1. STBHUCCB_38510- hypothetical protein S. Typhi
The hypothetical STBHUCCB_38510 gene of P-stx-12, CT 18 and Ty2 strains of S. Typhi has been used as a target to detect S. Typhi via LAMP (Abdullah et al., 2015 and Frickmann et al., 2019). Three sets of primers were designed and their specificity was confirmed using BLAST. Positive LAMP products were successfully digested with HinfI enzyme that was specific only to the amplified STBHUCCB_38510 gene of the S. Typhi, thus allowing its differentiation from closely related bacteria species (e.g., S. Typhimurium and S. Paratyphi A). After in-vitro confirmation of binding characteristics of both LAMP primer sets with culture isolates (n = 112), sensitivity and specificity were 100%. However, low sensitivity and specificity were recorded in an assay of 170 EDTA blood samples using one of the primer sets and some cross-reactivity was also observed.
2. STY2879-Putative Reverse Transcriptase S. Typhi
Kaur et al.,2017 targeted the Gene STY2879 that encodes for a reverse transcriptase protein confirmed to be present in all S. Typhi isolates. Highly sensitive detection of S. Typhi in blood with a 50 CFU/mL titre was achieved using their protocol involving a magnetic nanoparticle-based pre-concentration. The specificity and cross-reactivity were tested against other bacterial isolates of E. coli, S. aureus, P. aeruginosa, A. baumanni, E. faecalis, S. Paratyphi A and K. pneumonia. The proposed method was also evaluated against clinical samples and no cross-reactivity was observed at a high concentration of 106 CFU/mL of other pathogenic bacterial species as compared to a positive control of S. typhi DNA. 
3. STY1607-hypothetical protein S. Typhi
Fan et al., 2015, developed an RT-LAMP method to detect S. Typhi infection but initially performed regular PCR on 48 S. Typhi strains and 75 other strains  including  34 other common Salmonella serotypes, primary enteric pathogens, and some critical febrile microorganisms , in order to test the specificity of primers for their selected target gene(STY1607). The STY1607 gene was amplified from all S. Typhi strains but no others. Sequencing of the PCR amplicons (531 bp) randomly selected from 15 S. Typhi strains showed 100% sequence identity indicating that STY1607 is conserved and can be used as a marker gene for detecting Salmonella Typhi. It also performed well as an RT-LAMP target with a detection limit of 3 CFU/ml in simulated blood and 30 CFU/g in simulated stool samples, which is 10-fold more sensitive than the RT-PCR method.
4. STY0201 -putative fimbrial-like adhesin protein S. typhi
S. typhi-specific qPCR targeting the STY0201 region was carried out by Nga et al., (2010) and Tennant et al.,(2015), reported positive LAMP results using the same region.  However, some false-positive results were recorded for other STY0201 primer sets reported by Frickmann et al., 2019. Even though the focus was on specificity, Both LAMP primer sets showed excellent sensitivity with incubated blood culture materials using the Genie II Mk2 system(Frickmann et al., 2019 ).
5. InvA- Secretory protein S. Typhi
Francois et al., 2011 evaluated the robustness of LAMP targeting the invA gene of S. Typhi. The primers exhibited excellent performance (accurate, sensitive, and specific detection) at a DNA concentration of 0.5pg and were robust to manipulation of sample and reaction parameters.  However, cross-reactivity wasn’t extensively tested as only E. coli strains were used.
6. SSPA2539-Hypothetical Protein S. Paratyphi
Kaur et al., 2019 targeted the SPA2539 gene using a LAMP assay, demonstrating good sensitivity and specificity to S. paratyphi as verified by culture and biochemical tests as well as by qPCR . It was also able to detect the viability of the cells. Cross-reactivity was checked against  E. coli, S. havana, P. aeruginosa, S. typhimurium, A. baumanni, E. faecalis, K. pneumonia, S. aureus, and S. Paratyphi B and no cross-reactivity was observed even at high concentrations (i.e. 106 CFU/mL).
7&8. SSPA2308-Hypothetical Protein and SSPA 1724-ATP Dependent Protease Binding Unit of S.  Paratyphi 
Rojak et al., 2019 designed LAMP primers targeting two genes from S. Paratyphi A: SSPA 2308 hypothetical protein and the SSPA 1724-ATP Dependent Protease Binding Unit.  The primers were tested with DNA from culture isolates and spiked blood cultures against published PCR protocols targeting the same micro-organisms. LAMP proved to be more sensitive and specific (80.0 to 100.0% and 96.1 to 100.0%) using these targets than PCR (65 to 100% and 98.7 to 100%). For the spiked blood LAMP also showed similar results although slightly lower with some primer pairs than PCR. Some cross-reactivity was also observed with one of th e LAMP primers for S. Paratyphi A with S. havana.

Molecular targets for detecting AMR in S. Typhi

Fluoroquinolones and cephalosporins have been reported to be dominantly used antibiotics for the treatment of typhoid fever in Cameroon (Stakeholders engagement). We, therefore, selected AMR target genes affiliated with resistance to fluoroquinolones and cephalosporins. Studies of AMR in Cameroon are limited, so our choice of AMR genes was largely based on studies done in countries neighbouring Cameroon and other African countries. In this study, we test for three AMR target regions in S. Typhi: i) point mutation in gyrA leading to fluoroquinolone resistance, ii) plasmid mediated qnrS gene, and iii) the blaCTX-M gene for CTX-M-1,  (summarized in Table \ref{386515}). The rationale for this is laid out below:
1. Nonsynonymous mutations in the DNA gyrase genes (gyrA) 
The point mutations in DNA gyrases (gyrA and gyrB) and DNA topoisomersae (paraA and paraC) results in reduction of the drug-enzyme binding, and as such, the ability for fluoroquinolones to inhibit DNA ligation is totally restricted \citep{Aldred2012,Barnard_2001} Such mutations have been reported in several African regions including Ghana  \citet{Acheampong2019}, Congo \citet{Phoba2017}\citet{Phoba2017}, Kenya and South Africa  \citet{Al-Emran2016}. A  point mutation in the 83 Ser to Phe in gyrA is the most commonly reported. In this test, we design our primers to address two challenges that would be widely applied to detect point mutations: