Simulating the impact of non-pharmaceutical interventions limiting transmission in COVID-19 epidemics using a membrane computing model.

Epidemics caused by microbial organisms are part of the natural phenomena of increasing biological complexity. The heterogeneity and constant variability of hosts, in terms of age, immunological status, family structure, lifestyle, work activities, social and leisure habits, daily division of time and other demographic characteristics make it extremely difficult to predict the evolution of epidemics. Such prediction is, however, critical for implementing intervention measures in due time and with appropriate intensity. General conclusions should be precluded, given that local parameters dominate the flow of local epidemics. Membrane computing models allows us to reproduce the objects (viruses and hosts) and their interactions (stochastic but also with defined probabilities) with an unprecedented level of detail. Our LOIMOS model helps reproduce the demographics and social aspects of a hypothetical town of 10 320 inhabitants in an average European country where COVID-19 is imported from the outside. The above-mentioned characteristics of hosts and their lifestyle are minutely considered. For the data in the Hospital and the ICU we took advantage of the observations at the Nursery Intensive Care Unit of the Consortium University General Hospital, Valencia, Spain (included as author). The dynamics of the epidemics are reproduced and include the effects on viral transmission of innate and acquired immunity at various ages. The model predicts the consequences of delaying the adoption of non-pharmaceutical interventions (between 15 and 45 days after the first reported cases) and the effect of those interventions on infection and mortality rates (reducing transmission by 20, 50 and 80%) in immunological response groups. The lockdown for the elderly population as a single intervention appears to be effective. This modeling exercise exemplifies the application of membrane computing for designing appropriate multilateral interventions in epidemic situations.

Evolutionary Pathways and Trajectories in Antibiotic Resistance.

Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.

Successful treatment of intrauterine cytomegalovirus infection with an intraventricular cyst in a dichorionic diamniotic twin gestation using cytomegalovirus immunoglobulin.

Congenital cytomegalovirus (CMV) infection is the leading cause of severe congenital abnormalities. CMV immunoglobulin (CMVIG) may lower risk for symptomatic disease in congenital CMV infection. In a twin pregnancy, only one fetus shows CMV infection, raising a dilemma about intervention since the uninfected fetus would be exposed to treatment unnecessarily. CMVIG (2 × 200 U/kg) was given due to high viral load and development of an intraventricular cyst. The cyst growth plateaued, no other brain damage developed, and at 8 months, the infant was symptom-free. CMVIG appears appropriate to treat intrauterine CMV infection in this setting.

The refusal of the Society to accept antibiotic toxicity: missing opportunities for therapy of severe infections.

Over the last decade the emergence and spread of antibiotic resistance in bacteria has led to a new fear in the scientific and medical communities as well as among members of the general public. Due to the lack of development of new antibiotics, there is a need to reconsider old drugs or dosages rejected because of their toxicity. As a society, if we tolerate the potential toxicity of other drugs, such as anticancer drugs, why do we refuse to accept the use of toxic but effective antibiotics in life-threatening infections? The aim of this review is to provide insight into the reasons why the medical community remains unjustifiably unwilling to accept the risk of toxicity and the adverse effects of antibiotics that, nonetheless, might be required to treat severe infections, including those due to multidrug-resistant bacteria.

Escherichia coli: an old friend with new tidings.

Escherichia coli is one of the most-studied microorganisms worldwide but its characteristics are continually changing. Extraintestinal E. coli infections, such as urinary tract infections and neonatal sepsis, represent a huge public health problem. They are caused mainly by specialized extraintestinal pathogenic E. coli (ExPEC) strains that can innocuously colonize human hosts but can also cause disease upon entering a normally sterile body site. The virulence capability of such strains is determined by a combination of distinctive accessory traits, called virulence factors, in conjunction with their distinctive phylogenetic background. It is conceivable that by developing interventions against the most successful ExPEC lineages or their key virulence/colonization factors the associated burden of disease and health care costs could foreseeably be reduced in the future. On the other hand, one important problem worldwide is the increase of antimicrobial resistance shown by bacteria. As underscored in the last WHO global report, within a wide range of infectious agents including E. coli, antimicrobial resistance has reached an extremely worrisome situation that 'threatens the achievements of modern medicine'. In the present review, an update of the knowledge about the pathogenicity, antimicrobial resistance and clinical aspects of this 'old friend' was presented.

The global threat of antimicrobial resistance: science for intervention.

