Elizabethkingia bruuniana Infections in Humans, Taiwan, 2005-2017

Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission

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Identification of closely related (< 50 SNV) clinical and environmental aquatic Elizabethkingia anophelis isolates.

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Identification of a provisional novel species Elizabethkingia umaracha.

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Novel bla_GOB and bla_B carbapenemases and extended spectrum β-lactamase bla_CME alleles identified in Elizabethkingia spp.

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Analysis of the global phylogeny and pangenome of Elizabethkingia spp.

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Identification of novel ICE elements carrying uncharacterised genetic cargo in 67 / 94 (71.3%) of the aquatic environments Elizabethkingia spp.

Elizabethkingia species are ubiquitous in aquatic environments, colonize water systems in healthcare settings and are emerging opportunistic pathogens with reports surfacing in 25 countries across six continents. Elizabethkingia infections are challenging to treat, and case fatality rates are high. Chromosomal bla_B, bla_GOB and bla_CME genes encoding carbapenemases and cephalosporinases are unique to Elizabethkingia spp. and reports of concomitant resistance to aminoglycosides, fluoroquinolones and sulfamethoxazole-trimethoprim are known. Here, we characterized whole-genome sequences of 94 Elizabethkingia isolates carrying multiple wide-spectrum metallo-β-lactamase (bla_Band bla_GOB) and extended-spectrum serine‑β-lactamase (bla_CME) genes from Australian aquatic environments and performed comparative phylogenomic analyses against national clinical and international strains. qPCR was performed to quantify the levels of Elizabethkingia species in the source environments. Antibiotic MIC testing revealed significant resistance to carbapenems and cephalosporins but susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole. Phylogenetics show that three environmental E. anophelis isolates are closely related to E. anophelis from Australian clinical isolates (∼36 SNPs), and a new species, E. umeracha sp. novel, was discovered. Genomic signatures provide insight into potentially shared origins and a capacity to transfer mobile genetic elements with both national and international isolates.

Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019

Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.

Molecular Characteristics and Antimicrobial Susceptibility Profiles of Elizabethkingia Clinical Isolates in Shanghai, China

Purpose

To investigate molecular characteristics and antimicrobial susceptibility profiles of clinical isolates of Elizabethkingia in Shanghai, China.

Methods

Elizabethkingia isolates were collected in a university-affiliated hospital in 2012–2015 and 2017–2018. They were re-identified to species level by 16S rRNA gene and species-specific gene sequencing. Antimicrobial susceptibility testing, screening for metallo-beta-lactamase production, identification of antimicrobial resistance genes and pulsed-field gel electrophoresis (PFGE) were performed.

Results

Among 52 Elizabethkingia isolates, E. anophelis was the most prevalent species (67.3%), followed by E. meningoseptica (26.9%). High carriage rates of bla_CME, bla_BlaB and bla_GOB genes were consistent with the poor in vitro activity of most β-lactams including carbapenems. Nevertheless, β-lactamase inhibitors increased susceptibility rates significantly for cefoperazone and piperacillin. Susceptibility rates for minocycline, tigecycline, rifampin and levofloxacin were 100%, 78.8%, 76.9% and 71.2%, respectively. Ser83Ile or Ser83Arg substitution in the DNA gyrase A unit was associated with resistance to fluoroquinolones. MIC₅₀/MIC₉₀ values of vancomycin and linezolid were 16/16 mg/L and 16/32 mg/L, respectively. Molecular typing showed twenty-one different types of PFGE and more than one indistinguishable isolates were observed in each of the eight subtypes.

Conclusion

Tetracyclines, tigecycline, β-lactam/β-lactamase inhibitor combinations, rifampin and fluoroquinolones demonstrated high rates of in vitro activity against clinical isolates of Elizabethkingia. Both genetic diversity and clonality were observed from this health-care facility. Our report provides potential alternative treatment options for Elizabethkingia infections.

Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence

Bacteria of the genus Elizabethkingia are emerging infectious agents that can cause infection in humans. The number of published whole-genome sequences of Elizabethkingia is rapidly increasing. In this study, we used comparative genomics to investigate the genomes of the six species in the Elizabethkingia genus, namely E. meningoseptica, E. anophelis, E. miricola, E. bruuniana, E. ursingii, and E. occulta. In silico DNA–DNA hybridization, whole-genome sequence-based phylogeny, pan genome analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, and clusters of orthologous groups were evaluated. Of the 86 whole-genome sequences available in GenBank, 21 were complete genome sequences and 65 were shotgun sequences. In silico DNA–DNA hybridization clearly delineated the six Elizabethkingia species. Phylogenetic analysis confirmed that E. bruuniana, E. ursingii, and E. occulta were closer to E. miricola than to E. meningoseptica and E. anophelis. A total of 2,609 clusters of orthologous groups were identified among the six type strains of the Elizabethkingia genus. Metabolism-related clusters of orthologous groups accounted for the majority of gene families in KEGG analysis. New genes were identified that substantially increased the total repertoire of the pan genome after the addition of 86 Elizabethkingia genomes, which suggests that Elizabethkingia has shown adaptive evolution to environmental change. This study presents a comparative genomic analysis of Elizabethkingia, and the results of this study provide knowledge that facilitates a better understanding of this microorganism.

Elizabethkingia Infections in Humans: From Genomics to Clinics

The genus Elizabethkingia has recently emerged as a cause of life-threatening infections in humans, particularly in immunocompromised patients. Several new species in the genus Elizabethkingia have been proposed in the last decade. Numerous studies have indicated that Elizabethkingia anophelis, rather than Elizabethkingia meningoseptica, is the most prevalent pathogen in this genus. Matrix-assisted laser desorption/ionization–time of flight mass spectrometry systems with an extended spectrum database could reliably identify E. anophelis and E. meningoseptica, but they are unable to distinguish the remaining species. Precise species identification relies on molecular techniques, such as housekeeping gene sequencing and whole-genome sequencing. These microorganisms are usually susceptible to minocycline but resistant to most β-lactams, β-lactam/β-lactam inhibitors, carbapenems, and aminoglycosides. They often exhibit variable susceptibility to piperacillin, piperacillin-tazobactam, fluoroquinolones, and trimethoprim-sulfamethoxazole. Accordingly, treatment should be guided by antimicrobial susceptibility testing. Target gene mutations are markedly associated with fluoroquinolone resistance. Knowledge on the genomic characteristics provides valuable insights into in these emerging pathogens.