Identification and quantification of bacterial genomes carrying antibiotic resistance genes and virulence factor genes for aquatic microbiological risk assessment

AbstractGenes capable of conferring resistance to clinically used antibiotics have been found in many different natural environments. However, a concise overview of the resistance genes found in common human bacterial pathogens is lacking, which complicates risk ranking of environmental reservoirs. Here, we present an analysis of potential antibiotic resistance genes in the 17 most common bacterial pathogens isolated from humans. We analyzed more than 20,000 bacterial genomes and defined a clinical resistome as the set of resistance genes found across these genomes. Using this database, we uncovered the co-occurrence frequencies of the resistance gene clusters within each species enabling identification of co-dissemination and co-selection patterns. The resistance genes identified in this study represent the subset of the environmental resistome that is clinically relevant and the dataset and approach provides a baseline for further investigations into the abundance of clinically relevant resistance genes across different environments. To facilitate an easy overview the data is presented at the species level at www.resistome.biosustain.dtu.dk.

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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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Investigation of the antibiotic resistance and biofilm formation of Staphylococcus aureus strains isolated from gangrenous mastitis of ewes

Acta Veterinaria Hungarica ◽

10.1556/avet.2012.016 ◽

2012 ◽

Vol 60 (2) ◽

pp. 189-197 ◽

Cited By ~ 7

Author(s):

Osman Tel ◽

Özkan Aslantaş ◽

Oktay Keskin ◽

Ebru Yilmaz ◽

Cemil Demir

Keyword(s):

Staphylococcus Aureus ◽

Antibiotic Resistance ◽

Virulence Factor ◽

Resistance Genes ◽

Biofilm Formation ◽

Antibiotic Resistance Genes ◽

Penicillin G ◽

Beta Lactamase ◽

Potential Virulence Factor ◽

Amoxicillin Clavulanic Acid

In this study,Staphylococcus aureusstrains (n = 110) isolated from seven ewe flocks in Sanliurfa, Turkey were screened for antibiotic resistance and biofilmforming ability as well as for genes associated with antibiotic resistance and biofilm-forming ability. All isolates were found to be susceptible to oxacillin, gentamicin, clindamycin, cefoxitin, tetracycline, vancomycin, amoxicillin-clavulanic acid, ciprofloxacin and sulphamethoxazole-trimethoprim. The percent proportions of strains resistant to penicillin G, ampicillin and erythromycin were 27.2% (n = 30), 25.4% (n = 28) and 6.3% (n = 7), respectively. Regarding the antibiotic resistance genes, 32 (29%) isolates carried theblaZ and 8 (7.2%) theermC gene. Other resistance genes were not detected in the isolates. All isolates showed biofilm-forming ability on Congo red agar (CRA), while 108 (98.18%) and 101 (91.81%) of them were identified as biofilm producers by the use of standard tube (ST) and microplate (MP) methods, respectively. All isolates carried theicaA andicaD genes but none of them harboured thebapgene. The results demonstrated thatS. aureusisolates from gangrenous mastitis were mainly resistant to penicillins (which are susceptible to the staphylococcal beta-lactamase enzyme), and less frequently to erythromycin. Furthermore, all of theS. aureusisolates produced biofilm which was considered a potential virulence factor in the pathogenesis of staphylococcal mastitis.

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ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01310-13 ◽

2013 ◽

Vol 58 (1) ◽

pp. 212-220 ◽

Cited By ~ 581

Author(s):

Sushim Kumar Gupta ◽

Babu Roshan Padmanabhan ◽

Seydina M. Diene ◽

Rafael Lopez-Rojas ◽

Marie Kempf ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Gene Sequence ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Genetic Determinants ◽

