Comparative genomic analyses of two novel qnrVC6 carrying multidrug-resistant Pseudomonas. spp strains

AbstractKlebsiella pneumoniae(Kp) has emerged as an important cause of two distinct public health threats: multidrug resistant (MDR) healthcare-associated infections1and community-acquired invasive infections, particularly pyogenic liver abscess2. The majority of MDR hospital outbreaks are caused by a subset ofKpclones with a high prevalence of acquired antimicrobial resistance (AMR) genes, while the majority of community-acquired invasive infections are caused by ‘hypervirulent’ clones that rarely harbour acquired AMR genes but have high prevalence of key virulence loci3–5. Worryingly, the last few years have seen increasing reports of convergence of MDR and the key virulence genes within individualKpstrains6, but it is not yet clear whether these represent a transient phenomenon or a significant ongoing threat. Here we perform comparative genomic analyses for 28 distinctKpclones, including 6 hypervirulent and 8 MDR, to better understand their evolutionary histories and the risks of convergence. We show that MDR clones are highly diverse with frequent chromosomal recombination and gene content variability that far exceeds that of the hypervirulent clones. Consequently, we predict a much greater risk of virulence gene acquisition by MDRKpclones than of resistance gene acquisition by hypervirulent clones.

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Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids

Genes ◽

10.3390/genes10110850 ◽

2019 ◽

Vol 10 (11) ◽

pp. 850 ◽

Cited By ~ 1

Author(s):

Krzysztof Romaniuk ◽

Michal Styczynski ◽

Przemyslaw Decewicz ◽

Oliwia Buraczewska ◽

Witold Uhrynowski ◽

...

Keyword(s):

Transposable Elements ◽

Horizontal Transfer ◽

Comparative Genomic ◽

Narrow Host Range ◽

Antarctic Soils ◽

Pseudomonas Spp ◽

Genomic Analyses ◽

Genes Encoding ◽

Pilin Protein ◽

Functional Analyses

Pseudomonas spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of Pseudomonas spp. have been sequenced, but only 12 of them were isolated from psychrotolerant strains. In this study, 15 novel plasmids of cold-active Pseudomonas spp. originating from the King George Island (Antarctica) were characterized using a combined, structural and functional approach, including thorough genomic analyses, functional analyses of selected genetic modules, and identification of active transposable elements localized within the plasmids and comparative genomics. The analyses performed in this study increased the understanding of the horizontal transfer of plasmids found within Pseudomonas populations inhabiting Antarctic soils. It was shown that the majority of the studied plasmids are narrow-host-range replicons, whose transfer across taxonomic boundaries may be limited. Moreover, structural and functional analyses enabled identification and characterization of various accessory genetic modules, including genes encoding major pilin protein (PilA), that enhance biofilm formation, as well as active transposable elements. Furthermore, comparative genomic analyses revealed that the studied plasmids of Antarctic Pseudomonas spp. are unique, as they are highly dissimilar to the other known plasmids of Pseudomonas spp.

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Functional and comparative genome analysis reveals clade-specific genome innovations in the killer fungus Candida auris

10.1101/2021.01.29.428909 ◽

2021 ◽

Author(s):

Aswathy Narayanan ◽

Rakesh Netha Vadnala ◽

Promit Ganguly ◽

Pavitra Selvakumar ◽

Shivaprakash M Rudramurthy ◽

...

Keyword(s):

Genome Analysis ◽

Multidrug Resistant ◽

Comparative Genomic ◽

Candida Auris ◽

Evolutionary Trajectory ◽

Molecular Events ◽

Genomic Analyses ◽

Centromere Inactivation ◽

Chromosomal Changes ◽

Systemic Infections

AbstractThe thermotolerant multidrug-resistant ascomycete Candida auris rapidly emerged since 2009 and simultaneously evolved in different geographical zones worldwide, causing superficial as well as systemic infections. The molecular events that orchestrated this sudden emergence of the killer fungus remain mostly elusive. Here, we identify centromeres in C. auris and related species, using a combined approach of chromatin immunoprecipitation and comparative genomic analyses. We find that C. auris and multiple other species in the Clavispora/Candida clade shared a conserved small regional centromere landscape lacking pericentromeres. Further, a centromere inactivation event led to karyotypic alterations in this species complex. Inter-species genome analysis identified several structural chromosomal changes around centromeres. In addition, centromeres are found to be rapidly evolving loci among the different geographical clades of the same species of C. auris. Finally, we reveal an evolutionary trajectory of the unique karyotype associated with clade 2 that consists of the drug susceptible isolates of C. auris.

