Distinct Phylogroups Research Articles

Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution

An international collection of Staphylococcus aureus of clonal complex (CC) 398 from diverse hosts spanning all continents and a 30 year-period is studied based on whole-genome sequencing (WGS) data. The collection consists of publicly available genomic data from 2994 strains and 134 recently sequenced Swiss methicillin-resistant S. aureus (MRSA) CC398 strains. A time-calibrated phylogeny reveals the presence of distinct phylogroups present in Asia, North and South America and Europe. European MRSA diverged from methicillin-susceptible S. aureus (MSSA) at the beginning of the 1950s. Two major European phylogroups (EP4 and EP5), which diverged approximately 1974, are the main drivers of MRSA CC398 spread in Europe. Within EP5, an emergent MRSA lineage spreading among the European horse population (EP5-Leq) diverged approximately 1996 from the pig lineage (EP5-Lpg), and also contains human-related strains. EP5-Leq is characterized by staphylococcal cassette chromosome mec (SCCmec) IVa and spa type t011 (CC398-IVa-t011), and EP5-Lpg by CC398-SCCmecVc-t011. The lineage-specific antibiotic resistance and virulence gene patterns are mostly mediated by the acquisition of mobile genetic elements like SCCmec, S. aureus Genomic Islands (SaGIs), prophages and transposons. Different combinations of virulence factors are present on S. aureus pathogenicity islands (SaPIs), and novel antimicrobial resistance gene containing elements are associated with certain lineages expanding in Europe. This WGS-based analysis reveals the actual evolutionary trajectory and epidemiological trend of the international MRSA CC398 population considering host, temporal, geographical and molecular factors. It provides a baseline for global WGS-based One-Health studies of adaptive evolution of MRSA CC398 as well as for local outbreak investigations.

Plant virus diversity in bee and pollen samples from apple (Malus domestica) and sweet cherry (Prunus avium) agroecosystems.

Honey bee (Apis mellifera) pollination is widely used in tree fruit production systems to improve fruit set and yield. Many plant viruses can be associated with pollen or transmitted through pollination, and can be detected through bee pollination activities. Honey bees visit multiple plants and flowers in one foraging trip, essentially sampling small amounts of pollen from a wide area. Here we report metagenomics-based area-wide monitoring of plant viruses in cherry (Prunus avium) and apple (Malus domestica) orchards in Creston Valley, British Columbia, Canada, through bee-mediated pollen sampling. Plant viruses were identified in total RNA extracted from bee and pollen samples, and compared with profiles from double stranded RNA extracted from leaf and flower tissues. CVA, PDV, PNRSV, and PVF coat protein nucleotide sequences were aligned and compared for phylogenetic analysis. A wide array of plant viruses were identified in both systems, with cherry virus A (CVA), prune dwarf virus (PDV), prunus necrotic ringspot virus (PNRSV), and prunus virus F (PVF) most commonly detected. Citrus concave gum associated virus and apple stem grooving virus were only identified in samples collected during apple bloom, demonstrating changing viral profiles from the same site over time. Different profiles of viruses were identified in bee and pollen samples compared to leaf and flower samples reflective of pollen transmission affinity of individual viruses. Phylogenetic and pairwise analysis of the coat protein regions of the four most commonly detected viruses showed unique patterns of nucleotide sequence diversity, which could have implications in their evolution and management approaches. Coat protein sequences of CVA and PVF were broadly diverse with multiple distinct phylogroups identified, while PNRSV and PDV were more conserved. The pollen virome in fruit production systems is incredibly diverse, with CVA, PDV, PNRSV, and PVF widely prevalent in this region. Bee-mediated monitoring in agricultural systems is a powerful approach to study viral diversity and can be used to guide more targeted management approaches.

Comparing the genetic typing methods for effective surveillance and rabies control in Georgia.

