Antimicrobial resistance dissemination associated with intensive animal production practices in Argentina: A systematic review and meta-analysis

Resumen El abuso y mal uso de los antimicrobianos aceleró la propagación de bacterias resistentes. La asociación entre las infecciones que presentan resistencia a antimicrobianos (RAM) en humanos y el uso de antimicrobianos en la producción agropecuaria es compleja, pero está bien documentada. Proporcionamos una revisión sistemática y metaanálisis sobre la diseminación de la resistencia a antimicrobianos designados como críticamente importantes por la Organización Mundial de la Salud (OMS) en cerdos, aves y bovinos de producción intensiva y extensiva en Argentina. Se buscó información en bases de datos electrónicas (Medline-PubMed, Web of Science, SciELO, Sistema Nacional de Repositorios Digitales de Argentina) y en la literatura gris. Se incluyeron estudios epidemiológicos sobre la RAM en las principales bacterias transmitidas por los alimentos - Salmonella spp., Campylobacter spp., Escherichia coli y Enterococcus spp. - y bacterias causantes de mastitis aisladas de cerdos, pollos y bovinos. Los resultados de este estudio apoyan la hipótesis de que la RAM de las bacterias transmitidas por los alimentos alcanza niveles alarmantes. Los metaanálisis seguidos de análisis por subgrupos mostraron asociación entre la RAM y (a) el animal (p<0,01) para estreptomicina, ampicilina y tetraciclina o (b) el sistema productivo (p<0,05) para estreptomicina, cefotaxima, ampicilina, ácido nalidíxico y tetraciclina. La mayor prevalencia conjunta de multirresistencia se detectó en cerdos (0,47 [0,29; 0,66]) y producción intensiva (0,62 [0,34; 0,83]), mientras que la menor correspondió a bovinos de leche (0,056 [0,003; 0,524]) y producción extensiva (0,107 [0,043; 0,240]). Se observó un vacío de información respecto de los bovinos de feedlot. Es urgente adoptar medidas políticas para coordinar y armonizar la vigilancia de la RAM y regular el uso de antimicrobianos en animales.

Abstract Abuse and misuse of antimicrobial agents has accelerated the spread of antimicrobial-resistant bacteria. The association between antimicrobial-resistant infections in humans and antimicrobial use in agriculture is complex, but well-documented. This study provides a systematic review and meta-analysis of the dissemination of antimicrobial resistance (AMR) to antimicrobials defined as critically important by the WHO, in swine, chicken, and cattle from intensive and extensive production systems in Argentina. We conducted searches in electronic databases (MEDLINE-PubMed, Web of Science, SciELO, the National System of Digital Repositories from Argentina) as well as in the gray literature. Inclusion criteria were epidemiological studies on AMR in the main food-transmitted bacteria, Salmonella spp., Campylobacter spp., Escherichia coli and Enterococcus spp., and mastitis-causing bacteria, isolated from swine, chicken, dairy and beef cattle from Argentina. This study gives evidence for supporting the hypothesis that AMR of common food-transmitted bacteria in Argentina is reaching alarming levels. Meta-analyses followed by subgroup analyses confirmed the association between the prevalence of AMR and (a) animal species (p<0.01) for streptomycin, ampicillin and tetracycline or (b) the animal production system (p<0.05) for streptomycin, cefotaxime, nalidixic acid, ampicillin and tetracycline. Moreover, swine (0.47 [0.29; 0.66]) and intensive production (0.62 [0.34; 0.83]) showed the highest pooled prevalence of multidrug resistance while dairy (0.056 [0.003; 0.524]) and extensive production (0.107 [0.043; 0.240]) showed the lowest. A research gap regarding beef-cattle from feedlot was identified. Finally, there is an urgent need for political measures meant to coordinate and harmonize AMR surveillance and regulate antimicrobial use in animal production.

Antimicrobial resistance dissemination associated with intensive animal production practices in Argentina: A systematic review and meta-analysis.

