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Anokwah D, Asante-Kwatia E, Asante J, Obeng-Mensah D, Danquah CA, Amponsah IK, Ameyaw EO, Biney RP, Obese E, Oberer L, Amoako DG, Abia ALK, Mensah AY. Antibacterial, Resistance Modulation, Anti-Biofilm Formation, and Efflux Pump Inhibition Properties of Loeseneriella africana (Willd.) N. Halle (Celastraceae) Stem Extract and Its Constituents. Microorganisms 2023; 12:7. [PMID: 38276176 PMCID: PMC10819663 DOI: 10.3390/microorganisms12010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/02/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
This study investigated the antibacterial, resistance modulation, biofilm inhibition, and efflux pump inhibition potentials of Loeseneriella africana stem extract and its constituents. The antimicrobial activity was investigated by the high-throughput spot culture growth inhibition (HT-SPOTi) and broth microdilution assays. The resistance modulation activity was investigated using the anti-biofilm formation and efflux pump inhibition assays. Purification of the extract was carried out by chromatographic methods, and the isolated compounds were characterized based on nuclear magnetic resonance, Fourier transform infrared and mass spectrometry spectral data and comparison with published literature. The whole extract, methanol, ethyl acetate, and pet-ether fractions of L. africana all showed antibacterial activity against the test bacteria with MICs ranging from 62.5 to 500.0 µg/mL The whole extract demonstrated resistance modulation effect through strong biofilm inhibition and efflux pump inhibition activities against S. aureus ATCC 25923, E. coli ATCC 25922 and P. aeruginosa ATCC 27853. Chromatographic fractionation of the ethyl acetate fraction resulted in the isolation of a triterpenoid (4S,4αS,6αR,6βS,8αS,12αS,12βR,14αS,14βR)-4,4α,6β,8α,11,11,12β,14α-Octamethyloctadecahydropicene-1,3(2H,4H)-dione) and a phytosterol (β-sitosterol). These compounds showed antibacterial activity against susceptible bacteria at a MIC range of 31-125 µg/mL and potentiated the antibacterial activity of amoxicillin (at ¼ MIC of compounds) against E. coli and P. aeruginosa with modulation factors of 32 and 10, respectively. These compounds also demonstrated good anti-biofilm formation effect at a concentration range of 3-100 µg/mL, and bacterial efflux pump inhibition activity at ½ MIC and ¼ MIC against E. coli and P. aeruginosa. Loeseneriella africana stem bark extracts and constituents elicit considerable antibacterial, resistance modulation, and biofilm and efflux pump inhibition activities. The results justify the indigenous uses of L. africana for managing microbial infections.
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Affiliation(s)
- Daniel Anokwah
- School of Pharmacy and Pharmaceutical Sciences, College of Health and Allied Sciences, University of Cape Coast, PMB, Cape Coast, Ghana; (J.A.); (D.O.-M.); (E.O.A.); (R.P.B.); (E.O.)
| | - Evelyn Asante-Kwatia
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana; (E.A.-K.); (I.K.A.); (A.Y.M.)
| | - Jonathan Asante
- School of Pharmacy and Pharmaceutical Sciences, College of Health and Allied Sciences, University of Cape Coast, PMB, Cape Coast, Ghana; (J.A.); (D.O.-M.); (E.O.A.); (R.P.B.); (E.O.)
| | - Daniel Obeng-Mensah
- School of Pharmacy and Pharmaceutical Sciences, College of Health and Allied Sciences, University of Cape Coast, PMB, Cape Coast, Ghana; (J.A.); (D.O.-M.); (E.O.A.); (R.P.B.); (E.O.)
| | - Cynthia Amaning Danquah
- Department of Pharmacology, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana;
| | - Isaac Kingsley Amponsah
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana; (E.A.-K.); (I.K.A.); (A.Y.M.)
| | - Elvis Ofori Ameyaw
- School of Pharmacy and Pharmaceutical Sciences, College of Health and Allied Sciences, University of Cape Coast, PMB, Cape Coast, Ghana; (J.A.); (D.O.-M.); (E.O.A.); (R.P.B.); (E.O.)
| | - Robert Peter Biney
- School of Pharmacy and Pharmaceutical Sciences, College of Health and Allied Sciences, University of Cape Coast, PMB, Cape Coast, Ghana; (J.A.); (D.O.-M.); (E.O.A.); (R.P.B.); (E.O.)
| | - Ernest Obese
- School of Pharmacy and Pharmaceutical Sciences, College of Health and Allied Sciences, University of Cape Coast, PMB, Cape Coast, Ghana; (J.A.); (D.O.-M.); (E.O.A.); (R.P.B.); (E.O.)
| | - Lukas Oberer
- Novartis Institutes for BioMedical Research, CH-4056 Basel, Switzerland;
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (D.G.A.); (A.L.K.A.)
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (D.G.A.); (A.L.K.A.)
- Environmental Research Foundation, Westville 3630, South Africa
| | - Abraham Yeboah Mensah
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana; (E.A.-K.); (I.K.A.); (A.Y.M.)
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Asare Yeboah EE, Agyepong N, Mbanga J, Amoako DG, Abia ALK, Owusu-Ofori A, Essack SY. Multidrug-resistant Gram-negative bacterial colonization in patients, carriage by healthcare workers and contamination of hospital environments in Ghana. J Infect Public Health 2023; 16 Suppl 1:2-8. [PMID: 37953109 DOI: 10.1016/j.jiph.2023.10.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Patients already colonized with multidrug-resistant (MDR) Gram-negative bacteria (GNB) on admission to critical care units may be an important source of transmission of these bacteria in hospitals. We sought to determine the prevalence of MDR GNB colonization in patients, staff and the ward environment and to assess the risk factors for colonization of patients in wards. METHODS The study was conducted from April 2021 to July 2021 in a teaching hospital in Ghana. MDR GNB were isolated from rectal, and hand swabs were taken from patients on admission and after 48 h. Swabs from HCW's hands and the ward environment were also taken. Risk factors for colonization with MDR GNB were assessed using univariate and multivariate analysis. RESULTS MDR GNB rectal colonization rate among patients was 50.62% on admission and 44.44% after 48 h. MDR GNB were isolated from 6 (5.26%) and 24 (11.54%) of HCW's hand swabs and environmental swabs, respectively. Previous hospitalization (p-value = 0.021, OR, 95% CI= 7.170 (1.345-38.214) was significantly associated with colonization by MDR GNB after 48 h of admission. Age (21-30 years) (p-value = 0.022, OR, 95% CI = 0.103 (0.015-0.716) was significantly identified as a protective factor associated with a reduced risk of rectal MDR GNB colonization. CONCLUSION The high colonization of MDR GNB in patients, the carriage of MDR GNB on HCW's hands, and the contamination of hospital environments highlights the need for patient screening and stringent infection prevention and control practices to prevent the spread of MDR GNB in hospitals.