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Comparative Genomic Analyses Reveal Potential Factors Responsible for the ST6 Oxacillin-Resistant Staphylococcus lugdunensis Endemic in a Hospital

Frontiers in Microbiology ◽

10.3389/fmicb.2021.765437 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shih-Cheng Chang ◽

Lee-Chung Lin ◽

Jang-Jih Lu

Keyword(s):

Multidrug Resistant ◽

Comparative Genomic ◽

Staphylococcus Lugdunensis ◽

Healthcare Settings ◽

Resistant Genes ◽

Similar Drug ◽

Genomic Analyses ◽

Life Threatening ◽

Potential Factors ◽

Successful Colonization

Oxacillin-resistant Staphylococcus lugdunensis (ORSL) is considered a life-threatening isolate in healthcare settings. Among ORSL clones, ST6-SCCmec II strains are associated with an endemic spread in hospitals. We analyzed the complete genome of ORSL CGMH-SL118, a representative strain. Results revealed that this strain contained three MGEs (two prophages and one plasmid) other than the SCCmec II element, which showed remarkable differences in genome organization compared to the reference strains from NCBI. Eight multidrug-resistant genes were identified. All but blaZ were carried by MGEs, such as the SCCmec II element [mecA, ant (9)-Ia, and ermA] and the prophage φSPbeta [aac (6')-aph (2'), aph (3')-III, and ant (6)-Ia], indicating that MGEs carrying multidrug-resistant genes may be important for ST6 strains. The prophage φSPbeta contains sasX gene, which was responsible for the pathogenesis of Staphylococcus aureus. A phage-mediated resistant island containing fusB (SlRIfusB-118) was found near φSPbeta, which was highly homologous to type III SeRIfusB-5907 of Staphylococcus epidermidis. In contrast to previous studies, over 20% of ST6 isolates showed a fusidic acid-resistant phenotype, suggesting that phage-mediated intraspecies transmission of resistant islands may become an important issue for ST6 strains. Sixty-eight clinical isolates of ST6 Staphylococcus lugdunensis (50 OSSL, oxacillin-sensitive S. lugdunensis, and 18 ORSL, including CGMH-SL118) collected from various types of specimens in the hospital were studied. Among these isolates in this study, ORSL showed similar drug-resistant genes and phenotypes as CGMH-SL118. The comparative genomic analyses highlight the contribution of MGEs in the development and dissemination of antimicrobial resistance in ST6 strains, suggesting that resistance determinants and virulence factors encoded by MGEs provide a survival advantage for successful colonization and spread in healthcare settings.

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The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

Horticulture Research ◽

10.1038/s41438-021-00544-9 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Josué Barrera-Redondo ◽

Guillermo Sánchez-de la Vega ◽

Jonás A. Aguirre-Liguori ◽

Gabriela Castellanos-Morales ◽

Yocelyn T. Gutiérrez-Guerrero ◽

...

Keyword(s):

Defense Mechanisms ◽

Population Level ◽

Growth Hormones ◽

Comparative Genomic ◽

Structural Variants ◽

Closely Related Species ◽

Level Data ◽

Genomic Analyses ◽

Genotype By Sequencing ◽

Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

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Complete chloroplast genomes of Leptodermis scabrida complex: comparative genomic analyses and phylogenetic relationships

Gene ◽

10.1016/j.gene.2021.145715 ◽

2021 ◽

pp. 145715

Author(s):

Ying Zhang ◽

Zhengfeng Wang ◽

Yanan Guo ◽

Sheng Chen ◽

Xianyi Xu ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Comparative Genomic ◽

Chloroplast Genomes ◽

Genomic Analyses

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Prevalence of Antimicrobial Resistant Bacteria from Conjunctival Flora in an Eye Infection Prone Breed (Saint Bernard)

Molecules ◽

10.3390/molecules26082219 ◽

2021 ◽

Vol 26 (8) ◽

pp. 2219

Author(s):

George Cosmin Nadăș ◽

Cristiana Ștefania Novac ◽

Ioana Adriana Matei ◽

Cosmina Maria Bouari ◽

Zoltan Miklos Gal ◽

...

Keyword(s):

