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Okwu MU, Akpoka AO, Mitsan O, Izevbuwa OE, Osamede A, Tkadlec J. High Frequency of Methicillin-Resistant and Multidrug-Resistant Strains of Staphylococcus aureus Colonizing Students in Okada, Edo State, Nigeria. Microb Drug Resist 2023; 29:516-522. [PMID: 37713290 DOI: 10.1089/mdr.2023.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023] Open
Abstract
Staphylococcus aureus is one of the most common bacterial pathogens, often asymptomatically colonizing healthy people, but capable of causing fatal disease. The ability to treat S. aureus infections is limited by the rapid spread of multidrug-resistant strains. This study aimed to determine the prevalence of S. aureus carriage among students from Okada, Edo State, Nigeria, to analyze the antibiotic resistance patterns and molecular characteristics of S. aureus isolates. One hundred healthy students from Okada, Nigeria, were tested for nasal colonization by S. aureus. Isolates were identified using standard microbiological methods. The susceptibilities of the isolates to a panel of 22 antimicrobials were tested. spa and staphylococcal cassette chromosome mec typing were performed. The prevalence of S. aureus and methicillin-resistant S. aureus (MRSA) among the students was 23% and 6%, respectively. Of the six (26.1%; 6/23) MRSA isolates detected, CC88-MRSA-IVa (n = 2) and CC7-MRSA-V (n = 2) were the most frequent clones. The CC7-MRSA-V isolates were resistant to multiple antimicrobials. Overall, resistance to beta-lactams, tetracyclines, fluoroquinolones, and aminoglycosides was detected among the S. aureus and MRSA isolates. The high prevalence of MRSA and methicillin-susceptible isolates with resistance to multiple antimicrobial classes observed among the students is an alarming finding. This study indicated the circulation of resistant clones of S. aureus in Nigerian educational institutions and the community.
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Affiliation(s)
- Maureen Uchechukwu Okwu
- Department of Biological Sciences (Microbiology), College of Natural and Applied Sciences, Igbinedion University Okada, Okada, Edo State, Nigeria
| | - Augustine Obhioze Akpoka
- Department of Biological Sciences (Microbiology), College of Natural and Applied Sciences, Igbinedion University Okada, Okada, Edo State, Nigeria
| | - Olley Mitsan
- Department of Laboratory Medicine, Igbinedion University Teaching Hospital, Okada, Edo State, Nigeria
| | - Osazee Ekundayo Izevbuwa
- Department of Biological Sciences (Microbiology), College of Natural and Applied Sciences, Igbinedion University Okada, Okada, Edo State, Nigeria
| | - Anita Osamede
- Department of Biological Sciences (Microbiology), College of Natural and Applied Sciences, Igbinedion University Okada, Okada, Edo State, Nigeria
| | - Jan Tkadlec
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
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Jans C, Wambui J, Stevens MJA, Tasara T. Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore. Front Microbiol 2022; 13:923080. [PMID: 36046020 PMCID: PMC9421002 DOI: 10.3389/fmicb.2022.923080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus infection is considered to be a neglected tropical disease with huge impact on human and animal health alike. Dairy production in sub-Saharan Africa (SSA) relies heavily on various animals such as cows, goats, and camels, depending on the region. S. aureus causes mastitis and exhibits high prevalence in raw milk. The population structure including genotypic and phenotypic traits of dairy S. aureus in relation to animal and human isolates is, however, unknown for SSA. In this work, 20 S. aureus dairy isolates from East and West Africa were selected for comparative genomics and phenotypic analysis. Comparing their population structure revealed a large diversity of different origins suggesting milk to be a reservoir for human and animal strains alike. Furthermore, a novel putative siderophore was detected in multiple strains in a distinct animal-clade with strains of global origin. This putative siderophore shares a high genetic identity with that from Streptococcus equi suggesting possible horizontal gene transfer. These findings combined with the virulence genes harbored by these dairy-derived strains such as pvl, human evasion factor scn, various enterotoxin, leucocidin and antibiotic resistance genes, stresses the need for an integrative One Health approach to tackle the problem of S. aureus infections in animals and humans in sub-Saharan Africa.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Switzerland
| | - Joseph Wambui
- Institute of Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Marc J. A. Stevens
- Institute of Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Taurai Tasara
- Institute of Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
- *Correspondence: Taurai Tasara,
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Development of sustainable research excellence with a global perspective on infectious diseases: Centre de Recherches Médicales de Lambaréné (CERMEL), Gabon. Wien Klin Wochenschr 2021; 133:500-508. [PMID: 33398458 PMCID: PMC7781170 DOI: 10.1007/s00508-020-01794-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022]
Abstract
Medical research in sub-Saharan Africa is of high priority for societies to respond adequately to local health needs. Often enough it remains a challenge to build up capacity in infrastructure and human resources to highest international standards and to sustain this over mid-term to long-term periods due to difficulties in obtaining long-term institutional core funding, attracting highly qualified scientists for medical research and coping with ever changing structural and political environments. The Centre de Recherches Médicales de Lambaréné (CERMEL) serves as model for how to overcome such challenges and to continuously increase its impact on medical care in Central Africa and beyond. Starting off as a research annex to the Albert Schweitzer Hospital in Lambaréné, Gabon, it has since then expanded its activities to academic and regulatory clinical trials for drugs, vaccines and diagnostics in the field of malaria, tuberculosis, and a wide range of poverty related and neglected tropical infectious diseases. Advancing bioethics in medical research in Africa and steadily improving its global networks and infrastructures, CERMEL serves as a reference centre for several international consortia. In close collaboration with national authorities, CERMEL has become one of the main training hubs for medical research in Central Africa. It is hoped that CERMEL and its leitmotiv “to improve medical care for local populations” will serve as an inspiration to other institutions in sub-Saharan Africa to further increase African capacity to advance medicine.
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Monemo P, Demba N, Touré FS, Traoré A, Avi C, N’Guessan MA, Tadet JO, Gobey AR, Anoh AE, Diarrassouba A, Tuo MN, Cissé A, Saric J, Utzinger J, Tia H, Kouassi-N’Djeundo J, Becker SL, Akoua-Koffi C. Pharyngeal Carriage of Beta-Haemolytic Streptococcus Species and Seroprevalence of Anti-Streptococcal Antibodies in Children in Bouaké, Côte d’Ivoire. Trop Med Infect Dis 2020; 5:tropicalmed5040177. [PMID: 33261048 PMCID: PMC7709589 DOI: 10.3390/tropicalmed5040177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 11/24/2022] Open
Abstract
The pharynx of the child may serve as a reservoir of pathogenic bacteria, including beta-haemolytic group A streptococci (GAS), which can give rise to upper airway infections and post-streptococcal diseases. The objective of this study was to determine the prevalence of beta-haemolytic Streptococcus spp. in pharyngeal samples stemming from children aged 3–14 years in Bouaké, central Côte d’Ivoire. Oropharyngeal throat swabs for microbiological culture and venous blood samples to determine the seroprevalence of antistreptolysin O antibodies (ASO) were obtained from 400 children in March 2017. Identification was carried out using conventional bacteriological methods. Serogrouping was performed with a latex agglutination test, while an immunological agglutination assay was employed for ASO titres. The mean age of participating children was 9 years (standard deviation 2.5 years). In total, we detected 190 bacteria in culture, with 109 beta-haemolytic Streptococcus isolates, resulting in an oropharyngeal carriage rate of 27.2%. Group C streptococci accounted for 82.6% of all isolates, whereas GAS were rarely found (4.6%). The ASO seroprevalence was 17.3%. There was no correlation between serology and prevalence of streptococci (p = 0.722). In conclusion, there is a high pharyngeal carriage rate of non-GAS strains in children from Bouaké, warranting further investigation.
