Competition of Listeria monocytogenes Serotype 1/2a and 4b Strains in Mixed-Culture Biofilms

The majority of Listeria monocytogenes isolates recovered from foods and the environment are strains of serogroup 1/2, especially serotypes 1/2a and 1/2b. However, serotype 4b strains cause the majority of human listeriosis outbreaks. Our investigation of L. monocytogenes biofilms used a simulated food-processing system that consisted of repeated cycles of growth, sanitation treatment, and starvation to determine the competitive fitness of strains of serotypes 1/2a and 4b in pure and mixed-culture biofilms. Selective enumeration of strains of a certain serotype in mixed-culture biofilms on stainless steel coupons was accomplished by using serotype-specific quantitative PCR and propidium monoazide treatment to prevent amplification of extracellular DNA or DNA from dead cells. The results showed that the serotype 1/2a strains tested were generally more efficient at forming biofilms and predominated in the mixed-culture biofilms. The growth and survival of strains of one serotype were not inhibited by strains of the other serotype in mixed-culture biofilms. However, we found that a cocktail of serotype 4b strains survived and grew significantly better in mixed-culture biofilms containing a specific strain of serotype 1/2a (strain SK1387), with final cell densities averaging 0.5 log₁₀ CFU/cm² higher than without the serotype 1/2a strain. The methodology used in this study contributed to our understanding of how environmental stresses and microbial competition influence the survival and growth of L. monocytogenes in pure and mixed-culture biofilms.A prominent food-borne pathogen, Listeria monocytogenes can cause severe infections in humans, primarily in high-risk populations, though the disease (listeriosis) is relatively rare (11, 30, 43). Outbreaks of listeriosis have resulted from the contamination of a variety of foods by L. monocytogenes, especially meat and dairy products (27). L. monocytogenes is ubiquitous in the environment, able to grow at refrigeration temperature, and tolerant of the low pHs (3 to 4) typical of acidified foods (28, 32, 44). The capacity to produce biofilms confers protection against stresses common in the food-processing environment (13, 33).Biofilms are characterized by dense clusters of bacterial cells embedded in extracellular polymeric substances which are secreted by cells to aid in adhesion to surfaces and to other cells (4, 5). Strains of L. monocytogenes have been known to persist for years in food-processing environments, presumably in biofilms. Of the 13 known serotypes of L. monocytogenes, three (1/2a, 1/2b, and 4b) account for >95% of the isolates from human illness (21). Serotype 1/2a accounts for >50% of the L. monocytogenes isolates recovered from foods and the environment, while most major outbreaks of human listeriosis have been caused by serotype 4b strains (1, 3, 14, 15, 17, 22, 29, 31, 41, 47, 49,). No correlation between L. monocytogenes strain fitness and serotype has been identified (16, 19). Some studies have reported that strains repeatedly isolated from food and environmental samples (defined as persistent strains) had a higher adherence capacity than strains that were sporadically isolated (2, 36), while this phenomenon was not observed by others (7). Serotype 4b strains exhibited a higher capacity for biofilm formation than did serotype 1/2a strains (36), whereas this was not observed by Di Bonaventura and colleagues (6). It has been suggested that serotype 1/2a strains could be more robust than serotype 4b strains in biofilm formation under a variety of environmental conditions. Furthermore, strains of these serotypes differ in terms of the medium that promotes biofilm formation. Biofilm formation by serotype 4b strains was higher in full-strength tryptic soy broth than in diluted medium, whereas the opposite was observed with serotype 1/2a strains, which produced more biofilm in diluted medium (12).There is limited information on microbial competition between strains of different serotypes in biofilms or on how the environmental stresses present in food-processing environments may affect the biofilm formation and survival of L. monocytogenes of different serotypes. In food-processing plants, the environmental stresses encountered by bacteria are more complex and variable than most laboratory systems used for microbial ecology and biofilm studies. A simulated food-processing (SFP) system has been developed to address this issue (38). The SFP system incorporates several stresses that may affect bacteria in biofilms in the food-processing environment, including exposure to sanitizing agents, dehydration, and starvation. When biofilms were subjected to the SFP regimen over a period of several weeks, the cell numbers of L. monocytogenes strains in the biofilms initially were reduced and then increased as the culture adapted (38). The development of resistance to sanitizing agents was specific to the biofilm-associated cells and was not apparent in the detached cells (38). This suggested that extracellular polymeric substances present in the biofilm matrix were responsible for the resistance to sanitizing agents. It was subsequently found that real-time PCR, in combination with propidium monoazide (PMA) treatment of samples prior to DNA isolation, was an effective method for enumerating viable cells in biofilms (37).The objective of this study was to determine if strains of serotype 1/2a or 4b have a selective advantage under stress conditions. We investigated and compared the initial attachment and biofilm formation capabilities of L. monocytogenes strains of these two serotypes and analyzed the survival and growth of bacteria of each serotype in mixed-serotype biofilms in the SFP system by using PMA with quantitative PCR.     

A New Borrelia Species Defined by Multilocus Sequence Analysis of Housekeeping Genes

Analysis of Lyme borreliosis (LB) spirochetes, using a novel multilocus sequence analysis scheme, revealed that OspA serotype 4 strains (a rodent-associated ecotype) of Borrelia garinii were sufficiently genetically distinct from bird-associated B. garinii strains to deserve species status. We suggest that OspA serotype 4 strains be raised to species status and named Borrelia bavariensis sp. nov. The rooted phylogenetic trees provide novel insights into the evolutionary history of LB spirochetes.Multilocus sequence typing (MLST) and multilocus sequence analysis (MLSA) have been shown to be powerful and pragmatic molecular methods for typing large numbers of microbial strains for population genetics studies, delineation of species, and assignment of strains to defined bacterial species (4, 13, 27, 40, 44). To date, MLST/MLSA schemes have been applied only to a few vector-borne microbial populations (1, 6, 30, 37, 40, 41, 47).Lyme borreliosis (LB) spirochetes comprise a diverse group of zoonotic bacteria which are transmitted among vertebrate hosts by ixodid (hard) ticks. The most common agents of human LB are Borrelia burgdorferi (sensu stricto), Borrelia afzelii, Borrelia garinii, Borrelia lusitaniae, and Borrelia spielmanii (7, 8, 12, 35). To date, 15 species have been named within the group of LB spirochetes (6, 31, 32, 37, 38, 41). While several of these LB species have been delineated using whole DNA-DNA hybridization (3, 20, 33), most ecological or epidemiological studies have been using single loci (5, 9-11, 29, 34, 36, 38, 42, 51, 53). Although some of these loci have been convenient for species assignment of strains or to address particular epidemiological questions, they may be unsuitable to resolve evolutionary relationships among LB species, because it is not possible to define any outgroup. For example, both the 5S-23S intergenic spacer (5S-23S IGS) and the gene encoding the outer surface protein A (ospA) are present only in LB spirochete genomes (36, 43). The advantage of using appropriate housekeeping genes of LB group spirochetes is that phylogenetic trees can be rooted with sequences of relapsing fever spirochetes. This renders the data amenable to detailed evolutionary studies of LB spirochetes.LB group spirochetes differ remarkably in their patterns and levels of host association, which are likely to affect their population structures (22, 24, 46, 48). Of the three main Eurasian Borrelia species, B. afzelii is adapted to rodents, whereas B. valaisiana and most strains of B. garinii are maintained by birds (12, 15, 16, 23, 26, 45). However, B. garinii OspA serotype 4 strains in Europe have been shown to be transmitted by rodents (17, 18) and, therefore, constitute a distinct ecotype within B. garinii. These strains have also been associated with high pathogenicity in humans, and their finer-scale geographical distribution seems highly focal (10, 34, 52, 53).In this study, we analyzed the intra- and interspecific phylogenetic relationships of B. burgdorferi, B. afzelii, B. garinii, B. valaisiana, B. lusitaniae, B. bissettii, and B. spielmanii by means of a novel MLSA scheme based on chromosomal housekeeping genes (30, 48).     

