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Complete genome sequences and genomic characterization of five plasmids harbored by environmentally persistent Cronobacter sakazakii strains ST83 H322 and ST64 GK1025B obtained from powdered infant formula manufacturing facilities
Gut Pathogens ( IF 4.3 ) Pub Date : 2022-06-06 , DOI: 10.1186/s13099-022-00500-5
Flavia J Negrete 1, 2 , Katie Ko 1, 2 , Hyein Jang 1 , Maria Hoffmann 3 , Angelika Lehner 4 , Roger Stephan 4 , Séamus Fanning 5, 6 , Ben D Tall 1 , Gopal R Gopinath 1
Affiliation  

Cronobacter sakazakii is a foodborne pathogen that causes septicemia, meningitis, and necrotizing enterocolitis in neonates and infants. The current research details the full genome sequences of two extremely persistent C. sakazakii strains (H322 and GK1025B) isolated from powdered infant formula (PIF) manufacturing settings. In addition, the genetic attributes associated with five plasmids, pH322_1, pH322_2, pGK1025B_1, pGK1025B_2, and pGK1025B_3 are described. Using PacBio single-molecule real-time (SMRT®) sequencing technology, whole genome sequence (WGS) assemblies of C. sakazakii H322 [Sequence type (ST)83, clonal complex [CC] 83) and GK1025B (ST64, CC64) were generated. Plasmids, also sequenced, were aligned with phylogenetically related episomes to determine, and identify conserved and missing genomic regions. A truncated ~ 13 Kbp type 6 secretion system (T6SS) gene cluster harbored on virulence plasmids pH322_2 and pGK1025B_2, and a second large deletion (~ 6 Kbp) on pH322_2, which included genes for a tyrosine-type recombinase/integrase, a hypothetical protein, and a phospholipase D was identified. Within the T6SS of pH322_2 and pGK1025B_2, an arsenic resistance operon was identified which is in common with that of plasmids pSP291_1 and pESA3. In addition, PHASTER analysis identified an intact 96.9 Kbp Salmonella SSU5 prophage gene cluster in pH322_1 and pGK1025B_1 and showed that these two plasmids were phylogenetically related to C. sakazakii plasmids: pCS1, pCsa767a, pCsaC757b, pCsaC105731a. Plasmid pGK1025B_3 was identified as a novel conjugative Cronobacter plasmid. Furthermore, WGS analysis identified a ~ 16.4 Kbp type 4 secretion system gene cluster harbored on pGK1025B_3, which contained a phospholipase D gene, a key virulence factor in several host–pathogen diseases. These data provide high resolution information on C. sakazakii genomes and emphasizes the need for furthering surveillance studies to link genotype to phenotype of strains from previous investigations. These results provide baseline data necessary for future in-depth investigations of C. sakazakii that colonize PIF manufacturing facility settings and genomic analyses of these two C. sakazakii strains and five associated plasmids will contribute to a better understanding of this pathogen's survival and persistence within various “built environments” like PIF manufacturing facilities.

中文翻译:

