Lego-Inspired Glass Capillary Microfluidic Device: A Technique for Bespoke Microencapsulation of Phase Change Materials.

We report a Lego-inspired glass capillary microfluidic device capable of encapsulating both organic and aqueous phase change materials (PCMs) with high reproducibility and 100% PCM yield. Oil-in-oil-in-water (O/O/W) and water-in-oil-in-water (W/O/W) core-shell double emulsion droplets were formed to encapsulate hexadecane (HD, an organic PCM) and salt hydrate SP21EK (an aqueous PCM) in a UV-curable polymeric shell, Norland Optical Adhesive (NOA). The double emulsions were consolidated through on-the-fly polymerization, which followed thiol-ene click chemistry for photoinitiation. The particle diameters and shell thicknesses of the microcapsules were controlled by manipulating the geometry of glass capillaries and fluid flow rates. The microcapsules were monodispersed and exhibited the highest encapsulation efficiencies of 65.4 and 44.3% for HD and SP21EK-based materials, respectively, as determined using differential scanning calorimetry (DSC). The thermogravimetric (TGA) analysis confirmed much higher thermal stability of both encapsulated PCMs compared to pure PCMs. Polarization microscopy revealed that microcapsules could sustain over 100 melting-crystallization cycles without any structural changes. Bifunctional microcapsules with remarkable photocatalytic activity along with thermal energy storage performance were produced after the addition of 1 wt % titanium dioxide (TiO2) nanoparticles (NPs) into the polymeric shell. The presence of TiO2 NPs in the shell was confirmed by higher opacity and whiteness of these microcapsules and was quantified by energy dispersive X-ray (EDX) spectroscopy. Young's modulus of HD-based microcapsules estimated using micromanipulation analysis increased from 58.5 to 224 MPa after TiO2 incorporation in the shell.

Construction of hydrophobic fire retardant coating on cotton fabric using a layer-by-layer spray coating method.

Multifunctional cotton fabric was prepared through a two-step layer-by-layer spray coating method, where the first layer of the coating comprising chitosan and ammonium phytate provided fire retardancy, and the second one with PDMS-ZnO composite imparted hydrophobicity to the fabric. A molecular dynamics (MD) simulation study was carried out to calculate interfacial adhesion of different components of the coating, based on which the sequencing of the coating layers was determined and used to prepare coated samples. The coated fabric demonstrated a significant improvement in fire retardancy through an increase in LOI from 18 % in control to 30 %, a reduction in char length from 30 cm to 7 cm, and a decrease in peak and total heat release rate values by 75 % and 33 %, respectively. The hydrophobicity of coated fabric was tested via water drop test where coated sample maintained a contact angle of 148° for up to 120 s, while the control sample showed 0°.

Understanding the core-shell interactions in macrocapsules of organic phase change materials and polysaccharide shell.

The main objective of this work is to prepare completely biodegradable macrocapsules containing organic phase change materials (PCMs) for thermal energy storage applications. Three different PCMs hexadecane (paraffin), butyl stearate (ester) and caprylic acid (fatty acid) were encapsulated inside barium crosslinked pectin shell using ionic gelation method. Millimeter size(≤2 mm) pectin-PCM capsules were prepared with highest encapsulation efficiency of 83.66 wt% (H5), 83.21 wt% (B5) and 84.39 wt% (C5) containing hexadecane, butyl stearate and caprylic acid respectively as core, while corresponding melting enthalpies were 184.89 kJ kg-1 (H5), 116 kJ kg-1 (B5) and 118 kJ kg-1 (C5). Pectin encapsulation improved thermal stability of PCM-capsules by 70 °C-130 °C compared to core PCMs. 25 g of H5, B5 and C5 capsules provided thermal buffering of 62 min, 50 min and 51mins respectively during discharge experiments. Thus, the prepared biodegradable pectin-PCM capsules are effective for thermal energy storage.

Zirconia- and ceria-based electrolytes for fuel cell applications: critical advancements toward sustainable and clean energy production.

