Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens

Journal of Clinical Microbiology, Год журнала: 2024, Номер 62(5)

Опубликована: Март 5, 2024

ABSTRACT Whole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) gained prominence may offer advantages over sequencing, particularly recent introduction R10 chemistry, which promises much lower error rates than R9 chemistry. However, limited information is available on its performance single-nucleotide polymorphism (SNP)-based investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) ( https://github.com/BioinformaticsPlatformWIV-ISP/PACU ), constructing SNP phylogenies and/or ONT R9/R10 data. The workflow was evaluated data sets Shiga toxin-producing Escherichia coli Listeria monocytogenes by comparing each technology not only separately but also integrating samples sequenced different technologies/chemistries into same phylogenomic analysis. Additionally, minimum time required to obtain accurate phylogenetic results nanopore evaluated. PACU allowed identification clusters both species all technologies/chemistries, deviated slightly more from results. showed trends very similar Illumina, we found that either or isolates analysis produced stable highly resulting these two outbreaks stabilized after ~20 hours ~8 R10. This study provides a proof concept R10, in isolation combination rapid SNP-based

Язык: Английский

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Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS

Genes, Год журнала: 2021, Номер 12(5), С. 644 - 644

Опубликована: Апрель 26, 2021

Sequencing of whole microbial genomes has become a standard procedure for cluster detection, source tracking, outbreak investigation and surveillance many microorganisms. An increasing number laboratories are currently in transition phase from classical methods towards next generation sequencing, generating unprecedented amounts data. Since the precision downstream analyses depends significantly on quality raw data generated sequencing instrument, comprehensive, meaningful primary control is indispensable. Here, we present AQUAMIS, Snakemake workflow an extensive assembly Illumina data, allowing to automatize initial analysis their whole-genome AQUAMIS performs all steps sequence analysis, consisting read trimming, (QC), taxonomic classification, de-novo assembly, reference identification, QC contamination both level. The results visualized interactive HTML report including species-specific thresholds, non-bioinformaticians assess experiments at glance. All also available as standard-compliant JSON file, facilitating easy exchange. We have applied analyze ~13,000 isolates well ~1000 in-silico contaminated datasets, proving workflow’s ability perform high throughput routine environments reliably predict contaminations. found that intergenus intragenus contaminations can be detected most accurately using combination different metrics within AQUAMIS.

Язык: Английский

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Metagenomics Approaches for Improving Food Safety: A Review

Journal of Food Protection, Год журнала: 2021, Номер 85(3), С. 448 - 464

Опубликована: Окт. 27, 2021

Язык: Английский

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Non‐antibiotic approaches to combat motile Aeromonas infections in aquaculture: Current state of knowledge and future perspectives

Reviews in Aquaculture, Год журнала: 2022, Номер 15(1), С. 333 - 366

Опубликована: Авг. 7, 2022

Abstract Inland aquaculture contributed by three major fish groups, including carps, tilapias, and catfish plays a vital role in global food security nutrition, particularly low middle‐income countries. However, the sustainable development of this sector is hampered disease epidemics, especially those caused bacteria such as Aeromonas species. At least eight pathogenic motile species ( A. hydrophila , veronii jandaei caviae sobria bestiarum dhakensis schubertii ) have been reported with some causing up to 100% mortality during outbreaks. Simultaneously, emerging multidrug‐resistant due long‐inappropriate use antibiotics alarming highlights public health concern negative socioeconomic impacts. Here, we provide comprehensive overview infections, antibiotic antimicrobial resistance . This contribution also non‐antibiotic approaches (the solutions for preventing or treating bacterial diseases without resorting use) control infections. In addition current state knowledge limitations each prophylaxis/therapy, perspectives future research are discussed critically, oral/immersion multivalent vaccines, microencapsulated synbiotics, exogenous metabolites, novel lytic bacteriophage cocktails. Some applicable nanotechnology themes nanovaccines, nanobioactive compounds, nanobubbles included review. summary, combating infections aquaculture, aeromonads, well other diseases, lengthy battle that requires strategic combination multiple coherent One Health philosophy.

