Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel

Zubair, Saima; Fischer, Anne; Liljander, Anne; Meens, Jochen; Hegerman, Jan; Gourlé, Hadrien; Bishop, Richard P.; Roebbelen, Ina; Younan, Mario; Mustafa, Mudassir Imran; Mushtaq, Muhammad; Bongcam‐Rudloff, Erik; Jores, Joerg

doi:10.1186/s40793-015-0098-6

Cited by 11 publications

(6 citation statements)

References 55 publications

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“…In comparison of pangenome, high proportion of core genes in this study were functionally characterized and assigned to COGs category. Similar results have been observed in previous studies on Staphylococcus aureus (Zubair et al, 2015) Helicobacter 43 . J category enriched in core genome across the Leptospira clades support previous studies that translational machinery remains conserved and close to original form in evolution (Liu et al, 2012;Ouzounis and Kyrpides, 1996).…”

Section: Identification Of Clad Specific Genessupporting

confidence: 92%

Comparative analysis of whole genome sequences ofLeptospiraspp. from RefSeq database provide interspecific divergence and repertoire of virulence factors

Abdullah

Kadivella

Sharma

et al. 2021

Preprint

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Leptospirosis is an emerging zoonotic and neglected disease across the world causing huge loss of life and economy. The disease is caused by Leptospira of which 605 sequenced genomes representing 72 species are available in RefSeq database. A comparative genomics approach based on Average Amino acid Identity (AAI), Average Nucleotide Identity (ANI), and Insilco DNA-DNA hybridization provide insight that taxonomic and evolutionary position of few genomes needs to be changed and reclassified. Clustering on the basis of AAI of core and pan-genome contradict clustering pattern on basis of ANI into 4 clusters. Amino acid identity based hierarchical clustering clearly established 3 clusters of Leptospira correlating with level of virulence. Whole genome tree supported three cluster classifications and grouped Leptospira into three clades termed as pathogenic, intermediate and saprophytic. Leptospira genus consist of diverse species and exist in heterogeneous environment, it contains relatively large and closed core genome of 1038 genes. Analysis provided pan genome remains open with 20822 genes. COG analysis revealed that mobilome related genes were found mainly in pan-genome of pathogenic clade. Clade specific genes mined in the study can be used as marker for determining clade and associating level of virulence of any new Leptospira species. Many known Leptospira virulent genes were absent in set of 78 virulent factors mined using Virulence Factor database. A deep search approach provided a repertoire of 496 virulent genes in pan-genome. Further validation of virulent genes will help in accurately targeting pathogenic Leptospira and controlling leptospirosis.Graphical Abstract

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Section: Identification Of Clad Specific Genessupporting

confidence: 92%

Comparative analysis of whole genome sequences ofLeptospiraspp. from RefSeq database provide interspecific divergence and repertoire of virulence factors

Abdullah

Kadivella

Sharma

et al. 2021

Preprint

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“…1 ). Read coverage inspection using reference Sa_ILRI (ST30) ( 21 ) and whole-genome alignment confirmed a large 30-kb deletion corresponding to the prophage Sa ϕ2, indicating phage excision occurring late over the course of the infection. All deleted genes were hypothetical proteins or encoded phage proteins.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Genomic Investigation of Adaptive Mutations Driving the Low-Level Oxacillin Resistance Phenotype in Staphylococcus aureus

