Determination of Enterococcus faecalis and Enterococcus faecium Antimicrobial Resistance and Virulence Factors and Their Association with Clinical and Demographic Factors in Kenya
Background. Enterococci are clinically significant because of their increasing antibiotic resistance and their ability to cause severe infections due to an arsenal of virulence genes. Few studies in the developing world have examined virulence factors that may significantly impact patient outcomes. This study describes the antimicrobial resistance profiles and prevalence of five key Enterococcal virulence genes gelE, asa, cylA, esp, and hyl in forty-four clinical Enterococcus faecalis and E. faecium isolates in Kenya and their association with patients’ demographic and clinical characteristics. Results. All E. faecium isolates were obtained from hospital-acquired skin and soft tissue infections. While E. faecalis was associated with community-acquired urinary tract infections. All isolates were resistant to erythromycin, whereas 11/44 (27.5%), 25/44 (56.8%), 28/44 (63.6%), 37/44 (84.1%), 40/44 (90.0%), and 43/44 (97.5%) were susceptible to tetracycline, levofloxacin, gentamicin, ampicillin, nitrofurantoin, and teicoplanin, respectively. All isolates were susceptible to tigecycline, vancomycin, and linezolid. There was little difference in the antibiotic resistance profiles between E. faecalis and E. faecium. The prevalence of the virulence genes among the 44 isolates were 27 (61.4%) for gelE, 26 (59.1%) for asa1, 16 (36.3%) for esp, 11 (25.0%) for cylA, and 1 (2.3%) for hyl. 72.9% of E. faecalis isolates had multiple virulence genes compared to 57% of E. faecium isolates with no virulence genes. The hyl gene was only detected in E. faecium, while cylA and asa1 were only detected in E. faecalis. A significant correlation was observed between the presence of asa1 and esp virulence genes and tetracycline resistance ( and 0.0363, respectively). A significant correlation was also observed between the presence of virulence genes gelE and asa1 and nitrofurantoin resistance ( and 0.0225, respectively) and ampicillin resistance ( and 0.0008, respectively). Conclusion. The study highlights the high levels of erythromycin resistance in E. faecalis and E. faecium, the demographic factors influencing the species distribution among patients, and the accumulation of multiple virulence genes in E. faecalis. The significant association of gelE, asa1, and esp virulence genes with drug resistance could explain the pathogenic success of E. faecalis and provides a guide for future studies.
Enterococcal species bacteria are Gram-positive cocci typically found in the gut, bowel, throat, mouth, and vagina as commensals [1–4]. E. faecalis and E. faecium are the main pathogenic species of the eighteen-known species of enterococci. However, only the E. faecalis and E. faecium strains harboring virulence genes are associated with human infections , including urinary tract (UTI), pelvic, blood, intraabdominal, and skin and soft tissue infections (SSTI) . The main virulence factors that have been described in Enterococci are aggregation substance (asa1), gelatinase (gelE), cytolysin (cylA), enterococcal surface protein (esp), and hyaluronidase (hyl). asa1 is an aggregation substance that enhances adherence to renal tubular cells . Gelatinase is a zinc metalloprotease that hydrolyzes fibrin, collagen, and other peptides  and has been linked to biofilm formation . The secretion of hemolysins such as cytolysin causes the breakdown of blood cells and has been linked with increased toxicity in human infection . Hyaluronidase facilitates the colonization of host tissue by breaking down hyaluronic acid, a critical component of connective tissue . Enterococcal surface protein (esp) is a high molecular weight surface protein associated with biofilm formation that is specific to enterococci . esp also plays a role in colonization and persistence in the urinary tract . The enterococcal virulence gene gelE is the most common in E. faecalis isolates, while hyl and esp are more common in E. faecium than in E. faecalis . Most of what is known about Enterococci species virulence is based on studies outside Africa [14, 15].