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Affiliation(s)
- Esther Eyram Asare Yeboah
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Pharmaceutical Sciences, School of Pharmacy, Central University, Miotso, Ghana.
| | - Nicholas Agyepong
- Department of Pharmaceutical Sciences, Sunyani Technical University, Sunyani, Ghana
| | - Joshua Mbanga
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; National University of Science and Technology, Department of Applied Biology & Biochemistry, P Bag AC939, Bulawayo, Zimbabwe
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Integrative Biology and Bioinformatics, University of Guelph, Ontario, Canada
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Environmental Research Foundation, Westville 3630, South Africa
| | - Alexander Owusu-Ofori
- Department of Clinical Microbiology, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana; Clinical Microbiology Unit, Laboratory Services Directorate, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Yousif M, Rachida S, Taukobong S, Ndlovu N, Iwu-Jaja C, Howard W, Moonsamy S, Mhlambi N, Gwala S, Levy JI, Andersen KG, Scheepers C, von Gottberg A, Wolter N, Bhiman JN, Amoako DG, Ismail A, Suchard M, McCarthy K. SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses. Nat Commun 2023; 14:6325. [PMID: 37816740 PMCID: PMC10564906 DOI: 10.1038/s41467-023-41369-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/30/2023] [Indexed: 10/12/2023] Open
Abstract
As global SARS-CoV-2 burden and testing frequency have decreased, wastewater surveillance has emerged as a key tool to support clinical surveillance efforts. The aims of this study were to identify and characterize SARS-CoV-2 variants in wastewater samples collected from urban centers across South Africa. Here we show that wastewater sequencing analyses are temporally concordant with clinical genomic surveillance and reveal the presence of multiple lineages not detected by clinical surveillance. We show that wastewater genomics can support SARS-CoV-2 epidemiological investigations by reliably recovering the prevalence of local circulating variants, even when clinical samples are not available. Further, we find that analysis of mutations observed in wastewater can provide a signal of upcoming lineage transitions. Our study demonstrates the utility of wastewater genomics to monitor evolution and spread of endemic viruses.
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Affiliation(s)
- Mukhlid Yousif
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa.
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Said Rachida
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Setshaba Taukobong
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nkosenhle Ndlovu
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Chinwe Iwu-Jaja
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Wayne Howard
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shelina Moonsamy
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nompilo Mhlambi
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sipho Gwala
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Cathrine Scheepers
- SAMRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel Gyamfi Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa
| | - Melinda Suchard
- Department of Chemical Pathology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Kerrigan McCarthy
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Christoffels A, Mboowa G, van Heusden P, Makhubela S, Githinji G, Mwangi S, Onywera H, Nnaemeka N, Amoako DG, Olawoye I, Diallo A, Mbala-Kingebeni P, Oyola SO, Adu B, Mvelase C, Ondoa P, Dratibi FA, Sow A, Gumede N, Tessema SK, Ouma AO, Tebeje YK. A pan-African pathogen genomics data sharing platform to support disease outbreaks. Nat Med 2023; 29:1052-1055. [PMID: 37161068 DOI: 10.1038/s41591-023-02266-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Alan Christoffels
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia.
- South African National Bioinformatics Institute, SAMRC Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa.
| | - Gerald Mboowa
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia
| | - Peter van Heusden
- South African National Bioinformatics Institute, SAMRC Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa
| | | | - George Githinji
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Sarah Mwangi
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia
| | - Harris Onywera
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia
| | | | - Daniel Gyamfi Amoako
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- College of Health Sciences, University of KwaZulu Natal, Durban, South Africa
| | - Idowu Olawoye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | | | - Placide Mbala-Kingebeni
- Institut National de Recherche Biomédicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Samuel O Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | | | - Pascale Ondoa
- African Society for Laboratory Medicine (ASLM), Addis Ababa, Ethiopia
| | | | | | - Nicksy Gumede
- WHO Regional Office for Africa, Brazzaville, Republic of Congo
| | - Sofonias K Tessema
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia.
| | - Ahmed Ogwell Ouma
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia
| | - Yenew Kebede Tebeje
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia
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5
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Ismael N, van Wyk S, Tegally H, Giandhari J, San JE, Moir M, Pillay S, Utpatel C, Singh L, Naidoo Y, Ramphal U, Mabunda N, Abílio N, Arnaldo P, Xavier J, Amoako DG, Everatt J, Ramphal Y, Maharaj A, de Araujo L, Anyaneji UJ, Tshiabuila D, Viegas S, Lessells R, Engelbrecht S, Gudo E, Jani I, Niemann S, Wilkinson E, de Oliveira T. Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique. PLOS Glob Public Health 2023; 3:e0001593. [PMID: 36963096 PMCID: PMC10021167 DOI: 10.1371/journal.pgph.0001593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/20/2023] [Indexed: 03/08/2023]
Abstract
Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020 and it has since spread to all provinces in the country. To investigate the introductions and spread of SARS-CoV-2 in Mozambique, 1 142 whole genome sequences sampled within Mozambique were phylogenetically analyzed against a globally representative set, reflecting the first 25 months of the epidemic. The epidemic in the country was marked by four waves of infection, the first associated with B.1 ancestral lineages, while the Beta, Delta, and Omicron Variants of Concern (VOCs) were responsible for most infections and deaths during the second, third, and fourth waves. Large-scale viral exchanges occurred during the latter three waves and were largely attributed to southern African origins. Not only did the country remain vulnerable to the introductions of new variants but these variants continued to evolve within the borders of the country. Due to the Mozambican health system already under constraint, and paucity of data in Mozambique, there is a need to continue to strengthen and support genomic surveillance in the country as VOCs and Variants of interests (VOIs) are often reported from the southern African region.
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Affiliation(s)
- Nalia Ismael
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - James Emmanuel San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Lavanya Singh
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Nuro Abílio
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Joicymara Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brasil
| | - Daniel Gyamfi Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - Josie Everatt
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa
| | - Yajna Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Arisha Maharaj
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Leonardo de Araujo
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Ugochukwu J. Anyaneji
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Derek Tshiabuila
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Sofia Viegas
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Richard Lessells
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eduardo Gudo
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Ilesh Jani
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Túlio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
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6
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Wolter N, Jassat W, Walaza S, Welch R, Moultrie H, Groome M, Amoako DG, Everatt J, Bhiman JN, Scheepers C, Tebeila N, Chiwandire N, du Plessis M, Govender N, Ismail A, Glass A, Mlisana K, Stevens W, Treurnicht FK, Makatini Z, Hsiao NY, Parboosing R, Wadula J, Hussey H, Davies MA, Boulle A, von Gottberg A, Cohen C. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study. Lancet 2022; 399:437-446. [PMID: 35065011 PMCID: PMC8769664 DOI: 10.1016/s0140-6736(22)00017-4] [Citation(s) in RCA: 613] [Impact Index Per Article: 306.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/24/2021] [Accepted: 01/04/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND The SARS-CoV-2 omicron variant of concern was identified in South Africa in November, 2021, and was associated with an increase in COVID-19 cases. We aimed to assess the clinical severity of infections with the omicron variant using S gene target failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy. METHODS We did data linkages for national, South African COVID-19 case data, SARS-CoV-2 laboratory test data, SARS-CoV-2 genome data, and COVID-19 hospital admissions data. For individuals diagnosed with COVID-19 via TaqPath PCR tests, infections were designated as either SGTF or non-SGTF. The delta variant was identified by genome sequencing. Using multivariable logistic regression models, we assessed disease severity and hospitalisations by comparing individuals with SGTF versus non-SGTF infections diagnosed between Oct 1 and Nov 30, 2021, and we further assessed disease severity by comparing SGTF-infected individuals diagnosed between Oct 1 and Nov 30, 2021, with delta variant-infected individuals diagnosed between April 1 and Nov 9, 2021. FINDINGS From Oct 1 (week 39), 2021, to Dec 6 (week 49), 2021, 161 328 cases of COVID-19 were reported in South Africa. 38 282 people were diagnosed via TaqPath PCR tests and 29 721 SGTF infections and 1412 non-SGTF infections were identified. The proportion of SGTF infections increased from two (3·2%) of 63 in week 39 to 21 978 (97·9%) of 22 455 in week 48. After controlling for factors associated with hospitalisation, individuals with SGTF infections had significantly lower odds of admission than did those with non-SGTF infections (256 [2·4%] of 10 547 vs 121 [12·8%] of 948; adjusted odds ratio [aOR] 0·2, 95% CI 0·1-0·3). After controlling for factors associated with disease severity, the odds of severe disease were similar between hospitalised individuals with SGTF versus non-SGTF infections (42 [21%] of 204 vs 45 [40%] of 113; aOR 0·7, 95% CI 0·3-1·4). Compared with individuals with earlier delta variant infections, SGTF-infected individuals had a significantly lower odds of severe disease (496 [62·5%] of 793 vs 57 [23·4%] of 244; aOR 0·3, 95% CI 0·2-0·5), after controlling for factors associated with disease severity. INTERPRETATION Our early analyses suggest a significantly reduced odds of hospitalisation among individuals with SGTF versus non-SGTF infections diagnosed during the same time period. SGTF-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. Some of this reduced severity is probably a result of previous immunity. FUNDING The South African Medical Research Council, the South African National Department of Health, US Centers for Disease Control and Prevention, the African Society of Laboratory Medicine, Africa Centers for Disease Control and Prevention, the Bill & Melinda Gates Foundation, the Wellcome Trust, and the Fleming Fund.