The Prevalence of Multidrug Resistance Is Higher among Bovine than Human Salmonella enterica Serotype Newport,Typhimurium, and 4,5,12:i:? Isolates in the United States but Differs by Serotype and Geographic Region

Salmonella represents an important zoonotic pathogen worldwide, but the transmission dynamics between humans and animals as well as within animal populations are incompletely understood. We characterized Salmonella isolates from cattle and humans in two geographic regions of the United States, the Pacific Northwest and the Northeast, using three common subtyping methods (pulsed-field gel electrophoresis [PFGE], multilocus variable number of tandem repeat analysis [MLVA], and multilocus sequence typing [MLST]). In addition, we analyzed the distribution of antimicrobial resistance among human and cattle Salmonella isolates from the two study areas and characterized Salmonella persistence on individual dairy farms. For both Salmonella enterica subsp. enterica serotypes Newport and Typhimurium, we found multidrug resistance to be significantly associated with bovine origin of isolates, with the odds of multidrug resistance for Newport isolates from cattle approximately 18 times higher than for Newport isolates from humans. Isolates from the Northwest were significantly more likely to be multidrug resistant than those from the Northeast, and susceptible and resistant isolates appeared to represent distinct Salmonella subtypes. We detected evidence for strain diversification during Salmonella persistence on farms, which included changes in antimicrobial resistance as well as genetic changes manifested in PFGE and MLVA pattern shifts. While discriminatory power was serotype dependent, the combination of PFGE data with either MLVA or resistance typing data consistently allowed for improved subtype discrimination. Our results are consistent with the idea that cattle are an important reservoir of multidrug-resistant Salmonella infections in humans. In addition, the study provides evidence for the value of including antimicrobial resistance data in epidemiological investigations and highlights the benefits and potential problems of combining subtyping methods.Salmonella is an important human and animal pathogen worldwide. In the United States, Salmonella causes an estimated 1.4 million human cases, 15,000 hospitalizations, and more than 400 deaths each year (44, 75). Human infections can be acquired through contact with animals or humans shedding Salmonella or through contaminated environments, but the majority of human infections are food-borne, and a large number of human outbreaks have been linked to foods of animal origin (20). Beef represents one well-recognized source of human infection (71). In addition, a number of human cases have been linked to dairy products or cattle contact, for instance at state fairs or on dairy farms (for example, see references 25, 35, and 61).Salmonella enterica subsp. enterica serotypes Typhimurium and Newport are commonly isolated from human cases, including those linked to cattle (20, 61). In 2006, Salmonella serotypes Typhimurium and Newport were isolated from 17 and 8% of reported human salmonellosis cases in the United States, respectively, making them the first and third most common human disease-associated serotypes in the United States (15). S. enterica serotype 4,5,12:i:− is both genetically and antigenically closely related to Salmonella serotype Typhimurium, of which it represents a monophasic variant (62). Salmonella enterica serotype 4,5,12:i:− is characterized by a deletion of flagellar genes fliA and fliB, which prevents expression of the phase 2 flagellar antigen (60). In the United States, the prevalence of Salmonella serotype 4,5,12:i:− has increased considerably over the past 10 years, and in 2006, Salmonella serotype 4,5,12:i:− represented the sixth most commonly isolated serotype from humans in the United States (15, 60).Salmonella serotype Newport represents two distinct clonal groups or lineages—one predominantly associated with isolates from cattle (i.e., Newport lineage A) and one associated with isolates from birds (i.e., Newport lineage B) (1, 33). Members of both lineages cause human infections (1, 33). The two Newport lineages can be clearly distinguished by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE), and some correlation between genetic lineage and antimicrobial resistance profile seems to exist (1, 33). In general, Newport lineage B isolates are pansusceptible or resistant to only a few antimicrobial drugs. In contrast, lineage A is strongly associated with multidrug resistance and includes a Newport subtype commonly referred to as Newport MDR-AmpC (1, 33).The prevalence of antimicrobial resistance among Salmonella serotype Newport and Typhimurium isolates has increased worldwide during the last 2 decades, predominantly as a result of emerging multidrug-resistant (MDR) strains (14, 52, 65). During the 1990s, Salmonella serotype Typhimurium phage type DT104 with pentaresistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline (ACSSuT) increased considerably in prevalence around the world, and some isolates acquired resistance to additional antimicrobial agents, including trimethoprim or ciprofloxacin (52). MDR Salmonella serotype Typhimurium DT104 has been isolated from a wide variety of host species and caused numerous large human outbreaks around the world (65). Salmonella serotype Newport MDR-AmpC, characterized by resistance to ACSSuT and carrying a plasmid encoding resistance to amoxicillin-clavulanic acid, cefoxitin, ceftiofur, and cephalothin emerged in the United States during the late 1990s, where it quickly became widespread among humans and cattle, leading to several large human outbreaks (14).Whether antimicrobial drug use in animals facilitates the emergence of MDR human pathogens is still subject to debate. Some studies report a temporal association between the introduction of new antimicrobial agents in veterinary medicine and the emergence of antimicrobial resistance (for instance, see references 22 and 58), but questions regarding the underlying evolutionary mechanisms, the origin and distribution of naturally occurring resistance genes, and the role of antimicrobial usage among humans remain (for example, see references 2 and 66 for reviews on this topic). Moreover, some studies report a higher prevalence of antimicrobial resistance among Salmonella isolates from farm animals than humans. Gebreyes et al. (26), for instance, found a higher prevalence of antimicrobial resistance among Salmonella isolates from pigs than humans, but potential effects attributable to differences in serotype distribution are difficult to assess in this study. In recent years, risk factors for MDR have received considerable attention. Infections with MDR Salmonella strains can lead to treatment failures, may be of longer duration, and may result in more severe clinical disease. Hence, such infections lead more often to hospitalization or death than infections with susceptible Salmonella strains, but serotype or subtype differences between resistant and susceptible Salmonella strains complicate the interpretation of clinical data (34, 41, 68).Subtyping methods allow characterization of Salmonella isolates and include phenotypic methods (e.g., serotyping or phage typing) as well as molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), ribotyping, multilocus variable number of tandem repeat analysis (MLVA), and multilocus sequence typing (MLST) (5). PFGE is widely used and robust, and rigorous standardization allows comparison between laboratories (5). However, the method is time-intensive and laborious, requires careful standardization and analysis, does not allow phylogenetic inference, and can in rare cases be affected by endogenous nucleases or DNA methylation (for a review of this topic, see reference 5). MLVA and MLST are rapid, allow for easy data exchange between laboratories, and provide some phylogenetic information (5). MLVA is highly discriminatory but subject to rapid diversification and therefore most appropriate for the analysis of closely related isolates. While MLST lacks discriminatory power within Salmonella serotypes, it is highly reproducible and allows for phylogenetic analysis of more distantly related isolates (1, 5, 33). PFGE and MLST can be performed regardless of serotype, but MLVA protocols are serotype specific and have so far only been validated for a limited number of Salmonella serotypes. Moreover, MLVA can be complicated by inaccurate sizing of DNA fragments, and the degree of reliability can be considerably influenced by nucleotide composition and fragment length (5). Overall, these subtyping methods differ considerably in discriminatory power and sometimes yield conflicting results, and the most appropriate subtyping method or combination thereof strongly depends on serotype and chosen application (19, 56, 72, 76). Other genetic or phenotypic characteristics, such as antimicrobial resistance patterns or the presence of specific plasmids, have also been used successfully for subtyping in outbreak investigations and other epidemiological studies and can provide valuable additional information (7, 8, 40, 63, 64).Here we describe the distribution and subtype diversity of Salmonella serotypes Newport, 4,5,12:i:−, and Typhimurium among cattle and humans in two geographic regions of the United States, and we assess common risk factors for multidrug resistance. In addition, we utilize three Salmonella subtyping methods (PFGE, MLVA, and MLST), analyze their usefulness for characterizing isolates representing three common human-associated Salmonella serotypes, and compare the combined discriminatory power of PFGE and MLVA to that of PFGE and antimicrobial resistance patterns.     

Regulatory Diversity of TUP1 in Cryptococcus neoformans

Cryptococcus neoformans serotype A strains, the major cause of cryptococcosis, are distributed worldwide, while serotype D strains are more concentrated in Central Europe. We have previously shown that deletion of the global regulator TUP1 in serotype D isolates results in a novel peptide-mediated, density-dependent growth phenotype that mimics quorum sensing and is not known to exist in other fungi. Unlike for tup1Δ strains of serotype D, the density-dependent growth phenotype was found to be absent in tup1Δ strains of serotype A which had been derived from several different genetic clusters. The serotype A H99 tup1Δ strain showed less retardation in the growth rate than tup1Δ strains of serotype D, but the mating efficiency was found to be similar in both serotypes. Deletion of TUP1 in the H99 strain resulted in significantly enhanced capsule production and defective melanin formation and also revealed a unique regulatory role of the TUP1 gene in maintaining iron/copper homeostasis. Differential expression of various genes involved in capsule formation and iron/copper homeostasis was observed between the wild-type and tup1Δ H99 strains. Furthermore, the H99 tup1Δ strain displayed pleiotropic effects which included sensitivity to sodium dodecyl sulfate, susceptibility to fluconazole, and attenuated virulence. These results demonstrate that the global regulator TUP1 has pathobiological significance and plays both conserved and distinct roles in serotype A and D strains of C. neoformans.The fungal Tup1 proteins function as global repressors which regulate a large number of genes associated with growth, morphological differentiation, and sexual and asexual reproduction. As a consequence, tup1 mutants are known to display numerous phenotypes (9, 19, 42). The deletion of TUP1 in Candida albicans results in constitutive filamentous growth with no budding yeast cells and is accompanied by loss of virulence (2, 32). In Penicillium marneffei, the only dimorphic species known in the genus Penicillium, deletion of the TUP1 homolog, tupA, confers reduced filamentation and abnormality in yeast morphogenesis (38). In the filamentous fungi Aspergillus nidulans and Neurospora crassa, deletion of the TUP1 homologs, rcoA and rco-1, respectively, severely affects growth and sexual and asexual reproduction (12, 46).Cryptococcus neoformans is a bipolar heterothallic basidiomycetous yeast with two serotypes, A and D, and the function of Tup1 has been studied only for serotype D strains (26, 27). While disruption of TUP1 in strains of serotype D did not affect yeast or hyphal cell morphology, it resulted in mating-type-dependent differences, including temperature-dependent growth, sensitivity to 0.8 M KCl, and expression of genes in several other biological pathways (26). Most importantly, tup1Δ strains displayed a peptide-mediated quorum-sensing-like phenomenon in both mating types of serotype D strains which has not been reported for any other fungal species (27).According to genome sequence data, the serotype A reference strain H99 shares 95% sequence identity with the serotype D reference strain JEC21 (29). However, serotype-specific differences between the two strains have been demonstrated in two major signaling pathways, the pheromone-responsive Cpk1 mitogen-activated protein kinase and cyclic AMP (cAMP) (5, 13, 41, 47). In addition, the high-osmolarity glycerol (HOG) pathway also showed regulatory disparity between the two serotypes (1, 8). Since the regulation of peptide-mediated quorum sensing by TUP1 is reported only for serotype D strains, we sought to determine whether the deletion of TUP1 in serotype A strains would have similar consequences. Surprisingly, we found striking differences in the phenotypes manifested by tup1Δ strains of the two serotypes. We report here the serotype-specific differences in TUP1 regulation between A and D strains and the novel regulatory role of TUP1 in maintaining iron/copper homeostasis in C. neoformans.     

