Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

Abstract Background Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results. Results The genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD-type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene. Conclusions The sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea. The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control.

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The shared resistome of human and pig microbiota is mobilized by distinct genetic elements

Applied and Environmental Microbiology ◽

10.1128/aem.01910-20 ◽

2020 ◽

Author(s):

Chao Wang ◽

Yuqin Song ◽

Na Tang ◽

Gang Zhang ◽

Sébastien Olivier Leclercq ◽

...

Keyword(s):

Antibiotic Resistance ◽

Intestinal Microbiota ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

Antibiotic Resistance Genes ◽

Mobile Genetic Elements ◽

Human Pathogens ◽

Genetic Elements ◽

Metagenomics Data ◽

Genetic Context

The extensive use of antibiotics in hospitals and in the animal breeding industry has promoted antibiotic resistance in bacteria, which resulted in the emergence of a large number of antibiotic resistance genes in the intestinal tract of human and farmed animals. Genetic exchange of resistance genes between the two ecosystems is now well documented for pathogenic bacteria, but the repertoire of shared resistance genes in the commensal bacterial community and by which genetic modules they are disseminated are still unclear. By analyzing metagenomics data of human and pig intestinal samples both collected in Shenzhen, China, a set of 27 highly prevalent antibiotic resistance genes was found to be shared between human and pig intestinal microbiota. The mobile genetic context for 11 of these core antibiotic resistance genes could be identified by mining their carrying scaffolds constructed from the two datasets, leading to the detection of seven integrative and conjugative/mobilizable elements and two IS-related transposons. The comparison of the relative abundances between these detected mobile genetic elements and their associated antibiotic resistance genes revealed that for many genes, the estimated contribution of the mobile elements to the gene abundance differs strikingly depending on the host. These findings indicate that although some antibiotic resistance genes are ubiquitous across microbiota of human and pig populations, they probably relied on different genetic elements for their dissemination within each population. IMPORTANCE There is growing concern that antibiotic resistance genes could spread from the husbandry environment to human pathogens through dissemination mediated by mobile genetic elements. In this study, we investigated the contribution of mobile genetic elements to the abundance of highly prevalent antibiotic resistance genes found in commensal bacteria of both human and pig intestinal microbiota originating from the same region. Our results reveal that for most of these antibiotic resistance genes, the abundance is not explained by the same mobile genetic element in each host, suggesting that the human and pig microbial communities promoted a different set of mobile genetic carriers for the same antibiotic resistance genes. These results deepen our understanding of the dissemination of antibiotic resistance genes among and between human and pig gut microbiota.

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Multiplex characterization of human pathogens including species and antibiotic-resistance gene identification

Journal of Medical Microbiology ◽

10.1099/jmm.0.000192 ◽

2016 ◽

Vol 65 (1) ◽

pp. 48-55 ◽

Cited By ~ 3

Author(s):

Ivan Barišić ◽

Josefine Petzka ◽

Silvia Schoenthaler ◽

Klemens Vierlinger ◽

Christa Noehammer ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Gene ◽

Antibiotic Resistance Gene ◽

Gene Identification ◽

Human Pathogens

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Antibiotic resistance gene transfer during anaerobic digestion with added copper: Important roles of mobile genetic elements

The Science of The Total Environment ◽

10.1016/j.scitotenv.2020.140759 ◽

2020 ◽

Vol 743 ◽

pp. 140759 ◽

Cited By ~ 1

Author(s):

Ranran Zhang ◽

Jie Gu ◽

Xiaojuan Wang ◽

Yang Li

Keyword(s):

Antibiotic Resistance ◽

Anaerobic Digestion ◽

Gene Transfer ◽

Resistance Gene ◽

Antibiotic Resistance Gene ◽

Mobile Genetic Elements ◽

Genetic Elements

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Resistance Genes and Genetic Elements Associated with Antibiotic Resistance in Clinical and Commensal Isolates of Streptococcus salivarius

Applied and Environmental Microbiology ◽

10.1128/aem.00415-15 ◽

2015 ◽

Vol 81 (12) ◽

pp. 4155-4163 ◽

Cited By ~ 21

Author(s):

Fanny Chaffanel ◽

Florence Charron-Bourgoin ◽

Virginie Libante ◽

Nathalie Leblond-Bourget ◽

Sophie Payot

Keyword(s):

Antibiotic Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Genetic Linkage ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Streptococcus Salivarius ◽

