Search

Background: The direct identification of uropathogens from urine samples, in combination with the rapid detection of resistance, would allow early adjustment of empirical antimicrobial treatment. Methods: Two hundred and ninety-eight urine samples processed between 1 June and 31 December 2020, selected with flow cytometry, with direct identification by MALDI-TOF mass spectrometry, and rapid detection of extended-spectrum beta-lactamase (ESBL) and carbapenemases-producing strains by lateral flow were analyzed. Results: The positive predictive value of the direct identification of the 86 samples that met the flow cytometry criterion (>5000 bacteria/µL) was 96.4%. Reliable direct identification was obtained in 14 of the 27 (51.8%) urinary source bacteraemias. There was 100% agreement between the lateral flow and antibiogram in the detection of ESBL and carbapenemases. Conclusion: the protocol for the direct identification and rapid detection of ESBL and carbapenemases-producing strains from urine samples is a reliable and useful tool.

Treballs finals del Màster de Fonaments de Ciència de Dades, Facultat de matemàtiques, Universitat de Barcelona. Curs: 2022-2023. Tutor: Miquel Duran Frigola i Jordi Vitrià i Marca, [en] Predictive modelling of antimicrobial activity of molecules is a crucial step towards the discovery of anti-infective medicines. Unfortunately, there is a shortage of models covering endemic pathogens of the Global South, reflecting the existing bias in research towards diseases prevalent in wealthy countries. This project has developed a pipeline to systematically build drug discovery models, in particular antimicrobial activity prediction models for small molecule compounds. The data of assay results on a selected pathogen is extracted from a publicly available database: ChEMBL. This data is then cleaned and processed in order to build predictive models with various Automated Machine Learning (AutoML) techniques using the ZairaChem tool from the Ersilia Open Data Initiative. The pipeline has been applied on 6 pathogens of great relevance to global health known as ESKAPE, for which the data has been obtained and processed, and baseline models created. We have built the full set of final models for one of these pathogens, Staphylococcus aureus. The pipeline can be used on any other pathogen for which ChEMBL has sufficient data. This pipeline will be used to deploy models in the Ersilia Model Hub, a repository of pre-trained ML for drug discovery in global health. This will be an opportunity to compensate for the shortage of ML models adapted to the needs of the Global South.

The ability of MALDI-TOF for the identification of nontuberculous mycobacteria (NTM) has improved recently thanks to updated databases and optimized protein extraction procedures. Few multicentre studies on the reproducibility of MALDI-TOF have been performed so far, none on mycobacteria. The aim of this study was to evaluate the reproducibility of MALDI-TOF for the identification of NTM in 15 laboratories in 9 European countries. A total of 98 NTM clinical isolates were grown on Löwenstein-Jensen. Biomass was collected in tubes with water and ethanol, anonymized and sent out to the 15 participating laboratories. Isolates were identified using MALDI Biotyper (Bruker Daltonics). Up to 1330 MALDI-TOF identifications were collected in the study. A score ≥ 1.6 was obtained for 100% of isolates in 5 laboratories (68.2–98.6% in the other). Species-level identification provided by MALDI-TOF was 100% correct in 8 centres and 100% correct to complex-level in 12 laboratories. In most cases, the misidentifications obtained were associated with closely related species. The variability observed for a few isolates could be due to variations in the protein extraction procedure or to MALDI-TOF system status in each centre. In conclusion, MALDI-TOF showed to be a highly reproducible method and suitable for its implementation for NTM identification.

The purpose of the present study was to examine the inactivation of Salmonella enterica (50 μL; 109 CFU g−1), Listeria monocytogenes (50 μL; 109 CFU g−1), and murine norovirus (MNV-1; 50 μL; 107 50% tissue culture infectious dose (TCID50) mL−1) on whole and fresh-cut strawberries after 2 min disinfection treatments (water (H2O), chlorine 200 mg L−1 (NaClO), water-assisted ultraviolet-C (UV-C) (WUV), and the combination WUV and 40 mg L−1 of PA (WUV + PA)) in a water tank (15 L) equipped with 4 UV-C lamps (17.2 W each), and after 7 days of cold storage (4 and 10 °C). For MNV-1, dry UV-C treatment (DUV) was also tested. For all UV-C treatments, an irradiation dose of 1.3 kJ m−2 was used. RESULTS: When strawberries were washed with WUV, L. monocytogenes and S. enterica were reduced by 2.8 and 2.2 log CFU g−1, respectively. The addition of 40 mg L−1 of PA to WUV (WUV + PA) increased the reduction range of L. monocytogenes and S. enterica by 1.9 and 0.8 log, respectively. Regarding the wash water, no pathogens were recovered after the WUV + PA treatment (detection limit 50 CFU mL−1). Depending on storage conditions (7 days at 4 or 10 °C), reductions observed were 0.5 to 2.0 log for S. enterica and 0.5 to 3.0 log for L. monocytogenes. The reductions in MNV-1 titer after disinfection treatments ranged from 1.3 to 1.7 log. No significant differences between storage conditions were observed for MNV-1: titers did not decline or were reduced up to 0.3 log after 7 days of cold storage. CONCLUSION: The three-way action for disinfecting strawberries by UV-C irradiation and PA, plus the physical removal of the microorganisms by agitated water, are effective against foodborne pathogens on strawberries and water wash. During storage, WUV had a larger impact on the inactivation kinetics of S. enterica. Storage had little impact on MNV-1 inactivation. The authors are grateful to the Spanish government (Ministerio deEconomía y Competitividad, research project AGL2016-78086-R)and the Centres de Recerca de Catalunya (CERCA) Programmeof‘Generalitat de Catalunya’for itsfinancial support. J. Ortiz-Solàthanks the University of Lleida for its PhD grant (BOU186-243/2017 UdL) and M. Anguera thanks them for their techni-cal support. I. Nicolau-Lapeña is in receipt of a predoctoral grantawarded by the‘Ministerio de Economía, Industria y Competitivi-dad’(grant number BES-2017-079779). The authors gratefullyacknowledged the assistance of Gloria Sánchez and Susana Guixfor teaching them the methodologies related to MNV-1 andRAW 264.7 assays.

Cefiderocol is a catechol-substituted siderophore cephalosporin combining rapid penetration into the periplasmic space with increased stability against β-lactamases. This study provides additional data on the in vitro antimicrobial activity of cefiderocol and commercially available comparators against an epidemiologically diverse collection of Acinetobacter baumannii clinical isolates. Antimicrobial susceptibility was tested using pre-prepared frozen 96-well microtiter plates containing twofold serial dilutions of: cefepime, ceftazidime/avibactam, imipenem/relebactam, ampicillin/sulbactam, meropenem, meropenem/vaborbactam, ciprofloxacin, minocycline, tigecycline, trimethoprim/sulfamethoxazole and colistin using the standard broth microdilution procedure in cation-adjusted Mueller–Hinton broth (CAMHB). For cefiderocol, iron-depleted CAMHB was used. A collection of 113 clinical strains of A. baumannii isolated from Argentina, Azerbaijan, Croatia, Greece, Italy, Morocco, Mozambique, Peru and Spain were included. The most active antimicrobial agents against our collection were colistin and cefiderocol, with 12.38% and 21.23% of non-susceptibility, respectively. A high proportion of multidrug-resistant (76.77%) and carbapenem-resistant (75.28%) A. baumannii isolates remained susceptible to cefiderocol, which was clearly superior to novel β-lactam/β-lactamase inhibitor combinations. Cefiderocol-resistance was higher among carbapenem-resistant isolates and isolates belonging to ST2, but could not be associated with any particular resistance mechanism or clonal lineage. Our data suggest that cefiderocol is a good alternative to treat infections caused by MDR A. baumanni, including carbapenem-resistant strains.

Background: Quantitative (q) polymerase chain reaction (PCR) cycle threshold (Ct) values represent the number of amplification cycles required for a positive PCR result and are a proxy of pathogen quantity in the tested sample. The clinical utility of Ct values remains unclear for gastrointestinal infections.Objectives: This systematic review assesses the global medical literature for associations between Ct values of gastrointestinal pathogens and patient presentation and clinical outcomes.Data Sources: MEDLINE, EMBASE, Cochrane library databases: searched January 14–17, 2020.Study Eligibility Criteria: Studies reporting on the presence or absence of an association between Ct values and clinical outcomes in adult and pediatric populations were included. Animal studies, reviews, meta-analyses, and non-English language studies were excluded.Participants: Humans infected with gastrointestinal pathogens, detected with qPCR.Interventions: Diagnostics assessing Ct values. Extracted data were reported narratively.Results: Thirty-three eligible studies were identified; the most commonly studied pathogens were Clostridioides difficile (n = 15), norovirus (n = 10), and rotavirus (n = 9). Statistically significant associations between low C. difficile Ct values and increased symptom severity or poor outcome were reported in 4/8 (50%) studies, and increased risk of death in 1/2 (50%) studies; no significant associations were found between Ct value and duration of symptoms or length of hospital stay. Among studies of norovirus, 5/7 (71%), mainly genogroup II, reported symptomatic cases with significantly lower median Ct values than controls. Significantly lower rotavirus Ct values were also observed in symptomatic cases vs. controls in 3/7 (43%) studies, and associated with more severe symptoms in 2/2 studies. Contradictory associations were identified for non-C. difficile bacterial and parasitic pathogens.Conclusions: In conclusion, some studies reported clinically useful associations between Ct values and patient or healthcare outcomes; additional, well-designed, large-scale trials are warranted based on these findings.Systematic Review Registration: [PROSPERO], identifier [CRD42020167239].