Solid oxide fuel cells (SOFCs) are emerging as energy conversion devices for large-scale electrical power generation because of their high energy conversion efficiency, excellent ability to minimize air pollution, and high fuel flexibility. In this context, this critical review has focussed on the recent advancements in developing a suitable electrolyte for SOFCs which has been required for the commercialization of SOFC technology after emphasizing the literature from the prior studies. In particular, the significant developments in the field of solid oxide electrolytes for SOFCs, particularly zirconia- and ceria-based electrolytes, have been highlighted as important advancements toward the production of sustainable and clean energy. It has been reported that among various electrolyte materials, zirconia-based electrolytes have the potential to be utilized as the electrolyte in SOFC because of their high thermal stability, non-reducing nature, and high mechanical strength, along with acceptable oxygen ion conductivity. However, some studies have proved that the zirconia-based electrolytes are not suitable for low and intermediate-temperature working conditions because of their poor ionic conductivity to below 850 °C. On the other hand, ceria-based electrolytes are being investigated at a rapid pace as electrolytes for intermediate and low-temperature SOFCs due to their higher oxygen ion conductivity with good electrode compatibility, especially at lower temperatures than stabilized zirconia. In addition, the most emerging advancements in electrolyte materials have demonstrated that the intermediate temperature SOFCs as next-generation energy conversion technology have great potential for innumerable prospective applications.

Distinct Potentially Adaptive Accumulation of Truncation Mutations in Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A.

Gene inactivation through the accumulation of truncation (or premature stop codon) mutations is a common mode of evolution in bacteria. It is frequently believed to result from reductive evolutionary processes allowing purging of superfluous traits. However, several works have demonstrated that, similar to the occurrences of inactivating nonsynonymous (i.e., amino acid replacement) mutations under positive selection pressures, truncation mutations can also be adaptive where specific traits deleterious in particular environmental conditions need to be inactivated for survival. Here, we performed a comparative analysis of genome-wide accumulation of truncation mutations in Salmonella enterica serovar Typhi and Salmonella enterica serovar Paratyphi A. Considering the known convergent evolutionary trajectories in these two serovars, we expected a strong overlap of truncated genes in S. Typhi and S. Paratyphi A, emerging through either reductive or adaptive dynamics. However, we detected a distinct set of core truncated genes encoding different overrepresented functional clusters in each serovar. In 54% and 28% truncated genes in S. Typhi and S. Paratyphi A, respectively, inactivating mutations were acquired by only different subsets of isolates, instead of all isolates analyzed for that serovar. Importantly, 62% truncated genes (P < 0.001) in S. Typhi and S. Paratyphi A were also targeted by convergent amino acid mutations in different serovars, suggesting those genes to be under selection pressures. Our findings indicate significant presence of potentially adaptive truncation mutations in conjunction with the ones emerging due to reductive evolution. Further experimental and large-scale bioinformatic studies are necessary to better explore the impact of such adaptive footprints of truncation mutations in the evolution of bacterial virulence. IMPORTANCE Detecting the adaptive mutations leading to gene inactivation or loss of function is crucial for understanding their contribution in the evolution of bacterial virulence and antibiotic resistance. Such inactivating mutations, apart from being of nonsynonymous (i.e., amino acid replacement) nature, can also be truncation mutations, abruptly trimming the length of encoded proteins. Importantly, the notion of reductive evolutionary dynamics is primarily accepted toward the accumulation of truncation mutations. However, our case study on S. Typhi and S. Paratyphi A, two human-restricted systemically invasive pathogens exerting similar clinical manifestations, indicated that a significant proportion of truncation mutations emerge from positive selection pressures. The candidate genes from our study will enable directed functional assays for deciphering the adaptive role of truncation mutations in S. Typhi and S. Paratyphi A pathogenesis. Also, our genome-level analytical approach will pave the way to understand the contribution of truncation mutations in the adaptive evolution of other bacterial pathogens.

Complex Polymeric Microstructures with Programmable Architecture via Pickering Emulsion-Templated In Situ Polymerization.

