Evaluation of patient risk factors for infection with carbapenem-resistant Enterobacteriaceae

The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children

Antibiotic resistance is a global threat driven primarily by antibiotic use. We evaluated the effects of antibiotic exposures on the gut microbiomes and resistomes of children at high risk of colonization by antibiotic-resistant bacteria. We performed shotgun metagenomic sequencing of 691 serially collected fecal samples from 80 children (<18 years) undergoing hematopoietic cell transplantation. We evaluated the effects of aerobic (cefepime, vancomycin, fluoroquinolones, aminoglycosides, macrolides, and trimethoprim-sulfamethoxazole) and anaerobic (piperacillin-tazobactam, carbapenems, metronidazole, and clindamycin) antibiotic exposures on the diversity and composition of the gut microbiome and resistome. We identified 372 unique antibiotic resistance genes (ARGs); the most frequent ARGs identified encode resistance to tetracyclines (n = 88), beta-lactams (n = 84), and fluoroquinolones (n = 79). Both aerobic and anaerobic antibiotic exposures were associated with a decrease in the number of bacterial species (aerobic, β = 0.71, 95% CI: 0.64, 0.79; anaerobic, β = 0.66, 95% CI: 0.53, 0.82) and the number of unique ARGs (aerobic, β = 0.81, 95% CI: 0.74, 0.90; anaerobic, β = 0.73, 95% CI: 0.61, 0.88) within the gut metagenome. However, only antibiotic regimens that included anaerobic activity were associated with an increase in acquisition of new ARGs (anaerobic, β = 1.50; 95% CI: 1.12, 2.01) and an increase in the relative abundance of ARGs in the gut resistome (anaerobic, β = 1.62; 95% CI: 1.15, 2.27). Specific antibiotic exposures were associated with distinct changes in the number and abundance of ARGs for individual antibiotic classes. Our findings detail the impact of antibiotics on the gut microbiome and resistome and demonstrate that anaerobic antibiotics are particularly likely to promote acquisition and expansion of antibiotic-resistant bacteria.

Who should be screened for carbapenemase-producing Enterobacterales and when? A systematic review

Carbapenemase-producing Enterobacterales (CPE) cases increases every year in Denmark and the proportion of CPE-positive cases with a travel history decreases. Several epidemiological links show transmission in Danish healthcare setting indicating infection prevention and control challenges and raising questions about the Danish CPE screening protocol. The aim of this review was to identify additional risk factors to those described in the Danish CPE-screening protocol in order to detect the Danish CPE-positive patients and thereby reduce the risk of transmission and outbreaks. A systematic literature search was conducted in PubMed, Embase and Cochrane Library during March 2022. A total of 1487 articles were screened, and 19 studies were included. Retrieved studies dealt with patients with laboratory-confirmed CPE (colonization and/or infection) and associated risk factors. Antimicrobial therapy, especially broad-spectrum antimicrobial agents, prior or current hospitalization of approximately one week in ICU and 20-28 days in other wards and travel history with or without hospitalization abroad were significant risk factors associated with CPE acquisition. Comorbidities and invasive procedures were identified as risk factors, but without identifying specific comorbidities or invasive procedures associated with risk for CPE-acquisition. This study suggests the need to develop an additional algorithm for CPE-screening in Denmark. In addition to risk-based screening on admission, screening of inpatients should be considered. The screening protocol might include screening of inpatients with comorbidities who are hospitalized >1 week in ICU or >3 weeks in other wards and who have previously received or currently are receiving antibiotic treatment. Further research is needed to develop a new CPE-screening algorithm.

Cefiderocol, a Siderophore Cephalosporin, as a Treatment Option for Infections Caused by Carbapenem-Resistant Enterobacterales

Carbapenem-resistant Enterobacterales (CRE) remain a significant public health threat, and, despite recent approvals, new antibiotics are needed. Severe infections caused by CRE, such as nosocomial pneumonia and bloodstream infections, are associated with a relatively high risk of morbidity and mortality. The recent approval of ceftazidime-avibactam, imipenem-relebactam, meropenem-vaborbactam, plazomicin, eravacycline and cefiderocol has broadened the armamentarium for the treatment of patients with CRE infections. Cefiderocol is a siderophore cephalosporin with overall potent in vitro activity against CRE. It is taken up via iron transport channels through active transport, with some entry into bacteria through traditional porin channels. Cefiderocol is relatively stable against hydrolysis by most serine- and metallo-beta-lactamases, including KPC, NDM, VIM, IMP and OXA carbapenemases-the most frequent carbapenemases detected in CRE. The efficacy and safety of cefiderocol has been demonstrated in three randomised, prospective, parallel group or controlled clinical studies in patients at risk of being infected by multidrug-resistant or carbapenem-resistant Gram-negative bacteria. This paper reviews the in vitro activity, emergence of resistance, preclinical effectiveness, and clinical experience for cefiderocol, and its role in the management of patients with CRE infections.