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Affiliation(s)
- Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard Welch
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Harry Moultrie
- Centre for Tuberculosis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michelle Groome
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Daniel Gyamfi Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Josie Everatt
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cathrine Scheepers
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Naume Tebeila
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nicola Chiwandire
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nevashan Govender
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Koleka Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy Stevens
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Florette K Treurnicht
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Zinhle Makatini
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Nei-Yuan Hsiao
- National Health Laboratory Service, Johannesburg, South Africa; Division of Medical Virology, University of Cape Town, Cape Town, South Africa
| | - Raveen Parboosing
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Virology, University of KwaZulu-Natal, Durban, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Jeannette Wadula
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa; Department of Clinical Microbiology and Infectious Diseases, CH Baragwanath Academic Hospital, Johannesburg, South Africa
| | - Hannah Hussey
- Western Cape Government Health and School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Mary-Ann Davies
- Western Cape Government Health and School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrew Boulle
- Western Cape Government Health and School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Fatoba DO, Amoako DG, Akebe ALK, Ismail A, Essack SY. Genomic analysis of antibiotic-resistant Enterococcus spp. reveals novel enterococci strains and the spread of plasmid-borne Tet(M), Tet(L) and Erm(B) genes from chicken litter to agricultural soil in South Africa. J Environ Manage 2022; 302:114101. [PMID: 34800768 DOI: 10.1016/j.jenvman.2021.114101] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Manure from food animals exposed to antibiotics is often used as soil fertiliser, potentially releasing antibiotic-resistant bacteria (ARB) with diverse antibiotic-resistance genes (ARGs) into the soil. To determine the impact of chicken litter application on the soil resistome, Enterococcus spp. isolated from chicken litter and soil samples collected before and after the soil amendment were characterised, using whole-genome sequencing and bioinformatics tools. Nineteen Enterococcus spp. isolates from the three sources were sequenced on Illumina Miseq platform to ascertain the isolates' resistome, mobilome, virulome, clonality, and phylogenomic relationships. Multilocus sequence typing (MLST) analysis revealed eight novel sequence types (STs) (ST1700, ST1752, ST1753, ST1754, ST1755, ST1756, ST1004, and ST1006). The isolates harboured multiple resistance genes including those conferring resistance to inter alia macrolides-lincosamide-streptogramin (erm(B), lnu(B), lnu(G), lsaA, lsaE, eat(A), msr(C)), tetracycline (tet(M), tet(L), tet(S)), aminoglycosides (aac(6')-Ii, aac(6')-Iih, ant(6)-Ia, aph(3')-III, ant(9)-Ia), fluoroquinolones (efmA, and emeA), vancomycin (VanC {VanC-2, VanXY, VanXYC-3, VanXYC-4, VanRC}), and chloramphenicol (cat). The litter-amended soil harboured new ARB (particularly E. faecium) and ARGs (ant(6)-Ia, aac(6')-Ii, aph(3')-III), lnu(G), msr(C), and eat(A), efmA) that were not previously detected in the soil. The identified ARGs were associated with diverse mobile genetic elements (MGEs) such as insertion sequences (IS6, ISL3, IS256, IS30), transposons (Tn3 and Tn916) and plasmids (repUS43, repUS1, rep9b, and rep 22). Twenty-eight virulence genes encoding adherence/biofilm formation (ebpA, ebpB, ebpC), antiphagocytosis (elrA) and bacterial sex pheromones (Ccf10, cOB1, cad, and camE), were detected in the genomes of the isolates. Phylogenomic analysis revealed a close relationship between a few isolates from litter-amended soil and the chicken litter isolates. The differences in the ARG and ARB profiles in the soil before and after the litter amendment and their association with diverse MGEs indicate the mobilisation and transmission of ARGs and ARB from the litter to the soil.
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Affiliation(s)
- Dorcas Oladayo Fatoba
- Antimicrobial Research Unit, College of Health Science, University of KwaZulu-Natal, Durban, South Africa.
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Science, University of KwaZulu-Natal, Durban, South Africa; Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Abia Luther King Akebe
- Antimicrobial Research Unit, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
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Aduah M, Adzitey F, Amoako DG, Abia ALK, Ekli R, Teye GA, Shariff AHM, Huda N. Not All Street Food Is Bad: Low Prevalence of Antibiotic-Resistant Salmonella enterica in Ready-to-Eat (RTE) Meats in Ghana Is Associated with Good Vendors' Knowledge of Meat Safety. Foods 2021; 10:foods10051011. [PMID: 34066440 PMCID: PMC8148193 DOI: 10.3390/foods10051011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022] Open
Abstract
Foodborne infections due to the consumption of meat is a significant threat to public health. However, good vendor and consumer knowledge of meat safety could prevent meat contamination with and transmission of foodborne pathogens like Salmonella. Thus, this study investigated the vendor and consumer perception, knowledge, and practices of meat safety regarding ready-to-eat (RTE) meat and how this affected the prevalence and antibiotic susceptibility of Salmonella enterica in RTE meats in the streets of Ghana. A semi-structured questionnaire was used to obtain the demographics, knowledge, and practices of meat safety data from RTE meat vendors (n = 300) and consumers (n = 382). Salmonella enterica detection was done according to the United State of America (USA)-Food and Drugs Administration (FDA) Bacteriological Analytical Manual. The disk diffusion method was used for antibiotic resistance testing. The results revealed that most of the respondents had heard of meat safety (98.3% vendors, 91.8% consumers) and knew that meat could be contaminated by poor handling (100.0% vendors, 88.9% consumers). The respondents knew that regular hand washing reduced the risk of meat contamination (100.0% vendors, 94.0% consumers). Responses to the practices of meat safety by vendors were generally better. A very low Salmonella enterica prevalence was observed in the samples, ranging between 0.0 and 4.0% for guinea fowl and beef, respectively. However, the six isolates obtained were resistant to five of the nine antibiotics tested, with all isolates displaying different resistance profiles. Overall, the good knowledge and practice of meat safety demonstrated by the respondents corroborated the negligible prevalence of Salmonella in this study, reiterating the importance of vendor meat safety knowledge. However, the presence of resistant Salmonella enterica in some of the meat samples, albeit in a very low prevalence, warrants stricter sanitary measures and greater meat safety awareness in the general population to prevent meat-borne infections and potential transmission of drug-resistant bacteria to humans.
