Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis

Multilocus sequence typing (MLST) has become a useful tool for studying the genetic diversity of important public health pathogens, such as Chlamydia trachomatis (Ct). Four MLST schemes have been proposed for Ct (data available from Chlamydiales MLST databases). However, the lack of a sole standardized scheme represents the greatest limitation regarding typing this species. This study was thus aimed at evaluating the usefulness of the four MLST schemes available for Ct, describing each molecular marker's pattern and its contribution toward a description of intra-specific genetic diversity and population structure. The markers for each scheme, showed a variable power of dicrimination, exhibiting in some cases over estimation in the determination of Sequence Types (STs). However, individual analysis of each locus's typing efficiency and discrimination power led to identifying 8 markers as having a suitable pattern for intra-specific typing. analyzing the 8 candidate markers gave a combination of 3 of these loci as an optimal scheme for identifying a large amount of STs, maximizing discrimination power whilst maintaining suitable typing efficiency. One scheme was compared against core genome phylogenies, finding a higher typing resolution through the last approach. These results confirm once again that although complete genome data, in particular from core genome MLST (cgMLST) allow a high resolution clustering for Ct isolates. There are combinations of molecular markers that could generate equivalent results, with the advantage of representing an easy implementation strategy and lower costs leading to contribute to the monitoring and molecular epidemiology of Ct

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Genomic and transcriptomic comparative in Leishmania species from Colombia

La Leishmaniasis es una enfermedad tropical ocasionada por parásitos protozoarios del género Leishmania. En Colombia esta enfermedad representa un grave problema de salud pública debido al elevado número de casos reportados anualmente, la cantidad de especies encontradas y la aparición de cepas resistentes, principalmente frente a los medicamentos de primera línea: antimoniato N-metil glucamina (Glucantime®). Hasta el momento, varios estudios utilizando técnicas de secuenciación de última generación y basados en herramientas como las “omicas” han proporcionado información crucial con respecto a los mecanismos de resistencia y adaptación utilizados por estos parásitos frente a los antimoniales. Sin embargo, este conocimiento en especies de Leishmania del nuevo mundo son escasos, así como estudios que permitan describir la arquitectura genómica intra-especifica en estas especies. Teniendo en cuenta lo anterior, este estudio evaluó el comportamiento genómico y transcriptómico de las principales especies de Leishmania que circulan en Colombia bajo la presión al N-metil glucamina (Glucantime® (SbIII), así como la arquitectura genómica de estas especies, obtenidas a partir de aislamientos clínicos. Los resultados producto de esta tesis permitieron describir que (i) la distribución de las especies de Leishmania a nivel urbano/selvático es diferente, (ii) los cambios genómicos y transcriptómicos en respuesta a los antimoniales trivalentes es una característica compartida entre especies del viejo y del nuevo mundo y (iii) describir la baja variación estructural encontrada en Leishmania braziliensis y Leishmania panamensis. Finalmente, consideramos que estudios adicionales son necesarios con el propósito de seguir ampliando el conocimiento acerca de los mecanismos de adaptación de este parásito.Leishmaniasis is a tropical disease caused by protozoan parasites of the genus Leishmania. In Colombia, this disease represents a serious public health problem due to the high number of cases reported annually, the number of species found and the appearance of resistant strains, mainly compared to first-line drugs: N-methyl glucamine antimoniato (Glucantime®) . So far, several studies using next generation sequencing and tools based on “omicas” have provided crucial information regarding the resistance and adaptation mechanisms used by these parasites against antimonials. However, this knowledge in Leishmania species of the new world is scarce, as well as studies that allow to describe the intra-specific genomic architecture in these species. Taking into account the above, this study evaluated the genomic and transcriptomic behavior of the main Leishmania species that circulate in Colombia under the pressure of N-methyl glucamine (Glucantime® (SbIII), as well as the genomic architecture of these species, obtained at from clinical isolates. The results of this thesis allowed us to describe that (i) the distribution of Leishmania species at urban / jungle level is different, (ii) genomic and transcriptomic changes in response to trivalent antimonials is a characteristic shared between species of the old and of the new world and (iii) describe the low structural variation found in Leishmania braziliensis and Leishmania panamensis. Finally, we consider that additional studies are necessary in order to continue expanding the knowledge about the adaptation mechanisms of this parasite.Departamento administrativo de Ciencia, Tecnología e Innovación (Colciencias), dentro del marco del Programa Nacional para promover la formación en la investigación (convocatoria 647)Dirección Académica de la Universidad del RosarioDirección de Investigación e Innovación de la Universidad del Rosari

