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Stenhouse GE, Keddy KH, Bengtsson RJ, Hall N, Smith AM, Thomas J, Iturriza-Gómara M, Baker KS. The genomic epidemiology of shigellosis in South Africa. Nat Commun 2023; 14:7715. [PMID: 38001075 PMCID: PMC10673971 DOI: 10.1038/s41467-023-43345-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.
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Affiliation(s)
- George E Stenhouse
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
| | | | - Rebecca J Bengtsson
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Miren Iturriza-Gómara
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK
| | - Kate S Baker
- Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK.
- Department of Genetics, University of Cambridge, CB23EH, Cambridge, UK.
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Dikoumba AC, Onanga R, Mangouka LG, Boundenga L, Ngoungou EB, Godreuil S. Molecular epidemiology of antimicrobial resistance in central africa: A systematic review. Access Microbiol 2023; 5:acmi000556.v5. [PMID: 37691840 PMCID: PMC10484317 DOI: 10.1099/acmi.0.000556.v5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 07/21/2023] [Indexed: 09/12/2023] Open
Abstract
Background In Central Africa, it is difficult to tackle antibiotic resistance, because of a lack of data and information on bacterial resistance, due to the low number of studies carried out in the field. To fill this gap, we carried out a systematic review of the various studies, and devised a molecular epidemiology of antimicrobial resistance from humans, animals and the environmental samples. Method A systematic search of all publications from 2005 to 2020 on bacterial resistance in Central Africa (Gabon, Cameroon, Democratic Republic of Congo, Central African Republic, Chad, Republic of Congo, Equatorial Guinea, São Tomé and Príncipe, Angola) was performed on Pubmed, Google scholar and African Journals Online (AJOL). All circulating resistance genes, prevalence and genetic carriers of these resistances were collected. The study area was limited to the nine countries of Central Africa. Results A total of 517 studies were identified through a literature search, and 60 studies carried out in eight countries were included. Among all articles included, 43 articles were from humans. Our study revealed not only the circulation of beta-lactamase and carbapenemase genes, but also several other types of resistance genes. To finish, we noticed that some studies reported mobile genetic elements such as integrons, transposons, and plasmids. Conclusion The scarcity of data poses difficulties in the implementation of effective strategies against antibiotic resistance, which requires a health policy in a 'One Health' approach.
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Affiliation(s)
- Annicet-Clotaire Dikoumba
- Département de biologie médicale, Hôpital d’Instruction des Armées Omar Bongo Ondimba, B.P 20404 Libreville, Gabon
- Unité de recherche et d’Analyses Médicales (URAM), Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), B.P. 679 Franceville, Gabon
| | - Richard Onanga
- Unité de recherche et d’Analyses Médicales (URAM), Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), B.P. 679 Franceville, Gabon
| | - Laurette G. Mangouka
- Département de Médecine, Hôpital d’Instruction des Armées Omar Bongo Ondimba, B.P 20404 Libreville, Gabon
| | - Larson Boundenga
- Groupe Evolution et Transmission Inter-espèces des Pathogènes, Département de Parasitologie du Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
- Unité Maladies Émergentes Virales, Département de Virologie du Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Edgard-Brice Ngoungou
- Unité de Recherche en Epidémiologie des Maladies Chroniques et Santé Environnement (UREMCSE), Département d’Epidémiologie, Biostatistiques et Informatique Médicale (DEBIM), Faculté de Médecine, Université des Sciences de la Santé, BP 4009 Libreville, Gabon
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 191 Avenue du Doyen Gaston Giraud, 34 295 Montpellier Cedex 5, France
- MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
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Zhu Z, Wang W, Cao M, Zhu Q, Ma T, Zhang Y, Liu G, Zhou X, Li B, Shi Y, Zhang J. Virulence factors and molecular characteristics of Shigella flexneri isolated from calves with diarrhea. BMC Microbiol 2021; 21:214. [PMID: 34271864 PMCID: PMC8285881 DOI: 10.1186/s12866-021-02277-0] [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: 02/19/2021] [Accepted: 06/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background The natural hosts of Shigella are typically humans and other primates, but it has been shown that the host range of Shigella has expanded to many animals. Although Shigella is becoming a major threat to animals, there is limited information on the genetic background of local strains. The purpose of this study was to assess the presence of virulence factors and the molecular characteristics of S. flexneri isolated from calves with diarrhea. Results Fifty-four S. flexneri isolates from Gansun, Shanxi, Qinghai, Xinjiang and Tibet obtained during 2014 to 2016 possessed four typical biochemical characteristics of Shigella. The prevalences of ipaH, virA, ipaBCD, ial, sen, set1A, set1B and stx were 100 %, 100 %, 77.78 %, 79.63 %, 48.15 %, 48.15 and 0 %, respectively. Multilocus variable number tandem repeat analysis (MLVA) based on 8 variable number of tandem repeat (VNTR) loci discriminated the isolates into 39 different MLVA types (MTs), pulsed field gel electrophoresis (PFGE) based on NotI digestion divided the 54 isolates into 31 PFGE types (PTs), and multilocus sequence typing (MLST) based on 15 housekeeping genes differentiated the isolates into 7 MLST sequence types (STs). Conclusions The findings from this study enrich our knowledge of the molecular characteristics of S. flexneri collected from calves with diarrhea, which will be important for addressing clinical and epidemiological issues regarding shigellosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02277-0.
