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Abstract：
BACKGROUND: Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS).
RESULTS: We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently.
CONCLUSIONS: Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.
RESULTS: We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently.
CONCLUSIONS: Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.
摘要：
背景：培养分离株的可靠菌种鉴定在临床细菌学中至关重要。我们建立了一种名为NOVA-新型生物体验证和分析的新研究算法，以系统分析无法通过常规鉴定程序MALDI-TOFMS和使用全基因组测序（WGS）的部分16SrRNA基因测序进行表征的细菌分离株。
结果：我们总共鉴定了35个代表潜在新物种的细菌菌株。棒状杆菌属。（n=6）和Schaaliasp。(n=5)是优势属。在缺氧球菌属中各鉴定出2株,梭菌属,Desulfovibrio,和Peptoniphilus，在柠檬酸杆菌中发现了一个新物种，Dermabacter,Helcococcus,Lancefieldella,奈瑟菌,嗜铬杆菌(布鲁氏菌),拟芽孢杆菌,泛菌,卟啉单胞菌,假杆菌,假单胞菌,嗜冷杆菌,Pusillimonas,Rothia,Sneathia,还有Tessaracocus.从深层组织标本或血液培养物中分离出35个菌株中的27个。鉴定的35个分离菌株中有7个是临床相关的。此外,使用WGS分析只能在物种水平上鉴定的26种细菌菌株，主要是最近被鉴定/分类的生物。
结论：我们的新算法被证明是检测和鉴定新型细菌生物的强大工具。公开的临床和基因组数据可能有助于更好地了解其临床和生态作用。我们鉴定了35个新菌株，其中7种似乎与临床相关，显示了尚未定义的各种未描述的病原体。
结果：我们总共鉴定了35个代表潜在新物种的细菌菌株。棒状杆菌属。（n=6）和Schaaliasp。(n=5)是优势属。在缺氧球菌属中各鉴定出2株,梭菌属,Desulfovibrio,和Peptoniphilus，在柠檬酸杆菌中发现了一个新物种，Dermabacter,Helcococcus,Lancefieldella,奈瑟菌,嗜铬杆菌(布鲁氏菌),拟芽孢杆菌,泛菌,卟啉单胞菌,假杆菌,假单胞菌,嗜冷杆菌,Pusillimonas,Rothia,Sneathia,还有Tessaracocus.从深层组织标本或血液培养物中分离出35个菌株中的27个。鉴定的35个分离菌株中有7个是临床相关的。此外,使用WGS分析只能在物种水平上鉴定的26种细菌菌株，主要是最近被鉴定/分类的生物。
结论：我们的新算法被证明是检测和鉴定新型细菌生物的强大工具。公开的临床和基因组数据可能有助于更好地了解其临床和生态作用。我们鉴定了35个新菌株，其中7种似乎与临床相关，显示了尚未定义的各种未描述的病原体。
