Abstract
Background
Urinary tract infections (UTIs) are among the most prevalent infectious diseases worldwide, exacerbated by rising antimicrobial resistance (AMR) as a result of overuse and misuse of antibiotics. This study aims to assess local bacterial etiologies and their resistance and sensitivity patterns to commonly used antibiotics in Sudan.
Methodology
This retrospective study utilized secondary data from the Nile Medical Compound in Port Sudan. Total coverage of all data from June/2023 to March/2024 were included, which yielded 328 samples.
Results
Most of the samples were from females (64.3%), and significant differences were found in pathogen detection between genders (p = 0.001). 69.8% was positive for a single pathogen, with Escherichia coli (31.3%) being the most common, followed by Pseudomonas aeruginosa (9.5%), and Staphylococcus aureus (8.8%). Females had higher rates of E.coli, Pseudomonas aureginosa and Enterococci spp. Notably, 23.7% of positive samples were resistant to 4–6 antibiotic classes, with females having significantly higher percentages of antibiotic resistance than males. Gentamicin showed the highest sensitivity (74.1%) among cultures, as two-thirds of E. coli were sensitive to it. Sensitivity patterns also revealed that the majority of Staphylococcus aureus and Enterococcus faecalis had notable sensitivity to gentamicin. Almost all detected pathogens were resistant to 4–6 classes of drugs with Enterococcus faecalis having the highest percentage of resistance and Staphylococcus aureus having the least.
Conclusion
Despite some high sensitivity rates, resistance to multiple antibiotic classes remains a concern, underscoring the need for continuous surveillance and localized treatment guidelines. Moreover, our study highlights the significant difference in resistance patterns between males and females, which suggests that more research is needed to elaborate on the reasons.
Keywords: Urinary tract infection, Antibiotic resistance, Sudan, Cultures
Introduction
Urinary tract infections (UTIs) are among the most prevalent infectious diseases worldwide [1], affecting millions of individuals each year. They involve infections in any part of the urinary tract, including the bladder (cystitis), urethra (urethritis), and kidneys (pyelonephritis) [1]. 50–60% of women experience UTI at least once in their lives [2]. The majority of UTIs are caused by gram-negative bacteria, with Escherichia coli (E.coli) being the leading pathogen responsible for these infections [3–5]. Due to anatomical and physiological factors, women are particularly susceptible to UTIs [5]. These factors include a shorter urethra, which facilitates easier bacterial entry, and hormonal changes during pregnancy that increase the risk of infection [6].
The global burden of UTIs is compounded by the growing issue of antimicrobial resistance (AMR). The overuse and misuse of antibiotics have led to an increase in AMR, making it more challenging to treat bacterial infections effectively. Inappropriate antibiotic use, such as not completing prescribed courses or using antibiotics without medical guidance, contributes to the development of resistant bacterial strains [7]. This problem is exacerbated in resource-limited settings where access to appropriate medical care and diagnostic facilities is limited, leading to higher rates of resistance and inadequate management of infections [8].
The rise in antimicrobial resistance poses a significant threat to the treatment of UTIs, making many commonly used antibiotics ineffective. Resistance to first-line antibiotics, such as trimethoprim-sulfamethoxazole and fluoroquinolones, has been increasing, leading to higher treatment failure rates and prolonged illness. This resistance crisis is particularly severe in developing regions where surveillance systems for tracking resistance patterns are often underdeveloped or non-existent. Studies from various geographic regions, including sub-Saharan Africa and parts of Asia, have documented high prevalence rates of multidrug-resistant (MDR) -strains, which are resistant to 3 or more subclasses of antibiotics [9, 10]- UTI pathogens, which complicates treatment protocols and challenges public health efforts [10–12].