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Affiliation(s)
- Martin Aduah
- Department of Animal Science, University for Development Studies, Tamale P.O. Box TL 1882, Ghana; (M.A.); (R.E.); (G.A.T.)
| | - Frederick Adzitey
- Department of Animal Science, University for Development Studies, Tamale P.O. Box TL 1882, Ghana; (M.A.); (R.E.); (G.A.T.)
- Department of Veterinary Science, University for Development Studies, Tamale P.O. Box TL 1882, Ghana
- Correspondence: (F.A.); (N.H.); Tel.: +233-249-995-310 (F.A.); +60-124-843-144 (N.H.)
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (D.G.A.); (A.L.K.A.)
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (D.G.A.); (A.L.K.A.)
| | - Rejoice Ekli
- Department of Animal Science, University for Development Studies, Tamale P.O. Box TL 1882, Ghana; (M.A.); (R.E.); (G.A.T.)
| | - Gabriel Ayum Teye
- Department of Animal Science, University for Development Studies, Tamale P.O. Box TL 1882, Ghana; (M.A.); (R.E.); (G.A.T.)
| | - Amir H. M. Shariff
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia;
| | - Nurul Huda
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia;
- Department of Food Science, Faculty of Agriculture, Universitas Sebalas Maret, Surakarta 57126, Central Java, Indonesia
- Correspondence: (F.A.); (N.H.); Tel.: +233-249-995-310 (F.A.); +60-124-843-144 (N.H.)
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9
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Phiri AF, Abia ALK, Amoako DG, Mkakosya R, Sundsfjord A, Essack SY, Simonsen GS. Burden, Antibiotic Resistance, and Clonality of Shigella spp. Implicated in Community-Acquired Acute Diarrhoea in Lilongwe, Malawi. Trop Med Infect Dis 2021; 6:tropicalmed6020063. [PMID: 33925030 PMCID: PMC8167763 DOI: 10.3390/tropicalmed6020063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022] Open
Abstract
Although numerous studies have investigated diarrhoea aetiology in many sub-Saharan African countries, recent data on Shigella species’ involvement in community-acquired acute diarrhoea (CA-AD) in Malawi are scarce. This study investigated the incidence, antibiotic susceptibility profile, genotypic characteristics, and clonal relationships of Shigella flexneri among 243 patients presenting with acute diarrhoea at a District Hospital in Lilongwe, Malawi. Shigella spp. were isolated and identified using standard microbiological and serological methods and confirmed by identifying the ipaH gene using real-time polymerase chain reaction. The isolates’ antibiotic susceptibility to 20 antibiotics was determined using the VITEK 2 system according to EUCAST guidelines. Genes conferring resistance to sulfamethoxazole (sul1, sul2 and sul3), trimethoprim (dfrA1, dfrA12 and dfrA17) and ampicillin (oxa-1 and oxa-2), and virulence genes (ipaBCD, sat, ial, virA, sen, set1A and set1B) were detected by real-time PCR. Clonal relatedness was assessed using ERIC-PCR. Thirty-four Shigella flexneri isolates were isolated (an overall incidence of 14.0%). All the isolates were fully resistant to sulfamethoxazole/trimethoprim (100%) and ampicillin (100%) but susceptible to the other antibiotics tested. The sul1 (79%), sul2 (79%), sul3 (47%), dfrA12 (71%) and dfrA17 (56%) sulfonamide and trimethoprim resistance genes were identified; Oxa-1, oxa-2 and dfrA1 were not detected. The virulence genes ipaBCD (85%), sat (85%), ial (82%), virA (76%), sen (71%), stx (71%), set1A (26%) and set1B (18%) were detected. ERIC-PCR profiling revealed that the Shigella isolates were genetically distinct and clonally unrelated, indicating the potential involvement of genetically distinct S. flexneri in CA-AD in Malawi. The high percentage resistance to ampicillin and sulfamethoxazole/trimethoprim and the presence of several virulence determinants in these isolates emphasises a need for continuous molecular surveillance studies to inform preventive measures and management of Shigella-associated diarrhoeal infections in Malawi.
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Affiliation(s)
- Abel F.N.D. Phiri
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.F.N.D.P.); (D.G.A.); (S.Y.E.)
- National Microbiology Reference Laboratory, Ministry of Health, Lilongwe 3, Malawi
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.F.N.D.P.); (D.G.A.); (S.Y.E.)
- Correspondence:
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.F.N.D.P.); (D.G.A.); (S.Y.E.)
| | - Rajab Mkakosya
- Department of Pathology, College of Medicine, University of Malawi, Blantyre 3, Malawi;
| | - Arnfinn Sundsfjord
- Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway; (A.S.); (G.S.S.)
- Faculty of Health Sciences, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.F.N.D.P.); (D.G.A.); (S.Y.E.)
| | - Gunnar Skov Simonsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway; (A.S.); (G.S.S.)
- Faculty of Health Sciences, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway
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Sithole V, Amoako DG, Abia ALK, Perrett K, Bester LA, Essack SY. Occurrence, Antimicrobial Resistance, and Molecular Characterization of Campylobacter spp. in Intensive Pig Production in South Africa. Pathogens 2021; 10:pathogens10040439. [PMID: 33917115 PMCID: PMC8067824 DOI: 10.3390/pathogens10040439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/16/2022] Open
Abstract
Campylobacter spp. are among the leading foodborne pathogens, causing campylobacteriosis, a zoonotic infection that results in bacterial gastroenteritis and diarrheal disease in animals and humans. This study investigated the molecular epidemiology of antibiotic-resistant Campylobacter spp. isolated across the farm-to-fork-continuum in an intensive pig production system in South Africa. Following ethical approval, samples were collected over sixteen weeks from selected critical points (farm, transport, abattoir, and retail) using a farm-to-fork sampling approach according to WHO-AGISAR guidelines. Overall, 520 samples were investigated for the presence of Campylobacter spp., which were putatively identified using selective media with identity and speciation confirmed by polymerase chain reaction (PCR) of specific genes. Resistance profiles were ascertained by the Kirby-Bauer disk diffusion method. Antibiotic resistance and virulence genes were identified using PCR and DNA sequencing. Clonal relatedness was determined using ERIC-PCR. Altogether, 378/520 (72.7%) samples were positive for Campylobacter spp., with Campylobacter coli being the predominant species (73.3%), followed by Campylobacter jejuni (17.7%); 8.9% of the isolates were classified as "other spp". Relatively high resistance was observed in C. coli and C. jejuni to erythromycin (89% and 99%), streptomycin (87% and 93%), tetracycline (82% and 96%), ampicillin (69% and 85%), and ciprofloxacin (53% and 67%), respectively. Multidrug resistance (MDR) was noted in 330 of the 378 (87.3%) isolates. The antibiotic resistance genes observed were tetO (74.6%), blaOXA-61 (2.9%), and cmeB (11.1%), accounting for the resistance to tetracycline and ampicillin. The membrane efflux pump (cmeB), conferring resistance to multiple antibiotics, was also detected in most resistant isolates. Chromosomal mutations in gyrA (Thr-86-Ile) and 23S rRNA (A2075G and A2074C) genes, conferring quinolone and erythromycin resistance, respectively, were also found. Of the virulence genes tested, ciaB, dnaJ, pldA, cdtA, cdtB, cdtC, and cadF were detected in 48.6%, 61.1%, 17.4%, 67.4%, 19.3%, 51%, and 5% of all Campylobacter isolates, respectively. Clonal analysis revealed that isolates along the continuum were highly diverse, with isolates from the same sampling points belonging to the same major ERIC-types. The study showed relatively high resistance to antibiotics commonly used in intensive pig production in South Africa with some evidence, albeit minimal, of transmission across the farm-to-fork continuum. This, together with the virulence profiles present in Campylobacter spp., presents a challenge to food safety and a potential risk to human health, necessitating routine surveillance, antibiotic stewardship, and comprehensive biosecurity in intensive pig production.
