<正>Dear Editor,Bacteriophages predominate in the biosphere and outnumber their hosts by at least one order of magnitude(Srinivasiah et al.,2008).They have been used for over90 years as an ...alternative to antibiotics in Eastern Europe(Deresinski,2009).With the increasing emergence of antibiotic resistance,the therapeutic potential of bacteriophages is being reevaluated(Kutter et al.,2010).Until recently,phages possessing ds DNA genomes have been
Deep Omics Tran, Ngoc Hieu; Zhang, Xianglilan; Li, Ming
Proteomics,
January 2018, 2018-01-00, 20180101, Volume:
18, Issue:
2
Journal Article
Peer reviewed
Open access
Deep learning has revolutionized research in image processing, speech recognition, natural language processing, game playing, and will soon revolutionize research in proteomics and genomics. Through ...three examples in genomics, protein structure prediction, and proteomics, we demonstrate that deep learning is changing bioinformatics research, shifting from algorithm‐centric to data‐centric approaches.
Bacillus anthracis (B. anthracis) is a gram-positive bacterium responsible for the acute disease anthrax. Rapid and reliable identification of pathogenic B. anthracis is important in the detection of ...natural infectious disease cases or bio-threats. Herein, a DNA endonuclease targeted CRISPR trans reporter (DETECTR) detection platform based on recombinase polymerase amplification (RPA) was studied. The DETECTR system targeted three sequences from B. anthracis (the BA_5345 chromosomal specific marker, the protective antigen gene pag A from pXO1 plasmid and the capsule-biosynthesis-related gene cap A from pXO2 plasmid). We developed a rapid (<40 min), easy-to-implement and accurate identification method for of B. anthracis nucleic acid with near two-copies sensitivity. The combination of tripartite primer sets is effective for the reliable identification of B. anthracis but also for fast screening of pathogenic strains. More importantly, DETECTR correctly detected simulated clinical blood samples and firstly detected positive samples collected from the location of world War-II site, preserved at north-east China (45°36′55.940″ N, 126°38′33.738″ E) with high sensitivity and specificity. Our study provides insight into the DETECTR-based detection of B. anthracis. We present a novel screening and diagnostic option for pathogenic B. anthracis that can be performed on a user-friendly portable device. Based on its proven reliability, sensitivity, specificity and simplicity, our proposed method can be readily adapted to detect pathogenic B. anthracis, anthrax and biothreats.
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•A novel DETECTR-based pathogenic B. anthracis detection method with three targets was developed.•The method was capable of pathogenic B. anthracis detection with proved ultrasensitive, rapid and specificity.•We firstly use DETECTR to detect B. anthracis genomic DNA from soil samples collected from the world War-II site in China.
A temperate bacteriophage, IME1320_01, was induced by mitomycin C treatment from
Corynebacterium striatum.
This phage possesses a double-stranded DNA genome of 40,086 bp with a G+C content of 58%. A ...total of 53 putative open reading frames (ORFs) were identified in its genome. BLASTn analysis revealed that IME1320_01 had the highest sequence similarity to
Corynebacterium striatum
strain 216, with a genome homology coverage of 44% and highest sequence identity of 95%. The termini of the phage genome was non-redundant, with a 13-nt 3’-protruding cohesive end. To the best of our knowledge, phage IME1320_01 is the first inducible phage to be identified in
Corynebacterium striatum
.
Diarrheal cases caused by non-toxigenic Vibrio cholerae have been reported globally. Lineages L3b and L9, characterized as ctxAB-negative and tcpA-positive (CNTP), pose the highest risk and have ...caused long-term epidemics in different regions worldwide. From 2001 to 2018, two waves (2001–2012 and 2013–2018) of epidemic caused by non-toxigenic V. cholerae occurred in the developed city of Hangzhou, China. In this study, through the integrated analysis of 207 genomes of Hangzhou isolates from these two waves (119 and 88) and 1573 publicly available genomes, we showed that L3b and L9 lineages together caused the second wave as had happened in the first wave, but the dominant lineage shifted from L3b (first wave: 69%) to L9 (second wave: 50%). We further found that the genotype of a key virulence gene, tcpF, in the L9 lineage during the second wave shifted to type I, which may have enhanced bacterial colonization in humans and potentially promoted the pathogenic lineage shift. Moreover, we found that 21% of L3b and L9 isolates had changed to predicted cholera toxin producers, providing evidence that gain of complete CTXφ-carrying ctxAB genes, rather than ctxAB gain in pre-CTXφ-carrying isolates, led to the transition. Taken together, our findings highlight the possible public health risk associated with L3b and L9 lineages due to their potential to cause long-term epidemics and turn into high-virulent cholera toxin producers, which necessitates a more comprehensive and unbiased sampling in further disease control efforts.
•There were two waves of epidemic caused by CNTP V. cholerae.•The first wave (2001–2012) was mainly caused by L3b, and L9 was dominant during the second one (2013–2018).•There was a shift of dominant population occurring in Hangzhou from L3b to L9.•The shift may be caused by acquisition of a virulence gene type I tcpF, and an antimicrobial resistance gene, qnrS.•The ratio of identified ctxAB positive V. cholerae in the CNTP lineage L3b has increased.
