Genotypic profiling of an ongoing outbreak of multidrug-resistant linezolid resistant Staphylococcus capitis in private hospitals

This dataset displays data gathered and illustrated in tables and figures format. Table3.1: The distribution of the 119 linezolid resistant multidrug-resistant <em>Staphylococcus capitis</em> isolates arranged by the year of collection, along with age groups, gender and region of the hospitals. Female = F; Male = M; Unknown = U; A = Pretoria; B = Centurion; C = Midrand; D = Johannesburg; E = Limpopo; F = Rustenburg; G = Trichardt Table 3.2: Genes, primers and PCR conditions that were used for the amplification of fragments to identify <em>Staphylococcus capitis</em> and detect plasmid-mediated linezolid resistant mechanisms in <em>S. capitis</em> isolates Table 3.3: The Master mix reaction composition for the M-PCR assay to identify the <em>Staphylococcus capitis</em> isolates and for the detection of the <em>cfr</em> gene in <em>S. capitis</em> isolates Table 3.4: Distribution of 119 linezolid resistant, multidrug-resistant <em>Staphylococcus capitis</em> isolates by year of collection, linezolid resistant minimum inhibitory concentration, and number of antimicrobial agents resistant (MDR). n = number of isolates; U = unknown Figure 3.1: The map displays the locations of hospitals in the greater Gauteng area where isolates were collected. Regions are labelled A to G, hospitals are sub-labelled by numbers and differentiated by color. The size of each label corresponds to the number of isolates collected from that hospital. The map was created using Tableau (Salesforce Inc, USA). Figure 3.2: Dendrogram showing the genetic relatedness of the <em>Staphylococcus capitis</em> isolates in the study. The various pulsotypes are labelled A to E. The blue box outline indicates the isolates that were chosen for WGS.

本数据集收录了以表格与图表形式整理呈现的实验数据。
表3.1：按采集年份分组的119株利奈唑胺耐药多重耐药头状葡萄球菌（*Staphylococcus capitis*）分离株分布情况，同时统计了受试患者的年龄组、性别及所属医院所在地区。性别标注规则为：女性=F，男性=M，未知=U；地区标注规则为：A=比勒陀利亚，B=森图里翁，C=米德兰，D=约翰内斯堡，E=林波波，F=勒斯滕堡，G=特里查德特。
表3.2：用于扩增特异性片段以鉴定头状葡萄球菌，并检测头状葡萄球菌分离株中质粒介导利奈唑胺耐药机制的基因、引物及聚合酶链式反应（Polymerase Chain Reaction，PCR）条件。
表3.3：多重聚合酶链式反应（Multiplex Polymerase Chain Reaction，M-PCR）检测体系的主反应混合液组成，用于鉴定头状葡萄球菌分离株，以及检测头状葡萄球菌分离株中的*cfr*耐药基因。
表3.4：按采集年份、利奈唑胺耐药最低抑菌浓度以及抗菌药物耐药数目（多重耐药，MDR）分组的119株利奈唑胺耐药多重耐药头状葡萄球菌分离株分布情况。其中n代表分离株数量，U代表未知项。
图3.1：展示了分离株采集地——大豪登地区范围内的医院分布地图。地区以A至G标注，医院以数字作为子标注并通过颜色区分，每个标注的尺寸代表从对应医院采集的分离株数量。本地图由美国Salesforce公司旗下的Tableau制作完成。
图3.2：树状聚类图展示了本研究中头状葡萄球菌分离株的遗传相关性。不同脉冲型以A至E标注，蓝色方框框选出了用于全基因组测序（Whole Genome Sequencing，WGS）的分离株。