Infectious diseases in the genomic era

Indexación: Web of Science; Scielo.La nueva generación de secuenciadores (NGS) ha llegado para cambiar el modo de realizar investigación. Particularmente en Infectología, estas tecnologías modernas la han dirigido a una próxima era, denominada la "era de la genómica". En países desarrollados, las NGS se están utilizando en un gran número de aplicaciones, las que incluyen diagnóstico clínico, epidemiología y microbiología. En la actualidad, secuenciar el genoma de un microorganismo completo, ya sea bacteriano o viral, cuesta aproximadamente $100 dólares, precio bastante asequible en comparación a los precios de las tecnologías más antiguas. En esta revisión se describen algunas publicaciones recientes que han utilizado la secuenciación de genomas completos para, (i) rastrear brotes de enfermedades transmitidas por alimentos, (ii) la preparación de base de datos de genomas para los Gobiernos (iii) investigación de enfermedades nosocomiales, y (iv) en diagnóstico clínico. La era de la genómica está aquí, y llegó para quedarse, por lo cual se debe enfocar todos los esfuerzos en aprender a utilizar la gran cantidad de "datos masivos" generados por estas tecnologías, para reducir el impacto de las enfermedades infecciosas y así, mejorar la salud de personas y animales.Next generation sequencing (NGS) technologies have arrived, changing research and infectious disease research into a new era, the "genomic era". Currently, the developed world is introducing NGS in a number of applications, including clinical diagnostics, epidemiology, and microbiology. In developing countries NGS is being progressively introduced. Technologies currently available allow to sequence the whole genome of bacterial and viral strains for an approximate cost of$100 USD, which is highly cost savings compared to old-technologies for genome sequencing. Here we review recent publication of whole genome sequencing used for, (i) tracking of foodborne outbreaks, with emphasis in Salmonella and Listeria monocytogenes, (ii) building genomic databases for Governments, (iii) investigating nosocomial infections, and (iv) clinical diagnosis. The genomic era is here to stay and researchers should use these "massive databases" generated by this technology to decrease infectious diseases and thus improve health of humans and animals.http://ref.scielo.org/dwxt9

Animal contact as a source of human non-typhoidal salmonellosis

Non-typhoidal Salmonella represents an important human and animal pathogen world-wide. Most human salmonellosis cases are foodborne, but each year infections are also acquired through direct or indirect animal contact in homes, veterinary clinics, zoological gardens, farm environments or other public, professional or private settings. Clinically affected animals may exhibit a higher prevalence of shedding than apparently healthy animals, but both can shed Salmonella over long periods of time. In addition, environmental contamination and indirect transmission through contaminated food and water may complicate control efforts. The public health risk varies by animal species, age group, husbandry practice and health status, and certain human subpopulations are at a heightened risk of infection due to biological or behavioral risk factors. Some serotypes such as Salmonella Dublin are adapted to individual host species, while others, for instance Salmonella Typhimurium, readily infect a broad range of host species, but the potential implications for human health are currently unclear. Basic hygiene practices and the implementation of scientifically based management strategies can efficiently mitigate the risks associated with animal contacts. However, the general public is frequently unaware of the specific disease risks involved, and high-risk behaviors are common. Here we describe the epidemiology and serotype distribution of Salmonella in a variety of host species. In addition, we review our current understanding of the public health risks associated with different types of contacts between humans and animals in public, professional or private settings, and, where appropriate, discuss potential risk mitigation strategies

Comparative analysis of 37 Acinetobacter bacteriophages

© 2017 by the authors. Licensee MDPI, Basel, Switzerland. Members of the genus Acinetobacter are ubiquitous in the environment and the multipledrug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A comparative bioinformatics analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades

The COVID-19 Pandemic and Global Food Security

We present scientific perspectives on the impact of the COVID-19 pandemic and global food security. International organizations and current evidence based on other respiratory viruses suggests COVID-19 is not a food safety issue, i.e., there is no evidence associating food or food packaging with the transmission of the virus causing COVID-19 (SARS-CoV-2), yet an abundance of precaution for this exposure route seems appropriate. The pandemic, however, has had a dramatic impact on the food system, with direct and indirect consequences on lives and livelihoods of people, plants, and animals. Given the complexity of the system at risk, it is likely that some of these consequences are still to emerge over time. To date, the direct and indirect consequences of the pandemic have been substantial including restrictions on agricultural workers, planting, current and future harvests; shifts in agricultural livelihoods and food availability; food safety; plant and animal health and animal welfare; human nutrition and health; along with changes in public policies. All aspects are crucial to food security that would require “One Health” approaches as the concept may be able to manage risks in a cost-effective way with cross-sectoral, coordinated investments in human, environmental, and animal health. Like climate change, the effects of the COVID-19 pandemic will be most acutely felt by the poorest and most vulnerable countries and communities. Ultimately, to prepare for future outbreaks or threats to food systems, we must take into account the Sustainable Development Goals of the United Nations and a “Planetary Health” perspective

