Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities.

Integration of genomic technologies into routine antimicrobial resistance (AMR) surveillance in health-care facilities has the potential to generate rapid, actionable information for patient management and inform infection prevention and control measures in near real time. However, substantial challenges limit the implementation of genomics for AMR surveillance in clinical settings. Through a workshop series and online consultation, international experts from across the AMR and pathogen genomics fields convened to review the evidence base underpinning the use of genomics for AMR surveillance in a range of settings. Here, we summarise the identified challenges and potential benefits of genomic AMR surveillance in health-care settings, and outline the recommendations of the working group to realise this potential. These recommendations include the definition of viable and cost-effective use cases for genomic AMR surveillance, strengthening training competencies (particularly in bioinformatics), and building capacity at local, national, and regional levels using hub and spoke models.

Genomics for public health and international surveillance of antimicrobial resistance.

Historically, epidemiological investigation and surveillance for bacterial antimicrobial resistance (AMR) has relied on low-resolution isolate-based phenotypic analyses undertaken at local and national reference laboratories. Genomic sequencing has the potential to provide a far more high-resolution picture of AMR evolution and transmission, and is already beginning to revolutionise how public health surveillance networks monitor and tackle bacterial AMR. However, the routine integration of genomics in surveillance pipelines still has considerable barriers to overcome. In 2022, a workshop series and online consultation brought together international experts in AMR and pathogen genomics to assess the status of genomic applications for AMR surveillance in a range of settings. Here we focus on discussions around the use of genomics for public health and international AMR surveillance, noting the potential advantages of, and barriers to, implementation, and proposing recommendations from the working group to help to drive the adoption of genomics in public health AMR surveillance. These recommendations include the need to build capacity for genome sequencing and analysis, harmonising and standardising surveillance systems, developing equitable data sharing and governance frameworks, and strengthening interactions and relationships among stakeholders at multiple levels.

Innovations in genomic antimicrobial resistance surveillance.

Whole-genome sequencing of antimicrobial-resistant pathogens is increasingly being used for antimicrobial resistance (AMR) surveillance, particularly in high-income countries. Innovations in genome sequencing and analysis technologies promise to revolutionise AMR surveillance and epidemiology; however, routine adoption of these technologies is challenging, particularly in low-income and middle-income countries. As part of a wider series of workshops and online consultations, a group of experts in AMR pathogen genomics and computational tool development conducted a situational analysis, identifying the following under-used innovations in genomic AMR surveillance: clinical metagenomics, environmental metagenomics, gene or plasmid tracking, and machine learning. The group recommended developing cost-effective use cases for each approach and mapping data outputs to clinical outcomes of interest to justify additional investment in capacity, training, and staff required to implement these technologies. Harmonisation and standardisation of methods, and the creation of equitable data sharing and governance frameworks, will facilitate successful implementation of these innovations.

Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group.

Nearly a century after the beginning of the antibiotic era, which has been associated with unparalleled improvements in human health and reductions in mortality associated with infection, the dwindling pipeline for new antibiotic classes coupled with the inevitable spread of antimicrobial resistance (AMR) poses a major global challenge. Historically, surveillance of bacteria with AMR typically relied on phenotypic analysis of isolates taken from infected individuals, which provides only a low-resolution view of the epidemiology behind an individual infection or wider outbreak. Recent years have seen increasing adoption of powerful new genomic technologies with the potential to revolutionise AMR surveillance by providing a high-resolution picture of the AMR profile of the bacteria causing infections and providing real-time actionable information for treating and preventing infection. However, many barriers remain to be overcome before genomic technologies can be adopted as a standard part of routine AMR surveillance around the world. Accordingly, the Surveillance and Epidemiology of Drug-resistant Infections Consortium convened an expert working group to assess the benefits and challenges of using genomics for AMR surveillance. In this Series, we detail these discussions and provide recommendations from the working group that can help to realise the massive potential benefits for genomics in surveillance of AMR.

Exploiting genomics for antimicrobial resistance surveillance at One Health interfaces.