Abuse and misuse of antimicrobial agents has accelerated the spread of antimicrobial-resistant bacteria. The association between antimicrobial-resistant infections in humans and antimicrobial use in agriculture is complex, but well-documented. This study provides a systematic review and meta-analysis of the dissemination of antimicrobial resistance (AMR) to antimicrobials defined as critically important by the WHO, in swine, chicken, and cattle from intensive and extensive production systems in Argentina. We conducted searches in electronic databases (MEDLINE-PubMed, Web of Science, SciELO, the National System of Digital Repositories from Argentina) as well as in the gray literature. Inclusion criteria were epidemiological studies on AMR in the main food-transmitted bacteria, Salmonella spp., Campylobacter spp., Escherichia coli and Enterococcus spp., and mastitis-causing bacteria, isolated from swine, chicken, dairy and beef cattle from Argentina. This study gives evidence for supporting the hypothesis that AMR of common food-transmitted bacteria in Argentina is reaching alarming levels. Meta-analyses followed by subgroup analyses confirmed the association between the prevalence of AMR and (a) animal species (p<0.01) for streptomycin, ampicillin and tetracycline or (b) the animal production system (p<0.05) for streptomycin, cefotaxime, nalidixic acid, ampicillin and tetracycline. Moreover, swine (0.47 [0.29; 0.66]) and intensive production (0.62 [0.34; 0.83]) showed the highest pooled prevalence of multidrug resistance while dairy (0.056 [0.003; 0.524]) and extensive production (0.107 [0.043; 0.240]) showed the lowest. A research gap regarding beef-cattle from feedlot was identified. Finally, there is an urgent need for political measures meant to coordinate and harmonize AMR surveillance and regulate antimicrobial use in animal production.

Socio-cognitive constraints and opportunities for sustainable intensification in South Asia: insights from fuzzy cognitive mapping in coastal Bangladesh.

Appreciating and dealing with the plurality of farmers' perceptions and their contextual knowledge and perspectives of the functioning and performance of their agroecosystems-in other words, their 'mental models'-is central for appropriate and sustainable agricultural development. In this respect, the sustainable development goals (SDGs) aim to eradicate poverty and food insecurity by 2030 by envisioning social inclusivity that incorporates the preferences and knowledge of key stakeholders, including farmers. Agricultural development interventions and policies directed at sustainable intensification (SI), however, do not sufficiently account for farmers' perceptions, beliefs, priorities, or interests. Considering two contrasting agroecological systems in coastal Bangladesh, we used a fuzzy cognitive mapping (FCM)-based simulation and sensitivity analysis of mental models of respondents of different farm types from 240 farm households. The employed FCM mental models were able to (1) capture farmers' perception of farming system concepts and relationships for each farm type and (2) assess the impact of external interventions (drivers) on cropping intensification and food security. We decomposed the FCM models' variance into the first-order sensitivity index (SVI) and total sensitivity index (TSI) using a winding stairs algorithm. Both within and outside polder areas, the highest TSIs (35-68%) were observed for effects of agricultural extension on changes in other concepts in the map, particularly food security and income (SI indicators), indicating the importance of extension programs for SI. Outside polders, drainage and micro-credit were also influential; within polders, the availability of micro-credit appears to affect farmer perceptions of SI indicators more than drainage. This study demonstrated the importance of reflection on the differing perspectives of farmers both within and outside polders to identify entry points for development interventions. In addition, the study underscores the need for micro-farming systems-level research to assess the context-based feasibility of introduced interventions as perceived by farmers of different farm types. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10668-021-01342-y.

The importance of the traditional milpa in food security and nutritional self-sufficiency in the highlands of Oaxaca, Mexico.

Around 30% of global food is produced by smallholder farmers, yet they constitute the most food-insecure group. In Mexico, food self-sufficiency is declining. Rural policies in the country have stimulated the production of cash crops to the detriment of the traditional intercropping system, the milpa. Such a decline may have negative consequences for the food security of subsistence farmers. This study aimed to assess changes in nutritional self-sufficiency over the last 30 years and the role of milpa systems in food security for two communities in the highlands of Oaxaca, Mexico. The study used satellite images, censuses, and field data to estimate food production. Three cropping systems, monoculture of maize, monoculture of common bean, and the milpa were compared in terms of nutrients and vitamins produced. Furthermore, a household typology was developed for each community to contrast nutritional self-sufficiency levels between the different household types. Results showed that the milpa produced more volume of food per area compared to the other systems. The milpa also produced all the nutrients and vitamins (except for B12) required to feed at least 2 persons ha-1. Monocultures of maize lacked vitamins A, B9, B12, and C, and the common bean lacked vitamins A, B12, and C. While farmers recognized the importance of the milpa, they preferred monocultures due to the reduced labor demands of this system. Households that obtained most of their income from off-farm activities had the lowest nutritional self-sufficiency. Enhancing nutritional self-sufficiency through crop diversification has the potential to not only improve the nutrition of subsistence farmers, but also to enhance ecosystem service provision, promote biodiversity conservation and restoration, and improve resilience to climate change.

