All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy

In prokaryotic taxonomy, a set of criteria is commonly used to delineate species. These criteria are generally based on cohesion at the phylogenetic, phenotypic and genomic levels. One such criterion shown to have promise in the genomic era is average nucleotide identity (ANI), which provides an average measure of similarity across homologous regions shared by a pair of genomes. However, despite the popularity and relative ease of using this metric, ANI has undergone numerous refinements, with variations in genome fragmentation, homologue detection parameters and search algorithms. To test the robustness of a 95–96 % species cut-off range across all the commonly used ANI approaches, seven different methods were used to calculate ANI values for intra- and interspecies datasets representing three classes in the Proteobacteria . As a reference point, these methods were all compared to the widely used blast-based ANI (i.e. ANIb as implemented in JSpecies), and regression analyses were performed to investigate the correlation of these methods to ANIb with more than 130000 individual data points. From these analyses, it was clear that ANI methods did not provide consistent results regarding the conspecificity of isolates. Most of the methods investigated did not correlate perfectly with ANIb, particularly between 90 and 100% identity, which includes the proposed species boundary. There was also a difference in the correlation of methods for the different taxon sets. Our study thus suggests that the specific approach employed needs to be considered when ANI is used to delineate prokaryotic species. We furthermore suggest that one would first need to determine an appropriate cut-off value for a specific taxon set, based on the intraspecific diversity of that group, before conclusions on conspecificity of isolates can be made, and that the resulting species hypotheses be confirmed with analyses based on evolutionary history as part of the polyphasic approach to taxonomy.

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A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078

mBio ◽

10.1128/mbio.02790-18 ◽

2019 ◽

Vol 10 (2) ◽

Cited By ~ 16

Author(s):

Kate E. Dingle ◽

Xavier Didelot ◽

T. Phuong Quan ◽

David W. Eyre ◽

Nicole Stoesser ◽

...

Keyword(s):

Clostridium Difficile ◽

Evolutionary History ◽

Selective Pressure ◽

Tetracycline Resistance ◽

Clonal Expansion ◽

Human Pathogen ◽

Content Type ◽

Resistance Determinants ◽

Ribotype 078 ◽

Human Infections

ABSTRACT The increasing clinical importance of human infections (frequently severe) caused by Clostridium difficile PCR ribotype 078 (RT078) was first reported in 2008. The severity of symptoms (mortality of ≤30%) and the higher proportion of infections among community and younger patients raised concerns. Farm animals, especially pigs, have been identified as RT078 reservoirs. We aimed to understand the recent changes in RT078 epidemiology by investigating a possible role for antimicrobial selection in its recent evolutionary history. Phylogenetic analysis of international RT078 genomes (isolates from 2006 to 2014, n = 400), using time-scaled, recombination-corrected, maximum likelihood phylogenies, revealed several recent clonal expansions. A common ancestor of each expansion had independently acquired a different allele of the tetracycline resistance gene tetM. Consequently, an unusually high proportion (76.5%) of RT078 genomes were tetM positive. Multiple additional tetracycline resistance determinants were also identified (including efflux pump tet40), frequently sharing a high level of nucleotide sequence identity (up to 100%) with sequences found in the pig pathogen Streptococcus suis and in other zoonotic pathogens such as Campylobacter jejuni and Campylobacter coli. Each RT078 tetM clonal expansion lacked geographic structure, indicating rapid, recent international spread. Resistance determinants for C. difficile infection-triggering antimicrobials, including fluoroquinolones and clindamycin, were comparatively rare in RT078. Tetracyclines are used intensively in agriculture; this selective pressure, plus rapid, international spread via the food chain, may explain the increased RT078 prevalence in humans. Our work indicates that the use of antimicrobials outside the health care environment has selected for resistant organisms, and in the case of RT078, has contributed to the emergence of a human pathogen. IMPORTANCE Clostridium difficile PCR ribotype 078 (RT078) has multiple reservoirs; many are agricultural. Since 2005, this genotype has been increasingly associated with human infections in both clinical settings and the community. Investigations of RT078 whole-genome sequences revealed that tetracycline resistance had been acquired on multiple independent occasions. Phylogenetic analysis revealed a rapid, recent increase in numbers of closely related tetracycline-resistant RT078 (clonal expansions), suggesting that tetracycline selection has strongly influenced its recent evolutionary history. We demonstrate recent international spread of emergent, tetracycline-resistant RT078. A similar tetracycline-positive clonal expansion was also identified in unrelated nontoxigenic C. difficile, suggesting that this process may be widespread and may be independent of disease-causing ability. Resistance to typical C. difficile infection-associated antimicrobials (e.g., fluoroquinolones, clindamycin) occurred only sporadically within RT078. Selective pressure from tetracycline appears to be a key factor in the emergence of this human pathogen and the rapid international dissemination that followed, plausibly via the food chain.

