Antibiotic Susceptibility Pattern of Shigella spp. Isolated from Patients Suspected of Acute Gastroenteritis

Shigellosis, an intestinal infection caused by Shigella species, is manifested by bloody diarrhea. Due to the surge in multidrug-resistant (MDR) Shigella species, the control of shigellosis has been a big challenge. This study aims to determine the prevalence and assess the antibiotic susceptibility pattern of Shigella species. During our study period of five months from April 2014 to August 2014 at Sukraraj Tropical and Infectious Disease Hospital, Teku, Kathmandu, a total of 653 stool samples were collected from the patients suspected of acute gastroenteritis. The standard microbiological procedure was followed for the isolation and identification of Shigella species. Assessment of antibiotic susceptibility pattern of the Shigella species was done by Kirby-Bauer disk diffusion method following CLSI guidelines. The study found 25(3.82%) cases were Shigella positive. Among them, 18(72%) were S. flexneri, 6(24%) were S. dysenteriae, and 1(4%) was S. sonnei. The patients in the age group 16-45 years were highly susceptible to infection as the higher proportion 16(64%) of Shigella species were isolated from this age group (p> 0.05). Shigella species were found to be highly susceptible to Cefotaxime (100%), a third-generation cephalosporin. Nalidixic acid, on the other hand, was the least effective antibiotic as 20(80%) of the Shigella isolates were resistant, followed by Ampicillin 18(72%), Cotrimoxazole 13(52%), and Ciprofloxacin 9(36%). A higher proportion of [10(40%)] of our study isolates were MDR. Our results show that Nalidixic acid, Ampicillin, Cotrimoxazole, Ciprofloxacin, and Ofloxacin cannot be used as empirical therapy for the treatment of Shigella infection as Shigella species were highly resistant to these antibiotics. So, for the MDR Shigella infection, we suggest third-generation cephalosporin as an option.

Reclassification of Shigella species as later heterotypic synonyms of Escherichia coli in the Genome Taxonomy Database

Members of the genus Shigella have high genomic similarity to Escherichia coli and are often considered to be atypical members of this species. In an attempt to retain Shigella species as recognizable entities, they were reclassified as Escherichia species in the Genome Taxonomy Database (GTDB) using an operational average nucleotide identity (ANI)-based approach nucleated around type strains. This resulted in nearly 80% of E. coli genomes being reclassified to new species including the common laboratory strain E. coli K-12 (to 'E. flexneri') because it is more closely related to the type strain of Shigella flexneri than it is to the type strain of E. coli. Here we resolve this conundrum by treating Shigella species as later heterotypic synonyms of E. coli, present evidence supporting this reclassification, and show that assigning E. coli/Shigella strains to a single species is congruent with the GTDB-adopted genomic species definition.

Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK

Shigellosis in men who have sex with men (MSM) is caused by multidrug resistant Shigellae, exhibiting resistance to antimicrobials including azithromycin, ciprofloxacin and more recently the third-generation cephalosporins. We sequenced four bla CTX-M-27-positive MSM Shigella isolates (2018–20) using Oxford Nanopore Technologies; three S. sonnei (identified as two MSM clade 2, one MSM clade 5) and one S. flexneri 3a, to explore AMR context. All S. sonnei isolates harboured Tn7/Int2 chromosomal integrons, whereas S. flexneri 3a contained the Shigella Resistance Locus. All strains harboured IncFII pKSR100-like plasmids (67-83kbp); where present bla CTX-M-27 was located on these plasmids flanked by IS26 and IS903B, however bla CTX-M-27 was lost in S. flexneri 3a during storage between Illumina and Nanopore sequencing. IncFII AMR regions were mosaic and likely reorganised by IS26; three of the four plasmids contained azithromycin-resistance genes erm(B) and mph(A) and one harboured the pKSR100 integron. Additionally, all S. sonnei isolates possessed a large IncB/O/K/Z plasmid, two of which carried aph(3’)-Ib/aph(6)-Id/sul2 and tet(A). Monitoring the transmission of mobile genetic elements with co-located AMR determinants is necessary to inform empirical treatment guidance and clinical management of MSM-associated shigellosis.

