Browsing by Author "Mbanga, J."

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    A study of scavenging poultry gastrointestinal and ecto-parasites in rural areas of Matebeleland Province, Zimbabwe.
    (Asian Network for Scientific Information, 2010) Dube, S.; Zindi, P.; Mbanga, J.; Dube, C.
    A study was carried out to determine endo and ecto-parasites in Matebeleland North and South from free range chickens (Gallus domesticus). Only adult chickens were selected for determination of parasite. For intestinal parasites microscopic studies of eggs and faecal egg counts were done using the salt floatation technique. The endo parasites encountered in the study were Tetrameres americana, Acuaria hamulosa, Ascaridia galli, Heterakis gallinarum, H. dispar, Allodapa suctoria, Capillaria annulate, Raillietina echinobothrida and R. tetragona. A commercially prepared insecticide constituted as follows (0.02% Tetamethrin, 0.03% pramethrin and 0.034% Imiprothrin) was applied for 2 seconds and feathers were then gentle unruffled so that ectoparasites could be counted and identified. Ecto parasites recorded in this study were Menopon gallinae, Menacanthus stramineus, Dermanyssus gallinae, Argas persicus, Ornithonyssus bursa, Cnemidocoptes mutans, Echidnophaga gallinacean, Gonocoites gallinae and Gonocoites hologester.
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    Genomic Analysis of Enterococcus spp. Isolated From a Wastewater Treatment Plant and Its Associated Waters in Umgungundlovu District, South Africa
    (Frontiers in Microbiology, 2021-06-14) Mbanga, J.; Amoako, D.G.; Abia, A.L.; Allam, M.; Ismail, A.; Essack, S.Y.
    We investigated the antibiotic resistome, mobilome, virulome, and phylogenomic lineages of Enterococcus spp. obtained from a wastewater treatment plant and its associated waters using whole-genome sequencing (WGS) and bioinformatics tools. The whole genomes of Enterococcus isolates including Enterococcus faecalis (n = 4), Enterococcus faecium (n = 5), Enterococcus hirae (n = 2), and Enterococcus durans (n = 1) with similar resistance patterns from different sampling sites and time points were sequenced on an Illumina MiSeq machine. Multilocus sequence typing (MLST) analysis revealed two E. faecalis isolates that had a common sequence type ST179; the rest had unique sequence types ST841, and ST300. The E. faecium genomes belonged to 3 sequence types, ST94 (n = 2), ST361 (n = 2), and ST1096 (n = 1). Detected resistance genes included those encoding tetracycline [tet(S), tet(M), and tet(L)], and macrolides [msr(C), msr(D), erm(B), and mef(A)] resistance. Antibiotic resistance genes were associated with insertion sequences (IS6, ISL3, and IS982), and transposons (Tn3 and Tn6000). The tet(M) resistance gene was consistently found associated with a conjugative transposon protein (TcpC). A total of 20 different virulence genes were identified in E. faecalis and E. faecium including those encoding for sex pheromones (cCF10, cOB1, cad, and came), adhesion (ace, SrtA, ebpA, ebpC, and efaAfs), and cell invasion (hylA and hylB). Several virulence genes were associated with the insertion sequence IS256. No virulence genes were detected in E. hirae and E. durans. Phylogenetic analysis revealed that all Enterococcus spp. isolates were more closely related to animal and environmental isolates than clinical isolates. Enterococcus spp. with a diverse range of resistance and virulence genes as well as associated mobile genetic elements (MGEs) exist in the wastewater environment in South Africa.
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    Genomic Characterization of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Implicated in Bloodstream Infections, KwaZulu-Natal, South Africa: A Pilot Study
    (MDPI, 2024-08-23) Hetsa, B.A.; Asante, J.; Mbanga, J.; Ismail, A.; Abia, A.L.; Amoako, D.G.; Essack, S.Y.
