Quantifying within-household transmission of extended-spectrum β-lactamase-producing bacteria

Modeling the transmission of antibiotic-resistant Enterobacterales in the community: A systematic review

BACKGROUND

Antibiotic-resistant Enterobacterales (ARE) are a public health threat worldwide. Dissemination of these opportunistic pathogens has been largely studied in hospitals. Despite high prevalence of asymptomatic colonization in the community in some regions of the world, less is known about ARE acquisition and spread in this setting. As explaining the community ARE dynamics has not been straightforward, mathematical models can be key to explore underlying phenomena and further evaluate the impact of interventions to curb ARE circulation outside of hospitals.

METHODS

We conducted a systematic review of mathematical modeling studies focusing on the transmission of AR-E in the community, excluding models only specific to hospitals. We extracted model features (population, setting), formalism (compartmental, individual-based), biological hypotheses (transmission, infection, antibiotic impact, resistant strain specificities) and main findings. We discussed additional mechanisms to be considered, open scientific questions, and most pressing data needs.

RESULTS

We identified 18 modeling studies focusing on the human transmission of ARE in the community (n=11) or in both community and hospital (n=7). Models aimed at (i) understanding mechanisms driving resistance dynamics; (ii) identifying and quantifying transmission routes; or (iii) evaluating public health interventions to reduce resistance. To overcome the difficulty of reproducing observed ARE dynamics in the community using the classical two-strains competition model, studies proposed to include mechanisms such as within-host strain competition or a strong host population structure. Studies inferring model parameters from longitudinal carriage data were mostly based on models considering the ARE strain only. They showed differences in ARE carriage duration depending on the acquisition mode: returning travelers have a significantly shorter carriage duration than discharged hospitalized patient or healthy individuals. Interestingly, predictions across models regarding the success of public health interventions to reduce ARE rates depended on pathogens, settings, and antibiotic resistance mechanisms. For E. coli, reducing person-to-person transmission in the community had a stronger effect than reducing antibiotic use in the community. For Klebsiella pneumoniae, reducing antibiotic use in hospitals was more efficient than reducing community use.

CONCLUSIONS

This study raises the limited number of modeling studies specifically addressing the transmission of ARE in the community. It highlights the need for model development and community-based data collection especially in low- and middle-income countries to better understand acquisition routes and their relative contribution to observed ARE levels. Such modeling will be critical to correctly design and evaluate public health interventions to control ARE transmission in the community and further reduce the associated infection burden.

Evaluation of antimicrobial selective pressure using the multicenter semiautomatic surveillance system Japan surveillance for infection prevention and healthcare epidemiology

BACKGROUND

Evaluating the selective pressure of antimicrobials on bacteria is important for promoting antimicrobial stewardship programs (ASPs). The aim of this study was to assess the selective pressure of antimicrobials by evaluating their use (carbapenem [CBP] and CBP-sparing therapy) over time and the detection status of CBP-resistant organisms using multicenter data.

METHODS

Among the facilities whose data were registered in the Japan Surveillance for Infection Prevention and Healthcare Epidemiology from 2017 to 2020, those that had data on the use of CBP and CBP-sparing therapy (fluoroquinolones [FQs], cefmetazole [CMZ], piperacillin-tazobactam [PIP/TAZ], ampicillin-sulbactam [ABPC/SBT], ceftriaxone/cefotaxime [CTRX/CTX], CAZ (ceftazidime), cefepime [CFPM], and aminoglycosides [AGs]) as well as on CBP-resistant Enterobacterales (CRE) and CBP-resistant Pseudomonas aeruginosa (CRPA) detection were included. Alcohol-based hand rubbing (ABHR) usage was also analyzed. Regression analyses, including multivariable regression analysis, were performed to evaluate trends. The association of antimicrobial use density (AUD) with CRE and CRPA detection rates was evaluated.

RESULTS

In 28 facilities nationwide, CBP, FQ, CAZ, AG, and PIP/TAZ use decreased over the 3-year period, whereas the use of CMZ, ABPC/SBT, CTRX/CTX, CFPM, and ABHR as well as the rates of CRE and CRPA detection increased. The average AUD did not significantly correlate with CRE and CRPA detection rates. The multivariable regression analysis did not reveal any significant correlation between each AUD or ABHR and CRE or CRPA detection.

CONCLUSION

CBP and ABHR use showed a decreasing and an increasing trend, respectively, while CRPA and CRE detection rates exhibited a gradual increase. The considerably low CRE and CRPA detection rates suggest that slight differences in numbers may have been observed as excessive trend changes. Further investigation is warranted to evaluate selective pressure while considering the characteristics of ASP and the mechanisms underlying resistance.

Carriage Rate of Enterobacterales Resistant to Extended-Spectrum Cephalosporins in the Tunisian Population

Enterobacterales resistant to extended-spectrum cephalosporins (ESC) are a marker of the antimicrobial resistance (AMR) burden. They are infecting humans, but the intestinal microbiota can also be transiently colonized without developing symptoms. Healthy carriage can promote silent dissemination of resistant bacteria, and data on this colonization are often lacking. Between 2021 and 2023, a sampling of healthy Tunisian people was carried out. Fecal samples (n = 256) were plated on selective agar, and all collected isolates were characterized by phenotypic (antibiograms) and genomic (whole-genome sequencing) methods. A total of 26 (26/256, 10.2%) isolates were collected, including 24 Escherichia coli and 2 Klebsiella pneumoniae. In total, 17 isolates (15 E. coli and 2 K. pneumoniae) presented an ESBL phenotype conferred by the blaCTX-M-15 gene, and 9 E. coli isolates presented an AmpC phenotype conferred by the blaDHA-1 gene. K. pneumoniae belonged to ST1564 and ST313, while E. coli belonged to diverse STs including the pandemic ST131 clone. Clonally related ST349 E. coli isolates carrying the blaDHA-1 gene were found in nine individuals. In parallel, four blaCTX-M-15 -positive E. coli isolates carried this ESC-resistance gene on an epidemic plasmid IncF/F-:A-:B53 previously identified in Tunisian pigeons and fish. These findings highlight the spread of genetically diverse ESC-resistant Enterobacterales as well as an epidemic plasmid in Tunisia, emphasizing the need for antimicrobial stewardship to limit the transmission of these resistances in the Tunisian population.

Antimicrobial consumption and resistance in bacteria from humans and food-producing animals: Fourth joint inter-agency report on integrated analysis of antimicrobial agent consumption and occurrence of antimicrobial resistance in bacteria from humans and food-producing animals in the EU/EEA JIACRA IV - 2019-2021

The fourth joint inter-agency report on integrated analysis of antimicrobial consumption (AMC) and the occurrence of antimicrobial resistance (AMR) in bacteria from humans and food-producing animals (JIACRA) addressed data obtained by the Agencies' EU-wide surveillance networks for 2019-2021. The analysis also sought to identify whether significant trends in AMR and AMC were concomitant over 2014-2021. AMC in both human and animal sectors, expressed in mg/kg of estimated biomass, was compared at country and European level. In 2021, the total AMC was assessed at 125.0 mg/kg of biomass for humans (28 EU/EEA countries, range 44.3-160.1) and 92.6 mg/kg of biomass for food-producing animals (29 EU/EEA countries, range 2.5-296.5). Between 2014 and 2021, total AMC in food-producing animals decreased by 44%, while in humans, it remained relatively stable. Univariate and multivariate analyses were performed to study associations between AMC and AMR for selected combinations of bacteria and antimicrobials. Positive associations between consumption of certain antimicrobials and resistance to those substances in bacteria from both humans and food-producing animals were observed. For certain combinations of bacteria and antimicrobials, AMR in bacteria from humans was associated with AMR in bacteria from food-producing animals which, in turn, was related to AMC in animals. The relative strength of these associations differed markedly between antimicrobial class, microorganism and sector. For certain antimicrobials, statistically significant decreasing trends in AMC and AMR were concomitant for food-producing animals and humans in several countries over 2014-2021. Similarly, a proportion of countries that significantly reduced total AMC also registered increasing susceptibility to antimicrobials in indicator E. coli from food-producing animals and E. coli originating from human invasive infections (i.e., exhibited 'complete susceptibility' or 'zero resistance' to a harmonised set of antimicrobials). Overall, the findings suggest that measures implemented to reduce AMC in food-producing animals and in humans have been effective in many countries. Nevertheless, these measures need to be reinforced so that reductions in AMC are retained and further continued, where necessary. This also highlights the importance of measures that promote human and animal health, such as vaccination and better hygiene, thereby reducing the need for use of antimicrobials.