Genomic and transcriptomic comparative in Leishmania species from Colombia

La Leishmaniasis es una enfermedad tropical ocasionada por parásitos protozoarios del género Leishmania. En Colombia esta enfermedad representa un grave problema de salud pública debido al elevado número de casos reportados anualmente, la cantidad de especies encontradas y la aparición de cepas resistentes, principalmente frente a los medicamentos de primera línea: antimoniato N-metil glucamina (Glucantime®). Hasta el momento, varios estudios utilizando técnicas de secuenciación de última generación y basados en herramientas como las “omicas” han proporcionado información crucial con respecto a los mecanismos de resistencia y adaptación utilizados por estos parásitos frente a los antimoniales. Sin embargo, este conocimiento en especies de Leishmania del nuevo mundo son escasos, así como estudios que permitan describir la arquitectura genómica intra-especifica en estas especies. Teniendo en cuenta lo anterior, este estudio evaluó el comportamiento genómico y transcriptómico de las principales especies de Leishmania que circulan en Colombia bajo la presión al N-metil glucamina (Glucantime® (SbIII), así como la arquitectura genómica de estas especies, obtenidas a partir de aislamientos clínicos. Los resultados producto de esta tesis permitieron describir que (i) la distribución de las especies de Leishmania a nivel urbano/selvático es diferente, (ii) los cambios genómicos y transcriptómicos en respuesta a los antimoniales trivalentes es una característica compartida entre especies del viejo y del nuevo mundo y (iii) describir la baja variación estructural encontrada en Leishmania braziliensis y Leishmania panamensis. Finalmente, consideramos que estudios adicionales son necesarios con el propósito de seguir ampliando el conocimiento acerca de los mecanismos de adaptación de este parásito.Leishmaniasis is a tropical disease caused by protozoan parasites of the genus Leishmania. In Colombia, this disease represents a serious public health problem due to the high number of cases reported annually, the number of species found and the appearance of resistant strains, mainly compared to first-line drugs: N-methyl glucamine antimoniato (Glucantime®) . So far, several studies using next generation sequencing and tools based on “omicas” have provided crucial information regarding the resistance and adaptation mechanisms used by these parasites against antimonials. However, this knowledge in Leishmania species of the new world is scarce, as well as studies that allow to describe the intra-specific genomic architecture in these species. Taking into account the above, this study evaluated the genomic and transcriptomic behavior of the main Leishmania species that circulate in Colombia under the pressure of N-methyl glucamine (Glucantime® (SbIII), as well as the genomic architecture of these species, obtained at from clinical isolates. The results of this thesis allowed us to describe that (i) the distribution of Leishmania species at urban / jungle level is different, (ii) genomic and transcriptomic changes in response to trivalent antimonials is a characteristic shared between species of the old and of the new world and (iii) describe the low structural variation found in Leishmania braziliensis and Leishmania panamensis. Finally, we consider that additional studies are necessary in order to continue expanding the knowledge about the adaptation mechanisms of this parasite.Departamento administrativo de Ciencia, Tecnología e Innovación (Colciencias), dentro del marco del Programa Nacional para promover la formación en la investigación (convocatoria 647)Dirección Académica de la Universidad del RosarioDirección de Investigación e Innovación de la Universidad del Rosari

Minor temperature shifts do not affect chromosomal ploidy but cause transcriptomic changes in Leishmania braziliensis promastigotes in vitro