Frequency and Antimicrobial Resistance of Shigella Species in Iran During 2000 - 2020

Context: Numerous studies have shown the high frequency and antibiotic-resistant patterns of Shigella species in different provinces of Iran. In this study, we performed a comprehensive review from 2000 to 2020 in Iran to describe the prevalence rate and antibiotic-resistant patterns of S. sonnei, S. dysenteriae, S. flexneri, and S. boydii. Evidence Acquisition: We systematically searched the biomedical databases including Scopus, Google Scholar, PubMed, SID, and Web of Science for related articles published in English or Persian. Finally, out of 70 articles, 34 studies were included in the study. Results: From 44,292 clinical specimens, 2,742 cases were introduced as positive samples for Shigella species in Iran during 2000 - 2020. Also, S. sonnei (n = 1484, 54.1%) was the predominant species in Iran, followed by S. flexneri (n = 1100, 40.1%), S. dysenteriae (n = 80,3%), and S. boydii (n = 78, 2.8%). These Shigella species showed maximum resistance to ampicillin (n = 1759, 64% - 96%), cotrimoxazole (n = 1220, 87% - 100%), nalidixic acid (n = 649, 10% - 82%), trimethoprim-sulfamethoxazole (n = 459, 80% - 98.5%), cefotaxime (n = 410, 53% - 63%), and tetracycline (n = 386, 36% - 94%). No resistances were found against imipenem, meropenem, cefoxitin, norfloxacin, levofloxacin, azithromycin, and amoxicillin. Also, 308 and 359 cases were introduced as multidrug resistance (MDR) and extended spectrum beta lactamase (ESBL) producing species, respectively. Conclusions: Evaluation of endemic shigellosis and antibiotic-resistant patterns through epidemiological studies are necessary to promote infection control strategies. These data may be useful to avoid empirical treatment, revise treatment guidelines, and decrease antimicrobial resistance of Shigella spp. in human societies.

Informing shigellosis prevention and control through pathogen genomics

Shigella spp. are the leading bacterial cause of severe childhood diarrhoea in low- and middle- income countries (LMIC), are increasingly antimicrobial resistant and have no licensed vaccine. We performed genomic analyses of 1246 systematically collected shigellae from seven LMIC to inform control and identify factors that could limit the effectiveness of current approaches. We found that S. sonnei contributes ≥20-fold more disease than other Shigella species relative to its genomic diversity and highlight existing diversity and adaptative capacity among S. flexneri that may generate vaccine escape variants in <6 months. Furthermore, we show convergent evolution of resistance against the current recommended antimicrobial among shigellae. This demonstrates the urgent need to integrate existing genomic diversity into vaccine and treatment plans for Shigella, and other pathogens.

Insight into the Stunting vis a vis Salmonella and Shigella Species among Children of Pakistan

Pakistan is one of the leading countries where the high childhood mortality (under the age of 5 years) as well as is a country where >33% of children are underweight and 38% show stunted growth. The current study investigated the presence or absence of Salmonella and Shigella sp. in stunted children under five years of age from the lower socioeconomic background of Pakistan. Besides, the antibiotics susceptibility patterns were studied along with the sociodemographic and clinical information demographic factors using a questionnaire. The stool samples from stunted children have processed following standard bacteriological protocols and presumptive colonies of Salmonella and Shigella species were identified and sub-cultured on selective media and confirmed by using the standard biochemical test as well as molecular tests. Antibiotics susceptibility of the isolates to 10 antibiotics was tested using disk diffusion assay. The results suggested that 10.5% and 5.7% of the stool samples were positive for Salmonella and Shigella sp. respectively. Moreover, the antibiotics susceptibility test results of the isolates showed that Salmonella sp., were showing higher resistance to amoxicillin whereas Shigella sp. were more resistant to gentamycin. All Salmonella and Shigella isolates were resistant to Rifampicin and 80% of isolates of both were susceptible to ciprofloxacin and cefotaxime. The study suggested that environmental enteric dysfunction (EED), is widespread among malnourished children and may result in stunted growth. The contributory factors such as unsafe farming practices or close association to poultry or livestock animals and prevailing sanitation & hygiene conditions are the potential source of entero-pathogens.