Structural and Genetic Basis for the Serological Differentiation of Pasteurella multocida Heddleston Serotypes 2 and 5

Pasteurella multocida is classified into 16 serotypes according to the Heddleston typing scheme. As part of a comprehensive study to define the structural and genetic basis of this scheme, we have determined the structure of the lipopolysaccharide (LPS) produced by P. multocida strains M1404 (B:2) and P1702 (E:5), the type strains for serotypes 2 and 5, respectively. The only difference between the LPS structures made by these two strains was the absence of a phosphoethanolamine (PEtn) moiety at the 3 position of the second heptose (Hep II) in M1404. Analysis of the lpt-3 gene, required for the addition of this PEtn residue, revealed that the gene was intact in P1702 but contained a nonsense mutation in M1404. Expression of an intact copy of lpt-3 in M1404 resulted in the attachment of a PEtn residue to the 3 position of the Hep II residue, generating an LPS structure identical to that produced by P1702. We identified and characterized each of the glycosyltransferase genes required for assembly of the serotype 2 and 5 LPS outer core. Monoclonal antibodies raised against serotype 2 LPS recognized the serotype 2/5-specific outer core LPS structure, but recognition of this structure was inhibited by the PEtn residue on Hep II. These data indicate that the serological classification of strains into Heddleston serotypes 2 and 5 is dependent on the presence or absence of PEtn on Hep II.Pasteurella multocida is a gram-negative pathogen that causes serious diseases in animals and humans. It is the causative agent of fowl cholera (7), hemorrhagic septicemia in cattle (9), atrophic rhinitis in pigs (6), and dog and cat bite infections in humans (28).P. multocida isolates may be grouped serologically based on capsular antigens into five serogroups—A, B, D, E, and F—using a passive hemagglutination test with erythrocytes sensitized with capsular antigen. Structural information is available for the capsular polysaccharides synthesized by serogroups A (hyaluronic acid) (22), D (heparin) (10), and F (chondroitin) (10). The genes involved in biosynthesis of the capsules have been identified for all five serogroups (27), and capsule is a critical virulence factor for serogroups A (8) and B (3).Lipopolysaccharide (LPS) is also an important virulence factor in P. multocida (13) and can be used for the identification of strains, with two main somatic typing systems reported (14, 17). The Namioka system is based on a tube agglutination test and is able to recognize 11 serotypes (17), whereas the Heddleston system uses a gel diffusion precipitation test and can recognize 16 serotypes; the Heddleston system is currently the preferred method (14). Current classification of P. multocida strains combines capsular typing with Heddleston somatic typing. Strains are given a designation in which the first letter indicates the capsular group and the number designates the Heddleston LPS serotype (e.g., A:1 indicates a strain that is capsular group A and LPS serotype 1). LPS produced by each of the 16 Heddleston serotype strains has been examined previously for sugar content and reactivity with LPS antisera (21). The LPS isolated from serotype 2 and 5 strains was virtually identical in sodium dodecyl sulfate-polyacrylamide gel electrophoresis migration profile (19), sugar composition, and serological reactivity with anti-LPS antibodies (21). Interestingly, serotypes 2 and 5 were the only serotypes found to elaborate two isomers of heptose in their LPS, namely l-glycero-d-manno-heptose (ld-Hep) and d-glycero-d-manno-heptose (dd-Hep) (21). The aims of this study were to determine whether the LPS molecules made by these two serotypes were structurally distinct and to compare the LPS structures with those previously determined for P. multocida serotypes 1 and 3 (24-26). Furthermore, we identified the transferase genes responsible for the assembly of the outer core LPS structure in each of these strains and characterized the function of each glycosyltransferase.     

Evidence for Rare Capsular Switching in Streptococcus agalactiae

The polysaccharide capsule is a major antigenic factor in Streptococcus agalactiae (Lancefield group B streptococcus [GBS]). Previous observations suggest that exchange of capsular loci is likely to occur rather frequently in GBS, even though GBS is not known to be naturally transformable. We sought to identify and characterize putative capsular switching events, by means of a combination of phenotypic and genotypic methods, including pulsed-field gel electrophoretic profiling, multilocus sequence typing, and surface protein and pilus gene profiling. We show that capsular switching by horizontal gene transfer is not as frequent as previously suggested. Serotyping errors may be the main reason behind the overestimation of capsule switching, since phenotypic techniques are prone to errors of interpretation. The identified putative capsular transformants involved the acquisition of the entire capsular locus and were not restricted to the serotype-specific central genes, the previously suggested main mechanism underlying capsular switching. Our data, while questioning the frequency of capsular switching, provide clear evidence for in vivo capsular transformation in S. agalactiae, which may be of critical importance in planning future vaccination strategies against this pathogen.Streptococcus agalactiae (group B streptococcus [GBS]) is primarily a colonizing agent of the genitourinary and gastrointestinal tracts, but it is also a leading cause of bacterial sepsis and meningitis in neonates and is increasingly associated with invasive infections in adults (39). The capsular polysaccharide is a major GBS virulence factor and also the main target of antibody-mediated killing (11). In the last decade, conjugated multivalent vaccines have been developed and proved to be highly immunogenic, raising the possibility of the prevention of perinatal GBS disease through maternal immunization (38).Nine capsular types are recognized: Ia, Ib and II to VIII, along with a new provisional serotype IX, recently proposed (19). Comparison of the capsular locus genes suggested that the structural diversity of the capsular polysaccharide is associated with the genetic diversity of the capsular locus, possibly driven by horizontal gene transfer (9, 24). Capsular serotyping has been the classical method used in epidemiological studies to differentiate GBS isolates, although further characterization of GBS diversity includes the use of a broad range of DNA-based typing methods, such as restriction fragment length polymorphisms (RFLP), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Both PFGE and MLST have provided new clues about the population structure of S. agalactiae, particularly the recognition of diverse lineages among serotype III that were shown to differ in virulence potential and tropism (16, 25, 26, 31, 41). Although the distinction of lineages within a particular serotype has proved useful, a complete correlation between capsular type and the lineages defined by MLST was not found (4, 21, 22). Moreover, whole-genome comparative analysis of isolates expressing different serotypes showed that they sometimes share more genes than strains of the same serotype, suggesting a serotype-independent clustering of strains (43). These observations support the hypothesis that closely and divergently related clones may share the genes coding for a particular capsular type, suggesting that exchange of capsular genes in vivo may have occurred (16, 21, 22). We refer to these phenomena here as capsular switching in vivo, recognizable by the expression of different serotypes and the presence of different capsular loci in otherwise indistinguishable isolates when sampling a set of 11 loci distributed in the genome.The changes at the capsular locus were proposed to be driven by the equilibrium between the selective pressure imposed by host immunity and conservation of a particular capsular polysaccharide, as an adaptive advantage of virulent clones (4, 9, 21). Capsular switching by homologous recombination would be facilitated by the organization of the locus encoding the capsular polysaccharide synthesis genes (cps), where the highly variable serotype determining region (cpsG-cpsK) is flanked by conserved genes (9, 24). This led to the suggestion that genetic exchange of the central part of the cps operon could be driving capsular switching (9, 22). According to Luan et al., who specifically addressed this issue, horizontal transfer of capsular genes occurs at a high level within a population without restriction to genetic background. The authors of that study also suggest that since only advantageous combinations of genotype-serotype persist, these altered serotypes, due to capsular switching, are recognized at a lower frequency among stable clones (21).Capsular switching is well established in other streptococcal species such as Streptococcus pneumoniae, where spontaneous in vivo capsular transformation events were observed and characterized (28, 34). In contrast to GBS, S. pneumoniae is naturally transformable, and this is widely believed to be responsible for the ease with which this species exchanges DNA. Capsular switching may have serious impact in pneumococcal vaccination programs since it may provide the selective pressure for virulent genotypes to switch capsules and escape vaccine coverage (6), and a similar response could be seen with a future introduction of GBS vaccination (38).The aim of the present study was to evaluate the concordance between serotype and the clusters defined by PFGE and to further characterize any putative transformants to establish unequivocally that capsular switching occurs in GBS. We combined PFGE with the analysis of multiple genes spread across the GBS genome in order to identify capsular transformants and concluded that capsular switching events occur less frequently than previously thought.     