There is limited published data on the prevalence and distribution of virulence genes among clinical enterococci in Africa. However, studies in Ethiopia have demonstrated that Enterococcal isolates from animals carry the gelE virulence genes , contribute to hospital-associated infections  and profiled their antimicrobial susceptibility . Enterococci species are not major clinical pathogens in Africa as reports in Nigeria and Kenya indicate a point prevalence of 5–11% . Despite this, resistance to glycopeptides, aminoglycosides, β-lactams, and fluoroquinolone antibiotic classes is on the rise globally [10, 20] and could pose challenge to the treatment of these infections given that the remaining treatment options, such as linezolid, daptomycin quinupristin/dalfopristin, and vancomycin, are expensive with limited availability in primary care centers in Kenya. Although rare, there have been reports of vancomycin resistance in Kenya , indicating the possibility of growing resistance to these last-line drugs. The interplay of virulence genes and antimicrobial resistance in clinical infections is worth examining as hypervirulent and multidrug-resistant Enterococci isolates leading to infections with adverse clinical outcomes could emerge. Zou et al. examined the correlation between erythromycin resistance and virulence genes and found a positive association between the presence of gelE and resistance to erythromycin . This study was therefore conducted to examine clinical isolates of E. faecalis and E. faecium in Kenya to understand the prevalence and distribution of the virulence genes and determine if there is an association between antimicrobial resistance, clinical presentation, demographic factors, and virulence genes.
2.1. Study Design and Population
This cross-sectional study is nested in a multi-hospital surveillance study where patients over two months old with UTIs or SSTIs were recruited between May 2015 and December 2019 from six hospitals in five Kenyan counties. Urine samples, pus, and swabs from soft tissue infections were collected from study subjects after they consented to participate in the study. In addition, demographic and clinical data were collected for each patient, including gender, age, infection type, in- or outpatient status, infection acquisition in the community or hospital, and immune status.
2.2. Bacterial Isolation and Identification
Samples were shipped to the Kenya Medical Research Institute (KEMRI) laboratories at 2–8°C for pus and wound swabs and at room temperature for urine samples in boric acid. All samples were inoculated on MacConkey (BD, New Jersey, United States of America), cysteine lactose electrolyte deficient agar (HIMEDIA, Mumbai, India), and sheep blood agar (SBA) and incubated for 24 to 48 hrs at 37°C. Colony morphology and culture characteristics were observed macroscopically. Preliminary identification of Enterococci was made based on observation of Gram-positive cocci in chains on Gram stain and a negative catalase test. Confirmation of the identification and Enterococcus speciation were performed on the VITEK 2 automated platform (bioMérieux, Marcy-l’Étoile, France).
2.3. Antimicrobial Susceptibility Testing
Antimicrobial susceptibility tests were performed on the VITEK2 (bioMérieux, Marcy-l’Étoile, France) platform using the AST-P586 card panel consisting of thirteen antibiotics: benzylpenicillin, ampicillin, gentamicin, streptomycin, levofloxacin, erythromycin, quinupristin/dalfopristin, linezolid, vancomycin, teicoplanin, tetracycline, tigecycline, and nitrofurantoin. Results were interpreted based on Clinical & Laboratory Standards Institute (CLSI 2018) guidelines and the VITEK2 advanced expert system.
2.4. Detection of Virulence Genes
DNA was extracted from pure Enterococcus spp. isolate cultures using the Quick-DNA/Fungal/Bacterial extraction kit (ZymoResearch, California, USA) according to the manufacturer’s instructions and quantified using the Nanodrop (Thermofisher, Massachusetts, USA) spectrophotometer. A multiplex PCR targeting the five genes (cylA, asa1, gelE, esp, and hyl) was performed on Applied Biosystems 9700 thermocycler (Thermofisher, Massachusetts, USA) using published primers by Vankerkhoven et al. 2004 . Each 25 μl of the PCR mixture consisted of 12 μl of Dream Taq DNA polymerase (Thermofisher, Massachusetts, USA). 2.5 μl of DNA, 0.1 μl of cylA, asa1, gelE, and hyl. 0.2 μl of esp specific primers . The positive and negative controls were E. faecalis ATCC 29212 and E. coli ATCC 25922, respectively. The PCR conditions were: initial activation at 95°C for 15 min, 30 cycles of denaturation at 94°C for 1 min, annealing at 56°C for 1 min, extension at 72°C for 1 min, and finally, one extension cycle at 72°C for 7 mins. The PCR products were observed by running 15 μl of the PCR reaction on a 1% agarose gel alongside a 100 bp ladder (Thermofisher, Massachusetts, United States) and visualizing on an E-box gel documentation station (Vilber, Marne-la-Vallée, France).
