Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance

Antimicrobial resistance is one of the major threats to Public Health worldwide. Understanding the transfer and maintenance of antimicrobial resistance genes mediated by mobile genetic elements is thus urgent. In this work, we focus on the ColE1-like plasmid family, whose distinctive replication and multicopy nature has given rise to key discoveries and tools in molecular biology. Despite being massively used, the hosts, functions, and evolutionary history of these plasmids remain poorly known. Here, we built specific Hidden Markov Model(HMM) profiles to search ColE1 replicons within genomes. We identified 1,035 ColE1 plasmids in five Orders of γ-Proteobacteria, several of which are described here for the first time. The phylogenetic analysis of these replicons and their characteristic MOBP5/HEN relaxases suggest that ColE1 plasmids have diverged apart, with little transfer across orders, but frequent transfer across families. Additionally, ColE1 plasmids show a functional shift over the last decades, losing their characteristic bacteriocin production while gaining several antimicrobial resistance genes, mainly enzymatic determinants and including several extended-spectrum betalactamases and carbapenemases. Furthermore, ColE1 plasmids facilitate the intragenomic mobilization of these determinants, as various replicons were identified co-integrated with large non-ColE1 plasmids, mostly via transposases. These results illustrate how families of plasmids evolve and adapt their gene repertoires to bacterial adaptive requirements.

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Serotype distribution, antimicrobial susceptibility, antimicrobial resistance genes and virulence genes of Salmonella isolated from a pig slaughterhouse in Yangzhou, China

AMB Express ◽

10.1186/s13568-019-0936-9 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Quan Li ◽

Jian Yin ◽

Zheng Li ◽

Zewei Li ◽

Yuanzhao Du ◽

...

Keyword(s):

Public Health ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Antimicrobial Susceptibility ◽

Virulence Genes ◽

Multidrug Resistant ◽

Resistance Rate ◽

Economic Losses ◽

Production Chain ◽

Antimicrobial Resistance Genes

AbstractSalmonella is an important food-borne pathogen associated with public health and high economic losses. To investigate the prevalence and the characteristics of Salmonella in a pig slaughterhouse in Yangzhou, a total of 80 Salmonella isolates were isolated from 459 (17.43%) samples in 2016–2017. S. Derby (35/80, 43.75%) was the most prevalent, followed by S. Rissen (16/80, 20.00%) and S. Newlands (11/80, 13.75%). The highest rates of susceptibility were observed to cefoxitin (80/80, 100.0%) and amikacin (80/80, 100.0%), followed by aztreonam (79/80, 98.75%) and nitrofurantoin (79/80, 98.75%). The highest resistance rate was detected for tetracycline (65/80, 81.25%), followed by ampicillin (60/80, 75.00%), bactrim (55/80, 68.75%), and sulfisoxazole (54/80, 67.50%). Overall, 91.25% (73/80) of the isolates were resistant to at least one antibiotic, while 71.25% (57/80) of the isolate strains were multidrug resistant in the antimicrobial susceptibility tested. In addition, 86.36% (19/22) of the 22 antimicrobial resistance genes in the isolates were identified. Our data indicated that the resistance to certain antimicrobials was significantly associated, in part, with antimicrobial resistance genes. Furthermore, 81.25% (65/80) isolates harbored the virulence gene of mogA, of which 2 Salmonella Typhimurium isolates carried the mogA, spvB and spvC virulence genes at the same time. The results showed that swine products in the slaughterhouse were contaminated with multidrug resistant Salmonella commonly, especially some isolates carry the spv virulence genes. The virulence genes might facilitate the dissemination of the resistance genes to consumers along the production chain, suggesting the importance of controlling Salmonella during slaughter for public health.