The situation in Sudan reflects similar concerns. A 2008 study reported high antibiotic resistance, with 67% of gram-negative organisms and 44% of gram-positive isolates exhibiting resistance [13]. More recent findings indicate a persistent trend, showing 62.3% resistance to amoxicillin-clavulanate and 47.2% resistance to nitrofurantoin [14]. Additionally, another study confirmed high resistance levels in E. coli strains against first-line antibiotics, including amoxicillin-clavulanate and nitrofurantoin [15]. Empirical treatment, which is often used in settings lacking the capability for culture and sensitivity testing, relies heavily on local resistance data to guide the choice of antibiotics. Without current and specific data on resistance patterns, healthcare providers may continue to use ineffective antibiotics, leading to suboptimal treatment outcomes and further resistance development. Therefore, continuous surveillance and detailed local data are essential for adapting treatment guidelines and improving patient care [16, 17].
Understanding local bacterial etiologies and their resistance patterns is critical for the effective management of UTIs. Therefore, this study aims to assess the prevalence of bacterial pathogens associated with UTIs cases and their antibiotic sensitivity pattern.
Methods
Study design and population
This is a retrospective institutional-based cross-sectional study that involved the detection of Gram-positive and Gram-negative organisms in urinary isolates. The study was conducted using secondary data obtained from laboratory records in the Nile Medical Compound in Port Sudan City. We included all urine cultures and sensitivity tests performed for all patients who were tested for UTI between June 2023 to March 2024, a total of 328 cultures.
Sample size and sampling technique
All available records meeting the inclusion criteria during the study period were included in the analysis. No sampling technique was applied, as total coverage was used instead of random sampling. A total of 323 laboratory records were reviewed. Relevant data were extracted from the laboratory records, including demographic information (sex), urine culture results, and antibiotic sensitivity test results.
Urine collection and processing
Clean voided midstream urine samples were collected in sterile special urine collection cups with the assistance of trained laboratory staff at the Sea Ports Corporation Hospital. Before sample collection, each patient was provided with a brochure and instructions explaining how to collect correct midstream urine samples to avoid contamination. All urine samples were inoculated using a calibrated inoculation with 10 µL of urine, and each sample was inoculated on Cysteine Lactose Electrolyte Deficient (CLED) agar. All plates were incubated at 37 °C for 24–48 h for visible growth [18].
Identification of isolated microorganisms
Urine samples showing a colony count of more than 100 CFU/mL were considered positive for UTI isolates. They were identified following standard biochemical tests and Gram stain. Samples with mixed growth of two uropathogens were considered as mixed co-infections and included in the analysis. However, samples with polymicrobial growth suggestive of contamination (more than two organisms or significant epithelial cell presence) were excluded, and patients were requested to provide a repeat midstream clean-catch sample. Gram-negative isolates were assessed for lactose and glucose fermentation, urease, oxidase, indole synthesis, and citrate utilization. Gram-positive bacteria were evaluated using catalase, coagulase, mannitol fermentation, and bile esculin tests.
In this study, co-infection was defined as the isolation of two distinct uropathogens from the same urine culture sample, based on clear colony morphology, Gram stain differences, and identification through biochemical testing. Only samples with two clinically relevant pathogens and no evidence of contamination (e.g., absence of mixed skin flora or more than two morphologically distinct colonies without clinical correlation) were considered true co-infections. Contaminated samples were excluded from the analysis.
Antimicrobial susceptibility testing (Kirby-Bauer’s disc diffusion testing)
Antibiotic sensitivity of the isolated bacteria was determined using the disc diffusion method. Discs were evenly distributed 20 mm apart on Mueller-Hinton Agar using sterile forceps and incubated at 37 °C for 18–24 h. The diameter of the zone of inhibition around the disc was measured using a ruler. Results were interpreted as Sensitive and Resistant based on CLSI M100 guidelines (Clinical and Laboratory Standards Institute) [19]. Antibiotic disks used were: amikacin (AK, 30 µg), amoxiclav (AMC, 20/10 µg), ceftriaxone (CTR, 30 µg), co-trimoxazole (COT, 1.25/23.75 µg), gentamicin (GEN, 30 µg), nitrofurantoin (NIT, 300 µg), meropenem (MEM, 10 µg), imipenem (IPM, 10 µg), ciprofloxacin (CIP, 5 µg), tetracycline (TE, 30 µg), doxycycline (DOX, 30 µg), azithromycin (AZM, 15 µg) piperacillin (PRL, 100 µg), vancomycin (VA, 30 µg), ofloxacin (OFX, 5 µg), chloramphenicol (C, 30 µg), cefotaxime (CTX, 30 µg), levofloxacin (LEV, 5 µg), norfloxacin (NOR, 10 µg), ceftazidime (CAZ, 30 µg), cefixime (CFM, 5 µg), and ampicillin (AMP, 10 µg).