3. Data Analysis
Demographic and clinical data were extracted from study questionnaires and displayed in an Excel spreadsheet. Quantitative data were analyzed in Excel. The association between virulence genes, demographic factors, and antimicrobial susceptibility phenotypes was assessed using the Fisher’s exact test with a considered significant.
4.1. Demographic and Clinical Characteristics of Patients with Enterococcal Infections
Enterococcus isolates were obtained from six hospitals within five counties: Nairobi (16), Kisumu (18), Kericho (2), Kisii (7), and Kilifi (1). Thirty-seven E. faecalis isolates and 7 E. faecium isolates were isolated from forty-four patients with a mean age of 37 years during the study period which represented only 1.89% of the total isolates obtained during the same period. The majority of isolates 29/44 (65.1%) were from the skin and soft tissue infections (SSTIs) while 15/44 (34.9%) were isolated from urinary tract infections (UTIs). Ten out of forty-four patients (23%) were immunocompromised individuals, 28/44 (63.7%) were hospitalized, and 10/44 (23.0%) had hospital-associated infections. E. faecalis was isolated more from females 21 (56.7%) than males. In contrast, 6 of the 7 E. faecium isolates were from males. All seven E. faecium isolates were from hospitalized patients and 6/7 from patients with SSTIs. Among the 44 patients, most had community-acquired enterococci infections, but E. faecium infections accounted for most of the hospital-associated infections. Only one UTI was hospital-associated compared with six SSTIs (Table 1).
Age was significantly associated with Enterococci infections (). The age group between 14 and 29 years contributed the largest proportion of infections, followed by the age group between 31 and 49 years and above 50 years. There was no association between gender and the species of Enterococcus or between immunocompromised status or type of infection with enterococcal species. There was a significant association between species type, the source of infections (), and the patient status (inpatient/out-patient). Community-acquired Enterococci infections were more likely to be caused by E. faecalis than E. faecium whereas E. faecalis were more likely to be HAI with all E. faecalis infections identified in hospitalized patients (Table 1).
4.2. Phenotypic Characteristics and Antimicrobial Susceptibility Profiles of the Enterococci spp. Isolates
All 37 E. faecalis and 7 E. faecium colonies appeared as smooth, nonhemolytic yellow colonies with entire edges on CLED media indicating lactose fermentation. They were all Gram-positive cocci in short chains microscopically. Among the 44 isolates, there was 100% susceptibility to three antibiotics (linezolid, tigecycline, and vancomycin). There was 97.5%, 90.0%, 84.1%, 63.6%, 56.8%, and 27.5% susceptibility to teicoplanin, nitrofurantoin, ampicillin, gentamicin, levofloxacin, and tetracycline, respectively. Complete resistance to erythromycin was also observed (Figure 1). Supplementary Table 1 contains raw data of phenotypic antibiotic resistance data.
4.3. Detection of Virulence Genes
All the five virulence genes screened were detected among the E. faecalis and E. faecium isolates based on the presence of expected band sizes (Figure 2). Data indicating the presence or absence of the virulence genes for all the isolates is shown in Supplementary Table 1.
gelE was the most frequently detected gene at 27 (61.4%) followed by asa1 26 (59.1%), esp 16 (36.3%), cylA 11 (25.0%) and hyl 1 (2.3%) (Table 2). All the asa1 and cylA genes detected were in E. faecalis. gelE gene was detected in 26/27 (96.3%) E. faecalis isolates. 9/37 (24.3%) of E. faecalis isolates had only one of the virulence genes, 15/37 (40.54%) had two genes, 10/37 (27.03%) had three genes, and 2/37 (5.45%) had four genes. The most common gene combinations were gelE and asaI (35.1%) followed by asa1, cylA, and esp at 13/44 (24.3%) both found only in E. faecalis. E. faecium carried fewer virulence genes than E. faecalis, with 4/7 (57.0%) having none of the genes, two isolates having only one gene, and a single isolate having two genes (gelE, and esp). Notably, hyl was only detected in an E. faecium isolate. In contrast, cylA and asa1 were only detected in E. faecalis.
