Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean.

Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.

Population structure of Neisseria meningitidis ST-9493 identified in Colombian isolates.

INTRODUCTION: Neisseria meningitidis is associated with invasive infections causing high mortality rates. The objective of this study was to describe the population structure of Colombian invasive isolates with ST-9493, a potentially emerging clonal group in the country. METHODS: The complete genomes of 34 invasive isolates of serogroup B with ST-9493 and its variants at one or two loci were sequenced by Illumina to describe the phenotypic and genotypic characteristics of these isolates. RESULTS: The relationship of a clonal group associated with ST-136 CC41/44 was phylogenetically established, identifying two main clades composed of isolates from an outbreak or endemic. The most frequent alleles and peptides included porA 17, porB 44, fHbp 2.24, NHBA 10, and the FetA F5-17 variant. Most of the isolates were susceptible to the antibiotics evaluated. CONCLUSION: This study shows that meningococcal isolates with ST-9493 are an autochthonous clonal group with population dynamics and the capacity to cause endemic and epidemic meningococcal disease in Colombia.

Leading causes of excess mortality in Mexico during the COVID-19 pandemic 2020-2021: A death certificates study in a middle-income country.

Background: The death toll after SARS-CoV-2 emergence includes deaths directly or indirectly associated with COVID-19. Mexico reported 325,415 excess deaths, 34.4% of them not directly related to COVID-19 in 2020. In this work, we aimed to analyse temporal changes in the distribution of the leading causes of mortality produced by COVID-19 pandemic in Mexico to understand excess mortality not directly related to the virus infection. Methods: We did a longitudinal retrospective study of the leading causes of mortality and their variation with respect to cause-specific expected deaths in Mexico from January 2020 through December 2021 using death certificate information. We fitted a Poisson regression model to predict cause-specific mortality during the pandemic period, based on the 2015-2019 registered mortality. We estimated excess deaths as a weekly difference between expected and observed deaths and added up for the entire period. We expressed all-cause and cause-specific excess mortality as a percentage change with respect to predicted deaths by our model. Findings: COVID-19 was the leading cause of death in 2020-2021 (439,582 deaths). All-cause total excess mortality was 600,590 deaths (38⋅2% [95% CI: 36·0 to 40·4] over expected). The largest increases in cause-specific mortality, occurred in diabetes (36·8% over expected), respiratory infections (33·3%), ischaemic heart diseases (32·5%) and hypertensive diseases (25·0%). The cause-groups that experienced significant decreases with respect to the expected pre-pandemic mortality were infectious and parasitic diseases (-20·8%), skin diseases (-17·5%), non-traffic related accidents (-16·7%) and malignant neoplasm (-5·3%). Interpretation: Mortality from COVID-19 became the first cause of death in 2020-2021, the increase in other causes of death may be explained by changes in the health service utilization patterns caused by hospital conversion or fear of the population using them. Cause-misclassification cannot be ruled out. Funding: This study was funded by Conacyt.

Implementation of a COVID-19 Genomic Surveillance Regional Network for Latin America and Caribbean region.

The timely release of SARS-CoV-2 first genomic sequences allowed the identification of the etiologic agent and development of diagnostic protocols. Genomic sequencing was a crucial step in generating data for driving laboratory response and detections of SARS-CoV-2 since the start of the COVID-19 pandemic. Because of all the progression and achievements that timely release of genetic sequence data represents in the public health response, the Pan American Health Organization (PAHO) in collaboration with countries' public health laboratories, started implementation of a network for strengthening the Latin America and Caribbean (LAC) region on timely generation of SARS-CoV-2 genomic data. Here we describe the implementation of the COVID-19 Genomic Surveillance Regional Network in the Americas region during the beginning of the pandemic. The establishment of this network has strengthened laboratory response capacity at the country level, as well as facilitated timely release of SARS-CoV-2 genomic information to be used to complement the multiple response strategies for COVID-19 pandemic mitigation. As genomic epidemiology is useful for guiding public health decisions on outbreak and response, we also analysed the first SARS-CoV-2 genomic sequence data from countries of the Latin America and Caribbean Region.

COVID-19 laboratory preparedness and response in the Americas Region: Lessons learned.

By the time the etiologic agent of the COVID-19 was identified as a novel coronavirus, no country in the Americas Region had laboratory capacity for detecting this new virus. A strategic multilevel approach with specific reagent purchase and delivery, regional trainings, in-country missions, and the provision of technical support was established for timely preparedness of national reference laboratories for SARS-CoV-2 detection. All countries should be prepared to timely detect any potential pandemic emerging agent. The rapid SARS-CoV-2 molecular detection implementation throughout the Americas showed the importance of an efficient and coordinated laboratory response for preparedness. Here we present how in 25 days the Americas Region went from no SARS-CoV-2 diagnostic capacity, to molecular detection fully implemented in 28 Member States, under the coordinated strategy of the Pan American Health Organization and collaborative work at regional and country level with national authorities and public health laboratories.