Improved feeding and forages at a crossroads: Farming systems approaches for sustainable livestock development in East Africa.

Dairy development provides substantial potential economic opportunities for smallholder farmers in East Africa, but productivity is constrained by the scarcity of quantity and quality feed. Ruminant livestock production is also associated with negative environmental impacts, including greenhouse gas (GHG) emissions, air pollution, high water consumption, land-use change, and loss of biodiversity. Improved livestock feeding and forages have been highlighted as key entry point to sustainable intensification, increasing food security, and decreasing environmental trade-offs including GHG emission intensities. In this perspective article, we argue that farming systems approaches are essential to understand the multiple roles and impacts of forages in smallholder livelihoods. First, we outline the unique position of forages in crop-livestock systems and systemic obstacles to adoption that call for multidisciplinary thinking. Second, we discuss the importance of matching forage technologies with agroecological and socioeconomic contexts and niches, and systems agronomy that is required. Third, we demonstrate the usefulness of farming systems modeling to estimate multidimensional impacts of forages and for reducing agro-environmental trade-offs. We conclude that improved forages in East Africa are at a crossroads: if adopted by farmers at scale, they can be a cornerstone of pathways toward sustainable livestock systems in East Africa.

The risk posed by Xanthomonas wilt disease of banana: Mapping of disease hotspots, fronts and vulnerable landscapes.

Banana production landscapes in the African Great Lakes Region (AGLR) have been under immense pressure from Xanthomonas wilt (XW) disease over the past two decades. XW, first reported on banana in central Uganda and eastern DR Congo in 2001, has since spread to the entire AGLR. XW is currently spreading westwards from hot spots in eastern DR Congo highlands, putting the plantain (Musa AAB genome) belt of central and west Africa at risk. In-depth understanding of the key variables responsible for disease spread, current hotspots, and vulnerable landscapes is crucial for disease early warning and management. We mapped aggregated disease distribution and hotspots in the AGLR and identified vulnerable landscapes across African banana production zones. Available data on disease prevalence collected over 11 years was regressed against environmental and expert developed covariates to develop the AGLR XW hotspots map. For the Africa-wide risk map, precipitation, distance to hotspots, degree of trade in fresh banana products, production zone interconnectedness and banana genotype composition were used as covariates. In the AGLR, XW was mainly correlated to precipitation and disease/banana management. Altitude and temperature had unexpectedly low effects, possibly due to an overriding impact of tool-mediated spread which is part of the management covariate. In the AGLR, the eastern part of DR Congo was a large hotspot with highest vulnerability. Apart from endemic zones in the AGLR and Ethiopia, northern Mozambique was perceived as a moderate risk zone mainly due to the predominance of 'Bluggoe' (Musa ABB type) which is highly susceptible to insect-vectored transmission. Presence of XW hotspots (e.g. eastern DR Congo) and vulnerable areas with low (e.g. north-western Tanzania) or no disease (e.g. Congo basin, western DR Congo and northern Mozambique) pressure suggest key areas where proactive measures e.g. quarantines and information sharing on XW diagnosis, epidemiology, and control could be beneficial.

Risks Posed by Intercrops and Weeds as Alternative Hosts to Xanthomonas campestris pv. musacearum in Banana Fields.

Alternative host plants are important in the survival and perpetuation of several crop pathogens and have been suspected to play a role in the survival of Xanthomonas campestris pv. musacearum (Xcm) and perpetuation of Xanthomonas wilt (XW) disease of banana and enset. This study determined the potential risk posed by two weeds (Canna spp. and wild sorghum) and common banana intercrops (maize, millet, sorghum, taro, and sugarcane) as alternative hosts to Xcm. The study employed screenhouse experiments, laboratory procedures and diagnosis of banana fields in XW-affected landscapes. Typical XW symptoms were only observed in artificially inoculated Canna sp., with an incidence of 96%. Leaf lesions characteristic of xanthomonads occurred on millet (50%) and sorghum (35%), though the plants recovered. No symptoms occurred in maize, sugarcane, taro or wild sorghum. However, Xcm was recovered from all these plant species, with higher recoveries in Canna sp. (47%), millet (27%), sugarcane (27%), and wild sorghum (25%). Only isolates recovered from Canna sp., millet, sorghum and wild sorghum caused disease in banana plantlets. The presence and incidence of XW on-farm was positively associated with the presence of susceptible ABB Musa genotypes and negatively with number of banana cultivars on farm and household access to training on XW management. Only 0.02% of field sampled Canna spp. plants had Xcm. Risk posed by Canna spp. on-farm could be limited to tool transmission as it has persistent floral bracts that prevent insect-mediated infections. Given the high susceptibility, perennial nature and propagation through rhizomes of Canna sp., it could pose a moderate-high risk, thus warranting some attention in the management of XW disease. Sugarcane could offer a low-moderate risk due to its perennial nature and propagation through rhizomes while risk from maize, millet, and sorghum was deemed zero-low due to their annual nature, wind-mediated mode of pollination and propagation through seed. Understanding the interactions of a crop pathogen with other plants is thus important when diversifying agroecosystems. The study findings also suggest other factors such as cultivar composition and management of the disease at farm and landscape level to be important in the perpetuation of XW disease.

