21 research outputs found

    Additional file 1 of Highly sensitive and rapid point-of-care testing for HIV-1 infection based on CRISPR-Cas13a system

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    Additional file 1: Figure S1. The HIV-1 RNA template was diluted in gradient and amplified separately using 9 pairs of RT-RAA primers. The amplification products are shown in the red dashed boxes. Figure S2. Fluorescence CRISPR detection different concentrations of HIV-1 RNA. Fluorescence CRISPR/Cas13a detection result at 10 min. NC: Negative control, "****" means P < 0.0001, "***", "**" means P < 0.005, and "ns" means no significant difference. The above experiments were carried out 3 independent repeated experiments. Figure S3. Agarose gel electrophoresis of HIV-1 RNA with different concentrations after RT-PCR and RT-RAA. Figure S4. RT-RAA-CRISPR/Cas13a detected 158 plasma clinical samples. For fluorescence readings, we set a threshold for the signal-to-noise (S/N) ratio of fluorescence intensity (blue line) (noise is the fluorescence intensity from negative samples performed in parallel with water as input), and positive results are 3. In the lateral-flow strip strip, “T” represents for test bands, and “C” represents for control bands. Figure S5. Standard curve for detection of HIV-1 by RT-qPCR. The standard was detected with HIV-1 Nucleic Acid Assay Kit (DaAn Gene Co., Ltd) and a standard curve was drawn. Copy number conversion: 1 IU/mL = 0.51 copy/μL. Supplementary Table 1. Sequence information of HIV-1 detected by RT-RAA-CRISPR/Cas13a system. Supplementary Table 2. The template sequences used in this study. Supplementary Table 3. The crRNA (CRF07_BC, CRF01_AE, B subtype) and primer sequences used in this study

    Dominant serotype distribution and antimicrobial resistance profile of <i>Shigella</i> spp. in Xinjiang, China

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    <div><p><i>Shigella</i> represents one of the major diarrhea-inducing pathogens threatening public health, but its prevalence and antimicrobial resistance profile in Xinjiang Uygur Autonomous region, China, remains unclear. We conducted comprehensive investigation of <i>Shigella</i> serotype distribution and antimicrobial resistance pattern in Xinjiang, identifying 458 <i>Shigella</i> isolates between 2008 to 2014. <i>Shigella flexneri</i> was identified as predominant species, and several <i>S</i>. <i>flexneri</i> serotypes were isolated, including atypical serotypes 1c, 2c, and 4s. Dominant <i>S</i>. <i>flexneri</i> serotypes were 2a, 1b, 2b, and Xv, different from those generally dominant in China. A hybrid serotype pattern was observed, which included the major Chinese serotypes (2a, Xv) and those predominant in Pakistan (1b, 2b). <i>Shigella sonnei</i> was shown to have a lower frequency compared with that generally observed in China, but an increasing trend of infections associated with this pathogen was observed. Furthermore, a high frequency of drug resistance and different <i>Shigella</i> antimicrobial resistance patterns were demonstrated as well, including very severe resistance phenotypes, such as multidrug resistance and resistance to frontline antibiotics. Seventy-five cephalosporin-resistant <i>Shigella</i> isolates were frequently identified with the resistance determinants that can undergo horizontal transfer, such as <i>bla</i><sub>OXA</sub>, <i>bla</i><sub>TEM</sub>, <i>bla</i><sub>CTX-M</sub>, and integrons, facilitating the development of cephalosporin resistance among <i>Shigella</i> subtypes. Additionally, genetic analyses demonstrated that all 86 quinolone-resistant <i>S</i>. <i>flexneri</i> isolates possess 3–4 mutation sites in quinolone resistance-determining regions, primarily contributing to their resistance to quinolone. However, <i>S</i>. <i>sonnei</i> isolates were not shown to be quinolone resistant. Co-resistance to cephalosporins and quinolones was detected in 17 <i>S</i>. <i>flexneri</i> isolates, and these isolates were additionally multidrug resistant and carried β-lactamase genes and quinolone-resistance determinants. As is demonstrated in this study, dominant serotypes of <i>Shigella</i> were distributed in unique trend with dangerous drug resistance patterns. Novel strategies are urgently required to prevent the development of drug resistance among diarrhea-inducing pathogens.</p></div

    Trends in <i>Shigella</i> prevalence in isolates collected in Xinjiang between 2008 and 2014.

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    <p>Variations in the frequencies of <i>S</i>. <i>flexneri</i> and <i>S</i>. <i>sonnei</i> with time are presented. In each column, frequencies of <i>S</i>. <i>flexneri</i> and <i>S</i>. <i>sonnei</i> are shown.</p