Emergence of MDR invasive Neisseria meningitidis in El Salvador, 2017-19.

BACKGROUND: Invasive meningococcal disease (IMD) is an acute, highly transmissible and potentially fatal disease caused by Neisseria meningitidis. Prompt antimicrobial therapy and prophylaxis are recommended, where penicillin or ciprofloxacin are the available choices. However, the emergence of resistant isolates of N. meningitidis poses a challenge for antimicrobial therapy. OBJECTIVES: To describe the clinical, epidemiological and biological characteristics of six penicillin- and ciprofloxacin-resistant, culture-confirmed IMD cases reported in El Salvador, Central America, between 2017 and 2019. METHODS: Following the detection of six patients presenting with IMD in El Salvador, clinical data were collected and epidemiological action plans conducted. Isolates were subjected to antimicrobial susceptibility testing by broth microdilution and WGS for genotyping and molecular characterization analysis, including phylogeny comparison with global sequences available from public databases. RESULTS: A total of six IMD cases caused by N. meningitidis serogroup Y, resistant to both penicillin (MIC >8.0 mg/L) and ciprofloxacin (MIC 0.125 mg/L), were detected from 2017 to 2019. Genomic analysis showed that penicillin resistance was mediated by the production of ß-lactamase ROB-1. Ciprofloxacin resistance was attributed to an amino acid substitution in DNA gyrase (T91I). All isolates were classified as ST3587, clonal complex 23, and were genetically highly similar, based on core-genome SNP analysis. CONCLUSIONS: To the best of our knowledge, we report the first cases of MDR N. meningitidis causing IMD in Latin America. Our findings highlight the emergence of this potential public health threat, with a profound impact on the efficacy of IMD treatment and prophylaxis protocols.

Molecular characterization of Neisseria meningitidis isolates recovered from patients with invasive meningococcal disease in Colombia from 2013 to 2016.

BACKGROUND: Neisseria meningitidis is a significant cause of morbidity and mortality worldwide. Meningococcal isolates have a highly dynamic population structure and can be phenotypically and genetically differentiated into serogroups and clonal complexes. The aim of this study was to describe the phenotypic and genotypic characteristics of invasive isolates recovered in Colombia from 2013 to 2016. METHODOLOGY: A total of 193 invasive isolates were analyzed. Phenotypic and genotypic characteristics were determined by serotyping, antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. RESULTS: Based on the results, meningococcal serogroups C, B and Y were responsible for 47.9%, 41.7%, and 9.4% of cases, respectively, and the distribution of serogroups B and C changed over time. Fifteen clonal groups and 14 clonal complexes (cc) were identified by PFGE and genome sequencing. The main clonal group included serogroup B isolates with sequence type (ST)-9493 and its four single-locus variants, which has only been identified in Colombian isolates. The clonal population structure demonstrates that the isolates in this study mainly belong to four clonal complexes: ST-11 cc, ST-32 cc, ST-35 cc and ST-41/44 cc. Thirty-eight penA alleles were identified, but no correlation between MICs and specific sequences was observed. CONCLUSION: This study shows that most meningococcal isolates recovered from patients with invasive meningococcal disease in Colombia are strains associated with distinct globally disseminated hyperinvasive clones.

Carriage of Neisseria meningitidis and other Neisseria species among children and young adults in Paraguay.

Introduction. Colonization by Neisseria meningitidis is the pre-requisite for the development of disease. We present the findings of a cross-sectional investigation onto the oropharyngeal carriage of N. meningitidis and Neisseria species in the population aged 3 to 21 in Paraguay.Aim. Carriage prevalence by age groups, risk factors associated with carriage, and phenotypic and genotypic characteristics of strains are described.Methodology. We collected 2011 oropharyngeal swabs from consenting participants aged 3-21 years. Infants were recruited at immunization clinics, and older children and young adults were identified at schools and universities. A single oropharyngeal swab was collected and processed for the identification and isolation of Neisseria. Additionally, participants, or their legal guardian if these were minors, were requested to fill a standardized questionnaire.Results. N. meningitidis was isolated in 42/2011 (2.1 %) participants, while other Neisseria spp. were identified in 306/2011 (15.2 %) subjects: N. cinerea and N. lactamica were identified in 39/2011 (1.9 %) and 43/2011 (2.2 %), respectively. Meningococcal strains belonged to ten different clonal complexes, of which six are associated with invasive disease (ST-32/ET5 complex, ST-11/ET37 complex, ST-103 complex, ST-167 complex, ST-35 complex and ST-41/44 complex/lineage 3).Conclusion. Prevalence of N. meningitidis carriage was low compared to that reported from other settings, however, the overall carriage of Neisseria spp. (including N. meningitidis) was comparable to meningococcal carriage prevalence reported in the literature. This study is the first of its kind conducted in Paraguay, and one of the few known in the Southern Cone of Latin America.

Increase of Neisseria meningitidis W:cc11 invasive disease in Chile has no correlation with carriage in adolescents.

