Project description:Salmonella genomic island 1 (SGI1) and variants (SGI1-I and the new variant SGI1-O) were mapped in five strains of Proteus mirabilis isolated from humans and food in China. Sequencing showed that SGI1 and variants were integrated at the 3' end of the chromosomal thdF gene as previously described for Salmonella strains.

| S-EPMC2223879 | biostudies-literature

SGI1-K, a variant of the SGI1 genomic island carrying a mercury resistance region, in Salmonella enterica serovar Kentucky.

Project description:A multiple-antibiotic-resistant Salmonella enterica serovar Kentucky strain was found to contain SGI1-K, a variant form of the Salmonella genomic island 1 (SGI1) with an In4-type class 1 integron that contains only one cassette array, aacCA5-aadA7, and an adjacent mercury resistance module. Part of the 3'-conserved segment (3'-CS) of the integron, together with the inverted short segment from the right-hand end of the integron transposition module normally found between the 3'-CS and IS6100 in In4 family integrons, has been removed by an IS6100-mediated deletion. IRt, the right-hand inverted repeat found at the outer end of the integron, abuts a mercury resistance region instead of the usual SGI1 backbone segment. The mer module is a hybrid of those found in Tn501 and Tn21. This mer region and a further uncharacterized segment of at least 10 kb appear to have been incorporated between IRt and the SGI1 backbone. These findings demonstrate that the multidrug resistance region in SGI1 can incorporate new DNA segments in the same way as multiple antibiotic resistance regions in plasmids.

| S-EPMC1797678 | biostudies-literature

Emergence of Extensively Drug-Resistant Proteus mirabilis Harboring a Conjugative NDM-1 Plasmid and a Novel Salmonella Genomic Island 1 Variant, SGI1-Z.

Project description:Acquisition of blaNDM-1 in bacterial species, such as Proteus mirabilis that is intrinsically resistant to tetracycline, tigecycline and colistin, will make clinical treatment extremely difficult. Here, we characterized an NDM-1-producing clinical isolate of P. mirabilis (PM58) that displayed an extensively drug-resistant (XDR) phenotype, susceptible only to aztreonam. Molecular analysis revealed that PM58 harbored both a conjugative NDM-1 plasmid and a novel Salmonella genomic island 1 variant on chromosome.

| S-EPMC4576069 | biostudies-literature

Salmonella genomic island 1 variant SGI1-L

Project description:Salmonella genomic island 1 variant SGI1-L of Morganella morganii subsp morganii strain LIM90

| PRJEB15529 | ENA

Emergence of Neoteric Serotypes Among Multidrug Resistant Strains of Streptococcus pneumoniae Prevalent in Egypt.

Project description:BackgroundStreptococcus pneumoniae is still one of the major causes of morbidity and mortality worldwide. The prevalent serotype distribution had shown variation along different studies conducted at different time intervals. In order to efficiently assess the epidemiology of the diseases for effective preventive and treatment strategies, serotype prevalence need to be periodically reassessed.ObjectivesConducting a reassessment of the prevalent S. pneumoniae serotypes in Egypt as an essential step in the search for a regional vaccine. In addition, monitoring the antibiotic susceptibility patterns of pneumococcal strains currently causing infections as an evaluation of therapeutic strategies applied.Materials and methodsA total of 100 specimens of different sources were collected in Cairo, Egypt, from 2011 to 2013, representing almost all different types of diseases caused by S. pneumoniae such as meningitis, pneumonia, otitis media and sinusitis. Conventional and molecular identification methods were performed, the antimicrobial susceptibility patterns were assessed and serotyping was done using PCR assays to identify the most prevalent types. In addition, detection of certain virulence genes for the most prevalent serotypes was carried out.ResultsOur results revealed that in Egypt, currently, the most prevalent serotypes were serogroup 6 and serotype 19F as they represented 58% of all isolates. High rates of resistance were found to different antibiotic classes. The lytA and psaA genes were found to be more sensitive for S. pneumoniae identification than ply.ConclusionsOur study illustrates the importance of constantly monitoring the prevalent serotypes in any region in order to aid in the development of more effective vaccines.

| S-EPMC4902850 | biostudies-literature

Emergence of Multidrug Resistant Hypervirulent ST23 Klebsiella pneumoniae: Multidrug Resistant Plasmid Acquisition Drives Evolution.