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Affiliation(s)
- Viwe Sithole
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (V.S.); (S.Y.E.)
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (V.S.); (S.Y.E.)
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
- Correspondence: (D.G.A.); (A.L.K.A.); Tel.: +27-(0)8-4330-8957 (D.G.A.); +27-(0)7-3440-3343 (A.L.K.A.)
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (V.S.); (S.Y.E.)
- Correspondence: (D.G.A.); (A.L.K.A.); Tel.: +27-(0)8-4330-8957 (D.G.A.); +27-(0)7-3440-3343 (A.L.K.A.)
| | - Keith Perrett
- Epidemiology Section, KwaZulu-Natal Agriculture & Rural Development-Veterinary Service, Pietermaritzburg 3201, South Africa;
| | - Linda A. Bester
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (V.S.); (S.Y.E.)
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Sineke N, Asante J, Amoako DG, Abia ALK, Perrett K, Bester LA, Essack SY. Staphylococcus aureus in Intensive Pig Production in South Africa: Antibiotic Resistance, Virulence Determinants, and Clonality. Pathogens 2021; 10:pathogens10030317. [PMID: 33800367 PMCID: PMC8000748 DOI: 10.3390/pathogens10030317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Although Staphylococcus aureus is a major threat to the veterinary, agricultural, and public health sectors because of its zoonotic potential, studies on its molecular characterisation in intensive animal production are rare. We phenotypically and genotypically characterised antibiotic-resistant S. aureus in intensive pig production in South Africa, using the farm-to-fork approach. Samples (n = 461) were collected from the farm, transport vehicles, and the abattoir using the World Health Organisation on Integrated Surveillance of Antimicrobial Resistance (WHO-AGISAR) sampling protocol. Bacteria were isolated using selective media and identified using biochemical tests and polymerase chain reaction (PCR). Phenotypic resistance was determined using the disk diffusion method. Selected resistance and virulence genes were investigated using PCR. Clonality among the isolates was determined using the repetitive element sequence-PCR. In all, 333 presumptive staphylococcal isolates were obtained, with 141/333 (42.3%) identified as staphylococci biochemically. Ninety-seven (97; 68.8%) were confirmed as S. aureus using PCR, 52.6% of which were identified as methicillin-resistant S. aureus (MRSA) through the mecA gene. All the 97 S. aureus isolates (100%) were resistant to at least one of the antibiotics tested, with the highest resistance observed against erythromycin and clindamycin (84.50% each), and the lowest observed against amikacin (2.10%); 82.47% (80/97) were multidrug-resistant with an average multiple antibiotic resistance index of 0.50. Most of the phenotypically resistant isolates carried at least one of the corresponding resistance genes tested, ermC being the most detected. hla was the most detected virulence gene (38.14%) and etb was the least (1.03%). Genetic fingerprinting revealed diverse MRSA isolates along the farm-to-fork continuum, the major REP types consisting of isolates from different sources suggesting a potential transmission along the continuum. Resistance to antibiotics used as growth promoters was evidenced by the high prevalence of MDR isolates with elevated multiple antibiotic resistance indices >0.2, specifically at the farm, indicating exposure to high antibiotic use environments, necessitating antibiotic stewardship and proper infection control measures in pig husbandry and intensive pig production.
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Affiliation(s)
- Ncomeka Sineke
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (N.S.); (J.A.); (S.Y.E.)
| | - Jonathan Asante
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (N.S.); (J.A.); (S.Y.E.)
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (N.S.); (J.A.); (S.Y.E.)
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg 2131, South Africa
- Correspondence: (D.G.A.); (A.L.K.A.)
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (N.S.); (J.A.); (S.Y.E.)
- Correspondence: (D.G.A.); (A.L.K.A.)
| | - Keith Perrett
- Epidemiology Section, KwaZulu-Natal Agriculture & Rural Development-Veterinary Service, Pietermaritzburg 3201, South Africa;
| | - Linda A. Bester
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (N.S.); (J.A.); (S.Y.E.)
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Mbanga J, Abia ALK, Amoako DG, Essack SY. 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. Microb Drug Resist 2021; 27:904-918. [PMID: 33512279 DOI: 10.1089/mdr.2020.0380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
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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Affiliation(s)
- Joshua Mbanga
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Mbanga J, Abia ALK, Amoako DG, Essack SY. Quantitative microbial risk assessment for waterborne pathogens in a wastewater treatment plant and its receiving surface water body. BMC Microbiol 2020; 20:346. [PMID: 33183235 PMCID: PMC7663859 DOI: 10.1186/s12866-020-02036-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/05/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Access to safe water for drinking and domestic activities remains a challenge in emerging economies like South Africa, forcing resource-limited communities to use microbiologically polluted river water for personal and household purposes, posing a public health risk. This study quantified bacterial contamination and the potential health hazards that wastewater treatment plant (WWTP) workers and communities may face after exposure to waterborne pathogenic bacteria in a WWTP and its associated surface water, respectively. RESULTS Escherichia coli (Colilert®-18/ Quanti-Tray® 2000) and enterococci (Enterolert®/ Quanti-Tray® 2000) were quantified and definitively identified by real-time polymerase chain reaction targeting the uidA and tuf genes, respectively. An approximate beta-Poisson dose-response model was used to estimate the probability of infection (Pi) with pathogenic E. coli. Mean E. coli concentration ranged from 2.60E+ 02/100 mL to 4.84E+ 06/100 mL; enterococci ranged from 2.60E+ 02/100 mL to 3.19E+ 06/100 mL across all sampled sites. Of the 580 E. coli isolates obtained from this study, 89.1% were intestinal, and 7.6% were extraintestinal pathogenic E. coli. The 579 enterococci obtained were 50.4% E. faecalis (50.4%), 31.4% E. faecium, 3.5%, E. casseliflavus and 0.7% E. gallinarum. The community health risk stemming from the use of the water for recreational and domestic purposes revealed a greater health risk (Pi) from the ingestion of 1 mL of river water from upstream (range, 55.1-92.9%) than downstream (range, 26.8-65.3%) sites. The occupational risk of infection with pathogenic E. coli for workers resulting from a once-off unintentional consumption of 1 mL of water was 0% (effluent) and 23.8% (raw influent). Multiple weekly exposures of 1 mL over a year could result in a Pi of 1.2 and 100% for the effluent and influent, respectively. CONCLUSION Our findings reveal that there is a potentially high risk of infection for WWTP workers and communities that use river water upstream and downstream of the investigated WWTP.