Gut microbiome dynamics in index patients colonized with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales after hospital discharge and their household contacts

IMPORTANCE

Colonization with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) often precedes infections and is therefore considered as a great threat for public health. Here, we studied the gut microbiome dynamics in eight index patients colonized with ESBL-PE after hospital discharge and the impact of exposure to this index patient on the gut microbiome dynamics of their household contacts. We showed that the microbiome composition from index patients is different from their household contacts upon hospital discharge and that, in some of the index patients, their microbiome composition over time shifted toward the composition of their household contacts. In contrast, household contacts showed a stable microbiome composition over time irrespective of low-level extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) or extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) gut colonization, suggesting that, in healthy microbiomes, colonization resistance is able to prevent ESBL-PE expansion.

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

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

Neonatal acquisition of extended-spectrum beta-lactamase-producing Enterobacteriaceae in the community of a low-income country (NeoLIC): protocol for a household cohort study in Moramanga, Madagascar

INTRODUCTION

Data regarding the acquisition of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) in neonates at the community level are scarce in low-income and middle-income countries (LMICs), where the burden of neonatal sepsis is high.Our study aims at identifying and quantifying the role of the different routes of ESBL-PE transmission for neonates, which are still undefined in the community in LMICs.

METHODS AND ANALYSIS

In a semirural community in Madagascar, 60 mothers and their neonates will be recruited at delivery, during which a maternal stool sample and meconium of the newborn will be collected. Home visits will be planned the day of the delivery and next at days 3, 7, 14, 21 and 28. Stool samples from the newborn, the mother and every other household member will be collected at each visit, as well as samples from the environment in contact with the newborn (food, surfaces and objects). Sociodemographic data and factors which might drive ESBL-PE acquisition will also be collected.We will analyse the isolated ESBL-PE using DNA sequencing methods to characterise clones, resistance genes and plasmids of ESBL-PE. To analyse these data globally, we will develop novel analytical approaches combining mathematical modelling and statistics. Finally, mathematical simulations will be performed to test different strategies of control of ESBL-PE transmission to neonates.In complement, we will conduct an anthropological investigation to understand local environments and practices that would contribute to neonatal ESBL-PE acquisition. In-depth interviews with members of 16 households will be conducted and 4 mother-newborn pairs will be followed by a participants' observations methodology.

ETHICS AND DISSEMINATION

The study was approved by the ethical committee in Madagascar and by the institutional review board of Institut Pasteur, Paris, France.Findings will be reported to participating families, collaborators and local government; presented at national and international conferences and disseminated by peer-review publications.

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

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

Does plasmid-based beta-lactam resistance increase E. coli infections: Modelling addition and replacement mechanisms

Infections caused by antibiotic-resistant bacteria have become more prevalent during past decades. Yet, it is unknown whether such infections occur in addition to infections with antibiotic-susceptible bacteria, thereby increasing the incidence of infections, or whether they replace such infections, leaving the total incidence unaffected. Observational longitudinal studies cannot separate both mechanisms. Using plasmid-based beta-lactam resistant E. coli as example we applied mathematical modelling to investigate whether seven biological mechanisms would lead to replacement or addition of infections. We use a mathematical neutral null model of individuals colonized with susceptible and/or resistant E. coli, with two mechanisms implying a fitness cost, i.e., increased clearance and decreased growth of resistant strains, and five mechanisms benefitting resistance, i.e., 1) increased virulence, 2) increased transmission, 3) decreased clearance of resistant strains, 4) increased rate of horizontal plasmid transfer, and 5) increased clearance of susceptible E. coli due to antibiotics. Each mechanism is modelled separately to estimate addition to or replacement of antibiotic-susceptible infections. Fitness costs cause resistant strains to die out if other strain characteristics are maintained equal. Under the assumptions tested, increased virulence is the only mechanism that increases the total number of infections. Other benefits of resistance lead to replacement of susceptible infections without changing the total number of infections. As there is no biological evidence that plasmid-based beta-lactam resistance increases virulence, these findings suggest that the burden of disease is determined by attributable effects of resistance rather than by an increase in the number of infections.

High levels of gut carriage of antimicrobial-resistant Escherichia coli in community settings in Rio de Janeiro, Brazil

The prevalence and risk factors for gut carriage of antimicrobial-resistant Escherichia coli among individuals living in the community in Rio de Janeiro, Brazil, are unknown. The aim of this study was to determine the prevalence of colonization with antimicrobial-resistant E. coli, including isolates producing ESBL and harboring plasmid-mediated quinolone resistant (PMQR) genes in this community. We performed a cross-sectional study and analyzed fecal specimens of individuals attending outpatient clinics in the city from January 2015 to July 2019. We investigated susceptibility to antimicrobial agents by disc diffusion tests and used PCR to determine ESBL types, PMQR, and the virulence genes that characterize an isolate as extraintestinal pathogenic E. coli (ExPEC). Among the 623 subjects, 212 (34%) carried an isolate resistant to at least one of the tested antimicrobial agents, with the highest frequencies of resistance to ampicillin (26%), trimethoprim-sulfamethoxazole (19%), cefazolin (14%), and ciprofloxacin (CIP, 9%). In addition, 13% (81) of subjects carried a multidrug-resistant-E.coli (MDR-E), including 47 (8% of all isolates) ESBL-producing E. coli (ESBL-E), mainly of CTX-M-8 (15, 32%) and CTX-M-15 (9, 20%) types. PMQR genes were present in 7% (42) of all isolates, including 60% (32) of the 53 resistant to CIP. Previous use of antimicrobial agents, particularly fluoroquinolones, was a risk factor for colonization with MDR-E (25%, 20/81 vs 13%, 70/542, p = 0.01), ESBL-E (28%, 13/47, vs 13%, 77/576, p = 0.01), and resistance to CIP (26%, 14/53, vs 12%, 70/570, p = 0.01). The most pathogenic phylogroups B2, C, and D were 37% of the MDR-E, 30% of the ESBL-E, 38% of the CIP-resistant, and 31% of PMQR gene carrying E. coli isolates. We show that carriage of MDR-E (mostly ESBL-E) reached high levels in the community in Rio de Janeiro, increased by the selection of antimicrobial agents. Much of the resistant E. coli isolates are potential pathogenic strains. The widespread use of antimicrobial agents during the COVID-19 pandemic in Brazil may have worsened this picture.

Carriage of ESBL-producing Enterobacterales in wastewater treatment plant workers and surrounding residents - the AWARE Study

To investigate whether wastewater treatment plant (WWTP) workers and residents living in close proximity to a WWTP have elevated carriage rates of ESBL-producing Enterobacterales, as compared to the general population. From 2018 to 2020, we carried out a cross-sectional study in Germany, the Netherlands, and Romania among WWTP workers (N = 344), nearby residents (living ≤ 300 m away from WWTPs; N = 431) and distant residents (living ≥ 1000 m away = reference group; N = 1165). We collected information on potential confounders via questionnaire. Culture of participants' stool samples was performed with ChromID®-ESBL agar plates and species identification with MALDI-TOF-MS. We used logistic regression to estimate the odds ratio (OR) for carrying ESBL-producing E. coli (ESBL-EC). Sensitivity analyses included stratification by country and interaction models using country as secondary exposure. Prevalence of ESBL-EC was 11% (workers), 29% (nearby residents), and 7% (distant residents), and higher in Romania (28%) than in Germany (7%) and the Netherlands (6%). Models stratified by country showed that within the Romanian population, WWTP workers are about twice as likely (aOR = 2.34, 95% CI: 1.22-4.50) and nearby residents about three times as likely (aOR = 3.17, 95% CI: 1.80-5.59) to be ESBL-EC carriers, when compared with distant residents. In stratified analyses by country, we found an increased risk for carriage of ESBL-EC in Romanian workers and nearby residents. This effect was higher for nearby residents than for workers, which suggests that, for nearby residents, factors other than the local WWTP could contribute to the increased carriage.