Data analysis and management
Data was collected using Excel, then cleaned and organized using SPSS version 26. Classification of antibiotics into classes was done according to the WHO classification in 2023 [20]. Frequency tables were used to present the data. Chi-squire and Fisher exact tests were used to determine the differences across urine culture results regarding gender and also antibiotic resistance. All tests considered 0.05 as the level of significance.
Results
Urine cultures’ characteristics
Of the 328 urine culture samples collected in this study, more than half were from females (211, 64.3%). Regarding urine culture, more than two-thirds of the samples (229, 69.8%) were positive cultures with only one detected pathogen. The most common detected pathogens were: E. coli (102, 31.3%), Pseudomonas spp (31, 9.5%) and Staphylococcus aureus(29, 8.8%). The most commonly reported co-infection was infection by both E coli and Enterococci spp (11, 3.4%). All the pathogens detected were resistant to at least 1–2 antibiotics, with only 28.7% (94) of samples being resistant to 4–6 classes of antibiotics. Only one case was sensitive to all antibiotics (0 resistance), and the patient was found to have Pseudomonas spp.
When comparing the culture results against gender, there was a significant difference between male and female regarding the pathogen detected in the culture (p-value = 0.001). Females tended to have a higher percentage of E coli, Pseudomonas spp., Enterococci spp. and co-infections (35.1%, 10.9%, 11.4% and 12.8%, respectively). Females also had significantly higher percentages of positive results, either with one pathogen (154, 73%) or co-infection (27, 12.8%), than males (p-value = 0.012). Moreover, females’ cultures tended to have significantly higher percentages of antibiotic resistance across all classes (0–2, 3 and 4–6) (p-value = 0.037) (Table 1).
Table 1.
The table shows the urine culture results against gender (N = 328)
| Variables | Frequency (%) | Male | Female | p-value | |||
|---|---|---|---|---|---|---|---|
| frequency | Column% | frequency | Column% | ||||
| Urine culture results | Negative result | 62 (18.9%) | 32 | 27.4% | 30 | 14.2% | 0.012* |
| Positive result with one pathogen | 229 (69.8%) | 75 | 64.1% | 154 | 73% | ||
| Positive result with co-infection | 37 (11.3%) | 10 | 8.5% | 27 | 12.8% | ||
| Pathogen detected | No pathogen | 62 (18.9%) | 32 | 27.4% | 30 | 14.2% | 0.001* |
| Staphylococcuss aureus | 29 (8.8%) | 15 | 12.8% | 14 | 6.6% | ||
| Enterococci spp. | 28 (8.5%) | 5 | 4.3% | 23 | 10.9% | ||
| Pseudomonas spp. | 31 (9.5%) | 7 | 6% | 24 | 11.4% | ||
| E coli | 102 (31.1%) | 28 | 23.9% | 74 | 35.1% | ||
| Klebsiella spp. | 13 (4%) | 7 | 6% | 6 | 2.8% | ||
| Othersa | 27(8.2%) | 13 | 11.1% | 14 | 6.6% | ||
| Co-infection of two pathogens | 35 (11.3%) | 10 | 8.5% | 25 | 12.8% | ||
| If co-infection, what were they? | Single pathogen | 291 (88.7%) | 107 | 91.5% | 184 | 87.2% | 0.753 |
| E coli and Enterococci spp. | 11 (3.4%) | 2 | 1.7% | 9 | 4.3% | ||
| E coli and Staphylococcus aureus | 7 (2.1%) | 3 | 2.6% | 4 | 1.9% | ||
