Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer

Ampicillin resistance has greatly contributed to the recent dramatic increase of a cluster of human adapted Enterococcus faecium lineages (ST17, ST18, and ST78) in hospital-based infections. Changes in the chromosomal pbp5 gene have been associated with different levels of ampicillin susceptibility, leading to protein variants (designated as PBP5 C-types to keep the nomenclature used in previous works) with diverse degrees of reduction in penicillin affinity. Our goal was to use a comparative genomics approach to evaluate the relationship between the diversity of PBP5 among E. faecium isolates of different phylogenomic groups as well as to assess the pbp5 transferability among isolates of disparate clonal lineages. The analyses of 78 selected E. faecium strains as well as published E. faecium genomes, suggested that the diversity of pbp5 mirrors the phylogenomic diversification of E. faecium. The presence of identical PBP5 C-types as well as similar pbp5 genetic environments in different E. faecium lineages and clones from quite different geographical and environmental origin was also documented and would indicate their horizontal gene transfer among E. faecium populations. This was supported by experimental assays showing transfer of large (≈180–280 kb) chromosomal genetic platforms containing pbp5 alleles, ponA (transglycosilase) and other metabolic and adaptive features, from E. faecium donor isolates to suitable E. faecium recipient strains. Mutation profile analysis of PBP5 from available genomes and strains from this study suggests that the spread of PBP5 C-types might have occurred even in the absence of a significant ampicillin resistance phenotype. In summary, genetic platforms containing pbp5 sequences were stably maintained in particular E. faecium lineages, but were also able to be transferred among E. faecium clones of different origins, emphasizing the growing risk of further spread of ampicillin resistance in this nosocomial pathogen.This work was supported by Fundação para a Ciência e a Tecnologia (FCT)/Ministério da Educacão e Ciência (MEC) through national funds and co-financed by Fundo Europeu de Desenvolvimento Regional (FEDER) under the Partnership Agreement PT2020 with the reference UID/ MULTI/04378/2013–POCI/01/0145/FERDER/007728 to CN and LP, Instituto de Salud Carlos III (Plan Estatal de I+D+i 2013-2016), Grant PI12-01581 and PI15-01307 to TMC and CIBERESP (CB06/02/0053) to FB, European Commission, Seventh Framework Program (EVOTARFP7-HEALTH-282004) to TMC and FB and the Regional Government of Madrid in Spain (PROMPT- S2010/BMD2414) to FB and TMC.Peer reviewedPeer Reviewe

PipX, the coactivator of NtcA, is a global regulator in cyanobacteria

To modulate the expression of genes involved in nitrogen assimilation, the cyanobacterial PII-interacting protein X (PipX) interacts with the global transcriptional regulator NtcA and the signal transduction protein PII, a protein found in all three domains of life as an integrator of signals of the nitrogen and carbon balance. PipX can form alternate complexes with NtcA and PII, and these interactions are stimulated and inhibited, respectively, by 2-oxoglutarate, providing a mechanistic link between PII signaling and NtcA-regulated gene expression. Here, we demonstrate that PipX is involved in a much wider interaction network. The effect of pipX alleles on transcript levels was studied by RNA sequencing of S. elongatus strains grown in the presence of either nitrate or ammonium, followed by multivariate analyses of relevant mutant/control comparisons. As a result of this process, 222 genes were classified into six coherent groups of differentially regulated genes, two of which, containing either NtcA-activated or NtcA-repressed genes, provided further insights into the function of NtcA–PipX complexes. The remaining four groups suggest the involvement of PipX in at least three NtcA-independent regulatory pathways. Our results pave the way to uncover new regulatory interactions and mechanisms in the control of gene expression in cyanobacteria.This work was supported by the Spanish Ministry of Economy and Competitivity (Grants BFU2009-07371, BFU2012-33364, and BFU2011-26608) and the European Seventh Framework Program (Grants 289326/FP7-KBBE-2011-5 and 282004/FP7-HEALTH-2011-2.3.1-2)

Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences

This is an open-access article distributed under the terms of the Creative Commons Attribution License.Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ–proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages.Work was financed by the Spanish Ministry of Economy and Competitivity (BFU2011-26608 to FdlC, FIS-PI09/01273 and AGL2013-47852-R to JB and FIS-PI12-01581 and CB06/02/0053 to TMC), by the European Seventh Framework Program (612146/FP7-ICT-2013-10 to FdlC and 282004/FP7-HEALTH-2011-2.3.1-2 to FdlC and TMC); by Red Española de Investigación en Patología­ Infecciosa (REIPI RD06/0008/1018-1016) to JB, by Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia and European Regional Development Fund, ERDF (CN2012/303 and EM2014/001) to JB and by the regional government of Madrid (PROMPT-S2010/BMD2414) to TMC. We are also grateful to the Spanish Network for the Study of Plasmids and Extrachromosomal Elements (REDEEX) for funding cooperation among Spanish microbiologists working on the biology of MGEs (Spanish Ministry of Science and Innovation BFU2011-14145-E).Peer Reviewe

High genomic diversity and heterogenous origins of pathogenic and antibiotic-resistant Escherichia coli in household settings represent a challenge to reducing transmission in low-income settings

Escherichia coli; is present in multiple hosts and environmental compartments as a normal inhabitant, temporary or persistent colonizer, and as a pathogen. Transmission of; E. coli; between hosts and with the environment is considered to occur more often in areas with poor sanitation. We performed whole-genome comparative analyses on 60; E. coli; isolates from soils and fecal sources (cattle, chickens, and humans) in households in rural Bangladesh. Isolates from household soils were in multiple branches of the reconstructed phylogeny, intermixed with isolates from fecal sources. Pairwise differences between all strain pairs were large (minimum, 189 single nucleotide polymorphisms [SNPs]), suggesting high diversity and heterogeneous origins of the isolates. The presence of multiple virulence and antibiotic resistance genes is indicative of the risk that; E. coli; from soil and feces represent for the transmission of variants that pose potential harm to people. Analysis of the accessory genomes of the Bangladeshi; E. coli; relative to; E. coli; genomes available in NCBI identified a common pool of accessory genes shared among; E. coli; isolates in this geographic area. Together, these findings indicate that in rural Bangladesh, a high level of; E. coli; in soil is likely driven by contributions from multiple and diverse; E. coli; sources (human and animal) that share an accessory gene pool relatively unique to previously published; E. coli; genomes. Thus, interventions to reduce environmental pathogen or antimicrobial resistance transmission should adopt integrated One Health approaches that consider heterogeneous origins and high diversity to improve effectiveness and reduce prevalence and transmission.; IMPORTANCE; Escherichia coli; is reported in high levels in household soil in low-income settings. When; E. coli; reaches a soil environment, different mechanisms, including survival, clonal expansion, and genetic exchange, have the potential to either maintain or generate; E. coli; variants with capabilities of causing harm to people. In this study, we used whole-genome sequencing to identify that; E. coli; isolates collected from rural Bangladeshi household soils, including pathogenic and antibiotic-resistant variants, are diverse and likely originated from multiple diverse sources. In addition, we observed specialization of the accessory genome of this Bangladeshi; E. coli; compared to; E. coli; genomes available in current sequence databases. Thus, to address the high level of pathogenic and antibiotic-resistant; E. coli; transmission in low-income settings, interventions should focus on addressing the heterogeneous origins and high diversity

Simulating the Influence of Conjugative-Plasmid Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model

