MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications

Coagulase-negative staphylococci (CoNS) have emerged as major pathogens in healthcare-associated facilities, being S. epidermidis, S. haemolyticus and, more recently, S. lugdunensis, the most clinically relevant species. Despite being less virulent than the well-studied pathogen S. aureus, the number of CoNS strains sequenced is constantly increasing and, with that, the number of virulence factors identified in those strains. In this regard, biofilm formation is considered the most important. Besides virulence factors, the presence of several antibiotic-resistance genes identified in CoNS is worrisome and makes treatment very challenging. In this review, we analyzed the different aspects involved in CoNS virulence and their impact on health and food.

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Diversity, abundances and distribution of antibiotic resistance genes and virulence factors in the South China Sea revealed by metagenomic sequencing

The Science of The Total Environment ◽

10.1016/j.scitotenv.2021.152803 ◽

2022 ◽

pp. 152803

Author(s):

Haochang Su ◽

Xiaojuan Hu ◽

Wujie Xu ◽

Yu Xu ◽

Guoliang Wen ◽

...

Keyword(s):

Antibiotic Resistance ◽

South China Sea ◽

Virulence Factors ◽

South China ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

The South China Sea ◽

Metagenomic Sequencing ◽

The South ◽

China Sea

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Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis

mSystems ◽

10.1128/msystems.00821-19 ◽

2020 ◽

Vol 5 (3) ◽

Cited By ~ 3

Author(s):

Yu Pan ◽

Jiaxiong Zeng ◽

Liguan Li ◽

Jintao Yang ◽

Ziyun Tang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Virulence Factors ◽

Resistance Genes ◽

Large Scale ◽

Antibiotic Resistance Genes ◽

Comprehensive Analysis ◽

Health Concern ◽

Human Pathogens ◽

Bacterial Genomes ◽

Gene Acquisition

ABSTRACT Widespread use of antibiotics has enhanced the evolution of highly resilient pathogens and poses a severe risk to human health via coselection of antibiotic resistance genes (ARGs) and virulence factors (VFs). In this study, we rigorously evaluate the abundance relationship and physical linkage between ARGs and VFs by performing a comprehensive analysis of 9,070 bacterial genomes isolated from multiple species and hosts. The coexistence of ARGs and VFs was observed in bacteria across distinct phyla, pathogenicities, and habitats, especially among human-associated pathogens. The coexistence patterns of gene elements in different habitats and pathogenicity groups were similar, presumably due to frequent gene transfer. A shorter intergenic distance between mobile genetic elements and ARGs/VFs was detected in human/animal-associated bacteria, indicating a higher transfer potential. Increased accumulation of exogenous ARGs/VFs in human pathogens highlights the importance of gene acquisition in the evolution of human commensal bacteria. Overall, the findings provide insights into the genic features of combinations of ARG-VF and expand our understanding of ARG-VF coexistence in bacteria. IMPORTANCE Antibiotic resistance has become a serious global health concern. Despite numerous case studies, a comprehensive analysis of ARG and VF coexistence in bacteria is lacking. In this study, we explore the coexistence profiles of ARGs and VFs in diverse categories of bacteria by using a high-resolution bioinformatics approach. We also provide compelling evidence of unique ARG-VF gene pairs coexisting in specific bacterial genomes and reveal the potential risk associated with the coexistence of ARGs and VFs in organisms in both clinical settings and environments.

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Draft Genome Sequences of Five Pseudomonas aeruginosa Clinical Strains Isolated from Sputum Samples from Cystic Fibrosis Patients: TABLE 1

Genome Announcements ◽

10.1128/genomea.01528-15 ◽

2016 ◽

Vol 4 (1) ◽

Author(s):

M. B. Couger ◽

Anna Wright ◽

Erika I. Lutter ◽

Noha Youssef

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Antibiotic Resistance ◽

Virulence Factors ◽

Resistance Genes ◽

Draft Genome ◽

Antibiotic Resistance Genes ◽

Genome Sequences ◽

Clinical Strains ◽

Chronic Colonization

We report here the draft genome sequences of five Pseudomonas aeruginosa isolates obtained from sputum samples from two cystic fibrosis patients with chronic colonization. These closely related strains harbor 225 to 493 genes absent from the P. aeruginosa POA1 genome and contain 178 to 179 virulence factors and 29 to 31 antibiotic resistance genes.

