WGS-Based Analysis of Carbapenem-Resistant Acinetobacter baumannii in Vietnam and Molecular Characterization of Antimicrobial Determinants and MLST in Southeast Asia

Antibiotics, Год журнала: 2021, Номер 10(5), С. 563 - 563

Опубликована: Май 11, 2021

Carbapenem-resistant Acinetobacter baumannii (A. baumannii, CRAb) is an emerging global threat for healthcare systems, particularly in Southeast Asia. Next-generation sequencing (NGS) technology was employed to map genes associated with antimicrobial resistance (AMR) and identify multilocus sequence types (MLST). Eleven strains isolated from humans Vietnam were sequenced, their AMR MLST compared published genomes of originating Asia, i.e., Thailand (n = 49), Myanmar 38), Malaysia 11), Singapore 4) Taiwan 1). Ten out eleven Vietnamese CRAb susceptible only colistin. All harbored ant(3”)-IIa, armA, aph(6)-Id aph(3”) conferring aminoglycosides, blaOXA-51 variants blaADC-25 ß-lactams. More than half the that confer tetracyclines, sulfonamides macrolides. The showed high diversity, where six assigned type (ST)/2, two allocated new STs (ST/1411-1412). analyses 108 Asia identified 19 (ST), ST/2 most prevalent found 62 strains. A broad range mediating ß-lactams, including cephalosporins carbapenems (e.g., blaOXA-51-like, blaOXA-23, blaADC-25, blaADC-73, blaTEM-1, blaNDM-1), aminoglycosides aph(3”)-Ib, aph(6)-Id, armA aph(3’)-Ia), phenicoles catB8), tetracyclines tet.B tet.39), sul.1 sul.2), macrolides lincosamide mph.E, msr.E abaF). core genome (cgMLST) extreme diversity among Several different countries clustered together by cgMLST; however, clusters shared same ST. Developing action plan on AMR, increasing awareness prohibiting selling antibiotics without prescription must be mandatory this region. Such efforts are critical enforcing targeted policies rational use carbapenem compounds controlling dissemination emergence general.

Язык: Английский

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Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal Escherichia coli

Microorganisms, Год журнала: 2021, Номер 9(3), С. 598 - 598

Опубликована: Март 14, 2021

Antimicrobial resistance (AMR) is a major threat to public health worldwide. Currently, AMR typing changes from phenotypic testing whole-genome sequence (WGS)-based detection of determinants for better understanding the isolate diversity and elements involved in gene transmission (e.g., plasmids, bacteriophages, transposons). However, use WGS data monitoring purposes requires suitable techniques, standardized parameters approved guidelines reliable prediction their association with mobile genetic (plasmids). In this study, different sequencing assembly strategies were tested suitability Escherichia coli routines German National Reference Laboratory Resistances. To assess outcomes approaches, results silico predictions compared conventional phenotypic- genotypic-typing data. With focus on (fluoro)quinolone-resistant E.coli, five qnrS-positive isolates multiple extrachromosomal subjected NextSeq (Illumina), PacBio (Pacific BioSciences) ONT (Oxford Nanopore) depth characterization qnrS1-carrying plasmids. Raw reads short- long-read assembled individually by Unicycler or Flye combination both (hybrid assembly). The generated contigs bioinformatics analysis. Based data, sequences are error prone can yield loss small plasmid genomes. contrast, short-read was shown be insufficient linkage genes qnrS1) specific sequences. Furthermore, failed detect certain duplications unsuitable genome finishing. Overall, hybrid led most comprehensive results, especially predicting associations elements. Thus, technologies assemblies currently represents best approach risk assessment.

Язык: Английский

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Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features

Microbiology Spectrum, Год журнала: 2023, Номер 11(3)

Опубликована: Май 16, 2023

Identification of plasmids in bacterial genomes is critical for many factors, including horizontal gene transfer, antibiotic resistance genes, host-microbe interactions, cloning vectors, and industrial production. There are several silico methods to predict plasmid sequences assembled genomes. However, existing have evident shortcomings, such as unbalance sensitivity specificity, dependency on species-specific models, performance reduction shorter than 10 kb, which has limited their scope applicability. In this work, we proposed Plasmer, a novel predictor based machine-learning shared k-mers genomic features. Unlike k-mer or genomic-feature methods, Plasmer employs the random forest algorithm make predictions using percent with chromosome databases combined other features, alignment E value replicon distribution scores (RDS). can multiple species achieved an average area under curve (AUC) 0.996 accuracy 98.4%. Compared tests both sliding simulated de novo assemblies consistently shown that outperforming stable across long short contigs above 500 bp, demonstrating its applicability fragmented assemblies. also excellent balanced specificity (both >0.95 bp) highest F1-score, eliminated bias was common methods. provides taxonomy classification help identify origin plasmids. IMPORTANCE study, prediction tool named Plasmer. Technically, unlike features-based first combine advantages score This given (i) improvement compared best F1-score sequences, contigs, assemblies; (ii) bp accuracy, enabling short-read (iii) between commonly existed methods; (iv) no training models. We believe more reliable alternative genome

