Uropathogens and the antibiogram profile from a tertiary care hospital: A 2-month study post conversion of a COVID dedicated center to a non-COVID one

Bineeta Kashyap; NP Singh; Kirti Nirmal; Manoj Kumar Meena

doi:10.4103/injms.injms_145_21

ORIGINAL ARTICLE

Year : 2022 | Volume : 13 | Issue : 3 | Page : 169-175

Uropathogens and the antibiogram profile from a tertiary care hospital: A 2-month study post conversion of a COVID dedicated center to a non-COVID one

Bineeta Kashyap, NP Singh, Kirti Nirmal, Manoj Kumar Meena
Department of Microbiology, University College of Medical Sciences and Guru Tag Bahadur Hospital, Delhi, India

Date of Submission	20-Dec-2021
Date of Decision	31-Jan-2022
Date of Acceptance	01-Feb-2022
Date of Web Publication	28-Jul-2022

Correspondence Address:
Dr. Bineeta Kashyap
Department of Microbiology, University College of Medical Sciences and Guru Tag Bahadur Hospital, Delhi - 110 095
India

Source of Support: None, Conflict of Interest: None

DOI: 10.4103/injms.injms_145_21

Abstract

Background: Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, both in the community and the hospital settings. The distribution of antimicrobial susceptibility data of UTI-causing microorganisms changes from time to time and from place to place. The susceptibility data provided by regional microbiology laboratories helps to choose the empirical antimicrobials to treat UTI. Aim and Objectives: To determine the prevalence and antimicrobial drug susceptibility pattern of the bacterial uropathogens isolated from a tertiary care hospital. Material and Methods: A retrospective analysis over a period of two months (Jan-Feb 2021) was performed in the Department of Microbiology of a tertiary care hospital, East part of Delhi. These two months were immediately following conversion of this facility to a non COVID centre from a dedicated COVID centre. Culture results of the urine samples received during the study period were analyzed. The samples were processed according to standard guidelines. The data were entered into micro soft excel for analysis. Results: A total of 1650 urine samples from suspected UTIs were analyzed retrospectively for isolation and identification of bacteria and antimicrobial susceptibility testing. 271 (16.4%) grew significant microorganisms including fungus. In both male and female patients E. coli (n = 46, 17%) was the most commonly isolated microorganism, followed by Staphylococcus spp. (n = 45, 16%). Isolated resistance to uropathogens was common with Cotrimoxazole (60%), Nitrofurantoin (50%), ciprofloxacin (50%), tetracycline (45%), Imipenem and cefotaxime (35%) Conclusions: UTI is one of the most common infectious diseases that clinicians are dealing with. Increasing antimicrobial resistance among uropathogens implicated in UTI is a matter of concern. Periodic monitoring of etiology and drug susceptibility is recommended.

Keywords: Antibiogram profile, COVID-19, uropathogens

How to cite this article:
Kashyap B, Singh N P, Nirmal K, Meena MK. Uropathogens and the antibiogram profile from a tertiary care hospital: A 2-month study post conversion of a COVID dedicated center to a non-COVID one. Indian J Med Spec 2022;13:169-75

How to cite this URL:
Kashyap B, Singh N P, Nirmal K, Meena MK. Uropathogens and the antibiogram profile from a tertiary care hospital: A 2-month study post conversion of a COVID dedicated center to a non-COVID one. Indian J Med Spec [serial online] 2022 [cited 2023 Jun 9];13:169-75. Available from: http://www.ijms.in/text.asp?2022/13/3/169/352631

Introduction

Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, both in the community and the hospital settings.^[1] UTI is the most common bacterial infectious disease in the community with increased morbidity and a huge financial cost. It is estimated that globally, 26% of deaths are due to infectious diseases such as UTIs of which 98% occur in the low-income countries.^[2] It has been estimated that 150 million people were infected with UTI per annum worldwide costing global economy more than 6 billion US dollars.^[2] The prevalence of pediatric UTI in Asian countries was reported high. In Nepal, two studies done at different times from different areas showed the prevalence of 15.88% and 57%, respectively. An Indian study southern part of India documented 48% prevalence of UTI.^[3]

