1
|
Dong W, Fan X, Guo Y, Wang S, Jia S, Lv N, Yuan T, Pan Y, Xue Y, Chen X, Xiong Q, Yang R, Zhao W, Zhu B. An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases. Nat Commun 2024; 15:8084. [PMID: 39278950 PMCID: PMC11402979 DOI: 10.1038/s41467-024-51864-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 08/16/2024] [Indexed: 09/18/2024] Open
Abstract
Virulence factor genes (VFGs) play pivotal roles in bacterial infections and have been identified within the human gut microbiota. However, their involvement in chronic diseases remains poorly understood. Here, we establish an expanded VFG database (VFDB 2.0) consisting of 62,332 nonredundant orthologues and alleles of VFGs using species-specific average nucleotide identity ( https://github.com/Wanting-Dong/MetaVF_toolkit/tree/main/databases ). We further develop the MetaVF toolkit, facilitating the precise identification of pathobiont-carried VFGs at the species level. A thorough characterization of VFGs for 5452 commensal isolates from healthy individuals reveals that only 11 of 301 species harbour these factors. Further analyses of VFGs within the gut microbiomes of nine chronic diseases reveal both common and disease-specific VFG features. Notably, in type 2 diabetes patients, long HiFi sequencing confirms that shared VF features are carried by pathobiont strains of Escherichia coli and Klebsiella pneumoniae. These findings underscore the critical importance of identifying and understanding VFGs in microbiome-associated diseases.
Collapse
Affiliation(s)
- Wanting Dong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinyue Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaqiong Guo
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, Beijing, 100089, China
| | - Siyi Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shulei Jia
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Na Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Yuan
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China
| | - Yuanlong Pan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Xue
- National Engineering and Technology Research Center for Fruits and Vegetables, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xi Chen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Xiong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Weigang Zhao
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China.
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250117, China.
- Beijing Key Laboratory of Antimicrobial Resistance and Pathogen Genomics, Beijing, 100101, China.
| |
Collapse
|
2
|
Ketkhao P, Utrarachkij F, Parikumsil N, Poonchareon K, Kerdsin A, Ekchariyawat P, Narongpun P, Nakajima C, Suzuki Y, Suthienkul O. Phylogenetic diversity and virulence gene characteristics of Escherichia coli from pork and patients with urinary tract infections in Thailand. PLoS One 2024; 19:e0307544. [PMID: 39052658 PMCID: PMC11271939 DOI: 10.1371/journal.pone.0307544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC), especially uropathogenic E. coli (UPEC) are responsible for urinary tract infections (UTIs), while diarrheagenic E. coli (DEC) cause foodborne illnesses. These pathogenic E. coli are a serious threat to human health and a public concern worldwide. However, the evidence on pork E. coli (PEC) harboring UPEC virulence-associated genes is currently limited. Therefore, this study aimed to determine the phylogroups, virulence genes, and their association between PEC and UPEC from UTI patients. In this study, 330 E. coli were obtained from archived stock culture isolated from pork (PEC; n = 165) and urine of patients with UTIs (UPEC; n = 165) during 2014-2022. Phylogroups, UPEC- and diarrheagenic E. coli (DEC) associated virulence genes were assessed using PCR assays. The results showed that phylogroups A (50.3%), and B1 (32.1%) were commonly found among PEC whereas phylogroups B2 (41.8%), and C (25.5%) were commonly detected in the UPEC. PEC and UPEC carried similar virulence-associated genes with different percentages. The most frequent UPEC virulence-associated gene among UPEC, and PEC strains was fimH, (93.3%, and 92.1%), followed by iucC (55.2%, and 12.7%), papC (21.8%, and 4.2%), afaC (22.4%, and 0%), hlyCA (17%, and 0.6%), cnf (16.4%, and 0.6%), and sfa/focDE (8.5%, and 4.8%). Additionally, 6 of 27 UPEC virulence-associated gene patterns were found in both PEC and UPEC strains regardless of phylogroups. Furthermore, the DEC virulence-associated genes were found in only 3 strains, one from PEC harboring eae, and two from UPEC carried fimH-bfpA or afaC-CVD432 indicating hybrid strains. Cluster analysis showed a relationship between PEC and UPEC strains and demonstrated that PEC harboring UPEC virulence-associated genes in pork may be associated with UPEC in humans. Food safety and hygiene practices during pork production chain are important procedures for minimizing cross-contamination of these strains that could be transmitted to the consumers.