Production of Extracellular Polysaccharides by CAP Mutants of Cryptococcus neoformans

The human pathogen Cryptococcus neoformans causes meningoencephalitis. The polysaccharide capsule is one of the main virulence factors and consists of two distinct polysaccharides, glucuronoxylomannan (GXM) and galactoxylomannan (GalXM). How capsular polysaccharides are synthesized, transported, and assembled is largely unknown. Previously, it was shown that mutations in the CAP10, CAP59, CAP60, and CAP64 genes result in an acapsular phenotype. Here, it is shown that these acapsular mutants do secrete GalXM and GXM-like polymers. GXM and GalXM antibodies specifically reacted with whole cells and the growth medium of the wild type and CAP mutants, indicating that the capsule polysaccharides adhere to the cell wall and are shed into the environment. These polysaccharides were purified from the medium, either with or without anion-exchange chromatography. Monosaccharide analysis of polysaccharide fractions by gas-liquid chromatography/mass spectrometry showed that wild-type cells secrete both GalXM and GXM. The CAP mutants, on the other hand, were shown to secrete GalXM and GXM-like polymers. Notably, the GalXM polymers were shown to contain glucuronic acid. One-dimensional ¹H nuclear magnetic resonance confirmed that the CAP mutants secrete GalXM and also showed the presence of O-acetylated polymers. This is the first time it is shown that CAP mutants secrete GXM-like polymers in addition to GalXM. The small amount of this GXM-like polymer, 1 to 5% of the total amount of secreted polysaccharides, may explain the acapsular phenotype.Cryptococcus neoformans of the A (var. grubii [24]) and D (var. neoformans [36]) serotypes are the causative agents of cryptococcosis, of which the most common clinical form is meningoencephalitis. This disease is related to immunocompromised patients but can also occur in immunocompetent individuals (4, 19, 38). One of the main virulence factors is the polysaccharide capsule (2, 5, 17, 21, 27, 35). This capsule enables the yeast-like fungus to survive the harsh environment of the human body by using its immunomodulatory properties that enable immune evasion and by preventing killing through phagocytosis by macrophages (44, 45).The capsule consists of a low percentage of mannoproteins (46) and the polysaccharides glucuronoxylomannan (GXM) and galactoxylomannan (GalXM) in a mass ratio of about 10:1 (14, 16, 17). Little is known about the synthesis of GXM and GalXM and their transport toward the cell surface. A mutation in the Sec4/Rab8 GTPase homologue was recently shown to affect protein secretion as well as polysaccharide secretion and resulted in intracellular accumulation of vesicles containing GXM (51). From this and the fact that GXM has been detected in extracellular vesicles, it was proposed that polysaccharides are packaged in such vesicles to cross the cell wall to reach the extracellular environment (47).Mutation analysis has revealed four genes, called CAP10, CAP59, CAP60, and CAP64, which give an acapsular phenotype when inactivated (7, 9-13). The precise role of the encoded Cap proteins is unknown. Cap59 has been suggested to play a role in extracellular trafficking of multimeric forms of GXM molecules (26). Moreover, it may play a role in the assembly of GXM, since it shares homology with a mannosyltransferase (48). Like Cap59, Cap60 is a putative mannosyltransferase. Cap10 shares homology with a xylosyltransferase and therefore may also be involved in capsule assembly (34), like the recently identified xylosyltransferase encoded by CXT1 (33). This transferase has been shown to play a direct role in the synthesis of both of the capsular polysaccharides but is especially active in the addition of xyloses to the GalXM polysaccharide. CAP64 shares homology with so-called CAS genes, encoding proteins involved in O acetylation of GXM (40).Structural analysis has revealed a relatively clear picture of the buildup of the GXM and GalXM polysaccharides (14, 50) (Fig. ​(Fig.1).1). Some variability in the chemical structures of the capsular polysaccharides has been described, even within the capsule of a particular strain (40, 50). In addition, GalXM has been shown to also contain, besides galactopyranose, galactofuranose in trace amounts (1, 29). The two C. neoformans serotypes A and D are distinguished based on variation in the position of the different xylose residues in the GXM repeating unit (30). The structure of the GalXM repeating unit was analyzed by using a fraction of purified polysaccharides secreted in the medium by a mutant of the D serotype called the CAP67 mutant. This strain is mutated in the same gene as a serotype A CAP59 mutant. The number of xylose residues can vary from zero up to six within the GalXM repeating unit (Fig. ​(Fig.1)1) (50).Open in a separate windowFIG. 1.Chemical structure of GXM and GalXM monomers. Large strands of these monomers form polymers of up to 1 × 10⁶ to 7 × 10⁶ daltons for GXM and 1 × 10⁵ daltons for GalXM. Ratios vary between serotypes. Shown are serotype A GXM, Man 3/Xyl 2/GlcA 1, and GalXM, Gal 6/Man 4/Xyl 1.6 (shown are three xyloses). The degree of O acetylation is not shown. The picture is based on data from reference 3.So far, secreted polysaccharides in the medium of the serotype D CAP67 mutant and the corresponding serotype A CAP59 mutant have been analyzed (41, 50). It was shown that these mutants secrete GalXM but not GXM in the medium. However, it is shown here that these mutants, as well as the serotype A CAP10, CAP60, and CAP64 mutants, also secrete GXM-like polymers in addition to GalXM. Moreover, part of GalXM seems to contain glucuronic acid, supporting earlier findings (16, 49).     

Synergistic Effects of Sodium Chloride,Glucose, and Temperature on Biofilm Formation by Listeria monocytogenes Serotype 1/2a and 4b Strains

Biofilm formation by Listeria monocytogenes is generally associated with its persistence in the food-processing environment. Serotype 1/2a strains make up more than 50% of the total isolates recovered from food and the environment, while serotype 4b strains are most often associated with major outbreaks of human listeriosis. Using a microplate assay with crystal violet staining, we examined biofilm formation by 18 strains of each serotype in tryptic soy broth with varying concentrations of glucose (from 0.25% to 10.0%, wt/vol), sodium chloride (from 0.5% to 7.0%, wt/vol) and ethanol (from 1% to 5.0%, vol/vol), and at different temperatures (22.5°C, 30°C, and 37°C). A synergistic effect on biofilm formation was observed for glucose, sodium chloride, and temperature. The serotype 1/2a strains generally formed higher-density biofilms than the 4b strains under most conditions tested. Interestingly, most serotype 4b strains had a higher growth rate than the 1/2a strains, suggesting that the growth rate may not be directly related to the capacity for biofilm formation. Crystal violet was found to stain both bacterial cells and biofilm matrix material. The enhancement in biofilm formation by environmental factors was apparently due to the production of extracellular polymeric substances instead of the accumulation of viable biofilm cells.Listeria monocytogenes, a Gram-positive bacterium, is capable of causing severe food-borne infections in both humans and animals. The organism is ubiquitous in the environment and can grow in a wide variety of foods, including those stored at refrigeration temperatures. It is particularly difficult to eliminate this bacterium from ready-to-eat foods and food-processing equipment (19). The ability to form biofilms protects the bacterium from stresses in food-processing environments (13, 25). Among the 13 different serotypes described, serotypes 1/2a, 1/2b, and 4b are involved in the majority of human cases of listeriosis. Serotype 4b strains have accounted for most human outbreaks, whereas the majority of L. monocytogenes strains isolated from foods or food-processing plants belong to serotype 1/2a (19).Comparative studies to link the phenotypic attributes of L. monocytogenes strains to serotypes have obtained variable results. Buncic et al. (4) have shown that serotype 1/2a isolates were more resistant to antilisterial bacteriocins than serotype 4b strains at 4°C. They also found that 4b isolates exhibited greater resistance to heat treatments at 60°C and were easier to recover than 1/2a strains immediately following cold storage. Bruhn et al. (3) observed that 1/2a strains (lineage II) grew faster than 4b and 1/2b (lineage I) strains in commonly used enrichment broth media (University of Vermont media I and II). However, other studies have indicated that similar differences could not be linked to a serotype (14), and sequencing results have shown a syntenic relationship between strains of the two serotypes (27).Some L. monocytogenes strains have consistently been isolated from food-processing plants over many years (1, 28). Although several studies have been carried out to identify differences in cell adherence and biofilm formation among different serotypes, conflicting results were obtained. Lineage I isolates (including serotypes 4b, 1/2b, 3c, and 3b) were found to produce higher-density biofilms than lineage II isolates (including serotypes 1/2a, 1/2c, and 3a) (8, 28). However, this conclusion was not supported by other studies (1, 7, 18). For serotype 4b strains, the capacity to form biofilms was reduced when the nutrient level in a medium decreased, while serotype 1/2a strains were not similarly affected (11).It has been suggested that the formation of a biofilm is a stress response by bacterial cells (15, 16). Biofilm research under laboratory conditions may not reflect biofilm formation in the environment. To investigate the behavior of L. monocytogenes in biofilms, a simulated food-processing (SFP) system including several stresses was designed (30). The SFP system was used to study 1/2a and 4b strains in mixed-culture biofilms (31). Bacterial cells from a 1/2a cocktail predominated over 4b strains when exposed to the SFP system for 4 weeks, but no competitive inhibition was observed. Environmental factors, including temperature, sugar, salt, pH, and nutrients that are common in foods and food-processing environments, have been demonstrated to have impacts on L. monocytogenes adhesion and biofilm formation (25). The objectives of this study were to investigate and compare biofilm formation between L. monocytogenes serotype 1/2a strains and serotype 4b strains under a variety of environmental conditions, including different temperatures and varying concentrations of salt, sugar, and ethanol, and to examine the synergistic effects of these factors on biofilm formation by both serotypes.     

