An Antibiogram Study for Urine Culture Testing in Makkah Region Hospitals

Background: The antibiogram profile could be helpful in the selection of the most appropriate antimicrobial treatment for microbial infection and even useful to monitor antibiotic resistance. Objective: This study aims to identify the bacteria in the urine through urine culture and perform their antibiogram to determine the resistance profile between antibiotics and urine tract infection (UTI)-causing bacteria and to determine the effective and non-effective antibiotics. Methods: The study was based on urine culture data from five Makkah hospitals in the Kingdom of Saudi Arabia (KSA). Results: A total of 1000 pathogens were found in the urine culture; 899 were bacterial isolates, and 101 were Candida spp. Seven hundred and seventy-seven of the 899 bacteria isolates were gram-positive, while 122 were gram-negative bacteria. Escherichia coli (44%) was the most frequent UTI-causing bacteria, followed by Klebsiella spp. (20%), Pseudomonas aeruginosa (6%), S. aureus (5.5%), Enterococcus faecalis (4.5%), Enterobacter spp. (2%), and Proteus spp. (1%). There was clear evidence that ampicillin, cefepime, erythromycin, and moxifloxacin were not effective antibiotics for uropathogens in the Makkah area, KSA. The multiple drug resistance (MDR), extensively drug-resistant (XDR), extended spectrum beta lactamase (ESBL), CR, and quinolones resistance (QR) were higher in the gram-negative bacilli. The pandrug resistance (PDR) and AmpC seemed to have fewer ratios of UTIs caused by gram-negative bacteria. On the other hand, S. aureus of the gram-positive type was also involved in the UTI and had a higher ratio of MDR, QR, and methicillin-resistant Staphylococcus aureus (MRSA).


Introduction
UTIs are frequent illnesses that develop when bacteria enter the urethra and infect the urinary system. These germs are frequently found on the skin or rectum. Although the infections can affect different regions of the urinary system, a bladder infection (cystitis) is the most prevalent. Another kind of UTI is a kidney infection, often known as pyelonephritis [1]. Urine testing is the main element in diagnosing an UTI. It includes collecting midstream urine with an aseptic method followed by urine culture, which involves identification of the causative pathogen and sensitivity testing. Urine dipsticks and urine microscopy are two of the most frequently used methods of diagnostic testing, especially when there is suspicion that a patient is suffering from an UTI [1,2]. In the urinary tract, bacteria enter through the urethra and grow rapidly to develop an infection. Generally, the infection begins in the urethra or bladder, but it has the ability to spread to other parts of the system [2][3][4].
Multiple drug resistance (MDR) is bacterial antimicrobial resistance to at least one antimicrobial drug in three or more antimicrobial categories. Extensively drug-resistant (XDR) is defined as nonsusceptibility to at least one agent in all but two or fewer antimicrobial categories. Pandrug Resistance (PDR) is the nonsusceptibility to all agents in all antimicrobial categories (i.e., bacterial isolates are not susceptible to any clinically available drug). An antibiogram is an overall profile of antimicrobial susceptibility testing results for a specific microorganism to many antimicrobial drugs. This profile is generated by the laboratory using aggregate data from a hospital or healthcare system; the data are summarized periodically and presented, showing percentages of organisms tested that are susceptible to a particular antimicrobial drug. Only results for antimicrobial drugs that are routinely tested and clinically useful should be presented to clinicians. The overall antimicrobial susceptibility testing profile of any microorganism to a series of anti-microbial drugs is termed an antibiogram [5]. The laboratory obtains the data from a healthcare system or hospital and produces that profile by aggregating the data. It shows the ratio of the organism that is susceptible to a specific type of drug. This antibiogram profile helps the pharmacist and clinician to select the most appropriate antimicrobial treatment for a microbial infection. This tool is quite useful to detect and monitor antibiotic resistance [6][7][8][9]. This is a research-based study in which the urine culture antibiogram has been generated with urine pathogens against the different antibiotics in Makkah city hospitals, KSA, and the antibiotic resistance, as well as the most MDRs of different types of urine pathogens, have been discussed. This retrospective study was performed using data from the Saudi hospitals in the Makkah region through a surveillance network for antimicrobial resistance (AMR) in pathogenic bacteria in the urine. In this study, urine culture data has been collected in outpatient clinics and inpatient departments from five tertiary hospitals in Makkah, KSA, during the period of 1 January 2020 to 31 December 2020. Data collection, including demographic data (age, gender, education, and type of pathogen), was performed manually from the databases of the two departments of the laboratory and medical records corresponding to urine samples that were positive for urine pathogens. A total of 1000 non-duplicated urine pathogens from 1000 patients were identified in hospitals during the study period. Most of the patients were males: 641 (64.1%), while the females were 359 (35.9%). The majority of patients with UTI were above 60 years old, representing 351 (35.1%) of the total number of patients, whereas 249 (24.9%) of the patients were between 41 and 50 years, 200 (20%) were between 51 and 60 years, 148 (14.8%) were between 20 and 40 years, whereas 62 (6.2%) patients were younger than 20 years.