[EN] Bacterial plasmids harboring antibiotic resistance genes are critical in the spread of antibiotic resistance. It is known that plasmids differ in their kinetic values, i.e., conjugation rate, segregation rate by copy number incompatibility with related plasmids, and rate of stochastic loss during replication. They also differ in cost to the cell in terms of reducing fitness and in the frequency of compensatory mutations compensating plasmid cost. However, we do not know how variation in these values influences the success of a plasmid and its resistance genes in complex ecosystems, such as the microbiota. Genes are in plasmids, plasmids are in cells, and cells are in bacterial populations and microbiotas, which are inside hosts, and hosts are in human communities at the hospital or the community under various levels of cross-colonization and antibiotic exposure. Differences in plasmid kinetics might have consequences on the global spread of antibiotic resistance. New membrane computing methods help to predict these consequences. In our simulation, conjugation frequency of at least 10(-3) influences the dominance of a strain with a resistance plasmid. Coexistence of different antibiotic resistances occurs if host strains can maintain two copies of similar plasmids. Plasmid loss rates of 10(-4) or 10(-5) or plasmid fitness costs of >= 0.06 favor plasmids located in the most abundant species. The beneficial effect of compensatory mutations for plasmid fitness cost is proportional to this cost at high mutation frequencies (10(-3) to 10(-5)). The results of this computational model clearly show how changes in plasmid kinetics can modify the entire population ecology of antibiotic resistance in the hospital setting.F. Baquero, M. Campos, and T. M. Coque were supported by EU Joint Programming Initiative JPIAMR2016-AC16/00043 (JPIonAMR-Third call on Transmission, ST131TS project), the Health Institute Carlos III of Spain (grants PI15-00818 and PI18-01942 and CIBER [CIBER in Epidemiology and Public Health, CIBERESP; CB06/02/0053]), and the Regional Government of Madrid (InGEMICS-C; S2017/BMD-3691), all of them cofinanced by the European Development Regional Fund (ERDF) "A Way to Achieve Europe." A. San Millan was supported by the European Research Council under the European Union's Horizon 2020 Research and Innovation Program (ERC grant agreement number 757440-PLASREVOLUTION)Campos Frances, M.; San Millan, A.; Sempere Luna, JM.; Lanza, VF.; Coque, TM.; Llorens, C.; Baquero, F. (2020). Simulating the Influence of Conjugative-Plasmid Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model. 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F., Mizrahi, I., & Dagan, T. (2019). Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance. Nature Communications, 10(1). doi:10.1038/s41467-019-10600-7Yano, H., Shintani, M., Tomita, M., Suzuki, H., & Oshima, T. (2019). Reconsidering plasmid maintenance factors for computational plasmid design. Computational and Structural Biotechnology Journal, 17, 70-81. doi:10.1016/j.csbj.2018.12.001Gumpert, H., Kubicek-Sutherland, J. Z., Porse, A., Karami, N., Munck, C., Linkevicius, M., … Sommer, M. O. A. (2017). Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment. Frontiers in Microbiology, 8. doi:10.3389/fmicb.2017.01852Durão, P., Balbontín, R., & Gordo, I. (2018). Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance. Trends in Microbiology, 26(8), 677-691. doi:10.1016/j.tim.2018.01.005Campos, M., Llorens, C., Sempere, J. 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Journal of General Microbiology, 136(11), 2319-2325. doi:10.1099/00221287-136-11-2319Levin, B. R., Stewart, F. M., & Rice, V. A. (1979). The kinetics of conjugative plasmid transmission: Fit of a simple mass action model. Plasmid, 2(2), 247-260. doi:10.1016/0147-619x(79)90043-xTurner, P. E., Williams, E. S. C. P., Okeke, C., Cooper, V. S., Duffy, S., & Wertz, J. E. (2014). Antibiotic resistance correlates with transmission in plasmid evolution. Evolution, 68(12), 3368-3380. doi:10.1111/evo.12537Porse, A., Schønning, K., Munck, C., & Sommer, M. O. A. (2016). Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts. Molecular Biology and Evolution, 33(11), 2860-2873. doi:10.1093/molbev/msw163Smillie, C., Garcillán-Barcia, M. P., Francia, M. V., Rocha, E. P. C., & de la Cruz, F. (2010). Mobility of Plasmids. Microbiology and Molecular Biology Reviews, 74(3), 434-452. doi:10.1128/mmbr.00020-1038. Taylor DE, Gibreel A, Tracz DM, Lawley TD. 2004. Antibiotic resistance plasmids, p 473–492. In Funnell BE, Phillips GJ (ed), Plasmid biology. American Society of Microbiology, Washington, DC.Million-Weaver, S., & Camps, M. (2014). Mechanisms of plasmid segregation: Have multicopy plasmids been overlooked? Plasmid, 75, 27-36. doi:10.1016/j.plasmid.2014.07.002Lau, B. T. C., Malkus, P., & Paulsson, J. (2013). New quantitative methods for measuring plasmid loss rates reveal unexpected stability. Plasmid, 70(3), 353-361. doi:10.1016/j.plasmid.2013.07.007Vogwill, T., & MacLean, R. C. (2014). The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach. Evolutionary Applications, 8(3), 284-295. doi:10.1111/eva.12202Andersson, D. I., & Levin, B. R. (1999). The biological cost of antibiotic resistance. Current Opinion in Microbiology, 2(5), 489-493. doi:10.1016/s1369-5274(99)00005-3Andersson, D. I., & Hughes, D. (2010). Antibiotic resistance and its cost: is it possible to reverse resistance? Nature Reviews Microbiology, 8(4), 260-271. doi:10.1038/nrmicro2319Loftie-Eaton, W., Bashford, K., Quinn, H., Dong, K., Millstein, J., Hunter, S., … Top, E. M. (2017). Compensatory mutations improve general permissiveness to antibiotic resistance plasmids. Nature Ecology & Evolution, 1(9), 1354-1363. doi:10.1038/s41559-017-0243-2Zwanzig, M., Harrison, E., Brockhurst, M. A., Hall, J. P. J., Berendonk, T. U., & Berger, U. (2019). Mobile Compensatory Mutations Promote Plasmid Survival. mSystems, 4(1). doi:10.1128/msystems.00186-18Yang, Q. E., MacLean, C., Papkou, A., Pritchard, M., Powell, L., Thomas, D., … Walsh, T. R. (2020). Compensatory mutations modulate the competitiveness and dynamics of plasmid-mediated colistin resistance in Escherichia coli clones. The ISME Journal, 14(3), 861-865. doi:10.1038/s41396-019-0578-6Gama, J. A., Zilhão, R., & Dionisio, F. (2018). Impact of plasmid interactions with the chromosome and other plasmids on the spread of antibiotic resistance. Plasmid, 99, 82-88. doi:10.1016/j.plasmid.2018.09.009Harrison, E., Dytham, C., Hall, J. P. J., Guymer, D., Spiers, A. J., Paterson, S., & Brockhurst, M. A. (2016). Rapid compensatory evolution promotes the survival of conjugative plasmids. Mobile Genetic Elements, 6(3), e1179074. doi:10.1080/2159256x.2016.1179074Hall, J. P. J., Brockhurst, M. A., Dytham, C., & Harrison, E. (2017). The evolution of plasmid stability: Are infectious transmission and compensatory evolution competing evolutionary trajectories? Plasmid, 91, 90-95. doi:10.1016/j.plasmid.2017.04.00354. Shintani M, Suzuki H. 2019. Plasmids and their hosts, p 109–133. In Nishida H, Oshima T (ed), DNA traffic in the environment. Springer, Singapore.Komp Lindgren, P., Karlsson, A., & Hughes, D. (2003). Mutation Rate and Evolution of Fluoroquinolone Resistance in Escherichia coli Isolates from Patients with Urinary Tract Infections. Antimicrobial Agents and Chemotherapy, 47(10), 3222-3232. doi:10.1128/aac.47.10.3222-3232.2003Krone, S. M., Lu, R., Fox, R., Suzuki, H., & Top, E. M. (2007). Modelling the spatial dynamics of plasmid transfer and persistence. Microbiology, 153(8), 2803-2816. doi:10.1099/mic.0.2006/004531-0Baquero, F., Coque, T. M., & de la Cruz, F. (2011). Ecology and Evolution as Targets: the Need for Novel Eco-Evo Drugs and Strategies To Fight Antibiotic Resistance. Antimicrobial Agents and Chemotherapy, 55(8), 3649-3660. doi:10.1128/aac.00013-11Buckner, M. M. C., Ciusa, M. L., & Piddock, L. J. V. (2018). Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing. FEMS Microbiology Reviews, 42(6), 781-804. doi:10.1093/femsre/fuy031Bush, K. (2008). Extended-spectrum β-lactamases in North America, 1987–2006. Clinical Microbiology and Infection, 14, 134-143. doi:10.1111/j.1469-0691.2007.01848.xJacoby, G. A., & Han, P. (1996). Detection of extended-spectrum beta-lactamases in clinical isolates of Klebsiella pneumoniae and Escherichia coli. Journal of clinical microbiology, 34(4), 908-911. doi:10.1128/jcm.34.4.908-911.1996Valverde, A., Coque, T. M., Sanchez-Moreno, M. P., Rollan, A., Baquero, F., & Canton, R. (2004). Dramatic Increase in Prevalence of Fecal Carriage of Extended-Spectrum  -Lactamase-Producing Enterobacteriaceae during Nonoutbreak Situations in Spain. Journal of Clinical Microbiology, 42(10), 4769-4775. doi:10.1128/jcm.42.10.4769-4775.2004Hernández, J. R., Martínez-Martínez, L., Cantón, R., Coque, T. M., & Pascual, A. (2005). Nationwide Study of Escherichia coli and Klebsiella pneumoniae Producing Extended-Spectrum β-Lactamases in Spain. Antimicrobial Agents and Chemotherapy, 49(5), 2122-2125. doi:10.1128/aac.49.5.2122-2125.2005PEREZ, F., ENDIMIANI, A., HUJER, K., & BONOMO, R. (2007). The continuing challenge of ESBLs. 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Genomics of Serratia marcescens isolates causing outbreaks in the same pediatric unit 47 years apart: Position in an updated phylogeny of the species