One of the main targets for the use of phytogenics in aquafeeds is the mucosal tissues as they constitute a physical and biochemical shield against environmental and pathogenic threats, comprising elements from both the innate and acquired immunity. In the present study, the modulation of the skin transcriptional immune response, the bacterial growth capacity in skin mucus, and the overall health condition of gilthead seabream (Sparus aurata) juveniles fed a dietary supplementation of garlic essential oil, carvacrol, and thymol were assessed. The enrichment analysis of the skin transcriptional profile of fish fed the phytogenic-supplemented diet revealed the regulation of genes associated to cellular components involved in the secretory pathway, suggesting the stimulation, and recruitment of phagocytic cells. Genes recognized by their involvement in non-specific immune response were also identified in the analysis. The promotion of the secretion of non-specific immune molecules into the skin mucus was proposed to be involved in thein vitrodecreased growth capacity of pathogenic bacteria in the mucus of fish fed the phytogenic-supplemented diet. Although the mucus antioxidant capacity was not affected by the phytogenics supplementation, the regulation of genes coding for oxidative stress enzymes suggested the reduction of the skin oxidative stress. Additionally, the decreased levels of cortisol in mucus indicated a reduction in the fish allostatic load due to the properties of the tested additive. Altogether, the dietary garlic, carvacrol, and thymol appear to promote the gilthead seabream skin innate immunity and the mucus protective capacity, decreasing its susceptibility to be colonized by pathogenic bacteria.

Xylem vascular wilt pathogens cause devastating diseases in plants. Proliferation of these pathogens in the xylem causes massive disruption of water and mineral transport, resulting in severe wilting and death of the infected plants. Upon reaching the xylem vascular tissue, these pathogens multiply profusely, spreading vertically within the xylem sap, and horizontally between vessels and to the surrounding tissues. Plant resistance to these pathogens is very complex. One of the most effective defense responses in resistant plants is the formation of physico-chemical barriers in the xylem tissue. Vertical spread within the vessel lumen is restricted by structural barriers, namely, tyloses and gels. Horizontal spread to the apoplast and surrounding healthy vessels and tissues is prevented by vascular coating of the colonized vessels with lignin and suberin. Both vertical and horizontal barriers compartmentalize the pathogen at the infection site and contribute to their elimination. Induction of these defenses are tightly coordinated, both temporally and spatially, to avoid detrimental consequences such as cavitation and embolism. We discuss current knowledge on mechanisms underlying plant-inducible structural barriers against major xylem-colonizing pathogens. This knowledge may be applied to engineer metabolic pathways of vascular coating compounds in specific cells, to produce plants resistant towards xylem colonizers., Research in the lab is funded by the Spanish Ministry of Economy and Competitiveness with grants 2016-78002-R (AGL) and RyC 2014–16158 (NSC), by the Ministry of Science and Innovation / Spanish State Research Agency PID2019-108595RB-I00 / AEI / 10.13039/501100011033, and through the “Severo Ochoa Programme for Centres of Excellence in R&D” (SEV-2015-0533). AK is the recipient of a Netaji Subhas—Indian Council of Agricultural Research (ICAR) International Fellowship. This work was also supported by the CERCA Programme / Generalitat de Catalunya.

Nontypeable Haemophilus influenzae (NTHi) is a Gram-negative human pathogen that causes infections mainly in the upper and lower respiratory tract. The bacterium is associated with bronchitis and exacerbations in patients suffering from chronic obstructive pulmonary disease and frequently causes acute otitis media in preschool children. We have previously demonstrated that the binding of C4b binding protein (C4BP) is important for NTHi complement evasion. In this study, we identified outer membrane protein 5 (P5) of NTHi as a novel ligand of C4BP. Importantly, we observed significantly lower C4BP binding and decreased serum resistance in P5-deficient NTHi mutants. Surface expression of recombinant P5 on Escherichia coli conferred C4BP binding and consequently increased serum resistance. Moreover, P5 expression was positively correlated with C4BP binding in a series of clinical isolates. We revealed higher levels of P5 surface expression and consequently more C4BP binding in isolates from the lower respiratory tract of chronic obstructive pulmonary disease patients and tonsil specimens compared with isolates from the upper respiratory tract and the bloodstream (invasive strains). Our results highlight P5 as an important protein for protecting NTHi against complement-mediated killing., This work was supported by the Swedish Heart Lung Foundation (20180401), the Swedish Research Council (2019-01053 to K.R.; 2018-02392 to A.M.B.), the Anna och Edwin Berger foundation (to K.R.), the Torsten Söderberg Foundation (to A.M.B.), the Royal Physiographical Society in Lund Hedda and John Forssman Foundation (to O.T. and S.B.), the O. E. och Edla Johanssons Foundation (to S.B.), the Längmanska Kulturfonden (to S.B.), the Tore Nilsson’s Foundation (to S.B.), and Skåne County Council’s Research and Development Foundation (to K.R. and A.M.B.).

Tesis doctoral.-- Universidad de Barcelona. Programa de doctorado en biotecnología., Mycoplasma pneumoniae y Mycoplasma genitalium son dos patógenos humanos que infectan tejido pulmonar y urogenital respectivamente. El mecanismo principal para llevar a cabo la infección es a través de la adhesión a las células huésped por una pequeña protuberancia llamada Organela terminal (OT). En la membrana de esta OT se encuentra un complejo multiproteico, denominado Nap, compuesto por un dímero de heterodímeros de las proteínas P1 y P40/P90 en M. pneumoniae, o P140 y P110 en M. genitalium. P1 ha sido el foco de numerosos estudios, identificándola como la adhesina principal del complejo Nap en M. pneumoniae. Además de la función de adhesión, las proteínas de los Naps también participan en otros procesos esenciales para la patogenicidad, como son la motilidad y la evasión del sistema inmune. En nuestro laboratorio se determinó hace unos años la estructura del ectodominio de la proteína P110 de M. genitalium (Aparicio et al., Nature comm. 2018). Continuando la investigación sobre las proteínas que componen el Nap, el objetivo principal de esta Tesis doctoral ha sido determinar la estructura tridimensional de P140 (M. genitalium) y de P1 y P40/P90 (M. pneumoniae), estudiando también el papel que desempeñan estas proteínas en adhesión, motilidad e inmunogenicidad. El primer capítulo presenta la obtención, mediante cristalografía de rayos X, de la estructura del dominio C de P140. La estructura se resolvió en dos grupos espaciales cristalográficos diferentes: I) tetragonal I422, a 1.43 Å de resolución, con una molécula en la unidad asimétrica y II) monoclínico C2, a 1.92 Å, con ocho moléculas en la unidad asimétrica. El análisis estructural ha proporcionado dos resultados que cabe destacar aquí: I) El dominio C de P140 puede formar oligómeros (octámeros) compactos; II) Por otro lado, las grandes diferencias entre las diversas conformaciones halladas del dominio C, cuando a posteriori se pudo disponer de la estructura del ectodominio completo de P140, indican la gran plasticidad de este dominio y sugieren un papel importante de esa plasticidad en el funcionamiento del Nap. El segundo capítulo corresponde a la determinación de la estructura de P140 y del complejo P110-P140. P140 se resolvió a través de un procedimiento en el cual fue crítica la información proporcionada por crio-tomografía electrónica (crio-ET) del Nap y por diversos cristales tanto de P140 como de P1. En este trabajo también se pudieron modelar diversas conformaciones del Nap a través del “docking” de las estructuras de P140 y P110 en los correspondientes mapas de crio-ET y de crio-microscopía electrónica (crio-EM).

A polyphasic taxonomic study was conducted on three strains isolated from drinking water systems that had previously been deposited as Chryseobacterium species at the Spanish Type Culture Collection in order to complete their classification. Strains CECT 9293T, CECT 9390T and CECT 9393T were isolated from sites in Barcelona, Spain, in the framework of a project aimed at generating the first MALDI-TOF database specific for bacteria present in water for human consumption. Their partial 16S rRNA sequences showed that their closest relatives among the type strains of Chryseobacterium exhibited 98 % similarity or less, supporting their taxonomic novelty. At the same time, comparison between them revealed that strains CECT 9293T and CECT 9393T could perhaps be related at the species level as they shared 99.5 % similarity. However, whole genome sequencing was performed and the subsequent calculation of relatedness indices, average nucleotide identity and estimated DNA–DNA hybridization, ruled out that possibility and confirmed instead that each of the strains should be considered a separate species in the genus Chryseobacterium . Having clarified their status, we also performed phylogenomic analyses and searched for possible environmental or non-type material sequences that could be related to any of them at the species level. In parallel, the strains were characterized phenotypically and compared to their closest relatives to determine diagnostic traits to support their formal proposal. The proposed species are Chryseobacterium potabilaquae sp. nov. with the type strain CECT 9293T (=LMG 32084T), Chryseobacterium aquaeductus sp. nov. with the type strain CECT 9390T (=LMG 32085T) and Chryseobacterium fistulae sp. nov. with the type strain CECT 9393T (=LMG 32086T).

