Ribosomal MLST nucleotide identity (rMLST-NI), a rapid bacterial species identification method: application to Klebsiella and Raoultella genomic species validation

Bacterial genomics is making an increasing contribution to the fields of medicine and public health microbiology. Consequently, accurate species identification of bacterial genomes is an important task, particularly as the number of genomes stored in online databases increases rapidly and new species are frequently discovered. Existing database entries require regular re-evaluation to ensure that species annotations are consistent with the latest species definitions. We have developed an automated method for bacterial species identification that is an extension of ribosomal multilocus sequence typing (rMLST). The method calculates an ‘rMLST nucleotide identity’ (rMLST-NI) based on the nucleotides present in the protein-encoding ribosomal genes derived from bacterial genomes. rMLST-NI was used to validate the species annotations of 11839 publicly available Klebsiella and Raoultella genomes based on a comparison with a library of type strain genomes. rMLST-NI was compared with two whole-genome average nucleotide identity methods (OrthoANIu and FastANI) and the k-mer based Kleborate software. The results of the four methods agreed across a dataset of 11839 bacterial genomes and identified a small number of entries (n=89) with species annotations that required updating. The rMLST-NI method was 3.5 times faster than Kleborate, 4.5 times faster than FastANI and 1600 times faster than OrthoANIu. rMLST-NI represents a fast and generic method for species identification using type strains as a reference.

Metabacillus rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants

A Gram-positive, endospore-forming, rod-shaped and aerobic bacterium, with swarming and swimming motility, designated strain DBTR6^T, was isolated from the rhizosphere soil of tomato plants. Strain DBTR6^T grew at 20-45 ℃ (optimum 30-37℃), pH 4-9 (optimum 7-8) and at salinities from 0 to 5% (optimum 1%). Phylogenetic analysis using 16S rRNA gene sequences showed this strain belonged to the genus Metabacillus and was most closely related to Metabacillus litoralis DSM 16303 ^T (98.3%) and Metabacillus sediminilitoris MCCC 1K03777^T (98.3%). The DNA G + C content of the genomic DNA was 36.4%. The digital DNA-DNA hybridization value between strain DBTR6^T and reference strains M. sediminilitoris MCCC 1K03777^T and "M. bambusae" BG109^T were less than 70% (26.7% and 26.0%), and the average nucleotide identity score were less than 95% (78.55% and 78.38%), and the Amino Acid Identity values calculated were less than 96% (79.99% and 80.18%), respectively, suggesting that strain DBTR6^T represented a novel species in the genus Metabacillus. Chemotaxonomic analysis showed that strain DBTR6^T contained MK-7 as the major respiratory quinone. The predominant fatty acids (> 10.0%) were iso-C_15:0, anteiso-C_15:0 and C_16:0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), glycolipids (GL) and three unidentified lipids (L). Based on the differential physiological properties, biochemical characteristics and genotypic data, strain DBTR6^T represents a novel species of the genus Metabacillus, for which the name Metabacillus rhizolycopersici sp. nov. is proposed. The type strain is DBTR6^T (= ACCC 61900 ^T = JCM 35080 ^T).

Klebsiella oxytoca Complex: Update on Taxonomy, Antimicrobial Resistance, and Virulence

Klebsiella oxytoca is actually a complex of nine species-Klebsiella grimontii, Klebsiella huaxiensis, Klebsiella michiganensis, K. oxytoca, Klebsiella pasteurii, Klebsiella spallanzanii, and three unnamed novel species. Phenotypic tests can assign isolates to the complex, but precise species identification requires genome-based analysis. The K. oxytoca complex is a human commensal but also an opportunistic pathogen causing various infections, such as antibiotic-associated hemorrhagic colitis (AAHC), urinary tract infection, and bacteremia, and has caused outbreaks. Production of the cytotoxins tilivalline and tilimycin lead to AAHC, while many virulence factors seen in Klebsiella pneumoniae, such as capsular polysaccharides and fimbriae, have been found in the complex; however, their association with pathogenicity remains unclear. Among the 5,724 K. oxytoca clinical isolates in the SENTRY surveillance system, the rates of nonsusceptibility to carbapenems, ceftriaxone, ciprofloxacin, colistin, and tigecycline were 1.8%, 12.5%, 7.1%, 0.8%, and 0.1%, respectively. Resistance to carbapenems is increasing alarmingly. In addition to the intrinsic bla_OXY, many genes encoding β-lactamases with varying spectra of hydrolysis, including extended-spectrum β-lactamases, such as a few CTX-M variants and several TEM and SHV variants, have been found. bla_KPC-2 is the most common carbapenemase gene found in the complex and is mainly seen on IncN or IncF plasmids. Due to the ability to acquire antimicrobial resistance and the carriage of multiple virulence genes, the K. oxytoca complex has the potential to become a major threat to human health.

Proposal for reunification of the genus Raoultella with the genus Klebsiella and reclassification of Raoultella electrica as Klebsiella electrica comb. nov

The order Enterobacterales was divided into seven families including the family Enterobacteriaceae in 2016. The genus Klebsiella within the family Enterobacteriaceae was divided into two genera Klebsiella and Raoultella in 2001. Here, our phylogenomic analysis shows that the genus Raoultella is nested within the genus Klebsiella. Klebsiella and Raoultella together are monophyletic and share average amino acid identities (AAIs) of 86.9-89.6% above the AAI threshold (86%) for genus delimitation within the family Enterobacteriaceae. Klebsiella and Raoultella share AAIs of 79.9%-85.0% with the other genera within the subfamily "Klebsiella clade", which are in the range of inter-genus AAIs (74‒85%) within the family Enterobacteriaceae. Klebsiella and Raoultella also share six known conserved signature indels. Therefore, we propose to reunify Klebsiella and Raoultella to the single genus Klebsiella and reclassify Raoultella electrica as Klebsiella electrica comb. nov. Our genome-based taxonomic analyses also identified seven potential novel species within the unified genus Klebsiella.

Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae

During a citywide microbiological screening project in Pavia (Italy) a bacterial strain isolated from the surface of an Automated Teller Machine was classified as a Klebsiella sp. by MALDI-TOF spectrometry, and shown to be susceptible to the most antimicrobial classes by phenotypic testing. After Illumina genome sequencing and subsequent assembly, a high-quality draft genome was obtained (size = 5,051,593 bp, N50 = 615,571 bp, largest contig = 1,328,029 bp, N_contig = 17, GC content = 51.58%, coverage = 141.42), absence of antimicrobial resistance genes was confirmed, but the strain resulted to be highly divergent from all Klebsiella, and more related to other Enterobacteriaceae. The higher values of 16S rRNA identity were with members of the genera Citrobacter, Salmonella, and “Superficieibacter.” An ortholog-based phylogenomic analysis indicated a sister group relationship with “Superficieibacter electus,” in a distinct clade from other members of the Enterobacteriaceae family. In order to evaluate whether the novel genome represents a new species of “Superficiebacter,” average nucleotide identity (ANI) and Hadamard analysis were performed on a dataset of 78 Enterobacteriaceae. The novel genome showed an ANI of 87.51% with S. electus, which compared on identity values between other members of the family, clearly indicates that the genome represents a new species within the genus “Superficieibacter.” We propose for the new species the name “Superficieibacter maynardsmithii.”