Phenotypic and genetic changes in the life cycle of small colony variants of Salmonella enterica serotype Typhimurium induced by streptomycin

Abstract

BackgroundSmall colony variants (SCVs), constituting a slow-growing subpopulation of bacteria that facilitates persistence in lethal environmental conditions, are able to revert to the phenotype of rapid growth for further proliferation and transmission. Salmonella enterica serotype Typhimurium is one of the most important foodborne pathogens. This study investigated the genetic mechanisms how SCVs induced by streptomycin reverted to the fast-growing phenotype and the phenotypic changes of SCVs among their complete life cycle in S.Typhimurium.MethodsSalmonella Typhimurium SCVs were obtained by streptomycin treatment and their revertants were collected in the absence of antibiotics. The fitness, antimicrobial susceptibility, biofilm formation, and the biofilm-related genes expression were analyzed in comparison to their wild type strain, and the whole genome sequencing was performed to identify the genetic changes in the life cycle of S. Typhimurium SCVs.ResultsSmall colony variants were characterized by an increased antimicrobial resistance to streptomycin (64-fold), imipenem (twofold), and gentamicin (fourfold). A significant increase in biofilm production with higher expression of csgB was observed in SCVs (P < 0.01). The genetic alterations of all SCVs occurred in ubiE gene (coenzyme Q8 and menaquinone synthesis) with frameshift mutations. However, all fast-growing revertants again lost the trait of increased biofilm production (P > 0.05), in which two modes of the genetic changes for reversing to the rapidly growing form were observed: four revertants harbored a secondary mutation in ubiE, which reinstated most of the amino acid sequence of the ubiE, and other four revertants harbored a mutation in prfB.ConclusionsSalmonella Typhimurium could switch to the phenotype of SCVs under the treatment of streptomycin by a mutation in ubiE, partially combined with increased production of biofilm, and these SCVs could escape from growth restriction by a compensatory mutation in prfB or a new mutation in ubiE. These findings may contribute to establishing phenotype-directed treatments against SCVs of S.Typhimurium.Electronic supplementary materialThe online version of this article (doi:10.1186/s12941-016-0151-3) contains supplementary material, which is available to authorized users.

Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance

“…Mutations in ubiF have been shown to produce pleiotropic E. coli phenotypes resistant to STR and GEN (Soballe and Poole, 1999). Similarly, Li et al (2016) found mutations in genes ubiE and prfB, associated with STR induction of a small colony variant (SCV) phenotype, resulted in two-to four-fold increases in STR MIC of isolates. BLAST analyses of the coenzyme Q redox gene ubiE found no frameshift or nonsynonymous mutations in isolates from this study.…”

“…Sequences with < 100% amino acid identity to the DNA gyrase subunit A gene (gyrA) were reviewed to determine whether they matched known nalidixic acid-resistant (NalR) mutations ( Table 2). This analysis was also conducted for the 111 S. enterica strains to search for mutations in aroD, cyoB, cyoC, fusA, glnA, gidB, ispA, nuoE, nuoF, prfB, rpsL, trkH, ubiA, ubiE, and ubiF genes which have a reported role in conversion of Salmonella to a small colony variant (SCV) phenotype and/or confer streptomycin resistance (Soballe and Poole, 1999;Springer et al, 2001;Cano et al, 2003;Okamoto et al, 2007;Koskiniemi et al, 2011;Lázár et al, 2013;Li et al, 2016;Aurass et al, 2017).…”

“…Blocking of the ubiquinone biosynthesis pathway results in a defect in electron transport and aerobic respiration which has been found to increase aminoglycoside resistance (Paradise et al, 1998;Li et al, 2016). Mutations in ubiF have been shown to produce pleiotropic E. coli phenotypes resistant to STR and GEN (Soballe and Poole, 1999).…”

The Uptake and Release of Amino Acids by Staphylococcus aureus at Mid-Exponential and Stationary Phases and Their Corresponding Responses to Changes in Temperature, pH and Osmolality

“…(von Eiff, 2008;Onyango et al, 2012;Onyango et al, 2013;Proctor et al, 2014). The occurrence of SCVs have been observed in medical samples, animals (Tkadlec et al, 2015) and even food (Li et al, 2016). SCVs are a slow-growing sub-population of bacteria that are characterized with decreased metabolic activity and increased resistance to antimicrobial agents (von Eiff et al, 2000).…”

“…Further, biofilm formation can occur in response to other non-ideal growth conditions such as exposure to alkaline environments (Jones et al, 2015;Jaishankar and Srivastava, 2017). Both SCV phenotypes and biofilm greatly contribute to the profound resistance and stable adhesion, which eventually assist the bacteria to survive under changed environmental conditions (Yao et al, 2005;Li et al, 2016).…”