La tularemia es una enfermedad zoonótica del hemisferio norte causada por Francisella tularensis, una bacteria intracelular facultativa, que requiere una dosis infectiva muy baja y que puede causar una enfermedad potencialmente grave si no es tratada. Típicamente, las infecciones humanas y animales son causadas por cepas de la subespecie tularensis, que ocasiona brotes principalmente en América del Norte, y la holarctica, distribuida en todo el hemisferio norte, incluyendo Europa. Aunque no se conoce el reservorio natural, se ha visto que F. tularensis puede infectar una gran variedad de especies, destacando a pequeños roedores, lagormorfos y garrapatas como reservorios (y vectores) clave para esta bacteria e implicados en gran parte de los brotes reportados. Sin embargo, en Europa se ha descrito otro tipo de transmisión vectorial de la tularemia; la transmisión por mosquito, que implicaría a estos artrópodos pero también a cierto tipo de protozoos acuáticos como potenciales vectores y reservorios ambientales para F. t. holarctica. Este modo de transmisión, hasta la fecha, solo se ha documentado en regiones concretas del norte del continente europeo como Suecia o Finlandia, y no se ha podido demostrar su relevancia en otras regiones endémicas como España. Este trabajo de revisión ha consistido en hacer una recopilación de los estudios observacionales y experimentales más recientes de la literatura acerca de varios aspectos relacionados con el mantenimiento y la transmisión de F. t. holarctica en el entorno acuático, con el objetivo de poder conocer con más detalle el papel epidemiológico de los mosquitos y protozoos, así como la interacción entre ambos y el patógeno e intentar explicar el porqué de las diferencias geográficas entre diversos países en cuanto a este tipo de transmisión así como documentar las lagunas que aún siguen habiendo y proponer posibles estudios que ayuden a esclarecerlas.

Medical records of 101 blood culture-confirmed bacteremic foals were reviewed to determine whether foals with Actinobacillus sp. bacteremia are affected at an earlier age, have more severe signs of disease, and have a worse prognosis than do foals with bacteremia of other causes. Thirty percent (30/101) of bacteremic foals had Actinobacillus sp. cultured, and these were 2 times more likely to die (crude odds ratio [ORCR] 0.8, 4; P 5 .14), with a survival rate of 43% (13/30) compared to the overall survival rate of 55% (56/101). When compared to other bacteremic foals, foals with actinobacillosis were 7 times more likely to have been sick from birth (adjusted odds ratio [ORADJ] 2, 26; P 5 .003) and 6 times more likely to have diarrhea (ORADJ 1, 22; P 5 .009). By bivariate analysis, foals with Actinobacillus sp. bacteremia were 5 times more likely to have a sepsis score .11 (ORCR 1, 18; P 5 .007), 6 times more likely to be obtunded (ORCR 2, 20; P 5 .005), and 3 times more likely to have pneumonia (ORCR 1, 7; P 5 .03). Furthermore, Actinobacillus sp. bacteremic foals were 27 times more likely to have a segmented neutrophil count ,3.3 3 109 cells/L (ORADJ 4, 166; P , .0001) and were 4.5 times more likely to have a band neutrophil count .0.46 3 109 cells/L (ORADJ 1, 17; P 5 .02) when compared to foals that had bacteremia caused by either gram-negative enteric or gram-positive organisms. Sepsis score was #11 in 49% (29/59) of bacteremia foals aged ,13 days for which a discernible sepsis score was calculable. Results of this study should improve the diagnostic sensitivity of clinical examinations of neonatal foals, thereby facilitating treatment decisions

Bacterial plant pathogens are among the most devastating threats to agriculture. To date, there are no effective means to control bacterial plant diseases due to the restrictions in the use of antibiotics in agriculture. A novel strategy under study is the use of chemical compounds that inhibit the expression of key bacterial virulence determinants. The type III secretion system is essential for virulence of many Gram-negative bacteria because it injects into the plant host cells bacterial proteins that interfere with their immune system. Here, we describe the methodology to identify bacterial type III secretion inhibitors, including a series of protocols that combine in planta and in vitro experiments. We use Ralstonia solanacearum as a model because of the number of genetic tools available in this organism and because it causes bacterial wilt, one of the most threatening plant diseases worldwide. The procedures presented can be used to evaluate the effect of different chemical compounds on bacterial growth and virulence.

Bacteria present in the human body are innocuous, providing beneficial functions, some of which are necessary for correct body function. However, other bacteria are able to colonize, invade, and cause damage to different tissues, and these are categorised as pathogens. These pathogenic bacteria possess several factors that enable them to be more virulent and cause infection. Bacteria have a great capacity to adapt to different niches and environmental conditions (presence of antibiotics, iron depletion, etc.). Antibiotic pressure has favoured the emergence and spread of antibiotic-resistant bacteria worldwide. Several studies have reported the presence of a relationship (both positive and negative, and both direct and indirect) between antimicrobial resistance and virulence among bacterial pathogens. This review studies the relationship among the most important Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) taking into account two points of view: (i) the effect the acquisition of resistance has on virulence, and (ii) co-selection of resistance and virulence. The relationship between resistance and virulence among bacteria depends on the bacterial species, the specific mechanisms of resistance and virulence, the ecological niche, and the host.

CD38 is a multifunctional protein widely expressed in cells from the immune system and as a soluble form in biological fluids. CD38 expression is up-regulated by an array of inflammatory mediators, and it is frequently used as a cell activation marker. Studies in animal models indicate that CD38 functional expression confers protection against infection by several bacterial and parasitic pathogens. In addition, infectious complications are associated with anti-CD38 immunotherapy. Although CD38 displays receptor and enzymatic activities that contribute to the establishment of an effective immune response, recent work raises the possibility that CD38 might also enhance the immunosuppressive potential of regulatory leukocytes. This review integrates the current knowledge on the diversity of functions mediated by CD38 in the host defense to infection.

Ralstonia solanacearum is the causative agent of bacterial wilt disease on a wide range of plant species. Besides the numerous bacterial activities required for host invasion, those involved in the adaptation to the plant environment are key for the success of infection. R. solanacearum ability to cope with the oxidative burst produced by the plant is likely one of the activities required to grow parasitically. Among the multiple reactive oxygen species (ROS)-scavenging enzymes predicted in the R. solanacearum GMI1000 genome, a single monofunctional catalase (KatE) and two KatG bifunctional catalases were identified. In this work, we show that these catalase activities are active in bacterial protein extracts and demonstrate by gene disruption and mutant complementation that the monofunctional catalase activity is encoded by katE. Different strategies were used to evaluate the role of KatE in bacterial physiology and during the infection process that causes bacterial wilt. We show that the activity of the enzyme is maximal during exponential growth in vitro and this growth-phase regulation occurs at the transcriptional level. Our studies also demonstrate that katE expression is transcriptionally activated by HrpG, a central regulator of R. solanacearum induced upon contact with the plant cells. In addition, we reveal that even though both KatE and KatG catalase activities are induced upon hydrogen peroxide treatment, KatE has a major effect on bacterial survival under oxidative stress conditions and especially in the adaptive response of R. solanacearum to this oxidant. The katE mutant strain also exhibited differences in the structural characteristics of the biofilms developed on an abiotic surface in comparison to wild-type cells, but not in the overall amount of biofilm production. The role of catalase KatE during the interaction with its host plant tomato is also studied, revealing that disruption of this gene has no effect on R. solanacearum virulence or bacterial growth in leave tissues, which suggests a minor role for this catalase in bacterial fitness in planta. Our work provides the first characterization of the R. solanacearum catalases and identifies KatE as a bona fide monofunctional catalase with an important role in bacterial protection against oxidative stress., This work was supported by the Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT PICT 2014-2487 to EO and PICT 2014-2485 to MLT) and the Spanish Ministry of Economy and Competitiveness (AGL2016-78002-R and PID2019-108595RB-I00 to MV). We also acknowledge financial support from the “Severo Ochoa Program for Centers of Excellence in R&D” (SEV/2015/0533), and the CERCA Program from the Catalan Government (Generalitat de Catalunya). EO and MLT are staff members and AV is Fellow of the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET, Argentina).