Bacterial Genomes ◽

Content Type ◽

A Genome ◽

Bioinformatic Tool

ABSTRACTARG-ANNOT (Antibiotic Resistance Gene-ANNOTation) is a new bioinformatic tool that was created to detect existing and putative new antibiotic resistance (AR) genes in bacterial genomes. ARG-ANNOT uses a local BLAST program in Bio-Edit software that allows the user to analyze sequences without a Web interface. All AR genetic determinants were collected from published works and online resources; nucleotide and protein sequences were retrieved from the NCBI GenBank database. After building a database that includes 1,689 antibiotic resistance genes, the software was tested in a blind manner using 100 random sequences selected from the database to verify that the sensitivity and specificity were at 100% even when partial sequences were queried. Notably, BLAST analysis results obtained using thermtFgene sequence (a new aminoglycoside-modifying enzyme gene sequence that is not included in the database) as a query revealed that the tool was able to link this sequence to short sequences (17 to 40 bp) found in other genes of thermtfamily with significant E values. Finally, the analysis of 178Acinetobacter baumanniiand 20Staphylococcus aureusgenomes allowed the detection of a significantly higher number of AR genes than the Resfinder gene analyzer and 11 point mutations in target genes known to be associated with AR. The average time for the analysis of a genome was 3.35 ± 0.13 min. We have created a concise database for BLAST using a Bio-Edit interface that can detect AR genetic determinants in bacterial genomes and can rapidly and easily discover putative new AR genetic determinants.

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Genome Sequence of Kocuria palustris Strain CD07_3 Isolated from the Duodenal Mucosa of a Celiac Disease Patient

Genome Announcements ◽

10.1128/genomea.00210-16 ◽

2016 ◽

Vol 4 (2) ◽

Cited By ~ 4

Author(s):

Atul Munish Chander ◽

Ramesan Girish Nair ◽

Gurwinder Kaur ◽

Rakesh Kochhar ◽

Shanmugam Mayilraj ◽

...

Keyword(s):

Antibiotic Resistance ◽

Celiac Disease ◽

Virulence Factor ◽

Disease Patient ◽

Antibiotic Resistance Genes ◽

Duodenal Mucosa ◽

Celiac Disease Patient ◽

Pathogenic Potential ◽

Specific Virulence ◽

Virulence Factor Genes

We report here the 2.8-Mb genome of Kocuria palustris strain CD07_3 isolated from the duodenal mucosa of a celiac disease (CD) patient. The genome of the bacterium consists of specific virulence factor genes and antibiotic resistance genes that depict its pathogenic potential.

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Forecasting the dissemination of antibiotic resistance genes across bacterial genomes

Nature Communications ◽

10.1038/s41467-021-22757-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Mostafa M. H. Ellabaan ◽

Christian Munck ◽

Andreas Porse ◽

Lejla Imamovic ◽

Morten O. A. Sommer

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Gram Negative Bacteria ◽

Bacterial Genomes ◽

Exchange Networks ◽

Gram Positive Bacteria ◽

Physiological Constraints ◽

Statistical Framework ◽

Genes Encoding

AbstractAntibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes (ARGs). Here, we set out to determine predictive features of ARG transfer among bacterial clades. We use a statistical framework to identify putative horizontally transferred ARGs and the groups of bacteria that disseminate them. We identify 152 gene exchange networks containing 22,963 bacterial genomes. Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes. Certain ARGs appear to be frequently mobilised by different mobile genetic elements. We characterise the phylogenetic reach of these mobilisation elements to predict the potential future dissemination of known ARGs. Using a separate database with 472,798 genomes from Streptococcaceae, Staphylococcaceae and Enterobacteriaceae, we confirm 34 of 94 predicted mobilisations. We explore transfer barriers beyond mobilisation and show experimentally that physiological constraints of the host can explain why specific genes are largely confined to Gram-negative bacteria although their mobile elements support dissemination to Gram-positive bacteria. Our approach may potentially enable better risk assessment of future resistance gene dissemination.

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Molecular Identification and Quantification of Tetracycline and Erythromycin Resistance Genes in Spanish and Italian Retail Cheeses

BioMed Research International ◽

10.1155/2014/746859 ◽

2014 ◽

Vol 2014 ◽

pp. 1-10 ◽

Cited By ~ 18

Author(s):

Ana Belén Flórez ◽

Ángel Alegría ◽

Franca Rossi ◽

Susana Delgado ◽

Giovanna E. Felis ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Denaturing Gradient Gel Electrophoresis ◽

