Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates

2017 ◽  
Vol 20 (3) ◽  
pp. 857-865 ◽  
Author(s):  
Cedric C Laczny ◽  
Valentina Galata ◽  
Achim Plum ◽  
Andreas E Posch ◽  
Andreas Keller
Keyword(s):  
Antibiotic Resistance ◽  
In Silico ◽  
Pathogenic Bacteria ◽  
Antibiotic Resistance Genes ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Chromosomal Dna ◽  
Accurate Identification ◽  
Resistance Factors ◽  
The Individual

AbstractHigh-throughput next-generation shotgun sequencing of pathogenic bacteria is growing in clinical relevance, especially for chromosomal DNA-based taxonomic identification and for antibiotic resistance prediction. Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identification of plasmids from whole-genome sequencing (WGS) data remains one of the major challenges for sequencing-based precision medicine in infectious diseases. Here, we assess the heterogeneity of four state-of-the-art tools (cBar, PlasmidFinder, plasmidSPAdes and Recycler) for the in silico prediction of plasmid-derived sequences from WGS data. Heterogeneity, sensitivity and precision were evaluated by reference-independent and reference-dependent benchmarking using 846 Gram-negative clinical isolates. Interestingly, the majority of predicted sequences were tool-specific, resulting in a pronounced heterogeneity across tools for the reference-independent assessment. In the reference-dependent assessment, sensitivity and precision values were found to substantially vary between tools and across taxa, with cBar exhibiting the highest median sensitivity (87.45%) but a low median precision (27.05%). Furthermore, integrating the individual tools into an ensemble approach showed increased sensitivity (95.55%) while reducing the precision (25.62%). CBar and plasmidSPAdes exhibited the strongest concordance with respect to identified antibiotic resistance factors. Moreover, false-positive plasmid predictions typically contained only few antibiotic resistance factors. In conclusion, while high degrees of heterogeneity and variation in sensitivity and precision were observed across the different tools and taxa, existing tools are valuable for investigating the plasmid-borne resistome. Nevertheless, additional studies on representative clinical data sets will be necessary to translate in silico plasmid prediction approaches from research to clinical application.

scholarly journals Comparative Genomics of Klebsiella pneumoniae Strains with Different Antibiotic Resistance Profiles

2011 ◽  
Vol 55 (9) ◽  
pp. 4267-4276 ◽  
Author(s):  
Vinod Kumar ◽  
Peng Sun ◽  
Jessica Vamathevan ◽  
Yong Li ◽  
Karen Ingraham ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Susceptible Strain ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Content Type ◽  
Extended Spectrum

ABSTRACTThere is a global emergence of multidrug-resistant (MDR) strains ofKlebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. While the epidemiology ofK. pneumoniaestrains and occurrences of specific antibiotic resistance genes, such as plasmid-borne extended-spectrum β-lactamases (ESBLs), have been extensively studied, only four complete genomes ofK. pneumoniaeare available. To better understand the multidrug resistance factors inK. pneumoniae, we determined by pyrosequencing the nearly complete genome DNA sequences of two strains with disparate antibiotic resistance profiles, broadly drug-susceptible strain JH1 and strain 1162281, which is resistant to multiple clinically used antibiotics, including extended-spectrum β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, and sulfamethoxazoles. Comparative genomic analysis of JH1, 1162281, and other publishedK. pneumoniaegenomes revealed a core set of 3,631 conserved orthologous proteins, which were used for reconstruction of whole-genome phylogenetic trees. The close evolutionary relationship between JH1 and 1162281 relative to otherK. pneumoniaestrains suggests that a large component of the genetic and phenotypic diversity of clinical isolates is due to horizontal gene transfer. Using curated lists of over 400 antibiotic resistance genes, we identified all of the elements that differentiated the antibiotic profile of MDR strain 1162281 from that of susceptible strain JH1, such as the presence of additional efflux pumps, ESBLs, and multiple mechanisms of fluoroquinolone resistance. Our study adds new and significant DNA sequence data onK. pneumoniaestrains and demonstrates the value of whole-genome sequencing in characterizing multidrug resistance in clinical isolates.

