Factors Associated With Peripartum Virologic Suppression in Eastern Cape Province, South Africa: A Retrospective Cross-Sectional Analysis.

BACKGROUND: This study describes the characteristics of pregnant women on antiretroviral therapy (ART) and the rate of peripartum virologic suppression in a large prevention of mother-to-child transmission cohort who delivered in some selected maternity centers in Eastern Cape Province, South Africa. In addition, the study examines the factors associated with virologic suppression in the cohort. METHODS: This multicenter, retrospective cross-sectional analysis included medical data of 1709 women with human immunodeficiency virus between September 2015 and May 2016 in Eastern Cape Province. The main outcome measure was the rate of peripartum virologic suppression, defined as viral load (VL) <1000 copies/mL and undetectable viremia (VL <20 copies/mL). Correlates of peripartum virologic suppression and undetectable viremia were examined by fitting logistic regression model analysis. RESULTS: Of 1463 women with available VL results, the overall rate of peripartum suppression was 82%, and undetectable viremia was 56.9%. Being aged 24 years or younger (adjusted odds ratio [AOR], 0.68 [95% confidence interval {CI}, .48-.94]), smoking during pregnancy (AOR, 0.50 [95% CI, .28-.90]), and starting ART in the first trimester were associated with lower odds of viral suppression (<1000 copies/mL). Women who had never defaulted ART had an increased odds of having an undetectable VL (AOR, 3.09 [95% CI, 2.12-4.49]) and virologic suppression (AOR, 3.88 [95% CI, 2.62-5.74]) compared to those who defaulted. CONCLUSIONS: More than half of the women achieved undetectable VL, and 4 in 5 women achieved viral suppression at delivery in the region. Early antenatal booking, combined with enhanced adherence support for pregnant women on ART, would be crucial toward achieving the goal of elimination of mother-to-child transmission in the region.

Analyses of HIV-1 integrase gene sequences among treatment-naive patients in the Eastern Cape, South Africa.

Drug resistance has been recognized in all available therapeutic class of medications for the management of human immunodeficiency virus-1 (HIV-1) infected patients. This makes the continuous study of HIV drug resistance and new treatment options pertinent to patients and researchers globally. The aim of this study is to analyze the complete HIV-1 integrase gene for the possible occurrence of resistance mutations or polymorphisms. We performed genetic analyses on 48 treatment-naive HIV-1-infected patients using nested polymerase chain reaction. Integrase drug-related resistance mutation (DRMs) analysis was performed on all generated sequences according to Stanford HIV drug interpretation program and the International AIDS Society-USA guidelines while phylogenetic analysis was inferred using MEGA 6. The study revealed no major resistance-associated mutation. However, E157Q (2.1%), L74M/I (4.2%), and P142T (2.1%) were the observed accessory and polymorphic mutations. Naturally occurring polymorphism observed were E11D, K14R, D25E, V31I, M50I, V72I, P90T, F100Y, L101I, T124A, T125A, K136Q, D167E, V201I, L234I, A265V, A269K, D278A, and S283G. Phylogenetic analysis delineated all the sequences as HIV-1 subtype C. The study revealed the absence of major integrase inhibitors associated resistance mutations in a setting where integrase inhibitor is administered as salvage therapy in patients developing resistance to first and second-line antiretroviral treatment. However minor and natural polymorphisms were observed and thus may influence the outcome of each treatment regimen. However, additional studies are required to precisely evaluate the impact of these mutations on integrase inhibitors in the Eastern Cape of South Africa.

Prevalence and capsular type distribution of Streptococcus agalactiae isolated from pregnant women in Namibia and South Africa.

