Carolina Duarte

Whole-Genome Sequencing to Determine Origin of Multinational Outbreak of Sarocladium kiliense Bloodstream Infections.

Next-generation technologies and bioinformatics enabled source attribution and implementation of effective control strategies.

Characterization of Streptococcus pneumoniae invasive serotype 19A isolates recovered in Colombia

The aim of this study was to determine the molecular characterization of invasive penicillin non-susceptible Streptococcus pneumoniae serotype 19A isolates, collected in Colombia between 1994 and 2012. A total of 115 isolates serotype 19A were analyzed. Genetic relationship of 80 isolates with minimal inhibitory concentration (MIC) to penicillin ≥0.125 μg/was determined by pulsed-field gel electrophoresis (PFGE) and selected strains were studied by multilocus sequence typing (MLST). Among the 115 isolates, resistance to penicillin in meningitis was 64.2%, in non-meningitis 32.2% were intermediate and 1.1% were high resistance. The most frequent sequence types were ST320 (33.7%), ST276 (21.5%), and ST1118 (11.2%). Five isolates were associated with the Spain(9V)-ST156 clone, and two isolates were related to Colombia(23F)-ST338 clone. S. pneumoniae serotype 19A increased in Colombia was associated with the spread of isolates genetically related to ST320 and ST276, and emergence of capsular variants of worldwide-disseminated clones.

Characterization of Carriage Isolates of Neisseria meningitidis in the Adolescents and Young Adults Population of Bogota (Colombia)

Background Meningococcal carriage studies are important to improve our understanding of the epidemiology of meningococcal disease. The aim of this study was to determine the prevalence of meningococcal carriage and the phenotypic and genotypic characteristics of isolates collected from a sample of students in the city of Bogotá, Colombia. Materials and Methods A total of 1459 oropharyngeal samples were collected from students aged 15–21 years attending secondary schools and universities. Swabs were plated on a Thayer Martin agar and N. meningitidis was identified by standard microbiology methods and PCR. Results The overall carriage prevalence was 6.85%. Carriage was associated with cohabitation with smokers, and oral sex practices. Non-groupable and serogroup Y isolates were the most common capsule types found. Isolates presented a high genetic diversity, and circulation of the hypervirulent clonal complexes ST-23, ST-32 and ST-41/44 were detected. Conclusion The meningococcal carriage rate was lower than those reported in Europe and Africa, but higher than in other Latin American countries. Our data also revealed antigenic and genetic diversity of the isolates and the circulation of strains belonging to clonal complexes commonly associated with meningococcal disease.

Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance

Abstract Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene blaNDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of blaNDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes.

First Complete Providencia rettgeri Genome Sequence, the NDM-1-Producing Clinical Strain RB151

ABSTRACT Providencia rettgeri is an opportunistic bacterial pathogen of clinical significance due to its association with urinary tract infections and multidrug resistance. Here, we report the first complete genome sequence of P. rettgeri. The genome of strain RB151 consists of a 4.8-Mbp chromosome and a 108-kbp blaNDM-1-positive plasmid.

Genomic and Molecular Characterization of Clinical Isolates of Enterobacteriaceae Harboring mcr-1 in Colombia, 2002 to 2016

ABSTRACT Polymyxins are last-resort antimicrobial agents used to treat infections caused by carbapenem-resistant Enterobacteriaceae. Due to the worldwide dissemination of polymyxin resistance in animal and human isolates, we aimed to characterize polymyxin resistance associated with the presence of mcr-1 in Enterobacteriaceae 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 mcr-1-positive isolates, and these were further subjected to whole-genome sequencing (WGS). The localization of mcr-1 was confirmed by S1 pulsed-field gel electrophoresis (S1-PFGE) and CeuI-PFGE hybridization. Transferability was evaluated by mating assays. A total of 12 colistin-resistant isolates recovered after 2013 harbored mcr-1, including 8 Escherichia coli, 3 Salmonella enterica serovar Typhimurium, and 1 Klebsiella pneumoniae isolate. E. coli isolates were unrelated by PFGE and belonged to 7 different sequence types (STs) and phylogroups. S. Typhimurium and K. pneumoniae isolates belonged to ST34 and ST307, respectively. The mcr-1 gene was plasmid borne in all isolates but two E. coli isolates which harbored it on the chromosome. Conjugation of mcr-1 was successful in 8 of 10 isolates (8.2 × 10−5 to 2.07 × 10−1 cell per recipient). Plasmid sequences showed that the mcr-1 plasmids belonged to four different Inc groups (a new IncP-1 variant and the IncFII, IncHI1, and IncH families). Our results indicate that mcr-1 is circulating in clinical isolates of colistin-resistant Enterobacteriaceae in Colombia and is mainly harbored in transferable plasmids.

