Phylogenetic Types Research Articles

Assessment of β-tubulin gene as a complementary molecular marker for desert truffle identification: a study case on Tunisian samples

Tunisian desert truffles have been identified on the basis of the internal transcribed spacer (ITS) locus as Tirmania nivea, Terfezia bouderii and T. arenaria. ITS and, for the first time, β-tubulin gene were employed in the phylogenetic analyses of these species to assess whether β-tubulin gene could be a complementary molecular tool for resolution of phylogenetic species. From their comparison, both markers showed to be suitable to distinguish Tirmania nivea from Terfezia bouderii and T. arenaria and, focusing on the T. boudieri complex, to assign the phylogenetic types previously described. In addition to give a first glimpse into the distribution of desert truffles from north to south of Tunisia, we then suggest to use the β-tubulin gene as a complementary marker to ITS. This indication can be useful above all for the phylogenetic reconstruction of the T. boudieri complex.

Clinical characteristics and genetic variation in respiratory syncytial virus isolated from infants hospitalized due to acute bronchiolitis in Korea during winter season 2016–2017

Purpose: Circulating patterns of predominant respiratory syncytial virus (RSV) genotypes in the community may be helpful in un derstanding molecular epidemiology and predicting future outbreaks of the RSV genotype. We investigated the association of ge netic variations in RSV with acute severe bronchiolitis in infants. Methods: We reviewed medical records of infants younger than 1 year of age hospitalized due to acute bronchiolitis between No vember 2016 and February 2017. Subjects were classified as severe or mild based on the use of mechanical or noninvasive ventila tion. The associations between severity of the disease, sex, age at admission, oxygen saturation at admission and laboratory test re sults were analyzed. RSV sequence analysis was performed in the severe group. Results: Among 114 infants, 80 underwent respiratory viral polymerase chain reaction using nasopharyngeal swab; of these, 53 (66.3%) showed positive for RSV. Of the 53 RSV-positive samples, 9 were categorized as the severe group and 44 were categorized as the mild group. Male sex, young age, longer duration of admission, minimum SaO2 at admission and bronchiolitis severity score were significantly correlated with disease severity in the severe group than in the mild group (all variables, P<0.001). Phylogenetic and sequence analysis in the severe group revealed 8 RSV-A, ON1 genotype and 1 RSV-B, BA4 genotype. Conclusion: Phylogenetic types of RSV in subjects of the severe group were RSV-A, ON1 genotype or RSV-B, BA4 genotype which were prevalent in the Korean community at the same time. Our study showed that disease severity was not significantly associated with RSV genotypic evolution or antigenic drift in Korea during winter season 2016-17. (Allergy Asthma Respir Dis 2018;6:110-115)

Investigating biogeographical patterns using point‐based cartograms

AbstractAimVisualization is an important tool in the investigation of phylogenetic distributions of species. Several tools have been developed that allow a researcher to overlay species distributions and phylogenetic trees on a map. However, when samples span a large range but also have high density in some regions, it can be difficult to appreciate both the global and the local context of biodiversity in a single view.InnovationWe have developed an algorithm for cartogram construction that extends the Gastner–Newman approach to point‐based rather than region‐based data. Cartogram construction is controlled by parameters that impact the magnitude and extent of the distortion. We also introduce the geographically coupled phylogenetic distance (GCPD), a quantitative measure that combines phylogenetic diversity with geographical distance, as a criterion for distorting a map.Main conclusionsWe used our cartogram approach to develop enhanced geographical visualizations of datasets, including an outbreak of Vibrio cholerae in Haiti and the distribution of the salamander Aneides lugubris in California, U.S.A. In both examples, our cartogram approach allowed the concurrent visualization of local distributional patterns while preserving the broader context of the survey. Our implementation in the GenGIS software package allows joint visualization of cartogram, phylogenetic and other types of data.

Free Fatty Acids Profiles Are Related to Gut Microbiota Signatures and Short-Chain Fatty Acids.