UTI is defined as the microbial invasion of urinary tract that can be upper or lower based on the anatomy, whether symptomatic or asymptomatic and complicated or uncomplicated clinically.^[4] The spectrum of bacteria causing complicated UTI is much broader than the uncomplicated one. However, the commonly encountered ones are Escherichia ^{More Details} coli, Citrobacter spp., Enterobacter aerogenes, Pseudomonas aeruginosa, and Proteus vulgaris, whereas the less common causes include Klebsiella spp., Staphylococcus aureus, and Salmonella ^{More Details} spp.^[4],[5]

An emerging significant public health problem is the increasing evidence of multidrug resistance among the bacterial uropathogens. The Infectious Disease Society of America identified some microorganisms called the “ESKAPE pathogens” (Enterococcus faecium, S. aureus, Klebsiella spp., Acinetobacter spp., Pseudomonas spp., and Enterobacter spp.) witnessing increasing drug resistance in UTI that need regular monitoring of the antibiotic susceptibility of uropathogens in a particular area. Various factors such as the type of UTI (complicated or uncomplicated), gender, age, or the previous history of antibiotic therapy should be considered to estimate the correct global data on susceptibility.^[6] The distribution of antimicrobial susceptibility data of UTI-causing microorganisms changes from time to time and from place to place.^[7] The susceptibility data provided by regional microbiology laboratories helps to choose the empirical antimicrobials to treat UTI.

Many hospitals all over the world have targeted their attention on the use of certain antimicrobial agents to change this worrying trend.^[8],[9] Most of the times, there is a need to initiate empirical antimicrobial treatment before one could obtain the microbiological results. Surveillance studies provide information of the causative agents of UTIs and their antimicrobial resistance patterns which may aid clinicians in choosing the appropriate antimicrobial empirical treatment.^[10] Important contributors to increasing microbial resistance are improper use of antibiotics and incorrect or unreasonable antibiotics prescription.^[11] Time, appropriate dose, or the manner of administration would contribute to a rational drug prescription. Studies have shown that 30%–60% of the prescribed and use of antibiotics has been improper.^[12] With tens of millions of people being tested positive for severe acute respiratory syndrome coronavirus-2 and possibly millions of fatal cases, if current trends continue, antibiotic use in the clinical management of COVID-19 will be enormous globally.^[12] The long-term rehabilitation and management of health consequences of COVID-19 are unknown; some individuals may suffer from long-term effects leading to susceptibility to bacterial or fungal infections. There is a huge likelihood that this pandemic will exacerbate the rise of antibiotic resistant superbugs. The pandemic still continues with newer waves; countries globally must embrace the practice of antibiotic stewardship even stronger and do their best to avoid the emergence or spread of resistant bacteria post pandemic.

In view of the above dilemma, it is worthwhile that the degree of susceptibility of these uropathogens to various antibiotics be known to the clinicians for effective treatment of infections so as to avoid antibiotic misuse. This increased antimicrobial resistance, the result of an irrational and an uncontrolled use of the antimicrobials, is a threat to the public health. This study is aimed at determining the prevalence and antimicrobial drug susceptibility pattern of the bacterial uropathogens isolated from a tertiary care hospital. This was a dedicated COVID center and the data that we reflect here are for 2 months after this setting was converted to a non-COVID facility.

Subjects and Methods

A retrospective analysis over a period of 2 months (January–February 2021) was performed in the department of microbiology of a tertiary care hospital, East part of Delhi. These 2 months were immediately following conversion of this facility to a non-COVID center from a dedicated COVID center. Culture results of the urine samples received during the study period were analyzed. The age and sex of the patients, the organisms isolated, and the antimicrobial susceptibility profile were collected from the records using a standard data collection form. The data were entered into Microsoft Excel for analysis.

