Klebsiella spp. are frequently enriched in the gut microbiota of preterm neonates, and overgrowth is associated with necrotizing enterocolitis (NEC), nosocomial infections and late-onset sepsis. Little is known about the genomic and phenotypic characteristics of preterm-associated Klebsiella , as previous studies have focused on the recovery of antimicrobial-resistant isolates or culture-independent molecular analyses. The aim of this study was to better characterize preterm-associated Klebsiella populations using phenotypic and genotypic approaches. Faecal samples from a UK cohort of healthy and sick preterm neonates (n=109) were screened on MacConkey agar to isolate lactose-positive Enterobacteriaceae . Whole-genome sequences were generated for Klebsiella spp., and virulence and antimicrobial resistance genes identified. Antibiotic susceptibility profiling and in vitro macrophage and iron assays were undertaken for the Klebsiella strains. Metapangenome analyses with a manually curated genome dataset were undertaken to examine the diversity of Klebsiella oxytoca and related bacteria in a publicly available shotgun metagenome dataset. Approximately one-tenth of faecal samples harboured Klebsiella spp. ( Klebsiella pneumoniae , 7.3 %; Klebsiella quasipneumoniae , 0.9 %; Klebsiella grimontii , 2.8 %; Klebsiella michiganensis , 1.8 %). Isolates recovered from NEC- and sepsis-affected infants and those showing no signs of clinical infection (i.e. ‘healthy’) encoded multiple β-lactamases. No difference was observed between isolates recovered from healthy and sick infants with respect to in vitro siderophore production (all encoded enterobactin in their genomes). All K. pneumoniae , K. quasipneumoniae , K. grimontii and K. michiganensis faecal isolates tested were able to reside and persist in macrophages, indicating their immune evasion abilities. Metapangenome analyses of published metagenomic data confirmed our findings regarding the presence of K. michiganensis in the preterm gut. There is little difference in the phenotypic and genomic characteristics of Klebsiella isolates recovered from healthy and sick infants. Identification of β-lactamases in all isolates may prove problematic when defining treatment regimens for NEC or sepsis, and suggests that healthy preterm infants contribute to the resistome. Refined analyses with curated sequence databases are required when studying closely related species present in metagenomic data.

中文翻译：

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早产儿拥有多种克雷伯氏菌种群，包括编码和产生一系列抗菌素耐药性和毒力相关因子的非典型物种。


克雷伯菌属早产儿肠道微生物群中经常富集，过度生长与坏死性小肠结肠炎 (NEC)、医院感染和迟发性败血症有关。人们对早产相关克雷伯氏菌的基因组和表型特征知之甚少，因为之前的研究重点是抗菌素耐药菌株的恢复或不依赖于培养物的分子分析。本研究的目的是利用表型和基因型方法更好地表征与早产相关的克雷伯氏菌群体。在麦康凯琼脂上对英国健康和患病早产新生儿队列 ( n = 109) 的粪便样本进行筛选，以分离出乳糖阳性肠杆菌科细菌。生成了克雷伯菌属的全基因组序列，并鉴定了毒力和抗菌素耐药性基因。对克雷伯氏菌菌株进行了抗生素敏感性分析以及体外巨噬细胞和铁测定。使用手动整理的基因组数据集进行元泛基因组分析，以检查公开可用的鸟枪法宏基因组数据集中催产克雷伯氏菌和相关细菌的多样性。大约十分之一的粪便样本含有克雷伯菌属。 （肺炎克雷伯菌，7.3%；准肺炎克雷伯菌，0.9%；格里蒙克雷伯氏菌，2.8%；密歇根克雷伯氏菌，1.8%）。从受 NEC 和败血症影响的婴儿以及那些没有表现出临床感染迹象（即“健康”）的婴儿中回收的分离株编码多种 β-内酰胺酶。从健康婴儿和患病婴儿中回收的分离株在体外铁载体产生方面没有观察到差异（基因组中均编码肠杆菌素）。所有测试的肺炎克雷伯菌、准肺炎克雷伯菌、格里蒙氏克雷伯菌和密歇根克雷伯菌粪便分离株都能够在巨噬细胞中驻留并持续存在，表明它们具有免疫逃避能力。对已发表的宏基因组数据的宏基因组分析证实了我们关于早产儿肠道中存在密歇根克雷伯菌的发现。从健康婴儿和患病婴儿中回收的克雷伯氏菌分离株的表型和基因组特征几乎没有差异。在确定 NEC 或败血症的治疗方案时，对所有分离株中的 β-内酰胺酶进行鉴定可能会产生问题，并表明健康的早产儿对耐药组有贡献。在研究宏基因组数据中存在的密切相关物种时，需要使用精选的序列数据库进行精细分析。