Neisseria meningitidis is a human exclusive pathogen that can lead to invasive meningococcal disease or may be carried in the upper respiratory tract without symptoms. The relationship between carriage and disease remains poorly understood but it is widely accepted that decreasing carriage by immunization should lead to a reduction of invasive cases. Latin America has experienced an increased incidence of serogroup W invasive cases of Neisseria meningitidis in the last decade. Specifically in Chile, despite low total incidence of invasive cases, serogroup W has become predominant since 2011 and has been associated with elevated mortality. Expecting to gain insight into the epidemiology of this disease, this study has used molecular typing schemes to compare Neisseria meningitidis isolates causing invasive disease with those isolates collected from adolescent carriers during the same period in Chile. A lower carriage of the serogroup W clonal complex ST-11/ET37 than expected was found; whereas, the same clonal complex accounted for 66% of total invasive meningococcal disease cases in the country that year. A high diversity of PorA variable regions and fHbp peptides was also ascertained in the carrier isolates compared to the invasive ones. According to the results shown here, the elevated number of serogroup W invasive cases in our country cannot be explained by a rise of carriage of pathogenic isolates. Overall, this study supports the idea that some strains, as W:cc11 found in Chile, possess an enhanced virulence to invade the host. Notwithstanding hypervirulence, this strain has not caused an epidemic in Chile. Finally, as genetic transfer occurs often, close surveillance of Neisseria meningitidis strains causing disease, and particularly hypervirulent W:cc11, should be kept as a priority in our country, in order to prepare the best response to face genetic changes that could lead to enhanced fitness of this pathogen.

Identifying the social and environmental determinants of plague endemicity in Peru: insights from a case study in Ascope, La Libertad.

BACKGROUND: Plague remains a public health problem in specific areas located in Bolivia, Brazil, Ecuador and Peru. Its prevention and control encompasses adequate clinical management and timely laboratory diagnosis. However, understanding communities' interaction with its surrounding ecosystem as well as the differences between community members and institutional stakeholders regarding the root causes of plague might contribute to understand its endemicity. We aim at bridging the traditionally separate biological and social sciences by elucidating communities' risk perception and identifying knowledge gaps between communities and stakeholders. This approach has been used in other areas but never in understanding plague endemicity, nor applied in the Latin American plague context. The objectives were to identify (i) plague risk perception at community level, (ii) perceived social and environmental determinants of plague endemicity, and (iii) institutions that need to be involved and actions needed to be taken as proposed by stakeholders and community members. The study was performed in 2015 and took place in Ascope rural province, La Libertad Region, in Peru, where the study areas are surrounded by intensive private sugarcane production. METHODS: We propose using a multi-level discourse analysis. Community households were randomly selected (n = 68). Structured and semi-structured questionnaires were applied. A stakeholder analysis was used to identify policy makers (n = 34). In-depth interviews were performed, recorded and transcribed. Descriptive variables were analyzed with SPSS®. Answers were coded following variables adapted from the Commission on Social Determinants of Health and analyzed with the assistance of ATLAS.ti®. RESULTS: Results showed that risk perception was low within the community. Policy-makers identified agriculture and sugarcane production as the root cause while community answers ranked the hygiene situation as the main cause. Stakeholders first ranked governmental sectors (education, housing, agriculture and transport) and the community prioritized the health sector. Social surveillance and improving prevention and control were first cited by policy-makers and community members, respectively. CONCLUSIONS: The determinants of plague endemicity identified by the two groups differed. Similarly, actions and sectors needed to be involved in solving the problem varied. The gaps in understanding plague root causes between these two groups might hinder the efficiency of current plague prevention and control strategies.

A qualitative socio-ecological characterization of the plague threat at Hermelinda Market, La Libertad, Peru

[ABSTRACT]. Objective. To identify 1) the main determinants of persistent Yersinia pestis circulation and the associated threat of plague at Hermelinda Market—a large farmers’ market in the city of Trujillo, La Libertad, Peru—and the main actions taken against it, as perceived by local stakeholders; 2) the level of plague risk perception among local actors; and 3) recommended actions to solve the plague threat at the market. Methods. A conceptual framework was developed combining a social determinants approach with a complex systems-thinking framework and a knowledge management perspective. A four-step qualitative protocol was carried out (literature review; stakeholder mapping; 37 semi-structured interviews; and coding/analysis). In the fourth step, the data collected in the semi-structured interviews were coded for eight social determinants of health (SDH) variables and analyzed with ATLAS.ti®, and an emerging category analysis was performed to identify risk perception levels. Results. Based on analysis by SDH variable, the three main determinants of the plague threat at Hermelinda Market were: 1) local (Trujillo City) governance, 2) infrastructure and basic services, and 3) local culture. According to the same analysis, actions most frequently undertaken against plague involved 1) infrastructure and basic services, 2) social vigilance, and 3) communication. The emerging category analysis indicated local risk perception levels were low, with most of the data pointing to “unhygienic” (“naturalized”) lifestyles and a general lack of awareness about the disease prior to plague-related health concerns at the market as the cause. Conclusions. The results indicate that the persistent circulation of Yersinia pestis at Hermelinda Market is not simply a technical matter but more of a managerial and cultural problem. As local governance was found to be a main factor in the persistence of this public health threat, future efforts against it should focus on sustainable inter-sectoral planning and education. Actions taken exclusively by the health sector and the improvement of infrastructure and basic services alone will not be enough to reduce the threat of plague at the market.

