The American Journal of Tropical Medicine and Hygiene
ABSTRACT. The Countrywide Mortality Surveillance for Action project aims to implement a child mor... more ABSTRACT. The Countrywide Mortality Surveillance for Action project aims to implement a child mortality surveillance program through strengthening vital registration event reporting (pregnancy, birth, and death) and investigating causes of death (CODs) based on verbal autopsies. In Quelimane (central Mozambique), Minimally Invasive Tissue Sampling (MITS) procedures were added to fine-tune the COD approaches. Before the implementation of MITS, an evaluation of the acceptability and ethical considerations of child mortality surveillance was considered fundamental. A socio-anthropological study was conducted in Quelimane, using observations, informal conversations, semi-structured interviews, and focus group discussions with healthcare providers, nharrubes (traditional authorities who handle bodies before the funeral), community and religious leaders, and traditional birth attendants to understand the locally relevant potential facilitators and barriers to the acceptability of MITS. Au...
Streptococcus pneumoniaeis a common cause of acute bacterial infections in Malawi. Understanding ... more Streptococcus pneumoniaeis a common cause of acute bacterial infections in Malawi. Understanding the underlying molecular mechanisms of the pathogen’s invasive behavior is crucial for designing new therapeutic strategies. We conducted a pan-genome analysis to identify potential virulence genes inS. pneumoniaeby comparing the gene pool of the isolates from carriers’ nasopharyngeal secretions to isolates from the blood and cerebrospinal fluid of patients. We identified 56 serotypes in the cohort. Most serotypes showed a similar prevalence in carriage and disease groups. However, serotypes 1, 5, and 12F were disproportionately more commonly detected in specimens from patients compared to the carriage group, as expected, given the known invasiveness of these serotypes. These serotypes were genetically distinct from other isolates of other serotypes. The lack of genes from a genomic island known as RD8a was the most pronounced difference between serotypes 1, 5, and 12F compared to signif...
Considering the early inequity in global COVID-19 vaccine distribution, we compared the level of ... more Considering the early inequity in global COVID-19 vaccine distribution, we compared the level of population immunity to SARS-CoV-2 with vaccine uptake and refusal between rural and urban Kenya two years after the pandemic onset. A population-based seroprevalence study was conducted in the city of Nairobi (n = 781) and a rural western county (n = 810) between January and February 2022. The overall SARS-CoV-2 seroprevalence was 90.2% (95% CI, 88.6–91.2%), including 96.7% (95% CI, 95.2–97.9%) among urban and 83.6% (95% CI, 80.6–86.0%) among rural populations. A comparison of immunity profiles showed that >50% of the rural population were strongly immunoreactive compared to <20% of the urban population, suggesting more recent infections or vaccinations in the rural population. More than 45% of the vaccine-eligible (≥18 years old) persons had not taken a single dose of the vaccine (hesitancy), including 47.6% and 46.9% of urban and rural participants, respectively. Vaccine refusal ...
Various efforts to increase COVID-19 vaccination rates have been employed in the United States. W... more Various efforts to increase COVID-19 vaccination rates have been employed in the United States. We sought to rapidly investigate public reactions to these efforts to increase vaccination, including self-reported responses to widespread reduced masking behavior, monetary incentive programs to get vaccinated, and work vaccination requirements. Using a unique method for data collection (Random Domain Intercept Technology), we captured a large (N = 14,152), broad-based sample of the United States Web-using population (data collected from June 30 –July 26, 2021). About 3/4 of respondents reported being vaccinated. The likelihood of vaccination and vaccination intention differed across various demographic indicators (e.g., gender, age, income, political leaning). We observed mixed reactions to efforts aimed at increasing vaccination rates among unvaccinated respondents. While some reported that specific efforts would increase their likelihood of getting vaccinated (between 16% and 32%), o...
Additional file 2. Description of sensitivity analysis looking at potential gestational age measu... more Additional file 2. Description of sensitivity analysis looking at potential gestational age measurement error.
