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ACTA MICROBIOLOGICA BULGARICA Volume 37 / 3 (2021)
149
Volume 37 / 1 (2021)
* Corresponding author: id–dhanashreeltmmc@gmail.com
Epidemiological Prole, Speciation and Antibiogram of Enterococcus
Species in the Era of Resistance
Dhanashree Padmanabh Inamdar1*, Anuradha Basavaraju1, Malatesh Undi2
1Department of Microbiology, Mamata Medical College and Hospital, Khammam, Telangana, India
2Department of Community Medicine, Karwar Institute of Medical Sciences, Uttara Kannada, Karnataka,
India
Abstract
Enterococcus species have now emerged as leading causes of nosocomial infections. Speciation and
antibiotic susceptibility testing (AST) are needed for these organisms due to their increasing resistance to
various antibiotics. As geographic diversity contributes to varied resistant patterns in these organisms, the
present study was conducted with the objective to analyse the prevalence, clinicodemographic prole, and
speciation of enterococci from various clinical samples, and to assess their antimicrobial resistance (AMR)
pattern at our setting. A prospective observational study was carried out for a period of six months at a tertiary
care hospital in Telangana, India. Clinical samples which showed growth of pathogens during the study peri-
od were included. Enterococcus spp. were identied by appropriate biochemical tests followed by AST. 106
Enterococcus spp. were isolated among 1864 samples with growth during the study period. Prevalence of en-
terococcal infections was 5.6%. Male population, age distribution (31-40 yrs), gynaecology ward inpatients,
and urine samples had signicant (p value <0.05) enterococcal isolation. Enterococcus faecalis (61.3%) was
the commonest isolate. High-level streptomycin (HLS) resistance was 33.01% and high-level gentamicin
(HLG) resistance was 37.7%. Although resistance to commonly used antibiotics was high, vancomycin re-
sistance was only 6.6%, and linezolid resistance was 0% at our setting. The clinicodemographic prole of
patients has to be scrutinized when dealing with enterococcal infections. There is geographic variation in the
resistance patterns of enterococci, which needs to be addressed before institution of denitive therapy. Spe-
ciation not only helps epidemiology, but also guides in tracking resistance patterns emerging among them.
Keywords: Enterococcus spp., antibiotic susceptibility testing (AST), antimicrobial resistance (AMR),
vancomycin, vancomycin resistant Enterococcus (VRE).
Резюме
Eнтерококите са водещи причинители при вътреболничните инфекции. Поради тяхната
нарастваща резистентност към различни антибиотици е необходимо тестиране на специфичността
и чувствителността им към антибиотици (AST). Тъй като географското разнообразие допринася за
различни модели на резистентност при тези микроорганизми, настоящото проучване е проведено с
цел да се анализира разпространението, клинично-демографския профил и видовата характеристика
на ентерококи от различни клинични проби и да се оцени моделът на тяхната антимикробна
резистентност (AMR). За период от шест месеца е проведено проспективно обсервационно
проучване в болница за третични грижи в Телангана, Индия. Включени са клинични проби, които
показват растеж на патогени през изследвания период. Видовете ентерококи са идентифицирани
чрез подходящи биохимични тестове, последвани от AST. Изолирани са 106 вида ентерококи от
общо 1864 проби. Разпространението на ентерококовите инфекции е 5.6%. Половото и възрастовото
разпределение (31-40 години), пациентите в гинекологичното отделение и пробите от урина
показват значитело достоверно (р <0.05) изолиране на ентерококи. Най -често срещаният изолат е
Enterococcus faecalis (61.3%). Резистентността към HLS (високо ниво на стрептомицин) е 33.01%, а
резистентност към HLG (високо ниво на гентамицин) е 37.7%. Въпреки че резистентността към чес-
то използваните антибиотици е висока, резистентността към ванкомицин е само 6.6%, а резистент-
ността към линезолид е 0%. Клинично-демографският профил на пациентите трябва да се изследва
150
Introduction
Group D Streptococci includes Gram-posi-
tive cocci, of which the genus Enterococcus is clin-
ically signicant. These organisms are normal res-
idents of the gastrointestinal, biliary and urogenital
tracts in humans (Ross, 2006; Rasovic, 2018). With
19 species within this genus, Enterococcus faecalis
contributes to the majority of infections - up to 80-
90%, followed by Enterococcus faecium 10-15%,
Enterococcus avium, Enterococcus casseliavus,
Enterococcus durans, and Enterococcus gallinar-
um (Udo et al., 2003; Upadhyaya et al., 2009). This
speciation helps not only in evidence-based diag-
nosis, but is particularly useful with regard to treat-
