Emergence of carbapenemase-producing Enterobacteriaceae in Malawi

Lewis, Jessica; Lester, Rebecca; Mphasa, Madalitso; Banda, Rachel; Edwards, Thomas; Thomson, Nicholas R.; Feasey, Nicholas A.

doi:10.1016/j.jgar.2019.12.017

Cited by 13 publications

(19 citation statements)

References 5 publications

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“…This raises the possibility that co-location of genes conferring ESBL and co-trimoxazole could select for ESBL resistance even in the absence of beta-lactam use. No genes conferring resistance to carbapenemases were identified, though the carbapenemase blaNDM-5 has been described in E. coli in Blantyre contemporaneously with this study40 , and the carbapenemases blaKPC-2 in ST340 K. pneumoniae and blaOXA-48 in K. variicola have been described in Central Malawi 41 in 2016/17. Carbapenems are increasingly available in QECH, and it seems very likely that increasing exposure will result in rapid expansion of carbapenemases in K. pneumoniae especially given the likely unrestricted global flow of Klebsiella strains suggested by our data 8.…”

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confidence: 46%

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

Lewis

Mphasa

Banda

et al. 2021

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Klebsiella pneumoniae is an antimicrobial resistance (AMR) associated pathogen of global importance, and polyvalent vaccines targeting K. pneumoniae O-antigens are in development. Genomes from sub-Saharan Africa (sSA) are underrepresented in global sequencing efforts. We therefore carried out a genomic analysis of extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae complex isolates colonising adults in Blantyre, Malawi, 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 multicountry collection of 484 K. pneumoniae genomes sampled to cover maximum diversity of the species, 150 previously sequenced Malawian and 66 Kenyan isolates from blood or sterile sites. We inferred phylogenetic relationships and analysed the diversity of genetic loci linked to AMR, virulence, capsule (K-) and LPS O-antigen (O-types). We find that the diversity of Malawian Klebsiella isolates is representative of the species population structure, but with local success and expansion of sequence types (STs) ST14, ST15, ST340 and ST307. Siderophore and hypermucoidy genes were more frequent in invasive versus carriage isolates (present in 13% vs 1%, p < 0.001) but still generally lacking in most invasive isolates. The population structure and distribution of O-antigen types was similar in Malawian invasive and carriage isolates, with O4 being more common in Malawian isolates (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 highlights the need for geographically aware sampling to robustly define secular trends in Klebsiella diversity. Colonising and invasive isolates in Blantyre are similar and hence O-typing of colonising Klebsiella isolates may be a rapid and cost-effective approach to describe global diversity and guide vaccine development.

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confidence: 46%

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

Lewis

Mphasa

Banda

et al. 2021

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“…Concurrently, we present the first report of the following carbapenemase resistance genes bla OXA-48 (n=94), bla IMP (n=13), bla NDM (n=8) and bla KPC (n=3) in Malawian river water, although bla NDM have previously been reported clinically (Lewis et al, 2020). Whilst the ARGs detected cannot be attributed to a specific bacterial species, water sources are susceptible to anthropogenic pressures and are often polluted with antibiotics and both commensal and pathogenic bacteria associated with humans (Sanderson et al, 2018).…”