A full nucleoprotein gene sequencing of 68 isolates collected from passive rabies surveillance system in Georgia between 2015 and 2016 identified two distinct dog rabies phylogroups, GEO_V1 and GEO_V2, which both belonged to the cosmopolitan dog clade. GEO_V1 was found throughout the country and was further divided into four sub-phylogroups that overlapped geographically; GEO_V2 was found in the southeast region and was closely related to dog rabies in Azerbaijan. A sequence analysis of the full N gene, partial nucleoprotein gene of N-terminal and C-terminal, and the amplicon sequences of pan-lyssavirus RT-qPCR LN34 showed that all four sequencing approaches provided clear genetic typing results of canine rabies and could further differentiate GEO_V1 and GEO_V2. The phylogenetic analysis results vary and were affected by the length of the sequences used. Amplicon sequencing of the LN34 assay positive samples provided a rapid and cost-effective method for rabies genetic typing, which is important for improving rabies surveillance and canine rabies eradication globally.

Extraction-free LAMP assays for generic detection of Old World Orthopoxviruses and specific detection of Mpox virus

Mpox is a neglected zoonotic disease endemic in West and Central Africa. The Mpox outbreak with more than 90,000 cases worldwide since 2022 generated great concern about future outbreaks and highlighted the need for a simple and rapid diagnostic test. The Mpox virus, MPV, is a member of the Orthopoxvirus (OPV) genus that also contains other pathogenic viruses including variola virus, vaccinia virus, camelpox virus, and cowpox virus. Phylogenomic analysis of 200 OPV genomes identified 10 distinct phylogroups with the New World OPVs placed on a very long branch distant from the Old World OPVs. Isolates derived from infected humans were found to be distributed across multiple phylogroups interspersed with isolates from animal sources, indicating the zoonotic potential of these viruses. In this study, we developed a simple and sensitive colorimetric LAMP assay for generic detection of Old World OPVs. We also developed an MPV-specific probe that differentiates MPV from other OPVs in the N1R LAMP assay. In addition, we described an extraction-free protocol for use directly with swab eluates in LAMP assays, thereby eliminating the time and resources needed to extract DNA from the sample. Our direct LAMP assays are well-suited for low-resource settings and provide a valuable tool for rapid and scalable diagnosis and surveillance of OPVs and MPV.

Comparative Phylogeography, Historical Demography, and Population Genetics of Three Common Coastal Fauna in Spartina Marshes of the Northwestern Gulf of Mexico

Coastal wetlands worldwide are experiencing high rates of loss and degradation that may lead to a reduction in diversity in faunal populations. Since salt marsh habitats are subject to a multitude of stressors, evaluations of the genetic diversity, connectivity, and potential resilience of faunal communities within salt marsh habitats are relevant. This study characterizes mitochondrial DNA (mtDNA) diversity for three common faunal residents of salt marshes along the northern Gulf of Mexico. Gulf Killifish (Fundulus grandis) samples were characterized for 1077 bp of the concatenated nucleotide sequence corresponding to the Control Region and Nitrogen Dehydrogenase, Subunits 2 and 5. Daggerblade grass shrimp (Palaemon pugio) samples were characterized using 466 bp of 16sRNA sequence, and phloem-feeding planthoppers (Prokelisia marginata) were characterized using 372 bp of Cytochrome c Oxidase Subunit I (COI) sequence. For F. grandis, our data revealed high levels of haplotypic diversity, evidence of isolation by distance (IBD), and regional population structuring associated with the distribution of two distinct phylogroups and distinct historical demography signatures. P. pugio and P. marginata displayed low levels of haplotypic diversity and evidence of population structure, but both appear to contain only snapshots of the total potential diversity for these species in the Gulf of Mexico. Greater resolution of the patterns of historical demography of Gulf Killifish may be obtained in future studies by including localities from Florida and Mexico. For both P. pugio and planthoppers, future studies would benefit from the characterization of genetic markers with a higher degree of polymorphism. We conclude that despite these three species inhabiting the same habitats along the same stretch of coast, each is subject to a different combination of evolutionary forces, and this study was able to reconstruct differences in how the genetic variation in each of these species emerged, and how it is maintained.

