Taking the next-gen step: Comprehensive antimicrobial resistance detection from Burkholderia pseudomallei

Madden, Danielle; Webb, Jessica R.; Steinig, Eike J.; Currie, Bart J.; Price, Erin P.; Sarovich, Derek S.

doi:10.1016/j.ebiom.2020.103152

Cited by 20 publications

(42 citation statements)

References 39 publications

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“…We infer that all the mutations found in amrR may relate with varied level of resistance to macrolides or meropenem in B. pseudomallei except for AmrR V222M which has been proved not to cause AMR [55]. This assumption needs to be experimentally verified in the future.…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

“…PenA T147A was identified in 987 genomes (59.7 %) in current study, including 64 (52 %) newly sequenced Hainan genomes (supplementary data table S9). However, multiple studies [53,55] have proved that PenA T147A was a natural variant present in >50 % B. pseudomallei genomes and did not confer clinically relevant AMR. The sequence analysis of PBP3 of the 1654 genomes showed that there was a duplicate copy of PBP3 residing in two contigs of an Australian genome MSHR2138, and the result also revealed nine deletions to varying degrees in nine genomes, including five newly sequenced Hainan genomes (Fig.…”

Section: Virulence Factors and Antimicrobial Resistancementioning

confidence: 99%

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Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis

et al. 2021

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Burkholderia pseudomallei is a Gram-negative soil-dwelling bacillus that causes melioidosis, a frequently fatal infectious disease, in tropical and subtropical regions. Previous studies have identified the overall genetic and evolutionary characteristics of B. pseudomallei on a global scale, including its origin and transmission routes. However, beyond its known hyperendemicity foci in northern Australia and Southeast Asia, the distribution and genetic characteristics of B. pseudomallei in most tropical regions remain poorly understood, including in southern China. Here, we sequenced the genomes of 122 B. pseudomallei strains collected from Hainan, an island in southern China, in 2002–2018, to investigate the population structure, relationships with global strains, local epidemiology, and virulence and antimicrobial-resistance factors. A phylogenetic analysis and hierarchical clustering divided the Hainan strains into nine phylogenic groups (PGs), 80 % of which were concentrated within five major groups (group 1: corresponding to minor sequence types [STs], 12.3 %; group 3: ST46 and ST50, 31.1 %; group 9: ST58, 13.1 %; group 11: ST55, 8.2 %; group 15: mainly ST658, 15.6%). A phylogenetic analysis that included global strains suggested that B. pseudomallei in Hainan originated from Southeast Asian countries, transmitted in multiple historical importation events. We also identified several mutual transmission events between Hainan and Southeast Asian countries in recent years, including three importation events from Thailand and Singapore to Hainan and three exportation events from Hainan to Singapore, Malaysia, and Taiwan island. A statistical analysis of the temporal distribution showed that the Hainan strains of groups 3, 9, and 15 have dominated the disease epidemic locally in the last 5 years. The spatial distribution of the Hainan strains demonstrated that some PGs are distributed in different cities on Hainan island, and by combining phylogenic and geographic distribution information, we detected 21 between-city transmission events, indicating its frequent local transmission. The detection of virulence factor genes showed that 56 % of the Hainan strains in group 1 encode a B. pseudomallei -specific adherence factor, boaB, confirming the specific pathogenic characteristics of the Hainan strains in group 1. An analysis of the antimicrobial-resistance potential of B. pseudomallei showed that various kinds of alterations were identified in clinically relevant antibiotic resistance factors, such as AmrR, PenA and PBP3, etc. Our results clarify the population structure, local epidemiology, and pathogenic characteristics of B. pseudomallei in Hainan, providing further insight into its regional and global transmission networks and improving our knowledge of its global phylogeography.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Virulence Factors and Antimicrobial Resistancementioning

confidence: 99%

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Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis

et al. 2021

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“…Though the success of the Darwin treatment protocol is clear from improved treatment outcomes, high levels of intrinsic antimicrobial resistance and concerns about emerging acquired resistant have prompted the application of genomics to predict antimicrobial resistance in B. pseudomallei 24 . Moreover, the ability of B. pseudomallei to sequestrate in cells and tissues where Figure 2.…”

Section: Treatmentmentioning

confidence: 99%

Melioidosis in Australia

Inglis¹

2021

Microbiol. Aust.

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Melioidosis is a potentially fatal bacterial infection caused by the Gram-negative bacillus, Burkholderia pseudomallei following contact with a contaminated environmental source, normally soil or water in tropical and subtropical locations. The disease spectrum varies from rapidly progressive bacteraemic infection with or without pneumonia, to focal lesions in deep soft tissues and internal organs to superficial soft tissue infection and asymptomatic seroconversion with possible long-term dormancy. Most infections occur with a background of chronic illness such as diabetes, chronic kidney disease and alcoholic liver disease. Improvements in diagnosis, targeted antimicrobial treatment and long term follow up have improved clinical outcomes. Environmental controls following rare point source case clusters and heightened awareness of melioidosis appear to have reduced the disease burden in some parts of northern Australia. However, the impact of climate change on dispersal of environmental B. pseudomallei, and changing land use in tropical Australia is expected to change the epidemiology of melioidosis in future.

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“…In this issue of EBioMedicine, Madden and colleagues report the development of a tool, which they call ARDaP, for detecting antimicrobial resistance (AMR) determinants in next generation sequencing (NGS) data for B. pseudomallei, having found shortcomings with existing tools for this purpose [5]. They found that ARDaP accurately detected all the previously described SNP, indel, CNV, inversion, and gene loss AMR determinants in the B. pseudomallei isolates studied, and accurately predicted three previously undescribed determinants.…”

mentioning

confidence: 99%

Harnessing genomics in the battle against antimicrobial resistance and neglected tropical diseases

Dance

Batty

2021

EBioMedicine

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Taking the next-gen step: Comprehensive antimicrobial resistance detection from Burkholderia pseudomallei

Cited by 20 publications

References 39 publications

Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis

Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis

Melioidosis in Australia

Harnessing genomics in the battle against antimicrobial resistance and neglected tropical diseases

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