BACKGROUND: Streptococcus agalactiae or Group B Streptococcus (GBS) is the leading cause of neonatal morbidity and mortality resulting in septicaemia, bacteraemia and meningitis. Long term problems in children range from loss of hearing to mental retardation. While Intrapartum Antibiotic Prophylaxis (IAP) has reduced the incidence of S. agalactiae infection, it still remains the leading cause of disease in neonates. GBS has ten capsular types whose distribution varies across the world. Therefore, this study sought to determine the prevalence of GBS in Namibia and South Africa amongst pregnant women between 35 and 37 weeks gestation and elucidate the capsular types. METHODS: Lower vaginal and rectal swabs were collected from pregnant women between 35 and 37 weeks gestation. Five hundred and thirty pregnant women were recruited into the study in Windhoek, Namibia while one hundred pregnant women were recruited in the Eastern Cape, South Africa. The swabs were cultured on 5% sheep blood agar (Biomerieux, New Jersey, USA) for isolation of GBS. Presumptive isolates were confirmed using both the Vitek (2) and molecular techniques targeting the scpB gene. Capsular typing was performed in a multiplex PCR with capsular specific primer pairs. RESULTS: The prevalence of GBS in Namibia was 13.6 and 37% in South Africa respectively. In both countries most women were dually colonised with GBS. Capsular types II, III and V were the most prevalent. CONCLUSIONS: The prevalence of GBS in Namibia was lower than in South Africa in this study. The prevalence in both countries was not different from those reported in other African countries and around the world. The predominant capsular types in this study are the ones commonly associated with adverse maternal outcomes.

The activity of commercial antimicrobials, and essential oils and ethanolic extracts of Olea europaea on Streptococcus agalactiae isolated from pregnant women.

BACKGROUND: Streptococcus agalactiae also known as Group B Streptococcus (GBS) is a major cause of disease in pregnant women and new born babies where it causes early and late onset disease characterised by sepsis, pneumonia and meningitis. Ten to 37 % of pregnant women in the world are colonised with GBS while intrapartum antibiotic prophylaxis has led to significant reduction in early onset disease. The increase in drug resistant microorganisms has become a major threat. Development of vaccines is still in progress so there is need for new and safer alternatives to treatment. METHODS: Benzyl penicillin, Ampicillin, Cefotaxime, Ceftriaxone, Levofloxacin, Erythromycin, Clindamycin, Linezolid, Vancomycin, Tetracycline and Cotrimoxazole, Olea europaea leaf extracts and essential oil were tested against GBS isolates from South Africa and Namibia. RESULTS: The isolates showed 100% sensitivity to benzyl penicillin, ampicillin, ceftriaxone, levofloxacin, linezolid, vancomycin, O. europaea leaf extracts and essential oils. Only one isolate (0.6%) was resistant to cefotaxime and 23.4 and 10.4% were resistant to clindamycin and erythromycin respectively. CONCLUSION: GBS isolates showed sensitivity to O. europaea extracts at low minimum inhibitory concentrations. Β lactams are still the drugs of choice for treatment of GBS disease but O. europaea extracts potent as an alternative source of antimicrobials.

Molecular detection of Porcine circovirus type 2 in swine herds of Eastern Cape Province South Africa.

BACKGROUND: Porcine circovirus type 2 (PCV2) remains the main causative viral pathogen of porcine circovirus-associated diseases (PCVAD) of great economic importance in pig industry globally. This present study aims at determining the occurrence of the viral pathogen in swine herds of the Province. RESULTS: The data obtained revealed that 15.93% of the screened samples (54/339) from the swine herds of the studied areas were positive for PCV2; while the severity of occurrence of the viral pathogen as observed at farm level ranges from approximately 5.6 to 60% in the studied farms. The majority (15 out of 17 = 88%) of the analyzed sequences were found clustering with other PCV2b strains in the phylogenetic analysis. More interestingly, two other sequences obtained were also found clustering within PCV2d genogroup, which is presently another fast-spreading genotype with observable higher virulence in global swine herds. CONCLUSION: This is the first report of PCV2 in swine herds of the Province and the first detection of PCV2b and PCV2d in South African swine herds. It follows the first reported case of PCV2a in an outbreak of porcine multisystemic wasting syndrome (PMWS) in Gauteng Province, South Africa more than one decade ago. This finding confirmed the presence of this all-important viral pathogen in pigs of the region; which could result in a serious outbreak of PCVAD and huge economic loss at the instances of triggering factors if no appropriate measures are taken to effectively curb its spread.

Genetic profiling for Anaplasma and Ehrlichia species in ticks collected in the Eastern Cape Province of South Africa.