Bovine mastitis is one of the most costly diseases in dairy cows worldwide. It can be caused by over 150 different microorganisms, where
Staphylococcus aureus
is the most frequently isolated and a ...major pathogen responsible for heavy economic losses in dairy industry. Although antibiotic therapy is most widely used, alternative treatments are necessary due to the increasing antibiotic resistance. Using phage for pathogen control is a promising tool in the fight against antibiotic resistance. Mainly using high-throughput sequencing, bioinformatics and our proposed phage termini identification method, we have isolated and characterized a novel virulent phage, designated as vB_SauS_IMEP5, from manure collected from dairy farms in Shihezi, Xinjiang, China, for use as a biocontrol agent against
Staphylococcus aureus
infections. Its latent period was about 30 min and its burst size was approximately 272PFU/cell. Phage vB_SauS_IMEP5 survives in a wide pH range between 3 and 12. A treatment at 70 °C for 20 min can inactive the phage. Morphological analysis of vB_SauS_IMEP5 revealed that phage vB_SauS_IMEP5 morphologically resembles phages in the family
Siphoviridae
. Among our tested multiplicity of infections (MOIs), the optimal multiplicity of infection (MOI) of this phage was determined to be 0.001, suggesting that phage vB_SauS_IMEP5 has high bacteriolytic potential and good efficiency for reducing bacterial growth. The complete genome of IME-P5 is a 44,677-bp, linear, double-stranded DNA, with a G+C content of 34.26%, containing 69 putative ORFs. The termini of genome were determined with next-generation sequencing data using our previously proposed termini identification method, which suggests that this phage has non-redundant termini with 9nt 3′ protruding cohesive ends. The genomic and proteomic characteristics of IMEP5 demonstrate that this phage does not belong to any of the previously recognized
Siphoviridae Staphylococcus
phage groups, suggesting the creation of a new lineage, thus adding to the knowledge on the diversity of
Staphylococcus
phages. An
N
-acetylmuramoyl-
l
-alanine amidase gene and several conserved genes were predicted, while no virulence or antibiotic resistance genes were identified. This study isolated and characterized a novel
S. aureus
phage vB_SauS_IMEP5, and our findings suggest that this phage may be potentially utilized as a therapeutic or prophylactic candidate against
S.aureus
infections.
Pseudomonas aeruginosa
(
P. aeruginosa
) infection has imposed a great threat to patients with cystic fibrosis. With the emergence of multidrug-resistant
P. aeruginosa
, developing an alternative ...anti-microbial strategy is indispensable and more urgent than ever. In this study, a lytic
P. aeruginosa
phage was isolated from the sewage of a hospital, and one protein was predicted as the depolymerase-like protein by genomic sequence analysis, it includes two catalytic regions, the Pectate lyase_3 super family and Glycosyl hydrolase_28 super family. Further analysis demonstrated that recombinant depolymerase-like protein degraded
P. aeruginosa
exopolysaccharide and enhanced bactericidal activity mediated by serum in vitro. Additionally, this protein disrupted host bacterial biofilms. All of these results showed that the phage-derived depolymerase-like protein has the potential to be developed into an anti-microbial agent that targets
P. aeruginosa
.
Abstract
Infectious diseases emerge unprecedentedly, posing serious challenges to public health and the global economy. Virulence factors (VFs) enable pathogens to adhere, reproduce and cause damage ...to host cells, and antibiotic resistance genes (ARGs) allow pathogens to evade otherwise curable treatments. Simultaneous identification of VFs and ARGs can save pathogen surveillance time, especially in situ epidemic pathogen detection. However, most tools can only predict either VFs or ARGs. Few tools that predict VFs and ARGs simultaneously usually have high false-negative rates, are sensitive to the cutoff thresholds and can only identify conserved genes. For better simultaneous prediction of VFs and ARGs, we propose a hybrid deep ensemble learning approach called HyperVR. By considering both best hit scores and statistical gene sequence patterns, HyperVR combines classical machine learning and deep learning to simultaneously and accurately predict VFs, ARGs and negative genes (neither VFs nor ARGs). For the prediction of individual VFs and ARGs, in silico spike-in experiment (the VFs and ARGs in real metagenomic data), and pseudo-VFs and -ARGs (gene fragments), HyperVR outperforms the current state-of-the-art prediction tools. HyperVR uses only gene sequence information without strict cutoff thresholds, hence making prediction straightforward and reliable.
A novel virulent bacteriophage named vB_EfaP_IME199 that specifically infects
Enterococcus faecium
was isolated and characterized. Its optimal multiplicity of infection was 0.01, and it had a ...30 minute outbreak period. High-throughput sequencing revealed that the phage has a dsDNA genome of 18,838 bp with 22 open reading frames. The genome has very low homology to all other bacteriophage sequences in the GenBank database. Run-off sequencing experiments confirmed that vB_EfaP_IME199 has short inverted terminal repeats. Phylogenetic analysis indicated that vB_EfaP_IME199 can be taxonomically classified as a new member of the genus
Ahjdlikevirus
of family
Podoviridae
.
•Neotropical Mansoniini mosquitoes harbor different viral families.•Mansonia wilsoni from northeast of Brazil showed at least 6 known viral families.•Viral sequences showed phylogenetic relationship ...with insect-specific viruses found in mosquitoes from different locations.•Almost all segments of an Orthomyxovirus from Ma. wilsoni were identified.
Mosquitoes interact with a wide range of viruses including both arboviruses and insect-specific viruses. This study aimed to characterize the RNA viruses that are interacting with Mansonia wilsoni and Coquillettidia hermanoi mosquito species. The total RNA extracted from mosquito pools were sequenced on a Ion torrent platform. Viral contigs were identified against viral databases and their evolutionary relationship were reconstructed. We identified a total of 107 viral sequences, 11 of which were assigned as endogenous viral elements, and at least six known viral families were identified. Phylogenetic reconstructions were performed for 4 viral families. All Mansoniini viruses investigated through phylogenetic analysis are closely related to insect-specific viruses found in other mosquito species although with considerable divergence at the amino acid level, suggesting that we have detected new viral lineages. This study enhanced our understanding about the virome of two sylvatic Mansoniini mosquitoes.
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