Characterization of antibiotic determinants and heavy metal resistance genes in Escherichia coli from pigs in Catalonia

Microbial Genomics, Год журнала: 2025, Номер 11(3)

Опубликована: Март 25, 2025

More antibiotics are administered to livestock animals than treat human infections. Industrialization, large animal densities and early weaning mean pigs exposed more any other animal. Consequently, antimicrobial resistance (AMR) is common among commensal pathogenic bacteria. Heavy metals (HMs) also often used as feed additives for growth promotion infection prevention alongside antimicrobials, increased exposure copper, zinc cadmium can further encourage AMR through co-selection. In this study, we sequenced an archived collection of 112 Escherichia coli isolates from in Catalonia using short- long-read sequencing methods detect HM tolerance genes. The most genes were mdfA (84.8%), aph(3″)-Ib (52.7%), bla TEM-1B (45.6%) aph(6)-Id (45.6%). Genes relevant public health, such the extended-spectrum β -lactamases (15.4%), CTX-M type or SHV , mobile colistin ( mcr ) (13.4%), mcr-1 found. present almost every genome but rarely located plasmids, and, cases, not on same plasmids. Of predicted increase HMs, only those with activity mercury co-located plasmids determinants. However, pig farming does support a scenario where co-selected. Finally, identified exclusive association between mcr-4 ColE10 plasmid, which may help target interventions curtail its spread .

Язык: Английский

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Genomic analysis of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) causing infections in children—a Spanish multicenter study

Frontiers in Microbiology, Год журнала: 2025, Номер 16

Опубликована: Май 9, 2025

Objectives Staphylococcus aureus is one of the most common human pathogens causing skin and soft tissue infections (SSTIs) among children. This study investigated molecular traits community-associated methicillin-resistant S. (CA-MRSA) isolates in children Spain. Methods Antibiotic susceptibility testing whole-genome sequencing were performed 98 CA-MRSA (4.2 median age, 52% males). The phylogenetic relationship, antibiotic resistance, virulence, plasmid replicon genes content investigated. Results Resistance rates found as follows: Erythromycin, 42.9%, which could be explained due to presence erm(C) , mph(C) msr(A) genes; tobramycin, 27.5%, aac(6′)-Ie/aph(2″)-Ia aadD1 tetracycline, 25.5%, mainly tet(K) levofloxacin moxifloxacin, 19.4%, primarily mutations gyrA parC gentamicin, 15.3%, gene. prevalent lineage was ST8-IVc t008. Most genetically diverse, except for three groups from same hospital group different hospitals. These had less than or equal 5 allele differences by core-genome multilocus sequence typing (cgMLST) analysis 0–6 core single-nucleotide polymorphisms (SNPs) SNP-based analysis. Phage-encoded Panton–Valentine leukocidin (PVL) 75.5% isolates. Other virulence related adhesion ( capA capP ), lipid degradation geh hemolysis hlb hld hlgABC hly/hla destruction sspAB ). Conclusion observed a high genetic diversity community-acquired Spain, with lineage. Nevertheless, relatedness some well hospitals suggests dissemination contact.

Язык: Английский

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Comparative study of mcr-10 plasmids in Enterobacter spp. with the mcr-10_ter locus from wastewater and clinical samples: implications for antimicrobial resistance and fitness

Journal of Global Antimicrobial Resistance, Год журнала: 2025, Номер unknown

Опубликована: Май 1, 2025

Язык: Английский

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Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

Microorganisms, Год журнала: 2021, Номер 9(8), С. 1613 - 1613

Опубликована: Июль 28, 2021

The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance is often mediated acquisition and maintenance plasmids. study plasmid epidemiology genomics requires long-read sequencing information, but recently a number tools that allow prediction from short-read data have been developed. Here, we reviewed 25 available categorized them into binary plasmid/chromosome classification reconstruction tools. We benchmarked six (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP SCAPP) aim to reliably reconstruct distinct plasmids, with special focus on plasmids carrying antibiotic genes (ARGs) such as extended-spectrum beta-lactamase genes. found two thirds (n = 425, 66.3%) all were correctly reconstructed at least one tools, range 92 (14.58%) 317 (50.23%) predicted However, majority carried 85, 57.8%) could not be completely recovered any MOB-suite was only tool able 317, 50.23%), performed best reconstructing large 166, 46.37%) ARG-plasmids 41, 27.9%), predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes highest fraction smaller than 18 kbp 168, 61.54%). Large ARG-plasmids, however, merged sequences derived replicons. Available bioinformatic can provide valuable insight also important limitations. This work will serve guideline for selecting most appropriate studies focusing absence data.