Aside from smooth and spherical microcapsules, the concept of tailoring complex polymeric microstructures is being taken a step ahead due to their great demand in various applications and fundamental studies in the subjects of microfluidics and nanotechnology. Size, shape, and morphology are of paramount importance for their functional performance and various applications. However, simple, inexpensive, versatile, and high-throughput techniques for fabricating microcapsules with controlled morphology remain a bottleneck for discoveries in the subject of polymer colloids. In this paper, we directly fulfill this need by reporting a novel approach of Pickering emulsion-templated in situ polymerization for tailoring complex polymeric microstructures comprised of a composite shell of titanium dioxide nanoparticle (TiO2 NP)-embedded poly(melamine-urea-formaldehyde) (polyMUF) and a core of hexadecane (HD, soft template). At first, we hydrophobize TiO2 NPs by chemisorbing long-chain biobased myristic acid via a bidentate chelating complex and precisely tune their wettability by varying the grafting density of myristic acid to obtain highly stable oil-in-water (O/W) Pickering emulsion. Thereafter, we employ the optimized TiO2 NPs in the intended encapsulation strategy that enables various microstructures and morphologies with the particle diameter ranging from 5 to 20 µm. Careful manipulation of reaction parameters and copolymer components leads to novel complex microstructures: smooth, raspberry-like, partially budded, hollow, filled, single-holed, and closed-cell-like microstructures. Particle properties such as morphology, size, shell thickness, and core content are governed by the TiO2 NP content, core-to-shell ratio, copolymer component, conversion, and pH value. Based on the results of a series of control experiments, novel mechanisms for the formation of various such microstructures are proposed.

Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae.

Sulfolobaceae family, comprising diverse thermoacidophilic and aerobic sulfur-metabolizing Archaea from various geographical locations, offers an ideal opportunity to infer the evolutionary dynamics across the members of this family. Comparative pan-genomics coupled with evolutionary analyses has revealed asymmetric genome evolution within the Sulfolobaceae family. The trend of genome streamlining followed by periods of differential gene gains resulted in an overall genome expansion in some species of this family, whereas there was reduction in others. Among the core genes, both Sulfolobus islandicus and Saccharolobus solfataricus showed a considerable fraction of positively selected genes and also higher frequencies of gene acquisition. In contrast, Sulfolobus acidocaldarius genomes experienced substantial amount of gene loss and strong purifying selection as manifested by relatively lower genome size and higher genome conservation. Central carbohydrate metabolism and sulfur metabolism coevolved with the genome diversification pattern of this archaeal family. The autotrophic CO2 fixation with three significant positively selected enzymes from S. islandicus and S. solfataricus was found to be more imperative than heterotrophic CO2 fixation for Sulfolobaceae. Overall, our analysis provides an insight into the interplay of various genomic adaptation strategies including gene gain-loss, mutation, and selection influencing genome diversification of Sulfolobaceae at various taxonomic levels and geographical locations.

Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19?

The dire need of effective preventive measures and treatment approaches against SARS-CoV-2 virus, causing COVID-19 pandemic, calls for an in-depth understanding of its evolutionary dynamics with attention to specific geographic locations, since lockdown and social distancing to prevent the virus spread could lead to distinct localized dynamics of virus evolution within and between countries owing to different environmental and host-specific selection pressures. To decipher any correlation between SARS-CoV-2 evolution and its epidemiology in India, we studied the mutational diversity of spike glycoprotein, the key player for the attachment, fusion and entry of virus to the host cell. For this, we analyzed the sequences of 630 Indian isolates as available in GISAID database till June 07, 2020 (during the time-period before the start of Unlock 1.0 in India on and from June 08, 2020), and detected the spike protein variants to emerge from two major ancestors - Wuhan-Hu-1/2019 and its D614G variant. Average stability of the docked spike protein - host receptor (S-R) complexes for these variants correlated strongly (R2 = 0.96) with the fatality rates across Indian states. However, while more than half of the variants were found unique to India, 67% of all variants showed lower stability of S-R complex than the respective ancestral variants, indicating a possible fitness loss in recently emerged variants, despite a continuous increase in mutation rate. These results conform to the sharply declining fatality rate countrywide (>7-fold during April 11 - June 28, 2020). Altogether, while we propose the potential of S-R complex stability to track disease severity, we urge an immediate need to explore if SARS-CoV-2 is approaching mutational meltdown in India.

