1
|
Owusu D, Ndegwa LK, Ayugi J, Kinuthia P, Kalani R, Okeyo M, Otieno NA, Kikwai G, Juma B, Munyua P, Kuria F, Okunga E, Moen AC, Emukule GO. Use of Sentinel Surveillance Platforms for Monitoring SARS-CoV-2 Activity: Evidence From Analysis of Kenya Influenza Sentinel Surveillance Data. JMIR Public Health Surveill 2024; 10:e50799. [PMID: 38526537 PMCID: PMC11002741 DOI: 10.2196/50799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND Little is known about the cocirculation of influenza and SARS-CoV-2 viruses during the COVID-19 pandemic and the use of respiratory disease sentinel surveillance platforms for monitoring SARS-CoV-2 activity in sub-Saharan Africa. OBJECTIVE We aimed to describe influenza and SARS-CoV-2 cocirculation in Kenya and how the SARS-CoV-2 data from influenza sentinel surveillance correlated with that of universal national surveillance. METHODS From April 2020 to March 2022, we enrolled 7349 patients with severe acute respiratory illness or influenza-like illness at 8 sentinel influenza surveillance sites in Kenya and collected demographic, clinical, underlying medical condition, vaccination, and exposure information, as well as respiratory specimens, from them. Respiratory specimens were tested for influenza and SARS-CoV-2 by real-time reverse transcription polymerase chain reaction. The universal national-level SARS-CoV-2 data were also obtained from the Kenya Ministry of Health. The universal national-level SARS-CoV-2 data were collected from all health facilities nationally, border entry points, and contact tracing in Kenya. Epidemic curves and Pearson r were used to describe the correlation between SARS-CoV-2 positivity in data from the 8 influenza sentinel sites in Kenya and that of the universal national SARS-CoV-2 surveillance data. A logistic regression model was used to assess the association between influenza and SARS-CoV-2 coinfection with severe clinical illness. We defined severe clinical illness as any of oxygen saturation <90%, in-hospital death, admission to intensive care unit or high dependence unit, mechanical ventilation, or a report of any danger sign (ie, inability to drink or eat, severe vomiting, grunting, stridor, or unconsciousness in children younger than 5 years) among patients with severe acute respiratory illness. RESULTS Of the 7349 patients from the influenza sentinel surveillance sites, 76.3% (n=5606) were younger than 5 years. We detected any influenza (A or B) in 8.7% (629/7224), SARS-CoV-2 in 10.7% (768/7199), and coinfection in 0.9% (63/7165) of samples tested. Although the number of samples tested for SARS-CoV-2 from the sentinel surveillance was only 0.2% (60 per week vs 36,000 per week) of the number tested in the universal national surveillance, SARS-CoV-2 positivity in the sentinel surveillance data significantly correlated with that of the universal national surveillance (Pearson r=0.58; P<.001). The adjusted odds ratios (aOR) of clinical severe illness among participants with coinfection were similar to those of patients with influenza only (aOR 0.91, 95% CI 0.47-1.79) and SARS-CoV-2 only (aOR 0.92, 95% CI 0.47-1.82). CONCLUSIONS Influenza substantially cocirculated with SARS-CoV-2 in Kenya. We found a significant correlation of SARS-CoV-2 positivity in the data from 8 influenza sentinel surveillance sites with that of the universal national SARS-CoV-2 surveillance data. Our findings indicate that the influenza sentinel surveillance system can be used as a sustainable platform for monitoring respiratory pathogens of pandemic potential or public health importance.