| Pseudomonas spp. and Enterococci spp. | 5 (1.5%) | 1 | 0.9% | 4 | 1.9% | ||
| Enterococci spp. and Proteus spp. | 3 (0.9%) | 1 | 0.9% | 2 | 0.9% | ||
| Othersab | 11 (3.4%) | 3 | 2.6% | 8 | 3.8% | ||
| Number of antibiotic classes the pathogen is resistant to | No detected pathogens | 62 (18.9%) | 32 | 27.4% | 30 | 14.2% | 0.037* |
| 0–2 classes of antibiotics | 78 (23.8%) | 30 | 21.4% | 53 | 25.1% | ||
| 3 classes of antibiotics | 94 (28.7%) | 30 | 25.6% | 64 | 30.3% | ||
| 4–6 classes of antibiotics | 94 (28.7%) | 30 | 25.6% | 64 | 30.3% | ||
aOthers are low frequency pathogens such as Staphylococcus epidermidis, Staphylococcus saprophyticus, Acinetobacter baumannii
Others are low frequency co-infections such as E coli and Staphylococcus epidermidis, E. coli and Pseudomonas spp., Enterococci spp. and Klebsiella spp., Pseudomonas spp. and Gonococci spp., Pseudomonas spp. and Staphylococcus aureus
*p-value <0.05
Antibiotic sensitivity and resistance
When presenting the different pathogens detected against the tested antibiotics, the antibiotics that showed the highest sensitivity among cultures were: gentamicin (198, 60.4%), cotrimoxazole (128, 39%), Other antibiotics (128, 39%), nitrofurantoin (110, 33.5%) and ciprofloxacin (103, 31.4%). The majority of the Staphylococcus aureus pathogens (79.3%) and enterococci spp. (93.3%) were sensitive to gentamicin. More than half of the Pseudomonas spp. samples were sensitive to both gentamicin (64.5%), other antibiotics (67.7%), cotrimoxazole (85.1%), meropenem (54.8%) and ciprofloxacin (54.8%). Almost two-thirds of E coli samples (68.6%) were sensitive to gentamicin, and more than two-thirds of Klebsiella spp. samples (69.2%) were sensitive to the same drug (Table 2).
Table 2.
The table shows the different pathogens detected in the urine cultures and their sensitivity to the used antibiotics (N = 328)
| Antibiotics | Frequency of sensitivity (%) | Number cultures sensitive to the antibiotic (%)c | ||||||
|---|---|---|---|---|---|---|---|---|
| Staphylococcus aureus | Enterococci spp. | Pseudomonas spp. | E coli | Klebsiella spp. | Othersb | Co-infection | ||
| Gentamicin | 198 (60.4%) | 23 (79.3%) | 28 (93.3%) | 20 (64.5%) | 70 (68.6%) | 9 (69.2%) | 16 (59.3%) | 32 (94.1%) |
| Meropenem | 95 (29%) | 0 (0%) | 0 (0%) | 17 (54.8%) | 42 (41.2%) | 7 (53.8%) | 13 (48.1%) | 16 (47.1%) |
| Imipenem | 63 (19.2%) | 0 (0%) | 1 (3.3%) | 11 (35.5%) | 28 (27.5%) | 6 (46.2%) | 7 (25.9%) | 10 (29.4%) |
| Amikacin | 75 (22.9%) | 5 (17.2%) | 1 (3.3%) | 14 (45.2%) | 36 (35.3%) | 4 (30.8%) | 13 (48.1%) | 2 (5.9%) |
| Nitrofurantoin | 110 (33.5%) | 17 (58.6%) | 26 (86.7%) | 1 (3.2%) | 45 (44.1%) | 2 (15.4%) | 4 (14.8%) | 15 (44.1%) |
| Ciprofloxacin | 103 (31.4%) | 6 (20.7%) | 1 (3.3%) | 17 (54.8%) | 36 (35.3%) | 8 (61.5%) | 14 (51.9%) | 21 (61.8%) |
| Tetracycline | 86 (26.2%) | 15 (51.7%) | 14 (46.7%) | 8 (25.8%) | 27 (26.5%) | 4 (30.8%) | 11 (40.7%) | 7 (20.6%) |
| Cotrimoxazole | 128 (39%) | 12 (41.4%) | 10 (33.3%) | 18 (58.1%) | 54 (52.9%) | 3 (23.1%) | 12 (44.4%) | 19 (55.9%) |
| Amoxicillin/clavulanic acid | 44 (13.4%) | 10 (34.5%) | 11 (36.7%) | 0 (0%) | 11 (10.8%) | 2 (15.4%) | 0 (0%) | 10 (29.4%) |
