Establishing a molecular laboratory in COVID-19 pandemic: The experience of a regional laboratory in Spain.

The high demand for COVID-19 diagnosis overwhelmed reference hospitals. Regional laboratories had to incorporate molecular technology to respond to the emergency. This work described the implementation of molecular diagnostic tools and the detection of SARS-CoV-2, in a regional hospital with no previous experience, from October 2020 to March 2022. The laboratory structure was significantly modified. The staff grew from 3 to 4 clinical microbiologists, and from 7 to 17 laboratory technicians to provide 24/7 coverage. A total of 144,442 samples were processed during the period of study. The highest peaks were reached in July 2021 with 25,285 samples processed, and between December 2021 and January 2022, with 32,245. COVID-19 pandemic has represented not only the challenge, but the opportunity to introduce Nucleic Acid Amplification Techniques (NAAT) in inexperienced laboratories. These secondary settings have shown an extraordinary ability to adapt and cannot be left behind in the progress of diagnostic techniques.

Altered blood glucose concentration is associated with risk of death among patients with community-acquired Gram-negative rod bacteremia.

BACKGROUND: Altered blood glucose concentration is commonly observed in patients with sepsis, even among those without hypoglycemic treatments or history of diabetes mellitus. These alterations in blood glucose are potentially detrimental, although the precise relationship with outcome in patients with bacteremia has not been yet determined. METHODS: A retrospective cohort study design for analyzing patients with Gram negative rod bacteremia was employed, with the main outcome measure being in-hospital mortality. Patients were stratified in quintiles accordingly deviation of the blood glucose concentration from a central value with lowest mortality. Cox proportional-hazards regression model was used for determining the relationship of same day of bacteremia blood glucose and death. RESULTS: Of 869 patients identified 63 (7.4%) died. Same day of bacteremia blood glucose concentration had a U-shaped relationship with in-hospital mortality. The lowest mortality (2%) was detected in the range of blood glucose concentration from 150 to 160 mg/dL. Greater deviation of blood glucose concentration from the central value of this range (155 mg/dL, reference value) was directly associated with higher risk of death (p = 0.002, chi for trend). The low-risk group (quintile 1) had a mortality of 3.3%, intermediate-risk group (quintiles 2, 3 and 4) a mortality of 7.1%, and the high-risk group (quintile 5) a mortality of 12.05%. In a multivariable Cox regression model, the hazard ratio for death among patients in the intermediate-risk group as compared with that in the low risk group was 2.88 (95% confidence interval, 1.01 to 8.18; P = 0.048), and for the high risk group it was 4.26 (95% confidence interval, 1.41 to 12.94; P = 0.01). CONCLUSIONS: Same day of bacteremia blood glucose concentration is related with outcome of patients with Gram-negative rod bacteremia. Lowest mortality is detected in patients with blood glucose concentration in an interval of 150-160 mg/dL. Deviations from these values are associated with an increased risk of death.

Impact of antibiotic resistance and of adequate empirical antibiotic treatment in the prognosis of patients with Escherichia coli bacteraemia.

BACKGROUND: Escherichia coli is the most frequent Gram-negative organism causing bacteraemia. There are few data about prognostic factors of bloodstream infections due to E. coli. In particular, the consequences of antibiotic resistance and of adequate empirical antibiotic treatment on outcome remain broadly unknown. METHODS: We conducted a retrospective cohort study of patients with E. coli bacteraemia between January 1997 and June 2005 to identify any association between antibiotic resistance, adequacy of empirical antibiotic therapy and mortality. RESULTS: Of 663 patients with E. coli bacteraemia, 36 (5.4%) died. Patients with multidrug-resistant (MDR) E. coli bacteraemia had a significantly lower frequency of correct empirical antibiotic treatment than patients with non-MDR E. coli bacteraemia [relative risk (RR) 0.53; 95% confidence interval (CI) 0.48-0.67], and also had a significantly higher mortality (RR 3.31; 95% CI 1.72-6.36). An association between the number of antibiotics to which E. coli was resistant with adequacy of empirical antibiotic (P < 0.001) and with mortality (P < 0.001) was detected. After adjustment for other significant risk factors and confounders, the inadequacy of empirical antibiotic treatment was associated with an increased mortality (adjusted OR 2.98; 95% CI 1.25-7.11). When the adequacy of empirical treatment was excluded from the model, the presence of MDR E. coli in blood cultures was also associated with the prognosis (adjusted OR 3.11; 95% CI 1.3-7.44). In multivariate analysis, other variables associated with the outcome were age, the presence of severe sepsis or shock, Charlson index score and a non-urinary origin of the bacteraemia. CONCLUSIONS: Adequacy of empirical antibiotic treatment is an independent risk factor for mortality in patients with E. coli bacteraemia. MDR E. coli bacteraemia had a worse prognosis due, at least in part, to a lower frequency of correct empirical treatment.

A polymorphic tandem repeat potentially useful for typing in the chromosome of Yersinia enterocolitica.

The hexanucleotide CCAGCA was found repeated 15 times in tandem on the 5' side of the virginiamycin acetyl transferase gene of Yersinia enterocolitica strain Y56. The corresponding region was analysed by PCR from 54 clinical strains belonging to the same biotype and serotype, and others from this laboratory collection belonging to different biotypes and serotypes. Each strain produced a single amplification product whose size was variable among strains, revealing that the locus was polymorphic. Nucleotide sequence determination of selected PCR products showed that the polymorphism was due to the precise expansion or reduction in the number of hexanucleotide repeats. Analysis of this locus in a few strains showing the same PFGE pattern showed that it was also polymorphic. These results suggest that this method could be valuable to increase the discriminatory power of current Y. enterocolitica typing schemes.