Background
Shigella spp. the members of
Enterobacteriaceae family are rod-shaped, non-spore-forming, non-motile, and facultative anaerobic Gram-negative bacterium that is capable of intracellular infection [
1].
Shigella species are a major public health concern as they rank high among the causes of diarrhea across the globe. Ninety-nine percent of the roughly 167 million yearly instances of
Shigella infection occur in developing nations [
2]. Compared to other enteric pathogens such as
Salmonella and
Vibrio which typically require a dose of 10
5–10
8 organisms,
Shigellosis poses a severe public health threat due to its infective dose being as low as 10 to 100 organisms [
3]. There are four subgroups of
Shigella spp., consisting of group A (
Shigella dysenteriae), group B (
Shigella flexneri), group C
(Shigella boydii), and group D (
Shigella sonnei), with each subgroup containing multiple serotypes [
4].The use of antibiotics has resulted in benefits for patients infected with Shigella, including reduced duration and severity of diarrheal illness. Based on current guidelines from the World Health Organization (WHO) and a systematic review, the recommended treatment for Shigellosis is the administration of ciprofloxacin and azithromycin, two recommended oral antibiotics, for a duration of 5 days [
5,
6]. Typically, shigellosis clears up without intervention or treatment, yet it can be dangerous for people with immunocompromised status those without adequate healthcare.
Shigella can impact anyone, with children under five especially at risk because of inadequate hygiene practices, underdeveloped immune systems, and lack of prior exposure.
Antibiotics play a vital role in lowering diseases and death by treating bacterial infections, yet their improper and excessive use in managing diarrhea is a factor in the growing issue of antibiotic resistance. There is an escalating worry about the resistance of intestinal pathogens, including
Shigella spp.
, Enteropathogenic E. coli (EPEC),
Vibrio cholerae, and
Salmonella spp. [
3,
7,
8].
A systematic review and meta-analysis was conducted in Iran between 2008 and 2021, revealing the prevalence rates of resistance to ciprofloxacin, azithromycin, and ceftriaxone among
Shigella spp. as 3%, 30%, and 28%, respectively. Drug resistance in
Shigella spp. can manifest through diverse mechanisms including active efflux pumps expelling drugs, reduced cellular permeability, increased production of drug-modifying or drug-inactivating enzymes, and target mutation leading to modification [
3]. These strains commonly exhibit resistance to multiple antibiotics, leading in increasing of morbidity. Therefore, there is a strong need for the surveillance and control of these strains [
3,
9]. Examining both the phenotypic and genotypic antimicrobial resistance profiles of
Shigella is of utmost importance for accurately identifying appropriate antibiotics for the treatment of shigellosis, particularly given the ongoing alterations in resistance profiles [
10]. Molecular typing techniques have been used with increasing frequency in studies of the epidemiology
Shigella spp. and also for a better understanding of the evolutionary relationships among clones. Gaining knowledge about the prevalent strains linked to human infections and their origins within various environments holds significance for enhancing our comprehension of this pathogen's epidemiology and addressing related issues. Consequently, precise and swift epidemiological typing is imperative for tracking the evolution of these bacterium strains [
10‐
12]. One of the suitable tools for genetic analysis and genetic relatedness evaluation among bacteria, especially the
Enterobacteriaceae family, is the ERIC-PCR method. The objective of this study was to analyze the antibiotic susceptibility patterns and clonal relationships among clinical strains of
Shigella spp. isolated from patients with diarrhea in the Hormozgan province, located in the southern region of Iran.
Discussion
Throughout the duration of our study,
S. flexneri continued to maintain its dominance as the primary serogroup, consistent with previous records [
3]. This research has confirmed the prevalence of
S. flexneri in low- and middle-income countries (LMIC), while
S. sonnei demonstrated a higher prevalence in high-income countries [
21]. Therefore, the findings of this study validate the aforementioned assumption.
Over the past few decades in Iran, the predominant causative agent of shigellosis has been identified as
S. flexneri. However, contemporary studies have revealed a notable surge in shigellosis cases associated with
S. sonnei [
22‐
24]. In this study, it was found that 40.3% of
S.
flexneri strains were isolated from children under 10 years of age, indicating a significant prevalence within this particular age group. The observed variations in the occurrence of
Shigella spp. could potentially be attributed to factors such as age, economic development level, geographical location, climate, and numerous other environmental conditions [
23].
Shigella boydii has been reported in Iran in less than 3% of the total shigellosis cases [
9], whereas in our study,
S. boydii accounted for 22.58%. In line with our study, research conducted in Iran in 2018 revealed that the occurrence rate of
S. boydii among
Shigella strains was 23.8% [
25]. Similar to other studies in Iran,
S. dysenteriae was not detected in stool samples [
3,
23].
Shigella dysenteriae exhibits a higher frequency in outbreak scenarios linked to civil unrest and refugee crises [
26].
In previous studies, it has been demonstrated that fever was the predominant presenting symptom [
27,
28]. Our cases had a low rate of hospitalization and death was not observed. In contrast to previous research findings [
29,
30], our study observed a high occurrence of bloody diarrhea (56.43%).
Various mechanisms contribute to the development of drug resistance in
Shigella isolates. One example is the interference with DNA replication through the inhibition of DNA topoisomerase IV and gyrase by quinolone antibacterial agents, such as nalidixic acid, ofloxacin, and ciprofloxacin [
3]. The emergence of antimicrobial resistance poses a critical challenge to public health. The results of antibiotic susceptibility testing revealed high resistance rates among
Shigella isolates, particularly against ampicillin (90.78%), piperacillin–tazobactam (87.1%), cefixime (83.87%), trimethoprim–sulfamethoxazole(co-trimoxazole) (83.87%), cefotaxime (82.26%), and ceftriaxone (80.65%). These rates were in line with previous studies from Iran and various countries [
3,
23,
31]. However, the resistance rates for different
Shigella species exhibited the expected variations.