Superhydrophobic Surfaces: Insights from Theory and Experiment.

Biomimetic nanosurfaces with distinct wettability and versatility have found special enthusiasm in both fundamental research and industrial applications. With the advent of nanotechnology, it is doable to acclimate surface architecture and surface chemistry to attain superhydrophobicity. The uniqueness of superhydrophobic surfaces arises from various phenomenal advances, and its progress is expected to continue for decades in the future. In this Review Article, we discuss recent progress made in defining physical aspects of numerical modeling, experimental practices adopted, and applications of superhydrophobic surfaces. First, we revisit various classical models of superhydrophobicity and recent theoretical advances achieved related to the wetting phenomena. Subsequently, we emphasize various precursors and advance fabrication strategies adopted to fabricate superhydrophobic surfaces. In the following section, we take up various potential applications and appropriate working principles to explain wettability phenomena. Finally, some general conclusions are drawn along with proposed guidelines for designing robust superhydrophobic coatings.

Gene duplication and deletion, not horizontal transfer, drove intra-species mosaicism of Bartonella henselae.

Bartonella henselae is a facultative intracellular pathogen that occurs worldwide and is responsible primarily for cat-scratch disease in young people and bacillary angiomatosis in immunocompromised patients. The principal source of genome-level diversity that contributes to B. henselae's host-adaptive features is thought to be horizontal gene transfer events. However, our analyses did not reveal the acquisition of horizontally-transferred islands in B. henselae after its divergence from other Bartonella. Rather, diversity in gene content and genome size was apparently acquired through two alternative mechanisms, including deletion and, more predominantly, duplication of genes. Interestingly, a majority of these events occurred in regions that were horizontally transferred long before B. henselae's divergence from other Bartonella species. Our study indicates the possibility that gene duplication, in response to positive selection pressures in specific clones of B. henselae, might be linked to the pathogen's adaptation to arthropod vectors, the cat reservoir, or humans as incidental host-species.

Protein-polysaccharide based microencapsulated phase change material composites for thermal energy storage.

Microencapsulated phase change material (MPCM) composites of capric acid were synthesized utilizing protein (Gelatin, GE)-polysaccharide (Gum Arabic, GA) interactions as shell material. Mechanical and thermal stabilities of these MPCM composites were achieved using glutaraldehyde cross-linker and silica coating respectively. Thermal properties (enthalpy and, melting/crystallization and cyclic tests) were estimated using differential scanning calorimeter (DSC) while, thermal stability was obtained from thermogravimetric analyzer (TGA). Morphology and particle size were analyzed using scanning electron microscope (SEM). FTIR and EDX (energy-dispersive X-ray) data interpreted nature of chemical bonds while crystalloid structures were obtained from XRD (X-Ray Diffraction). Based on morphology and thermal stability, the composite made with the core: shell ratio of 2:3 was chosen for analyzing the role of process parameters i.e. cross-linker amount and duration of cross-link reaction, and surfactant amount influencing encapsulation ratio. The composite tested and found stable for 50 heating/cooling cycles.

T4SS-dependent TLR5 activation by Helicobacter pylori infection.

Toll-like receptor TLR5 recognizes a conserved domain, termed D1, that is present in flagellins of several pathogenic bacteria but not in Helicobacter pylori. Highly virulent H. pylori strains possess a type IV secretion system (T4SS) for delivery of virulence factors into gastric epithelial cells. Here, we show that one of the H. pylori T4SS components, protein CagL, can act as a flagellin-independent TLR5 activator. CagL contains a D1-like motif that mediates adherence to TLR5+ epithelial cells, TLR5 activation, and downstream signaling in vitro. TLR5 expression is associated with H. pylori infection and gastric lesions in human biopsies. Using Tlr5-knockout and wild-type mice, we show that TLR5 is important for efficient control of H. pylori infection. Our results indicate that CagL, by activating TLR5, may modulate immune responses to H. pylori.