Molecular Epidemiology of Candida auris in Colombia Reveals a Highly Related, Countrywide Colonization With Regional Patterns in Amphotericin B Resistance

Background Candida auris is a multidrug-resistant yeast associated with hospital outbreaks worldwide. During 2015-2016, multiple outbreaks were reported in Colombia. We aimed to understand the extent of contamination in healthcare settings and to characterize the molecular epidemiology of C. auris in Colombia. Methods We sampled patients, patient contacts, healthcare workers, and the environment in 4 hospitals with recent C. auris outbreaks. Using standardized protocols, people were swabbed at different body sites. Patient and procedure rooms were sectioned into 4 zones and surfaces were swabbed. We performed whole-genome sequencing (WGS) and antifungal susceptibility testing (AFST) on all isolates. Results Seven of the 17 (41%) people swabbed were found to be colonized. Candida auris was isolated from 37 of 322 (11%) environmental samples. These were collected from a variety of items in all 4 zones. WGS and AFST revealed that although isolates were similar throughout the country, isolates from the northern region were genetically distinct and more resistant to amphotericin B (AmB) than the isolates from central Colombia. Four novel nonsynonymous mutations were found to be significantly associated with AmB resistance. Conclusions Our results show that extensive C. auris contamination can occur and highlight the importance of adherence to appropriate infection control practices and disinfection strategies. Observed genetic diversity supports healthcare transmission and a recent expansion of C. auris within Colombia with divergent AmB susceptibility.

Whole-Genome Sequence of a Colombian Acinetobacter baumannii Strain, a Coproducer of OXA-72 and OXA-255-Like Carbapenemases.

ABSTRACT Colombian Acinetobacter baumannii strain ST920 was isolated from the sputum of a 68-year-old male patient. This isolate possessed blaOXA-72 and blaOXA-255-like genes. The assembled genome contained 4,104,098 pb and 38.79% G+C content. This is the first case reported of the coproduction (blaOXA-72 and blaOXA-255-like) of carbapenem-hydrolyzing class D β-lactamases (CHDLs) in Acinetobacter baumannii.

Whole-Genome Sequence of Multidrug-Resistant Campylobacter coli Strain COL B1-266, Isolated from the Colombian Poultry Chain

ABSTRACT Campylobacter coli is considered one of the main causes of food-borne illness worldwide. We report here the whole-genome sequence of multidrug-resistant Campylobacter coli strain COL B1-266, isolated from the Colombian poultry chain. The genome sequences encode genes for a variety of antimicrobial resistance genes, including aminoglycosides, β-lactams, lincosamides, fluoroquinolones, and tetracyclines.

Response to letter by Moreira et al., regarding “PHiD-CV effectiveness against Invasive Pneumococcal Disease caused by Serotype 19A: Further evidence in Colombia”

We thank the comments made by Moreira et al., regarding the rticle published in this journal that shows the importance of the urveillance of Streptococcus pneumoniae serotypes distribution. owever, we think that the data that we published in no way onstitute a further evidence in Colombia of the PHiD-CV effeciveness against IPD caused by serotype 19A for the reasons that ollow. In Colombia, this surveillance has been performing through he SIREVA II network of the Pan American Health Organization, hich the main objective is to generate reliable information on neumococcal serotype distribution in the region. However, refernce lab-based surveillance systems may have limitations as regard dherence to the program by local institutions and underreporting f isolates, which could affect representativeness of data. Considring that the surveillance program started since 1994 and in the rst years were included isolates from children under five years nd from 2000 it was extended to all age groups, with an average f 243 isolates/year [range 127 (1996) – 384 (2012)] [1] sent by 6 public health laboratories, the data show the general trend of S. neumoniae serotype distribution in the country. As we said in the article, during the surveillance we observed n increase of serotype 19A isolates among patients with invasive neumococcal disease. Result that was similar when the analyis of S. pneumoniae serotype distribution was done from 2005 o 2010 [2] and during 2013 (5.5%) [1]. Therefore, the results howed do not depend on a systematic subtraction of vaccine erotypes. Capsular switching is a genetic event in S. pneumoniae with the otential to reduce the efficacy of anti-pneumococcal conjugated accines on the long term [3,4]. Our results offer evidence on the apsular switching between the capsular type of the Spain9V ST156 lone and the 19A capsular type. The Spain9V ST156 clone was he most successful among S. pneumoniae invasive isolates before onjugated vaccines introduction in Colombia [2], therefore, it is