Analysis of indigenous plasmid sequences of A. baumannii DS002 reveals the existence of lateral mobility and extensive genetic recombination among Acinetobacter plasmids

Genome sequence of Acinetobacter baumannii DS002 revealed the existence of seven contigs with features of indigenous plasmids. Of the seven contigs, three of them have shown size and sequence identity. They appeared to have been generated due to the unique recombination events leading to a large-scale recombination and sequence inversions. The rest of the indigenous plasmids have shown significant size variations and contained the genetic repertoire required for the detoxification of formaldehyde and biosynthesis of exopolysaccharides. Genetic modules encoding novel toxin–antitoxin systems were found in most of the plasmids to ensure their survival in the host. In some instances, the toxin and antitoxin coding sequences were found on two different plasmids promoting the cosegregation of these two plasmids into the daughter cells

Mobile genetic elements associated with carbapenemase genes in South American Enterobacterales

ABSTRACT Introduction: Carbapenem resistance in members of order Enterobacterales is a growing public health problem causing high mortality in developing and industrialized countries. Its emergence and rapid propagation worldwide was due to both intercontinental spread of pandemic strains and horizontal dissemination via mobile genetic elements (MGE) such as plasmids and transposons. Objective: To describe MGE carrying carbapenem resistance genes in Enterobacterales which have been reported in South America. Search strategy and selection criteria: A search of the literature in English or Spanish published until 2019 in PubMed, Google Scholar, LILACS and SciELO databases was performed for studies of MGE in Enterobacterales reported in South American countries. Results: Seven South American countries reported MGE related to carbapenemases. Carbapenemase-producing Klebsiella pneumoniae belonging to clonal complex 258 were the most prevalent pathogens reported; others carbapenemase-producing Enterobacterales such as Escherichia coli, Serratia marcescens, and Providencia rettgeri also have been reported. The MGE implicated in the spread of the most prevalent carbapenemase genes are Tn4401 and non-Tn4401 elements for bla KPC and ISAba125 for bla NDM, located in different plasmid incompatibility groups, i.e. L/M, A/C, FII and bacterial clones. Conclusion: This review indicates that, like in other parts of the world, the most commonly reported carbapenemases in Enterobacterales from South America are being disseminated through clones, plasmids, and transposons which have been previously reported in other parts of the world.

Overview of antibiotic resistance genes database / 生物工程学报

The discovery of antibiotics is a big revolution in human history, and its clinical application has saved countless lives. However, with the widespread and abuse of antibiotics, many pathogens have developed resistance, and even "Super Bacteria" resistance to multiple drugs have evolved. In the arms race between humans and pathogens, humans are about to face a situation where no medicine is available. Research on microbial antibiotic resistance genes, resistance mechanisms, and the spread of resistance has attracted the attention of many scientific researchers, and various antibiotic resistance gene databases and analysis tools have emerged. In this review, we collect the current databases that focus on antibiotics resistance genes, and discuss these databases in terms of database types, data characteristics, antibiotics resistance gene prediction models and the types of analyzable sequences. In addition, a few gene databases of anti-metal ions and anti-biocides are also involved. It is believed that this summary will provide a reference for how to select and use antibiotic resistance gene databases.

Presence & mobility of antimicrobial resistance in Gram-negative bacteria from environmental samples in coastal Karnataka, India

To understand antimicrobial resistance (AMR) patterns and mechanisms of horizontal gene transfer in human-associated environments is essential to AMR surveillance. Gram-negative bacteria (1122 isolates) from food-animal environments were characterized for antimicrobial susceptibility and AMR genes. Seventy five per cent of the isolates (837 of 1122) were resistant to at least one of the antibiotics tested. Resistance to more than three groups of antimicrobials (multidrug resistance) was observed in 43 isolates with most often encountered (12 of 43) resistance to ?-lactams, tetracycline, quinolones and nitrofurantoin. The profile of frequently reported plasmid-mediated resistance gene in these isolates was determined. The mobility of these elements as plasmids or phages was examined. The blaCTX-M gene was present in the plasmid of 61 per cent and packed in induced phage fractions in 72 per cent of the isolates and blaTEMin 69 per cent phage fractions compared to 15 per cent presence in the plasmid.