scholarly journals COVID-19 Lockdowns May Reduce Resistance Genes Diversity in the Human Microbiome and the Need for Antibiotics

2021 ◽  
Vol 22 (13) ◽  
pp. 6891
Author(s):  
João S. Rebelo ◽  
Célia P. F. Domingues ◽  
Francisco Dionisio ◽  
Manuel C. Gomes ◽  
Ana Botelho ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Bacterial Resistance ◽  
Human Microbiome ◽  
Antibiotic Resistance Genes ◽  
Public Health Problem ◽  
Small World ◽  
Physical Contact ◽  
Hygiene Measures

Recently, much attention has been paid to the COVID-19 pandemic. Yet bacterial resistance to antibiotics remains a serious and unresolved public health problem that kills hundreds of thousands of people annually, being an insidious and silent pandemic. To contain the spreading of the SARS-CoV-2 virus, populations confined and tightened hygiene measures. We performed this study with computer simulations and by using mobility data of mobile phones from Google in the region of Lisbon, Portugal, comprising 3.7 million people during two different lockdown periods, scenarios of 40 and 60% mobility reduction. In the simulations, we assumed that the network of physical contact between people is that of a small world and computed the antibiotic resistance in human microbiomes after 180 days in the simulation. Our simulations show that reducing human contacts drives a reduction in the diversity of antibiotic resistance genes in human microbiomes. Kruskal–Wallis and Dunn’s pairwise tests show very strong evidence (p < 0.000, adjusted using the Bonferroni correction) of a difference between the four confinement regimes. The proportion of variability in the ranked dependent variable accounted for by the confinement variable was η2 = 0.148, indicating a large effect of confinement on the diversity of antibiotic resistance. We have shown that confinement and hygienic measures, in addition to reducing the spread of pathogenic bacteria in a human network, also reduce resistance and the need to use antibiotics.

scholarly journals Monitoring and Evaluation of Antibiotic Resistance Genes in Three Rivers in Northeast China

2021 ◽  
Author(s):  
Chen Zhao ◽  
Chenyu Li ◽  
Xiaoming Wang ◽  
Zhuosong Cao ◽  
Chao Gao ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
River Water ◽  
Resistance Genes ◽  
Northeast China ◽  
Pathogenic Bacteria ◽  
Respiratory Infections ◽  
Antibiotic Resistance Genes ◽  
Distribution Characteristics ◽  
Beta Lactam ◽  
Three Rivers

Abstract Background: Antibiotic resistance genes (ARGs) have become an important public health problem. In this study, we used metagenomic sequencing to analyze the composition of ARGs in certain original habitats of northeast China, comprising three different rivers and riverbank soils of the Heilongjiang River, Tumen River, and Yalu River. Results: Twenty types of ARG were detected in every water sample. The major ARGs were multidrug resistance genes, at approximately 0.5 copies/16s rRNA, accounting for 57.5% of the total ARG abundance. The abundance of multidrug, bacitracin, beta-lactam, macrolide‑lincosamide‑streptogramin, sulfonamide, fosmidomycin, and polymyxin resistance genes covered 96.9% of the total ARG abundance. No significant ecological boundary of ARG diversity was observed. The compositions of the resistance genes in the three rivers were very similar to each other, and 92.1% of ARG subtypes were shared by all water samples. Except for vancomycin resistance genes, almost all ARGs in riverbank soils were detected in the river water. About 31.05% ARGs were carried by Pseudomonas. Opportunistic pathogenic bacteria carrying resistance genes were mainly related to diarrhea and respiratory infections. Multidrug and beta-lactam resistance genes correlated positively with mobile genetic elements (MGEs), indicating a potential risk of diffusion.Conclusions: The composition of ARGs in three different rivers was similar, indicating that climate played an important role in ARG occurrence. ARG subtypes in river water were almost completely the same as those in riverbank soil. ARGs had no significant geographical distribution characteristics. Many ARGs were carried by human pathogenic bacteria related to human diarrhea and respiratory infections, such as Pseudomonas aeruginosa and Aeromonas caviae. In general, our results provide a valuable dataset of river water ARG distribution in northeast China. The related ecological geography distribution characteristics should be further explored.

