Carolina Duarte

Background. Infections caused by Streptococcus pneumoniae are a public health problem worldwide, and penicillin-non-susceptible isolates are a priority for the World Health Organization, which requires further research and development of new antibiotics and vaccines. Aim. To describe the global pneumococcal sequence clusters (GPSCs) among penicillin non-susceptible S. pneumoniae isolates obtained from patients with invasive pneumococcal disease in Colombia after the introduction of PCV10 (Synflorix, GlaxoSmithKline) to generate data on the genetic structure of pneumococcal populations with different antimicrobial susceptibilities. Methods. A subset of 313 pneumococcal isolates with values of Minimum Inhibitory Concentration to penicillin of ≥0.125 µg ml ⁻¹ , collected through the National Reference Laboratory at the National Health Institute of Colombia, were characterized by whole-genome sequencing to determine the GPSCs, serotypes, sequence types, antimicrobial resistance determinants and pilus islets. Results. Most of the isolates (80%, n =251) were clustered in seven GPSCs: multidrug-resistant GPSC1 (40.6%, n =127) conformed principally to serotype 19A isolates and ST320, GPSC5 (10.5%, n =33) associated with ST338 and isolates of serogroups 23 and 6, GPSC13 (7.3%, n =23) which clustered 68% of 6A isolates, GPSC10 (7.0%, n =22) with 19A and 24F isolates, GPSC6 (5.4%, n =17) related to ST156, GPSC9 (4.8%, n =15) conformed to isolates 15A, 19 F/A and 6A and GPSC47 (4.5%, n =14) with 6C isolates. Only three isolates with PCV10 serotypes were recovered from children younger than 5 years old. Conclusion. The results revealed changes in the population structure expected after PCV10 introduction, with GPSC1 being the most important clone due to its association with multidrug resistance. Genome sequencing of clinical multidrug-resistant isolates contributes to elucidating the antibiotic resistance mechanism and understanding the global pneumococcal population structure.

Background: PCV10 was introduced in Colombia in 2011, and PCV13 in 2022; however, there is limited evidence on long-term pneumococcal serotype dynamics and potential impact of new PCVs. Methods: We conducted a retrospective analysis using national surveillance data on IPD isolates from children and adults collected between 2005 and 2023. The study period included a pre‑vaccine era (2005–2009) and four subsequent periods during which PCV7, PCV10, and PCV13 were successively introduced. Temporal trends in serotype distribution were assessed using χ² tests. Theoretical vaccine coverage was estimated for licensed PCVs (10, 13, 15, 20, and 21) and for forthcoming formulations (PCV24 and PCV25). Results: 7,824 IPD isolates were included in the analysis. Following universal introduction of PCV10, most PCV10 serotypes declined across all age groups. By contrast, serotype 19A increased substantially over the study period. It rose from 3% of all isolates in 2005–2009 to 33% in 2023. Non‑PCV13 serotypes—especially 6C, 23A, and 15A—increased from 22% in 2005–2009 to 46% in 2013–2018. PCV21, PCV24, and PCV25 covered approximately 82–87% of all serotypes detected between 2019–2023 among infants <2 years and 74–78% among adults. Among antimicrobial‑resistant serotypes, 19A became the predominant serotype. Consequently, most next‑generation PCVs provide substantial coverage of antimicrobial resistance. Conclusions: In Colombia, PCV 10 vaccination was followed by a decrease in PCV10 serotypes and a substantial increase in 19A and Non-PCV13 serotypes. Continued nationwide surveillance remains critical to tracking serotype trends and informing vaccination policy about new PCVs introduction.

Background: Invasive non-typhoidal Salmonella disease is a leading cause of morbidity and mortality worldwide, primarily affecting children, the elderly, and immunocompromised adults, particularly those living with HIV. Salmonella meningitis is rare, except in sub-Saharan Africa. Salmonella arizonae is associated with reptiles and exceptionally causes meningitis in humans. Case Summary: We present the case of an adult man living with HIV who presented five episodes of bacterial meningitis due to S. arizonae within a period of 8 months. The patient improved after performing cholecystectomy and with optimization of antiretroviral treatment and prolonged antibiotic therapy. Genomic study confirmed that S. arizonae is sensitive to antibiotics. Conclusion: This case illustrates a rare form of S. arizonae meningitis. The identity of the etiological agent was confirmed by next-generation sequencing analysis.