Collapse
Affiliation(s)
- Pramualchai Ketkhao
- Faculty of Public Health, Department of Microbiology, Mahidol University, Bangkok, Thailand
| | - Fuangfa Utrarachkij
- Faculty of Public Health, Department of Microbiology, Mahidol University, Bangkok, Thailand
| | | | - Kritchai Poonchareon
- Division of Biochemistry, School of Medical Sciences, University of Phayao, Phayao, Thailand
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermprakiat Sakon Nakhon Province Campus, Sakhon Nakhon, Thailand
| | - Peeraya Ekchariyawat
- Faculty of Public Health, Department of Microbiology, Mahidol University, Bangkok, Thailand
| | - Pawarut Narongpun
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
| | | |
Collapse
|
3
|
Siqueira JAM, Teixeira DM, da Piedade GJL, Souza CDO, Moura TCF, Bahia MDNM, Brasiliense DM, Santos DSADS, Morais LLCDS, da Silva DDFL, Carneiro BS, Pinheiro KDC, Junior ECS, Catete CP, Souza E Guimarães RJDP, Ferreira JL, Chagas Junior WDD, Machado RS, Tavares FN, Resque HR, Dos Santos Lobo P, Guerra SDFDS, Soares LS, da Silva LD, Gabbay YB. Environmental health of water bodies from a Brazilian Amazon Metropolis based on a conventional and metagenomic approach. J Appl Microbiol 2024; 135:lxae101. [PMID: 38627246 DOI: 10.1093/jambio/lxae101] [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: 09/08/2023] [Revised: 04/03/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
AIMS The present study aimed to use a conventional and metagenomic approach to investigate the microbiological diversity of water bodies in a network of drainage channels and rivers located in the central area of the city of Belém, northern Brazil, which is considered one of the largest cities in the Brazilian Amazon. METHODS AND RESULTS In eight of the analyzed points, both bacterial and viral microbiological indicators of environmental contamination-physical-chemical and metals-were assessed. The bacterial resistance genes, drug resistance mechanisms, and viral viability in the environment were also assessed. A total of 473 families of bacteria and 83 families of viruses were identified. Based on the analysis of metals, the levels of three metals (Cd, Fe, and Mn) were found to be above the recommended acceptable level by local legislation. The levels of the following three physicochemical parameters were also higher than recommended: biochemical oxygen demand, dissolved oxygen, and turbidity. Sixty-three bacterial resistance genes that conferred resistance to 13 different classes of antimicrobials were identified. Further, five mechanisms of antimicrobial resistance were identified and viral viability in the environment was confirmed. CONCLUSIONS Intense human actions combined with a lack of public policies and poor environmental education of the population cause environmental degradation, especially in water bodies. Thus, urgent interventions are warranted to restore the quality of this precious and scarce asset worldwide.