    Staphylococcus aureus is an opportunistic pathogen and a leading cause of bloodstream infections, with its capacity to acquire antibiotic resistance genes posing significant treatment challenges. This pilot study characterizes the genomic profiles of S. aureus isolates from patients with bloodstream infections in KwaZulu-Natal, South Africa, to gain insights into their resistance mechanisms, virulence factors, and clonal and phylogenetic relationships. Six multidrug-resistant (MDR) S. aureus isolates, comprising three methicillin-resistant S. aureus (MRSA) and three methicillin-susceptible S. aureus (MSSA), underwent whole genome sequencing and bioinformatics analysis. These isolates carried a range of resistance genes, including blaZ, aac(6′)-aph(2″), ant(9)-Ia, ant(6)-Ia, and fosB. The mecA gene, which confers methicillin resistance, was detected only in MRSA strains. The isolates exhibited six distinct spa types (t9475, t355, t045, t1265, t1257, and t7888) and varied in virulence gene profiles. Panton–Valentine leukocidin (Luk-PV) was found in one MSSA isolate. Two SCCmec types, IVd(2B) and I(1B), were identified, and the isolates were classified into four multilocus sequence types (MLSTs), with ST5 (n = 3) being the most common. These sequence types clustered into two clonal complexes, CC5 and CC8. Notably, two MRSA clones were identified: ST5-CC5-t045-SCCmec_I(1B) and the human-associated endemic clone ST612-CC8-t1257-SCCmec_IVd(2B). Phylogenomic analysis revealed clustering by MLST, indicating strong genetic relationships within clonal complexes. These findings highlight the value of genomic surveillance in guiding targeted interventions to reduce treatment failures and mortality.
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    Genomic Insights of Multidrug-Resistant Escherichia coli From Wastewater Sources and Their Association With Clinical Pathogens in South Africa
    (Frontiers in Veterinary Science, 2021-02-26) Mbanga, J.; Amoako, D.G.; Abia, A.L.; Allam, M.; Ismail, A.; Essack, S. Y.
    There is limited information on the comparative genomic diversity of antibiotic-resistant Escherichia coli from wastewater. We sought to characterize environmental E. coli isolates belonging to various pathotypes obtained from a wastewater treatment plant (WWTP) and its receiving waters using whole-genome sequencing (WGS) and an array of bioinformatics tools to elucidate the resistomes, virulomes, mobilomes, clonality, and phylogenies. Twelve multidrug-resistant (MDR) diarrheagenic E. coli isolates were obtained from the final effluent of a WWTP, and the receiving river upstream and downstream of the WWTP were sequenced on an Illumina MiSeq machine. The multilocus sequence typing (MLST) analysis revealed that multiple sequence types (STs), the most common of which was ST69 (n = 4) and ST10 (n = 2), followed by singletons belonging to ST372, ST101, ST569, ST218, and ST200. One isolate was assigned to a novel ST ST11351. A total of 66.7% isolates were positive for β-lactamase genes with 58.3% harboring the blaTEM1B gene and a single isolate the blaCTX−M−14 and blaCTX−M−55 extended-spectrum β-lactamase (ESBL) genes. One isolate was positive for the mcr-9 mobilized colistin resistance gene. Most antibiotic resistance genes (ARGs) were associated with mobile genetic support: class 1 integrons (In22, In54, In191, and In369), insertion sequences (ISs), and/or transposons (Tn402 or Tn21). A total of 31 virulence genes were identified across the study isolates, including those responsible for adhesion (lpfA, iha, and aggR), immunity (air, gad, and iss), and toxins (senB, vat, astA, and sat). The virulence genes were mostly associated with IS (IS1, IS3, IS91, IS66, IS630, and IS481) or prophages. Co-resistance to heavy metal/biocide, antibiotics were evident in several isolates. The phylogenomic analysis with South African E. coli isolates from different sources (animals, birds, and humans) revealed that isolates from this study mostly clustered with clinical isolates. Phylogenetics linked with metadata revealed that isolates did not cluster according to source but according to ST. The occurrence of pathogenic and MDR isolates in the WWTP effluent and the associated river is a public health concern.