There are three subgroups of
Shigella spp. isolates
: S. flexneri, S. sonnei, and
S. boydii. These subgroups have shown higher rates of resistance against ampicillin (64.9%) and co-trimoxazole. The data indicate a significant increase in resistance to various classes of antibiotics among the
Shigella isolates. Based on our study findings, and considering that co-trimoxazole and ampicillin are commonly used as first-line treatments for
Shigella-induced diarrhea, we discourage the use of these antibiotics for empirical therapy due to their high resistance rates [
3]. In line with our findings, a significant resistance rate to different antibiotics had been previously reported in the southwestern and central regions of Iran [
23,
32].
The resistance to ciprofloxacin has significantly risen (by 56.45%) when compared to previous studies [
30,
33]. The occurrence of drug resistance in
Shigella spp. is a significant risk, particularly in developing nations with health and nutritional challenges.
The findings of our study revealed a concerning trend with the high prevalence of MDR-
Shigella isolates and their emergence within the respective hospitals. Similar to our results, a study conducted in Cambodia found that 91% of
Shigella spp. isolates were multidrug-resistant [
34].
In line with our study, a study conducted by Shahin et al. during 2015–2016 on 70
Shigella spp. isolates revealed that at least 50 percent of the
S. sonnei strains were resistant to ceftazidime, cefotaxime, cefuroxime, ampicillin, tetracycline, nalidixic acid, and ciprofloxacin, according to the results of the antimicrobial [
35].
A study conducted on
S. flexneri and
S. sonnei strains isolated from bacillary dysentery cases in Southeast Brazil found that 90% of them exhibited multiple drug resistance phenotypes [
36].
Furthermore, across Iran, 11 studies identified a total of 667 clinical isolates as species producing both MDR and ESBLs [
9]. There have been reports of the emergence of extensively drug-resistant (XDR) and multidrug-resistant (MDR)
S. flexneri serotypes in England [
37].
Similar to the isolates isolated from human sources, unfortunately, the isolates isolated from water sources have also shown high antibiotic resistance. For example, Shahin et al. from Iran showed that all
Shigella isolates collected from water samples were MDR [
38].
In a study with a wide range of food samples demonstrated that the incidence of Shigella spp. is more frequent in raw vegetables and also multidrug resistance phenotypes were noticeably frequent and observed in 17 isolates (89.5%) out of 19 isolates.
A study conducted on various food samples reveals a high prevalence of
Shigella spp. in raw vegetables, with a remarkable prevalence of multidrug resistance phenotypes detected in 17 out of 19 isolates (89.5%). The spread of
Shigella is notably affected by suboptimal health standards, limited personal hygiene awareness, and water quality of lower quality. Although most cases of Shigella-induced foodborne illnesses are typically mild and resolve independently, the emergence of severe cases raises significant concerns, particularly in high-risk patient populations [
39].
In this current investigation, ERIC-PCR was utilized for the molecular characterization of
Shigella spp. isolates, offering a swift and cost-effective approach that has demonstrated its worth as a valuable genotyping method for
Enterobacteriaceae [
40]. It is a powerful method for molecular typing of
Shigella strains and has been shown to be a plausible alternative strategy to PFGE [
41]. This study aimed to understand the molecular epidemiology of
Shigella spp. in hospitals. The objective was to identify the main clonal lineages that are currently circulating in this region.
Isolates in this study with ERIC profiles A3, A5, A6, A8 and A11 were believed to be endemic in our study region. All isolates belonging to the same genotype exhibited consistent resistance patterns. They demonstrated co-resistance to antimicrobial agents, including ampicillin, piperacillin–tazobactam, trimethoprim–sulfamethoxazole, cefixime, and ceftriaxone (Table
6). This remarkably similar pattern suggests that the same species might be circulating within the communities. Also, based on the ERIC profile results of all isolates presented in Fig.
1, clusters A2, A4, and sub cluster A6-1 (87.5%) were prevalent in the winter season, while clusters A1, A3, A9, A10 and sub cluster A6-2 were prevalent in the autumn season. Maybe this reason is one of the factors contributing to the high similarity of these isolates.
Wei et al. documented a strong correlation between antimicrobial resistance patterns and PFGE genotypes in clinically derived
Shigella isolates [
42].
Shigella isolates with the same antimicrobial resistance patterns, as well as similar PFGE genotypes, have contributed to the shigellosis that has been circulating in an area for a longer period.
In another study conducted by Zhu et al., a notable correlation was observed between the antimicrobial resistance phenotypes and genotyping of
Shigella spp. isolates obtained from clinical samples [
43].
In our research, groups A1 and A9 showed complete resistance to seven different antibiotics, as detailed in Table
6. Corresponding with our results, another investigation used RAPD-PCR to group
Shigella strains into five main clusters and found that those in cluster R4 exhibited the most antibiotic resistance. This study also suggested a connection between the clusters and their resistance to antimicrobials [
44]. Therefore, molecular genotyping patterns can be used to predict antimicrobial resistance in
Shigella strains.
In the last 20 years, numerous studies have applied the ERIC-PCR assay as a quick genetic typing technique to evaluate genetic connections between bacterial species from various origins such as the environment, food products, and humans [
20,
45,
46]. In this study, ERIC-PCR showed remarkable differentiation among unrelated
Shigella spp., making it a valuable DNA fingerprinting approach for discerning
Shigella species isolated from diverse samples. It can provide genotyping profiles and contribute to understanding the genetic diversity and relatedness of
Shigella strains.
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