL-genes included the plasmid-mediated CTX-M-15 in all isolates, and the SHV-12 allele. Other AMR genes included blaOXA-1, blaTEM-1, as well as genes encoding resistance against aminoglycosides, quinolones, chloramphenicol, rifampicin, tetracyclines, sulfonamides and trimethoprim.

Conclusion

Current data confirm the clonal spread of ESBL-producing ST131 and ST405 clones in patients from South Kivu, and the acquisition of resistance and virulence genes. A closer survey of AMR and virulence should therefore be prompted in this high-risk area.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-3763-3) contains supplementary material, which is available to authorized users.

Duration of travel-associated faecal colonisation with ESBL-producing Enterobacteriaceae - A one year follow-up study

Background

In a previous study, we found that 30% of individuals travelling outside Scandinavia acquired extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) in their faecal flora. The aim of this study was to determine the duration of travel-associated faecal colonisation with ESBL-PE, to assess risk factors for prolonged colonisation and to detect changes in antibiotic susceptibility during prolonged colonisation.

Methods

Individuals with travel-associated colonisation with ESBL-PE submitted faecal samples every 3rd month over a one-year period. A questionnaire was completed at the beginning and end of follow-up. All specimens were analysed for ESBL-PE, and all isolates underwent confirmatory phenotype testing as well as molecular characterisation of ESBL-genes. Minimum inhibitory concentrations (MIC) for beta-lactam and non-beta-lactam agents were determined using the Etest.

Results

Among 64 participants with travel-associated colonisation with ESBL-PE, sustained carriage was seen in 20/63 (32%), 16/63 (25%), 9/63 (14%) and 7/64 (11%) at 3, 6, 9 and 12 months after return from their journey, respectively. The majority, 44 (69%) of travellers were short-term carriers with ESBL-PE only detected in the initial post-travel stool sample. Evaluation of risk factors demonstrated a decreased risk of becoming a long-term carrier among travellers with diarrhoea while abroad and a history of a new journey during the follow-up period. High susceptible rates were demonstrated to carbapenems (97–100%), temocillin (95%), mecillinam (97%), amikacin (98%), fosfomycin (98%), nitrofurantoin (99%) and tigecycline (97%).

Conclusion

Travel-associated faecal colonisation with ESBL-PE appears to be transient and generally brief. Diarrhoea while abroad or a new trip abroad during the follow-up period decreased the risk of becoming a long-term carrier. Only 11% of travellers who acquired ESBL-PE during their travels had sustained colonisation 12 months after return.

Responses of the Human Gut Escherichia coli Population to Pathogen and Antibiotic Disturbances

Research on human-associated E. coli tends to focus on pathogens, such as enterotoxigenic E. coli (ETEC) strains, which are a leading cause of diarrhea in developing countries. However, the severity of disease caused by these pathogens is thought to be influenced by the microbiome. The nonpathogenic E. coli community that resides in the human gastrointestinal tract may play a role in pathogen colonization and disease severity and may become a reservoir for virulence and antibiotic resistance genes. Our study used whole-genome sequencing of E. coli before, during, and after challenge with an archetype ETEC isolate, H10407, and antibiotic treatment to explore the diversity and resiliency of the resident E. coli population in response to the ecological disturbances caused by pathogen invasion and antibiotic treatment.

Studies of Escherichia coli in the human gastrointestinal tract have focused on pathogens, such as diarrhea-causing enterotoxigenic E. coli (ETEC), while overlooking the resident, nonpathogenic E. coli community. Relatively few genomes of nonpathogenic E. coli strains are available for comparative genomic analysis, and the ecology of these strains is poorly understood. This study examined the diversity and dynamics of resident human gastrointestinal E. coli communities in the face of the ecological challenges presented by pathogen (ETEC) challenge, as well as of antibiotic treatment. Whole-genome sequences obtained from E. coli isolates from before, during, and after ETEC challenge were used in phylogenomic and comparative genomic analyses to examine the diversity of the resident E. coli communities, as well as the dynamics of the challenge strain, H10407, a well-studied ETEC strain (serotype O78:H11) that produces both heat-labile and heat-stable enterotoxins. ETEC failed to become the dominant E. coli clone in two of the six challenge subjects, each of whom exhibited limited or no clinical presentation of diarrhea. The E. coli communities of the remaining four subjects became ETEC dominant during the challenge but reverted to their original, subject-specific populations following antibiotic treatment, suggesting resiliency of the resident E. coli population following major ecological disruptions. This resiliency is likely due in part to the abundance of antibiotic-resistant ST131 E. coli strains in the resident populations. This report provides valuable insights into the potential interactions of members of the gastrointestinal microbiome and its responses to challenge by an external pathogen and by antibiotic exposure.

