Plasmid evolution in carbapenemase‐producing Enterobacteriaceae : a review

Please read abstract in the article.Table S1. Metadata of plasmids deposited at GenBank and included in this study.Supplementary dataset. Nucleotide sequences of plasmids included in this study and obtained from Genbank.https://nyaspubs.onlinelibrary.wiley.com/journal/174966322020-12-01hj2019Medical Microbiolog

Symbiotic performance and characterization of Pigeonpea (Cajanus cajan L. Millsp.) Rhizobia occurring in South African soils

Pigeonpea (Cajanus cajan (L.) Millsp.) is an important grain legume, which, like several other legumes, depends on the process of biological nitrogen fixation for its nitrogen (N2 ) requirement by forming a symbiotic association with rhizobia. Compared to other tropical legumes, however, the productivity of pigeonpea in South Africa is low, despite the extensive interests in developing it for wider markets. To assist this process, the objectives of the current study were to (i) characterize putative indigenous rhizobial strains that were previously derived from local soils with no previous history of legume cultivation and (ii) confirm their nodulation abilities on a local landrace and a genetically improved (exotic) genotype of pigeonpea. DNA-based analyses using the 16S rRNA and recA genes showed that the strains predominantly represented Rhizobium and Bradyrhizobium, although we also recovered Phyllobacterium and Paraburkholderia. These rhizobia nodulated both the local landrace and the improved pigeonpea genotype that were included for comparative purposes. In many cases, rhizobia performed similarly on the two genotypes, although the locally sourced landrace mostly performed better in terms of nodulation and plant biomass. While the current study generated vital information regarding the diversity of indigenous rhizobia associating with pigeonpea, further screening (including field inoculation trials) would be necessary to identify possible elite nitrogen-fixing rhizobial strains for development as inoculants to enhance South African pigeonpea production.The University of Venda Research and Publications Committee.The University of Venda Research and Publications CommitteeBiochemistryGenetic

Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains

Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP in South Africa and globally were characterized. CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex PCR, genotyping by repetitive element palindromic (REP)-PCR, plasmid size, number, incompatibility and mobility analyses, and PacBio’s SMRT sequencing (n=6). There were 56 multidrug-resistant CRKP, having blaOXA-48-like and blaNDM-1/7 carbapenemases on self-transmissible IncF, A/C, IncL/M and IncX3 plasmids endowed with prophages, traT, resistance islands, and type I and II restriction modification systems (RMS). Plasmids and clades detected in this study were respectively related to globally established/ disseminated plasmids clades/clones, evincing transboundary horizontal and vertical dissemination. Reduced susceptibility to colistin occurred in 23 strains. Common clones included ST307, ST607, ST17, ST39 and ST3559. IncFIIk virulent plasmid replicon was present in 56 strains. Whole-genome sequencing of six strains revealed least 41 virulence genes, extensive ompK36 mutations, and four different K- and O-loci types: KL2, KL25, KL27, KL102, O1, O2, O4 and O5. Types I, II and III RMS, conferring m6A (GATC, GATGNNNNNNTTG, CAANNNNNNCATC motifs) and m4C (CCWGG) modifications on chromosomes and plasmids, were found. The nature of plasmid-mediated, clonal and multi-clonal dissemination of blaOXA-48-like and blaNDM-1 mirrors epidemiological trends observed for closely related plasmids and sequence types internationally. Worryingly, the presence of both blaOXA-48 and blaNDM-1 in the same isolates was observed. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity and resistance, threatening infection treatment. The influence of RMS on antimicrobial and bacteriophage therapy needs urgent investigation.The NHLS, NRF (National Research Foundation) and the University of Pretoria.https://www.microbiologyresearch.org/content/journal/mgenMedical Microbiolog

Outbreak and control of Achromobacter denitrificans at an academic hospital in Pretoria, South Africa

OBJECTIVE : In this study, we sought to determine the source of an outbreak of Achromobacter denitrificans infections in patients at a tertiary-care academic hospital. DESIGN : Outbreak report study with intervention. The study period extended from February 2018 to December 2018. SETTING : The study was conducted at a tertiary-care academic hospital in Pretoria, South Africa. PATIENTS AND PARTICIPANTS : All patients who cultured A. denitrificans from any site were included in this study. During the study period, 43 patients met this criterion. INTERVENTIONS :Once an outbreak was confirmed, the microbiology laboratory compiled a list of affected patients. A common agent, chlorhexidine-and-water solution, was used as a disinfectant–antiseptic for all affected patients. The laboratory proceeded to culture this solution. Environmental and surface swabs were also cultured from the hospital pharmacy area where this solution was prepared. Repetitive-element, sequence-based, polymerase chain reaction (rep-PCR) was performed on the initial clinical isolates to confirm the relatedness of the isolates. RESULTS : In total, 43 isolates of A. denitrificans were cultured from patient specimens during the outbreak. The laboratory cultured A. denitrificans from all bottles of chlorhexidine-and-water solutions sampled from the wards and the pharmacy. The culture of the dispenser device used to prepare this solution also grew A. denitrificans. The rep-PCR confirmed the clonality of the clinical isolates with 2 genotypes dominating. CONCLUSIONS : Contaminated chlorhexidine-and-water solutions prepared at the hospital pharmacy was determined to be the source of the outbreak. Once this item was removed from the hospital, the laboratory did not culture any further A. denitrificans isolates from patient specimens.http://journals.cambridge.org/ICE2023-07-01hj2023Medical Microbiolog

Symbiotic Performance and Characterization of Pigeonpea (<i>Cajanus cajan</i> L. Millsp.) Rhizobia Occurring in South African Soils

Pigeonpea (Cajanus cajan (L.) Millsp.) is an important grain legume, which, like several other legumes, depends on the process of biological nitrogen fixation for its nitrogen (N2) requirement by forming a symbiotic association with rhizobia. Compared to other tropical legumes, however, the productivity of pigeonpea in South Africa is low, despite the extensive interests in developing it for wider markets. To assist this process, the objectives of the current study were to (i) characterize putative indigenous rhizobial strains that were previously derived from local soils with no previous history of legume cultivation and (ii) confirm their nodulation abilities on a local landrace and a genetically improved (exotic) genotype of pigeonpea. DNA-based analyses using the 16S rRNA and recA genes showed that the strains predominantly represented Rhizobium and Bradyrhizobium, although we also recovered Phyllobacterium and Paraburkholderia. These rhizobia nodulated both the local landrace and the improved pigeonpea genotype that were included for comparative purposes. In many cases, rhizobia performed similarly on the two genotypes, although the locally sourced landrace mostly performed better in terms of nodulation and plant biomass. While the current study generated vital information regarding the diversity of indigenous rhizobia associating with pigeonpea, further screening (including field inoculation trials) would be necessary to identify possible elite nitrogen fixing rhizobial strains for development as inoculants to enhance South African pigeonpea production