The molecular characterisation of methicillin-resistant Staphylococcus aureus from hospitals in Cape Town

Comprehensive molecular epidemiological data are prerequisite for establishing control over methicillin-resistant S. aureus (MRSA) in the hospital setting; however, there is currently a paucity of molecular epidemiological data available on MRSA from South Africa. A molecular characterisation of one hundred MRSA isolates collected between January 2007 and December 2008 from patients in five hospitals in Cape Town was carried out in this study

Genetic basis of rifampicin resistance in methicillin-resistant Staphylococcus aureus suggests clonal expansion in hospitals in Cape Town, South Africa

<p>Abstract</p> <p>Background</p> <p>Since 2001, several studies have reported high rifampicin resistance rates (45 - 100%) among methicillin-resistant <it>Staphylococcus aureus </it>(MRSA) isolates from South Africa. The authors previously characterised 100 MRSA isolates from hospitals in Cape Town, South Africa; forty-five percent of these isolates were rifampicin-resistant. The majority (44/45) corresponded to ST612-MRSA-IV, which is prevalent in South Africa, but has not been reported frequently elsewhere. The remaining rifampicin-resistant isolate corresponded to ST5-MRSA-I. The aim of this study was to investigate further the prevalence and genetic basis of rifampicin-resistance in MRSA isolates from hospitals in Cape Town.</p> <p>Results</p> <p>Between July 2007 and June 2011, the prevalence of rifampicin-resistant MRSA in hospitals in Cape Town ranged from 39.7% to 46.4%. Based on the results of the aforementioned study, nine ST612-MRSA-IV isolates, the rifampicin-resistant ST5-MRSA-I isolate, and two rifampicin-susceptible MRSA isolates were investigated. Four previously described ST612-MRSA-IV isolates, including two each from South Africa and Australia, were also included.</p> <p>The ST5-MRSA-I isolate carried a single mutational change, H₄₈₁Y, commonly associated with high-level rifampicin resistance. All ST612-MRSA-IV isolates carried an uncommon double amino acid substitution in RpoB, H₄₈₁N, I₅₂₇M, whilst one of the Australian ST612-MRSA-IV isolates carried an additional mutation within <it>rpoB</it>, representing a novel <it>rpoB </it>genotype: H₄₈₁N, I₅₂₇M, K₅₇₉R. All ST612-MRSA-IV isolates also shared a unique silent single nucleotide polymorphism (SNP) within <it>rpoB</it>.</p> <p>Conclusions</p> <p>That local ST612-MRSA-IV isolates described here share an uncommon <it>rpoB </it>genotype and a unique silent SNP suggests this clone may have undergone clonal expansion in hospitals in Cape Town. Further, the data suggest that these isolates may be related to rifampicin-resistant ST612-MRSA-IV previously described in South Africa and Australia.</p

Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure

Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonisation, disease, antimicrobial resistance, and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30,976 genomes and contextual data for carriage and disease pneumococci recovered between 1916-2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1,222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds, and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme, and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen. Impact statement Many thousands of pneumococcal genomes are available in the public domain, and this creates opportunities for the scientific community to re-use existing data; however, these data are most useful when the contextual data (provenance and phenotype) are also linked to the genomes. Therefore, we created a curated, open-access database in PubMLST that contained nearly 31,000 published pneumococcal genomes and the corresponding contextual data for each genome. This large and diverse pneumococcal database was used to create a novel cgMLST scheme and multilevel clustering method to define genetic lineages with high resolution and a standardised nomenclature. These are open-access resources for all to use and provide a unified framework for the characterisation of global pneumococcal populations

Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked DownloadUnderstanding the structure of a bacterial population is essential in order to understand bacterial evolution. Estimating the core genome (those genes common to all, or nearly all, strains of a species) is a key component of such analyses. The size and composition of the core genome varies by dataset, but we hypothesized that the variation between different collections of the same bacterial species would be minimal. To investigate this, we analyzed the genome sequences of 3,118 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (United States), and Maela (Thailand). The analyses revealed a "supercore" genome (genes shared by all 3,118 pneumococci) of 558 genes, although an additional 354 core genes were shared by pneumococci from Reykjavik, Southampton, and Boston. Overall, the size and composition of the core and pan-genomes among pneumococci recovered in Reykjavik, Southampton, and Boston were similar. Maela pneumococci were distinctly different in that they had a smaller core genome and larger pan-genome. The pan-genome of Maela pneumococci contained several >25 Kb sequence regions (flanked by pneumococcal genes) that were homologous to genomic regions found in other bacterial species. Overall, our work revealed that some subsets of the global pneumococcal population are highly heterogeneous, and our hypothesis was rejected. This is an important finding in terms of understanding genetic variation among pneumococci and is also an essential point of consideration before generalizing the findings from a single dataset to the wider pneumococcal population.Wellcome Trust Biomedical Research Fund award Wellcome Trust Research Fellowship University of Oxford John Fell Fund award Wellcome Trust Eimskipa University Fund GlaxoSmithKline Biologicals SA Landspitali University Hospital Research Fun

The global meningitis genome partnership.

Genomic surveillance of bacterial meningitis pathogens is essential for effective disease control globally, enabling identification of emerging and expanding strains and consequent public health interventions. While there has been a rise in the use of whole genome sequencing, this has been driven predominately by a subset of countries with adequate capacity and resources. Global capacity to participate in surveillance needs to be expanded, particularly in low and middle-income countries with high disease burdens. In light of this, the WHO-led collaboration, Defeating Meningitis by 2030 Global Roadmap, has called for the establishment of a Global Meningitis Genome Partnership that links resources for: N. meningitidis (Nm), S. pneumoniae (Sp), H. influenzae (Hi) and S. agalactiae (Sa) to improve worldwide co-ordination of strain identification and tracking. Existing platforms containing relevant genomes include: PubMLST: Nm (31,622), Sp (15,132), Hi (1935), Sa (9026); The Wellcome Sanger Institute: Nm (13,711), Sp (> 24,000), Sa (6200), Hi (1738); and BMGAP: Nm (8785), Hi (2030). A steering group is being established to coordinate the initiative and encourage high-quality data curation. Next steps include: developing guidelines on open-access sharing of genomic data; defining a core set of metadata; and facilitating development of user-friendly interfaces that represent publicly available data

Common variants at 12p11, 12q24, 9p21, 9q31.2 and in ZNF365 are associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers

Abstract Introduction Several common alleles have been shown to be associated with breast and/or ovarian cancer risk for BRCA1 and BRCA2 mutation carriers. Recent genome-wide association studies of breast cancer have identified eight additional breast cancer susceptibility loci: rs1011970 (9p21, CDKN2A/B), rs10995190 (ZNF365), rs704010 (ZMIZ1), rs2380205 (10p15), rs614367 (11q13), rs1292011 (12q24), rs10771399 (12p11 near PTHLH) and rs865686 (9q31.2). Methods To evaluate whether these single nucleotide polymorphisms (SNPs) are associated with breast cancer risk for BRCA1 and BRCA2 carriers, we genotyped these SNPs in 12,599 BRCA1 and 7,132 BRCA2 mutation carriers and analysed the associations with breast cancer risk within a retrospective likelihood framework. Results Only SNP rs10771399 near PTHLH was associated with breast cancer risk for BRCA1 mutation carriers (per-allele hazard ratio (HR) = 0.87, 95% CI: 0.81 to 0.94, P-trend = 3 &#215; 10-4). The association was restricted to mutations proven or predicted to lead to absence of protein expression (HR = 0.82, 95% CI: 0.74 to 0.90, P-trend = 3.1 &#215; 10-5, P-difference = 0.03). Four SNPs were associated with the risk of breast cancer for BRCA2 mutation carriers: rs10995190, P-trend = 0.015; rs1011970, P-trend = 0.048; rs865686, 2df-P = 0.007; rs1292011 2df-P = 0.03. rs10771399 (PTHLH) was predominantly associated with estrogen receptor (ER)-negative breast cancer for BRCA1 mutation carriers (HR = 0.81, 95% CI: 0.74 to 0.90, P-trend = 4 &#215; 10-5) and there was marginal evidence of association with ER-negative breast cancer for BRCA2 mutation carriers (HR = 0.78, 95% CI: 0.62 to 1.00, P-trend = 0.049). Conclusions The present findings, in combination with previously identified modifiers of risk, will ultimately lead to more accurate risk prediction and an improved understanding of the disease etiology in BRCA1 and BRCA2 mutation carriers