The intersection of human, animal, and ecosystem health at One Health interfaces is recognised as being of key importance in the evolution and spread of antimicrobial resistance (AMR) and represents an important, and yet rarely realised opportunity to undertake vital AMR surveillance. A working group of international experts in pathogen genomics, AMR, and One Health convened to take part in a workshop series and online consultation focused on the opportunities and challenges facing genomic AMR surveillance in a range of settings. Here we outline the working group's discussion of the potential utility, advantages of, and barriers to, the implementation of genomic AMR surveillance at One Health interfaces and propose a series of recommendations for addressing these challenges. Embedding AMR surveillance at One Health interfaces will require the development of clear beneficial use cases, especially in low-income and middle-income countries. Evidence of directionality, risks to human and animal health, and potential trade implications were also identified by the working group as key issues. Addressing these challenges will be vital to enable genomic surveillance technology to reach its full potential for assessing the risk of transmission of AMR between the environment, animals, and humans at One Health interfaces.

A global assembly of adult female mosquito mark-release-recapture data to inform the control of mosquito-borne pathogens.

BACKGROUND: Pathogen transmission by mosquitos is known to be highly sensitive to mosquito bionomic parameters. Mosquito mark-release-recapture (MMRR) experiments are a standard method for estimating such parameters including dispersal, population size and density, survival, blood feeding frequency and blood meal host preferences. METHODS: We assembled a comprehensive database describing adult female MMRR experiments. Bibliographic searches were used to build a digital library of MMRR studies and selected data describing the reported outcomes were extracted. RESULTS: The resulting database contained 774 unique adult female MMRR experiments involving 58 vector mosquito species from the three main genera of importance to human health: Aedes, Anopheles and Culex. Crude examination of these data revealed patterns associated with geography as well as mosquito genus, consistent with bionomics varying by species-specific life history and ecological context. Recapture success varied considerably and was significantly different amongst genera, with 8, 4 and 1% of adult females recaptured for Aedes, Anopheles and Culex species, respectively. A large proportion of experiments (59%) investigated dispersal and survival and many allowed disaggregation of the release and recapture data. Geographic coverage was limited to just 143 localities around the world. CONCLUSIONS: This MMRR database is a substantial contribution to the compilation of global data that can be used to better inform basic research and public health interventions, to identify and fill knowledge gaps and to enrich theory and evidence-based ecological and epidemiological studies of mosquito vectors, pathogen transmission and disease prevention. The database revealed limited geographic coverage and a relative scarcity of information for vector species of substantial public health relevance. It represents, however, a wealth of entomological information not previously compiled and of particular interest for mosquito-borne pathogen transmission models.

Temporal and micro-spatial heterogeneity in the distribution of Anopheles vectors of malaria along the Kenyan coast.

BACKGROUND: The distribution of anopheline mosquitoes is determined by temporally dynamic environmental and human-associated variables, operating over a range of spatial scales. Macro-spatial short-term trends are driven predominantly by prior (lagged) seasonal changes in climate, which regulate the abundance of suitable aquatic larval habitats. Micro-spatial distribution is determined by the location of these habitats, proximity and abundance of available human bloodmeals and prevailing micro-climatic conditions. The challenge of analysing--in a single coherent statistical framework--the lagged and distributed effect of seasonal climate changes simultaneously with the effects of an underlying hierarchy of spatial factors has hitherto not been addressed. METHODS: Data on Anopheles gambiae sensu stricto and A. funestus collected from households in Kilifi district, Kenya, were analysed using polynomial distributed lag generalized linear mixed models (PDL GLMMs). RESULTS: Anopheline density was positively and significantly associated with amount of rainfall between 4 to 47 days, negatively and significantly associated with maximum daily temperature between 5 and 35 days, and positively and significantly associated with maximum daily temperature between 29 and 48 days in the past (depending on Anopheles species). Multiple-occupancy households harboured greater mosquito numbers than single-occupancy households. A significant degree of mosquito clustering within households was identified. CONCLUSIONS: The PDL GLMMs developed here represent a generalizable framework for analysing hierarchically-structured data in combination with explanatory variables which elicit lagged effects. The framework is a valuable tool for facilitating detailed understanding of determinants of the spatio-temporal distribution of Anopheles. Such understanding facilitates delivery of targeted, cost-effective and, in certain circumstances, preventative antivectorial interventions against malaria.

The role of Anopheles arabiensis and Anopheles coustani in indoor and outdoor malaria transmission in Taveta District, Kenya.