Язык: Английский

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Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam

Microbial Genomics, Год журнала: 2022, Номер 8(5)

Опубликована: Май 5, 2022

Non-typhoidal Salmonella (NTS) is a major cause of bacterial enterocolitis globally but also causes invasive bloodstream infections. Antimicrobial resistance (AMR) hampers the treatment these infections and understanding how AMR spreads between NTS may help in developing effective strategies. We investigated isolates associated with disease, diarrhoeal disease asymptomatic carriage animals humans from Vietnam. Isolates included multiple serovars both common rare phenotypic profiles; long- short-read sequencing was used to investigate genetic mechanisms genomic backgrounds profiles. demonstrate concordance most genotypes phenotypes identified large genotypic diversity clinically relevant high mobility potential genes (ARGs) this setting. found that 84 % ARGs were located on plasmids, commonly those containing IncHI1A_1 IncHI1B(R27)_1_R27 replicons (33%), IncHI2_1 IncHI2A_1 (31%). The vast majority (95%) ARGS within 10 kbp IS6/IS26 elements, which provide plasmids mechanism exchange other parts genome. Whole genome targeted long-read applied One Health context comparatively limited number insertion sequences plasmid AMR. Therefore, Vietnam likely for settings as well, by move contribute more successful profile than specific ARGs, facilitating adaptation bacteria different environments or selection pressures.

Язык: Английский

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Detection of plasmid contigs in draft genome assemblies using customized Kraken databases

Microbial Genomics, Год журнала: 2021, Номер 7(4)

Опубликована: Апрель 7, 2021

Plasmids play an important role in bacterial evolution and mediate horizontal transfer of genes including virulence antimicrobial resistance genes. Although short-read sequencing technologies have enabled large-scale genomics, the resulting draft genome assemblies are often fragmented into hundreds discrete contigs. Several tools approaches been developed to identify plasmid sequences such assemblies, but require trade-off between sensitivity specificity. Here we propose using Kraken classifier, together with a custom database comprising known chromosomal Klebsiella pneumoniae species complex (KpSC), plasmid-derived contigs assemblies. We assessed performance Illumina-based for 82 KpSC isolates, which complete genomes were available supply ground truth. When benchmarked against five other classifiers (Centrifuge, RFPlasmid, mlplasmids, PlaScope Platon), showed balanced terms overall specificity (90.8 99.4 %, respectively, contig count; 96.5 >99.9 cumulative length), highest accuracy (96.8% vs 91.8-96.6% 99.8% 99.0-99.7 % F1-score (94.5 84.5-94.1 98.0 88.9-96.7 length). also achieved consistent across our collection. Furthermore, demonstrate that expanding additional can further improve classification performance. focused here on KpSC, this methodology could easily be applied sufficient number completed genomes.

Язык: Английский

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Widespread Detection of Yersiniabactin Gene Cluster and Its Encoding Integrative Conjugative Elements (ICE Kp ) among Nonoutbreak OXA-48-Producing Klebsiella pneumoniae Clinical Isolates from Spain and the Netherlands

Microbiology Spectrum, Год журнала: 2023, Номер 11(4)