Phylogroup typing and carbapenem resistance of Escherichia coli from agricultural samples in Metro Manila, Philippines

Primary production environment is considered as reservoir of Escherichia coli contamination of produce. E. coli is classified into eight phylogroups which differ in ecological niches, evolutionary history, and phenotypic properties. To understand the population genetic structure and composition of E. coli in primary production environments in Metro Manila, Philippines, a total of 80 E. coli recovered from irrigation water, soil, vegetables, and feces of cat, carabao, chicken, dog, and goat were allocated into distinct phylogroups based on the presence and absence of genetic markers. Results showed that the most prevalent phylogroup was B1 (71.3%), followed by A (18.6%), D (6.3%), B2 (1.3%), E (1.3%), and an unknown phylogroup (1.3%). The most prevalent genetic marker was arpA, followed by TspE4.C2, yjaA, and chuA. The carbapenem resistance of 24 E. coli isolates representing different phylogroups was also evaluated. Intriguingly, all isolates exhibited uniform susceptibility. This is the first report to provide insights into the phylogroup structure and composition, as well as carbapenem resistance of E. coli from primary production in the Philippines, which highlights possible source of and solution for gastrointestinal and enteric diseases.

Comparative Phylogeography of Birds Across the Tocantins–Araguaia Interfluve Reveals a New Biogeographic Suture in the Amazon Far East

Few phylogeographic studies have focused on understanding the role of the Tocantins–Araguaia Interfluve (TAI) in the diversification of Amazonian biodiversity. Herein we evaluate the phylogeographic relationships of 14 avian lineages present in the TAI and its two neighboring Amazonian Areas of Endemism: the Xingu (XAE) and Belém (BAE). Four alternative scenarios coupling degree of genetic differentiation and area relationships were tested: (1) populations distributed in TAI, BAE, and XAE are not genetically differentiated from each other (assumed as the null hypothesis); (2) populations from TAI are more closely related to those from BAE; (3) populations from TAI are more closely related to those from XAE; and (4) TAI populations represent independent or endemic lineages not present in either the BAE or XAE. Molecular analyses considered Bayesian Inference methods and Bayesian Information Criterion (BIC) evolutionary models, haplotype sharing and genetic differentiation estimates. We found three distinct phylogeographic patterns: (i) four lineages presented no population structure across XAE, TAI and BAE; (ii) six lineages were represented in the TAI with distinct phylogroups replacing each other between XAE and BAE, but with varying degrees of contact and evidence of gene-flow within the TAI; and (iii) for four lineages, the Tocantins River acted as a barrier isolating BAE phylogroups from those inhabiting both TAI and XAE. These different patterns demonstrate a heterogeneous response to the barrier effects posed by both the Tocantins and Araguaia rivers on the local fauna. Historical geomorphological and hydromorphological factors, such as the presence and absence of paleochannels and anastomosed channel stretches and variations in sedimentation rates support a dynamic history for the Araguaia-Tocantins floodplains, likely accounting for the observed heterogeneity in species’ specific responses. Finally, the scenario of phylogeographic breaks and population subdivision recovered herein along the Tocantins and Araguaia rivers, associated with the existence of contact zones and the occurrence of gene flow, define the TAI as hitherto unknown biogeographic suture zone, localized in southeasternmost Amazonia.

Linear plasmids in Klebsiella and other Enterobacteriaceae.

Linear plasmids are extrachromosomal DNA elements that have been found in a small number of bacterial species. To date, the only linear plasmids described in the family Enterobacteriaceae belong to Salmonella , first found in Salmonella enterica Typhi. Here, we describe a collection of 12 isolates of the Klebsiella pneumoniae species complex in which we identified linear plasmids. Screening of assembly graphs assembled from public read sets identified linear plasmid structures in a further 13 K . pneumoniae species complex genomes. We used these 25 linear plasmid sequences to query all bacterial genome assemblies in the National Center for Biotechnology Information database, and discovered an additional 61 linear plasmid sequences in a variety of Enterobacteriaceae species. Gene content analysis divided these plasmids into five distinct phylogroups, with very few genes shared across more than two phylogroups. The majority of linear plasmid-encoded genes are of unknown function; however, each phylogroup carried its own unique toxin–antitoxin system and genes with homology to those encoding the ParAB plasmid stability system. Passage in vitro of the 12 linear plasmid-carrying Klebsiella isolates in our collection (which include representatives of all five phylogroups) indicated that these linear plasmids can be stably maintained, and our data suggest they can transmit between K. pneumoniae strains (including members of globally disseminated multidrug-resistant clones) and also between diverse Enterobacteriaceae species. The linear plasmid sequences, and representative isolates harbouring them, are made available as a resource to facilitate future studies on the evolution and function of these novel plasmids.

Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant

BackgroundEmergence of new variant of SARS-CoV-2, namely omicron, has posed a global concern because of its high rate of transmissibility and mutations in its genome. Researchers worldwide are trying to understand the evolution and emergence of such variants to understand the mutational cascade events. MethodsWe have considered all omicron genomes (n = 302 genomes) available till 2nd December 2021 in the public repository of GISAID along with representatives of variants of concern (VOC), i.e., alpha, beta, gamma, delta, and omicron; variant of interest (VOI) mu and lambda; and variant under monitoring (VUM). Whole genome-based phylogeny and mutational analysis were performed to understand the evolution of SARS CoV-2 leading to emergence of omicron variant. ResultsWhole genome-based phylogeny depicted two phylogroups (PG-I and PG-II) forming variant specific clades except for gamma and VUM GH. Mutational analysis detected 18,261 mutations in the omicron variant, majority of which were non-synonymous mutations in spike (A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H), followed by RNA dependent RNA polymerase (rdrp) (A1892T, I189V, P314L, K38R, T492I, V57V), ORF6 (M19M) and nucleocapsid protein (RG203KR). ConclusionDelta and omicron have evolutionary diverged into distinct phylogroups and do not share a common ancestry. While, omicron shares common ancestry with VOI lambda and its evolution is mainly derived by the non-synonymous mutations.

Phylotyping and Determining the Antimicrobial Susceptibility of Cutibacterium acnes Isolated from Patients with Acne Vulgaris

Cutibacterium acnes (formerly known as Propionibacterium acnes), obligate anaerobic gram-positive diphtheroid, is a member of normal skin microbiota and frequently isolated from acne lesions and also in various infections as an opportunist pathogen. Within the last decade, distinct phylogroups of C.acnes have been discovered, and specific strains associated with human disease were defined. Increasing resistance to antimicrobials used in the treatment of C.acnes infections has been reported. Resistance rates vary among isolates from different geographic locations. However, knowledge about the antimicrobial susceptibility patterns of C.acnes is limited in Turkey. Determining the phylotypes of C.acnes isolates and providing antimicrobial susceptibility data will be very useful in understanding the pathogenesis of the disease, preventing the development of resistance, and applying rational and effective empirical treatment. The aim of this study was to determine the phylotypes and antimicrobial susceptibility patterns of C.acnes and to investigate the relationship among C.acnes phylotypes, the severity of acne and the antimicrobial resistance. C.acnes isolates cultivated from the acne lesions of 57 patients who admitted to the dermatology outpatient clinic of our university hospital and from the skin of 62 healthy control group in a six-month period were included in the study. The acne lesions on the face and chest/upper back were given a score according to the Global acne grading system (GAGS) for describing the severity of acne. The severity was graded as mild if the score was 1-18, moderate with scores from 19 to 30, severe with scores from 31 to 38, and as very severe if the score is more than 39. The isolates were identified by using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) . Phylotype analysis was performed by polymerase chain reaction (PCR) using specific primers. The minimum inhibitory concentrations (MICs) of clindamycin, erythromycin, azithromycin, tetracycline and doxycycline were determined by agar dilution technique recommended by Clinical and Laboratory Standards Institute (CLSI) for anaerobic bacteria. The majority of the isolates (patient; n= 47, control; n= 47) in both of the patient and control groups were phylotype IA, followed by type IB and type II, respectively and no type III C.acnes was detected. There was no correlation between acne severity and bacterial phylotypes. The resistance rates of clindamycin, erythromycin, azithromycin, tetracycline and doxycycline were found to be 22.8%, 29.8%, 35.2%, 3.5% and 5.3% in the acne patients group, respectively, whereas in the control group the incidence of resistance to these antimicrobials was 11.3%, 21%, 38.7%, 1.6% and 1.6%, respectively. There was no significant difference in antimicrobial resistance between the patient and control groups, except erythromycin (p= 0.043, Fisher's exact) as well as no relationship was found between antimicrobial resistance and phylotypes in both of the groups. The number of isolates, resistant to two or more antimicrobials, was higher in the patients with acne. C.acnes isolates were highly resistant to clindamycin, erythromycin and azithromycin. Type IA constituted the majority of the phylotypes. There was no significant relationship between C.acnes phylotype, antimicrobial resistance and acne severity.

High Mutation Frequency and Significant Population Differentiation in Papaya Ringspot Virus-W Isolates.