Ressenya sobre la tecnologia més avançada dins del camp dels biosensors electroquímics i la seva aplicació per a la detecció de bacteris patògens encarregats de causar malalties infeccioses. Durant l’anàlisi del funcionament dels biosensors, s’han estudiat les diferents tècniques capdavanteres de detecció utilitzades actualment al camp de la biomedicina, les diferents rutes de síntesi utilitzades per a la fabricació de polímers conductors i les seves funcions dins dels biosensors. S'han analitzat les estratègies i metodologies aplicades al disseny de biosensors capaços de detectar diferents malalties infeccioses de forma selectiva. S’ha estudiat com la intervenció de polímers conductors per a la fabricació de sensors aporta nombrosos avantatges i millores que han estat analitzades durant la ressenya. D’igual manera, s’han interpretat els resultats obtinguts durant els diferents experiments analitzats i totes les variables relacionades. El treball realitzat s’ha redactat en format article i enviat com treball de revisió ("review") a la revista científica Journal of Materials Chemistry B (Factor d’impacte: 5.047) publicada per la Royal Society of Chemistry. Dins d’aquesta revista científica s’hi pot trobar tota mena d’informació sobre propietats, aplicacions i síntesis de materials presents a l’àmbit de la biologia i la medicina. Amb aquest projecte s’ha volgut redactar una ressenya amb un contingut innovador que serveixi com a referència de consulta dins del sector biomèdic en l’aplicació de biosensors modificats amb polímers conductors. Reseña sobre la tecnología más avanzada dentro del campo de los biosensores electroquímicos y su aplicación para la detección de bacterias patogénicas encargadas de causar enfermedades infecciosas. Durante el análisis del funcionamiento de los biosensores, se han estudiado las diferentes técnicas de detección utilizadas actualmente en el campo de la biomedicina, las diferentes rutas de síntesis utilizadas para la fabricación de polímeros conductores y sus funciones dentro de los biosensores. Se han analizado las estrategias y metodologías aplicadas al diseño de biosensores capaces de detectar diferentes enfermedades infecciosas de forma selectiva. Se ha estudiado como la intervención de polímeros conductores para la fabricación de sensores aporta numerosas ventajas y mejoras analizadas durante la reseña. Del mismo modo, se han interpretado los resultados obtenidos durante los diferentes experimentos analizados y todas las variables relacionadas. El trabajo realizado se ha redactado en formato artículo y enviado como trabajo de revisión (“review”) a la revista científica Journal of Materials Chemistry B (Factor de impacto: 5.047) publicada por la Royal Society of Chemistry. Dentro de esta revista científica se puede encontrar todo tipo de información sobre propiedades, aplicaciones y síntesis de materiales presentes en el ámbito de la biología y la medicina. Con este proyecto se ha querido redactar una reseña con un contenido innovador que sirva como referencia de consulta dentro del sector biomédico en la aplicación de biosensores modificados con polímeros conductores. Review of the most advanced technology in the field of electrochemical biosensors and its application for the detection of pathogenic bacteria responsible for causing infectious diseases. During the analysis of the functioning of biosensors, the different detection techniques currently used in the field of biomedicine have been studied, the different synthesis pathways used for the manufacture of conductive polymers and their functions within the biosensors. The strategies and methodologies applied to the design of biosensors capable of detecting different infectious diseases in a selective way have been analyzed. It has been studied as the intervention of conductive polymers for the manufacture of sensors brings numerous advantages and improvements analyzed during the review. Similarly, the results obtained during the different experiments analyzed and all the related variables have been interpreted. The work has been written in article format and sent as a review paper to the scientific Journal of Materials Chemistry B (Impact Factor: 5,047) published by the Royal Society of Chemistry. Within this scientific journal you can find all kinds of information on properties, applications and synthesis of materials present in the field of biology and medicine. The aim of this project was to produce a review with an innovative content that serves as a reference for consultation within the biomedical sector in the application of biosensors modified with conductive polymers.

Pathogenic bacteria and metastasic tumor cells try to spread to new parts of the human body and survive to the immune response. Since both need to overcome the same obstacles, the aim of the study is to find common characteristics between both processes, starting from the so called moonlighting proteins. Moonlighting proteins are multifunctional proteins and in bacteria are usually virulence factors. Therefore, functions associated with them are related to the infection and survival of the pathogen. It is wanted to identify the functions that are mostly shared between virulence moonlighting proteins and metastasic proteins. In order to perform this comparison, metastasic proteins were divided according to the processes in which they were involved: glucose metabolism, remodeling/regeneration of tissues, interaction with plasminogen and interaction with extracellular matrix. Subsequently, their GO terms were compared to those of the moonlighting proteins, differentiating which of them were virulence factors. The results obtained showed that GO terms related to the binding to extracelullar matrix, such as collagen, fibronectin or laminin, are widely represented among virulence moonlighting proteins and metastasic proteins. Further investigation is needed to prove if the binding sites used by both types of proteins are the same, if they share binding sequences or to discover new blocker drugs specific of these binding sites. Tanto las bacterias patógenas como las células tumorales metastásicas luchan por diseminarse por el cuerpo humano y sobrevivir a la respuesta del Sistema Inmunitario. Al tener que superar los mismos obstáculos, el objetivo del estudio es encontrar los puntos comunes entre ambos procesos, partiendo de las proteínas moonlighting. Las proteínas moonlighting son proteínas multifuncionales que en bacterias suelen actuar como factores de virulencia, por lo que las funciones asociadas a ellas están relacionadas con la infección y la supervivencia del patógeno. Se quiere comprobar qué funciones están compartidas en mayor medida entre proteínas moonlighting de virulencia y proteínas relacionadas con la metástasis. Para realizar la comparación, las proteínas metastásicas se dividieron por procesos en las que estaban involucradas: metabolismo de glucosa, remodelación/regeneración de tejidos, interacción con plasminógeno e interacción con la matriz extracelular. Posteriormente, se compararon sus códigos GO con los de las proteínas moonlighting, diferenciando las que son factores de virulencia de las que no. Los resultados obtenidos indican que los códigos GO relacionados con la unión a proteínas de la matriz extracelular, como el colágeno, fibronectina o laminina, están ampliamente representados entre las proteínas moonlighting de virulencia y proteínas metastásicas. Son necesarios más estudios para comprobar si los sitios de unión que utilizan ambos tipos de proteínas son los mismos, si comparten secuencias de unión, descubrir nuevos fármacos bloqueadores de sitios de unión etc. Tant els bacteris patògens com les cèl·lules tumorals metastàsiques lluiten per disseminar-se pel cos humà i sobreviure a la resposta del Sistema Immunitari. En haver de superar els mateixos obstacles, l'objectiu de l'estudi és trobar els punts comuns entre tots dos processos, partint de les proteïnes moonlighting. Les proteïnes moonlighting són proteïnes multifuncionals que en bacteris solen actuar com a factors de virulència, per la qual cosa les funcions associades a elles estan relacionades amb la infecció i la supervivència del patogen. Es vol comprovar quines funcions estan compartides en major mesura entre proteïnes moonlighting de virulència i proteïnes relacionades amb la metàstasi. Per a realitzar la comparació, les proteïnes metastàsiques es van dividir per processos en les quals estaven involucrades: metabolisme de glucosa, remodelació/regeneració de teixits, interacció amb plasminogen i interacció amb la matriu extracelul·lar. Posteriorment, es van comparar els seus codis GO amb els de les proteïnes moonlighting, diferenciant les que són factors de virulència de les quals no. Els resultats obtinguts indiquen que els codis GO relacionats amb la unió a proteïnes de la matriu extracelul·lar, com el col·lagen, fibronectina o laminina, estan àmpliament representats entre les proteïnes moonlighting de virulència i proteïnes metastásicas. Són necessaris més estudis per a comprovar si els llocs d'unió que utilitzen tots dos tipus de proteïnes són els mateixos, si comparteixen seqüències d'unió, descobrir nous fàrmacs blocadors de llocs d'unió etc.

Intracellular invasion is an advantageous mechanism used by pathogens to evade host defense and antimicrobial therapy. In patients, the intracellular microbial lifestyle can lead to infection persistence and recurrence, thus worsening outcomes. Lung infections caused by Pseudomonas aeruginosa, especially in cystic fibrosis (CF) patients, are often aggravated by intracellular invasion and persistence of the pathogen. Proliferation of the infectious species relies on a continuous deoxyribonucleotide (dNTP) supply, for which the ribonucleotide reductase enzyme (RNR) is the unique provider. The large genome plasticity of P. aeruginosa and its ability to rapidly adapt to different environments are challenges for studying the pathophysiology associated with this type of infection. Using different reference strains and clinical isolates of P. aeruginosa independently combined with alveolar (A549) and bronchial (16HBE14o- and CF-CFBE41o-) epithelial cells, we analyzed host–pathogen interactions and intracellular bacterial persistence with the aim of determining a cell type-directed infection promoted by the P. aeruginosa strains. The oscillations in cellular toxicity and oxygen consumption promoted by the intracellular persistence of the strains were also analyzed among the different infectious lung models. Significantly, we identified class II RNR as the enzyme that supplies dNTPs to intracellular P. aeruginosa. This discovery could contribute to the development of RNR-targeted strategies against the chronicity occurring in this type of lung infection. Overall our study demonstrates that the choice of bacterial strain is critical to properly study the type of infectious process with relevant translational outcomes.

Ralstonia solanacearum is a bacterial plant pathogen causing important economic losses worldwide. In addition to the polar flagella responsible for swimming motility, this pathogen produces type IV pili (TFP) that govern twitching motility, a flagellum-independent movement on solid surfaces. The implication of chemotaxis in plant colonization, through the control flagellar rotation by the proteins CheW and CheA, has been previously reported in R. solanacearum. In this work, we have identified in this bacterium homologues of the Pseudomonas aeruginosa pilI and chpA genes, suggested to play roles in TFP-associated motility analogous to those played by the cheW and cheA genes, respectively. We demonstrate that R. solanacearum strains with a deletion of the pilI or the chpA coding region show normal swimming and chemotaxis but altered biofilm formation and reduced twitching motility, transformation efficiency, and root attachment. Furthermore, these mutants displayed wild-type growth in planta and impaired virulence on tomato plants after soil-drench inoculations but not when directly applied to the xylem. Comparison with deletion mutants for pilA and fliC—encoding the major pilin and flagellin subunits, respectively—showed that both twitching and swimming are required for plant colonization and full virulence. This work proves for the first time the functionality of a pilus-mediated pathway encoded by pil-chp genes in R. solanacearum, demonstrating that pilI and chpA genes are bona fide motility regulators controlling twitching motility and its three related phenotypes: virulence, natural transformation, and biofilm formation., This study was funded by grants BIO2016-77011-R and AGL2016-78002-R (Spanish Ministry of Economy and Competitiveness). We acknowledge financial support from the Severo Ochoa Program for Centers of Excellence in R&D (SEV‐2015‐0533) and the CERCA Program from the Catalan Government (Generalitat de Catalunya). J.A. is a Serra Húnter Fellow (Generalitat de Catalunya). The project that gave rise to these results received the support of a fellowship (code is LCF/BQ/IN17/11620004) from la Caixa Foundation (identifier [ID] 100010434). This project has received funding from the European Union's Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement no. 713673.