| Ceftriaxone and/or cefepime | 38 (11.6%) | 1 (3.4%) | 0 (0%) | 7 (22.6%) | 15 (14.7%) | 3 (23.1%) | 5 (18.5%) | 7 (20.6%) |
| Azithromycin | 31 (9.5%) | 4 (13.8%) | 4 (13.3%) | 1 (3.2%) | 16 (15.7%) | 2 (15.4%) | 3 (11.1%) | 1 (2.9%) |
| Doxycycline | 25 (7.6%) | 5 (17.2%) | 1 (3.3%) | 1 (3.2%) | 13 (12.7%) | 2 (15.4%) | 2 (7.4%) | 1 (2.9%) |
| Othersa | 128 (39%) | 23 (79.3%) | 11 (36.7%) | 21 (67.7%) | 45 (44.1%) | 7 (53.8%) | 14 (51.9%) | 7 (20.6%) |
aOthers are low frequency sensitive antibiotics which are piperacillin, vancomycin, Ofloxacin, chloramphenicol, cefotaxime, levofloxacin, norfloxacin, ceftazidime, cefixime, ampicillin, cephalosporins
bOthers are low frequency pathogens such as Staphylococcus epidermidis, Staphylococcus saprophyticus, Acinetobacter baumannii, Enterobacter spp., Gonococci spp., Proteus spp
cPathogens were sensitive to more than one drug
In analysing the association between the detected pathogen and antibiotic resistance, we excluded negative culture results, making the total number 266 instead of 328. Out of 266 positive cultures, almost all detected pathogens were resistant to 4–6 classes of drugs, with Enterococci spp. having the highest percentage of resistance (15, 50%) and Staphylococcus aureus having the least (6, 20.7%). When comparing the detected pathogens to the number of antibiotic classes they are resistant to, no significance was detected across all pathogens (p-value = 0.339). The pathogens with the highest percentages of resistance in 3–6 classes were: Enterococci spp. (22, 80%), other pathogens (21, 77.7.%) and Klebsiella spp. (10, 77%) (Table 3).
Table 3.
The table shows the chi-squire test for the detected pathogens against number of antibiotics classes they are resistant to (N = 266)
| Pathogen detected a | Number of antibiotic classes the pathogen is resistant | ||||||
|---|---|---|---|---|---|---|---|
| 0–2 classes | 3 classes | 4–6 classes | P -value | ||||
| Frequency | Row % | Frequnecy | Row % | Frequency | Row % | ||
| Staphylococcuss aureus | 11 | 37.9% | 12 | 41.4% | 6 | 20.7% | 0.339 |
| Enterococci spp. | 6 | 21.4% | 7 | 25% | 15 | 53.6% | |
| Pseudomonas spp. | 7 | 23.3% | 13 | 43.3% | 10 | 33.3% | |
| E coli | 29 | 28.4% | 37 | 36.3% | 36 | 35.3% | |
| Klebsiella spp. | 3 | 23.1% | 6 | 46.2% | 4 | 30.8% | |
| Others | 6 | 22.2% | 11 | 40.7% | 10 | 37% | |
| Co-infection | 16 | 43.2% | 8 | 21.6% | 13 | 35.1% | |
aWe excluded the negative culture results to enable the chi-squire test to be performed
Discussion
Urinary tract infections (UTIs) remain one of the most common bacterial infections globally, and the growing threat of antimicrobial resistance (AMR) has heightened the importance of localized data to inform effective treatment. This study assessed the bacterial etiology of Urinary Tract Infections and their sensitivity patterns toward commonly used antibiotics in Port Sudan City. By identifying the most common uropathogens and their resistance profiles, the study provides crucial evidence to support empirical treatment strategies and antimicrobial stewardship in eastern Sudan.
