Training of anti-Staphylococcus aureus phages against S. epidermidis multidrug-resistant isolates is associated with inter- and intra-sequence type host range specificity

Phage therapy is considered a promising option in the face of antibiotic multidrug-resistant bacteria, including staphylococci. However, most anti-staphylococcal phages have been characterized in S. aureus, while a limited number of studies investigated phage activity against S. epidermidis. We studied the potential of phage training to extend the host range of two types of anti-S. aureus phages against S. epidermidis isolates. The Appelmans protocol was applied to a mixture of Kayvirus and a mixture of Silviavirus phages repeatedly exposed to seven S. epidermidis strains representative of nosocomial-associated sequence types (ST), including ST2. We observed increased activity only for the Kayvirus mixture against two of these strains (ST2 or ST35). Phage subpopulations isolated from the training mixture using these two strains (five/strain) exhibited different evolved phenotypes, active only against their isolation strain or strains against which they had never been exposed but of the same ST. Of note, 16/47 ST2 strains were susceptible to one of the groups of trained phages. Genomic analyses were conducted to identify potential bacterial determinants of this specificity. A comparative analysis of ancestral and trained phage genomes found numerous recombination events between two of the three ancestors. A small number of trained phage genes had nucleotide sequence modifications impacting the corresponding protein compared to ancestral phages, two-to-four of them being specific of each group of phage subpopulations exhibiting different host range. The results suggest that anti-S. aureus phages can be adapted to S. epidermidis isolates but with inter- and intra-ST specificity.噬菌体疗法（Phage therapy）被视为应对包括葡萄球菌（staphylococci）在内的抗生素多重耐药菌（multidrug-resistant bacteria）的极具前景的治疗选择。然而，绝大多数抗葡萄球菌噬菌体的研究均以金黄色葡萄球菌（S. aureus）为对象，针对表皮葡萄球菌（S. epidermidis）开展噬菌体活性研究的报道相对有限。本研究旨在探究通过噬菌体驯化拓展两类抗金黄色葡萄球菌噬菌体对表皮葡萄球菌分离株的宿主范围（host range）的可行性。本研究采用Appelmans方案，将凯病毒属（Kayvirus）混合噬菌体与西尔维亚病毒（Silviavirus）混合噬菌体反复暴露于7株代表医院相关序列型（sequence types, ST）的表皮葡萄球菌菌株，其中包含ST2型菌株。结果显示，仅凯病毒属混合噬菌体对其中2株菌株（ST2型或ST35型）的裂解活性有所提升。利用这2株菌株从驯化混合噬菌体中分离得到的噬菌体亚群（phage subpopulations，每株菌株分离得到5个亚群）呈现出不同的进化表型：部分仅能裂解其分离所用的菌株，另一部分则可裂解从未接触过但属于同一序列型的菌株。值得注意的是，47株ST2型表皮葡萄球菌中有16株可被某一组驯化噬菌体裂解。为明确该宿主特异性潜在的细菌决定因子，本研究开展了基因组分析（genomic analyses）。对祖先噬菌体与驯化噬菌体的基因组进行比较分析后发现，3株祖先噬菌体中的2株之间发生了大量重组事件（recombination events）。与祖先噬菌体相比，少量驯化噬菌体基因发生了影响对应蛋白功能的核苷酸序列修饰（nucleotide sequence modifications），其中每一组具有不同宿主范围的噬菌体亚群均带有2~4个特异性突变基因。本研究结果表明，抗金黄色葡萄球菌噬菌体可被改造为可裂解表皮葡萄球菌分离株的噬菌体，但这种改造后的宿主范围具有序列型间和序列型内的特异性。