Household Transmission of Carbapenemase-producing Enterobacterales in Ontario, Canada

BACKGROUND

Data on household transmission of carbapenemase-producing Enterobacterales (CPE) remain limited. We studied risk of CPE household co-colonization and transmission in Ontario, Canada.

METHODS

We enrolled CPE index cases (identified via population-based surveillance from January 2015 to October 2018) and their household contacts. At months 0, 3, 6, 9, and 12, participants provided rectal and groin swabs. Swabs were cultured for CPE until September 2017, when direct polymerase chain reaction (PCR; with culture of specimens if a carbapenemase gene was detected) replaced culture. CPE risk factor data were collected by interview and combined with isolate whole-genome sequencing to determine likelihood of household transmission. Risk factors for household contact colonization were explored using a multivariable logistic regression model with generalized estimating equations.

RESULTS

Ninety-five households with 177 household contacts participated. Sixteen (9%) household contacts in 16 (17%) households were CPE-colonized. Household transmission was confirmed in 3/177 (2%) cases, probable in 2/177 (1%), possible in 9/177 (5%), and unlikely in 2/177 (1%). Household contacts were more likely to be colonized if they were the index case's spouse (odds ratio [OR], 6.17; 95% confidence interval [CI], 1.05-36.35), if their index case remained CPE-colonized at household enrollment (OR, 7.00; 95% CI, 1.92-25.49), or if they had at least 1 set of specimens processed after direct PCR was introduced (OR, 6.46; 95% CI, 1.52-27.40).

CONCLUSIONS

Nine percent of household contacts were CPE-colonized; 3% were a result of household transmission. Hospitals may consider admission screening for patients known to have CPE-colonized household contacts.

National point prevalence study on carriage of multidrug-resistant microorganisms in Dutch long-term care facilities in 2018

OBJECTIVES

Long-term care facilities (LTCFs) may act as a reservoir of ESBL-producing Enterobacterales (ESBL-E) and carbapenemase-producing Enterobacterales (CPE) for hospitals and the general population. In this study, we estimated the prevalence and molecular epidemiology of rectal carriage with ESBL-E and CPE in residents of Dutch LTCFs between March 2018 and December 2018.

METHODS

LTCFs were geographically selected across the country. For each LTCF, a random sample of residents were tested for ESBL-E and CPE in 2018. To identify risk factors for high carriage prevalence and/or individual carriage, characteristics of LTCFs and of a subset of the tested residents were collected. WGS was conducted on isolates from LTCFs with an ESBL-E prevalence of >10% and all CPE isolates to identify institutional clonal transmission.

RESULTS

A total of 4420 residents of 159 LTCFs were included. The weighted mean ESBL-E prevalence was 8.3% (95% CI: 6.8-10.0) and no CPE were found. In 53 LTCFs (33%), where ESBL-E prevalence was >10%, MLST using WGS (wgMLST) was performed. This included 264 isolates, the majority being Escherichia coli (n = 224) followed by Klebsiella pneumoniae (n = 30). Genetic clusters were identified in more than half (30/53; 57%) of high ESBL-positive LTCFs. Among the E. coli isolates, blaCTX-M-15 (92/224; 41%) and blaCTX-M-27 (40/224; 18%) were the most prevalent ESBL-encoding genes. For K. pneumoniae isolates, the most common was blaCTX-M-15 (23/30; 80%).

CONCLUSIONS

The estimated prevalence of ESBL-E rectal carriage in Dutch LTCFs is 8.3% and resistance is observed mainly in E. coli with predominance of blaCTX-M-15 and blaCTX-M-27. ESBL-E prevalence in LTCFs seems comparable to previously reported prevalence in hospitals and the general population.

Household transmission of carbapenemase-producing Enterobacteriaceae: a prospective cohort study

OBJECTIVES

To estimate the transmission rate of carbapenemase-producing Enterobacteriaceae (CPE) in households with recently hospitalized CPE carriers.

METHODS

We conducted a prospective case-ascertained cohort study. We identified the presence of CPE in stool samples from index subjects, household contacts and companion animals and environmental samples at regular intervals. Linked transmissions were identified by WGS. A Markov model was constructed to estimate the household transmission potential of CPE.

RESULTS

Ten recently hospitalized index patients and 14 household contacts were included. There were seven households with one contact, two households with two contacts, and one household with three contacts. Index patients were colonized with blaOXA-48-like (n = 4), blaKPC-2 (n = 3), blaIMP (n = 2), and blaNDM-1 (n = 1), distributed among divergent species of Enterobacteriaceae. After a cumulative follow-up time of 9.0 years, three family members (21.4%, 3/14) acquired four different types of CPE in the community (hazard rate of 0.22/year). The probability of CPE transmission from an index patient to a household contact was 10% (95% CI 4%-26%).

CONCLUSIONS

We observed limited transmission of CPE from an index patient to household contacts. Larger studies are needed to understand the factors associated with household transmission of CPE and identify preventive strategies.

Transmission of ESBL-producing Escherichia coli between broilers and humans on broiler farms

BACKGROUND

ESBL and AmpC β-lactamases are an increasing concern for public health. Studies suggest that ESBL/pAmpC-producing Escherichia coli and their plasmids carrying antibiotic resistance genes can spread from broilers to humans working or living on broiler farms. These studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these isolates.

METHODS

Eleven suspected transmission events among broilers and humans living/working on eight broiler farms were investigated using whole-genome short-read (Illumina) and long-read sequencing (PacBio). Core genome MLST (cgMLST) was performed to investigate the occurrence of strain transmission. Horizontal plasmid and gene transfer were analysed using BLAST.

RESULTS

Of eight suspected strain transmission events, six were confirmed. The isolate pairs had identical ESBL/AmpC genes and fewer than eight allelic differences according to the cgMLST, and five had an almost identical plasmid composition. On one of the farms, cgMLST revealed that the isolate pairs belonging to ST10 from a broiler and a household member of the farmer had 475 different alleles, but that the plasmids were identical, indicating horizontal transfer of mobile elements rather than strain transfer. Of three suspected horizontal plasmid transmission events, one was confirmed. In addition, gene transfer between plasmids was found.

CONCLUSIONS

The present study confirms transmission of strains as well as horizontal plasmid and gene transfer between broilers and farmers and household members on the same farm. WGS is an important tool to confirm suspected zoonotic strain and resistance gene transmission.

Do vegetarians less frequently carry ESBL/pAmpC-producing Escherichia coli/Klebsiella pneumoniae compared with non-vegetarians?

BACKGROUND

ESBL and plasmid-mediated AmpC (pAmpC)-producing Enterobacteriaceae are frequently found on meat products in Dutch retail, especially on poultry.

OBJECTIVES

We investigated whether vegetarians are at lower risk of carrying ESBL/pAmpC-producing Escherichia coli/Klebsiella pneumoniae (ESBL-E/K) compared with persons who consume meat.

METHODS

Vegetarians, pescatarians (vegetarians who eat fish) and non-vegetarians (persons who eat meat at least three times per week) were asked to send in a faecal sample and a questionnaire. ESBL-E/K were cultured and MLSTs were determined. ESBL/pAmpC genes were analysed using PCR and sequencing. The risk of ESBL-E/K carriage in the three study groups was analysed using multivariable logistic regression.

RESULTS

Prevalence of ESBL-E/K carriage was 8.0% in vegetarians (63/785; 95% CI 6.3-10.1), 6.9% in pescatarians (27/392; 95% CI 4.8-9.8) and 3.8% in non-vegetarians (14/365; 95% CI 2.3-6.3). Multivariable analysis showed an OR for ESBL-E/K carriage of 2.2 for vegetarians (95% CI 1.2-4.0) and 1.6 for pescatarians (95% CI 0.8-3.2) compared with non-vegetarians. The predominant MLST was E. coli ST131 and the most common ESBL genes were blaCTX-M-15, blaCTX-M-27, blaCTX-M-14 and blaCTX-M-1 in all diet groups. Independent risk factors for ESBL-E/K carriage were travel to Africa/Latin America/Asia (OR 4.6; 95% CI 2.8-7.7) in the past 6 months and rarely/never washing hands before food preparation (OR 2.5; 95% CI 1.2-5.0).

CONCLUSIONS

Vegetarians and pescatarians did not have a lower risk of ESBL-E/K carriage compared with non-vegetarians, indicating that eating meat is not an important risk factor for ESBL-E/K carriage.

