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1.
Front Cell Infect Microbiol ; 12: 933006, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35909954

RESUMO

For the first time, we describe the whole genome of a yellow-pigmented, capsule-producing, pathogenic, and colistin-resistant Chryseobacterium gallinarum strain MGC42 isolated from a patient with urinary tract infection in India. VITEK 2 automated system initially identified this isolate as C. indologenes. However, 16S rRNA gene sequencing revealed that MGC42 shared 99.67% sequence identity with C. gallinarum-type strain DSM 27622. The draft genome of the strain MGC42 was 4,455,926 bp long with 37.08% Guanine-Cytosine (GC) content and was devoid of any plasmid. Antibiotic resistance, virulence, and toxin genes were predicted by implementing a machine learning classifier. Potential homologs of 340 virulence genes including hemolysin secretion protein D, metalloprotease, catalase peroxidases and autotransporter adhesins, type VI secretion system (T6SS) spike proteins, and 27 toxin factors including a novel toxin domain Ntox23 were identified in the genome. Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs of 110 transporter proteins were predicted that were in agreement with moderate efflux activity. Twelve antibiotic resistance genes including two potentially novel putative ß-lactamase genes sharing low similarity with known ß-lactamase genes were also identified in the genome of this strain. The strain MGC42 was also resistant to several classes of antibiotics along with carbapenems and polymyxin. We also identified mutations in the orthologs of pmrB (M384T) and lpxD (I66V) that might be responsible for colistin resistance. The MGC42 strain shared 683 core genes with other environmental and clinical strains of Chryseobacterium species. Our findings suggest that the strain MGC42 is a multidrug-resistant, virulent pathogen and recommend 16S rRNA gene sequencing to identify clinical specimens of Chryseobacterium species.


Assuntos
Antibacterianos , Chryseobacterium , Colistina , Farmacorresistência Bacteriana Múltipla , Infecções por Flavobacteriaceae , RNA Ribossômico 16S , Antibacterianos/farmacologia , Chryseobacterium/genética , Chryseobacterium/isolamento & purificação , Colistina/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Infecções por Flavobacteriaceae/tratamento farmacológico , Infecções por Flavobacteriaceae/genética , Genoma Bacteriano/genética , Humanos , Testes de Sensibilidade Microbiana , RNA Ribossômico 16S/genética , beta-Lactamases/genética
2.
BMC Bioinformatics ; 23(1): 313, 2022 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-35918655

RESUMO

BACKGROUND: DIRs are mysterious protein that have the ability to scavenge free radicals, which, are highly reactive with molecules in their vicinity. What is even more fascinating is that they carry out from these highly unstable species, a selective reaction (i.e., stereoenantioselective) from a well-defined substrate to give a very precise product. Unfortunately, to date, only three products have been demonstrated following studies on DIRs from the plant world, which until now was the kingdom where these proteins had been demonstrated. Within this kingdom, each DIR protein has its own type of substrate. The products identified to date, have on the other hand, a strong economic impact: in agriculture for example, the biosynthesis of (+)-gossypol could be highlighted (a repellent antifood produced by the cotton plant) by the DIRs of cotton. In forsythia plant species, it is the biosynthesis of (-)-pinoresinol, an intermediate leading to the synthesis of podophyllotoxine (a powerful anicancerous agent) which has been revealed. Recently, a clear path of study, potentially with strong impact, appeared by the hypothesis of the potential existence of protein DIR within the genomes of prokaryotes. The possibility of working with this type of organism is an undeniable advantage: since many sequenced genomes are available and the molecular tools are already developed. Even easier to implement and working on microbes, of less complex composition, offers many opportunities for laboratory studies. On the other hand, the diversity of their environment (e.g., soil, aquatic environments, extreme environmental conditions (pH, temperature, pressure) make them very diverse and varied subjects of study. Identifying new DIR proteins from bacteria means identifying new substrate or product molecules from these organisms. It is the promise of going further in understanding the mechanism of action of these proteins and this will most likely have a strong impact in the fields of agricultural, pharmaceutical and/or food chemistry. RESULTS: Our goal is to obtain as much information as possible about these proteins to unlock the secrets of their exceptional functioning. Analyzes of structural and functional genomic data led to the identification of the Pfam PF03018 domain as characteristic of DIR proteins. This domain has been further identified in the sequence of bacterial proteins therefore named as DIR-like (DIRL). We have chosen a multidisciplinary bioinformatic approach centered on bacterial genome identification, gene expression and regulation signals, protein structures, and their molecular information content. The objective of this study was to perform a thorough bioinformatic analysis on these DIRLs to highlight any information leading to the selection of candidate bacteria for further cloning, purification, and characterization of bacterial DIRs. CONCLUSIONS: From studies of DIRL genes identification, primary structures, predictions of their secondary and tertiary structures, prediction of DIRL signals sequences, analysis of their gene organization and potential regulation, a list of primary bacterial candidates is proposed.


