Carbapenemase dendogram fragment
Typing Services

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Similar to its close relative E. coli, Shigella species are a common cause of diarrheal disease, which is often bloody and may be severe enough to require hospitilization (1). Shigella are atypical, however, in that their only animal hosts are primates. Hence, transmission is primarily fecal-oral, involving water and foods contaminated with sewage or through contact with infected individuals (who may be asymptomatic but continue to shed Shigella). Most infections acquired domestically involve children (e.g., within day care centers), with the remainder commonly associated with travel to developing countries.  On the other hand, a 2010 outbreak involving over 100 culture-confirmed cases of shigellosis was traced to an Illinois Subway restaurant and specifically two of its food handlers (2).  More recently, U.S. outbreaks have been identified in homeless persons and men who have sex with men (3).  A contributing factor is Shigella’s notably low infectious dose, estimated at <100 bacteria.


Shigella infection is routinely diagnosed by culture from stool specimens, although this is being challenged by the emergence of culture-independent diagnostic tests, in particular multiplex GI panels based on stool DNA (4,5).  In the U.S. and other developed countries, the two most commonly encountered Shigella species, identified by conventional serotyping, are S. sonnei (Group D) and S. flexneri (Group B), responsible for roughly two-thirds and one-third of infections, respectively.  In the  developing world, these are joined by S. boydii (Group C) and S. dysenteriae (Group A), the latter notorious for causing deadly epidemics.

For Shigella outbreak detection and investigation, and for source and epidemiological tracking, strain typing is required. Conventional typing methods include serotyping, phage typing, and PFGE.  Their limitations, however, have motivated the development of additional methods including MLST (6), MLVA (7), and whole genome sequencing-based SNP analysis (8,9).  The latter offers the highest resolution, but its high cost – for reagents, equipment, and highly trained laboratory and bioinformatics personnel – precludes its widespread use.  Each of these methods require pure cultures, and hence are incompatible with culture-independent diagnosis.

To address the need for an affordable, user-friendly Shigella typing service, MicrobiType offers ShMT1 and ShMT2.  Both yield high strain resolution, general concordance with serotype, and ability to distinquish epidemiologically related and unrelated strains (see ShMT1 dendrogram and ShMT2 dendrogram).  These strengths are further enhanced by combining these services (at discounted price).  Furthermore, as with other PLST services, they offer the potential for typing directly from stool DNA (contact us for further information regarding culture-independent services).


With respect to treatment, shigellosis is generally self-limiting; however, more serious cases require antibiotics, most commonly ciprofloxacin or azithromycin.  This is complicated by resistance, particularly in strains acquired through international travel, but increasingly recognized in domestic cases as well (1).  MicrobiType offers Ent-gyrA and 23S-rDNA sequencing services that can be used to confirm and identify molecular mechanisms of resistance to ciprofloxacin and azithromycin, respectively, and epidemiologically track their spread.

Results are reported in sequence alignment and dendrogram formats, illustrating the relatedness of the submitted isolate to concurrently or previously submitted isolates from your lab, and to representative GenBank database strains.

(3) Hines JZ et al, 2016. Shigellosis outbreak among men who have sex with men and homeless persons - Oregon, 2015–2016. MMWR 65:812.
(4) Zhang H et al, 2015. Multiplex polymerase chain reaction tests for detection of pathogens associated with gastroenteritis. Clin Lab Med 35:461.
(5) Huang RS et al, 2016. Performance of the Verigene enteric pathogens test, Biofire FilmArray gastrointestinal panel and Luminex xTAG gastrointestinal pathogen panel for detection of common enteric pathogens. Diagn Microbiol Infect Dis 86:336.
(6) Yang J et al, 2007. Revisiting the molecular evolutionary history of Shigella spp. J Mol Evol 64:71.
(7) Chiou CS et al, 2009. Utility of multilocus variable-number tandem-repeat analysis as a molecular tool for phylogenetic analysis of Shigella sonnei. J Clin Microbiol 47:1149.
(8) McDonnell J et al, 2013. Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK. Epidemiol Infect 141:2568.

(9) Zhang N et al, 2014. Genomic portrait of the evolution and epidemic spread of a recently emerged multidrug-resistant Shigella flexneri clone in China. J Clin Microbiol 52:1119.

(MicrobiType services are for research/investigational use only.)