Vibrio vulnificus (Vv) is a multi-host pathogenic species currently subdivided into three biotypes (Bts). The three Bts are human-pathogens, but only Bt2 is also a fish-pathogen, an ability that is conferred by a transferable virulence-plasmid (pVvbt2). Here we present a phylogenomic analysis from the core genome of 80 Vv strains belonging to the three Bts recovered from a wide range of geographical and ecological sources. We have identified five well-supported phylogenetic groups or lineages (L). LI comprises a mixture of clinical and environmental Bt1 strains, most of them involved in human clinical cases related to raw seafood ingestion. LII is linked to the aquaculture industry and includes Bt3 strains exclusively, mostly related to wound infections or secondary septicemia after farmed-fish handling. LIII is formed by a mixture of Bt1 and Bt2 strains from various sources, including diseased fish, and is also related to the aquaculture industry. Lastly, LIV and LV include a few strains of Bt1 associated with specific geographical areas. The phylogenetic trees for ChrI and II are not congruent to one another, which suggests that inter- and/or intra-chromosomal rearrangements have been produced along Vv evolution. Further, the phylogenetic trees for each chromosome and the virulence plasmid were also not congruent, which also suggests that pVvbt2 has been acquired independently by different clones, probably in fish farms. From all these clones, the one with zoonotic capabilities (Bt2-Serovar E) has successfully spread worldwide. From these results, we propose a new updated classification of the species based on phylogenetic lineages rather than on Bts, as well as the inclusion of all Bt2 strains in a pathovar with the particular ability to cause fish vibriosis, for which we suggest the name 'piscis'.

The coexistence between species that occurs in some infections remains hard to achieve in vitro since bacterial fitness differences eventually lead to a single organism dominating the mixed culture. Pseudomonas aeruginosa and Staphylococcus aureus are major pathogens found growing together in biofilms in disease-affected lungs or wounds. Herein, we tested and analyzed different culture media, additives and environmental conditions to support P. aeruginosa and S. aureus coexistence in vitro. We have unraveled the potential of DMEM to support the growth of these two organisms in mature cocultured biofilms (three days old) in an environment that dampens the pH rise. Our conditions use equal initial inoculation ratios of both strains and allow the stable formation of separate S. aureus microcolonies that grow embedded in a P. aeruginosa biofilm, as well as S. aureus biofilm overgrowth when bovine serum albumin is added to the system. Remarkably, we also found that S. aureus survival is strictly dependent on a well-characterized phenomenon of oxygen stratification present in the coculture biofilm. An analysis of differential tolerance to gentamicin and ciprofloxacin treatment, depending on whether P. aeruginosa and S. aureus were growing in mono- or coculture biofilms, was used to validate our in vitro coculture conditions.

Migratory birds may have a vital role in the spread of antimicrobial resistance across habitats and regions, but empirical data remain scarce. We investigated differences in the gut microbiome composition and the abundance of antibiotic resistance genes (ARGs) in faeces from four migratory waterbirds wintering in South-West Spain that differ in their habitat use. The white stork Ciconia ciconia and lesser black-backed gull Larus fuscus are omnivorous and opportunistic birds that use highly anthropogenic habitats such as landfills and urban areas. The greylag goose Anser anser and common crane Grus grus are herbivores and use more natural habitats. Fresh faeces from 15 individuals of each species were analysed to assess the composition of bacterial communities using 16S rRNA amplicon-targeted sequencing, and to quantify the abundance of the Class I integron integrase gene (intI1) as well as genes encoding resistance to sulfonamides (sul1), beta-lactams (blaTEM, blaKPC and blaNDM), tetracyclines (tetW), fluoroquinolones (qnrS), and colistin (mcr-1) using qPCR. Bacterial communities in gull faeces were the richest and most diverse. Beta diversity analysis showed segregation in faecal communities between bird species, but those from storks and gulls were the most similar, these being the species that regularly feed in landfills. Potential bacterial pathogens identified in faeces differed significantly between bird species, with higher relative abundance in gulls. Faeces from birds that feed in landfills (stork and gull) contained a significantly higher abundance of ARGs (sul1, blaTEM, and tetW). Genes conferring resistance to last resort antibiotics such as carbapenems (blaKPC) and colistin (mcr-1) were only observed in faeces from gulls. These results show that these bird species are reservoirs of antimicrobial resistant bacteria and suggest that waterbirds may disseminate antibiotic resistance across environments (e.g., from landfills to ricefields or water supplies), and thus constitute a risk for their further spread to wildlife and humans.

Multidrug-resistant Escherichia coli ST131 fimH30 responsible for extra-intestinal pathogenic (ExPEC) infections is globally distributed. However, the occurrence of a subclone fimH27 of ST131 harboring both ExPEC and enteroaggregative E. coli (EAEC) related genes and belonging to commonly reported O25:H4 and other serotypes causing bacteremia in African children remain unknown. We characterized 325 E. coli isolates causing bacteremia in Mozambican children between 2001 and 2014 by conventional multiplex polymerase chain reaction and whole genome sequencing. Incidence rate of EAEC bacteremia was calculated among cases from the demographic surveillance study area. Approximately 17.5% (57/325) of isolates were EAEC, yielding an incidence rate of 45.3 episodes/105 children-years-at-risk among infants; and 44 of isolates were sequenced. 72.7% (32/44) of sequenced strains contained simultaneously genes associated with ExPEC (iutA, fyuA and traT); 88.6% (39/44) harbored the aggregative adherence fimbriae type V variant (AAF/V). Sequence type ST-131 accounted for 84.1% (37/44), predominantly belonging to serotype O25:H4 (59% of the 37); 95.6% (35/44) harbored fimH27. Approximately 15% (6/41) of the children died, and five of the six yielded ST131 strains (83.3%) mostly (60%; 3/5) due to serotypes other than O25:H4. We report the emergence of a new subclone of ST-131 E. coli strains belonging to O25:H4 and other serotypes harboring both ExPEC and EAEC virulence genes, including agg5A, associated with poor outcome in bacteremic Mozambican children, suggesting the need for prompt recognition for appropriate management., Author summary Escherichia coli ST131 has emerged as a globally disseminated multi-drug resistant clone associated with extra-intestinal infections acquired in the community or hospital. In Manhiça district, E. coli is among the top five leading bloodstream pathogens in children. We characterized E. coli strains causing bacteremia in young children in a rural hospital of Mozambique, providing novel information on the occurrence of a new subclone of ST131 harboring both ExPEC and EAEC related genes and belonging to commonly reported O25:H4 and other serotypes. These data suggest the need for further understanding of pathogenesis and clinical impact of this new entity to inform prompt recognition and appropriate treatment.

Bacterial wilt caused by the bacterial pathogen Ralstonia solanacearum is one of the most devastating crop diseases worldwide. The molecular mechanisms controlling the early stage of R. solanacearum colonization in the root remain unknown. Aiming to better understand the mechanism of the establishment of R. solanacearum infection in root, we established four stages in the early interaction of the pathogen with Arabidopsis roots and determined the transcriptional profiles of these stages of infection. A total 2,698 genes were identified as differentially expressed genes during the initial 96 h after infection, with the majority of changes in gene expression occurring after pathogen-triggered root-hair development observed. Further analysis of differentially expressed genes indicated sequential activation of multiple hormone signaling cascades, including abscisic acid (ABA), auxin, jasmonic acid, and ethylene. Simultaneous impairment of ABA receptor genes promoted plant wilting symptoms after R. solanacearum infection but did not affect primary root growth inhibition or root-hair and lateral root formation caused by R. solanacearum. This indicated that ABA signaling positively regulates root defense to R. solanacearum. Moreover, transcriptional changes of genes involved in primary root, lateral root, and root-hair formation exhibited high temporal dynamics upon infection. Taken together, our results suggest that successful infection of R. solanacearum on roots is a highly programmed process involving in hormone crosstalk., This study was supported by the National Natural Science Foundation of China (No. 31601703), the Start-up Funds of Northwest A&F University (Z111021601), the Fundamental Research Fund for the Central Universities of China (Z109021706) and External Science and Technology Cooperation Program of Ningxia Academy of Agriculture and Forestry Sciences (DW-X-2018012). We also acknowledge financial support from the Spanish Ministry of Economy and Competitiveness (grants AGL2016-78002-R and SEV-2015-0533) and from the CERCA project of the Catalan Government (Generalitat de Catalunya).