BACKGROUND: The scaling up of malaria vector control efforts in Africa has resulted in changing the malaria vectorial systems across different ecological settings. In view of the ongoing trends in vector population dynamics, abundance, species composition and parasite infectiousness, there is a need to understand vector distribution and their contribution to malaria transmission to facilitate future planning of control strategies. We studied indoor and outdoor malaria transmission dynamics and vector population variability of Anopheles mosquitoes in Taveta district along the Kenyan Coast. METHODS: Anopheles mosquitoes were collected indoors and outdoors in 4 ecologically different villages using CDC light traps (both indoor and outdoor) and aspiration method (day resting indoors; DRI) methods. Mosquitoes were examined for infection with P. falciparum sporozoites and blood feeding preferences using enzyme linked immunosorbent assay (ELISA). The An. gambiae and An. funestus complexes were identified by PCR technique to determine the sibling species composition. RESULTS: A total of 4,004 Anopheles mosquitoes were collected consisting of 34.9%% (n = 1,397) An. gambiae s.1., 28.1% (n = 1,124) An. funestus s.l., 33.5% (n = 1,340) An. coustani and 3.6% (n = 143) An. pharoensis. A total of 14,654 culicine mosquitoes were collected, mainly Cx. quinquefasciatus. Of the total Anopheles collected, 3,729 were tested for P. falciparum sporozoite infection. The sporozoite transmission was found to be occurring both indoors and outdoors. The overall sporozoite infectivity was 0.68% (n = 2,486) indoors and 1.29% (n = 1,243) outdoors. Indoor and outdoor sporozoite infectivity and the vectorial systems varied across the 4 ecological villages. Entomological inoculation rates for the 4 villages indicate that there was site-to-site variation. In the 4 villages, Mwarusa had the highest EIRs with An. arabiensis, An. funestus and An. coustani contributing to 23.91, 11.96 and 23.91 infectious bites per person per year ib/p/year respectively. In Kiwalwa and Njoro outdoor EIR was significantly higher than indoors. CONCLUSIONS: This study shows that malaria transmission is occurring both indoors and outdoors. The main vectors are An. arabiensis, An. funestus and An. coustani indoors while An. coustani is playing a major role in outdoor transmission. Effective malaria control programmes, should therefore include tools that target both indoor and outdoor transmission.

Shifts in malaria vector species composition and transmission dynamics along the Kenyan coast over the past 20 years.

BACKGROUND: Over the past 20 years, numerous studies have investigated the ecology and behaviour of malaria vectors and Plasmodium falciparum malaria transmission on the coast of Kenya. Substantial progress has been made to control vector populations and reduce high malaria prevalence and severe disease. The goal of this paper was to examine trends over the past 20 years in Anopheles species composition, density, blood-feeding behaviour, and P. falciparum sporozoite transmission along the coast of Kenya. METHODS: Using data collected from 1990 to 2010, vector density, species composition, blood-feeding patterns, and malaria transmission intensity was examined along the Kenyan coast. Mosquitoes were identified to species, based on morphological characteristics and DNA extracted from Anopheles gambiae for amplification. Using negative binomial generalized estimating equations, mosquito abundance over the period were modelled while adjusting for season. A multiple logistic regression model was used to analyse the sporozoite rates. RESULTS: Results show that in some areas along the Kenyan coast, Anopheles arabiensis and Anopheles merus have replaced An. gambiae sensu stricto (s.s.) and Anopheles funestus as the major mosquito species. Further, there has been a shift from human to animal feeding for both An. gambiae sensu lato (s.l.) (99% to 16%) and An. funestus (100% to 3%), and P. falciparum sporozoite rates have significantly declined over the last 20 years, with the lowest sporozoite rates being observed in 2007 (0.19%) and 2008 (0.34%). There has been, on average, a significant reduction in the abundance of An. gambiae s.l. over the years (IRR = 0.94, 95% CI 0.90-0.98), with the density standing at low levels of an average 0.006 mosquitoes/house in the year 2010. CONCLUSION: Reductions in the densities of the major malaria vectors and a shift from human to animal feeding have contributed to the decreased burden of malaria along the Kenyan coast. Vector species composition remains heterogeneous but in many areas An. arabiensis has replaced An. gambiae as the major malaria vector. This has important implications for malaria epidemiology and control given that this vector predominately rests and feeds on humans outdoors. Strategies for vector control need to continue focusing on tools for protecting residents inside houses but additionally employ outdoor control tools because these are essential for further reducing the levels of malaria transmission.

