The prevalence of carbapenem resistance is increasing indicating a very alarming situation. Eight years ago the emergence of CRE in clinical isolates was reported in two intensive care unit patients in a cancer hospital in Cairo in Egypt [12]. Since then, the frequency increased within few years reaching 62.7% (47/75) in Tanta University Hospitals [13]. More recently, a survey for hospital acquired infections (HAIs) that included 310 ICUs in 72 hospitals across 25 governorates in Egypt showed that 64% of the hospitals had at least one CRE isolate and 47.9% of Enterobacteriaceae isolates were CRE. This rate is higher than estimates reported from other Arab, African or Asian countries. The incidence of CRE HAI was estimated as (3.7/10,000 patient days) which is also much higher than the overall incidence of all CRE (HAI and non-HAI) reported from other countries all over the world; United States (0.1–0.4/10,000 patient-days), Canada (0.2 per 10,000 patient-days) and China (0.4 per 10,000 patient-days) [14].
CRE carriers in rectal swab samples are recognized as a high risk group, as they can spread CRE by intimate contact and via travel [15]. Furthermore, a 6.5% risk of infection with CRE amongst colonized patients has been documented [7]. Therefore, it becomes essential to identify CRE carriers in hospital settings because identifying asymptomatic colonizers and applying contact isolation precautions is mandatory to reduce transmission and to improve patient outcome [16]
The aim of the current study was to determine the frequency of CRE intestinal colonization in patients upon admission to TBRI hospital, assess the genotypic diversity of CPE and to determine the main risk factors related to intestinal colonization with CRE.
Twenty-eight of screened patients gave positive rectal swabs culture on chromogenic agar “CARBA SMART” media yielding 36 CRE isolates. Thus, the prevalence of colonization by CRE was 28%. Studies assessing CRE colonization in Egypt are limited; however, the result of the current study is comparable to a recently published one that was carried in a paediatric ICU in Cairo that showed a prevalence rate of 24% [17]. This was also in agreement with a previous Brazilian study showing a prevalence rate of 30.4% [18]. Higher rate of CRE colonization (52%) was reported among patients admitted to Vietnamese hospitals [19]. On the contrary, this figure was relatively higher than that reported in a rehabilitation Italian hospital (10.2%) and much higher than that reported from outpatient children in Shanghai (3.6%) [15, 20].
Also this was higher than figures obtained from patients in ICUs of two hospitals in Kuwait; 7.8% (25 / 320) at Adan Hospital, and 12.2% (33/270) at Mubarak Al Kabeer Hospital [21].
In a recently published review, Egypt showed the highest prevalence of CRE (28% of 796 isolates) compared to other African countries including Algeria, Libya, Morocco, Mauritania and Tunisia showing a prevalence rate of 2% or less [22]. This high level of resistance in the current study can be attributed to the massive abuse of antibiotics in Egypt [23].
In the current study and following CLSI breakpoints revealed that all the studied isolates harboring carbapenemase-producing genes showed resistance to at least one carbapenem with best sensitivity to ertapenem (97.2%) [8]. However, upon applying the “ECOFFs” screening cut-off values to the three carbapenems, a more sensitive result was obtained covering 100% of CRE with ertapenem and meropenem [9]. This is of much importance to healthcare facilities where screening for CRE to apply prompt infection control contact precautions is of tremendous priority. Moreover, it is worth mentioning that the recent document released by EUCAST in 2017 recommended the use of ertapenem and meropenem to screen for CRE and not imipenem that matches with the finding in this study [24].
The Rapidec Carba NP test is a reliable confirmation tool of CPE isolates, especially NDM producers, with lower sensitivity (as it gave negative results with six OXA-48-like producers) which could be attributed to their weak hydrolytic carbapenemase activity. These findings agree with another study which revealed lower sensitivity with class D Ambler carbapenemase producers [25].
The detection of CPE by Rapidec Carba NP test in six isolates, which were negative by PCR of the tested carbapenem resistance genes, suggested the possibility of the presence of other mechanisms of resistance other than carbapenemase production such as porin loss or over production of ESBLs or of AmpCs. As we tested the main five resistance genes (KPC, NDM, VIM, IMP and OXA-48 genes) only, other uncommon untested resistance genes such as GES, NMC-A, SME, SCF-1, IMI-1 and IMI-2 genes may be involved in resistance to carbapenems.