Comparative evaluation of Assays for Broad Detection of Molecular Resistance Mechanisms in Enterobacterales Isolates

2021 ◽  
Author(s):  
J. N. Brazelton de Cardenas ◽  
C. D. Garner ◽  
Y Su ◽  
L Tang ◽  
R. T. Hayden
Keyword(s):  
Antibiotic Resistance ◽  
Rapid Evolution ◽  
Antibiotic Resistance Genes ◽  
Resistance Mechanisms ◽  
Beta Lactam ◽  
Accurate Identification ◽  
Gram Negative ◽  
Diagnostic Role ◽  
Clinically Significant ◽  
Third Generation Cephalosporins

Rapid detection of antimicrobial resistance in both surveillance and diagnostic settings is still a major challenge for the clinical lab, compounded by the rapid evolution of antibiotic resistance mechanisms. This study compares four methods for the broad detection of antibiotic resistance genes in Enterobacterales isolates: two multiplex PCR assays, (the Streck ARM-D® beta-lactamase kit and the OpGen Acuitas AMR Gene Panel u5.47 (research use only (RUO)), and one microarray assay (the Check-MDR CT103XL assay), with whole genome sequencing as a reference standard. A total of 65 Gram-negative bacterial isolates, from 56 patients, classified by phenotypic AST as showing resistance to beta-lactam antimicrobials (ESBL positive, resistance to third generation cephalosporins or carbapenems), were included in the study. Overall concordance between the molecular assays and sequencing was high. While all three assays had similar performance, the OpGen Acuitas AMR assay had the highest overall percent concordance with sequencing results. The primary differences between the assays tested were the number and diversity of targets, ranging from 9 for Streck to 34 for OpGen. This study shows that commercially available PCR-based assays can provide accurate identification of antimicrobial resistant loci in clinically significant Gram-negative bacteria. Further studies are needed to determine the clinical diagnostic role and potential benefit of such methods.

Genome Assessment of Antibiotic Resistance Genes in Probiotic Bacteria and a Literature Review

2021 ◽  
Author(s):  
Mehdi Fatahi-Bafghi ◽  
Sara Naseri ◽  
Ali Alizehi
Keyword(s):  
Antibiotic Resistance ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Antibiotic Resistance Genes ◽  
Probiotic Bacteria ◽  
Whole Genome Sequence ◽  
Probiotic Properties ◽  
Antibiotic Resistant ◽  
To Come

Abstract Having various clinical applications, probiotic bacteria are currently used in the diet. There are reports of antibiotic resistance genes (ARGs) in these bacteria that can be transferred to other microflora and pathogenic bacteria. The aim of the study is to examine whole-genome sequence analysis in bacteria with probiotic properties. Moreover, this study follows existing issues about the importance and presence of ARGs in these bacteria the dangers of which may affect human health in the years to come. In the present study, 126 complete probiotic bacterial genomes were collected and analysed for ARGs. The results of the study shows there are various antibiotic resistant genes of in these bacteria some of which can be transmitted to other bacteria. We propose microorganisms be applied as a probiotic element in various types of products, antibiogram be conducted for a large number of antibiotics and analysis of complete genome sequence for ARGs prediction.

Metagenomic analysis of effects of oxytetracycline and copper on antibiotic resistance genes and associated pathogenic hosts in swine manure compost

2020 ◽  
Author(s):  
Honghong Guo ◽  
jie gu ◽  
Xiaojuan Wang ◽  
Zilin Song ◽  
Xun Qian ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Swine Manure ◽  
Antibiotic Resistance Genes ◽  
Feed Additives ◽  
Poultry Feed ◽  
Risk Scores ◽  
Composting Process ◽  
Positive Effects

