The epidemiology of carbapenem-resistant Enterobacterales in a single center in Oman

Background : Carbapenem-resistant Enterobacterales (CRE) are a global public health threat associated with significant morbidity and mortality. Objectives : The study aims to describe the epidemiology, microbiology and outcome of patients with CRE infection or colonization during an active surveillance program and to determine the risk factors for the acquisition of such organisms in a single center in Oman. Method : A retrospective case–control study was conducted in a tertiary care hospital in 2015 and 2016. Cases included patients who had a positive screening or clinical sample for CRE and controls included patients who were screened during the same period and never had a positive screening or clinical sample for CRE. Risk factors analyzed were demographics, comorbidities, instrumentation, and antibiotic exposures. Data were analyzed using SPSS for Windows (version 11.5). Variables of interest were analyzed by univariate analysis

C arbapenem-resistant Enterobacterales (CRE) are a global public health threat associated with significant morbidity and mortality. In the absence of safe and effective treatment options, infection prevention remains the primary means of mitigating CRErelated morbidity and mortality (1).
In Oman, CRE was reported for the first time in 2011 among Klebsiella pneumoniae harbouring NDM-1 and OXA-181 carbapenemases (2,3). Other reports described the molecular epidemiology of CRE in the country, where the predominant isolates were Klebsiella pneumoniae, followed by Escherichia coli, Enterobacter cloacae and others that carried bla NDM, bla OXA48-like and to a lesser extent bla VIM carbapenemases (4,5). In addition, Balkhair et al. reported in 2013 an overall prevalence rate of 10.8 (95% CI: 9.3-12.4) of multidrug resistant gram-negative bacteria cases per 1,000 admissions (6).
Data regarding the incidence of CRE in Oman and risk factors for CRE infection or colonization are lacking. This study aims to describe the epidemiology, microbiology, and outcome of patients who acquired CRE infection or colonization during an active surveillance program and determine the risk factors for the acquisition of such organisms in a single center in Oman.

Methods
The Royal Hospital is a tertiary care hospital with 769bed capacity delivering care to the Omani population through the divisions of Child Health, Medicine, Surgery, Obstetrics and Gynecology, Oncology and Cardiothoracic Surgery. The hospital has 25 adult intensive care unit (ICU) beds (16 beds covering medical and surgical service and nine adult post-cardiac surgery beds). The paediatric ICU has 25 beds (nine medical and surgical beds, 10 neonatal and six paediatric post-cardiac surgery). In addition, the hospital has a step-down unit for critical adult patients that is located within the Adult ICU, which sometimes admits ventilated patients and accommodates chronically ventilated patients. The critical patients move between these two units frequently, and staff are shared between them. Therefore, the infection prevention and control department (IPCD) consider the two units as one when looking at the epidemiological link to acquisition and infection control interventions.
The hospital has well-established CRE surveillance that commenced in 2012 and is conducted by the IPCD. The surveillance criteria have changed over the years except during 2015 and 2016 when there was no change in screening indications and no outbreaks encountered. Surveillance involves screening patients at risk of CRE at admission and patients who have had contact with a CRE-positive case not under contact precautions. Weekly CRE screening is applied during outbreak situations. This is a retrospective case-control study. We followed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) recommendations (Appendix I: The completed STROBE checklist) (7). The study was approved by the hospital's Ethics and Research Committee (SRC#114/2017). The cases included all patients who had a positive CRE screening or grew CRE from any clinical samples at admission or after admission during the study period. Only one sample is included for each case with repeated positive cultures if they remained positive from screening samples. Only a clinical sample is included for patients who had a positive culture from screening and then were positive from another clinical sample. The controls were selected randomly from patients admitted during the same study period who had negative CRE screening and never grew CRE from any clinical samples during their hospital stay and throughout the study period. The case-to-control ratio was 1:1 because of the large number of cases identified.
Demographic data and clinical characteristics were extracted from the hospital information system (AL Shifa #3+, The Omani Health Information System). We studied the various risk factors that patients were exposed to in the 3 months prior to the detection of a CRE sample. We included presence of a nasogastric tube, central line, tracheostomy, urinary catheter, surgery, endoscopy, ICU admission or previous ICU admission (abroad and local), and antibiotic use. Case records were reviewed by an experienced microbiologist to categorise cases as infection versus colonization.

