Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physicochemical observations. Samples and observations were collected monthly over 3 years at a welldescribed ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible 'keystone' species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes.

Uropathogenic Escherichia coli (UPEC) strain CFT073 contains 13 large genomic islands ranging in size from 32 kb to 123 kb. Eleven of these genomic islands were individually deleted from the genome, and nine isogenic mutants were tested for their ability to colonize the CBA/J mouse model of ascending urinary tract infection. Three genomic island mutants (⌬PAI-aspV, ⌬PAI-metV, and ⌬PAI-asnT) were significantly outcompeted by wild-type CFT073 in the bladders and/or kidneys following transurethral cochallenge (P < 0.0139). The PAI-metV mutant also showed significant attenuation in the ability to independently colonize the kidneys (P ‫؍‬ 0.0011). Specific genes within these islands contributed to the observed phenotype, including a previously uncharacterized iron acquisition cluster, fbpABCD (c0294 to c0297 [c0294-97]), autotransporter, picU (c0350), and RTX family exoprotein, tosA (c0363) in the PAI-aspV island. The double deletion mutant with deletions in both copies of the fbp iron acquisition operon (⌬c0294-97 ⌬c2518-15) was significantly outcompeted by wild-type CFT073 in cochallenge. Strains with mutations in a type VI secretion system within the PAI-metV island did not show attenuation. The attenuation of the PAI-metV island was localized to genes c3405-10, encoding a putative phosphotransferase transport system, which is common to UPEC and avian pathogenic E. coli strains but absent from E. coli K-12. We have shown that, in addition to encoding virulence genes, genomic islands contribute to the overall fitness of UPEC strain CFT073 in vivo.Escherichia coli, a versatile microbe, can colonize the intestinal tract with no harmful effects to the host or can cause devastating and life-threatening disease (34). E. coli can be classified into one of three groups: commensal (nonpathogenic) E. coli strains that coexist with the host without causing overt disease, intestinal pathogenic (diarrheagenic) E. coli, and extraintestinal pathogenic E. coli (ExPEC). The latter category, ExPEC, was proposed in 2000 to classify E. coli isolates capable of causing disease outside of the intestinal tract, including uropathogenic E. coli (UPEC), sepsis-associated E. coli, and neonatal meningitis-associated E. coli (63). Within the human intestinal tract, ExPEC may colonize without causing disease. However, this subset of E. coli has the ability to disseminate to other sites of the body, including the urinary tract, bloodstream, and central nervous system, and elicit pathogenesis (77).Urinary tract infections (UTIs), the most common type of bacterial infection (16), affect 11% of adult women every year, with an estimated one-third of women requiring antibiotic therapy for a clinician-diagnosed UTI by 24 years of age (17). Approximately 60% of all women will experience a UTI during their lifetime (17). Nearly 7 million physician office visits, 1 million emergency room visits, and 100,000 hospitalizations per year are attributed to UTIs, with women twice as likely as men to seek medical treatment for infections of the urinary tract (6...

The structure and genetic diversity of marine protistan assemblages were investigated in the upper 500 m of the water column at a Pacific Ocean time-series station off the coast of Southern California. Deoxyribonucleic acid sequence-based microbial eukaryote diversity was examined in January, April, July, and October of 2001 at four depths (5 m, chlorophyll maximum [CM], 150 m, and 500 m). A total of 2956 partial 18S ribosomal ribonucleic acid gene sequences yielded representatives from most of the major eukaryotic lineages. Notable among the taxonomic groups were recently described lineages of stramenopiles, alveolates, and euglenozoa. A large number of polycystine and acantharean sequences were observed at depth. Pairwise sequence analysis was performed to establish operational taxonomic units (OTUs) that were then used to estimate the unsampled protistan diversity by parametric and nonparametric techniques. A total of 2246 protistan sequences grouped into 377 distinct OTUs, with remaining sequences attributed to metazoa. Protistan richness estimates ranged from , 600 to 1500 OTUs when all depths and seasons were combined into a single data set. Seasonal and depth-related trends in the observed protistan diversity were apparent from comparisons of univariate and multivariate analyses. Cluster analysis combined with nonmetric multidimensional scaling and analysis of similarity testing identified distinct protistan assemblages at the shallowest depths (5 m and CM) for each season, which were significantly different (p , 0.03) from assemblages at the two deepest depths (150 and 500 m) where seasonal changes in the protistan assemblage were not apparent.