Giulieri

Guérillot

Kwong

et al. 2020

mBio

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Antistaphylococcal penicillins such as oxacillin are the key antibiotics in the treatment of invasive methicillin-susceptible Staphylococcus aureus (MSSA) infections; however, mec gene-independent resistance adaptation can cause treatment failure. Despite its clinical relevance, the basis of this phenomenon remains poorly understood. Here, we investigated the genomic adaptation to oxacillin at an unprecedented scale using a large collection of 503 clinical mec-negative isolates and 30 in vitro-adapted isolates from independent oxacillin exposures. By combining comparative genomics, evolutionary convergence, and genome-wide association analysis, we found 21 genetic loci associated with low-level oxacillin resistance, underscoring the polygenic nature of this phenotype. Evidence of adaptation was particularly strong for the c-di-AMP signal transduction pathways (gdpP and dacA) and in the clpXP chaperone-protease complex. The role of mutations in gdpP in conferring low-level oxacillin resistance was confirmed by allele-swapping experiments. We found that resistance to oxacillin emerges at high frequency in vitro (median, 2.9 × 10−6; interquartile range [IQR], 1.9 × 10−6 to 3.9 × 10−6), which is consistent with a recurrent minimum inhibitory concentration (MIC) increase across the global phylogeny of clinical isolates. Nevertheless, adaptation in clinical isolates appears sporadically, with no stably adapted lineages, suggesting a high fitness cost of resistance, confirmed by growth assessment of mutants in rich media. Our data provide a broader understanding of the emergence and dynamics of oxacillin resistance adaptation in S. aureus and a framework for future surveillance of this clinically important phenomenon. IMPORTANCE The majority of Staphylococcus aureus strains causing human disease are methicillin-susceptible (MSSA) and can be treated with antistaphylococcal penicillins (such as oxacillin). While acquisition of the mec gene represents the main resistance mechanism to oxacillin, S. aureus can acquire low-level resistance through adaptive mutations in other genes. In this study, we used genomic approaches to understand the basis of S. aureus adaption to oxacillin and its dynamic at the population level. By combining a genome analysis of clinical isolates from persistent MSSA infections, in vitro selection of oxacillin resistance, and genome-wide association analysis on a large collection of isolates, we identified 21 genes linked to secondary oxacillin resistance. Adaptive mutations in these genes were easy to select when S. aureus was exposed to oxacillin, but they also came at a substantial cost in terms of bacterial fitness, suggesting that this phenotype emerges preferentially in the setting of sustained antibiotic exposure.

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“…This flexibility also leads to divergence of bacterial strains within species. Thus, a large part of strain-specific DNA are associated with prophage sequences (Casjens, 2003; Zubair et al, 2015). Both intact and incomplete prophages can impart important biological properties of their host.…”

Section: Resultsmentioning

confidence: 99%

Comparative Genome Analysis of Uropathogenic Morganella morganii Strains

Миннуллина

Pudova

Shagimardanova

et al. 2019

Front. Cell. Infect. Microbiol.

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Morganella morganii is an opportunistic bacterial pathogen shown to cause a wide range of clinical and community-acquired infections. This study was aimed at sequencing and comparing the genomes of three M. morganii strains isolated from the urine samples of patients with community-acquired urinary tract infections. Draft genome sequencing was conducted using the Illumina HiSeq platform. The genomes of MM 1, MM 4, and MM 190 strains have a size of 3.82–3.97 Mb and a GC content of 50.9–51%. Protein-coding sequences (CDS) represent 96.1% of the genomes, RNAs are encoded by 2.7% of genes and pseudogenes account for 1.2% of the genomes. The pan-genome containes 4,038 CDS, of which 3,279 represent core genes. Six to ten prophages and 21–33 genomic islands were identified in the genomes of MM 1, MM 4, and MM 190. More than 30 genes encode capsular biosynthesis proteins, an average of 60 genes encode motility and chemotaxis proteins, and about 70 genes are associated with fimbrial biogenesis and adhesion. We determined that all strains contained urease gene cluster ureABCEFGD and had a urease activity. Both MM 4 and MM 190 strains are capable of hemolysis and their activity correlates well with a cytotoxicity level on T-24 bladder carcinoma cells. These activities were associated with expression of RTX toxin gene hlyA , which was introduced into the genomes by a phage similar to Salmonella phage 118970_sal4.

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Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel

Cited by 11 publications

References 55 publications

Comparative analysis of whole genome sequences ofLeptospiraspp. from RefSeq database provide interspecific divergence and repertoire of virulence factors

Comparative analysis of whole genome sequences ofLeptospiraspp. from RefSeq database provide interspecific divergence and repertoire of virulence factors

Comprehensive Genomic Investigation of Adaptive Mutations Driving the Low-Level Oxacillin Resistance Phenotype in Staphylococcus aureus

Comparative Genome Analysis of Uropathogenic Morganella morganii Strains

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