Project description:BackgroundIn recent years, the emergence of multidrug resistant hypervirulent K. pneumoniae (MDR hvKp) isolates poses severe therapeutic challenge to global public health. The present study used the complete genome sequence of two MDR hvKp isolates belonging to ST23 to characterize the phylogenetic background and plasmid diversity.MethodsTwo hvKp isolates from patients with bacteremia were sequenced using Ion Torrent PGM and Oxford Nanopore MinION platforms and assembled by hybrid genome assembly approach. Comparative genomics approaches were used to investigate the population structure, evolution, virulence, and antimicrobial resistance of MDR hvKp strains.ResultsThe study isolates exhibited typical features of hvKp phenotypes associated with ST23. The convergence of multidrug resistance and hypervirulence were attributed by the presence of multiple plasmids including a 216 kb virulence plasmid and MDR plasmids belonging to IncA/C2, IncFIB, IncX3, and ColKP3 groups. The insertion of catA1 gene into virulence plasmid was observed along with genetic factors such as aerobactin, salmochelin, and rmpA2 that confer hvKp's hypervirulent phenotype. The core genome single nucleotide polymorphism (SNP) phylogenetic analyses of the isolates showed the evolution of ST23 hvKp was predominantly driven by ICEKp acquisitions.ConclusionTo the best of our knowledge, this is the first report of MDR hvKp isolates of ST23 with insertion of catA1 gene into the virulence plasmid which presents the possibility of hotspot integration sites on the plasmids to aid acquisition of AMR genes. ST23 is no longer confined to susceptible strains of hvKp. Our findings emphasize the need for more studies on recombinant events, plasmid transmission dynamics and evolutionary process involving hvKp.

| S-EPMC7718023 | biostudies-literature

Polyclonal Multidrug ESBL-Producing Klebsiella pneumoniae and Emergence of Susceptible Hypervirulent Klebsiella pneumoniae ST23 Isolates in Mozambique.

Project description:Globally, antibiotic-resistant Klebsiella spp. cause healthcare-associated infections with high mortality rates, and the rise of hypervirulent Klebsiella pneumoniae (hvKp) poses a significant threat to human health linked to community-acquired infections and increasing non-susceptibility. We investigated the phenotypic and genetic features of 36 Klebsiella isolates recovered from invasive infections at Hospital Central of Maputo in Mozambique during one year. The majority of the isolates displayed multidrug resistance (MDR) (29/36) to cephalosporins, gentamicin, ciprofloxacin, and trimethoprim-sulfamethoxazole but retained susceptibility to amikacin, carbapenems, and colistin. Most isolates were ESBLs-producing (28/36), predominantly carrying the blaCTX-M-15 and other beta-lactamase genes (blaSHV, blaTEM-1, and blaOXA-1). Among the 16 genomes sequenced, multiple resistance genes from different antibiotic classes were identified, with blaCTX-M-15, mostly in the ISEcp1-blaCTX-M-15-orf477 genetic environment, co-existing with blaTEM-1 and aac(3)-IIa in five isolates. Our results highlight the presence of polyclonal MDR ESBL-producing K. pneumoniae from eight sequence types (ST), mostly harbouring distinct yersiniabactin within the conjugative integrative element (ICE). Further, we identified susceptible hvKp ST23, O1-K1-type isolates carrying yersiniabactin (ybt1/ICEKp10), colibactin, salmochelin, aerobactin, and hypermucoid locus (rmpADC), associated with severe infections in humans. These findings are worrying and underline the importance of implementing surveillance strategies to avoid the risk of the emergence of the most threatening MDR hvKp.

| S-EPMC10525843 | biostudies-literature

SGI2, a relative of Salmonella genomic island SGI1 with an independent origin.

Project description:Multiply antibiotic-resistant Salmonella enterica serovar Emek strains isolated in Australia and the United Kingdom had similar features, suggesting that they all belong to a single clone. These strains all contain SGI2 (formerly SGI1-J), an independently formed relative of Salmonella genomic island SGI1. In SGI2, the complex class 1 integron which includes all of the resistance genes is not located between tnpR (S027) and S044 as in SGI1 and SGI1 variants. Instead, tnpR was found to be adjacent to S044, and the integron is located 6.9 kb away, within S023. In both SGI1 and SGI2, the 25-bp inverted repeats that mark the outer ends of class 1 integrons are flanked by a 5-bp duplication of the target, indicating that incorporation of the integron was by transposition. A small number of differences between the sequences of the backbones of SGI1 and SGI2 were also found. Hence, a class 1 integron has entered two different variants of the SGI backbone to generate two distinct lineages. Despite this, the integron in SGI2 has a complex structure that is very similar to that of In104 in SGI1. Differences are in the cassette arrays and in the gene which encodes the chloramphenicol and florfenicol efflux protein. The CmlA9 protein, encoded by InEmek, is only 92.8% identical to FloRc (also a CmlA family protein) from SGI1. A variant form of SGI2, SGI2-A, which has lost the tet(G) and cmlA9 resistance determinants, was found in one strain.

| S-EPMC2443934 | biostudies-literature

Biochemical Characterization of VIM-39, a VIM-1-Like Metallo-β-Lactamase Variant from a Multidrug-Resistant Klebsiella pneumoniae Isolate from Greece.

Project description:VIM-39, a VIM-1-like metallo-β-lactamase variant (VIM-1 Thr33Ala His224Leu) was identified in a clinical isolate of Klebsiella pneumoniae belonging to sequence type 147. VIM-39 hydrolyzed ampicillin, cephalothin, and imipenem more efficiently than did VIM-1 and VIM-26 (a VIM-1 variant with the His224Leu substitution) because of higher turnover rates.

| S-EPMC4649142 | biostudies-literature