The gram-negative enteric bacterium Proteus mirabilis is a frequent cause of urinary tract infections in individuals with long-term indwelling catheters or with complicated urinary tracts (e.g., due to spinal cord injury or anatomic abnormality). P. mirabilis bacteriuria may lead to acute pyelonephritis, fever, and bacteremia. Most notoriously, this pathogen uses urease to catalyze the formation of kidney and bladder stones or to encrust or obstruct indwelling urinary catheters. Here we report the complete genome sequence of P. mirabilis HI4320, a representative strain cultured in our laboratory from the urine of a nursing home patient with a long-term (>30 days) indwelling urinary catheter. The genome is 4.063 Mb long and has a G؉C content of 38.88%. There is a single plasmid consisting of 36,289 nucleotides. Annotation of the genome identified 3,685 coding sequences and seven rRNA loci. Analysis of the sequence confirmed the presence of previously identified virulence determinants, as well as a contiguous 54-kb flagellar regulon and 17 types of fimbriae. Genes encoding a potential type III secretion system were identified on a low-G؉C-content genomic island containing 24 intact genes that appear to encode all components necessary to assemble a type III secretion system needle complex. In addition, the P. mirabilis HI4320 genome possesses four tandem copies of the zapE metalloprotease gene, genes encoding six putative autotransporters, an extension of the atf fimbrial operon to six genes, including an mrpJ homolog, and genes encoding at least five iron uptake mechanisms, two potential type IV secretion systems, and 16 two-component regulators.Proteus mirabilis is not a common cause of urinary tract infections (UTI) in normal hosts (65). Surveys of uncomplicated cystitis or acute pyelonephritis show that P. mirabilis causes only a few percent of cases. Even in patients with recurrent UTI, the incidence of infection by this organism is only a few percentage points higher. However, this organism infects a very high proportion of patients with complicated urinary tracts, that is, urinary tracts with functional or anatomic abnormalities or with chronic instrumentation. In these patients, not only does this bacterium cause cystitis and acute pyelonephritis (20-22, 65, 73), but the production of urinary stones, a hallmark of infection with this organism (23), further compromises the already complicated urinary tract. P. mirabilis has sporadically been reported to be a causative agent of bacteremia and nosocomial infections (59); additional evidence suggests that this species is associated with rheumatoid arthritis (62).

Proteus mirabilis, a Gram-negative rod-shaped bacterium most noted for its swarming motility and urease activity, frequently causes catheter-associated urinary tract infections (CAUTI) that are often polymicrobial. These infections may be accompanied by urolithiasis, development of bladder or kidney stones due to alkalinization of urine from urease-catalyzed urea hydrolysis. Adherence of the bacterium to epithelial and catheter surfaces is mediated by 17 different fimbriae, most notably MR/P fimbriae. Repressors of motility are often encoded by these fimbrial operons. Motility is mediated by flagella encoded on a single contiguous 54 kb chromosomal sequence. On agar plates, P. mirabilis undergoes a morphological conversion to a filamentous swarmer cell expressing hundreds of flagella. When swarms from different strains meet, a line of demarcation, a “Dienes line”, develops due to the killing action of each strain’s type VI secretion system. During infection, histological damage is caused by cytotoxins including hemolysin and a variety of proteases, some autotransported. The pathogenesis of infection, including assessment of individual genes or global screens for virulence or fitness factors has been assessed in murine models of ascending UTI or CAUTI using both single-species and polymicrobial models. Global gene expression studies carried out in culture and in the murine model have revealed the unique metabolism of this bacterium. Vaccines, using MR/P fimbria and its adhesin, MrpH, have been shown to be efficacious in the murine model. A comprehensive review of factors associated with urinary tract infection is presented, encompassing both historical perspectives and current advances.

Proteus mirabilis is a Gram-negative bacterium which is well-known for its ability to robustly swarm across surfaces in a striking bulls’-eye pattern. Clinically, this organism is most frequently a pathogen of the urinary tract, particularly in patients undergoing long-term catheterization. This review covers P. mirabilis with a focus on urinary tract infections (UTI), including disease models, vaccine development efforts, and clinical perspectives. Flagella-mediated motility, both swimming and swarming, is a central facet of this organism. The regulation of this complex process and its contribution to virulence is discussed, along with the type VI-secretion system-dependent intra-strain competition which occurs during swarming. P. mirabilis uses a diverse set of virulence factors to access and colonize the host urinary tract, including urease and stone formation, fimbriae and other adhesins, iron and zinc acquisition, proteases and toxins, biofilm formation, and regulation of pathogenesis. While significant advances in this field have been made, challenges remain to combatting complicated UTI and deciphering P. mirabilis pathogenesis.