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Affiliation(s)
- Pacôme Monemo
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
- Unité de Formation et Recherche des Sciences Médicales, Université Alassane Ouattara, Bouaké, Cote d’Ivoire; (A.R.G.); (J.K.-N.)
- Correspondence: (P.M.), (S.L.B.)
| | - Nadia Demba
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
| | - Fidèle S. Touré
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
| | - Adjartou Traoré
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
| | - Christelle Avi
- Service de Pédiatrie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire;
| | - Micheline A. N’Guessan
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
| | - Juste O. Tadet
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
| | - Arthur R. Gobey
- Unité de Formation et Recherche des Sciences Médicales, Université Alassane Ouattara, Bouaké, Cote d’Ivoire; (A.R.G.); (J.K.-N.)
- Laboratoire d’Immunologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire
| | - Augustin E. Anoh
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
| | - Abdoulaye Diarrassouba
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
- Unité de Formation et Recherche des Sciences Médicales, Université Alassane Ouattara, Bouaké, Cote d’Ivoire; (A.R.G.); (J.K.-N.)
| | - Marie N. Tuo
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
| | - Amadou Cissé
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
| | - Jasmina Saric
- Swiss Tropical and Public Health Institute, CH-4002 Basel, Switzerland; (J.S.); (J.U.)
- University of Basel, CH-4003 Basel, Switzerland
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, CH-4002 Basel, Switzerland; (J.S.); (J.U.)
- University of Basel, CH-4003 Basel, Switzerland
| | - Honoré Tia
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
- Unité de Formation et Recherche des Sciences Médicales, Université Alassane Ouattara, Bouaké, Cote d’Ivoire; (A.R.G.); (J.K.-N.)
| | - Judith Kouassi-N’Djeundo
- Unité de Formation et Recherche des Sciences Médicales, Université Alassane Ouattara, Bouaké, Cote d’Ivoire; (A.R.G.); (J.K.-N.)
- Service d’Oto-Rhino-Laryngologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire
| | - Sören L. Becker
- Swiss Tropical and Public Health Institute, CH-4002 Basel, Switzerland; (J.S.); (J.U.)
- University of Basel, CH-4003 Basel, Switzerland
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421 Homburg/Saar, Germany
- Correspondence: (P.M.), (S.L.B.)
| | - Chantal Akoua-Koffi
- Laboratoire de Bactériologie-Virologie, Centre Hospitalier Universitaire de Bouaké, Bouaké, Cote d’Ivoire; (N.D.); (F.S.T.); (A.T.); (M.A.N.); (J.O.T.); (A.E.A.); (A.D.); (M.N.T.); (A.C.); (H.T.); (C.A.-K.)
- Unité de Formation et Recherche des Sciences Médicales, Université Alassane Ouattara, Bouaké, Cote d’Ivoire; (A.R.G.); (J.K.-N.)
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Omwenga I, Aboge GO, Mitema ES, Obiero G, Ngaywa C, Ngwili N, Wamwere G, Wainaina M, Bett B. Antimicrobial Usage and Detection of Multidrug-Resistant Staphylococcus aureus, Including Methicillin-Resistant Strains in Raw Milk of Livestock from Northern Kenya. Microb Drug Resist 2020; 27:843-854. [PMID: 33185504 DOI: 10.1089/mdr.2020.0252] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The association of antimicrobial usage (AMU) with prevalence of antimicrobial-resistant (AMR) Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA) in livestock raw milk consumed by pastoralists in Kenya remains unclear. We investigated the relationship between AMU and emergence of multidrug-resistant (MDR) S. aureus, including MRSA in raw milk of livestock. AMU data were obtained using sales records from veterinary pharmacies. S. aureus was isolated from 603 milk samples from various livestock species, including sheep, goat, cow, and camel reared in Isiolo and Marsabit counties in Kenya. Resistant phenotypes and genotypes were determined by disc diffusion and molecular methods, respectively. Correlation between AMU and occurrence of resistance was determined by Pearson's correlation coefficient (r) method. The consumption of various antimicrobial classes were as follows; 4,168 kg of oxytetracycline, 70 kg of sulfonamides, 49.7 kg of aminoglycosides, 46 kg of beta-lactams, 39.4 kg of macrolides, and 0.52 kg for trimethoprim. The S. aureus isolates were mainly resistant to tetracycline (79%), ampicillin (58%), and oxacillin (33%), respectively. A few isolates (5-18%) were resistant to clindamycin, cephalexin, erythromycin, kanamycin, and ciprofloxacin. Most of the MDR-S. aureus isolates were MRSA (94%). The genetic determinants found in the AMR isolates included tetK/tetM (96.5%/19%) for tetracycline, blaZ (79%) for penicillin, aac (6')/aph (2'')/aph (3')-IIIa (53%) for aminoglycosides, mecA (41%) for oxacillin, and msrA/ermA (24%/7%) for macrolides. Oxytetracycline usage was correlated to tetK/tetM (r = 0.62/1) detection, penicillins to mecA/blaZ (r = 0.86/0.98), aminoglycoside to aac (6')/aph (2'')/aph (3')-IIIa (r = 0.76/-13), and macrolide usages for detection of ermA/msrA (r = 0.94/0.77). AMU appeared to be associated with occurrence of MDR-SA and the tetM detection. Consumption of raw milk contaminated with MRSA could pose a serious public health risk in pastoral communities in northern Kenya.
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Affiliation(s)
- Isaac Omwenga
- International Livestock Research Institute, Nairobi, Kenya.,Department of Public Health Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Gabriel O Aboge
- Department of Public Health Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya.,Center for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, University of Nairobi, Nairobi, Kenya
| | - Eric S Mitema
- Department of Public Health Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - George Obiero
- Center for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, University of Nairobi, Nairobi, Kenya
| | - Catherine Ngaywa
- International Livestock Research Institute, Nairobi, Kenya.,Center for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, University of Nairobi, Nairobi, Kenya
| | | | - George Wamwere
- International Livestock Research Institute, Nairobi, Kenya
| | | | - Bernard Bett
- International Livestock Research Institute, Nairobi, Kenya
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Gawlik D, Ruppelt-Lorz A, Müller E, Reißig A, Hotzel H, Braun SD, Söderquist B, Ziegler-Cordts A, Stein C, Pletz MW, Ehricht R, Monecke S. Molecular investigations on a chimeric strain of Staphylococcus aureus sequence type 80. PLoS One 2020; 15:e0232071. [PMID: 33052925 PMCID: PMC7556507 DOI: 10.1371/journal.pone.0232071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/21/2020] [Indexed: 11/18/2022] Open
Abstract
A PVL-positive, methicillin-susceptible Staphylococcus aureus was cultured from pus from cervical lymphadenitis of a patient of East-African origin. Microarray hybridisation assigned the isolate to clonal complex (CC) 80 but revealed unusual features, including the presence of the ORF-CM14 enterotoxin homologue and of an ACME-III element as well as the absence of etD and edinB. The isolate was subjected to both, Illumina and Nanopore sequencing allowing characterisation of deviating regions within the strain´s genome. Atypical features of this strain were attributable to the presence of two genomic regions that originated from other S. aureus lineages and that comprised, respectively, 3% and 1.4% of the genome. One deviating region extended from walJ to sirB. It comprised ORF-CM14 and the ACME-III element. A homologous but larger fragment was also found in an atypical S. aureus CC1/ST567 strain whose lineage might have served as donor of this genomic region. This region itself is a chimera comprising fragments from CC1 as well as fragments of unknown origin. The other deviating region comprised the region from htsB to ecfA2, i.e., another 3% of the genome. It was very similar to CC1 sequences. Either this suggests an incorporation of CC1 DNA into the study strain, or alternatively a recombination event affecting “canonical” CC80. Thus, the study strain bears witness of several recombination events affecting supposedly core genomic genes. Although the exact mechanism is not yet clear, such chimerism seems to be an additional pathway in the evolution of S. aureus. This could facilitate also a transmission of virulence and resistance factors and therefore offer an additional evolutionary advantage.