Increased risk of acquisition and transmission of ESBL-producing Enterobacteriaceae in malnourished children exposed to amoxicillin

OBJECTIVES

Routine amoxicillin for children with uncomplicated severe acute malnutrition raises concerns of increasing antibiotic resistance. We performed an ancillary study nested within a double-blind, placebo-controlled trial in Niger testing the role of routine 7 day amoxicillin therapy in nutritional recovery of children 6 to 59 months of age with uncomplicated severe acute malnutrition.

METHODS

We screened 472 children for rectal carriage of ESBL-producing Enterobacteriaceae (ESBL-E) as well as their household siblings under 5 years old, at baseline and Week 1 (W1) and Week 4 (W4) after start of therapy, and characterized strains by WGS. ClinicalTrials.gov: NCT01613547.

RESULTS

Carriage in index children at baseline was similar in the amoxicillin and the placebo groups (33.8% versus 27.9%, P = 0.17). However, acquisition of ESBL-E in index children at W1 was higher in the amoxicillin group than in the placebo group (53.7% versus 32.2%, adjusted risk ratio = 2.29, P = 0.001). Among 209 index and sibling households possibly exposed to ESBL-E transmission, 16 (7.7%) had paired strains differing by ≤10 SNPs, suggesting a high probability of transmission. This was more frequent in households from the amoxicillin group than from the placebo group [11.5% (12/104) versus 3.8% (4/105), P = 0.04].

CONCLUSIONS

Among children exposed to amoxicillin, ESBL-E colonization was more frequent and the risk of transmission to siblings higher. Routine amoxicillin should be carefully balanced with the risks associated with ESBL-E colonization.

Comparative Analysis of Consumer Exposure to Resistant Bacteria through Chicken Meat Consumption in Germany

Human exposure to bacteria carrying antimicrobial resistance (AMR) genes through the consumption of food of animal origin is a topic which has gained increasing attention in recent years. Bacterial transmission can be enhanced, particularly in situations in which the consumer pays less attention to hygiene practices, and consumer exposure to foodborne resistant bacteria through ready-to-eat foods could be increased. It has been demonstrated that even methicillin-resistant Staphylococcus aureus (MRSA) bacteria, which have low prevalence and concentration in raw chicken meat in Germany, may reach the consumer during barbecue events after failures in hygiene practices. This study aimed to quantify the consumer exposure to extended-spectrum beta-lactamase- (ESBL) or ampicillinase class C (AmpC) beta-lactamase-producing E. coli in Germany through the consumption of chicken meat and bread during household barbecues. The study considered cross-contamination and recontamination processes from raw chicken meat by using a previously-developed probabilistic consumer exposure model. In addition, a comparative analysis of consumer exposure was carried out between ESBL-/AmpC-producing E. coli and MRSA. Our results demonstrated that the probability of ESBL-/AmpC-producing E. coli reaching the consumer was 1.85 × 10^-5 with the number of bacteria in the final serving averaging 332. Given the higher prevalence and concentration of ESBL-/AmpC-producing E. coli in raw chicken meat at retail compared to MRSA, comparative exposure assessment showed that the likelihood and extent of exposure were significantly higher for ESBL-/AmpC-producing E. coli than for MRSA. ESBL-/AmpC-producing E. coli was determined to be 7.6 times likelier (p-value < 0.01) than MRSA to reach the consumer, with five times the concentration of bacteria in the final serving (p-value < 0.01).

Quinolone Consumption by Mothers Increases Their Children's Risk of Acquiring Quinolone-Resistant Bacteriuria

BACKGROUND

Quinolone resistance has been documented in the pediatric population, although their use is limited in children. This study investigated the effect of maternal quinolone use on gram-negative bacterial resistance to quinolones in their offspring.

METHODS

We conducted a population-based, unmatched case-control study during 2010-2017. Cases were all children aged 0.5-17 years with community acquired, gram-negative quinolone-resistant bacteriuria. Controls were similar children with quinolone-sensitive bacteriuria. Only the first positive urine cultures for each child were included. Data on quinolones dispensed to the mother, any antibiotics dispensed to the children, age, sex, ethnicity, and prior hospitalizations were collected. Children with previous quinolone use were excluded.

RESULTS

The study population consisted of 40 204 children. Quinolone resistance was detected in 2182 (5.3%) urine cultures. The median age was 5 years, with 93.7% females and 77.6% Jewish. A total of 26 937 (65%) of the children received any antibiotic and 1359 (3.2%) of the mothers received quinolones in the 6 months preceding bacteriuria. Independent risk factors were quinolone dispensed to the mothers (odds ratio [OR], 1.50 [95% confidence interval {CI}, 1.22-1.85]), Arab ethnicity (OR, 1.99 [95% CI, 1.81-2.19]), and antibiotic dispensed to the child (OR, 1.54 [95% CI, 1.38-1.71]). Compared with children aged 12-17 years, younger children had 1.33-1.43 increased odds for quinolone-resistant bacteriuria.

CONCLUSIONS

Quinolone prescription to mothers was linked to increased risk of community-acquired, quinolone-resistant bacteria in their offspring, by about 50%. This is another example of the deleterious ecological effects of antibiotic use and should be considered when prescribing antibiotics.

Household acquisition and transmission of extended-spectrum β-lactamase (ESBL) -producing Enterobacteriaceae after hospital discharge of ESBL-positive index patients

OBJECTIVES

This study aimed to determine rates and risk factors of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) acquisition and transmission within households after hospital discharge of an ESBL-PE-positive index patient.

METHODS

Two-year prospective cohort study in five European cities. Patients colonized with ESBL-producing Escherichia coli (ESBL-Ec) or Klebsiella pneumoniae (ESBL-Kp), and their household contacts were followed up for 4 months after hospital discharge of the index case. At each follow up, participants provided a faecal sample and personal information. ESBL-PE whole-genome sequences were compared using pairwise single nucleotide polymorphism-based analysis.

RESULTS

We enrolled 71 index patients carrying ESBL-Ec (n = 45), ESBL-Kp (n = 20) or both (n = 6), and 102 household contacts. The incidence of any ESBL-PE acquisition among household members initially free of ESBL-PE was 1.9/100 participant-weeks at risk. Nineteen clonally related household transmissions occurred (case to contact: 13; contact to case: 6), with an overall rate of 1.18 transmissions/100 participant-weeks at risk. Most of the acquisition and transmission events occurred within the first 2 months after discharge. The rate of ESBL-Kp household transmission (1.16/100 participant-weeks) was higher than of ESBL-Ec (0.93/100 participant-weeks), whereas more acquisitions were noted for ESBL-Ec (1.06/100 participant-weeks) compared with ESBL-Kp (0.65/100 participant-weeks). Providing assistance for urinary and faecal excretion to the index case by household members increased the risk of ESBL-PE transmission (adjusted prevalence ratio 4.3; 95% CI 1.3-14.1).

CONCLUSIONS

ESBL-PE cases discharged from the hospital are an important source of ESBL-PE transmission within households. Most acquisition and transmission events occurred during the first 2 months after hospital discharge and were causally related to care activities at home, highlighting the importance of hygiene measures in community settings.

CLINICAL STUDY REGISTRATION

German Clinical Trials Register, DRKS-ID: DRKS00013250.

Urban Migrant Labourers as Potential Source for Transfer of Antimicrobial Resistance to Rural Community

The aim of the study was to investigate potential evidence for spread of antimicrobial resistance (AMR) from urban migrant labourers to labourers from local resident rural community due to sharing of common residential premises and other civic amenities. Two groups of unskilled labourers, enrolled for civil construction in a peri-urban area viz. (i) labourers having migrated from urban zone and (ii) labourers from local resident village community were compared in terms of demographic profile, history of various risk factors towards acquisition of AMR and prevalence of extended-spectrum beta-lactamase (ESBL), carbapenemase and New Delhi metallo-beta-lactamase type 1 (NDM-1) categories of AMR at enrolment and after one year of sharing of common residential premises with associated sanitation facilities using Escherichia coli as indicator organism. Higher percentage of urban migrant labourers were characterised by low literacy level, history of inhabitation in makeshift shelters without dedicated access to drinking water or cooking space, practice of defecation in open, episodes of illness suggestive of bacterial infections, faulty treatment seeking behaviour and intestinal carriage rate of E. coli with various categories of AMR compared to the non-migrant labourers from rural community. The later group showed an increase in the prevalence of carbapenem resistance with NDM-1 production during the duration of co-inhabitation with urban migrant labourers. The present study provided potential evidence for transfer of AMR by urban migrant labourers to non-migrant labourers from rural community that may serve as vehicle for further transmission of AMR to the rural community hitherto unexposed or less exposed to the problem.

