Draft genome sequences of Salmonella enterica subsp. enterica serovar Give sequence type 516 isolated from blood and brain abscess of a child from North India

TL;DR

This paper presents draft genome sequences of a Salmonella strain isolated from a child's blood and brain abscess in North India.

Contribution

The study provides new genomic data for Salmonella Give sequence type 516, including its antibiotic resistance gene aac(6′)-Iaa.

Findings

The draft genomes are 4,690,901 bp and 4,703,054 bp in size.

The genomes were assembled into 64 and 67 contigs respectively.

The genomes contain the antibiotic resistance gene aac(6′)-Iaa.

Abstract

Invasive non-typhoidal Salmonellae remains a substantial cause of morbidity and mortality. Here, we present the draft genome sequences of Salmonella Give ST516, isolated from blood and brain abscess of a child. The genome sizes are 4,690,901 bp and 4,703,054 bp, assembled in 64 and 67 contigs respectively, and possess aac(6′)-Iaa.

Figures

(a) Circular genome of S. Give ST516 study strains (OSS 712 and OSS 713), compared with S. Typhimurium LT2 (reference strain) plotted from the Artemis tool (version 1.8.0.0) using DNA plotter, with default parameter (14). The outer scale is marked in megabases. The tracks from the outside represent (1) Salmonella Typhimurium LT2 forward CDS; (2) Salmonella Typhimurium LT2 reverse CDS; (3) Salmonella Give (OSS-712) forward CDS; (4) Salmonella Give (OSS-712) reverse CDS; (5) Salmonella Give (OSS-713) forward CDS; (6) Salmonella Give (OSS-713) reverse CDS; (7) %GC plot; and (8) GC skew. (b) WGS-based SNP phylogenetic tree of S. Give ST516 study strains (OSS-712 and OSS-713) were compared with S. Typhimurium LT2 (reference strain) and global blood isolates (n = 10) available at EnteroBase (version 1.2.0). The SNP analysis was done using CSI phylogeny (version 1.4) tool, and the phylogenetic tree was visualized in iTOL (version 6.0).

Tables

TABLE 1. Result of antimicrobial susceptibility testing (AST) and summary of genome characteristics of Salmonella Give (n = 2) clinical isolates

AST and genome characteristic	Result for sample ID:
	OSS-712	OSS-713
Source of isolation	Blood	Brain abscess
AST profilea	Amp (S), C (S), T (S), Q (S), Nal (S), Cip (S), 3Cs (S), St (S), G (S), Ak (S), Az (S), AmC (S)	Amp (s), C (s), T (s), Q (S), Nal (S), Cip (S), 3Cs (S), St (S), G (S), Ak (S), Az (S), AmC (S)
Genome size (bp)	4,690,901	4,703,054
No. of reads	983,448	1,118,588
Mean read length (bp)	268	261
No. of contigs	64	67
G+C content (%)	52.22	52.21
N 75	94,979	79,869
N 50	283,930	283,928
Genes (total)	4,589	4,592
CDSs (total)	4,479	4,485
Genes (coding)	4,298	4,311
CDSs (with protein)	4,298	4,311
rRNA (5S, 16S, 23S)	8, 11, 10	8, 9, 10
tRNA	72	71
ncRNAs	9	9
Virulence genes	fimA, pefB, safB, mgtB, misL, invA, ssaC, cdtB, pltA	fimA, pefB, safB, mgtB, misL, invA, ssaC, cdtB, pltA
AMR gene	aac(6′)Iaa	aac(6′)Iaa
ST type (MLST)	516 (aroC_84, dnaN_11, hemD_16, hisD_42, purE_40, sucA_71, thrA_4)	516 (aroC_84, dnaN_11, henD_16, hisD_42, purE_40, sucA_71, thrA_4)
GenBank accession number	JAYGAW000000000	JAYGAX000000000
SRA accession number	SRR28409737	SRR28409736

Full text

ANNOUNCEMENT

Invasive non-typhoidal salmonellosis can be fatal, particularly in children and elderly adults (1). Salmonella enterica subsp. enterica serovar Give was previously reported from ruminants and pigs in Quebec (2, 3). Human infection through consumption of contaminated meat products was reported in the US and Europe (4). Here, we report the draft genome sequences of Salmonella Give ST516, isolated from a child.