Sample processing

A calibrated loop method was used for the isolation of bacterial pathogens from urine samples. A sterile 4.0 mm platinum-wired calibrated loop was used which delivered 0.01 or 0.001 mL of urine. A loopful urine sample was placed on cystine–lactose–electrolyte deficient agar (HiMedia Laboratories, Mumbai, Maharashtra, India). The plates after inoculation were incubated at 37°C for 24 h (48 h for the negative ones). The number of isolated bacterial colonies was multiplied by 100 or 1000 for the estimation of bacterial load/mL of the urine sample. A sample was considered positive if the organism was growing at a concentration of ≥10⁵ cfu/mL or when an organism was growing at a concentration of 10⁴ cfu/mL along with >5 pus cells per high-power field on direct microscopic examination of the urine.

Identification of urine isolates

Identification of bacterial isolates was done on the basis of their cultural and biochemical characteristics.^[13] Gram-negative and Gram-positive microorganisms were identified by the standard biochemical tests.^[14]

Antimicrobial susceptibility tests

According to the standard operational procedures, antimicrobial susceptibility tests were done on Mueller–Hinton agar (HiMedia, Laboratories Pvt., Ltd., Mumbai, Maharashtra, India) using Kirby–Bauer disk-diffusion method. Standard inoculums matching 0.5 McFarland were swabbed on Mueller–Hinton agar plates, antibiotic disks were placed and pressed gently on the surface. Culture plates were incubated at 37°C for 24 h. The zones of inhibition were measured after 24 h and interpreted as per the recommendations by the Clinical Laboratory Standards Institute (CLSI). The antimicrobial agents tested were nitrofurantoin (300 μg), fosfomycin (200 μg), cefotaxime (30 μg), gentamicin (10 μg), imipenem (10 μg), tobramycin (10 μg), ceftazidime (30 μg), ceftriaxone (30 μg), cotrimoxazole (1.25/23.75 μg), ciprofloxacin (5 μg), tetracycline (30 μg), linezolid (30 μg), teicoplanin (30 μg), tigecycline (10 μg), clindamycin (2 μg), erythromycin (15 μg), ampicillin (10 μg), and norfloxacin (5 μg). Antimicrobial susceptibility was interpreted according to the latest Clinical Laboratory Standards Institute guidelines.^[15]

Reference strains of E. coli ATCC 25922, S. aureus ATCC 25923, and P. aeruginosa (ATCC 27853) were used for quality control for antimicrobial susceptibility tests.

Statistical analysis

The results were expressed as percentages for analysis of various epidemiological details and for analyzing the distribution of different bacterial isolates and their sensitivity pattern. Microsoft Excel was used for the computation of these results.

Results

During January 2021–February 2021, a total of 1650 urine samples from suspected UTIs were analyzed retrospectively for isolation and identification of bacteria and antimicrobial susceptibility testing. Two hundred and seventy-one (16.4%) grew significant microorganisms including fungus. The isolates from these 271 patients are being discussed here.

The age of the patients ranged from 1 year to 85 years, with the mean age of 35.26 years. The most common age group was 33–55 years (33%), followed by 12–35 years (26%) with the lowest number from the age group of new born to 2 years (6%). The male-to-female ratio was 1:2. The age-wise distribution of study group with suspected UTI is shown in [Figure 1].

Figure 1: Age-wise distribution of study group with suspected urinary tract infection (n = 271

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Majority of the urine isolates, 119 (44%), were isolated from the outpatient department (OPD) followed by the wards (23%), casualty (12%), medical intensive care unit (ICU) (8%), pediatric ICU (7%), critical care unit (4%), and neonatal ICU (3%) [Figure 2].

Figure 2: Ward-wise frequency percentage distribution of the uropathogens

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In both male and female patients, E. coli was the most commonly isolated microorganism (17%), followed by Staphylococcus spp. (16%), Candida spp. (14%), Klebsiella spp. (11.65%), Group D Streptococcus spp. (6%), Proteus spp. (9%), P. aeruginosa (7%), Acinetobacter spp. (6%), Enterococcus spp. (5%), Enterobacter and Citrobacter spp. (4% each), and Streptococcus pneumoniae (3%) [Figure 3].

