Molecular epidemiology of multidrug-resistant , and outbreak among neonates in Tembisa hospital, South Africa.

Background: An outbreak of multidrug-resistant infections in a neonatal ward within a tertiary hospital in South Africa resulted in the mortality of 10 patients within six months. In this work, the genomic epidemiology of and the molecular factors mediating this outbreak were investigated.

Methods: Bacterial cultures obtained from clinical samples collected from the infected neonates underwent phenotypic and molecular analyses to determine their species, sensitivity to antibiotics, production of carbapenemases, complete resistance genes profile, clonality, epidemiology, and evolutionary relationships.

Molecular Screening of Clinical Multidrug-Resistant Gram-Negative Bacteria Shows Endemicity of Carbapenemases, Coexistence of Multiple Carbapenemases, and Rarity of in South Africa.

Extensive use of carbapenems to treat multidrug-resistant (MDR) Gram-negative bacteria (GNB) facilitates the wide dissemination of carbapenemase-producing carbapenem-resistant GNB. Colistin was reintroduced into clinical settings to manage these GNB infections. However, there is currently an increase in the dissemination of mobile colistin resistance (-producing colistin-resistant GNB isolates in clinical settings.

Global epidemiology, genetic environment, risk factors and therapeutic prospects of genes: A current and emerging update.

Background: Mobile colistin resistance () genes modify Lipid A molecules of the lipopolysaccharide, changing the overall charge of the outer membrane.

Results And Discussion: Ten genes have been described to date within eleven Enterobacteriaceae species, with , , and species being the most predominant. They are present worldwide in 72 countries, with animal specimens currently having the highest incidence, due to the use of colistin in poultry for promoting growth and treating intestinal infections.

Current and emerging polymyxin resistance diagnostics: A systematic review of established and novel detection methods.

The emergence of polymyxin resistance, due to transferable mcr genes, threatens public and animal health as there are limited therapeutic options. As polymyxin is one of the last-line antibiotics, there is a need to contain the spread of its resistance to conserve its efficacy. Herein, we describe current and emerging polymyxin resistance diagnostics to inform faster clinical diagnostic choices.

Emerging Transcriptional and Genomic Mechanisms Mediating Carbapenem and Polymyxin Resistance in : a Systematic Review of Current Reports.

The spread of carbapenem- and polymyxin-resistant poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. A systematic review of all studies published in PubMed database between 2015 to October 2020 was performed.

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

Carbapenem-resistant (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 (=6).

Emergence of in Extended-Spectrum-β-Lactamase-Producing Clinical in Pretoria, South Africa: Global Evolutionary Phylogenomics, Resistome, and Mobilome.

Extended-spectrum-β-lactamase (ESBL)-producing are critical-priority pathogens that cause substantial fatalities. With the emergence of mobile genes mediating resistance to colistin in , clinicians are now left with few therapeutic options. Eleven clinical strains with resistance to cephems and/or colistin were genomically analyzed to determine their resistomes, mobilomes, and evolutionary relationships to global strains.

Comparative Evaluation of CHROMagar COL-APSE, MicroScan Walkaway, ComASP Colistin, and Colistin MAC Test in Detecting Colistin-resistant Gram-Negative Bacteria.

Colistin has become a critical antibiotic for fatal Gram-negative infections owing to the proliferation of multidrug-resistant carbapenemase-producing bacteria. Thus, cheaper, faster, efficient and easier-to-use colistin diagnostics are required for clinical surveillance, diagnoses and therapeutics. The sensitivity, specificity, major error (ME), very major error (VME), categorial agreement, essential agreement, turnaround time (TAT), average cost, and required skill for four colistin resistance diagnostics viz.

Pathogenomics and Evolutionary Epidemiology of Multi-Drug Resistant Clinical Klebsiella pneumoniae Isolated from Pretoria, South Africa.

Antibiotic-resistant Klebsiella pneumoniae is increasingly being implicated in invasive infections worldwide with high mortalities. Forty-two multidrug resistant (MDR) K. pneumoniae isolates were collected over a 4-month period.

Publisher Correction: The Resistome, Mobilome, Virulome and Phylogenomics of Multidrug-Resistant Escherichia coli Clinical Isolates from Pretoria, South Africa.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A Comparative Evaluation of the New Genexpert MTB/RIF Ultra and other Rapid Diagnostic Assays for Detecting Tuberculosis in Pulmonary and Extra Pulmonary Specimens.

Studies evaluating the new GeneXpert Ultra with other rapid diagnostic assays are limited, particularly in different geographical settings. The performance of the GeneXpert Ultra, the GeneXpert G4, the Line probe assays (LPA) and auramine smear microscopy in detecting TB in pulmonary and extra-pulmonary samples were thus evaluated. Remnants (n = 205 samples) of pulmonary (n = 125 samples) and extra-pulmonary (n = 80 samples) specimens from TB suspects were prospectively collected.