Capturing farm diversity with hypothesis-based typologies: An innovative methodological framework for farming system typology development.

Creating typologies is a way to summarize the large heterogeneity of smallholder farming systems into a few farm types. Various methods exist, commonly using statistical analysis, to create these typologies. We demonstrate that the methodological decisions on data collection, variable selection, data-reduction and clustering techniques can bear a large impact on the typology results. We illustrate the effects of analysing the diversity from different angles, using different typology objectives and different hypotheses, on typology creation by using an example from Zambia's Eastern Province. Five separate typologies were created with principal component analysis (PCA) and hierarchical clustering analysis (HCA), based on three different expert-informed hypotheses. The greatest overlap between typologies was observed for the larger, wealthier farm types but for the remainder of the farms there were no clear overlaps between typologies. Based on these results, we argue that the typology development should be guided by a hypothesis on the local agriculture features and the drivers and mechanisms of differentiation among farming systems, such as biophysical and socio-economic conditions. That hypothesis is based both on the typology objective and on prior expert knowledge and theories of the farm diversity in the study area. We present a methodological framework that aims to integrate participatory and statistical methods for hypothesis-based typology construction. This is an iterative process whereby the results of the statistical analysis are compared with the reality of the target population as hypothesized by the local experts. Using a well-defined hypothesis and the presented methodological framework, which consolidates the hypothesis through local expert knowledge for the creation of typologies, warrants development of less subjective and more contextualized quantitative farm typologies.

Enhancing agroecosystem productivity with woody perennials in semi-arid West Africa. A meta-analysis.

Soil degradation in semi-arid West Africa can be reversed through an intensified application of organic matter, especially on coarse soils. Woody perennials have been promoted in the region to secure organic matter sources and improve soil productive capacity, yet the mechanisms by which perennials provide benefits to soils and crops remain poorly understood, and no effective, generalizable agronomic recommendations exist. Here, we reviewed the effects of trees and shrubs on soil properties and on crop yields in semi-arid West Africa (< 1000 mm year-1). Specific objectives of this meta-analysis were to (i) describe and (ii) quantify the effects of the presence of woody perennials and of ramial wood amendments on crop productivity and soil characteristics, and (iii) identify general recommendations on the integration of perennials with crops. An iterative keyword search was conducted to gather relevant literature. The search string consisted of four parts: source, practice, responses, and countries of interest. In total, 26 references on agroforestry parklands and 21 on woody amendments were included in the meta-database (314 entries, 155 for parklands, and 159 for ramial wood). We show that (1) the presence of shrubs and trees on agricultural fields had an overall positive but variable effect on soil total C (i.e. + 20 to 75%); (2) millet and sorghum yields were often higher in the presence of shrubs (- 25 to + 120%); (3) more variability was observed in the presence of trees (- 100 to + 200%); and (4) the use of shrub- and tree-based ramial wood resulted in equal or higher cereal yields as compared to the control (- 30 to + 100%). Upscaling the use of biodiversity-driven processes in farming systems of West Africa may provide benefits to overall ecosystems, but species' choice and trade-offs perceived at the farm level, including labour management and low ramial wood availability, should be addressed through future research.

Towards a new generation of agricultural system data, models and knowledge products: Design and improvement.

This paper presents ideas for a new generation of agricultural system models that could meet the needs of a growing community of end-users exemplified by a set of Use Cases. We envision new data, models and knowledge products that could accelerate the innovation process that is needed to achieve the goal of achieving sustainable local, regional and global food security. We identify desirable features for models, and describe some of the potential advances that we envisage for model components and their integration. We propose an implementation strategy that would link a "pre-competitive" space for model development to a "competitive space" for knowledge product development and through private-public partnerships for new data infrastructure. Specific model improvements would be based on further testing and evaluation of existing models, the development and testing of modular model components and integration, and linkages of model integration platforms to new data management and visualization tools.