Polymerase chain reaction for the in vitro detection of the pESI plasmid associated with the globally circulating Salmonella Infantis outbreak strain

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.

Clinical and molecular epidemiology of Acinetobacter baumannii bloodstream infections in an endemic setting

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.

Adapting experimental ontologies for molecular epidemiology

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.