Log Jam Formation and Flood Damage to House by Detour Flood Flow around a Bridge

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchive

Diversity and microevolution of CRISPR loci in <i>Helicobacter cinaedi</i>

<div><p><i>Helicobacter cinaedi</i> is associated with nosocomial infections. The CRISPR-Cas system provides adaptive immunity against foreign genetic elements. We investigated the CRISPR-Cas system in <i>H</i>. <i>cinaedi</i> to assess the potential of the CRISPR-based microevolution of <i>H</i>. <i>cinaedi</i> strains. A genotyping method based on CRISPR spacer organization was carried out using 42 <i>H</i>. <i>cinaedi</i> strains. The results of sequence analysis showed that the <i>H</i>. <i>cinaedi</i> strains used in this study had two CRISPR loci (CRISPR1 and CRISPR2). The lengths of the consensus direct repeat sequences in CRISPR1 and CRISPR2 were both 36 bp-long, and 224 spacers were found in the 42 <i>H</i>. <i>cinaedi</i> strains. Analysis of the organization and sequence similarity of the spacers of the <i>H</i>. <i>cinaedi</i> strains showed that CRISPR arrays could be divided into 7 different genotypes. Each genotype had a different ancestral spacer, and spacer acquisition/deletion events occurred while isolates were spreading. Spacer polymorphisms of conserved arrays across the strains were instrumental for differentiating closely-related strains collected from the same hospital. MLST had little variability, while the CRISPR sequences showed remarkable diversity. Our data revealed the structural features of <i>H</i>. <i>cinaedi</i> CRISPR loci for the first time. CRISPR sequences constitute a valuable basis for genotyping, provide insights into the divergence and relatedness between closely-related strains, and reflect the microevolutionary process of <i>H</i>. <i>cinaedi</i>.</p></div

CRISPR-Cas locus architecture in <i>H</i>. <i>cinaedi</i> PAGU597^T strain.

<p>CRISPR loci in <i>H</i>. <i>cinaedi</i>: (A) CRISPR1, (B) CRISPR2. CRISPR1 and CRISPR2 loci were present in <i>H</i>. <i>cinaedi</i> genomes (AP012492) in 1362505–1364592 and 1889862–1890162, respectively. The signature gene for each type is shown in red (<i>cas</i>9 and RAMP for Type II and III, respectively). The universal <i>cas</i>1 and <i>cas</i>2 genes are blue. Accessory genes are white. CRISPR loci are shown in green. The arrows indicate the directions of the coding sequences.</p

Phylogenetic tree of 11 STs of <i>H</i>. <i>cinaedi</i> isolates using MLST analysis.

<p>Phylogenetic analysis was generated with the neighbor-joining method. Numbers at the nodes represent bootstrap values > 50% (obtained from 100 resamplings). All sequences are labeled by strain number, hospital, and year of isolation in parentheses. The colors represent the different hospitals. Bars: 0.001 substitutions per nucleotide position.</p

CRISPR spacer content and polymorphisms in CRISPR2.

<p>The CRISPR2 arrays from 42 <i>H. cinaedi</i> strains are represented graphically. Identical spacers are shown as squares representing the same combination of numerals and letters, and are aligned so that they have same number (apart from duplicate spacers). Spacer numbering is initiated at the ancestral (right) end towards the most recently acquired spacers per strain (left).</p