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Affiliation(s)
- Darius Gawlik
- Institute of Infectious Diseases and Infection Control, University Hospital, Jena, Germany
- PTC—Phage Technology Center GmbH, Bönen, Germany
| | - Antje Ruppelt-Lorz
- Institute for Medical Microbiology and Hygiene, Technical University of Dresden, Dresden, Germany
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Annett Reißig
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Bo Söderquist
- School of Medical Sciences, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Claudia Stein
- Institute of Infectious Diseases and Infection Control, University Hospital, Jena, Germany
| | - Mathias W. Pletz
- Institute of Infectious Diseases and Infection Control, University Hospital, Jena, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- Institute of Physical Chemistry, Jena University, Jena, Germany
| | - Stefan Monecke
- Institute for Medical Microbiology and Hygiene, Technical University of Dresden, Dresden, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- * E-mail:
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Shittu A, Deinhardt‐Emmer S, Vas Nunes J, Niemann S, Grobusch MP, Schaumburg F. Tropical pyomyositis: an update. Trop Med Int Health 2020; 25:660-665. [DOI: 10.1111/tmi.13395] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Adebayo Shittu
- Department of Microbiology Obafemi Awolowo University Ile‐Ife Nigeria
- Institute of Medical Microbiology University Hospital Münster Münster Germany
| | | | - Jonathan Vas Nunes
- Masanga Hospital Masanga Sierra Leone
- Masanga Medical Research Unit Masanga Sierra Leone
| | - Silke Niemann
- Institute of Medical Microbiology University Hospital Münster Münster Germany
| | - Martin P. Grobusch
- Masanga Medical Research Unit Masanga Sierra Leone
- Center of Tropical Medicine University of Amsterdam Amsterdam The Netherlands
| | - Frieder Schaumburg
- Institute of Medical Microbiology University Hospital Münster Münster Germany
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8
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Kateete DP, Asiimwe BB, Mayanja R, Mujuni B, Bwanga F, Najjuka CF, Källander K, Rutebemberwa E. Nasopharyngeal carriage, spa types and antibiotic susceptibility profiles of Staphylococcus aureus from healthy children less than 5 years in Eastern Uganda. BMC Infect Dis 2019; 19:1023. [PMID: 31791276 PMCID: PMC6889221 DOI: 10.1186/s12879-019-4652-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/22/2019] [Indexed: 01/13/2023] Open
Abstract
Background Staphylococcus aureus carriage is a known risk factor for staphylococcal disease. However, the carriage rates vary by country, demographic group and profession. This study aimed to determine the S. aureus carriage rate in children in Eastern Uganda, and identify S. aureus lineages that cause infection in Uganda. Methods Nasopharyngeal samples from 742 healthy children less than 5 years residing in the Iganga/Mayuge Health and Demographic Surveillance Site in Eastern Uganda were processed for isolation of S. aureus. Antibiotic susceptibility testing based on minimum inhibitory concentrations (MICs) was determined by the BD Phoenix™ system. Genotyping was performed by spa and SCCmec typing. Results The processed samples yielded 144 S. aureus isolates (one per child) therefore, the S. aureus carriage rate in children was 19.4% (144/742). Thirty one percent (45/144) of the isolates were methicillin resistant (MRSA) yielding a carriage rate of 6.1% (45/742). All isolates were susceptible to rifampicin, vancomycin and linezolid. Moreover, all MRSA were susceptible to vancomycin, linezolid and clindamycin. Compared to methicillin susceptible S. aureus (MSSA) isolates (68.8%, 99/144), MRSA isolates were more resistant to non-beta-lactam antimicrobials –trimethoprim/sulfamethoxazole 73.3% (33/45) vs. 27.3% (27/99) [p < 0.0001]; erythromycin 75.6% (34/45) vs. 24.2% (24/99) [p < 0.0001]; chloramphenicol 60% (27/45) vs. 19.2% (19/99) [p < 0.0001]; gentamicin 55.6% (25/45) vs. 25.3% (25/99) [p = 0.0004]; and ciprofloxacin 35.6% (16/45) vs. 2% (2/99) [p < 0.0001]. Furthermore, 42 MRSA (93.3%) were multidrug resistant (MDR) and one exhibited high-level resistance to mupirocin. Overall, 61 MSSA (61.6%) were MDR, including three mupirocin and clindamycin resistant isolates. Seven spa types were detected among MRSA, of which t037 and t064 were predominant and associated with SCCmec types I and IV, respectively. Fourteen spa types were detected in MSSA which consisted mainly of t645 and t4353. Conclusions S. aureus carriage rate in healthy children in Eastern Uganda is high and comparable to rates for hospitalized patients in Kampala. The detection of mupirocin resistance is worrying as it could rapidly increase if mupirocin is administered in a low-income setting. S. aureus strains of spa types t064, t037 (MRSA) and t645, t4353 (MSSA) are prevalent and could be responsible for majority of staphylococcal infections in Uganda.
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Affiliation(s)
- David Patrick Kateete
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda. .,Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda.
| | - Benon B Asiimwe
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Raymond Mayanja
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda.,Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda.,Makerere University Walter Reed Project, Kampala, Uganda
| | - Brian Mujuni
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda.,Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Freddie Bwanga
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda.,Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Christine F Najjuka
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Karin Källander
- Malaria Consortium, London, UK.,Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
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9
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Casimiro-Soriguer CS, Loucera C, Perez Florido J, López-López D, Dopazo J. Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples. Biol Direct 2019; 14:15. [PMID: 31429791 PMCID: PMC6701120 DOI: 10.1186/s13062-019-0246-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 08/06/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacterial abundance profiles. RESULTS Here we use a transformation of the conventional bacterial strain or gene abundance profiles to functional profiles that account for bacterial metabolism and other cell functionalities. These profiles are used as features for city classification in a machine learning algorithm that allows the extraction of the most relevant features for the classification. CONCLUSIONS We demonstrate here that the use of functional profiles not only predict accurately the most likely origin of a sample but also to provide an interesting functional point of view of the biogeography of the microbiota. Interestingly, we show how cities can be classified based on the observed profile of antibiotic resistances. REVIEWERS Open peer review: Reviewed by Jin Zhuang Dou, Jing Zhou, Torsten Semmler and Eran Elhaik.
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Affiliation(s)
- Carlos S. Casimiro-Soriguer
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Carlos Loucera
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Javier Perez Florido
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Daniel López-López
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Joaquin Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013 Sevilla, Spain
- Functional Genomics Node (INB), FPS, Hospital Virgen del Rocio, 41013 Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER). FPS, Hospital Virgen del Rocio, 41013 Sevilla, Spain
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10
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Kateete DP, Bwanga F, Seni J, Mayanja R, Kigozi E, Mujuni B, Ashaba FK, Baluku H, Najjuka CF, Källander K, Rutebemberwa E, Asiimwe BB, Joloba ML. CA-MRSA and HA-MRSA coexist in community and hospital settings in Uganda. Antimicrob Resist Infect Control 2019; 8:94. [PMID: 31171965 PMCID: PMC6547506 DOI: 10.1186/s13756-019-0551-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/28/2019] [Indexed: 01/17/2023] Open
Abstract
Background Methicillin resistant Staphylococcus aureus (MRSA) strains were once confined to hospitals however, in the last 20 years MRSA infections have emerged in the community in people with no prior exposure to hospitals. Strains causing such infections were novel and referred to as community-associated MRSA (CA-MRSA). The aim of this study was to determine the MRSA carriage rate in children in eastern Uganda, and to investigate coexistence between CA-MRSA and hospital-associated (HA-MRSA). Methods Between February and October 2011, nasopharyngeal samples (one per child) from 742 healthy children under 5 years in rural eastern Uganda were processed for isolation of MRSA, which was identified based on inhibition zone diameter of ≤19 mm on 30 μg cefoxitin disk. SCCmec and spa typing were performed for MRSA isolates. Results A total of 140 S. aureus isolates (18.9%, 140/742) were recovered from the children of which 5.7% (42/742) were MRSA. Almost all (95.2%, 40/42) MRSA isolates were multidrug resistant (MDR). The most prevalent SCCmec elements were types IV (40.5%, 17/42) and I (38.1%, 16/42). The overall frequency of SCCmec types IV and V combined, hence CA-MRSA, was 50% (21/42). Likewise, the overall frequency of SCCmec types I, II and III combined, hence HA-MRSA, was 50% (21/42). Spa types t002, t037, t064, t4353 and t12939 were detected and the most frequent were t064 (19%, 8/42) and t037 (12%, 5/42). Conclusion The MRSA carriage rate in children in eastern Uganda is high (5.7%) and comparable to estimates for Mulago Hospital in Kampala city. Importantly, HA-MRSA (mainly of spa type t037) and CA-MRSA (mainly of spa type t064) coexist in children in the community in eastern Uganda, and due to high proportion of MDR detected, outpatient treatment of MRSA infection in eastern Uganda might be difficult.