A growing body of evidence highlights the relevance of free fatty acids (FFA) for human health, and their role in the cross talk between the metabolic status and immune system. Altered serum FFA profiles are related to several metabolic conditions, although the underlying mechanisms remain unclear. Recent studies have highlighted the link between gut microbiota and host metabolism. However, although most of the studies have focused on different clinical conditions, evidence on the role of these mediators in healthy populations is lacking. Therefore, we have addressed the analysis of the relationship among gut microbial populations, short-chain fatty acid (SCFA) production, FFA levels, and immune mediators (IFNγ, IL-6, and MCP-1) in 101 human adults from the general Spanish population. Levels of selected microbial groups, representing the major phylogenetic types present in the human intestinal microbiota, were determined by quantitative PCR. Our results showed that the intestinal abundance of Akkermansia was the main predictor of total FFA serum levels, displaying a negative association with total FFA and the pro-inflammatory cytokine IL-6. Similarly, an altered FFA profile, identified by cluster analysis, was related to imbalanced levels of Akkermansia and Lactobacillus as well as increased fecal SCFA, enhanced IL-6 serum levels, and higher prevalence of subclinical metabolic alterations. Although no differences in nutritional intakes were observed, divergent patterns in the associations between nutrient intakes with intestinal microbial populations and SCFA were denoted. Overall, these findings provide new insights on the gut microbiota–host lipid metabolism axis and its potential relevance for human health, where FFA and SCFA seem to play an important role.

Comparative Analysis of Phylogenetic Assignment of Human and Avian ExPEC and Fecal Commensal Escherichia coli Using the (Previous and Revised) Clermont Phylogenetic Typing Methods and its Impact on Avian Pathogenic Escherichia coli (APEC) Classification.

The Clermont scheme has been used for subtyping of Escherichia coli since it was initially described in early 2000. Since then, researchers have used the scheme to type and sub-type commensal E. coli and pathogenic E. coli, such as extraintestinal pathogenic E. coli (ExPEC), and compare their phylogenetic assignment by pathogenicity, serogroup, distribution among ExPEC of different host species and complement of virulence and resistance traits. Here, we compare assignments of human and avian ExPEC and commensal E. coli using the old and revised Clermont schemes to determine if the new scheme provides a refined snapshot of isolate classification. 1,996 E. coli from human hosts and poultry, including 84 human neonatal meningitis E. coli isolates, 88 human vaginal E. coli, 696 human uropathogenic E. coli, 197 healthy human fecal E. coli, 452 avian pathogenic E. coli (APEC), 200 retail poultry E. coli, 80 crop and gizzard E. coli from healthy poultry at slaughter and 199 fecal E. coli from healthy birds at slaughter. All isolates were subject to phylogenetic analysis using the Clermont et al. (2000, 2013) schemes and compared to determine the effect of the new classification on strain designation. Most of the isolates’ strain designation remained where they were originally assigned. Greatest designation change occurred in APEC where 53.8% of isolates were reclassified; while classification rates among human strains ranged from 8 to 14%. However, some significant changes were observed for UPEC associated strains with significant (P < 0.05) designation changes observed from A to C and D to E or F phylogenetic types; a similar designation change was noted among NMEC for D to F designation change. Among the APEC significant designation changes were observed from A to C and D to E and F. These studies suggest that the new scheme provides a tighter and more meaningful definition of some ExPEC; while the new typing scheme has a significant impact on APEC classification. A comparison of phylogenetic group assignment by content of virulence, resistance, replicon and pathogenicity island genes in APEC suggests that insertion of pathogenicity islands into the genome appears to correlate closely with revised phylogenetic assignment.

Escherichia coli sequence type 73 as a cause of community acquired urinary tract infection in men and women in Rio de Janeiro, Brazil

Escherichia coli clones ST131, ST69, ST95, and ST73 are frequent causes of urinary tract infections (UTI) and bloodstream infections. Specific clones and virulence profiles of E. coli causing UTI in men has been rarely described. The aim of this study was to characterize patient and clonal characteristics of community-acquired UTI caused by E. coli in men (n=12) and women (n=127) in Rio de Janeiro, Brazil, complementing a previous work. We characterized isolates in phylogenetic groups, ERIC2-PCR and PFGE types, MLST, genome similarity and virulence gene-profiles. UTI from men were more frequently caused by phylogenetic group B2 isolates (83% versus 42%, respectively, P = 0.01), a group with significantly higher virulence scores compared with women. ST73 was the predominant clone in men (50%) and the second most frequent in women (12%), with the highest virulence score (mean and median=9) among other clones. ST73 gnomes formed at least six clusters. E. coli from men carried significantly higher numbers of virulence genes, such as sfa/focDE (67% versus 27%), hlyA (58% versus 24%), cnf 1 (58% versus 16%), fyuA (100% versus 82%) and MalX (92% versus 44%), compared with isolates from women. These data suggest the predominance and spread of ST73 isolates likely relates to an abundance of virulence determinants.