The prevalence of a new hypervirulent and hypermucoviscous K. pneumoniae phenotype (Hmv) is increasing worldwide, mainly linked to serotypes K1 and K2. Since capsular thickness can directly affect the capability to form biofilms, we aimed to evaluate the association between the Hmv phenotype with adhesion and biofilm formation in a collection of clinical K. pneumoniae isolates. We selected 38 Hmv clinical isolates [15 serotype K1; 9 serotype K2; 3 non-K1/K2 (rmpA(+)); 11 non-K1/K2 (rmpA(-))] and 7 non-Hmv clinical isolates. The Hmv phenotype was assessed through the mucoviscosity test. Serum resistance was determined by bacterial viability tests in pooled human serum. Adhesion was evaluated with the Biofilm Ring Test (R), and biofilm formation was identified by crystal violet staining (Solid-Liquid, SLI-biofilm) or visual examination (Air-Liquid, ALI-biofilm). This study linked for the first time the formation of robust ALI-biofilm plugs by K. pneumoniae to the capsular serotype K1, a group of hypervirulent strains which are generally highly susceptible to the antimicrobial agents. Among all the studied isolates, the capsular serotype K1 presented lower initial adhesion despite having the adhesins mrkD and fimH but higher ALI-biofilm formation than isolates with other capsular serotypes (K2 or non-K1/K2). This structure might confer increased resistance to a group of hypervirulent K. pneumoniae serotype K1.

Ralstonia solanacearum is a devastating bacterial vascular pathogen causing bacterial wilt. In the field, resistance against this disease is quantitative and only available for breeders in tomato and eggplant. To understand the basis of resistance in tomato, we have investigated the spatio-temporal bacterial colonization dynamics using non-invasive live monitoring techniques coupled to grafting of susceptible and resistant varieties. We revealed four different restrictions to the bacterium in resistant tomato: root colonization, vertical movement from roots to shoots, circular vascular bundle invasion and radial apoplastic spread in the cortex. We also show that the radial invasion of cortical extracellular spaces occurs mostly at late disease stages but is observed throughout plant infection. This work shows that resistance is expressed both in root and shoot tissues and highlights the importance of structural constraints to bacterial spread as a resistance mechanism. It also shows that R. solanacearum is not only a vascular pathogen but spreads "out of the xylem", occupying the plant apoplast niche. Our work will help elucidate the complex genetic determinants of resistance, setting the foundations to decipher the molecular mechanisms that limit pathogen colonization, which may provide new potential precision tools to fight bacterial wilt in the field.

[Background]: Potato, the third most important crop worldwide, plays a critical role in human food security. Brown rot, one of the most destructive potato diseases caused by Ralstonia solanacearum, results in huge economic losses every year. A quick, stable, low cost and high throughout method is required to meet the demands of identification of germplasm resistance to bacterial wilt in potato breeding programs., [Results]: Here we present a novel R. solanacearum hydroponic infection assay on potato plants grown in vitro. Through testing wilt symptom appearance and bacterial colonization in aerial part of plants, we found that the optimum conditions for in vitro potato infection were using an OD600 0.01 bacterial solution suspended with tap water for infection, broken potato roots and an open container. Infection using R. solanacearum strains with differential degree of aggressivity demonstrated that this infection system is equally efficient as soil-drench inoculation for assessment of R. solanacearum virulence on potato. A small-scale assessment of 32 potato germplasms identified three varieties highly resistant to the pathogen, which indicates this infection system is a useful method for high-throughout screening of potato germplasm for resistance. Furthermore, we demonstrate the utility of a strain carrying luminescence to easily quantify bacterial colonization and the detection of latent infections in hydroponic conditions, which can be efficiently used in potato breeding programs., [Conclusions]: We have established a quick and efficient in vitro potato infection system, which may facilitate breeding for new potato cultivars with high resistance to R. solanacearum., This study was supported by the National Natural Science Foundation of China (No. 31601703), the Start-up Funds of Northwest A&F University (Z111021601), the Fundamental Research Fund for the Central Universities of China (Z109021706) and External Science and Technology Cooperation Program of Ningxia Academy of Agriculture and Forestry Sciences (DW-X-2018012). N.S.C. and M.V. work was funded by projects AGL2016-78002-R. (Spanish Ministry of Economy and Competitiveness) and financial support from the “Severo Ochoa Programme for Centres of Excellence in R&D” (SEV‐2015‐0533) and the CERCA Programme from the Catalan Government (Generalitat de Catalunya).

Bacterial resistance to antibiotics is a global public health concern. New treatments are needed to combat resistant strains, among which phage therapy is a promising option. Probably the main advantages of phage therapy are its high specificity as well as rapid viral adaptability, which in principle allows using phage evolution to overcome resistance. Here, we have performed serial coevolution passages between Escherichia coli and its phage T7 to investigate the ability of coevolved phages to reduce the emergence of resistances. We find that the initial bacterial population is less likely to undergo resistance when challenged with experimentally coevolved phages than when challenged with the wild-type phage. Hence, our findings suggest that coevolved phage preparations could be used to increase the efficacy of phage therapy.

Wastewater is an important resource in water-scarce regions of the world, and its use in agriculture requires the guarantee of acceptable public health risks. The use of fecal indicator bacteria to evaluate safety does not represent viruses, the main potential health hazards. Viral pathogens could complement the use of fecal indicator bacteria in the evaluation of water quality. In this study, we characterized the concentration and removal of human adenovirus (HAdV) and norovirus genogroup II (NoV GII), highly abundant and important viral pathogens found in wastewater, in two wastewater treatment plants (WWTPs) that use different tertiary treatments (constructed wetland vs conventional UV, chlorination and Actiflo® treatments) for a year in Catalonia. The main objective of this study was to develop a Quantitative Microbial Risk Assessment for viral gastroenteritis caused by norovirus GII and adenovirus, associated with the ingestion of lettuce irrigated with tertiary effluents from these WWTPs. The results show that the disease burden of NoV GII and HAdV for the consumption of lettuce irrigated with tertiary effluent from either WWTP was higher than the WHO recommendation of 10−6 DALYs for both viruses. The WWTP with constructed wetland showed a higher viral reduction on average (3.9 and 2.8 logs for NoV GII and HAdV, respectively) than conventional treatment (1.9 and 2.5 logs) but a higher variability than the conventional WWTP. Sensitivity analysis demonstrated that the input parameters used to estimate the viral reduction by treatment and viral concentrations accounted for much of the model output variability. The estimated reductions required to reach the WHO recommended levels in tertiary effluent are influenced by the characteristics of the treatments developed in the WWTPs, and additional average reductions are necessary (in WWTP with a constructed wetland: A total of 6.7 and 5.1 logs for NoV GII and HAdV, respectively; and in the more conventional treatment: 7 and 5.6 logs). This recommendation would be achieved with an average quantification of 0.5 genome copies per 100 mL in reclaimed water for both viruses. The results suggest that the analyzed reclaimed water would require additional treatments to achieve acceptable risk in the irrigation of vegetables with reclaimed water.

Escherichia coli (E. coli) is a common microorganism of the human intestinal microbiota. A new pathotype called AIEC (Adherent Invasive Escherichia coli) associated with Crohn's disease (CD) has been described. It has the ability to adhere to and invade intestinal epithelial cells, as well as to survive and replicate inside macrophages. Most studies have been done using a murine cell line (J774), but recent studies demonstrate its ability to replicate in human cell lines such as THP1. No study comparing the bacterial replication in the two types of cell lines with a broad set of AIEC strains exist. Additionally, there is no sufficient knowledge of the survival and replication abilities in macrophages of non-adherent (non-AIEC) strains that inhabit in the intestine. For these reasons, we wanted to study and compare the survival and replication of E. coli strains, including AIEC and non-AIEC, in human and murine macrophages. A total of 50 strains, 21 AIEC and 29 non-AIEC (isolated from patients with CD and controls, the same from which the AIEC strains have been isolated) have been tested. An AIEC reference LF82 and commensal laboratory strain K12 (non-AIEC) have been used as control strains. The murine macrophages J774 and the human monocyte THP1 cell lines have been tested. The survival and replication index (I_REPL) is measured based on the bacterial infection of these cell cultures using gentamicin to eliminate the extracellular bacteria. It is calculated as the percentage of intracellular bacteria after 24h of the infection with respect to the internalized ones (1h post-infection). To analyze the replication capacity in J774 and THP1 according to the pathotype, a t-test has been performed. To compare frequency data, Pearson's χ2 has been used, and the possible relationship between cell lines has been determined by Pearson or Spearman correlation study. In this study, it has been possible to verify that AIEC strains presented high replication capacity in J774 macrophages (with an average of I_REPL = 1146%), but it replicated less in THP1 (mean of I_REPL = 89%). In contrast, non-AIEC strains did not show large differences in replication between both cell lines (mean of I_REPL = 116% in THP1 and mean of I_REPL = 281% in J774). Finally, it has been possible to establish a possible categorization threshold (I_REPL = 500%) that allows the classification of E. coli strains according to pathotype. In conclusion, THP1 is not a good option for conducting these studies with E. coli and, therefore, the difference between cell lines determines that the ability of survival and replication of these bacteria is not independent of the host but depends on the infected cell

The definition of species boundaries constitutes an important challenge in biodiversity studies. In this work we applied the Generalized Mixed Yule Coalescent (GMYC) method, which determines a divergence threshold to delimit species in a phylogenetic tree. Based on the tree branching pattern, the analysis fixes the transition threshold between speciation and the coalescent process associated with the intra-species diversification. This approach has been widely used to delineate eukaryote species and establish their diversification process from sequence data. Nevertheless, there are few examples in which this analysis has been applied to a bacterial population. Although the GMYC method was originally designed to assume a constant (Yule) model of diversification at between-species level, it was later evaluated simulating other conditions. Our aim was therefore to determine the species delineation in Aeromonas using the GMYC method and asses which model best explains the speciation process in this bacterial genus. The application of the GMYC method allowed us to clearly delineate the Aeromonas species boundaries, even in the controversial groups, such as the A. veronii or A. media species complexes.

