Claudia Gonzalez

Snakebite envenoming is a major neglected public health problem in Panama, yet culture-independent data on the oral microbiota of medically important viperid snakes remain limited. We characterized the oral microbiota of four captive species native to Panama (Bothrops asper, Bothriechis nigroviridis, Cerrophidion sasai, and Porthidium lansbergii) using forward-read analysis of 16S rRNA V3–V4 amplicons and compositional methods. Among 68 retained oral samples, communities were dominated by Pseudomonadota, Bacillota, Actinomycetota, and Bacteroidota. Observed ASV richness differed among species (Kruskal–Wallis H = 21.87, p < 0.001), whereas no significant differences were detected in Shannon diversity or Pielou’s evenness. Richness differences require caution because sequenced negative controls were unavailable and no independent depth-aware sensitivity analysis was performed. Community composition was significantly associated with host species (PERMANOVA R² = 0.197, p = 0.001), although PERMDISP detected heterogeneous within-group dispersion (p = 0.005), requiring cautious interpretation. ANCOM-BC2 identified 21 differentially abundant genera, including Providencia, Morganella, Pseudomonas, Stenotrophomonas, and Staphylococcus, with high relative abundance of Mycoplasma in a subset of P. lansbergii samples. These findings provide a culture-independent taxonomic baseline for future culture-based, antimicrobial-susceptibility, and paired snake-oral/human-wound investigations in Panama.

This study provides a comprehensive overview of SARS-CoV-2 genomic surveillance in Central America and the Dominican Republic from February 2020 to January 2023, highlighting the collaborative efforts of the Pan American Health Organization (PAHO), and the Council of Ministers of Health of Central America (COMISCA). A total of 26, 595 sequences from the GISAID database were analyzed, correlating findings with key events reported by participating entities. The genomic analysis reveals significant co-circulation of variants, with notable lineage diversity observed throughout the pandemic. Variants of concern (VOC) like Alpha, Gamma, Delta and Omicron were identified alongside variants of interest (VOI) like Lambda and Mu. The emergence of recombinant lineages further illustrates the ongoing evolution of the virus and its spread across the region, underscoring the interconnectedness of Central America and the Dominican Republic. The collaborative model facilitated broader sequencing coverage, enabling more extensive surveillance than individual countries could achieve alone. Despite the successes of regional collaborations, challenges remain, particularly regarding sequencing capacity in countries impacted by socioeconomic inequalities. Addressing these gaps is essential to enhance public health responses to current and future pandemics.

Rickettsia rickettsii is the most virulent agent of the genus Rickettsia that causes one of the most relevant vector-borne diseases in the Americas (RRSF). RRSF manifests with many non-specific acute clinical symptoms complicating its diagnosis and can lead to death if not treated appropriately. RRSF has been reported in Canada, the United States of America, Mexico, Costa Rica, Panama, Colombia, Brazil, and Argentina. In addition to R. rickettsii, mild and severe spotted fever group rickettsioses (SFGR) have been reported in the Americas; however, the true prevalence of these diseases is unknown. In Panama, RRSF have been reported in four of 14 provinces during two outbreak periods: five cases including two fatalities were identified in 1950–1951, and 23 cases including 17 fatalities between 2004 and 2025. This paper presents the clinical characterization of a fatal case of RRSF in Coclé province and a severe case of SFGR in a mountainous area of the Gnäbe Buglé Indigenous Comarca (GBIC). Laboratory confirmation was performed by molecular analysis of tissues obtained from necropsies in the case of RRSF and by immunofluorescence assay (IFA) in the case of SFGR. Furthermore, this paper identifies existing gaps in the initial clinical suspicion and pertinent to SFGR in Panama, which may be applicable to other countries in the region. In the last 21 years, cases have occurred upon contact with ticks in rural areas (13), urban and suburban locations (7), rural woodlands (2), and forests (1). Provinces with more cases are Panamá (7 of 23, 6 died), Coclé (5 of 23, 5 died), Colón (3 of 23, 1 died), Panamá Oeste (1 of 23, 1 died), and GBIC (7 of 23, 4 died), including a cluster of seven cases in 2019. Therefore, Coclé province is considered one of the endemic areas for RRSF in Panama, while the latest cases from the GBIC since 2019 indicate that mountainous areas are an eco-epidemiological scenario to include in the transmission of these diseases. Although this disease has a low prevalence, patients who present symptoms commonly associated with more common diseases such as dengue, other arboviruses, malaria, and leptospirosis, among others, should be included in the diagnostic suspicion. Without diagnostic suspicion and adequate treatment, the patient can die.