Wind direction and proximity to larval sites determines malaria risk in Kilifi District in Kenya.

Studies of the fine-scale spatial epidemiology of malaria consistently identify malaria hotspots, comprising clusters of homesteads at high transmission intensity. These hotspots sustain transmission, and may be targeted by malaria-control programmes. Here we describe the spatial relationship between the location of Anopheles larval sites and human malaria infection in a cohort study of 642 children, aged 1-10-years-old. Our data suggest that proximity to larval sites predict human malaria infection, when homesteads are upwind of larval sites, but not when homesteads are downwind of larval sites. We conclude that following oviposition, female Anophelines fly upwind in search for human hosts and, thus, malaria transmission may be disrupted by targeting vector larval sites in close proximity, and downwind to malaria hotspots.

Population structure of Anopheles gambiae along the Kenyan coast.

In the tropics, Anopheles mosquito abundance is greatest during the wet season and decline significantly during the dry season as larval habitats shrink. Population size fluctuations between wet and dry seasons may lead to variation in distribution of specific alleles within natural Anopheles populations, and a possible effect on the population genetic structure. We used 11 microsatellite markers to examine the effect of seasonality on population genetic structure of Anopheles gambiae s.s. at two sites along the Kenyan coast. All loci were highly polymorphic with the total number of alleles for pooled samples ranging from 7 (locus ND36) to 21 (locus AG2H46). Significant estimates of genetic differentiation between sites and seasons were observed suggesting the existence of spatio-temporal subpopulation structuring. Genetic bottleneck analysis showed no indication of excess heterozygosity in any of the populations. These findings suggest that along the Kenyan coast, seasonality and site specific ecological factors can alter the genetic structure of A. gambiae s.s. populations.

Efficacy of vectobac DT and culinexcombi against mosquito larvae in unused swimming pools in Malindi, Kenya.

The efficacy and persistence of 2 bacterial larvicides, Vectobac-DT (Bacillus thuringiensis israelensis [Bti]) and CulinexCombi (Bti and Bacillus sphaericus [Bs]), were tested against Anopheles gambiae and Culex quinquefasciatus in temporarily unused swimming pools with rainwater in Malindi, Kenya. Pre- and posttreatment larval densities were recorded by sampling with the standard WHO dipping technique for 8 consecutive days. The larvicides were applied to the pools with a knapsack sprayer. The data showed that Vectobac-DT was highly effective against early instars of An. gambiae with 89% reduction within 24 h but not as effective against the early stages of Cx. quinquefasciatus with reduction of only 46%. CulinexCombi resulted in high mortalities to early instars of both species with over 97% reduction within 24 h, but showed a drastic reduction 48 h after application. Both Vectobac-DT and CulinexCombi were highly effective against late instars of both species, whereby Vectobac-DT persisted much longer than CulinexCombi. Anopheles gambiae was found to be more susceptible to both larvicides than Cx. quinquefasciatus. By their high efficacy and good persistence against mosquito larvae, both Vectobac-DT and CulinexCombi can be recommended for use in integrated mosquito control programs.

Estimating dispersal and survival of Anopheles gambiae and Anopheles funestus along the Kenyan coast by using mark-release-recapture methods.

Mark-release-recapture (MRR) experiments were conducted with emerging Anopheles gambiae s.l. and Anophelesfunestus Giles at Jaribuni and Mtepeni in Kilifi, along the Kenyan Coast. Of 739 and 1246 Anopheles released at Jaribuni and Mtepeni, 24.6 and 4.33% were recaptured, respectively. The daily survival probability was 0.96 for An. funestus and 0.95 for An. gambiae in Jaribuni and 0.83 and 0.95, respectively, in Mtepeni. The maximum flight distance recorded was 661 m. The high survival probability of An. gambiae and An. funestus estimated accounts for the continuous transmission of malaria along the Kenyan coast. This study also shows that the release of young, emergent female Anopheles improves the recapture rates and may be a better approach to MRR studies.