Screening the Presence of Non-Typhoidal Salmonella in Different Animal Systems and the Assessment of Antimicrobial Resistance.

Salmonella is a major bacterial foodborne pathogen that causes the majority of worldwide food-related outbreaks and hospitalizations. Salmonellosis outbreaks can be caused by multidrug-resistant (MDR) strains, emphasizing the importance of maintaining public health and safer food production. Nevertheless, the drivers of MDR Salmonella serovars have remained poorly understood. In this study, we compare the resistance profiles of Salmonella strains isolated from 4047 samples from domestic and wild animals in Chile. A total of 106 Salmonella strains (2.61%) are isolated, and their serogroups are characterized and tested for susceptibility to 16 different antimicrobials. The association between antimicrobial resistance (AMR) and a subset of independent variables is evaluated using multivariate logistic models. Our results show that 47 antimicrobial-resistant strains were found (44.3% of the total strains). Of the 47, 28 correspond to single-drug resistance (SDR = 26.4%) and 19 are MDR (17.9%). S. Enteritidis is highly persistent in animal production systems; however, we report that serogroup D strains are 18 times less likely to be resistant to at least one antimicrobial agent than the most common serogroup (serogroup B). The antimicrobials presenting the greatest contributions to AMR are ampicillin, streptomycin and tetracycline. Additionally, equines and industrial swine are more likely to acquire Salmonella strains with AMR. This study reports antimicrobial-susceptible and resistant Salmonella in Chile by expanding the extant literature on the potential variables affecting antimicrobial-resistant Salmonella

Mec-Positive Staphylococcus Healthcare-Associated Infections Presenting High Transmission Risks for Antimicrobial-Resistant Strains in an Equine Hospital.

Healthcare-associated infections caused by Staphylococcus, particularly Staphylococcus aureus, represent a high risk for human and animal health. Staphylococcus can be easily transmitted through direct contact with individual carriers or fomites, such as medical and non-medical equipment. The risk increases if S. aureus strains carry antibiotic resistance genes and show a phenotypic multidrug resistance behavior. The aim of the study was to identify and characterize methicillin resistant coagulase-positive staphylococci (MRSA) and coagulase-negative staphylococci (MRCoNS) in equine patients and environmental sources in an equine hospital to evaluate the genetic presence of multidrug resistance and to understand the dissemination risks within the hospital setting. We explored 978 samples for MRSA and MRCoNS using Oxacillin Screen Agar in an equine hospital for racehorses in Chile, which included monthly samples (n = 61-70) from equine patients (246) and hospital environments (732) in a one-year period. All isolates were PCR-assessed for the presence of methicillin resistance gene mecA and/or mecC. Additionally, we explored the epidemiological relatedness by Pulsed Field Gel Electrophoresis (PFGE) in MRSA isolates. Phenotypic antibiotic resistance was evaluated using the Kirby-Bauer disk diffusion method. We estimated the unadjusted and adjusted risk of acquiring drug-resistant Staphylococcus strains by employing logistic regression analyses. We identified 16 MRSA isolates and 36 MRCoNS isolates. For MRSA, we detected mecA and mecC in 100% and 87.5 % of the isolates, respectively. For MRCoNS, mecA was detected among 94% of the isolates and mecC among 86%. MRSA and MRCoNS were isolated from eight and 13 equine patients, respectively, either from colonized areas or compromised wounds. MRSA strains showed six different pulse types (i.e., A1-A3, B1-B2, C) isolated from different highly transited areas of the hospital, suggesting potential transmission risks for other patients and hospital staff. The risk of acquiring drug-resistant Staphylococcus species is considerably greater for patients from the surgery, equipment, and exterior areas posing higher transmission risks. Tackling antimicrobial resistance (AMR) using a One Health perspective should be advocated, including a wider control over antimicrobial consumption and reducing the exposure to AMR reservoirs in animals, to avoid cross-transmission of AMR Staphylococcus within equine hospitals

