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The present study aims to employ a multiplex PCR-based method for phylogenetic typing of Shigella and determine the frequency of several virulence genes among Shigella phylogenetic clades and species. Species identification, phylogenetic typing of 44 previously diagnosed Shigella isolates, and frequency of virulence genes and loci, virA, virB, virF, ipaBCD, ial, sen, and set1A were investigated through performing several PCR assays. Distribution of virulence genes among Shigella phylogenetic clades and species was determined by the statistical analysis. The identities of 40 isolates out of 44 were confirmed as Shigella, and these isolates were classified in four phylogenetic clades, S1 (7.5%), S2 (52.5%), S3 (20%), and S5 (20%) and 4 species, S. sonnei (52.5%), S. flexneri (22.5%), S. dysenteriae (20%), and S. boydii (5%). The prevalence of virA, virB, virF, ipaBCD, ial, sen, and set1A was determined as 67.5%, 72.5%, 72.5%, 65%, 75%, 40%, and 5%, respectively. The presence of sen, uidA, or set1A was found to be statistically correlated with either of Shigella phylogenetic clades or species. A significant statistically association was also determined between set1A and Shigella phylogenetic clades. Furthermore, the nucleotide sequence of invasion-associated locus (ial) was determined and mapped on Shigella genome through in silico analysis. The current study shows the distribution of Shigella isolates and its key virulence genes within the five recently described phylogenetic clades for the first time in the Asia. This is also the first description of ial nucleotide sequence and its exact location on Shigella genome after its initial identification.

Infection with Shigella is considered a major cause of morbidity and mortality in children with diarrhea in developing countries, especially in Iran. Due to the importance of country-level epidemiological data, molecular characterization of genetic determinants of Shigella spp. is a necessity. The aim of the present study was to investigate the prevalence of integron types, bla-CTX-M, bla-SHV and blaTEM β-lactamase genes of Shigella isolates in pediatric patients in Tehran, Iran. In a time period of 18 months from May 2015 to August 2017, 75 Shigella spp. were isolated from non-duplicative diarrheal stool specimens in six different hospitals in Tehran. The isolates from patients were further analyzed for their antibiotic susceptibility and extended-spectrum beta-lactamase (ESBL) production. Polymerase chain reaction was performed for amplification of the integrons (I, II, III), TEM, SHV, CTX-M15. The prevalence of S. sonnei, S. flexneri, S. dysenteriae and S. boydii were 40 (53.3%), 33 (44%), 1 (1.3%) and 1 (1.3%), respectively. The results of an antimicrobial resistance test showed that the high percentage of resistance to nalidixic acid (NA), ampicillin (AMP) and trimethoprim/sulfamethoxazole (SXT) included 38 (50.6%), 59 (81.3%) and 64 (88%) isolates, respectively. Further results revealed that 52% and 76% of Shigella isolates carried intI and intII genes, respectively. In this study, the rates of CTX-M (10.7%), SHV (28%) and TEM (21.3%) were determined, all of which were positive for blaCTX-M15. This study showed the high prevalence of multidrug resistant S. sonnei and S. flexneri. Furthermore, it highlighted the increasing integrons (intI and intII) and ESBL genes, especially blaCTX-M15, in Shigella isolates.

Fluoroquinolone (FQ) resistance in clinical isolates of Shigella species has been increasing reported in recent years. This study was carried out to find the mutations within the quinolone resistance-determining regions (QRDRs) and the prevalence of plasmid-mediated quinolone resistance (PMQR) determinants among the clinical isolates of Shigella sp. in Tehran, Iran. A total of 50 Shigella isolates were collected from five teaching therapeutic centers in Tehran, Iran and analyzed for antibiotic susceptibility over a period of 20 months from July 2015 to January 2017. The PCR and direct nucleotide sequencing were used for genetic alterations in the QRDRs. The PMQR genes were detected using PCR. The results revealed four types of mutations in the QRDR of gyrA: 20 (40%) had a S83L mutation, 1 (2%) had a S83A mutation, 2 (4%) had a D87G mutation, and 1 (2%) isolate had a D87Y mutation. Mutations were also found at codon N57D, D200N, and E210K in three isolates. Seven hospitalized children had qnrS determinants, and one isolates had the mutation S83A, while two isolates had double mutations at S83L and/or D87G (Ser83Leu and Asp-87Gly). The PMQR gene-positive isolates had the single replacement of serine with leucine. In hospitalized children, two isolates had two types of PMQR determinants (qnrS and qnrA) and (qnrS and qnrB) at once. The results of this study indicate that the emergence of strains with mutations in the QRDR regions and the capture of PMQR determinants in strains may lead to failure in therapy with FQ and the widespread emergence of strains with high-level FQ resistance.