Collapse
Affiliation(s)
- Daniel Owusu
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Linus K Ndegwa
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Jorim Ayugi
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Rosalia Kalani
- Disease Surveillance and Response Unit, Ministry of Health, Nairobi, Kenya
| | - Mary Okeyo
- National Influenza Centre Laboratory, National Public Health Laboratories, Ministry of Health, Nairobi, Kenya
| | - Nancy A Otieno
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Gilbert Kikwai
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Bonventure Juma
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Peninah Munyua
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Francis Kuria
- Directorate of Public Health, Ministry of Health, Nairobi, Kenya
| | - Emmanuel Okunga
- Disease Surveillance and Response Unit, Ministry of Health, Nairobi, Kenya
| | - Ann C Moen
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gideon O Emukule
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
| |
Collapse
|
2
|
Hunsperger E, Osoro E, Munyua P, Njenga MK, Mirieri H, Kikwai G, Odhiambo D, Dayan M, Omballa V, Agogo GO, Mugo C, Widdowson MA, Inwani I. Seroconversion and seroprevalence of TORCH infections in a pregnant women cohort study, Mombasa, Kenya, 2017-2019. Epidemiol Infect 2024; 152:e68. [PMID: 38305089 PMCID: PMC11077605 DOI: 10.1017/s0950268824000165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Women infected during pregnancy with TORCH (Toxoplasmosis, Other, Rubella, Cytomegalovirus, and Herpes simplex viruses) pathogens have a higher risk of adverse birth outcomes including stillbirth / miscarriage because of mother-to-child transmission. To investigate these risks in pregnant women in Kenya, we analyzed serum specimens from a pregnancy cohort study at three healthcare facilities. A sample of 481 participants was selected for TORCH pathogen antibody testing to determine seroprevalence. A random selection of 285 from the 481 participants was selected to measure seroconversion. These sera were tested using an IgG enzyme-linked immunosorbent assay against 10 TORCH pathogens. We found that the seroprevalence of all but three of the 10 TORCH pathogens at enrollment was >30%, except for Bordetella pertussis (3.8%), Treponema pallidum (11.4%), and varicella zoster virus (0.5%). Conversely, very few participants seroconverted during their pregnancy and were herpes simplex virus type 2 (n = 24, 11.2%), parvovirus B19 (n = 14, 6.2%), and rubella (n = 12, 5.1%). For birth outcomes, 88% of the participant had live births and 12% had stillbirths or miscarriage. Cytomegalovirus positivity at enrolment had a statistically significant positive association with a live birth outcome (p = 0.0394). Of the 10 TORCH pathogens tested, none had an association with adverse pregnancy outcome.
Collapse
Affiliation(s)
- Elizabeth Hunsperger
- Division of Global Health Protection, US Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Eric Osoro
- Washington State University (WSU) Global Health Kenya, Nairobi, Kenya
- Paul G. Allen School for Global Health, Washington State University (WSU), Pullman, WA, USA
| | - Peninah Munyua
- Division of Global Health Protection, US Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - M. Kariuki Njenga
- Washington State University (WSU) Global Health Kenya, Nairobi, Kenya
- Paul G. Allen School for Global Health, Washington State University (WSU), Pullman, WA, USA
| | - Harriet Mirieri
- Washington State University (WSU) Global Health Kenya, Nairobi, Kenya
| | - Gilbert Kikwai
- Kenya Medical Research Institute (KEMRI), Center for Global Health Research, Nairobi, Kenya
| | - Dennis Odhiambo
- Kenya Medical Research Institute (KEMRI), Center for Global Health Research, Nairobi, Kenya
| | - Moshe Dayan
- Kenya Medical Research Institute (KEMRI), Center for Global Health Research, Nairobi, Kenya
| | - Victor Omballa
- Kenya Medical Research Institute (KEMRI), Center for Global Health Research, Nairobi, Kenya
| | - George O. Agogo
- Division of Global Health Protection, US Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Cyrus Mugo
- Department of Paediatrics and Child Health/Kenyatta National Hospital, University of Nairobi, Nairobi, Kenya
| | - Marc-Alain Widdowson
- Division of Global Health Protection, US Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Irene Inwani
- Department of Paediatrics and Child Health/Kenyatta National Hospital, University of Nairobi, Nairobi, Kenya
| |
Collapse
|
3
|
Munywoki PK, Bigogo G, Nasimiyu C, Ouma A, Aol G, Oduor CO, Rono S, Auko J, Agogo GO, Njoroge R, Oketch D, Odhiambo D, Odeyo VW, Kikwai G, Onyango C, Juma B, Hunsperger E, Lidechi S, Ochieng CA, Lo TQ, Munyua P, Herman-Roloff A. Heterogenous transmission and seroprevalence of SARS-CoV-2 in two demographically diverse populations with low vaccination uptake in Kenya, March and June 2021. Gates Open Res 2023; 7:101. [PMID: 37990692 PMCID: PMC10661969 DOI: 10.12688/gatesopenres.14684.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2023] [Indexed: 11/23/2023] Open
Abstract