Characterization of NDM-7 Carbapenemase-Producing Escherichia coli Isolates in the Arabian Peninsula.

The purpose of this study was to characterize the New Delhi metallo-beta lactamase (NDM)-7-producing Enterobacteriaceae isolated in the Arabian Peninsula. Enterobacteriaceae identified to carry blaNDM-7 in a collection of 157 NDM-producing isolates from Kuwait, Oman, Saudi Arabia, and the United Arab Emirates (UAE) were investigated for their antibiotic and disinfectant susceptibility, and resistance gene content. The virulence profile, phylogenetic and sequence types of the isolates were also determined. The plasmids carrying the blaNDM-7 were transferred, and their complete nucleotide sequence was determined. Four NDM-7-producing Escherichia coli isolated in Kuwait, Oman, and the UAE, respectively, were identified. They were clonally unrelated, carried a few virulence determinants only, and belonged to clonal complexes CC10 and CC23, or ST448. They were all multi-drug resistant but remained susceptible to fosfomycin, tigecycline, and colistin. In all isolates, blaNDM-7 was located on IncX3 type plasmids of a variable size, not harboring any further resistance genes. The plasmids exhibited a high degree of similarity to each other and to pKpN01-NDM7 from Canada, with various size deletions and insertions. Our findings show that IncX3 type plasmids play an important role in the spread of the currently rare NDM-7 variant in the Arabian Peninsula. This association of blaNDM-7 with the IncX3-type plasmid is particularly worrisome, as this type of plasmid was proved to spread other carbapenemases in various species of Enterobacteriaceae worldwide at a high efficiency.

Virulence Markers and Phylogenetic Analysis of Escherichia coli Strains with Hybrid EAEC/UPEC Genotypes Recovered from Sporadic Cases of Extraintestinal Infections.

Virulence genes from different E. coli pathotypes are blended in hybrid strains. E. coli strains with hybrid enteroaggregative/uropathogenic (EAEC/UPEC) genotypes have sporadically emerged causing outbreaks of extraintestinal infections, however their association with routine infections is yet underappreciated. We assessed 258 isolates of E. coli recovered from 86 consecutive cases of extraintestinal infections seeking EAEC and hybrid genotype (EAEC/UPEC) strains. Extensive virulence genotyping was carried out to detect 21 virulence genes, including molecular predictors of EAEC and UPEC strains. Phylogenetic groups and sequence types (STs) were identified, as well as it was performed phylogenetic analyses in order to evaluate whether hybrid EAEC/UPEC strains belonged to intestinal or extraintestinal lineages of E. coli. Adhesion assays were performed to evaluate the biofilm formation by hybrid strains in human urine and cell culture medium (DMEM). Molecular predictors of UPEC were detected in more than 70% of the strains (chuA in 85% and fyuA in 78%). Otherwise, molecular predictors of EAEC (aatA and aggR) were detected in only 3.4% (9/258) of the strains and always along with the UPEC predictor fyuA. Additionally, the pyelonephritis-associated pilus (pap) gene was also detected in all of the hybrid EAEC/UPEC strains. EAEC/UPEC strains were recovered from two cases of community-onset urinary tract infections (UTI) and from a case of bacteremia. Analyses revealed that hybrid EAEC/UPEC strains were phylogenetically positioned in two different clades. Two representative strains, each recovered from UTI and bacteremia, were positioned into a characteristic UPEC clade marked by strains belonging to phylogenetic group D and ST3 (Warwick ST 69). Another hybrid EAEC/UPEC strain was classified as phylogroup A-ST478 and positioned in a commensal clade. Hybrid EAEC/UPEC strains formed biofilms at modest, but perceptible levels either in DMEM or in urine samples. We showed that different lineages of E. coli, at least phylogenetic group A and D, can acquire and gather EAEC and UPEC virulence genes promoting the emergence of hybrid EAEC/UPEC strains.