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Mathematical Modelling to Study the Horizontal Transfer of Antimicrobial Resistance Genes in Bacteria: Current State of the Field and Recommendations

10.20944/preprints201904.0161.v2 ◽

2019 ◽

Author(s):

Quentin J. Leclerc ◽

Jodi A. Lindsay ◽

Gwenan M. Knight

Keyword(s):

Public Health ◽

Antimicrobial Resistance ◽

Mathematical Modelling ◽

Resistance Genes ◽

Horizontal Transfer ◽

Evolutionary Dynamics ◽

Research Field ◽

Contact Transformation ◽

Current State ◽

Antimicrobial Resistance Genes

Antimicrobial resistance (AMR) is one of the greatest public health challenges we are currently facing. To develop effective interventions against this, it is essential to understand the processes behind the spread of AMR. These are partly dependent on the dynamics of horizontal transfer of resistance genes between bacteria, which can occur by conjugation (direct contact), transformation (uptake from the environment) or transduction (mediated by bacteriophages). Mathematical modelling is a powerful tool to investigate the dynamics of AMR, however its application to study the horizontal transfer of AMR genes is currently unclear. In this systematic review, we searched for mathematical modelling studies which focused on horizontal transfer of AMR genes. We compared their aims and methods using a list of predetermined criteria, and utilized our results to assess the current state of this research field. Of the 43 studies we identified, most focused on the transfer of single genes by conjugation in Escherichia coli in culture, and its impact on the bacterial evolutionary dynamics. Our findings highlight the existence of an important research gap on the dynamics of transformation and transduction, and the overall public health implications of horizontal transfer of AMR genes. To further develop this field and improve our ability to control AMR, it is essential that we clarify the structural complexity required to study the dynamics of horizontal gene transfer, which will require cooperation between microbiologists and modellers.

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Presence and Characterization of a Novel cfr-Carrying Tn558 Transposon Derivative in Staphylococcus delphini Isolated From Retail Food

Frontiers in Microbiology ◽

10.3389/fmicb.2020.598990 ◽

2021 ◽

Vol 11 ◽

Author(s):

Feng Zhang ◽

Shi Wu ◽

Jiahui Huang ◽

Runshi Yang ◽

Jumei Zhang ◽

...

Keyword(s):

Public Health ◽

Multidrug Resistance ◽

Antimicrobial Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Poultry Meat ◽

Whole Genome ◽

Chloramphenicol Resistance ◽

Antimicrobial Resistance Genes ◽

Retail Food

Antimicrobial resistance has become a major public health threat. Food-related Staphylococcus species have received much attention due to their multidrug resistance. The cfr gene associated with multidrug resistance has been consistently detected in food-derived Staphylococcus species. In this retrospective study, we examined the prevalence of cfr-positive Staphylococcus strains isolated from poultry meat in different geographical areas of China from 2011 to 2016. Two cfr-positive Staphylococcus delphini strains were identified from poultry meat in China. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in the two S. delphini isolates 245-1 and 2794-1. Whole-genome sequencing showed that they both harbored a novel 20,258-bp cfr-carrying Tn558 transposon derivative on their chromosomes. The Tn558 derivative harbors multiple antimicrobial resistance genes, including the transferable multiresistance gene cfr, chloramphenicol resistance gene fexA, aminoglycoside resistance genes aacA-aphD and aadD, and bleomycin resistance gene ble. Surprisingly, within the Tn558 derivative, an active unconventional circularizable structure containing various resistance genes and a copy of a direct repeat sequence was identified by two-step PCR. Furthermore, core genome phylogenetic analysis revealed that the cfr-positive S. delphini strains were most closely related to S. delphini 14S03313-1 isolated from Japan in 2017 and 14S03319-1 isolated from Switzerland in 2017. This study is the first report of S. delphini harboring a novel cfr-carrying Tn558 derivative isolated from retail food. This finding raises further concerns regarding the potential threat to food safety and public health safety. The occurrence and dissemination of similar cfr-carrying transposons from diverse Staphylococcus species need further surveillance.

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A Virulence and Antimicrobial Resistance DNA Microarray Detects a High Frequency of Virulence Genes in Escherichia coli Isolates from Great Lakes Recreational Waters

Applied and Environmental Microbiology ◽

10.1128/aem.00137-06 ◽

2006 ◽

Vol 72 (6) ◽

pp. 4200-4206 ◽

Cited By ~ 82

Author(s):

Katia Hamelin ◽

Guillaume Bruant ◽

Abdel El-Shaarawi ◽

Stephen Hill ◽

Thomas A. Edge ◽

...