Pertussis and COVID-19 are respiratory diseases with similar clinical manifestations, complicating diagnosis. In Colombia, pertussis surveillance is based on probable cases confirmed through laboratory detection of Bordetella pertussis . During the COVID-19 pandemic, pertussis incidence declined sharply. Given limited data on coinfections with COVID-19 and pertussis, this study aimed to estimate the positivity of Bordetella spp. in SARS-CoV-2-positive samples collected in Colombia during 2021–2022. A retrospective analysis was conducted on samples collected between January 2021 and December 2022 through simple random sampling from specimens stored at the National Reference Laboratory (NRL). Demographic data, symptoms, complications, and race were obtained from the National Surveillance System (SIVIGILA), and PCR results were used to identify Bordetella spp. coinfections. National and departmental positivity rates were estimated with Clopper-Pearson confidence intervals. PCR testing for Bordetella spp. was positive in 0.54% (6/1,102) of samples, with four cases involving B. pertussis and two involving B. parapertussis ; no B. holmesii coinfections were detected. The national positivity rate of SARS-CoV-2 and Bordetella spp. coinfections was 1.92% in 2021, decreasing to 1.25% in 2022. Although coinfections with viral agents and B. pertussis are common, this study found low positivity of SARS-CoV-2 and Bordetella spp. coinfections in Colombia during 2021–2022, likely due to non-pharmacological interventions, the cyclical pattern of B. pertussis , and possible underestimation related to the geographic and demographic scope of the sample. This is the first report of such coinfections in Colombia, offering a reference for future studies in Latin America. IMPORTANCE: This is the first report of SARS-CoV-2 and Bordetella spp. coinfections in Colombia, providing key evidence of their low occurrence during 2021–2022. Given that both diseases share clinical features and may complicate differential diagnosis, these findings underscore the importance of integrated surveillance for respiratory pathogens. The observed decrease in positivity may be linked to non-pharmaceutical interventions and the cyclical nature of pertussis, while also highlighting potential limitations in the geographic and demographic representativeness of the sample. This study offers a valuable baseline for future research in Latin America and reinforces the need to strengthen diagnostic capacity to detect coinfections, particularly in epidemic or pandemic contexts.

Globally, the increasing reports of resistance to ceftazidime-avibactam (CZA) in Enterobacterales are concerning. In this paper we describe an isolate of Klebsiella quasipneumoniae (GMR-RA-2034.23) highly resistant to ceftazidime-avibactam, ceftolozane-tazobactam, ceftazidime and cefotaxime in which a new variant of the PAC ß-lactamase, designated PAC-2 by the NCBI, was identified. The bla PAC-2 gene is encoded in a non-conjugative plasmid type IncQ (9,452 bp). The GMR-RA-2034.23 isolate did not present mutations in the OmpK 35 or OmpK 36 porins, associated with resistance to CZA. This is the first description of PAC-type ß-lactamase in Colombia. Continuous monitoring of mechanisms of resistance to CZA is crucial to prevent its spread.

Introducción: Ante la alerta epidemiológica emitida por la Organización Panamericana de la Salud / Organización Mundial de la Salud (OPS/OMS) sobre mucormicosis asociada a COVID-19 (CAM) el Instituto Nacional de Salud (INS) implementó la vigilancia nacional por laboratorio obligatoria para esta micosis. Objetivo: Describir los hallazgos de la vigilancia por laboratorio de CAM en Colombia durante julio 2021 a enero de 2022. Métodos: De acuerdo con los lineamientos emitidos por el INS, se realizó el diagnóstico de mucormicosis por histopatología y cultivo de pacientes que cumplían la sospecha clínica y previo diagnóstico de la micosis realizado por personal de los laboratorios de las Unidades Primarias Generadoras de Datos (UPGD). Resultados: En Colombia se notificaron 16 casos de CAM, de los cuales 10 fueron confirmados y 6 descartados, provenientes de siete departamentos del país. Conclusiones: Los resultados confirman la presencia de casos de CAM en nuestro país, haciendo énfasis en la necesidad de realizar una rápida intervención diagnóstica y terapéutica multidisciplinaria derivada de la toma de acciones de prevención y control oportunas.

Foodborne diseases represent a link between environmental, animal, and human health interfaces from the One Health perspective. Whole genome sequencing (WGS) is becoming the gold standard in foodborne surveillance, worldwide. WGS than provides precision data from pathogens allows laboratories to resolve the genetic relations among all sources from One Health perspective, especially during outbreak investigations, getting insights into their transmission routes and pathogenicity. Salmonella spp. is the most prevalent foodborne bacteria in Colombia, in 2020, 268 foodborne outbreaks were reported to National health institute (INS) and 3079 invasive and faecal salmonellosis samples from 81% of the Colombian geographical regions. Several studies in different food sources exhibited an increase of contamination with Salmonella , a public health concern due to the steady development of antimicrobial resistance associated to specific serovars. However, integration of Salmonella spp . data including food-chain supply and clinical interfaces is very scarce in Colombia. This study carried out a national comparison of Salmonella isolates collected from food-chain supply and clinical sources. Using an epidemiological and phenotypic approach, we demonstrated the higher resolution of WGS compared with PFGE, routinely used in Salmonella surveillance in Colombia. For example, the resolution of PFGE allowed the description of two main clusters of food Salmonella Enteritidis isolates which were expanded to eight clades by using WGS. Virulence factors and antimicrobial determinant genes observed in the foodborne clades should be considered a public health concern in Colombia. WGS is a technology that provides precise and valid evidence for the establishment of dissemination routes of foodborne high-risk Salmonella clades, but it requires an integrative and continued collaboration between the stakeholders across the One Health interfaces to promote and support integrated real-time actions in public health.