ISEM, Université de Montpellier, CNRS, IRD, 34095 Montpellier, France.
Service de Dermatologie, Centre Hospitalier Andrée Rosemon, Cayenne 97306, French Guiana.
Int J Mol Sci. 2023 Sep 6;24(18):13727. doi: 10.3390/ijms241813727.
The identification of an emerging pathogen in humans can remain difficult by conventional methods such as enrichment culture assays that remain highly selective, require appropriate medium and cannot avoid misidentifications, or serological tests that use surrogate antigens and are often hampered by the level of detectable antibodies. Although not originally designed for this purpose, the implementation of polymerase-chain-reaction (PCR) has resulted in an increasing number of diagnostic tests for many diseases. However, the design of specific molecular assays relies on the availability and reliability of published genetic sequences for the target pathogens as well as enough knowledge on the genetic diversity of species and/or variants giving rise to the same disease symptoms. Usually designed for clinical isolates, molecular tests are often not suitable for environmental samples in which the target DNA is mixed with a mixture of environmental DNA. A key challenge of such molecular assays is thus to ensure high specificity of the target genetic markers when focusing on clinical and environmental samples in order to follow the dynamics of disease transmission and emergence in humans. Here we focus on the Buruli ulcer (BU), a human necrotizing skin disease mainly affecting tropical and subtropical areas, commonly admitted to be caused by worldwide although other mycolactone-producing mycobacteria and even mycobacterium species were found associated with BU or BU-like cases. By revisiting the literature, we show that many studies have used non-specific molecular markers (IS, IS, KR-B) to identify from clinical and environmental samples and propose that all mycolactone-producing mycobacteria should be definitively considered as variants from the same group rather than different species. Importantly, we provide evidence that the diversity of mycolactone-producing mycobacteria variants as well as mycobacterium species potentially involved in BU or BU-like skin ulcerations might have been underestimated. We also suggest that the specific variants/species involved in each BU or BU-like case should be carefully identified during the diagnosis phase, either via the key to genetic identification proposed here or by broader metabarcoding approaches, in order to guide the medical community in the choice for the most appropriate antibiotic therapy.
人类新兴病原体的鉴定仍然很困难，常规方法如富集培养检测法具有高度选择性，需要适当的培养基，并且不能避免错误鉴定，或者血清学检测法使用替代抗原，并且经常受到可检测抗体水平的限制。虽然最初不是为此目的设计的，但聚合酶链反应（PCR）的实施已经导致针对许多疾病的诊断测试数量不断增加。然而，特定分子检测的设计依赖于目标病原体的已发表遗传序列的可用性和可靠性，以及对引起相同疾病症状的物种和/或变体的遗传多样性的足够了解。分子检测通常是为临床分离株设计的，因此通常不适合于目标 DNA 与环境 DNA 混合的环境样本。因此，此类分子检测的一个关键挑战是在关注临床和环境样本时确保目标遗传标记的高度特异性，以跟踪人类疾病传播和出现的动态。在这里，我们专注于布鲁里溃疡（BU），这是一种主要影响热带和亚热带地区的人类坏死性皮肤病，尽管发现其他产生杀白细胞素的分枝杆菌甚至分枝杆菌物种与 BU 或类似 BU 的病例有关，但通常被认为是由引起的。通过重新审视文献，我们表明，许多研究使用非特异性分子标记物（IS、IS、KR-B）来鉴定从临床和环境样本中分离出的 ，并提出所有产生杀白细胞素的分枝杆菌都应被明确视为同一组的变体，而不是不同的物种。重要的是，我们提供的证据表明，与 BU 或类似 BU 的皮肤溃疡有关的产生杀白细胞素的分枝杆菌变体以及分枝杆菌物种的多样性可能被低估了。我们还建议，在诊断阶段，应仔细鉴定每个 BU 或类似 BU 病例中涉及的特定变体/物种，无论是通过这里提出的遗传鉴定关键，还是通过更广泛的代谢组学方法，以便为医学界提供指导在选择最合适的抗生素治疗方面。