ment, as beta lactamases are now widespread in this
genus and glycopeptide resistance to vancomycin
can result in therapeutic failure in treating urinary
tract infections, hospital acquired bacteraemia and
endocarditis caused by this organism (Gordon et
al.,1992; Low et al., 2001). Although Escherichia
coli is the most common pathogen causing commu-
nity acquired or nosocomial urinary tract infections
(UTI), the Centers for Disease Control and Preven-
tion (CDC) mention Enterococcus spp. as the sec-
ond most common causative agent of nosocomial
UTI next to it in a survey (Oberoi and Aggarwal,
2010; Aljicevic et al., 2019). Treating enterococcal
infections is one of the greatest challenges faced
by clinicians of 21st century. This is due to the in-
creasing resistance in this organism, which can be
intrinsic or acquired. The drug used for empiri-
cal treatment of enterococcal infections is usually
beta-lactam antibiotic. Vancomycin is clinically
indicated in serious infections when the patient
does not respond to preliminary antibiotics like
beta-lactams or has beta-lactam allergy (Kristich
et al., 2014). Thus, antibiotic susceptibility testing
(AST) is obligatory, as it guides in initiating anti-
biotics and aids in evidence-based treatment. VanA
gene cluster, which is carried on transposons or via
conjugative plasmids, is responsible for vancomy-
cin resistance, which can otherwise be inducible
also (Salem-Bekhit et al., 2012).
Many literature sources make reference to the
emergence of glycopeptide resistance like vanco-
mycin-resistant enterococci (VRE) and high-lev-
el aminoglycoside resistance (HLAR) along with
methods to detect the resistance genes involved.
Studies of antimicrobial susceptibility patterns are
now referred to as antimicrobial resistance (AMR)
studies due to the huge shift from susceptible to re-
sistant bacterial populations (Jaiswal et al., 2017;
Naruka et al., 2019). The World Health Organisa-
tion (WHO) has declared antimicrobial resistance
(AMR) as one of the top ten global threats facing
humanity, which requires urgent collaboration at
multisectoral level. This issue has its grave conse-
quences on patients, as it increases the cost, length
of hospital stays, and causes adverse outcome of pa-
tient recovery (Schouten et al., 2000). Not only the
presence of beta-lactamase genes, van genes circu-
lating in Enterococcus contribute to resistance, but
also different geographic locations have varied re-
sistance patterns due to diverse antibiotic prescrib-
ing policy by general practitioners and disparity in
empirical treatment being initiated for infections
caused by this microbe (Gangurde et al., 2014).
Thus, there is a need to know their resistance pat-
tern so that early treatment can be initiated, as VRE
poses a great challenge in clinical settings. Hence,
the present study was undertaken with the aim to
check the antimicrobial resistance (AMR) pattern
in enterococci at our setup along with clinicodemo-
graphic prole, prevalence, and its speciation from
various clinical samples. The aim was to study the
prevalence, clinicodemographic prole, speciation
of Enterococci from various clinical samples and to
assess the antibiogram in those isolates.
Materials and Methods
Institutional ethical committee clearance was
obtained before the start of the study. A prospective
observational study was carried out in the Depart-
ment of Microbiology, Mamata Medical College
and Hospital, Khammam, Telangana, from June
2019 to January 2020, which caters patients mainly
belonging to rural background.
Sample processing
Clinical samples collected in this period were
subjected to Gram stain, ZN stain and special stains
wherever required. All samples were inoculated on
routine media like blood agar and MacConkey agar
for bacterial culture and incubated at 37°C for 18-
24hrs. Chocolate agar was incubated for 48-72 hrs
in a candle jar. Genus’s identication along with
speciation was done by routine and special bio-
chemical tests for all isolates. Enterococcus spp.
внимателно при наличие на ентерококови инфекции. Съществуват географски различия в моделите
на резистентност на ентерококите, които трябва да бъдат разгледани преди въвеждане на окончател-
на терапия. Видовата характеристика не само помага на епидемиологията, но е и ръководеща при
проследяването на възникващите модели на резистентност.
151
was identied by colony morphology, catalase test,
growth in 6.5% NaCl broth, PYR test and bile escu-
lin test. Further speciation was performed by motili-
ty, sugar fermentation test with mannitol, arabinose,
rafnose, lactose, sucrose, deamination of arginine
on Moellers decarboxylase broth and pigment pro-
duction on white Dacron swab (Ross, 2006).
