<i>Shigella</i> Detection and Molecular Serotyping With a Customized TaqMan Array Card in the Enterics for Global Health (EFGH): <i>Shigella</i> Surveillance Study
Jie Liu, Paul F. Garcia Bardales, Kamrul Islam, Sheikh Jarju, Jane Juma, Chimwemwe Mhango, Queen Saidi Naumanga, Sonia Qureshi, Catherine Sonye, Naveed Ahmed, Fátima Aziz, Md Taufiqur Rahman Bhuiyan, Mary Charles, Nigel A. Cunliffe, Mahamadou Abdou, Sean R. Galagan, Ensa Gitteh, Ibréhima Guindo, M Jahangir Hossain, Abdoulie Jabang, Khuzwayo C. Jere, Flywell Kawonga, Mariama Keita, Noumou Yakhouba Keita, Karen L. Kotloff, Wagner V Shapiama Lopez, Stephen Munga, Maribel Paredes Olórtegui, Richard Omore, Patricia B. Pavlinac, Firdausi Qadri, Farah Naz Qamar, Saifa Raz, Laura Riziki, Francesca Schiaffino, Suzanne Stroup, Sarata Nassoun Traore, Tackeshy Pinedo Vasquez, Mohammad Tahir Yousafzai, Martín Antonio, Jennifer Cornick, Furqan Kabir, Farhana Khanam, Margaret Kosek, John B. Ochieng, James A Platts-Mills, Sharon M. Tennant, Eric R. Houpt
Abstract
Abstract 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.