Язык: Английский

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Intestinal colonization with multidrug-resistant Enterobacterales: screening, epidemiology, clinical impact, and strategies to decolonize carriers

European Journal of Clinical Microbiology & Infectious Diseases, Год журнала: 2023, Номер 42(3), С. 229 - 254

Опубликована: Янв. 21, 2023

Abstract The clinical impact of infections due to extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing Enterobacterales ( Ent ) has reached dramatic levels worldwide. Infections these multidrug-resistant (MDR) pathogens—especially Escherichia coli and Klebsiella pneumoniae —may originate from a prior asymptomatic intestinal colonization that could also favor transmission other subjects. It is therefore desirable gut carriers are rapidly identified try preventing both the occurrence serious endogenous potential transmission. Together with infection prevention control countermeasures, any strategy capable effectively eradicating MDR- tract would be desirable. In this narrative review, we present summary different aspects linked . particular, culture- molecular-based screening techniques identify carriers, data on prevalence risk factors in populations, impact, length colonization, contribution various settings will overviewed. We discuss standard strategies (selective digestive decontamination, fecal microbiota transplant) those still development (bacteriophages, probiotics, microcins, CRISPR-Cas-based) might used decolonize carriers.

Язык: Английский

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Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

Antibiotics, Год журнала: 2023, Номер 12(11), С. 1580 - 1580

Опубликована: Окт. 30, 2023

Recent advancements in sequencing technology and data analytics have led to a transformative era pathogen detection typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming standard for analysis control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into epidemiology emergence antimicrobial-resistant strains. Antimicrobial resistance (AMR) is pressing global public health issue. While clinical laboratories traditionally relied on culture-based antimicrobial susceptibility testing, integration AMR holds immense promise. Genomic-based furnish swift, consistent, highly accurate predictions phenotypes specific strains or populations, all while contributing invaluable surveillance. Moreover, genome assumes pivotal role investigation hospital outbreaks. It aids identification infection sources, unveils genetic connections among isolates, informs strategies The One Health initiative, with its focus intricate interconnectedness humans, animals, environment, seeks develop comprehensive approaches disease surveillance, control, prevention. When integrated epidemiological systems, forecast expansion bacterial populations species transmissions. Consequently, this provides evolution relationships pathogens, hosts, environment.

Язык: Английский

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Antimicrobial Resistance in Aquaculture: Risk Mitigation within the One Health Context

Foods, Год журнала: 2024, Номер 13(15), С. 2448 - 2448

Опубликована: Авг. 2, 2024

The application of antimicrobials in aquaculture primarily aims to prevent and treat bacterial infections fish, but their inappropriate use may result the emergence zoonotic antibiotic-resistant bacteria subsequent transmission resistant strains humans via food consumption. aquatic environment serves as a potential reservoir for bacteria, providing an ideal breeding ground development antimicrobial resistance (AMR). mutual inter-connection intensive fish-farming systems with terrestrial environments, processing industry human population creates pathways exacerbating problem further. aim this study was provide overview most effective available risk mitigation strategies tackle AMR aquaculture, based on One Health (OH) concept. stringent guidelines, promoting disease control methods like enhanced farm biosecurity measures vaccinations, alternatives antibiotics (ABs) (prebiotics, probiotics, immunostimulants, essential oils (EOs), peptides phage therapy), feeding practices, genetics, monitoring water quality, improving wastewater treatment, rather than applying excessive antimicrobials, can effectively release into food. contribution traditionally receives less attention, and, therefore, environmental aspects should be included more prominently OH efforts predict, detect risks health. This is particular importance low middle-income countries lack integration national action plans (NAPs) aquaculture-producing environment. Integrated fisheries approach contribute substantial decrease resistance, such case Asia, where percentage compounds exceeding 50% (P50) decreased from 52% 22% within period previous two decades.