[RESUMEN]. Objetivo. Establecer: 1) los principales determinantes de la circulación persistente de Yersinia pestis y la amenaza asociada de peste en el mercado La Hermelinda, un gran mercado de agricultores en la ciudad de Trujillo, Departamento de La Libertad en Perú, y las medidas más adecuadas para combatir la bacteria, según la percepción de los interesados directos locales; 2) el grado de percepción del riesgo de peste entre los actores locales; y 3) las medidas recomendadas para resolver la amenaza de peste en el mercado. Métodos. Se elaboró un marco conceptual que combinaba un enfoque de determinantes sociales con un complejo marco de pensamiento sistémico y una perspectiva de gestión del conocimiento. Se llevó a cabo un protocolo cualitativo de cuatro pasos (revisión bibliográfica; mapeo de interesados directos; 37 entrevistas semiestructuradas y codificación y análisis). En el cuarto paso, los datos recopilados en las entrevistas semiestructuradas fueron codificados conforme a ocho variables de los determinantes sociales de la salud y analizados con el programa ATLAS.ti ®, y luego se realizó un análisis de las categorías emergentes para establecer los grados de percepción del riesgo. Resultados. Sobre la base del análisis de las variables de los determinantes sociales de la salud, los tres principales determinantes de la amenaza de peste en el mercado La Hermelinda fueron: 1) la gobernanza local (Ciudad de Trujillo), 2) la infraestructura y los servicios básicos y 3) la cultura local. Según el mismo análisis, las acciones emprendidas con mayor frecuencia contra la peste se vincularon con 1) la infraestructura y los servicios básicos, 2) la vigilancia social y 3) la comunicación. El análisis de las categorías emergentes indicó que los grados locales de percepción del riesgo fueron bajos y la mayoría de los datos apuntaron como causas a los modos de vida “antihigiénicos” (“naturalizados”) y a una falta general de concientización acerca de la enfermedad antes de la preocupación acerca de la salud relacionada con la peste en el mercado. Conclusiones. Los resultados indican que la circulación persistente de Yersinia pestis en el mercado La Hermelinda no es sencillamente un asunto técnico sino sobre todo un problema cultural y de gestión. Como se encontró que la gobernanza local era un factor importante en la persistencia de esta amenaza a la salud pública, las actividades futuras para combatirla deben centrarse en la planificación y la educación intersectoriales sostenibles. Las medidas adoptadas exclusivamente por el sector de la salud y el mejoramiento de la infraestructura y los servicios básicos por sí solos no serán suficientes para reducir la amenaza de la peste en el mercado.

[RESUMO]. Objetivo. Identificar 1) os principais determinantes da circulação persistente de Yersinia pestis e o risco associado de ocorrência da peste no Mercado Hermelinda, um grande mercado de produtos agrícolas no município de Trujillo, La Libertad, Peru, e as principais medidas adotadas para enfrentar esta situação, segundo a percepção dos interessados diretos locais, 2) o nível de percepção do risco de ocorrência da peste entre os atores locais e 3) as ações recomendadas para eliminar o risco de ocorrência da peste no mercado. Métodos. Foi desenvolvida uma estrutura conceitual formada pela combinação de um enfoque de determinantes sociais, um enquadramento complexo de reflexão sistêmica e uma perspectiva de gestão do conhecimento. Foi conduzido um protocolo qualitativo de quatro etapas (revisão literária, mapeamento de interessados diretos, 37 entrevistas semiestruturadas e codificação/análise). Na quarta etapa, os dados coletados nas entrevistas semiestruturadas foram codificados para oito variáveis de determinantes sociais da saúde (DSS) e analisados com o programa ATLAS.ti®. Uma análise de categorias emergentes foi realizada para identificar os níveis de percepção de risco. Resultados. A partir da análise segundo as variáveis de DSS, os três principais determinantes do risco de ocorrência da peste no Mercado Hermelinda foram: 1) governança local (município de Trujillo), 2) infraestrutura e serviços básicos e 3) cultura local. Segundo a mesma análise, as medidas adotadas com maior frequência para evitar a peste foram: 1) infraestrutura e serviços básicos, 2) vigilância social e 3) comunicação. A análise de categorias emergentes indicou que o nível de percepção local do risco de ocorrência era baixo, sendo que a maioria dos dados apontou como causa hábitos de vida anti-higiênicos (“naturalizados”) e falta geral de consciência da doença anterior às preocupações de saúde relacionadas com a peste no mercado. Conclusões. Os resultados do estudo indicam que a circulação persistente de Yersinia pestis no Mercado Hermelinda não é simplesmente uma questão técnica, sendo mais um problema administrativo e cultural. Verificou-se que a governança local é um dos principais fatores para a persistência desta ameaça à saúde pública e os esforços futuros devem visar o planejamento intersetorial sustentável e a educação. Medidas adotadas exclusivamente pelo setor da saúde e a melhoria da infraestrutura e serviços básicos por si só não serão suficientes para reduzir o risco de ocorrência da peste no mercado.