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Affiliation(s)
- Joshua Mbanga
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
- Department of Applied Biology and Biochemistry, National University of Science and Technology, P.O Box AC 939 Ascot, Bulawayo, 00263, Zimbabwe.
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of Kwazulu-Natal, Private Bag X54001, Durban, 4000, South Africa
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Sosibo S, Amoako DG, Somboro AM, Sun DD, Ngila JC, Kumalo H. Understanding the Binding Mechanism of Antagonist (AZD3293) Against BACE-1: Molecular Insights into Alzheimer’s Drug Discovery. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666191029142640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
β-site amyloid precursor protein cleaving enzyme (BACE 1) is the ratelimiting
enzyme in the formation of neurotoxic β-amyloid (Aβ) residues (Aβ1-40 or Aβ1-42)
considered as key players in the onset of Alzheimer’s Disease (AD). Consequently, BACE 1 is one
of the principal targets of anti-AD therapy with many small molecule BACE 1 inhibitors (BACE
1Is) in clinical trials. AZD3293 (Lanabecestat) is a BACE 1I that concluded in phase 2/3 clinical
trials. Due to the limited knowledge about the interaction of this drug with the BACE 1 enzyme, in
the present study, we performed comprehensive Molecular Dynamics (MD) analysis to understand
the binding mechanism of AZD3293 to BACE 1.
Methods:
A production run of 120 ns is carried out and results are analysed using Root Mean
Square Deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg) to
explain the stability of enzyme ligand complex. Further, the distance (d1) between the flap tip
(Thr72) and the hinge residue of the flexible loop (Thr328), in relation to θ1 (Thr72–Asp228-
Thr328), and to the dihedral angle δ (Thr72-Asp35-Asp228-Thr328) were measured.
Results:
The presence of the ligand within the active site restricted conformational changes as
shown by decreased values of RMSF and average RMSD of atomic positions when compared to the
values of the apoenzyme. Further analysis via the flap dynamics approach revealed that the
AZD3293 decreases the flexibility of binding residues and made them rigid by altering the
conformational changes.
Conclusion:
The prospective binding modes of AZD3293 from this study may extend the
knowledge of the BACE 1-drug interaction and pave the way to design analogues with similar
inhibitory properties needed to slow the progression of Alzheimer’s disease.
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Affiliation(s)
- Sphelele Sosibo
- School of Applied Chemistry, University of Johannesburg, Doornfontein, Johannesburg 2001, South Africa
| | - Daniel Gyamfi Amoako
- Drug Research and Innovation Research Unit, School of Medical Biochemistry, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
| | - Anou Moise Somboro
- Drug Research and Innovation Research Unit, School of Medical Biochemistry, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
| | - Darren Delai Sun
- School of Applied Chemistry, University of Johannesburg, Doornfontein, Johannesburg 2001, South Africa
| | - Jane Catherine Ngila
- School of Applied Chemistry, University of Johannesburg, Doornfontein, Johannesburg 2001, South Africa
| | - Hezekiel Kumalo
- Drug Research and Innovation Research Unit, School of Medical Biochemistry, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
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Adzitey F, Teye GA, Amoako DG. Prevalence, phylogenomic insights, and phenotypic characterization of Salmonella enterica isolated from meats in the Tamale metropolis of Ghana. Food Sci Nutr 2020; 8:3647-3655. [PMID: 32724627 PMCID: PMC7382109 DOI: 10.1002/fsn3.1647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/11/2020] [Accepted: 04/14/2020] [Indexed: 12/26/2022] Open
Abstract
Characterization of foodborne pathogens including Salmonella species allows for the determination of their relationship and/or relatedness with others. This study characterized Salmonella enterica (S. enterica) isolated from five meat types (mutton, beef, chevon, guinea fowl, and local chicken) obtained from Tamale metropolis, Ghana. The S. enterica were characterized phenotypically (n = 44) based on their antibiotic resistance pattern with the disc diffusion method and genetically (n = 16) using whole-genome sequencing (WGS) as well as with bioinformatic analysis for the prediction of their clonal and phylogenomic relationship. Of the 225 meat samples examined, 107 (47.56%) were positive for S. enterica. Mutton was the most contaminated meat type and the least was local chicken. The 44 S. enterica isolates exhibited five different antibiotic patterns with multiple antibiotic resistance (MAR) index ranging from 0.13 to 0.63. Resistant to only erythromycin was most common and was exhibited by 34 isolates (77.27%). Four isolates were resistant to four different antibiotics (TeAmpSxtECro) with a percentage of 9.09%, while two isolates (4.55%) were resistant to none of the antibiotics. The sequenced S. enterica isolates consisted of 7 serovars and 8 clonal lineages with the S. enterica subsp. enterica serovar Hato (ST5308) being the predominate strain. Phylogenomic analysis showed that the isolates clustered according to their serovars and sequence types (clonal lineages). However, further metadata insights coupled with the phylogenomics revealed a complex intraspread of multiple S. enterica subsp. enterica serovars in diverse meat sources in areas in Tamale which is very worrying for infection management. In summary, our study provides useful insights into S. enterica in meat reservoirs obtained from Tamale metropolis, Ghana.
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Affiliation(s)
- Frederick Adzitey
- Department of Veterinary ScienceUniversity for Development StudiesTamaleGhana
- Department of Animal ScienceUniversity for Development StudiesTamaleGhana
| | - Gabriel Ayum Teye
- Department of Animal ScienceUniversity for Development StudiesTamaleGhana
| | - Daniel Gyamfi Amoako
- Infection Genomics and Applied Bioinformatics Division, Antimicrobial Research UnitUniversity of KwaZulu‐NatalDurbanSouth Africa
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Amoako DG, Somboro AM, Abia ALK, Molechan C, Perrett K, Bester LA, Essack SY. Antibiotic Resistance in Staphylococcus aureus from Poultry and Poultry Products in uMgungundlovu District, South Africa, Using the "Farm to Fork" Approach. Microb Drug Resist 2019; 26:402-411. [PMID: 31647362 DOI: 10.1089/mdr.2019.0201] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background: This study determined the prevalence and antibiotic susceptibility profiles of Staphylococcus aureus isolated from selected critical control points (farm, transport, abattoir, and retail product) in an intensive poultry production system in the uMgungundlovu District, South Africa, using the "farm to fork" approach. Materials and Methods: Three hundred eighty-four samples from poultry and poultry products were examined across the "farm to fork" continuum for S. aureus using selective media, biochemical tests, and API Staph kit and confirmed by polymerase chain reaction identification of the nuc gene. Antibiotic susceptibility testing of the isolates was determined by the Kirby-Bauer disc diffusion method to 19 antimicrobials and to vancomycin by the broth microdilution technique. Results: The overall prevalence rate of S. aureus was 31.25% (n = 120/384), distributed across the continuum: farm site (40), transport (15), abattoir (30), and retail point (35). The isolates were resistant to tetracycline (61.67%), penicillin G (55.83%), erythromycin (54.17%), clindamycin (43.33%), doxycycline (36.67%), ampicillin (34.17%), moxifloxacin (30.83%), amikacin (30.83%), trimethoprim-sulfamethoxazole (30.00%), and levofloxacin (23.33%). A 100% susceptibility to tigecycline, teicoplanin, vancomycin, nitrofurantoin, chloramphenicol, and linezolid was observed in all isolates. The rate of multidrug resistance and the multiple antibiotic resistance index of the strains were 39.17% and 0.23%, respectively. The isolates showed similar patterns of resistance to commonly used growth promoters and antibiotics in veterinary and human medicine belonging to the same class. Conclusion: It is evident that the different antibiotics and growth promoters used in poultry production are exerting selection pressure for the emergence and co-selection of antibiotic-resistant bacteria in the production system, necessitating efficient antibiotic stewardship guidelines to streamline their use.