Section: Args In Malawian River Watermentioning

confidence: 75%

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

Byrne

Cocker²,

Alyayyoussi³

et al. 2021

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BackgroundEnvironmental water samples are increasingly recognised as an important reservoir of antimicrobial resistance (AMR) genes. Polymerase chain reaction (PCR) and next generation sequencing (NGS) offer a potentially inclusive surveillance platform for a wide range of AMR genes. However, molecular methods are dependent upon the extraction of DNA of high yield and quality. Current options for DNA extraction from complex environmental matrices for downstream molecular applications are either expensive or low yielding. We present here a novel magnetic bead-based DNA extraction method, for the detection of antimicrobial resistance genes (ARGs) from river water in Malawi, named MagnaExtract.MethodsMagnaExtract involves initial filtration of 250ml freshwater, followed by an overnight incubation of the filter in 15ml buffered peptone water (BPW), common procedure in microbiology laboratories. 200µl is then taken for a boil (95°C) and spin step and mixed with magnetic beads to bind DNA. Following washes with ethanol, the DNA is eluted in nuclease-free water. To determine the effectiveness of this method, 98 freshwater samples were collected from two rivers in Southern Malawi, and DNA was isolated using the MagnaExtract method, two commercial Qiagen (Germany) kits; PowerWater and DNeasy Blood and tissue, alongside a boil and spin of BPW, and a boil and spin from bacterial isolate grown on agar media. All samples were screened with a high-resolution melt (HRM) PCR panel previously validated for the detection of third generation cephalosporin and carbapenem ARGs. We compared the DNA yield obtained using all extraction methods, as well as the identification of each ARG.ResultsDNA yield using MagnaExtract was statistically greater than both boil and spin methods and DNeasy Blood & Tissue (Qiagen, Germany). DNA yield was slightly lower than using PowerWater (Qiagen) but the difference was not statistically significant. MagnaExtract was the only method to identify ARGs in all 98 water samples compared with PowerWater (n=82), DNeasy (n=95) boilate of BPW (n=75) and boilate of bacterial isolate (n=87). The most commonly detected ARG was OXA-48 (n=93). In addition, we found overnight incubation in non-selective enrichment broth (BPW) to promote the growth of bacteria harbouring extended spectrum beta lactamase (ESBL) genes and reduction in the detection of carbapenemase genes.ConclusionThe MagnaExtract approach offers a simple, affordable, high yielding DNA extraction method for the detection of ARGs isolated from river water samples.

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“…We find that the diversity of E. coli in Blantyre broadly reflects global diversity, but with a suggestion of local subclades that highlights a need for further targeted sequencing of isolates from Malawi and sSA to understand local, regional, and global E. coli transmission. Carbapenem resistance is present in Malawi 11,45 , and it likely that increased carbapenem use (driven by ESBL resistance) will select for it. There is a critical need for robust stewardship strategies plus ongoing surveillance, as these agents are introduced.…”

Section: Discussionmentioning

confidence: 99%

“…Our study is set in Blantyre, Malawi, where carbapenem use is not routine, but the 3GC antimicrobial ceftriaxone has been widely used in the hospital setting since its introduction to the Malawian national formulary in 2005 9 . Since that time, ESBL-producing E. coli have become an increasing problem in clinical practice and now represent 31% of invasive E. coli in Blantyre 10 , whereas carbapenem resistance has so far only been sporadically described 11 . There is a significant unmet need for access to carbapenem antimicrobials to treat resistant infections, but the example of ceftriaxone shows that carbapenem resistance may be likely to disseminate rapidly if carbapenem use is increased.…”

Section: Introductionmentioning

confidence: 99%

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

Lewis

Mphasa

Banda

et al. 2021

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Escherichia coli is a ubiquitous bacterial species, associated with drug resistant infections; hundreds of thousands of genomes are now available, but are biased towards high-income countries and clinical isolates. Data from sub-Saharan Africa (sSA) are underrepresented in global sequencing efforts and may represent a major source of genetic diversity with respect to transmissible antimicrobial resistance (AMR). We carried out a genomic investigation of extended-spectrum beta-lactamase (ESBL)-producing E. coli colonising adults in Blantyre, Malawi to assess the diversity and AMR determinants and to place these isolates in the context of globally available genomes. We carried out short-read whole-genome sequencing of 473 colonising ESBL E. coli isolated from stool and placed them in the context of a previous curated species wide collection of 10,146 isolates using the popPUNK clustering algorithm and by constructing a core gene phylogeny. The most frequently identified STs in Malawian isolates were the globally successful ST131 and ST410, and blaCTX-M were the dominant ESBL genes, mirroring global trends. However, 37% of Malawian isolates did not cluster with any isolates in the global collection, and the core gene phylogeny was consistent with local subclades including in ST410 and several phylogroup A lineages. Apparent undescribed diversity in Malawian E. coli could be due to local selection pressures or sampling biases in global E. coli collections. Taking a one health approach to further sampling of E. coli from Malawi and sSA, and principled incorporation into unbiased global collections is necessary to understand local, regional and global transmission of both E. coli and priority AMR genes.

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Emergence of carbapenemase-producing Enterobacteriaceae in Malawi

Cited by 13 publications

References 5 publications

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

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

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

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

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