A total of 101 papaya ringspot virus-W (PRSV-W) isolates were collected from five different cucurbit hosts in six counties of Oklahoma during the 2016–2018 growing seasons. The coat protein (CP) coding region of these isolates was amplified by reverse transcription-polymerase chain reaction, and 370 clones (3–5 clones/isolate) were sequenced. Phylogenetic analysis revealed three phylogroups while host, location, and collection time of isolates had minimal impact on grouping pattern. When CP gene sequences of these isolates were compared with sequences of published PRSV isolates (both P and W strains), they clustered into four phylogroups based on geographical location. Oklahoman PRSV-W isolates formed one of the four distinct major phylogroups. The permutation-based tests, including Ks, Ks *, Z *, Snn, and neutrality tests, indicated significant genetic differentiation and polymorphisms among PRSV-W populations in Oklahoma. The selection analysis confirmed that the CP gene is undergoing purifying selection. The mutation frequencies among all PRSV-W isolates were within the range of 1 × 10−3. The substitution mutations in 370 clones of PRSV-W isolates showed a high proportion of transition mutations, which gave rise to higher GC content. The N-terminal region of the CP gene mostly contained the variable sites with numerous mutational hotspots, while the core region was highly conserved.

Recent population differentiation in the habitat specialist Glossy Antshrike (Aves: Thamnophilidae) across Amazonian seasonally flooded forests.

We assessed population structure and the spatio‐temporal pattern of diversification in the Glossy Antshrike Sakesphorus luctuosus (Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. By targeting ultraconserved elements (UCEs) from 32 specimens of S. luctuosus, we identified independent lineages and estimated their differentiation, divergence times, and migration rates. We also estimated current and past demographic histories for each recovered lineage. We found evidence confirming that S. luctuosus consists of a single species, comprising at least four populations, with some highly admixed individuals and overall similar levels of migration between populations. We confirmed the differentiation of the Araguaia River basin population (S. l. araguayae) and gathered circumstantial evidence indicating that the taxon S. hagmanni may represent a highly introgressed population between three distinct phylogroups of S. luctuosus. Divergences between populations occurred during the last 1.2 mya. Signs of population expansions were detected for populations attributed to subspecies S. l. luctuosus, but not for the S. l. araguayae population. Our results support that S. luctuosus has had a complex population history, resulting from a high dependence on southeastern “clear water” seasonally flooded habitats and their availability through time. Spatial and demographic expansions toward the western “white water” flooded forests might be related to recent changes in connectivity and availability of these habitats. Our study reinforces the view that isolation due to absence of suitable habitat has been an important driver of population differentiation within Amazonian flooded forests, but also that differences between várzeas (“white water” floodplains, mostly in southwestern Amazonia) and igapós (“clear water” floodplains, especially located in the east) should be further explored as drivers of micro‐evolution for terrestrial species.

Variation in Accessory Genes Within the Klebsiella oxytoca Species Complex Delineates Monophyletic Members and Simplifies Coherent Genotyping.

Members of the Klebsiella oxytoca species complex (KoSC) are emerging human pathogens causing infections of increasing significance especially in healthcare settings. KoSC strains are affiliated with distinct phylogroups based on genetic variation at the beta-lactamase gene (blaOXY) and it has been proposed that each major phylogroup represents a unique species. However, since the typing methods applied in clinical settings cannot differentiate every species within the complex, existing clinical, epidemiological and DNA sequence data is frequently misclassified. Here we systematically examined the phylogenetic relationship of KoSC strains to evaluate robustness of existing typing methods and to provide a simple typing strategy for KoSC members that cannot be differentiated biochemically. Initial analysis of a collection of K. oxytoca, K. michiganensis, K. pasteurii, and K. grimontii strains of environmental origin showed robust correlation of core phylogeny and blaOXY grouping. Moreover, we identified species-specific accessory gene loci for these strains. Extension of species correlation using database entries initially failed. However, assessment of average nucleotide identities (ANI) and phylogenetic validations showed that nearly one third of isolates in public databases have been misidentified. Reclassification resulted in a robust reference strain set for reliable species identification of new isolates or for retyping of strains previously analyzed by multi-locus sequence typing (MLST). Finally, we show convergence of ANI, core gene phylogeny, and accessory gene content for available KoSC genomes. We conclude that also the monophyletic members K. oxytoca, K. michiganensis, K. pasteurii and K. grimontii can be simply differentiated by a PCR strategy targeting blaOXY and accessory genes defined here.