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Affiliation(s)
- Zhen Zhu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China.,College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Weiwei Wang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China
| | - Mingze Cao
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Qiqi Zhu
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Tenghe Ma
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Yongying Zhang
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Guanhui Liu
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Xuzheng Zhou
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China
| | - Bing Li
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China
| | - Yuxiang Shi
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, 056038, Handan, China
| | - Jiyu Zhang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, 730050, Lanzhou, China.
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Guglielmino CJD, Kakkanat A, Forde BM, Rubenach S, Merone L, Stafford R, Graham RMA, Beatson SA, Jennison AV. Outbreak of multi-drug-resistant (MDR) Shigella flexneri in northern Australia due to an endemic regional clone acquiring an IncFII plasmid. Eur J Clin Microbiol Infect Dis 2021; 40:279-286. [PMID: 32888117 PMCID: PMC7473701 DOI: 10.1007/s10096-020-04029-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/27/2020] [Indexed: 11/12/2022]
Abstract
Epidemiological surveillance of Shigella spp. in Australia is conducted to inform public health response. Multi-drug resistance has recently emerged as a contributing factor to sustained local transmission of Shigella spp. All data were collected as part of routine public health surveillance, and strains were whole-genome sequenced for further molecular characterisation. 108 patients with an endemic regional Shigella flexneri strain were identified between 2016 and 2019. The S. flexneri phylogroup 3 strain endemic to northern Australia acquired a multi-drug resistance conferring blaDHA plasmid, which has an IncFII plasmid backbone with virulence and resistance elements typically found in IncR plasmids. This is the first report of multi-drug resistance in Shigella sp. in Australia that is not associated with men who have sex with men. This strain caused an outbreak of multi-drug-resistant S. flexneri in northern Australia that disproportionality affects Aboriginal and Torres Strait Islander children. Community controlled public health action is recommended.
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Affiliation(s)
- Christine J D Guglielmino
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Brisbane, Australia.
