Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence

Abstract

The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.

Actinotignum schaalii: Relation to Concomitants and Connection to Patients’ Conditions in Polymicrobial Biofilms of Urinary Tract Catheters and Urines

“…Since the species richness was higher in UC with both approaches (presence/absence-based PCR-DGGE-S combined with culture, as well as abundance-based NGS), as expected (see Figure 2 , Supplementary Figures S4–S7 ), we do not assume any underestimation in UCs’ species richness. This finding can refer to A. schaalii ’s ability to be present in any catheters’ biofilm (including nephrostomy) [ 2 , 9 , 12 , 18 , 22 , 37 ], regardless of the catheter type. To confirm this hypothesis in non-infected but colonized patients, the cohort with non-catheterized individuals should be examined, although the case series and clinical observations have already defined unspecified catheterization as a risk factor for A. schaalii infection [ 6 , 9 , 12 , 19 , 34 , 35 ].…”

“…We hypothesize that A. schaalii acts as a colonizer of early biofilm formation stages, co-aggregating with F. nucleatum, and cohabitating with others. Two clusters of tight adhesion genes (tad) in A. schaalii's genome, encoding the machinery required to assemble pili, and genes for adhesive fimbriae construction [2] are present. Evidence showing, that tad loci are important for either early, middle or late colonization in various species, is accumulating [67].…”

“…Actinotignum schaalii (formerly Actinobaculum ) is a Gram-positive, rod-shaped, facultatively anaerobic, bacillus [ 1 ]. The toxin-antitoxin system and attachment pilli genes together with genes of resistance to reactive oxygen radicals [ 2 ] refer to biofilm-forming features and the ability to survive under oxidative stress—common for the inflammatory environment [ 2 ].…”

“…Patients' characteristics. Patient is considered as A. schaalii positive if at least one of his/her sample is A. schaalii positive;2 We tested by Fisher's exact test whether there is a statistically significant association between A. schaalii presence in patients (A. schaalii-positive vs. -negative patients) and sex (males vs. females), type of catheterization (urinary vs. ureteral), and respective diagnosis (present vs. absent). n.s.-not statistically important difference when comparing A. schaalii-positive and -negative patients.…”

“…Distal and proximal DJC tip were sonicated and analyzed separately (297 samples in total). However, merged A. schaalii results are shown in this table;2 We tested by Fisher's exact test whether there is a statistically significant association between A. schaalii presence and a sample type (urine sample vs. catheter sonicate), for UC and DJC samples separately.…”