The enteric bacterium Proteus mirabilis is a common cause of complicated urinary tract infections. In this study, microarrays were used to analyze P. mirabilis gene expression in vivo from experimentally infected mice. Urine was collected at 1, 3, and 7 days postinfection, and RNA was isolated from bacteria in the urine for transcriptional analysis. Across nine microarrays, 471 genes were upregulated and 82 were downregulated in vivo compared to in vitro broth culture. Genes upregulated in vivo encoded mannose-resistant Proteus-like (MR/P) fimbriae, urease, iron uptake systems, amino acid and peptide transporters, pyruvate metabolism enzymes, and a portion of the tricarboxylic acid (TCA) cycle enzymes. Flagella were downregulated. Ammonia assimilation gene glnA (glutamine synthetase) was repressed in vivo, while gdhA (glutamate dehydrogenase) was upregulated in vivo. Contrary to our expectations, ammonia availability due to urease activity in P. mirabilis did not drive this gene expression. A gdhA mutant was growth deficient in minimal medium with citrate as the sole carbon source, and loss of gdhA resulted in a significant fitness defect in the mouse model of urinary tract infection. Unlike Escherichia coli, which represses gdhA and upregulates glnA in vivo and cannot utilize citrate, the data suggest that P. mirabilis uses glutamate dehydrogenase to monitor carbon-nitrogen balance, and this ability contributes to the pathogenic potential of P. mirabilis in the urinary tract.

Moraxella (Branhamella) catarrhalis is an important cause of disease in both the upper and lower respiratory tracts (35,48). This unencapsulated gram-negative coccobacillus has been shown to express a number of different outer membrane proteins on its cell surface, some of which are antigenically conserved (47, 49). At present, information about the M. catarrhalis gene products that are involved in the ability of this organism to colonize the mucosa of the nasopharynx and survive in this hostile environment is limited at best. Much effort has been expended recently on documenting the human immune response to selected M. catarrhalis surface-exposed proteins (6,12,25,53,65), providing evidence that these particular gene products are expressed in vivo during otitis media or infections of the bronchial tree. A few of these outer membrane proteins now have a function ascribed to them, mainly with respect to iron acquisition (7,9,10,15,42,43).In contrast, there is relatively little known about other surface proteins of M. catarrhalis that might be involved in the ability of this organism to colonize and survive in the nasopharynx (35). The CD outer membrane protein (33) has been shown to bind middle ear mucin in vitro (51), a function that could be involved in the colonization process or in the development of otitis media. The UspA1 protein has been shown to be an adhesin, at least in vitro (38), whereas both the UspA2 protein (38) and outer membrane protein E (50) have been implicated in serum resistance. Both UspA1 and UspA2, consistent with their functional activities, have been localized to the surface of M. catarrhalis, where they are accessible to antibodies (2, 45).Scott and colleagues (16, 17) correlated both hemagglutination activity and the expression of a 200-kDa protein by some M. catarrhalis isolates with the presence of a fibrillar surface array. In addition, Sasaki and colleagues reported that the 200-kDa protein expressed by M. catarrhalis was subject to phase variation in vitro (K. Sasaki, L. Myers, S. M. Loosmore, and M. H. Klein, Abstr. 99th Gen. Meet. Am. Soc. Microbiol., abstr. B/D-306, 1999) and determined the nucleotide sequence of the gene encoding this protein (54). In the present study, we used analysis of mutants to show that this protein, designated Hag (hemagglutinin), is involved not only in hemagglutination but also in autoagglutination and the binding of human immunoglobulin D (IgD) by M. catarrhalis strain O35E. In addition, we determined that the Hag protein, together with the UspA1 and UspA2 proteins (3), all form fibrillar projections on the M. catarrhalis cell surface.

Swarming motility by the urinary tract pathogen Proteus mirabilis has been a long-studied but little understood phenomenon. On agar, a P. mirabilis colony grows outward in a bull's-eye pattern formed by consecutive waves of rapid swarming followed by consolidation into shorter cells. To examine differential gene expression in these growth phases, a microarray was constructed based on the completed genome sequence and annotation. RNA was extracted from broth-cultured, swarming, and consolidation-phase cells to assess transcription during each of these growth states. A total of 587 genes were differentially expressed in broth-cultured cells versus swarming cells, and 527 genes were differentially expressed in broth-cultured cells versus consolidationphase cells (consolidate). Flagellar genes were highly upregulated in both swarming cells and consolidationphase cells. Fimbriae were downregulated in swarming cells, while genes involved in cell division and anaerobic growth were upregulated in broth-cultured cells. Direct comparison of swarming cells to consolidation-phase cells found that 541 genes were upregulated in consolidate, but only nine genes were upregulated in swarm cells. Genes involved in flagellar biosynthesis, oligopeptide transport, amino acid import and metabolism, cell division, and phage were upregulated in consolidate. Mutation of dppA, oppB, and cysJ, upregulated during consolidation compared to during swarming, revealed that although these genes play a minor role in swarming, dppA and cysJ are required during ascending urinary tract infection. Swarming on agar to which chloramphenicol had been added suggested that protein synthesis is not required for swarming. These data suggest that the consolidation phase is a state in which P. mirabilis prepares for the next wave of swarming.Proteus mirabilis, a member of the Enterobacteriaceae and an opportunistic pathogen, is especially problematic as a urinary tract pathogen in catheterized patients, those with spinal cord injury, or those with anatomical abnormality of the urinary tract (reviewed in reference 16). This urease-positive bacterium causes an increase in urinary pH and the production of kidney and bladder stones (25, 39). In addition, urinary catheters become encrusted and even blocked during P. mirabilis infections (45). As our population continues to age, resulting in larger numbers of catheterized patients in hospitals and nursing homes, this organism will likely be of special concern as an agent of nosocomial infections. Particularly worrisome is the more frequent appearance of multidrug-resistant strains of P. mirabilis (17, 47).P. mirabilis was first characterized in 1885 by G. Hauser for its ability to swarm over agar surfaces, resulting in a characteristic bull's-eye pattern (reviewed in reference 65). During the swarm process, P. mirabilis differentiates into very long (Ͼ50 m), multinucleate, highly motile hyperflagellated cells (65). At intervals, swarm cells slow down or cease movement and dedifferentiate into shorter rod-shaped ce...