Assuntos
Biologia Computacional , Proteínas de Plantas , Genoma Bacteriano , Humanos , Proteínas de Plantas/metabolismo
4.
Brief Bioinform ; 23(4)2022 07 18.
Artigo em Inglês | MEDLINE | ID: mdl-35809555

RESUMO

The pan-genome analysis of bacteria provides detailed insight into the diversity and evolution of a bacterial population. However, the genomes involved in the pan-genome analysis should be checked carefully, as the inclusion of confounding strains would have unfavorable effects on the identification of core genes, and the highly similar strains could bias the results of the pan-genome state (open versus closed). In this study, we found that the inclusion of highly similar strains also affects the results of unique genes in pan-genome analysis, which leads to a significant underestimation of the number of unique genes in the pan-genome. Therefore, these strains should be excluded from pan-genome analysis at the early stage of data processing. Currently, tens of thousands of genomes have been sequenced for Escherichia coli, which provides an unprecedented opportunity as well as a challenge for pan-genome analysis of this classical model organism. Using the proposed strategies, a high-quality E. coli pan-genome was obtained, and the unique genes was extracted and analyzed, revealing an association between the unique gene clusters and genomic islands from a pan-genome perspective, which may facilitate the identification of genomic islands.


Assuntos
Escherichia coli , Ilhas Genômicas , Escherichia coli/genética , Genoma Bacteriano , Família Multigênica , Filogenia
5.
Genome Biol Evol ; 14(7)2022 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-35776426

RESUMO

Bacterial genome organization is primarily driven by chromosomal replication from a single origin of replication. However, chromosomal rearrangements, which can disrupt such organization, are inevitable in nature. Long DNA repeats are major players mediating rearrangements, large and small, via homologous recombination. Since changes to genome organization affect bacterial fitness-and more so in fast-growing than slow-growing bacteria-and are under selection, it is reasonable to expect that genomic positioning of long DNA repeats is also under selection. To test this, we identified identical DNA repeats of at least 100 base pairs across ∼6,000 bacterial genomes and compared their distribution in fast- and slow-growing bacteria. We found that long identical DNA repeats are distributed in a non-random manner across bacterial genomes. Their distribution differs in the overall number, orientation, and proximity to the origin of replication, between fast- and slow-growing bacteria. We show that their positioning-which might arise from a combination of the processes that produce repeats and selection on rearrangements that recombination between repeat elements might cause-permits less disruption to the replication-dependent genome organization of bacteria compared with random suggesting it as a major constraint to positioning of long DNA repeats.


Assuntos
Replicação do DNA , Genoma Bacteriano , DNA , Replicação do DNA/genética , DNA Bacteriano/genética , Rearranjo Gênico , Genômica
6.
BMC Genomics ; 23(1): 537, 2022 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-35870884

