Rapid methods for detection of bacterial resistance to antibiotics. / Métodos rápidos para la detección de la resistencia bacteriana a antibióticos.

The most widely used antibiotic susceptibility testing methods in Clinical Microbiology are based on the phenotypic detection of antibiotic resistance by measuring bacterial growth in the presence of the antibiotic being tested. These conventional methods take typically 24hours to obtain results. Here we review the main techniques for rapid determination of antibiotic susceptibility. Data obtained with different methods such as molecular techniques, microarrays, commercial methods used in work routine, immunochromatographic methods, colorimetric methods, image methods, nephelometry, MALDI-TOF mass spectrometry, flow cytometry, chemiluminescence and bioluminescence, microfluids and methods based on cell disruption are analysed in detail.

[Rapid antibiotic susceptibility test in Clinical Microbiology]. / Antibiograma rápido en Microbiología Clínica.

The most widely used antibiotic susceptibility testing methods in Clinical Microbiology are based on the phenotypic detection of antibiotic resistance by measuring bacterial growth in the presence of the antibiotic being tested. These conventional methods take typically 24hours to obtain results. A review is presented here of recently developed techniques for the rapid determination of antibiotic susceptibility. Data obtained with different methods such as molecular techniques, flow cytometry, chemiluminescence, mass spectrometry, commercial methods used in routine work, colorimetric methods, nephelometry, microarrays, microfluids, and methods based on cell disruption and sequencing, are analyzed and discussed in detail.

A two-hour antibiotic susceptibility test by ATP-bioluminescence.

The antibiotic susceptibility test (AST) in Clinical Microbiology laboratories is still time-consuming, and most procedures take 24h to yield results. In this study, a rapid antimicrobial susceptibility test using ATP-bioluminescence has been developed. The design of method was performed using five ATCC collection strains of known susceptibility. This procedure was then validated against standard commercial methods on 10 strains of enterococci, 10 staphylococci, 10 non-fermenting gram negative bacilli, and 13 Enterobacteriaceae from patients. The agreement obtained in the sensitivity between the ATP-bioluminescence method and commercial methods (E-test, MicroScan and VITEK2) was 100%. In summary, the preliminary results obtained in this work show that the ATP-bioluminescence method could provide a fast and reliable AST in two hours.

New procedure for rapid identification of microorganisms causing urinary tract infection from urine samples by mass spectrometry (MALDI-TOF).

INTRODUCTION: Matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry is widely established as a technique in clinical microbiology laboratories for the identification of microorganisms. Using this technique, it is also possible to obtain the identification of microorganisms from untreated urine samples. METHODS: In this study, a differential centrifugation protocol and a criterion for validation of the results in order to achieve microbial identification from untreated urine samples are proposed. Additionally, the sensitivity of the analytical procedure in monobacterial urine samples has been evaluated. RESULTS: A 90% sensitivity (confidence interval of 81.96%-94.84%) was obtained in urine samples with bacterial counts of ≥1×10(5)CFU/ml, and it was possible to improve the percentages of direct identifications from urine samples with bacterial counts of <1×10(5)CFU/ml. CONCLUSION: It is concluded that the MALDI-TOF system is both fast and reliable in the identification of individual microorganisms from untreated urine samples with counts of ≥1×10(5)CFU/ml.

Bacterial/fungal infection in hospitalized patients with COVID-19 in a tertiary hospital in the Community of Castilla y León, Spain.

INTRODUCTION: Bacterial/fungal coinfection and superinfections contribute to the increased morbi-mortality of viral respiratory infections (RIs). The main objective of this study was to determine the incidence of these infections in hospitalized patients with COVID-19. METHOD: Retrospective observational study of all patients admitted for COVID-19 and bacterial/fungal infections at the Hospital Clínico Universitario of Valladolid, Spain (March 1-May 31, 2020). Demographic, clinical and microbiological data were compared based on Intensive Care Unit (ICU) admission and predictors of mortality by were identified using multivariate logistic regression analyses. RESULTS: Of the 712 COVID-19 patients, 113 (16%) presented bacterial/fungal coinfections or superinfections. Their median age was 73 years (IQR 57-89) and 59% were men. The profiles of ICU patients (44%) included male, SARS-CoV-2 pneumonia, leukocytosis, elevated inteleukin-6, with interferon ß-1b and tocilizumab and superinfection (p < 0.05). Coinfections were diagnosed in 5% (39/712) patients. Most common pathogens of respiratory coinfection (18) were Streptococcus pneumoniae (6) and Staphylococcus aureus (6). Superinfections were detected in 11% (80/712) patients. Urinary (53) and RI (39) constituted the majority of superinfections Acinetobacter baumannii multidrug-resistant was the main agent of IR and bacteremia. An outbreak of A. baumannii contributed to this result. Three patients were considered to have probable pulmonary aspergillosis. Mortality was higher in UCI patients (50% vs. 29%, p = 0.028). The predictive factors of mortality included being a male with various comorbidities, SARS-CoV-2 pneumonia, bacteremia and superinfections from A. baumannii. CONCLUSION: The outbreak of A. baumannii was a determining factor in the increases of the incidence of infection and the morbi-mortality of ICU patients.