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Analysis of virulence factors and antibiotic resistance genes in Group B Streptococcus from clinical samples

10.21203/rs.2.21004/v1 ◽

2020 ◽

Author(s):

Raymond Mudzana ◽

Rooyen T Mavenyengwa ◽

Muchaneta Gudza-Mugabe

Keyword(s):

Antibiotic Resistance ◽

Pregnant Women ◽

Virulence Factors ◽

Resistance Genes ◽

Virulence Genes ◽

Group B Streptococcus ◽

Antibiotic Resistance Genes ◽

Virulence Gene ◽

Clinical Samples ◽

Group B

Abstract Background: Streptococcus agalacticae is one of the most important causative agents of serious infections among neonates. Group B Streptococcus (GBS) virulence factors are important in the development of vaccines, whilst antibiotic resistance genes are necessary in understanding the resistance mechanisms used by these pathogens. This study was carried out to identify the virulence genes and antibiotic resistance genes associated with GBS isolated from pregnant women.Methods: A total of 43 GBS isolates were obtained from vaginal samples that were collected from all HIV positive and HIV negative women who were 13-35 weeks pregnant attending Antenatal Care at both Chitungwiza and Harare Central Hospitals in Zimbabwe. Identification tests of GBS isolates was done using standard bacteriological methods including molecular tests. Antibiotic susceptibility testing using 3 antibiotics was done using the modified Kirby-Bauer method. The boiling method was used to extract DNA and Polymerase Chain Reaction (PCR) was used to screen for 13 genes in the isolates. Data was fed into SPSS 24.0 and the Spearman rank correlation test used to determine any correlation among genes.Results: Nine distinct virulence gene profiles were identified. The profiles hly-scpB-bca-rib 37.2% (16/43) and hly-scpB-bca 18.6% (8/43) were common among GBS isolates. The following virulence gene frequencies were obtained namely hly 97.8% (42/43), scpB 90.1% (39/43), bca 86.0% (37/43), rib 69.8% (30/43) and bac 11.6% (5/43). Antibiotic resistance genes showed high frequencies for tetM 97.6% (41/42) and low frequencies for ermB 34.5% (10/29), ermTR 10.3% (3/29), mefA 3.4% (1/29), tetO 2.4% (1/42) and linB 0% (0/35). The atr housekeeping gene amplification yielded 100% (43/43) positive results, whilst the mobile genetic element IS1548 yielded a low 9.3% (4/43).Conclusion: The study showed a high prevalence of multiple virulence genes hly, scpB, bca and rib in S. agalactiae strains isolated from pregnant women. Tetracycline resistance was found to be predominantly caused by the tetM gene, whilst macrolide resistance was predominantly due to the presence of erm methylase, with the ermB gene being more prevalent. It was also observed that in vitro phenotypic resistance is not always accurately predicted by resistance genotypes.

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Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen

10.1101/2020.09.15.297663 ◽

2020 ◽

Author(s):

Robin B. Guevarra ◽

Stefan Magez ◽

Eveline Peeters ◽

Mi Sook Chung ◽

Kyung Hyun Kim ◽

...

Keyword(s):

Antibiotic Resistance ◽

Virulence Factors ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Genomic Analysis ◽