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Affiliation(s)
- Daniel Gyamfi Amoako
- Antimicrobial Research Unit and College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anou M Somboro
- Antimicrobial Research Unit and College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Akebe L K Abia
- Antimicrobial Research Unit and College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Chantal Molechan
- Antimicrobial Research Unit and College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Keith Perrett
- Epidemiology Section, KwaZulu-Natal, Agriculture & Rural Development-Veterinary Service, Pietermaritzburg, South Africa
| | - Linda A Bester
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit and College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Amoako DG, Somboro AM, Abia ALK, Allam M, Ismail A, Bester LA, Essack SY. Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa. Pathogens 2019; 8:E166. [PMID: 31569754 PMCID: PMC6963616 DOI: 10.3390/pathogens8040166] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/19/2022] Open
Abstract
This study undertook genome mining and comparative genomics to gain genetic insights into the dominance of the methicillin-resistant Staphylococcus aureus (MRSA) endemic clone ST612-CC8-t1257-SCCmec_IVd(2B), obtained from the poultry food chain in South Africa. Functional annotation of the genome revealed a vast array of similar central metabolic, cellular and biochemical networks within the endemic clone crucial for its survival in the microbial community. In-silico analysis of the clone revealed the possession of uniform defense systems, restriction-modification system (type I and IV), accessory gene regulator (type I), arginine catabolic mobile element (type II), and type 1 clustered, regularly interspaced, short palindromic repeat (CRISPR)Cas array (N = 7 ± 1), which offer protection against exogenous attacks. The estimated pathogenic potential predicted a higher probability (average Pscore ≈ 0.927) of the clone being pathogenic to its host. The clone carried a battery of putative virulence determinants whose expression are critical for establishing infection. However, there was a slight difference in their possession of adherence factors (biofilm operon system) and toxins (hemolysins and enterotoxins). Further analysis revealed a conserved environmental tolerance and persistence mechanisms related to stress (oxidative and osmotic), heat shock, sporulation, bacteriocins, and detoxification, which enable it to withstand lethal threats and contribute to its success in diverse ecological niches. Phylogenomic analysis with close sister lineages revealed that the clone was closely related to the MRSA isolate SHV713 from Australia. The results of this bioinformatic analysis provide valuable insights into the biology of this endemic clone.
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Affiliation(s)
- Daniel Gyamfi Amoako
- Infection Genomics and Applied Bioinformatics Division, Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal; Durban 4000, South Africa.
| | - Anou M Somboro
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal; Durban 4000, South Africa.
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa.
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa.
| | - Linda A Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal; Durban 4000, South Africa.
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
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Mbelle NM, Osei Sekyere J, Amoako DG, Maningi NE, Modipane L, Essack SY, Feldman C. Genomic analysis of a multidrug-resistant clinical Providencia rettgeri (PR002) strain with the novel integron ln1483 and an A/C plasmid replicon. Ann N Y Acad Sci 2019; 1462:92-103. [PMID: 31549428 DOI: 10.1111/nyas.14237] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/26/2019] [Accepted: 08/31/2019] [Indexed: 11/29/2022]
Abstract
Whole-genome sequence analysis was performed on a multidrug-resistant Providencia rettgeri PR002 clinical strain isolated from the urine of a hospitalized patient in Pretoria, South Africa, in 2013. The resistome, mobilome, pathogenicity island(s), as well as virulence and heavy-metal resistance genes of the isolate, were characterized using whole-genome sequencing and bioinformatic analysis. PR002 had a genome assembly size of 4,832,624 bp with a GC content of 40.7%, an A/C2 plasmid replicase gene, four integrons/gene cassettes, 17 resistance genes, and several virulence and heavy metal resistance genes, confirming PR002 as a human pathogen. A novel integron, In1483, harboring the gene blaOXA-2 , was identified, with other uncharacterized class 1 integrons harboring aacA4cr and dfrA1. Aac(3')-IIa and blaSCO-1 , as well as blaPER-7 , sul2, and tet(B), were found bracketed by composite Tn3 transposons, and IS91, IS91, and IS4 family insertion sequences, respectively. PR002 was resistant to all antibiotics tested except amikacin, carbapenems, cefotaxime-clavulanate, ceftazidime-clavulanate, cefoxitin, and fosfomycin. PR002 was closely related to PR1 (USA), PRET_2032 (SPAIN), DSM_1131, and NCTC7477 clinical P. rettgeri strains, but not close enough to suggest it was imported into South Africa from other countries. Multidrug resistance in P. rettgeri is rare, particularly in clinical settings, making this case an important incident requiring urgent attention. This is also the first report of an A/C plasmid in P. rettgeri. The array, multiplicity, and diversity of resistance and virulence genes in this strain are concerning, necessitating stringent infection control, antibiotic stewardship, and periodic resistance surveillance/monitoring policies to preempt further horizontal and vertical spread of these resistance genes.
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Affiliation(s)
- Nontombi Marylucy Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.,National Health Laboratory Services, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Daniel Gyamfi Amoako
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Lesedi Modipane
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Charles Feldman
- Department of Internal Medicine, University of the Witwatersrand, Johannesburg, South Africa
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Agyepong N, Govinden U, Owusu-Ofori A, Amoako DG, Allam M, Janice J, Pedersen T, Sundsfjord A, Essack S. Genomic characterization of multidrug-resistant ESBL-producing Klebsiella pneumoniae isolated from a Ghanaian teaching hospital. Int J Infect Dis 2019; 85:117-123. [DOI: 10.1016/j.ijid.2019.05.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/13/2019] [Accepted: 05/20/2019] [Indexed: 10/26/2022] Open
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Amoako DG, Somboro AM, Abia ALK, Allam M, Ismail A, Bester L, Essack SY. Genomic analysis of methicillin-resistant Staphylococcus aureus isolated from poultry and occupational farm workers in Umgungundlovu District, South Africa. Sci Total Environ 2019; 670:704-716. [PMID: 30909047 DOI: 10.1016/j.scitotenv.2019.03.110] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
This study detected methicillin-resistant Staphylococcus aureus (MRSA) isolates circulating in poultry and farm workers at an intensive poultry production system in uMgungundlovu, South Africa and established the genetic relatedness and characteristics of the isolates using whole genome sequencing (WGS). A total of 145 S. aureus were isolated from poultry (120) and occupational workers (25) in the "farm to fork" continuum (farm, transport, slaughterhouse, and retail points). Twelve MRSA (12/145; 8.3%) isolates were found in the poultry food-chain. MRSA isolates were subjected to antibiotic susceptibility testing against a panel of 20 antibiotics using the broth dilution method and their whole genome was sequenced via the Illumina MiSeq. All the MRSA isolates were multi-drug resistant (MDR) and carried the mecA gene on the SCCmec mobile genetic element (MGE). The majority (11/12) of the MRSA isolates circulating between humans and animals in the continuum belonged to a human-associated clone, ST612-CC8-t1257-SCCmec_IVd (2B), previously reported in South Africa. Other MGEs present in the isolates included: plasmid replicons based on Rep 7 and 20, insertion sequences (IS1182), and prophages (phi2958PVL). Genomic analysis identified a distinct acquired antibiotic resistome in the clone, which accurately predicted the phenotypic antibiograms. Phylogenetic analysis clustered the isolates within the major cluster (I), suggesting the spread of the local dominant multidrug resistance MRSA clone ST612-CC8-t1257-SCCmec_IVd (2B) between humans and animals along the 'farm to fork' continuum. The findings of this study suggest the need to establish appropriate control measures to curb the spread of MDR-MRSA in the food chain.