The overall isolation rate for uropathogens was 69.5%. This is considerably higher than the rate reported in a recent study conducted at Wed Madani city, the Capital of Al Gezira state in Sudan (41.8%), and Khartoum state (21.8%) [21, 22], as well as the isolation rate reported in studies from Kuwait (26.6%), Pakistan (36.1%), Ethiopia (9.8%), and Yemen (18%) [23–26]. However, our result is similar to a study conducted in four different cities in Sudan that reported an overall isolation rate of 68%, and a recent study from Bangladesh (71%) [27, 28].
As for gender, females exhibited higher percentages of positive results, and particularly higher percentages of E. coli, Pseudomonas spp. and Enterococci spp., reinforcing existing evidence of gender-based differences in UTI susceptibility. This result is in line with existing research that suggests UTIs are more prevalent in females due to anatomical and physiological factors [29–32]. Interestingly, we also observed significantly higher rates of antibiotic resistance among female isolates across all antimicrobial classes (p = 0.037). This finding stands in contrast to several studies conducted in higher-resource settings, where male patients have been shown to harbor more resistant strains. For instance, Lee et al. in South Korea identified male sex as a significant risk factor for resistance to second- and third-generation cephalosporins in febrile UTIs [33], while McGregor et al. in the U.S. and Linhares et al. in Portugal similarly reported higher resistance rates in males across various antibiotics [34, 35]. However, our findings are consistent with a 7-year retrospective study conducted in Khartoum State, which also found significantly higher resistance among female patients [36]. This discrepancy may be attributed to context-specific factors such as more frequent empirical antibiotic use among women, self-medication, and prescribing behaviors in low-resource settings. These results highlight the importance of gender-sensitive antibiotic stewardship and the need to encourage culture-guided therapy, particularly among female patients, to mitigate the growing threat of resistance.
Antibiotic resistance
There was very high resistance to carbapenems across all UTI-causing pathogens, with only 29% of positive cultures being sensitive to meropenem and only 19.2% being sensitive to imipenem. In contrast, gentamicin showed the highest overall sensitivity at 60.4%, followed by a notable decline to 39% for other specific agents and 39% for cotrimoxazole. Among Gram-negative bacteria, Gentamicin was the most effective antibiotic, showing lower resistance compared to meropenem, colistin, and amikacin, which were found to be the most effective by El-Arif et al., Mohammedkheir et al., and Hamadalneel, respectively [1, 9, 37]. While the majority of detected pathogens were resistant to multiple classes of antibiotics, more than a quarter (28.7%) were resistant to 4–6 classes. Based on the number of antibiotic classes, Enterococci spp. showed the highest resistance in the 4–6 class group (15 isolates; 53.6%), followed by E.coli (36 isolates; 35.3%), Pseudomonas spp. (10 isolates; 33.3%), and Klebsiella spp. (4 isolates; 30.8%). Staphylococcus aureus demonstrated the lowest level of multidrug resistance, with only 6 isolates (20.7%) falling into the 4–6 class resistance range. These results are particularly concerning given the global rise in multidrug-resistant (MDR) and extended-spectrum beta-lactamase (ESBL) producing strains, as documented in other regions [38, 39], and emphasize the vulnerability of current treatment options. The wide sensitivity gap between gentamicin and other antibiotics further highlights a dangerous vulnerability: If resistance to gentamicin increases due to overuse, few effective alternatives will remain. This underscores the urgent need to shift from blind empirical treatment to culture-guided antibiotic selection and implement stewardship policies aimed at preserving the existing antibiotic efficacy.
Gram-negative bacteria
ُE.coli was the most frequently isolated pathogen in our study (31.3%), which is consistent with the global pattern. A systematic review confirmed E. coli as the most common isolated pathogen in 55.2% of cases in low-income countries in Asia and Africa [40]. Even though it is lower than regional prevalence, our findings align with a multi-center Sudanese study conducted in 2020 (26.3%) [28], and another study conducted in Khartoum state, which reported E. coli in 72.7% of community cases and 32.3% of hospitalized cases [14]. Similar results were reported from studies in Saudi Arabia (33.7%), Ethiopia (42.7%), and Khartoum state (49.1%) [14, 41, 42]. This, however, contradicts the results of the study conducted at Gezira state, Sudanwhere Staphylococcus aureus was the most commonly isolated pathogen. This, however, could be attributed to differences in population characteristics, as their study was conducted in hospitalized patients [21].