Collapse
Affiliation(s)
| | - Dielle Monteiro Teixeira
- Laboratório de Vírus Gastroentéricos, Seção de Virologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | | | - Cintya de Oliveira Souza
- Laboratório de Enteroinfecções Bacterianas II, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | - Tuane Carolina Ferreira Moura
- Laboratório de Enteroinfecções Bacterianas II, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | - Marcia de Nazaré Miranda Bahia
- Laboratório de Enteroinfecções Bacterianas II, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | - Danielle Murici Brasiliense
- Laboratório de Patógenos Especiais, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | | | | | | | - Bruno Santana Carneiro
- Laboratório de Indicadores Físico-Químicos de Qualidade da Água, Seção de Meio Ambiente, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | - Kenny da Costa Pinheiro
- Laboratório de Bioinformática, Seção de Virologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | - Edivaldo Costa Sousa Junior
- Laboratório de Epidemiologia em Leishmanioses, Seção de Parasitologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | - Clístenes Pamplona Catete
- Laboratório de Geoprocessamento, Seção de Epidemiologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | | | - James Lima Ferreira
- Laboratório de Enterovírus, Seção de Virologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | | | - Raiana Scerni Machado
- Laboratório de Enterovírus, Seção de Virologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | - Fernando Neto Tavares
- Laboratório de Enterovírus, Seção de Virologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | - Hugo Reis Resque
- Laboratório de Vírus Gastroentéricos, Seção de Virologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | - Patrícia Dos Santos Lobo
- Laboratório de Vírus Gastroentéricos, Seção de Virologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | | | - Luana Silva Soares
- Laboratório de Vírus Gastroentéricos, Seção de Virologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | - Luciana Damascena da Silva
- Laboratório de Vírus Gastroentéricos, Seção de Virologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| | - Yvone Benchimol Gabbay
- Laboratório de Vírus Gastroentéricos, Seção de Virologia, Instituto Evandro Chagas (SVSA/MS), CEP 67030-000, Brazil
| |
Collapse
|
4
|
Liu X, Mo J, Yang X, Peng L, Zeng Y, Zheng Y, Song G. Causal relationship between gut microbiota and chronic renal failure: a two-sample Mendelian randomization study. Front Microbiol 2024; 15:1356478. [PMID: 38633704 PMCID: PMC11021586 DOI: 10.3389/fmicb.2024.1356478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
Background Observational studies and some experimental investigations have indicated that gut microbiota are closely associated with the incidence and progression of chronic renal failure. However, the causal relationship between gut microbiota and chronic renal failure remains unclear. The present study employs a two-sample Mendelian randomization approach to infer the causal relationship between gut microbiota and chronic renal failure at the genetic level. This research aims to determine whether there is a causal effect of gut microbiota on the risk of chronic renal failure, aiming to provide new evidence to support targeted gut therapy for the treatment of chronic renal failure. Methods Employing genome-wide association study (GWAS) data from the public MiBioGen and IEU OpenGWAS platform, a two-sample Mendelian randomization analysis was conducted. The causal relationship between gut microbiota and chronic renal failure was inferred using five different methods: Inverse Variance Weighted, MR-Egger, Weighted Median, Simple Mode, and Weighted Mode. The study incorporated sensitivity analyses that encompassed evaluations for pleiotropy and heterogeneity. Subsequently, the results of the Mendelian randomization analysis underwent a stringent correction for multiple testing, employing the False Discovery Rate method to enhance the validity of our findings. Results According to the results from the Inverse Variance Weighted method, seven bacterial genera show a significant association with the outcome variable chronic renal failure. Of these, Ruminococcus (gauvreauii group) (OR = 0.82, 95% CI = 0.71-0.94, p = 0.004) may act as a protective factor against chronic renal failure, while the genera Escherichia-Shigella (OR = 1.22, 95% CI = 1.08-1.38, p = 0.001), Lactococcus (OR = 1.1, 95% CI = 1.02-1.19, p = 0.013), Odoribacter (OR = 1.23, 95% CI = 1.03-1.49, p = 0.026), Enterorhabdus (OR = 1.14, 95% CI = 1.00-1.29, p = 0.047), Eubacterium (eligens group) (OR = 1.18, 95% CI = 1.02-1.37, p = 0.024), and Howardella (OR = 1.18, 95% CI = 1.09-1.28, p < 0.001) may be risk factors for chronic renal failure. However, after correction for multiple comparisons using False Discovery Rate, only the associations with Escherichia-Shigella and Howardella remain significant, indicating that the other genera have suggestive associations. Sensitivity analyses did not reveal any pleiotropy or heterogeneity. Conclusion Our two-sample Mendelian randomization study suggests that the genera Escherichia-Shigella and Howardella are risk factors for chronic renal failure, and they may serve as potential targets for future therapeutic interventions. However, the exact mechanisms of action are not yet clear, necessitating further research to elucidate their precise roles fully.