The first documented nosocomial outbreak caused by Serratia marcescens in Spain occurred in 1969 at the neonatal intensive care unit (NICU) of the tertiary La Paz Children’s Hospital in Madrid, Spain, and based on the available phenotyping techniques at this time, it was considered as a monoclonal outbreak. Only 47 years later, another S. marcescens outbreak of an equivalent dimension occurred at the same NICU. The aim of the present study was to study isolates from these historical and contemporary outbreaks by phenotypic analysis and whole-genome sequencing techniques and to position these strains along with 444 publicly available S. marcescens genomes, separately comparing core genome and accessory genome contents. Clades inferred by both approaches showed high correlation, indicating that core and accessory genomes seem to evolve in the same manner for S. marcescens. Nine S. marcescens clusters were identified, and isolates were grouped in two of them according to sampling year. One exception was isolate 13F-69, the most genetically distant strain, located in a different cluster. Categorical functions in the annotated accessory genes of both collections were preserved among all isolates. No significant differences in frequency of insertion sequences in historical (0.18–0.20)—excluding the outlier strain—versus contemporary isolates (0.11–0.19) were found despite the expected resting effect. The most dissimilar isolate, 13F-69, contains a highly preserved plasmid previously described in Bordetella bronchiseptica. This strain exhibited a few antibiotic resistance genes not resulting in a resistant phenotype, suggesting the value of gene down expression in adaptation to long-term starvation.CS was supported by “Fundación Mutua Madrileña” grant to RC achieved in 2017 call with reference number AP165902017. MP-A was supported by the Programa Operativo de Empleo Juvenil, cofinanced by the European Social Fund Investing in your future (ESF) and ERDF (PEJD-2018-PRE/BMD-8237). BP-V was funded by H2020 FTIPilot 2016 project no. 730713 “FAST-bact “A novel fast and automated test for antibiotic susceptibility testing for Gram positive and negative bacteria” and co-funded by Instituto de Salud Carlos III and the European Regional Development Fund (ERDF, “A way to achieve Europe”). FB was supported by grants from the Madrid Regional Government (InGEMICS-C; S2017/BMD-3691) and CIBER (CIBER in Epidemiology and Public Health, CIBERESP; CB06/02/0053), co-funded by Instituto de Salud Carlos III and the European Regional Development Fund (ERDF, “A way to achieve Europe”). This work was supported by the Instituto de Salud Carlos III, PI17/00115 (RC), and REIPI (RD16/0016/0011) actions, cofinanced by the European Development Regional Fund “A way to achieve Europe” (ERDF