Novel fluorescent-based reporter cell line engineered for monitoring homologous recombination events.

Homologous recombination (HR) faithfully restores DNA double-strand breaks. Defects in this HR repair pathway are associated with cancer predisposition. In genetic engineering, HR has been used extensively to study gene function and it represents an ideal method of gene therapy for single gene disorders. Here, we present a novel assay to measure HR in living cells. The HR substrate consisted of a non-fluorescent 3' truncated form of the eGFP gene and was integrated into the AAVS1 locus, known as a safe harbor. The donor DNA template comprised a 5' truncated eGFP copy and was delivered via AAV particles. HR mediated repair restored full-length eGFP coding sequence, resulting in eGFP+ cells. The utility of our assay in quantifying HR events was validated by exploring the impact of the overexpression of HR promoters and the siRNA-mediated silencing of genes known to play a role in DNA repair on the frequency of HR. We conclude that this novel assay represents a useful tool to further investigate the mechanisms that control HR and test continually emerging tools for HR-mediated genome editing.

Bacterial/fungal infection in hospitalized patients with COVID-19 in a tertiary hospital in the Community of Castilla y León, Spain. / Infección bacteriana/fúngica en pacientes con COVID-19 ingresados en un hospital de tercer nivel de Castilla y León, España.

INTRODUCTION: Bacterial/fungal coinfection and superinfections contribute to the increased morbi-mortality of viral respiratory infections (RIs). The main objective of this study was to determine the incidence of these infections in hospitalized patients with COVID-19. METHOD: Retrospective observational study of all patients admitted for COVID-19 and bacterial/fungal infections at the Hospital Clínico Universitario of Valladolid, Spain (March 1-May 31, 2020). Demographic, clinical and microbiological data were compared based on Intensive Care Unit (ICU) admission and predictors of mortality by were identified using multivariate logistic regression analyses. RESULTS: Of the 712 COVID-19 patients, 113 (16%) presented bacterial/fungal coinfections or superinfections. Their median age was 73 years (IQR 57-89) and 59% were men. The profiles of ICU patients (44%) included male, SARS-CoV-2 pneumonia, leukocytosis, elevated inteleukin-6, with interferon ß-1b and tocilizumab and superinfection (p < 0.05). Coinfections were diagnosed in 5% (39/712) patients. Most common pathogens of respiratory coinfection (18) were Streptococcus pneumoniae (6) and Staphylococcus aureus (6). Superinfections were detected in 11% (80/712) patients. Urinary (53) and RIs (39) constituted the majority of superinfections Acinetobacter baumannii multidrug-resistant was the main agent of IR and bacteremia. An outbreak of A. baumannii contributed to this result. Three patients were considered to have probable pulmonary aspergillosis. Mortality was higher in UCI patients (50 vs. 29%; p = 0.028). The predictive factors of mortality included being a male with various comorbidities, SARS-CoV-2 pneumonia, bacteremia and superinfections from A. baumannii. CONCLUSION: The outbreak of A. baumannii was a determining factor in the increases of the incidence of infection and the morbi-mortality of ICU patients.

Anti-infectives for systemic use prescribed in a Spanish hospital between 2009-2013.

The overuse and misuse of antimicrobials contribute to the emergence of antibiotic-resistant bacteria. The aim of this work was to analyse all the anti-infectives for systemic use (J ATC group) prescribed at the University Clinic Hospital of Valladolid (Spain) for the years 2009-2013. Amounts of anti-infectives (antibacterials, antifungals and antivirals) used in the period 2009-2013 were expressed as defined daily doses (DDDs) and as total expenditure, and the significance of the difference in consumption of anti-infectives and the relevant expenditure between years was evaluated from the overlapping of the corresponding confidence intervals at 95% confidence level of DDDs and expenditure. The results obtained showed that DDDs and expenditure of antibacterials decreased in the period 2009-2013. Antimycotics showed an upward trend in expenditure and DDDs in the five-year study period, but with major oscillations. The consumption of antivirals was practically constant in the period 2009-2011; in 2012, a significant reduction was observed and this reduction was conserved in 2013, although their expenditure increased year by year. In conclusion, in the period 2009-2013, expenditure on anti-infectives increased year to year. However, this increase in expenditure resulted in a downward trend of DDDs.

A two-hour procedure for determining the susceptibility of enterococci and staphylococci to antibiotics by a colourimetric method.

