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

Comparative genomics, in particular, pan-genome analysis, provides an in-depth understanding of the genetic variability and dynamics of a bacterial species. Coupled with whole-genome-based taxonomic analysis, these approaches can help to provide comprehensive, detailed insights into a bacterial species. Here, we report whole-genome-based taxonomic classification and comparative genomic analysis of potential human pathogenic Enterobacter hormaechei subsp. hoffmannii isolated from chlorinated wastewater. Genome Blast Distance Phylogeny (GBDP), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) confirmed the identity of the isolates. The algorithm PathogenFinder predicted the isolates to be human pathogens with a probability of greater than 0.78. The potential pathogenic nature of the isolates was supported by the presence of biosynthetic gene clusters (BGCs), aerobactin, and aryl polyenes (APEs), which are known to be associated with pathogenic/virulent strains. Moreover, analysis of the genome sequences of the isolates reflected the presence of an arsenal of virulence factors and antibiotic resistance genes that augment the predictions of the algorithm PathogenFinder. The study comprehensively elucidated the genomic features of pathogenic Enterobacter isolates from wastewaters, highlighting the role of wastewaters in the dissemination of pathogenic microbes, and the need for monitoring the effectiveness of the wastewater treatment process.

Phylogenomic analyses and comparative genomics of Pseudomonas syringae associated with almond (Prunus dulcis) in California

“…Taxonomic assignment of the isolates was based on dDDH, and ANIb, which were in congruence (A3 and A4 in S1 Data ). Whole genome sequencing-based phylogenomic analyses greatly improves the identification of isolates through the elucidation of functional profiles of taxonomic groups, and this can resolve ambiguities in the phylogeny of higher taxa, that would be difficult using traditional approaches [ 8 , 9 , 50 ]. Of the four designated clades, only the P. syringae species complex clade is known to include plant pathogenic bacteria.…”

Augmenting Bacterial Similarity Measures Using a Graph-Based Genome Representation

“…Current taxonomy and identification improvements have focused on using whole genome alignments instead of 16S sequences, particularly for pathogen outbreak tracking and variant differentiation [37, 38]. Some techniques make use of solely vertically transferred genes, which illustrates a choice of genes for phylogenetics [39].…”

Application of Biological Nanopore Sequencing Technology in the Detection of Microorganisms†

“…This study indicated that all strains of pond species were considered multidrug resistant and could lead to the emergence of ESBL bacteria, posing a threat to human health upon exposure. Furthermore, nanopore sequencing technology has also been applied to industrial wastewater, [ 93 ] activated sludge, [ 94 ] animal husbandry, [ 95 ] medical waste, [ 96 ] and other environments.…”