Carbapenem-resistant Acinetobacter baumannii is the top-ranked pathogen in the World Health Organization priority list of antibiotic-resistant bacteria. It emerged as a global pathogen due to the successful expansion of a few epidemic lineages, or international clones (ICs), producing acquired class D carbapenemases (OXA-type). During the past decade, however, reports regarding IC-I isolates in Latin America are scarce and are non-existent for IC-II and IC-III isolates. This study evaluates the molecular mechanisms of carbapenem resistance and the epidemiology of 80 non-duplicate clinical samples of A. baumannii collected from February 2014 through April 2016 at two tertiary care hospitals in Lima. Almost all isolates were carbapenem-resistant (97.5%), and susceptibility only remained high for colistin (95%). Pulsed-field gel electrophoresis showed two main clusters spread between both hospitals: cluster D containing 51 isolates (63.8%) associated with sequence type 2 (ST2) and carrying OXA-72, and cluster F containing 13 isolates (16.3%) associated with ST79 and also carrying OXA-72. ST2 and ST79 were endemic in at least one of the hospitals. ST1 and ST3 OXA-23-producing isolates were also identified. They accounted for sporadic hospital isolates. Interestingly, two isolates carried the novel OXA-253 variant of OXA-143 together with an upstream novel insertion sequence (ISAba47). While the predominant A. baumannii lineages in Latin America are linked to ST79, ST25, ST15, and ST1 producing OXA-23 enzymes, we report the emergence of highly resistant ST2 (IC-II) isolates in Peru producing OXA-72 and the first identification of ST3 isolates (IC-III) in Latin America, both considered a serious threat to public health worldwide. This study was supported by Cienciactiva of CONCYTEC, contract no. 164-2016-FONDECYT; Planes Nacionales de I+D+i 2008-2011/2013-2016, Instituto de Salud Carlos III, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Economía y Competitividad, Spanish Network for Research in Infectious Diseases (REIPI RD12/0015/0013 and REIPI RD16/0016/ 0010); the 2017 call for Strategic Action on Health (PI17/01932), co-financed by European Development Regional Fund “A way to achieve Europe” and operative program Intelligent Growth 2014-2020; and grant 2014 SGR 0653 from the Departament d’Universitats, Recerca i Societat de la Informació, of the Generalitat de Catalunya. I.R. was supported by the Department of Health, Generalitat de Catalunya, grant SLT002/16/00349. Part of these data have been presented as a poster communication at the 18th International Congress on Infectious Diseases, 3–4 March, 2018, Buenos Aires, Argentina, and at the XXVIII-European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Madrid (Spain), 21–24 April, 2018 Revisión por pares

Campylobacter jejuni is the causal agent of the food-borne infection with the highest incidence in Europe. Both poultry and wild birds are a major reservoir. To gain insight into the population structure, virulence potential, and antimicrobial resistance (AMR), a collection of 150 isolates from three different ecological niches (broilers, wild birds, and human patients) was studied. Despite the high genetic diversity found, the population structure defined two distinct clusters, one formed mostly by broiler and human isolates and another one by most wild bird isolates. The ST-21 complex exhibits highest prevalence (in humans and broilers), followed by ST-1275 complex (only in wild birds). The ST-48, -45, and -354 complexes were found in all three niches, but represent only 22 out of 150 studied strains. A higher occurrence of AMR and multidrug resistance was detected among broiler and human isolates. Moreover, significant differences were found in the distribution of certain putative virulence genes. Remarkably, many wild bird strains were negative for either cdtA, cdtB, or cdtC from the canonical strain 81-176, whereas all broiler and human strains were positive. These data suggest that the different variants of the cdt genes might be relevant for the efficient colonization of certain hosts by C. jejuni. Our study contributes to the understanding of the role of the diverse Campylobacter reservoirs in the transmission of campylobacteriosis to humans info:eu-repo/semantics/publishedVersion

Carbapenem-resistant Acinetobacter baumannii has recently been defined by the World Health Organization as a critical pathogen. The aim of this study was to compare clonal diversity and carbapenemase-encoding genes of A. baumannii isolates collected from colonized or infected patients and hospital environment in two intensive care units (ICUs) in Morocco. The patient and environmental sampling was carried out in the medical and surgical ICUs of Mohammed V Military teaching hospital from March to August 2015. All A. baumannii isolates recovered from clinical and environmental samples, were identified using routine microbiological techniques and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Antimicrobial susceptibility testing was performed using disc diffusion method. The carbapenemase-encoding genes were screened for by PCR. Clonal relatedness was analyzed by digestion of the DNA with low frequency restriction enzymes and pulsed field gel electrophoresis (PFGE) and the multi locus sequence typing (MLST) was performed on two selected isolates from two major pulsotypes. A total of 83 multidrug-resistant A. baumannii isolates were collected: 47 clinical isolates and 36 environmental isolates. All isolates were positive for the bla OXA51-like and bla OXA23-like genes. The coexistence of bla NDM-1 /bla OXA-23-like and bla OXA 24-like /bla OXA-23-like were detected in 27 (32.5%) and 2 (2.4%) of A. baumannii isolates, respectively. The environmental samples and the fecally-colonized patients were significantly identified (p

MagicBullet Working Group WP4., [Objectives] To investigate the molecular epidemiology, antimicrobial susceptibility and carbapenem resistance determinants of Acinetobacter baumannii isolates from respiratory tract samples of patients diagnosed with ventilator-associated pneumonia (VAP) who were enrolled in the MagicBullet clinical trial., [Methods] A. baumannii isolates were prospectively cultured from respiratory tract samples from 65 patients from 15 hospitals in Greece, Italy and Spain. Susceptibility testing was performed by broth microdilution. Carbapenem resistance determinants were identified by PCR and sequencing. Molecular epidemiology was investigated using rep-PCR (DiversiLab) and international clones (IC) were identified using our in-house database., [Results] Of 65 isolates, all but two isolates (97%) were resistant to imipenem and these were always associated with an acquired carbapenemase, OXA-23 (80%), OXA-40 (4.6%), OXA-58 (1.5%) or OXA-23/58 (1.5%). Resistance to colistin was 47.7%. Twenty-two isolates were XDR, and 20 isolates were pandrug-resistant (PDR). The majority of isolates clustered with IC2 (n = 54) with one major subtype comprising isolates from 12 hospitals in the three countries, which included 19 XDR and 16 PDR isolates., [Conclusions] Carbapenem resistance rates were very high in A. baumannii recovered from patients with VAP. Almost half of the isolates were colistin resistant, and 42 (64.6%) isolates were XDR or PDR. Rep-PCR confirmed IC2 is the predominant clonal lineage in Europe and suggests the presence of an epidemic XDR/PDR A. baumannii clone that has spread in Greece, Italy and Spain. These data highlight the difficulty in empirical treatment of patients with A. baumannii VAP in centres with a high prevalence of carbapenem-resistant A. baumannii., This work was supported by the MagicBullet study. MagicBullet is a project funded by the European Union Directorate-General for Research and Innovation through the Seventh Framework Program for Research and Development (grant agreement 278232) and has been running since 1 January 2012 (duration, 48 months). Paul G. Higgins was supported by grant FOR2251 from the German Research Council (DFG) (www.acinetobacter.de).

Vibrio vulnificus biotype 2-serovar E is a zoonotic clonal complex that can cause death by sepsis in humans and fish. Unlike other biotypes, Bt2 produces a unique type of MARTXVv (Multifunctional-Autoprocessive-Repeats-in-Toxin; RtxA13), which is encoded by a gene duplicated in the pVvBt2 plasmid and chromosome II. In this work, we analyzed the activity of this toxin and its role in human sepsis by performing in vitro, ex vivo, and in vivo assays. First, we demonstrated that the ACD domain, present exclusively in this toxin variant, effectively has an actin-cross-linking activity. Second, we determined that the whole toxin caused death of human endotheliocytes and monocytes by lysis and apoptosis, respectively. Finally, we tested the hypothesis that RtxA13 contributes to human death caused by this zoonotic serovar by triggering an early cytokine storm in blood. To this end, we used a Bt2-SerE strain (R99) together with its rtxA13 deficient mutant, and a Bt1 strain (YJ016) producing RtxA11 (the most studied MARTXVv) together with its rtxA11 deficient mutant, as controls. Our results showed that RtxA13 was essential for virulence, as R99ΔΔrtxA13 was completely avirulent in our murine model of infection, and that R99, but not strain YJ016, induced an early, strong and dysregulated immune response involving the up-regulation of a high number of genes. This dysregulated immune response was directly linked to RtxA13. Based on these results and those obtained ex vivo (human blood), we propose a model of infection for the zoonotic serovar of V. vulnificus, in which RtxA13 would act as a sepsis-inducing toxin.

The chemical structure and genomics of the lipopolysaccharide (LPS) core oligosaccharide of pathogenic Edwardsiella tarda strain EIB 202 were studied for the first time. The complete gene assignment for all LPS core biosynthesis gene functions was acquired. The complete structure of core oligosaccharide was investigated by 1H and 13C nuclear magnetic resonance (NMR) spectroscopy, electrospray ionization mass spectrometry MSn, and matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry. The following structure of the undecasaccharide was established: The heterogeneous appearance of the core oligosaccharide structure was due to the partial lack of β-d-Galp and the replacement of α-d-GlcpNAcGly by α-d-GlcpNGly. The glycine location was identified by mass spectrometry.