Antibiotic susceptibility testing
This was carried out by Kirby Bauer disc
diffusion method on Muller Hinton agar (MHA)
plates with broth turbidity matching 0.5 McFarland
standard as per CLSI 2019-2020 guidelines. Anti-
biotic discs required for testing AMR testing were
procured from Himedia (Mumbai, India). ATCC E.
faecalis 25912 was used for quality control (QC)
check on MHA plates. Plates were inoculated and
incubated at 37°C for 16-18 hrs for all antibiotics
except for vancomycin, where incubation was ex-
tended to 24 hrs. The plates were read with reected
light a few inches above black background except
for vancomycin, which was read under transmitted
light. The area showing no obvious, visible growth
to unaided eye was considered as zone diameter.
Those isolates which showed intermediate and re-
sistant zones with vancomycin were further sub-
jected to Epsilometer (E MIC strip) test procured
from Himedia (Mumbai, India) on Muller Hinton
agar plates for 24 hrs and results were reported as
per MIC values
Reporting based on CLSI guidelines:
The following antibiotics were interpreted as
per the Clinical and Laboratory Standards Institute
(CLSI, 2019).
Group A = penicillin and ampicillin (for all
clinical isolates)
Group B = vancomycin and linezolid (for all
clinical isolates)
Group C = high-level gentamicin resistance
(HLG), high-level streptomycin resistance (HLS),
doxycycline (for all clinical isolates).
Group U = ciprooxacin, levooxacin, nitro-
furantoin (Primarily/used only for urinary isolates)
and fosfomycin (for urinary isolates of E. faecalis
only).
HLG and HLS resistance was detected when
the organism showed no zone, was inconclusive for
7-9 mm, and susceptible if >10 mm diameter was
measured on AST (mentioned separately as Table
3J in CLSI).
Statistical analysis
Data were coded and entered into Microsoft
Excel 2019 (v16.0) (Microsoft, 2019). The data
were analysed using SPSS Statistics for Windows,
version 16.0 (SPSS Inc., Chicago, Ill., USA) (SPSS
Inc, 2007). The results were described using mean
standard deviation and percentages. A chi-square
test of independence was performed to examine the
relation between categorical variables. The relation
between these variables was considered statistical-
ly signicant if p<0.05.
Results
Epidemiological prole
Among the 1864 culture positive samples
during the study period, 106 Enterococcus spp.
were isolated. Prevalence of the Enterococcus spp.
in our institute was 5.6%. A chi-square test of in-
dependence showed that there was a signicant
association between sex and enterococcal isolates,
χ2 (1, N=1864)=10.631, p=0.0011, with male popu-
lation showing increased isolation. There was also
a signicant association between age and entero-
coccal isolates, χ2 (5, N=1864)=12.01, p=0.03467,
with the 31-40 yrs age group showing more isola-
tion. Though the enterococcal isolates did not differ
signicantly by overall clinical settings (outpatient
department (OPD)/inpatient department (IPD)), χ2
(1, N=1864)=2.21, p=0.1370, there was a signi-
cant association between different inpatient wards
and enterococcal isolates, χ2 (4, N=1864)=92.36, p
<.0001, showing gynaecology patients harbouring
more infection. There was a signicant association
between the type of sample and enterococcal iso-
lates, χ2 (3, N=1864)=26.710, p <.0001. Among the
106 enterococcal isolates obtained, urine samples
(86, 81.13%) had the highest enterococcal isolates
followed by pus (17, 16.04%), blood (2, 1.89%),
and ET aspirate (1, 0.94%) (Table 1).
Speciation
Overall E. faecalis (61.3%) was the pre-
dominant species isolated in our setting followed
by E. faecium (25.4%), E. gallinarum (3.7%), E.
rafnosus (2.8%), E. durans (2.8%), E. casselia-
vus (2.8%), and E. avium (0.9%) (Table 2).
Figure 1 depicts the distribution of various
enterococcal isolates in clinical samples. E. faecalis
was the most predominant isolate from urine, pus,
blood, and ET aspirate followed E. faecium.
Antibiogram
Figure 2 depicts the antimicrobial resistance
(AMR) pattern of enterococcal isolates to vari-
ous antimicrobial agents. Resistance to penicillin
was 86.7% (92/106) and to ampicillin was 83.9%
(89/106). None of the isolates was resistant to line-
zolid (0/106). Nitrofurantoin was tested for urinary
152
isolates only, with 30.23% (26/86) of the isolates
showing resistance. Fosfomycin was tested for
urinary isolates of E. faecalis only, which showed
29.62% (16/54) resistance. Fluoroquinolones and
tetracycline resistance was high, with ciprooxa-
cin 71.6% (76/106), levooxacin 67.9% (72/106),
and doxycycline 69.8% (74/106) at our setting.
