A Peek into the Plasmidome of Global Sewage

Kirstahler, Philipp; Teudt, Frederik; Otani, Saria; Aarestrup, Frank Møller; Pamp, Sünje Johanna

doi:10.1128/msystems.00283-21

Cited by 20 publications

(42 citation statements)

References 51 publications

(58 reference statements)

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“…The most frequently observed AMR genes related to these three classes were ermB , ermT , and ermF (macrolide–lincosamide–streptogramin B). The higher frequency of these genes in plasmidome samples suggests that they are more frequently found on plasmids in general or on smaller plasmids compared to larger ones ( Kirstahler et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Characterization of Carbapenem-Resistant Enterobacteriaceae Cultured From Retail Meat Products, Patients, and Porcine Excrement in China

Feng

Xiang

et al. 2021

Front. Microbiol.

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The emergence and dissemination of carbapenem-resistant Enterobacteriaceae (CRE) is a growing concern to animal and public health. However, little is known about the spread of CRE in food and livestock and its potential transmission to humans. To identify CRE strains from different origins and sources, 53 isolates were cultured from 760 samples including retail meat products, patients, and porcine excrement. Antimicrobial susceptibility testing was carried out, followed by phylogenetic typing, whole-genome sequencing, broth mating assays, and plasmids analyses. Forty-three Escherichia coli, nine Klebsiella pneumoniae, and one Enterobacter cloacae isolates were identified, each exhibiting multidrug-resistant phenotypes. Genetically, the main sequence types (STs) of E. coli were ST156 (n = 7), ST354 (n = 7), and ST48 (n = 7), and the dominant ST of K. pneumoniae is ST11 (n = 5). blaNDM–5 (n = 40) of E. coli and blaKPC–2 (n = 5) were the key genes that conferred carbapenem resistance phenotypes in these CRE strains. Additionally, the mcr-1 gene was identified in 17 blaNDM-producing isolates. The blaNDM–5 gene from eight strains could be transferred to the recipients via conjugation assays. Two mcr-1 genes in the E. coli isolates could be co-transferred along with the blaNDM–5 genes. IncF and IncX3 plasmids have been found to be predominantly associated with blaNDM gene in these strains. Strains isolated in our study from different sources and regions tend to be concordant and overlap. CRE strains from retail meat products are a reservoir for transition of CRE strains between animals and humans. These data also provide evidence of the dissemination of CRE strains and carbapenem-resistant genes between animal and human sources.

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Section: Discussionmentioning

confidence: 99%

Characterization of Carbapenem-Resistant Enterobacteriaceae Cultured From Retail Meat Products, Patients, and Porcine Excrement in China

Feng

Xiang

et al. 2021

Front. Microbiol.

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“…Circular elements were scanned for Pfam domains, these domain predictions have been used previously to classify elements as plasmids or phages 16 . Briefly, Prodigal (version 2.6.3) 24 was used to predict proteins, which were scanned against the Pfam database (version 33) 25 using hmmscan from HMMER (version 3.3.1) 26 .…”

Section: Methodsmentioning

confidence: 99%

“…Pfam domains were used classify the putative proteins on the circular elements (as in our previous publication, the e-value cutoff was 0.000001 16 . If multiple domains with acceptable e-values were predicted in a protein, the domain with the lowest e-value was chosen.…”

Section: Methodsmentioning

confidence: 99%

“…The color of the nodes were based on Pfam function. The classification scheme was adapted from previous publications 16,31 . The scheme was updated to include toxin-antitoxin systems as a separate group, and potential ARG domains found in the CARD databases.…”

Section: Methodsmentioning

confidence: 99%

“…We have recently suggested urban sewage as a comparable matrix and used that successfully to study the global occurrence of antimicrobial resistance, the virome, and human populations [13][14][15] . We recently applied long read sequencing to explore the occurrence and diversity of the small plasmidome in 24 globally obtained sewage samples and assembled 165,302 contigs (159,322 circular), of which 58,429 carried genes encoding for plasmid-related and 11,222 for virus/phage-related proteins 16 . These plasmidomes were compared to conventional whole community metagenomic extractions from the corresponding samples, elucidating which AMR classes was preferentially found in the plasmidome of sewage communities.…”

Section: Introductionmentioning

confidence: 99%

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Global distribution and diversity of prevalent sewage water plasmidomes

Teudt

Otani

Aarestrup

2022

Preprint

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Sewage water from around the world contains an abundance of short plasmids, a number of which harbor antimicrobial resistance genes (ARGs). The global dynamics of plasmid-derived antimicrobial resistance and functions is only starting to be unveiled. Here, we utilized a previously created dataset of 159,332 assumed small plasmids from 24 different globally collected sewage samples. We investigated the detailed phylogeny as well as the interplay between their protein domains, ARGs, and predicted bacterial host genera to help understand the global sewage plasmidome dynamics. A total of 58,429 circular elements carried genes encoding for plasmid-related features, and MASH distance analyses showed a very high degree of diversity. A single very diverse cluster of 520 predicted Acinetobacter plasmids was predominant among the European sewage water. Based on functional domain network analysis, we identified three groups of plasmids, mainly replication and mobilization domains. However, these backbone domains were not exclusive to any given group. Acinetobacter was the dominant host genus among theta-replicating plasmids at these size ranges. They contained a reservoir of the macrolide resistance gene pair msr(E) and mph(E). Macrolide resistance genes were the most common resistance genes in sewage plasmidomes and found in the largest number of unique plasmids. While msr(E) and mph(E) were limited to Acinetobacter, erm(B) was disseminated among a range of Firmicutes plasmids, including Staphylococcus and Streptococcus, highlighting a potential reservoir of antibiotics resistance for these pathogens from around the globe.

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