Keyword(s):

Public Health ◽

Escherichia Coli ◽

Antimicrobial Resistance ◽

Great Lakes ◽

Dna Microarray ◽

Resistance Genes ◽

Virulence Genes ◽

Recreational Waters ◽

E Coli ◽

Antimicrobial Resistance Genes

ABSTRACT Escherichia coli is generally described as a commensal species with occasional pathogenic strains. Due to technological limitations, there is currently little information concerning the prevalence of pathogenic E. coli strains in the environment. For the first time, using a DNA microarray capable of detecting all currently described virulence genes and commonly found antimicrobial resistance genes, a survey of environmental E. coli isolates from recreational waters was carried out. A high proportion (29%) of 308 isolates from a beach site in the Great Lakes carried a pathotype set of virulence-related genes, and 14% carried antimicrobial resistance genes, findings consistent with a potential risk for public health. The results also showed that another 8% of the isolates had unusual virulence gene combinations that would be missed by conventional screening. This new application of a DNA microarray to environmental waters will likely have an important impact on public health, epidemiology, and microbial ecology in the future.

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Mathematical modelling to study the horizontal transfer of antimicrobial resistance genes in bacteria: current state of the field and recommendations

Journal of The Royal Society Interface ◽

10.1098/rsif.2019.0260 ◽

2019 ◽

Vol 16 (157) ◽

pp. 20190260 ◽

Cited By ~ 9

Author(s):

Quentin J. Leclerc ◽

Jodi A. Lindsay ◽

Gwenan M. Knight

Keyword(s):

Public Health ◽

Antimicrobial Resistance ◽

Mathematical Modelling ◽

Resistance Genes ◽

Horizontal Transfer ◽

Evolutionary Dynamics ◽

Research Field ◽

Contact Transformation ◽

Current State ◽

Antimicrobial Resistance Genes

Antimicrobial resistance (AMR) is one of the greatest public health challenges we are currently facing. To develop effective interventions against this, it is essential to understand the processes behind the spread of AMR. These are partly dependent on the dynamics of horizontal transfer of resistance genes between bacteria, which can occur by conjugation (direct contact), transformation (uptake from the environment) or transduction (mediated by bacteriophages). Mathematical modelling is a powerful tool to investigate the dynamics of AMR; however, the extent of its use to study the horizontal transfer of AMR genes is currently unclear. In this systematic review, we searched for mathematical modelling studies that focused on horizontal transfer of AMR genes. We compared their aims and methods using a list of predetermined criteria and used our results to assess the current state of this research field. Of the 43 studies we identified, most focused on the transfer of single genes by conjugation in Escherichia coli in culture and its impact on the bacterial evolutionary dynamics. Our findings highlight the existence of an important research gap in the dynamics of transformation and transduction and the overall public health implications of horizontal transfer of AMR genes. To further develop this field and improve our ability to control AMR, it is essential that we clarify the structural complexity required to study the dynamics of horizontal gene transfer, which will require cooperation between microbiologists and modellers.

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Mathematical Modelling to Study the Horizontal Transfer of Antimicrobial Resistance Genes in Bacteria: Current State of the Field and Recommendations

10.20944/preprints201904.0161.v1 ◽

2019 ◽

Author(s):

Quentin J. Leclerc ◽

Jodi A. Lindsay ◽

Gwenan M. Knight

Keyword(s):

Public Health ◽

Antimicrobial Resistance ◽

Mathematical Modelling ◽

Resistance Genes ◽

Horizontal Transfer ◽

Evolutionary Dynamics ◽

Research Field ◽

Contact Transformation ◽

Current State ◽

Antimicrobial Resistance Genes

Antimicrobial resistance (AMR) is one of the greatest public health challenges we are currently facing. To develop effective interventions against this, it is essential to understand the processes behind the spread of AMR. These are partly dependent on the dynamics of horizontal transfer of resistance genes between bacteria, which can occur by conjugation (direct contact), transformation (uptake from the environment) or transduction (mediated by bacteriophages). Mathematical modelling is a powerful tool to investigate the dynamics of AMR, however its application to study the horizontal transfer of AMR genes is currently unclear. In this systematic review, we searched for mathematical modelling studies which focused on horizontal transfer of AMR genes. We compared their aims and methods using a list of predetermined criteria, and utilized our results to assess the current state of this research field. Of the 26 studies we identified, most focused on the transfer of single genes by conjugation in Escherichia coli in culture, and its impact on the bacterial evolutionary dynamics. Our findings highlight the existence of an important research gap on the dynamics of transformation and transduction, and the overall public health implications of horizontal transfer of AMR genes. To further develop this field and improve our ability to control AMR, it is essential that we clarify the structural complexity required to study the dynamics of horizontal gene transfer, which will require cooperation between microbiologists and modellers.

