Colonization with CRE was not associated with higher 1-year mortality in our study. Similar results were observed for shorter follow-up of 30-day mortality. Nonetheless, CRE colonized patients experienced higher frequency of infections of any cause with a PS-weighted OR of 1.65 (95% CI 1.06–2.56). Of interest is the increased risk for BSI, that was twice the risk in CRE carriers compared to their respective controls. Days of hospital stay in the year following CRE acquisition was higher among CRE colonized patients compared to controls in those who survived, PS-weighted OR 1.52 (95% CI 1. 01–2.10). In a subgroup analysis of CPE carriers and their controls, significantly increased risks for BSIs with PS-weighted OR of 2.36 (95% CI1.11–5.00) and for clinical infections with PS weighted OR of 1.71 (95% CI 1.03–2.85, p = 0.038) were observed.

CRE colonization can persist for a long duration. In a meta-analysis assessing CRE colonization duration, 73.9% (95% CI 64–81.8) and 55.2% (95% CI 37.7–71.9) of patients continued carriage at 1 and 6 months after colonization detection [8]. Long-term mortality is the ultimate toll of CRE carriage, encompassing the burden of CRE infections that cannot be treated optimally, isolation in healthcare facilities and delays or even avoidance of certain procedures and opportunities due to the carriage state and contact isolation.

Similar to our findings, colonization with CRE was no longer significantly associated with increased mortality after adjusting for patients’ characteristics in previous studies. CRE colonization was shown to be a strong predictor of CRE infection in intensive care unit (ICU) patients but was not associated with 90 days all-cause mortality [9]. A higher OR for mortality was observed (adjusted OR 2.3, 95% CI 0.1–5.3) in that study, evaluating ICU patients, but only 36 CRE carriers were included [10]. In another study comparing 164 CRE carriers to 62 controls in the ICU setting, CRE colonization was not associated with mortality but with increased length of hospital stay [10]. Excess mortality in CRE colonized patents was observed in specific patient groups, following liver transplantation [11], and patients with acute leukemia [11, 12]. These patients might cope worse with clinical CRE infection, relying more heavily on effective antibiotic therapy that was unavailable for CRE. In contrast to previous studies, in our study, we analyzed the association between CRE colonization and mortality in a large and heterogenous patient group.

As to the risk of developing clinical infection, most studies focus on the risk of CRE-infection among colonized patients; a systematic review by Tischendrof et al. described a cumulative incidence of 16.5% for CRE infection among colonized patients [13]. Moreover, numerous studies assessing risk for CRE-infection include patients diagnosed both in the colonization and the infection states. We describe for the first time the risk of clinical infection, irrespective of the causative pathogen measured following acquisition of CRE colonization. Our current findings show a strong association between CRE acquisition and development of clinical infections. This might be related to the limitations imposed on CRE carriers due to isolation requirement, or a reflection of the differences between CRE carriers and non-carriers. We attempted to overcome the inherent differences between CRE colonized and non-colonized patients by selecting similar controls who were screened for CRE, and by adjusting for confounders using propensity score overlap weighting [7]. When CRE causes a clinical infection, as in 4% of CRE carriers in our study who developed CRE BSI, the burden of disease becomes even more evident due to the limited treatment options available. Broad-spectrum antibiotics are often prescribed, promoting further selective pressure both in the same patient and in other patients in the corresponding hospitalization ward.

In our study, CRE colonized patients who survived for 1 year, required longer hospital stays than controls. We measured days of hospital stay starting from colonization detection (or index day for controls) and adjusted it for previous hospitalization days through matching, as well as other confounders. The increased hospital stay of CRE colonized patients has multiple implications: first, the potential of cross-transmission and spreading CRE to other hospitalized patients is increased. This is of special concern in light of recent evidence on horizontal plasmid transfer occurring almost in every colonized patient [14], and might be leading to underestimation of cross-transmission risks in the current literature. Implementation of antimicrobial stewardship and infection prevention interventions could not be overemphasized in CRE carrier patients. Moreover, the resources and dedicated staff needed for treating these patients are higher, and lastly the daily isolation costs can sum up to significant amounts [15]. Of note, in CPE carriers the longer hospital stays among 1-year survivors was not maintained, hinting to differences between CPE and non-CP-CRE carriers.

The main strengths of our investigation build up upon the fact that intensive screening enabled detection of CRE colonization state prior to infection in a large number of patients, in an endemic setting. We included a large and heterogenous sample of patients acquiring colonization in different settings (ICU, hemotological and other wards). We evaluated important outcomes relevant in both patients’ and hospital’s perspectives. We used PS overlap weighting to overcome the inherent differences between CRE colonized patients and controls; and were able to define excess infection risk and excess length of stay associated with CRE colonization, adding up to the already known burden of CRE infection.

Despite our study findings, caution should be taken when linking severe outcomes solely to the state of CRE colonization, as causality cannot be determined. It is not clear to what extent the colonizing bacterium plays a role in the context of host factors. Patients who acquire CRE, and multidrug resistant organisms in general, tend to have high morbidity rates prolonged exposure to the healthcare system, often carry invasive instrumentation and are prone to adverse health outcomes. Yet, this does not need to influence the need for infection prevention and antimicrobial stewardship in these patients. As a single center study, our findings might not be generalizable to other settings. Despite our efforts, the generated estimates might still be subject to residual confounding. We did not follow the patients outside our hospital, however, as it is the only tertiary hospital in northern Israel, patients tend to be re-admitted to the same facility, but we still might have missed community-onset infections that did not require hospitalization. Last, the majority of the included cases carried CPE rather than non-CP-CRE, thus our findings tend to less reflect the latter.

No decolonization approach had achieved long term effect on CRE carriage in previous studies [8]. Further research should tackle novel decolonization strategies. Vaccines could be an interesting option for colonized or at-risk patients, but the current pipeline is lacking candidate agents for Enterobacterales in advanced stages of development [16]. Further research should evaluate optimal interventions to limit cross-transmissions in the healthcare settings. The optimal strategies to screen patients for multi-drug resistant organisms and CRE colonization, in particular, should be defined in cluster randomized trials. Future studies should also define better indicators for increased CRE cross-transmission rather than occurrence of CRE clinical infections and cumbersome and costly patient screening, such as wastewater and environmental surveillance. Finally, the actual costs of CRE colonization and cost-effectiveness of surveillance and infection prevention efforts should be investigated.

In summary, in our study CRE colonization was not associated with mortality but with higher risk of clinical infections and longer hospital stays. Infection prevention and antimicrobial stewardship are of utmost importance to prevent colonization and prevent infections in colonized patients.