High-level streptomycin (HLS) resistance was
33.01% (35/106) and high-level gentamicin (HLG)
resistance was 37.7% (40/106) at our setting.
Image 1 shows antibiotic susceptibility testing
done as per CLSI guidelines for E. faecalis on
Muller Hinton agar plate (100 mm) by Kirby Bauer
disc diffusion method with six antibiotic discs.
Although resistance to commonly used anti-
biotics was high in our setting, one interesting ob-
Table 2: Distribution of Enterococcus spp. in various samples
E.
faecalis
E.
faecium
E.
gallinarum
E.
ranosus
E.
durans
E.
casseliavus
E.
avium
Urine (n=86) 54 21 2 3 3 2 1
Pus
(n=17) 9 5 2 - -- 1
Blood (n=2) 1 1 - - - -
ETϯaspirate
(n=1) 1 - - - - -
Total=106 65
(61.3)
27
(25.4)
4
(3.7)
3
(2.8)
3
(2.8)
3
(2.8)
1
(0.9)
ϯET= Endotracheal
CharacteristicsFrequency Negative
ϯ
(%)
Positive
ϯ
(%)
χ2* (df) p-value*
Sex
Male 1102 1017
(92.29)
65 (5.9) 10.631
(1)
0.0011**
Female 762 741 (97.24) 41 (2.76)
Age(in completed years)
<1843 38 (88.37) 05 (11.63) 12.01
(5)
0.03467**
18-30 93 85 (91.40) 08 (8.60)
31-40 822 781 (95.01) 41 (4.99)
41-50 618 591 (95.63) 27 (4.37)
51-60 176 160 (90.91) 16 (9.09)
>60 112 103 (91.96) 09 (8.04)
Department
OPD 995 931 (93.57) 64 (6.43) 2.211
(1)
0.1370
IPD 869 827 (95.17) 42 (4.83)
IPD 1Paediatric ward 11 09 (81.82) 02 (18.18) 92.36
(4)
< 0.00001**
IPD 2Gynaecology
ward
478 462 (96.65) 16 (3.35)
IPD 3Medicine ward 351 339 (96.58) 12 (3.42)
IPD 4Surgery ward19 11 (57.89) 08 (42.11)
IPD 5Orthopaedics
ward
10 06 (60.00) 04 (40.00)
Samples
Urine 1098 1012
(92.17)
86 (7.83) 26.710
(3)
< 0.00001**
Pus 691 674 (97.54) 17 (2.46)
Blood 71 69 (97.18) 02 (2.82)
ET aspirate 04 03 (75.00) 01 (25.00)
Table 1. Clinicodemographic prole of patients (n=1864)
Note: ϯ for Enterococcus isolation, *Chi-square test for independence, **statistically signicant (p<0.05).
Total samples with growth - 1864, Enterococcus spp. Isolated - 106
153
servation was the resistance to vancomycin, which
was unexceptionally low. On a total of seven (7)
isolates, of which three isolates showed complete
resistance on disc diffusion method and four iso-
lates showed intermediate resistance pattern, van-
comycin E MIC strip test was performed. All iso-
lates had Minimum Inhibitory Concentration (MIC)
breakpoint of ≥ 32µg/ml, indicating vancomycin
resistance. Vancomycin resistant Enterococcus
(VRE) isolation at our setting was 6.6% (7/106).
Thus, VRE was much less (6.6%) compared to
HLG (37.7%) and HLS (33.01%) resistance at our
setting. E. faecium showed the highest vancomycin
resistance followed by E. faecalis.
Discussion
The epidemiological pattern of enterococci
varies with different geographic locations (Gan-
gurde et al., 2014). Once susceptible, this genus has
now acquired widespread resistance with many lit-
erature sources mentioning antimicrobial resistance
patterns, characterization and phenotyping meth-
ods as a title (Jaiswal et al., 2017; Naruka et al.,
2019). The prevalence of enterococci in our study
was 5.6%, which was high compared to Mukher-
jee et al. (2016), which was 4.8% and Sreeja et al.
(2012), which was 2.3%, and less compared to De-
sai et al. (2001), which was 22.19 % and Jada and
Jayakumar (2012), which was 15.46%.
The present study showed signicant distri-
bution of enterococcal isolation with sex (p val-
Fig. 1. Distribution of Enterococcus spp. isolated from various samples
Fig. 2. Antibiogram of Enterococcus spp., P=Penicillin, AMP=Ampicillin, VA=Vancomycin, LZ=Linezolid,
CIP=Ciprooxacin, LE=Levooxacin, HLG=High level gentamicin, HLS=High level streptomycin,
DO=Doxycycline, FO=Fosfomycin, NIT=Nitrofurantoin.