BACKGROUND: Anaplasma and Ehrlichia are emerging tick-borne pathogens that cause anaplasmosis and ehrlichiosis in humans and other animals worldwide. Infections caused by these pathogens are deadly if left untreated. There has been relatively no systematic survey of these pathogens among ticks in South Africa, thus necessitating this study. The presence of Anaplasma and Ehrlichia species were demonstrated by PCR in ticks collected from domestic ruminants at some selected communities in the Eastern Cape of South Africa. The ticks were identified by morphological characteristics and thereafter processed to extract bacterial DNA, which was analyzed for the presence of genetic materials of Anaplasma and Ehrlichia. RESULTS: Three genera of ticks comprising five species were identified. The screening yielded 16 positive genetic materials that were phylogenetically related to Ehrlichia sequences obtained from GenBank, while no positive result was obtained for Anaplasma. The obtained Ehrlichia sequences were closely related to E. chaffeensis, E. canis, E. muris and the incompletely described Ehrlichia sp. UFMG-EV and Ehrlichia sp. UFMT. CONCLUSION: The findings showed that ticks in the studied areas were infected with Ehrlichia spp. and that the possibility of transmission to humans who might be tick infested is high.

Chemical constituents, antibacterial and antioxidant properties of the essential oil flower of Tagetes minuta grown in Cala community Eastern Cape, South Africa.

BACKGROUND: Tagetes minuta has a long record of human use for the treatment of stomach and intestinal diseases. Most drugs used for diseases treatment are less efficacious with side effects and this brought the search for new treatment regimens mainly from medicinal plants. METHOD: The essential oil (EO) was extracted by Clevenger's-type apparatus and its chemical composition, antioxidant and antibacterial properties were determined by GC-MS, spectrophotometric and broth dilution methods respectively. S. uberis, E. cloacae, S. aureus, M. smegmatis, L. ivanovii, Vibrio spp. and E. coli bacteria strains were used as test bacteria. RESULTS: GC-MS analysis revealed 98 compounds in the EO flower of T. minuta and ß-Ocimene (14. 40%) was the major chemical constituents. The EO exhibited highest inhibitory effect against DPPH radical, followed by its effect on ABTS, while LP radical showed the least sensitivity with IC50 values of 2.45 mg/mL, 2.76 mg/mL and 3.23 mg/mL respectively. The EO showed antibacterial activities against all test organisms with MIC value for S. aureus, M. smegatis and S. uberis at 0.125 mg/mL and for L. ivanovii, Vibrio spp., E. cloacae and E. coli at 0.06 mg/mL. The EO showed MBC against E. cloacae and E. coli at 0.06 mg/mL at 0.5 mg/mL for S. uberis and 0.125 mg/mL for Vibrio spp. CONCLUSION: Findings from this study suggest that the EO of T. minuta flower may be a useful candidate in the search for lead constituents for the synthesis of new potent antibacterial and antioxidant agent.

Virulence and antimicrobial resistance factors of Enterococcusspp. isolated from fecal samples from piggery farms in Eastern Cape, South Africa.

BACKGROUND: Enterococci have emerged as an important opportunistic pathogen causing life-threatening infections in hospitals. The emergence of this pathogen is associated with a remarkable capacity to accumulate resistance to antimicrobials and multidrug-resistance particularly to vancomycin, erythromycin and streptomycin have become a major cause of concern for the infectious diseases community. In this paper, we report the prevalence of Enterococcus in respect to species distribution, their virulence and antibiogram profiles. METHODS: Four hundred fecal samples were collected from two piggery farms in the Eastern Cape Province of South Africa. Enterococcus species were isolated and confirmed with generic specific primers targeting the tuf gene (encoding elongation factor). The confirmed isolates were speciated with enterococci species specific primers that aimed at delineating them into six species that are commonly associated with infections in humans. Antibiotic susceptibility testing was performed by disc diffusion method. Six virulence genes and antimicrobial resistance profiles of the isolates were evaluated molecularly. RESULTS: Molecular identification of the presumptive isolates confirmed 320 isolates as Enterococcus spp. Attempt at speciation of the isolates with primers specific for E. faecalis, E. durans, E. casseliflavus, E. hirae and E. faecium delineated them as follows: E. faecalis (12.5 %), E. hirae (31.25 %), E. durans (18.75 %) and E. faecium (37.5 %) while E. casseliflavus was not detected. All the isolates were resistant to vancomycin, streptomycin and cloxacillin, and to at least two different classes of antibiotics, with 300 (93.8 %) isolates being resistant to five or more antibiotics. Also, three out of the six virulence genes were detected in majority of the isolates and they are Adhesion of collagen in E. faecalis (ace) (96.88 %), gelatinase (gelE) (93.13 %) and surface protein (esp) (67.8 %). CONCLUSION: There was high prevalence of multi-resistant vancomycin Enterococcus spp. (VREs) in the fecal samples of pigs in the farms studied, and this poses health implications as vancomycin is an important drug in human medicine. Further studies are needed to determine the spread of vancomycin resistance among bacteria of human origin in the communities.