Table S1. Comparison of pneumococcal colonization between the 2009 and 2010 surveys. Table S2. Se... more Table S1. Comparison of pneumococcal colonization between the 2009 and 2010 surveys. Table S2. Serotype distribution of non-vaccine type pneumococci (N = 497). Table S3. Antibiotic resistance patterns of multidrug-resistant pneumococcal isolates (N = 103). Table S4. Factors associated with cotrimoxazole nonsusceptibility among children in Lwak and Kibera, 2009. Table S5. Factors associated with multidrug-resistance among children in Lwak and Kibera, 2009. (DOCX 40 kb)
A One Health (OH) approach that integrates human,animal and environmental approaches to managemen... more A One Health (OH) approach that integrates human,animal and environmental approaches to management of zoonotic diseases has gained momentum in the last decadeas part of a strategy to prevent and control emerging infectious diseases. However, there are few examples of howan OH approach can be established in a country. Kenya establishment of an OH office, referred to asthe Zoonotic Disease Unit (ZDU) in 2011. The ZDU bridges theanimal and human health sectors with a senior epidemiologist deployed from each ministry; and agoal of maintaining collaboration at the animal and human health interface towards better prevention and control of zoonoses.The country is adding an ecologist to the ZDU to ensure that environmental risks are adequately addressed in emerging disease control.
BackgroundThe prioritization of vaccine eligibility for different subpopulations is an important ... more BackgroundThe prioritization of vaccine eligibility for different subpopulations is an important decision to curb spread and severe outcomes of epidemic infectious diseases for which vaccines become available. Using COVID-19 as a prototype, this study evaluates the public health impact of various vaccine prioritization schemes of elderly and high-risk individuals with different vaccination start dates and rollout speeds. MethodsAn agent-based simulation model was adapted and used to project the number of infections, hospitalizations, and deaths under various vaccination start dates, rollout speeds, and prioritization schemes, including (A)no prioritization, (B)two-staged prioritization of elderly population, and (C)multi-staged prioritization of elderly and then high-risk population. The study period was February 18th, 2020 –June 1st, 2021, and the state of Georgia was used as a case study. ResultsThe relative effectiveness of the prioritization schemes depends on the outcome consid...
Background The current burden of >5 million deaths yearly is the focus of the Sustainable Deve... more Background The current burden of >5 million deaths yearly is the focus of the Sustainable Development Goal (SDG) to end preventable deaths of newborns and children under 5 years old by 2030. To accelerate progression toward this goal, data are needed that accurately quantify the leading causes of death, so that interventions can target the common causes. By adding postmortem pathology and microbiology studies to other available data, the Child Health and Mortality Prevention Surveillance (CHAMPS) network provides comprehensive evaluations of conditions leading to death, in contrast to standard methods that rely on data from medical records and verbal autopsy and report only a single underlying condition. We analyzed CHAMPS data to characterize the value of considering multiple causes of death. Methods and findings We examined deaths identified from December 2016 through November 2020 from 7 CHAMPS sites (in Bangladesh, Ethiopia, Kenya, Mali, Mozambique, Sierra Leone, and South Af...
Background Sub-Saharan Africa and south Asia contributed 81% of 5•9 million under-5 deaths and 77... more Background Sub-Saharan Africa and south Asia contributed 81% of 5•9 million under-5 deaths and 77% of 2•6 million stillbirths worldwide in 2015. Vital registration and verbal autopsy data are mainstays for the estimation of leading causes of death, but both are non-specific and focus on a single underlying cause. We aimed to provide granular data on the contributory causes of death in stillborn fetuses and in deceased neonates and children younger than 5 years, to inform child mortality prevention efforts. Methods The Child Health and Mortality Prevention Surveillance (CHAMPS) Network was established at sites in seven countries (
Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the... more Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use of vaccines in > 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 stool samples from children aged <13 years admitted with diarrheal illness to Kilifi County Hospital, coastal Kenya. Antigen screening detected RVA in 55 samples (22.2%). Of these, VP7 (G) and VP4 (P) segments were successfully sequenced in 48 (87.3%) and phylogenetic analysis based on the VP7 sequences identified seven genetic clusters with six different GP combinations; G3P[8], G1P[8], G2P[4], G2P[8], G9P[8] and G12P[8]. The G3P[8] strains predominated the season (n=37, 67.2%) and comprised three G3 genetic clusters that fell within Lineage I and IX (the latter also known as equine-like G3 lineage). Both two G3 lineages have been recently detected in several countries. Our study is the first to d...