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Affiliation(s)
- David Patrick Kateete
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Freddie Bwanga
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Jeremiah Seni
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
- Catholic University of Health and Allied Sciences – Bugando, Mwanza, Tanzania
| | - Raymond Mayanja
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Brian Mujuni
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred K. Ashaba
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Hannington Baluku
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Christine F. Najjuka
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Karin Källander
- Malaria Consortium, London, UK
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | | | - Benon B. Asiimwe
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Moses L. Joloba
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
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11
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Kazimoto T, Abdulla S, Bategereza L, Juma O, Mhimbira F, Weisser M, Utzinger J, von Müller L, Becker SL. Causative agents and antimicrobial resistance patterns of human skin and soft tissue infections in Bagamoyo, Tanzania. Acta Trop 2018; 186:102-106. [PMID: 30006029 DOI: 10.1016/j.actatropica.2018.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 11/29/2022]
Abstract
Few epidemiological studies have been carried out to assess the aetiology and antimicrobial susceptibility patterns of pathogens giving rise to skin and soft tissue infections (SSTIs) in sub-Saharan Africa. In the present study from six healthcare facilities in Bagamoyo, Tanzania, wound swabs from outpatients with SSTIs were analysed by a suite of methods, including microbiological culture techniques, matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and resistance testing. Among 185 patients with SSTIs, 179 (96.8%) swabs showed microbiological growth. In total, 327 organisms were found, of which 285 were of potential aetiological relevance. Staphylococcus aureus was the predominant pathogen (prevalence: 71.4%), followed by the Gram-negative bacteria Enterobacter cloacae complex (14.6%), Klebsiella pneumoniae (12.4%) and Pseudomonas aeruginosa (11.8%). While one out of three isolates of S. aureus showed resistance to macrolides, tetracyclines, cotrimoxazole and clindamycin, only a single methicillin-resistant S. aureus (MRSA) strain was found. In Gram-negative bacteria, resistance to ampicillin and cotrimoxazole was common, while extended-spectrum beta-lactamases were rarely detected (<1%). We conclude that S. aureus was the most frequently detected pathogen in community-acquired SSTIs in Bagamoyo, Tanzania. Resistance to commonly prescribed oral antibiotics was considerable, but multi-resistant strains were rarely encountered. Monitoring of antibiotic susceptibility patterns in SSTIs is important to provide specific data for tailoring treatment recommendations.
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Affiliation(s)
- Theckla Kazimoto
- Ifakara Health Institute, Bagamoyo Branch, P.O. Box 74, Bagamoyo, Tanzania; Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Building 43, 66421 Homburg/Saar, Germany.
| | - Salim Abdulla
- Ifakara Health Institute, Bagamoyo Branch, P.O. Box 74, Bagamoyo, Tanzania
| | - Leah Bategereza
- Ifakara Health Institute, Bagamoyo Branch, P.O. Box 74, Bagamoyo, Tanzania
| | - Omar Juma
- Ifakara Health Institute, Bagamoyo Branch, P.O. Box 74, Bagamoyo, Tanzania
| | - Francis Mhimbira
- Ifakara Health Institute, Bagamoyo Branch, P.O. Box 74, Bagamoyo, Tanzania
| | - Maja Weisser
- Ifakara Health Institute, Bagamoyo Branch, P.O. Box 74, Bagamoyo, Tanzania; Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel, Switzerland; University of Basel, P.O. Box, CH-4003 Basel, Switzerland; Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel, Switzerland; University of Basel, P.O. Box, CH-4003 Basel, Switzerland
| | - Lutz von Müller
- Institute for Laboratory Medicine, Microbiology and Hygiene, Christophorus Kliniken, Südring 41, 48653 Coesfeld, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Building 43, 66421 Homburg/Saar, Germany; Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel, Switzerland; University of Basel, P.O. Box, CH-4003 Basel, Switzerland
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12
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Alabi A, Kazimoto T, Lebughe M, Vubil D, Phaku P, Mandomando I, Kern WV, Abdulla S, Mellmann A, Peitzmann L, Bischoff M, Peters G, Herrmann M, Grobusch MP, Schaumburg F, Rieg S. Management of superficial and deep-seated Staphylococcus aureus skin and soft tissue infections in sub-Saharan Africa: a post hoc analysis of the StaphNet cohort. Infection 2018; 46:395-404. [PMID: 29667040 DOI: 10.1007/s15010-018-1140-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/12/2018] [Indexed: 10/17/2022]
Abstract
PURPOSE The incidence of Staphylococcus aureus skin and soft tissue infection (SSTI) is high in sub-Saharan Africa. This is fueled by a high prevalence of Panton-Valentine leukocidin (PVL), which can be associated with necrotizing disease. The aim was to describe the clinical presentation and the treatment of SSTI in the African setting and to identify challenges in the management. METHODS Patients (n = 319) were recruited in DR Congo (n = 56, 17.6%), Gabon (n = 89, 27.9%), Mozambique (n = 79, 24.8%) and Tanzania (n = 95, 29.8%) during the prospective observational StaphNet cohort study (2010-2015). A physician recorded the clinical management in standardized questionnaires and stratified the entity of SSTI into superficial (sSSTI) or deep-seated (dSSTI). Selected virulence factors (PVL, β hemolysin) and multilocus sequence types (MLST) were extracted from whole genome sequencing data. RESULTS There were 220/319 (69%) sSSTI and 99/319 (31%) dSSTI. Compared to sSSTI, patients with dSSTI were more often hospitalized (13.2 vs. 23.5%, p = 0.03), HIV-positive (7.6 vs. 15.9%, p = 0.11), and required more often incision and drainage (I&D, 45.5 vs. 76.5%, p = 0.04). The proportion of an adequate antimicrobial therapy increased marginally from day 1 (empirical therapy) to day 3 (definite therapy), for sSSTI (70.7 to 72.4%) and dSSTI (55.4 to 58.9%). PVL was a risk factor for I&D (OR = 1.7, p = 0.02) and associated with MLST clonal complex CC121 (OR = 2.7, p < 0.001). CONCLUSION Appropriate antimicrobial agents and surgical services to perform I&D were available for the majority of patients. Results from susceptibility testing should be considered more efficiently in the selection of antimicrobial therapy.