Uropathogenic Escherichia coli (UPEC) is responsible for the majority of uncomplicated urinary tract infections (UTI) and represents the most common bacterial infection in adults. UPEC utilizes a wide range of virulence factors to colonize the host, including the novel repeat-in-toxin (RTX) protein TosA, which is specifically expressed in the host urinary tract and contributes significantly to the virulence and survival of UPEC. tosA, found in strains within the B2 phylogenetic subgroup of E. coli, serves as a marker for strains that also contain a large number of well-characterized UPEC virulence factors. The presence of tosA in an E. coli isolate predicts successful colonization of the murine model of ascending UTI, regardless of the source of the isolate. Here, a detailed analysis of the function of tosA revealed that this gene is transcriptionally linked to genes encoding a conserved type 1 secretion system similar to other RTX family members. TosA localized to the cell surface and was found to mediate (i) adherence to host cells derived from the upper urinary tract and (ii) survival in disseminated infections and (iii) to enhance lethality during sepsis (as assessed in two different animal models of infection). An experimental vaccine, using purified TosA, protected vaccinated animals against urosepsis. From this work, it was concluded that TosA belongs to a novel group of RTX proteins that mediate adherence and host damage during UTI and urosepsis and could be a novel target for the development of therapeutics to treat ascending UTIs. R epeat-in-toxin (RTX) proteins are widespread among Gramnegative bacteria, with more than 1,000 family members detected in a survey of genome sequences from 251 bacterial species (21). Two common features present in known RTX family members are a characteristic glycine-and aspartate-rich repeat near the C terminus of the protein and a conserved type 1 secretion system (T1SS) that exports the protein into the extracellular environment, bypassing the periplasmic space (21, 37). The model protein for the RTX family, alpha-hemolysin, inserts into host membranes and forms pores that allow an influx of Ca 2ϩ into host cells, altering host physiology or leading to cell death (37). Additional RTX family members have displayed a wide array of functions in bacterial pathogens; secreted proteases (24, 29) and lipases (9, 40), cross-linkers of cellular actin that cause host cell rounding (28), and surface-associated coats of protein that form the bacterial S-layer (26, 30) represent a few examples of these diverse functions. However, most RTX family members remain uncharacterized. Given the widespread distribution and diverse roles that known family members contribute to bacterial pathogenesis, the identification and characterization of novel RTX family members remains an important area of research.One of the best characterized RTX family members, alphahemolysin, enhances host damage in the urinary tract during an Escherichia coli infection (32). In addition, this protein contributes to...

Home-based specimen collection could result in similar levels of index case management for CT or NG infection when compared with clinic-based specimen collection. Increases in the proportion of individuals tested as a result of home-based, compared with clinic-based, specimen collection are offset by a lower proportion of positive results. The harms of home-based specimen collection compared with clinic-based specimen collection have not been evaluated. Future RCTs to assess the effectiveness of home-based specimen collection should be designed to measure biological outcomes of STI case management, such as proportion of participants with negative tests for the relevant STI at follow-up.

No abstract

Uropathogenic Escherichia coli (UPEC) strains, which cause the majority of uncomplicated urinary tract infections (UTIs), carry a unique assortment of virulence or fitness genes. However, no single defining set of virulence or fitness genes has been found in all strains of UPEC, making the differentiation between UPEC and fecal commensal strains of E. coli difficult without the use of animal models of infection or phylogenetic grouping. In the present study, we consider three broad categories of virulence factors simultaneously to better define a combination of virulence factors that predicts success in the urinary tract. A total of 314 strains of E. coli, representing isolates from fecal samples, asymptomatic bacteriuria, complicated UTIs, and uncomplicated bladder and kidney infections, were assessed by multiplex PCR for the presence of 15 virulence or fitness genes encoding adhesins, toxins, and iron acquisition systems. The results confirm previous reports of gene prevalence among isolates from different clinical settings and identify several new patterns of gene associations. One gene, tosA, a putative repeat-in-toxin (RTX) homolog, is present in 11% of fecal strains but 25% of urinary isolates. Whereas tosA-positive strains carry an unusually high number (11.2) of the 15 virulence or fitness genes, tosA-negative strains have an average of only 5.4 virulence or fitness genes. The presence of tosA was predictive of successful colonization of a murine model of infection, even among fecal isolates, and can be used as a marker of pathogenic strains of UPEC within a distinct subset of the B2 lineage.

Uncomplicated urinary tract infections (UTI) are caused most commonly by uropathogenic Escherichia coli (UPEC). Whole-genome screening approaches, including transcriptomic, proteomic, and signature-tagged mutagenesis, have shown that UPEC highly expresses or requires genes for translational machinery, capsule, lipopolysaccharide, type 1 fimbriae, and iron acquisition systems during UTI. To identify additional genes expressed by UPEC during UTI, an immunoscreening approach termed in vivo-induced antigen technology (IVIAT) was employed to identify antigens produced during experimental infection that are not produced during in vitro culture. An inducible protein expression library, constructed from genomic DNA isolated from UPEC strain CFT073, was screened using exhaustively adsorbed pooled sera from 20 chronically infected female CBA/J mice. Using this approach, we identified 93 antigens induced by UPEC in vivo. A representative subset of these genes was tested by quantitative PCR for expression by CFT073 in vivo and during growth in human urine or LB medium in vitro; proWX, narJI, lolA, lolD, tosA (upxA), c2432, katG, ydhX, kpsS, and yddQ were poorly expressed in vitro but highly expressed in vivo. Of these, tosA, a gene encoding a predicted repeat-in-toxin family member, was expressed exclusively during UTI. Deletion of tosA in UPEC strain CFT073 resulted in significant attenuation in bladder and kidney infections during ascending UTI. By screening for in vivo-induced antigens, we identified a novel UPEC virulence factor and additional proteins that could be useful as potential vaccine targets.