Data analysis
The data has been used in the laboratory to develop the antibiogram for all of the mentioned bacteria against different antibiotic variables extracted, including bacterial species, susceptibility categories (susceptible or resistant) to each tested antibiotic, and resistant threats such as MDR, XDR, PDR, ESBL, AmpC, Carbapenemase Resistance (CR), MRSA, Vancomycin-Resistant Enterococcus (VRE), and Quinolones Resistance (QR). After getting the antibiogram from the laboratory test, a chart has been developed showing the profile of all the antibiotics against the bacteria in percentage.

Results
The result of the present study showed that there were 13 gram-negative bacilli (E. coli, Klebsiella spp., Proteus spp., Enterobacter spp., Citobacter spp., Serratia marcescens, Morganella, Providencia spp., Salmonella spp., P. aeruginosa, Acinetobacter, Burkholderia cepacian, N. gonorrhoeae) and six gram-positive cocci (namely, S. aureus, S. saprophyticus, S. haemolyticus, Enterococcus faecalis, E. faecium, and S. agalactiae) one candida isolate have been isolated during the studied period. During the Urine Cultural Test, there were 1000 total pathogens found, out of which 101 were Candida spp., while the remaining 899 were bacterial isolates, which are further divided into gram-negative and gram-positive, 777 and 122, respectively. Table 1 presents the urine cultural bacterial isolates.
The second major part of the bacterial isolate was gram-positive cocci, which is mainly based on the S. aureus, which has a ratio of 5.3% (53), followed by Enterococcus faecalis with a ratio of 4.4% (44), followed by the E. faecium, which has a ratio of 0.5% (5), S. saprophiticus with 0.8% (8) of the total gram-positive, the S. heamolyticus is 0.4% (4), and the S. agalactae is 1% (9) of the total gram-positive cocci. The result of antimicrobial susceptibility testing showed that 100% of gram-positive bacteria were sensitive to vancomycin and linezolid, followed by levofloxacin (90%) and tigecycline (82%), as shown in Table 2. It was found that 42.6% of gram-positive bacteria were resistant to oxacillin, while 34.4% of them were resistant to moxifloxacin and erythromycin (

TABLE 2: Antimicrobial Susceptibility Testing Results of Gram-Positive Cocci
The results also showed that 99.7% of gram-negative bacteria were sensitive to colistin, followed by meropenem (96.5%) and imipenem (94%), as shown in Table 3. It was found that 56.5% of gram-negative bacteria were resistant to ampicillin, while 45.6% of them were resistant to cefepime ( Table 3).