4.4. Distribution and Association of Virulence Factors with Antibiotic Resistance
Data on virulence factors and antibiotic resistance are summarized in Supplementary Table 1. There was a significant association between tetracycline resistance and the presence of asa1 and esp ( and 0.0363, respectively), nitrofurantoin resistance and the presence of gel E and asa1 genes ( and 0.0225, respectively) and ampicillin resistance and the presence of gel E and asa1 ( and 0.0008, respectively) (Table 3). The associations between the other antibiotics were not tested because of complete or almost complete resistance or susceptibility to erythromycin, teicoplanin, nitrofurantoin, linezolid, vancomycin, and tigecycline.
This study was conducted to evaluate the prevalence and distribution of known Enterococcus spp. virulence genes among clinical E. faecalis and E. faecium isolates obtained in a 5-year antimicrobial resistance surveillance study. The study found that Enterococcus spp. are uncommon clinical pathogens in the sampled Kenyan population given that the E. faecalis and E. faecium isolates represented <2% of the isolates recovered from clinical samples in the parent study. This is consistent with previous research in Africa that showed a 2.7% prevalence of Enterococcus spp. infections among pediatrics  much lower compared to a 13.6% prevalence reported in East Asia. The isolates in this study were obtained from SSTIs and UTIs consistent with the known infections caused by Enterococci spp. . However, we observed that E. faecalis was the predominant pathogen of the two species with E. faecalis isolated five times more than E. faecium. E. faecalis’s dominance is consistent with studies by Goel et al. in North India , that identified E. faecalis as the main uropathogen in community-acquired UTIs (CA-UTIs). This abundance of E. faecalis in CA-UTI could be attributed to the predominance of E. faecalis in the patient’s commensal flora [25, 26]. E. faecium though less frequently isolated, was found predominantly in male hospitalized patients with SSTIs, indicating its significance as a hospital-associated pathogen compared to other Enterococcus species.
Despite having fewer of the virulence genes tested than E. faecalis, E. faecium infections were associated with inpatient infections which implies infections of greater severity. This apparent disparity was also reported by Higuita et al. , who observed that E. faecium caused more severe infections and had a higher mortality rate than E. faecalis. Based on our observations we hypothesize that hospital-associated E. faecium infections could be opportunistic, affecting already vulnerable patients and leading to more adverse outcomes, and could have little to do with the presence or absence of virulence factors.
When we examined the antibiotic resistance patterns we found no significant differences between the two species in contrast to studies that found that E. faecium isolates are more efficient in accumulating resistance genes , resulting in greater resistance to penicillin, ampicillin, piperacillin, imipenem, and ciprofloxacin than E. faecalis isolates The lack of difference in resistance between species could reflect the rarity of human enterococcal infections and the high number of community-acquired infections which do not experience the antibiotic pressure that would drive antibiotic resistance to drugs typically used in hospital settings. The AST results indicated many available treatment options for the clinical management of Enterococcal infections since all the isolates tested were susceptible to vancomycin, tigecycline, and linezolid. The samples also had high susceptibility to teicoplanin, nitrofurantoin, ampicillin, gentamycin, and levofloxacin. Variable E. faecalis antibiotic resistance results for rifampin (60.7%), tetracycline (17.9%), erythromycin (14.3%), and chloramphenicol (10.7%) have been documented in Kenya . A high incidence of antibiotic resistance to ampicillin (80%) and doxycycline (73.3%) have also been reported in Ethiopia .