Soil, rhizosphere, and plant-associated microorganisms can enhance plant growth and health. A genomic analysis of these microbes revealed the key characteristics contributing to their beneficial effects. Following a field survey in Panama, four bacterial isolates with plant growth-promoting traits (PGPT) in rice (Oryza sativa L.) were identified. In this study, we sequenced, assembled, and annotated the genomes of Lysinibacillus fusiformis C6 and 24, and Bacillus cereus D23 and 59. The C6 genome was 4,754,472 bp long with 10 contigs, 37.62% guanine-cytosine (GC) content, and 4657 coding sequences (CDS). The 24 genome was 4,683,219 bp with five contigs, 37.65% GC content, and 4550 CDS. The D23 genome was 6,199,908 bp long with 18 contigs, 34.84% GC content, and 6141 CDS. The 59 genome was 6,194,462 bp with 21 contigs, 34.87% GC content, and 6122 CDS. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) confirmed that C6 and 24 belong to Lysinibacillus fusiformis, whereas D23 and 59 belong to the Bacillus cereus species. Further results revealed that these bacteria contained genes characteristic of plant growth-promoting bacteria, such as siderophore, phytohormone auxin (IAA) production, and nitrogen-fixing abilities that promote plant growth. Moreover, the antiSMASH database identified gene clusters involved in secondary metabolite production (biosynthetic gene clusters), such as betalactone, NRPS-like, NRP-siderophore, terpene, and RiPP-like clusters. Moreover, diverse and novel biosynthetic clusters (BCGs) have included non-ribosomal peptides (NRPs), polyketides (PKs), bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). This work offers new insights into the genomic basis of the studied strains’ plant growth-promoting capabilities.

Chlamydia trachomatis (CT) is a bacterium that causes one of the most common sexually transmitted infections (STIs) worldwide. In Panama, the prevalence of genital Chlamydia trachomatis (CT) among adolescents is 15.8%. However, no data describing circulating CT genotypes or evaluating molecular resistance are available. This study aims to determine the genotypes of genital CT infections and explore the macrolide resistance-associated mutations in this population to contribute to baseline information about CT circulating strains and antimicrobial resistance. Genomic analysis was performed on CT-positive, first-void urine specimens from school-going adolescents (14–19 years) in urban regions in Panama. The ompA gene was used for genotype and phylogenetic analysis, and the rplD, rplV, and 23S rRNA genes were used for molecular resistance analysis. Five genotypes were found: D, 15 (47%); F, 9 (28%); E, 4 (13%); Ia, 2 (6%); and Ja, 2 (6%) genotype Ja. A triple mutation (G52S, R65C, and V77A) was found in the rplV gene, though no mutations of interest were found for the rplD and 23S rRNA genes. The present study indicated CT genotype D had increased circulation within the population; mutations indicative of macrolide resistance were not found. Follow-up studies and implementation of active surveillance are necessary to understand the circulation of CT in Panama.

Low-frequency mutations associated with drug resistance have been related to virologic failure in subjects with no history of pre-treatment and recent HIV diagnosis. In total, 78 antiretroviral treatment (ART)-naïve subjects with a recent HIV diagnosis were selected and followed by CD4+ T lymphocytes and viral load tests to detect virologic failure. We sequenced the basal samples retrospectively using next-generation sequencing (NGS), looking for low-frequency mutations that had not been detected before using the Sanger sequencing method (SSM) and describing the response to ART. Twenty-two subjects developed virologic failure (VF), and thirteen of them had at least one drug-resistance mutation associated with Reverse Transcriptase Inhibitors (RTI) and Protease Inhibitors (PIs) at frequency levels ≤ 1%, not detected previously in their basal genotyping test. No resistance mutations were observed to Integrase Strand Transfer Inhibitors (INSTIs). We identified a possible cause of VF in ART-naïve subjects with low-frequency mutations detected. To our knowledge, this is the first evaluation of pre-existing drug resistance for HIV-1 minority variants carried out on ART-naïve people living with HIV/AIDS (PLWHA) by analyzing the HIV-1 pol gene using NGS in the country.

