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

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

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

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

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

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

Peer reviewe

Taxonomy of prokaryotic viruses : 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.Peer reviewe

Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

<p>Abstract</p> <p>Background</p> <p>Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of <it>Salmonella enterica </it>subsp. <it>enterica </it>subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of <it>Salmonella enterica </it>subsp. <it>enterica</it>, and identify clade-specific genes that may be the result of ecological specialization.</p> <p>Results</p> <p>Multi-locus sequence analysis (MLSA) and single nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of <it>S. enterica </it>subsp. <it>enterica </it>into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a β-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20% belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of β-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment.</p> <p>Conclusions</p> <p><it>S. enterica </it>subsp. <it>enterica </it>consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.</p

Lysis Profiles of <i>Salmonella</i> Phages on <i>Salmonella</i> Isolates from Various Sources and Efficiency of a Phage Cocktail against <i>S.</i> Enteritidis and <i>S.</i> Typhimurium

Salmonella enterica serovar Enteritidis and Salmonella enterica serovar Typhimurium are major foodborne pathogens of concern worldwide. Bacteriophage applications have gained more interest for biocontrol in foods. This study isolated 36 Salmonella phages from several animal farms in Thailand and tested them on 47 Salmonella strains from several sources, including farms, seafood processing plant and humans in Thailand and USA. Phages were classified into three major groups. The estimated phage genome size showed the range from 50 &#177; 2 to 200 &#177; 2 kb. An effective phage cocktail consisting of three phages was developed. Approximately 4 log CFU/mL of S. Enteritidis and S. Typhimurium could be reduced. These phages revealed a burst size of up to 97.7 on S. Enteritidis and 173.7 PFU/cell on S. Typhimurium. Our phage cocktail could decrease S. Enteritidis on chicken meat and sunflower sprouts by 0.66 log CFU/cm2 and 1.27 log CFU/g, respectively. S. Typhimurium on chicken meat and sunflower sprouts were decreased by 1.73 log CFU/cm2 and 1.17 log CFU/g, respectively. Overall, animal farms in Thailand provided high abundance and diversity of Salmonella phages with the lysis ability on Salmonella hosts from various environments and continents. A developed phage cocktail suggests a potential biocontrol against Salmonella in fresh foods