Definitions
Colonization: positive culture from a clinical non-sterile site sample or screening sample without the presence of signs and symptoms of infection and the patient received no antibiotic treatment for the duration of admission.
Infection: positive culture from clinical sterile and or non-sterile samples with the presence of symptoms and signs of infection. If the patient was treated with antibiotics by the caring clinician, the event was considered an infection.
Community acquired: acquisition of CRE with no identified epidemiological link to healthcare institutions and the positive culture was collected within the first 48 h of admission.
Hospital-acquired: acquisition of CRE with the presence of an epidemiological link to healthcare institutions such as admission, dialysis, or daycare or the positive culture for CRE was obtained 48 h after admission.

Microbiology
Patients with risk factors were screened on admission with rectal swabs in addition to endotracheal tube secretions for ventilated patients, catheter urine for patients with urinary catheter, and wound swab for patients with chronic wounds. Samples were collected by staff nurses as per infection prevention and control screening criteria described in Appendix II. CRE swabs were directly inoculated in CRE chromogenic agar plates (CHROMagar™ mSuperCARBA™ Medisinale, Chromagar, Paris, France). The plates were incubated at aerobic conditions at 35-37°C for 18-24 h. Typical colonies as per colony forming units (CFUs) were identified and susceptibility tested using the BD Phoenix ™ automated identification and susceptibility testing system (Becton, Dickinson and Company, Franklin Lakes, NJ, USA). Carbapenemase production is suspected based on Clinical and Laboratory Standards Institute (CLSI) breakpoints of 2-4 mg/L for imipenem and meropenem and 2 mg/L for ertapenem with no routine confirmatory tests done (8).

Statistical analysis
Data were analyzed using SPSS Statistics for Windows version 11.5 (SPSS Inc., Chicago, IL, USA).
Statistical analysis included frequency and percent distributions. Significant variables in the univariate analysis were included in the logistic regression model for the multivariate analysis. P-values were interpreted together with 95% confidence interval (CI) for the logistic regression model. Statistical significance was set at a P-value of ≤ 0.05.

Demographic characteristics of CRE cases and controls
The total number of CRE-positive cases identified during the study period was 728. Males comprised 417 (57.3%) cases and females 311 (42.7%). The majority of CRE cases were adult patients 644 (88.5%) compared to 84 (11.5%) in the pediatric age group. The mean age of CRE carriage was 51 ± 21. The total number of controls was 749 patients. The majority of the control group were adults 611 (81.6%) compared to 138 (18.4%) pediatric patients. The percentages of underlying diseases were much higher in the cases compared to the controls as shown in Table 1.

Incidence of CRE
The number of patients screened during the study period was 8,431 in 2015 and 10,231 in 2016, with a positivity rate of 4.2% in 2015 and 3.5% in 2016 ( Table 2). The total numbers of admissions, CRE cases identified through active surveillance, the incidence rates, and the incidence density of CRE, in 2015 and 2016 are shown in Table 2.
The vast majority of CRE cases were healthcare-acquired 724 (99.5%), and only four (0.5%) were attributed to community acquisition. Approximately 53.6% were acquired at Royal Hospital, 31.3% acquired from other local hospitals and 14.6% acquired from hospitals abroad.
Although the highest percentage of CRE cases acquired at Royal Hospital was in the adult medical service for both years (35.8% in 2015, 43.5% in 2016), the highest incidence density of acquisition was in adult critical care service (3.05 per 1,000 patient days in 2015, 3.82 per 1,000 patient days in 2016) ( Table 3). Table 3 shows the services where cases acquired CRE at Royal Hospital. The incidence density of bacteremia was 0.12 per 1,000 patient days in 2015 and 0.11 per 1000 patient days in 2016, as shown in Table 4.