IMPORTANCE Research on human-associated E. coli tends to focus on pathogens, such as enterotoxigenic E. coli (ETEC) strains, which are a leading cause of diarrhea in developing countries. However, the severity of disease caused by these pathogens is thought to be influenced by the microbiome. The nonpathogenic E. coli community that resides in the human gastrointestinal tract may play a role in pathogen colonization and disease severity and may become a reservoir for virulence and antibiotic resistance genes. Our study used whole-genome sequencing of E. coli before, during, and after challenge with an archetype ETEC isolate, H10407, and antibiotic treatment to explore the diversity and resiliency of the resident E. coli population in response to the ecological disturbances caused by pathogen invasion and antibiotic treatment.

Prevalence of CTX-M-Type Extended-Spectrum β-Lactamase-Producing Escherichia coli B2-O25-ST131 H30R Among Residents in Nonacute Care Facilities in Japan

We investigated the prevalence and characteristics of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli among 258 residents of long-term care facilities (LTCFs) in Japan. Out of 258 fecal samples collected from nine LTCFs between November 2015 and March 2017, we recovered 59 ESBL-producing E. coli isolates. All isolates carried bla_CTX-M genes, mainly bla_CTX-M-27 (42.4%), bla_CTX-M-14 (23.7%), and bla_CTX-M-15 (18.6%). The isolates showed 7 serotypes (STs), including ST131 (n = 49, 83.1%) and ST38 (n = 4, 6.8%), and 47 (79.7%) out of 49 isolates belonging to ST131 were identified as H30R. The 59 ESBL producers were divided into four groups, B2 (86.4%), D (8.5%), A (3.4%), and C (1.7%); 44 (74.6%) were epidemic clone B2-O25-ST131 H30R, of which 21, 11, and 6 harbored bla_CTX-M-27, bla_CTX-M-15, and bla_CTX-M-14, respectively. Most plasmids were of IncF replicon types (n = 33), and 22 bla_CTX-M-27-carrying plasmids showed multiple replicon types, including IncFII, FIA, and FIB. The ESBL producers were susceptible to imipenem, amikacin, and fosfomycin, but resistant to ceftazidime (49.2%), and ciprofloxacin (88.1%); in particular, the isolates harboring the bla_CTX-M-15 gene showed significantly high resistance rate to ceftazidime (p < 0.01). Our findings indicate that a considerable proportion of the examined LTCF residents carried ESBL-producing E. coli isolates in feces and had high prevalence of epidemic clone B2-O25-ST131. Furthermore, continuous investigations would be very necessary to monitor actual carriage states of ESBL-producers among the LTCF residents from the viewpoint of both public health and healthcare viewpoints.

Environmental and genetic modulation of the phenotypic expression of antibiotic resistance

Antibiotic resistance can be acquired by mutation or horizontal transfer of a resistance gene, and generally an acquired mechanism results in a predictable increase in phenotypic resistance. However, recent findings suggest that the environment and/or the genetic context can modify the phenotypic expression of specific resistance genes/mutations. An important implication from these findings is that a given genotype does not always result in the expected phenotype. This dissociation of genotype and phenotype has important consequences for clinical bacteriology and for our ability to predict resistance phenotypes from genetics and DNA sequences. A related problem concerns the degree to which the genes/mutations currently identified in vitro can fully explain the in vivo resistance phenotype, or whether there is a significant additional amount of presently unknown mutations/genes (genetic ‘dark matter’) that could contribute to resistance in clinical isolates. Finally, a very important question is whether/how we can identify the genetic features that contribute to making a successful pathogen, and predict why some resistant clones are very successful and spread globally? In this review, we describe different environmental and genetic factors that influence phenotypic expression of antibiotic resistance genes/mutations and how this information is needed to understand why particular resistant clones spread worldwide and to what extent we can use DNA sequences to predict evolutionary success.