Widespread Environmental Presence of Multidrug-Resistant Salmonella in an Equine Veterinary Hospital That Received Local and International Horses

Indexación: Scopus.Salmonella enterica is a highly infectious microorganism responsible for many outbreaks reported in equine hospitals. Outbreaks are characterized by high morbidity and mortality rates, nosocomial transmission to other patients, zoonotic transmission to hospital personnel, and even closure of facilities. In this study, 545 samples (environmental and hospitalized patients) were collected monthly during a 1-year period from human and animal contact surfaces in an equine hospital that received local and international horses. A total of 22 Salmonella isolates were obtained from human contact surfaces (e.g., offices and pharmacy) and animal contact surfaces (e.g., stalls, surgery room, and waterers), and one isolate from a horse. Molecular serotyping revealed 18 isolates as Salmonella Typhimurium and three as Salmonella Infantis. Nineteen isolates were resistant to at least one antimicrobial class, and only two isolates were susceptible to all antimicrobials tested. In addition, we identified nine multidrug-resistant (MDR) isolates in S. Typhimurium, which displayed resistance to up to eight antimicrobials (i.e., amoxicillin/clavulanate, ampicillin, ciprofloxacin, chloramphenicol, streptomycin, gentamicin, trimethoprim/sulfamethoxazole, and tetracycline). Pulsed-field gel electrophoresis (PFGE) revealed the presence of three PFGE patterns permanently present in the environment of the hospital during our study. The persistent environmental presence of MDR Salmonella isolates, along with the fact that local and international horses are attended in this hospital, highlights the importance of improving biosecurity programs to prevent disease in horses and the hospital personnel and also for the global dissemination and acquisition of MDR Salmonella. © Copyright © 2020 Soza-Ossandón, Rivera, Tardone, Riquelme-Neira, García, Hamilton-West, Adell, González-Rocha and Moreno-Switt.https://www.frontiersin.org/articles/10.3389/fvets.2020.00346/ful

A proposed new bacteriophage subfamily: “Jerseyvirinae”

© 2015, Springer-Verlag Wien. Based on morphology and comparative nucleotide and protein sequence analysis, a new subfamily of the family Siphoviridae is proposed, named “Jerseyvirinae” and consisting of three genera, “Jerseylikevirus”, “Sp3unalikevirus” and “K1glikevirus”. To date, this subfamily consists of 18 phages for which the genomes have been sequenced. Salmonella phages Jersey, vB_SenS_AG11, vB_SenS-Ent1, vB_SenS-Ent2, vB_SenS-Ent3, FSL SP-101, SETP3, SETP7, SETP13, SE2, SS3e and wksl3 form the proposed genus “Jerseylikevirus”. The proposed genus “K1glikevirus” consists of Escherichia phages K1G, K1H, K1ind1, K1ind2 and K1ind3. The proposed genus “Sp3unalikevirus” contains one member so far. Jersey-like phages appear to be widely distributed, as the above phages were isolated in the UK, Canada, the USA and South Korea between 1970 and the present day. The distinguishing features of this subfamily include a distinct siphovirus morphotype, genomes of 40.7-43.6kb (49.6-51.4mol% G+C), a syntenic genome organisation, and a high degree of nucleotide sequence identity and shared proteins. All known members of the proposed subfamily are strictly lytic

ECOPHAGE: Combating Antimicrobial Resistance Using Bacteriophages for Eco-Sustainable Agriculture and Food Systems

The focus of this meeting was to discuss the suitability of using bacteriophages as alternative antimicrobials in the agrifood sector. Following a One Health approach, the workshop explored the possibilities of implementing phage application strategies in the agriculture, animal husbandry, aquaculture, and food production sectors. Therefore, the meeting had gathered phage researchers, representatives of the agrifood industry, and policymakers to debate the advantages and potential shortcomings of using bacteriophages as alternatives to traditional antimicrobials and chemical pesticides. Industry delegates showed the latest objectives and demands from consumers. Representatives of regulatory agencies (European Medicines Agency (EMA) and Spanish Agency of Medicines and Health Products (AEMPS)) presented an update of new regulatory aspects that will impact and support the approval and implementation of phage application strategies across the different sectors

Taxonomy of prokaryotic viruses : 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

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