Biology subjects

He, K.

Publications and source records attributed to He, K..

3 recordsLinked to original sources

bioRxiv2018

Colistin resistance prevalence in Escherichia coli from domestic animals in intensive breeding farms of Jiangsu Province, China

The global dissemination of colistin resistance has received a great deal of attention. Recently, the plasmid-mediated colistin resistance encoded by mcr-1 and mcr-2 genes in Escherichia coli (E.coli) strains from animals, food, and patients in China have been reported continuously. To make clear the colisin resistance and mcr gene spread in domestic animals in Jiangsu Province, we collected fecael swabs from pigs, chicken and cattle at different age distributed in intensive feeding farms. The selected chromogenic agar and mcr-PCR were used to screen the colisin resistance and mcr gene carriage. Colistin resistant E.coli colonies were identified from 54.25 % (440/811) pig faecal swabs, from 35.96 % (443/1232) chicken faecal swabs, and 26.92 % (42/156) from cattle faecal swabs. Of all the colisin resistant E.coli colonies, the positive amplifications of mcr-1 were significantly higher than mcr-2. The mcr-1 prevalence was 68.86 % (303/440) in pigs, 87.58 % (388/443) in chicken, and 71.43 % (30/42), compared with 46.82 % (206/440) in pigs, 14.90 % (66/443) in chicken, and 19.05 % (8/42) in cattle of prevalence of mcr-2. Co-occurrence of mcr-1 and mcr-2 was identified in 20 % (88/440) in pigs, 7.22 % (32/443) in chickens, and in 9.52 % (4/42) cattle. These data indicate that mcr was the most important colistin resistance mechanism. Interventions and alternative options are necessary to minimise further dissemination of mcr between food-producing animals and human.\n\nIMPORTANCEColistin is recognized one of the last defence lines for the treatment of highly resistant bacteria, but the emergence of resistance that conferred by a transferable plasmid-mediated mcr genes to this vital antibiotic is extremely disturbing. Here, we used E. coli as an index to monitor drug resistance in domestic animals (pigs, chicken and cattle). It was found that the colistin resistance widely occurred at all ages of domestic animals and the mcr-dependent mechanism dominated in E.coli. We also found that the elder and adult animals were a reservoir of resistant strains, suggesting a potential food safety issue and greater public health problems.

epidemiology↗

bioRxiv2017

Cryptic phylogeographic history sheds light on the generation of species diversity in sky-island mountains

Biodiversity hotspots should be given high priority for conservation under the situation of global climate change. The sky islands in southwestern China are characterized by extraordinarily high species diversity and are among one of the worlds top biodiversity hotspots. However, neither the actual species diversity in this region or mechanisms generating this diversity are well explored. Here, we report on the phylogeographic analysis of the long-tailed mole (Scaptonyx fusicaudus), a semi-fossorial mammal that inhabits the montane cool forests across the Chinese sky islands and is considered to represent one species divided into two subspecies. Analyses using DNA sequence data from one mitochondrial and six nuclear genes revealed that populations inhabiting different mountains exhibited exceptionally strong geographic structure. The lowlands and large rivers act as \"soft\" and \"hard\" barriers to dispersal, respectively, isolating evolutionary lineages for up to 11 million years. Our results suggest that the mountain ranges act as interglacial refugia buffering populations from climate fluctuations, further facilitating allopatric diversification. Strikingly, species delimitation analyses suggests that the long-tailed mole may comprise 18 operational taxonomic units and 17 putative species. Our results suggest that for low-vagility species, the complex topography of the Chinese sky islands has shaped genetic diversity and structure and promoted exceptional diversification through a combination of eco-environmental stability as well as geographic fragmentation. The patterns observed in S. fusicaudus may be representative for other cold- adapted species, reflecting the generation of mammalian faunal diversity in the sky-island mountains of southwestern China.

zoology↗

bioRxiv2016

An improved de novo pipeline for enrichment of high diversity mitochondrial genomes from Amphibia to high-throughput sequencing

We present an improved de novo pipeline by combining long-range polymerase chain reaction (LR-PCR) and capture hybridization for enriching mitochondrial DNA to high-throughput sequencing. We test a new set of primers and hybridizing long-range library (LR-HY) with 112 mitochondrial genomes (MtG) representing three orders, 12 families, 54 genera, and 106 species of Amphibia. The primers are used for obtaining wide taxonomic MtG amplicons to sequence directly and/or make probes for closely related species. LR-HY is compared to standard hybridization. The primers successfully amplify 82 MtGs from all three order, all families, 92.6% (50/54) of the genera, and 74.5% (79/106) of the species, despite some DNA degradation and gene rearrangement. We observe a significantly negative correlation between sequence depth and gene variation. The pattern of highly variable regions is separately distributed in different regions within the length of < 4 kb in the 33-pooled sample. We demonstrate that using 2 kb libraries generate deeper sequence coverage in the highly variable loci than using 400 bp libraries. In total, the pipeline successfully recovers 83 complete and 14 almost complete MtGs from 53 of 54 genera, including 14 MtGs had rearranged protein-coding genes. This universal primers combined with LR-HY is an efficient way to enrich complete MtGs across the entire Amphibia.

genomics↗