Acquisition of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in intensive care units in Thailand

This study aimed to assess the prevalence and associated risk factors for extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae (ESBL-EK) acquisition among patients staying in medical and surgical Intensive Care Units (ICU) in Northern Thailand. Rectal swabs were collected from 206 ICU patients upon admission and discharge. Overall, the ESBL-EK acquisition rate among patients during ICU stay was 29.6%. Acquisition rate was significantly higher for K. pneumoniae (20.9%) than that of E. coli (12.1%) (p = 0.024). Multivariate logistic regression analysis identified the use of third generation cephalosporin (p = 0.008) as a risk factor for ESBL-EK acquisition. Sixty-eight ESBL-EK isolates (25 E. coli and 43 K. pneumoniae) were recovered. The majority of ESBL-EK isolates (≥88%) were resistant to ceftazidime, cefepime and aztreonam. Fifty-two acquired ESBL-EK isolates (76.5%) were positive for bla_CTX-M and 4 K. pneumoniae isolates simultaneously carried bla_NDM-1. Our results reveal that ICU patients could acquire ESBL-EK during hospitalization and the use of third generation cephalosporin should be strictly controlled to prevent the acquisition of ESBL-EK among ICU patients.

Hand hygiene improvement or antibiotic restriction to control the household transmission of extended-spectrum β-lactamase-producing Escherichia coli: a mathematical modelling study

Background

The best strategy to control ESBL-producing Escherichia coli (ESBL-EC) spread in the community is lacking.

Methods

We developed an individual-based transmission model to evaluate the impact of hand hygiene (HH) improvement and reduction in antibiotic use on the within-household transmission of ESBL-EC. We used data from the literature and incorporated key elements of ESBL-EC transmission such as the frequency and nature of contacts among household members, antibiotic use in the community and hand hygiene behaviour. We introduced in a household a single ESBL-EC colonised person and simulated the transmission dynamics of ESBL-EC over a one-year time horizon.

Results

The probability of ESBL-EC transmission depended on the household composition and the profile of the initial carrier. In the two-person household, the probability of ESBL-EC transmission was 5.3% (95% CI 5.0–5.6) or 6.6% (6.3–6.9) when the index person was a woman or a man, respectively. In a four-person household, the probability of transmission varied from 61.4% (60.9–62.0) to 68.8% (68.3–69.3) and was the highest when the index patient was the baby. Improving HH by 50% reduced the probability of transmission by 33–62%. Antibiotic restriction by 50% reduced the transmission by 2–6%.

Conclusions

The transmission of ESBL-EC is frequent in households and especially those with a baby. Antibiotic reduction had little impact on ESBL-EC. Improvement of hygiene in the community could help prevent transmission of ESBL-EC.

Prevalence and associated factors for carriage of Enterobacteriaceae producing ESBLs or carbapenemase and methicillin-resistant Staphylococcus aureus in Hong Kong community

OBJECTIVES

We conducted a cross-sectional study in Hong Kong community to estimate the carriage prevalence, associated factors and genotypes of extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E), methicillin-resistant Staphylococcus aureus (MRSA) and carbapenemase-producing Enterobacteriaceae (CPE).

METHODS

Seemingly healthy subjects were asked to provide nasal, handprint and stool samples from March to April 2017. Isolates were characterized by molecular methods. We used multivariable logistic regression models within a generalized estimating equation framework to identify risk factors for ESBL-E carriage. Characteristics of MRSA/CPE carriage were summarized.

RESULTS

The prevalence of ESBL-E, MRSA and CPE were 52.8% (104/197), 2.5% (5/197) and 0.5% (1/197) respectively. Most ESBL-E isolates were E. coli (85.6%; 113/132). Most ESBL genes belonged to bla_CTX-M-G9 (68.9%) and bla_TEM (53.0%) types. Self-reported antibiotic consumption (≥2 courses) in the past six months was associated with ESBL-E carriage (adjusted odds ratio: 4.71-5.47).

CONCLUSIONS

Abundance of ESBL-E in the community are causes of concern, and antibiotic use is associated with its carriage. Presence of MRSA and CPE in community members without clear healthcare exposure hints on a change in their epidemiology. This study establishes a baseline to formulate infection control policies and future studies in combating antimicrobial resistance.

Transmission Routes of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in a Neonatology Ward in Madagascar

The diffusion of extended-spectrum beta-lactamase (E-ESBL)-producing Enterobacteriaceae is a major concern worldwide, especially in low-income countries, where they may lead to therapeutic failures. In hospitals, where colonization is the highest, E-ESBL transmission is poorly understood, limiting the possibility of establishing effective control measures. We assessed E-ESBL-acquisition routes in a neonatalogy ward in Madagascar. Individuals from a neonatology ward were longitudinally followed-up (August 2014-March 2015). Newborns' family members' and health-care workers (HCWs) were stool-sampled and tested for E-ESBL colonization weekly. Several hypothetical acquisition routes of newborns-e.g. direct contact with family members and HCWs and indirect contact with other newborns through environmental contamination, colonization pressure, or transient hand carriage-were examined and compared using mathematical modeling and Bayesian inference. In our results, high E-ESBL acquisition rates were found, reaching > 70% for newborns, > 55% for family members, and > 75% for HCWs. Modeling analyses indicated transmission sources for newborn colonization to be species dependent. Health-care workers' route were selected for Klebsiella pneumoniae and Escherichia coli, with respective estimated transmission strengths of 0.05 (0.008; 0.14) and 0.008 (0.001; 0.021) ind^-1 day^-1. Indirect transmissions associated with ward prevalence, e.g. through hand carriage or environment, were selected for Enterobacter cloacae, E. coli, and K. pneumoniae (range 0.27-0.41 ind^-1 day^-1). Importantly, family members were not identified as transmission source. To conclude, E-ESBL acquisition sources are strongly species dependent. Escherichia coli and E. cloacae involve more indirect contamination, whereas K. pneumoniae also spreads through contact with colonized HCWs. These findings should help improve control measures to reduce in-hospital transmission.

Incidence of health care-associated extended-spectrum β-lactamase-positive patients before and after discontinuation of contact precautions

BACKGROUND

Isolation of patients with multidrug-resistant organisms has been recommended in several guidelines. Recent evidence has suggested potential negative effects of isolation on patient well-being and facility throughput. Published literature shows a difference in transmission risk of extended-spectrum β-lactamase (ESBL)-producing organisms, suggesting that contact precautions may not be necessary for all ESBL-positive organisms.

METHODS

Incidence rates of health care-associated ESBL organisms were measured before and after eliminating the use of contact precautions for patients with only ESBL-positive organisms. The National Healthcare Safety Network surveillance methodology was used to measure incidence. Surgical site infections and carbapenem-resistant Enterobacteriaceae were excluded from the surveillance incidence.

RESULTS

The incidence of health care-associated ESBL infections from January 2014 through November 2015 was 3.71 per 10,000 patient days. The incidence from December 2015 through August 2017 was 3.00 per 10,000 patient days. This rate change was statistically significant (P = .022) CONCLUSIONS: This study found that discontinuing the use of contact precautions for patients colonized or infected with ESBL-positive organisms did not lead to an increased rate of health care-associated ESBL-positive infections or colonization.

Household carriage and acquisition of extended-spectrum β-lactamase-producing Enterobacteriaceae: A systematic review

OBJECTIVE

The epidemiology of ESBL-producing Enterobacteriaceae (ESBL-PE) has been extensively studied in hospitals, but data on community transmission are scarce. We investigated ESBL-PE cocarriage and acquisition in households using a systematic literature review.

METHODS

We conducted a systematic literature search to retrieve cross-sectional or cohort studies published between 1990 and 2018 evaluating cocarriage proportions and/or acquisition rates of ESBL-PE among household members, without language restriction. We excluded studies focusing on animal-to-human transmission or conducted in nonhousehold settings. The main outcomes were ESBL-PE cocarriage proportions and acquisition rates, stratified according to phenotypic or genotypic assessment of strain relatedness. Cocarriage proportions of clonally related ESBL-PE were transformed using the double-arcsine method and were pooled using a random-effects model. Potential biases were assessed manually.