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An empirical investigation of repeat buying behavior of customers of two brands in India

Journal of Indian Business Research ◽

10.1108/jibr-05-2013-0043 ◽

2014 ◽

Vol 6 (3) ◽

pp. 255-268 ◽

Cited By ~ 1

Author(s):

Mehir Baidya ◽

Gautam Ghosh

Keyword(s):

No Value ◽

Empirical Investigation ◽

Primary Data ◽

Buying Behavior ◽

Content Type ◽

Fund Allocation ◽

Total Process ◽

Data Points ◽

Repeat Purchase ◽

Practical Implications

Purpose – The purpose of this paper is to attempt to test whether price and quality have any influence on customer repeat purchase probability. Managers should know the strategic determinants of repeat purchase probability to retain customers. Design/methodology/approach – Primary data were gathered on repeat purchase, price and quality via a survey of 400 customers of two brands in the Business-to-customer (B2C) sector. Then 380 × 4 data points to a logit model were fitted to estimate the effects of price and quality on customer repeat purchase probability. Findings – It was found that price, quality and price × quality influence customer repeat purchase probability substantially. Furthermore, the elasticities of repeat purchase probability to price and quality are quite high in both cases. Practical implications – Managers should use elasticities to determine how to allocate funds between price and quality to maximize repeat purchase probability. Originality/value – In view of the complexity of customer repeat buying behavior, this study deals with one aspect or feature of the total process, which does not mean that it has no value. By confirming two strategic determinants of customer repeat purchase probability and suggesting a simple rule of fund allocation, this work definitely adds some research of value to the relevant marketing literature.

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KKCL: exploring growth opportunities

Emerald Emerging Markets Case Studies ◽

10.1108/eemcs-09-2014-0234 ◽

2015 ◽

Vol 5 (4) ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Jyoti Kainth ◽

Gautam Kainth

Keyword(s):

Subject Area ◽

Growth Strategy ◽

Situational Analysis ◽

Product Management ◽

Growth Strategies ◽

Content Type ◽

Data Points ◽

Fashion Apparel ◽

To Come ◽

Internal And External Factors

Subject area Product Management, Marketing Strategy, Growth Strategies. Study level/applicability Bachelor of Business Studies, MBA, Executive MBA. Case overview The case documents the humble beginning of Kewal Kiran Clothing Limited (KKCL) in 1981 to its current position as a leading fashion apparel brand in India. However, competition from new national players, emergence of global players in India, private labels of retailers and dawn of Internet retailing has created significant growth challenges for the firm. Mr Jain, the Managing Director of KKCL, is contemplating the growth strategies for the firm and possible changes in the business model, as he is developing the 2014-2015 strategic plan for KKCL. This is imperative to reach the ambitious sales target of INR 10 billion by 2018-2019. The students are expected to assess the performance of KKCL on multiple quantitative and qualitative data points given in the case and exhibits. It encourages them to come up with possible growth strategies for the firm. Expected learning outcomes The case is expected to guide students in comprehending the multi-thronged challenges pertaining to fashion apparel industry; in Situational Analysis of the firm, which includes assessing internal and external factors; and in recommending the best possible growth strategy after due evaluation and deliberation using Ansoff's Matrix. Supplementary materials Teaching notes are available for educators only. Please contact your library to gain login details or email [email protected] to request teaching notes.

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Human Origin for Livestock-Associated Methicillin-Resistant Staphylococcus aureus

mBio ◽

10.1128/mbio.00082-12 ◽

2012 ◽

Vol 3 (2) ◽

Cited By ~ 28

Author(s):

J. Ross Fitzgerald

Keyword(s):

Staphylococcus Aureus ◽

Evolutionary History ◽

Methicillin Resistant Staphylococcus Aureus ◽

Agricultural Practices ◽

Methicillin Resistant ◽

Content Type ◽

Zoonotic Infections ◽

Ancestral Origin ◽

Important Study ◽

History Of

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of human morbidity and mortality worldwide. The emergence in the last decade of a livestock-associated MRSA (LA-MRSA) clone which also has the capacity to cause zoonotic infections in humans has raised important questions regarding its origin and its potential to cause human epidemics. An important study by L. B. Price et al. [mBio 3(1):e00305-11, 2012] provides evidence for a human ancestral origin for LA-MRSA, raising concerns about agricultural practices that may have contributed to its emergence and expansion. The study highlights the potential for comparative whole-genome sequencing of closely related strains to provide valuable insights into the evolutionary history of bacterial pathogens.