Microbiologic and clinical characteristics of CRE Species
The majority of CRE samples 480 (66%) represent colonization mainly from active surveillance screening cultures (97%), and only 3% of patients were colonized in urine, sputum, and wounds. Infection was identified in 248 (34%) of the cases. The most common sites of infections were urine and wound comprising 29% each, followed by respiratory (21%) and blood (17%). Klebsiella pneumoniae (n = 578, 79%) was the predominant organism in both colonized and infected patients accounting for 82% and 74%, respectively. Escherichia coli (n = 101, 14%) was the second most commonly isolated organism in 2.1% of colonization and 13% of infections. The microbiological characteristics are summarised in Table 5.

Discussion
Our hospital initiated the continuous active CRE screening surveillance program as part of a multifaceted approach to control the spread of CRE since 2012. The annual incidence of CRE acquisition per 100 admissions and the incidence density per 1,000 patient days remained stable during the study period with minor trending downward. The majority of the CRE identified in this study were healthcare acquired, and only a minority were community acquired. The finding of community-acquired CRE is of concern although highlighted previously by Tang et al. (9) who reported 29.5% of CRE were community acquired and Kelly et al. (10) who reported the percentage of community-associated or community-onset CRE ranged from 0 to 29.5%, with the percentage of community-based CRE highest in parts of Asia. The highest incidence density of CRE acquisition, found amongst adult ICU patients followed by adult medical service, should lead the IPCD to prioritise infection control interventions in these two services. Adesanya et al. (11) found the highest proportion of carbapenem-resistant infections from patients in surgical wards as well as in the ICU although they did not report the incidence density in their study.
In our study, the significant risk factors for acquisition of CRE infection and/or colonization were presence of invasive devices (urinary catheter, central line, intubation), antibiotic exposure, previous abroad hospital admission, other local hospital admission, and previous or current ICU admission. Our findings for risk factors are similar to those reported by Teo et al. (12). Our study did not address other risk factors such as duration of hospital stay prior to acquisition or comorbidities per se as reported in the literature although we noticed the number of comorbidities were higher among cases than controls (131 [4][5][6][7][8][9][10][11][12][13][14][15]. The most common CRE in our study was Klebsiella pneumoniae followed by Escherichia coli and Enterobacter species. which is more or less the same finding reported by  (14) and but slightly different to Tang et al. (10) who reported Enterobacter species as the second most common followed by Escherichia coli as the third. The most common clinical samples from which CRE was isolated because of infection were wound/tissue and urine followed by blood and sputum, which is similar to other studies (1,5).
In this study, the overall mortality among patients who acquired CRE was high as reported by other investigators (14,16). Not surprisingly, the mortality among bacteremia patients was high. Tamma et al. (17) found that the odds of dying within 14 days were more than three times greater in Carbapenemase-producing CRE compared with non-Carbapenemase-producing CRE bacteremic patients (OR: 3.20; 95% CI: 1.06-9.61) and Li et al. (18) reported 65% mortality among CRE bloodstream infections. The cases in this study had more comorbidities than the controls, and we assessed all-cause mortality, which might explain the higher mortality. The strength of our study is that it included large numbers of patients in both paediatric and adult groups and a case-control design that enabled the identification of risk factors specific to our population. However, several limitations are observed. Firstly, the study is retrospective in nature. Secondly, we could not identify the risk factors for infection per se as we included one sample for each case and we took the infection sample if the case had previous colonization with same organism. Thirdly, the molecular typing of the strains that caused infections were not performed. Fourthly, this is a single centre study that may not represent the national epidemiology of the CRE. A multicentre prospective design that includes molecular epidemiology could enrich the epidemiology of these organisms in our setting.

Conclusion
The annual incidence of CRE acquisition in our facility is high with a high mortality rate among bacteremic patients. The risk factors identified significantly for acquisition of CRE were invasive devices (urinary catheter, central line, ventilation), antibiotic exposure, and previous healthcare admission (other hospital and abroad). A multifaceted strategy to control the spread of CRE is fundamental, considering the specific epidemiology of this organism related to our institution and country.

Ethical approval
The study was approved by the Royal Hospital Ethics and Research Committee (SRC#114/2017). The participants have not consented as there were no interventions done in the study. Only their data were extracted from the electronic medical records.