Glycopeptide resistance which is mediated by the Van gene clusters has rarely been reported in studies from Kenya [28, 29] and we did not observe any resistance in this study. Enterococci expressing the vanA gene are highly resistant to vancomycin and teicoplanin antibiotics, while enterococci expressing the vanB gene show high resistance to vancomycin and susceptibility to teicoplanin . In this study, there was no resistance to vancomycin, but teicoplanin nonsusceptible isolates were observed in a few isolates and confirmed by repeat testing. Discordant resistance to the glycopeptide antibiotics is a rare but reported occurrence attributed in a study by Loong et al.  to novel point mutations and deletions in the regulatory regions for the Van genes located in the Tn1546 type transposon. Analysis of the presence of vancomycin resistance genes and the regulatory components could offer clues on the mechanisms at play in the unusual discordance observed among the study isolates.
The study observed high susceptibility (75%) to nitrofurantoin, the second most common drug to treat bacterial infections in the urinary tract in Kenya after beta-lactam drugs . This high susceptibility in Kenya compared to other countries such as Iran with resistance levels of 35.5%  suggests that nitrofurantoin use is still not as common in Kenya as in other countries. Erythromycin is a relatively inexpensive broad-spectrum antibiotic used to treat many infections, so it was not surprising that resistance levels were high. This study shows that this drug is no longer effective for the treatment of Enterococcus spp. infections. A study in Nigeria also showed 100% erythromycin resistance, indicating that this trend is prevalent in more than one region of sub-Saharan Africa . This study on clinical isolates found tetracycline resistance levels (72.5%) markedly higher than the 17.9% percent reported in the 2018 survey by Wambui et al. performed on slaughterhouse cattle  but consistent with studies done in a Kenyan hospital in 2009 that found tetracycline resistance rates of 80% for E. faecalis and 71% for E. faecium . These high rates can be attributed to tetracycline being commonly used to treat infections because it is affordable and readily available. The high tetracycline resistance rate has also been linked to the widespread use of tetracycline in livestock , evidenced by its presence in animal products [35, 36] and among poultry in Europe  which could drive antibiotic resistance in bacteria including Enterococci.
This study reports gentamicin resistance of 36.4%, which suggests close to a two-fold increase in resistance in less than ten years based on a reported 19% resistance level in Kenya in 2012 . Since aminoglycosides (e.g., gentamicin) monotherapy is known to have poor uptake into the cytoplasm, a combination of penicillin/gentamicin therapy is recommended for the treatment of patients with Enterococcal infections to improve the penetration of gentamicin through the bacterial cell-wall using the cell-wall active penicillins, resulting in synergistic activity . A study done in Kenya in 2020 by Maina et al.  reported that combinations of penicillin and gentamicin were predominant in the neonatal unit (58%). Resistance to ampicillin was roughly comparable to resistance to gentamycin in this study, implying corresponding use.
After observing that the antibiotic resistance levels were low except for erythromycin and tetracycline we considered whether the pathogenicity of the organisms were a significant threat by examining the virulence gene profiles. The gene encoding gelatinase gelE was the most prevalent virulence gene (36.3%). This is consistent with the findings of numerous studies conducted around the world, all of which found gelE to be more prevalent than the other genes measured in this study . In terms of dominance, the agglutination substance gene asa1 came in second. Both genes were present only in E. faecalis. gelE and asa1 are the predominant virulence genes in similar studies performed among clinical isolates in India and Iran and also in pigs from a study in China [21, 40, 41]. The hyl gene was found in only one E. faecium isolate, which was not a surprise given earlier studies that observed that the hyl gene was predominantly found in E. faecium isolates from clinical samples in the United States . Although esp is known for its function in adhesion to the urinary tract wall  in this study, it was equally present in isolates from UTIs and SSTIs.