Abstract Background: The proliferation of antibiotic resistance genes (ARGs) in compost and their horizontal transfer to human pathogenic bacteria (HPB) may lead to the failure of human antibiotics. However, the antibiotic resistome in compost has not been comprehensively characterized. This study used a metagenomic approach to obtain new insights into the effects of oxytetracycline (OTC) and copper (Cu) on the antibiotic resistome during swine manure composting and the risks posed to human health. Results: The results showed that composting reduced the abundances and diversity of ARGs and HPB in swine manure. In total, 289 ARG subtypes and 19 ARG types were detected in the samples with abundances ranging from 1.08 ´ 10 –1 to 9.39 ´ 10 –1 copies/16S rRNA, which mainly encoded tetracycline, aminoglycoside, and macrolide–lincosamide–streptogramin (MLS) resistance genes. The application of OTC and Cu, especially the combined application, exacerbated the compost resistome risk scores and specific ARG subtypes responded differently. Tetracycline, multidrug, and MLS resistance genes mainly affected resistance profiles of HPB throughout the composting process. HPB and intI1 had significant positive effects on determining the ARG profiles during the composting process, and the co-selective effect of heavy metals may increase the abundances of ARGs via strong positive effects on intI1 . In addition, the effect of mobile genetic elements on the horizontal gene transfer of ARGs should not be ignored. Conclusions: This study of the antibiotic resistome in compost indicates the need for effective regulation of the misuse of livestock and poultry feed additives in order to minimize the spread of the antibiotic resistome in agro-ecosystems and decrease the potential risk to public health. Keywords: Antibiotic resistome; Composting; Metagenome; Pathogenic host; Swine manure

scholarly journals Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates

2019 ◽  
Vol 17 (2) ◽  
pp. 169-182 ◽  
Author(s):  
Valentina Galata ◽  
Cédric C. Laczny ◽  
Christina Backes ◽  
Georg Hemmrich-Stanisak ◽  
Susanne Schmolke ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Isolates ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data

scholarly journals Phylogenetic Analysis of Antibiotic Resistance Genes and Virulence Genes of Klebsiella species in silico

2017 ◽  
Vol 16 (1) ◽  
pp. 119-127 ◽  
Author(s):  
Nusrat Nahar ◽  
Ridwan Bin Rashid
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
In Silico ◽  
Iron Uptake ◽  
Virulence Genes ◽  
Antibiotic Resistance Genes ◽  
Genotype 1 ◽  
Klebsiella Species ◽  
Tract Infections ◽  
Klebsiella Infections

A total of twelve isolates were screened for virulence and antibiotic resistance genes associated with Klebsiella pneumoniae infections. Virulence and antibiotic resistance genes were detected by in silico PCR amplification. Iron uptake protein entB was detected in 66.67% (n=8) of the isolates while no isolate was found to harbour chelating agent irp2. Iron uptake system kfu, involved in purulent tissue infections and capsule formation, was identified in 25% (n=3) of the isolates. Regulator of mucoid phenotype A, rmpA was not found in any of the isolates. The wabG gene, responsible for urinary tract infections was found in seven K. pneumoniae strains. Five uge positive strains might play role in the pathogenicity of K. pneumoniae infections. About 83.33% of the isolates were positive for type 1 fimbriae fimH1 while no type 3 fimbriae mrkD gene was found. Complement reaction blocked by plasmid traT gene was not observed in Klebsiella species while eight isolates harboured outer membrane lipoprotein, ycfM which protects Klebsiella species from antibiotics. Antibiotic resistance genes blaTEM and blaSHV were detected in 33.33% (n=4) and 66.67% (n=8) of the isolates while 25% isolates carried both blaTEM and blaSHV genes. Genotype 1 carried fimH1 and ycfM genes while all the virulence genes studied were present in genotype 2 and 3. The blaSHV gene was detected in all the genotypes while blaTEM gene was found in only genotype 1 and 3. The findings of this study would be helpful to predict virulence gene associated with Klebsiella infections. This data also helps us to choose antibiotics for treating Klebsiella infections. By assessing the genotypic distribution of antibiotic resistance gene, correct antibiotic can be used to treat the infection. This could help reduce emergence of antibiotic resistance since it is known that incorrect choice of antibiotics contributes to antibiotic resistance.Dhaka Univ. J. Pharm. Sci. 16(1): 119-127, 2017 (June)

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