RESUMO

BACKGROUND: The implementation of whole genome sequencing (WGS) by PulseNet, the molecular subtyping network for foodborne diseases, has transformed surveillance, outbreak detection, and public health laboratory practices in the United States. In 2017, the New Hampshire Public Health Laboratories, a member of PulseNet, commenced the use of WGS in tracking foodborne pathogens across the state. We present some of the initial results of New Hampshire's initiative to transition to WGS in tracking Salmonella enterica, a bacterial pathogen that is responsible for non-typhoidal foodborne infections and enteric fever. We characterize the population structure and evolutionary history of 394 genomes of isolates recovered from human clinical cases in New Hampshire from 2017 to 2020. RESULTS: The New Hampshire S. enterica population is phylogenetically diverse, consisting of 78 sequence types (ST) and 67 serotypes. Six lineages dominate the population: ST 11 serotype Enteritidis, ST 19 Typhimurium, ST 32 Infantis, ST 118 Newport, ST 22 Braenderup, and ST 26 Thompson. Each lineage is derived from long ancestral branches in the phylogeny, suggesting their extended presence in the region and recent clonal expansion. We detected 61 genes associated with resistance to 14 antimicrobial classes. Of these, unique genes of five antimicrobial classes (aminocoumarins, aminoglycosides, fluoroquinolones, nitroimidazoles, and peptides) were detected in all genomes. Rather than a single clone carrying multiple resistance genes expanding in the state, we found multiple lineages carrying different combinations of independently acquired resistance determinants. We estimate the time to the most recent common ancestor of the predominant lineage ST 11 serotype Enteritidis (126 genomes) to be 1965 (95% highest posterior density intervals: 1927-1982). Its population size expanded until 1978, followed by a population decline until 1990. This lineage has been expanding since then. Comparison with genomes from other states reveal lack of geographical clustering indicative of long-distance dissemination. CONCLUSIONS: WGS studies of standing pathogen diversity provide critical insights into the population and evolutionary dynamics of lineages and antimicrobial resistance, which can be translated to effective public health action and decision-making. We highlight the need to strengthen efforts to implement WGS-based surveillance and genomic data analyses in state public health laboratories.


Assuntos
Salmonella enterica , Febre Tifoide , Animais , Antibacterianos/farmacologia , Genoma Bacteriano , Humanos , Laboratórios , New Hampshire , Filogenia , Saúde Pública , Estados Unidos , Sequenciamento Completo do Genoma/métodos
7.
Genome Biol ; 23(1): 147, 2022 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-35791022

RESUMO

There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 samples from three bacterial species and an outbreak of 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate on a large (N=13k) M. tuberculosis cohort, building a map of non-synonymous SNPs and indels in a region where all such variants are assumed to cause rifampicin resistance. We quantify the correlation with phenotypic resistance and then replicate in a second cohort (N=10k).


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Mycobacterium tuberculosis , Genoma Bacteriano , Genótipo , Humanos , Mutação INDEL , Mycobacterium tuberculosis/genética , Polimorfismo de Nucleotídeo Único
8.
Org Lett ; 24(27): 4943-4948, 2022 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-35776528

RESUMO

Cationic nonribosomal lipopeptides (CNRLPs) from Paenibacillus spp. have been a rewarding source of Gram-negative-active antibiotics. Here we systematically screened sequenced bacterial genomes for CNRLP biosynthetic gene clusters (BGCs) that we predicted might encode additional Gram-negative-active antibiotics. Total chemical synthesis of the bioinformatically predicted products of seven such BGCs led to our identification of new laterocidine, tridecaptin, and paenibacterin-like antibiotics with potent activity against both multiple-drug-resistant Gram-negative and Gram-positive pathogens.


Assuntos
Antibacterianos , Paenibacillus , Antibacterianos/farmacologia , Genoma Bacteriano , Lipopeptídeos/farmacologia , Família Multigênica , Paenibacillus/genética
9.
Nat Methods ; 19(7): 823-826, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35789207

RESUMO

Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.


Assuntos
Metagenoma , Nanoporos , Genoma Bacteriano , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de DNA
10.
Microbiology (Reading) ; 168(7)2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35849532

RESUMO

CRISPR-Cas systems provide bacteria with both specificity and adaptability in defence against invading genetic elements. From a theoretical perspective, CRISPR-Cas systems confer many benefits. However, they are observed at an unexpectedly low prevalence across the bacterial domain. While these defence systems can be gained horizontally, fitness costs may lead to selection against their carriage. Understanding the source of CRISPR-related fitness costs will help us to understand the evolutionary dynamics of CRISPR-Cas systems and their role in shaping bacterial genome evolution. Here, we review our current understanding of the potential fitness costs associated with CRISPR-Cas systems. In addition to potentially restricting the acquisition of genetic material that could confer fitness benefits, we explore five alternative biological factors that from a theoretical perspective may influence the fitness costs associated with CRISPR-Cas system carriage: (1) the repertoire of defence mechanisms a bacterium has available to it, (2) the potential for a metabolic burden, (3) larger-scale population and environmental factors, (4) the phenomenon of self-targeting spacers, and (5) alternative non-defence roles for CRISPR-Cas.


