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Eleven FIme plasmids representative of those identified in epidemic strains of Salmonella wien and Salmonella typhimurium isolated in North Africa, Europe, and the Middle East have been examined for the presence of determinants of toxigenicity, adherence, and iron-sequestering mechanisms. Chemical and genetic data indicated that all plasmids code for a hydroxamate-mediated iron assimilation system. Detailed analysis of derivative plasmids and cloned fragments of FIme plasmid pZM61 demonstrated that the general genetic and structural organization of the DNA region containing the genes for hydroxamate biosynthesis and cloacin DF13 receptor was virtually identical to that described for the aerobactin-mediated iron uptake system of pColV-K30. This DNA region is part of a composite element that is 16.7 kilobases long and carries its IS] modules as inverted repeats. A very similar element is present in either orientation in all nine FIme plasmids analyzed.

Hfq is an RNA-binding protein known to regulate a variety of cellular processes by interacting with small RNAs (sRNAs) and mRNAs in prokaryotes. Stenotrophomonas maltophilia is an important opportunistic pathogen affecting primarily hospitalized and immunocompromised hosts. We constructed an hfq deletion mutant (⌬hfq) of S. maltophilia and compared the behaviors of wild-type and ⌬hfq S. maltophilia cells in a variety of assays. This revealed that S. maltophilia Hfq plays a role in biofilm formation and cell motility, as well as susceptibility to antimicrobial agents. Moreover, Hfq is crucial for adhesion to bronchial epithelial cells and is required for the replication of S. maltophilia in macrophages. Differential RNA sequencing analysis (dRNA-seq) of RNA isolated from S. maltophilia wild-type and ⌬hfq strains showed that Hfq regulates the expression of genes encoding flagellar and fimbrial components, transmembrane proteins, and enzymes involved in different metabolic pathways. Moreover, we analyzed the expression of several sRNAs identified by dRNA-seq in wild-type and ⌬hfq S. maltophilia cells grown in different conditions on Northern blots. The accumulation of two sRNAs was strongly reduced in the absence of Hfq. Furthermore, based on our dRNA-seq analysis we provide a genomewide map of transcriptional start sites in S. maltophilia. Stenotrophomonas maltophilia is a Gram-negative environmental gammaproteobacterium that has been recognized as an important opportunistic pathogen in the last decade, affecting primarily hospitalized and immunocompromised hosts (3). S. maltophilia is frequently isolated from the lungs of cystic fibrosis patients, and its multidrug-resistant phenotype complicates the eradication of S. maltophilia infections (35). Factors that may contribute to the pathogenicity of S. maltophilia include a wide range of extracellular enzymes potentially involved in the colonization process, such as fibrolysin, lipases, and proteases (6), the ability to adhere to and form biofilms on epithelial cells (31), and replication and persistence in the lung (34). Deterioration of lung function associated with S. maltophilia infections has been demonstrated by infection assays carried out in mice (10).Whole genome sequences of three S. maltophilia strains are available: (i) R551-3, a strain which was isolated from Populus trichocarpa (46); (ii) SKA14, which was isolated from the Baltic Sea (15); and (iii) K279a, a strain isolated from a cancer patient (6). Comparative genome-wide analyses revealed that the R551-3 and K279a genomes share a conserved backbone but contain different sets of genomic islands (GEIs) (33).Hfq (host factor I protein) is a highly conserved RNA chaperone that was first identified as a protein required for the replication of the RNA phage Q␤ in Escherichia coli (13). Hfq plays an important role in the fitness and virulence of many pathogenic bacteria, and hfq mutants often exhibit pleiotropic phenotypes, including defects in quorum sensing, growth rate, stress tolerance, and virulence ...