Phylogenetic analysis of Ganoderma australe complex in a Bornean tropical rainforest and implications for mechanism of coexistence of various phylogenetic types

We hypothesized that different phylogenetic types of the Ganoderma australe complex can coexist and that their coexistence is promoted by resource partitioning among them. Our field survey and phylogenetic analysis revealed six phylogenetic types coexisting within a 3 ha primary forest plot in a Bornean tropical rainforest. Two of the six have been reported previously, whereas the remaining four are new. Fruit bodies of all dominant phylogenetic types appeared more frequently from fresh coarse woody debris than expected. Comparison of resource use patterns between the observed fungal community and the null community did not provide significant evidence of niche partitioning. Although we found high genetic diversity within the plot, the phylogenetic types at the site share resources. Resource partitioning on phylogenetic types of host trees or stochastic processes during colonization of pieces of coarse woody debris might play an important role in forming the community structure of phylogenetic types of G. australe.

Genotyping of Escherichia Coli Isolated From Clinical and Hospitals Environment

Pathogenic Escherichia coli (E. coli) strains are known to cause intestinal and extraintestinal infections in human. A wide variety of infectious diseases could be caused by E. coli strains, including urinary tract infection, septicemia, newborn meningitis, central nervous system and respiratory system infections.Several bacterial agents can cause diarrheal and urinary tract infections, among these E.coli strains are detected as an important cause of morbidity and mortality of diarrhoea and UTI throughout the world.A total of 318 samples were collected during the period from September 2012 to march 2013 .All specimens were screened for the presence of E. coli by cultured on MacConkey agar and Eosin-methylene blue agar then identified by biochemical tests and confirmed by API 20E system which revealed that:90/318(28.33%) gave positive growth for E.coli )15 (16.63%) environmental isolates and 75(83.33%) clinical isolates( as fallowing:1/42(2.38%)was obtained from burns,7/25(28%)from High vaginal swabs ,11/41 (26.82%) from Wounds infections,18/33(54.54%)from Diarrheal infections and38/67(56.71 %)from Urinary tract infections, while 15/110 (13.63%) from environmental isolates, The isolated were subjected to molecular identification as E.coli by used the intergenic spacer region primer(ITS). The confirmed isolates were examined to detect the phylogenetic group based on triplex PCR by using a combination of two genes (chuA and yjaA) and an anonymous DNA fragment.Universal primers (ITS) indicated that all isolates 90(100%) gave positive results.The phylogenetic analysis revealed that 90 E.coli isolates belonged to three phylogenetic groups A &amp;D 36(40%)for each, while B2 18 (20%) and no one isolates belong to B1 phylogenetic types .

Phylogenetic group determination of Escherichia coli isolated from broilers and layers with colibacillosis.

Colibacillosis is of the most common infectious bacterial diseases of poultry.A total of 170 Escherichia coli isolates obtained from broiler and layer flocks implicated with colibacillosis between 2011 and 2014 were subjected to phylogenetic analysis. Among 150 E. coli isolates from typical lesions of local and systemic colibacillosis, 54 (31.8%), 37 (21.7%), 36 (21.2%) and 43 (25.3%) isolates determined as belonged to groups A, B1, B2 and D, respectively. The distribution of phylogenetic types for 20 isolates, obtained from apparently healthy birds as controls, were 9 (45%), 5 (25%), 1 (5%) and 5 (25%) for A, B1, B2 and D, respectively. Overall, the phylogenetic Determination revealed the B2 groups as predominant isolates in diseased birds, whereas the A group was apparently predominant in healthy birds. Results of this study represent genotypic diversity among different manifestations of avian colibacillosis.

Virulence of carbapenem-resistant Escherichia coli isolated in the Arabian Peninsula