Overview of Staphylococcus aureus mobile genetic elements and horizontal gene transfer of antimicrobial resistance genes / 中华预防医学杂志

The mechanism of antimicrobial resistance transmission mediated by mobile genetic elements (MGEs) in Staphylococcus aureus is highly complicated, leading a significant challenge for controlling the spread of the resistant Staphylococcus aureus strains. Based on the latest literature acquired in this work, we have overviewed the transmission mechanism of antimicrobial resistance encoding MGEs. It is notably that there are a number of MGEs, which may encode different antimicrobial resistance determinants and possess specific transmission mechanism. In spite of this specificity of the strains to their host (human or animal), some Staphylococcus aureus strains can be transmitted from animals to humans or vice versa. This ability of cross staphylococci transfer is an additional means to acquire new genetic material encoded by MGE. It was suggested in this review that study on transmission mechanism of MGEs mediated antimicrobial resistance genes could provide important biological information of their spreading and effectively help prevent and control of the resistant strains and/or resistance genes among human, animals and ecologies.

Mobile genetic elements related to carbapenem resistance in Acinetobacter baumannii

Abstract Acinetobacter baumannii is widely recognized as an important pathogen associated with nosocomial infections. The treatment of these infections is often difficult due to the acquisition of resistance genes. A. baumannii presents a high genetic plasticity which allows the accumulation of these resistance determinants leading to multidrug resistance. It is highlighted the importance of the horizontal transfer of resistance genes, through mobile genetic elements and its relationship with increased incidence of multidrug resistant A. baumannii in hospitals. Considering that resistance to carbapenems is very important from the clinical and epidemiological point of view, the aim of this article is to present an overview of the current knowledge about genetic elements related to carbapenem resistance in A. baumannii such as integrons, transposons, resistance islands and insertion sequences.

Detecção e caracterização de elementos conjugativos integrativos em bactérias isoladas de amostras ambientais / Detection and characterization of integrative conjugative elements in bacteria isolated from environmental samples

O reconhecimento da resistência antimicrobiana como um fenômeno emergente em saúde pública, tem constituído um problema em nível mundial. O abuso na utilização de antibióticos na medicina humana e veterinária, e na agricultura, tem originado incremento na diversidade de micro-organismos resistentes, refletindo em falha terapêutica. Os mecanismos de resistência a antibióticos em micro-organismos são mediados principalmente por genes adquiridos de DNA exógeno. A dinâmica da transferência horizontal é realizada por meio de elementos genéticos móveis que carregam genes de resistência. A ampla distribuição deste tipo de estruturas, como o elemento SXT, isolado inicialmente em V. cholerae, tem contribuído para a disseminação de complexos específicos clonais em determinadas áreas geográficas. Este estudo pioneiro no Brasil pesquisou a presença de elementos SXT, em espécies bacterianas do grupo das gama proteobactérias em espécies ambientais, determinou suas características estruturais e funcionais, incluindo genes de resistência a antibióticos, bem como a sensibilidade aos antibióticos dentre os isolados bacterianos que os abrigam. O resultado foi a classificação de 43 elementos SXT obtidos no Brasil, através da comparação com aqueles descritos na literatura. Dentre os elementos SXT obtidos, quatro são albergados por Morganella morganii, fato inédito na literatura. O conhecimento da evolução bacteriana constitui importante ferramenta para estabelecer estratégias eficazes de controle e tratamento de infecções, sem aumentar a pressão seletiva sobre os micro-organismos, bem como instrumento preciso e de grande importância para subsidiar estudos epidemiológicos.

Recognition of antimicrobial resistance as an emerging phenomenon in public health has been a problem worldwide. The abuse in the use of antibiotics in human and veterinary medicine, and agriculture, has caused an increase in the diversity of resistant microorganisms, reflecting in treatment failure. The mechanisms of antibiotic resistance in microorganisms are primarily mediated by genes acquired from exogenous DNA. The dynamics of the horizontal transfer is performed by mobile genetic elements which carry resistance genes. The wide distribution of these structures, such as the SXT element originally isolated from V. cholerae, has contributed to the spread of specific clonal complexes in certain geographical areas. This pioneering study in Brazil researched the presence of SXT elements in the group of bacterial species in environmental gamma-proteobacteria species, determined their structural and functional characteristics, including genes for resistance to antibiotics and the antibiotic susceptibility among bacterial isolates that harbor them. The result was the classification of 43 SXT elements found in Brazil, by comparison with those found in the literature. Among the SXT elements found, four are sheltered by Morganella morganii, unprecedented in the literature. Knowledge of bacterial evolution is an important to establish effective strategies to control and treat infections without increasing the selective pressure on microorganisms, as well as a precise instrument and very important tool to support epidemiological studies.