Content Type ◽

Clinical Strains ◽

Genetic Elements

ABSTRACTThe diversity of clinical (n= 92) and oral and digestive commensal (n= 120) isolates ofStreptococcus salivariuswas analyzed by multilocus sequence typing (MLST). No clustering of clinical or commensal strains can be observed in the phylogenetic tree. Selected strains (92 clinical and 46 commensal strains) were then examined for their susceptibilities to tetracyclines, macrolides, lincosamides, aminoglycosides, and phenicol antibiotics. The presence of resistance genestet(M),tet(O),erm(A),erm(B),mef(A/E), andcatQand associated genetic elements was investigated by PCR, as was the genetic linkage of resistance genes. High rates of erythromycin and tetracycline resistance were observed among the strains. Clinical strains displayed either theerm(B) (macrolide-lincosamide-streptogramin B [MLSB] phenotype) ormef(A/E) (M phenotype) resistance determinant, whereas almost all the commensal strains harbored themef(A/E) resistance gene, carried by a macrolide efflux genetic assembly (MEGA) element. A genetic linkage between a macrolide resistance gene and genes of Tn916was detected in 23 clinical strains and 5 commensal strains, with a predominance of Tn3872elements (n= 13), followed by Tn6002(n= 11) and Tn2009(n= 4) elements. Four strains harboring amef(A/E) gene were also resistant to chloramphenicol and carried acatQgene. Sequencing of the genome of one of these strains revealed that these genes colocalized on an IQ-like element, as already described for other viridans group streptococci. ICESt3-related elements were also detected in half of the isolates. This work highlights the potential role ofS. salivariusin the spread of antibiotic resistance genes both in the oral sphere and in the gut.

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Genome-based taxonomic reclassification of Acinetobacter species using type and reference strains

10.21203/rs.3.rs-677553/v1 ◽

2021 ◽

Author(s):

Masato Suzuki ◽

Shotaro Maehana ◽

Hidero Kitasato

Keyword(s):

Genome Sequence ◽

Dna Hybridization ◽

Type Strain ◽

Genomic Analysis ◽

Clinical Settings ◽

Human Pathogens ◽

Acinetobacter Species ◽

Antimicrobial Resistance Genes ◽

Reference Strains ◽

Genome Comparisons

Abstract Acinetobacter species are widely distributed in the environment and clinical settings worldwide and serve as natural reservoirs of antimicrobial resistance genes and occasional human pathogens responsible for nosocomial infections. In this study, we performed genomic analysis of Acinetobacter seohaensis DSM 16313, a type strain of the proposed Acinetobacter species. This species was estimated to be evolutionary close to Acinetobacter towneri but the genome sequence of A. seohaensis was not publicly available. Pangenome analysis of the genome sequence of A. seohaensis along with those of genome-available type and reference strains of 82 Acinetobacter species including A. towneri suggested that three groups of Acinetobacter species, A. seohaensis and A. towneri; Acinetobacter pullorum and Acinetobacter portensis; and Acinetobacter idrijaensis, Acinetobacter mesopotamicus, and Acinetobacter lwoffii, were phylogenetically very similar to each other. Genome comparisons based on in silico DNA-DNA hybridization and the average nucleotide identity confirmed that these three groups of Acinetobacter species are conspecific. Based on the rules of priority, A. seohaensis, A. pullorum, and A. idrijaensis/A. mesopotamicus should be reclassified as later heterotypic synonyms of A. towneri, A. portensis, and A. lwoffii, respectively.

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Distribution of Medically Relevant Antibiotic Resistance Genes and Mobile Genetic Elements in Soils of Temperate Forests and Grasslands Varying in Land Use

Genes ◽

10.3390/genes11020150 ◽

2020 ◽

Vol 11 (2) ◽

pp. 150 ◽

Cited By ~ 1

Author(s):

Inka M. Willms ◽

Jingyue Yuan ◽

Caterina Penone ◽

Kezia Goldmann ◽

Juliane Vogt ◽

...

Keyword(s):