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Separate F-Type Plasmids Have Shaped the Evolution of the H30 Subclone of Escherichia coli Sequence Type 131

mSphere ◽

10.1128/msphere.00121-16 ◽

2016 ◽

Vol 1 (4) ◽

Cited By ~ 42

Author(s):

Timothy J. Johnson ◽

Jessica L. Danzeisen ◽

Bonnie Youmans ◽

Kyle Case ◽

Katharine Llop ◽

...

Keyword(s):

Escherichia Coli ◽

Real Time ◽

Single Molecule ◽

Convergent Evolution ◽

Evolutionary History ◽

Gene Clusters ◽

Content Type ◽

E Coli ◽

History Of ◽

Evolutionary Success

ABSTRACT A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131’s evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical lineages of ST131. From this work, it was determined that a series of plasmid gains, losses, and recombinational events has led to the currently circulating plasmids of ST131 strains. These plasmids appear to have evolved to acquire similar gene clusters on multiple occasions, suggesting possible plasmid-mediated convergent evolution leading to evolutionary success. These plasmids also appear to be better suited to exist in specific strains of ST131 due to coadaptive mutations. Overall, a series of events has enabled the evolution of ST131 plasmids, possibly contributing to the lineage’s success. The extraintestinal pathogenic Escherichia coli (ExPEC) H30 subclone of sequence type 131 (ST131-H30) has emerged abruptly as a dominant lineage of ExPEC responsible for human disease. The ST131-H30 lineage has been well described phylogenetically, yet its plasmid complement is not fully understood. Here, single-molecule, real-time sequencing was used to generate the complete plasmid sequences of ST131-H30 isolates and those belonging to other ST131 clades. Comparative analyses revealed separate F-type plasmids that have shaped the evolution of the main fluoroquinolone-resistant ST131-H30 clades. Specifically, an F1:A2:B20 plasmid is strongly associated with the H30R/C1 clade, whereas an F2:A1:B− plasmid is associated with the H30Rx/C2 clade. A series of plasmid gene losses, gains, and rearrangements involving IS26 likely led to the current plasmid complements within each ST131-H30 sublineage, which contain several overlapping gene clusters with putative functions in virulence and fitness, suggesting plasmid-mediated convergent evolution. Evidence suggests that the H30Rx/C2-associated F2:A1:B− plasmid type was present in strains ancestral to the acquisition of fluoroquinolone resistance and prior to the introduction of a multidrug resistance-encoding gene cassette harboring bla CTX-M-15. In vitro experiments indicated a host strain-independent low frequency of plasmid transfer, differential levels of plasmid stability even between closely related ST131-H30 strains, and possible epistasis for carriage of these plasmids within the H30R/Rx lineages. IMPORTANCE A clonal lineage of Escherichia coli known as ST131 has emerged as a dominating strain type causing extraintestinal infections in humans. The evolutionary history of ST131 E. coli is now well understood. However, the role of plasmids in ST131’s evolutionary history is poorly defined. This study utilized real-time, single-molecule sequencing to compare plasmids from various current and historical lineages of ST131. From this work, it was determined that a series of plasmid gains, losses, and recombinational events has led to the currently circulating plasmids of ST131 strains. These plasmids appear to have evolved to acquire similar gene clusters on multiple occasions, suggesting possible plasmid-mediated convergent evolution leading to evolutionary success. These plasmids also appear to be better suited to exist in specific strains of ST131 due to coadaptive mutations. Overall, a series of events has enabled the evolution of ST131 plasmids, possibly contributing to the lineage’s success.

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Exploratory Study on Plasma Immunomodulator and Antibody Profiles in Tuberculosis Patients

Clinical and Vaccine Immunology ◽

10.1128/cvi.00213-13 ◽

2013 ◽

Vol 20 (8) ◽

pp. 1283-1290 ◽

Cited By ~ 13

Author(s):

Resmi Ravindran ◽

Viswanathan V. Krishnan ◽

Azra Khanum ◽

Paul A. Luciw ◽

Imran H. Khan

Keyword(s):

