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.

Tawanda E Maguvu,Cornelius C Bezuidenhout

doi:10.3390/microorganisms9091928

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.

Highlights

The genus Enterobacter comprises common human pathogens, with the Enterobacter cloacae complex (ECC) species (Enterobacter cloacae subsp. cloacae, Enterobacter asburiae, Enterobacter kobei, Enterobacter hormaechei, Enterobacter ludwigii among others) being notoriously found in hospitals, causing a wide range of infections such as lower respiratory tract infections, urinary tract infections, bacteremia, and meningitis [1,2,3]
The ECC strains are of clinical significance, global surveillance and characterization of the virulence factors associated with these species are still limited [6]
We present whole-genome-based taxonomic classification and comparative genomic analysis of potential human pathogenic E. hormaechei subsp. hoffmannii isolated from chlorinated wastewater

Summary

Introduction

The genus Enterobacter comprises common human pathogens, with the Enterobacter cloacae complex (ECC) species (Enterobacter cloacae subsp. cloacae, Enterobacter asburiae, Enterobacter kobei, Enterobacter hormaechei, Enterobacter ludwigii among others) being notoriously found in hospitals, causing a wide range of infections such as lower respiratory tract infections, urinary tract infections, bacteremia, and meningitis [1,2,3]. Cloacae, Enterobacter asburiae, Enterobacter kobei, Enterobacter hormaechei, Enterobacter ludwigii among others) being notoriously found in hospitals, causing a wide range of infections such as lower respiratory tract infections, urinary tract infections, bacteremia, and meningitis [1,2,3]. The ECC strains are of clinical significance, global surveillance and characterization of the virulence factors associated with these species are still limited [6]. Taxonomic classification of the genus Enterobacter is complicated; recently, Wu et al (2020) updated the taxonomy of Enterobacter species and subspecies based on whole-genome taxonomic analysis [7]. The complexity resulted from the fact that classification in the genus Enterobacter had been defined based on low-resolution analytical methods, and is in need of careful re-examination [8,9,10]. As shown with the current severe acute respiratory syndrome

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