Sixty-two invasive Streptococcus pyogenes strains, including 32 strains isolated from patients wi... more Sixty-two invasive Streptococcus pyogenes strains, including 32 strains isolated from patients with streptococcal toxic shock syndrome (STSS), were analyzed for the following phenotypic and genotypic characteristics: M-protein type, serum opacity factor production, protease production, the presence of streptococcal pyrogenic exotoxin (Spe) genes A, B, and C, and in vitro production of SpeA and SpeB. These characteristics were analyzed for possible associations with each other as well as with clinical components of STSS. M-type 1, the most commonly isolated M-type, was significantly associated with protease production. Protease activity was significantly associated with the clinical sign of soft tissue necrosis. M-type 1 and 3 strains from STSS patients were significantly associated with the clinical signs of shock and organ involvement as well as with SpeA production in vitro. Finally, the production of SpeA was significantly associated with the clinical component of shock and organ...
International Journal of Environmental Research and Public Health, 2020
Diarrheal disease remains a major cause of childhood mortality and morbidity causing poor health ... more Diarrheal disease remains a major cause of childhood mortality and morbidity causing poor health and economic outcomes. In low-resource settings, young children are exposed to numerous risk factors for enteric pathogen transmission within their dwellings, though the relative importance of different transmission pathways varies by pathogen species. The objective of this analysis was to model associations between five household-level risk factors—water, sanitation, flooring, caregiver education, and crowding—and infection status for endemic enteric pathogens in children in five surveillance studies. Data were combined from 22 sites in which a total of 58,000 stool samples were tested for 16 specific enteropathogens using qPCR. Risk ratios for pathogen- and taxon-specific infection status were modeled using generalized linear models along with hazard ratios for all-cause diarrhea in proportional hazard models, with the five household-level variables as primary exposures adjusting for c...
Background Kenya introduced the monovalent G1P [8] Rotarix® vaccine into the infant immunization ... more Background Kenya introduced the monovalent G1P [8] Rotarix® vaccine into the infant immunization schedule in July 2014. We examined trends in rotavirus group A (RVA) genotype distribution pre- (January 2010–June 2014) and post- (July 2014–December 2018) RVA vaccine introduction. Methods Stool samples were collected from children aged < 13 years from four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic Nairobi, Lwak Mission Hospital, and Siaya County Referral Hospital (children aged < 5 years only). Samples were screened for RVA using enzyme linked immunosorbent assay (ELISA) and VP7 and VP4 genes sequenced to infer genotypes. Results We genotyped 614 samples in pre-vaccine and 261 in post-vaccine introduction periods. During the pre-vaccine introduction period, the most frequent RVA genotypes were G1P [8] (45.8%), G8P [4] (15.8%), G9P [8] (13.2%), G2P [4] (7.0%) and G3P [6] (3.1%). In the post-vaccine introduction period, the most frequent genotypes wer...
Some protozoans isolated from aquatic habitats, including domestic water supplies, can support th... more Some protozoans isolated from aquatic habitats, including domestic water supplies, can support the intracellular replication of autochthonous legionellae in vitro. We studied the effect of incubating water samples containing amoebae on the sensitivity of culture for legionellae. Samples collected during investigations of legionellosis epidemics and shown by conventional culture procedures to contain amoebae, but not legionellae, were incubated at 35 degrees C and replated. Legionellae were recovered from 59 of 144 such samples. Species isolated included L. pneumophila, L. anisa, L. bozemanii, L. gormanii, L. micdadei, L. rubrilucens, L. sainthelensi, L. steigerwaltii, and an unnamed species. Acanthamoeba polyphaga, Acanthamoeba hatchetti, a Rosculus sp., Hartmannella vermiformis, and Vahlkampfia spp. were among the autochthonous amoebae identified. Legionellae were recovered by this procedure from only 3 of 63 samples that were negative for amoebae by conventional culture procedures...
