scholarly journals Comparative Pathogenomics of Aeromonas veronii from Pigs in South Africa: Dominance of the Novel ST657 Clone

2020 ◽  
Vol 8 (12) ◽  
pp. 2008
Author(s):  
Yogandree Ramsamy ◽  
Koleka P. Mlisana ◽  
Daniel G. Amoako ◽  
Akebe Luther King Abia ◽  
Mushal Allam ◽  
...  
Keyword(s):  
South Africa ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Illumina Miseq ◽  
Aeromonas Veronii ◽  
Carbapenem Resistant ◽  
Kwazulu Natal ◽  
Miseq Platform ◽  
Differential Ability ◽  
Potential Pathogenicity

The pathogenomics of carbapenem-resistant Aeromonas veronii (A. veronii) isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The pan-genome analysis showed that the isolates formed a total of 4349 orthologous gene clusters, 4296 of which were shared; no unique clusters were observed. All the isolates had similar resistance phenotypes, which corroborated their chromosomally mediated resistome (blaCPHA3 and blaOXA-12) and belonged to a novel sequence type, ST657 (a satellite clone). Isolates in the same sub-clades clustered according to their clonal lineages and host. Mobilome analysis revealed the presence of chromosome-borne insertion sequence families. The estimated pathogenicity score (Pscore ≈ 0.60) indicated their potential pathogenicity in humans. Furthermore, these isolates carried several virulence factors (adherence factors, toxins, and immune evasion), in different permutations and combinations, indicating a differential ability to establish infection. Phylogenomic and metadata analyses revealed a predilection for water environments and aquatic animals, with more recent reports in humans and food animals across geographies, making A. veronii a potential One Health indicator bacterium.

scholarly journals Pathogenomic Analysis of a Novel Extensively Drug-Resistant Citrobacter freundii Isolate Carrying a blaNDM-1 Carbapenemase in South Africa

Pathogens ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 89 ◽  
Author(s):  
Yogandree Ramsamy ◽  
Koleka P. Mlisana ◽  
Daniel G. Amoako ◽  
Mushal Allam ◽  
Arshad Ismail ◽  
...  
Keyword(s):  
South Africa ◽  
Acquired Resistance ◽  
Carbapenem Resistance ◽  
Illumina Miseq ◽  
Tertiary Hospital ◽  
Phylogenomic Analysis ◽  
Citrobacter Freundii ◽  
Class 1 Integron ◽  
Pathogenic Potential ◽  
Carbapenem Resistant

Pathogenomic analysis was performed on a novel carbapenem-resistant Citrobacter freundii isolate (H2730R) from a rectal swab of an adult male patient admitted to a tertiary hospital, Durban, South Africa. H2730R was identified using selective media and API 20e kit. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK II. H2730R was whole-genome sequenced on the Illumina MiSeq platform. H2730R was resistant to all tested antibiotics except tigecycline and was defined as ST498 by the C. freundii multilocus sequence typing (MLST) database. The estimated pathogenic potential predicted a higher probability (Pscore ≈ 0.875), supporting H2730R as a human pathogen. H2730R harbored 25 putative acquired resistance genes, 4 plasmid replicons, 4 intact prophages, a class 1 integron (IntI1), 2 predominant insertion sequences (IS3 and IS5), numerous efflux genes, and virulome. BLASTn analysis of the blaNDM-1 encoding contig (00022) and its flanking sequences revealed the blaNDM-1 was located on a plasmid similar to the multireplicon p18-43_01 plasmid reported for the spread of carbapenem resistance in South Africa. Phylogenomic analysis showed clustering of H2730R with CF003/CF004 strains in the same clade, suggesting a possible association between C. freundii strains/clones. Acquiring the p18-43_01 plasmid containing blaNDM-1, the diversity, and complex resistome, virulome, and mobilome of this pathogen makes its incidence very worrying regarding mobilized resistance. This study presents the background genomic information for future surveillance and tracking of the spread of carbapenem-resistant Enterobacteriaceae in South Africa.

scholarly journals Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1260
Author(s):  
Milton T. Mogotsi ◽  
Peter N. Mwangi ◽  
Phillip A. Bester ◽  
M. Jeffrey Mphahlele ◽  
Mapaseka L. Seheri ◽  
...  
Keyword(s):  
South Africa ◽  
Genomic Analysis ◽  
Illumina Miseq ◽  
Viral Population ◽  
Early Developmental Stage ◽  
Health State ◽  
North West ◽  
Viral Shedding ◽  
Healthy Infants ◽  
Miseq Platform