| | - Asha Kakkanat
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Brisbane, Australia
| | - Brian M Forde
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Sally Rubenach
- Tropical Public Health Services, Queensland Health, Cairns, Australia
| | - Lea Merone
- Rural and Remote Clinical Support Unit, Apunipima Cape York Health Council, Cairns, Australia
| | - Russell Stafford
- Communicable Diseases Unit, Queensland Health, Brisbane, Australia
| | - Rikki M A Graham
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Brisbane, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Amy V Jennison
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Brisbane, Australia
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5
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Cao M, Wang W, Zhang L, Liu G, Zhou X, Li B, Shi Y, Zhu Z, Zhang J. Epidemic and molecular characterization of fluoroquinolone-resistant Shigella dysenteriae 1 isolates from calves with diarrhea. BMC Microbiol 2021; 21:6. [PMID: 33407134 PMCID: PMC7789508 DOI: 10.1186/s12866-020-02050-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Background The widespread distribution of antimicrobial-resistant Shigella has become a recurrent challenge in many parts of the developing world. Previous studies indicate that the host of Shigella has expanded from humans to animals. This study aimed to investigate the prevalence of fluoroquinolone resistance and associated molecular characterization of S. dysenteriae 1 isolated from calves. Results All 38 unduplicated S. dysenteriae 1 isolates were collected from calves in Gansu Province from October 2014 to December 2016. According to MLST and PFGE analysis, these isolates were separated into 4 and 28 genotypes, respectively. The most common STs identified were ST228 (34.21%, 13/38) and ST229 (39.47%, 15/38), which were first found in the present study. All isolates harbored virulence genes, and the incidence of the seven virulence genes were ipaH (100%), ipaBCD (92.11%), stx (73.68%), ial (57.89%), sen (28.95%), set1A and set1B (0%). According to the results of antimicrobial susceptibilities, 76.32% (29/38) were resistant to fluoroquinolone and showed multidrug resistance. In a study on the polymorphism of quinolone resistance–determining region (QRDR) of gyrA/B and parC/E genes, we identified two mutations in gyrA (Ser83 → Leu and Asp87 → Asn) and parC (Ser80 → Ile and Ser83 → Leu), respectively. Among them, 55.17% (16/29) of resistant strains had the gyrA point mutations (Ser83 → Leu) and parC point mutation (Ser83 → Leu). Moreover, 41.38% (12/29) of isolates had all five point mutations of gyrA and parC. In addition, the prevalence of the plasmid-mediated quinolone resistance (PMQR) determinant genes was also investigated. All 29 fluoroquinolone-resistant isolates were positive for the aac (6′)-Ib-cr gene but negative for qepA, except for SD001. In addition, only 6 (20.69%, 6/29) isolates harbored the qnr gene, including two with qnrB (6.90%, 2/29) and four with qnrS (13.79%, 4/29). Conclusion Given the increased common emergence of multidrug resistant isolates, uninterrupted surveillance will be necessary to understand the actual epidemic burden and control this infection. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02050-9.
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Affiliation(s)
- Mingze Cao
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, Lanzhou, 730050, China.,College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, Handan, 056038, China
| | - Weiwei Wang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, Lanzhou, 730050, China
| | - Liwei Zhang
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, Handan, 056038, China
| | - Guanhui Liu
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, Handan, 056038, China
| | - Xuzheng Zhou
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, Lanzhou, 730050, China
| | - Bing Li
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, Lanzhou, 730050, China
| | - Yuxiang Shi
- College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, Handan, 056038, China
| | - Zhen Zhu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, Lanzhou, 730050, China. .,College of Life Science and Food Engineering, Hebei University of Engineering, Hanshan District, Handan, 056038, China.
| | - Jiyu Zhang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development of the Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Jiangouyan, Qilihe District, Lanzhou, 730050, China.
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6
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Wang MF, Ma GQ, Shao F, Liu RH, Chen LY, Liu Y, Yang L, Meng XW. Neoflavonoids from the heartwood of Dalbergia melanoxylon. Nat Prod Res 2020; 36:735-741. [PMID: 32744091 DOI: 10.1080/14786419.2020.1800692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Three new neoflavonoids, named (1S,8R,9S)-1,5-dihydroxy-4,12-dimethoxy-8-vinyl-tricyclo[7.3.1.02,7]trideca-2,4,6,11-tetraen-10-one (1), 2,5,2',5'-tetrahydroxy-4-methoxybenzophenone (2) and 2,5,3'-trihydroxy-4-methoxybenzophenone (3), were isolated from the heartwood of Dalbergia melanoxylon. Their structures were established by spectroscopic methods, including UV, IR, HRMS, 1 D and 2 D-NMR. Compounds 1-3 were evaluated for inhibitory activity against three fungal strains Candida albicans, Mucor ramosissimus, Saccharomycopsis fermentans and seven bacterial strains Shigella dysenteriae, Salmonella enteri, Bacillus cereus, Staphylococcus epidermidis, Bacillus sphaericus, Staphylococcus aureus, Escherichia coli using the broth dilution method. However, none of compounds 1-3 showed potential antimicrobial activities in vitro.