Detection of Minority Variants and Mixed Infections in Mycobacterium tuberculosis by Direct Whole-Genome Sequencing on Noncultured Specimens Using a Specific-DNA Capture Strategy

Detection of mixed Mycobacterium tuberculosis (MTB) infections is essential, particularly when resistance mutations are present in minority bacterial populations that may affect patients' disease evolution and treatment. Whole-genome sequencing (WGS) has extended the amount of key information available for the diagnosis of MTB infection, including the identification of mixed infections. Having genomic information at diagnosis for early intervention requires carrying out WGS directly on the clinical samples. However, few studies have been successful with this approach due to the low representation of MTB DNA in sputa. In this study, we evaluated the ability of a strategy based on specific MTB DNA enrichment by using a newly designed capture platform (MycoCap) to detect minority variants and mixed infections by WGS on controlled mixtures of MTB DNAs in a simulated sputum genetic background. A pilot study was carried out with 12 samples containing 98% of a DNA pool from sputa of patients without MTB infection and 2% of MTB DNA mixtures at different proportions. Our strategy allowed us to generate sequences with a quality equivalent to those obtained from culture: 62.5× depth coverage and 95% breadth coverage (for at least 20× reads). Assessment of minority variant detection was carried out by manual analysis and allowed us to identify heterozygous positions up to a 95:5 ratio. The strategy also automatically distinguished mixed infections up to a 90:10 proportion. Our strategy efficiently captures MTB DNA in a nonspecific genetic background, allows detection of minority variants and mixed infections, and is a promising tool for performing WGS directly on clinical samples. IMPORTANCE We present a new strategy to identify mixed infections and minority variants in Mycobacterium tuberculosis by whole-genome sequencing. The objective of the strategy is the direct detection in patient sputum; in this way, minority populations of resistant strains can be identified at the time of diagnosis, facilitating identification of the most appropriate treatment for the patient from the first moment. For this, a platform for capturing M. tuberculosis-specific DNA was designed to enrich the clinical sample and obtain quality sequences

Mge-cluster: a reference-free approach for typing bacterial plasmids

Extrachromosomal elements of bacterial cells such as plasmids are notorious for their importance in evolution and adaptation to changing ecology. However, high-resolution population-wide analysis of plasmids has only become accessible recently with the advent of scalable long-read sequencing technology. Current typing methods for the classification of plasmids remain limited in their scope which motivated us to develop a computationally efficient approach to simultaneously recognize novel types and classify plasmids into previously identified groups. Here, we introduce mge-cluster that can easily handle thousands of input sequences which are compressed using a unitig representation in a de Bruijn graph. Our approach offers a faster runtime than existing algorithms, with moderate memory usage, and enables an intuitive visualization, classification and clustering scheme that users can explore interactively within a single framework. M ge-cluster platform for plasmid analysis can be easily distributed and replicated, enabling a consistent labelling of plasmids across past, present, and future sequence collections. We underscore the advantages of our approach by analysing a population-wide plasmid data set obtained from the opportunistic pathogen Escherichia coli, studying the prevalence of the colistin resistance gene mcr-1.1 within the plasmid population, and describing an instance of resistance plasmid transmission within a hospital environment