Gene Diversity ◽

Antibiotic Resistance Gene ◽

Antibiotic Resistance Genes ◽

Resistant Bacteria ◽

Gene Pools ◽

Erythromycin Resistance ◽

Identification And Quantification

Large antibiotic resistance gene pools in the microbiota of foods may ultimately pose a risk for human health. This study reports the identification and quantification of tetracycline- and erythromycin-resistant populations, resistance genes, and gene diversity in traditional Spanish and Italian cheeses, via culturing, conventional PCR, real-time quantitative PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). The numbers of resistant bacteria varied widely among the antibiotics and the different cheese varieties; in some cheeses, all the bacterial populations seemed to be resistant. Up to eight antibiotic resistance genes were sought by gene-specific PCR, six with respect to tetracycline, that is,tet(K),tet(L),tet(M),tet(O),tet(S), andtet(W), and two with respect to erythromycin, that is,erm(B) anderm(F). The most common resistance genes in the analysed cheeses weretet(S),tet(W),tet(M), anderm(B). The copy numbers of these genes, as quantified by qPCR, ranged widely between cheeses (from 4.94 to10.18log⁡10/g). DGGE analysis revealed distinct banding profiles and two polymorphic nucleotide positions fortet(W)-carrying cheeses, though the similarity of the sequences suggests thistet(W) to have a monophyletic origin. Traditional cheeses would therefore appear to act as reservoirs for large numbers of many types of antibiotic resistance determinants.

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Risk assessment of antibiotic resistance genes in the drinking water system

The Science of The Total Environment ◽

10.1016/j.scitotenv.2021.149650 ◽

2021 ◽

pp. 149650

Author(s):

Yaru Hu ◽

Lei Jiang ◽

Xiaoyan Sun ◽

Jianqiang Wu ◽

Lei Ma ◽

...

Keyword(s):

Risk Assessment ◽

Drinking Water ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Water System ◽

Antibiotic Resistance Genes ◽

Drinking Water System

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The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes

Applied and Environmental Microbiology ◽

10.1128/aem.01802-16 ◽

2016 ◽

Vol 82 (22) ◽

pp. 6672-6681 ◽

Cited By ~ 108

Author(s):

Yongfei Hu ◽

Xi Yang ◽

Jing Li ◽

Na Lv ◽

Fei Liu ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Synergistic Effects ◽

Bacterial Species ◽

Antibiotic Resistance Genes ◽

Farm Animals ◽

Human Pathogens ◽

Bacterial Genomes ◽

Bacterial Phyla ◽

Bacterial Phylogeny

ABSTRACTHorizontally acquired antibiotic resistance genes (ARGs) in bacteria are highly mobile and have been ranked as principal risk resistance determinants. However, the transfer network of the mobile resistome and the forces driving mobile ARG transfer are largely unknown. Here, we present the whole profile of the mobile resistome in 23,425 bacterial genomes and explore the effects of phylogeny and ecology on the recent transfer (≥99% nucleotide identity) of mobile ARGs. We found that mobile ARGs are mainly present in four bacterial phyla and are significantly enriched inProteobacteria. The recent mobile ARG transfer network, which comprises 703 bacterial species and 16,859 species pairs, is shaped by the bacterial phylogeny, while an ecological barrier also exists, especially when interrogating bacteria colonizing different human body sites. Phylogeny is still a driving force for the transfer of mobile ARGs between farm animals and the human gut, and, interestingly, the mobile ARGs that are shared between the human and animal gut microbiomes are also harbored by diverse human pathogens. Taking these results together, we suggest that phylogeny and ecology are complementary in shaping the bacterial mobile resistome and exert synergistic effects on the development of antibiotic resistance in human pathogens.IMPORTANCEThe development of antibiotic resistance threatens our modern medical achievements. The dissemination of antibiotic resistance can be largely attributed to the transfer of bacterial mobile antibiotic resistance genes (ARGs). Revealing the transfer network of these genes in bacteria and the forces driving the gene flow is of great importance for controlling and predicting the emergence of antibiotic resistance in the clinic. Here, by analyzing tens of thousands of bacterial genomes and millions of human and animal gut bacterial genes, we reveal that the transfer of mobile ARGs is mainly controlled by bacterial phylogeny but under ecological constraints. We also found that dozens of ARGs are transferred between the human and animal gut and human pathogens. This work demonstrates the whole profile of mobile ARGs and their transfer network in bacteria and provides further insight into the evolution and spread of antibiotic resistance in nature.

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