Review of emUvarovistia/em (Orthoptera: Tettigoniidae; Tettigoniinae): genetic data indicate a new cryptic species, emUvarovistia/em emmunzurensis/em sp.n.

Genus Uvarovistia ranged along the Zagros Mountain belt. We presented first genetic data from three species of the genus and a taxonomic rectification indicated by these data. Sequences of three mitochondrial and two nuclear gene segments were obtained from different populations. Phylogenetic and automatic species delimitation analyses consistently suggested three distinct phylogroups as U. zebra, U. satunini and the third a new species, U. munzurensis Uluar Yahyaoğlu sp. n. Time estimation and population genetic analyses supported consistent results. The following conclusions were reached: (i) five species in the genus constitute two distinct species groups named as Zebra Group and Satunini Group, (ii) data suggest intra generic relationships as U. zebra + ((U. satunini + U. munzurensis) + (U. bakhtiara +U. iraka)), (iii) molecular clock estimations indicated a deep divergence time and no gene flow between U. satunini and U. munzurensis, (iv) although these two species cannot be clearly distinguished by morphology, range of U. munzurensis seems to be isolated from other by lowlands of Euphrates Valley, and (v) age of generic ancestor is around five million years a time corresponding to connection of Anatolian and Zagros plates, and genus radiated along Zagros belt after dispersal of ancestral stock here.

Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups

In this study, more than one hundred thousand Escherichia coli and Shigella genomes were examined and classified. This is, to our knowledge, the largest E. coli genome dataset analyzed to date. A Mash-based analysis of a cleaned set of 10,667 E. coli genomes from GenBank revealed 14 distinct phylogroups. A representative genome or medoid identified for each phylogroup was used as a proxy to classify 95,525 unassembled genomes from the Sequence Read Archive (SRA). We find that most of the sequenced E. coli genomes belong to four phylogroups (A, C, B1 and E2(O157)). Authenticity of the 14 phylogroups is supported by several different lines of evidence: phylogroup-specific core genes, a phylogenetic tree constructed with 2613 single copy core genes, and differences in the rates of gene gain/loss/duplication. The methodology used in this work is able to reproduce known phylogroups, as well as to identify previously uncharacterized phylogroups in E. coli species.

Locality Effect of Coral-Associated Bacterial Community in the Kuroshio Current From Taiwan to Japan

The Kuroshio Current (KC) is one of the fastest water currents in the world, running through the western boundary of the North Pacific Ocean. The KC strongly influences the regional hydroclimate by creating temperature, salinity, and pH gradients from tropical to subtropical and temperate zones, including regions with rich coral reef habitats. Microbial community composition of corals is influenced by various environmental factors, including salinity, pH, and geographical location. However, to date, it is unclear how coral-associated microbial communities would respond to the same water current running through different locations with a time lag. Therefore, we hypothesized that the locations subjected to the KC at higher latitudes experience similar but delayed environmental conditions compared to those at lower latitudes, and thus the coral communities of both will respond similarly, but at different times. In this yearlong study, we compared the bacterial communities of Acropora muricata at Taiwan, Okinawa, and Kochi subjected to the KC. We found that site-specific conditions and site latitude may have stronger effects on bacterial composition and dynamics than a water current. Consequently, we suggest that latitude largely determines the temperature tolerance range of coral microbiota. Additionally, among the dominant coral associated bacteria, Endozoicomonas from A. muricata and Stylophora pistillata forms distinct phylogroups, while Acinetobacter is more likely a host generalist.

Phylogenetic Analysis and Antimicrobial Resistance Profiles of Escherichia coli Strains Isolated from UTI-Suspected Patients.