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    Genotyping Human Papillomavirus in Women Attending Cervical Cancer Screening Clinic in Harare, Zimbabwe
    (2023) Matuvhunye, T.; Dube-Mandishora, R.S.; Chin’ombe, N.; Chakafana, G.; Mbanga, J.; Zumbika, E.; Stray-Pedersen, B.
    Aim: To determine the prevalence of human papillomavirus genotypes in women attending a cervical cancer screening VIAC (visual inspection with acetic acid) clinic. Study Design: Cross-sectional studyPlace and Duration of Study: VIAC clinic at Parirenyatwa Referral Hospital in Harare in Zimbabwe between February and April 2015. Methodology: Sexually active women were recruited and they provided their socio-demographic data and self-collected vaginal swabs. HIV status of the participants was determined. DNA was extracted from the swabs using the standard phenol-chloroform method. HPV DNA was detected using the standard consensus MY09/11-GP5+/GP6+ nested polymerase chain reaction. Amplicons were sequenced and sequences analyzed using bioinformatics tools to identify the HPV genotypes. Results: Sixty women were recruited. Their age ranged from 21-83 years, with a mean of 40.1 years. Most of the women were married and resided in the urban areas. Of the 60 participants, 50% (30/60) were HIV-positive. The prevalence of HPV genotypes in the study subjects was 56.7% (34/60). HPVs were most prevalent in women aged 30 years and below, and became less prevalent as the age increased. The predominant genotypes detected were HPV-16, -58, -52, -45, 18, -33, -51, -6, -81, -11, -70, -62, -32 and -40. Conclusion: A number of HPV genotypes were detected in half of women tested. There was no significance association between risk-factors (parity, level of education, residence, history of STI, contraceptive use and sexual debut) and HPV infection. The findings of this study showed that consensus nested PCR and DNA sequencing could be used to detect HPV genotypes in women in cervical cancer screening programs. Although this method is sensitive, it is inefficient at detecting multiple HPV infections.
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    Mbanga, J., Abia, A.L.K., Amoako, D.G. and Essack, S.Y., 2021. Longitudinal surveillance of antibiotic resistance in Escherichia coli and Enterococcus spp. from a wastewater treatment plant and its associated waters in KwaZulu-Natal, South Africa. Microbial Drug Resistance, 27(7), pp.904-918.
    (Microbial Drug Resistance, 2021) Mbanga, J.; Abia, A.L.K.; Amoako, D.G.; Essack, S.Y.
    We assessed the prevalence, distribution, and antibiotic resistance patterns of Escherichia coli and Enterococcus spp. isolated from raw and treated wastewater of a major wastewater treatment plant (WWTP) in KwaZulu-Natal, South Africa and the receiving river water upstream and downstream from the WWTP discharge point. Escherichia coli and enterococci were isolated and counted using the Colilert®-18 Quanti-Tray® 2000 and Enterolert®-18 Quanti-Tray 2000 systems, respectively. A total of 580 quantitative PCR-confirmed E. coli and 579 enterococci were randomly chosen from positive samples and tested for in vitro antibiotic susceptibility using the disk diffusion assay against 20 and 16 antibiotics, respectively. The removal success of the bacterial species through the treatment procedure at the WWTP was expressed as log removal values (LRVs). Most E. coli were susceptible to meropenem (94.8%) and piperacillin-tazobactam (92.9%), with most Enterococcus susceptible to ampicillin (97.8%) and vancomycin (96.7%). In total, 376 (64.8%) E. coli and 468 (80.8%) Enterococcus isolates showed multidrug resistance (MDR). A total of 42.4% (246/580) E. coli and 65.1% (377/579) enterococci isolates had multiple antibiotic resistance indices >0.2. The LRV for E. coli ranged from 2.97 to 3.99, and for enterococci the range was observed from 1.83 to 3.98. A high proportion of MDR E. coli and enterococci were present at all sampled sites, indicating insufficient removal during wastewater treatment. There is a need to appraise the public health risks associated with bacterial contamination of environmental waters arising from such WWTPs to protect the health of users of the receiving water bodies.