In the last decade we have witnessed a dramatic increase in the proportion and absolute number of bacterial pathogens resistant to multiple antibacterial agents. Multidrug-resistant bacteria are currently considered as an emergent global disease and a major public health problem. The B-Debate meeting brought together renowned experts representing the main stakeholders (i.e. policy makers, public health authorities, regulatory agencies, pharmaceutical companies and the scientific community at large) to review the global threat of antibiotic resistance and come up with a coordinated set of strategies to fight antimicrobial resistance in a multifaceted approach. We summarize the views of the B-Debate participants regarding the current situation of antimicrobial resistance in animals and the food chain, within the community and the healthcare setting as well as the role of the environment and the development of novel diagnostic and therapeutic strategies, providing expert recommendations to tackle the global threat of antimicrobial resistance.

In vivo attenuation and genetic evolution of a ST247-SCCmecI MRSA clone after 13 years of pathogenic bronchopulmonary colonization in a patient with cystic fibrosis: implications of the innate immune response.

Methicillin-resistant Staphylococcus aureus (MRSA) causes chronic pulmonary infections in patients with cystic fibrosis (CF). This study tracks the 13-year evolution (1996-2009) of a single MRSA clone in a male patient with CF, evaluating both the host immunogenic response and the microbial variations. Whole-genome sequencing was performed for the initial (CF-96) and evolved (CF-09) isolates. The immunogenicity of CF-96 and CF-09 was evaluated by incubation with innate immune cells from healthy volunteers. We also studied the patient's innate immune response profile, cytokine production, expression of triggering receptor expressed on myeloid cells-1 (TREM-1), and phagocytosis. A total of 30 MRSA ST247-SCCmecI-pvl(-) isolates were collected, which evidenced a genome size reduction from the CF-96 ancestor to the evolved CF-09 strain. Up to six changes in the spa-type were observed over the course of the 13-year evolution. Cytokine production, TREM-1 expression, and phagocytosis were significantly lower for the healthy volunteer monocytes exposed to CF-09, compared with those exposed to CF-96. Patient monocytes exhibited a reduced inflammatory response when challenged with CF-09. Genetic changes in MRSA, leading to reduced immunogenicity and entry into the refractory state, may contribute to the attenuation of virulence and efficient persistence of the bacteria in the CF lung.

Corrigendum to "The global threat of antimicrobial resistance: science for intervention" [New Microbes New Infect 6 (2015): 22-29].

[This corrects the article DOI: 10.1016/j.nmni.2015.02.007.].

The microbiome as a human organ.

The human organism is a complex structure composed of cells belonging to all three domains of life on Earth, Eukarya, Bacteria and Archaea, as well as their viruses. Bacterial cells of more than a thousand taxonomic units are condensed in a particular functional collective domain, the intestinal microbiome. The microbiome constitutes the last human organ under active research. Like other organs, and despite its intrinsic complexity, the microbiome is readily inherited, in a process probably involving 'small world' power law dynamics of construction in newborns. Like any other organ, the microbiome has physiology and pathology, and the individual (and collective?) health might be damaged when its collective population structure is altered. The diagnostic of microbiomic diseases involves metagenomic studies. The therapeutics of microbiome-induced pathology include microbiota transplantation, a technique increasingly available. Perhaps a new medical specialty, microbiomology, is being born.

Metagenomic epidemiology: a public health need for the control of antimicrobial resistance.

The intestine is an 'environment', a shared space where the interior and the exterior of the organism merge. The complexity of the intestinal microbiome modulates such interaction, and reflects the coordinated evolution of animals and intestinal microbes. The intestinal microbiome is exposed to the environmental resistome, to intestinal organisms from other hosts and also to microbiome-damaging agents, such as antibiotics. The result is a 'genetic-genomic-metagenomic reactor' where resistance genes flow among different biological units of different hierarchical levels, such as integrons, transposons, plasmids, clones, species or genetic exchange communities. Metagenomics provides the possibility to explore the presence of antibiotic resistance genes in all these biological and evolutionary units, and to identify possible 'high risk associations'. Multi-layered metagenomic epidemiology is required to understand and eventually to predict and apply interventions aiming to limit antibiotic resistance.

High-density fecal Enterococcus faecium colonization in hospitalized patients is associated with the presence of the polyclonal subcluster CC17.