Pantoea Agglomerans ◽

Whole Genome ◽

Tnf Α ◽

Wide Range ◽

Depth Analysis

AbstractPantoea agglomerans is a Gram-negative aerobic bacillus causing a wide range of opportunistic infections in humans including septicemia, pneumonia, septic arthritis, wound infections and meningitis. To date, the determinants of virulence, antibiotic resistance, metabolic features conferring survival and host-associated pathogenic potential of this bacterium remain largely underexplored. In this study, we sequenced and assembled the whole-genome of P. agglomerans KM1 isolated from kimchi in South Korea. The genome contained one circular chromosome of 4,039,945 bp, 3 mega plasmids, and 2 prophages. The phage-derived genes encoded integrase, lysozyme and terminase. Six CRISPR loci were identified within the bacterial chromosome. Further in-depth analysis showed that the genome contained 13 antibiotic resistance genes conferring resistance to clinically important antibiotics such as penicillin G, bacitracin, rifampicin, vancomycin, and fosfomycin. Genes involved in adaptations to environmental stress were also identified which included factors providing resistance to osmotic lysis, oxidative stress, as well as heat and cold shock. The genomic analysis of virulence factors led to identification of a type VI secretion system, hemolysin, filamentous hemagglutinin, and genes involved in iron uptake and sequestration. Finally, the data provided here show that, the KM1 isolate exerted strong immunostimulatory properties on RAW 264.7 macrophages in vitro. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-α, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-α, IL-6, IL-10, and NO depended on TLR4 and TLR1/2. While production of TNF-α, IL-6 and NO involved solely activation of the NF-κB, IL-10 secretion was largely dependent on NF-κB and to a lesser extent on MAPK Kinases. Taken together, the analysis of the whole-genome and immunostimulatory properties provided in-depth characterization of the P. agglomerans KM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic hosts.

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2602. Genetic Basis of Staphylococcus aureus Virulence

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.2280 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S904-S904

Author(s):

Edward W Adams ◽

Doyle V Ward ◽

Bruce A Barton ◽

Richard T Ellison ◽

Oladapo Olaitan

Keyword(s):

Staphylococcus Aureus ◽

Antibiotic Resistance ◽

Virulence Factors ◽

Resistance Genes ◽

Gene Frequency ◽

Academic Medical Center ◽

Clinical Manifestations ◽

Antibiotic Resistance Genes ◽

Convenience Sample ◽

Tract Infections

Abstract Background Although multiple different virulence factors have been identified for Staphylococcus aureus, there is limited information on genetic variation present between different strains of S. aureus in the clinical setting. To better define whether differing virulence factors could contribute to differing clinical manifestations of S. aureus infections we undertook a comparison of the frequency of virulence and antibiotic resistance genes present in S. aureus isolates from different clinical sites. Methods Whole-genome sequencing was performed on a convenience sample of S. aureus isolates from clinical or surveillance cultures obtained at an academic medical center over a 27-month period. Genomic assemblies were generated and annotated to define protein-coding regions. The prevalence of 28 genes previously defined as being associated with S. aureus virulence or antimicrobial resistance, including MSCRAMM genes, was then analyzed in relation to nine specific culture sources including only a single isolate from each culture source per patient using a likelihood ratio χ 2 analysis. Results There were 1286 S. aureus isolates with draft assemblies and annotations, and there was a statistically significant (P < 0.01) difference in gene frequencies between culture sources for 18 genes that included 13 of 19 virulence factors, 4 of 7 antibiotic resistance genes and 1 of 2 MSCRAMM genes. The most notable variation was seen for the presence of the sec, sep, entB, lukS, lufK, fosB, mecA, and ermA genes (all with P < 0.0001). There were also significant variations in overall gene frequency patterns between isolates from wound, blood, and respiratory isolates (P < 0.0001), as well as significant differences in the frequency of cna and hlY genes between surveillance and clinical isolates (P < 0.0001). Conclusion This study demonstrates a difference in the prevalence of virulence and antibiotic resistance genes in S. aureus isolates based on the culture source. As the culture location can be considered a surrogate for different types of infections (such as bacteremia, pneumonia, urinary tract infections) these differences in gene frequency may contribute to variation in the clinical manifestations of infections by differing S. aureus strains. Disclosures All authors: No reported disclosures.

