Whole genome sequencing indicates Corynebacterium jeikeium comprises 4 separate genomospecies and identifies a dominant genomospecies among clinical isolates

Abstract

Corynebacterium jeikeium is an opportunistic pathogen which has been noted for significant genomic diversity. The population structure within this species remains poorly understood. Here we explore the relationships among fifteen clinical isolates of C. jeikeium (reference strains K411 and ATCC 43734, and 13 primary isolates collected over a period of 7 years) through genetic, genomic, and phenotypic studies. We report a high degree of divergence among strains based on 16S ribosomal RNA (rRNA) gene and rpoB gene sequence analysis, supporting the presence of genetically distinct subgroups. Whole genome sequencing indicates genomic-level dissimilarity among subgroups, which qualify as 4 separate and distinct Corynebacterium species based on an Average Nucleotide Identity (ANIb) threshold of < 95%. Functional distinctions in antibiotic susceptibilities and metabolic profiles characterize two of these genomospecies, allowing their differentiation from others through routine laboratory testing. The remaining genomospecies can be classified through a biphasic approach integrating phenotypic testing and rpoB gene sequencing. The genomospecies predominantly recovered from patient specimens does not include either of the existing C. jeikeium reference strains, implying that studies of this pathogen would benefit from examination of representatives from the primary disease-causing group. The clinically dominant genomospecies also has the smallest genome size and gene repertoire, suggesting the possibility of increased virulence relative to the other genomospecies. The ability to classify isolates to one of the four C. jeikeium genomospecies in a clinical context provides diagnostic information for tailoring antimicrobial therapy and may aid in identification of species-specific disease associations.

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

“…Although none of the classifications by the clinical laboratory were overtly different from the closest-matched genome identified for any given isolate, 12% (76/612) of isolates receiving a species-level classification displayed <95% ANIb to the specified taxon, and thus represented a genomospecies distinct from the given clinical classification. Novel genomospecies were unevenly distributed across bacterial genera; at the extremes, all isolates from the genera Escherichia , Lactobacillus , and Proteus were grouped with a previously reported genome, whereas all isolates from the genera Neisseria and Corynebacterium fell below a 95% ANIb identity to previously reported genomes ( S3 Fig ), likely reflecting the high degree of genomic diversity inherent to those lineages [ 29 , 30 ].…”

“…After the completion of isolate collection, sequencing libraries were constructed in serial batches of ~192 organisms each, using the same lots of reagents in order to limit batch effects. Sequencing libraries were prepared as described elsewhere [ 30 ], with the addition of a size selection step to enrich for library fragments 400–900 bp in size. Sequencing was performed using Illumina HiSeq 2000 and Illuimina MiSeq platforms with 101 bp paired end reads.…”

Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases

“…The most common applications of NGS in diagnostic microbiology laboratories ( Figure 2) include (1) whole-genome sequencing (sequencing and assembly of the genome of a pathogen of interest [eg, evaluating genetic relatedness during outbreak investigations, identification of new species]) [5][6][7]; (2) targeted NGS with different methods for enrichment including amplification or probe hybridization (ie, 16S rDNA bacterial profiling or PCR amplification of other specified targets followed by NGS) [7,8]; or (3) mNGS (defined in more detail below) [9]. We refer the reader to other publications on this topic that summarize common terms and approaches used in DNA sequence analysis [10], the different NGS technologies [11][12][13], and the various NGS methods, bioinformatics tools [14] and clinical applications [10,15].…”

Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents

“…However, these authors emphasized that human and animal strains do vary in their biochemical properties and 16S rRNA gene sequence analysis lacks the precision and accuracy offered by whole-genome sequencing (WGS) [16]. WGS (using “next-generation” DNA sequencing technologies) has allowed the broad examination of the genomic content and population structure of bacterial species [17]. The use of comparative genomics facilitates the differentiation of bacteria at the molecular level allowing for the characterization of the pangenome, i.e., the entire gene set of all strains of a given species, and the evolutionary relationships among related species [18].…”