Burden, Antibiotic Resistance, and Clonality of Shigella spp. Implicated in Community-Acquired Acute Diarrhoea in Lilongwe, Malawi

Although numerous studies have investigated diarrhoea aetiology in many sub-Saharan African countries, recent data on Shigella species’ involvement in community-acquired acute diarrhoea (CA-AD) in Malawi are scarce. This study investigated the incidence, antibiotic susceptibility profile, genotypic characteristics, and clonal relationships of Shigella flexneri among 243 patients presenting with acute diarrhoea at a District Hospital in Lilongwe, Malawi. Shigella spp. were isolated and identified using standard microbiological and serological methods and confirmed by identifying the ipaH gene using real-time polymerase chain reaction. The isolates’ antibiotic susceptibility to 20 antibiotics was determined using the VITEK 2 system according to EUCAST guidelines. Genes conferring resistance to sulfamethoxazole (sul1, sul2 and sul3), trimethoprim (dfrA1, dfrA12 and dfrA17) and ampicillin (oxa-1 and oxa-2), and virulence genes (ipaBCD, sat, ial, virA, sen, set1A and set1B) were detected by real-time PCR. Clonal relatedness was assessed using ERIC-PCR. Thirty-four Shigella flexneri isolates were isolated (an overall incidence of 14.0%). All the isolates were fully resistant to sulfamethoxazole/trimethoprim (100%) and ampicillin (100%) but susceptible to the other antibiotics tested. The sul1 (79%), sul2 (79%), sul3 (47%), dfrA12 (71%) and dfrA17 (56%) sulfonamide and trimethoprim resistance genes were identified; Oxa-1, oxa-2 and dfrA1 were not detected. The virulence genes ipaBCD (85%), sat (85%), ial (82%), virA (76%), sen (71%), stx (71%), set1A (26%) and set1B (18%) were detected. ERIC-PCR profiling revealed that the Shigella isolates were genetically distinct and clonally unrelated, indicating the potential involvement of genetically distinct S. flexneri in CA-AD in Malawi. The high percentage resistance to ampicillin and sulfamethoxazole/trimethoprim and the presence of several virulence determinants in these isolates emphasises a need for continuous molecular surveillance studies to inform preventive measures and management of Shigella-associated diarrhoeal infections in Malawi.

Antibiotic susceptibility and genetic relatedness of Shigella species isolated from food and human stool samples in Qazvin, Iran

Objective The aim of this study was to investigate the genetic relatedness and antimicrobial resistance among Shigella species isolated from food and stool samples. Using cross sectional study method, Shigella spp. were isolated from food and clinical samples using culture-based, biochemical and serological methods. Antimicrobial susceptibility and genetic relatedness among the isolates were evaluated using disk diffusion and RAPD-PCR methods respectively. Results The prevalence of Shigella spp. were 4.84 and 7.7% in food and stool samples respectively. All food isolates were Sh. sonnei. 91.42% of the Shigella stool isolates were Sh. sonnei. 62.5% of food isolates were resistant to tetracycline. 46.8, 50 and 65.8% of clinical isolates were resistant to imipenem, amikacin and azithromycin respectively. 50 and 85.7% of the food and clinical isolates respectively were MDR. Dendrogram generated by RAPD-PCR showed that the isolates from food and stool samples were categorized in a same group. Close genetic relatedness between MDR Shigella isolates from food and clinical samples indicate that foods can be considered as one of the main vehicles for transmission of MDR Shigella to human causing acute diseases. Survey of MDR Shigella among food and clinical samples is strongly suggested to be implemented.