The American Journal of Tropical Medicine and Hygiene
ABSTRACT. The Countrywide Mortality Surveillance for Action project aims to implement a child mor... more ABSTRACT. The Countrywide Mortality Surveillance for Action project aims to implement a child mortality surveillance program through strengthening vital registration event reporting (pregnancy, birth, and death) and investigating causes of death (CODs) based on verbal autopsies. In Quelimane (central Mozambique), Minimally Invasive Tissue Sampling (MITS) procedures were added to fine-tune the COD approaches. Before the implementation of MITS, an evaluation of the acceptability and ethical considerations of child mortality surveillance was considered fundamental. A socio-anthropological study was conducted in Quelimane, using observations, informal conversations, semi-structured interviews, and focus group discussions with healthcare providers, nharrubes (traditional authorities who handle bodies before the funeral), community and religious leaders, and traditional birth attendants to understand the locally relevant potential facilitators and barriers to the acceptability of MITS. Au...
Streptococcus pneumoniaeis a common cause of acute bacterial infections in Malawi. Understanding ... more Streptococcus pneumoniaeis a common cause of acute bacterial infections in Malawi. Understanding the underlying molecular mechanisms of the pathogen’s invasive behavior is crucial for designing new therapeutic strategies. We conducted a pan-genome analysis to identify potential virulence genes inS. pneumoniaeby comparing the gene pool of the isolates from carriers’ nasopharyngeal secretions to isolates from the blood and cerebrospinal fluid of patients. We identified 56 serotypes in the cohort. Most serotypes showed a similar prevalence in carriage and disease groups. However, serotypes 1, 5, and 12F were disproportionately more commonly detected in specimens from patients compared to the carriage group, as expected, given the known invasiveness of these serotypes. These serotypes were genetically distinct from other isolates of other serotypes. The lack of genes from a genomic island known as RD8a was the most pronounced difference between serotypes 1, 5, and 12F compared to signif...
Considering the early inequity in global COVID-19 vaccine distribution, we compared the level of ... more Considering the early inequity in global COVID-19 vaccine distribution, we compared the level of population immunity to SARS-CoV-2 with vaccine uptake and refusal between rural and urban Kenya two years after the pandemic onset. A population-based seroprevalence study was conducted in the city of Nairobi (n = 781) and a rural western county (n = 810) between January and February 2022. The overall SARS-CoV-2 seroprevalence was 90.2% (95% CI, 88.6–91.2%), including 96.7% (95% CI, 95.2–97.9%) among urban and 83.6% (95% CI, 80.6–86.0%) among rural populations. A comparison of immunity profiles showed that >50% of the rural population were strongly immunoreactive compared to <20% of the urban population, suggesting more recent infections or vaccinations in the rural population. More than 45% of the vaccine-eligible (≥18 years old) persons had not taken a single dose of the vaccine (hesitancy), including 47.6% and 46.9% of urban and rural participants, respectively. Vaccine refusal ...
Various efforts to increase COVID-19 vaccination rates have been employed in the United States. W... more Various efforts to increase COVID-19 vaccination rates have been employed in the United States. We sought to rapidly investigate public reactions to these efforts to increase vaccination, including self-reported responses to widespread reduced masking behavior, monetary incentive programs to get vaccinated, and work vaccination requirements. Using a unique method for data collection (Random Domain Intercept Technology), we captured a large (N = 14,152), broad-based sample of the United States Web-using population (data collected from June 30 –July 26, 2021). About 3/4 of respondents reported being vaccinated. The likelihood of vaccination and vaccination intention differed across various demographic indicators (e.g., gender, age, income, political leaning). We observed mixed reactions to efforts aimed at increasing vaccination rates among unvaccinated respondents. While some reported that specific efforts would increase their likelihood of getting vaccinated (between 16% and 32%), o...
Additional file 2. Description of sensitivity analysis looking at potential gestational age measu... more Additional file 2. Description of sensitivity analysis looking at potential gestational age measurement error.