Multiple antibiotic resistances among Shiga toxin producing Escherichia coli O157 in feces of dairy cattle farms in Eastern Cape of South Africa.

BACKGROUND: Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a well-recognized cause of bloody diarrhea and hemolytic-uremic syndrome (HUS). The ability of STEC strains to cause human disease is due to the production of Shiga toxins. The objectives of this study were to determinate the prevalence, serotypes, antibiotic susceptibility patterns and the genetic capability for Shiga toxin production in Escherichia coli (STEC) strains isolated from dairy cattle farms in two rural communities in the Eastern Cape Province of South Africa. METHODS: Fecal samples were collected between March and May 2014, from individual cattle (n=400) in two commercial dairy farms having 800 and 120 cattle each. Three hundred presumptive isolates obtained were subjected to polymerase chain reactions (PCR) for identification of O157 serogroup and Shiga toxin producing genes (stx1, stx2) on genomic DNA extracted by boiling method. Susceptibility of the isolates to 17 antibiotics was carried out in vitro by the standardized agar disc-diffusion method. RESULTS: Based on direct PCR detection, 95 (31.7%) isolates were identified as O157 serogroup. The genetic repertoire for Shiga toxin production was present in 84 (88.42%) isolates distributed as stx1 (37), stx2 (38) and stx1/2 (9) respectively while 11 of the isolates did not harbor Shiga toxin producing genes. Multiple antibiotic resistances were observed among the isolates and genetic profiling of resistance genes identified bla ampC 90%, blaCMY 70%, blaCTX-M 65%, blaTEM 27% and tetA 70% and strA 80% genes among the antimicrobial resistance determinants examined. CONCLUSION: We conclude that dairy cattle farms in the Eastern Cape Province are potential reservoirs of antibiotic resistance determinants in the province.

Assessment of Biofilm Forming Capability and Antibiotic Resistance in Proteus mirabilis Colonizing Indwelling Catheter.

<b>Background and Objective:</b> Urinary tract infections from the use of an indwelling urinary catheter are one of the most common infections caused by <i>Proteus mirabilis</i>. Due to their biofilm-producing capacity and the increasing antimicrobial resistance in this microorganism, this study aimed to determine the prevalence, biofilm-producing capacity, antimicrobial resistance patterns, multidrug resistance and plasmid mediated resistance of the recovered isolates. <b>Materials and Methods:</b> A total of 50 urinary samples were collected from May to August, 2018 from patients on indwelling urinary catheters. Using routine microbiological and biochemical methods, 37 <i>P. mirabilis</i> were isolated. Biofilm forming capability was determined among the isolates using the tube method while antimicrobial susceptibility and plasmid curing were also performed. <b>Results:</b> All isolates were biofilm producers with 17(46%) being moderate producers while 20(54%) were strong biofilm formers. The study isolates exhibited a high resistance rate to empiric antibiotics, including ceftazidime (75.8%), cefuroxime (54.5%), ampicillin (69.7%) and amoxicillin-clavulanic acid (51.5%). Low resistance was seen in the fluoroquinolones, gentamicin and nitrofurantoin. Plasmid curing experiment revealed that most isolates lost their resistance indicating that resistance was borne on plasmids. Plasmid carriage is likely the reason for the high MDR rate of 56.8% observed. <b>Conclusion:</b> These findings necessitate the provision of infection control programs which will guide and implement policies.

Identification of South African Plant-Based Bioactive Compounds as Potential Inhibitors against the SARS-CoV-2 Receptor.