>Figure 3: Distribution of the uropathogens among the isolates from suspected urinary tract infection in the study group (n = 271)

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Among the isolates from the ICU, P. aeruginosa (45%) was the most common Gram-negative organism followed by S. aureus accounting for 16% of the isolates. Among the OPD patients, Proteus spp. (25%) and Klebsiella spp. (20%) were the common organisms isolated. P. aeruginosa (20%) and Citrobacter spp. (20%) were commonly isolated from the inpatients [Table 1].

Table 1: Ward-wise distribution of the isolated uropathogens (n=271)

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One eighty-seven (70%) urine samples from which some uropathogens were isolated came from female patients, whereas 84 (30%) were from male patients. Among the males, S. aureus (58%) followed by Klebsiella pneumoniae and P. aeruginosa (50%), respectively, were the most common microorganism isolated. Among the females, Acinetobacter baumannii (100%), Candida spp. (67%), Proteus spp. (60%), and E. coli (10%) were the most common organism isolated [Table 2].

Table 2: Age- and gender-wise distribution of uropathogens in suspected urinary tract infections patients (n=271)

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The overall resistance pattern of the various antimicrobials used among the isolated uropathogens was as follows: cotrimoxazole (60%), nitrofurantoin (50%), ciprofloxacin (50%), tetracycline (45%), and imipenem and cefotaxime (35%) followed by fosfomycin (30%), ceftazidime (30%), teicoplanin (30%), tigecycline (30%), erythromycin (25%), and clindamycin (20%) [Figure 4].

Figure 4: Antibiogram of uropathogens in suspected Urinary tract infections patients (n = 271)

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E. coli, the most frequently isolated bacterium, showed high resistance (>60%) to erythromycin and tetracycline. The other three most common isolates exhibited resistance rates of 80%–100% to erythromycin and amoxicillin. Majority of E. coli isolates (85%) were susceptible to nitrofurantoin with resistance of 15%. The other isolates were sensitive to gentamicin and ciprofloxacin with resistance of 28%–30% and 30%–32%, respectively [Table 3].

Table 3: Organism wise antimicrobial susceptibility pattern among suspected urinary tract infections patients (n=271)

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Among the isolates from the ICUs, the susceptibility to Imipenem was 84% followed by Fosfomycin and Cotrimoxazole (80%); however, the isolates from the wards had the maximum susceptibility of 80% to tobramycin and tigecycline and 75% to ampicillin. While the isolates from the OPD patients had the maximum susceptibility of 90% to clindamycin, cefotaxime, and fosfomycin whereas a susceptibility of 80% to cotrimoxazole [Figure 5].

Figure 5: Comparative depiction of the antibiotic susceptibility pattern of uropathogens to various antibiotics among the outpatient department, ward, and intensive care units isolates (n = 271

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Discussion

UTIs are one of the most common diseases diagnosed worldwide. Availability of new antimicrobials has improved the management of UTIs. However, the management of UTI infections has been jeopardized by increase in emergence of antimicrobial drug resistance. The present study provides an overview on the prevalence and antibiogram of uropathogens which can vary dramatically from time to time and place to place even within the same country. Various factors such as the type of UTI (complicated or uncomplicated), gender, age, and previous history of antibiotic therapy or instrumentation of each patient should also be considered to find out the correct global data on susceptibility. Increasing drug resistance due to empirical treatment in UTI needs regular monitoring of the antibiotic susceptibility of uropathogens in a particular area. To ensure appropriate therapy, current knowledge of the pathogens that cause UTI in an area and their susceptibility pattern is mandatory.