Introduction: It is generally assumed that multidrug-resistant bacteria are less virulent. However, little is known about the virulence traits of carbapenem-resistant Escherichia coli . Objectives: To reveal the distribution of virulence factors of carbapenem-resistant extraintestinal pathogenic E. coli isolated in the Arabian Peninsula. Materials and methods: Thirty independent carbapenem-resistant E. coli samples were collected between 2009 and 2013 from Saudi Arabia (n =3), Kuwait (n =5), Oman (n =7) and the United Arab Emirates (UAE) (n =15). Carbapenemase production was confirmed by the carba-NP test. Genes of KPC, NDM, OXA-48-like, VIM, IMP carbapenemases, the lipopolysaccharide core types and the phylogenetic types were identified by polymerase chain reaction (PCR). Clonal relations were established by pulsed-field gel electrophoresis (PFGE) using an 80% similarity threshold. Virulence factor-encoding genes were detected by multiplex PCRs. Biofilm production was assessed in a stationary model. Results: Of the 30 isolates, 11 produced OXA-48-like, seven NDM-1 and one VIM-4 carbapenemases, and 11 of them did not produce carbapenemases. The strains exhibited 27 different PFGE patterns, with only three pairs of strains exhibiting clustering. Although strains belonged to all four phylogenetic groups and all five core types were detected, remarkably all OXA-48-like positive isolates belonged to phylogenetic group D and carried core type R4. The virulence factor score for the carbapenemase producers did not differ from that of the carbapenemase non-producer strains. However, members of the former group were significantly more likely to carry the yersiniabactin siderophore gene (P =0.01), to possess the virulence associated K5 capsular type (P =0.02) and to produce biofilm in anaerobic conditions (P =0.02). Conclusions: Carbapenem-resistant E. coli strains exhibit a variety of virulence factors. Those promoting intestinal colonization, i.e. K5 capsular type, and biofilm production under anaerobic conditions show some association with carbapenemase production.

Diversity of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during composting of municipal sludge

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) play an important role in the oxidation of ammonia. The diversity and relative abundance of AOA and AOB in compost samples from four composting stages [initial (day 0), heating (day 3), thermophilic (day 12), and cooling (day 28) stage ] were analyzed using the amoA gene as a functional marker. The number of operational taxonomic units (OTUs) found in each stage during sewage sludge composting was 33.3 % to 66.6 % of the total OTUs for AOB and 43.8 % to 62.5 % for AOA, with OTUs defined on the basis of a 5 % difference in nucleotides. Phylogenetic analysis showed that the AOB amoA sequences related to the Nitrosomonas lineage were dominant throughout the entire composting process. Most of the AOA amoA sequences fell into a soil/sediment cluster containing “Candidatus Nitrososphaera gargensis”. These results indicate that different ammonia oxidizers were present in different stages during composting, but that the dominant phylogenetic types were stable.

Using phylogenetic diversity to identify ancient rain forest refugia and diversification zones in a biodiversity hotspot

AbstractAimThe plight of the world's biodiversity hotspots has been paralleled by a debate over how to best prioritize or maximize gain of biodiversity for conservation. Approaches to date have focused on quantifying species, habitat, phylogenetic or other types of diversity. The importance of preserving evolutionary distinctiveness or phylogenetic diversity (PD) has gained popularity due to its ability to identify evolutionary patterns in the landscape that traditional taxon richness measures cannot. Here, we expand upon the application of PD as a biodiversity index and incorporate data on historical biogeography to understand the processes that shaped the assembly of a tropical flora.LocationTropical north‐east Queensland, Australia.MethodsWe generated a genus‐level molecular phylogeny for the bioregion to calculate PD. We then integrated data on historical biogeography into a model to explain the distribution of PD and the PD residuals and further tested for a correlation between rain forest stability through time and community assembly.ResultsWe identified a strong correlation between PD residuals and the biogeographic origin of the lineages in the extant flora. Areas with higher PD than expected based on generic richness (GR) contain a higher proportion of immigrant plant lineages dispersed into northern Australia mostly from Southeast Asia within the past few million years. Areas with lower PD than predicted by genus richness are rich in ancient Australian relict lineages and are correlated with previously identified rain forest refugia that have remained stable throughout the last glacial cycle.Main conclusionsMaximizing PD without historical interpretation may yield unintended or undesirable conservation outcomes such as deprioritizing ancient refugia with lower PD values. By understanding the biome assembly of a region, better‐informed decisions can be made to ensure different stages of a region's evolutionary history are preserved.

IncA/C plasmid-mediated spread of CMY-2 in multidrug-resistant Escherichia coli from food animals in China.