Risk factors for carbapenem-resistant Enterobacterales infection among hospitalized patients with previous colonization

BACKGROUND

We aimed to identify the risk factors for subsequent carbapenem-resistant Enterobacterales (CRE) infections in patients with initial rectal colonization with CRE.

METHODS

We conducted a retrospective case-control study on inpatients with rectal CRE colonization between January 2019 and December 2020. Clinical and microbiological data were extracted from hospital patients' medical records and the clinical microbiology laboratory. Risk factors were assessed and compared between patients with CRE colonization who had subsequent infections and those who did not have infections.

RESULTS

Among 1064 patients screened for CRE, we enrolled 205 patients with rectal CRE colonization. Among the 205 colonized bacteria, 78.5% were Klebsiella pneumoniae, with 62.9% of them producing Klebsiella pneumoniae carbapenemase (KPC). Multivariate logistic regression analysis revealed that more than three times hospitalization (p = 0.026), being in a coma (p = 0.019), and exposure to carbapenems (p = 0.015) were independent risk factors for CRE clinical infection among CRE rectal carriers.

CONCLUSION

This is the first study to report that more than three times hospitalization is an independent risk factor for subsequent CRE clinical infection in CRE intestinal carriers. Carbapenem-resistant Klebsiella pneumoniae is the most important species isolated from hospitalized CRE rectal carriers and is the most common cause of subsequent infections.

Association between Antimicrobial Consumption and the Prevalence of Nosocomial Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae in a Tertiary Hospital in Northern Taiwan

Carbapenem-resistant Enterobacteriales has become a threat in Taiwan. This is the first local study focusing on the association between carbapenem-resistant Enterobacteriales and antimicrobial consumption. From January 2012 to December 2020, data were collected in a tertiary care hospital in Taipei, Taiwan. Antimicrobial consumption was estimated by the defined daily dose/1,000 patient-days. During the same period, the prevalence of carbapenem-resistant Escherichia coli (CREC) and carbapenem-resistant Klebsiella pneumoniae (CRKP) were collected through routine surveillance data. The following retrospective analyses were conducted: 1) analysis of antimicrobial consumption over time, (2) analysis and forecast of CREC and CRKP prevalence over time, and 3) analysis of correlation between antimicrobial consumption and the prevalence of CREC and CRKP. The consumption of piperacillin/tazobactam (β = 0.615), fluoroquinolones (β = 0.856), meropenem (β = 0.819), and doripenem (β = 0.891) increased during the observation period (P < 0.001), and the consumption of aminoglycosides (β = -0.852) and imipenem/cilastatin (β = -0.851) decreased (P < 0.001). The prevalence of CRKP rose over time (β = 0.522, P = 0.001) and correlated positively with the consumption of fluoroquinolones, levofloxacin, penicillin/β-lactamase inhibitor, piperacillin/tazobactam, meropenem, and doripenem (P < 0.05). The prevalence of CRKP and CREC both correlated negatively with consumption of aminoglycosides (P < 0.01). The prevalence of CRKP in our hospital increased as the forecast predicted based on an autoregressive integrated moving average model. This study provides alarming messages for members participating in antimicrobial stewardship programs, including the increasing prevalence of CRKP, the increasing consumption of broad-spectrum antibiotics, and the positive correlation between them.

Modelling of the transmission dynamics of carbapenem-resistant Klebsiella pneumoniae in hospitals and design of control strategies

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as a major threat to global public health. Epidemiological and infection controls associated with CRKP are challenging because of several potential elements involved in a complicated cycle of transmission. Here, we proposed a comprehensive mathematical model to investigate the transmission dynamics of CRKP, determine factors affecting the prevalence, and evaluate the impact of interventions on transmission. The model includes the essential compartments, which are uncolonized, asymptomatic colonized, symptomatic colonized, and relapsed patients. Additionally, symptomatic colonized and relapsed patients were further classified into subpopulations according to their number of treatment failures or relapses. We found that the admission of colonized patients and use of antibiotics significantly impacted the endemic transmission in health care units. Thus, we introduced the treatment efficacy, defined by combining the treatment duration and probability of successful treatment, to characterize and describe the effects of antibiotic treatment on transmission. We showed that a high antibiotic treatment efficacy results in a significantly reduced likelihood of patient readmission in the health care unit. Additionally, our findings demonstrate that CRKP transmission with different epidemiological characteristics must be controlled using distinct interventions.