Assuntos
Bactérias , Sistemas CRISPR-Cas , Bactérias/genética , Genoma Bacteriano/genética
12.
Anal Chem ; 94(29): 10479-10486, 2022 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-35834188

RESUMO

As the key player of a new restriction modification system, DNA phosphorothioate (PT) modification, which swaps oxygen for sulfur on the DNA backbone, protects the bacterial host from foreign DNA invasion. The identification of PT sites helps us understand its physiological defense mechanisms, but accurately quantifying this dynamic modification remains a challenge. Herein, we report a simple quantitative analysis method for optical mapping of PT sites in the single bacterial genome. DNA molecules are fully stretched and immobilized in a microfluidic chip by capillary flow and electrostatic interactions, improving the labeling efficiency by maximizing exposure of PT sites on DNA while avoiding DNA loss and damage. After screening 116 candidates, we identified a bifunctional chemical compound, iodoacetyl-polyethylene glycol-biotin, that can noninvasively and selectively biotinylate PT sites, enabling further labeling with streptavidin fluorescent nanoprobes. With this method, PT sites in PT+ DNA can be easily detected by fluorescence, while almost no detectable ones were found in PT- DNA, achieving real-time visualization of PT sites on a single DNA molecule. Collectively, this facile genome-wide PT site detection method directly characterizes the distribution and frequency of DNA modification, facilitating a better understanding of its modification mechanism that can be potentially extended to label DNAs in different species.


Assuntos
Genoma Bacteriano , Microfluídica , DNA , DNA Bacteriano/genética , Enxofre
13.
Proc Natl Acad Sci U S A ; 119(30): e2205068119, 2022 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-35857876

RESUMO

Bifidobacterium is a commensal bacterial genus ubiquitous in the human gastrointestinal tract, which is associated with a range of health benefits. The advent of CRISPR-based genome editing technologies provides opportunities to investigate the genetics of important bacteria and transcend the lack of genetic tools in bifidobacteria to study the basis for their health-promoting attributes. Here, we repurpose the endogenous type I-G CRISPR-Cas system and adopt an exogenous CRISPR base editor for genome engineering in B. animalis subsp. lactis, demonstrating that both genomic and epigenetic contexts drive editing outcomes across strains. We reprogrammed the endogenous type I-G system to screen for naturally occurring large deletions up to 27 kb and to generate a 500-bp deletion in tetW to abolish tetracycline resistance. A CRISPR-cytosine base editor was optimized to install C•G-to-T•A amber mutations to resensitize multiple B. lactis strains to tetracycline. Remarkably, we uncovered epigenetic patterns that are distributed unevenly among B. lactis strains, despite their genomic homogeneity, that may contribute to editing efficiency variability. Insights were also expanded to Bifidobacterium longum subsp. infantis to emphasize the broad relevance of these findings. This study highlights the need to develop individualized CRISPR-based genome engineering approaches for distinct bacterial strains and opens avenues for engineering of next generation probiotics.


Assuntos
Bifidobacterium , Sistemas CRISPR-Cas , Edição de Genes , Probióticos , Bifidobacterium/genética , Edição de Genes/métodos , Genoma Bacteriano/genética , Genômica , Humanos
14.
Microb Genom ; 8(7)2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35894927

RESUMO

Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.


Assuntos
Archaea , Metagenômica , Bactérias , Florestas , Genoma Bacteriano , Metano/metabolismo , Solo , Microbiologia do Solo
15.
Artif Intell Med ; 130: 102326, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35809965

