Shigella Detection and Molecular Serotyping With a Customized TaqMan Array Card in the Enterics for Global Health (EFGH): Shigella Surveillance Study

Background

Quantitative polymerase chain reaction (qPCR) targeting ipaH has been proven to be highly efficient in detecting Shigella in clinical samples compared to culture-based methods, which underestimate Shigella burden by 2- to 3-fold. qPCR assays have also been developed for Shigella speciation and serotyping, which is critical for both vaccine development and evaluation.

Methods

The Enterics for Global Health (EFGH) Shigella surveillance study will utilize a customized real-time PCR-based TaqMan Array Card (TAC) interrogating 82 targets, for the detection and differentiation of Shigella spp, Shigella sonnei, Shigella flexneri serotypes, other diarrhea-associated enteropathogens, and antimicrobial resistance (AMR) genes. Total nucleic acid will be extracted from rectal swabs or stool samples, and assayed on TAC. Quantitative analysis will be performed to determine the likely attribution of Shigella and other particular etiologies of diarrhea using the quantification cycle cutoffs derived from previous studies. The qPCR results will be compared to conventional culture, serotyping, and phenotypic susceptibility approaches in EFGH.

Conclusions

TAC enables simultaneous detection of diarrheal etiologies, the principal pathogen subtypes, and AMR genes. The high sensitivity of the assay enables more accurate estimation of Shigella-attributed disease burden, which is critical to informing policy and in the design of future clinical trials.

Imported spring onions related to the first recorded outbreak of enteroinvasive Escherichia coli in Denmark, November to December 2021

Between November and December 2021, the first ever recorded outbreak of enteroinvasive Escherichia coli in Denmark occurred at national scale. We describe the investigation of this outbreak, which was initially recognised in early December 2021. A total of 88 cases (58 female; 30 male) with a median age of 52 years (range: 0-91) were detected by PCR-based diagnostic methods. Case ascertainment was complicated by current culture-free diagnostic procedures, with only 34 cases confirmed by culture, serotyping and whole genome sequencing. Isolates from cases grouped into two serotypes (O136:H7 and O96:H19), which was supported by whole-genome-sequence-phylogeny, also yielding two clusters. Interviews of 42 cases and traceback investigation pointed towards consumption of ready-to-eat salads as the outbreak cause. While the ready-to-eat salads comprised different vegetables, imported spring onions were the only common ingredient and thus the likely source. Environmental investigations failed to recover outbreak strains. This report highlights the value of fast typing (here O-typing) to confirm cases in an outbreak situation. Timely communication and data sharing are also important, and were facilitated by the national collaboration between relevant laboratories, the public health institute and the veterinary and food administration. High hygiene standards for imported fresh vegetables intended for ready-to-eat products are essential.

Outbreak of gastroenteritis highlighting the diagnostic and epidemiological challenges of enteroinvasive Escherichia coli, County of Halland, Sweden, November 2017

An outbreak of gastroenteritis with 83 cases occurred at a conference venue in November 2017 in Halland County, Sweden. Stool samples from two venue visitors and a symptomatic secondary case attributed to household transmission were PCR-positive for the ipaH gene, a target found in both Shigella spp. and enteroinvasive Escherichia coli (EIEC). EIEC was isolated from stool samples and whole genome sequencing analysis confirmed EIEC O96:H19 to be the aetiological agent. A cohort study was conducted among venue attendees and employees and the findings implicated contaminated leafy greens as the vehicle of infection, however, no microbiological evidence could support the study results. Here, we report the investigation into the first recorded EIEC outbreak in Sweden and illustrate the challenges associated with the differential laboratory diagnostics of Shigella/EIEC in an outbreak setting.

High Rates of Antimicrobial Resistance and Virulence Gene Distribution Among Shigella spp. Isolated from Pediatric Patients in Tehran, Iran

Background

Shigella continues to be important causes of acute pediatric diarrhea worldwide. Shigella produces numerous virulence factors involved in colonization and invasion into epithelial cells which eventually result in the disease. The present study was conducted to evaluate the prevalence of virulence genes and to investigate antibiotic resistance profiles among Shigella isolates obtained from pediatric patients in Iran.