INTRODUCTION: Rapid determination of the antibiotic susceptibility test in bacteria remains a challenge for Clinical Microbiology laboratories. METHODS: An improvement in the colorimetric antimicrobial susceptibility testing performed with resazurin in enterococci and staphylococci has been carried out. The design of method was performed using two collection strains, which have a known susceptibility. This procedure was then validated against standard commercial methods on 15 strains of staphylococci and 15 strains of enterococci from patients. RESULTS: The essential agreement between the colorimetric method and commercial methods (E-test, MicroScan and VITEK2) was 100%. CONCLUSION: Resazurin allows us to obtain a reliable antibiotic susceptibility test in staphylococci and enterococci in less than two hours.

[How to fight parasitic infectious diseases with bacteria. The case of Wolbachia pipientis]. / Cómo combatir con bacterias a las enfermedades infecciosas parasitarias. El caso de Wolbachia pipientis.

In Nature, no individual can live in isolation; hence, living organisms are forced to interact with each other. This necessity has led many organisms to establish heterogeneous relations to enhance their ability to adapt to the environment, thus acquiring evolutionary advantages. These relationships are sometimes so intense, that on the long term the organisms may lose their individual identity. An example of these associations is the endosymbiotic ones, where eukaryote organisms generally harbor different prokaryote organisms. The endosymbiotic bacterium Wolbachia pipientis is a species described by Hertig and Wolbach in 1924. This microorganism can be isolated in a large variety of eukaryote organisms, with which it maintains different links. Until now, this species has only been described with 11 serogroups numbered from A to K within the Wolbachia genus. This work is intended to illustrate the relationship of Wolbachia pipientis with human pathogenic filaria and with arthropods, as well as to describe the implications of this bacterium in the treatment of filariasis. Finally, this work tries to describe recent studies that have targeted the use of artificially-created Wolbachia pipientis virulent strains that, once inoculated in infectious diseases-transmitting vectors, develop negative effects within them in order to, in this way, erradicate mosquito-transmitted infectious diseases for which no treatment is available at the moment or the prevention of its transmissibility has not been achieved.

En la naturaleza ningún individuo puede vivir de forma aislada, de tal forma que los organismos vivos se ven obligados a interactuar unos con otros. Esta necesidad ha llevado a que diferentes organismos establezcan relaciones heterogéneas para mejorar su capacidad de adaptación al medio, obteniendo así ventajas evolutivas. Estas relaciones a veces son tan intensas que a la larga los organismos pueden perder su identidad individual. Un ejemplo de estas asociaciones son las endosimbióticas, en las cuales generalmente organismos eucariotas albergan a diferentes organismos procariotas. La bacteria endosimbiótica Wolbachia pipientis es una especie descrita en 1924 por Hertig y Wolbach. Este microorganismo se puede aislar en gran variedad de organismos eucariotas, con los que mantiene diferentes vínculos. Hasta el momento solo se ha descrito esta especie con 11 serogrupos enumerados de la A a la K dentro del género Wolbachia. En este trabajo se pretende ilustrar la relación de Wolbachia pipientis con las filarias patógenas humanas y con los artrópodos, así como describir las implicaciones de esta bacteria en el tratamiento de las filariasis. Finalmente, se pretende exponer los estudios recientes que han apuntado el uso de cepas virulentas de Wolbachia pipientis creadas artificialmente que una vez inoculadas en los vectores transmisores de enfermedades desarrollan efectos negativos en estos, para de esa forma lograr la erradicación de enfermedades infecciosas transmitidas por mosquitos para las cuales de momento no existe tratamiento o no se ha logrado impedir su transmisibilidad.

Procedure for microbial identification based on Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry from screening-positive urine samples.

Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry is a widely used proteomic technique in clinical microbiology laboratories, and enables microbial identification directly from clinical samples. This study seeks to establish a protocol for bacterial identification from monomicrobial urine samples that have tested positive in the screening with Sysmex UF-1000i (Sysmex Corporation, Kobe, Japan). Sysmex UF-1000i counts ≥1 × 10(7) bacteria/mL indicate a sufficient bacterial concentration to allow direct identification from urine, with 87.5% sensitivity. Microbial identification from urine with Sysmex UF-1000i counts between 1 × 10(5) and 1 × 10(7) bacteria/ml requires preincubation to obtain the adequate amount of bacteria needed for analysis, and 91.7% sensitivity thus being achieved.

[Quorum sensing in bacteria and yeast]. / Quorum sensing en bacterias y levaduras.

Bacterial sets are complex dynamic systems, which interact with each other and through the interaction, bacteria coexist, collaborate, compete and share information in a coordinated manner. A way of bacterial communication is quorum sensing. Through this mechanism the bacteria can recognize its concentration in a given environment and they can decide the time at which the expression of a particular set of genes should be started for developing a specific and simultaneous response. The result of these interconnections raises properties that cannot be explained from a single isolated bacterial cell.