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Long-read shotgun metagenome sequencing using PromethION uncovers novel bacteriophages, their abundance, and interaction with host bacterial immunity in the oral microbiota

10.1101/2020.03.13.989996 ◽

2020 ◽

Author(s):

Koji Yahara ◽

Masato Suzuki ◽

Aki Hirabayashi ◽

Yutaka Suzuki ◽

Yusuke Okazaki

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Human Saliva ◽

Oral Microbiota ◽

Cellular Processes ◽

Antimicrobial Resistance Genes ◽

Long Read ◽

Bacterial Viruses ◽

Metagenome Sequencing ◽

First Time

AbstractBacteriophages (phages), or bacterial viruses, are very diverse and highly abundant worldwide, including human microbiomes. Although a few metagenomic studies have focused on oral phages, they relied on short-read sequencing. Here, we conducted a long-read metagenomic study of human saliva for the first time using PromethION that requires a smaller amount of DNA than PacBio. Our analyses, which integrated both PromethION and HiSeq data of >30 Gb per sample, revealed N50 ranging from 187-345 kb and thousands of contigs with >1 kb accounting for > 99% of all contigs on which 94-96% of HiSeq reads were mapped. We identified hundreds of viral contigs (95 phages and 333 prophages on an average per sample); 0-43.8% and 12.5-56.3% of the “most confident” phages and prophages, respectively, didn’t cluster with those reported previously and were identified as novel. Our integrated analyses identified highly abundant oral phages/prophages, including a novel Streptococcus phage cluster and nine jumbo phages/prophages. Interestingly, 86% of the phage cluster and 67% of the jumbo phages/prophages contained remote homologs of antimicrobial resistance genes, suggesting their potential role as a source of recombination to generate new resistance genes. Pan-genome analysis of the phages/prophages revealed remarkable diversity, identifying 0.3% and 86.4% of the genes as core and singletons, respectively. Functional annotation revealed that the highest fraction of the core genes was enriched in phage morphogenesis, followed by the fraction enriched in host cellular processes. Furthermore, our study suggested that oral phages present in human saliva are under selective pressure for escaping CRISPR immunity.ImportanceDespite the abundance and grave implications oral bacterial viruses in health and disease, little is known regarding the different groups of oral bacterial viruses, their relative abundances under various conditions, and their activities. We provided answers to these questions for the first time utilizing a recently developed sequencer that can capture and sequence long DNA fragments, including viruses, and requires only a small amount of DNA input, making it suitable for analyzing human oral samples. We identified hundreds of viral sequences, including “jumbo” viruses and a distinctive group of highly abundant oral viruses, which often contained parts of antimicrobial resistance genes; the entire repertoire of these viral genes showed remarkable diversity and supported a recently proposed hypothesis that phages modulate oral microbiota through multiple mechanisms. We also revealed genomic signs of coevolution of viruses and host bacteria that have been missed in large viromic studies in humans.

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Vegetable-derived carbapenemase-producing high-risk Klebsiella pneumoniae ST15 and Acinetobacter baumannii ST2 clones in Japan: co-existence of blaNDM-1, blaOXA-66, blaOXA-72, and AbaR4-like resistance island from the same sample

Applied and Environmental Microbiology ◽

10.1128/aem.02166-20 ◽

2021 ◽

Author(s):

Ahmed M. Soliman ◽

Hirofumi Nariya ◽

Daiki Tanaka ◽

Liansheng Yu ◽

Junzo Hisatsune ◽

...

