Are uropathogenic enterococci becoming smarter day by day? Changing trends of antimicrobial resistance and species distribution among uropathogenic Enterococcus species

INTRODUCTION

Enterococci are Gram-positive cocci (GPC) that have been recognized as important human pathogens. They were initially classified as Streptococcus members, but in the 1980s, they were reclassified as Enterococcus members due to their distinct biochemical and genetic characteristics.^[1] Enterococci are characterized by their ability to grow in the presence of bile salts and their ability to hydrolyze esculin.^[2] They are catalase negative and oxidase negative, distinguishing them from other GPCs such as staphylococci and micrococci.^[3]

The enterococci produce a variety of enzymes and metabolic products, including hemolysins, gelatinases, and cytolysins.^[4] They are also able to produce biofilms, which can further protect them from the action of antibiotics and are able to evade the host immune system.^[3] The enterococci are also known for their ability to exchange genetic material with various other bacterial species. Antibiotic resistance and virulence factors transmission among enterococcal populations may be aided by the horizontal transfer of genetic material. The antibiotic resistance genes spread among enterococci are well documented, and these bacteria are frequently linked to healthcare-associated infections (HCAI).^[4] Enterococcal infections have continued to be a major public health concern, particularly in healthcare settings, especially causing infections in patients with weakened immune systems or who have undergone invasive medical procedures. Urinary tract infections (UTIs) are the most common infections caused by enterococci among HCAIs. These infections have become even more difficult to treat in recent years due to the emergence of strains resistant to multiple antibiotics, including vancomycin-resistant enterococci (VRE).^[5]

Despite the challenges posed by enterococcal infections, ongoing research is helping to improve our understanding of the biology and pathogenesis of these bacteria as well as their mechanisms of antibiotic resistance.^[6] This research is critical for the selection of appropriate antimicrobials for treatment and prevention strategies to combat enterococcal infections. The identification of enterococci up to species level is also important along with their antimicrobial resistance pattern in the form of an antibiogram for the selection of appropriate antimicrobials for empirical treatment. The less frequently isolated species including Enterococcus casseliflavus and Enterococcus gallinarum are usually misdiagnosed on conventional methods due to overlapping biochemical properties. These rare species have different resistance patterns leading to treatment failure due to the selection of the wrong antibiotic based on the antibiogram of misidentified species. This study was planned to observe the trends in the frequency distribution of various Enterococcus species along with their antimicrobial susceptibility patterns implicated in UTI among the patients presenting to our tertiary care medical teaching hospital.

MATERIAL AND METHODS

This was a cross-sectional observational study, which was conducted in the Microbiology Department of our hospital and the duration of the study was 1 year (August 2022–July 2023). The prior approval from the institutional ethical committee was taken before the commencement of this study vide letter No. SMC/UECM/2022/403/202 dated April 01, 2022. The midstream clean catch urine samples were collected aseptically from suspected cases of UTI from intensive care units, outpatient departments (OPDs), and inpatient departments of the hospital after taking informed and written consent, following inclusion and exclusion criteria.

RESULTS

A total of 4961 urine samples were collected from the clinically suspected patients of UTI during the study period of 1 year. Out of the total urine samples collected, clinically significant pathogens were grown in 1477 samples comprising 29.77% of overall culture positivity among urine samples. The distribution of various pathogens revealed 17% of GPC among all pathogens isolated [Figure 1].

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Figure 1:

Distribution of various pathogenic organisms isolated from urine.

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Among total 257 GPC isolates grown on culture from urine specimens, most of the isolates were Enterococcus species comprising 89.49%. Among enterococci, E. faecalis was the most commonly isolated species, followed by Enterococcus faecium comprising 49% and 41%, respectively [Figure 2].

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Figure 2:

Species distribution of enterococci isolated from urine.

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Among all enterococci isolates, 46.09% were isolated from male patients, while 53.91% were from female patients. The majority of isolates from urine samples belonged to patients more than 60 years of age comprising 35.65% [Table 1]. The AST results of various Enterococcus species revealed overall higher resistance of E. casseliflavus and E. gallinarum to ciprofloxacin (100%) [Tables 2 and 3].

DISCUSSION

The enterococci previously considered as traditional commensal bacteria are now understood to be capable of causing serious infections in humans, especially among the patients admitted in the healthcare settings. With rising vancomycin resistance and rising mortality rates, enterococci have become an important pathogen, especially implicated among HCAIs.^[7-9]

In this study, significant growth of different pathogenic organisms implicated in UTI was observed in 29.77% of urine cultures. This culture positivity rate was found to be consistent with the culture positivity rate of other studies including Sharma et al. in 2023 from adjacent geographical regions comprising 29.1%.^[10] The culture positivity among urine samples from nearby geographical regions was also observed almost similar to our study with slight variations, including the reported culture positivity of 34.0% and 22.93% by Rajni et al. in 2022 and Ahirwar et al. in 2024, respectively.^[11,12] The culture positivity depends on many factors, including the factors related to the healthcare setting as well as patient-related factors such as age, gender, immunity status, and geographical distribution of the individuals.^[13]

In our study, the species distribution of all enterococci comprised 48.48% E. faecalis, 40.69% E. faecium, 7.79% E. gallinarum, and 2.5% E. casseliflavus. The rates of isolation of various Enterococcus species from urine as reported in other studies were consistent with our findings, highlighting the predominance of E. faecalis over E. faecium, including the studies by Smout et al. in 2023, Sumangala et al. in 2020, and Yenisehirli et al. in 2016.^[14-16] We observed a significant proportion of other enterococci comprising around 8% of E. gallinarum and 2.5% of E. casseliflavus in this study, which were rarely reported in other studies from the recent past. The emergence of new species of enterococci causing UTI can be a changing trend.