Three cases of mcr-1-positive colistin-resistant Escherichia coli bloodstream infections in Italy, August 2016 to January 2017

We describe three cases of bloodstream infection caused by colistin-resistant Escherichia coli in patients in a tertiary hospital in Italy, between August 2016 and January 2017. Whole genome sequencing detected the mcr-1 gene in three isolated strains belonging to different sequence types (STs). This occurrence of three cases with mcr-1-positive E. coli belonging to different STs in six months suggests a widespread problem in settings where high multidrug resistance is endemic such as in Italy.

Fecal carriage of extended spectrum β-lactamase producing Escherichia coli and Klebsiella pneumoniae after urinary tract infection - A three year prospective cohort study

We have performed a prospective cohort study to investigate the duration of and risk factors for prolonged fecal carriage of ESBL-producing Escherichia coli or Klebsiella pneumoniae in patients with community acquired urinary tract infection caused by these bacteria. From 2009 to 2011, 101 Norwegian patients were recruited. Stool swabs and questionnaires were collected every three months for one year and at the end of the study in 2012. Information on antibiotic prescriptions was collected from the Norwegian Prescription Database. Stool samples were cultured directly on ChromID ESBL agar as well as in an enrichment broth, and culture positive isolates were examined by blaCTX-M multiplex PCR. Isolates without blaCTX-M were investigated for alternative ESBL-determinants with a commercial microarray system. Time to fecal clearance of ESBL producing Enterobacteriaceae was also analysed using Kaplan-Meier estimates. Uni- and multivariate logistic regression was used to compare groups according to previously described risk factors. The ESBL point prevalence of fecal carriage were 61% at 4 months, 56% at 7 months, 48% at 10 months, 39% at 13 months, 19% after two years, and 15% after three years or more. We found no correlation between duration of carriage, comorbidity, antibiotic use or travel to ESBL high-prevalence countries. Prolonged carriage was associated with E. coli isolates of phylogroup B2 or D. Importantly, comparative MLST and MLVA analyses of individual paired urine and fecal E. coli isolates revealed that ESBL production commonly occurred in diverse strains within the same host. When investigating cross-transmission of ESBL producing bacteria in health care institutions, this notion should be taken into account.

Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis

In a whole genome-based phylogeny, clinical and fecal isolates of Escherichia coli sequence type 131 (H30R1 and H30Rx subclones) from six households formed household-specific clusters, interspersed among reference ST131 genomes. This supported the fecal-urethral hypothesis and confirmed within-household strain sharing.

Background. Within-household sharing of strains from the resistance-associated H30R1 and H30Rx subclones of Escherichia coli sequence type 131 (ST131) has been inferred based on conventional typing data, but it has been assessed minimally using whole genome sequence (WGS) analysis.

Methods. Thirty-three clinical and fecal isolates of ST131-H30R1 and ST131-H30Rx, from 20 humans and pets in 6 households, underwent WGS analysis for comparison with 52 published ST131 genomes. Phylogenetic relationships were inferred using a bootstrapped maximum likelihood tree based on core genome sequence polymorphisms. Accessory traits were compared between phylogenetically similar isolates.

Results. In the WGS-based phylogeny, isolates clustered strictly by household, in clades that were distributed widely across the phylogeny, interspersed between H30R1 and H30Rx comparison genomes. For only 1 household did the core genome phylogeny place epidemiologically unlinked isolates together with household isolates, but even there multiple differences in accessory genome content clearly differentiated these 2 groups. The core genome phylogeny supported within-household strain sharing, fecal-urethral urinary tract infection pathogenesis (with the entire household potentially providing the fecal reservoir), and instances of host-specific microevolution. In 1 instance, the household's index strain persisted for 6 years before causing a new infection in a different household member.

Conclusions. Within-household sharing of E coli ST131 strains was confirmed extensively at the genome level, as was long-term colonization and repeated infections due to an ST131-H30Rx strain. Future efforts toward surveillance and decolonization may need to address not just the affected patient but also other human and animal household members.