Table 3.

Sample storage and processing descriptions

Specimen collected	Purpose	Tests performed
Stool/flocked rectal swabs	Bacterial ID and storage for AST	Fresh samples/rectal swabs will be cultured to identify Shigella spp., Salmonella spp., Campylobacter spp. and Escherichia coli using standard microbiological methods and biochemically confirmed using bioMérieux’s API strips. All Shigella spp., Salmonella s pp. and Campylobacter spp. isolates, as well as a random subset of E. coli isolates will undergo antibiotic resistance testing using disc diffusion for the following antibiotics: amoxicillin–clavulanic acid (augmentin), ampicillin, azithromycin, chloramphenicol, ciprofloxacin, ceftriaxone, ceftazidime, cefoxitin, gentamicin, imipenem, trimethoprim-sulfamethoxazole, ceftazidime/clavulanate (ESBL), cefotaxime/clavulanate (ESBL). Categorisations of susceptible, intermediate and resistant will be determined using zone-size cut-offs outlined in CLSI interpretive standards.
	Parasite detection	Fresh stool and rectal swabs will be tested for Giardia and Cryptosporidium using the immunoassay Giardia/Cryptosporidium QUIK CHEK.
	Storage	Stool/flocked swabs and colonies of E. coli, Shigella spp., Salmonella spp. and Campylobacter spp. will be stored at −80°C.
Nasopharyngeal swabs	Bacterial isolation, storage and resistance testing	S. pneumoniae colonies will be isolated using standard microbiological or molecular diagnostic protocols and susceptibility testing performed using standard microbiological or molecular techniques. A random subset of S. pneumoniae isolates will undergo antimicrobial resistance testing using disc diffusion for the following antibiotics: amoxicillin–clavulanic acid (Augmentin), ampicillin, azithromycin, chloramphenicol, ciprofloxacin, ceftriaxone, ceftazidime, cefoxitin, imipenem and trimethoprim–sulfamethoxazole. Categorisations of susceptible, intermediate and resistant will be determined using zone-size cut-offs outlined in CLSI interpretive standards.
	Storage	Back-up sample and S. pneumoniae colonies will be will be stored at −80°C.
Blood	HIV and malaria testing	HIV testing will be performed per Kenyan National Guidelines and malaria microscopy performed using standard methods.
	Storage	Plasma and buffy coat will be stored at −80°C. Dried blood spots will be stored at room temperature.

AST, antibiotic susceptibility testing; CLSI, Clinical and Laboratory Standards Institute; E.coli, Escherichia coli; ID, identification; S. pnuemoniae, Streptococcus pneumoniae; spp., species.