VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria

Li, Jun; Tai, Cui; Deng, Zixin; Zhong, Weihong; He, Yongqun; Ou, Hong‐Yu

doi:10.1093/bib/bbw141

Cited by 88 publications

(86 citation statements)

References 51 publications

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“…UPEC isolates from patients with different disease severities were obtained from the Manges collection (Manges et al, , , ; Manges, Dietrich, et al, ; Manges, Johnson, et al, ). Although UPEC strains are heterogeneous, clinical isolates from UTIs predominantly belong to E. coli phylogenetic groups B2 and D (Johnson, Delavari, Kuskowski, & Stell, ).…”

Section: Resultsmentioning

confidence: 99%

Identification and characterization of OmpT‐like proteases in uropathogenic Escherichia coli clinical isolates

et al. 2019

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Bacterial colonization of the urogenital tract is limited by innate defenses, including the production of antimicrobial peptides (AMPs). Uropathogenic Escherichia coli (UPEC) resist AMP‐killing to cause a range of urinary tract infections (UTIs) including asymptomatic bacteriuria, cystitis, pyelonephritis, and sepsis. UPEC strains have high genomic diversity and encode numerous virulence factors that differentiate them from non‐UTI‐causing strains, including ompT. As OmpT homologs cleave and inactivate AMPs, we hypothesized that UPEC strains from patients with symptomatic UTIs have high OmpT protease activity. Therefore, we measured OmpT activity in 58 clinical E. coli isolates. While heterogeneous OmpT activities were observed, OmpT activity was significantly greater in UPEC strains isolated from patients with symptomatic infections. Unexpectedly, UPEC strains exhibiting the greatest protease activities harbored an additional ompT‐like gene called arlC (ompTp). The presence of two OmpT‐like proteases in some UPEC isolates led us to compare the substrate specificities of OmpT‐like proteases found in E. coli. While all three cleaved AMPs, cleavage efficiency varied on the basis of AMP size and secondary structure. Our findings suggest the presence of ArlC and OmpT in the same UPEC isolate may confer a fitness advantage by expanding the range of target substrates.

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Section: Resultsmentioning

confidence: 99%

Identification and characterization of OmpT‐like proteases in uropathogenic Escherichia coli clinical isolates

et al. 2019

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“…Regions with nucleotide sequence similarity above 50% are shown on the map. Four genomic islands (GIs) were identified based on comparative analysis in VRprofile (Li et al, 2017). The upstream and downstream regions of each GI were then retrieved and manually searched for the presence of conserved regions or signature genes (such as tRNA, integrase or transposase).…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles

Zhong

et al. 2017

Front. Microbiol.

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Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and extreme temperature. However, the molecular mechanisms for their environmental adaption are poorly understood. Archaeal species is commonly considered as primitive organism. The evolutional placement of archaea is a fundamental and intriguing scientific question. We sequenced the genomes of Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland, respectively. Comparative genomic analysis revealed genetic diversity and instability implicated in niche adaption, including a number of transporter- and integrase/transposase-related genes. Pan-genome analysis also defined the gene pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity impacting cognate genomic architecture. We believe that Methanopyrus genomics could facilitate efficient investigation/recognition of archaeal phylogenetic diverse patterns, as well as improve understanding of biological roles and significance of these versatile microbes.

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“…In silico identification of T6SS-encoding genes T6SS gene clusters were identified by SecReT6 [10] and VRprofile [9] algorithms,. considering e-value ≤10 − 10 and identity ≥70%..…”

Section: K Pneumoniae Genomic Sequencesmentioning

confidence: 99%

“…In silico analyses have demonstrated the presence of T6SS genes in several Gram-negative bacteria, with the numbers of orthologs varying in each bacterium [7,[9][10][11]. Besides, the genomes of some bacteria can encode the set of T6SS genes in more than one locus [7,12].…”

Section: Introductionmentioning

confidence: 99%

Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

Barbosa

Lery

2019

BMC Genomics

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Background Klebsiella pneumoniae (KP) is an opportunistic pathogen that mainly causes respiratory and urinary tract infections. The frequent occurrence of simultaneously virulent and multiple drug-resistant isolates led WHO to include this species in the list of top priorities for research and development of therapeutic alternatives. The comprehensive knowledge of the molecular mechanisms underlying KP virulence may lead to the proposal of more efficient and specific drugs. One of its virulence factors is the Type VI Secretion System (T6SS), which contributes to bacterial competition, cell invasion and in vivo colonisation. Despite the few studies showing the involvement of T6SS in KP pathogenesis, little is known concerning the regulation of its expression. The understanding of regulatory mechanisms may give more clues about the function of the system and the possibilities of future interference in this process. This work aimed to standardise the annotation of T6SS genes in KP strains and identify mechanisms of their transcriptional regulation through computational predictions. Results We analyzed the genomes of Kp52.145, HS11286 and NTUH-K2044 strains to perform a broad prediction and re-annotation of T6SS genes through similarity searches, comparative and linear discriminant analysis. 38 genes were found in Kp52.145, while 29 in HS11286 and 30 in NTUH-K2044. Genes coding for iron uptake systems are encoded in adjacencies of T6SS, suggesting that KP T6SS might also play a role in ion import. Some of the T6SS genes are comprised in syntenic regions. 17 sigma 70-dependent promoter regions were identified in Kp52.145, 12 in HS11286 and 12 in NTUH-K2044. Using VirtualFootprint algorithm, binding sites for 13 transcriptional regulators were found in Kp52.145 and 9 in HS11286 and 17 in NTUH-K2044. Six of them are common to the 3 strains: OxyR, H-NS, RcsAB, GcvA, Fis, and OmpR. Conclusions The data presented herein are derived from computational analysis. Although future experimental studies are required to confirm those predictions, they suggest that KP T6SS might be regulated in response to environmental signals that are indeed sensed by the bacteria inside the human host: temperature (H-NS), nutrition-limitation (GcvA and Fis), oxidative stress (OxyR) and osmolarity (RscAB and OmpR). Electronic supplementary material The online version of this article (10.1186/s12864-019-5885-9) contains supplementary material, which is available to authorized users.

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VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria

Cited by 88 publications

References 51 publications

Identification and characterization of OmpT‐like proteases in uropathogenic Escherichia coli clinical isolates

Identification and characterization of OmpT‐like proteases in uropathogenic Escherichia coli clinical isolates

Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles

Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation

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