Detection, Identification and Diagnostic Characterization of the Staphylococcal Small Colony-Variant (SCV) Phenotype

Abstract

While modern molecular methods have decisively accelerated and improved microbiological diagnostics, phenotypic variants still pose a challenge for their detection, identification and characterization. This particularly applies if they are unstable and hard to detect, which is the case for the small-colony-variant (SCV) phenotype formed by staphylococci. On solid agar media, staphylococcal SCVs are characterized by tiny colonies with deviant colony morphology. Their reduced growth rate and fundamental metabolic changes are the result of their adaptation to an intracellular lifestyle, regularly leading to specific auxotrophies, such as for menadione, hemin or thymidine. These alterations make SCVs difficult to recognize and render physiological, biochemical and other growth-based methods such as antimicrobial susceptibility testing unreliable or unusable. Therefore, diagnostic procedures require prolonged incubation times and, if possible, confirmation by molecular methods. A special approach is needed for auxotrophy testing. However, standardized protocols for SCV diagnostics are missing. If available, SCVs and their putative parental isolates should be genotyped to determine clonality. Since their detection has significant implications for the treatment of the infection, which is usually chronic and relapsing, SCV findings should be specifically reported, commented on, and managed in close collaboration with the microbiological laboratory and the involved clinicians.

Klebsiella pneumoniaeexhibiting a phenotypic hyper-splitting phenomenon including the formation of small colony variants

“…In this context, macrophage and neutrophil assays would be valuable for assessing both the extent of immune response and the presence of persistent cells. Moreover, the determination of the auxotrophism (13, 17) of K. pneumoniae SCVs and of the molecular mechanisms that drive SCV formation and the resulting antibiotic resistance in this species require further investigation. Integrating a comprehensive range of approaches encompassing genomics, transcriptomics, and proteomics, the utilization of experimental evolutionary models can yield valuable insights into the genetic determinants and regulatory networks orchestrating SCV phenotypes.…”

“…Another non-classical mechanism leading to functional resistance is the formation of the small colony variant (SCV) phenotype. SCVs are subpopulations of bacteria that exhibit slow growth, reduced colony size, and altered phenotypic properties compared to their normal-growing counterparts, making them difficult to detect and treat effectively (12, 13). Their ability to evade the host’s immune surveillance and to undermine the effectiveness of antimicrobial interventions by host cell internalization results in intracellular persistence, which contributes significantly to the recurrence and chronicity of the infection (14, 15).…”

Integrative omics analysis reveals insights into small colony variants of Staphylococcus aureus induced by sulfamethoxazole-trimethoprim

“…Since the formation of S . aureus SCVs are usually linked with deficiencies in the utilization of menadione, hemin or thymidine by bacteria, we conducted the auxotrophism test on the induced SCVs to find the possible mechanisms [ 12 ]. The results showed that the colony sizes of the 3 induced SCVs strains on MH plates supplemented with each compound separately were not significantly different from those on the plates without these agents, as shown in Fig.…”

Klebsiella pneumoniae exhibiting a phenotypic hyper-splitting phenomenon including the formation of small colony variants

“…In this context, macrophage and neutrophil assays would be valuable for assessing both the extent of immune response and the presence of persistent cells. Moreover, the determination of the auxotrophism ( Kriegeskorte et al., 2014 ; Becker, 2023 ) of K. pneumoniae SCVs and of the molecular mechanisms that drive SCV formation and the resulting antibiotic resistance in this species require further investigation. Integrating a comprehensive range of approaches encompassing genomics, transcriptomics, and proteomics, the utilization of experimental evolutionary models can yield valuable insights into the genetic determinants and regulatory networks orchestrating SCV phenotypes.…”

“…Another non-classical mechanism leading to antibiotic tolerance is the formation of the small colony variant (SCV) phenotype. SCVs are subpopulations of bacteria that exhibit slow growth, reduced colony size, and altered phenotypic properties compared to their normal-growing counterparts, making them difficult to detect and treat effectively ( Proctor et al., 2006 ; Becker, 2023 ). Their ability to evade the host’s immune surveillance and to undermine the effectiveness of antimicrobial interventions by host cell internalization results in intracellular persistence, which contributes significantly to the recurrence and chronicity of the infection ( Tuchscherr et al., 2011 ; Kahl et al., 2016 ).…”