Background:Escherichia coli as one of the most predominant pathogens is the major cause of urinary tract infections (UTI) worldwide. E. coli strains could be classified into distinct phylo-groups based on PCR method. Additionally, studying the antimicrobial resistance profiles of these strains is essential for finding the effective selection of treatment and evaluating the differences among resistance patterns of particular phylogenetic groups. This study aimed to determine the phylogroups of E. coli isolated from patients with UTI in Tehran, Iran.Methods:The urine samples were collected from patients suspected to UTI from four hospitals in Tehran, Iran; Mofid, Vali-Asr, Bu-Ali and Tehran Heart Center (THC) Hospitals during 2014–2016. Assessing the antimicrobial resistance profile of the identified strains was accomplished using ampicillin, ceftriaxone, cefotaxime, and ceftazidime among β-lactam group; gentamicin, and streptomycin among aminoglycosides; nalidixic acid and norfloxacin from quinolones; and chloramphenicol disks. The phylogenetic characterization of 60 E. coli isolates obtained from patients with UTI was done by triplex PCR method.Results:E. coli strains showed high resistance toward streptomycin (93.33%), ampicillin (86.6%) and nalidixic acid (73.33%) while resistance against chloramphenicol showed the lowest (10%). The prevalent groups were B2 (n=50/60, 83%), followed by D (n=6/60, 10%), B1 (n=3/60, 5%), and A (n=1, 1.6%).Conclusion:The most predominant phylogenetic group was B2 with the major frequent detected with the major drug resistant (48%) compared to other Phylogenetic groups.

Comparative Phylogeography and Integrative Taxonomy of Ochlerotatus caspius (Dipera: Culicidae) and Ochlerotatus dorsalis

Given that accurately identifying pathogen vectors is vital for designing efficient mosquito control programs based on the proper surveillance of the epidemiologically important species, it has been suggested the complementary use of independently evolving genes and morphometric traits as a reliable approach for the characterization and delimitation of related species. Hence, we examined the spatial distribution of COI mtDNA and ITS2 rDNA variation from the historical perspective of Ochlerotatus caspius (Pallas, 1771) and O. dorsalis (Meigen, 1830), while simultaneously testing the utility of the two markers in integrative species delimitation when combined with phenotypic character analyses of larvae and adults. Despite the striking difference in haplotype diversity (high in COI mtDNA, low in ITS2 rDNA), no evident phylogeographic structure was apparent in the Palearctic O. caspius. The Holarctic O. dorsalis species was subdivided into two highly distinctive COI mtDNA phylogroups which corresponded to the Nearctic and Palearctic regions. Strong support for the independence of the two allopatric evolutionary lineages suggested that geographical barrier and climatic changes during Pleistocene caused vicariance of the ancestral range. COI mtDNA reliably distinguished O. caspius and O. dorsalis, while ITS2 rDNA yet again lacked the proper resolution for solving this problem. An integrative approach based on the larval and adult morphological traits have varying taxonomic applications due to their differential diagnostic values. Thus, by the implementation of an integrative taxonomic approach, we successfully detected species borders between the two epidemiologically relevant species and uncovered the presence of cryptic diversity within O. dorsalis.

Environmental DNA reveals cryptic diversity within the subterranean amphipod genus Pseudocrangonyx Akatsuka & Komai, 1922 (Amphipoda: Crangonyctoidea: Pseudocrangonyctidae) from central Japan

Abstract An environmental DNA (eDNA) detection method confirms the presence of the subterranean amphipod genus PseudocrangonyxAkatsuka & Komai, 1922 in the city of Kyoto, Honshu, Japan for the first time in more than 90 years. Phylogenetic trees using partial sequences of the 16S rRNA gene of eDNA samples from Kyoto and specimens collected from various locations in Japan and Korea highlight that two genetically distinct taxonomic units inhabit Kyoto’s subterranean environments. Results reveal that the ranges of distinct phylogroups of Pseudocrangonyx widely overlap with each other around Lake Biwa in central western Honshu. The eDNA results increase our understanding of the species richness and complicated evolutionary history of these stygobitic amphipods.

The speciation and hybridization history of the genus Salmonella

Bacteria and archaea make up most of natural diversity, but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genus Salmonella , an ecologically diverse bacterial lineage, within which S. enterica subsp. enterica is responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified 11 distinct phylogroups, 3 of which were previously undescribed. Strains assigned to S. enterica subsp. salamae are polyphyletic, with two distinct lineages that we designate Salamae A and B. Strains of the subspecies houtenae are subdivided into two groups, Houtenae A and B, and are both related to Selander’s group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large-scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages, but detected subtler signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence are not sufficient to account for Salmonella evolution.