Background SARS-CoV-2 has extensively spread in cities and rural communities, and studies are needed to quantify exposure in the population. We report seroprevalence of SARS-CoV-2 in two well-characterized populations in Kenya at two time points. These data inform the design and delivery of public health mitigation measures. Methods Leveraging on existing population based infectious disease surveillance (PBIDS) in two demographically diverse settings, a rural site in western Kenya in Asembo, Siaya County, and an urban informal settlement in Kibera, Nairobi County, we set up a longitudinal cohort of randomly selected households with serial sampling of all consenting household members in March and June/July 2021. Both sites included 1,794 and 1,638 participants in the March and June/July 2021, respectively. Individual seroprevalence of SARS-CoV-2 antibodies was expressed as a percentage of the seropositive among the individuals tested, accounting for household clustering and weighted by the PBIDS age and sex distribution. Results Overall weighted individual seroprevalence increased from 56.2% (95%CI: 52.1, 60.2%) in March 2021 to 63.9% (95%CI: 59.5, 68.0%) in June 2021 in Kibera. For Asembo, the seroprevalence almost doubled from 26.0% (95%CI: 22.4, 30.0%) in March 2021 to 48.7% (95%CI: 44.3, 53.2%) in July 2021. Seroprevalence was highly heterogeneous by age and geography in these populations-higher seroprevalence was observed in the urban informal settlement (compared to the rural setting), and children aged <10 years had the lowest seroprevalence in both sites. Only 1.2% and 1.6% of the study participants reported receipt of at least one dose of the COVID-19 vaccine by the second round of serosurvey-none by the first round. Conclusions In these two populations, SARS-CoV-2 seroprevalence increased in the first 16 months of the COVID-19 pandemic in Kenya. It is important to prioritize additional mitigation measures, such as vaccine distribution, in crowded and low socioeconomic settings.
Collapse
Affiliation(s)
- Patrick K. Munywoki
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Godfrey Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Carolyne Nasimiyu
- Global Health Program, Washington State University – Global Health Kenya (WSU-GH Kenya), Nairobi, Kenya
- Paul G. Allen School of Global Health, Washington State University, Pullman, Washington, USA
| | - Alice Ouma
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - George Aol
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Clifford O. Oduor
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Samuel Rono
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Joshua Auko
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - George O. Agogo
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Ruth Njoroge
- Global Health Program, Washington State University – Global Health Kenya (WSU-GH Kenya), Nairobi, Kenya
| | - Dismas Oketch
- Global Health Program, Washington State University – Global Health Kenya (WSU-GH Kenya), Nairobi, Kenya
| | - Dennis Odhiambo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Victor W. Odeyo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Gilbert Kikwai
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Clayton Onyango
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Bonventure Juma
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Elizabeth Hunsperger
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Shirley Lidechi
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | | | - Terrence Q. Lo
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Peninah Munyua
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Amy Herman-Roloff
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| |
Collapse
|
4
|
Murunga N, Nyawanda B, Nyiro JU, Otieno GP, Kamau E, Agoti CN, Lewa C, Gichuki A, Mutunga M, Otieno N, Mayieka L, Ochieng M, Kikwai G, Hunsperger E, Onyango C, Emukule G, Bigogo G, Verani JR, Chaves SS, Nokes DJ, Munywoki PK. Surveillance of respiratory viruses at health facilities from across Kenya, 2014. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17908.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Acute respiratory illnesses (ARI) are a major cause of morbidity and mortality globally. With (re)emergence of novel viruses and increased access to childhood bacterial vaccines, viruses have assumed greater importance in the aetiology of ARI. There are now promising candidate vaccines against some of the most common endemic respiratory viruses. Optimal delivery strategies for these vaccines, and the need for interventions against other respiratory viruses, requires geographically diverse data capturing temporal variations in virus circulation. Methods: We leveraged three health facility-based respiratory illness surveillance platforms operating in 11 sites across Kenya. Nasopharyngeal (NP) and/or oropharyngeal (OP) specimens, patient demographic, and clinical characteristics were collected in 2014 from individuals of various ages presenting with respiratory symptoms at the surveillance facilities. Real time multiplex polymerase chain reaction was used to detect rhinoviruses, respiratory syncytial virus (RSV), influenza virus, human coronaviruses (hCoV), and adenoviruses. Results: From 11 sites, 5451 NP/OP specimens were collected and tested from patients. Of these, 40.2% were positive for at least one of the targeted respiratory viruses. The most frequently detected were rhinoviruses (17.0%) and RSV A/B (10.5%), followed by influenza A (6.2%), adenovirus (6.0%) and hCoV (4.2%). RSV was most prevalent among infants aged <12 months old (18.9%), adenovirus among children aged 12–23 months old (11.0%), influenza A among children aged 24–59 months (9.3%), and rhinovirus across all age groups (range, 12.7–19.0%). The overall percent virus positivity varied by surveillance site, health facility type and case definition used in surveillance. Conclusions: We identify rhinoviruses, RSV, and influenza A as the most prevalent respiratory viruses. Higher RSV positivity in inpatient settings compared to outpatient clinics strengthen the case for RSV vaccination. To inform the design and delivery of public health interventions, long-term surveillance is required to establish regional heterogeneities in respiratory virus circulation and seasonality.
