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A globally circulating strain of Salmonella enterica serotype Infantis containing the pESI plasmid has increased in prevalence in poultry meat samples and cases of human infections. In this study, a polymerase chain reaction (PCR) protocol was designed to detect the pESI plasmid and confirm the Infantis serotype of Salmonella isolates. Primers were tested bioinformatically to predict specificity, sensitivity, and precision. A total of 54 isolates of Salmonella serotypes Infantis, Senftenberg, and Alachua were tested, with and without the pESI plasmid carriage. Isolates of 31 additional serotypes were also screened to confirm specificity to Infantis. Specificity, sensitivity, and precision of each primer were >0.95. All isolates tested produced the expected band sizes. This PCR protocol provides a rapid and clear result for the detection of the pESI plasmid and serotype Infantis and will allow for the in vitro detection for epidemiological studies where whole-genome sequencing is not available., (© The Author(s) 2023. Published by Oxford University Press on behalf of Applied Microbiology International.)

Study Objective: In the United States, alcohol use disorder adversely affects 5.6% of all adults. Excessive alcohol consumption adversely affects organ functions critical for adaptation to stress induced by surgery. Colorectal resection is one of the most common major surgeries in patients at risk for alcohol use disorder. The objective of this study was to assess the impact of alcohol use disorder on hospital outcomes after colectomy using a population-based discharge database., Setting: Population-based discharge database., Patients: The Premier Healthcare Database was queried for the 603,730 adult patients who underwent colectomy from 2016 to 2019., Interventions: None., Measurements: Multiple logistic regressions estimated the associations between in-hospital mortality, length of stay, and hospitalization cost with alcohol use disorder as the primary predictor, adjusting for other substance use disorders, psychotic disorders, depression, other Elixhauser comorbidities, age, payor, race, gender, non-elective surgery, and other unbalanced variables., Main Results: A discharge code for alcohol use disorder was identified in 2.9% of colectomy patients and the overall in-hospital mortality rate in all sampled colectomy patients was 1.4%. Alcohol use disorder was associated with a significantly increased risk of in-hospital mortality after adjusting for other factors (AOR 1.36, 95% CI 1.24-1.48, p < 0.0001). Alcohol use disorder was also significantly associated with long length of stay (AOR 1.45, 95% CI 1.39-1.52, p < 0.0001) and high hospitalization costs (AOR 1.63, 95% CI 1.56-1.70, p < 0.0001)., Conclusions: Alcohol use disorder is associated with an increased risk of in-hospital mortality in patients undergoing colectomy, one of the most common major surgeries. Future research should examine if enhanced efforts to identify patients with alcohol use disorder could enable anesthesiologists to provide worthwhile perioperative interventions for this high-risk population., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Legionella pneumophila serogroup 1 (Lp1) sequence type (ST) 23 is one of the most commonly detected STs in Italy where it currently causes all investigated outbreaks. ST23 has caused both epidemic and sporadic cases between 1995 and 2018 and was analysed at genomic level and compared with ST23 isolated in other countries to determine possible similarities and differences. A core genome multi-locus sequence typing (cgMLST), based on a previously described set of 1,521 core genes, and single-nucleotide polymorphisms (SNPs) approaches were applied to an ST23 collection including genomes from Italy, France, Denmark and Scotland. DNAs were automatically extracted, libraries prepared using NextEra library kit and MiSeq sequencing performed. Overall, 63 among clinical and environmental Italian Lp1 isolates and a further seven and 11 ST23 from Denmark and Scotland, respectively, were sequenced, and pangenome analysed. Both cgMLST and SNPs analyses showed very few loci and SNP variations in ST23 genomes. All the ST23 causing outbreaks and sporadic cases in Italy and elsewhere, were phylogenetically related independent of year, town or country of isolation. Distances among the ST23s were further shortened when SNPs due to horizontal gene transfers were removed. The Lp1 ST23 isolated in Italy have kept their monophyletic origin, but they are phylogenetically close also to ST23 from other countries. The ST23 are quite widespread in Italy, and a thorough epidemiological investigation is compelled to determine sources of infection when this ST is identified in both LD sporadic cases and outbreaks., (© 2022 Ricci et al.)