Development and implementation of the Caribbean Laboratory Quality Management Systems Stepwise Improvement Process (LQMS-SIP) Towards Accreditation.

BACKGROUND: Implementing quality management systems and accrediting laboratories in the Caribbean has been a challenge. OBJECTIVES: We report the development of a stepwise process for quality systems improvement in the Caribbean Region. METHODS: The Caribbean Laboratory Stakeholders met under a joint Pan American Health Organization/US Centers for Disease Control and Prevention initiative and developed a user-friendly framework called 'Laboratory Quality Management System - Stepwise Improvement Process (LQMS-SIP) Towards Accreditation' to support countries in strengthening laboratory services through a stepwise approach toward fulfilling the ISO 15189: 2012 requirements. RESULTS: This approach consists of a three-tiered framework. Tier 1 represents the minimum requirements corresponding to the mandatory criteria for obtaining a licence from the Ministry of Health of the participating country. The next two tiers are quality improvement milestones that are achieved through the implementation of specific quality management system requirements. Laboratories that meet the requirements of the three tiers will be encouraged to apply for accreditation. The Caribbean Regional Organisation for Standards and Quality hosts the LQMS-SIP Secretariat and will work with countries, including the Ministry of Health and stakeholders, including laboratory staff, to coordinate and implement LQMS-SIP activities. The Caribbean Public Health Agency will coordinate and advocate for the LQMS-SIP implementation. CONCLUSION: This article presents the Caribbean LQMS-SIP framework and describes how it will be implemented among various countries in the region to achieve quality improvement.

A qualitative socio-ecological characterization of the plague threat at Hermelinda Market, La Libertad, Peru.

OBJECTIVE: To identify 1) the main determinants of persistent Yersinia pestis circulation and the associated threat of plague at Hermelinda Market-a large farmers' market in the city of Trujillo, La Libertad, Peru-and the main actions taken against it, as perceived by local stakeholders; 2) the level of plague risk perception among local actors; and 3) recommended actions to solve the plague threat at the market. METHODS: A conceptual framework was developed combining a social determinants approach with a complex systems-thinking framework and a knowledge management perspective. A four-step qualitative protocol was carried out (literature review; stakeholder mapping; 37 semi-structured interviews; and coding/analysis). In the fourth step, the data collected in the semi-structured interviews were coded for eight social determinants of health (SDH) variables and analyzed with ATLAS.ti®, and an emerging category analysis was performed to identify risk perception levels. RESULTS: Based on analysis by SDH variable, the three main determinants of the plague threat at Hermelinda Market were: 1) local (Trujillo City) governance, 2) infrastructure and basic services, and 3) local culture. According to the same analysis, actions most frequently undertaken against plague involved 1) infrastructure and basic services, 2) social vigilance, and 3) communication. The emerging category analysis indicated local risk perception levels were low, with most of the data pointing to "unhygienic" ("naturalized") lifestyles and a general lack of awareness about the disease prior to plague-related health concerns at the market as the cause. CONCLUSIONS: The results indicate that the persistent circulation of Yersinia pestis at Hermelinda Market is not simply a technical matter but more of a managerial and cultural problem. As local governance was found to be a main factor in the persistence of this public health threat, future efforts against it should focus on sustainable inter-sectoral planning and education. Actions taken exclusively by the health sector and the improvement of infrastructure and basic services alone will not be enough to reduce the threat of plague at the market.

A qualitative socio-ecological characterization of the plague threat at Hermelinda Market, La Libertad, Peru / Caracterización socioecológica cualitativa de la amenaza de peste en el mercado La Hermelinda, Departamento de La Libertad Perú / Caracterização socioecológica qualitativa do risco de ocorrência da peste no Mercado Hermelinda, La Libertad, Peru

Objective To identify 1) the main determinants of persistent Yersinia pestis circulation and the associated threat of plague at Hermelinda Market—a large farmers' market in the city of Trujillo, La Libertad, Peru—and the main actions taken against it, as perceived by local stakeholders; 2) the level of plague risk perception among local actors; and 3) recommended actions to solve the plague threat at the market. Methods A conceptual framework was developed combining a social determinants approach with a complex systems-thinking framework and a knowledge management perspective. A four-step qualitative protocol was carried out (literature review; stakeholder mapping; 37 semi-structured interviews; and coding/analysis). In the fourth step, the data collected in the semi-structured interviews were coded for eight social determinants of health (SDH) variables and analyzed with ATLAS.ti®, and an emerging category analysis was performed to identify risk perception levels. Results Based on analysis by SDH variable, the three main determinants of the plague threat at Hermelinda Market were: 1) local (Trujillo City) governance, 2) infrastructure and basic services, and 3) local culture. According to the same analysis, actions most frequently undertaken against plague involved 1) infrastructure and basic services, 2) social vigilance, and 3) communication. The emerging category analysis indicated local risk perception levels were low, with most of the data pointing to "unhygienic" ("naturalized") lifestyles and a general lack of awareness about the disease prior to plague-related health concerns at the market as the cause. Conclusions The results indicate that the persistent circulation of Yersinia pestis at Hermelinda Market is not simply a technical matter but more of a managerial and cultural problem. As local governance was found to be a main factor in the persistence of this public health threat, future efforts against it should focus on sustainable inter-sectoral planning and education. Actions taken exclusively by the health sector and the improvement of infrastructure and basic services alone will not be enough to reduce the threat of plague at the market.