Collapse
Affiliation(s)
- Xingzheng Liu
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Jinying Mo
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Xuerui Yang
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Ling Peng
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Youjia Zeng
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Yihou Zheng
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Gaofeng Song
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| |
Collapse
|
5
|
Du C, Liao Y, Ding C, Huang J, Zhou S, Xu Y, Yang Z, Shi X, Li Y, Jiang M, Zuo L, Li M, Bian S, Xiao N, Li L, Xu Y, Hu Q, Li Q. Molecular serotyping of diarrheagenic Escherichia coli with a MeltArray assay reveals distinct correlation between serotype and pathotype. Gut Microbes 2024; 16:2401944. [PMID: 39292565 DOI: 10.1080/19490976.2024.2401944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/13/2024] [Accepted: 09/04/2024] [Indexed: 09/20/2024] Open
Abstract
Diarrheagenic Escherichia coli serotypes are associated with various clinical syndromes, yet the precise correlation between serotype and pathotype remains unclear. A major barrier to such studies is the reliance on antisera-based serotyping, which is culture-dependent, low-throughput, and cost-ineffective. We have established a highly multiplex PCR-based serotyping assay, termed the MeltArray E. coli serotyping (EST) assay, capable of identifying 163 O-antigen-encoding genes and 53 H-antigen-encoding genes of E. coli. The assay successfully identified serotypes directly from both simulated and real fecal samples, as demonstrated through spike-in validation experiments and a retrospective study. In a multi-province study involving 637 E. coli strains, it revealed that the five major diarrheagenic pathotypes have distinct serotype compositions. Notably, it differentiated 257 Shigella isolates into four major Shigella species, distinguishing them from enteroinvasive E. coli based on their distinct serotype profiles. The assay's universality was further corroborated by in silico analysis of whole-genome sequences from the EnteroBase. We conclude that the MeltArray EST assay represents a paradigm-shifting tool for molecular serotyping of E. coli, with potential routine applications for comprehensive serotype analysis, disease diagnosis, and outbreak detection.
Collapse
Affiliation(s)
- Chen Du
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yiqun Liao
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Congcong Ding
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Jiayu Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Shujuan Zhou
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Yiyan Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Zhaohui Yang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Xiaolu Shi
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yinghui Li
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Min Jiang
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Le Zuo
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Minxu Li
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | | | - Na Xiao
- Laboratory Department, Yantian District Center for Disease Control and Prevention, Shenzhen, China
| | - Liqiang Li
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Qinghua Hu
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| |
Collapse
|
6
|
Zhuo W, Zhao Y, Zhao X, Yao Z, Qiu X, Huang Y, Li H, Shen J, Zhu Z, Li T, Li S, Huang Q, Zhou R. Enteropathogenic Escherichia coli is a predominant pathotype in healthy pigs in Hubei Province of China. J Appl Microbiol 2023; 134:lxad260. [PMID: 37962953 DOI: 10.1093/jambio/lxad260] [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: 07/26/2023] [Revised: 10/29/2023] [Accepted: 11/13/2023] [Indexed: 11/16/2023]
Abstract
AIM This study aims to investigate the prevalence of intestinal pathogenic Escherichia coli (InPEC) in healthy pig-related samples and evaluate the potential virulence of the InPEC strains. METHODS AND RESULTS A multiplex PCR method was established to identify different pathotypes of InPEC. A total of 800 rectal swab samples and 296 pork samples were collected from pig farms and slaughterhouses in Hubei province, China. From these samples, a total of 21 InPEC strains were isolated, including 19 enteropathogenic E. coli (EPEC) and 2 shiga toxin-producing E. coli (STEC) strains. By whole-genome sequencing and in silico typing, it was shown that the sequence types and serotypes were diverse among the strains. Antimicrobial susceptibility assays showed that 90.48% of the strains were multi-drug resistant. The virulence of the strains was first evaluated using the Galleria mellonella larvae model, which showed that most of the strains possessed medium to high pathogenicity. A moderately virulent EPEC isolate was further selected to characterize its pathogenicity using a mouse model, which suggested that it could cause significant diarrhea. Bioluminescence imaging (BLI) was then used to investigate the colonization dynamics of this EPEC isolate, which showed that the EPEC strain could colonize the mouse cecum for up to 5 days.
