Correction: Implementation of Genomic Surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings.

[This corrects the article DOI: 10.1371/journal.pgph.0001455.].

Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings.

The COVID-19 pandemic highlighted the importance of global genomic surveillance to monitor the emergence and spread of SARS-CoV-2 variants and inform public health decision-making. Until December 2020 there was minimal capacity for viral genomic surveillance in most Caribbean countries. To overcome this constraint, the COVID-19: Infectious disease Molecular epidemiology for PAthogen Control & Tracking (COVID-19 IMPACT) project was implemented to establish rapid SARS-CoV-2 whole genome nanopore sequencing at The University of the West Indies (UWI) in Trinidad and Tobago (T&T) and provide needed SARS-CoV-2 sequencing services for T&T and other Caribbean Public Health Agency Member States (CMS). Using the Oxford Nanopore Technologies MinION sequencing platform and ARTIC network sequencing protocols and bioinformatics pipeline, a total of 3610 SARS-CoV-2 positive RNA samples, received from 17 CMS, were sequenced in-situ during the period December 5th 2020 to December 31st 2021. Ninety-one Pango lineages, including those of five variants of concern (VOC), were identified. Genetic analysis revealed at least 260 introductions to the CMS from other global regions. For each of the 17 CMS, the percentage of reported COVID-19 cases sequenced by the COVID-19 IMPACT laboratory ranged from 0·02% to 3·80% (median = 1·12%). Sequences submitted to GISAID by our study represented 73·3% of all SARS-CoV-2 sequences from the 17 CMS available on the database up to December 31st 2021. Increased staffing, process and infrastructural improvement over the course of the project helped reduce turnaround times for reporting to originating institutions and sequence uploads to GISAID. Insights from our genomic surveillance network in the Caribbean region directly influenced non-pharmaceutical countermeasures in the CMS countries. However, limited availability of associated surveillance and clinical data made it challenging to contextualise the observed SARS-CoV-2 diversity and evolution, highlighting the need for development of infrastructure for collecting and integrating genomic sequencing data and sample-associated metadata.

Frequency and characteristics of selected enteropathogens in fecal and rectal specimens from childhood diarrhea in Trinidad, 1998-2000.

OBJECTIVE: To determine the prevalence and characteristics of selected enteric pathogens in diarrheic children in six counties of the island of Trinidad. METHODS: This cross-sectional study was conducted from April 1998 through March 2000. Fecal or rectal swab specimens from children (<12 years) were collected and then processed, using standard methods, to detect Salmonella spp., Shigella spp., enteropathogenic Escherichia coli (EPEC), Campylobacter spp., Yersinia spp., Cryptosporidium parvum, and parasite ova. The antibiograms of the enteropathogens were determined using the disk diffusion method. RESULTS: A total of 236 samples were processed; 86 samples originated directly from 17 heath centers in two counties (St. George East and St. George West), while 150 samples were obtained from the Trinidad Public Health Laboratory, having been submitted by private practitioners and personnel from six counties in Trinidad. Of the 236 samples, 33 (14.0%) were positive for Shigella, 4 (1.7%) for Salmonella, and 1 (0.4%) for EPEC. Two of the samples (0.8%) were positive for Campylobacter jejuni, while 1 sample (0.4%) was positive for hookworm ova. All the samples were negative for Cryptosporidium parvum and Yersinia spp. With the 86 samples collected directly from the health centers, in St. George East County the frequency of Shigella was 20.0% (12 of 60), compared with 26.9% (7 of 26) for samples from St. George West County, but the difference was not statistically significant (P>0.05 with the chi-square test). For the 150 samples from the six counties that had been submitted directly to the Trinidad Public Health Laboratory, 14 of them (9.3%) were positive for Shigella, a figure statistically significantly lower than that found with the samples sampled directly from the health centers (P<0.05 with the chi-square test). Sh. sonnei was the predominant serotype detected, accounting for 28 of the 33 Shigella isolates (84.8%) recovered from the 236 samples. Overall, the frequency of detection of enteropathogens had no seasonal pattern nor relationship to the county of origin. Of the 37 isolates of Salmonella and Shigella tested for antimicrobial sensitivity, all of them were sensitive to ciprofloxacin, gentamicin, and cefotaxime. In terms of resistance, 3 of the 37 isolates (8.1%) exhibited resistance to ampicillin, 1 (2.7%) to chloramphenicol, and 1 (2.7%) to sulfamethoxazole/ trimethoprim. CONCLUSION: Of the enteropathogens for which assays were done, Shigella sonnei was the most prevalent, and it has the highest probability of being an important etiological agent of childhood diarrhea in Trinidad.