The overall culture isolation rate of uropathogens in this study was 16.4% which was comparable with the findings of Sood and Gupta from Jaipur.^[16] A lower culture positivity was documented from Aligarh, Bangalore, Ethiopia, and Portugal,^{[3],[17],[18],[19]} whereas a higher culture positivity rate was recorded from Odisha, Meerut, and Pondicherry.^{[15],[20],[21]} The rate of isolation was higher in females (70%), thus revealing increased susceptibility of females to UTIs. The highest isolation was found in 33–55 years (33%), followed by 12–35 years (26%), thus revealing the increased susceptibility of sexually active females who are more prone to UTIs due to short urethra, proximity to anus and urethral trauma during the intercourse. The increase vulnerability of the geriatric population to UTI is presumably due to various age-related physiological changes, waning of the immune system, and other infirmities such as diabetes and enlarged prostate, as depicted in some studies.^{[22],[23],[24]}

The department-wise isolation rate was the highest in the OPD group (44%) followed by the ward (23%) and ICUs (22.8%); this may be due to the surgical procedures, instrumentation, increased hospital stay, and immunosuppressive drugs. Such similar trends have been reported from other studies too.^[25],[26] P. aeruginosa was the most common organism isolated from the ICUs settings (45%) and inpatient departments (20%). From the outpatient departments, Proteus spp. (25%) followed by Klebsiella pneumoniae were predominately (20%) isolated. Our findings are correlating with the study done by Akram et al. from Aligarh.^[19]

In the present study, Gram-negative organisms, Gram-positive bacteria, and yeast were responsible for 64%, 20%, and 14% of the isolates, respectively. Gram-negative bacteria were predominantly responsible for UTI and this finding is in agreement with the findings from previous studies.^[1],[27] E. coli (17%) and S. aureus (16%), followed by Candida spp.(14%), similar to other studies, were the most prevalent in UTI.^[27],[28] Among Gram-negative organisms, E. coli (17%) was the most predominant pathogen isolated followed by Klebsiella spp.(11%), Proteus spp.(9%), and Pseudomonas spp.(7%), while among Gram-positive organisms, S. aureus (16%), Enterobacter spp., and Citrobacter spp. (4%) were the predominant ones. The isolation rates of E. coli and other pathogens in this study were comparable to the rates documented previously.^[27],[28] However, the rates were generally lower than other reports.^{[10],[29],[30],[31]} Differences in identification methods are known to influence the relative prevalence of bacteria which makes comparison difficult.^[32] Bacterial etiologies of UTI can show geographic variations and may even vary over time within a population.^[13],[15]

The overall susceptibility profile of the bacterial isolates is shown in [Table 3]. Erythromycin had the highest overall resistance of 60%, followed by tetracycline (60%). Nitrofurantoin, gentamicin, and ciprofloxacin had overall resistance rates of 15%, 22%, and 32%, respectively. This result is similar to the result documented in Kolkata and Bangalore.^[22],[23] E. coli, the most frequently isolated bacterium, showed high resistance rates (>60%) to erythromycin and tetracycline. Majority (85%) of E. coli isolates were susceptible to nitrofurantoin with resistance rate of 15%. High rates of sensitivity to nitrofurantoin,^[33] ciprofloxacin,^[34] and gentamicin^[35] have been documented from earlier studies. Klebsiella spp., Proteus spp., and Pseudomonas spp. were found to be resistant to erythromycin and tetracycline but sensitive to gentamicin and ciprofloxacin. These rates are higher than reported from studies in Kolkata,^[26] Bangalore,^[19] and Italy.^[28] Increasing antimicrobial resistance has been documented globally.^{[1],[19],[26],[27],[28],[29],[30]} Resistance among bacterial pathogens is more likely in case, there is a past infection history of patients and/or inpatient status.^[19],[20] This study provides valuable data to compare and monitor the status of antimicrobial resistance among uropathogens to improve efficient empirical treatment.

Conclusion

UTI is one of the most common infectious diseases that clinicians are dealing with. Increasing antimicrobial resistance among uropathogens implicated in UTI is a matter of concern. This study showed that the prevalence of UTI was high in all age groups. The most frequently isolate bacterium was sensitive to nitrofurantoin and the other isolates were sensitive to gentamicin. Nitrofurantoin, gentamicin, and ciprofloxacin are considered as appropriate antimicrobials for the empirical treatment of UTI in the area. Periodic monitoring of etiology and drug susceptibility is recommended.

Financial support and sponsorship

None.

Conflicts of interest

There are no conflicts of interest.

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