从粉状婴儿配方奶粉生产设施中获得的环境持久性阪崎克罗诺杆菌菌株 ST83 H322 和 ST64 GK1025B 所携带的五个质粒的完整基因组序列和基因组特征

阪崎克罗杆菌是一种食源性病原体,可引起新生儿和婴儿的败血症、脑膜炎和坏死性小肠结肠炎。目前的研究详细介绍了从婴儿配方奶粉 (PIF) 制造环境中分离出的两种极其持久的阪崎肠杆菌菌株(H322 和 GK1025B)的全基因组序列。此外,还描述了与五个质粒 pH322_1、pH322_2、pGK1025B_1、pGK1025B_2 和 pGK1025B_3 相关的遗传属性。使用 PacBio 单分子实时 (SMRT®) 测序技术,对 C. sakazakii H322 [序列类型 (ST)83、克隆复合物 [CC] 83) 和 GK1025B (ST64、CC64) 的全基因组序列 (WGS) 组装生成。质粒也被测序,与系统发育相关的附加体进行比对,以确定和鉴定保守和缺失的基因组区域。截短的~13 Kbp 6 型分泌系统 (T6SS) 基因簇包含在毒力质粒 pH322_2 和 pGK1025B_2 上,以及 pH322_2 上的第二个大缺失 (~ 6 Kbp),其中包括酪氨酸型重组酶/整合酶的基因,一种假设的蛋白质, 并鉴定出磷脂酶 D。在 pH322_2 和 pGK1025B_2 的 T6SS 中,鉴定出与质粒 pSP291_1 和 pESA3 相同的抗砷操纵子。此外,PHASTER 分析在 pH322_1 和 pGK1025B_1 中鉴定了一个完整的 96.9 Kbp 沙门氏菌 SSU5 前噬菌体基因簇,并表明这两个质粒在系统发育上与 C. sakazakii 质粒相关:pCS1、pCsa767a、pCsaC757b、pCsaC105731a。质粒 pGK1025B_3 被鉴定为一种新型的共轭克罗诺杆菌质粒。此外,WGS 分析确定了约 16 个。4 Kbp 4 型分泌系统基因簇包含在 pGK1025B_3 上,其中包含一个磷脂酶 D 基因,这是几种宿主-病原体疾病的关键毒力因子。这些数据提供了有关 C. sakazakii 基因组的高分辨率信息,并强调需要进一步开展监测研究,将基因型与先前研究中菌株的表型联系起来。这些结果为未来深入研究 C. sakazakii 提供了必要的基线数据,这些 C. sakazakii 定植于 PIF 制造设施设置和这两种 C. sakazakii 菌株和五个相关质粒的基因组分析将有助于更好地了解这种病原体在各种环境中的存活和持久性“建筑环境”,如 PIF 制造设施。几种宿主-病原体疾病的关键毒力因子。这些数据提供了有关 C. sakazakii 基因组的高分辨率信息,并强调需要进一步开展监测研究,将基因型与先前研究中菌株的表型联系起来。这些结果为未来深入研究 C. sakazakii 提供了必要的基线数据,这些 C. sakazakii 定植于 PIF 制造设施设置和这两种 C. sakazakii 菌株和五个相关质粒的基因组分析将有助于更好地了解这种病原体在各种环境中的存活和持久性“建筑环境”,如 PIF 制造设施。几种宿主-病原体疾病的关键毒力因子。这些数据提供了有关 C. sakazakii 基因组的高分辨率信息,并强调需要进一步开展监测研究,将基因型与先前研究中菌株的表型联系起来。这些结果为未来深入研究 C. sakazakii 提供了必要的基线数据,这些 C. sakazakii 定植于 PIF 制造设施设置和这两种 C. sakazakii 菌株和五个相关质粒的基因组分析将有助于更好地了解这种病原体在各种环境中的存活和持久性“建筑环境”,如 PIF 制造设施。sakazakii 基因组,并强调需要进一步的监测研究,将基因型与先前研究中菌株的表型联系起来。这些结果为未来深入研究 C. sakazakii 提供了必要的基线数据,这些 C. sakazakii 定植于 PIF 制造设施设置和这两种 C. sakazakii 菌株和五个相关质粒的基因组分析将有助于更好地了解这种病原体在各种环境中的存活和持久性“建筑环境”,如 PIF 制造设施。sakazakii 基因组,并强调需要进一步的监测研究,将基因型与先前研究中菌株的表型联系起来。这些结果为未来深入研究 C. sakazakii 提供了必要的基线数据,这些 C. sakazakii 定植于 PIF 制造设施设置和这两种 C. sakazakii 菌株和五个相关质粒的基因组分析将有助于更好地了解这种病原体在各种环境中的存活和持久性“建筑环境”,如 PIF 制造设施。
更新日期:2022-06-06
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