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Affiliation(s)
- Meng-Fei Wang
- Key Laboratory of Innovation Drug and Efficient Energy-saving Pharmaceutical Equipment, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Guang-Qiang Ma
- College of Basic Medical, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Feng Shao
- Key Laboratory of Innovation Drug and Efficient Energy-saving Pharmaceutical Equipment, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Rong-Hua Liu
- Key Laboratory of Innovation Drug and Efficient Energy-saving Pharmaceutical Equipment, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Lan-Ying Chen
- National Engineering Research Center, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Yang Liu
- Key Laboratory of Innovation Drug and Efficient Energy-saving Pharmaceutical Equipment, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Li Yang
- Key Laboratory of Innovation Drug and Efficient Energy-saving Pharmaceutical Equipment, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Xiao-Wei Meng
- Key Laboratory of Innovation Drug and Efficient Energy-saving Pharmaceutical Equipment, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
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Parajuli P, Rajput MI, Verma NK. Plasmids of Shigella flexneri serotype 1c strain Y394 provide advantages to bacteria in the host. BMC Microbiol 2019; 19:86. [PMID: 31035948 PMCID: PMC6489325 DOI: 10.1186/s12866-019-1455-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 04/11/2019] [Indexed: 11/29/2022] Open
Abstract
Background Shigella flexneri has an extremely complex genome with a significant number of virulence traits acquired by mobile genetic elements including bacteriophages and plasmids. S. flexneri serotype 1c is an emerging etiological agent of bacillary dysentery in developing countries. In this study, the complete nucleotide sequence of two plasmids of S. flexneri serotype 1c strain Y394 was determined and analysed. Results The plasmid pINV-Y394 is an invasive or virulence plasmid of size 221,293 bp composed of a large number of insertion sequences (IS), virulence genes, regulatory and maintenance genes. Three hundred and twenty-eight open reading frames (ORFs) were identified in pINV-Y394, of which about a half (159 ORFs) were identified as IS elements. Ninety-seven ORFs were related to characterized genes (majority of which are associated with virulence and their regulons), and 72 ORFs were uncharacterized or hypothetical genes. The second plasmid pNV-Y394 is of size 10,866 bp and encodes genes conferring resistance against multiple antibiotics of clinical importance. The multidrug resistance gene cassette consists of tetracycline resistance gene tetA, streptomycin resistance gene strA-strB and sulfonamide-resistant dihydropteroate synthase gene sul2. Conclusions These two plasmids together play a key role in the fitness of Y394 in the host environment. The findings from this study indicate that the pathogenic S. flexneri is a highly niche adaptive pathogen which is able to co-evolve with its host and respond to the selection pressure in its environment. Electronic supplementary material The online version of this article (10.1186/s12866-019-1455-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pawan Parajuli
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Munazza I Rajput
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Naresh K Verma
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, ACT, Australia.
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Ma QP, Su L, Liu JW, Yao MX, Yuan GY. Study on the association between drug‑resistance and gene mutations of the active efflux pump acrAB‑tolC gene and its regulatory genes. Mol Med Rep 2018; 17:8228-8236. [PMID: 29693161 PMCID: PMC5983997 DOI: 10.3892/mmr.2018.8916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/22/2017] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to investigate the correlation between the multi‑drug resistance of Shigella flexneri and the drug‑resistant gene cassette carried by integrons; in the meanwhile, to detect the associations between drug‑resistance and gene mutations of the active efflux pump acrAB‑tolC gene and its regulatory genes, including marOR, acrR and soxS. A total of 158 isolates were isolated from the stool samples of 1,026 children with diarrhoea aged 14 years old between May 2012 and October 2015 in Henan. The K‑B method was applied for the determination of drug resistance of Shigella flexneri, and polymerase chain reaction amplification was used for class 1, 2 and 3 integrase genes. Enzyme digestion and sequence analysis were performed for the variable regions of positive strains. Based on the drug sensitivity assessment, multi‑drug resistant strains that were resistant to five or more antibiotics, and sensitive strains were selected for amplification. Their active efflux pump genes, acrA and acrB, and regulatory genes, marOR, acrR and soxS, were selected for sequencing. The results revealed that 91.1% of the 158 strains were multi‑resistant to ampicillin, chloramphenicol, tetracycline and streptomycin, and 69.6% of the strains were multi‑resistant to sulfamethoxazole/trimethoprim. The resistance to ceftazidime, ciprofloxacin and levofloxacin was <32.9%. All strains (100%) were sensitive to cefoxitin, cefoperazone/sulbactam and imipenem. The rate of the class 1 integron positivity was 91.9% (144/158). Among these class 1 integron‑positive strains, 18 strains exhibited the resistance gene cassette dfrV in the variable region of the strain, four strains exhibited dfrA17‑aadA5 in the variable region and 140 strains exhibited blaOXA‑30‑aadA1 in the variable region. Four strains showed no resistance gene in the variable regions. The rate of class 2 integron positivity was 86.1% (136/158), and all positive strains harboured the dfrA1‑sat1‑aadA resistance gene cassette in the variable region. The class 3 integrase gene was not detected in these strains. The gene sequencing showed the deletion of base CATT in the 36, 37, 38, 39 site in the marOR gene, which is a regulatory gene of the active efflux pump, AcrAB‑TolC. Taken together, the multi‑drug resistance of Shigella flexneri was closely associated with gene mutations of class 1 and 2 integrons and the marOR gene.