Enterococcus faecium belonging to the polyclonal subcluster CC17, with a typical ampicillin-resistant E. faecium (AREfm) phenotype, have become prevalent among nosocomial infections around the world. High-density intestinal AREfm colonization could be one of the factors contributing to the successful spread of these pathogens. We aimed to quantify the enterococcal intestinal colonization densities in stool samples from AREfm-colonized and non-colonized patients using fluorescent in situ hybridization (FISH). Stool samples were collected from AREfm-colonized (n = 8) and non-colonized (n = 8) patients. The relative number of Enterococcus faecalis and E. faecium was determined by FISH using specific 16S rRNA probes, while the total amount of bacterial cells was counted by staining the sample with 4',6-diamidino-2-phenylindole (DAPI). The median bacterial cell numbers in fecal samples, counted by DAPI staining, were 7.7 × 10(9) and 4.8 × 10(9) cells/g for AREfm-colonized and non-colonized patients, respectively (p = 0.34). The E. faecium densities in AREfm-colonized patients, accounting for 0.5-7% of all fecal bacterial cells, exceeded E. faecalis levels by over ten-fold. E. faecium was not detected in non-colonized patients. This study demonstrated high E. faecium cell densities in stool samples from patients colonized with AREfm. Increased cell densities may contribute to host-to-host transmission and environmental contamination, facilitating the spread of AREfm in the hospital setting.

Escherichia coli and Staphylococcus aureus: bad news and good news from the European Antimicrobial Resistance Surveillance Network (EARS-Net, formerly EARSS), 2002 to 2009.

Based on data collected by the European Antimicrobial Resistance Surveillance Network (EARS-Net) and the former EARSS, the present study describes the trends in antimicrobial susceptibility patterns and occurrence of invasive infections caused by Escherichia coli and Staphylococcus aureus in the period from 2002 to 2009. Antimicrobial susceptibility results from 198 laboratories in 22 European countries reporting continuously on these two microorganisms during the entire study period were included in the analysis. The number of bloodstream infections caused by E. coli increased remarkably by 71% during the study period, while bloodstream infections caused by S. aureus increased by 34%. At the same time, an alarming increase of antimicrobial resistance in E. coli was observed, whereas for S. aureus the proportion of meticillin resistant isolates decreased. The observed trend suggests an increasing burden of disease caused by E. coli. The reduction in the proportion of meticillin-resistant S. aureus and the lesser increase in S. aureus infections, compared with E. coli, may reflect the success of infection control measures at hospital level in several European countries.

Molecular analysis of community-acquired methicillin-susceptible and resistant Staphylococcus aureus isolates recovered from bacteraemic and osteomyelitis infections in children from Tunisia.

Thirty-six children (27 boys, nine girls) that fulfilled CDC criteria for community-acquired infections were diagnosed with bacteraemia and/or osteomyelitis caused by Staphylococcus aureus during an 18-month period (2006-2008). Antibiotic susceptibility was determined by an agar dilution method. SCCmec type, carriage of pvl genes, agr type and spa-typing were determined using specific PCR protocols. Clonal relatedness was examined by pulsed field gel electrophoresis-SmaI and mutilocus sequence typing techniques. From the 36 isolates, eight (22%) corresponded to methicillin-resistant Staphylococcus aureus (MRSA) -t044/042-CC80/CC5-IVc-pvl(+) -agrIII/II. The highest genetic diversity was observed among the 28 community-acquired methicillin-susceptible S. aureus (CA-MSSA) isolates: 22 spa-variants that also grouped by multilocus sequence typing in CC1, CC5, CC6, CC8, CC30, CC80, CC97 and the singletons ST464, ST1467, ST1468 and ST1469. The pvl genes were detected in all eight CA-MRSA isolates and in eight CA-MSSA isolates (28%), being significantly more frequent among isolates causing osteoarticular infection (11 of 12, 92%) than in the bacteraemic isolates (six of 24, 25%). Based on patients' age, three groups were considered: newborns, infants and children. Bacteraemia was diagnosed in all newborns and infants, whereas in 42% of the children group osteomyelitis was the unique presentation. In most cases, the portal of entry was either the skin or unknown. In general, favourable outcome was observed, except in four cases-three of whom had severe complications and one died. In summary, we analysed the epidemiological and genetic background of community-acquired staphylococcal strains causing bacteraemic and/or osteomyelitis infections in children from Tunisia, describing three new sequence types and one novel spa type.

Stationary biofilm growth normalizes mutation frequencies and mutant prevention concentrations in Pseudomonas aeruginosa from cystic fibrosis patients.