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    Mobile genetic elements-mediated Enterobacterales-associated carbapenemase antibiotic resistance genes propagation between the environment and humans: A One Health South African study
    (Elsevier, 2021-09-23) Ramsamy, Y.; Mlisana, K.P.; Amoako, D.G.; Abia, A.L.K.; Ismail, A.; Allam, M.; Mbanga, J.; Singh, R.; Essack, S.Y.
    We, (1) studied carbapenem-resistant Enterobacterales (CRE) in the environment, humans, and animals, within the same geographical area and, (2) delineated the isolates' resistome, mobilome, virulome, and phylogeny. Following ethical approval, 587 samples (humans = 230, pigs = 345, and water = 12) were collected and cultured on CRE selective media. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK 2 automated platform. The resistomes, virulomes, mobilomes, and phylogenies were ascertained by whole genome sequencing. Nineteen (3.2%), i.e., 15/19 humans and 4/19 environmental, but no pig, CRE were obtained. CREs included Klebsiella pneumoniae 9/19 (47%), Enterobacter hormaechei 6/19 (32%), Klebsiella quasipneumoniae 2/19 (11%), a novel ST498 Citrobacter freundii 1/19 (5%) and Serratia marcescens 1/19 (5%). Eleven isolates were extensively drug-resistant; eight were multidrug-resistant. Sixteen CRE harbored the blaOXA-181, blaOXA-48, blaOXA-484, blaNDM-1, and blaGES-5 genes. Multiple species/clones carried blaOXA-48 and blaNDM-1 carbapenemase-encoding genes with respective mobile genetic elements (MGEs). The IncFIB(K) plasmid replicon was found in most human K. pneumoniae strains (7/9) and all environmental K. quasipneumoniae isolates; most K. pneumoniae produced OXA-181 (5/9). The (Col440I) plasmid replicon, identified in 11 (26.82%) isolates, mainly E. hormaechei (n = 6), predominated both sectors. Most β-lactamase-encoding genes were associated with class 1 integrons IntI1, insertion sequences (IS) (IS91, IS5075, IS30, IS3000, IS3, IS19, ISKpn19, IS5075) and transposons (Tn3). The IncL/M(pMU407) and IncL/M(pOXA48) plasmid replicons were found exclusively in K. pneumoniae; all but one of these strains produced OXA-181. Also, the Klebsiella spp. harbored 80 virulence genes. Phylogenomic clustered identified isolates with other carbapenemase-producing K. pneumoniae, E. hormaechei, S. marcescens, and C. freundii from different South African sources (animals, environment, and humans). We delineated the resistome, mobilome, virulome, and phylogeny of carbapenemase-producing Enterobacterales in humans and environment, highlighting antibiotic resistance genes propagation via MGEs across sectors, emphasizing a One Health approach to AMR.
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    Molecular Identification of Mycobacterium Species of Public Health Importance in Cattle in Zimbabwe by 16S rRNA Gene Sequencing
    (2015) Padya, L.; Chin’ombe, N.; Magwenzi, M.; Mbanga, J.; Ruhanya, V.; Nziramasanga, P.
    Mycobacterium species are naturally found in the environment as well as in domestic animals such as cattle. So far, more than 150 species of Mycobacterium, some of which are pathogenic, have been identified. Laboratory isolation, detection and identification of Mycobacterium species are therefore critical if human and animal infections are to be controlled. The objective of this study was to identify Mycobacterium species isolated in cattle in Zimbabwe using 16S ribosomal RNA gene amplification and sequencing. A total of 134 cow dung samples were collected throughout Zimbabwe and mycobacteria were isolated by culture. Only 49 culture isolates that were found to be acid-fast bacilli positive by Ziehl-Neelsen staining. The 16S rRNA gene was successfully amplified by PCR in 41 (84%) of the samples. There was no amplification in 8 (16%) of the samples. Out of the 41 samples that showed amplification, 26 (63%) had strong PCR bands and were selected for DNA sequencing. Analysis of the DNA sequences showed that 7 (27%) belonged to Mycobacterium neoaurum, 6 (23%) belonged to Mycobacterium fortuitum, 3 (12%) to Mycobacterium goodii, 2 (1%) to Mycobacterium arupense, 2 (1%) to Mycobacterium peregrinum or M. septicum and 1 isolate (0.04%) to Mycobacterium elephantis. There were 5 (19%) isolates that were non-mycobacteria and identified as Gordonia terrae, a close relative of Mycobacterium. The study therefore provided a molecular basis for detection and identification of Mycobacterium species in animals and humans
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    Virulence gene profiles of avian pathogenic Escherichia coli isolated from chickens with colibacillosis in Bulawayo, Zimbabwe
    (Scielo, 2015) Mbanga, J.; Nyararai, Y.O.