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Affiliation(s)
- Quan-Ping Ma
- Department of Clinical Laboratory, Jinan Fourth People's Hospital, Jinan, Shandong 250031, P.R. China
| | - Liang Su
- Department of Clinical Laboratory, Jinan Infectious Disease Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
| | - Jing-Wen Liu
- Department of Clinical Laboratory, Jinan Infectious Disease Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
| | - Ming-Xiao Yao
- Bacteria Laboratory, Shandong Center for Disease Control and Prevention, Shandong 250014, P.R. China
| | - Guang-Ying Yuan
- Department of Clinical Laboratory, Jinan Infectious Disease Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
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Rajpara N, Nair M, Chowdhury G, Mukhopadhyay AK, Ramamurthy T, Niyogi SK, Bhardwaj AK. Molecular analysis of multidrug resistance in clinical isolates of Shigella spp. from 2001-2010 in Kolkata, India: role of integrons, plasmids, and topoisomerase mutations. Infect Drug Resist 2018; 11:87-102. [PMID: 29391815 PMCID: PMC5769595 DOI: 10.2147/idr.s148726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To understand the genetic basis of high drug resistance in Shigella, 95 clinical isolates of Shigella spp. (2001-2010) were obtained from the Infectious Diseases Hospital, Kolkata, India. Ninety-three isolates were resistant to three or more antibiotics. Resistance to nalidixic acid, trimethoprim, streptomycin, and co-trimoxazole was most common in this population. Dendrogram analysis showed that S. sonnei strains were more clonally related when compared to the other Shigella species. The role of mobile genetic elements and chromosome-borne resistance factors was analyzed in detail. Integron analysis indicated the preponderance of class 2 and atypical class 1 integrons in that population. Typical class 1 integron was present in only one S. sonnei isolate and harbored trimethoprim resistance-encoding gene dfrV, while atypical class 1 integrons harbored dfrA1-aadA or blaOXA-aadA gene cassettes responsible for resistance to trimethoprim, aminoglycosides, and β-lactams. Class 2 integrons harbored either dfrA1-sat-aadA or dfrA1-sat gene cassettes. Most importantly, a novel gene cassette array InsE-InsO-dfrA1-sat was found in class 2 integron of S. sonnei NK4846. Many of the resistance traits for antibiotics such as trimethoprim, co-trimoxazole, kanamycin, ampicillin, and tetracycline were transferred from parent Shigella isolates to recipient Escherichia coli during conjugation, establishing the role of plasmids in horizontal transfer of resistance genes. Multiple mutations such as S80→I, S83→L, and D87→G/N/Y in quinolone resistance determining regions of topoisomerases from the representative quinolone-resistant isolates could explain the spectrum of minimal inhibitory concentration values for various quinolones. To the best of our knowledge, this is the first comprehensive report that describes the contribution of mobile (plasmids, integrons, and quinolone resistance genes named qnr) and innate genetic elements (mutations in topoisomerases) in determining the resistance phenotype of all the four species of Shigella over a span of ten years.