Roles of Minor Pilin Subunits Spy0125 and Spy0130 in the Serotype M1 Streptococcus pyogenes Strain SF370

Adhesive pili on the surface of the serotype M1 Streptococcus pyogenes strain SF370 are composed of a major backbone subunit (Spy0128) and two minor subunits (Spy0125 and Spy0130), joined covalently by a pilin polymerase (Spy0129). Previous studies using recombinant proteins showed that both minor subunits bind to human pharyngeal (Detroit) cells (A. G. Manetti et al., Mol. Microbiol. 64:968-983, 2007), suggesting both may act as pilus-presented adhesins. While confirming these binding properties, studies described here indicate that Spy0125 is the pilus-presented adhesin and that Spy0130 has a distinct role as a wall linker. Pili were localized predominantly to cell wall fractions of the wild-type S. pyogenes parent strain and a spy0125 deletion mutant. In contrast, they were found almost exclusively in culture supernatants in both spy0130 and srtA deletion mutants, indicating that the housekeeping sortase (SrtA) attaches pili to the cell wall by using Spy0130 as a linker protein. Adhesion assays with antisera specific for individual subunits showed that only anti-rSpy0125 serum inhibited adhesion of wild-type S. pyogenes to human keratinocytes and tonsil epithelium to a significant extent. Spy0125 was localized to the tip of pili, based on a combination of mutant analysis and liquid chromatography-tandem mass spectrometry analysis of purified pili. Assays comparing parent and mutant strains confirmed its role as the adhesin. Unexpectedly, apparent spontaneous cleavage of a labile, proline-rich (8 of 14 residues) sequence separating the N-terminal ∼1/3 and C-terminal ∼2/3 of Spy0125 leads to loss of the N-terminal region, but analysis of internal spy0125 deletion mutants confirmed that this has no significant effect on adhesion.The group A Streptococcus (S. pyogenes) is an exclusively human pathogen that commonly colonizes either the pharynx or skin, where local spread can give rise to various inflammatory conditions such as pharyngitis, tonsillitis, sinusitis, or erysipelas. Although often mild and self-limiting, GAS infections are occasionally very severe and sometimes lead to life-threatening diseases, such as necrotizing fasciitis or streptococcal toxic shock syndrome. A wide variety of cell surface components and extracellular products have been shown or suggested to play important roles in S. pyogenes virulence, including cell surface pili (1, 6, 32). Pili expressed by the serotype M1 S. pyogenes strain SF370 mediate specific adhesion to intact human tonsil epithelia and to primary human keratinocytes, as well as cultured keratinocyte-derived HaCaT cells, but not to Hep-2 or A549 cells (1). They also contribute to adhesion to a human pharyngeal cell line (Detroit cells) and to biofilm formation (29).Over the past 5 years, pili have been discovered on an increasing number of important Gram-positive bacterial pathogens, including Bacillus cereus (4), Bacillus anthracis (4, 5), Corynebacterium diphtheriae (13, 14, 19, 26, 27, 44, 46, 47), Streptococcus agalactiae (7, 23, 38), and Streptococcus pneumoniae (2, 3, 24, 25, 34), as well as S. pyogenes (1, 29, 32). All these species produce pili that are composed of a single major subunit plus either one or two minor subunits. During assembly, the individual subunits are covalently linked to each other via intermolecular isopeptide bonds, catalyzed by specialized membrane-associated transpeptidases that may be described as pilin polymerases (4, 7, 25, 41, 44, 46). These are related to the classical housekeeping sortase (usually, but not always, designated SrtA) that is responsible for anchoring many proteins to Gram-positive bacterial cell walls (30, 31, 33). The C-terminal ends of sortase target proteins include a cell wall sorting (CWS) motif consisting, in most cases, of Leu-Pro-X-Thr-Gly (LPXTG, where X can be any amino acid) (11, 40). Sortases cleave this substrate between the Thr and Gly residues and produce an intermolecular isopeptide bond linking the Thr to a free amino group provided by a specific target. In attaching proteins to the cell wall, the target amino group is provided by the lipid II peptidoglycan precursor (30, 36, 40). In joining pilus subunits, the target is the ɛ-amino group in the side chain of a specific Lys residue in the second subunit (14, 18, 19). Current models of pilus biogenesis envisage repeated transpeptidation reactions adding additional subunits to the base of the growing pilus, until the terminal subunit is eventually linked covalently via an intermolecular isopeptide bond to the cell wall (28, 41, 45).The major subunit (sometimes called the backbone or shaft subunit) extends along the length of the pilus and appears to play a structural role, while minor subunits have been detected either at the tip, the base, and/or at occasional intervals along the shaft, depending on the species (4, 23, 24, 32, 47). In S. pneumoniae and S. agalactiae one of the minor subunits acts as an adhesin, while the second appears to act as a linker between the base of the assembled pilus and the cell wall (7, 15, 22, 34, 35). It was originally suggested that both minor subunits of C. diphtheriae pili could act as adhesins (27). However, recent data showed one of these has a wall linker role (26, 44) and may therefore not function as an adhesin.S. pyogenes strain SF370 pili are composed of a major (backbone) subunit, termed Spy0128, plus two minor subunits, called Spy0125 and Spy0130 (1, 32). All three are required for efficient adhesion to target cells (1). Studies employing purified recombinant proteins have shown that both of the minor subunits, but not the major subunit, bind to Detroit cells (29), suggesting both might act as pilus-presented adhesins. Here we report studies employing a combination of recombinant proteins, specific antisera, and allelic replacement mutants which show that only Spy0125 is the pilus-presented adhesin and that Spy0130 has a distinct role in linking pili to the cell wall.     

Alignment of the c-Type Cytochrome OmcS along Pili of Geobacter sulfurreducens

Immunogold localization revealed that OmcS, a cytochrome that is required for Fe(III) oxide reduction by Geobacter sulfurreducens, was localized along the pili. The apparent spacing between OmcS molecules suggests that OmcS facilitates electron transfer from pili to Fe(III) oxides rather than promoting electron conduction along the length of the pili.There are multiple competing/complementary models for extracellular electron transfer in Fe(III)- and electrode-reducing microorganisms (8, 18, 20, 44). Which mechanisms prevail in different microorganisms or environmental conditions may greatly influence which microorganisms compete most successfully in sedimentary environments or on the surfaces of electrodes and can impact practical decisions on the best strategies to promote Fe(III) reduction for bioremediation applications (18, 19) or to enhance the power output of microbial fuel cells (18, 21).The three most commonly considered mechanisms for electron transfer to extracellular electron acceptors are (i) direct contact between redox-active proteins on the outer surfaces of the cells and the electron acceptor, (ii) electron transfer via soluble electron shuttling molecules, and (iii) the conduction of electrons along pili or other filamentous structures. Evidence for the first mechanism includes the necessity for direct cell-Fe(III) oxide contact in Geobacter species (34) and the finding that intensively studied Fe(III)- and electrode-reducing microorganisms, such as Geobacter sulfurreducens and Shewanella oneidensis MR-1, display redox-active proteins on their outer cell surfaces that could have access to extracellular electron acceptors (1, 2, 12, 15, 27, 28, 31-33). Deletion of the genes for these proteins often inhibits Fe(III) reduction (1, 4, 7, 15, 17, 28, 40) and electron transfer to electrodes (5, 7, 11, 33). In some instances, these proteins have been purified and shown to have the capacity to reduce Fe(III) and other potential electron acceptors in vitro (10, 13, 29, 38, 42, 43, 48, 49).Evidence for the second mechanism includes the ability of some microorganisms to reduce Fe(III) that they cannot directly contact, which can be associated with the accumulation of soluble substances that can promote electron shuttling (17, 22, 26, 35, 36, 47). In microbial fuel cell studies, an abundance of planktonic cells and/or the loss of current-producing capacity when the medium is replaced is consistent with the presence of an electron shuttle (3, 14, 26). Furthermore, a soluble electron shuttle is the most likely explanation for the electrochemical signatures of some microorganisms growing on an electrode surface (26, 46).Evidence for the third mechanism is more circumstantial (19). Filaments that have conductive properties have been identified in Shewanella (7) and Geobacter (41) species. To date, conductance has been measured only across the diameter of the filaments, not along the length. The evidence that the conductive filaments were involved in extracellular electron transfer in Shewanella was the finding that deletion of the genes for the c-type cytochromes OmcA and MtrC, which are necessary for extracellular electron transfer, resulted in nonconductive filaments, suggesting that the cytochromes were associated with the filaments (7). However, subsequent studies specifically designed to localize these cytochromes revealed that, although the cytochromes were extracellular, they were attached to the cells or in the exopolymeric matrix and not aligned along the pili (24, 25, 30, 40, 43). Subsequent reviews of electron transfer to Fe(III) in Shewanella oneidensis (44, 45) appear to have dropped the nanowire concept and focused on the first and second mechanisms.Geobacter sulfurreducens has a number of c-type cytochromes (15, 28) and multicopper proteins (12, 27) that have been demonstrated or proposed to be on the outer cell surface and are essential for extracellular electron transfer. Immunolocalization and proteolysis studies demonstrated that the cytochrome OmcB, which is essential for optimal Fe(III) reduction (15) and highly expressed during growth on electrodes (33), is embedded in the outer membrane (39), whereas the multicopper protein OmpB, which is also required for Fe(III) oxide reduction (27), is exposed on the outer cell surface (39).OmcS is one of the most abundant cytochromes that can readily be sheared from the outer surfaces of G. sulfurreducens cells (28). It is essential for the reduction of Fe(III) oxide (28) and for electron transfer to electrodes under some conditions (11). Therefore, the localization of this important protein was further investigated.     