    Colibacillosis, a disease caused by avian pathogenic Escherichia coli (APEC), is one of the main causes of economic losses in the poultry industry worldwide. This study was carried out in order to determine the APEC-associated virulence genes contained by E. coli isolates causing colibacillosis in chickens. A total of 45 E. coli isolates were obtained from the diagnostics and research branch of the Central Veterinary Laboratories, Bulawayo, Zimbabwe. These isolates were obtained from chickens with confirmed cases of colibacillosis after postmortem examination. The presence of the iutA, hlyF, ompT, frz, sitD, fimH, kpsM, sitA, sopB, uvrY, pstB and vat genes were investigated by multiplex polymerase chain reaction (PCR) assay. Of the 45 isolates, 93% were positive for the presence of at least one virulence gene. The three most prevalent virulence genes were iutA (80%), fimH (33.3%) and hlyF (24.4%). The kpsM, pstB and ompT genes had the lowest prevalence, having been detected in only 2.2% of the isolates. All 12 virulence genes studied were detected in the 45 APEC isolates. Virulence gene profiles were constructed for each APEC isolate from the multiplex data. The APEC isolates were profiled as 62.2% fitting profile A, 31.1% profile B and 6.7% profile C. None of the isolates had more than seven virulence genes. Virulence profiles of Zimbabwean APEC isolates are different from those previously reported. Zimbabwean APEC isolates appear to be less pathogenic and may rely on environmental factors and stress in hosts to establish infection.
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    Whole genome sequencing reveals insights into antibiotic resistant Klebsiella grimontii novel sequence type ST350 isolated from a wastewater source in South Africa
    (Journal of Biotech Research, 2022) Mbanga, J.; Amoako, D.G.; Abia, A.L.; Fatoba, D.; Essack, S.
    Klebsiella grimontii is a recently identified species that has been implicated in clinical infections. Few or no reports on environmental K. grimontii exist from Africa. This study was part of a broader longitudinal research that aimed to assess the distribution, antibiotic resistance patterns, and genomics of Enterobacterales obtained from raw and treated wastewater and the associated river water of a wastewater treatment plant (WWTP) in KwaZulu-Natal, South Africa. We reported the genomics of an antibiotic resistant Klebsiella grimontii isolate obtained from the raw influent of the WWTP. Following phenotypic characterisation and antibiotic susceptibility testing, the isolate was sequenced on an Illumina MiSeq machine. Raw reads were assembled de novo by using SPAdes (v3. 6.2) prior to bioinformatics analysis. The assembled K. grimontii INF139 genome was 6,369,878 bp, with 113 contiguous sequences (> 200 bp) and 55.4% GC content. The isolate was assigned a novel sequence type ST350. Genomic analysis revealed the presence of chromosomally encoded β-lactamase (blaOXY-6-1) and fluoroquinolone (oqxB) resistance genes. Virulence factors encoding antiphagocytic, iron acquisition, and Intracellular survival properties were identified. Mobilome analysis revealed the presence of plasmid replicons (ColRNAI, FIA (pBK30683), IncFII, IncFII (Yp)) and insertion sequences (ISIX2, ISSen9, ISIS, IS1A). To our knowledge, this is the first description of antibiotic resistant K. grimontii from the water environment from Africa. The presence of this antibiotic resistant and potentially pathogenic isolate in the water environment is worrying as it may be disseminated into river systems used by informal settlements.