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Affiliation(s)
- Neha Rajpara
- Department of Human Health and Diseases, Indian Institute of Advanced Research, Koba Institutional Area, Gandhinagar.,Department of Microbiology and Biotechnology Centre, Maharaja Sayaji Rao University of Baroda, Vadodara, Gujarat
| | - Mrinalini Nair
- Department of Microbiology and Biotechnology Centre, Maharaja Sayaji Rao University of Baroda, Vadodara, Gujarat
| | - Goutam Chowdhury
- Department of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata
| | - Asish K Mukhopadhyay
- Department of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata
| | - Thandavarayan Ramamurthy
- Center for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad, India
| | - Swapan Kumar Niyogi
- Department of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata
| | - Ashima Kushwaha Bhardwaj
- Department of Human Health and Diseases, Indian Institute of Advanced Research, Koba Institutional Area, Gandhinagar
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Seribelli AA, Frazão MR, Medeiros MIC, Stehling EG, Falcão JP. Molecular typing and occurrence of beta-lactam resistance genes of Shigella sonnei strains isolated from 1983 to 2014 in the São Paulo state of Brazil. Microbiol Immunol 2017; 61:547-553. [PMID: 29058340 DOI: 10.1111/1348-0421.12550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/03/2017] [Accepted: 10/19/2017] [Indexed: 11/29/2022]
Abstract
Shigella sonnei, which has generally been associated with dysentery in developed countries, has recently been emerging in developing countries. Specifically, in Brazil few published studies have that molecularly characterized this species. The aims of this study were to analyze the efficacy of typing using multiple-locus variable-number tandem-repeat analysis (MLVA), study the phylogeny by multi-locus sequence typing (MLST) and assess the presence of some beta-lactam resistance genes in S. sonnei strains isolated from human diarrhoeic faeces in the São Paulo State in Brazil between 1983 and 2014. Seventy-two such S. sonnei strains were typed by MLVA and grouped into two clusters. The discrimination index of MLVA was found to be 0.996. Twenty strains were typed by MLST as ST152. In addition, the blaTEM gene was detected in eight (72.7%) of the 11 S. sonnei strains that had previously been shown to be resistant to β-lactams. However, blaCTX-M-1group , blaCTX-M-9group and blaSHV genes were not found. MLVA results suggested the existence of two prevalent subtypes in the S. sonnei strains studied, confirming previous results. Moreover, MLVA efficiently discriminated monomorphic S. sonnei species. Because the S. sonnei strains studied belonged to clonal complex 152 and all isolates were typed as ST152, MLST is not a suitable method for studying the population structure of S. sonnei. Although, the rates of β-lactam resistance were not high in the present study, the frequency of blaTEM may represent a risk for patients receiving antimicrobial treatment. Taken together, the results provide better molecular characterization of this globally clinically important pathogen.
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Affiliation(s)
- Amanda Ap Seribelli
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, University of São Paulo, Café Avenue, 14040-903, Brazil
| | - Miliane R Frazão
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, University of São Paulo, Café Avenue, 14040-903, Brazil
| | | | - Eliana G Stehling
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, University of São Paulo, Café Avenue, 14040-903, Brazil
| | - Juliana P Falcão
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, University of São Paulo, Café Avenue, 14040-903, Brazil
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Gu B, Xu T, Kang H, Xu Y, Liu G, Pan S, Qian H, Ma P. A 10-year surveillance of antimicrobial susceptibility patterns in Shigella sonnei isolates circulating in Jiangsu Province, China. J Glob Antimicrob Resist 2017; 10:29-34. [PMID: 28606485 PMCID: PMC7103933 DOI: 10.1016/j.jgar.2017.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 02/19/2017] [Accepted: 03/06/2017] [Indexed: 11/30/2022] Open
Abstract
Long-term multicentre surveillance of antimicrobial susceptibility patterns in Shigella sonnei. Epidemic clones and integron types and resistance gene cassettes were characterised. PFGE indicated large-scale clonal transmission among different cities occurred several times during 10 years. Class 1, 2 and atypical class 1 integrons were detected in S. sonnei. High prevalence of integrons and gene cassettes was related to the increasing antimicrobial resistance.