The expected progress in SARS-CoV-2 vaccinations, as anticipated in 2020 and 2021, has fallen short, exacerbating global disparities due to a lack of universally recognized "safe and effective" vaccines. This study focuses on extracts of South African medicinal plants, Artemisia annua and Artemisia afra, to identify metabolomic bioactive compounds inhibiting the binding of the SARS-CoV-2 spike protein to ACE2 receptors. The extracts were monitored for cytotoxicity using a resazurin cell viability assay and xCELLigence real-time cell analyzer. Chemical profiling was performed using UPLC-MS/MS, orthogonal projection to latent structures (OPLS), and evaluated using principle component analysis (PCA) models. Identified bioactive compounds were subjected to in vitro SARS-CoV-2 enzyme inhibition assay using standard methods and docked into the spike (S) glycoprotein of SARS-CoV-2 using Schrodinger® suite followed by molecular dynamics simulation studies. Cell viability assays revealed non-toxic effects of extracts on HEK293T cells at lower concentrations. Chemical profiling identified 81 bioactive compounds, with compounds like 6″-O-acetylglycitin, 25-hydroxyvitamin D3-26,23-lactone, and sesaminol glucoside showing promising binding affinity. Molecular dynamics simulations suggested less stable binding, but in vitro studies demonstrated the ability of these compounds to interfere with SARS-CoV-2 spike protein's binding to the human ACE2 receptor. Sesaminol glucoside emerged as the most effective inhibitor against this interaction. This study emphasizes the importance of multiplatform metabolite profiling and chemometrics to understand plant extract composition. This finding is of immense significance in terms of unravelling metabolomics bioactive compounds inhibiting the binding of the SARS-CoV-2 spike protein to ACE2 receptors and holds promise for phytotherapeutics against SARS-CoV-2.

Molecular epidemiology of HIV in two highly endemic areas of northeastern South Africa.

There is paucity of data on the genetic landscape of HIV-1 viruses circulating in the Limpopo Province of northeastern South Africa. Here, we examine the genetic diversity of viruses from Bela-Bela and Musina, two towns with high HIV prevalence. Between June 2007 and March 2008, blood samples were collected from antiretroviral-drug-naïve individuals. Viruses were analyzed for genetic subtypes and drug resistance mutations. All of the viruses in these samples were shown by phylogenetic analysis based on gag p17, gag p24, reverse transcriptase, protease and envelope C2-C3 gene regions to belong to HIV-1 subtype C. Two of 44 reverse transcriptase sequences (4.5%) contained N rather than the consensus K at position 103. The K103N mutation is normally associated with resistance to NNRTIs. No major mutations were observed in the protease gene. However, several polymorphisms and amino acid changes normally considered to be minor drug resistance mutations were observed in the protease sequences. These results suggest that HIV-1 subtype C remains the predominant variant responsible for the epidemic in northeastern South Africa and that the prevalence of drug-resistant viruses among the naïve population is low.

The Emergence of Colistin- and Imipenem-Associated Multidrug Resistance in Escherichia coli Isolates from Retail Meat.

To determine the prevalence of Escherichia coli and their drug resistance profiles in fresh pork sold at two retail outlets (open-air market and closed retail stores) in Alice, South Africa. Retail meat samples (n = 176) collected from four shops (two from open-air markets and two from closed stores) were analyzed by conventional biochemical and PCR-based molecular confirmatory tests. The confirmed isolates were profiled for antimicrobial susceptibility to a panel of 12 commercial antibiotics: tetracycline, ampicillin, sulphamethoxazole trimethoprim, erythromycin, gentamycin, colistin sulphate, cefotaxime, chloramphenicol, norfloxacin, ciprofloxacin, cefuroxime, and imipenem. Colistin, ampicillin, and erythromycin resistance genes were profiled with the gene-specific primers. Multidrug resistance (MDR) and the association of imipenem and colistin in the MDR profile were determined. A total of 68 (39.08%) E. coli isolates were confirmed by PCR analysis. Resistance was most common to erythromycin (100%), followed by cefotaxime (95.58%), ampicillin (88.23%), cefuroxime (88.23%), trimethoprim-sulphamethoxazole (88.23%), and tetracycline (60.29%). Overall, 27/68 (39.70%) were MDR (≥ 3antibiotics classes). MDR E. coli isolates associated with imipenem resistance (50.00%) and colistin resistance (33.82%) were detected. The resistance genes were detected among the isolates though not in all the phenotypically resistant isolates. The detection of colistin resistance among MDR E. coli isolates from retail meat is troubling as the drug is a last resort antibiotic. Overall, the epidemiological implications of the findings are of public health importance.