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Affiliation(s)
- Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Anou Moise Somboro
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Pretoria, South Africa.
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Pretoria, South Africa.
| | - Linda Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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Somboro AM, Osei Sekyere J, Amoako DG, Kumalo HM, Khan R, Bester LA, Essack SY. In vitro potentiation of carbapenems with tannic acid against carbapenemase-producing enterobacteriaceae: exploring natural products as potential carbapenemase inhibitors. J Appl Microbiol 2018; 126:452-467. [PMID: 30365206 DOI: 10.1111/jam.14141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/17/2018] [Accepted: 10/19/2018] [Indexed: 02/03/2023]
Abstract
AIMS We hypothesized and confirmed that tannic acid (TA) reverses carbapenem resistance by inhibiting carbapenemases in class A and B carbapenemase-producing Enterobacteriaceae. METHODS AND RESULTS Minimum inhibitory concentrations of carbapenems in the presence and absence of TA and other efflux pump inhibitors, TA-carbapenemases inhibition assays and computational studies showed that TA had the greatest effect on metallo-β-lactamases (MBLs) followed by class A serine-β-lactamases (SBLs). TA completely reversed the MICs of MBL producers from between 32 and ≥512 mg l-1 to susceptible values (<4 mg l-1 ) while substantially reducing the MICs of SBLs from between 16 and >512 mg l-1 to <4 to 16 mg l-1 . Tolerable cytotoxic effect was observed for the concentrations tested (8-1024 mg l-1 ). TA inhibited enzymes with a marked difference of ≈50% inhibition (IC50 ) for NDM-1 (270 μmol l-1 ) and KPC-2 (15 μmol l-1 ). CONCLUSION TA inhibited both MBLs and SBLs by targeting their hydrophobic sites. Moreover, TA had a stronger binding affinity for MBLs than SBLs as the MBLs, specifically VIM-1 (-43·7220 ± 0·4513 kcal mol-1 ) and NDM-1(-44·2329 ± 0·3806 kcal mol-1 ), interact with a larger number of their catalytic active-site residues than that of OXA-48 (-22·5275 ± 0·1300 kcal mol-1 ) and KPC-2 (-22·1164 ± 0·0111 kcal mol-1 ). SIGNIFICANCE AND IMPACT OF THE STUDY Tannic acid or its analogues could be developed into carbapenemase-inhibiting adjuvants to restore carbapenem activity in CRE infections, save many lives and reduce healthcare associated costs.
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Affiliation(s)
- A M Somboro
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - J Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - D G Amoako
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - H M Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - R Khan
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - L A Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - S Y Essack
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Founou LL, Amoako DG, Founou RC, Essack SY. Antibiotic Resistance in Food Animals in Africa: A Systematic Review and Meta-Analysis. Microb Drug Resist 2018; 24:648-665. [PMID: 29683779 DOI: 10.1089/mdr.2017.0383] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES This study critically reviewed the published literature and performed a meta-analysis to determine the overall burden of antibiotic-resistant bacteria in food animals in Africa. METHODS English and French published articles indexed in EBSCOhost, PubMed, Web of Science, and African Journals Online were retrieved, with searches being conducted up to August, 2015. Data were pooled and meta-analysis performed using a random-effects model, and the results are described as event rates. RESULTS According to the predefined inclusion and exclusion criteria, 17 articles out of the 852 retrieved were eligible for the qualitative and quantitative analysis. The studies included were mainly conducted in Nigeria, with Escherichia coli, Salmonella spp., and Campylobacter spp. being the main bacteria. The pooled estimates showed high level of antibiotic resistance (ABR) (86%; p < 0.001) and multidrug resistance (73%; p = 0.003). CONCLUSION Our results suggest that ABR is substantively prevalent and poses a serious threat for food safety and security in Africa. These findings shed light on areas for future research concerning antibiotic-resistant and multidrug-resistant bacteria in food animals as etiological agents of infectious diseases in humans. They further yielded some interesting findings on the burden of ABR that could be useful in developing measures to contain this threat in the farm-to-plate continuum in Africa.
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Affiliation(s)
- Luria Leslie Founou
- 1 Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal , Durban, South Africa .,2 Department of Food Safety and Environmental Microbiology, Centre of Expertise and Biological Diagnostic of Cameroon , Yaoundé, Cameroon
| | - Daniel Gyamfi Amoako
- 1 Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal , Durban, South Africa
| | - Raspail Carrel Founou
- 1 Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal , Durban, South Africa .,3 Department of Clinical Microbiology, Centre of Expertise and Biological Diagnostic of Cameroon , Yaoundé, Cameroon
| | - Sabiha Yusuf Essack
- 1 Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal , Durban, South Africa
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Abstract
Resistance to fluoroquinolones (FQ) is being increasingly reported and found to be mediated by efflux pumps, plasmid-mediated quinolone resistance genes (PMQR) and mutations in gyrA, gyrB, parC and parE. However, studies reporting on FQ resistance mechanisms (FQRM), particularly in Africa, are focused mostly on Salmonella. This study used a whole-genome-based approach to describe FQRM in forty-eight clinical Enterobacteriaceae isolates comprising of Klebsiella pneumoniae (n = 21), Serratia marcescens (n = 12), Enterobacter spp. (n = 10), Citrobacter freundii (n = 3), Escherichia coli (n = 1), and Klebsiella michiganensis (n = 1) with reduced susceptibility to FQ in Enterobacteriaceae. All the isolates exhibited exceptionally high-level resistance (MIC of 4-512mg/L) to all three FQs, which could not be reversed by carbonyl cyanide m-chlorophenyl hydrazine (CCCP), verapamil (VRP) or reserpine (RSP). PMQR genes such as oqxAB (n = 43), aac(6’)-Ib-cr (n = 28), and qnr(S1, B1, B2, B9, B49, B66) (n = 23) were identified without transposons or integrons in their immediate environments. Multiple and diverse mutations were found in gyrA (including S83I/Y and T/I83I/T), gyrB, parC and parE, which were clonally specific. There were vertical and horizontal transmission of high-level FQ resistance in Enterobacteriaceae in hospitals in Durban, South Africa, which are mediated by efflux, PMQR genes, and gyrA, gyrB, parC and parE mutations.
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Affiliation(s)
- John Osei Sekyere
- Department of Pharmaceutics, Faculty of Pharmacy and Pharmaceutical Sciences, KNUST, Kumasi, Ghana
- * E-mail:
| | - Daniel Gyamfi Amoako
- Discipline of Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal; Durban, South Africa
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