Phylogenetic exploration of nosocomial transmission chains of 2009 influenza A/H1N1 among children admitted at Red Cross War Memorial Children's Hospital, Cape Town, South Africa in 2011

Traditional modes of investigating influenza nosocomial transmission have entailed a combination of confirmatory molecular diagnostic testing and epidemiological investigation. Common hospital-acquired infections like influenza require a discerning ability to distinguish between viral isolates to accurately identify patient transmission chains. We assessed whether influenza hemagglutinin sequence phylogenies can be used to enrich epidemiological data when investigating the extent of nosocomial transmission over a four-month period within a paediatric Hospital in Cape Town South Africa. Possible transmission chains/channels were initially determined through basic patient admission data combined with Maximum likelihood and time-scaled Bayesian phylogenetic analyses. These analyses suggested that most instances of potential hospital-acquired infections resulted from multiple introductions of Influenza A into the hospital, which included instances where virus hemagglutinin sequences were identical between different patients. Furthermore, a general inability to establish epidemiological transmission linkage of patients/viral isolates implied that identified isolates could have originated from asymptomatic hospital patients, visitors or hospital staff. In contrast, a traditional epidemiological investigation that used no viral phylogenetic analyses, based on patient co-admission into specific wards during a particular time-frame, suggested that multiple hospital acquired infection instances may have stemmed from a limited number of identifiable index viral isolates/patients. This traditional epidemiological analysis by itself could incorrectly suggest linkage between unrelated cases, underestimate the number of unique infections and may overlook the possible diffuse nature of hospital transmission, which was suggested by sequencing data to be caused by multiple unique introductions of influenza A isolates into individual hospital wards. We have demonstrated a functional role for viral sequence data in nosocomial transmission investigation through its ability to enrich traditional, non-molecular observational epidemiological investigation by teasing out possible transmission pathways and working toward more accurately enumerating the number of possible transmission events

Outbreak of multi-drug resistant Pseudomonas aeruginosa bloodstream infection in the haematology unit of a South African academic hospital

Objective: To describe an outbreak of multi-resistant Pseudomonas aeruginosa bloodstream infections (MRPA-BSI) that occurred in the haematology ward of a tertiary academic hospital in Cape Town, South Africa, and determine risk factors for acquisition of MRPA-BSI. METHODS: The outbreak investigation included a search for additional cases, review of patient records, environmental and staff screening, molecular typing using pulsed-field gel electrophoresis (PFGE) and Multi-locus sequencing (MLST) and a retrospective case-control study. RESULTS: Ten MRPA-BSI cases occurred in the haematology ward between January 2010 and January 2011. The case fatality rate was 80%. Staff screening specimens were negative for MRPA and an environmental source was not identified. PFGE showed that 9/10 isolates were related. MLST showed that 3 of these 9 isolates belonged to Sequence type (ST) 233 while the unrelated isolate belonged to ST260. CONCLUSION: We have described an outbreak of MRPA-BSI occurring over an extended period of time among neutropenic haematology patients. Molecular typing confirms that the outbreak was predominantly due to a single strain. The source of the outbreak was not identified, but the outbreak appears to have been controlled following intensive infection control measures

Persistent Chlamydia trachomatis, Neisseria gonorrhoeae or Trichomonas vaginalis positivity after treatment among human immunodeficiency virus-infected pregnant women, South Africa

The objective of this study is to assess the predictors and frequency of persistent sexually transmitted infection (STI) positivity in human immunodeficiency virus (HIV)-infected pregnant women treated for Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) or Trichomonas vaginalis (TV) infection. We enrolled HIV-infected pregnant women attending their first antenatal care visit and tested them for urogenital CT, NG and TV infection using Xpert® CT/NG and TV assays (Cepheid, Sunnyvale, CA). Those testing positive were treated. Participants either notified partners to seek treatment or were given extra medication to deliver to partners for treatment. Repeat testing was conducted approximately 21 days post-treatment or treatment initiation. Among 427 participants, 172 (40.3%) tested positive for any STI. Of the 136 (79.1%) that returned for repeat testing, 36 (26.5%) tested positive for the same organism: CT = 27 (26.5%), NG = 1 (6.3%), TV = 11 (16.7%). Persistent CT positivity was independently associated with having more than one sex partner in the preceding 12 months (adjusted-prevalence ratio [aPR] = 3.03, 95% CI: 1.44–6.37) and being newly diagnosed with HIV infection during the first antenatal care visit compared to those currently on antiretroviral therapy (aPR = 3.97, 95% CI: 1.09–14.43). Persistent TV positivity was associated with not knowing if a partner sought treatment following STI disclosure (aPR = 12.6, 95% CI: 2.16–73.5) and prior diagnosis of HIV but not currently on antiretroviral therapy. (aPR = 4.14; 95% CI: 1.25–13.79). We identified a high proportion of HIV-infected pregnant women with persistent CT or TV positivity after treatment. To decrease the risk of re-infection, enhanced strategies for partner treatment programmes are needed to improve the effectiveness of STI screening and treatment in pregnancy. The relationship between not being on antiretroviral therapy and persistent STI positivity needs further study.The Eunice Kennedy Shriver Institute of Child Health and Human Development, National Institutes of Health (NIH), award R21HD084274 and the President’s Emergency Plan for AIDS Relief through the United States Agency of the Cooperative Agreement AID 674-A-12-00017 funded this study. Noah Kojima was supported by the U.S. NIH Fogarty International Center (award number D43TW009343) and the University of California Global Health Institute. Christina A Muzny was supported by K23AI106957-01A1 from the National Institute of Allergy and Infectious Diseases.https://journals.sagepub.com/home/stdhj2021Medical MicrobiologyPaediatrics and Child Healt