Summary: Background: With more than 50000 accumulated cases, Panama has one of the highest incidences of SARS-CoV-2 in Central America, despite the fast implementation of disease control strategies. We investigated the early transmission patterns of the virus and the outcomes of mitigation measures in the country. Methods: We collected information from epidemiological surveillance, including contact tracing, and genetic data from SARS-CoV-2 whole genomes, of the first five weeks of the outbreak. These data were used to estimate the exponential growth rate, doubling time and the time-varying effective reproductive number (Rt) using date of symptom onset in a Bayesian framework. The time of most recent ancestor for the introduced and circulating lineages was estimated by Bayesian analysis. Findings: A total of 4210 subjects were SARS-CoV-2 positive during the period evaluated, of them we sequenced 313 cases, detecting the circulation of 10 SARS-CoV-2 lineages. Whole genomes analysis identified the local transmission of one cryptic lineage as early as 2 weeks before it was detected by surveillance systems. Analysis of transmission dynamics showed that lockdown reduced Rt and increased the doubling time, however, these measures did not stop the circulation of this lineage in the country. Interpretation: These results demonstrate the value of epidemiological modeling and genome surveillance to assess mitigation strategies. At the same time, an active search for cryptic transmission clusters is crucial to interrupt local transmission of SARS-CoV-2 in a region. Funding: Ministry of Health, Contribution from private donors and Secretaría Nacional de Ciencia y Tecnología. Research in Context: Evidence before this study: In May 2020, we searched for published studies in PubMed and web of Science related to genetic variability and dynamics of SARS-CoV-2 transmission in Latin America, and there was none. On July 2020, there was one study of this type on SARS-CoV-2 transmission in Brazil and none in Central America. We were particularly interested in SARS-CoV-2 cryptic transmission that could allow the virus spread through locals without being detected by respiratory health system surveillance, and no publication was reported. On July 2020, seven papers (five in preprint) were about SARS-CoV-2 cryptic transmission, one in China, another in UK and five in the US. None in Central America. All of them showed the importance of genomic surveillance to detect different lineage introductions, cryptic transmission and its role in early spread in a region or in health-care setting. Added value of this study: We integrate data collected from tested individual during national surveillance of COVID19 suspected cases or contact of cases, as part of the National COVID19 Laboratory network. This data was used to estimate epidemiological parameters of the outbreak as well as the effect of mitigation measures on the epidemic dynamic. We sequence the whole genome of SARS-COV-2 of 7.4% of RT-PCR confirmed cases at the national level, and with phylogenetic analysis we identified SARS-CoV-2 lineages introduced in the country and estimate date of their introductions. Epidemiological and genetic data was compared and we observed the cryptic transmission of one introduced lineage and the rise of a local lineage that was not detected by the active contact tracing implemented by the health system surveillance. This cryptic lineage could explain the fact that early implementation measures decreased the transmission rate and the increased the doubling time, however they were not able to eliminate totally the virus spread. Implications of all the available evidence: This is the first study that analyzed the epidemiology and transmission dynamics of the early COVID19 epidemic in a Central American country using both epidemiological and genomic surveillance. Our findings suggest that strict containment measures and movement restrictions in Panama might have contributed to decrease the early spread of the virus, but that cryptic local transmission allowed a continual basal virus diffusion that could explain, in part, the high incidence of cases in the country. More broadly, our findings are crucial to inform intervention policy in real-time, for countries in similar situations and the importance of constant monitoring of SARS-CoV-2 lineages to understand its transmission in a region.