Discussion
The present study has generated a urine culture antibiogram, including pathogens and their sensitivities against the different antibiotics in Makkah city hospitals. The result showed that the antibiogram of the urine culture was an indication of the antibiotic resistance of several microbial species and their effectiveness. The study showed that 100% of gram-positive bacteria were sensitive to vancomycin and linezolid, while 42.6% and 34.4% of them were resistant to oxacillin and erythromycin/moxifloxacin, respectively. In addition, the study also showed that 99.7% of gram-negative bacteria were sensitive to colistin, followed by meropenem (96.5%) and imipenem (94%), while 56.5% and 45.6% of them were resistant to ampicillin and cefepime, respectively ( Table 3).
Furthermore, the present study found that the Enterobacter spp. were MDR (22.6%), ESBL (22.6%), AMPC (13%), and QR (16%), except that all the antibiotics can be effective [13]. In addition, P. aeruginosa and Acinetobacter were both found as QR, while Acinetobacter was found to be XDR and QR simultaneously. In this connection, all the antibiotic resistance except the CR can be found in P. aeruginosa. However, other gram-negative bacilli, including Citrobacter spp., Serratia marcescens, Morganella, Providencia spp., Salmonella spp., Burkholderia cepacia, and N. gonorrhoeae, showed no resistance to any of the antibiotics, so it can be concluded that all of the mentioned antibiotic resistance may be found in these microbes [14].
For the gram-positive cocci, the present study found that S. aureus was the most MDR (39%), MRSA (39%), and QR (27.5%). All the other antibiotics are good for this microbe. After that, Enterococcus faecalis was found at QR (24.6%). Besides these two, all the cocci can be treated with any of the previously mentioned antibiotics.
In our study, we found E. coli to be the most frequent microbial that causes urinary tract infection (UTI). A similar result has been found by Gessese et al. [15]. They conducted a study on "Urinary pathogenic bacterial profile, antibiogram of isolates, and associated risk factors among pregnant women in Ambo town, Central Ethiopia: a cross-sectional study," where they studied 300 urine samples and found E. coli to be the most frequent microbial with a ratio of 46.6%. There are also some similarities in the microbes between our study and the study by Gessese et al. [10]. They found Proteus spp. and S. aureus too, in their study, just like ours. Gessese et al. also found a similarity with the most resistant antibiotic among gram-negative bacilli; in their study, the MDR found most of the resistant antibiotics among gram-negative bacteria, and our study also found similar findings.
A study is also made by Kibret and Abera [4]. They have made the antibiogram study on 1404 urine samples from Ethiopia. They have found that the most frequent and most infection-causing bacilli are named E. coli, with a ratio of 63.6%, followed by Klebsiella spp. and Proteus spp. This study also has similar findings to ours, not for the prevalence of microbes but for the resistance to antibiotics. They have noticed that the gramnegative bacteria are showing great resistance to MDR.
There are studies [16][17][18][19][20] with similar results to our study. Most studies found the most frequent bacilli to cause UTIs to be E. coli, Klebsiella spp., and Proteus spp. Most of them are related to the gram-negative type of bacteria, and they show high MDR.

Limitations and implications
This study is based on urine samples obtained from hospitals in the Makkah region, which sets a major limitation on the implication of this study. The antibiogram is showing the profile of the microbial and their possible treatment with antibiotics for a specific region of Makkah city. The result of this study did not represent the KSA country or other countries of the world. Similar studies are recommended to be undertaken in the other regions and cities of KSA.

Conclusions
The study showed clear evidence that ampicillin, cefepime, erythromycin, and moxifloxacin are not effective antibiotics for uropathogens in the Makkah area, KSA. The MDR, XDR, ESBL, CR, and QR were higher in the gram-negative bacteria. The PDR and AmpC seemed to have fewer ratios of UTI caused by gram-negative bacteria. On the other hand, S. aureus of the gram-positive type was also involved in the UTI and had a higher ratio of MDR, QR, and MRSA.

Additional Information Disclosures
Human subjects: All authors have confirmed that this study did not involve human participants or tissue. Animal subjects: All authors have confirmed that this study did not involve animal subjects or tissue.

Conflicts of interest:
In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work. Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work.