When are combinations of antibiotics clinically useful?

Intraspecific variation in antibiotic resistance potential within E. coli

Intraspecific genomic diversity brings the potential for an unreported and diverse reservoir of cryptic antibiotic resistance genes in pathogens, as cryptic resistance can occur without major mutations and horizontal transmission. Here, we predicted the differences in the types of antibiotics and genes that induce cryptic and latent resistance between micro-diverse Escherichia coli strains. For example, we hypothesize that known resistance genes will be the culprit of latent resistance within clinical strains. We used a modified functional metagenomics method to induce expression in eight E. coli strains. We found a total of 66 individual genes conferring phenotypic resistance to 11 out of 16 antibiotics. A total of 14 known antibiotic resistance genes comprised 21% of total identified genes, whereas the majority (52 genes) were unclassified cryptic resistance genes. Between the eight strains, 1.2% of core orthologous genes were positive (conferred resistance in at least one strain). Sixty-four percent of positive orthologous genes conferred resistance to only one strain, demonstrating high intraspecific variability of latent resistance genes. Cryptic resistance genes comprised most resistance genes among laboratory and clinical strains as well as natural, semisynthetic, and synthetic antibiotics. Known antibiotic resistance genes primarily conferred resistance to multiple antibiotics from varying origins and within multiple strains. Hence, it is uncommon for E. coli to develop cross-cryptic resistance to antibiotics from multiple origins or within multiple strains. We have uncovered prospective and previously unknown resistance genes as well as antibiotics that have the potential to trigger latent antibiotic resistance in E. coli strains from varying origins.IMPORTANCEIntraspecific genomic diversity may be a driving force in the emergence of adaptive antibiotic resistance. Adaptive antibiotic resistance enables sensitive bacterial cells to acquire temporary antibiotic resistance, creating an optimal window for the development of permanent mutational resistance. In this study, we investigate cryptic resistance, an adaptive resistance mechanism, and unveil novel (cryptic) antibiotic resistance genes that confer resistance when amplified within eight E. coli strains derived from clinical and laboratory origins. We identify the potential of cryptic resistance genes to confer cross-resistance to antibiotics from varying origins and within multiple strains. We discern antibiotic characteristics that promote latent resistance in multiple strains, considering intraspecific diversity. This study may help detect novel resistance genes and functional genes that could become responsible for cryptic resistance among diverse strains and antibiotics, thus also identifying potential novel antibiotic targets and mechanisms.

Use of monitoring indicators in hospital management of antimicrobials

Background

According to the literature, 25% to 50% of antimicrobials prescribed in hospitals are unnecessary or inappropriate, directly impacting antimicrobial resistance. Thus, the present study aimed to evaluate the use of antimicrobials in a university hospital in Northeast Brazil, using days of therapy (DOT) and length of therapy (LOT) indicators in accordance with the latest national and international recommendations for monitoring the use of antimicrobials.

Methods

This is an observational, prospective analytical study conducted in a teaching hospital, with 94 active beds, distributed between the intensive care unit (ICU), the surgical clinic (SUR), the medical clinic (MED), the pneumology/infectology department (PNE/INF) and pediatrics (PED). The duration of the study was from the beginning of January to the end of December 2018.

Results

During the study period, a total of 11,634 patient-days were followed up and 50.4% of the patients were found to have received some antimicrobial, with a significant reduction in use of 1% per month throughout the year. Patients were receiving antimicrobial therapy for 376 days in every 1000 days of hospitalization (LOT = 376/1000pd). Overall, the 1st-generation cephalosporins and fluoroquinolones were the most used in respect of the number of prescriptions and the duration of therapy. The calculated global DOT/LOT ratio showed that each patient received an average of 1.5 antimicrobials during the hospital stay. The incidence of antimicrobial resistance, globally, for both methicillin-resistant Staphylococcus aureus (methicillin R), Carbapenem-resistant Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii (Carbapenem R), was 1 per 1000 patient-days.

Conclusions

The results obtained from the analyses revealed that half of the patients admitted to the hospital who took part in the study were exposed to the use of antimicrobials at some point during their stay. Although moderate, it is noteworthy that there was a decline in the use of antimicrobials throughout the year. The indicators used in this study were found to be very effective for gathering data on the use of antimicrobials, and assessing the results of the initiatives taken as part of the Stewardship program.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06542-5.