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Affiliation(s)
- Abraham Alabi
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität, Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | | | - Marthe Lebughe
- Institut National de Recherche Bio-Médicale (INRB), Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Delfino Vubil
- Manhiça Health Research Center, Manhiça, Maputo, Mozambique
| | - Patrick Phaku
- Institut National de Recherche Bio-Médicale (INRB), Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Inacio Mandomando
- Manhiça Health Research Center, Manhiça, Maputo, Mozambique.,Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique
| | - Winfried V Kern
- Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Salim Abdulla
- Ifakara Health Institute (IHI), Dar es Salaam, Tanzania
| | | | - Lena Peitzmann
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Georg Peters
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Mathias Herrmann
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Martin P Grobusch
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität, Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.,Division of Internal Medicine, Department of Infectious Diseases, Center of Tropical Medicine and Travel Medicine, University of Amsterdam, Amsterdam, The Netherlands
| | - Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
| | - Siegbert Rieg
- Division of Infectious Diseases, Department of Medicine II, Medical Center, University of Freiburg Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
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13
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Origin, evolution, and global transmission of community-acquired Staphylococcus aureus ST8. Proc Natl Acad Sci U S A 2017; 114:E10596-E10604. [PMID: 29158405 PMCID: PMC5724248 DOI: 10.1073/pnas.1702472114] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
USA300 is a hypervirulent, community-acquired, multidrug-resistant Staphylococcus aureus clone that started to spread in the United States around 17 years ago. Many studies detected it also in South America, Europe, and the Asia-Pacific region. In this study, we show that USA300 is also circulating in sub-Saharan Africa. Locating the temporal and spatial origin of clonal lineages is important with respect to epidemiology and molecular evolution of pathogens. We show that USA300 evolved from a less virulent and less resistant ancestor circulating in Central Europe around 160 years ago. Constant surveillance of pathogen transmission routes is vital to prevent and control potential outbreaks. Whole genome sequencing proved to be a useful tool for epidemiological surveillance. USA300 is a pandemic clonal lineage of hypervirulent, community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) with specific molecular characteristics. Despite its high clinical relevance, the evolutionary origin of USA300 remained unclear. We used comparative genomics of 224 temporal and spatial diverse S. aureus isolates of multilocus sequence type (ST) 8 to reconstruct the molecular evolution and global dissemination of ST8, including USA300. Analyses of core SNP diversity and accessory genome variations showed that the ancestor of all ST8 S. aureus most likely emerged in Central Europe in the mid-19th century. From here, ST8 was exported to North America in the early 20th century and progressively acquired the USA300 characteristics Panton–Valentine leukocidin (PVL), SCCmec IVa, the arginine catabolic mobile element (ACME), and a specific mutation in capsular polysaccharide gene cap5E. Although the PVL-encoding phage ϕSa2USA was introduced into the ST8 background only once, various SCCmec types were introduced to ST8 at different times and places. Starting from North America, USA300 spread globally, including Africa. African USA300 isolates have aberrant spa-types (t112, t121) and form a monophyletic group within the clade of North American USA300. Large parts of ST8 methicillin-susceptible S. aureus (MSSA) isolated in Africa represent a symplesiomorphic group of ST8 (i.e., a group representing the characteristics of the ancestor), which are rarely found in other world regions. Isolates previously discussed as USA300 ancestors, including USA500 and a “historic” CA-MRSA from Western Australia, were shown to be only distantly related to recent USA300 clones.
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14
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Lebughe M, Phaku P, Niemann S, Mumba D, Peters G, Muyembe-Tamfum JJ, Mellmann A, Strauß L, Schaumburg F. The Impact of the Staphylococcus aureus Virulome on Infection in a Developing Country: A Cohort Study. Front Microbiol 2017; 8:1662. [PMID: 28900424 PMCID: PMC5581934 DOI: 10.3389/fmicb.2017.01662] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 08/16/2017] [Indexed: 12/31/2022] Open
Abstract
We performed a cohort study to analyze the virulome of Staphylococcus aureus from the Democratic Republic of the Congo using whole genome sequencing and to assess its impact on the course of S. aureus infections. Community-associated S. aureus from nasal colonization (n = 100) and infection (n = 86) were prospectively collected. Phenotypic susceptibility testing and WGS was done for each isolate. WGS data were used to screen for 79 different virulence factors and for genotyping purposes (spa typing, multilocus sequence typing). The majority of the 79 virulence factors were equally distributed among isolates from colonization and infection. Panton-Valentine leukocidin (PVL) and the non-truncated hemolysin β were associated with skin and soft tissue infection (SSTI) and recurrence of disease but did not influence the course of infection (i.e., mortality, surgical intervention). For the first time, we show that not only PVL but also hemolysin β could contribute to the development of SSTI in PVL-endemic areas such as Africa.
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Affiliation(s)
- Marthe Lebughe
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | - Patrick Phaku
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | - Silke Niemann
- Institute of Medical Microbiology, University Hospital MünsterMünster, Germany
| | - Dieudonné Mumba
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | - Georg Peters
- Institute of Medical Microbiology, University Hospital MünsterMünster, Germany
| | - Jean-Jacques Muyembe-Tamfum
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | | | - Lena Strauß
- Institute of Hygiene, University Hospital MünsterMünster, Germany
| | - Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital MünsterMünster, Germany
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15
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Ruffing U, Alabi A, Kazimoto T, Vubil DC, Akulenko R, Abdulla S, Alonso P, Bischoff M, Germann A, Grobusch MP, Helms V, Hoffmann J, Kern WV, Kremsner PG, Mandomando I, Mellmann A, Peters G, Schaumburg F, Schubert S, Strauß L, Tanner M, Briesen HV, Wende L, Müller LV, Herrmann M. Community-Associated Staphylococcus aureus from Sub-Saharan Africa and Germany: A Cross-Sectional Geographic Correlation Study. Sci Rep 2017; 7:154. [PMID: 28273954 PMCID: PMC5428059 DOI: 10.1038/s41598-017-00214-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/14/2017] [Indexed: 01/29/2023] Open
Abstract
Clonal clusters and gene repertoires of Staphylococcus aureus are essential to understand disease and are well characterized in industrialized countries but poorly analysed in developing regions. The objective of this study was to compare the molecular-epidemiologic profiles of S. aureus isolates from Sub-Saharan Africa and Germany. S. aureus isolates from 600 staphylococcal carriers and 600 patients with community-associated staphylococcal disease were characterized by DNA hybridization, clonal complex (CC) attribution, and principal component (PCA)-based gene repertoire analysis. 73% of all CCs identified representing 77% of the isolates contained in these CCs were predominant in either African or German region. Significant differences between African versus German isolates were found for alleles encoding the accessory gene regulator type, enterotoxins, the Panton-Valentine leukocidin, immune evasion gene cluster, and adhesins. PCA in conjunction with silhouette analysis distinguished nine separable PCA clusters, with five clusters primarily comprising of African and two clusters of German isolates. Significant differences between S. aureus lineages in Africa and Germany may be a clue to explain the apparent difference in disease between tropical/(so-called) developing and temperate/industrialized regions. In low-resource countries further clinical-epidemiologic research is warranted not only for neglected tropical diseases but also for major bacterial infections.
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Affiliation(s)
- Ulla Ruffing
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Abraham Alabi
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, Gabon
| | - Theckla Kazimoto
- Ifakara Health Research and Development Centre (IHRDC), Dar es Salaam, Tanzania
| | - Delfino C Vubil
- Manhiça Health Research Center, Manhiça, Manhiça, Mozambique
| | - Ruslan Akulenko
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Salim Abdulla
- Ifakara Health Research and Development Centre (IHRDC), Dar es Salaam, Tanzania
| | - Pedro Alonso
- Manhiça Health Research Center, Manhiça, Manhiça, Mozambique.,Department of Public Health, University of Barcelona, Barcelona, Spain
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Anja Germann
- Fraunhofer Institute for Biomedical Engineering, St. Ingbert, Germany
| | - Martin P Grobusch
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, Gabon.,Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Division of Internal Medicine, University of Amsterdam, Amsterdam, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Jonas Hoffmann
- Division of Infectious Diseases and Travel Medicine, University of Freiburg, Freiburg, Germany
| | - Winfried V Kern
- Division of Infectious Diseases and Travel Medicine, University of Freiburg, Freiburg, Germany
| | - Peter G Kremsner
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, Lambaréné, Gabon.,Institute of Tropical Medicine, University of Tübingen, Deutsches Zentrum für Infektionsforschung, Tübingen, Germany
| | | | | | - Georg Peters
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Sabine Schubert
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Lena Strauß
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Marcel Tanner
- Ifakara Health Research and Development Centre (IHRDC), Dar es Salaam, Tanzania.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Hagen von Briesen
- Fraunhofer Institute for Biomedical Engineering, St. Ingbert, Germany
| | - Laura Wende
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Lutz von Müller
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany.