ANTECEDENTES Las leishmaniasis son enfermedades descuidadas complejas causadas por parásitos protozoarios del género Leishmania. Leishmania braziliensis es el principal agente etiológico de la leishmaniasis cutánea en el Nuevo Mundo. En estudios recientes, los cambios genómicos, como las variaciones en el número de copias de genes y cromosomas (CNV), así como los cambios transcriptómicos se han destacado como mecanismos utilizados por las especies de Leishmania para adaptarse a situaciones de estrés. OBJETIVOS El objetivo de este estudio fue determinar el efecto de cambios de temperatura menores a corto plazo en las respuestas genómicas y transcriptómicas de promastigotes in vitro de L. braziliensis. MÉTODOS Se realizaron curvas de crecimiento, secuenciación del genoma y transcriptoma de promastigotes de L. braziliensis de cultivos expuestos a tres temperaturas diferentes (24ºC, 28ºC y 30ºC) en comparación con la temperatura de control (26ºC). HALLAZGOS Nuestros resultados mostraron una disminución en la proliferación de L. braziliensis a 30ºC, con alrededor del 3% de los genes que muestran CNV a cada temperatura, y cambios transcriptómicos en los genes que codifican las proteínas de superficie de amastina, proteínas de choque térmico y proteínas de transporte, lo que puede indicar una respuesta directa al estrés por temperatura. Conclusiones principales Este estudio proporciona evidencia de que los promastigotos de L. braziliensis exhiben una disminución en la densidad celular y cambios notables en los perfiles transcriptómicos. Sin embargo, no hubo cambios perceptibles en las CNV cromosómicas y solo ~ 3% de los genes cambiaron sus copias en cada tratamiento.BACKGROUND The leishmaniases are complex neglected diseases caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the main etiological agent of cutaneous leishmaniasis in the New World. In recent studies, genomic changes such as chromosome and gene copy number variations (CNVs), as well as transcriptomic changes have been highlighted as mechanisms used by Leishmania species to adapt to stress situations. OBJECTIVES The aim of this study was to determine the effect of short-term minor temperature shifts in the genomic and transcriptomic responses of L. braziliensis promastigotes in vitro. METHODS Growth curves, genome and transcriptome sequencing of L. braziliensis promastigotes were conducted from cultures exposed to three different temperatures (24ºC, 28ºC and 30ºC) compared with the control temperature (26ºC). FINDINGS Our results showed a decrease in L. braziliensis proliferation at 30ºC, with around 3% of the genes showing CNVs at each temperature, and transcriptomic changes in genes encoding amastin surface-like proteins, heat shock proteins and transport proteins, which may indicate a direct response to temperature stress. MAIN CONCLUSIONS This study provides evidence that L. braziliensis promastigotes exhibit a decrease in cell density, and noticeable changes in the transcriptomic profiles. However, there were not perceptible changes at chromosome CNVs and only ~3% of the genes changed their copies in each treatment

Unveiling the multilocus sequence typing (MLST) schemes and core genome phylogenies for genotyping chlamydia trachomatis

Multilocus sequence typing (MLST) has become a useful tool for studying the genetic diversity of important public health pathogens, such as Chlamydia trachomatis (Ct). Four MLST schemes have been proposed for Ct (data available from Chlamydiales MLST databases). However, the lack of a sole standardized scheme represents the greatest limitation regarding typing this species. This study was thus aimed at evaluating the usefulness of the four MLST schemes available for Ct, describing each molecular marker's pattern and its contribution toward a description of intra-specific genetic diversity and population structure. The markers for each scheme, showed a variable power of dicrimination, exhibiting in some cases over estimation in the determination of Sequence Types (STs). However, individual analysis of each locus's typing efficiency and discrimination power led to identifying 8 markers as having a suitable pattern for intra-specific typing. analyzing the 8 candidate markers gave a combination of 3 of these loci as an optimal scheme for identifying a large amount of STs, maximizing discrimination power whilst maintaining suitable typing efficiency. One scheme was compared against core genome phylogenies, finding a higher typing resolution through the last approach. These results confirm once again that although complete genome data, in particular from core genome MLST (cgMLST) allow a high resolution clustering for Ct isolates. There are combinations of molecular markers that could generate equivalent results, with the advantage of representing an easy implementation strategy and lower costs leading to contribute to the monitoring and molecular epidemiology of Ct. © 2018 Patiño, Camargo, Muñoz, Ríos-Chaparro, Patarroyo and Ramírez