Table S1. Comparison of pneumococcal colonization between the 2009 and 2010 surveys. Table S2. Se... more Table S1. Comparison of pneumococcal colonization between the 2009 and 2010 surveys. Table S2. Serotype distribution of non-vaccine type pneumococci (N = 497). Table S3. Antibiotic resistance patterns of multidrug-resistant pneumococcal isolates (N = 103). Table S4. Factors associated with cotrimoxazole nonsusceptibility among children in Lwak and Kibera, 2009. Table S5. Factors associated with multidrug-resistance among children in Lwak and Kibera, 2009. (DOCX 40 kb)
A One Health (OH) approach that integrates human,animal and environmental approaches to managemen... more A One Health (OH) approach that integrates human,animal and environmental approaches to management of zoonotic diseases has gained momentum in the last decadeas part of a strategy to prevent and control emerging infectious diseases. However, there are few examples of howan OH approach can be established in a country. Kenya establishment of an OH office, referred to asthe Zoonotic Disease Unit (ZDU) in 2011. The ZDU bridges theanimal and human health sectors with a senior epidemiologist deployed from each ministry; and agoal of maintaining collaboration at the animal and human health interface towards better prevention and control of zoonoses.The country is adding an ecologist to the ZDU to ensure that environmental risks are adequately addressed in emerging disease control.
BackgroundThe prioritization of vaccine eligibility for different subpopulations is an important ... more BackgroundThe prioritization of vaccine eligibility for different subpopulations is an important decision to curb spread and severe outcomes of epidemic infectious diseases for which vaccines become available. Using COVID-19 as a prototype, this study evaluates the public health impact of various vaccine prioritization schemes of elderly and high-risk individuals with different vaccination start dates and rollout speeds. MethodsAn agent-based simulation model was adapted and used to project the number of infections, hospitalizations, and deaths under various vaccination start dates, rollout speeds, and prioritization schemes, including (A)no prioritization, (B)two-staged prioritization of elderly population, and (C)multi-staged prioritization of elderly and then high-risk population. The study period was February 18th, 2020 –June 1st, 2021, and the state of Georgia was used as a case study. ResultsThe relative effectiveness of the prioritization schemes depends on the outcome consid...
Background The current burden of >5 million deaths yearly is the focus of the Sustainable Deve... more Background The current burden of >5 million deaths yearly is the focus of the Sustainable Development Goal (SDG) to end preventable deaths of newborns and children under 5 years old by 2030. To accelerate progression toward this goal, data are needed that accurately quantify the leading causes of death, so that interventions can target the common causes. By adding postmortem pathology and microbiology studies to other available data, the Child Health and Mortality Prevention Surveillance (CHAMPS) network provides comprehensive evaluations of conditions leading to death, in contrast to standard methods that rely on data from medical records and verbal autopsy and report only a single underlying condition. We analyzed CHAMPS data to characterize the value of considering multiple causes of death. Methods and findings We examined deaths identified from December 2016 through November 2020 from 7 CHAMPS sites (in Bangladesh, Ethiopia, Kenya, Mali, Mozambique, Sierra Leone, and South Af...
Background Sub-Saharan Africa and south Asia contributed 81% of 5•9 million under-5 deaths and 77... more Background Sub-Saharan Africa and south Asia contributed 81% of 5•9 million under-5 deaths and 77% of 2•6 million stillbirths worldwide in 2015. Vital registration and verbal autopsy data are mainstays for the estimation of leading causes of death, but both are non-specific and focus on a single underlying cause. We aimed to provide granular data on the contributory causes of death in stillborn fetuses and in deceased neonates and children younger than 5 years, to inform child mortality prevention efforts. Methods The Child Health and Mortality Prevention Surveillance (CHAMPS) Network was established at sites in seven countries (
Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the... more Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use of vaccines in > 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 stool samples from children aged <13 years admitted with diarrheal illness to Kilifi County Hospital, coastal Kenya. Antigen screening detected RVA in 55 samples (22.2%). Of these, VP7 (G) and VP4 (P) segments were successfully sequenced in 48 (87.3%) and phylogenetic analysis based on the VP7 sequences identified seven genetic clusters with six different GP combinations; G3P[8], G1P[8], G2P[4], G2P[8], G9P[8] and G12P[8]. The G3P[8] strains predominated the season (n=37, 67.2%) and comprised three G3 genetic clusters that fell within Lineage I and IX (the latter also known as equine-like G3 lineage). Both two G3 lineages have been recently detected in several countries. Our study is the first to d...