Image 1: Antibiotic susceptibility testing (AST) of
E. faecalis on Muller Hinton agar plate by Kirby
Bauer disc diffusion method.
154
ue<0.05), with male patients showing higher iso-
lation. Studies done by Ferede et al. (2018) and by
Salem Bekhit et al. (2012) showed no signicant
association of sex with enterococcal isolation, al-
though male population was predominant in their
study. The 31 to 40 years age group was associat-
ed with increased enterococcal isolation, showing
a signicant p value (<0.05) in the present study
in contrast to studies done by Balan et al. (2016),
which had 21-40 years age group affected, and
Ferede et al. (2018), where >59 years age group
was more commonly affected. IPD and OPD pa-
tient distribution was insignicant although gynae-
cology ward patients in the present study had high-
er isolation of enterococcal isolates followed by
medicine ward and surgery ward with a statistically
signicant p value (<0.05). Although the distribu-
tion among IPD and OPD was insignicant, noso-
comial infection by enterococcus was observed in
the present study as among IPD patient distribution
was signicant. Medical ward patients had higher
enterococcal isolation in the study done by Fere-
de et al. (2018), which contrasts with the present
study. Isolation of enterococci was the highest in
urine samples followed by pus, blood, and endotra-
cheal (ET) aspirates. This study is comparable to
studies done by Karmarkar et al. (2004), Anbumani
et al. (2005) and Mukherjee et al. (2016) where En-
terococci were isolated predominantly from urine
samples. Thus, the clinicodemographic prole con-
tributes signicantly when dealing with Enterococ-
cus spp. at any clinical setup, which is routinely
ignored.
E. faecalis was the predominant isolate in the
present study followed by E. faecium, E. gallinar-
um, E. rafnosus, E. durans, E. casseliavus, and
E. avium, which is similar to the study done by
Salem-Bekhit et al. (2012), and Mukherjee et al.
(2016). E. faecium was reported to be predominant
species in a study done by Aberna in 2018, which
contrasts to the present study.
The Enterococcus spp. are intrinsically resist-
ant to many antibiotics. They also develop resist-
ance very quickly compared to other organisms, re-
sulting in increased nosocomial infections (Morris
et al., 1995). Among 106 isolates tested in the pres-
ent study, resistance to beta lactams, uoroquinolo-
nes, tetracyclines(doxycycline) was 86.7%, 71.6%,
and 69.8%, which was high compared to other
studies (Mendiratta et al., 2008; Parameswarappa
et al., 2013). High-level resistance to streptomycin
and gentamicin was 33.01% and 37.7%, respective-
ly, which was also considerably higher compared
to other studies (Mittal et al., 2016; Maradia et al.,
2017). The incidence of nitrofurantoin (30.23%)
and fosfomycin (29.62%) resistance was compar-
atively less in urinary isolates, which is compara-
ble to the study done by Butch et al. in 2011 but
contrasts the study by Balan et al. in 2016. None
of the strains was resistant to linezolid, which is
comparable to most of the studies conducted in In-
dia (Srivastav et al., 2013; Lavanya et al., 2016).
In 1986, the rst case of VRE was observed and
reported from Europe (Leclercq et al., 1988). Since
then, many cases of VRE are being increasingly
reported from many parts of the world. India also
started reporting VRE from the early 20th century,
when few cases were observed in the beginning and
later on their number increased (Vidyalaxmi et al.,
2012). In the present study, the most notable nding
was VRE, which was 6.6%, which contrasts with
most of the recent studies published on enterococci
but similar to the study done by Balan et al. (2016),
Ferede et al. (2018), Asgin et al. (2020), and Gup-
ta et al. (2020). One of the reasons in the present
setting which may contribute to this antimicrobial
pattern may be due to hospital antibiogram policies
prescribing lesser use of vancomycin, which could
be due to its non-affordability for the patients.
Thus, geographic location matters for AMR in en-
terococci due to the local prescribing policy based
on affordability for patients. If followed properly,
mandatory AST, speciation, antimicrobial steward-
ship along with infection control practices play a
signicant role for reducing resistance in Entero-
coccus – a process which has a long way to go.
Conclusion
There was 5.6% prevalence of enterococcal
isolation in the present study, signicant associa-
tion of clinicodemographic prole of patients with
enterococcal infections and high level of resistance
to routinely used antibiotics with the exception of
vancomycin and linezolid. Routine screening of all
enterococcal isolates as per CLSI is recommended
due to evolving resistance in this organism by mul-
tiple mechanisms and due to widespread geograph-
ical variation.
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