Draft Genome Sequence of an Escherichia coli Sequence Type 155 Strain Isolated from Sewage in Kerala, India.

We report the draft genome sequence of Escherichia coli ASBT-1, a representative of E. coli sequence type 155 (ST155), obtained from India. Considering the known wide variety of pathogenic and antibiotic resistance potentials, this strain should be of great interest for detailed comparative genomic analysis.

Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci.

Global growth in antibiotic resistance is a major social problem. A high level of resistance to fluoroquinolones requires the concurrent presence of at least 3 mutations in the target proteins-2 in DNA gyrase (GyrA) and 1 in topoisomerase IV (ParC), which occur in a stepwise manner. In the Escherichia coli chromosome, the gyrA and parC loci are positioned about 1 Mb away from each other. Here we show that the 3 fluoroquinolone resistance mutations are tightly associated genetically in naturally occurring strains. In the latest pandemic uropathogenic and multidrug-resistant E. coli clonal group ST1193, the mutant variants of gyrA and parC were acquired not by a typical gradual, stepwise evolution but all at once. This happened as part of 11 simultaneous homologous recombination events involving 2 phylogenetically distant strains of E. coli, from an uropathogenic clonal complex ST14 and fluoroquinolone-resistant ST10. The gene exchanges swapped regions between 0.5 and 139 Kb in length (183 Kb total) spread along 976 Kb of chromosomal DNA around and between gyrA and parC loci. As a result, all 3 fluoroquinolone resistance mutations in GyrA and ParC have simultaneously appeared in ST1193. Based on molecular clock estimates, this potentially happened as recently as <12 y ago. Thus, naturally occurring homologous recombination events between 2 strains can involve numerous chromosomal gene locations simultaneously, resulting in the transfer of distant but tightly associated genetic mutations and emergence of a both highly pathogenic and antibiotic-resistant strain with a rapid global spread capability.

Mutational convergence acts as a major player in adaptive parallel evolution of Shigella spp.

Shigella spp., emerging from multiple origins of Escherichia coli, poses a significant health threat as a causative agent of bacillary dysentery. While multiple serotypes of four different species have evolved via independent lineages, Shigella spp. are designated as a single pathotype, primarily because of their common mode of pathogenesis. Convergent horizontal transfer events have so far been attributed to the commonalities in the evolution of virulence across diverse lineages. However, the role of mutational convergence in such parallel evolution is not yet well understood. Here we have carried out a genome-wide analysis of Shigella strains from all four species to detect the core genes (i.e. the ones present in all analyzed strains) acquiring convergent mutations of evolutionarily recent origin. Simulation studies show non-neutral accumulation of these convergent mutations across species, suggesting their adaptive role in the evolution of Shigella virulence. S. dysenteriae strain 197, representing highly virulent type 1 (Sd1) clone, carries excessively high number of core genes with recent convergent mutations compared to other analyzed strains. We propose that this high frequency of adaptive convergence in S. dysenteriae strain 197 could be linked to recent re-emergence of the Sd1 clone and its increased resistance to antimicrobials.

Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori.