RESUMEN Objetivo Establecer: 1) los principales determinantes de la circulación persistente de Yersinia pestis y la amenaza asociada de peste en el mercado La Hermelinda, un gran mercado de agricultores en la ciudad de Trujillo, Departamento de La Libertad en Perú, y las medidas más adecuadas para combatir la bacteria, según la percepción de los interesados directos locales; 2) el grado de percepción del riesgo de peste entre los actores locales; y 3) las medidas recomendadas para resolver la amenaza de peste en el mercado. Métodos Se elaboró un marco conceptual que combinaba un enfoque de determinantes sociales con un complejo marco de pensamiento sistémico y una perspectiva de gestión del conocimiento. Se llevó a cabo un protocolo cualitativo de cuatro pasos (revisión bibliográfica; mapeo de interesados directos; 37 entrevistas semiestructuradas y codificación y análisis). En el cuarto paso, los datos recopilados en las entrevistas semiestructuradas fueron codificados conforme a ocho variables de los determinantes sociales de la salud y analizados con el programa ATLAS.ti ®, y luego se realizó un análisis de las categorías emergentes para establecer los grados de percepción del riesgo. Resultados Sobre la base del análisis de las variables de los determinantes sociales de la salud, los tres principales determinantes de la amenaza de peste en el mercado La Hermelinda fueron: 1) la gobernanza local (Ciudad de Trujillo), 2) la infraestructura y los servicios básicos y 3) la cultura local. Según el mismo análisis, las acciones emprendidas con mayor frecuencia contra la peste se vincularon con 1) la infraestructura y los servicios básicos, 2) la vigilancia social y 3) la comunicación. El análisis de las categorías emergentes indicó que los grados locales de percepción del riesgo fueron bajos y la mayoría de los datos apuntaron como causas a los modos de vida "antihigiénicos" ("naturalizados") y a una falta general de concientización acerca de la enfermedad antes de la preocupación acerca de la salud relacionada con la peste en el mercado. Conclusiones Los resultados indican que la circulación persistente de Yersinia pestis en el mercado La Hermelinda no es sencillamente un asunto técnico sino sobre todo un problema cultural y de gestión. Como se encontró que la gobernanza local era un factor importante en la persistencia de esta amenaza a la salud pública, las actividades futuras para combatirla deben centrarse en la planificación y la educación intersectoriales sostenibles. Las medidas adoptadas exclusivamente por el sector de la salud y el mejoramiento de la infraestructura y los servicios básicos por sí solos no serán suficientes para reducir la amenaza de la peste en el mercado.

RESUMO Objetivo Identificar 1) os principais determinantes da circulação persistente de Yersinia pestis e o risco associado de ocorrência da peste no Mercado Hermelinda, um grande mercado de produtos agrícolas no município de Trujillo, La Libertad, Peru, e as principais medidas adotadas para enfrentar esta situação, segundo a percepção dos interessados diretos locais, 2) o nível de percepção do risco de ocorrência da peste entre os atores locais e 3) as ações recomendadas para eliminar o risco de ocorrência da peste no mercado. Métodos Foi desenvolvida uma estrutura conceitual formada pela combinação de um enfoque de determinantes sociais, um enquadramento complexo de reflexão sistêmica e uma perspectiva de gestão do conhecimento. Foi conduzido um protocolo qualitativo de quatro etapas (revisão literária, mapeamento de interessados diretos, 37 entrevistas semiestruturadas e codificação/análise). Na quarta etapa, os dados coletados nas entrevistas semiestruturadas foram codificados para oito variáveis de determinantes sociais da saúde (DSS) e analisados com o programa ATLAS.ti®. Uma análise de categorias emergentes foi realizada para identificar os níveis de percepção de risco. Resultados A partir da análise segundo as variáveis de DSS, os três principais determinantes do risco de ocorrência da peste no Mercado Hermelinda foram: 1) governança local (município de Trujillo), 2) infraestrutura e serviços básicos e 3) cultura local. Segundo a mesma análise, as medidas adotadas com maior frequência para evitar a peste foram: 1) infraestrutura e serviços básicos, 2) vigilância social e 3) comunicação. A análise de categorias emergentes indicou que o nível de percepção local do risco de ocorrência era baixo, sendo que a maioria dos dados apontou como causa hábitos de vida anti-higiênicos ("naturalizados") e falta geral de consciência da doença anterior às preocupações de saúde relacionadas com a peste no mercado. Conclusões Os resultados do estudo indicam que a circulação persistente de Yersinia pestis no Mercado Hermelinda não é simplesmente uma questão técnica, sendo mais um problema administrativo e cultural. Verificou-se que a governança local é um dos principais fatores para a persistência desta ameaça à saúde pública e os esforços futuros devem visar o planejamento intersetorial sustentável e a educação. Medidas adotadas exclusivamente pelo setor da saúde e a melhoria da infraestrutura e serviços básicos por si só não serão suficientes para reduzir o risco de ocorrência da peste no mercado.