Collapse
Affiliation(s)
- Wenxiao Zhuo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianglin Zhao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiming Yao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuxiu Qiu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yaxue Huang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Huaixia Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Shen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhihao Zhu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Li
- Hubei Animal Disease Prevention and Control Center, Wuhan 430070, China
| | - Shaowen Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Huang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, College of Veterinary Medicine, Wuhan 430070, China
- International Research Center for Animal Disease (Ministry of Science & Technology of China), College of Veterinary Medicine, Wuhan 430070, China
| | - Rui Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Cooperative Innovation Center of Sustainable Pig Production, College of Veterinary Medicine, Wuhan 430070, China
- International Research Center for Animal Disease (Ministry of Science & Technology of China), College of Veterinary Medicine, Wuhan 430070, China
- The HZAU-HVSEN Research Institute, Wuhan 430042, China
| |
Collapse
|
7
|
Köffer J, Frontzek A, Eigner U. Development and validation of a bacterial gastrointestinal multiplex RT-PCR assay for use on a fully automated molecular system. J Microbiol Methods 2023; 210:106754. [PMID: 37263528 DOI: 10.1016/j.mimet.2023.106754] [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] [Received: 04/04/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/03/2023]
Abstract
PCR-based enteric multiplex panels represent a rapid and reliable alternative to conventional "classical" phenotypic stool diagnostics. The aim of this study was to establish a laboratory-developed non-commercial multiplex Real-Time-PCR panel for the detection of the most important bacterial stool pathogens, Salmonella spp., Shigella spp., Yersinia enterocolitica/ pseudotuberculosis and Campylobacter jejuni/coli. on the "open" cobas omni Utility Channel (UC) of the cobas 6800 system (Roche). The aim was to replace the laborious phenotypical stool diagnostics with a high throughput Real-Time PCR method. The respective primers and probes were designed to cover conserved genomic regions of the pathogens and validated using Ultramer oligonucleotides, positive stool material and reference strains. To further validate the multiplex PCR-assay, the following parameters were evaluated: analytical-sensitivity and -specificity, cross-reactivity, linearity and inter- and intra-assay variance as well as limit of detection (LOD). In addition a retrospective analysis of culture positive and negative samples from daily routine was performed using 745 native stool samples. The Gastro assay was linear over a 5-log-unit and within the expected dynamic range with amplification efficiencies ranging from 94.6% to 120%. In addition, all targets showed excellent coefficients of repeatability (≤ 1.11%), intermediate precision (≤ 1.02%) and total variance (≤ 1.39%). In terms of analytical sensitivity the assay demonstrated detection limits ranging from 7.83 copies per reaction to 14.4 copies per reaction. The assay showed excellent agreement with culture methods (>95%) and a 100% sensitivity and specificity after resolution of discrepant results. The multiplex-PCR assay provides a comprehensive, rapid and sensitive alternative to conventional methods for the detection of the major bacterial stool pathogens in diagnostic laboratories.
