Nocardia huaxiensis sp. nov., an actinomycete isolated from human skin

Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021

A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.

Nocardia sputi sp. nov. isolated from the sputum of patients with pulmonary infection

Two Gram-stain-positive, aerobic and rod-shaped actinomycetes (strains CY18T and CY8) were isolated from the sputum of two patients with pulmonary infections, and their taxonomic status was investigated. The 16S rRNA gene sequences and the results of phylogenetic analyses indicated that CY18T and CY8 were identical (100 %) and were most closely related to Nocardia beijingensis CGMCC 4.1521T (99.9 %) and Nocardia araoensis NBRC 100135T (99.5 %). The predominant cellular fatty acids of CY18T and CY8 were C16 : 0, C18 : 0, C18 : 1ω9c and summed feature 3 (comprising C16 : 1ɷ7c and/or C16 : 1ɷ6c), and the major menaquinone was MK-8(H4ω-cycl).The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The whole-cell hydrolytic sugar pattern consisted of arabinose and glucose. The polar lipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two unidentified phospholipids, three unidentified glycolipids and two unidentified lipids.The DNA G+C contents of CY18T and CY8 were 67.9 and 68.0 % respectively. The digital DNA–DNA hybridization and average nucleotide identity values between the two novel strains and closely related species were well under the 70 % and 95–96 % thresholds, respectively, but these values between the two novel strains were 95.5 % and 99.5 %, respectively. On the basis of morphological and chemotaxonomic characteristics and the results of phylogenetic analyses, strains CY18T and CY8 represent a novel species of the genus Nocardia , for which the name Nocardia sputi sp. nov. is proposed. The type strain is CY18T (=GDMCC 1.3318T = JCM 33932T).

Case Report: First Case of Endophthalmitis Caused by an Emerging Pathogen: Nocardia huaxiensis

Nocardia endophthalmitis is a relatively uncommon form of endophthalmitis seen in clinical patients. In general, Nocardia endophthalmitis tends to carry a poor prognosis. Here, we report a 3-year-old child who was admitted to the hospital due to a rupture of the left eye. The suturing and anterior chamber formation were performed immediately. Approximately, 16 days after the operation, massive whitish plump and tufted exudates gathered in the pupil area and at the bottom of the anterior chamber, and the child was diagnosed with endophthalmitis. The infection was initially considered to be caused by fungal pathogens for that the hyphae and spores were observed in the smear. However, the isolate obtained after 4 days of culturation was identified as actinomycetes using MALDI–TOF. We further classified it as Nocardia huaxiensis by next-generation sequencing (NGS) based on the MinION platform. Amikacin and sulfamethoxazole tablets were used to control the infection and the ocular inflammation subsided gradually. Intraocular lens (IOL) implantation is planned to be performed at an appropriate future time to improve his vision. Nocardia endophthalmitis is rare and usually caused by ocular trauma or surgery. In conclusion, Nocardia huaxiensis should be considered as an emerging pathogen and deserves more attention.