By comparison of the Proteus mirabilis HI4320 genome with known lipopolysaccharide (LPS) phosphoethanolamine transferases, three putative candidates (PMI3040, PMI3576, and PMI3104) were identified. One of them, eptC (PMI3104) was able to modify the LPS of two defined non-polar core LPS mutants of Klebsiella pneumoniae that we use as surrogate substrates. Mass spectrometry and nuclear magnetic resonance showed that eptC directs the incorporation of phosphoethanolamine to the O-6 of l-glycero-d-mano-heptose II. The eptC gene is found in all the P. mirabilis strains analyzed in this study. Putative eptC homologues were found for only two additional genera of the Enterobacteriaceae family, Photobacterium and Providencia. The data obtained in this work supports the role of the eptC (PMI3104) product in the transfer of PEtN to the O-6 of l,d-HepII in P. mirabilis strains.

Lipopolysaccharides (LPSs) are an integral part of the Gram-negative outer membrane, playing important organizational and structural roles and taking part in the bacterial infection process. In Aeromonas hydrophila, piscicola, and salmonicida, three different genomic regions taking part in the LPS core oligosaccharide (Core-OS) assembly have been identified, although the characterization of these clusters in most aeromonad species is still lacking. Here, we analyse the conservation of these LPS biosynthesis gene clusters in the all the 170 currently public Aeromonas genomes, including 30 different species, and characterise the structure of a putative common inner Core-OS in the Aeromonadaceae family. We describe three new genomic organizations for the inner Core-OS genomic regions, which were more evolutionary conserved than the outer Core-OS regions, which presented remarkable variability. We report how the degree of conservation of the genes from the inner and outer Core-OS may be indicative of the taxonomic relationship between Aeromonas species.

The capability of clostridia spores to act as pathogen indicators in sewage sludge treatment was investigated. Sulfite-reducing clostridia and E. coli levels were monitored during waste activated sludge pre-treatments (alkali and ultrasound) and its subsequent mesophilic anaerobic digestion. E. coli was maintained or reduced depending on treatment type and intensity. However, alkali pre-treatment (35.3 gNaOH/kg TS) by itself and alkali (157 gNaOH/kg TS) and ultrasound (27,000 kJ/kg TS) pre-treatments followed by anaerobic digestion provoked reproducible clostridia increases. Specifically, up to 2.7 log 10 after 35.3 gNaOH/kg TS pre-treatment and up to 1.9 and 1.1 log 10 after digesting the 157 gNaOH/kg TS and 27,000 kJ/kg TS pre-treated sludge, respectively. Having rejected the hypotheses of sporulation and floc dissipation, the most plausible explanation for these clostridia increases is re-growth. These results question the suitability of clostridia spores as indicators of sludge treatment and other biological treatments where clostridia may have a role.

[eng] The regulation of the expression of virulence genes in Salmonella enterica serovar Typhimurium is an intensively studied feature of Salmonella lifestyle. How Salmonella integrates environmental signals to activate virulence-related genes within the host has been explored. The genes encoded in Salmonella pathogenicity island I (SPI-1) required for the invasion of epithelial cells are well characterized, and many regulators involved in the activation of SPI-1 genes have been described. However, little is known about mechanism involved in the repression of SPI-1 under conditions were Salmonella does not require the expression of virulence-related genes. The expression of SPI-1 encoded genes have been reported to be a burden for Salmonella physiology and therefore mechanism to control shut down of SPI-1 under non permissive conditions might play a crucial role in Salmonella physiology. Here we describe that at exponential phase, CRP-cAMP, which acts as an activator at stationary phase, represses the expression of SPI-1 genes. The overall objective of this thesis was to characterize how CRP-cAMP silences SPI-1 expression under non-permissive conditions and to describe the molecular mechanism behind this phenotypic observation. In this thesis we i) define the target gene for the CRP-mediated regulation of SPI-1 ii) elucidate at which level of regulation CRP-cAMP modulates the expression of the SPI-1 genes master regulator hilD iii) characterize the involvement of CRP-cAMP dependent sRNA in hilD regulation iv) characterize the interaction of the CRP-cAMP dependent sRNA Spot 42 with the hilD 3’UTR region to regulate SPI-1 and v) explore the role of CRP-cAMP in the modulation of the SPI-1 repressor CsrA through the regulation of the long non-coding RNA csrB and csrC. CRP-cAMP represses hilA expression at exponential phase (non-permissive conditions for SPI-1 expression) and acts as an activator at stationary phase (permissive conditions for SPI-1 expression). CRP-cAMP mediated repression of hilA causes a concomitant attenuation in the expression level of SPI-1 encoded effector proteins. The regulation of SPI-1 during logarithmic growth phase occurs upstream of HilA by repressing hilD, hilC and rtsA expression and is mediated by the regulation of hilD expression at the post transcriptional level through the hilD 3’UTR. CRP-cAMP mediated regulation of hilD requires, in addition to the hilD 3’UTR, the sRNA chaperone Hfq and the major endonuclease RNAse E. CRP-cAMP represses the expression of the sRNA Spot 42 at exponential phase. We show that Spot 42 positively regulates hilD expression at exponential growth phase and requires of the presence of the hilD 3’UTR, the sRNA chaperone Hfq and the major endonuclease RNAse E. Interestingly, Spot 42 and the hilD 3’UTR region physically bind to Hfq. Spot 42 physically interacts with the last 150 nt of the hilD 3’UTR and unstructured region III of Spot 42 is required for the regulation of hilD. CRP-cAMP represses csrC but not csrB expression at exponential phase to regulate the expression of hilD. Remarkably, the CRP-cAMP dependent sRNA Spot 42 positively regulates the expression of csrC., [spa] La regulación de la expresión de genes de virulencia en Salmonella enterica serovar Typhimurium es una característica intensamente estudiada en Salmonella. La forma en que Salmonella integra señales ambientales para activar los genes relacionados con la virulencia dentro del huésped ha sido explorada. Los genes codificados en la isla de patogenicidad I de Salmonella (SPI-1) son necesarios para la invasión de células epiteliales, están bien caracterizados y se han descrito muchos reguladores implicados en su activación. Sin embargo, poco se sabe sobre el mecanismo implicado en la represión de SPI-1 en condiciones en las que Salmonella no requiere la expresión de genes relacionados con la virulencia. Es sabido que la expresión de genes codificados por SPI-1 son una carga para la fisiología de Salmonella y por lo tanto el mecanismo para controlar la represión de SPI-1 en condiciones no permisivas podría desempeñar un papel crucial en la fisiología de Salmonella. Aquí se describe que en fase exponencial, CRP-cAMP, que actúa como un activador en fase estacionaria, reprime la expresión de los genes SPI-1. El objetivo general de esta tesis fue caracterizar cómo el CRP-cAMP silencia la expresión de SPI-1 en condiciones no permisivas y describir el mecanismo molecular detrás de esta observación fenotípica. El CRP-cAMP reprime la expresión de hilA en la fase exponencial (condiciones no permisivas para la expresión de SPI-1) y actúa como un activador en fase estacionaria (condiciones permisivas para la expresión de SPI-1). La represión mediada por CRP-cAMP de hilA provoca una atenuación concomitante en el nivel de expresión de proteínas efectoras codificadas por SPI-1. La regulación de SPI-1 durante la fase de crecimiento logarítmico se produce aguas arriba de HilA mediante la represión hilD, hilC y rtsA expresión y está mediada por la regulación de hilD a nivel post transcripcional a través de la hilD 3'UTR. La regulación mediada por CRP-cAMP de hilD requiere, además de la hilD 3'UTR, la chaperona Hfq y la endonucleasa RNAsa E. CRP-cAMP reprime la expresión del sRNA Spot 42 en la fase exponencial. Mostramos que Spot 42 regula positivamente la expresión hilD en la fase de crecimiento exponencial, Spot 42 interacciona físicamente con los últimos 150 nt de la hilD 3'UTR.

Background Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host. Results Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibrio vulnificus and Vibrio cholerae/Vibrio metoecus being the most abundant ones in SMS from estuary and lake, respectively. Functions encoded in the SMS-microbiome differed significantly from those in the W-microbiome and allowed us to predict that successful mucus colonizers should have specific genes for (i) attachment (mainly by forming biofilms), (ii) bacterial competence and communication, and (iii) resistance to mucosal innate immunity, predators (amoeba), and heavy metals/drugs. In addition, we found several mobile genetic elements (mainly integrative conjugative elements) as well as a series of evidences suggesting that bacteria exchange DNA in SMS. Further, we isolated and sequenced a V. metoecus strain from SMS. This isolate shares pathogenicity islands with V. cholerae O1 from intestinal infections that are absent in the rest of sequenced V. metoecus strains, all of them from water and extra-intestinal infections. Conclusions We have obtained metagenomic and genomic evidence in favor of the hypothesis on the role of fish mucosal surfaces as a specialized habitat selecting microbes capable of colonizing and persisting on other comparable mucosal surfaces, e.g., the human intestine. Electronic supplementary material The online version of this article (10.1186/s40168-017-0376-1) contains supplementary material, which is available to authorized users.