RESUMO

Whole genome sequencing (WGS) is quickly becoming the customary means for identification of antimicrobial resistance (AMR) due to its ability to obtain high resolution information about the genes and mechanisms that are causing resistance and driving pathogen mobility. By contrast, traditional phenotypic (antibiogram) testing cannot easily elucidate such information. Yet development of AMR prediction tools from genotype-phenotype data can be biased, since sampling is non-randomized. Sample provenience, period of collection, and species representation can confound the association of genetic traits with AMR. Thus, prediction models can perform poorly on new data with sampling distribution shifts. In this work -under an explicit set of causal assumptions- we evaluate the effectiveness of propensity-based rebalancing and confounding adjustment on antibiotic resistance prediction using genotype-phenotype AMR data from the Pathosystems Resource Integration Center (PATRIC). We select bacterial genotypes (encoded as k-mer signatures, i.e., DNA fragments of length k), country, year, species, and AMR phenotypes for the tetracycline drug class, preparing test data with recent genomes coming from a single country. We test boosted logistic regression (BLR) and random forests (RF) with/without bias-handling. On 10,936 instances, we find evidence of species, location and year imbalance with respect to the AMR phenotype. The crude versus bias-adjusted change in effect of genetic signatures on AMR varies but only moderately (selecting the top 20,000 out of 40+ million k-mers). The area under the receiver operating characteristic (AUROC) of the RF (0.95) is comparable to that of BLR (0.94) on both out-of-bag samples from bootstrap and the external test (n = 1085), where AUROCs do not decrease. We observe a 1 %-5 % gain in AUROC with bias-handling compared to the sole use of genetic signatures. In conclusion, we recommend using causally-informed prediction methods for modeling real-world AMR data; however, traditional adjustment or propensity-based methods may not provide advantage in all use cases and further methodological development should be sought.


Assuntos
Antibacterianos , Genoma Bacteriano , Antibacterianos/farmacologia , Farmacorresistência Bacteriana/genética , Genótipo , Testes de Sensibilidade Microbiana , Sequenciamento Completo do Genoma/métodos
16.
PLoS One ; 17(7): e0270499, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35793321

RESUMO

Burkholderia mallei is the etiological agent of glanders, a highly contagious and often fatal disease in equids. Due to the high genetic clonality of B. mallei, high-resolution typing assays are necessary to differentiate between individual strains. Here we report on the development and validation of a robust and reproducible core genome-based Multi Locus Sequence Typing Assay (cgMLST) for B. mallei, which is based on 3328 gene targets and enables high-resolution typing at the strain level. The assay was validated using a set of 120 B. mallei genomes from public databases and 23 newly sequenced outbreak strains from in-house strain collections. In this cgMLST analysis, strains from different geographic regions were clearly distinguished by at least 70 allele differences, allowing spatial clustering while closely related and epidemiologically related strains were separated by only zero to three alleles. Neither the different sequencing technologies nor the assembly strategies had an influence on the cgMLST results. The developed cgMLST is highly robust, reproducible and can be used for outbreak investigations, source tracking and molecular characterization of new B. mallei isolates.


Assuntos
Burkholderia mallei , Animais , Burkholderia mallei/genética , Variação Genética , Genoma Bacteriano , Genótipo , Tipagem de Sequências Multilocus/métodos
17.
Mar Drugs ; 20(6)2022 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-35736201

RESUMO

Large-scale genome-mining analyses have identified an enormous number of cryptic biosynthetic gene clusters (BGCs) as a great source of novel bioactive natural products. Given the sheer number of natural product (NP) candidates, effective strategies and computational methods are keys to choosing appropriate BGCs for further NP characterization and production. This review discusses genomics-based approaches for prioritizing candidate BGCs extracted from large-scale genomic data, by highlighting studies that have successfully produced compounds with high chemical novelty, novel biosynthesis pathway, and potent bioactivities. We group these studies based on their BGC-prioritization logics: detecting presence of resistance genes, use of phylogenomics analysis as a guide, and targeting for specific chemical structures. We also briefly comment on the different bioinformatics tools used in the field and examine practical considerations when employing a large-scale genome mining study.