ObjectivesTo obtain a broad molecular epidemiological characterization of plasmid-mediated AmpC β-lactamase CMY-2 in Escherichia coli isolates from food animals in China.MethodsA total of 1083 E. coli isolates from feces, viscera, blood, drinking water, and sub-surface soil were examined for the presence of CMY-2 β-lactamases. CMY-2-producing isolates were characterized as follows: the bla CMY-2 genotype was determined using PCR and sequencing, characterization of the bla CMY-2 genetic environment, plasmid sizing using S1 nuclease pulsed-field gel electrophoresis (PFGE), PCR-based replicon typing, phylogenetic grouping, XbaI-PFGE, and multi-locus sequence typing (MLST).ResultsAll 31 CMY-2 producers were only detected in feces, and presented with multidrug resistant phenotypes. All CMY-2 strains also co-harbored genes conferring resistance to other antimicrobials, including extended spectrum β-lactamases genes (bla CTX-M-14 or bla CTX-M-55), plasmid-mediated quinolone resistance determinants (qnr, oqxA, and aac-(6′)-Ib-cr), floR and rmtB. The co-transferring of bla CMY-2 with qnrS1 and floR (alone and together) was mainly driven by the Inc A/C type plasmid, with sizes of 160 or 200 kb. Gene cassette arrays inserted in the class 1 or class 2 integron were amplified among 12 CMY-2 producers. CMY-2 producers belonged to avirulent groups B1 (n = 12) and A (n = 11), and virulent group D (n = 8). There was a good correlation between phylogenetic groups and sequence types (ST). Twenty-four STs were identified, of which the ST complexes (STC) 101/B1 (n = 6), STC10/A (n = 5), and STC155/B1 (n = 3) were dominant.ConclusionsCMY-2 is the dominant AmpC β-lactamase in food animals and is associated with a transferable replicon IncA/C plasmid in the STC101, STC10, and STC155 strains.

Insufficient discriminatory power of MALDI-TOF mass spectrometry for typing of Enterococcus faecium and Staphylococcus aureus isolates

MALDI-TOF mass spectrometry (MALDI-TOF MS) is increasingly used as a reliable technique for species identification of bacterial pathogens. In this study we investigated the question of whether MALDI-TOF MS can be used for accurate sub-differentiation of strains and isolates of two important nosocomial pathogens Enterococcus faecium and Staphylococcus aureus. For this purpose, a selection of 112 pre-characterized E. faecium isolates (clonal complexes CC2, CC5, CC9, CC17, CC22, CC25, CC26, CC92 altogether 52 multilocus sequence types) and 59 diverse S. aureus isolates (mostly methicillin resistant; CC5, CC8, CC22, CC30, CC45, CC398) were studied using a combination of MALDI-TOF MS and advanced methods of spectral data analysis. The strategy of MS data evaluation included manual peak inspection on the basis of pseudo gel views, unsupervised hierarchical cluster analysis and supervised artificial neural network (ANN) analysis. We were capable of differentiating patterns of hospital-associated E. faecium isolates (CC17) from other strains of E. faecium with 87% accuracy, but failed to identify lineage-specific biomarker peaks. For S. aureus pattern analyses we were able to confirm a number of signals described in previous studies, but often failed to identify biomarkers that would allow a consistent and reliable identification of phylogenetic lineages, clonal complexes or sequence types. Hence, the discriminatory power of MALDI-TOF MS was found to be insufficient for reliably sub-differentiating E. faecium and S. aureus isolates to the level of distinct clones or clonal complexes, such as assessed by MLST. Further, a comparison between peak patterns of susceptible and resistant isolates did not identify statistically relevant marker peaks linked to glycopeptide resistance determinants (vanA, vanB) in E. faecium, or the methicillin resistance determinant (mecA) in S. aureus.

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes.

Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S ribosomal RNA gene. We show that there is a general pattern in phylogenetic signal in species ecological niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.