RESULTS

We included 13 studies. Among 863 household members of ESBL-PE positive index cases, prevalence of ESBL-PE cocarriage ranged from 8% to 37%. Overall, 12% (95% confidence interval [CI], 8%-16%) of subjects had a clonally related strain. Those proportions were higher for Klebsiella pneumoniae (20%-25%) than for Escherichia coli (10%-20%). Acquisition rates of clonally related ESBL-PE among 180 initially ESBL-PE-free household members of a previously identified carrier ranged between 1.56 and 2.03 events per 1,000 person weeks of follow-up. We identified multiple sources of bias and high heterogeneity (I2, 70%) between studies.

CONCLUSIONS

ESBL-PE household cocarriage is frequent, suggesting intrafamilial acquisition. Further research is needed to evaluate the risk and control of ESBL-PE household transmission.

Attributable sources of community-acquired carriage of Escherichia coli containing β-lactam antibiotic resistance genes: a population-based modelling study

BACKGROUND

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC), plasmid-mediated AmpC-producing E coli (pAmpC-EC), and other bacteria are resistant to important β-lactam antibiotics. ESBL-EC and pAmpC-EC are increasingly reported in animals, food, the environment, and community-acquired and health-care-associated human infections. These infections are usually preceded by asymptomatic carriage, for which attributions to animal, food, environmental, and human sources remain unquantified.

METHODS

In this population-based modelling study, we collected ESBL and pAmpC gene data on the Netherlands population for 2005-17 from published datasets of gene occurrences in E coli isolates from different sources, and from partners of the ESBL Attribution Consortium and the Dutch National Antimicrobial Surveillance System. Using these data, we applied an established source attribution model based on ESBL-EC and pAmpC-EC prevalence and gene data for humans, including high-risk populations (ie, returning travellers, clinical patients, farmers), farm and companion animals, food, surface freshwater, and wild birds, and human exposure data, to quantify the overall and gene-specific attributable sources of community-acquired ESBL-EC and pAmpC-EC intestinal carriage. We also used a simple transmission model to determine the basic reproduction number (R₀) in the open community.

FINDINGS

We identified 1220 occurrences of ESBL-EC and pAmpC-EC genes in humans, of which 478 were in clinical patients, 454 were from asymptomatic carriers in the open community, 103 were in poultry and pig farmers, and 185 were in people who had travelled out of the region. We also identified 6275 occurrences in non-human sources, including 479 in companion animals, 4026 in farm animals, 66 in wild birds, 1430 from food products, and 274 from surface freshwater. Most community-acquired ESBL-EC and pAmpC-EC carriage was attributed to human-to-human transmission within or between households in the open community (60·1%, 95% credible interval 40·0-73·5), and to secondary transmission from high-risk groups (6·9%, 4·1-9·2). Food accounted for 18·9% (7·0-38·3) of carriage, companion animals for 7·9% (1·4-19·9), farm animals (non-occupational contact) for 3·6% (0·6-9·9), and swimming in freshwater and wild birds (ie, environmental contact) for 2·6% (0·2-8·7). We derived an R₀ of 0·63 (95% CI 0·42-0·77) for intracommunity transmission.

INTERPRETATION

Although humans are the main source of community-acquired ESBL-EC and pAmpC-EC carriage, the attributable non-human sources underpin the need for longitudinal studies and continuous monitoring, because intracommunity ESBL-EC and pAmpC-EC spread alone is unlikely to be self-maintaining without transmission to and from non-human sources.

FUNDING

1Health4Food, Dutch Ministry of Economic Affairs, and the EU's Horizon-2020 through One-Health European Joint Programme.

The Relative Impact of Community and Hospital Antibiotic Use on the Selection of Extended-spectrum Beta-lactamase-producing Escherichia coli

Antibiotic stewardship programs have traditionally focused on reducing hospital antibiotic use. However, reducing community antibiotic prescribing could have substantial impacts in both hospital and community settings. We developed a deterministic model of transmission of extended-spectrum beta-lactamase-producing Escherichia coli in both the community and hospitals. We fit the model to existing, national-level antibiotic use and resistance prevalence data from Sweden. Across a range of conditions, a given relative change in antibiotic use in the community had a greater impact on resistance prevalence in both the community and hospitals than an equivalent relative change in hospital use. However, on a per prescription basis, changes in antibiotic use in hospitals had the greatest impact. The magnitude of changes in prevalence were modest, even with large changes in antimicrobial use. These data support the expansion of stewardship programs/interventions beyond the walls of hospitals, but also suggest that such efforts would benefit hospitals themselves.

High prevalence of colonisation with carbapenem-resistant Enterobacteriaceae among patients admitted to Vietnamese hospitals: Risk factors and burden of disease

BACKGROUND

Carbapenem-resistant Enterobacteriaceae (CRE) is an increasing problem worldwide, but particularly problematic in low- and middle-income countries (LMIC) due to limitations of resources for surveillance of CRE and infection prevention and control (IPC).

METHODS

A point prevalence survey (PPS) with screening for colonisation with CRE was conducted on 2233 patients admitted to neonatal, paediatric and adult care at 12 Vietnamese hospitals located in northern, central and southern Vietnam during 2017 and 2018. CRE colonisation was determined by culturing of faecal specimens on selective agar for CRE. Risk factors for CRE colonisation were evaluated. A CRE admission and discharge screening sub-study was conducted among one of the most vulnerable patient groups; infants treated at an 80-bed Neonatal ICU from March throughout June 2017 to assess CRE acquisition, hospital-acquired infection (HAI) and treatment outcome.

RESULTS

A total of 1165 (52%) patients were colonised with CRE, most commonly Klebsiella pneumoniae (n = 805), Escherichia coli (n = 682) and Enterobacter spp. (n = 61). Duration of hospital stay, HAI and treatment with a carbapenem were independent risk factors for CRE colonisation. The PPS showed that the prevalence of CRE colonisation increased on average 4.2% per day and mean CRE colonisation rates increased from 13% on the day of admission to 89% at day 15 of hospital stay. At the NICU, CRE colonisation increased from 32% at admission to 87% at discharge, mortality was significantly associated (OR 5·5, P < 0·01) with CRE colonisation and HAI on admission.

CONCLUSION

These data indicate that there is an epidemic spread of CRE in Vietnamese hospitals with rapid transmission to hospitalised patients.

Individual- and community-level risk factors for ESBL Enterobacteriaceae colonization identified by universal admission screening in London

OBJECTIVES

We evaluated risk factors for gastrointestinal carriage of Enterobacteriaceae which produce extended-spectrum β-lactamases (ESBL-E), including individual-level variables such as antibiotic use and foreign travel, and community-level variables such as housing and deprivation.

METHODS

In an observational study in 2015, all patients admitted to a London hospital group were approached to be screened for ESBL-E carriage using rectal swabs for 4 months. Patients completed a risk factor questionnaire. Those with a residential postcode in the local catchment area were linked to a database containing community-level risk factor data. Risk factors for ESBL-E carriage were determined by binary logistic regression.

RESULTS

Of 4006 patients, 360 (9.0%) carried ESBL-E. Escherichia coli was the most common organism (77.8%), and CTX-M-type ESBLs were the most common genes (57.9% CTX-M-15 and 20.7% CTX-M-9). In multivariable analysis, risk factors for phenotypic ESBL-E among the 1633 patients with a residential postcode within the local catchment area were: travel to Asia (OR 4.4, CI 2.5-7.6) or Africa (OR 2.4, CI 1.2-4.8) in the 12 months prior to admission, two or more courses of antibiotics in the 6 months prior to admission (OR 2.0, CI 1.3-3.0), and residence in a district with a higher-than-average prevalence of overcrowded households (OR 1.5, CI 1.05-2.2). .

CONCLUSIONS

Both individual and community variables were associated with ESBL-E carriage at hospital admission. The novel observation that household overcrowding is associated with ESBL-E carriage requires confirmation, but raises the possibility that targeted interventions in the community could help prevent transmission of antibiotic-resistant Gram-negative bacteria.