A 3-year-old female child with acute encephalopathy syndrome was admitted to the paediatric ward of PGIMER, Chandigarh, India, in December 2022. The patient’s paired peripheral blood samples were collected before starting antibiotic treatment. A brain abscess specimen was taken from the left-sided subdural abscess in operation theater under general anesthesia. The specimens were collected with parental consent and as a part of the treatment protocol. Samples were inoculated in sheep blood agar (BD BBL) and MacConkey agar (BD, Difco) followed by 16 hours of incubation at 37°C. The isolates were identified as Salmonella in MALDI-TOF (Biomerieux) and were sent to ICMR-NIRBI, where they were confirmed as S. Give by serotyping (5, 6). The isolates were susceptible to the tested antibiotics as detected by the Kirby-Bauer disk-diffusion method (Table 1). For the isolation of gDNA, bacterial colonies were inoculated into tryptic soy broth (BD, Bacto) and incubated at 37°C for 16 hours. gDNA was extracted using DNeasy blood and tissue kit (Qiagen), quantified in Qubit 3.0 fluorometer. DNA libraries were prepared for single-end sequencing (400 bp chemistry) using Ion Xpress Plus Fragment Library Kit as per the user manual (Thermo Fisher Scientific, TFS). First, the gDNA was sheared using Ion Shear Plus 10× Reaction Buffer and Enzyme Mix II (TFS) followed by adapter ligation and nick repairing. The DNA was size selected using E-Gel Size Select II Agarose Gel as per the NGS library size selection reference (400 bp) and sequenced on the IonTorrent-S5 platform using Ion530 chip (TFS). Read filtering and trimming were performed by BaseCaller module, inbuilt into Torrent-Suite Software (version 5.16.1) (7). Reads were assembled in contigs using the de novo assembler SPAdes (version 13.3.0) (8). Contigs were annotated by Prokaryotic Genome Annotation Pipeline (version 6.6) of NCBI (9). The annotated assemblies were investigated for the presence of antimicrobial resistance genes (ARGs), plasmids, and sequence types using ResFinder (4.6.0) (10), PlasmidFinder (2.1) (11), and MLST (2.0) (11), respectively, available at Centre for Genomic Epidemiology (11). The virulence genes were determined using Virulence Factor Database (4.0) (12). Default parameters were used for all the analyses.

The genome sizes of OSS-712 and OSS-713 were 4,690,901 bp and 4,703,054 bp, respectively, with an average G+C content of 52%. The genomic features and circular genome plot of the isolates are presented in Table 1; Fig. 1a, respectively. The isolates were pan-susceptible with no notable ARGs, except aac(6′)-Iaa, which is a chromosomal, cryptic gene present in most Salmonella serovars (13).

(a) Circular genome of S. Give ST516 study strains (OSS 712 and OSS 713), compared with S. Typhimurium LT2 (reference strain) plotted from the Artemis tool (version 1.8.0.0) using DNA plotter, with default parameter (14). The outer scale is marked in megabases. The tracks from the outside represent (1) Salmonella Typhimurium LT2 forward CDS; (2) Salmonella Typhimurium LT2 reverse CDS; (3) Salmonella Give (OSS-712) forward CDS; (4) Salmonella Give (OSS-712) reverse CDS; (5) Salmonella Give (OSS-713) forward CDS; (6) Salmonella Give (OSS-713) reverse CDS; (7) %GC plot; and (8) GC skew. (b) WGS-based SNP phylogenetic tree of S. Give ST516 study strains (OSS-712 and OSS-713) were compared with S. Typhimurium LT2 (reference strain) and global blood isolates (n = 10) available at EnteroBase (version 1.2.0). The SNP analysis was done using CSI phylogeny (version 1.4) tool, and the phylogenetic tree was visualized in iTOL (version 6.0).

The phylogenetic relationship of the study strains was compared by WGS-based SNP analysis with only the available blood isolates (n = 10) of S. Give ST516 available at EnteroBase (version 1.2.0) (15) in CSI phylogeny (version 1.4) (16). The phylogenetic tree (Fig. 1b) revealed that the Indian isolates were closely related to the USA isolate (SAMN07135360), which was also pan-susceptible. These sequences will serve as references from this region for comparative global genome analysis.