Sixty-two invasive Streptococcus pyogenes strains, including 32 strains isolated from patients wi... more Sixty-two invasive Streptococcus pyogenes strains, including 32 strains isolated from patients with streptococcal toxic shock syndrome (STSS), were analyzed for the following phenotypic and genotypic characteristics: M-protein type, serum opacity factor production, protease production, the presence of streptococcal pyrogenic exotoxin (Spe) genes A, B, and C, and in vitro production of SpeA and SpeB. These characteristics were analyzed for possible associations with each other as well as with clinical components of STSS. M-type 1, the most commonly isolated M-type, was significantly associated with protease production. Protease activity was significantly associated with the clinical sign of soft tissue necrosis. M-type 1 and 3 strains from STSS patients were significantly associated with the clinical signs of shock and organ involvement as well as with SpeA production in vitro. Finally, the production of SpeA was significantly associated with the clinical component of shock and organ...
International Journal of Environmental Research and Public Health, 2020
Diarrheal disease remains a major cause of childhood mortality and morbidity causing poor health ... more Diarrheal disease remains a major cause of childhood mortality and morbidity causing poor health and economic outcomes. In low-resource settings, young children are exposed to numerous risk factors for enteric pathogen transmission within their dwellings, though the relative importance of different transmission pathways varies by pathogen species. The objective of this analysis was to model associations between five household-level risk factors—water, sanitation, flooring, caregiver education, and crowding—and infection status for endemic enteric pathogens in children in five surveillance studies. Data were combined from 22 sites in which a total of 58,000 stool samples were tested for 16 specific enteropathogens using qPCR. Risk ratios for pathogen- and taxon-specific infection status were modeled using generalized linear models along with hazard ratios for all-cause diarrhea in proportional hazard models, with the five household-level variables as primary exposures adjusting for c...
Background Kenya introduced the monovalent G1P [8] Rotarix® vaccine into the infant immunization ... more Background Kenya introduced the monovalent G1P [8] Rotarix® vaccine into the infant immunization schedule in July 2014. We examined trends in rotavirus group A (RVA) genotype distribution pre- (January 2010–June 2014) and post- (July 2014–December 2018) RVA vaccine introduction. Methods Stool samples were collected from children aged < 13 years from four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic Nairobi, Lwak Mission Hospital, and Siaya County Referral Hospital (children aged < 5 years only). Samples were screened for RVA using enzyme linked immunosorbent assay (ELISA) and VP7 and VP4 genes sequenced to infer genotypes. Results We genotyped 614 samples in pre-vaccine and 261 in post-vaccine introduction periods. During the pre-vaccine introduction period, the most frequent RVA genotypes were G1P [8] (45.8%), G8P [4] (15.8%), G9P [8] (13.2%), G2P [4] (7.0%) and G3P [6] (3.1%). In the post-vaccine introduction period, the most frequent genotypes wer...
Some protozoans isolated from aquatic habitats, including domestic water supplies, can support th... more Some protozoans isolated from aquatic habitats, including domestic water supplies, can support the intracellular replication of autochthonous legionellae in vitro. We studied the effect of incubating water samples containing amoebae on the sensitivity of culture for legionellae. Samples collected during investigations of legionellosis epidemics and shown by conventional culture procedures to contain amoebae, but not legionellae, were incubated at 35 degrees C and replated. Legionellae were recovered from 59 of 144 such samples. Species isolated included L. pneumophila, L. anisa, L. bozemanii, L. gormanii, L. micdadei, L. rubrilucens, L. sainthelensi, L. steigerwaltii, and an unnamed species. Acanthamoeba polyphaga, Acanthamoeba hatchetti, a Rosculus sp., Hartmannella vermiformis, and Vahlkampfia spp. were among the autochthonous amoebae identified. Legionellae were recovered by this procedure from only 3 of 63 samples that were negative for amoebae by conventional culture procedures...
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Papers by Robert Breiman