The Clinical and Molecular Epidemiology of CTX-M-9 Group Producing Enterobacteriaceae Infections in Children

Introduction

The pandemic of extended-spectrum beta-lactamase-(ESBL)-producing Enterobacteriaceae (Ent) is strongly linked to the dissemination of CTX-M-type-ESBL-Ent. We sought to define the epidemiology of infections in children due to an emerging resistance type, CTX-M-9-group-producing-Ent (CTX-M-9-grp-Ent).

Methods

A retrospective matched case-control analysis of children with CTX-M-9-grp-Ent infections who received medical care at three Chicago area hospitals was performed. Cases were defined as children possessing extended-spectrum cephalosporin-resistant (ESC-R) infections due to bla_CTX-M-9. PCR and DNA analysis assessed beta-lactamase (bla) genes, multi-locus sequence types (MLST) and phylogenetic grouping of E. coli. Controls were children with ESC-susceptible (ESC-S)-Ent infections matched one case to three controls by age, source, and hospital. The clinical-epidemiologic predictors of CTX-M-9-grp-Ent infection were assessed.

Results

Of 356 ESC-R-Ent isolates from children (median age 4.1 years), the CTX-M-9-group was the solely detected bla gene in 44 (12.4%). The predominant species was E. coli (91%) of virulent phylogroups D (60%) and B2 (40%). MLST revealed multiple strain types. On multivariable analysis, CTX-M-9-grp-Ent occurred more often in E. coli than other Ent genera (OR 7.4, 95% CI 2.4, 27.2), children of non-Black-White-Hispanic race (OR 7.4, 95% CI 2.4, 28.2), and outpatients (OR 4.5, 95% CI 1.7, 12.3), which was a very unexpected finding for infections due to antibiotic-resistant bacteria. Residents of South Chicago had a 6.7 times higher odds of having CTX-M-9-grp-Ent infections than those in the reference region (West), while residence in Northwestern Chicago was associated with an 81% decreased odds of infection. Other demographic, comorbidity, invasive-device, and antibiotic use differences were not found.

Conclusion

CTX-M-9-grp-Ent infection may be associated with patient residence and is occurring in children without traditional in-patient exposure risk factors. This suggests that among children, the community environment may be a key contributor in the spread of these resistant pathogens.

High acquisition rate of extended-spectrum β-lactamase-producing Enterobacteriaceae among French military personnel on mission abroad, without evidence of inter-individual transmission

OBJECTIVES

Acquisition of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) by Europeans travelling individually in high-endemicity countries is common. However, how the different ESBL-E strains circulate in groups of travellers has not been studied. We investigated ESBL-E transmission within several groups of French military personnel serving overseas for 4-6 months.

METHODS

We conducted a prospective study among French military personnel assigned to Afghanistan, French Guiana or Côte d'Ivoire for 4-6 months. Faecal samples provided by volunteers before leaving and after returning were screened for ESBL-E isolates. ESBL Escherichia coli from each military group was characterized by repetitive element palindromic polymerase chain reaction (rep-PCR) fingerprinting followed, in the Afghanistan group, by whole-genome sequencing (WGS) if similarity was ≥97%.

RESULTS

Among the 189 volunteers whose samples were negative before departure, 72 (38%) were positive after return. The highest acquisition rates were observed in the Afghanistan (29/33, 88%) and Côte d'Ivoire (39/80, 49%) groups. Acquisition rates on return from French Guiana were much lower (4/76, 5%). WGS of the 20 strains from the Afghanistan group that clustered by rep-PCR identified differences in sequence type, serotype, resistance genes and plasmid replicons. Moreover, single-nucleotide polymorphism (SNP) differences across acquired strains from a given cluster ranged from 30 to 3641, suggesting absence of direct transmission.

CONCLUSIONS

ESBL-E. coli acquisition was common among military personnel posted overseas. Many strains clustered by rep-PCR but differed by WGS and SNP analysis, suggesting acquisition from common external sources rather than direct person-to-person transmission.

Multidrug-resistant CTX-M-15-producing Klebsiella pneumoniae ST231 associated with infection and persistent colonization of dog

Extended spectrum β-lactamase (ESBL)-producing bacterial infections in veterinary medicine are a clinical and epidemiological challenge. We report a case of CTX-M-15-producing Klebsiella pneumoniae infection followed by persistent colonization, in a dog presenting with bilateral purulent nasal discharge and dyspnea. In this regard, 5 broad-spectrum cephalosporin-resistant K. pneumoniae isolates were recovered from infection and surveillance cultures, collected during 1 year and eight months study. Genomic analysis of a representative clone of K. pneumoniae (KpPB76) revealed the presence of the human-associated lineage ST231, whereas resistome data confirmed the presence of genes conferring resistance to aminoglycosides, β-lactams, fluoroquinolones, fosfomycin, phenicols, sulfonamides, tetracyclines and trimethoprim. In the absence of therapeutic options, meropenem therapy was used, contributing to the control of infection during persistent carriage of K. pneumoniae CTX-M-15/ST231. Persistent colonization of companion animals with ESBL-producing bacteria could be result from a variety of situations, including multi introduction from the owner or household family members to pets, or from environmental exposure; whereas colonized animals may serve as an important source for the spread of ESBL-producing strains in the human-animal interface.

Current epidemiology, genetic evolution and clinical impact of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae

The worldwide spread of extended-spectrum β-lactamase (ESBL)-producing bacteria, particularly Escherichia coli and Klebsiella pneumoniae, is a critical concern for the development of therapies against multidrug-resistant bacteria. Since the 2000s, detection rates of CTX-M types ESBL-producing E. coli in the community have been high, possibly contributing to their nosocomial detection. Various factors, such as environmental sources, food animals, and international travel, accelerate the global ESBL spread in the community. The dramatic dissemination of ESBLs in the community is associated with the relatively recent emergence of CTX-M-15-producing ST131 E. coli clones, which often carry many other antibiotic resistance genes (including quinolone). The usefulness of β-lactam/β-lactamase inhibitor, particularly, piperacillin/tazobactam, has been considered as a carbapenem-sparing regimen for ESBL infections, although the global trend of AmpC β-lactamase-producing bacteria should be monitored carefully. Careful therapeutic selection and continued surveillance for the detection of multidrug-resistant bacteria are required.

Prevalence and risk factors for Extended-Spectrum Beta-Lactamase-producing- Enterobacteriaceae in French military and civilian travelers: A cross-sectional analysis

BACKGROUND

International travel is a risk factor for colonization with Extended-Spectrum Beta-Lactamase-producing- Enterobacteriaceae (ESBL-E). We describe the prevalence of and risk-factors for ESBL-E colonization in civilian and military travelers.

METHODS

Patients hospitalized in the infectious diseases department of Bégin Military Hospital (France) from May 2012 to November 2015, who had traveled abroad over the past two months, were screened for intestinal colonization with ESBL-E.

RESULTS

Forty-one out of 166 travelers (24.7%) had ESBL-E colonization, predominantly Escherichia coli. The risk factors for ESBL-E colonization in the univariate analysis were a treatment with any antibiotic in the last two months (OR 4.19, 95% CI 1.91-9.16) or with a beta-lactam in the same period (OR 3.35, 95% CI 1.44-7.82), and an hospitalization in the last two months (OR 3.96, 95% CI 1.91-9.16). The military status, military mission or military accommodation were not associated with an increased risk of ESBL-E colonization. In the multivariate analysis, a treatment with any antibiotic in the last two months was significantly associated with ESBL-E colonization (OR 6.71, 95% CI 3.36-19.08).

CONCLUSION

Antibiotic treatment in the two previous months is strongly predictive of ESBL-E colonization in international travelers, while the military status and its specific living conditions are not.

