Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex

Abstract

Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes isolated from their functional contexts. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and micro-synteny conservation analyses. This allowed to delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with, or are found preferentially in, the pathogenic ACB clade. They unveil, at an unprecedented resolution, the genetic makeup that coincides with the manifestation of the pathogenic phenotype in the last common ancestor of the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. Specifically, we could show that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. They disclose promising routes for future therapeutic strategies.

InvL, an Invasin-Like Adhesin, Is a Type II Secretion System Substrate Required for Acinetobacter baumannii Uropathogenesis

“…As virulence factors could differ among isolates, we assessed the distribution of invL across the Acinetobacter genus. Specifically, we performed a targeted ortholog search for invL and adjacent genes in 3,052 available genomes from the National Center for Biotechnology Information (NCBI) RefSeq Database ( 65 ). In genomes that encode InvL, the corresponding gene is flanked by genes encoding a TIGR01244 family phosphatase (D1G37_04390 in UPAB1) and a dihydrolipoyl dehydrogenase (D1G37_RS04400 in UPAB1) ( Fig.…”

“…Ortholog searches were performed across a database of 3,052 Acinetobacter genomes obtained from NCBI RefSeq as previously described ( 65 ). Briefly, the collection of orthologous groups that resulted from an all versus all ortholog search using OMA was screened to associate the group that harbors a particular protein sequence of interest ( 108 ).…”

InvL, an invasin-like adhesin, is a type II secretion system substrate required for Acinetobacter baumannii uropathogenesis

“…As virulence factors could differ among isolates, we assessed the distribution of InvL across the Acinetobacter genus. Specifically, we performed a targeted ortholog search for invL and adjacent genes in 3052 available genomes from the N ational C enter for B iotechnology Information (NCBI) RefSeq Database (64). In genomes where InvL is encoded, the corresponding gene is flanked by genes encoding a TIGR01244 family phosphatase (D1G37_04390 in UPAB1) and a dihydrolipoyl dehydrogenase (D1G37_RS04400 in UPAB1) ( Fig.…”

“…The proteins of interest comprise the translated sequences of D1G37_RS04395 (InvL), D1G37_RS0440, D1G37_RS04390, and A1 S_3863. Since the subset of genomes used by Djahanschiri et al did not include the strain UPAB1, the orthologs identified in the strain MDR-TJ via a reciprocal best blast hit approach were used to associate orthologous groups (64). The resulting presence/absence matrix together with the genus’ phylogeny served as the input for Vicinator v0.32 (https://github.com/BIONF/Vicinator) to trace the microsynteny of the InvL locus based on MDR-TJ and ATCC 17978 as the reference genomes.…”

“…Bioinformatic analysis of InvL distribution. Ortholog searches were performed across a database of 3052 Acinetobacter genomes obtained from NCBI RefSeq as previously described (64). Briefly, the collection of orthologous groups that resulted from an all vs all ortholog search using OMA were screened to associate the group that harbors a particular protein sequence of interest (105).…”