Frequency and characteristics of selected enteropathogens in fecal and rectal specimens from childhood diarrhea in Trinidad, 1998-2000 / Frecuencia y características de ciertos enteropatógenos en especímenes fecales y rectales obtenidos de niños con diarrea en Trinidad, 1998­2000

Objetivo. Determinar la frecuencia y las características de ciertos agentes enteropatógenos detectados en niños con diarrea en seis condados de la isla de Trinidad. Métodos. El presente estudio transversal se llevó a cabo de abril de 1998 a marzo de 2000. Especímenes de heces o hisopados rectales de niños menores de 12 años se obtuvieron y se procesaron usando métodos estándarizados para la detección de Salmonella spp., Shigella spp., Escherichia coli enteropatogénico (ECEP), Campylobacter spp., Yersinia spp., Cryptosporidium parvum, y huevos de parásitos. Los antibiogramas de los agentes enteropatógenos se determinaron mediante el método de difusión en un disco. Resultados. Se procesaron 236 muestras en total; 86 de ellas provinieron directamente de 17 centros de salud en dos condados (St. George East y St. George West), mientras que las otras 150 muestras se obtuvieron del Laboratorio de Salud Pública de Trinidad, al que fueron entregadas por médicos particulares y el personal en seis condados de la isla. De las 236 muestras, 33 (14,0%) mostraron positividad a Shigella, 4 (1,7%) a Salmonella, y 1 (0,4%) a ECEP. Dos de las muestras (0,8%) mostraron positividad a Campylobacter jejuni, y una (0,4%) tenía huevos de anquilostoma. Ninguna muestra salió positiva a Cryptosporidium parvum ni a Yersinia spp. De las 86 muestras obtenidas directamente de los centros de salud, el porcentaje con Shigella fue de 20% (12 muestras de 60) en el condado de St. George East, en comparación con 26,9% (7 muestras de 26) en el condado de St. George West, sin que la diferencia fuese estadísticamente significativa (P > 0,05 según la prueba de ji al cuadrado). De las 150 muestras procedentes de los seis condados que habían sido entregadas directamente al Laboratorio de Salud Pública de Trinidad, 14 (9,3%) salieron positivas a Shigella. Este porcentaje fue más pequeño, en grado estadísticamente significativo, que el hallado en las muestras tomadas directamente de los centros de salud (P < 0,05 según la prueba de ji al cudrado). El serotipo más frecuente fue Sh. sonnei, que se observó en 28 de las 33 (84,8%) cepas de Shigella aisladas de las 236 muestras. En términos generales, la frecuencia con que se detectaron enteropatógenos no varió con las estaciones del año ni mostró ninguna relación con el país de origen. Las 37 cepas de Salmonella y Shigella que se sometieron a pruebas de sensibilidad fueron sensibles en su totalidad a la ciprofloxacina, la gentamicina y la cefotaxima. Tres de las 37 cepas aisladas (8,1%) fueron resistentes a la ampicilina, 1 (2,7%) al cloramfenicol y 1 (2,7%) a la combinación de sufametoxazol con trimetoprima. Conclusión. De los enteropatógenos investigados mediante pruebas detectoras, Sh. sonnei fue el más frecuente y es, quizá, el principal agente causal de la diarrea infantil en Trinidad. Diarrea; infecciones bacterianas; resistencia microbiana a las drogas; Trinidad y Tobago

Objective. To determine the prevalence and characteristics of selected enteric pathogens in diarrheic children in six counties of the island of Trinidad. Methods. This cross-sectional study was conducted from April 1998 through March 2000. Fecal or rectal swab specimens from children (< 12 years) were collected and then processed, using standard methods, to detect Salmonella spp., Shigella spp., enteropathogenic Escherichia coli (EPEC), Campylobacter spp., Yersinia spp., Cryptosporidium parvum, and parasite ova. The antibiograms of the enteropathogens were determined using the disk diffusion method. Results. A total of 236 samples were processed; 86 samples originated directly from 17 heath centers in two counties (St. George East and St. George West), while 150 samples were obtained from the Trinidad Public Health Laboratory, having been submitted by private practitioners and personnel from six counties in Trinidad. Of the 236 samples, 33 (14.0%) were positive for Shigella, 4 (1.7%) for Salmonella, and 1 (0.4%) for EPEC. Two of the samples (0.8%) were positive for Campylobacter jejuni, while 1 sample (0.4%) was positive for hookworm ova. All the samples were negative for Cryptosporidium parvum and Yersinia spp. With the 86 samples collected directly from the health centers, in St. George East County the frequency of Shigella was 20.0% (12 of 60), compared with 26.9% (7 of 26) for samples from St. George West County, but the difference was not statistically significant (P > 0.05 with the chi-square test). For the 150 samples from the six counties that had been submitted directly to the Trinidad Public Health Laboratory, 14 of them (9.3%) were positive for Shigella, a figure statistically significantly lower than that found with the samples sampled directly from the health centers (P < 0.05 with the chi-square test). Sh. sonnei was the predominant serotype detected, accounting for 28 of the 33 Shigella isolates (84.8%) recovered from the 236 samples. Overall, the frequency of detection of enteropathogens had no seasonal pattern nor relationship to the county of origin. Of the 37 isolates of Salmonella and Shigella tested for antimicrobial sensitivity, all of them were sensitive to ciprofloxacin, gentamicin, and cefotaxime