Establishing a diverse gut microbiota after birth is essential for preventing illnesses later in life. However, little knowledge exists about the total viral population (virome) present in the gut of infants during the early developmental stage, with RNA viruses being generally overlooked. Therefore, this small pilot longitudinal study investigated the diversity and changes in the enteric RNA virome in healthy infants from South Africa. Faecal samples (n = 12) were collected from four infants at three time points (on average at 8, 13, and 25 weeks), and then sequenced on an Illumina MiSeq platform. The genomic analysis revealed a diverse population of human enteric viruses from the infants’ stools, and changes in the enteric virome composition were observed over time. The Reoviridae family, more specifically the Rotavirus genus, was the most common and could be linked to viral shedding due to the administration of live-attenuated oral vaccines in South Africa, followed by the Picornaviridae family including parechoviruses, echoviruses, coxsackieviruses, enteroviruses, and polioviruses. Polioviruses were also linked to vaccine-related shedding. Astroviridae (astroviruses) and Caliciviridae (noroviruses) were present at low abundance. It is evident that an infant’s gut is colonized by distinct viral populations irrespective of their health state. Further characterization of the human virome (with a larger participant pool) is imperative to provide more conclusive insights into the viral community structure and diversity that has been shown in the current study, despite the smaller sample size.

scholarly journals Diversity of carbapenem-resistant Klebsiella pneumoniae ST14 and emergence of a subgroup with KL64 capsular locus in the Arabian Peninsula

2021 ◽  
Author(s):  
Shaimaa F. Mouftah ◽  
Tibor Pál ◽  
Paul G. Higgins ◽  
Akela Ghazawi ◽  
Youssef Idaghdour ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Klebsiella Pneumoniae ◽  
United Arab Emirates ◽  
Core Genome ◽  
Arabian Peninsula ◽  
Illumina Miseq ◽  
Carbapenem Resistant ◽  
Distinct Cluster ◽  
Recent Emergence ◽  
Miseq Platform

AbstractTo understand the reasons of successful spread of carbapenem-resistant Klebsiella pneumoniae ST14 (CRKP-ST14) in countries of the Arabian Peninsula, the resistome, capsular locus, carbapenemase carrying plasmid types, and core genome of isolates from the region were compared to global isolates. Thirty-nine CRKP-ST14 strains isolated from 13 hospitals in the United Arab Emirates, Bahrain, and Saudi Arabia were selected for whole genome sequencing on Illumina MiSeq platform based on the variety of carbapenemase genes carried and plasmids bearing these genes. Their resistome, capsular locus, and core genome MLST were compared to 173 CRKP-ST14 genomes available in public databases. The selected 39 CRKP-ST14 produced either NDM-1, OXA-48, OXA-162, OXA-232, KPC-2, or co-produced NDM-1 and an OXA-48-like carbapenemase. cgMLST revealed three clusters: 16 isolates from five UAE cities (C1), 11 isolates from three UAE cities and Bahrain (C2), and 5 isolates from Saudi Arabia (C3), respectively, and seven singletons. Resistance gene profile, carbapenemase genes, and their plasmid types were variable in both C1 and C2 clusters. The majority of CRKP-ST14 had KL2, but members of the C2 cluster and two further singletons possessed KL64 capsular locus. Based on cgMLST comparison of regional and global isolates, CRKP-ST14 with KL64 from four continents formed a distinct cluster, suggesting a recent emergence and spread of this variant. Our findings confirmed clonal transmission coupled with likely horizontal gene transfer in carbapenem-resistant Klebsiella pneumoniae ST14. Dissemination of this genetically flexible, highly resistant clone warrants further monitoring.

scholarly journals Genome Sequence of Listeria innocua Strain MEZLIS26, Isolated from a Goat in South Africa

2019 ◽  
Vol 8 (44) ◽  
Author(s):  
Mohamed E. El Zowalaty ◽  
Rachel A. Hickman ◽  
Alexandra Moura ◽  
Marc Lecuit ◽  
Oliver T. Zishiri ◽  
...  
Keyword(s):  
South Africa ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Listeria Innocua ◽  
Eastern Cape ◽  
Content Type ◽  
Transfer Rnas ◽  
Miseq Platform

Here, we report the draft genome sequence of Listeria innocua strain MEZLIS26, isolated from a healthy goat in Flagstaff, Eastern Cape Province, South Africa. The genome was sequenced using the Illumina MiSeq platform and had a length of 2,800,777 bp, with a G+C content of 37.4%, 2,755 coding DNA sequences (CDSs), 49 transfer RNAs (tRNAs), and 4 noncoding RNAs (ncRNAs).