Our data showed that E. coli had high resistance to amoxicillin/clavulanic acid, ciprofloxacin, and nitrofurantoin — all drugs commonly used in UTI management — a pattern that mirrors findings from previous local studies [13, 21]. While susceptibility was relatively better for cotrimoxazole (52.9%) and gentamicin (68.8%), and nitrofurantoin (44.1%), low sensitivity to ciprofloxacin was particularly concerning (35.3%), given its frequent use in both community and hospital settings. Other studies showed similar patterns [13, 43, 44]. Alarmingly, E. coli also demonstrated reduced susceptibility to carbapenems, with only 41.2% and 27.5% of isolates sensitive to meropenem and imipenem, respectively. This contrasts sharply with studies from Morocco and Palestine, where E. coli isolates showed 100% sensitivity to these agents [44, 45]. Our findings contrast with previous studies conducted in Khartoum state, which reported lower sensitivity to gentamicin (40%) and nitrofurantoin (4%), but higher sensitivity to amikacin and meropenem (60%) compared to our results (35.3% and 41.2%, respectively) [22].
These discrepancies are likely due to differences in study populations, as the Khartoum study focused exclusively on hospitalized patients. This variation highlights the context-dependent nature of antibiotic resistance and underscores the urgent need for a robust and continuous surveillance system to monitor resistance patterns across different healthcare settings. Additionally, the diminishing effectiveness of broad-spectrum antibiotics, which are typically reserved as last–line options, raises serious concerns. These patterns highlight the growing challenge of managing uncomplicated and complicated UTIs in Sudan, particularly as resistance erodes the utility of first-line oral agents. They point toward a critical shift in local resistance dynamics. With only gentamicin and cotrimoxazole demonstrating over 50% sensitivity, our findings underscore the urgent need to revise empirical treatment protocols and strengthen antibiotic stewardship, especially in outpatient care.
Other Gram-negative bacteria also exhibited high resistance to some antibiotics. Pseudomonas spp. emerged as the most resistant pathogen in our study, showing near-complete resistance to amoxiclav, azithromycin, and doxycycline—mirroring national and global patterns and reinforcing its reputation as a major nosocomial threat in Sudan [39]. While it retained some sensitivity to aminoglycosides, carbapenems, cotrimoxazole, and ciprofloxacin, the reduced sensitivity to carbapenems (54.8%) is alarming. This decline likely reflects the inappropriate and excessive use of broad-spectrum antibiotics in intensive care settings, often as empirical therapy without adherence to evidence-based protocols [46]. Such misuse not only undermines treatment outcomes but accelerates the development of multidrug-resistant strains, underscoring the urgent need for revised and strictly enforced antibiotic stewardship policies.
Both Pseudomonas spp. And Klebsiella spp. demonstrated high resistance to nitrofurantoin—a drug commonly used for uncomplicated UTIs—further limiting first-line treatment options. However, Klebsiella spp. sensitivity to nitrofurantoin was reported to be high in studies from Ethiopia [22, 31, 47], contradicting our results. In contrast to earlier reports, our study found some retained sensitivity in Klebsiella spp. to aminoglycosides, and carbapenems, though both organisms displayed critically low susceptibility to third-generation cephalosporins in Khartoum, with sensitivity rates slightly lower than ours [14, 22]. These findings likely reflect the widespread, often unregulated use of cephalosporins like cefixime in Sudan [48], which has contributed to increasing resistance even to last-line agents such as cefepime. Given that cefepime remains one of the few effective options against Pseudomonas spp., this trend signals a looming public health crisis that demands immediate policy-level intervention.