Опубликована: Июнь 13, 2023

In this study, we determined the presence of virulence factors in nonoutbreak, high-risk clones and other isolates belonging to less common sequence types associated with spread OXA-48-producing Klebsiella pneumoniae clinical from The Netherlands (n = 61) Spain 53). Most shared a chromosomally encoded core factors, including enterobactin gene cluster, fimbrial fim mrk clusters, urea metabolism genes (ureAD). We observed high diversity K-Locus K/O loci combinations, KL17 KL24 (both 16%), O1/O2v1 locus (51%) being most prevalent our study. accessory factor was yersiniabactin cluster (66.7%). found seven lineages-ybt 9, ybt 10, 13, 14, 16, 17, 27-which were embedded integrative conjugative elements (ICEKp): ICEKp3, ICEKp4, ICEKp2, ICEKp5, ICEKp12, ICEKp10, ICEKp22, respectively. Multidrug-resistant lineages-ST11, ST101, ST405-were 10/ICEKp4, 9/ICEKp3, 27/ICEKp22, adhesin kpi operon (kpiABCDEFG) predominant among ST14, ST15, ST405 isolates, as well ferric uptake system kfuABC, which also ST101 isolates. No convergence hypervirulence resistance collection K. Nevertheless, two ST133 ST792, positive for genotoxin colibactin (ICEKp10). element, ICEKp, major vehicle clusters spreading. IMPORTANCE Convergence multidrug has been reported mostly related sporadic cases or small outbreaks. little is known about real prevalence carbapenem-resistant hypervirulent since these phenomena are often separately studied. gathered information on virulent content (i.e., ST11, ST405) STs study nonoutbreak can help us expand genomic landscape population by identifying markers their mechanisms spread. Surveillance should focus not only antimicrobial but characteristics avoid (hyper)virulent that may cause untreatable more severe infections.

Язык: Английский

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Stimulation of Nicotiana tabacum L. In Vitro Shoot Growth by Endophytic Bacillus cereus Group Bacteria

Microorganisms, Год журнала: 2021, Номер 9(9), С. 1893 - 1893

Опубликована: Сен. 6, 2021

In vitro plant tissue cultures face various unfavorable conditions, such as mechanical damage, osmotic shock, and phytohormone imbalance, which can be detrimental to culture viability, growth efficiency, genetic stability. Recent studies have revealed a presence of diverse endophytic bacteria, suggesting that engineering the microbiome in tissues has potential improve their acclimatization growth. Therefore, aim this study was identify cultivated tobacco (Nicotiana tabacum L.) bacteria isolates are capable promoting biomass accumulation shoots. Forty-five were obtained from greenhouse-grown leaves assigned seven Bacillus spp. one Pseudomonas sp. based on 16S rRNA or genome sequence data. To evaluate bacterial effect growth, shoots inoculated with 22 selected distinct taxonomic groups. Four cereus group species B. toyonensis, wiedmannii mycoides promoted shoot by 11–21%. Furthermore, contrasting found among several same species, strain-specific interaction host. Comparative analysis assemblies performed two closely related toyonensis growth-modulating properties. This structures genomic regions, including putative enzyme cluster involved biosynthesis linear azol(in)e-containing peptides polysaccharides. However, function these clusters significance plant-promoting activity remains elusive, observed effects more likely result variations leading differences metabolic gene expression activity. The shoot-growth-promoting properties application improving vitro.

Язык: Английский

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Genomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands

Pathogens, Год журнала: 2022, Номер 11(2), С. 123 - 123

Опубликована: Янв. 20, 2022

Acinetobacter baumannii is a nosocomial pathogen that frequently causes healthcare-acquired infections. The global spread of multidrug-resistant (MDR) strains with its ability to survive in the environment for extended periods imposes pressing public health threat. Two MDR A. outbreaks occurred 2012 and 2014 companion animal intensive care unit (caICU) Netherlands. Whole-genome sequencing (WGS) was performed on dog clinical isolates (n = 6), environmental 5), human reference 3) investigate if two were related. All shared identical resistance phenotypes displaying multidrug resistance. Multi-locus Sequence Typing (MLST) revealed all belonged sequence type ST2. core genome MLST (cgMLST) results confirmed not Comparative analysis showed outbreak contained different gene contents, including mobile genetic elements associated antimicrobial genes (ARGs). time-measured phylogenetic reconstruction diverged approximately 30 years before 2014. Our study shows importance WGS analyses combined molecular clock investigations reduce transmission infections clinics.

Язык: Английский

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First insights into antimicrobial resistance, toxigenic profiles, and genetic diversity in Bacillus cereus isolated from Chinese sausages

LWT, Год журнала: 2023, Номер 181, С. 114717 - 114717

Опубликована: Апрель 5, 2023

Язык: Английский

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