Adverse Events Reporting System as Experienced by Critical-Care Nurses in KwaZulu-Natal, South Africa

2018 ◽  
Vol 20 (1) ◽  
Author(s):  
Thusile Mabel Gqaleni ◽  
Busisiwe Rosemary Bhengu
Keyword(s):  
South Africa ◽  
Critical Care ◽  
Adverse Events ◽  
Patient Care ◽  
Family Involvement ◽  
Reporting System ◽  
Legal Framework ◽  
Critical Care Nurses ◽  
Kwazulu Natal ◽  
Life Threatening

Critically ill patients admitted to critical-care units (CCUs) might have life-threatening or potentially life-threatening problems. Adverse events (AEs) occur frequently in CCUs, resulting in compromised quality of patient care. This study explores the experiences of critical-care nurses (CCNs) in relation to how the reported AEs were analysed and handled in CCUs. The study was conducted in the CCUs of five purposively selected hospitals in KwaZulu-Natal, South Africa. A descriptive qualitative design was used to obtain data through in-depth interviews from a purposive sample of five unit managers working in the CCUs to provide a deeper meaning of their experiences. This study was a part of a bigger study using a mixed-methods approach. The recorded qualitative data were analysed using Tesch’s content analysis. The main categories of information that emerged during the data analysis were (i) the existence of an AE reporting system, (ii) the occurrence of AEs, (iii) the promotion of and barriers to AE reporting, and (iv) the handling of AEs. The findings demonstrated that there were major gaps that affected the maximum utilisation of the reporting system. In addition, even though the system existed in other institutions, it was not utilised at all, hence affecting quality patient care. The following are recommended: (1) a non-punitive and non-confrontational system should be promoted, and (2) an organisational culture should be encouraged where support structures are formed within institutions, which consist of a legal framework, patient and family involvement, effective AE feedback, and education and training of staff.

CHALLENGES TO BUILDING AUTHENTIC PARTNERSHIPS: LESSONS FROM BHAMBAYI, KWAZULU-NATAL, SOUTH AFRICA

2017 ◽  
Vol 26 (2) ◽  
pp. 124-140 ◽  
Author(s):  
Tanusha Raniga ◽  
Barbara Simpson ◽  
Ntokozo Mthembu
Keyword(s):  
South Africa ◽  
Social Services ◽  
Service Providers ◽  
Informal Settlement ◽  
Mutual Trust ◽  
Open Communication ◽  
Community Based ◽  
Individual Interviews ◽  
Kwazulu Natal ◽  
Qualitative Phase

In contemporary South Africa, partnerships between service providers in government, non-governmental organisations, the private sector and community based organisations have been identified as a means to strengthen communities and the sustainability of social services. However, the unequal power relations that exists between and within these organisations often leads to fragmentation, duplication, and lack of coordination of social services. Using Fowler’s (1998) conceptualisation of authentic partnerships, this qualitative phase of a larger study explored the challenges of building authentic partnerships in Bhambayi, a predominantly informal settlement in KwaZulu-Natal, South Africa. Individual interviews and a focus group held with nine service providers revealed that intraorganisational challenges, cross-boundary and inter-organisational relations as well as political influences were obstacles to the development of authentic partnerships. The article suggests that open communication, clarity of roles and mutual trust between service providers is vital.

Transforming the Rural Agricultural Landscape Through Groundwater Optimisation: Exploring A Chinese-South African Partnership

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Nirmala Dorasamy ◽  
Olayemi Bakre
Keyword(s):  
South Africa ◽  
South African ◽  
Agricultural Landscape ◽  
Agricultural Practices ◽  
Subsistence Farming ◽  
Water Shortages ◽  
Subsistence Farmers ◽  
Farming Communities ◽  
Standards Of Living ◽  
Kwazulu Natal

The majority of the South African rural populace is directly or indirectly engaged in agricultural practices to earn a livelihood. However, impediments such as climate change, water shortages, and inadequacy of institutional support have undermined these once thriving subsistence farming communities. Furthermore, poor leadership in hydrology, coupled with a lack of depth in skills at all government levels to facilitate the understanding of the importance of groundwater, has made it near impossible for subsistence farmers to benefit optimally from groundwater. The 2012 drought experienced in South Africa paralysed several subsistence farming communities in KwaZulu-Natal. To revamp subsistence farming and assist these farmers across South Africa, the Department of Water and Sanitation launched interventions, but despite the enormous resources expended, indicators (e.g. unsustainable farming practices, poor crop yield, pitiable living conditions, and poor standards of living) provide evidence that these interventions have not yielded the desired results. This paper seeks to suggest practicable interventions aimed at reducing the vulnerability of subsistence farmers in KwaZulu-Natal. The study pursued a qualitative approach in that it solicited the views of experts on groundwater and in related fields to gain an in-depth perspective. Some of the core challenges undermining the sustainability and growth of subsistence farming in the study area were found to be the inadequacy of experts on groundwater, water shortages, institutional deficiencies, lack of political will, and lack of coordination among stakeholders. Pragmatic recommendations are made to address these challenges, among other things to encourage a South African-Chinese partnership in the hydrology sector.

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