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16
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Jans C, Merz A, Johler S, Younan M, Tanner SA, Kaindi DWM, Wangoh J, Bonfoh B, Meile L, Tasara T. East and West African milk products are reservoirs for human and livestock-associated Staphylococcus aureus. Food Microbiol 2017; 65:64-73. [PMID: 28400021 DOI: 10.1016/j.fm.2017.01.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/12/2017] [Accepted: 01/29/2017] [Indexed: 12/13/2022]
Abstract
Staphylococcus aureus frequently isolated from milk products in sub-Saharan Africa (SSA) is a major pathogen responsible for food intoxication, human and animal diseases. SSA hospital-derived strains are well studied but data on the population structure of foodborne S. aureus required to identify possible staphylococcal food poisoning sources is lacking. Therefore, the aim was to assess the population genetic structure, virulence and antibiotic resistance genes associated with milk-derived S. aureus isolates from Côte d'Ivoire, Kenya and Somalia through spa-typing, MLST, and DNA microarray analysis. Seventy milk S. aureus isolates from the three countries were assigned to 27 spa (7 new) and 23 (12 new) MLST sequence types. Milk-associated S. aureus of the three countries is genetically diverse comprising human and livestock-associated clonal complexes (CCs) predominated by the CC5 (n = 10) and CC30 (n = 9) isolates. Panton-Valentine leukocidin, toxic shock syndrome toxin and enterotoxin encoding genes were predominantly observed among human-associated CCs. Penicillin, fosfomycin and tetracycline, but not methicillin resistance genes were frequently detected. Our findings indicate that milk-associated S. aureus in SSA originates from human and animal sources alike highlighting the need for an overarching One Health approach to reduce S. aureus disease burdens through improving production processes, animal care and hygienic measures.
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Affiliation(s)
- Christoph Jans
- ETH Zurich, Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Axel Merz
- University of Zurich, Institute of Food Safety and Hygiene, Winterthurerstrasse 272, 8057 Zurich, Switzerland
| | - Sophia Johler
- University of Zurich, Institute of Food Safety and Hygiene, Winterthurerstrasse 272, 8057 Zurich, Switzerland
| | - Mario Younan
- Vétérinaires Sans Frontières Germany, P.O. Box 25653, 00603 Nairobi, Kenya
| | - Sabine A Tanner
- ETH Zurich, Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Dasel Wambua Mulwa Kaindi
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, PO Box 29053, Nairobi, Kenya
| | - John Wangoh
- Department of Food Science, Nutrition and Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, PO Box 29053, Nairobi, Kenya
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), KM 17 route de Dabou, Adiopodoumé Yopougon, Abidjan - 01, B.P. 1303 Abidjan, Cote d'Ivoire
| | - Leo Meile
- ETH Zurich, Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, LFV C22, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Taurai Tasara
- University of Zurich, Institute of Food Safety and Hygiene, Winterthurerstrasse 272, 8057 Zurich, Switzerland.
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Vandendriessche S, De Boeck H, Deplano A, Phoba MF, Lunguya O, Falay D, Dauly N, Verhaegen J, Denis O, Jacobs J. Characterisation of Staphylococcus aureus isolates from bloodstream infections, Democratic Republic of the Congo. Eur J Clin Microbiol Infect Dis 2017; 36:1163-1171. [PMID: 28116552 DOI: 10.1007/s10096-017-2904-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/09/2017] [Indexed: 01/12/2023]
Abstract
Staphylococcus aureus is known worldwide as an invasive pathogen, but information on S. aureus from bloodstream infections in Central Africa remains scarce. A collection of S. aureus blood culture isolates recovered from hospitals in four provinces in the Democratic Republic of the Congo (2009-2013) was assessed. A total of 27/108 isolates were methicillin-resistant S. aureus (MRSA), of which >70% were co-resistant to aminoglycosides, tetracyclines, macrolides and lincosamides. For MRSA and methicillin-susceptible S. aureus (MSSA) isolates, resistance to chloramphenicol and trimethoprim-sulphamethoxazole (TMP-SMX) was <10%. However, 66.7% (72/108) of all isolates harboured the trimethoprim resistance gene dfrG. More than three-quarters (84/108, 77.8%) of isolates belonged to CC5, CC8, CC121 or CC152. Genetic diversity was higher among MSSA (31 spa types) compared to MRSA (four spa types). Most MRSA (23/27, 85.2%) belonged to CC8-spa t1476-SCCmec V and 17/23 (73.9%) MRSA ST8 were oxacillin susceptible but cefoxitin resistant. Among MRSA and MSSA combined, 49.1% (53/108) and 19.4% (21/108) contained the genes encoding for Panton-Valentine leucocidin (lukS-lukF PV, PVL) and toxic shock syndrome toxin-1 (tst, TSST-1), respectively. PVL was mainly detected among MSSA (51/53 isolates harbouring PVL were MSSA, 96.2%) and associated with CC121, CC152, CC1 and CC5. TSST-1 was associated with CC8-spa t1476-SCCmec V. The immune evasion cluster (IEC) genes scn, sak and chp were detected in 81.5% of isolates (88/108, equally represented among MSSA and MRSA). The present study confirms the occurrence of MRSA with high levels of multidrug co-resistance and PVL-positive MSSA among invasive S. aureus isolates in Central Africa.
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Affiliation(s)
- S Vandendriessche
- National Reference Centre for Staphylococcus aureus, Laboratory of Microbiology, Université Libre de Bruxelles (ULB), Brussels, Belgium.
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium.