The genomic epidemiology of Campylobacter from the Republic of South Africa

As the leading cause of bacterial gastroenteritis, Campylobacter represents a significant public health burden; however, our knowledge of its epidemiology in low- and middle-income countries remains limited. Recent studies have demonstrated the power of whole-genome sequencing (WGS) for public health microbiology. The primary aim of this thesis was to exploit WGS to improve our understanding of the epidemiology of Campylobacter from the Republic of South Africa, a middle-income country. In the first half of this thesis, in silico approaches were developed to evaluate diagnostic assays and methods of species identification. Large-scale analyses of publicly available WGS data identified a robust real-time PCR assay for the detection of Campylobacter jejuni and Campylobacter coli, the primary causes of human campylobacteriosis. Evaluation of in silico speciation methods demonstrated that the atpA gene and ribosomal multilocus sequence typing can be used to identify Campylobacter from WGS data. The second half of this thesis extended concepts developed in the first half to investigate the epidemiology of Campylobacter from animals and humans from South Africa. Isolates from a study of Campylobacter from free-range broiler carcasses belonged to the agriculture-associated ST-828 lineage, but were atypically homogenous and differed at only 46/1,513 (3%) loci, providing novel insights into clonal infections in chickens. Analyses of human disease isolates collected in Cape Town in 1991, 2011, and 2012 confirmed that the local epidemiology of Campylobacter is distinct from that of high-income countries: in addition to major agriculture-associated C. jejuni and C. coli lineages, a putative novel C. jejuni subsp. jejuni/C. jejuni subsp. doylei hybrid clade and genetically diverse C. jejuni subsp. doylei and C. upsaliensis isolates were identified. This work delivers further evidence of the utility of WGS for clinical microbiology, presents approaches that address general problems in Campylobacter diagnostics and public health microbiology, and provides insights into the epidemiology of this important group of pathogens in South Africa.</p

The genomic epidemiology of Campylobacter from the Republic of South Africa

As the leading cause of bacterial gastroenteritis, Campylobacter represents a significant public health burden; however, our knowledge of its epidemiology in low- and middle-income countries remains limited. Recent studies have demonstrated the power of whole-genome sequencing (WGS) for public health microbiology. The primary aim of this thesis was to exploit WGS to improve our understanding of the epidemiology of Campylobacter from the Republic of South Africa, a middle-income country. In the first half of this thesis, in silico approaches were developed to evaluate diagnostic assays and methods of species identification. Large-scale analyses of publicly available WGS data identified a robust real-time PCR assay for the detection of Campylobacter jejuni and Campylobacter coli, the primary causes of human campylobacteriosis. Evaluation of in silico speciation methods demonstrated that the atpA gene and ribosomal multilocus sequence typing can be used to identify Campylobacter from WGS data. The second half of this thesis extended concepts developed in the first half to investigate the epidemiology of Campylobacter from animals and humans from South Africa. Isolates from a study of Campylobacter from free-range broiler carcasses belonged to the agriculture-associated ST-828 lineage, but were atypically homogenous and differed at only 46/1,513 (3%) loci, providing novel insights into clonal infections in chickens. Analyses of human disease isolates collected in Cape Town in 1991, 2011, and 2012 confirmed that the local epidemiology of Campylobacter is distinct from that of high-income countries: in addition to major agriculture-associated C. jejuni and C. coli lineages, a putative novel C. jejuni subsp. jejuni/C. jejuni subsp. doylei hybrid clade and genetically diverse C. jejuni subsp. doylei and C. upsaliensis isolates were identified. This work delivers further evidence of the utility of WGS for clinical microbiology, presents approaches that address general problems in Campylobacter diagnostics and public health microbiology, and provides insights into the epidemiology of this important group of pathogens in South Africa

