Baborski Anna, Barth Stefanie A, Jung Elke Martina, Bloos Frank, Rödel Jürgen, Löffler Bettina, Bauer Michael, Busch Anne
Department of Anaesthesiology and Intensive Care Medicine, University Hospital Jena, Am Klinikum 1, 07747, Jena, Germany.
Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
BMC Genom Data. 2025 Aug 12;26(1):56. doi: 10.1186/s12863-025-01346-x.
Enterobacter cloacae complex is a group of common opportunistic pathogens on intensive care units. On intensive care units sepsis is treated with high doses of antibiotics. This treatment does not only eliminate pathogenic bacteria but parts of the microbiome community as well. This leads to an imbalance of the gut microbiome. However, some bacteria can survive such treatment due to certain survival and resistance mechanisms. Not only antibiotic resistance mechanisms but also forming strong communities via biofilm formation promotes cell survival. Here, we investigated the properties of the isolate AT70PIP076 from a sepsis patient treated with piperacillin and tazobactam. After biochemical analysis and MALDI-TOF analysis, the strain was found to be Enterobacter cloacae. In addition to in vitro, antimicrobial susceptibility testing the genome was further investigated in situ regarding antibiotic resistance. Further live/dead staining was performed, and the biofilm formation was investigated using confocal laser microscopy (cLSM). The genome shows the presence of biofilm-associated genes EU554560, bcsABZC_AP010953, ehaB, KF662843, and crl. The understanding of the underlying mechanism of survival of potential pathogens might contribute to elucidate potential treatment options.ObjectivesGenomic analysis of a bacterium that can survive antibiotic treatment within the gut of an antibiotictreated patient to elucidate survival and resistance mechanisms.Data descriptionThe isolate AT70PIP076 was isolated in 2021 from feces collected from a patient treated with Piperacillin and tazobactam. Whole genome DNA was isolated using the Nextera DNA Flex microbial colony extraction protocol and the Nextera Flex DNA preparation kit according to the manufacturer's instructions. Following paired-end sequencing was performed on the MiSeq platform (Illumina, Inc., San Diego, CA, USA) using a 300-cycle MiSeq reagent kit and a read length of 151 bp. Contamination check and identification of 16 S RNA sequences was done by using ContESt16S. The genomic sequence contained 4,988,237 bp and the G + C content is represented at 54.80%. This genome and its associated data set will serve as a useful resource for further analyses.
阴沟肠杆菌复合体是重症监护病房中一组常见的机会致病菌。在重症监护病房，败血症采用高剂量抗生素治疗。这种治疗不仅会消灭病原菌，还会破坏部分微生物群落。这会导致肠道微生物群失衡。然而，由于某些生存和耐药机制，一些细菌能够在这种治疗中存活下来。不仅抗生素耐药机制，而且通过形成生物膜形成强大的群落也能促进细胞存活。在此，我们研究了从一名接受哌拉西林和他唑巴坦治疗的败血症患者分离出的菌株AT70PIP076的特性。经过生化分析和基质辅助激光解吸电离飞行时间质谱分析，该菌株被鉴定为阴沟肠杆菌。除了进行体外抗菌药敏试验外，还对该基因组的抗生素耐药性进行了原位进一步研究。进一步进行了活/死染色，并使用共聚焦激光显微镜（cLSM）研究了生物膜的形成。该基因组显示存在与生物膜相关的基因EU554560、bcsABZC_AP010953、ehaB、KF662843和crl。了解潜在病原体生存的潜在机制可能有助于阐明潜在的治疗方案。
目的
对一名接受抗生素治疗的患者肠道内能够在抗生素治疗中存活的细菌进行基因组分析，以阐明其生存和耐药机制。
数据描述
菌株AT70PIP076于2021年从一名接受哌拉西林和他唑巴坦治疗的患者的粪便中分离得到。按照制造商的说明，使用Nextera DNA Flex微生物菌落提取方案和Nextera Flex DNA制备试剂盒分离全基因组DNA。随后，使用300循环的MiSeq试剂试剂盒和151 bp的读长，在MiSeq平台（美国加利福尼亚州圣地亚哥市Illumina公司）上进行双端测序。使用ContESt16S进行污染检查和16S RNA序列鉴定。基因组序列包含4,988,237 bp，G + C含量为54.80%。该基因组及其相关数据集将作为进一步分析的有用资源。