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Draft Genome Sequence of the Uropathogenic Herbaspirillum frisingense Strain ureolyticus VT-16-41

Genome Announcements ◽

10.1128/genomea.00279-17 ◽

2017 ◽

Vol 5 (17) ◽

Cited By ~ 3

Author(s):

Victor Tetz ◽

George Tetz

Keyword(s):

Antibiotic Resistance ◽

Urinary Tract ◽

Virulence Factors ◽

Genome Sequence ◽

Resistance Genes ◽

Draft Genome ◽

Antibiotic Resistance Genes ◽

Draft Genome Sequence ◽

Content Type

ABSTRACT Herbaspirillum frisingense strain ureolyticus VT-16-41 is a clinical cystitis isolate. Here, we report the draft genome sequence of the uropathogenic H. frisingense strain ureolyticus VT-16-41, which contains various antibiotic resistance genes and virulence factors that enable it to colonize and persist in the urinary tract.

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Virulence factors, antibiotic resistance genes and genetic relatedness of commensal Escherichia coli isolates from dogs and their owners

Microbial Pathogenesis ◽

10.1016/j.micpath.2018.01.041 ◽

2018 ◽

Vol 116 ◽

pp. 241-245 ◽

Cited By ~ 4

Author(s):

Abdollah Derakhshandeh ◽

Vida Eraghi ◽

Azar Motamedi Boroojeni ◽

Malihe Akbarzadeh Niaki ◽

Sahar Zare ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Virulence Factors ◽

Resistance Genes ◽

Genetic Relatedness ◽

Antibiotic Resistance Genes

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Genomic features underlying the evolutionary transitions of Apibacter to honey bee gut symbionts

10.1101/2020.09.30.321786 ◽

2020 ◽

Author(s):

Wenjun Zhang ◽

Xue Zhang ◽

Qinzhi Su ◽

Min Tang ◽

Hao Zheng ◽

...

Keyword(s):

Antibiotic Resistance ◽

Honey Bee ◽

Virulence Factors ◽

Resistance Genes ◽

Nitrate Reduction ◽

Crucial Role ◽

Antibiotic Resistance Genes ◽

Amino Acid Synthesis ◽

Gut Symbionts ◽

Close Relatives

AbstractThe symbiotic bacteria associated with honey bee gut have likely transformed from a free-living or parasitic lifestyle, through a close evolutionary association with the insect host. However, little is known about the genomic mechanism underlying bacterial transition to exclusive adaptation to the bee gut. Here we compared the genomes of bee gut symbionts Apibacter with their close relatives living in different lifestyles. We found that despite of general reduction in the Apibacter genome, genes involved in amino acid synthesis and monosaccharide detoxification were retained, which were likely beneficial to the host. Interestingly, the microaerobic Apibacter species have specifically acquired genes encoding for the nitrate respiration (NAR). The NAR system is also conserved in the cohabiting bee microbe Snodgrassella, although with a differed structure. This convergence implies a crucial role of respiratory nitrate reduction for microaerophilic microbiomes to colonize bee gut epithelium. Genes involved in lipid, histidine degradation are substantially lost in Apibacter, indicating a transition of the energy source utilization. Particularly, genes involved in the phenylacetate degradation to generate host toxic compounds, as well as other virulence factors were lost, suggesting the loss of pathogenicity. Antibiotic resistance genes were only sporadically distributed among Apibacter species, but condensed in their pathogenic relatives, which may be related to the remotely living feature and less exposure to antibiotics of their bee hosts. Collectively, this study advances our understanding of genomic transition underlying specialization in bee gut symbionts.ImportanceInvestigations aiming to uncover the genetic determinants underlying the transition to a gut symbiotic lifestyle were scarce. The vertical transmitted honey bee gut symbionts of genus Apibacter provided an rare opportunity to tackle this, as evolving from family Flavobacteriaceae, they had phylogenetic close relatives living various lifestyles. Here, we documented that Apibacter have both preserved and horizontally acquired host beneficial genes including monosaccharides detoxification that may have seeded a mutualistic relationship with the host. In contrast, multiple virulence factors and antibiotic resistance genes have been lost. Importantly, an highly efficient and genomic well organized respiratory nitrate reduction pathway is conserved across all Apibacter spp., as well as in majority of Snodgrassella, which colonize the same habitat as Apibacter, suggesting an crucial role it played in living inside the gut. These findings highlight genomic changes paving ways to the transition to a honey bee gut symbiotic lifestyle.

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