Epidemiological Characteristics, Antibiotic Resistance Patterns and Genomic Analysis of Shigella Isolated in Pudong, Shanghai During 2013–2024

TL;DR

This study analyzed Shigella bacteria in Shanghai from 2013 to 2024, finding high antibiotic resistance and common strains like S. sonnei and S. flexneri.

Contribution

The study provides a genomic and epidemiological analysis of Shigella isolates in Pudong, Shanghai, highlighting resistance trends and strain types.

Findings

High resistance rates (>90%) to multiple antibiotics like SXT, STR, NAL, AMP, and TET were observed in Shigella isolates.

Multidrug resistance was prevalent, with 97.87% of S. sonnei and 100% of S. flexneri isolates being resistant.

Genomic analysis showed isolates were phylogenetically similar to domestic and international strains of the same sequence types.

Abstract

Background: Shigella spp. are critical pathogens causing diarrheal diseases. This study analyzed the epidemiological characteristics, antimicrobial resistance profiles, virulence factor profiles, and molecular patterns of Shigella isolates in Pudong New Area, Shanghai, from 2013 to 2024. Materials and Methods: Antimicrobial susceptibility of Shigella isolates was determined using the broth microdilution method. All molecular characterization analyses were based on whole-genome next-generation sequencing of Shigella strains. Results: A total of 55 Shigella spp. isolates were obtained from 17,670 enrolled diarrheal cases between 2013 and 2024, including 47 S. sonnei and 8 S. flexneri isolates. Resistance rates to sulfamethoxazole-trimethoprim (SXT), streptomycin (STR), nalidixic acid (NAL), ampicillin (AMP), and tetracycline (TET) all exceeded 90.00%. The resistance rate to azithromycin (AZI) increased from 12.50% to 60.00% with a fluctuating upward trend from 2013 to 2019; 97.87% of S. sonnei and 100.00% of S. flexneri isolates were multidrug-resistant. These isolates harbored multiple resistance genes and virulence factors. S. sonnei was dominated by ST152, while S. flexneri was predominantly ST245. These isolates were phylogenetically close to domestic (Beijing) and international (USA) strains of the same sequence typing collected at different time points, suggesting a common origin and stable transmission characteristics. Conclusion: From 2013 to 2024, the prevalent Shigella species in Pudong were S. sonnei and S. flexneri. Shigella isolates exhibited high resistance rates, and the situation of multidrug resistance was severe. Therefore, strengthening antimicrobial resistance monitoring and controlling regional transmission are of great significance. Meanwhile, genomic surveillance of Shigella ST152/ST245 is recommended for Pudong’s enteric pathogen control programs.

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