Shigellosis is a considerable infectious disease with high morbidity and mortality among children worldwide. In this survey the prevalence of four important virulence genes including ial, ipaH, set1A, and set1B were investigated among Shigella strains and the related gene profiles identified in the present investigation, stool specimens were collected from children who were referred to two hospitals in Tehran, Iran. The samples were collected during 3 years (2008-2010) from children who were suspected to shigellosis. Shigella spp. were identified throughout microbiological and serological tests and then subjected to PCR for virulotyping. Shigella sonnei was ranking first (65.5%) followed by Shigella flexneri (25.9%), Shigella boydii (6.9%), and Shigella dysenteriae (1.7%). The ial gene was the most frequent virulence gene among isolated bacterial strains and was followed by ipaH, set1B, and set1A. S. flexneri possessed all of the studied virulence genes (ial 65.51%, ipaH 58.62%, set1A 12.07%, and set1B 22.41%). Moreover, the pattern of virulence gene profiles including ial, ial-ipaH, ial-ipaH-set1B, and ial-ipaH-set1B-set1A was identified for isolated Shigella spp. strains. The pattern of virulence genes is changed in isolated strains of Shigella in this study. So, the ial gene is placed first and the ipaH in second.

Over the past few years, the number of Shigella strains resistant to nalidixic acid has increased and has made the selection of effective antimicrobial therapy more difficult. The purpose of this study was to investigate the molecular mechanism of quinolone resistance in Shigella strains. Shigella strains isolated from 1100 diarrhoeal patients in Tehran, Iran, were assessed for their susceptibility to nalidixic acid prior to PCR-RFLP and sequence analysis of their quinolone resistance genes. Among 73 Shigella strains isolated, 23 (31.5%) were resistant to nalidixic acid. The most common Shigella spp. was Shigella sonnei (54; 74.0%). Of the 23 quinolone-resistant isolates, 4 (17.4%) (including 2 Shigella flexneri, 1 S. sonnei and 1 Shigella boydii) contained the qnrS gene. However, none of the isolates harboured qnrA or qnrB genes. PCR-RFLP analysis of gyrA showed a mutation profile in two nalidixic acid-resistant strains, including one S. sonnei and one S. flexneri. Sequencing of mutant gyrA genes revealed a point mutation at position 83, resulting in the replacement of serine by leucine. In conclusion, molecular mechanisms of resistance to quinolones were identified in 6 of 23 Shigella isolates. Other possible mechanisms of resistance should also be investigated for better characterisation of quinolone-resistant Shigella isolates., (Copyright © 2016. Published by Elsevier Ltd.)

The present study was conducted to determine the prevalence of serotypes and antibiotic resistance in Shigella spp. isolated from patients admitted to Bouali hospital, Tehran, Iran during 1999 to 2001. All cases of shigellosis that were diagnosed according to their clinical pictures and microbial cultures were included in current study. Patients' age ranged from 12 to 89 years. Overall, 52 patients (56%) and 41(44%) were males and female, respectively. From a total of 90 Shigella isolates, 40 strains were identified as S. sonnei (45%), 26 as S. flexneri (27.9%), 3 as S. boydii (3%) and 21 as S. dysenteriae (24%). More than 95% of the isolates were susceptible to ciprofloxacin, ceftriaxone and ceftizoxim, 70% to nalidixic acid and less than 50% to co-trimoxazole, tetracycline, ampicillin and fourazolodon.

Reza Ranjbar, Abbas Farahani Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, IranCorrespondence: Reza RanjbarMolecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, IranTel +98 21 8803 9883Email Ranjbarre@gmail.comAbstract: Shigella spp. are a common cause of diarrheal disease and have remained an important pathogen responsible for increased rates of morbidity and mortality caused by dysentery each year around the globe. Antibiotic treatment of Shigella infections plays an essential role in reducing prevalence and death rates of the disease. However, treatment of these infections remains a challenge, due to the global rise in broad-spectrum resistance to many antibiotics. Drug resistance in Shigella spp. can result from many mechanisms, such as decrease in cellular permeability, extrusion of drugs by active efflux pumps, and overexpression of drug-modifying and -inactivating enzymes or target modification by mutation. Therefore, there is an increasing need for identification and evolution of alternative therapeutic strategies presenting innovative avenues against Shigella infections, as well as paying further attention to this infection. The current review focuses on various antibiotic-resistance mechanisms of Shigella spp. with a particular emphasis on epidemiology and new mechanisms of resistance and their acquisition, and also discusses the status of novel strategies for treatment of Shigella infection and vaccine candidates currently under evaluation in preclinical or clinical phases.Keywords: Shigella, antibiotics, resistance, drug resistance, mechanism, treatment, biofilm, efflux pumps, prevention, vaccine