Collapse
|
5
|
Murunga N, Nyawanda B, Nyiro JU, Otieno GP, Kamau E, Agoti CN, Lewa C, Gichuki A, Mutunga M, Otieno N, Mayieka L, Ochieng M, Kikwai G, Hunsperger E, Onyango C, Emukule G, Bigogo G, Verani JR, Chaves SS, Nokes DJ, Munywoki PK. Surveillance of respiratory viruses at health facilities from across Kenya, 2014. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17908.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Acute respiratory illnesses (ARI) are a major cause of morbidity and mortality globally. With (re)emergence of novel viruses and increased access to childhood bacterial vaccines, viruses have assumed greater importance in the aetiology of ARI. There are now promising candidate vaccines against some of the most common endemic respiratory viruses. Optimal delivery strategies for these vaccines, and the need for interventions against other respiratory viruses, requires geographically diverse data capturing temporal variations in virus circulation. Methods: We leveraged three health facility-based respiratory illness surveillance platforms operating in 11 sites across Kenya. Nasopharyngeal (NP) and/or oropharyngeal (OP) specimens, patient demographic, and clinical characteristics were collected in 2014 from individuals of various ages presenting with respiratory symptoms at the surveillance facilities. Real time multiplex polymerase chain reaction was used to detect rhinoviruses, respiratory syncytial virus (RSV), influenza virus, human coronaviruses (hCoV), and adenoviruses. Results: From 11 sites, 5451 NP/OP specimens were collected and tested from patients. Of these, 40.2% were positive for at least one of the targeted respiratory viruses. The most frequently detected were rhinoviruses (17.0%) and RSV A/B (10.5%), followed by influenza A (6.2%), adenovirus (6.0%) and hCoV (4.2%). RSV was most prevalent among infants aged <12 months old (18.9%), adenovirus among children aged 12–23 months old (11.0%), influenza A among children aged 24–59 months (9.3%), and rhinovirus across all age groups (range, 12.7–19.0%). The overall percent virus positivity varied by surveillance site, health facility type and case definition used in surveillance. Conclusions: We identify rhinoviruses, RSV, and influenza A as the most prevalent respiratory viruses. Higher RSV positivity in inpatient settings compared to outpatient clinics strengthen the case for RSV vaccination. To inform the design and delivery of public health interventions, long-term surveillance is required to establish regional heterogeneities in respiratory virus circulation and seasonality.