BACKGROUND: Helicobacter pylori is a human stomach pathogen, naturally-competent for DNA uptake, and prone to homologous recombination. Extensive homoplasy (i.e., phylogenetically-unlinked identical variations) observed in H. pylori genes is considered a hallmark of such recombination. However, H. pylori also exhibits a high mutation rate. The relative adaptive role of homologous recombination and mutation in species diversity is a highly-debated issue in biology. Recombination results in homoplasy. While convergent mutation can also account for homoplasy, its contribution is thought to be minor. We demonstrate here that, contrary to dogma, convergent mutation is a key contributor to Helicobacter pylori homoplasy, potentially driven by adaptive evolution of proteins. RESULTS: Our present genome-wide analysis shows that homoplastic nonsynonymous (amino acid replacement) changes are not typically accompanied by homoplastic synonymous (silent) variations. Moreover, the majority of the codon positions with homoplastic nonsynonymous changes also contain different (i.e. non-homoplastic) nonsynonymous changes arising from mutation only. This indicates that, to a considerable extent, nonsynonymous homoplasy is due to convergent mutations. High mutation rate or limited availability of evolvable sites cannot explain this excessive convergence, as suggested by our simulation studies. Rather, the genes with convergent mutations are overrepresented in distinct functional categories, suggesting possible selective responses to conditions such as distinct micro-niches in single hosts, and to differences in host genotype, physiology, habitat and diet. CONCLUSIONS: We propose that mutational convergence is a key player in H. pylori's adaptation and extraordinary persistence in human hosts. High frequency of mutational convergence could be due to saturation of evolvable sites capable of responding to selection pressures, while the number of mutable residues is far from saturation. We anticipate a similar scenario of mutational vs. recombinational genome dynamics or plasticity for other naturally competent microbes where strong positive selection could favor frequent convergent mutations in adaptive protein evolution.

Development of a Web Tool for Escherichia coli Subtyping Based on fimH Alleles.

The aim of this study was to construct a valid publicly available method for in silico fimH subtyping of Escherichia coli particularly suitable for differentiation of fine-resolution subgroups within clonal groups defined by standard multilocus sequence typing (MLST). FimTyper was constructed as a FASTA database containing all currently known fimH alleles. The software source code is publicly available at https://bitbucket.org/genomicepidemiology/fimtyper, the database is freely available at https://bitbucket.org/genomicepidemiology/fimtyper_db, and a service implementing the software is available at https://cge.cbs.dtu.dk/services/FimTyper FimTyper was validated on three data sets: one containing Sanger sequences of fimH alleles of 42 E. coli isolates generated prior to the current study (data set 1), one containing whole-genome sequence (WGS) data of 243 third-generation-cephalosporin-resistant E. coli isolates (data set 2), and one containing a randomly chosen subset of 40 E. coli isolates from data set 2 that were subjected to conventional fimH subtyping (data set 3). The combination of the three data sets enabled an evaluation and comparison of FimTyper on both Sanger sequences and WGS data. FimTyper correctly predicted all 42 fimH subtypes from the Sanger sequences from data set 1 and successfully analyzed all 243 draft genomes from data set 2. FimTyper subtyping of the Sanger sequences and WGS data from data set 3 were in complete agreement. Additionally, fimH subtyping was evaluated on a phylogenetic network of 122 sequence type 131 (ST131) E. coli isolates. There was perfect concordance between the typology and fimH-based subclones within ST131, with accurate identification of the pandemic multidrug-resistant clonal subgroup ST131-H30. FimTyper provides a standardized tool, as a rapid alternative to conventional fimH subtyping, highly suitable for surveillance and outbreak detection.

Corrected Genome Annotations Reveal Gene Loss and Antibiotic Resistance as Drivers in the Fitness Evolution of Salmonella enterica Serovar Typhimurium.

Horizontal acquisition of novel chromosomal genes is considered to be a key process in the evolution of bacterial pathogens. However, the identification of gene presence or absence could be hindered by the inconsistencies in bacterial genome annotations. Here, we performed a cross-annotation of omnipresent core and mosaic accessory genes in the chromosome of Salmonella enterica serovar Typhimurium across a total of 20 fully assembled genomes deposited into GenBank. Cross-annotation resulted in a 32% increase in the number of core genes and a 3-fold decrease in the number of genes identified as mosaic genes (i.e., genes present in some strains only) by the original annotation. Of the remaining noncore genes, the vast majority were prophage genes, and 255 of the nonphage genes were actually of core origin but lost in some strains upon the emergence of the S Typhimurium serovar, suggesting that the chromosomal portion of the S Typhimurium genome acquired a very limited number of novel genes other than prophages. Only horizontally acquired nonphage genes related to bacterial fitness or virulence were found in four recently sequenced isolates, all located on three different genomic islands that harbor multidrug resistance determinants. Thus, the extensive use of antimicrobials could be the main selection force behind the new fitness gene acquisition and the emergence of novel Salmonella pathotypes. IMPORTANCE: Significant discrepancies in the annotations of bacterial genomes could mislead the conclusions about evolutionary origin of chromosomal genes, as we demonstrate here via a cross-annotation-based analysis of Salmonella Typhimurium genomes from GenBank. We conclude that despite being able to infect a broad range of vertebrate hosts, the genomic diversity of S Typhimurium strains is almost exclusively limited to gene loss and the transfer of prophage DNA. Only nonphage chromosomal genes acquired after the emergence of the serovar are linked to the genomic islands harboring multidrug resistance factors. Since the fitness factors could lead to increased virulence, this poses an important research question: could overuse or misuse of antimicrobials act as selection forces for the emergence of more pathogenic strains of Salmonella?