Strain-specific predation of Bdellovibrio bacteriovorus on Pseudomonas aeruginosa with a higher range for cystic fibrosis than for bacteremia isolates

7 p.-1 fig.This work aimed to evaluate the predatory activity of Bdellovibrio bacteriovorus 109J on clinical isolates of Pseudomonas aeruginosa selected from well-characterized collections of cystic fibrosis (CF) lung colonization (n = 30) and bloodstream infections (BSI) (n = 48) including strains selected by genetic lineage (frequent and rare sequence types), antibiotic resistance phenotype (susceptible and multidrug-resistant isolates), and colony phenotype (mucoid and non-mucoid isolates). The intraspecies predation range (I-PR) was defined as the proportion of susceptible strains within the entire collection. In contrast, the predation efficiency (PE) is the ratio of viable prey cells remaining after predation compared to the initial inoculum. I-PR was significantly higher for CF (67%) than for BSI P. aeruginosa isolates (35%) probably related to an environmental origin of CF strains whereas invasive strains are more adapted to humans. I-PR correlation with bacterial features such as mucoid morphotype, genetic background, or antibiotic susceptibility profile was not detected. To test the possibility of increasing I-PR of BSI isolates, a polyhydroxyalkanoate depolymerase deficient B. bacteriovorus bd2637 mutant was used. Global median I-PR and PE values remained constant for both predators, but 31.2% of 109J-resistant isolates were susceptible to the mutant, and 22.9% of 109J-susceptible isolates showed resistance to predation by the mutant, pointing to a predator–prey specificity process. The potential use of predators in the clinical setting should be based on the determination of the I-PR for each species, and the PE of each particular target strain.CH is supported by Comunidad Autónoma de Madrid (PEJD-2018-POST/BMD-8016). CS is granted by “Fundación Mutua Madrileña” achieved in 2017 call by RDC (AP165902017). SSB is a recipient of a predoctoral FPU grant (FPU17/03978) from the Spanish Ministry of Universities. This work was supported by the Instituto de Salud Carlos III, PI17/00115 and PI20/00164 to RdC, REIPI (RD16/0016/0011) actions, co-financed by the European Development Regional Fund “A way to achieve Europe” (ERDF), and Vertex Pharmaceuticals.Peer reviewe

Relationship of Diet to Gut Microbiota and Inflammatory Biomarkers in People with HIV

While changes in microbiome composition have been associated with HIV, the effect of diet and its potential impact on inflammation remains unclear. Methods: Twenty-seven people living with HIV (PWH) on antiretroviral therapy (ART) were studied. A comprehensive dietary analysis was performed and two types of dietary patterns were determined. We explored the associations of each dietary pattern with gut microbiota and plasma inflammatory biomarkers. Results: We appreciated two dietary patterns, Mediterranean-like (MEL) and one Western-like (WEL). Compared to participants with the WEL pattern, participants with MEL pattern showed higher abundance of Lachnospira (p-value = 0.02) and lower levels of the inflammatory biomarkers D-dimer (p-value = 0.050) and soluble TNF-alpha receptor 2 (sTNFR2) (p-value = 0.049). Men who have sex with men (MSM) with MEL pattern had lower abundance of Erysipelotrichaceae (p-value < 0.001) and lower levels of D-dimer (p-value = 0.026) than MSM with WEL pattern. Conclusion: MEL pattern favours Lachnospira abundance, and protects against Erysipelotrichaceae abundance and higher levels of the inflammatory biomarkers D-dimer and sTNFR2, precursors of inflammatory processes in HIV-infected patients. Our study contributes to understanding the determinants of a healthier diet and its connections with gut microbiota and inflammation