Collapse
|
6
|
Munywoki PK, Nasimiyu C, Alando MD, Otieno N, Ombok C, Njoroge R, Kikwai G, Odhiambo, D, Osita MP, Ouma A, Odour C, Juma B, Ochieng CA, Mutisya I, Ngere I, Dawa J, Osoro E, Njenga MK, Bigogo G, Munyua P, Lo TQ, Hunsperger E, Herman-Roloff A. Seroprevalence and risk factors of SARS-CoV-2 infection in an urban informal settlement in Nairobi, Kenya, December 2020. F1000Res 2022; 10:853. [PMID: 35528961 PMCID: PMC9065925 DOI: 10.12688/f1000research.72914.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/07/2022] [Indexed: 11/20/2022] Open
Abstract
Introduction: Urban informal settlements may be disproportionately affected by the COVID-19 pandemic due to overcrowding and other socioeconomic challenges that make adoption and implementation of public health mitigation measures difficult. We conducted a seroprevalence survey in the Kibera informal settlement, Nairobi, Kenya, to determine the extent of SARS-CoV-2 infection. Methods: Members of randomly selected households from an existing population-based infectious disease surveillance (PBIDS) provided blood specimens between 27
th November and 5
th December 2020. The specimens were tested for antibodies to the SARS-CoV-2 spike protein. Seroprevalence estimates were weighted by age and sex distribution of the PBIDS population and accounted for household clustering. Multivariable logistic regression was used to identify risk factors for individual seropositivity. Results: Consent was obtained from 523 individuals in 175 households, yielding 511 serum specimens that were tested. The overall weighted seroprevalence was 43.3% (95% CI, 37.4 – 49.5%) and did not vary by sex. Of the sampled households, 122(69.7%) had at least one seropositive individual. The individual seroprevalence increased by age from 7.6% (95% CI, 2.4 – 21.3%) among children (<5 years), 32.7% (95% CI, 22.9 – 44.4%) among children 5 – 9 years, 41.8% (95% CI, 33.0 – 51.1%) for those 10-19 years, and 54.9%(46.2 – 63.3%) for adults (≥20 years). Relative to those from medium-sized households (3 and 4 individuals), participants from large (≥5 persons) households had significantly increased odds of being seropositive, aOR, 1.98(95% CI, 1.17 – 1.58), while those from small-sized households (≤2 individuals) had increased odds but not statistically significant, aOR, 2.31 (95% CI, 0.93 – 5.74). Conclusion: In densely populated urban settings, close to half of the individuals had an infection to SARS-CoV-2 after eight months of the COVID-19 pandemic in Kenya. This highlights the importance to prioritize mitigation measures, including COVID-19 vaccine distribution, in the crowded, low socioeconomic settings.
Collapse
Affiliation(s)
- Patrick K Munywoki
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Caroline Nasimiyu
- Global Health Kenya, Washington State University, Nairobi, USA
- Paul G. Allen School of Global Health, Washington State University, Pullman, USA
| | - Moshe Dayan Alando
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Nancy Otieno
- Centre for Global Health Research,, Kenya Medical Research Institute, Kisumu, Kenya
| | - Cynthia Ombok
- Global Health Kenya, Washington State University, Nairobi, USA
| | - Ruth Njoroge
- Global Health Kenya, Washington State University, Nairobi, USA
| | - Gilbert Kikwai
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Dennis Odhiambo,
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Mike Powel Osita
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Alice Ouma
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Clifford Odour
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Bonventure Juma
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Caroline A Ochieng
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Immaculate Mutisya
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Isaac Ngere
- Global Health Kenya, Washington State University, Nairobi, USA
- Paul G. Allen School of Global Health, Washington State University, Pullman, USA
| | - Jeanette Dawa
- Global Health Kenya, Washington State University, Nairobi, USA
- Paul G. Allen School of Global Health, Washington State University, Pullman, USA
| | - Eric Osoro
- Global Health Kenya, Washington State University, Nairobi, USA
- Paul G. Allen School of Global Health, Washington State University, Pullman, USA
| | - M Kariuki Njenga
- Global Health Kenya, Washington State University, Nairobi, USA
- Paul G. Allen School of Global Health, Washington State University, Pullman, USA
| | - Godfrey Bigogo
- Centre for Global Health Research,, Kenya Medical Research Institute, Kisumu, Kenya
| | - Peninah Munyua
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Terrence Q Lo
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Elizabeth Hunsperger
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Amy Herman-Roloff
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| |
Collapse
|
7
|