The nucleotide sequence from the genome of Moraxella catarrhalis ATCC 43617 was annotated and used both to assess the metabolic capabilities and limitations of this bacterium and to design probes for a DNA microarray. An absence of gene products for utilization of exogenous carbohydrates was noteworthy and could be correlated with published phenotypic data. Gene products necessary for aerobic energy generation were present, as were a few gene products generally ascribed to anaerobic systems. Enzymes for synthesis of all amino acids except proline and arginine were present. M. catarrhalis DNA microarrays containing 70-mer oligonucleotide probes were designed from the genome-derived nucleotide sequence data. Analysis of total RNA extracted from M. catarrhalis ATCC 43617 cells grown under iron-replete and iron-restricted conditions was used to establish the utility of these DNA microarrays. These DNA microarrays were then used to analyze total RNA from M. catarrhalis cells grown in a continuous-flow biofilm system and in the planktonic state. The genes whose expression was most dramatically increased by growth in the biofilm state included those encoding a nitrate reductase, a nitrite reductase, and a nitric oxide reductase. Real-time reverse transcriptase PCR analysis was used to validate these DNA microarray results. These results indicate that growth of M. catarrhalis in a biofilm results in increased expression of gene products which can function not only in energy generation but also in resisting certain elements of the innate immune response.Moraxella catarrhalis is a gram-negative, unencapsulated bacterium that can colonize the mucosal surface of the human nasopharynx, most frequently in infants and very young children (22). When this organism traverses the eustachian tube in these very young individuals, it can cause otitis media (7). Alternatively, in colonized adults, M. catarrhalis gains access to the bronchi and there causes exacerbations of chronic obstructive pulmonary disease (48). This organism can also infrequently cause other types of infections (for reviews, see references 39 and 73).Information about the virulence mechanisms employed by this organism in the production of disease is still very limited, although a number of putative virulence factors have been identified, including proteins located in or attached to the outer membrane (1, 6, 9, 23, 24, 26, 32-34, 40, 44, 49, 51, 54, 57, 65, 71), as well as lipooligosaccharide (42, 59). Validation of the actual involvement of these different gene products in disease processes has been severely hindered by the lack of an appropriate animal model for M. catarrhalis disease (39). Similarly, little is known about how M. catarrhalis colonizes the nasopharynx, and while several M. catarrhalis adhesins which function in vitro have been identified (33,40,61,71), the relative importance of these macromolecules in the colonization process in vivo remains to be determined. Recent studies aimed at addressing this issue have included the use of reverse transcr...

Summary Proteus mirabilis alternates between motile and adherent forms. MrpJ, a transcriptional regulator previously reported to repress motility, is encoded at the 3' end of the mrp fimbrial operon in P. mirabilis. Sequencing of the P. mirabilis genome revealed 14 additional paralogs of mrpJ, ten of which are associated with fimbrial operons. Twelve of these genes, when overexpressed, repressed motility; several distinct patterns of swarming motility were noted. Expression of 10 of the 14 mrpJ paralogs repressed flagellin (FlaA) synthesis. Alignment of the predicted amino acid sequences of MrpJ and its fourteen paralogs revealed a conserved consensus motif (SQQQFSRYE) within the helix-turn-helix domain. Site-directed mutagenesis of these residues coupled with linker insertion mutagenesis of MrpJ confirmed the importance of this domain for repression of motility. Gel shift assays demonstrated that MrpJ and another paralog UcaJ bind directly to the promoter region of the flagellar master regulator flhDC. Thus, P. mirabilis appears to use a related mechanism to inhibit motility during the production of at least ten of its predicted fimbriae.