Risk factors for isolation of carbapenem-resistant Enterobacterales from normally sterile sites and urine

BACKGROUND

Invasive infections caused by carbapenem-resistant Enterobacterales (CRE) are of significant concern in health care settings. We assessed risk factors for a positive CRE culture from a sterile site (invasive infection) compared to isolation from urine in a large patient cohort in Atlanta from August 2011 to December 2015.

METHODS

CRE cases required isolation, from urine or a normally-sterile site, of E. coli, Klebsiella spp., or Enterobacter spp. that were carbapenem-nonsusceptible (excluding ertapenem) and resistant to all third-generation cephalosporins tested. Risk factors were compared between patients with invasive and urinary infections using multivariable logistic regression.

RESULTS

A total of 576 patients had at least 1 incident case of CRE, with 91 (16%) having an invasive infection. In multivariable analysis, the presence of a central venous catheter (OR 3.58; 95% CI: 2.06-6.23) or other indwelling device (OR 2.34; 95% CI: 1.35-4.06), and recent surgery within the last year (OR 1.81; 95% CI: 1.08-3.05) were associated with invasive infection when compared to urinary infection.

DISCUSSION

Health care exposures and devices were associated with invasive infections in patients with CRE, suggesting that targeting indwelling catheters, including preventing unwarranted insertion or encouraging rapid removal, may be a potential infection control intervention.

CONCLUSIONS

Future infection prevention efforts to decrease CRE cases in health care settings should focus on minimizing unnecessary devices.

Safety and Efficacy of Prophylactic Levofloxacin in Pediatric and Adult Hematopoietic Stem Cell Transplantation Patients

Levofloxacin has been widely used for bacteremia prophylaxis in the pre-engraftment setting for patients undergoing hematopoietic stem cell transplantation (HSCT), but data supporting this practice are inconsistent. In addition to concern for lack of benefit, there are also concerns that this practice could increase the rates of Clostridium difficile (C diff) infections, the incidence of multidrug-resistant organisms (MDRO) or lead to increased incidence of acute graft-versus-host disease (aGVHD) by disrupting the gut microbiome. This study aimed to assess the safety and efficacy of levofloxacin as bacterial prophylaxis in pediatric and young adult patients undergoing allogeneic or autologous HSCT at a single pediatric center. We conducted a retrospective chart review evaluating patients age ≥6 months who underwent HSCT at our center between January 1, 2016, and July 31, 2020. Patients who underwent transplantation before March 2018 did not receive levofloxacin prophylaxis, whereas those who underwent transplantation after April 2018 did receive levofloxacin prophylaxis. Each transplantation was included as a separate episode if the patient underwent more than 1 transplantation during the inclusion time. The primary outcome of this study was the proportion of patients who experienced at least 1 bacterial bloodstream infection (BSI) in the first 100 days post-transplantation. Secondary outcomes included the number of non-levofloxacin antibiotic days post-transplantation, the incidence of aGVHD, the occurrence of C diff infections, and development of MDRO. A total of 370 HSCT recipients with a median age of 6.7 years (range, 0.5 to 39 years) were included in this study. Seventy-two patients had undergone more than 1 transplantation, and thus we had 443 transplantations to observe. Of these, 216 did not include levofloxacin prophylaxis and 227 included levofloxacin prophylaxis. There were no differences in baseline characteristics between the 2 groups except for age; patients in the non-levofloxacin prophylaxis group were younger (8.1 years vs 9.6 years; P = .05). There were no between-group differences in rates of death at 100 days, antibiotic use, fungal infections, or MDRO infections. Patients in the non-prophylaxis group developed more bacterial BSI in the first 100 days post-HSCT (27% versus 17%; P = .004) and more C diff infections (20% versus 9%; P = .003) than patients who received levofloxacin prophylaxis. In addition, more acute GVHD was seen in the patients without levofloxacin prophylaxis (P = .014). Levofloxacin prophylaxis given from day -2 of HSCT through engraftment was significantly associated with decreased bacterial BSI in the first 100 days post-transplantation and was not associated with increased risks of C diff, acute GVHD, or MDRO. Our study supports the use of levofloxacin prophylaxis in the peritransplantation period. © 2021 American Society for Transplantation and Cellular Therapy. Published by Elsevier Inc.