Land Use ◽

Antibiotic Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Forest Soils ◽

Antibiotic Resistance Genes ◽

Mobile Genetic Elements ◽

Class 1 Integrons ◽

Genetic Elements ◽

Class 1

Antibiotic-resistant pathogens claim the lives of thousands of people each year and are currently considered as one of the most serious threats to public health. Apart from clinical environments, soil ecosystems also represent a major source of antibiotic resistance determinants, which can potentially disseminate across distinct microbial habitats and be acquired by human pathogens via horizontal gene transfer. Therefore, it is of global importance to retrieve comprehensive information on environmental factors, contributing to an accumulation of antibiotic resistance genes and mobile genetic elements in these ecosystems. Here, medically relevant antibiotic resistance genes, class 1 integrons and IncP-1 plasmids were quantified via real time quantitative PCR in soils derived from temperate grasslands and forests, varying in land use over a large spatial scale. The generated dataset allowed an analysis, decoupled from regional influences, and enabled the identification of land use practices and soil characteristics elevating the abundance of antibiotic resistance genes and mobile genetic elements. In grassland soils, the abundance of the macrolide resistance gene mefA as well as the sulfonamide resistance gene sul2 was positively correlated with organic fertilization and the abundance of aac(6′)-lb, conferring resistance to different aminoglycosides, increased with mowing frequency. With respect to forest soils, the beta-lactam resistance gene blaIMP-12 was significantly correlated with fungal diversity which might be due to the fact that different fungal species can produce beta-lactams. Furthermore, except blaIMP-5 and blaIMP-12, the analyzed antibiotic resistance genes as well as IncP-1 plasmids and class-1 integrons were detected less frequently in forest soils than in soils derived from grassland that are commonly in closer proximity to human activities.

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CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2020.0464 ◽

2021 ◽

Vol 377 (1842) ◽

Author(s):

Elizabeth Pursey ◽

Tatiana Dimitriu ◽

Fernanda L. Paganelli ◽

Edze R. Westra ◽

Stineke van Houte

Keyword(s):

Antibiotic Resistance ◽

System Analysis ◽

Bacterial Pathogens ◽

Genetic Material ◽

Antibiotic Resistance Genes ◽

Mobile Genetic Elements ◽

Multidrug Resistant ◽

Human Pathogens ◽

Genetic Elements ◽

Defence System

The acquisition of antibiotic resistance (ABR) genes via horizontal gene transfer (HGT) is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of ABR. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of ABR. We analysed approximately 40 000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens, including Enterococcus , Staphylococcus , Acinetobacter and Pseudomonas . We modelled the association between CRISPR-Cas and indicators of HGT, and found that pathogens with a CRISPR-Cas system were less likely to carry ABR genes than those lacking this defence system. Analysis of the mobile genetic elements (MGEs) targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of ABR. These results suggest a potential ‘immunocompromised’ state for multidrug-resistant strains that may be exploited in tailored interventions that rely on MGEs, such as phages or phagemids, to treat infections caused by bacterial pathogens. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

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The gut microbiota resistome provides development of drug resistance in causative agents of human infectious diseases

Nauchno-prakticheskii zhurnal «Patogenez» ◽

10.25557/gm.2017.3.8494 ◽

2017 ◽

pp. 20-32 ◽

Cited By ~ 1

Author(s):

Е.Н. Ильина ◽

Е.И. Олехнович ◽

А.В. Павленко

Keyword(s):

Drug Resistance ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Integrated Approach ◽

Modern Medicine ◽

Pathogenic Microorganisms ◽

Human Pathogens ◽

Potential Source ◽

Causative Agents ◽

Bacterial Genes

С течением времени подходы к изучению резистентности к антибиотикам трансформировались от сосредоточения на выделенных в виде чистой культуры патогенных микроорганизмах к исследованию резистентности на уровне микробных сообществ, составляющих биотопы человека и окружающей среды. По мере того, как продвигается изучение устойчивости к антибиотикам, возникает необходимость использования комплексного подхода для улучшения информирования мирового сообщества о наблюдаемых тенденциях в этой области. Все более очевидным становится то, что, хотя не все гены резистентности могут географически и филогенетически распространяться, угроза, которую они представляют, действительно серьезная и требует комплексных междисциплинарных исследований. В настоящее время резистентность к антибиотикам среди патогенов человека стала основной угрозой в современной медицине, и существует значительный интерес к определению ниши, в которых бактерии могут получить гены антибиотикорезистентности, и механизмов их передачи. В данном обзоре мы рассматриваем проблемы, возникшие на фоне широкого использования человечеством антибактериальных препаратов, в свете формирования микрофлорой кишечника резервуара генов резистентности. Over the time, studies of antibiotic resistance have transformed from focusing on pathogenic microorganisms isolated as a pure culture to analysis of resistance at the level of microbial communities that constitute human and environmental biotopes. Advancing studies of antibiotic resistance require an integrated approach to enhance availability of information about observed tendencies in this field to the global community. It becomes increasingly obvious that, even though not all resistance genes can geographically and phylogenetically spread, the threat they pose is indeed serious and requires complex interdisciplinary research. Currently, the antibiotic resistance of human pathogens has become a challenge to modern medicine, which is now focusing on determining a potential source for bacterial genes of drug resistance and mechanisms for the gene transmission. In this review, we discussed problems generated by the widespread use of antibacterial drugs in the light of forming a reservoir of resistance genes by gut microflora.

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