Bacterial biofilms play an important role in the persistent colonization of the respiratory tract in cystic fibrosis (CF) patients. The trade-offs among planktonic or sessile modes of growth, mutation frequency, antibiotic susceptibility and mutant prevention concentrations (MPCs) were studied in a well-defined collection of 42 CF Pseudomonas aeruginosa isolates. MICs of ciprofloxacin, tobramycin, imipenem and ceftazidime increased in the biofilm mode of growth, but not the MPCs of the same drugs. The mutation frequency median was significantly higher in planktonic conditions (1.1 × 10(-8)) than in biofilm (9.9 × 10(-9)) (p 0.015). Isolates categorized as hypomutable increased their mutation frequency from 3.6 × 10(-9) in the planktonic mode to 6 × 10(-8) in biofilm, whereas normomutators (from 9.4 × 10(-8) to 5.3 × 10(-8)) and hypermutators (from 1.6 × 10(-6) to 7.7 × 10(-7)) decreased their mutation frequencies in biofilm. High and low mutation frequencies in planktonic growth converge into the normomutable category in the biofilm mode of growth of CF P. aeruginosa, leading to stabilization of MPCs. This result suggests that once the biofilm mode of growth has been established, the propensity of CF P. aeruginosa populations to evolve towards resistance is not necessarily increased.

Clonal dissemination of Enterococcus faecalis ST201 and Enterococcus faecium CC17-ST64 containing Tn5382-vanB2 among 16 hospitals in Chile.

We report the clonal dissemination of ST201 Enterococcus faecalis carrying Tn5382-vanB2 and of CC17-ST64 Enterococcus faecium carrying Tn5382-vanB2-ISEnfa110 among 16 hospitals in four geographically distant regions in Chile. This is the first epidemiological characterization of vancomycin resistance in Chile, and also the first report of interhospital dissemination of enterococcal vanB2 in South America.

[Importance of the antimicrobial spectrum and the bacterial resistances in the antibiotic choice for the treatment of pediatric patients with communitary infections]. / Importancia de la cobertura antimicrobiana y de las resistencias bacterianas en la elección de antibióticos en Pediatría.

OBJECTIVE: This study aimed to know the importance of the antimicrobial spectrum and the bacterial resistances for the antibiotic choice in the extrahospitalary pediatric area, at the same time that establish the relationship with others therapeutics parameters. MATERIAL AND METHODS: Cross-sectional, observational study within the MUSA (Improvement of Use of Antimicrobial Agents in Primary Health Care) Project made by personal interview of 210 pediatrician doctors randomly selected with national representation. This target is included in a bigger universe (855 doctors) representative of the most doctors responsible of the antibiotic prescriptions in the extrahospitalary area (sample error of the 3.3% for a 95% confidence interval and maximum response dispersion: p=q=50). The results of the pediatric study were subjected to a comparative analysis with the results of a similar study made ten years ago and with the global results of the general study. The questionnaire used for the interview had two clearly different parts: in the first part, the questions were open with the objective to get spontaneous answers from the participants; the second part had questions with suggested answers. RESULTS: Clinical efficacy is the most spontaneously valued issue by the Spanish pediatricians when it comes to choosing an antimicrobial agent; efficacy is followed by tolerance/safety and posology. Antimicrobial spectrum is mentioned by one out of 4-5 pediatricians that have participated in the study (21.9%), while the bacterial resistances are only mentioned by a 3.8%. In a suggested level, clinical efficacy is still the most valued parameter, being identified by 7 out of 10 interviewed with the bacterial eradication. In this case, the antimicrobial spectrum is the following parameter on significance, appearing as a synonym of "activity against specific microorganisms" in 2 out of 3 cases. In relation to his own evaluation, 3 out of 4 pediatricians say they take "a lot" of the bacterial resistances into consideration, who are mostly understood as "global rate" for 5-6 out of 10 interviewed, whether the resistance showed by the pneumococcal is what worried the most to 4 out of 10 of them. This importance given to the bacterial resistances at the second part of the study contrasts with the low consideration showed when it is compared with other parameters and the valoration is treated in a spontaneous way. In relation to a similar study realized on 1997 (Urano Proyect), we observe that clinical efficacy has replaced tolerance/safety as a parameter to bear in mind, probably as a consequence of more experience and confidence with the most important antimicrobial agents in the antibiotic prescriptions in podiatry. On the other hand, the bacterial resistances still being left out on the pediatricians spontaneous consideration, a fact that is shared with the majority of the collectives participating on the general study. The rest of the parameters stay in a similar way. CONCLUSIONS: Is necessary to emphasize at the importance of bacterial resistances in the antimicrobials rational use on the pediatric patient. As the antimicrobial tolerance profile has been improving in the last ten years, clinical efficacy, understood as "bacterial eradication" has became the most determining parameter when choosing antimicrobial agents.