Emergence of Theileria species in ticks from free-ranging domestic animals in Raymond Mhlaba local municipality, South Africa.

Ticks infestation and diseases associated with it, are becoming a major life threatening concern to wildlife, domesticated animals and human health in general. Besides causing skin damage, ticks infestations have become a growing burden in food security and transmission of multiple pathogens. There is paucity of data on the occurrence of etiologic agents of tick-borne diseases in the Eastern Cape Province South Africa. We therefore carried out a molecular surveillance on Babesia and Theileria species in ticks obtained from livestock in Raymond Mhlaba District Municipality of the Province. A total of 962 ticks were collected and were morphologically identified and processed for DNA extraction using commercial DNA extraction kit. The extracted DNA samples were used to molecular identification of the ticks, and also to assess the occurrence of the Babesia and Theileria spp by PCR using genus specific primers. Positive amplicons obtained were sequenced, processed and characterised using appropriate bioinformatics tools. The molecular and morphological identifications of ticks obtained from the domestic animals in the study areas revealed that they belong to three different genera namely: Haemophalis, Rhipicephalus, and Amblyomma in ascending order of their abundance. Furthermore, the DNA of Theileria spp. was detected from 10 out of 962 ticks screened, with an overall infection of about 1% for Rhipicephalus spp., while none of the ticks was positive for Babesia spp. The phylogenetic analysis of the 10 theilerial sequences showed that nine (9) clustered distinctly within the T. orientalis complex clade, while only one (1) sequence formed a cluster with reference sequences of T. velifera. The findings from this study therefore expand the knowledge on recent emergence of Theileria spp. in livestock reared in the study area. This calls for an urgent effort in curbing the further spread of the pathogens in the area and beyond.

Prevalence of antiretroviral drug resistance mutations and HIV-I subtypes among newly-diagnosed drug-naïve persons visiting a voluntary testing and counselling centre in northeastern South Africa.

Data on antiretroviral drug resistance among drug-naive persons are important in developing sentinel and surveillance policies. This study was conducted to determine the prevalence of antiretroviral drug resistance mutations among drug-naïve HIV-infected individuals attending a voluntary testing and counselling centre at the Mankweng Hospital in northeastern South Africa. In total, 79 drug-naïve HIV-positive individuals were sequentially recruited during February 2008-December 2008. Drug resistance mutations were determined using the calibrated population resistance tool available on the Stanford HIV drug resistance database. Viral DNA was obtained from 57 (72%) of the 79 individuals. Reliable nucleotide sequences were obtained for 54 reverse transcriptase (RT) and 54 protease (PR) gene regions from 54 individuals. Overall, five sequences (9.3%) harboured drug resistance mutations (95% confidence interval -1.53 to 16.99). Four (7.4%) of these were nucleoside RT inhibitor mutations (D67G, D67E, T69D, and T215Y), and one (1.9%) was a PR inhibitor mutation (M46I). No major non-nucleoside RT resistance mutation was detected. Several minor resistance mutations and polymorphisms common in subtype C viruses were observed in the PR and RT genes. Phlyogenetic analysis of the partial pol sequences showed that 52 (96%) of the 54 isolates were HIV-1 subtype C. One isolate (08MB08ZA) was HIV-1 subtype B while another (08MB26ZA) was related to HIV-1 subtype J. HIV-1 subtype recombination analysis with REGA assigned the pol sequence to HIV subtype J (11_cpx) with a bootstrap value of 75%. The prevalence of drug resistance mutations observed in the population studied was relatively higher than previously reported from other parts of South Africa. In addition, this is apparently the first report of an HIV-1 subtype J-like virus from northeastern South Africa.

Genetic Characterization of HIV-1 Subtype A1/C/D/B/K Unique Recombinant Form from Eastern Cape, South Africa.