Time to acquire and lose carriership of ESBL/pAmpC producing E. coli in humans in the Netherlands

A subset of the study population from a cross-sectional study of carriership of ESBL/pAmpC-producing E. coli (ESBL-E) in the general population was followed up by five successive samples over an approximate half year period, leading to six samples in 333 persons. Fecal samples were cultured and analyzed for the presence of E. coli types as characterized by MLST, and ESBL/pAmpC genes were analysed by PCR and sequencing. The study included 255 persons who had a negative first sample, to allow observations of acquiring carriership of ESBL-E. Any individual record thus consisted of a series of snapshots of episodes of presence and absence of ESBL-E carriage. A survival model was built to estimate times to acquire or lose carriership, allowing for any combination of ESBL/pAmpC gene and E. coli MLST type. In carriers, the mean time to lose carriership was 1.1 (95% range 0.8-1.6) years. The estimated mean time to acquire carriership was 3.0 (95% range 1.6-6.3) years. Analysis of these times by ESBL/pAmpC gene found substantial variation among resistance genes both in persistence of carriership and in rates of acquiring carriership: blaCTX-M-1, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27 and blaSHV-12 were easily acquired, but blaCTX-M-1 and blaSHV-12 were also easily lost, while blaCTX-M-15, blaCTX-M-27 and blaCMY-2 were more likely to persist. When in addition bacterial host types were included, some combinations appeared more persistent than others (blaCTX-M-1 in ST10 and ST58; blaCTX-M-14, blaCMY-2, and blaSHV-12 in ST69), or were acquired with higher frequency (blaCTX-M-14 in ST38, ST69, and ST131; blaCTX-M-15 and blaCTX-M-27 in ST131; blaSHV-12 in ST69). The relatively short duration of carriership means that when an intervention drastically reduces the exposure of humans to ESBL-E, the prevalence will be halved in 0.66 years. The observed differences between carriage rates of ESBL/pAmpC genes and E. coli strains need further investigation.

High Prevalence of Intra-Familial Co-colonization by Extended-Spectrum Cephalosporin Resistant Enterobacteriaceae in Preschool Children and Their Parents in Dutch Households

Extended-spectrum cephalosporin-resistant (ESC^R) Enterobacteriaceae pose a serious infection control challenge for public health. The emergence of the ESC^R phenotype is mostly facilitated by plasmid-mediated horizontal extended-spectrum β-lactamases (ESBLs) and AmpC gene transfer within Enterobacteriaceae. Current data regarding the plasmid contribution to this emergence within the Dutch human population is limited. Hence, the aim of this study was to gain insight into the role of plasmids in the dissemination of ESBL/AmpC genes inside Dutch households with preschool children and precisely delineate co-colonization. In 87 ESC^REnterobacteriaceae from fecal samples of parents and preschool children within 66 Dutch households, genomic localization, plasmid type and insertion sequences linked to ESBL/AmpC genes were determined. Chromosomal location of ESBL/AmpC genes was confirmed when needed. An epidemiologically relevant subset of the isolates based on household co-carriage was assessed by Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis for genetic relatedness. The narrow-host range I1α and F plasmids were the major facilitators of ESBL/AmpC-gene dissemination. Interestingly, we documented a relatively high occurrence of chromosomal integration of typically plasmid-encoded ESBL/AmpC-genes. A high diversity of non-epidemic Escherichia coli sequence types (STs) was revealed; the predominant STs belonged to the pandemic lineages of extraintestinal pathogenic E. coli ST131 and ST69. Intra-familiar co-carriage by identical ESC^REnterobacteriaceae was documented in 7 households compared to 14 based on sole gene typing, as previously reported. Co-carriage was more frequent than expected based on pure chance, suggesting clonal transmission between children and parents within the household.

Quantifying Hospital-Acquired Carriage of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae Among Patients in Dutch Hospitals

BACKGROUND

Extended-spectrum β-lactamase–producing Enterobacteriaceae (ESBL-E) are emerging worldwide. Contact precautions are recommended for known ESBL-E carriers to control the spread of ESBL-E within hospitals.

OBJECTIVE

This study quantified the acquisition of ESBL-E rectal carriage among patients in Dutch hospitals, given the application of contact precautions.

METHODS

Data were used from 2 cluster-randomized studies on isolation strategies for ESBL-E: (1) the SoM study, performed in 14 Dutch hospitals from 2011 through 2014 and (2) the R-GNOSIS study, for which data were limited to those collected in a Dutch hospital in 2014. Perianal cultures were obtained, either during ward-based prevalence surveys (SoM), or at admission and twice weekly thereafter (R-GNOSIS). In both studies, contact precautions were applied to all known ESBL-E carriers. Estimates for acquisition of ESBL-E were based on the results of admission and discharge cultures from patients hospitalized for more than 2 days (both studies) and a Markov chain Monte Carlo (MCMC) model, applied to all patients hospitalized (R-GNOSIS).

RESULTS

The absolute risk of acquisition of ESBL-E rectal carriage ranged from 2.4% to 2.9% with an ESBL-E acquisition rate of 2.8 to 3.8 acquisitions per 1,000 patient days. In addition, 28% of acquisitions were attributable to patient-dependent transmission, and the per-admission reproduction number was 0.06.

CONCLUSIONS

The low ESBL-E acquisition rate in this study demonstrates that it is possible to control the nosocomial transmission of ESBL in a low-endemic, non-ICU setting whereEscherichia coliis the most prevalent ESBL-E and standard and contact precautions are applied for known ESBL-E carriers.

TRIAL REGISTRATION

Nederlands Trialregister, NTR2799,http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=2799; ISRCTN Registry, ISRCTN57648070,http://www.isrctn.com/ISRCTN57648070

Infect Control Hosp Epidemiol2018;39:32–39

The ecology of extended-spectrum β-lactamases (ESBLs) in the developed world

BACKGROUND

Since the initial appearance in the 1980s, Enterobacteriaceae producing extended-spectrum β-lactamase (ESBL) have increased in prevalence and emerged as a major antimicrobial-resistant pathogen. The source of these antimicrobial-resistant bacteria in the developed world is an area of active investigation.

METHODS

A standard internet search was conducted with a focus on the epidemiology and potential sources of ESBL-producing Enterobacteriaceae in the developed world.

RESULTS

The last decade has witnessed several major changes in the epidemiology of these bacteria: replacement of TEM and SHV-type ESBLs by CTX-M-family ESBLs, emergence of Escherichia coli ST131 as a prevalent vehicle of ESBL, and spread of ESBL-producing E. coli in the community. The most studied potential sources of ESBL-producing Enterobacteriaceae in humans in the community include food and companion animals, the environment and person-to-person transmission, though definitive links are yet to be established. Evidence is emerging that international travel may serve as a major source of introduction of ESBL-producing Enterobacteriaceae into the developed world.

CONCLUSIONS

ESBL-producing Enterobacteriaceae has become a major multidrug-resistant pathogen in the last two decades, especially in the community settings. The multifactorial nature of its expansion poses a major challenge in the efforts to control them.

ESBL/AmpC-producing Enterobacteriaceae in households with children of preschool age: prevalence, risk factors and co-carriage

OBJECTIVES

ESBL/AmpC-producing Enterobacteriaceae are an emerging public health concern. As households with preschool children may substantially contribute to the community burden of antimicrobial resistance, we determined the prevalence, risk factors and co-carriage of ESBL/AmpC-producing bacteria in preschool children and their parents.

METHODS

From April 2013 to January 2015, each month 2000 preschool children were randomly selected from Dutch population registries. The parents were invited to complete an epidemiological questionnaire and to obtain and send a faecal sample from the selected child and from one parent. Samples were tested for ESBL/AmpC-producing bacteria. Logistic regression was used to identify risk factors for ESBL/AmpC carriage in children and parents, and findings were internally validated by bootstrapping.

RESULTS

In total, 1016 families were included and ESBL/AmpC prevalence was 4.0% (95% CI 3.2%-5.0%); 3.5% (95% CI 2.5%-4.8%) in children and 4.5% (95% CI 3.4%-6.0%) in parents. Attending a daycare centre (DCC) was the only significant risk factor for children (OR 2.1, 95% CI 1.0-4.3). For parents, the only significant risk factor was having one or more children attending DCCs (OR 2.2, 95% CI 1.2-4.8). For parents of ESBL/AmpC-positive children the OR for ESBL/AmpC carriage was 19.7 (95% CI 9.2-42.4). Co-carriage of specific ESBL/AmpC genotypes in child and parent occurred more often than expected by chance (14.6% versus 1.1%, P < 0.001).

CONCLUSIONS

In this study, intestinal carriage with ESBL/AmpCs was detected in ∼4% of households with preschool children. DCC attendance was a risk factor in both children and parents and co-carriage of specific genotypes frequently occurred in child-parent pairs. These findings suggest household transmission or/and family-specific exposure to common sources of ESBL/AmpC-producing bacteria.