Importancia de la cobertura antimicrobiana y de las resistencias bacterianas en la elección de antibióticos en Pediatría / Importance of the antimicrobial spectrum and the bacterial resistances in the antibiotic Choice for the treatment of pediatric patients with comunitary infections

Objetivo. Conocer la importancia de la cobertura antimicrobianay de las resistencias bacterianas, así como su relacióncon otros parámetros terapéuticos, a la hora de elegirun tratamiento antimicrobiano en pacientes pediátricos.Material y métodos. Estudio obsevacional transversal,enmarcado en el Proyecto MUSA (Mejora del Uso de los Antimicrobianos)en la atención primaria de salud, realizadomediante entrevista personal a 210 pediatras, seleccionadosde forma aleatoria, con representatividad a nivel nacional.Esta muestra fue extraída de otra mayor (855 médicos), querepresentaba a la práctica totalidad de médicos responsablesde la prescripción de antimicrobianos en el ámbito extrahospitalario(error muestral del 3,3% para un margen de confianzadel 95% y un grado de dispersión de respuesta máximo:p=q=50).Los resultados del estudio en pediatría se sometieron a unanálisis comparativo con los obtenidos con un estudio de lasmismas características realizado 10 años atrás y con los resultadosglobales del estudio general.El cuestionario utilizado en la entrevista tenía dos partesclaramente diferenciadas: en la primera de ellas, se tratabade preguntas abiertas con objeto de conseguir respuestas espontáneasde los participantes; la segunda parte, conteníacuestiones con respuestas sugeridas.Resultados. La eficacia clínica es el aspecto más valoradode forma espontánea por los pediatras españoles a la hora deelegir un antimicrobiano; a la eficacia, le siguen la tolerancia/seguridad y la posología. La cobertura antimicrobiana escitada por uno de cada 4-5 pediatras participantes en el estudio(21,9%), mientras que las resistencias bacterianas sóloson citadas por el 3,8% (AU)

Objective. This study aimed to know the importanceof the antimicrobial spectrum and the bacterial resistances for the antibiotic choice in the extrahospitalarypediatric area, at the same time that establish the relationshipwith others therapeutics parameters.Material and methods. Cross-sectional, observationalstudy within the MUSA (Improvement of Use of AntimicrobialAgents in Primary Health Care) Project made bypersonal interview of 210 pediatrician doctors randomlyselected with national represantitivity. This target is includedin a bigger universe (855 doctors) representativeof the most doctors responsible of the antibiotic prescriptionsin the extrahospitalary area (sample error ofthe 3,3 % for a 95 % confidence interval and maximumresponse dispersion: p=q=50).The results of the pediatric study were subjected to acomparative analysis with the results of a similar studymade ten years ago and with the global results of thegeneral study.The questionnaire used for the interview had twocrearly differenced parts: in the first part, the questionswere open with the objective to get spontanious answersfrom the participants; the second part had questions withsuggested answers.Results. Clinical efficacy is the most spontaneouslyvalored issue by the spanish pediatricians when it comesto choosing an antimicrobial agent; efficacy is followedby tolerance/safety and posology. Antimicrobial spectrumis mentioned by one out of 4-5 pediatricians thathave participated in the study (21,9%), while the bacterialresistances are only mentioned by a 3,8% (AU)

Environmental stress and evolvability in microbial systems.

The sustainability of life on the planet depends on the preservation of the existing microbial systems, which constitutes our major "biological atmosphere". The detection of variations in microbial systems as a result of anthropogenic or natural changes is critical both to detect and assess risks and to programme specific interventions. Changes in microbial systems provokes stress, probably altering the local evolutionary time by changing evolvability (the possibilities of microbes to evolve). Methods should be refined to properly assess diversity in microbial systems. We propose that such diversity estimations should be done on a multi-hierarchical scale, encompassing not only organisms, but sub-cellular entities (e.g. chromosomal domains, plasmids, transposons, integrons, genes, gene modules) and supra-cellular organizations (e.g. clones, populations, communities, ecosystems), applying Hamiltonian criteria of inclusive fitness for the different ensembles. In any of these entities, we can generally identify, in a fractal manner, constant and variable parts. Variation in these entities and ensembles is probably both reduced and increased by environmental stress. Because of that, variation in microbial systems might serve as mirrors or symptoms of the health of the planet.