The genomic epidemiology of Campylobacter from the Republic of South Africa

As the leading cause of bacterial gastroenteritis, Campylobacter represents a significant public health burden; however, our knowledge of its epidemiology in low- and middle-income countries remains limited. Recent studies have demonstrated the power of whole-genome sequencing (WGS) for public health microbiology. The primary aim of this thesis was to exploit WGS to improve our understanding of the epidemiology of Campylobacter from the Republic of South Africa, a middle-income country. In the first half of this thesis, in silico approaches were developed to evaluate diagnostic assays and methods of species identification. Large-scale analyses of publicly available WGS data identified a robust real-time PCR assay for the detection of Campylobacter jejuni and Campylobacter coli, the primary causes of human campylobacteriosis. Evaluation of in silico speciation methods demonstrated that the atpA gene and ribosomal multilocus sequence typing can be used to identify Campylobacter from WGS data. The second half of this thesis extended concepts developed in the first half to investigate the epidemiology of Campylobacter from animals and humans from South Africa. Isolates from a study of Campylobacter from free-range broiler carcasses belonged to the agriculture-associated ST-828 lineage, but were atypically homogenous and differed at only 46/1,513 (3%) loci, providing novel insights into clonal infections in chickens. Analyses of human disease isolates collected in Cape Town in 1991, 2011, and 2012 confirmed that the local epidemiology of Campylobacter is distinct from that of high-income countries: in addition to major agriculture-associated C. jejuni and C. coli lineages, a putative novel C. jejuni subsp. jejuni/C. jejuni subsp. doylei hybrid clade and genetically diverse C. jejuni subsp. doylei and C. upsaliensis isolates were identified. This work delivers further evidence of the utility of WGS for clinical microbiology, presents approaches that address general problems in Campylobacter diagnostics and public health microbiology, and provides insights into the epidemiology of this important group of pathogens in South Africa.</p

Genome Reduction for Niche Association in Campylobacter Hepaticus, A Cause of Spotty Liver Disease in Poultry

The term “spotty liver disease” (SLD) has been used since the late 1990s for a condition seen in the UK and Australia that primarily affects free range laying hens around peak lay, causing acute mortality and a fall in egg production. A novel thermophilic SLD-associated Campylobacter was reported in the United Kingdom (UK) in 2015. Subsequently, similar isolates occurring in Australia were formally described as a new species, Campylobacter hepaticus. We describe the comparative genomics of 10 C. hepaticus isolates recovered from 5 geographically distinct poultry holdings in the UK between 2010 and 2012. Hierarchical gene-by-gene analyses of the study isolates and representatives of 24 known Campylobacter species indicated that C. hepaticus is most closely related to the major pathogens Campylobacter jejuni and Campylobacter coli. We observed low levels of within-farm variation, even between isolates collected over almost 3 years. With respect to C. hepaticus genome features, we noted that the study isolates had a ~140 Kb reduction in genome size, ~144 fewer genes, and a lower GC content compared to C. jejuni. The most notable reduction was in the subsystem containing genes for iron acquisition and metabolism, supported by reduced growth of C. hepaticus in an iron depletion assay. Genome reduction is common among many pathogens and in C. hepaticus has likely been driven at least in part by specialization following the occupation of a new niche, the chicken liver