| | - H De Boeck
- Department of Clinical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium
| | - A Deplano
- National Reference Centre for Staphylococcus aureus, Laboratory of Microbiology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - M-F Phoba
- Department of Clinical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium
| | - O Lunguya
- Department of Clinical Microbiology, National Institute for Biomedical Research Department of Microbiology, University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
- Department of Microbiology, University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - D Falay
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, Democratic Republic of the Congo
| | - N Dauly
- Department of Clinical Microbiology, National Institute for Biomedical Research Department of Microbiology, University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
- Department of Microbiology, University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - J Verhaegen
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - O Denis
- National Reference Centre for Staphylococcus aureus, Laboratory of Microbiology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - J Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
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18
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Hogan B, Rakotozandrindrainy R, Al-Emran H, Dekker D, Hahn A, Jaeger A, Poppert S, Frickmann H, Hagen RM, Micheel V, Crusius S, Heriniaina JN, Rakotondrainiarivelo JP, Razafindrabe T, May J, Schwarz NG. Prevalence of nasal colonisation by methicillin-sensitive and methicillin-resistant Staphylococcus aureus among healthcare workers and students in Madagascar. BMC Infect Dis 2016; 16:420. [PMID: 27526771 PMCID: PMC4986198 DOI: 10.1186/s12879-016-1733-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) clones pose a significant threat to hospitalised patients because the bacteria can be transmitted by asymptomatic carriers within healthcare facilities. To date, nothing is known about the prevalence of S. aureus and MRSA among healthcare workers in Madagascar. The objective of our study was to examine the prevalence and clonal epidemiology of nasal S. aureus and MRSA among healthcare workers and non-medical University students in Antananarivo, Madagascar. METHODS This cross sectional study screened nasal swabs taken from students and healthcare workers for S. aureus. Multiplex PCR was performed to identify S. aureus-specific (nuc), MRSA-specific mecA and mecC genes, Panton-Valentine leukocidin (PVL) (lukF-PV), and toxic shock syndrome toxin-1 (TSST-1) specific genes in methicillin-sensitive S. aureus (MSSA) and MRSA isolates. Staphylococcus protein A gene (spa) typing was performed for all confirmed MRSA isolates. The frequency distribution of nasal S. aureus and MRSA of healthcare workers and non-medical students was compared using Pearson's χ(2) test. RESULTS Of 1548 nasal swabs tested, 171 (11 %) were positive for S. aureus; 20 (1.3 %) of these isolates were identified as MRSA. S. aureus was detected in 91 of 863 healthcare workers (10.4 %) and in 80 (11.8 %) of 685 students; however, 14 (1.5 %) healthcare workers carried MRSA compared with six (0.9 %) students. Nasal carriage of S. aureus and MRSA was more prevalent in women than in men, and 21 (11.7 %) S. aureus isolates were PVL-positive and 36 (21 %) were TSST-1 positive. The mecC gene was not detected in any isolates. Five different spa types were identified, with spa type t186 being the predominant MRSA clone (16/20). CONCLUSION The results of the present study reveal a low frequency of S. aureus and MRSA nasal carriage in both students and healthcare workers from Antananarivo, Madagascar. The predominant MRSA clone (t186) was previously described in hospitalised patients in Madagascar.
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Affiliation(s)
- Benedikt Hogan
- Research Group Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359 Hamburg, Germany
| | | | - Hassan Al-Emran
- Research Group Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359 Hamburg, Germany
| | - Denise Dekker
- Research Group Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359 Hamburg, Germany
| | - Andreas Hahn
- Research Group Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359 Hamburg, Germany
| | - Anna Jaeger
- Research Group Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359 Hamburg, Germany
| | - Sven Poppert
- University Medical Center, Hamburg-Eppendorf, Martinistr. 52, 20251 Hamburg, Germany
| | - Hagen Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Bernhard-Nocht-Str. 74, D-20359 Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Hospital of Rostock, Schillingallee 70, D-18057 Rostock, Germany
| | - Ralf Matthias Hagen
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Bernhard-Nocht-Str. 74, D-20359 Hamburg, Germany
| | - Volker Micheel
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Bernhard-Nocht-Str. 74, D-20359 Hamburg, Germany
| | - Sabine Crusius
- Institute for Medical Microbiology, Virology and Hygiene, University Hospital of Rostock, Schillingallee 70, D-18057 Rostock, Germany
| | - Jean Noel Heriniaina
- Department of Microbiology and Parasitology, University of Antananarivo, B.P. 175, Antananarivo, Madagascar
| | | | - Tsiriniaina Razafindrabe
- Department of Microbiology and Parasitology, University of Antananarivo, B.P. 175, Antananarivo, Madagascar
| | - Jürgen May
- Research Group Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359 Hamburg, Germany
| | - Norbert Georg Schwarz
- Research Group Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine (BNITM), Bernhard-Nocht-Str. 74, D-20359 Hamburg, Germany
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19
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Phaku P, Lebughe M, Strauß L, Peters G, Herrmann M, Mumba D, Mellmann A, Muyembe-Tamfum JJ, Schaumburg F. Unveiling the molecular basis of antimicrobial resistance in Staphylococcus aureus from the Democratic Republic of the Congo using whole genome sequencing. Clin Microbiol Infect 2016; 22:644.e1-5. [PMID: 27102139 DOI: 10.1016/j.cmi.2016.04.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/29/2016] [Accepted: 04/08/2016] [Indexed: 11/25/2022]
Abstract
Staphylococcus aureus from sub-Saharan Africa is frequently resistant to antimicrobial agents that are commonly used to treat invasive infections in resource-limited settings. The underlying mechanisms of resistance are largely unknown. We therefore performed whole genome sequencing (WGS) on S. aureus from the Democratic Republic of the Congo (DRC) to analyse the genetic determinants of antimicrobial resistance. One hundred S. aureus samples were collected from community-associated asymptomatic nasal carriers in the metropolitan area of Kinshasa, DRC, between 2013 and 2014. Phenotypic resistance against 15 antimicrobial agents was compared to the genotypic results that were extracted from WGS data using Mykrobe predictor and the SeqSphere(+) software that screened for 106 target genes associated with resistance. Isolates were phenotypically resistant against penicillin (97%, n=97), trimethoprim (72%, n=72) and tetracycline (54%, n=45). Thirty-three isolates (33%) were methicillin-resistant S. aureus (MRSA). Of these, nine isolates (27.3%) were oxacillin-susceptible MRSA (OS-MRSA) and belonged to ST8 (t1476). The Y195F mutation of FemA was associated with OS-MRSA (p 0.015). The majority of trimethoprim resistant isolates carried dfrG. Tetracycline resistance was associated with tet(K). The concordance between phenotypic susceptibility testing and both WGS analysis tools was similar and ranged between 96% and 100%. In conclusion, a high proportion of OS-MRSA in the DRC was linked to mutations of FemA. Genotypic and phenotypical antimicrobial susceptibility testing showed high concordance. This encourages the future use of WGS in routine antimicrobial susceptibility testing.
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Affiliation(s)
- P Phaku
- Institut National de Recherche Bio-Médicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - M Lebughe
- Institut National de Recherche Bio-Médicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - L Strauß
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - G Peters
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - M Herrmann
- Institute of Medical Microbiology and Hygiene, University Hospital of Saarland, Homburg, Germany
| | - D Mumba
- Institut National de Recherche Bio-Médicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - A Mellmann
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - J-J Muyembe-Tamfum
- Institut National de Recherche Bio-Médicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - F Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
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20
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Detecting Staphylococcus aureus Virulence and Resistance Genes: a Comparison of Whole-Genome Sequencing and DNA Microarray Technology. J Clin Microbiol 2016; 54:1008-16. [PMID: 26818676 DOI: 10.1128/jcm.03022-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/21/2016] [Indexed: 12/31/2022] Open
Abstract
Staphylococcus aureusis a major bacterial pathogen causing a variety of diseases ranging from wound infections to severe bacteremia or intoxications. Besides host factors, the course and severity of disease is also widely dependent on the genotype of the bacterium. Whole-genome sequencing (WGS), followed by bioinformatic sequence analysis, is currently the most extensive genotyping method available. To identify clinically relevant staphylococcal virulence and resistance genes in WGS data, we developed anin silicotyping scheme for the software SeqSphere(+)(Ridom GmbH, Münster, Germany). The implemented target genes (n= 182) correspond to those queried by the IdentibacS. aureusGenotyping DNA microarray (Alere Technologies, Jena, Germany). Thein silicoscheme was evaluated by comparing the typing results of microarray and of WGS for 154 humanS. aureusisolates. A total of 96.8% (n= 27,119) of all typing results were equally identified with microarray and WGS (40.6% present and 56.2% absent). Discrepancies (3.2% in total) were caused by WGS errors (1.7%), microarray hybridization failures (1.3%), wrong prediction of ambiguous microarray results (0.1%), or unknown causes (0.1%). Superior to the microarray, WGS enabled the distinction of allelic variants, which may be essential for the prediction of bacterial virulence and resistance phenotypes. Multilocus sequence typing clonal complexes and staphylococcal cassette chromosomemecelement types inferred from microarray hybridization patterns were equally determined by WGS. In conclusion, WGS may substitute array-based methods due to its universal methodology, open and expandable nature, and rapid parallel analysis capacity for different characteristics in once-generated sequences.