The Determinants of Smallholder Farmers on the Functionality of Plant Health Clinics in the Vhembe District, South Africa

A plant health clinic is a system in which under-resourced and smallholder farmers can access basic services of plant healthcare from a plant clinic in relation to infected or symptomatic plants and plant products for pest diagnostic and identification purposes. The factors that influence smallholder farmers’ awareness and accessibility to plant health clinics in the Vhembe District Municipality of Limpopo Province, South Africa were examined in this study. The study also identified the constraints of the plant clinics that prevent their effective utilization. Three-hundred and twenty smallholder farmers (n = 320) from the population of 1600 were interviewed through a semi-structured questionnaire. A multistage random sampling technique was employed to select the 320 smallholder farmers from 8 irrigation schemes in the study area. To ensure representation, all categories of smallholder farmers were included in the study. Descriptive statistics such as frequency and percentages and Logit regression model were employed for the data analyses. The results revealed that there is a statistically significant and positive relation between communication channels and plant clinics awareness and accessibility among smallholder farmers. The distance to plant clinics has a negative influence on the accessibility of plant clinics among the farmers; however, the accessibility of plant clinic improves when visits by extension officers or plant doctors to farmers increase. The study pointed out some challenges affecting the functionality of plant clinics, which could be resolved through an efficient and effective plant clinic framework that involves major role players. An efficient and effective plant clinic framework was therefore developed by the study to improve its usefulness for diagnosing plant pest symptoms and diseases. The study concluded that plant clinic framework was important and should be considered and adopted by policy makers within the government, research institutes, and other NGOs

Phytosanitary risk associated with illegal importation of pest-infested commodities to the South African agricultural sector

We evaluated the phytosanitary risk associated with illegal importation of pest-infested plant commodities into South Africa. Samples were collected from different South African ports of entry over 8 years (2011 to 2019) and data were analysed descriptively using Statistical Software Package. Pests were frequently detected on commodity species such as Citrus (18.31%), Zea mays (13.22%), Phaseolus vulgaris (12.88%), Musa spp. (9.15%) and Fragaria ananassa (5.08%). The highest number of pests intercepted occurred on fresh fruits (44.06%), followed by grains (26.44%) and vegetables (14.23%). The most intercepted organisms were Callosobruchus rhodesianus (7.79%), Dysmicoccus brevipes (7.11%), Callosobruchus maculates (6.10%) and Phyllosticta citricarpa (4.74%). The majority of intercepted organisms were non-quarantine organisms (70.50%), followed by pests of unknown status (17.28%), quarantine pests (10.84%) and potential quarantine pests (1.35%). Phyllosticta citricarpa, Bactrocera dorsalis, Spodoptera frugiperda and Prostephanus truncatus were the only quarantine pests intercepted in terms of South African regulatory status. The interception was mainly from southern African countries, particularly Mozambique, Zimbabwe and Eswatini. The findings present the level of phytosanitary risk associated with illegal importation and/or non-compliance in regard to plants and plant commodities from different countries through South African ports of entry. Crop production, biodiversity, food security, existing export markets, and access to new export markets could be threatened as importing countries may impose stringent phytosanitary measures to limit the chances of introduction and establishment of quarantine pests into their territories. Significance Illegal importation of plant commodities may lead to the introduction, establishment and spread of pests that are of quarantine significance to South Africa. Introduction of pest species such as Phyllosticta citricarpa, Bactrocera dorsalis, Spodoptera frugiperda and Prostephanus truncatus into South Africa could result in undesirable impacts on the ecosystem, agriculture, biodiversity and economy of the country. Access to new export markets of plant commodities could be threatened as importing countries may impose stringent phytosanitary measures to limit the chances of introduction and establishment of these quarantine pests into their territories

Maximum Likelihood tree constructed using RAxMLv8.0 under GTR GAMMA model of nucleotide evolution.

<p>Four highly supported (by bootstrap score) probable transmission clusters involving sequences isolated from the study site (RXH and surrounding facilities) are highlighted in red.</p

RXH patient admission, Flu positivity and assumed source of viral acquisition (HAI/CAI) cases/viral isolate data grouped according to viral sequence phylogeny.

<p>RXH patient admission, Flu positivity and assumed source of viral acquisition (HAI/CAI) cases/viral isolate data grouped according to viral sequence phylogeny.</p

Time scaled maximum clade credibility (MCC) tree generated under GTR G + I and relaxed molecular clock in BEASTv1.7.5.

<p>The branch supports that are indicated are posterior probabilities (pp). Four significant putative transmission clusters containing sequences isolated from the study site (Red Cross Children’s Hospital and surrounding facilities) with pp support > 0.9 are highlighted in red.</p

Timeline displaying patient admission, movement and Influenza A (H1N1pdm) positivity within hospital (patient/isolate identity according to ML Cluster identity).

<p>Timeline displaying patient admission, movement and Influenza A (H1N1pdm) positivity within hospital (patient/isolate identity according to ML Cluster identity).</p