Methods

A total of 141 Shigella isolates were collected between March 2017 and September 2018 from stool of children under 14 who were suspected to have shigellosis. Shigella isolates were identified using standard microbiological and serological tests and antimicrobial susceptibility testing was carried out via Kirby–Bauer disk diffusion method. In addition, the presence of seven virulence determinants including ipaH, ipaB, ipaC, ipaD, ipgD, sen, and virA were evaluated using PCR.

Results

S. sonnei (78.7%) was the most prevalent shigella spp. among children with shigellosis followed by S. flexneri (19.9%) and S. boydii (1.4%). Antimicrobial susceptibility testing revealed that most of the isolates were considered as multidrug-resistant (MDR) strains. Our findings also showed a high resistance rate against trimethoprim-sulfamethoxazole in Shigella isolates. The prevalence of ipaH, ipaC, sen, ipaD, virA, ipaB, and ipgD were 100%, 95.7%, 95.7%, 94.3%, 93.6%, 92.9%, and 80.8%, respectively.

Conclusion

The current study revealed that S. sonnei was the predominant species isolated from children with shigellosis in Iran. Our results also indicated a high distribution of type III secretion system effector protein-encoding genes and high multidrug-resistance among shigella spp. in Iran. Therefore, it is suggested that antimicrobial susceptibility testing be performed prior to antibiotic prescription.

True Prevalence of Shigellosis in Indian Children with Acute Gastroenteritis: Have We Been Missing the Diagnosis?

BACKGROUND

Shigella is responsible for high morbidity and mortality among children, yet its true prevalence remains inconclusive. The aim of this study was to determine the actual prevalence of Shigella infection in childhood diarrhea and dysentery cases and assess the applicability of ipaH gene PCR in Indian settings.

METHODS

This study was conducted at Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi, India during 2011-12. A total of 385 children (207 with diarrhea, 118 with dysentery, and 60 matched controls) were enrolled. Stool samples were cultured, and the suspected colonies were analyzed using biochemical reactions and serotyping. Antimicrobial susceptibility testing was done using disc diffusion method. ipaH-gene PCR was performed directly on stool samples collected from 180 randomly selected patients (60 from each group).

RESULTS

Shigella was isolated using conventional culture methods in 8.2% (95% CI: 5.1%, 12.8%), 33.1% (95% CI: 25.2%, 42.0%), and 0% in the diarrhea, dysentery and control cases, respectively. High resistance was seen towards co-trimoxazole, nalidixic acid, fluoroquinolones, doxycycline and several beta-lactams drugs. Actual prevalence of shigellosis was determined using ipaH gene PCR to be 18.3% (95% CI: 10.4% - 30.1%) diarrhea cases and 56.7% (95% CI: 44.1, 68.4%) dysentery cases. One (1.7%, 95% CI: 0.01%, 9.7%) control specimen also yielded positive result in PCR.

CONCLUSIONS

Correct diagnosis of shigellosis is essential to start antimicrobial therapy in selected cases. The prevalence of Shigella / EIEC infection in children is much higher than previously estimated. Despite its high costs and other limitations, we recommend the use of ipaH-gene PCR as a routine tool in the management of childhood acute gastroenteritis cases.

Molecular detection of lactose fermenting enteroinvasive Escherichia coli from patients with diarrhea in Tehran-Iran

BACKGROUND AND OBJECTIVES

Enteroinvasive Escherichia coli (EIEC) is one the cause of acute diarrhea and bacillary dysentery in developing countries. Routine diagnostic microbiology tests are not capable to distinguish EIEC from other pathogenic or non-pathogenic E. coli. PCR, targeting ipaH, virF, virB and other virulence genes, is a diagnostic method for detecting E. coli pathotypes. Using PCR, we identified EIEC by PCR targeting ipaH and virF genes among E.coli isolates from patients with diarrhea at the selected hospitals in Tehran.

MATERIALS AND METHODS

Isolates of E. coli were cultured from 140 specimens of patients with diarrhea using culture and IMViC test. DNA was extracted using commercial kits and and tested for uidA, ipaH and virF genes by PCR.

RESULTS

Totally, 140 E. coli isolates were confirmed by IMViC tests and PCR targeting uidA gene. Of 140 E. coli isolates, 5 (3.6%) were positive for the ipaH gene, 4 (2.9%) contained virF gene and 4 (2.9%) were positive for both ipaH and virF genes.

CONCLUSION

These results indicated that EIEC is a considerable acute diarrheagenic pathogen in adults and infants. Moreover, virF gene is suggested for evaluation of invasiveness of EIEC.