Multidrug Resistant ◽

Ocular Disease ◽

Resistant Bacteria ◽

Human Populations ◽

Disease Treatment ◽

Pseudomonas Spp ◽

History Of ◽

External Sources ◽

Staphylococcus Spp ◽

Saint Bernard

The conjunctival bacterial resident and opportunistic flora of dogs may represent a major source of dissemination of pathogens throughout the environment or to other animals and humans. Nevertheless, contamination with bacteria from external sources is common. In this context, the study of the antimicrobial resistance (AMR) pattern may represent an indicator of multidrug resistant (MDR) strains exchange. The present study was focused on a single predisposed breed—Saint Bernard. The evaluated animals were healthy, but about half had a history of ocular disease/treatment. The swabs collected from conjunctival sacs were evaluated by conventional microbiological cultivation and antimicrobial susceptibility testing (AST). The most prevalent Gram-positive was Staphylococcus spp.; regardless of the history, while Gram-negative was Pseudomonas spp.; exclusively from dogs with a history of ocular disease/treatment. Other identified genera were represented by Bacillus, Streptococcus, Trueperella, Aeromonas and Neisseria. The obtained results suggest a possible association between the presence of mixed flora and a history of ocular disease/treatment. A high AMR was generally observed (90%) in all isolates, especially for kanamycin, doxycycline, chloramphenicol and penicillin. MDR was recorded in Staphylococcus spp. and Pseudomonas spp. This result together with a well-known zoonotic potential may suggest an exchange of these strains within animal human populations and the environment.

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Evidence from comparative genomic analyses indicating that Lactobacillus-mediated irritable bowel syndrome alleviation is mediated by the conjugated linoleic acid synthesis

Food & Function ◽

10.1039/d0fo02616f ◽

2021 ◽

Author(s):

Yang Liu ◽

Wei Xiao ◽

Leilei Yu ◽

Fengwei Tian ◽

Gang Wang ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Linoleic Acid ◽

Gut Microbiota ◽

Acid Synthesis ◽

Comparative Genomic ◽

Low Grade ◽

Genomic Analyses ◽

Irritable Bowel ◽

Low Grade Inflammation ◽

Gut Microbiota Dysbiosis

Irritable bowel syndrome (IBS) is a chronic intestinal disorder accompanied by low-grade inflammation, visceral hypersensitivity, and gut microbiota dysbiosis. Several studies have indicated that Lactobacillus supplementation can help to alleviate...

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Comparative genomic analyses of a virulent pseudorabies virus and a series of its in vitro passaged strains

Virology Journal ◽

10.1186/s12985-018-1102-8 ◽

2018 ◽

Vol 15 (1) ◽

Cited By ~ 1

Author(s):

Chao Ye ◽

Jiqiang Wu ◽

Wu Tong ◽

Tongling Shan ◽

Xuefei Cheng ◽

...

Keyword(s):

Pseudorabies Virus ◽

Comparative Genomic ◽

Genomic Analyses

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Rapid evolution and molecular convergence in cryptorchidism-related genes associated with inherently undescended testes in mammals

BMC Ecology and Evolution ◽

10.1186/s12862-021-01753-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Simin Chai ◽

Ran Tian ◽

Juanjuan Bi ◽

Shixia Xu ◽

Guang Yang ◽

...

Keyword(s):

Muscle Development ◽

Rapid Evolution ◽

Genetic Material ◽

Comparative Genomic ◽

Testicular Descent ◽

Ancestral State ◽

Undescended Testes ◽

Genomic Analyses ◽

Genetic Mechanisms ◽

Molecular Convergence

Abstract Background The mammalian testis is an important male exocrine gland and spermatozoa-producing organ that usually lies in extra-abdominal scrotums to provide a cooler environment for spermatogenesis and sperm storage. Testicles sometimes fail to descend, leading to cryptorchidism. However, certain groups of mammals possess inherently ascrotal testes (i.e. testes that do not descend completely or at all) that have the same physiological functions as completely descended scrotal testes. Although several anatomical and hormonal factors involved in testicular descent have been studied, there is still a paucity of comprehensive research on the genetic mechanisms underlying the evolution of testicular descent in mammals and how mammals with ascrotal testes maintain their reproductive health. Results We performed integrative phenotypic and comparative genomic analyses of 380 cryptorchidism-related genes and found that the mammalian ascrotal testes trait is derived from an ancestral scrotal state. Rapidly evolving genes in ascrotal mammals were enriched in the Hedgehog pathway—which regulates Leydig cell differentiation and testosterone secretion—and muscle development. Moreover, some cryptorchidism-related genes in ascrotal mammals had undergone positive selection and contained specific mutations and indels. Genes harboring convergent/parallel amino acid substitutions between ascrotal mammals were enriched in GTPase functions. Conclusions Our results suggest that the scrotal testis is an ancestral state in mammals, and the ascrotal phenotype was derived multiple times in independent lineages. In addition, the adaptive evolution of genes involved in testicular descent and the development of the gubernaculum contributed to the evolution of ascrotal testes. Accurate DNA replication, the proper segregation of genetic material, and appropriate autophagy are the potential mechanisms for maintaining physiological normality during spermatogenesis in ascrotal mammals. Furthermore, the molecular convergence of GTPases is probably a mechanism in the ascrotal testes of different mammals. This study provides novel insights into the evolution of the testis and scrotum in mammals and contributes to a better understanding of the pathogenesis of cryptorchidism in humans.

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