Objectives The rapid emergence of drug-resistant Shigella sonnei is a serious public health problem. This study aimed to characterise the antimicrobial resistance patterns, molecular subtypes, and integron types and resistance gene cassettes in S. sonnei from Jiangsu Province, China. Methods In total, 340 S. sonnei were collected in 2002–2011 throughout Jiangsu Province. Antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), PCR amplification of integrons, restriction fragment length polymorphism (RFLP) and DNA sequencing of cassette regions were performed. Results Resistance rates to ampicillin (67.7%), nalidixic acid (75.2%), tetracycline (73.7%) and trimethoprim/sulfamethoxazole (68.7%) remained high. Strains from Centre and South Jiangsu showed higher resistance and multiresistance rates compared with the North. PFGE analysis indicated that large-scale clonal transmission among different cities occurred several times during 10 years. Among all strains, 55.9% (190/340) harboured class 1 integrons, 80.3% (273/340) harboured class 2 integrons and 49.4% (168/340) harboured an atypical class 1 integron. Resistance rates to nine antimicrobials in the class 1 integron-positive group were significantly higher than in the negative group (P < 0.05). Seven different gene cassettes were detected in class 1 integrons. The most prevalent type was aacA4–cmlA1 (114/286). Class 2 integrons carried the gene cassette array dfrA1–sat1–aadA1, and the atypical class 1 integron carried blaOXA-30–aadA1. Conclusions The increasing antimicrobial resistance and significant clonal transmission of S. sonnei circulating in Jiangsu were closely related to the high prevalence of integrons and gene cassettes. Long-term cross-regional monitoring of antimicrobial resistance is urgently required for S. sonnei.
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Affiliation(s)
- Bing Gu
- Medical Technology Institute of Xuzhou Medical University, Xuzhou 221004, China; Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Ting Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Haiquan Kang
- Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Yanling Xu
- Department of General Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Genyan Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shiyang Pan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Huimin Qian
- Department of Acute Infectious Disease Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210029, China.
| | - Ping Ma
- Medical Technology Institute of Xuzhou Medical University, Xuzhou 221004, China; Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China.
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Zhang F, Ding G, Liu Z, Zhang C, Jiang B. Association between flood and the morbidity of bacillary dysentery in Zibo City, China: a symmetric bidirectional case-crossover study. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2016; 60:1919-1924. [PMID: 27121465 DOI: 10.1007/s00484-016-1178-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 03/30/2016] [Accepted: 04/17/2016] [Indexed: 06/05/2023]
Abstract
This study examined the relationship between daily morbidity of bacillary dysentery and flood in 2007 in Zibo City, China, using a symmetric bidirectional case-crossover study. Odds ratios (ORs) and 95 % confidence intervals (CIs) on the basis of multivariate model and stratified analysis at different lagged days were calculated to estimate the risk of flood on bacillary dysentery. A total of 902 notified bacillary dysentery cases were identified during the study period. The median of case distribution was 7-year-old and biased to children. Multivariable analysis showed that flood was associated with an increased risk of bacillary dysentery, with the largest OR of 1.849 (95 % CI 1.229-2.780) at 2-day lag. Gender-specific analysis showed that there was a significant association between flood and bacillary dysentery among males only (ORs >1 from lag 1 to lag 5), with the strongest lagged effect at 2-day lag (OR = 2.820, 95 % CI 1.629-4.881), and the result of age-specific indicated that youngsters had a slightly larger risk to develop flood-related bacillary dysentery than older people at one shorter lagged day (OR = 2.000, 95 % CI 1.128-3.546 in youngsters at lag 2; OR = 1.879, 95 % CI 1.069-3.305 in older people at lag 3). Our study has confirmed that there is a positive association between flood and the risk of bacillary dysentery in selected study area. Males and youngsters may be the vulnerable and high-risk populations to develop the flood-related bacillary dysentery. Results from this study will provide recommendations to make available strategies for government to deal with negative health outcomes due to floods.
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Affiliation(s)
- Feifei Zhang
- Department of Epidemiology, School of Public Health, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, China
- Shandong University Climate Change and Health Center, Jinan, Shandong Province, 250012, China
| | - Guoyong Ding
- Department of Epidemiology, School of Public Health, Taishan Medical University, Taian, Shandong Province, 271016, China
| | - Zhidong Liu
- Department of Epidemiology, School of Public Health, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, China
- Shandong University Climate Change and Health Center, Jinan, Shandong Province, 250012, China
| | - Caixia Zhang
- Department of Epidemiology, School of Public Health, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, China
- Shandong University Climate Change and Health Center, Jinan, Shandong Province, 250012, China
| | - Baofa Jiang
- Department of Epidemiology, School of Public Health, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, China.
- Shandong University Climate Change and Health Center, Jinan, Shandong Province, 250012, China.
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