Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Isolation, Whole-Genome Sequencing, and Analysis of Genomic Features
2.2. Whole Genome-Based Taxonomic Analysis
2.3. Comparative Genomics
3. Results and Discussions
3.1. Genomic Features and Assembling Metrics of the Genomes of the Isolates
3.2. Whole-Genome-Based Taxonomic Analysis
3.3. Predictions of Potential Human Pathogenicity, Resistome, Virulome, and Biosynthetic Gene Clusters
3.4. Comparative Genomics
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Isolate | S4 | S5 |
---|---|---|
Total Contigs | 71 | 132 |
Total Length (bp) | 4,658,088 | 4,442,534 |
Largest Contig (bp) | 329,202 | 135,452 |
N50 (bp) | 89,616 | 39,615 |
GC% | 55.26 | 55.35 |
Coding Genes | 4545 | 4341 |
Non Coding Repeats | 16 | 10 |
Non Coding RNA | 16 | 56 |
Query Strain | Subject Strain | dDDH (d4, in %) | C.I. (d4, in %) | G + C Content Difference (in %) |
---|---|---|---|---|
S4SPAdes.contigs.fa | Enterobacter hormaechei subsp. hoffmannii DSM 14563T | 92.9 | [90.9–94.4] | 0.07 |
S5SPAdes.contigs.fa | Enterobacter hormaechei subsp. hoffmannii DSM 14563T | 92.8 | [90.8–94.4] | 0.01 |
S4SPAdes.contigs.fa | Enterobacter hormaechei subsp. oharae DSM 16687T | 66. | [63.4–69.2] | 0.32 |
S5SPAdes.contigs.fa | Enterobacter hormaechei subsp. oharae DSM 16687T | 66.4 | [63.5–69.3] | 0.24 |
S4SPAdes.contigs.fa | Enterobacter hormaechei subsp. xiangfangensis LMG 27195T | 66.1 | [63.2–69.0] | 0.02 |
S5SPAdes.contigs.fa | Enterobacter hormaechei subsp. xiangfangensis LMG 27195T | 66.2 | [63.2–69.0] | 0.07 |
S4SPAdes.contigs.fa | Enterobacter hormaechei subsp. steigerwaltii DSM 16691T | 66 | [63.0–68.8] | 0.29 |
S5SPAdes.contigs.fa | Enterobacter hormaechei subsp. steigerwaltii DSM 16691T | 65.9 | [62.9–68.7] | 0.21 |
S4SPAdes.contigs.fa | Enterobacter hormaechei ATCC 49162T | 57.3 | [54.5–60.0] | 0.02 |
S5SPAdes.contigs.fa | Enterobacter hormaechei ATCC 49162T | 57.3 | [54.5–60.1] | 0.1 |
S4SPAdes.contigs.fa | Enterobacter bugandensis EB-247T | 35.1 | [32.7–37.6] | 0.74 |
S5SPAdes.contigs.fa | Enterobacter bugandensis EB-247T | 35.3 | [32.8–37.8] | 0.65 |
S4SPAdes.contigs.fa | Enterobacter mori LMG 25706T | 34.2 | [31.7–36.7] | 0.04 |
S5SPAdes.contigs.fa | Enterobacter mori LMG 25706T | 34.3 | [31.9–36.8] | 0.05 |
S4SPAdes.contigs.fa | Enterobacter roggenkampii DSM 16690T | 33.7 | [31.3–36.3] | 0.78 |
S5SPAdes.contigs.fa | Enterobacter roggenkampii DSM 16690T | 34 | [31.5–36.5] | 0.7 |
S4SPAdes.contigs.fa | Enterobacter oligotrophicus HUT 8142T | 33.4 | [31.0–35.9] | 0.96 |
S5SPAdes.contigs.fa | Enterobacter oligotrophicus HUT 8142T | 33.5 | [31.1–36.0] | 1.04 |
S4SPAdes.contigs.fa | Enterobacter cloacae subsp. dissolvens ATCC 23373T | 32 | [29.6–34.5] | 0.1 |
S5SPAdes.contigs.fa | Enterobacter cloacae subsp. dissolvens ATCC 23373T | 32.1 | [29.7–34.6] | 0.18 |
S4SPAdes.contigs.fa | Enterobacter cancerogenus ATCC 33241T | 31.3 | [28.9–33.8] | 0.42 |
S5SPAdes.contigs.fa | Enterobacter cancerogenus ATCC 33241T | 31.4 | [29.0–34.0] | 0.34 |
Virulence Factor Class | Virulence Factors | S4 | S5 |
---|---|---|---|
Type 3 fimbriae | 1 | 1 | |
Type I fimbriae | 8 | 6 | |
Adherence | Curli fibers(Escherichia) | 3 | 2 |
Hemorrhagic E. coli pilus (HCP) (Escherichia) | 2 | 2 | |
Type IV (pili) (Yersinia) | 1 | 1 | |
Antiphagocytosis | Capsule | 15 | 15 |
Efflux pump | AcrAB | 3 | 3 |
Aerobactin | 5 | 5 | |
Ent Siderophore | 12 | 12 | |
Salmochelin | 1 | 1 | |
Iron uptake | Heme transport (Shigella) | 1 | 1 |
Heme uptake (Escherichia) | 2 | 2 | |
Iron/Manganese transport (Escherichia) | 1 | 1 | |
Regulation | RcsAB | 2 | 1 |
T6SS-I | 10 | 9 | |
T6SS-II | 4 | 4 | |
T6SS-III | 0 | 2 | |
EPS type secretion system (Vibrio) | 1 | 1 | |
Flagella (cluster I) (Yersinia) | 32 | 32 | |
Secretion system | Hcp secretion island-1 encoded type VI secretion system (H-T6SS) (Pseudomonas) | 3 | 3 |
SCI-I T6SS (Escherichia) | 1 | 0 | |
T2SS (Yst1) (Yersinia) | 1 | 1 | |
T2SS (Aeromonas) | 1 | 1 | |
TTSS (SPI-encode) (Salmonela) | 1 | 0 | |
Serum resistance | LPS rfb locus | 1 | 1 |
Toxin | Heat-stable cytotonic toxin | 1 | 1 |
Autotransporter | EhaB | 1 | |
Endotoxin | LOS (Haemophilus) | 1 | 1 |
Agf/Csg (Salmonella) | 4 | 4 | |
Fim (Salmonella) | 5 | 5 | |
Fimbrial adherence determinants | Sti (Salmonella) | 1 | 1 |
Stj (Salmonella) | 1 | 0 | |
Stk (Salmonella) | 4 | 4 | |
Invasion | Flagella (Burkholderia) | 6 | 6 |
Motility | Flagella (Bordetella) | 1 | 1 |
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Maguvu, T.E.; Bezuidenhout, C.C. Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa. Microorganisms 2021, 9, 1928. https://doi.org/10.3390/microorganisms9091928
Maguvu TE, Bezuidenhout CC. Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa. Microorganisms. 2021; 9(9):1928. https://doi.org/10.3390/microorganisms9091928
Chicago/Turabian StyleMaguvu, Tawanda E., and Cornelius C. Bezuidenhout. 2021. "Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa" Microorganisms 9, no. 9: 1928. https://doi.org/10.3390/microorganisms9091928