This is the Fig 2 Location of the <i>bla</i>_NDM-1 gene and the IncX3 type of <i>bla</i>_NDM-1 plasmid.

<p>This is the Fig 2 Location of the <i>bla</i>_NDM-1 gene and the IncX3 type of <i>bla</i>_NDM-1 plasmid.</p

Arrangement of the <i>vrt</i> and <i>st</i> gene clusters in <i>Aspergillus ustus</i> and closely related species.

<p>vrt: viridicatumtoxin. st: sterigmatocystin. The arrow indicates the coding strand, the width of boxes and spaces were drawn in scale according to the genome annotation.</p

Secondary metabolites biosynthetic gene clusters in <i>Aspergillus ustus</i>.

<p>a. Two partial of such secondary biosynthetic gene cluster locate in the ends of scaffolds 43 and 37 of <i>Aspergillus ustus</i> draft assembly, respectively.</p><p>Secondary metabolites biosynthetic gene clusters in <i>Aspergillus ustus</i>.</p

Dissemination of NDM-1-Producing Enterobacteriaceae Mediated by the IncX3-Type Plasmid

<div><p>The emergence and spread of NDM-1-producing Enterobacteriaceae have resulted in a worldwide public health risk that has affected some provinces of China. China is an exceptionally large country, and there is a crucial need to investigate the epidemic of <i>bla</i>_NDM-1-positive Enterobacteriaceae in our province. A total of 186 carbapenem-resistant Enterobacteriaceae isolates (CRE) were collected in a grade-3 hospital in Zhejiang province. Carbapenem-resistant genes, including <i>bla</i>_KPC, <i>bla</i>_IMP, <i>bla</i>_VIM, <i>bla</i>_OXA-48 and <i>bla</i>_NDM-1 were screened and sequenced. Ninety isolates were identified as harboring the <i>bla</i>_KPC-2 genes, and five <i>bla</i>_NDM-1-positive isolates were uncovered. XbaI-PFGE revealed that three <i>bla</i>_NDM-1-positive <i>K</i>. <i>pneumoniae</i> isolates belonged to two different clones. S1-PFGE and southern blot suggested that the <i>bla</i>_NDM-1 genes were located on IncX3-type plasmids with two different sizes ranging from 33.3 to 54.7 kb (n=4) and 104.5 to 138.9 kb (n=1), respectively, all of which could easily transfer to <i>Escherichia coli</i> by conjugation and electrotransformation. The high-throughput sequencing of two plasmids was performed leading to the identification of a smaller 54-kb plasmid, which had high sequence similarity with a previously reported pCFNDM-CN, and a larger plasmid in which only a 7.8-kb sequence of a common gene environment around <i>bla</i>_NDM-1 (<i>bla</i>_NDM-1-<i>trpF</i>- <i>dsbC</i>-<i>cutA1</i>-<i>groEL</i>-Δ<i>InsE</i>,) was detected. PCR mapping and sequencing demonstrated that four smaller <i>bla</i>_NDM-1 plasmids contained a common gene environment around <i>bla</i>_NDM-1 (IS<i>5</i>-<i>bla</i>_NDM-1-<i>trpF</i>- <i>dsbC</i>-<i>cutA1</i>-<i>groEL</i>). We monitored the CRE epidemic in our hospital and determined that KPC-2 carbapenemase was a major risk to patient health and the IncX3-type plasmid played a vital role in the spread of the <i>bla</i>_NDM-1 gene among the CRE.</p></div

Gene content of the SCC<i>mec</i> element in <i>Staphylococcus haemolyticus</i> SH32.

1<p>gene position in the contig (accession number: KF006347).</p

A Genomics Based Discovery of Secondary Metabolite Biosynthetic Gene Clusters in <i>Aspergillus ustus</i>

<div><p>Secondary metabolites (SMs) produced by <i>Aspergillus</i> have been extensively studied for their crucial roles in human health, medicine and industrial production. However, the resulting information is almost exclusively derived from a few model organisms, including <i>A. nidulans</i> and <i>A. fumigatus</i>, but little is known about rare pathogens. In this study, we performed a genomics based discovery of SM biosynthetic gene clusters in <i>Aspergillus ustus</i>, a rare human pathogen. A total of 52 gene clusters were identified in the draft genome of <i>A. ustus</i> 3.3904, such as the sterigmatocystin biosynthesis pathway that was commonly found in <i>Aspergillus</i> species. In addition, several SM biosynthetic gene clusters were firstly identified in <i>Aspergillus</i> that were possibly acquired by horizontal gene transfer, including the <i>vrt</i> cluster that is responsible for viridicatumtoxin production. Comparative genomics revealed that <i>A. ustus</i> shared the largest number of SM biosynthetic gene clusters with <i>A. nidulans</i>, but much fewer with other <i>Aspergilli</i> like <i>A. niger</i> and <i>A. oryzae</i>. These findings would help to understand the diversity and evolution of SM biosynthesis pathways in genus <i>Aspergillus</i>, and we hope they will also promote the development of fungal identification methodology in clinic.</p></div

General features of <i>Aspergillus ustus</i> genome sequencing and annotation.

<p>General features of <i>Aspergillus ustus</i> genome sequencing and annotation.</p

Comparison of SCC<i>mec</i> elements in three <i>Staphylococcus haemolyticus</i> isolates.

<p>A: WCH1; B: SH32; C: JCSC 1435. <i>mec</i>(C1/C2): class C1/C2 <i>mec</i> complex. Rectangles with the same colors denote homologous regions. Dashed lines indicate their ends. Vertical solid lines indicate the site of integration site sequences. Green triangles denote insertion sequences.</p

Comparative proteomes across <i>Aspergillus</i> species.

<p>The phylogenetic tree was constructed based on 375 highly conserved proteins in the <i>Aspergillus</i> genus. The right section shows the number of homologous genes between <i>A. ustus</i> and other <i>Aspergillus</i> species, with the color indicating the sequence identity derived from BLASTP (cutoff E-value 1e-3, identity 25% and query coverage 50%).</p

General features of the SCC composite island in <i>Staphylococcus haemolyticus</i> SH32.

<p>(A) Distribution of the best-hit homologs of genes contained in the SH32 SCC composite island in staphylococci. The G+C content of the SCC region (from 70 to 120 kb) was calculated with a window size of 200 bp. 32.8% is the average G+C content of the whole chromosome. (B) Gene structure of the SH32 SCC composite island. Predicted genes in SCC elements are represented by triangles, while their direction indicates the encoding strands. Black triangles denote IS<i>431</i> genes. Abbreviations: DR, direct repeat sequence; IR, inverted repeat sequence.</p