Mutation-Driven Divergence and Convergence Indicate Adaptive Evolution of the Intracellular Human-Restricted Pathogen, Bartonella bacilliformis.

Among all species of Bartonella, human-restricted Bartonella bacilliformis is the most virulent but harbors one of the most reduced genomes. Carrión's disease, the infection caused by B. bacilliformis, has been afflicting poor rural populations for centuries in the high-altitude valleys of the South American Andes, where the pathogen's distribution is probably restricted by its sand fly vector's range. Importantly, Carrión's disease satisfies the criteria set by the World Health Organization for a disease amenable to elimination. However, to date, there are no genome-level studies to identify potential footprints of B. bacilliformis (patho)adaptation. Our comparative genomic approach demonstrates that the evolution of this intracellular pathogen is shaped predominantly via mutation. Analysis of strains having publicly-available genomes shows high mutational divergence of core genes leading to multiple sub-species. We infer that the sub-speciation event might have happened recently where a possible adaptive divergence was accelerated by intermediate emergence of a mutator phenotype. Also, within a sub-species the pathogen shows inter-clonal adaptive evolution evidenced by non-neutral accumulation of convergent amino acid mutations. A total of 67 non-recombinant core genes (over-representing functional categories like DNA repair, glucose metabolic process, ATP-binding and ligase) were identified as candidates evolving via adaptive mutational convergence. Such convergence, both at the level of genes and their encoded functions, indicates evolution of B. bacilliformis clones along common adaptive routes, while there was little diversity within a single clone.

A Novel 7-Single Nucleotide Polymorphism-Based Clonotyping Test Allows Rapid Prediction of Antimicrobial Susceptibility of Extraintestinal Escherichia coli Directly From Urine Specimens.

Background. Escherichia coli is a highly clonal pathogen. Extraintestinal isolates belong to a limited number of genetically related groups, which often exhibit characteristic antimicrobial resistance profiles. Methods. We developed a rapid clonotyping method for extraintestinal E coli based on detection of the presence or absence of 7 single nucleotide polymorphisms (SNPs) within 2 genes (fumC and fimH). A reference set of 2559 E coli isolates, primarily of urinary origin, was used to predict the resolving power of the 7-SNP-based typing method, and 582 representative strains from this set were used to evaluate test robustness. Results. Fifty-four unique SNP combinations ("septatypes") were identified in the reference strains. These septatypes yielded a clonal group resolution power on par with that of traditional multilocus sequence typing. In 72% of isolates, septatype identity predicted sequence type identity with at least 90% (mean, 97%) accuracy. Most septatypes exhibited highly distinctive antimicrobial susceptibility profiles. The 7-SNP-based test could be performed with high specificity and sensitivity using single or multiplex conventional polymerase chain reaction (PCR) and quantitative PCR. In the latter format, E coli presence and septatype identity were determined directly in urine specimens within 45 minutes with bacterial loads as low as 10(2) colony-forming units/mL and, at clinically significant bacterial loads, with 100% sensitivity and specificity. Conclusions. 7-SNP-based typing of E coli can be used for both epidemiological studies and clinical diagnostics, which could greatly improve the empirical selection of antimicrobial therapy.