Epidemiology, risk factors, and prediction score of carbapenem resistance among inpatients colonized or infected with 3rd generation cephalosporin resistant Enterobacterales

In this study, we determined the incidence and risk factors of Carbapenem-resistant Enterobacterales (CRE) acquisition in inpatients with 3rd generation cephalosporin-resistant (3GCR) Enterobacterales at a tertiary-care hospital in Lebanon, and suggested a risk prediction score for it. This is a retrospective matched case–control study of inpatients with 3GCR Enterobacterales that are carbapenem resistant (cases) versus those with carbapenem-sensitive isolates (controls). Data analysis was performed on IBM SPSS program, version 23.0 (Armonk, NY, USA: IBM Corp.). Categorical variables were compared between cases and controls through bivariate analysis and those with statistical significance (P < 0.05) were included in the forward stepwise multiple logistic regression analysis. To develop the CRE acquisition risk score, variables that maintained statistical significance in the multivariate model were assigned a point value corresponding to the odds ratio (OR) divided by the smallest OR identified in the regression model, and the resulting quotient was multiplied by two and rounded to the nearest whole number. Summation of the points generated by the calculated risk factors resulted in a quantitative score that was assigned to each patient in the database. Predictive performance was determined by assessing discrimination and calibration. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy were calculated for different cutoffs of the score. The incidence of CRE acquisition significantly increased with time from 0.21 cases/1000 patient-days (PD) in 2015 to 1.89 cases/1000PD in 2019 (r² = 0.789, P = 0.041). Multivariate analysis of matched data revealed that the history of cerebrovascular disease (OR 1.96; 95% CI 1.04–3.70; P = 0.039), hematopoietic cells transplantation (OR 7.75; 95% CI 1.52–39.36; P = 0.014), presence of a chronic wound (OR 3.38; 95% CI 1.73–6.50; P < 0.001), endoscopy done during the 3 months preceding the index hospitalization (OR 2.96; 95% CI 1.51–4.73; P = 0.01), nosocomial site of acquisition of the organism in question (OR 2.68; 95% CI 1.51–4.73; P = 0.001), and the prior use of meropenem within 3 months of CRE acquisition (OR 5.70; 95% CI 2.61–12.43; P < 0.001) were independent risk factors for CRE acquisition. A risk score ranging from 0 to 25 was developed based on these independent variables. At a cut-off of ≥ 5 points, the model exhibited a sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of 64.5%, 85.8%, 82%, 70.7% and 75%, respectively. We also showed that only meropenem consumption intensity and CRE acquisition incidence density showed a strong positive correlation(r = 0.798, P = 0.106), unlike imipenem (r = − 0.868, P = 0.056) and ertapenem (r = 0.385, P = 0.522). Patients with a score of ≥ 5 points in our model were likely to acquire CRE. Only meropenem was associated with CRE carriage. Our proposed risk prediction score would help target surveillance screening for CRE amongst inpatients at the time of hospital admission and properly guide clinicians on using anti-CRE therapy.

Risk factors for fecal carriage of extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli and Klebsiella pneumoniae strains among patients at hospital admission

AIM

Extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant (CR) Enterobacteriaceae are substantial problems in hospital-acquired infections worldwide. We analyzed the risk factors for fecal carriage of ESBL-positive and/or CR E. coli and K. pneumoniae (EcKp) strains in a hospital in Turkey, an endemic country for both resistances.

MATERIALS AND METHODS

A prospective cross-sectional study including the rectal swab samples of 168 patients, obtained at the day of admission, was conducted. ESBL-producing and CR EcKp were investigated with phenotypic tests and PCR, and the clonal relatedness of isolates was studied. Risk analysis was performed with logistic regression method.

RESULTS

A total of 67 (39.8%) and 21 (12.5%) patient samples tested positive for ESBL-producing and CR EcKp, respectively. CTX-M (n = 27) and OXA-48 (n = 12) were the dominant ESBL and carbapenemase types, and 4.5%-10.7% of the isolates were clonally-related. Among 15 potential risk factors studied, longer lengths of hospital stay and antimicrobial use, and receiving total parenteral nutrition in the last 6 months were determined as independent risk factors for fecal carriage of ESBL-producing and/or CR EcKp, while prior antimicrobial treatment was only a risk factor for ESBL producers.