Keyword(s):

Public Health ◽

Antimicrobial Resistance ◽

Klebsiella Pneumoniae ◽

Acinetobacter Baumannii ◽

Resistance Genes ◽

Safety Issue ◽

Health Concern ◽

Fresh Vegetables ◽

Antimicrobial Resistance Genes ◽

Resistance Island

This study was conducted to characterize carbapenemase-producing Klebsiella pneumoniae and Acinetobacter baumannii isolated from fresh vegetables in Japan. Two K. pneumoniae (AO15, and AO22) and one A. baumannii (AO22) isolates collected from vegetables in the Higashihiroshima city, Japan and subjected to antimicrobial susceptibility testing, conjugation experiments and complete genome sequence using Illumina MiniSeq and Oxford Nanopore sequencing platforms. The two K. pneumoniae isolates were clonal, belonging to ST15 and were detected to carry 19 different antimicrobial resistance genes, including blaNDM-1. Both the isolates carried blaNDM-1 on a self-transmissible IncFII(K):IncR plasmid of 122,804 bp in size with other antimicrobial resistance genes against aminoglycosides (aac(6')-Ib, aadA1, aph(3')-VI), β-lactams (blaCTXM-15, blaOXA-9, blaTEM-1A), fluoroquinolones (aac(6')-Ib-cr), and quinolones (qnrS1). A. baumannii AO22 carried blaOXA-66 on the chromosome, while blaOXA-72 was found as two copies on a GR2-type plasmid of 10,880 bp in size. Interestingly, A. baumannii AO22 harbored AbaR4-like genomic resistance island (GI) of 41,665 bp carrying antimicrobial resistance genes against tetracycline [tet(B)], sulfonamides (sul2), and streptomycin (strAB). Here, we identified Japanese carbapenemase-producing Gram-negative bacterias isolated from vegetables posing a food safety issue and a public health concern. Additionally, we reported a GR2-type plasmid carrying two copies of blaOXA-72 and an AbaR4-like resistance island from a foodborne A. baumannii. IMPORTANCE Carbapenemase-producing Gram-negative bacteria (CPGNB) cause severe health care-associated infections and constitute a major public health threat. Here, we investigated the genetic features of CPGNB isolated from fresh vegetable samples in Japan and found CPGNB, including Klebsiella pneumoniae and Acinetobacter baumannii, with dissimilar carbapenemases. The rarely described NDM carbapenemase in Japan was detected in two K. pneumoniae isolates. A. baumannii isolate, identified in this study, carried blaOXA-66 on the chromosome, while blaOXA-72 was found as two copies on a GR2-type plasmid. This study illustrated that even one fresh ready-to-eat vegetable sample might serve as a significant source of resistance genes (blaNDM-1, blaOXA-72, blaCTX-M-14b, and blaCTX-M-15) to frontline and clinically important antibiotics (carbapenems and cephalosporins). Furthermore, the detection of these organisms in fresh vegetables in Japan is alarming and poses a food safety issue and a public health concern.

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Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections

Microorganisms ◽

10.3390/microorganisms9040707 ◽

2021 ◽

Vol 9 (4) ◽

pp. 707

Author(s):

J. Christopher Noone ◽

Fabienne Antunes Ferreira ◽

Hege Vangstein Aamot

Keyword(s):

Staphylococcus Aureus ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Virulence Gene ◽

Orthopaedic Implant ◽

Metagenomic Sequencing ◽

Gene Detection ◽

Shotgun Metagenomic Sequencing ◽

Antimicrobial Resistance Genes ◽

Culture Independent

Our culture-independent nanopore shotgun metagenomic sequencing protocol on biopsies has the potential for same-day diagnostics of orthopaedic implant-associated infections (OIAI). As OIAI are frequently caused by Staphylococcus aureus, we included S. aureus genotyping and virulence gene detection to exploit the protocol to its fullest. The aim was to evaluate S. aureus genotyping, virulence and antimicrobial resistance genes detection using the shotgun metagenomic sequencing protocol. This proof of concept study included six patients with S. aureus-associated OIAI at Akershus University Hospital, Norway. Five tissue biopsies from each patient were divided in two: (1) conventional microbiological diagnostics and genotyping, and whole genome sequencing (WGS) of S. aureus isolates; (2) shotgun metagenomic sequencing of DNA from the biopsies. Consensus sequences were analysed using spaTyper, MLST, VirulenceFinder, and ResFinder from the Center for Genomic Epidemiology (CGE). MLST was also compared using krocus. All spa-types, one CGE and four krocus MLST results matched Sanger sequencing results. Virulence gene detection matched between WGS and shotgun metagenomic sequencing. ResFinder results corresponded to resistance phenotype. S. aureus spa-typing, and identification of virulence and antimicrobial resistance genes are possible using our shotgun metagenomics protocol. MLST requires further optimization. The protocol has potential application to other species and infection types.

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