Understanding factors that predispose to colonization of patients with CRE may help clinicians prevent transmission as well as reduce morbidity and mortality. Previous studies reported that exposure to hospital setting or/and antimicrobial agents might increase the risk of colonization and it would be easier to acquire CRE isolates [15]. In the current study, colonized and non-colonized patients did not significantly differ with respect to gender and associated comorbidities. However, patients colonized with CRE were significantly more likely than non-colonized patients to have a history of recent hospitalization within the previous 12 months, as well as having previous antibiotic intake within the previous month. This also confirms what has been reported lately that among colonized patients, ICU stay is one of the most important patient-related conditions associated with a significant risk of CRE infections, whereas prolonged exposure to broad spectrum antibiotics was among the main modifiable variables involved [7].
The variation in the study population and the epidemiological differences in various geographic regions was reflected in species distribution of CRE as in the present study, E. coli was the major species identified (83%), followed by K. pneumoniae (17%). This was similar to Perry et al. [26] who stated that E. coli was the major species found (47%) among faecal carriers of Enterobacteriaceae with blaNDM-1 at military hospitals in Pakistan. Opposite finding was reported in a Brazilian study where Klebsiella was the sole species identified, and in another study in USA where the majority of recovered isolates were K. pneumoniae (92%) [18, 27]. Other parts of the world showed also different results, where in Taiwan, K. pneumoniae (53.8%) was the main species followed by E. cloacae (30.8%) and lastly E. coli (14.1%) [28].
Although blaNDM is known to be endemic in the Middle East [5] in this study it was the second most common detected gene. While blaOXA-48-like was the main carbapenemase-producing gene (66.7%), mainly in E. coli (70%), blaNDM-like was the following gene (30.6%), mainly in K. pneumoniae (66.7%). Only 2.7% of the isolates harbored blaVIM-like. Similar findings were reported in a recent Egyptian study where blaOXA-48 showed dominance (33%) followed by blaNDM (27%) in CRE isolates from colonized pediatrics age group in ICU. However, both genes were detected mainly in Klebsiella pneumoniae isolates [17]. This finding could be different from the clinical situation in Egypt and in other parts of the world where carbapenem resistance is detected at higher frequencies in K. pneumoniae than in E. coli. In a more recent study, the most common pathogen for CRE cases of HAIs in Egypt was Klebsiella (85.1%), followed by E. coli (10.2%) [14]. Moreover, in a review that compares all multidrug resistant bacteria from different Arab countries, CRE was found in Egypt, as with other countries, more in Klebsiella than in E. coli isolates (40% vs 5%) [22]. Lately our team in TBRI also identified blaNDM as the main carbapenem resistance gene in K. pneumoniae clinical isolates [5]. The blaNDM is known to be endemic in our region with the first report in Cairo in Egypt being reported in 2013 from a K. pneumoniae isolate [12]. Later, it has been described repeatedly from various geographical areas in Egypt [5, 29]. Another Egyptian study reported blaOXA-48 as the dominant carbapenem resistance gene in K. pneumoniae clinical isolates (40.6%) and blaNDM-5 (9.6%) in E. coli [30].
Co-production of OXA-48-like and other carbapenemases (NDM, VIM) leads to the emergence of multidrug resistant strains. In this study, six isolates out of 36 (four E. coli and two K. pneumoniae) harbored two genes (blaNDM-like and blaOXA-48-like) while only one E. coli isolate harbored (blaOXA-48-like and blaVIM-like) genes. Similar co-production of genes was reported previously in several parts of the world [31, 32].
Early detection of CRE colonization allows for early and rapid setting of contact precautions to prevent CRE transmission to other patients. CRE carriage is an important risk factor to be detected rapidly, as this may permit early implementation of appropriate antimicrobial therapy, which is the strongest modifiable predictor for mortality in severe sepsis in CRE infections [16, 21]. Recent report from southeastern Brazil and Vietnam confirmed the importance of active CRE surveillance protocol as subsequent infection with CRE is frequent in hospitalized patients colonized with CRE isolates. However, its effective implementation depends on the appropriate preventive measures and feedback among its team members [19, 33]. Although the current study only enrolled 100 patients, yet we find this significant figure of colonization among the studied subjects is an important threat to public health and should be reported. Further studies including more patients from multiple centers should be considered in the future.
Current treatment options for CRE infections are very limited, as they are resistant to all β-lactam antibiotics as reported in the current study and as previously detected [34]. The highest in vitro sensitivity was shown to glycylclines (tigecycline) in this study followed by aminoglycosides (mainly amikacin and gentamicin) and nitrofurans (nitrofurantoin) which may represent possible treatment options.