Curso de gestión de calidad y buenas prácticas de laboratorio. 3. ed.

[INTRODUCCIÓN]. La vigilancia de la salud tanto individual como de la población general, el desarrollo de un número creciente de técnicas de laboratorio y la mejora continua de los métodos diagnósticos requieren la adopción de herramientas de gestión para su óptima implementación en los sistemas y laboratorios de salud. Por estas razones, entre otras, el concepto universal de calidad y el estudio de sus procesos se han extendido de la industria de la manufactura a las ciencias médicas. No sólo lo anteriormente mencionado, sino también el buen servicio y la satisfacción del cliente -o de los usuarios- son objetivos primordiales para los hospitales y laboratorios que tratan de establecer un sistema de gestión de la calidad que se adapte tanto a las necesidades operativas y fiduciarias de su organización, como a los requisitos prácticos de los usuarios: pacientes, médicos, epidemiólogos, autoridades sanitarias y comunidad entre otros. El objetivo de este curso es brindar capacitación en los principios básicos necesarios para la gestión de la calidad y la aplicación de buenas prácticas en los laboratorios. El contenido de los módulos incluye una información apropiada que, junto a la terminología descrita, permite la familiarización del participante con los conceptos esenciales sobre las principales áreas de un sistema de gestión de la calidad. El curso está diseñado para que los participantes puedan comenzar la planificación e implementación de un sistema de calidad en sus instituciones o en sus propios laboratorios, con la ayuda de actividades prácticas diseñadas especialmente para aplicar lo que han aprendido. El curso se desarrolla mediante un método de autoaprendizaje, por lo que las experiencias de cada participante desempeñan un papel muy importante. Tanto las actividades prácticas como los debates se concentran en el funcionamiento cotidiano del laboratorio...

Characterization of Carriage Isolates of Neisseria meningitides 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.

Effect of pneumococcal conjugate vaccination in Uruguay, a middle-income country.

BACKGROUND: In 2008, a 7-valent pneumococcal conjugate vaccine (PCV7) was introduced into the routine childhood immunization program in Uruguay, with a 2+1 schedule. In 2010, PCV13 replaced PCV7, and the same 2+1 schedule was used. The effect of these pneumococcal vaccines on the incidence of invasive pneumococcal infections (IPD) and on serotype distribution was analyzed retrospectively, based on passive national laboratory surveillance. METHODS: Data from 1,887 IPD isolates from 5 years before and 5 years after PCV7 introduction (7 before and 3 after PCV13 introduction) was examined to assess the incidence rate per 100,000 age-specific population of all IPD, PCV7-serotypes, and PCV13-serotypes associated IPD among children < 2 years and 2 to 4 years old, and patients ≥ 5 years old. Trends of frequency for each serotype were also analyzed. RESULTS: Comparison of pre-vaccination (2003-2007) and post-vaccination (2008-2012) periods showed a significant decrease in IPD incidence among children < 2 years old (IR 68.7 to IR 29.6, p<0.001) and children 2 to 4 years (p < 0.04). IPD caused by serotypes in PCV7 was reduced by 95.6% and IPD caused by 6 serotypes added in PCV13 was reduced by 83.9% in children <5 years old. Indirect effects of both conjugate vaccines were observed among patients ≥ 5 years old one year after the introduction of each vaccine, in 2010 for PCV7 and in 2012 for PCV13. Nevertheless, for reasons that still need to be explained, perhaps due to ascertainment bias, total IPD in this group increased after 2007. In 2012, the relative frequency of vaccine serotypes among vaccinated and unvaccinated population declined, except for serotype 3. Non vaccine serotypes with increasing frequency were identified, in rank order: 12F, 8, 24F, 22F, 24A, 15C, 9N, 10A and 33. CONCLUSION: Consecutive immunization with PCV7 and PCV13 has significantly reduced IPD in children < 5 years of age in Uruguay.

Where does human plague still persist in Latin America?