The Resistome, Mobilome, Virulome and Phylogenomics of Multidrug-Resistant Escherichia coli Clinical Isolates from Pretoria, South Africa.

Antibiotic-resistant Escherichia coli is a common occurrence in food, clinical, community and environmental settings worldwide. The resistome, mobilome, virulome and phylogenomics of 20 multidrug resistant (MDR) clinical E. coli isolates collected in 2013 from Pretoria, South Africa, were characterised.

Genomic analysis of a multidrug-resistant clinical Providencia rettgeri (PR002) strain with the novel integron ln1483 and an A/C plasmid replicon.

Whole-genome sequence analysis was performed on a multidrug-resistant Providencia rettgeri PR002 clinical strain isolated from the urine of a hospitalized patient in Pretoria, South Africa, in 2013. The resistome, mobilome, pathogenicity island(s), as well as virulence and heavy-metal resistance genes of the isolate, were characterized using whole-genome sequencing and bioinformatic analysis. PR002 had a genome assembly size of 4,832,624 bp with a GC content of 40.

Plasmid evolution in carbapenemase-producing Enterobacteriaceae: a review.

Carbapenem-resistant Enterobacteriaceae (CRE) have been listed by the WHO as high-priority pathogens owing to their high association with mortalities and morbidities. Resistance to multiple β-lactams complicates effective clinical management of CRE infections. Using plasmid typing methods, a wide distribution of plasmid replicon groups has been reported in CREs around the world, including IncF, N, X, A/C, L/M, R, P, H, I, and W.

Phylogenomic and epidemiological insights into two clinical Mycobacterium bovis BCG strains circulating in South Africa.

Background: Mycobacterium bovis BCG is a live, attenuated tuberculosis vaccine. While the vaccine protects infants from tuberculosis, complications including disseminated infections have been reported following vaccination. Genetically diverse BCG sub-strains now exist following continuous passaging of the original Pasteur strain for vaccine manufacture.

Molecular characteristics and genotypic diversity of enterohaemorrhagic Escherichia coli O157:H7 isolates in Gauteng region, South Africa.

Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 is one of the major foodborne and waterborne pathogens causing severe diseases and outbreaks worldwide. There is scarcity of EHEC O157:H7 data in South Africa. This study was carried out to determine the molecular characteristics and genotypic diversity of EHEC O157:H7 isolates in the Gauteng region, South Africa.

Klebsiella pneumoniae ST307 with bla South Africa, 2014-2016.

Klebsiella pneumoniae sequence type (ST) 307 is an emerging global antimicrobial drug-resistant clone. We used whole-genome sequencing and PCR to characterize K. pneumoniae ST307 with oxacillinase (OXA) 181 carbapenemase across several private hospitals in South Africa during 2014-2016.

Trends in the Genetic Background of Methicillin-Resistant Clinical Isolates in a South African Hospital: An Institutional-Based Observational Study.

Background: This study sought to understand the epidemio-ecological dynamics of MRSA isolates associated with a South African hospital over a period spanning year 2007-8 (a previous study reported in 2009) and year 2010-11 (this study).

Methods: One hundred and ninety three isolates were characterised by molecular fingerprinting methods including pulsed field gel electrophoresis (PFGE), typing, -typing, SCC-typing, and multilocus sequence typing (MLST). The Vitek-2 automated antibiogram of representative isolates was also performed.

Comparison of line probe assay to BACTEC MGIT 960 system for susceptibility testing of first and second-line anti-tuberculosis drugs in a referral laboratory in South Africa.

Background: The incidence of multidrug-resistant tuberculosis (MDR-TB) is increasing and the emergence of extensively drug-resistant tuberculosis (XDR-TB) is a major challenge. Controlling resistance, reducing transmission and improving treatment outcomes in MDR/XDR-TB patients is reliant on susceptibility testing. Susceptibility testing using phenotypic methods is labour intensive and time-consuming.

First Report of a Whole-Genome Shotgun Sequence of a Clinical Sequence Type 6 Strain from South Africa.

is a lactic acid-producing Gram-positive bacterium commonly found in the intestinal tract of humans and animals; it is implicated in multidrug-resistant nosocomial infections. The draft genome of this sequence type 6 (ST6) strain consists of 3,215,228 bp, with 37.20% GC content, 3,048 predicted coding sequences, and 61 RNA genes.

Draft Genome Sequence of a Clinical Sequence Type 18 Strain from South Africa.

We report the first draft genome sequence of an sequence type 18 (ST18) strain isolated from a tuberculosis patient in Africa. The genome is comprised of 3,202,539 bp, 501 contigs, 37.70% GC content, 3,202 protein-encoding genes, and 61 RNA genes.