Comparative Genomics and Transduction Potential of Enterococcus faecalis Temperate Bacteriophages

To determine the relative importance of temperate bacteriophage in the horizontal gene transfer of fitness and virulence determinants of Enterococcus faecalis, a panel of 47 bacteremia isolates were treated with the inducing agents mitomycin C, norfloxacin, and UV radiation. Thirty-four phages were purified from culture supernatants and discriminated using pulsed-field gel electrophoresis (PFGE) and restriction mapping. From these analyses the genomes of eight representative phages were pyrosequenced, revealing four distinct groups of phages. Three groups of phages, ΦFL1 to 3, were found to be sequence related, with ΦFL1A to C and ΦFL2A and B sharing the greatest identity (87 to 88%), while ΦFL3A and B share 37 to 41% identity with ΦFL1 and 2. ΦFL4A shares 3 to 12% identity with the phages ΦFL1 to 3. The ΦFL3A and B phages possess a high DNA sequence identity with the morphogenesis and lysis modules of Lactococcus lactis subsp. cremoris prophages. Homologs of the Streptococcus mitis platelet binding phage tail proteins, PblA and PblB, are encoded on each sequenced E. faecalis phage. Few other phage genes encoding potential virulence functions were identified, and there was little evidence of carriage of lysogenic conversion genes distal to endolysin, as has been observed with genomes of many temperate phages from the opportunist pathogens Staphylococcus aureus and Streptococcus pyogenes. E. faecalis JH2-2 lysogens were generated using the eight phages, and these were examined for their relative fitness in Galleria mellonella. Several lysogens exhibited different effects upon survival of G. mellonella compared to their isogenic parent. The eight phages were tested for their ability to package host DNA, and three were shown to be very effective for generalized transduction of naive host cells of the laboratory strains OG1RF and JH2-2.Enterococcus faecalis is a member of the natural flora of humans and colonizes the gastrointestinal and vaginal tracts and the oral cavity. In recent years it has emerged as an important opportunistic nosocomial pathogen and is a causative agent of bacteremia, infective endocarditis, and surgical wound and urinary tract infections. The accumulation of acquired antibiotic resistance determinants, in addition to its intrinsic resistance and tenacity, has given rise to the evolution of clinical isolates of E. faecalis that are therapeutically problematic (19). Greater notoriety was afforded to this species following the observed transfer of the conjugative transposon Tn1546 to Staphylococcus aureus, imparting vancomycin resistance (11). Subsequent analysis has revealed that multiple independent E. faecalis-dependent vanA transfers had occurred in the United States prior to 2007 (50). This places enterococci in an important and dynamic position within the health care system, warranting their increased study.The specific determinants that are proposed to contribute to the virulence of E. faecalis are not universally present, and expression of the cognate genes is variable (21, 37). For example, in a recent study of 106 clonally diverse strains of E. faecalis the metallopeptidase gelatinase (GelE) was shown to be expressed in less than 60% of 106 genotypically positive isolates, whereas expression of cytolysin was less frequently observed (expression in ∼25% of isolates, with 30% being genotypically positive) (33). A proposed pathogenicity island identified with E. faecalis V583 (49) is composed of a variable gene set encoding the virulence determinants enterococcal surface protein, cytolysin, and aggregation substance. This highly variable 150-kb mobile element contains many components of unknown function that are hypothesized to facilitate survival and/or transmission in the health care setting (34, 40, 49).Two sequenced and annotated genomes of E. faecalis have been completed and published to date. These are the blood isolate and first-observed vancomycin-resistant strain V583 (40) and the oral isolate OG1RF, used as a common laboratory strain (8). A major difference between these genomes is the presence in V583 of seven regions containing phage-associated sequences. In contrast, OG1RF contains only one phage remnant, which was proposed by McBride et al. (33) to form part of the core genome, a theory supported by the presence in OG1RF of this phage remnant region together with two CRISPR loci. CRISPR sequences provide sequence-specific resistance to bacteriophages via the assembly of phage DNA sequences interspersed as spacers between repeats, in concert with associated cas genes, which collectively operate as an RNA-based gene silencing mechanism (5, 6, 28, 30, 36, 42). This elegant heritable mechanism is proposed to limit horizontal gene transfer of bacteriophage, transposable elements, and conjugative plasmids (9, 10, 32).Within the firmicute division of Gram-positive bacteria, temperate bacteriophages are key vectors for the horizontal transfer of virulence genes. In Staphylococcus aureus, bacteriophages encode and mobilize an impressive array of immune evasion genes (54, 55) and Panton-Valentine leukocidin (43). Several bacteriophage-encoded virulence determinants also contribute to pathogenesis in group A Streptococcus (2, 3, 4).The role of bacteriophages in the virulence of E. faecalis is not clear. Encoded within seven phage-related sequences of strain V583, there are multiple reported homologs of the Streptococcus mitis platelet-binding proteins PblA and PblB (7) and a ferrochelatase (40). In contrast, the absence of mobile genetic elements (MGEs) in strain OG1RF led Bourgogne et al. (8) to speculate that they did not engender virulence in E. faecalis.In this study we determined the morphology and complete genome sequences of eight induced bacteriophages purified from clinical isolates of E. faecalis. We sought to determine the potential carriage of genes that might contribute to the virulence or fitness of this organism and characterize the capacity of these phages to participate in transduction.     

Transmission Networks and Population Turnover of Echovirus 30

Globally, echovirus 30 (E30) is one of the most frequently identified enteroviruses and a major cause of meningitis. Despite its wide distribution, little is known about its transmission networks or the dynamics of its recombination and geographical spread. To address this, we have conducted an extensive molecular epidemiology and evolutionary study of E30 isolates collected over 8 years from a geographically wide sample base (11 European countries, Asia, and Australia). 3Dpol sequences fell into several distinct phylogenetic groups, interspersed with other species B serotypes, enabling E30 isolates to be classified into 38 recombinant forms (RFs). Substitutions in VP1 and 3Dpol regions occurred predominantly at synonymous sites (ratio of nonsynonymous to synonymous substitutions, 0.05) with VP1 showing a rapid substitution rate of 8.3 × 10⁻³ substitutions per site per year. Recombination frequency was tightly correlated with VP1 divergence; viruses differing by evolutionary distances of >0.1 (or 6 years divergent evolution) almost invariably (>97%) had different 3Dpol groups. Frequencies of shared 3Dpol groups additionally correlated with geographical distances, with Europe and South Asia showing turnover of entirely distinct virus populations. Population turnover of E30 was characterized by repeated cycles of emergence, dominance, and disappearance of individual RFs over periods of 3 to 5 years, although the existence and nature of evolutionary selection underlying these population replacements remain unclear. The occurrence of frequent “sporadic” recombinants embedded within VP1 groupings of other RFs and the much greater number of 3Dpol groups than separately identifiable VP1 lineages suggest frequent recombination with an external diverse reservoir of non-E30 viruses.The genus Enterovirus in the family Picornaviridae is a group of nonenveloped RNA viruses that cause a wide range of diseases in humans and other mammals. Enteroviruses contain a positive-sense RNA genome of approximately 7,500 nucleotides encoding a polyprotein that after cleavage yields structural (capsid proteins VP1 to VP4) and nonstructural (2A to 3D) proteins. Primary infection with an enterovirus leads to viral replication in the tissue around the gastrointestinal tract, followed by a transient viremia and sometimes migration into other tissues (6, 44). Although infection in immunocompetent individuals is often asymptomatic or causes mild febrile illness, enteroviruses are a common etiological agent in aseptic meningitis, encephalitis, and paralysis in individuals of all ages, with persistent and/or widely disseminated systemic infection in immunosuppressed individuals and neonates (12, 19, 23).Enteroviruses were originally classified as polioviruses, coxsackie virus type A or B viruses, or echoviruses (enteric cytopathic human orphan viruses), depending upon the infectious properties of the virus such as pathogenicity in mice (reviewed in reference 22). From the 1960s onwards, enteroviruses within these groups were further differentiated into serotypes originally by using panels of specific neutralizing antisera and, more recently, by sequence comparisons of structural gene regions such as VP1 (9, 34, 38, 43). There are currently over 100 recognized human enterovirus serotypes that fall into four main species (designated A to D) using phylogenetic analysis (54). The Enterovirus genus additionally contains several other species infecting primates, cattle, and pigs and has recently been expanded to include the genetically related human rhinovirus A and B (54).The species B serotype, echovirus 30 (E30), is a major cause of meningitis in both children and adults. Among the many serotypes associated with this disease presentation, E30 is generally the most commonly isolated in Europe (8, 31, 49), the United States (10, 37), Asia (1, 60), and South America (33). E30 infections typically occur as a series of outbreaks every 3 to 5 years, frequently over large geographical areas. For example, high frequencies of E30 detection in meningitis cases and surveillance programs were reported for 2000 to 2001 throughout Europe, including Denmark (58), Belgium (57), Cyprus (45), Germany (46), and France (3, 5), and again in 2005 to 2006 (8). Similarly, in the United States, long-term surveillance by the Centers for Disease Control and Prevention revealed peaks of E30 isolation in 1981, 1991 to 1993, 1997, and 2003 (10, 37). The underlying basis for this periodicity in E30 infections and the possible association of different genetic variants of E30 with outbreaks are currently poorly understood.At any one time point, a range of different species B enterovirus serotypes circulate in human populations. The evolution of enteroviruses occurs through genetic drift and, over much longer periods, antigenic diversification in the structural gene region encoding the virus capsid (7, 14, 25, 30, 51, 55); it may also occur by recombination between the capsid and nonstructural coding parts of the genome and the 5′ untranslated region (2, 13, 16, 20, 26, 28, 29, 35, 39, 41, 47, 48, 53). To date, almost all documented examples of recombination have been limited to members of the same species (e.g., between species B serotypes), with the exception of the 5′ untranslated region, where only a single genetic group can be identified within human species A and B and a second with species C and D (48).In this study, we have carried out an extensive investigation of VP1 sequence divergence and recombination through sequencing the 3Dpol region of E30 isolates and samples collected from several European countries, Southeast Asia, and Australia over a combined 8-year observation period. Using this geographically diverse sample collection, our aims were to document the time span and geographical extent of different E30 variants as they emerged and spread during the observation period. The identification of individual recombinants of E30 provides the means to document in detail the dynamics of E30 population turnover, geographical ranges of enterovirus transmission networks, and, ultimately, the relationship between the emergence of new variants of E30 and longer-term changes in disease associations and pathogenicity.     