HIV-1 subtype C is the predominant circulating virus in South Africa. There are reports of non-C subtypes emerging in different regions of the country, however, very little information exists on the genetic diversity of HIV in the Eastern Cape Province, despite having the third largest HIV epidemic in the country. In the current study, a near full-length genomic sequence obtained from a heterosexual woman in the Eastern Cape (ADE/CMH/0032), was analyzed using two rapid online subtyping tools; REGA and the jumping Profile Hidden Markov Model (jpHMM). There was agreement between the two tools in the assignment of the pol, Vif, and vpr regions, identified as a C/D recombinant (pol) and subtype C (vif and vpr). Some degree of agreement existed in the assignment of the Gag region, as recombinant: A1/C/B/D by REGA, and A1/C/D by jPHMM, respectively. There was disparity between the two online tools in the subtype assignment of the remaining gene regions. Phylogenetic analysis with pure subtype reference sequences showed that the query sequence clustered with a subtype C reference strain, with a low bootstrap value of 43%. This is the first report from South Africa of a putative unique recombinant as classified by rapid online subtyping tools, involving subtype A1, C, D, B, and K. However, the clinical and epidemiological implications of this variant remain unclear. Further studies are needed to fully understand the genetic diversity of HIV in the Eastern Cape.

Rickettsia africae an Agent of African Tick Bite Fever in Ticks Collected from Domestic Animals in Eastern Cape, South Africa.

Background: Ticks transmit a plethora of pathogens of zoonotic implications. Their distribution, diversity and the pathogens they transmit differ from one ecological location to another. Rickettsia africae is the agent of African tick bite fever found in South Africa, a zoonotic infection that is frequently reported among travelers who have visited many sub-Saharan African countries where the pathogen is prevalent. Methods: Ticks were collected from domestic animals in Raymond Nkandla Municipality, Eastern Cape, South Africa. The ticks were identified morphologically prior to DNA extraction followed by molecular identification of randomly selected ticks from the morphologically delineated groups. To assess for the presence of tick-borne pathogens belonging to Rickettsia spp. by PCR (polymerase chain reaction), we used specific primer pairs targeting the gltA, ompA and ompB genes. The selected amplified ticks, all positive ompB and forty three ompA amplicons were sequenced in a commercial sequencing facility. The obtained nucleotide sequences were edited and subjected to BLASTn for homology search and phylogenetic analyses were performed with MEGA 7 Version for genetic relationships with curated reference sequences in GenBank. Results: A total of 953 ticks collected in the study were delineated into three genera consisting of Amblyomma, Rhipicephalus and Hyalomma in decreasing order of abundance. The presence of rickettsial DNA was detected in 60/953 (6.3%) from the three genera of ticks screened. Genetic analyses of the DNA sequences obtained showed that they have phylogenetic relationship to members of the spotted fever group rickettsiae with R. africae, being the predominant SFGR (spotted fever group rickettsiae) detected in the screened ticks. Conclusion: This report shows that R. africae is the predominant spotted fever group rickettsiae in ticks collected from domestic animals in the study area and the human health impacts are not known.

Antimicrobial Resistance Profiles of Diarrheagenic E. coli (DEC) and Salmonella Species Recovered from Diarrheal Patients in Selected Rural Communities of the Amathole District Municipality, Eastern Cape Province, South Africa.

PURPOSE: The emergence of multidrug-resistant bacteria remains as one of the major impediments towards the prevention and treatment of microbial infections and continues to be a serious threat to medicine. Henceforth, this study aimed at elucidating the antimicrobial resistance profiles of diarrheagenic E. coli (DEC) and Salmonella species recovered from diarrheal patients in selected rural communities of the Amathole District Municipality (ADM), Eastern Cape Province, South Africa (SA). METHODS: The antimicrobial resistance profiles of diarrheagenic E. coli (DEC) and Salmonella isolates were evaluated using antimicrobial susceptibility tests and the relevant antimicrobial resistance factors were elucidated by the Polymerase Chain Reaction technique. RESULTS: A sum of 324 diarrheagenic E. coli (DEC) and 62 Salmonella isolates were recovered from diarrheal stool specimens collected amongst diarrheal patients admitted in medical facilities/health-care centers within the ADM in the Eastern Cape Province, South Africa. Multiple antimicrobial resistance index mean values of 0.7 and 0.5 for DEC and Salmonella isolates, respectively, were observed in this study, indicating that these isolates were from sources where antimicrobials were frequently used. The antimicrobial resistance factors ampC, blaTEM, SulI and II, tet A and aadA were detected among antimicrobial-resistant DEC pathotypes and Salmonella isolates recovered in this study. CONCLUSION: The occurrence of the multiple antimicrobial-resistant DEC and Salmonella isolates with the relevant antimicrobial resistance factors in this study suggests a portentous human health threat associated with diarrhea and a major deterrent in medicine.