The study also sought to test the association of virulence genes with antibiotic resistance. In addition to the association described by Zou et al. between gel E and erythromycin, this study has identified other significant associations between the asa1 gene and esp and tetracycline and between nitrofurantoin, gelE, and asa1. The asa1, gelE, and esp genes encode biofilm-forming proteins involved in adhesion to the host cells [8, 42]. The positive association between asa1, gelE, and esp genes with nitrofurantoin and tetracycline resistance is interesting as the two drugs are effective against biofilm-forming isolates [43, 44]. Biofilm-forming Enterococci bacteria are generally more resistant to antibiotics than nonbiofilm-forming ones . We hypothesize that exposure of biofilm-forming isolates to nitrofurantoin and tetracycline could drive specific resistance to these agents. The association of asa1, esp, and gelE in antibiotic-resistant bacteria is advantageous as it provides a double arsenal for causing and surviving the treatment of clinical infections.
The study had a few limitations. First, there were only a few Enterococcus spp. isolates obtained in the study, which limited the statistical analysis and inferences that could be made. Second, some patients had coinfections with other pathogens, so the infections could not be solely attributed to Enterococcus spp. Third, the study only screened for five essential virulence genes, whereas more genes are involved in Enterococcal pathogenicity. Fourth, although most of the virulence genes tested are associated with biofilm formation, biofilm assays were not conducted to confirm the phenotype. A more extensive study combining phenotypic assays and whole-genome approaches would address virulence factors more comprehensively and provide the isolates’ strain types to address any clonality issues that could skew the detected associations.
The study has identified E. faecium as a predominantly health-care-associated infection affecting male patients and E. faecalis as an important etiology of community-acquired urinary tract infections. Enterococcal infections can be well managed due to the low-level resistance observed for most antibiotics except tetracycline and erythromycin. All five virulence genes tested were identified among the Kenyan isolates with E. faecalis carrying more and multiple genes. The importance of esp, asa1, and gelE virulence genes in virulence and their co-occurrence with antibiotic resistance could explain the clinical success of E. faecalis and provides an opportunity for further research.
|ATCC:||American Type Culture Collection|
|CLED:||Cysteine lactose electrolyte deficient agar|
|CLSI:||Clinical & Laboratory Standards Institute|
|E. faecalis:||Enterococcus faecalis|
|E. faecium:||Enterococcus faecium|
|esp:||Enterococcal surface protein|
|IRB:||Institutional Review Board|
|KEMRI:||Kenya Medical Research Institute|
|MLST:||Multilocus sequence typing|
|PCR:||Polymerase chain reaction|
|SBA:||Sheep blood agar|
|SERU:||Scientific and Ethics Review Unit|
|SSTIs:||Skin and soft tissue infections|
|UTIs:||Urinary tract infections|
|WRAIR:||Walter Reed Army Institute of Research.|
The graphs, figures, and tables data used to support the findings of this study are included within the article and also uploaded in the figures files section and supplemental files section.
This study was approved by the Scientific and Ethics Review Unit (SERU #2767) of the Kenya Medical Research Institute (KEMRI) and the Walter Reed Army Institute of Research (WRAIR #2089) IRB. Permission has been granted for the publication of this manuscript by the Director KEMRI. There is no objection to its publication. The investigators adhered to the policies for the protection of human subjects as prescribed in AR 70–25.
All subjects provided written consent to participate in the study and for their isolates and data to be used for research and publications.
The opinions or assertions contained herein are the author’s private views and are not to be construed as official or as reflecting the true views of the Department of Defense.
Conflicts of Interest
The authors declare that they have no conflicts of interest.
L.M. conceptualized the study and acquired the funding. M.G., D.M.M., D.M, F.T, E.O., and C.K investigated the study. M.G. and W.M analyzed the data. M.G. wrote the original draft. M.G., E.O., W.M., and L.M. reviewed and edited the manuscript. All the authors read and approved the final manuscript.
The authors would like to acknowledge the contribution of Amanda Roth in manuscript review, Cliff Momanyi, Fridah Kiage, Gladys Biwott, Catherine Muriuki, Alfred Odindo, Mitsanze IHA Thoya, and hospital staff for assistance with sample collection. This research was funded by the Armed Forces Health Surveillance Division (AFHSD) Global Emerging Infections Surveillance Branch under project no. PROMIS ID 20160270153 FY17-19.
Supplementary Table 1: infection types, antibiotic resistance profiles, and virulence genes for the Enterococcus spp. isolates. (Supplementary Materials)
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