Assuntos
Produtos Biológicos , Produtos Biológicos/metabolismo , Vias Biossintéticas/genética , Biologia Computacional/métodos , Genoma Bacteriano , Genômica , Família Multigênica
18.
Sci Rep ; 12(1): 9863, 2022 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-35701436

RESUMO

The unmapped readspace of whole genome sequencing data tends to be large but is often ignored. We posit that it contains valuable signals of both human infection and contamination. Using unmapped and poorly aligned reads from whole genome sequences (WGS) of over 1000 families and nearly 5000 individuals, we present insights into common viral, bacterial, and computational contamination that plague whole genome sequencing studies. We present several notable results: (1) In addition to known contaminants such as Epstein-Barr virus and phiX, sequences from whole blood and lymphocyte cell lines contain many other contaminants, likely originating from storage, prep, and sequencing pipelines. (2) Sequencing plate and biological sample source of a sample strongly influence contamination profile. And, (3) Y-chromosome fragments not on the human reference genome commonly mismap to bacterial reference genomes. Both experiment-derived and computational contamination is prominent in next-generation sequencing data. Such contamination can compromise results from WGS as well as metagenomics studies, and standard protocols for identifying and removing contamination should be developed to ensure the fidelity of sequencing-based studies.


Assuntos
Bacteriófagos , Infecções por Vírus Epstein-Barr , Biologia Computacional , Genoma Bacteriano , Genoma Humano , Genoma Viral , Herpesvirus Humano 4/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Sequenciamento Completo do Genoma
19.
Sci Data ; 9(1): 341, 2022 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-35705638

RESUMO

Whole genome sequencing (WGS) is a key tool in identifying and characterising disease-associated bacteria across clinical, agricultural, and environmental contexts. One increasingly common use of genomic and metagenomic sequencing is in identifying the type and range of antimicrobial resistance (AMR) genes present in bacterial isolates in order to make predictions regarding their AMR phenotype. However, there are a large number of alternative bioinformatics software and pipelines available, which can lead to dissimilar results. It is, therefore, vital that researchers carefully evaluate their genomic and metagenomic AMR analysis methods using a common dataset. To this end, as part of the Microbial Bioinformatics Hackathon and Workshop 2021, a 'gold standard' reference genomic and simulated metagenomic dataset was generated containing raw sequence reads mapped against their corresponding reference genome from a range of 174 potentially pathogenic bacteria. These datasets and their accompanying metadata are freely available for use in benchmarking studies of bacteria and their antimicrobial resistance genes and will help improve tool development for the identification of AMR genes in complex samples.


Assuntos
Antibacterianos , Bactérias , Antibacterianos/farmacologia , Bactérias/genética , Benchmarking , Farmacorresistência Bacteriana/genética , Genoma Bacteriano , Testes de Sensibilidade Microbiana , Sequenciamento Completo do Genoma
20.
Sci Rep ; 12(1): 10541, 2022 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-35732699

RESUMO

Whole genome sequencing (WGS) of methicillin-resistant Staphylococcus aureus (MRSA) provides high-resolution typing, facilitating surveillance and outbreak investigations. The aim of this study was to evaluate the genomic variation rate in MRSA, by comparing commonly used core genome multilocus sequencing (cgMLST) against single nucleotide polymorphism (SNP) analyses. WGS was performed on 95 MRSA isolates, collected from 20 carriers during years 2003-2019. To assess variation and methodological-related differences, two different cgMLST schemes were obtained using Ridom SeqSphere+ and the cloud-based 1928 platform. In addition, two SNP methods, 1928 platform and Northern Arizona SNP Pipeline (NASP) were used. The cgMLST using Ridom SeqSphere+ and 1928 showed a median of 5.0 and 2.0 allele variants/year, respectively. In the SNP analysis, performed with two reference genomes COL and Newman, 1928 showed a median of 13 and 24 SNPs (including presumed recombination) and 3.8 respectively 4.0 SNPs (without recombination) per individual/year. Accordantly, NASP showed a median of 5.5 and 5.8 SNPs per individual/year. In conclusion, an estimated genomic variation rate of 2.0-5.8 genetic events per year (without recombination), is suggested as a general guideline to be used at clinical laboratories for surveillance and outbreak investigations independently of analysis approach used.


Assuntos
Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas , Evolução Molecular , Genoma Bacteriano , Humanos , Staphylococcus aureus Resistente à Meticilina/classificação , Staphylococcus aureus Resistente à Meticilina/genética , Tipagem de Sequências Multilocus/métodos , Polimorfismo de Nucleotídeo Único , Infecções Estafilocócicas/microbiologia , Sequenciamento Completo do Genoma/métodos
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