Community exposure assessment to anti-microbial resistance (AMR); case study of Malawi

Anti-microbial resistance is currently one of the greatest global health threat (CDC, 2020, WHO, 2020). Efforts have previously focused on the healthcare sector through antibiotic stewardship and surveillance (Cueni, 2020). Poor water, sanitation and hygiene (WASH) practices and infrastructure contribute to the transmission of resistant bacteria (Iskandar et al., 2020). Low-and middle-income countries (LMICs) such as Malawi have pre-existing WASH challenges, which increase the risk of population exposure to AMR (Cassivi et al., 2020). There is an existing knowledge gap regarding the prevalence of AMR in the wider community environment (Ahammad et al., 2018)

Key environmental exposure pathways to antimicrobial resistant bacteria in southern Malawi : a SaniPath approach

Antimicrobial resistance (AMR) poses a severe global health threat, yet the transmission pathways of AMR within communal public environments, where humans and animals interact, remain poorly explored. This study investigated AMR risk pathways, prevalence, and seasonality of extended-spectrum β-lactamase (ESBL) producing E. coli and K. pneumoniae, and observed practices contributing to environmental contamination within urban, peri-urban, and rural Malawi. Using the SaniPath tool, in August 2020, transect walks across three Malawian study sites identified potential AMR exposure pathways, including drains, standing water, soil, and areas of communal hand contact. Subsequently, from September-2020 to August-2021, 1440 environmental samples were collected at critical points along exposure routes (n = 40/month from each site). These underwent microbiological analysis using chromogenic agar techniques to detect the presence of ESBL E. coli and ESBL K. pneumoniae. Results showed the highest ESBL prevalence in urban environments (68.1 %, 95%CI = 0.64–0.72, p < 0.001) with a higher ESBL presence seen in drains (58.8 %, 95%CI = 055–0.62, p < 0.001) and soil (54.1 %, 95%CI = 0.46–0.62, p < 0.001) compared to other pathways. Environmental contamination was attributed to unavailability and poor condition of sanitation and hygiene infrastructure based on key informant interviews with community leaders (n = 9) and confirmed by independent observation. ESBL prevalence varied between seasons (χ 2 (2,N = 1440) = 10.89, p = 0.004), with the highest in the hot-dry period (55.8 % (n = 201)). Prevalence also increased with increased rainfall (for ESBL E.coli). We highlight that community environments are likely to be a crucial component in AMR transmission, evident in the abundance of ESBL bacteria in identified exposure pathways. Additionally, poor sanitation infrastructure and practices coupled with seasonal dynamics further affect the presence of ESBLs in communal environments. Therefore, a context appropriate whole system approach that tackles infrastructure and behavioural factors, supported by effective surveillance is required to impact AMR and a range of aligned development challenges in these settings

Key environmental exposure pathways to antimicrobial resistant bacteria in southern Malawi: A SaniPath approach.

Antimicrobial resistance (AMR) poses a severe global health threat, yet the transmission pathways of AMR within communal public environments, where humans and animals interact, remain poorly explored. This study investigated AMR risk pathways, prevalence, and seasonality of extended-spectrum β-lactamase (ESBL) producing E. coli and K. pneumoniae, and observed practices contributing to environmental contamination within urban, peri-urban, and rural Malawi. Using the SaniPath tool, in August 2020, transect walks across three Malawian study sites identified potential AMR exposure pathways, including drains, standing water, soil, and areas of communal hand contact. Subsequently, from September-2020 to August-2021, 1440 environmental samples were collected at critical points along exposure routes (n = 40/month from each site). These underwent microbiological analysis using chromogenic agar techniques to detect the presence of ESBL E. coli and ESBL K. pneumoniae. Results showed the highest ESBL prevalence in urban environments (68.1 %, 95%CI = 0.64-0.72, p < 0.001) with a higher ESBL presence seen in drains (58.8 %, 95%CI = 055-0.62, p < 0.001) and soil (54.1 %, 95%CI = 0.46-0.62, p < 0.001) compared to other pathways. Environmental contamination was attributed to unavailability and poor condition of sanitation and hygiene infrastructure based on key informant interviews with community leaders (n = 9) and confirmed by independent observation. ESBL prevalence varied between seasons (χ (2,N = 1440) = 10.89, p = 0.004), with the highest in the hot-dry period (55.8 % (n = 201)). Prevalence also increased with increased rainfall (for ESBL E.coli). We highlight that community environments are likely to be a crucial component in AMR transmission, evident in the abundance of ESBL bacteria in identified exposure pathways. Additionally, poor sanitation infrastructure and practices coupled with seasonal dynamics further affect the presence of ESBLs in communal environments. Therefore, a context appropriate whole system approach that tackles infrastructure and behavioural factors, supported by effective surveillance is required to impact AMR and a range of aligned development challenges in these settings

Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity

Escherichia coli is one of the most prevalent Gram-negative species associated with drug resistant infections. Strains that produce extended-spectrum beta-lactamases (ESBLs) or carbapenemases are both particularly problematic and disproportionately impact resource limited healthcare settings where last-line antimicrobials may not be available. A large number of E. coli genomes are now available and have allowed insights into pathogenesis and epidemiology of ESBL E. coli but genomes from sub-Saharan Africa (sSA) are significantly underrepresented. To reduce this gap, we investigated ESBL-producing E. coli colonising adults in Blantyre, Malawi to assess bacterial diversity and AMR determinants and to place these isolates in the context of the wider population structure. We performed short-read whole-genome sequencing of 473 colonising ESBL E. coli isolated from human stool and contextualised the genomes with a previously curated multi-country collection of 10 146 E. coli genomes and sequence type (ST)-specific collections for our three most commonly identified STs. These were the globally successful ST131, ST410 and ST167, and the dominant ESBL genes were blaCTX-M, mirroring global trends. However, 37 % of Malawian isolates did not cluster with any isolates in the curated multicountry collection and phylogenies were consistent with locally spreading monophyletic clades, including within the globally distributed, carbapenemase-associated B4/H24RxC ST410 lineage. A single ST2083 isolate in this collection harboured a carbapenemase gene. Long read sequencing demonstrated the presence of a globally distributed ST410-associated carbapenemase carrying plasmid in this isolate, which was absent from the ST410 strains in our collection. We conclude there is a risk that carbapenem resistance in E. coli could proliferate rapidly in Malawi under increasing selection pressure, and that both ongoing antimicrobial stewardship and genomic surveillance are critical as local carbapenem use increases

Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity

Escherichia coli is one of the most prevalent Gram-negative species associated with drug resistant infections. Strains that produce extended-spectrum beta-lactamases (ESBLs) or carbapenemases are both particularly problematic and disproportionately impact resource limited healthcare settings where last-line antimicrobials may not be available. A large number of E. coli genomes are now available and have allowed insights into pathogenesis and epidemiology of ESBL E. coli but genomes from sub-Saharan Africa (sSA) are significantly underrepresented. To reduce this gap, we investigated ESBL-producing E. coli colonising adults in Blantyre, Malawi to assess bacterial diversity and AMR determinants and to place these isolates in the context of the wider population structure. We performed short-read whole-genome sequencing of 473 colonising ESBL E. coli isolated from human stool and contextualised the genomes with a previously curated multi-country collection of 10 146 E. coli genomes and sequence type (ST)-specific collections for our three most commonly identified STs. These were the globally successful ST131, ST410 and ST167, and the dominant ESBL genes were blaCTX-M, mirroring global trends. However, 37 % of Malawian isolates did not cluster with any isolates in the curated multicountry collection and phylogenies were consistent with locally spreading monophyletic clades, including within the globally distributed, carbapenemase-associated B4/H24RxC ST410 lineage. A single ST2083 isolate in this collection harboured a carbapenemase gene. Long read sequencing demonstrated the presence of a globally distributed ST410-associated carbapenemase carrying plasmid in this isolate, which was absent from the ST410 strains in our collection. We conclude there is a risk that carbapenem resistance in E. coli could proliferate rapidly in Malawi under increasing selection pressure, and that both ongoing antimicrobial stewardship and genomic surveillance are critical as local carbapenem use increases

Open defecation by proxy : tackling the increase of disposable diapers in waste piles in informal settlements

Disposable diapers are becoming increasingly popular and present an emerging challenge for global waste management, particularly within LMICs. They offer a cheap and convenient way for caregivers to manage child excreta; however, insufficient understanding of safe disposal methods, combined with limited access to waste management services results in hazardous disposal. Used diapers are being increasingly found dumped in the open environment, including in water bodies and in open fields, leading to faecal contamination of the environment and an enhanced risk of transmission of faecal-oral diseases such as cholera and typhoid. United Nations SDG 6 aims to end open defaecation globally by 2030; however, improper disposal of used diapers will hamper progress towards reaching this goal. In this review, we identify current trends in use and subsequent disposal of single use disposable diapers in LMICs, and critically discuss the environmental and public health impacts of current practices, and potential solutions to address these challenges. Contemporary methods for managing the disposal of single use diapers for communities in LMICs tend to be cost prohibitive with few alternative options other than dumping in the environment. Modern cloth diapers offer a low waste alternative to disposable diapers but often carry an unaffordable high upfront cost. Here, in addition to advocating improved efforts by governments to upgrade access and quality of waste management services, we recommend the design and implementation of intervention schemes aimed to increase awareness of safe and hygienic disposal practices for disposable diapers

Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi

Members of the Klebsiella pneumoniae species complex, particularly Klebsiella pneumoniae subsp. pneumoniae are antimicrobial resistance (AMR) associated pathogens of global importance, and polyvalent vaccines targeting Klebsiella O-antigens are in development. Whole-genome sequencing has provided insight into O-antigen distribution in the K. pneumoniae species complex, as well as population structure and virulence determinants, but genomes from sub-Saharan Africa are underrepresented in global sequencing efforts. We therefore carried out a genomic analysis of extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae species complex isolates colonising adults in Blantyre, Malawi. We placed these isolates in a global genomic context, and compared colonising to invasive isolates from the main public hospital in Blantyre. 203 isolates from stool and rectal swabs from adults were whole-genome sequenced and compared to a publicly available multicounty collection and previously sequenced Malawian and Kenyan isolates from blood or sterile sites. We inferred phylogenetic relationships and analysed the diversity of genetic loci linked to AMR, virulence, capsule and LPS O-antigen (O-types). We find that the diversity of Malawian Klebsiella pneumoniae subsp. pneumoniae isolates represents the species’ population structure, but shows distinct local signatures concerning clonal expansions. Siderophore and hypermucoidy genes were more frequent in invasive versus colonising isolates (present in 13% vs 1%) but still generally lacking in most invasive isolates. O-antigen population structure and distribution was similar in invasive and colonising isolates, with O4 more common (14%) than in previously published studies (2-5%). We conclude that host factors, pathogen opportunity or alternate virulence loci not linked to invasive disease elsewhere are likely to be the major determinants of invasive disease in Malawi. Distinct ST and O-type distributions in Malawi highlight the need to sample locations where the burden of invasive Klebsiella disease is greatest to robustly define secular trends in Klebsiella diversity to assist in the development of a useful vaccine. Colonising and invasive isolates in Blantyre are similar, hence O-typing of colonising Klebsiella isolates may be a rapid and cost-effective approach to describe global diversity and guide vaccine development

A novel, magnetic bead-based extraction method for the isolation of antimicrobial resistance genes with a case study in river water in Malawi

AimsThe environment is increasingly recognized as an important reservoir of antimicrobial resistance genes (ARGs), which can be identified using molecular platforms. Yet, environmental surveillance remains an underutilised tool as there is no agreement on the best strategy for sample processing. We aim to develop a low-cost extraction method independent to commercial kits or reagents.Methods and resultsWe present a novel, magnetic bead-based method for the isolation of ARGs from river water named MagnaExtract. We present this with analytic limit of detection as well as a case study in Southern Malawi. Here we compare the DNA yield from MagnaExtract with commercially available QIAGEN kits and the crude boil and spin method, using a high-resolution melt analysis PCR panel designed for the detection of third-generation cephalosporin and carbapenem-resistant genes from 98 water samples.ConclusionThe MagnaExtract method is comparable, and in some instance's superior to commercially available kits for the isolation of ARGs from river water samples.Significance and impact of the studyThe MagnaExtract approach offers a simple, affordable, high yielding extraction method that could be used for the detection of ARGs from river water samples in surveillance campaigns in East Africa

Colonization dynamics of extended-spectrum beta-lactamase-producing Enterobacterales in the gut of Malawian adults.

Drug-resistant bacteria of the order Enterobacterales which produce extended-spectrum beta-lactamase enzymes (ESBL-Enterobacterales, ESBL-E) are global priority pathogens. Antimicrobial stewardship interventions proposed to curb their spread include shorter courses of antimicrobials to reduce selection pressure but individual-level acquisition and selection dynamics are poorly understood. We sampled stool of 425 adults (aged 16-76 years) in Blantyre, Malawi, over 6 months and used multistate modelling and whole-genome sequencing to understand colonization dynamics of ESBL-E. Models suggest a prolonged effect of antimicrobials such that truncating an antimicrobial course at 2 days has a limited effect in reducing colonization. Genomic analysis shows largely indistinguishable diversity of healthcare-associated and community-acquired isolates, hence some apparent acquisition of ESBL-E during hospitalization may instead represent selection from a patient's microbiota by antimicrobial exposure. Our approach could help guide stewardship protocols; interventions that aim to review and truncate courses of unneeded antimicrobials may be of limited use in preventing ESBL-E colonization