Язык: Английский

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Dissemination of clinical Escherichia coli harboring the mcr-1 gene in Pakistan

Frontiers in Microbiology, Год журнала: 2025, Номер 15

Опубликована: Янв. 7, 2025

Colistin is an antibiotic used as a last resort to treat multidrug-resistant Gram-negative bacterial infections. Plasmid-mediated mobile colistin-resistant (mcr) genes in Escherichia coli (E. coli) are disseminated globally and considered be major public health threat. This study aimed determine the molecular characteristics of isolates clinical settings Pakistan. A total 240 E. strains isolated from urine pus cultures were collected two hospitals Faisalabad analyzed for phenotypic resistance colistin by cultivation on CHROMagar plates supplemented with 2 ug/ml. Molecular using conventional PCR, whole genome sequencing, bioinformatics analysis. PCR analysis confirmed presence mcr-1 gene 10 isolates. The minimum inhibitory concentration ranged 4 ug/ml 32 ResFinder revealed multiple determinants conferring co-resistance β-lactams, aminoglycosides, trimethoprim, sulfonamides, tetracycline, quinolones, florfenicol, macrolides. Hybrid genomic assembly indicated that carried IncI2 plasmids. Plasmid replicon typing IncI2-type plasmids (n = 10) most prevalent these strains, followed IncFIB 8), IncFIC 7), IncFIA 6), IncFII (4), IncQ1 3), IncI1 1), IncY IncN 1). Achtman MLST scheme large diversity STs among mcr-1-positive coli. VirulenceFinder numerous virulence factors ranging 19. Our emergence dissemination carrying hospital settings, posing potential risk anti-infective therapy. More efforts should taken monitor prevalence mcr-1-carrying bacteria

Язык: Английский

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Whole-genome sequencing of Listeria innocua recovered from retail milk and dairy products in Egypt

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Май 10, 2023

The similarity of the Listeria innocua genome with monocytogenes and their presence in same niche may facilitate gene transfer between them. A better understanding mechanisms responsible for bacterial virulence requires an in-depth knowledge genetic characteristics these bacteria. In this context, draft whole sequences were completed on five L. isolated from milk dairy products Egypt. assembled screened antimicrobial resistance genes, plasmid replicons multilocus sequence types (MLST); phylogenetic analysis sequenced isolates was also performed. sequencing results revealed only one gene, fosX, isolates. However, carried 13 genes involved adhesion, invasion, surface protein anchoring, peptidoglycan degradation, intracellular survival, heat stress; all lacked Pathogenicity Island 1 (LIPI-1) genes. MLST assigned into type (ST), ST-1085; however, single nucleotide polymorphism (SNP)-based 422-1,091 SNP differences our global lineages innocua. possessed ATP-dependent protease (clpL) which mediates resistance, a rep25 plasmids. Blast clpL-carrying contigs showed approximately 99% to corresponding parts plasmids strains 2015TE24968 N1-011A previously Italy United States, respectively. Although has been linked that serious outbreak, is first report containing Various among species other genera could raise possibility evolution virulent Such challenge processing preservation protocols pose health risks products. Ongoing genomic research necessary identify alarming changes develop preventive control measures.

Язык: Английский

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Antimicrobial resistance and genomic investigation of Salmonella isolated from retail foods in Guizhou, China

Frontiers in Microbiology, Год журнала: 2024, Номер 15

Опубликована: Март 6, 2024

Introduction Salmonella is a major foodborne pathogen worldwide that causes severe morbidity and mortality. It mainly caused by consuming contaminated food, with retail food considered the primary source. Methods In Guizhou, China, 102 strains isolated from 2016 to 2021 underwent phenotypic antimicrobial resistance testing whole-genome sequencing (WGS) understand diversity, including serotypes, types (STs), genes, virulence plasmid types, multi-locus sequence (MLST), core genome MLST (cgMLST). Results discussion S.Typhimurium was dominant serotype, O:4(B) leading serogroup. The most prevalent genotype ST40. Phenotypic identified 66.7% of sampled isolates as multi-drug resistant (MDR). S.Enteritidis ( n = 7), 1), S.Indiana S. Kentucky Uganda all which were MDR, Colistin. Resistance rates varied significantly across different particularly meat products exhibiting higher resistance. Notably, significant increases in observed for following: ≥ 1 P 0.001), MDR ampicillin tetracycline < chloramphenicol 0.030), trimethoprim/sulfamethoxazole 0.003). marked escalation drug over recent years, coupled varying among sources, underscores growing public health concern. Our findings highlight need coordinated approach effectively monitor respond infections China.

Язык: Английский

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