Integrating Scalable Genome Sequencing Into Microbiology Laboratories for Routine Antimicrobial Resistance Surveillance.

Antimicrobial resistance (AMR) is considered a global threat, and novel drug discovery needs to be complemented with systematic and standardized epidemiological surveillance. Surveillance data are currently generated using phenotypic characterization. However, due to poor scalability, this approach does little for true epidemiological investigations.

Complexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs.

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)'s 2013-2017 sample collection.

Methods: A total of 425 CRKP isolates from 21 departments were analyzed by HiSeq-X10®Illumina high-throughput sequencing.

An outbreak of Salmonella enterica subsp. enterica serovar Give associated with foodborne illness in the department of Vichada, Colombia, 2015.

Introduction: Salmonella enterica subsp. enterica serovar Give is found in ruminants, pigs, poultry, and aquatic environments, but rarely in humans. In Colombia, this serotype was ranked 11th.

Genomic and Molecular Characterization of Clinical Isolates of Enterobacteriaceae Harboring in Colombia, 2002 to 2016.

Polymyxins are last-resort antimicrobial agents used to treat infections caused by carbapenem-resistant Due to the worldwide dissemination of polymyxin resistance in animal and human isolates, we aimed to characterize polymyxin resistance associated with the presence of in and nonfermenter Gram-negative bacilli, using isolates collected retrospectively in Colombia from 2002 to 2016. A total of 5,887 Gram-negative clinical isolates were studied, and 513 were found to be resistant to the polymyxins. Susceptibility to colistin was confirmed by broth microdilution for all -positive isolates, and these were further subjected to whole-genome sequencing (WGS).