Immune Responses ◽

Ex Vivo ◽

Peripheral Circulation ◽

Computer Assisted ◽

Content Type ◽

Tuberculosis Patients ◽

Active Pulmonary Tuberculosis ◽

Host Immune Responses ◽

Data Points ◽

Apparently Healthy

ABSTRACTHost immune responses toMycobacterium tuberculosisare generally able to contain infection and maintain a delicate balance between protection and immunopathology. A shift in this balance appears to underlie active disease observed in about 10% of infected individuals. Effects of local inflammation, combined with anti-M. tuberculosissystemic immune responses, are directly detectable in peripheral circulation, withoutex vivostimulation of blood cells or biopsy of the affected organs. We studied plasma immunomodulator and antibody biomarkers in patients with active pulmonary tuberculosis (TB) by a combination of multiplex microbead immunoassays and computational tools for data analysis. Plasma profiles of 10 immunomodulators and antibodies against eightM. tuberculosisantigens (previously reported by us) were examined in active pulmonary TB patients in a country where TB is endemic, Pakistan. Multiplex analyses were performed on samples from apparently healthy individuals without active TB from the same community as the TB patients to establish the assay baselines for all analytes. Over 3,000 data points were collected from patients (n= 135) and controls (n= 37). The data were analyzed by multivariate and computer-assisted cluster analyses to reveal patterns of plasma immunomodulators and antibodies. This study shows plasma profiles that in most patients represented either strong antibody or strong immunomodulator biomarkers. Profiling of a combination of both immunomodulators and antibodies described here may be valuable for the analysis of host immune responses in active TB in countries where the disease is endemic.

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Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex

Microbial Genomics ◽

10.1099/mgen.0.000351 ◽

2020 ◽

Vol 6 (4) ◽

Cited By ~ 2

Author(s):

Maria Izabel A. Cavassim ◽

Sara Moeskjær ◽

Camous Moslemi ◽

Bryden Fields ◽

Asger Bachmann ◽

...

Keyword(s):

Species Complex ◽

Rhizobium Leguminosarum ◽

De Novo ◽

Gene Tree ◽

Species Boundaries ◽

Content Type ◽

Genomic Location ◽

Tree Traversal ◽

Four Blocks ◽

Core Genes

Rhizobia supply legumes with fixed nitrogen using a set of symbiosis genes. These can cross rhizobium species boundaries, but it is unclear how many other genes show similar mobility. Here, we investigate inter-species introgression using de novo assembly of 196 Rhizobium leguminosarum sv. trifolii genomes. The 196 strains constituted a five-species complex, and we calculated introgression scores based on gene-tree traversal to identify 171 genes that frequently cross species boundaries. Rather than relying on the gene order of a single reference strain, we clustered the introgressing genes into four blocks based on population structure-corrected linkage disequilibrium patterns. The two largest blocks comprised 125 genes and included the symbiosis genes, a smaller block contained 43 mainly chromosomal genes, and the last block consisted of three genes with variable genomic location. All introgression events were likely mediated by conjugation, but only the genes in the symbiosis linkage blocks displayed overrepresentation of distinct, high-frequency haplotypes. The three genes in the last block were core genes essential for symbiosis that had, in some cases, been mobilized on symbiosis plasmids. Inter-species introgression is thus not limited to symbiosis genes and plasmids, but other cases are infrequent and show distinct selection signatures.

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The past, present and future of ancient bacterial DNA

Microbial Genomics ◽

10.1099/mgen.0.000384 ◽

2020 ◽

Vol 6 (7) ◽

Cited By ~ 1

Author(s):

Nicolas Arning ◽

Daniel J. Wilson

Keyword(s):

Demographic Transition ◽

Dental Plaque ◽

Evolutionary History ◽

High Throughput Sequencing ◽

Industrial Revolution ◽

Environmental Isolates ◽

Bacterial Dna ◽

Content Type ◽

The Past ◽

History Of

Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis . Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.

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Stable Positions of Epigenetically Inherited Centromeres in the Emerging Fungal Pathogen Candida auris and Its Relatives

mBio ◽

10.1128/mbio.01036-21 ◽

2021 ◽

Author(s):

Laura N. Rusche

Keyword(s):

Fungal Pathogen ◽

Evolutionary History ◽

Comparative Genomic ◽

Candida Auris ◽

Content Type ◽

Genomic Study ◽

Comparative Genomic Study

Candida auris is an emerging fungal pathogen that is thermotolerant and often resistant to standard antifungal treatments. To trace its evolutionary history, the Sanyal lab conducted a comparative genomic study focusing on the positions of centromeres in C. auris and eight other species from the Clavispora / Candida clade of yeasts (A.

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Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat

10.1101/2021.01.10.426084 ◽

2021 ◽

Author(s):

Ekaterina D. Badaeva ◽

Fedor A. Konovalov ◽

Helmut Knüpffer ◽

Agostino Fricano ◽

Alevtina S. Ruban ◽

...

Keyword(s):

Evolutionary History ◽

Chromosomal Rearrangements ◽

Tetraploid Wheat ◽

Wheat Breeding ◽

Intraspecific Diversity ◽

Wheat Improvement ◽

Comprehensive Survey ◽

History Of ◽

Diversity Sampling ◽

Wheat Wild Relatives

AbstractBackgroundWheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite of its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement.ResultsWe report the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. We show that the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group-, and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. We discuss the origin and domestication history of the GGAtAt lineages in the context of state-of-the-art archaeobotanical finds.ConclusionsWe shed new light on the complex evolutionary history of the GGAtAt wheat genepool. We provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.

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