Munywoki PK, Nasimiyu C, Alando MD, Otieno N, Ombok C, Njoroge R, Kikwai G, Odhiambo, D, Osita MP, Ouma A, Odour C, Juma B, Ochieng CA, Mutisya I, Ngere I, Dawa J, Osoro E, Njenga MK, Bigogo G, Munyua P, Lo TQ, Hunsperger E, Herman-Roloff A. Seroprevalence and risk factors of SARS-CoV-2 infection in an urban informal settlement in Nairobi, Kenya, December 2020. F1000Res 2021; 10:853. [PMID: 35528961 PMCID: PMC9065925 DOI: 10.12688/f1000research.72914.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
Introduction: Urban informal settlements may be disproportionately affected by the COVID-19 pandemic due to overcrowding and other socioeconomic challenges that make adoption and implementation of public health mitigation measures difficult. We conducted a seroprevalence survey in the Kibera informal settlement, Nairobi, Kenya, to determine the extent of SARS-CoV-2 infection. Methods: Members of randomly selected households from an existing population-based infectious disease surveillance (PBIDS) provided blood specimens between 27th November and 5th December 2020. The specimens were tested for antibodies to the SARS-CoV-2 spike protein. Seroprevalence estimates were weighted by age and sex distribution of the PBIDS population and accounted for household clustering. Multivariable logistic regression was used to identify risk factors for individual seropositivity. Results: Consent was obtained from 523 individuals in 175 households, yielding 511 serum specimens that were tested. The overall weighted seroprevalence was 43.3% (95% CI, 37.4 – 49.5%) and did not vary by sex. Of the sampled households, 122(69.7%) had at least one seropositive individual. The individual seroprevalence increased by age from 7.6% (95% CI, 2.4 – 21.3%) among children (<5 years), 32.7% (95% CI, 22.9 – 44.4%) among children 5 – 9 years, 41.8% (95% CI, 33.0 – 51.1%) for those 10-19 years, and 54.9%(46.2 – 63.3%) for adults (≥20 years). Relative to those from medium-sized households (3 and 4 individuals), participants from large (≥5 persons) households had significantly increased odds of being seropositive, aOR, 1.98(95% CI, 1.17 – 1.58), while those from small-sized households (≤2 individuals) had increased odds but not statistically significant, aOR, 2.31 (95% CI, 0.93 – 5.74). Conclusion: In densely populated urban settings, close to half of the individuals had an infection to SARS-CoV-2 after eight months of the COVID-19 pandemic in Kenya. This highlights the importance to prioritize mitigation measures, including COVID-19 vaccine distribution, in the crowded, low socioeconomic settings.
Collapse
|
8
|
Omulo S, Lofgren ET, Mugoh M, Alando M, Obiya J, Kipyegon K, Kikwai G, Gumbi W, Kariuki S, Call DR. The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli. J Microbiol Methods 2017; 136:71-77. [PMID: 28323065 DOI: 10.1016/j.mimet.2017.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 10/19/2022]
Abstract
Investigators often rely on studies of Escherichia coli to characterize the burden of antibiotic resistance in a clinical or community setting. To determine if prevalence estimates for antibiotic resistance are sensitive to sample handling and interpretive criteria, we collected presumptive E. coli isolates (24 or 95 per stool sample) from a community in an urban informal settlement in Kenya. Isolates were tested for susceptibility to nine antibiotics using agar breakpoint assays and results were analyzed using generalized linear mixed models. We observed a <3-fold difference between prevalence estimates based on freshly isolated bacteria when compared to isolates collected from unprocessed fecal samples or fecal slurries that had been stored at 4°C for up to 7days. No time-dependence was evident (P>0.1). Prevalence estimates did not differ for five distinct E. coli colony morphologies on MacConkey agar plates (P>0.2). Successive re-plating of samples for up to five consecutive days had little to no impact on prevalence estimates. Finally, culturing E. coli under different conditions (with 5% CO2 or micro-aerobic) did not affect estimates of prevalence. For the conditions tested in these experiments, minor modifications in sample processing protocols are unlikely to bias estimates of the prevalence of antibiotic-resistance for fecal E. coli.
Collapse
Affiliation(s)
- Sylvia Omulo
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Community Health Analytics Initiative, Washington State University, Pullman, WA, USA
| | - Eric T Lofgren
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Community Health Analytics Initiative, Washington State University, Pullman, WA, USA
| | - Maina Mugoh
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Moshe Alando
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Joshua Obiya
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Korir Kipyegon
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Gilbert Kikwai
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Wilson Gumbi
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Douglas R Call
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Community Health Analytics Initiative, Washington State University, Pullman, WA, USA; The Nelson Mandela African Institute for Science and Technology, Arusha, Tanzania.