Язык: Английский

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Intensive care unit sinks are persistently colonized with multidrug resistant bacteria and mobilizable, resistance-conferring plasmids

mSystems, Год журнала: 2023, Номер unknown

Опубликована: Июль 13, 2023

ABSTRACT Contamination of hospital sinks with microbial pathogens presents a serious potential threat to patients, but our understanding sink colonization dynamics is largely based on infection outbreaks. Here, we investigate the patterns multidrug-resistant organisms (MDROs) in intensive care unit and water from two hospitals USA Pakistan collected over 27 months prospective sampling. Using culture-based methods, recovered 822 bacterial isolates representing 104 unique species genomospecies. Genomic analyses revealed long-term by Pseudomonas spp. Serratia marcescens strains across multiple rooms. Nanopore sequencing uncovered examples persistence resistance-conferring plasmids unrelated hosts. These data indicate that antibiotic resistance (AR) maintained both strain horizontal gene transfer (HGT), while HGT maintains AR within Acinetobacter Enterobacterales, independent colonization. results emphasize importance proactive, genomic-focused surveillance built environments mitigate MDRO spread. IMPORTANCE Hospital are frequently linked outbreaks antibiotic-resistant bacteria. used whole-genome track (ICU) We analyzed genomes, 100 different species. identified contamination opportunistic pathogens, as well transient appearance other common pathogens. found bacteria ICU had more genes (ARGs) their genomes compared matched community spaces. also many these ARGs harbored mobilizable plasmids, which were shared Overall, this study provides an in-depth view for nosocomial identifies specific targets surveillance.

Язык: Английский

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Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Дек. 22, 2023

Despite their crucial importance for human health, there is still relatively limited knowledge on how the gut resistome changes or responds to antibiotic treatment across ages, especially in latter case. Here, we use fecal metagenomic data from 662 Danish infants and 217 young adults fill this gap. The resistomes are characterized by a bimodal distribution driven E. coli composition. typical profile of differs significantly between infants, with distinguished higher gene plasmid abundances. However, predominant resistance genes (ARGs) same. Antibiotic reduces bacterial diversity increased ARG abundances both cohorts, core ARGs. effects treatments microbiome last longer than different antibiotics associated distinct impacts. Overall, study broadens our current understanding dynamics impact age groups.

Язык: Английский

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Identification of knowledge gaps in whole-genome sequence analysis of multi-resistant thermotolerant Campylobacter spp.

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Фев. 8, 2024

Abstract Background Campylobacter spp. is the most frequent cause of bacterial food-borne gastroenteritis and a high priority antibiotic resistant bacterium according to World Health Organization (WHO). European monitoring thermotolerant does not reflect global burden resistances already circulating within population worldwide. Methods We systematically compared whole genome sequencing with comprehensive phenotypic antimicrobial susceptibility, analyzing 494 poultry isolates from Vietnam Germany. Any discrepancy was checked by repeating wet lab improving dry part. Selected were additionally analyzed via long-read Oxford Nanopore technology, leading closed chromosomes plasmids. Results Overall, 22 different resistance genes gene variants (e. g. erm (B), aph(3’)-IIIa , aph(2’’)-If catA lnu (C), bla OXA sat4 ) point mutations in three distinct ( gyrA 23S rRNA, rpsL associated AMR present isolates. Two missing database one falsely resistance. Bioinformatic analysis based on short-read data partly failed identify tet (O) aadE when as duplicate or homologous variants. Intriguingly, also contained determinants, redundantly conferring chloramphenicol, gentamicin, kanamycin, lincomycin streptomycin. found novel (W) tetracycline sensitive strains, harboring mutations. Furthermore, assemblies impaired full length phase variable aad9 due variations poly-C tract gene. The genetic determinant responsible for gentamicin isolate Germany could be identified. GyrT86I, presenting main (fluoro-)quinolone led rare atypical phenotype ciprofloxacin but nalidixic acid sensitivity. Long-read predicted mainly located chromosome, rarely Predictions long- sequencing, respectively, often differed. organized multidrug islands (MDRI) partially proximity transposase genes, suggesting mobilization determinants natural transformation transposition . Conclusions results this study suggest that there duplication, mosaicism, mutation variation truncation strains have been reported previous studies are databases. need deciphering yet unknown mechanisms spread may pose challenge food safety.