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21
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Rao Q, Shang W, Hu X, Rao X. Staphylococcus aureus ST121: a globally disseminated hypervirulent clone. J Med Microbiol 2015; 64:1462-1473. [PMID: 26445995 DOI: 10.1099/jmm.0.000185] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus aureus is a leading cause of bacterial infections in hospitals and communities worldwide. With the development of typing methods, several pandemic clones have been well characterized, including the extensively spreading hospital-associated meticillin-resistant S. aureus (HA-MRSA) clone ST239 and the emerging hypervirulent community-associated (CA) MRSA clone USA300. The multilocus sequence typing method was set up based on seven housekeeping genes; S. aureus groups were defined by the sharing of alleles at ≥ 5 of the seven loci. In many cases, the predicted founder of a group would also be the most prevalent ST within the group. As a predicted founder of major S. aureus groups, approximately 90 % of ST121 strains was meticillin-susceptible S. aureus (MSSA). The majority of ST121 strains carry accessory gene regulator type IV, whereas staphylococcal protein A gene types for ST121 are exceptionally diverse. More than 90 % of S. aureus ST121 strains have Panton-Valentine leukocidin; other enterotoxins, haemolysins, leukocidins and exfoliative toxins also contribute to the high virulence of ST121 strains. Patients suffering from S. aureus ST121 infections often need longer hospitalization and prolonged antimicrobial therapy. In this review, we tried to summarize the epidemiology of the S. aureus clone ST121 and focused on the molecular types, toxin carriage and disease spectrum of this globally disseminated clone.
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Affiliation(s)
- Qing Rao
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, PR China
| | - Weilong Shang
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, PR China
| | - Xiaomei Hu
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, PR China
| | - Xiancai Rao
- Department of Microbiology, College of Basic Medical Sciences, Third Military Medical University, Chongqing, PR China
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22
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Schaumburg F, Alabi A, Peters G, Becker K. New epidemiology of Staphylococcus aureus infection in Africa. Clin Microbiol Infect 2014; 20:589-96. [DOI: 10.1111/1469-0691.12690] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Nurjadi D, Olalekan AO, Layer F, Shittu AO, Alabi A, Ghebremedhin B, Schaumburg F, Hofmann-Eifler J, Van Genderen PJJ, Caumes E, Fleck R, Mockenhaupt FP, Herrmann M, Kern WV, Abdulla S, Grobusch MP, Kremsner PG, Wolz C, Zanger P. Emergence of trimethoprim resistance gene dfrG in Staphylococcus aureus causing human infection and colonization in sub-Saharan Africa and its import to Europe. J Antimicrob Chemother 2014; 69:2361-8. [PMID: 24855123 DOI: 10.1093/jac/dku174] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Co-trimoxazole (trimethoprim/sulfamethoxazole) is clinically valuable in treating skin and soft tissue infections (SSTIs) caused by community-associated methicillin-resistant Staphylococcus aureus (MRSA). The genetic basis of emerging trimethoprim/sulfamethoxazole resistance in S. aureus from Africa is unknown. Such knowledge is essential to anticipate its further spread. We investigated the molecular epidemiology of trimethoprim resistance in S. aureus collected in and imported from Africa. METHODS Five hundred and ninety-eight human S. aureus isolates collected at five locations across sub-Saharan Africa [Gabon, Namibia, Nigeria (two) and Tanzania] and 47 isolates from travellers treated at six clinics in Europe because of SSTIs on return from Africa were tested for susceptibility to trimethoprim, sulfamethoxazole and trimethoprim/sulfamethoxazole, screened for genes mediating trimethoprim resistance in staphylococci [dfrA (dfrS1), dfrB, dfrG and dfrK] and assigned to spa genotypes and clonal complexes. RESULTS In 313 clinical and 285 colonizing S. aureus from Africa, 54% of isolates were resistant to trimethoprim, 21% to sulfamethoxazole and 19% to trimethoprim/sulfamethoxazole. We found that 94% of trimethoprim resistance was mediated by the dfrG gene. Of the 47 S. aureus isolates from travellers with SSTIs, 27 (57%) were trimethoprim resistant and carried dfrG. Markers of trimethoprim resistance other than dfrG were rare. The presence of dfrG genes in S. aureus was neither geographically nor clonally restricted. CONCLUSIONS dfrG, previously perceived to be an uncommon cause of trimethoprim resistance in human S. aureus, is widespread in Africa and abundant in imported S. aureus from ill returning travellers. These findings may foreshadow the loss of trimethoprim/sulfamethoxazole for the empirical treatment of SSTIs caused by community-associated MRSA.
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Affiliation(s)
- Dennis Nurjadi
- Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Tropenmedizin, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum, Elfriede-Aulhorn-Straße 6, 72076 Tübingen, Germany
| | - Adesola O Olalekan
- Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Tropenmedizin, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, PO Box 4000, Ogbomoso, Nigeria
| | - Franziska Layer
- Nationales Referenzzentrum für Staphylokokken und Enterokokken, Robert Koch Institut, Burgstraße 37, 38855 Wernigerode, Germany
| | - Adebayo O Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife 22005, Nigeria
| | - Abraham Alabi
- Centre de Recherches Médicales de Lambaréné (CERMEL), B.P. 118, Lambaréné, Gabon
| | - Beniam Ghebremedhin
- Institut für Medizinische Mikrobiologie, Universitätsklinikum, Leipziger Straße 44, 39120 Magdeburg, Germany/Department Humanmedizin, Universität Witten/Herdecke, Alfred-Herrhausen-Straße 50, 58448 Witten, Germany/Helios Clinic, Heusnerstraße 40, 42283 Wuppertal, Germany
| | - Frieder Schaumburg
- Institut für Medizinische Mikrobiologie, Universitätsklinikum Münster, Domagkstraße 10, 48149 Münster, Germany
| | - Jonas Hofmann-Eifler
- Bagamoyo Research and Training Center, Ifakara Health Institute, PO Box 74, Bagamoyo, Tanzania Universitätsklinikum Freiburg, Abteilung Infektiologie, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Perry J J Van Genderen
- Instituut voor Tropische Ziekten, Havenziekenhuis, Haringvliet 72, 3011 TG Rotterdam, The Netherlands
| | - Eric Caumes
- Service de Maladies Infectieuses et Tropicales, groupe hospitalier Pitié-Salpêtrière, 47-83 boulevard de l'Hôpital, 75651 Paris cedex 13, France/Sorbonne Universités, UPMC Univ Paris 06, F-75005, Paris, France
| | - Ralf Fleck
- Tropenklinik, Paul-Lechler-Krankenhaus, 72076 Tübingen, Germany
| | - Frank P Mockenhaupt
- Institut für Tropenmedizin und Internationale Gesundheit, Charité-Universitätsmedizin Berlin, Spandauer Damm 130, 14050 Berlin, Germany
| | - Mathias Herrmann
- Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum des Saarlandes, Kirrberger Straße, 66421 Homburg/Saar, Germany
| | - Winfried V Kern
- Universitätsklinikum Freiburg, Abteilung Infektiologie, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Salim Abdulla
- Bagamoyo Research and Training Center, Ifakara Health Institute, PO Box 74, Bagamoyo, Tanzania
| | - Martin P Grobusch
- Centre de Recherches Médicales de Lambaréné (CERMEL), B.P. 118, Lambaréné, Gabon Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 Amsterdam, The Netherlands
| | - Peter G Kremsner
- Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Tropenmedizin, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany Centre de Recherches Médicales de Lambaréné (CERMEL), B.P. 118, Lambaréné, Gabon
| | - Christiane Wolz
- Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum, Elfriede-Aulhorn-Straße 6, 72076 Tübingen, Germany
| | - Philipp Zanger
- Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Tropenmedizin, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany
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