Detection of Infectious Adenoviruses in Environmental Waters by Fluorescence-Activated Cell Sorting Assay

Methods for rapid detection and quantification of infectious viruses in the environment are urgently needed for public health protection. A fluorescence-activated cell-sorting (FACS) assay was developed to detect infectious adenoviruses (Ads) based on the expression of viral protein during replication in cells. The assay was first developed using recombinant Ad serotype 5 (rAd5) with the E1A gene replaced by a green fluorescent protein (GFP) gene. Cells infected with rAd5 express GFP, which is captured and quantified by FACS. The results showed that rAd5 can be detected at concentrations of 1 to 10⁴ PFU per assay within 3 days, demonstrating a linear correlation between the viral concentration and the number of GFP-positive cells with an r² value of >0.9. Following the same concept, FACS assays using fluorescently labeled antibodies specific to the E1A and hexon proteins, respectively, were developed. Assays targeting hexon showed greater sensitivity than assays targeting E1A. The results demonstrated that as little as 1 PFU Ads was detected by FACS within 3 days based on hexon protein, with an r² value greater than 0.9 over a 4-log concentration range. Application of this method to environmental samples indicated positive detection of infectious Ads in 50% of primary sewage samples and 33% of secondary treated sewage samples, but none were found in 12 seawater samples. The infectious Ads ranged in quantity between 10 and 165 PFU/100 ml of sewage samples. The results indicate that the FACS assay is a rapid quantification tool for detecting infectious Ads in environmental samples and also represents a considerable advancement for rapid environmental monitoring of infectious viruses.Waterborne viral infection is one of the most important causes of human morbidity in the world. There are hundreds of different types of human viruses present in human sewage, which, if improperly treated, may become the source of contamination in drinking and recreational waters (6, 12, 19). Furthermore, as water scarcity intensifies in the nation, so has consideration of wastewater reuse as a valid and essential alternative for resolving water shortages (31).Currently, routine viral monitoring is not required for drinking or recreational waters, nor is it required for wastewater that is discharged into the environment. This lack of a monitoring effort is due largely to the lack of methods that can rapidly and sensitively detect infectious viruses in environmental samples. In the past 20 years, tremendous progress has been made in detection of viruses in the environment based on molecular technology (32, 33, 35). PCR and quantitative real-time PCR (qPCR) methods have improved both the speed and sensitivity of viral detection compared with detection by the traditional tissue culture method (2, 11, 17, 18). However, they provide little information on viral infectivity, which is crucial for human health risk assessment (22-24, 35). Our previous work using a real-time PCR assay to detect human adenoviruses (Ads) in sewage could not differentiate the infectious viruses in the secondary treated sewage from those killed by chlorination disinfection (15). In this research, we pursued an innovative approach to detecting infectious viruses in water using fluorescence-activated cell sorting (FACS). This method is rapid and sensitive, with an established record in microbiological research (29, 34, 39).FACS is a specialized type of flow cytometry which provides a method for counting and sorting a heterogeneous mixture of biological cells into two or more kinds, one cell at a time, based upon the specific light-scattering and fluorescent characteristics of each cell (4, 25, 34, 38). It is a useful method since it provides fast and quantitative recording of fluorescent signals from individual cells (14, 16, 34, 47). The FACS viral assay is based on the expression of viral protein inside the recipient cell during viral replication (16). Specific antibody labeled with fluorescence is bound to the target viral protein, which results in fluorescence emission from infected cells. Viral particles outside the cell will not be captured, because the size of virus is below the detection limit of flow cytometry. Therefore, detection of cells, which can be captured with fluorescently labeled viral antibody, is a definitive indication of the presence of infectious virus.This research used human Ads as the target for development of the FACS method. The rationale for this choice is as follows. (i) Ads are important human pathogens that may be transmitted by water consumption and water spray (aerosols) (26, 32). The health hazard associated with exposure to Ads has been demonstrated by epidemiological data and clinical research (1, 7, 9, 35, 40, 43). (ii) Ads are among the most prevalent human viruses identified in human sewage and are frequently detected in marine waters and the Great Lakes (17, 32, 33, 35). (iii) Ads are more resistant to UV disinfection than any other bacteria or viruses (3, 5, 10, 24, 41, 42, 44). Thus, they may survive wastewater treatment as increasing numbers of wastewater treatment facilities switch from chlorination to UV to avoid disinfection by-products. (iv) Some serotypes of Ads, including enteric Ad 40 and 41, are fastidious. They are difficult to detect by plaque assay, and a routine assay of infectivity takes 7 to 14 days (8, 20).In this study, recombinant Ad serotype 5 (rAd5) with the E1A gene (the first transcribed gene after infection) replaced by a green fluorescent protein (GFP) gene was first used to test for sensitivity and speed of the assay. Two other viral proteins were then used as targets for development of FACS assays using Ad serotype 2 (Ad2) and Ad41. This study demonstrated the feasibility, sensitivity, and reliability of the assay for detection of infectious Ads in environmental samples.     

Genotype-Specific Neutralization and Protection by Antibodies against Dengue Virus Type 3

