Laboratory of Molecular Biology, Genomics and Bioinformatics, Department of Biology, Faculty of Nature and Life Sciences, University Hassiba Benbouali, Chlef, Algeria.
Pathogen Genomics Center, National Institute of Infectious Diseases (NIID), Tokyo, Japan.
BMC Microbiol. 2023 Nov 16;23(1):342. doi: 10.1186/s12866-023-03087-2.
Diabetic foot infections (DFIs) are the most common complications of diabetic foot ulcers (DFUs), and a significant cause of lower extremity amputation. In this study we used whole genome sequencing to characterize the clonal composition, virulence and resistance genetic determinants of 58 Staphylococcus/Mammaliicoccus spp. isolates from contralateral healthy skin and DFU from 44 hospitalized patients.
S. aureus (n = 32) and S. epidermidis (n = 10) isolates were recovered from both DFUs and healthy skin, whereas, S. haemolyticus (n = 8), M. sciuri (n = 1), S. hominis (n = 1) and S. simulans (n = 3) were recovered exclusively from healthy skin. In contrast, S. caprae (n = 2) and S. saprophyticus (n = 1) were recovered only from DFUs. Among S. aureus isolates, MRSA were present with high prevalence (27/32, 84.4%), 18 of which (66.7%) were from DFUs and 9 (33.3%) from healthy skin. In contrast, the coagulase-negative Staphylococcus (CoNS)/Mammaliicoccus isolates (n = 26), in particular S. epidermidis and S. haemolyticus were more prevalent in healthy skin, (10/26, 38.5%) and (8/26, 30.8%), respectively. MLST, spa and SCCmec typing classified the 32 S. aureus isolates into 6 STs, ST672, ST80, ST241, ST1, ST97, ST291 and 4 unknown STs (STNF); 8 spa types, t044, t037, t3841, t1247, t127, t639, t937 and t9432 and 2 SCCmec types, type IV and type III(A). Among CoNS, the S. epidermidis isolates belonged to ST54, ST35 and ST640. S. haemolyticus belonged to ST3, ST25, ST29, ST1 and ST56. The sole M. sciuri isolate was found to carry an SCCmec type III(A). A wide range of virulence genes and antimicrobial resistance genes were found among our isolates, with varying distribution between species or STs. The pan-genome analysis revealed a highly clonal population of Staphylococcus isolates, particularly among S. aureus isolates. Interestingly, the majority of S. aureus isolates including MRSA, recovered from the healthy skin and DFUs of the same patient belonged to the same clone and exhibited similar virulence/resistance genotype.
Our study provides clinically relevant information on the population profile, virulence and antibiotic resistance of Staphylococcus/Mammaliicoccus spp. in DFIs, which could serve as a basis for further studies on these as well as other groups of pathogens associated with DFIs.
糖尿病足感染（DFI）是糖尿病足溃疡（DFU）最常见的并发症，也是下肢截肢的重要原因。在这项研究中，我们使用全基因组测序技术来描述 44 名住院患者的对侧健康皮肤和 DFU 中 58 株金黄色葡萄球菌/乳球菌属分离株的克隆组成、毒力和耐药遗传决定因素。
从 DFU 和健康皮肤中均分离到金黄色葡萄球菌（n=32）和表皮葡萄球菌（n=10）分离株，而溶血葡萄球菌（n=8）、松鼠葡萄球菌（n=1）、人葡萄球菌（n=1）和相似葡萄球菌（n=3）仅从健康皮肤中分离到。相比之下，山羊葡萄球菌（n=2）和腐生葡萄球菌（n=1）仅从 DFU 中分离到。在金黄色葡萄球菌分离株中，耐甲氧西林金黄色葡萄球菌（MRSA）的患病率很高（27/32，84.4%），其中 18 株（66.7%）来自 DFU，9 株（33.3%）来自健康皮肤。相比之下，凝固酶阴性葡萄球菌（CoNS）/乳球菌属分离株（n=26），特别是表皮葡萄球菌和溶血葡萄球菌在健康皮肤中更为普遍，分别为 10/26（38.5%）和 8/26（30.8%）。MLST、spa 和 SCCmec 分型将 32 株金黄色葡萄球菌分离株分为 6 个 ST，ST672、ST80、ST241、ST1、ST97 和 ST291 和 4 个未知 ST（STNF）；8 个 spa 型，t044、t037、t3841、t1247、t127、t639、t937 和 t9432 和 2 个 SCCmec 型，IV 型和 III(A)型。在 CoNS 中，表皮葡萄球菌分离株属于 ST54、ST35 和 ST640。溶血葡萄球菌属于 ST3、ST25、ST29、ST1 和 ST56。唯一的松鼠葡萄球菌分离株携带 SCCmec III(A)型。我们的分离株中发现了广泛的毒力基因和抗生素耐药基因，其分布在不同的物种或 ST 之间存在差异。泛基因组分析显示，金黄色葡萄球菌分离株具有高度的克隆种群，特别是在金黄色葡萄球菌分离株中。有趣的是，从同一患者的健康皮肤和 DFU 中分离到的大多数金黄色葡萄球菌包括耐甲氧西林金黄色葡萄球菌（MRSA）都属于同一克隆，并且表现出相似的毒力/耐药基因型。
我们的研究提供了有关 DFIs 中金黄色葡萄球菌/乳球菌属的群体特征、毒力和抗生素耐药性的临床相关信息，可为进一步研究这些以及与 DFIs 相关的其他病原体组提供依据。
