Molecular diagnostics and next-generation sequencing reveal real etiological characteristics of invasive Salmonella infection in febrile illness in Freetown, Sierra Leone

Figures & data

Figure 1. Laboratory procedure and results from examining patient blood samples.

Table 1. Characteristics of the patients enrolled in this study.

Body temperature (°C), n (%)	37-37.5	37.5-38	38–39	39–40	>40
Total	53 (19.49%)	40 (14.71%)	122 (44.85%)	54 (19.85%)	3 (1.10%)
Widal test	28 (32.18%)	9 (10.34%)	26 (29.89%)	21 (24.14%)	3 (3.45%)
Age (years), n (%)	<5	6–18	19–30	31–50	51–60	>60	unknown
Total	16 (5.88%)	45 (16.54%)	86 (31.62%)	82 (30.15%)	15 (5.51%)	10 (3.68%)	18 (6.62%)
Widal test	11 (12.64%)	19 (21.84%)	26 (29.89%)	25 (28.74%)	4 (4.60%)	1 (1.15%)	1 (1.15%)
Occupations, n (%)	student	worker	housekeeper	trader	farmer	medical worker	teacher	fisherman	food maker	driver	police	sporadic children	others
Total	95 (34.93%)	40 (14.71%)	25 (9.19%)	20 (7.35%)	13 (4.78%)	11 (4.04%)	11 (4.04%)	9 (3.31%)	5 (1.84%)	2 (0.74%)	2 (0.74%)	2 (0.74%)	37 (13.60%)
Widal test	44 (50.57%)	14 (16.09%)	7 (8.05%)	0 (0%)	1 (1.15%)	5 (5.75%)	1 (1.15%)	2 (2.30%)	4 (4.60%)	0 (0%)	2 (2.30%)	0 (0%)	7 (8.05%)
Symptoms, n (%)	headache	chill	bellyache	jaundice	arthralgia	oliguria or anuria or gross	eyelid edema	diarrhea	relative infrequent pulse	purpura	petechiae or ecchymosi
Total	228 (83.82%)	139 (51.10%)	81 (29.78%)	64 (23.53%)	23 (8.46%)	18 (6.62%)	9 (3.31%)	9 (3.31%)	6 (2.21%)	6 (2.21%)	1 (0.37%)
Widal test	66 (75.86%)	36 (41.38%)	21 (24.14%)	18 (20.69%)	21 (24.14%)	14 (16.09%)	7 (8.05%)	4 (4.60%)	4 (4.60%)	0 (0%)	1 (1.15%)

Figure 2. Mapping of genome assemblies for P. putida, E. coli, and Salmonella generated from ONT MinION reads to the respective reference genomes (P. putida: NC_021505.1, E. coli: NC_000913.3, and Salmonella: NC_003197.2). The mean sequencing coverage for the P. putida, E. coli, and Salmonella genomes assembled in this study was approximately 39.8%, 80.1%, and 57.1%, respectively.

Figure 3. Comparison of the genome sequence of the WGH-01_Typhi isolate obtained in Sierra Leone with other S. Typhi complete genome sequences.

Figure 4. Phylogenetic analysis of the S. Typhi isolate obtained in the present study conducted with sequences from GenBank. The phylogenetic analysis was conducted on the S. Typhi isolate from our study outpatients and on another 105 S. Typhi sequences retrieved from GenBank. The genomes of S. Paratyphi A (GCA000026565), S. Typhimurium (GCA000006945), and S. Enteritidis (GCA000750395) were used as outgroups.