Heavy Metal Resistance Strategies of Acidophilic Bacteria and Their Acquisition: Importance for Biomining and Bioremediation

Microbial solubilizing of metals in acid environments is successfully used in industrial bioleaching of ores or biomining to extract metals such as copper, gold, uranium and others. This is done mainly by acidophilic and other microorganisms that mobilize metals and generate acid mine drainage or AMD, causing serious environmental problems. However, bioremediation or removal of the toxic metals from contaminated soils can be achieved by using the specific properties of the acidophilic microorganisms interacting with these elements. These bacteria resist high levels of metals by using a few "canonical" systems such as active efflux or trapping of the metal ions by metal chaperones. Nonetheless, gene duplications, the presence of genomic islands, the existence of additional mechanisms such as passive instruments for pH and cation homeostasis in acidophiles and an inorganic polyphosphate-driven metal resistance mechanism have also been proposed. Horizontal gene transfer in environmental microorganisms present in natural ecosystems is considered to be an important mechanism in their adaptive evolution. This process is carried out by different mobile genetic elements, including genomic islands (GI), which increase the adaptability and versatility of the microorganism. This mini-review also describes the possible role of GIs in metal resistance of some environmental microorganisms of importance in biomining and bioremediation of metal polluted environments such as Thiomonas arsenitoxydans, a moderate acidophilic microorganism, Acidithiobacillus caldus and Acidithiobacillus ferrooxidans strains ATCC 23270 and ATCC 53993, all extreme acidophiles able to tolerate exceptionally high levels of heavy metals. Some of these bacteria contain variable numbers of GIs, most of which code for high numbers of genes related to metal resistance. In some cases there is an apparent correlation between the number of metal resistance genes and the metal tolerance of each of these microorganisms. It is expected that a detailed knowledge of the mechanisms that these environmental microorganisms use to adapt to their harsh niche will help to improve biomining and metal bioremediation in industrial processes.

Correlation between acquired drug resistance-related genes and mobile genetic elements in pandrugresistant Acinetobacter baumannii / 中华临床感染病杂志

Objective To investigate the correlation between acquired drug resistance-related genes and mobile genetic elements from pandrug-resistant Acinetobacter baumannii. Methods Fifty-three horizontal transfer drug resistance-related genes ( β-lactamases,aminoglycoside and quinolones resistance related) and 12 mobile genetic elements (including zygosity plasmid,transposon,insertion sequence and integron) were detected by polymerase chain reaction (PCR) in 20 clinical isolates of pandrug-resistant Acinetobacter baumannii.Index cluster analysis was performed to explore the correlation.Results In 20 strains of pandrug-resistant Acinetobacter baumannii,there were 3 types of β-lactamases related genes (TEM-1,ADC-30,OXA-23 ),4 types of aminoglycoside modifying enzyme genes [ aac (3)-Ⅰ,aac(6′)-Ⅰ b,ant( 3″)-Ⅰ and aph( 3′)-Ⅰ ],and 5 kinds of mobile genetic elements ( int Ⅰ 1,tnpU,tnp513,IS26 and ISAba1 ). Index cluster analysis showed high correlations between resistance genes [TEM-1,ADC-30,aac( 6′)-Ⅰ b,ant( 3″)-Ⅰ,abeB,qacE Δ1] and mobile genetic elements ( int Ⅰ 1,tnpU,tnp513,IS26,ISAba1 ).Conclusion Clinical isolated pandrug-resistant Acinetobacter baumannii carries several acquired drug resistance-related genes and mobile genetic elements,and there may be a close association between them.

Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains

The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.

spa typing and enterotoxin gene profile of Staphylococcus aureus isolated from bovine raw milk in Korea

Staphylococcus aureus is a major etiological pathogen of bovine mastitis, which triggers significant economic losses in dairy herds worldwide. In this study, S. aureus strains isolated from the milk of cows suffering from mastitis in Korea were investigated by spa typing and staphylococcal enterotoxin (SE) gene profiling. Forty-four S. aureus strains were isolated from 26 farms in five provinces. All isolates grouped into five clusters and two singletons based on 14 spa types. Cluster 1 and 2 isolates comprised 38.6% and 36.4% of total isolates, respectively, which were distributed in more than four provinces. SE and SE-like toxin genes were detected in 34 (77.3%) isolates and the most frequently detected SE gene profile was seg, sei, selm, seln, and selo genes (16 isolates, 36.3%), which was comparable to one of the genomic islands, Type I nuSabeta. This is a first report of spa types and the prevalence of the recently described SE and SE-like toxin genes among S. aureus isolates from bovine raw milk in Korea. Two predominant spa groups were distributed widely and recently described SE and SE-like toxin genes were detected frequently.