Purpose: Although cesarean delivery is the most common surgical procedure in the United States, postoperative opioid prescribing varies greatly. We hypothesized that patient characteristics, procedural characteristics, or both would be associated with high vs low opioid use after discharge. This information could help individualize prescriptions., Methods: In this prospective cohort study, we quantified opioid use for 4 weeks following hospital discharge after cesarean delivery. Predischarge characteristics were obtained from health records, and patients self-reported total opioid use postdischarge on weekly questionnaires. Opioid use was quantified in milligram morphine equivalents (MMEs). Binomial and Poisson regression analyses were performed to assess predictors of opioid use after discharge., Results: Of the 233 patients starting the study, 203 (87.1%) completed at least 1 questionnaire and were included in analyses (86.3% completed all 4 questionnaires). A total of 113 patients were high users (>75 MMEs) and 90 patients were low users (≤75 MMEs) of opioids postdischarge. The group reporting low opioid use received on average 44% fewer opioids in the 24 hours before discharge compared with the group reporting high opioid use (mean = 33.0 vs 59.3 MMEs, P <.001). Only a minority of patients (11.4% to 15.8%) stored leftover opioids in a locked location, and just 31 patients disposed of leftover opioids., Conclusions: Knowledge of predischarge opioid use can be useful as a tool to inform individualized opioid prescriptions, help optimize nonopioid analgesia, and reduce opioid use. Additional studies are needed to evaluate the impact of implementing such measures on prescribing practices, pain, and functional outcomes., (© 2020 Annals of Family Medicine, Inc.)

Aim: The transmission dynamics of Acinetobacter baumannii in endemic settings, and the relation between microbial properties and patients' clinical outcomes, are yet obscure and hampered by insufficient metadata., Methods & Results: Of 20 consecutive patients with A. baumannii bloodstream infection that were thoroughly analyzed at a single center, at least one transmission opportunity was evident for 85% of patients. This implies that patient-to-patient transmission is the major mode of A. baumannii acquisitions in health facilities. Moreover, all patients who died immediately (<24 h of admission) were infected with a single clone (ST457; relative risk = 1.6; p = 0.05)., Conclusion: This preliminary analysis should prompt further investigation by mapping genomic virulence determinants among A. baumannii ST457 lineage compared with other strains.

Sequence-based methods for typing Staphylococcus aureus, such as multilocus sequence typing (MLST) and spa typing, have increased interlaboratory reproducibility, portability, and speed in obtaining results, but pulsed-field gel electrophoresis (PFGE), remains the method of choice in many laboratories due to the extensive experience with this methodology and the large body of data accumulated using the technique. Comparisons between typing methods have been overwhelmingly based on a qualitative assessment of the overall agreement of results and the relative discriminatory indexes. In this study, we quantitatively assess the congruence of the major typing methods for S. aureus, using a diverse collection of 198 S. aureus strains previously characterized by PFGE, spa typing, MLST, and, in the case of methicillin-resistant S. aureus (MRSA), SCCmec typing in order to establish the quantitative congruence between the typing methods. The results of most typing methods agree in that MRSA and methicillin-susceptible S. aureus (MSSA) differ in terms of diversity of genetic backgrounds, with MSSA being more diverse. Our results show that spa typing has a very good predictive power over the clonal relationships defined by eBURST, while PFGE is less accurate for that purpose but nevertheless provides better typeability and discriminatory power. The combination of PFGE and spa typing provided even better results. Based on these observations, we suggest the use of the conjugation of spa typing and PFGE typing for epidemiological surveillance studies, since this combination provides the ability to infer long-term relationships while maintaining the discriminatory power and typeability needed in short-term studies.

We have identified a set of indicators to track usage patterns of ontologies developed using the semantically explicit S3DB model (www.s3db.org, Nature Biotechnology (2006) 24(9):1070-1071). These indicators are quantitative measures that assess the maturity of the data model. As a case study, we have allowed experimental researchers working on molecular epidemiology to incubate a data model for molecular epidemiology by restructuring the underlying ontology and evaluating it with real data.