| |
Collapse
|
9
|
Waiboci LW, Mott JA, Kikwai G, Arunga G, Xu X, Mayieka L, Emukule GO, Muthoka P, Njenga MK, Fields BS, Katz MA. Which influenza vaccine formulation should be used in Kenya? A comparison of influenza isolates from Kenya to vaccine strains, 2007-2013. Vaccine 2016; 34:2593-601. [PMID: 27079931 DOI: 10.1016/j.vaccine.2016.03.095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 03/11/2016] [Accepted: 03/29/2016] [Indexed: 10/22/2022]
Abstract
INTRODUCTION Every year the World Health Organization (WHO) recommends which influenza virus strains should be included in a northern hemisphere (NH) and a southern hemisphere (SH) influenza vaccine. To determine the best vaccine formulation for Kenya, we compared influenza viruses collected in Kenya from April 2007 to May 2013 to WHO vaccine strains. METHODS We collected nasopharyngeal and oropharyngeal (NP/OP) specimens from patients with respiratory illness, tested them for influenza, isolated influenza viruses from a proportion of positive specimens, tested the isolates for antigenic relatedness to vaccine strains, and determined the percentage match between circulating viruses and SH or NH influenza vaccine composition and schedule. RESULTS During the six years, 7.336 of the 60,072 (12.2%) NP/OP specimens we collected were positive for influenza: 30,167 specimens were collected during the SH seasons and 3717 (12.3%) were positive for influenza; 2903 (78.1%) influenza A, 902 (24.2%) influenza B, and 88 (2.4%) influenza A and B positive specimens. We collected 30,131 specimens during the NH seasons and 3978 (13.2%) were positive for influenza; 3181 (80.0%) influenza A, 851 (21.4%) influenza B, and 54 (1.4%) influenza A and B positive specimens. Overall, 362/460 (78.7%) isolates from the SH seasons and 316/338 (93.5%) isolates from the NH seasons were matched to the SH and the NH vaccine strains, respectively (p<0.001). Overall, 53.6% and 46.4% SH and NH vaccines, respectively, matched circulating strains in terms of vaccine strains and timing. CONCLUSION In six years of surveillance in Kenya, influenza circulated at nearly equal levels during the SH and the NH influenza seasons. Circulating viruses were matched to vaccine strains. The vaccine match decreased when both vaccine strains and timing were taken into consideration. Either vaccine formulation could be suitable for use in Kenya but the optimal timing for influenza vaccination needs to be determined.
Collapse
Affiliation(s)
- Lilian W Waiboci
- US Centers for Disease Control and Prevention-Kenya, P.O. Box 606-00621, Nairobi, Kenya; Department of Biochemistry, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya.
| | - Joshua A Mott
- US Centers for Disease Control and Prevention-Kenya, P.O. Box 606-00621, Nairobi, Kenya; US Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30329-4027, USA
| | - Gilbert Kikwai
- Kenya Medical Research Institute/Centers for Diseases Control and Prevention, P.O. Box 54840-00200, Nairobi, Kenya
| | - Geoffrey Arunga
- Kenya Medical Research Institute/Centers for Diseases Control and Prevention, P.O. Box 54840-00200, Nairobi, Kenya
| | - Xiyan Xu
- US Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30329-4027, USA
| | - Lilian Mayieka
- Kenya Medical Research Institute/Centers for Diseases Control and Prevention, P.O. Box 54840-00200, Nairobi, Kenya
| | - Gideon O Emukule
- US Centers for Disease Control and Prevention-Kenya, P.O. Box 606-00621, Nairobi, Kenya
| | - Phillip Muthoka
- Kenya Ministry of Health, Afya House, P.O. Box 30016-00100, Nairobi, Kenya
| | - M Kariuki Njenga
- US Centers for Disease Control and Prevention-Kenya, P.O. Box 606-00621, Nairobi, Kenya; Kenya Medical Research Institute/Centers for Diseases Control and Prevention, P.O. Box 54840-00200, Nairobi, Kenya
| | - Barry S Fields
- US Centers for Disease Control and Prevention-Kenya, P.O. Box 606-00621, Nairobi, Kenya; US Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30329-4027, USA
| | - Mark A Katz
- US Centers for Disease Control and Prevention-Kenya, P.O. Box 606-00621, Nairobi, Kenya; US Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30329-4027, USA
| |
Collapse
|