Язык: Английский

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Tracing clinically-relevant antimicrobial resistances in Acinetobacter baumannii-calcoaceticus complex across diverse environments: A study spanning clinical, livestock, and wastewater treatment settings

Environment International, Год журнала: 2024, Номер 186, С. 108603 - 108603

Опубликована: Март 25, 2024

Acinetobacter baumannii has become a prominent nosocomial pathogen, primarily owing to its remarkable ability rapidly acquire resistance wide range of antimicrobial agents and persist in diverse environments. However, there is lack data on the molecular epidemiology potential implications for public health A. strains exhibiting clinically significant resistances that originate from non-clinical Therefore, genetic characteristics mechanisms 80 baumannii-calcoaceticus (ABC) complex isolates, sourced environments associated with poultry pig production, municipal wastewater treatment plants (WWTPs), clinical settings, were investigated. In total, our study classified 54 isolates into 29 previously described sequence types (STs), while 26 exhibited as-yet-unassigned STs. We identified broad STs originating production (e.g., ST10, ST238, ST240, ST267, ST345, ST370, ST372, ST1112 according Pasteur scheme). These have also been documented settings worldwide, highlighting their significance. findings raise concerns about zoonotic transmission certain livestock Furthermore, we observed highest diversity genes (ARGs). contrast typically carried significantly higher number ARGs, ranging 10 15. They exclusive carriers biocide acquired carbapenemases (blaOXA-23, blaOXA-58, blaOXA-72, blaGIM-1, blaNDM-1). Additionally, displayed an increased capacity carrying plasmids undergoing transformation. This heightened capability could be linked intense selective pressures commonly found within settings. Our provides comprehensive insights essential aspects ABC livestock-associated explored health, providing valuable knowledge addressing these critical issues.

Язык: Английский

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Comprehensive blueprint of Salmonella genomic plasticity identifies hotspots for pathogenicity genes

PLoS Biology, Год журнала: 2024, Номер 22(8), С. e3002746 - e3002746

Опубликована: Авг. 7, 2024

Understanding the dynamic evolution of Salmonella is vital for effective bacterial infection management. This study explores role flexible genome, organised in regions genomic plasticity (RGP), shaping pathogenicity lineages. Through comprehensive analysis 12,244 spp. genomes covering 2 species, 6 subspecies, and 46 serovars, we uncover distinct integration patterns pathogenicity-related gene clusters into RGP, challenging traditional views distribution. These RGP exhibit preferences specific spots, presence or absence such spots across lineages profoundly shapes strain pathogenicity. are guided by conserved flanking genes surrounding implicating their involvement regulatory networks functional synergies with integrated clusters. Additionally, emphasise multifaceted contributions plasmids prophages to diverse Overall, this provides a blueprint potential . unique insight identifies nonpathogenic that hold harbouring genes, providing foundation predicting future adaptations developing targeted strategies against emerging human pathogenic strains.

Язык: Английский

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Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads

Current Opinion in Microbiology, Год журнала: 2024, Номер 77, С. 102424 - 102424

Опубликована: Янв. 21, 2024

Early life represents a critical window for metabolic, cognitive and immune system development, which is influenced by the maternal microbiome as well infant gut microbiome. Antibiotic exposure, mode of delivery breastfeeding practices modulate reservoir antibiotic resistance genes (ARGs). Vertical horizontal microbial gene transfer during early mechanisms behind these transfers are being uncovered. In this review, we aim to provide an overview current knowledge on in mother–infant dyad through vertical transmission highlight main gaps challenges area.

Язык: Английский

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The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits

Microbiome, Год журнала: 2024, Номер 12(1)

Опубликована: Апрель 27, 2024

Abstract Background Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe detailed longitudinal study assessing the of ripening in three natural caves on microbiome resistome succession across different producers Cabrales blue-veined cheese. Results Both producer cave were ripened influenced cheese microbiome. Lactococcus former Lactobacillus genus, among other taxa, showed high abundance at initial stages ripening, either coming from raw material, starter culture used, and/or environment processing plants. Along caves, these taxa displaced by bacteria, such as Tetragenococcus , Corynebacterium Brevibacterium Yaniella Staphylococcus predominantly originating environments (mainly food contact surfaces), demonstrated source-tracking analysis, strain analysis read level, characterization 613 metagenome-assembled genomes. The koreensis halophilus detected has not been found previously metagenomes. Furthermore, level horizontal gene transfer with members microbiome, mainly involving genes related to carbohydrate metabolism functions. revealed that milk associated are rich reservoir antimicrobial resistance determinants, aminoglycosides, tetracyclines, β -lactam antibiotics harbored aerobic gram-negative bacteria relevance safety point view, Escherichia coli Salmonella enterica Acinetobacter Klebsiella pneumoniae displacement most milk-associated cave-associated during gave rise significant decrease load ARGs and, therefore, safer end product. Conclusion Overall, represented an important source non-starter microorganisms may play relevant role products. Among them, have identified novel regarded being dominant components ( spp.), providing very valuable information for authentication this protected designation origin artisanal

Язык: Английский

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