BACKGROUND: Plague is an epidemic-prone disease with a potential impact on public health, international trade, and tourism. It may emerge and re-emerge after decades of epidemiological silence. Today, in Latin America, human cases and foci are present in Bolivia, Brazil, Ecuador, and Peru. AIMS: The objective of this study is to identify where cases of human plague still persist in Latin America and map areas that may be at risk for emergence or re-emergence. This analysis will provide evidence-based information for countries to prioritize areas for intervention. METHODS: Evidence of the presence of plague was demonstrated using existing official information from WHO, PAHO, and Ministries of Health. A geo-referenced database was created to map the historical presence of plague by country between the first registered case in 1899 and 2012. Areas where plague still persists were mapped at the second level of the political/administrative divisions (counties). Selected demographic, socioeconomic, and environmental variables were described. RESULTS: Plague was found to be present for one or more years in 14 out of 25 countries in Latin America (1899-2012). Foci persisted in six countries, two of which have no report of current cases. There is evidence that human cases of plague still persist in 18 counties. Demographic and poverty patterns were observed in 11/18 counties. Four types of biomes are most commonly found. 12/18 have an average altitude higher than 1,300 meters above sea level. DISCUSSION: Even though human plague cases are very localized, the risk is present, and unexpected outbreaks could occur. Countries need to make the final push to eliminate plague as a public health problem for the Americas. A further disaggregated risk evaluation is recommended, including identification of foci and possible interactions among areas where plague could emerge or re-emerge. A closer geographical approach and environmental characterization are suggested.

Molecular characterization of invasive Neisseria meningitidis strains isolated in Chile during 2010-2011.

BACKGROUND: With the upcoming licensure of Outer Membrane Protein-based vaccines against meningococcal disease, data on disease incidence and molecular characteristic of circulating N. meningitidis strains in Latin American countries is needed. Chile is, to date, one of the few countries in the region that has performed this type of work in a comprehensive collection of disease-associated strains from two consecutive years, 2010-2011. METHODS: A total of 119 N. meningitidis strains isolated from patients with invasive disease in Chile in 2010-2011 were characterized by the National Reference Laboratory. Serogroup determination, MLST and porA typing were performed. RESULTS: Serogroup B was predominant in both study years, but W135 experienced a noticeable increase in 2011 compared to 2010. ST-11 complex, ST-41/44 complex ST-32 complex were the most prevalent among the isolates, and were strongly associated with serogroups W135 (ST-11 Complex) and B (ST-41/44 and ST-32 complexes). Likewise, the major porA types detected were strongly associated with these three clonal complexes: P1.5,2 was found exclusively among W135:ST-11 isolates, whereas P1.7, 2-3 was only detected in C:ST-11. ST-41/44 isolates mainly had P1.10-8, and ST-32 complex were associated with a P1.18-8 porA. CONCLUSIONS: Our data show disease-associated N. meningitidis circulating in Chile are similar to those found in other parts of the world. The increase on W135:ST-11 isolates observed in 2011 foretold the unusual epidemiological situation experienced in the country in 2012, and MLST data show that this strain is indistinguishable from the one linked to the global Hajj 2000-related outbreak that occurred in 2001. Finally, this work demonstrates the importance of maintaining a strong national surveillance program integrating clinical, epidemiological and laboratory data and incorporating gold standard diagnostic and characterization techniques that allow the data to be compared all over the world.

Phenotypic and genotypic characteristics of Neisseria meningitidis disease-causing strains in Argentina, 2010.

Phenotypic and genotypic characterization of 133 isolates of Neisseria meningitidis obtained from meningococcal disease cases in Argentina during 2010 were performed by the National Reference Laboratory as part of a project coordinated by the PAHO within the SIREVA II network. Serogroup, serotype, serosubtype and MLST characterization were performed. Minimum Inhibitory Concentration to penicillin, ampicillin, ceftriaxone, rifampin, chloramphenicol, tetracycline and ciprofloxacin were determined and interpreted according to CLSI guidelines. Almost 49% of isolates were W135, and two serotype:serosubtype combinations, W135:2a:P1.5,2:ST-11 and W135:2a:P1.2:ST-11 accounted for 78% of all W135 isolates. Serogroup B accounted for 42.1% of isolates, and was both phenotypically and genotypically diverse. Serogroup C isolates represented 5.3% of the dataset, and one isolate belonging to the ST-198 complex was non-groupable. Isolates belonged mainly to the ST-11 complex (48%) and to a lesser extent to the ST-865 (18%), ST-32 (9,8%) and the ST-35 complexes (9%). Intermediate resistance to penicillin and ampicillin was detected in 35.4% and 33.1% of isolates respectively. Two W135:2a:P1.5,2:ST-11:ST-11 isolates presented resistance to ciprofloxacin associated with a mutation in the QRDR of gyrA gene Thr91-Ile. These data show serogroup W135 was the first cause of disease in Argentina in 2010, and was strongly associated with the W135:2a:P1.5,2:ST-11 epidemic clone. Serogroup B was the second cause of disease and isolates belonging to this serogroup were phenotypically and genotypically diverse. The presence of isolates with intermediate resistance to penicillin and the presence of fluorquinolone-resistant isolates highlight the necessity and importance of maintaining and strengthening National Surveillance Programs.