CONCLUSION

Certain conditions in patients' medical backgrounds may be associated with increased likelihood of resistant bacterial colonization. Notably, questioning these situations at admission can help to identify potential carriers and proactively administer appropriate infection control measures.

Acquisition and carriage of multidrug-resistant organisms in dogs and cats presented to small animal practices and clinics in Switzerland

BACKGROUND

The emergence and spread of multidrug-resistant organisms (MDRO) present a threat to human and animal health.

OBJECTIVES

To assess acquisition, prevalence of and risk factors for MDRO carriage in dogs and cats presented to veterinary clinics or practices in Switzerland.

ANIMALS

Privately owned dogs (n = 183) and cats (n = 88) presented to 4 veterinary hospitals and 1 practice.

METHODS

Prospective, longitudinal, observational study. Oronasal and rectal swabs were collected at presentation and 69% of animals were sampled again at discharge. Methicillin-resistant (MR) staphylococci and macrococci, cephalosporinase-, and carbapenemase-producing (CP) Enterobacterales were isolated. Genetic relatedness of isolates was assessed by repetitive sequence-based polymerase chain reaction and multilocus sequence typing. Risk factors for MDRO acquisition and carriage were analyzed based on questionnaire-derived and hospitalization data.

RESULTS

Admission prevalence of MDRO carriage in pets was 15.5% (95% confidence interval [CI], 11.4-20.4). The discharge prevalence and acquisition rates were 32.1% (95% CI, 25.5-39.3) and 28.3% (95% CI, 22-35.4), respectively. Predominant hospital-acquired isolates were extended spectrum β-lactamase-producing Escherichia coli (ESBL-E coli; 17.3%) and β-lactamase-producing Klebsiella pneumoniae (13.7%). At 1 institution, a cluster of 24 highly genetically related CP (bla_oxa181 and bla_oxa48 ) was identified. Multivariate analysis identified hospitalization at clinic 1 (odds ratio [OR], 5.1; 95% CI, 1.6-16.8) and days of hospitalization (OR 3-5 days, 4.4; 95% CI, 1.8-10.9; OR > 5 days, 6.2; 95% CI, 1.3-28.8) as risk factors for MDRO acquisition in dogs.

CONCLUSIONS

Veterinary hospitals play an important role in the selection and transmission of MDRO among veterinary patients.

Risk factors and outcomes of patients colonized with carbapenemase-producing and non–carbapenemase-producing carbapenem-resistant Enterobacteriaceae

Objective:

To compare risk factors and outcome of patients colonized with carbapenemase-producing (CP) carbapenem-resistant Enterobactereaceae (CRE) and non–CP-CRE.

Design:

A comparative historical study.

Setting:

A 1,000-bed tertiary-care university hospital.

Patients:

Adults with CP-CRE positive rectal swab cultures, non–CP-CRE positive rectal swab cultures, and negative rectal swab cultures (non-CRE).

Methods:

CP-CRE and non–CP-CRE colonized adult patients versus patients not colonized with CRE hospitalized during 24 months were included. We identified patients retrospectively through the microbiology laboratory, and we reviewed their files for demographics, underlying diseases, Charlson Index, treatment, and outcome.

Results:

This study included 447 patients for whom a rectal swab for CRE was obtained: 147 positive for CP-CRE, 147 positive for non–CP-CRE, and 147 negative for both. Patients with CP-CRE and non–CP-CRE versus no CRE more frequently resided in nursing homes (P<0.001), received antibiotics 3 months prior to admission (P < .001), and received glucocorticosteroids 3 months prior to admission (P = .047 and P < .001, respectively). Risk factors unique for non–CP-CRE versus CP-CRE colonization included mechanical ventilation and patient movement between hospital departments. Non–CP-CRE was a predictor for mechanical ventilation 2.5 that of CP-CRE colonization. In-hospital mortality was highest among non–CP-CRE–colonized patients. On COX multivariate regression for mortality prediction age, Charlson index and steroid treatment 3 months before admission influenced mortality (P = .027, P = .023, and P = .013, respectively).

Conclusions:

Overlapping and unique risk factors are associated with CP-CRE and non–CP-CRE colonization. Non–CP-CRE colonized patients had a higher in-hospital mortality rate.