Unveiling the multilocus sequence typing (MLST) schemes and core genome phylogenies for genotyping chlamydia trachomatis

Multilocus sequence typing (MLST) has become a useful tool for studying the genetic diversity of important public health pathogens, such as Chlamydia trachomatis (Ct). Four MLST schemes have been proposed for Ct (data available from Chlamydiales MLST databases). However, the lack of a sole standardized scheme represents the greatest limitation regarding typing this species. This study was thus aimed at evaluating the usefulness of the four MLST schemes available for Ct, describing each molecular marker's pattern and its contribution toward a description of intra-specific genetic diversity and population structure. The markers for each scheme, showed a variable power of dicrimination, exhibiting in some cases over estimation in the determination of Sequence Types (STs). However, individual analysis of each locus's typing efficiency and discrimination power led to identifying 8 markers as having a suitable pattern for intra-specific typing. analyzing the 8 candidate markers gave a combination of 3 of these loci as an optimal scheme for identifying a large amount of STs, maximizing discrimination power whilst maintaining suitable typing efficiency. One scheme was compared against core genome phylogenies, finding a higher typing resolution through the last approach. These results confirm once again that although complete genome data, in particular from core genome MLST (cgMLST) allow a high resolution clustering for Ct isolates. There are combinations of molecular markers that could generate equivalent results, with the advantage of representing an easy implementation strategy and lower costs leading to contribute to the monitoring and molecular epidemiology of Ct. © 2018 Patiño, Camargo, Muñoz, Ríos-Chaparro, Patarroyo and Ramírez

Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries

Genomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage’s genomic and epidemiological characteristics. However, in South America, this variant’s arrival and genomic diversity are scarcely known. Therefore, this study determined the genomic diversity and phylogenetic relationships of 21,615 Omicron genomes available in public databases. We found that in South America, BA.1 (n = 15,449, 71%) and BA.1.1 (n = 6257, 29%) are the dominant sublineages, with several mutations that favor transmission and antibody evasion. In addition, these lineages showed cryptic transmission arriving on the continent in late September 2021. This event may have contributed to the dispersal of Omicron sublineages and the acquisition of new mutations. Considering the genomic and epidemiological characteristics of these lineages, especially those with a high number of mutations in their genome, it is important to conduct studies and surveillance on the dynamics of these lineages to identify the mechanisms of mutation acquisition and their impact on public health

Draft genomes of Blastocystis subtypes from human samples of Colombia

Background Blastocystis is one of the most common eukaryotic microorganisms colonizing the intestines of both humans and animals, but the conditions under which it may be a pathogen are unclear. Methods To study the genomic characteristics of circulating subtypes (ST) in Colombia, we established nine xenic cultures from Blastocystis isolated from human fecal samples, we identifed 10 diferent subtypes, since one sample had a mixed infection. Thus, the genomes of the subtypes ST1 (n=3), ST2 (n=1), ST3 (n=2), ST6 (n=1), ST7 (n=1), and ST8 (n=2) were sequenced using Illumina and Oxford Nanopore Technologies (ONT). Results Analyses of these draft nuclear genomes indicated remarkable diversity in terms of genome size and guanine-cytosine (GC) content among the compared STs. Illumina sequencing-only draft genomes contained 824 to 2077 scafolds, with total genome size ranging from 12 to 13.2 Mb and N50 values ranging from 10,585 to 29,404 base pairs (bp). The genome of one ST1 isolate was sequenced using ONT. This assembly was more contiguous, with a size of 20 million base pairs (Mb) spread over 116 scafolds, and an N50 of 248,997 bp. Conclusion This work represents one of the few large-scale comparative genomic analyses of Blastocystis isolates, providing an additional glimpse into its genomic diversity