Molecular and clinical characterization of plasmid-mediated AmpC β-lactamase-producing Escherichia coli bacteraemia: a comparison with extended-spectrum β-lactamase-producing and non-resistant E. coli bacteraemia

Plasmid-mediated AmpC β-lactamase-producing Escherichia coli (AmpC-E) bacteraemia was characterized by comparison with bacteraemia caused by extended-spectrum β-lactamase (ESBL)-producing E. coli (ESBL-E) and non-resistant E. coli (NR-E) in the era of the worldwide spread of the CTX-M-15-producing O25b-ST131-B2 clone. Of 706 bloodstream E. coli isolates collected between 2005 and 2010 in three Japanese university hospitals, 111 ESBL screening-positive isolates were analysed for AmpC and ESBL genes by PCR. A case–control study was performed in which the cases consisted of all of the patients with AmpC-E bacteraemia. Phylogenetic groups, sequence types and O25b serotype were determined. Twenty-seven AmpC-E isolates (26 of which were of the CMY-2 type) were identified, and 54 ESBL-E and 54 NR-E isolates were selected for the controls. Nineteen AmpC-E isolates were also positive for ESBL. CTX-M-14 was the most prevalent ESBL type among both the AmpC-E and ESBL-E isolates. The O25b-ST131-B2 clone was the most prevalent among the ESBL-E isolates (26%) and the second most prevalent among the NR-E isolates (13%), but only one O25b-ST131-B2 clone was found among the AmpC-E isolates. Twenty-three different sequence types were identified among the AmpC-E isolates. When compared with bacteraemia with ESBL-E, previous isolation of multidrug-resistant bacteria and intravascular catheterization were independently associated with a lower risk for AmpC-E. When compared with NR-E bacteraemia, prior use of antibiotics was the only significant risk factor for AmpC-E. Unlike the spread of the O25b-ST131-B2 clone between ESBL-E and NR-E, the AmpC-E isolates were not dominated by any specific clone.

Phylogenetic diversity of ammonia-oxidizing archaea and bacteria in biofilters of recirculating aquaculture systems

We constructed ammonia monooxygenase alpha subunit (amoA) gene clone libraries of ammonia-oxidizing archaea (AOA) and bacteria (AOB) from three biofiltration tanks used for closed marine fish culture systems. The number of operational taxonomic units (OTUs) found in any one place was 76%–80% of the total OTUs in each tank for AOA and 100% for AOB when OUTs were defined on the basis of a 5% nucleotide difference. In a phylogenetic tree, all of the AOA amoA sequences fell into a cluster, which contained Candidatus Nitrosopumilus maritimus. All of the AOB amoA sequences were related to the Nitrosospira lineage. These results indicated that different ammonia oxidizers were present in different tanks, but that the dominant phylogenetic types were stable. In a biofiltration tank to which a high concentration of ammonium chloride was added periodically to condition the biofilter materials, most of the AOA amoA sequences were different from the dominant one observed in the fish culture tanks. The AOB amoA sequences were also different, and were similar to those of Nitrosomonas aestuarii. These findings suggest that high concentration ammonia loads have a considerable affect on ammonia-oxidizer community composition.

Prevalence of Avian-Pathogenic Escherichia coli Strain O1 Genomic Islands among Extraintestinal and Commensal E. coli Isolates

Escherichia coli strains that cause disease outside the intestine are known as extraintestinal pathogenic E. coli (ExPEC) and include pathogens of humans and animals. Previously, the genome of avian-pathogenic E. coli (APEC) O1:K1:H7 strain O1, from ST95, was sequenced and compared to those of several other E. coli strains, identifying 43 genomic islands. Here, the genomic islands of APEC O1 were compared to those of other sequenced E. coli strains, and the distribution of 81 genes belonging to 12 APEC O1 genomic islands among 828 human and avian ExPEC and commensal E. coli isolates was determined. Multiple islands were highly prevalent among isolates belonging to the O1 and O18 serogroups within phylogenetic group B2, which are implicated in human neonatal meningitis. Because of the extensive genomic similarities between APEC O1 and other human ExPEC strains belonging to the ST95 phylogenetic lineage, its ability to cause disease in a rat model of sepsis and meningitis was assessed. Unlike other ST95 lineage strains, APEC O1 was unable to cause bacteremia or meningitis in the neonatal rat model and was significantly less virulent than uropathogenic E. coli (UPEC) CFT073 in a mouse sepsis model, despite carrying multiple neonatal meningitis E. coli (NMEC) virulence factors and belonging to the ST95 phylogenetic lineage. These results suggest that host adaptation or genome modifications have occurred either in APEC O1 or in highly virulent ExPEC isolates, resulting in differences in pathogenicity. Overall, the genomic islands examined provide targets for further discrimination of the different ExPEC subpathotypes, serogroups, phylogenetic types, and sequence types.