In this study, the majority of the isolates were isolated from urine samples belonging to patients more than 60 years of age group comprising 35.65%. More or less similar demographic observations were also observed in various other studies including a study done by Chanda et al.^[17]

We observed that 55.84% of enterococci were isolated from OPD and 22.07% of enterococci were isolated from the patient on indwelling urethral catheters, and similarly, 22.07% were isolated from other wards. There are variations in the reported data available, as these findings depend on various factors including the factors related to the type of healthcare facility and various patient-related factors such as catheterization status, immunity status, or demographic profile as mentioned by Yilema et al. and Medina-Polo et al. in 2017.^[18,19]

Due to emerging more resistant strains exhibiting higher resistance against most of the antibiotics used to treat enterococcal infections, particularly involving high-end antibiotics such as glycopeptides and linezolid, the treatment has become more difficult and challenging. As these bacteria are more resistant to antibiotics acting on cell walls than streptococci, species-level identification along with the susceptibility tests should be performed with penicillin or ampicillin. The approved treatment option for the treatment of simple as well as complicated UTIs such as chronic bacterial prostatitis, cystitis, and pyelonephritis is ciprofloxacin.^[20] In this study, we observed 93.91% of ciprofloxacin resistance among enterococci. More or less similar findings were reported in recent studies including the studies by Sattari-Maraji et al. in 2019, Perdana et al. in 2023, Anjum et al. in 2023, and Ohri et al. in 2023.^[21-24] The lower resistance against ciprofloxacin was also reported in previous studies including the reported data by Calgin and Cetincol, Yadav, and Agarwal comprising 51% and 60% of ciprofloxacin resistance, respectively.^[25,26] The drastically increasing resistance pattern of enterococci against commonly administered antibiotics is shown in recent literature as highlighted by Yadav and Agarwal.^[26]

Nitrofurantoin is an antibiotic that can be used to treat simple UTIs. The appropriate use of nitrofurantoin can reduce the emergence of resistance against newer high-end antibiotics by limiting their usage.^[27] In our study, we observed 31% of Enterococcus isolates exhibiting resistance against nitrofurantoin. A similar resistance against nitrofurantoin was also reported by Chanda et al. in 2022.^[17] The lower resistance was also reported against nitrofurantoin, including the study by Ahirwar et al. (2024).^[12]

The reported data highlight the increased resistance against glycopeptides (teicoplanin and vancomycin), and these antibiotics are still the most effective agents against Enterococcus species.^[17,25] We observed 29% and 18% of resistance against vancomycin and teicoplanin, respectively. The increasing trends of vancomycin resistance have been reported in various studies, including a systematic review and meta-analysis by Smout et al.^[14] in 2023 in which they reported and highlighted an upsurge in VRE over time in India from 2000 to 2020. The reported VRE was 4.8% between 2000 and 2010 while it was 14.1% between 2011 and 2020.^[14] We observed a further increase in the isolation rates of VRE in our study which is close to the reported resistance in recent studies, including the study by Jain in 2023 and Nair et al. in 2024.^[28,29] The possible reason for the increasing trends of VRE can be the indiscriminate use of glycopeptides to treat infections with Gram-positive bacteria. Antibiotic resistance patterns depend on many factors and can be different among healthcare facilities and geographical regions.^[29]

Linezolid, an antibiotic from the oxazolidinone class, is active against a variety of GPCs, including VRE.^[30] In our study, we reported 21.64% of enterococci resistant to linezolid. The use of linezolid should be limited only to appropriate indications and given in adequate doses after performing antibiotic susceptibility tests, preferably in combination with other antimicrobials, to prevent the development of resistance. As the resistance trends depend on a particular healthcare facility as well as the community, the understanding regarding the resistance trends among Enterococcus isolates is important to guide the policymakers in the formulation of policy guidelines to treat these infections.^[29,30] The continuous upsurge in the incidence of VRE and the emergence of linezolid resistance among enterococci has to be dealt with seriously. The appropriate guidelines for hospital infection prevention and control along with the antibiotic policy have to be strictly followed to prevent antimicrobial resistance and transmission of these strains in the hospital environment.

The emerging enterococcal species such as E. gallinarum and E. casseliflavus as observed in this study were comprised significant proportions and these species were observed to be more resistant against first-line antimicrobials including nitrofurantoin and fosfomycin which signifies the necessity of species-level identification and AST before initiation of antimicrobial chemotherapy. If the clinical condition is due to these unusual enterococci, the empirical antibiotic treatment may result in treatment failure.

CONCLUSION

Enterococci are among the common and important causes of UTI. The recent trends highlighting the emergence of newer species of enterococci, including E. gallinarum and E. casseliflavus exhibiting higher resistance against first-line antimicrobials, including nitrofurantoin and fosfomycin indicate an alarming situation leading to empirical treatment failure due to misidentification on conventional testing. The phenotypic characterization by automated methods or molecular characterization can serve as an important tool for the confirmation of these trends.