Dengue viruses (DENV) comprise a family of related positive-strand RNA viruses that infect up to 100 million people annually. Currently, there is no approved vaccine or therapy to prevent infection or diminish disease severity. Protection against DENV is associated with the development of neutralizing antibodies that recognize the viral envelope (E) protein. Here, with the goal of identifying monoclonal antibodies (MAbs) that can function as postexposure therapy, we generated a panel of 82 new MAbs against DENV-3, including 24 highly neutralizing MAbs. Using yeast surface display, we localized the epitopes of the most strongly neutralizing MAbs to the lateral ridge of domain III (DIII) of the DENV type 3 (DENV-3) E protein. While several MAbs functioned prophylactically to prevent DENV-3-induced lethality in a stringent intracranial-challenge model of mice, only three MAbs exhibited therapeutic activity against a homologous strain when administered 2 days after infection. Remarkably, no MAb in our panel protected prophylactically against challenge by a strain from a heterologous DENV-3 genotype. Consistent with this, no single MAb neutralized efficiently the nine different DENV-3 strains used in this study, likely because of the sequence variation in DIII within and between genotypes. Our studies suggest that strain diversity may limit the efficacy of MAb therapy or tetravalent vaccines against DENV, as neutralization potency generally correlated with a narrowed genotype specificity.Dengue viruses (DENV) cause the most common arthropod-borne viral infection in humans worldwide, with ∼50 million to 100 million people infected annually and ∼2.5 billion people at risk (13, 61). Infection by four closely related but serologically distinct viruses of the Flavivirus genus (DENV serotypes 1, 2, 3, and 4 [DENV-1 to -4, respectively]) cause dengue fever (DF), an acute, self-limiting, yet severe, febrile illness, or dengue hemorrhagic fever and dengue shock syndrome (DHF/DSS), a potentially fatal syndrome characterized by vascular leakage and a bleeding diathesis. Specific treatment or prevention of dengue disease is supportive, as there is no approved antiviral therapy or vaccine available.DENV has an ∼11-kb, single-stranded, positive-sense RNA genome that is translated into a polyprotein and is cleaved posttranslationally into three structural (envelope [E], pre/membrane [prM], and capsid [C]) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. The three structural proteins encapsidate a single infectious RNA of the DENV genome, whereas the nonstructural proteins have key enzymatic or regulatory functions that promote replication. Additionally, several DENV proteins are multifunctional and modulate cell-intrinsic and cell-extrinsic host immune responses (10).Most flavivirus-neutralizing antibodies recognize the structural E protein (reviewed in reference 40). Based on X-ray crystallographic analysis (32, 33), the DENV E protein is divided into three domains: domain I (DI), which is an 8-stranded β-barrel, domain II (DII), which consists of 12 β-strands, and domain III (DIII), which adopts an immunoglobulin-like fold. Mature DENV virions are covered by 90 antiparallel E protein homodimers, arranged flat along the surface of the virus with quasi-icosahedral symmetry (25). Studies with mouse monoclonal antibodies (MAbs) against DENV-1 and DENV-2 have shown that highly neutralizing anti-DENV antibodies are serotype specific and recognize primarily the lateral-ridge epitope on DIII (15, 49, 53). Additionally, subcomplex-specific MAbs, which recognize some but not all DENV serotypes, recognize a distinct, adjacent epitope on the A β-strand of DIII and also may be inhibitory (16, 28, 42, 53, 56). Complex-specific or flavivirus cross-reactive MAbs recognize epitopes in both DII and DIII and are generally less strongly neutralizing (8, 53).Beyond having genetic complexity (the E proteins of the four distinct serotypes are 72 to 80% identical at the amino acid level), viruses of each serotype can be further divided into closely related genotypes (43, 44, 57). DENV-3 is divided into 4 or 5 distinct genotypes (depending on the study), with up to 4% amino acid variation between genotypes and up to 2% amino acid variation within a genotype (26, 58, 62). The individual genotypes of DENV-3 are separated temporally and geographically (1), with genotype I (gI) strains located in Indonesia, gII strains in Thailand, and gIII strains in Sri Lanka and the Americas. Few examples of strains of gIV and gV exist from samples isolated after 1980 (26, 62). Infection with one DENV serotype is believed to confer long-term durable immunity against strains of the homologous but not heterologous DENV serotypes due to the specificity of neutralizing antibodies and protective CD8⁺ T cells (45). Indeed, epidemiological studies suggest that a preexisting cross-reactive antibody (7, 24) and/or T cells (34, 35, 64) can enhance the risk of DHF/DSS during challenge with a distinct DENV serotype. Nonetheless, few reports have examined how intergenotypic or even strain variation within a serotype affects the protective efficacy of neutralizing antibodies. This concept is important because the development of tetravalent DENV vaccines with attenuated prototype strains assumes that neutralizing antibody responses, which are lower during vaccination than during natural infection, will protect completely against all genotypes within a given serotype (60). However, a recent study showed markedly disparate neutralizing activities and levels of protection of individual anti-DENV-1 MAbs against different DENV-1 genotypes (49).Herein, we developed a panel of 82 new DENV-3 MAbs and examined their cross-reactivities, epitope specificities, neutralization potential at the genotype level in cell culture, and protective capacities in vivo. The majority of strongly neutralizing MAbs in this panel mapped to specific sites in DIII of the E protein. Remarkably, because of the scale of the sequence variation of DENV-3 strains, most of the protective antibodies showed significant strain specificity in their functional profiles.     

Rapid Microarray-Based Genotyping of Enterohemorrhagic Escherichia coli Serotype O156:H25/H?/Hnt Isolates from Cattle and Clonal Relationship Analysis

Since enterohemorrhagic Escherichia coli (EHEC) isolates of serogroup O156 have been obtained from human diarrhea patients and asymptomatic carriers, we studied cattle as a potential reservoir for these bacteria. E. coli isolates serotyped by agglutination as O156:H25/H−/Hnt strains (n = 32) were isolated from three cattle farms during a period of 21 months and characterized by rapid microarray-based genotyping. The serotyping by agglutination of the O156 isolates was not confirmed in some cases by the results of DNA-based serotyping as only 25 of the 32 isolates were conclusively identified as O156:H25. In the multilocus sequence typing (MLST) analysis, all EHEC O156:H25 isolates were characterized as sequence type 300 (ST300) and ST688, which differ by a single-nucleotide exchange in the purA gene. Oligonucleotide microarrays allow simultaneous detection of a wider range of EHEC-associated and other E. coli virulence markers than other methods. All O156:H25 isolates showed a wide spectrum of virulence factors typical for EHEC. The stx₁ genes combined with the EHEC hlyA (hlyA_EHEC) gene, the eae gene of the ζ subtype, as well as numerous other virulence markers were present in all EHEC O156:H25 strains. The behavior of eight different cluster groups, including four that were EHEC O156:H25, was monitored in space and time. Variations in the O156 cluster groups were detected. The results of the cluster analysis suggest that some O156:H25 strains had the genetic potential for a long persistence in the host and on the farm, while other strains did not. As judged by their pattern of virulence markers, E. coli O156:H25 isolates of bovine origin may represent a considerable risk for human infection. Our results showed that the miniaturized E. coli oligonucleotide arrays are an excellent tool for the rapid detection of a large number of virulence markers.Shiga toxin-producing Escherichia coli (STEC) strains comprise a group of zoonotic enteric pathogens (45). In humans, infections with some STEC serotypes may result in hemorrhagic or nonhemorrhagic diarrhea, which can be complicated by the hemolytic uremic syndrome (HUS) (32). These STEC strains are also designated enterohemorrhagic Escherichia coli (EHEC). Consequently, EHEC strains represent a subgroup of STEC with high pathogenic potential for humans. Although E. coli O157:H7 is the most frequent EHEC serotype implicated in HUS, other serotypes can also cause this complication. Non-O157:H7 EHEC strains including serotypes O26:H11/H−, O103:H2/H−, O111:H8/H10/H−, and O145:H28/H25/H− and sorbitol-fermenting E. coli O157:H− isolates are present in about 50% of stool cultures from German HUS patients (10, 42). However, STEC strains that cause human infection belong to a large number of E. coli serotypes, although a small number of STEC isolates of serogroup O156 were associated with human disease (7). Strains of the serotypes O156:H1/H8/H21/H25 were found in human cases of diarrhea or asymptomatic infections (9, 22, 25, 26). The detection of STEC of serogroup O156 from healthy and diseased ruminants such as cattle, sheep, and goats was reported by several authors (1, 11-13, 21, 39, 46, 50, 52). Additional EHEC-associated virulence genes such as stx, eae, hlyA_EHEC, or nlaA were found preferentially in the serotypes O156:H25 and O156:H− (11-13, 21, 22, 50, 52).Numerous methods exist for the detection of pathogenic E. coli, including genotypic and phenotypic marker assays for the detection of virulence genes and their products (19, 47, 55, 57). All of these methods have the common drawback of screening a relatively small number of determinants simultaneously. A diagnostic DNA microarray based on the ArrayTube format of CLONDIAG GmbH was developed as a viable alternative due to its ability to screen multiple virulence markers simultaneously (2). Further microarray layouts working with the same principle but different gene targets were developed for the rapid identification of antimicrobial resistance genes in Gram-negative bacteria (5) and for the rapid DNA-based serotyping of E. coli (4). In addition, a protein microarray for E. coli O serotyping based on the ArrayTube format was described by Anjum et al. (3).The aim of our study was the molecular genotyping of bovine E. coli field isolates of serogroup O156 based on miniaturized E. coli oligonucleotide arrays in the ArrayStrip format and to combine the screening of E. coli virulence markers, antimicrobial resistance genes, and DNA serotyping targets, some of which were partially described previously for separate arrays (2, 4, 5). The epidemiological situation in the beef herds from which the isolates were obtained and the spatial and temporal behavior of the clonal distribution of E. coli serogroup O156 were analyzed during the observation period. The potential risk of the isolates inducing disease in humans was assessed.     

Cultivation of Fastidious Bacteria by Viability Staining and Micromanipulation in a Soil Substrate Membrane System

Soil substrate membrane systems allow for microcultivation of fastidious soil bacteria as mixed microbial communities. We isolated established microcolonies from these membranes by using fluorescence viability staining and micromanipulation. This approach facilitated the recovery of diverse, novel isolates, including the recalcitrant bacterium Leifsonia xyli, a plant pathogen that has never been isolated outside the host.The majority of bacterial species have never been recovered in the laboratory (1, 14, 19, 24). In the last decade, novel cultivation approaches have successfully been used to recover “unculturables” from a diverse range of divisions (23, 25, 29). Most strategies have targeted marine environments (4, 23, 25, 32), but soil offers the potential for the investigation of vast numbers of undescribed species (20, 29). Rapid advances have been made toward culturing soil bacteria by reformulating and diluting traditional media, extending incubation times, and using alternative gelling agents (8, 21, 29).The soil substrate membrane system (SSMS) is a diffusion chamber approach that uses extracts from the soil of interest as the growth substrate, thereby mimicking the environment under investigation (12). The SSMS enriches for slow-growing oligophiles, a proportion of which are subsequently capable of growing on complex media (23, 25, 27, 30, 32). However, the SSMS results in mixed microbial communities, with the consequent difficulty in isolation of individual microcolonies for further characterization (10).Micromanipulation has been widely used for the isolation of specific cell morphotypes for downstream applications in molecular diagnostics or proteomics (5, 15). This simple technology offers the opportunity to select established microcolonies of a specific morphotype from the SSMS when combined with fluorescence visualization (3, 11). Here, we have combined the SSMS, fluorescence viability staining, and advanced micromanipulation for targeted isolation of viable, microcolony-forming soil bacteria.