Rotavirus and Cryptosporidium pathogens as etiological proxies of gastroenteritis in some pastoral communities of the Amathole District Municipality, Eastern Cape, South Africa.

OBJECTIVE: Cryptosporidium and Rotavirus agents have been associated with severe diarrheal illnesses and remain as one of the worst human health burdens in most developing regions. In the present study, we evaluated the incidences of Cryptosporidium and Rotavirus in diarrheal stool specimens of patients in some rural settlements of the Amathole District Municipality in the Eastern Cape Province, South Africa. Stool specimens from diarrheal children and elderly individuals were collected from clinics and hospitals within the rural communities of the region over a period of 21 months (February 2017-November 2018). Commercial enzyme-immuno-assays were used for the detection of Rotavirus and Cryptosporidium pathogens from processed diarrheal stool specimens. RESULTS: A total of 53 fresh stool samples from diarrheal patients were screened and 36% of the diarrheagenic stool specimens tested positive for Group A Rotavirus antigens, while 5.7% tested positive for Cryptosporidium antigens. Our findings reveal Rotavirus and Cryptosporidium pathogens as important etiological agents associated with diarrheal illnesses in children, among the rural hinterlands of the Amathole District Municipality.

Beta-Lactamase-Producing Escherichia coli Isolates Recovered from Pig Handlers in Retail Shops and Abattoirs in Selected Localities in Southern Nigeria: Implications for Public Health.

Antibiotic resistance evolution among pathogenic microorganisms has become a huge burden globally as it has increased the burden of diseases amongst humans and animals. The prevalence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) and metallo beta-lactamase-producing Escherichia coli (MBL-Ec) isolated from pig abattoir and handlers in retail shops was studied. In addition, the relationship between the isolates' prevalence and the background characteristics of the butchers/retailers was also investigated. Samples from 32 hand swabs of pork sellers at retail shops and 8 butchers at abattoirs, as well as 272 swabs taken from knives, tables, floors, water troughs, and carcasses from both retail shops and abattoirs, were collected. Escherichia coli (E. coli) was isolated from hand swabs, fomites, and carcasses and were identified by standard microbiological procedures. The isolates susceptibility to nitrofurantoin (300 µg), ciprofloxacin (5 µg), ceftazidime (30 µg), cefuroxime (30 µg), gentamicin (10 µg), cefixime (5 µg), ofloxacin (5 µg), amoxicillin/clavulanic acid (30 µg), imipenem (10 µg), and meropenem (10 µg) and their ability to produce ESBL and MBL was determined by phenotypic methods. Demographic information of the handlers was retrieved by means of a structured questionnaire and, in some cases, via face to face interviews. Out of 104 E. coli isolates from both sources, 52 (50.0%) and 8 (7.7%) were ESBL and MBL producers, respectively. ESBL was more prevalent on the hands of the retailers (40.6%) and butchers (75.0%). The isolates were 100% resistant to ceftazidime, cefotaxime, and amoxicillin-clavulanic acid and 4.8% resistant to nitrofurantoin. Diverse resistance patterns were observed among ESBL-Ec and MBL-Ec. It was found that 90% of ESBL-Ec and 100% of MBL-Ec were multidrug-resistant. A possible epidemiological link between the two sources was observed. The prevalence of E. coli ESBL- and MBL-producing isolates was associated with the duty performed by handlers (p = 0.012) and gender (p = 0.012). Our results provide evidence that the handlers' hands and abattoir environment had a great role to play in the high prevalence and resistance profiles of the microorganisms.