Phenotypic and Transcriptomic Analyses of Seven Clinical Stenotrophomonas maltophilia Isolates Identify a Small Set of Shared and Commonly Regulated Genes Involved in the Biofilm Lifestyle

Abstract

Stenotrophomonas maltophilia is one of the most frequently isolated multidrug resistant nosocomial opportunistic pathogens. It contributes to disease progression in cystic fibrosis patients and is frequently isolated from wounds, infected tissues or catheter surfaces. On these diverse surfaces S. maltophilia lives in single or multi-species biofilms. Since very little is known about common processes in biofilms of different S. maltophilia isolates, we analyzed the biofilm profiles of 300 clinical and environmental isolates from Europe of the recently identified main lineages Sgn3, Sgn4 and Sm2 - Sm18. The analysis of the biofilm architecture of 40 clinical isolates revealed the presence of multicellular structures and high phenotypic variability at a strain-specific level. Further, transcriptome analyses of biofilm cells of seven clinical isolates identified a set of 106 shared strongly expressed genes and 33 strain-specifically expressed genes. Surprisingly, the transcriptome profiles of biofilm versus planktonic cells revealed that just 9.43 ± 1.36 % of all genes were differentially regulated. This implies that just a small set of shared and commonly regulated genes is involved in the biofilm lifestyle. Strikingly, iron uptake appears to be a key factor involved in this metabolic shift. Further, metabolic analyses implied that S. maltophilia employs a mostly fermentative growth mode under biofilm conditions. The transcriptome data of this study together with the phenotypic and metabolic analysis represent so far the largest data set on S. maltophilia biofilm versus planktonic cells. This study will lay the foundation for the identification of strategies for fighting S. maltophilia biofilms in clinical and industrial settings. IMPORTANCE Microorganisms living in a biofilm are much more tolerant to antibiotics and antimicrobial substances than planktonic cells. Thus, the treatment of infections caused by microorganisms living in biofilms is extremely difficult. The nosocomial infections among others caused by S. maltophilia, particularly lung infection among CF patients, increased in prevalence in the last years. The intrinsic multidrug resistance of S. maltophilia and the increased tolerance to antimicrobial agents of its biofilm cells, makes the treatment of S. maltophilia infection difficult. The significance of our research is based in understanding the common mechanisms involved in biofilm formation of different S. maltophilia isolates, understanding the diversity of biofilm architectures among this species and in identifying the differently regulated processes in biofilm versus planktonic cells. These results will lay the foundation for the treatment of S. maltophilia biofilms.

Achromobacter xylosoxidans and Stenotrophomonas maltophilia: Emerging Pathogens Well-Armed for Life in the Cystic Fibrosis Patients’ Lung

“…Congruent with previous genomic evidence [ 61 ], the ability to form biofilm has been observed in 97.1% to 100% of CF Axc strains [ 79 , 84 , 87 ] and is shared by several species of the Axc , i.e., A. xylosoxidans ( Ax ), A. dolens / A. ruhlandii , A. insolitus , A. insuavis, and A. piechaudii [ 79 , 84 ], with one third to 58% of isolates being strong biofilm producers. A slightly lower percentage of CF Sm strains are able to form biofilm, although this remains a characteristic presented by 87.5% to 90.2% of strains [ 91 , 92 ], with a high level of variability observed both among strains analyzed and in biofilm architecture [ 93 ]. This ability to form biofilm favors persistence and dissemination through the maturation of the biofilm and subsequent detachment of bacterial cells from the mature biofilm, in accordance with the general stages of biofilm development [ 94 ].…”

“…In Sm , factors identified as influencing biofilm formation are cell motility, genes involved in lipopolysaccharide/exopolysaccharide biosynthesis, SmeYZ and MacABCsm efflux pumps, iron availability, histidin kinase, the two-component signal transduction system BfmAK, and the diffusible signal factor (DSF) quorum sensing (QS) system [ 93 , 103 , 104 ]. This is supported and completed by recent transcriptomic analyses revealing that a small set of commonly regulated genes are involved in the biofilm lifestyle of Sm, with 6% to 9% of all genes being upregulated and 1% to 3% of all genes being downregulated in biofilms versus planktonic cells [ 93 ]. Commonly, upregulated genes show a large functional distribution, and they are mostly involved in transcription and translation followed by a remarkably high number of genes involved in iron acquisition, then in metabolism/biosynthesis, membrane proteins/transporters, and respiration/energy [ 93 ].…”

“…Commonly, upregulated genes show a large functional distribution, and they are mostly involved in transcription and translation followed by a remarkably high number of genes involved in iron acquisition, then in metabolism/biosynthesis, membrane proteins/transporters, and respiration/energy [ 93 ]. In addition, the authors identified an extracellular protease activity up to 40 times higher in Sm biofilm compared with planktonic cultures; however, although such an activity has previously been associated with virulence and biofilm formation, they could not link the increased protease activity observed with any particular virulence or biofilm-forming profile [ 93 ].…”

Synthesis of Natural Rubrolides B, I, K, L, M, O and Analogues

“…Rubrolides B 1 , I 2 , K 3 , L 4 , M 5 , O 6 and the synthesized analogues were tested for their antibiofilm and antiviral properties. Investigating the reduction of virus replication of two different influenza A virus subtypes [28,29] and biofilm formation of Stenotrophomonas maltophilia [30–32] . For the virus inhibition, MDCK (Madin‐Darby canine kidney) cells were infected with p H1N1 or H3N2 influenza A viruses and cotreated with Ribavirin or the synthesized rubrolides (for all data see Supporting Information).…”

“…Investigating the reduction of virus replication of two different influenza A virus subtypes [28,29] and biofilm formation of Stenotrophomonas maltophilia. [30][31][32] For the virus inhibition, MDCK (Madin-Darby canine kidney) cells were infected with pH1N1 or H3N2 influenza A viruses and cotreated with Ribavirin or the synthesized rubrolides (for all data see Supporting Information). The viral titer of infected and PBS (phosphate buffer saline) (Ctrl 1) or 0.1 % DMSO (Ctrl 2) treated cells served as negative control.…”