Harnessing technology and portability to conduct molecular epidemiology of endemic pathogens in resource-limited settings

Faust, Christina L.; Brunker, Kirstyn; Ajambo, Diana; Ryan, Mary R.; Arinaitwe, Moses; Rowel, Candia; Wangoola, Robert Mandela; Wampande, Eddie M.; Guma, Andrew; Adriko, Moses; Lamberton, Poppy H. L.; Tukahebwa, Edridah M.; Mugenyi, Albert; Waiswa, Charles

doi:10.1093/trstmh/traa086

“…Furthermore, portable devices allow screening on-site and thus a much faster turnaround time. [87][88][89] Despite its wide use in research, PCR-based molecular screening for infections has led directly to interventions or policy change in only a few documented cases. In Myanmar, qPCR is usually applied to stratify villages into low or high prevalence, with the latter receiving mass drug administration (MDA).…”

Section: Prospective Use Cases For Molecular Toolsmentioning

confidence: 99%

Bridging the Gap from Molecular Surveillance to Programmatic Decisions for Malaria Control and Elimination

Golumbeanu,

Edi,

Hetzel

et al. 2023

The American Journal of Tropical Medicine and Hygiene

1

0

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An increasing number of molecular and genomic assays are available to study malaria parasite populations. However, so far they have played a marginal role in informing policy and programmatic decision-making. Currently, molecular data are mainly used for monitoring drug efficacy against Plasmodium falciparum; assessing molecular markers of drug and insecticide resistance; and assessing P. falciparum histidine-rich protein 2 and 3 genes (Pfhrp2/3) deletion. We argue that additional use cases for molecular routine surveillance could be implemented in the near future, especially in transmission settings approaching elimination. These would include using quantitative polymerase chain reaction to monitor the prevalence of sub-patent infections in asymptomatic carriers, monitoring parasite genetic diversity as transmission intensity is changing, using genomic data to determine the origin of imported infections and characterize transmission chains in settings with very low malaria transmission, and using serology to monitor recent and past exposures in low-transmission settings. Molecular surveillance could inform control programs on adapting novel strategies, such as reactive case detection or focal mass drug administration, and help evaluate the impact of interventions currently in place. To better integrate molecular and genomic data into control program decision-making, engagement of national malaria control experts is crucial. Local laboratory capacity needs to be strengthened, shortening the time from sample collection to data availability. Here, we discuss opportunities and challenges of the use of molecular and genomic data for supporting malaria control and elimination efforts, as well as the avenues to link molecular and genomic data with gold standard epidemiological measurements through mathematical modeling.

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“…In order to speed up time to result and enable in-country scientists and control programs to process samples, efforts are increasingly being made to bring laboratory capacity to field sites [16][17][18]. Numerous devices and protocols for molecular screening for pathogens are being developed and trialed.…”

Section: Introductionmentioning

confidence: 99%

qPCR in a suitcase for rapid Plasmodium falciparum and Plasmodium vivax surveillance in Ethiopia

Carlier

¹

,

Baker

²

,

Huwe

³

et al. 2022

PLOS Glob Public Health

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Many Plasmodium spp. infections, both in clinical and asymptomatic patients, are below the limit of detection of light microscopy or rapid diagnostic test (RDT). Molecular diagnosis by qPCR can be valuable for surveillance, but is often hampered by absence of laboratory capacity in endemic countries. To overcome this limitation, we optimized and tested a mobile qPCR laboratory for molecular diagnosis in Ziway, Ethiopia, where transmission intensity is low. Protocols were optimized to achieve high throughput and minimize costs and weight for easy transport. 899 samples from febrile patients and 1021 samples from asymptomatic individuals were screened by local microscopy, RDT, and qPCR within a period of six weeks. 34/52 clinical Plasmodium falciparum infections were missed by microscopy and RDT. Only 4 asymptomatic infections were detected. No hrp2 deletions were observed among 25 samples typed, but 19/24 samples carried hrp3 deletions. The majority (25/41) of Plasmodium vivax infections (1371 samples screened) were found among asymptomatic individuals. All asymptomatic P. vivax infections were negative by microscopy and RDT. In conclusion, the mobile laboratory described here can identify hidden parasite reservoirs within a short period of time, and thus inform malaria control activities.

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“…Molecular screening is thus seldom applied to select control strategies tailored to local conditions, or in response to outbreaks. In order to speed up time to result and enable in-country scientists and control programs to process samples, efforts are increasingly being made to bring laboratory capacity to field sites [16][17][18]. Numerous devices and protocols for molecular screening for pathogens are being developed and trialed.…”

Section: Introductionmentioning

confidence: 99%

qPCR in a suitcase for rapid Plasmodium falciparum and Plasmodium vivax surveillance in Ethiopia

Carlier

¹

,

Baker

²

,

Huwe

³

et al. 2022

Preprint

0

View full text Add to dashboard Cite

Many Plasmodium spp. infections, both in clinical and asymptomatic patients, are below the limit of detection of light microscopy or rapid diagnostic test (RDT). Molecular diagnosis by qPCR can be valuable for surveillance, but is often hampered by absence of laboratory capacity in endemic countries. To overcome this limitation, we optimized and tested a mobile qPCR laboratory for molecular diagnosis in Ziway, Ethiopia, where transmission intensity is low. Protocols were optimized to achieve high throughput and minimize costs and weight for easy transport. 899 samples from febrile patients and 1021 samples from asymptomatic individuals were screened by local microscopy, RDT, and qPCR within a period of six weeks. 34/52 clinical Plasmodium falciparum infections were missed by microscopy and RDT. Only 4 asymptomatic infections were detected. No hrp2 deletions were observed among 25 samples typed, but 19/24 samples carried hrp3 deletions. The majority (25/41) of Plasmodium vivax infections (1371 samples screened) were found among asymptomatic individuals. All asymptomatic P. vivax infections were negative by microscopy and RDT. In conclusion, the mobile laboratory described here can identify hidden parasite reservoirs within a short period of time, and thus inform malaria control activities.

show abstract

Harnessing technology and portability to conduct molecular epidemiology of endemic pathogens in resource-limited settings

Cited by 4 publications

References 6 publications

Bridging the Gap from Molecular Surveillance to Programmatic Decisions for Malaria Control and Elimination

Bridging the Gap from Molecular Surveillance to Programmatic Decisions for Malaria Control and Elimination

qPCR in a suitcase for rapid Plasmodium falciparum and Plasmodium vivax surveillance in Ethiopia

qPCR in a suitcase for rapid Plasmodium falciparum and Plasmodium vivax surveillance in Ethiopia

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