The overall decline in antibiotic sensitivity among Gram-negative bacteria is particularly critical. In our study, sensitivity to commonly used antibiotics such as amoxicillin/clavulanic acid and nitrofurantoin was markedly low, ranging between 0 and 16% across different Gram-negative species. In contrast, a study conducted in Khartoum between 2014 and 2015 reported much higher sensitivity rates among Gram-negative bacteria, with amoxiclav sensitivity reaching 98.8% [49]. This stark difference highlights a clear downward trend in antibiotic effectiveness over time. The decline is likely driven by the increasing misuse and overprescription of antibiotics, which accelerates the emergence of resistant strains.
Gram-positive bacteria
Gram-positive organisms in our study demonstrated complete resistance to carbapenems and cephalosporins, which is notably higher than the resistance rate reported by El-Erifi et al. in Khartoum in 2021 [14]. While both studies showed similar sensitivity to nitrofurantoin and gentamicin, a striking difference was observed in meropenem susceptibility: 75% of gram-positive isolates in their study were sensitive, whereas our findings revealed complete resistance. A comparable pattern emerged with cephalosporins, where their study found 34% sensitivity, while ours showed near-total resistance. This trend signals a concerning rise in antibiotic resistance among gram-positive organisms in recent years. Despite this, the highest sensitivities in our data were observed with specific last-resort antibiotics such as piperacillin, vancomycin, and ofloxacin. Notably, high vancomycin sensitivity has also been reported in neighbouring regions like Eritrea and Saudi Arabia [50, 51], and similar resistance patterns were reflected in recent national studies [21, 52]. This likely reflects their limited routine use in clinical settings.
Limitations
Our current study has some limitations, including a study design that depends solely on secondary data, a lack of sociodemographic information, and data gathered from only one centre. Although all urine samples were collected, the study is susceptible to selection bias because some patient groups who are previously diagnosed with UTI and did not undergo urine analysis may be underrepresented.
Conclusion
The study highlights critical insights into the prevalence and resistance patterns of bacterial pathogens causing UTIs in Port Sudan, Sudan. Escherichia coli remain the predominant pathogen, with variable sensitivity across different antibiotics. The high sensitivity to gentamicin, nitrofurantoin, and other antibiotics underscores its potential for empirical treatment, though the observed resistance to common antibiotics like fluoroquinolones and trimethoprim-sulfamethoxazole calls for caution. Moreover, our study highlights the significant difference in resistance patterns between males and females, which suggests more research to elaborate on the reasons behind this. The study’s findings support the implementation of localized surveillance programs and continuous monitoring to adapt treatment protocols and address AMR effectively. Further research is needed to explore resistance trends over time and develop comprehensive antimicrobial stewardship programs.
Recommendations
Our study’s findings suggest that enhancing antibiotic monitoring programs should be the initial measure taken. Equally important is raising awareness about the risks of self-medication with antibiotics through improved public health education. Improving access to healthcare can also reduce the use of self-medication. Considering the growing risk of antibiotic resistance, it is crucial to promote research into alternative treatment options, whether new antibiotics or non-antibiotic treatments. We also recommend regular surveillance for antibiotic resistance, both locally in Sudan and globally. Ultimately, the provision of tailored treatment services should be guided by local antimicrobial resistance patterns.
Acknowledgements
Not applicable.
Authors’ contributions
A.I conceptualized the study, collected the data, and wrote the first draft. M. E conducted data analysis. H.A, N.E and E.K wrote the final manuscript.
Funding
The authors received no funding for this study.
Data availability
Data sets used and/or analyzed during the current study are available upon reasonable request from the corresponding author.
Declarations
Ethical approval and consent to participate
This research is retrospective and involved collection of existing data and records; no additional samples were obtained specifically for research purposes. This study was carried out following the Helsinki Declaration. All patient-related data were anonymized to protect their privacy, and no identifiable patient information was included in the study. The ethical committee at the community department, Faculty of Medicine, University of Khartoum had approved all procedures of the study and provided a waiver for written informed consent.
Consent for publication
Not applicable.
Competing interests
The authors declare no competing interests.
Footnotes
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
Data sets used and/or analyzed during the current study are available upon reasonable request from the corresponding author.