Collapse
Affiliation(s)
| | - André Frontzek
- Roche Diagnostics (formerly, during study: Labor Stein, Mönchengladbach, Germany), Mannheim, Germany
| | | |
Collapse
|
8
|
Bose N, Moore SD. Variable Region Sequences Influence 16S rRNA Performance. Microbiol Spectr 2023; 11:e0125223. [PMID: 37212673 PMCID: PMC10269663 DOI: 10.1128/spectrum.01252-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/03/2023] [Indexed: 05/23/2023] Open
Abstract
16S rRNA gene sequences are commonly analyzed for taxonomic and phylogenetic studies because they contain variable regions that can help distinguish different genera. However, intra-genus distinction using variable region homology is often impossible due to the high overall sequence identities among closely related species, even though some residues may be conserved within respective species. Using a computational method that included the allelic diversity within individual genomes, we discovered that certain Escherichia and Shigella species can be distinguished by a multi-allelic 16S rRNA variable region single nucleotide polymorphism (SNP). To evaluate the performance of 16S rRNAs with altered variable regions, we developed an in vivo system that measures the acceptance and distribution of variant 16S rRNAs into a large pool of natural versions supporting normal translation and growth. We found that 16S rRNAs containing evolutionarily disparate variable regions were underpopulated both in ribosomes and in active translation pools, even for an SNP. Overall, this study revealed that variable region sequences can substantially influence the performance of 16S rRNAs and that this biological constraint can be leveraged to justify refining taxonomic assignments of variable region sequence data. IMPORTANCE This study reevaluates the notion that 16S rRNA gene variable region sequences are uninformative for intra-genus classification and that single nucleotide variations within them have no consequence to strains that bear them. We demonstrated that the performance of 16S rRNAs in Escherichia coli can be negatively impacted by sequence changes in variable regions, even for single nucleotide changes that are native to closely related Escherichia and Shigella species; thus, biological performance is likely constraining the evolution of variable regions in bacteria. Further, the native nucleotide variations we tested occur in all strains of their respective species and across their multiple 16S rRNA gene copies, suggesting that these species evolved beyond what would be discerned from a consensus sequence comparison. Therefore, this work also reveals that the multiple 16S rRNA gene alleles found in most bacteria can provide more informative phylogenetic and taxonomic detail than a single reference allele.
Collapse
Affiliation(s)
- Nikhil Bose
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Sean D. Moore
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| |
Collapse
|
9
|
The changing epidemiology of shigellosis in Australia, 2001-2019. PLoS Negl Trop Dis 2023; 17:e0010450. [PMID: 36857390 PMCID: PMC10010521 DOI: 10.1371/journal.pntd.0010450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/13/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
Shigellosis is an increasing cause of gastroenteritis in Australia, with prolonged outbreaks reported in remote Aboriginal and Torres Strait Islander (hereafter "First Nations") communities and among men who have sex with men (MSM) in major cities. To determine associations between Shigella species and demographic and geographic factors, we used multivariate negative binomial regression to analyse national case notifications of shigellosis from 2001 to 2019. Between 2001 and 2019, Australian states and territories reported 18,363 shigellosis cases to the National Notifiable Diseases Surveillance System (NNDSS), of which age, sex and organism information were available for >99% (18,327/18,363) of cases. Of the cases included in our analysis, 42% (7,649/18,327) were S. sonnei, 29% (5,267/18,327) were S. flexneri, 1% (214/18,327) were S. boydii, less than 1% (87/18,327) were S. dysenteriae, and species information was unknown for 28% (5,110/18,327) of cases. Males accounted for 54% (9,843/18,327) of cases, and the highest proportion of cases were in children aged 0-4 years (19%; 3,562/18,327). Crude annual notification rates ranged from 2.2 cases per 100,000 in 2003 and 2011 to 12.4 cases per 100,000 in 2019. Nationally, notification rates increased from 2001 to 2019 with yearly notification rate ratios of 1.04 (95% CI 1.02-1.07) for S. boydii and 1.05 (95% CI 1.04-1.06) for S. sonnei. Children aged 0-4 years had the highest burden of infection for S. flexneri, S. sonnei and S. boydii; and males had a higher notification rate for S. sonnei (notification rate ratio 1.24, 95% CI 1.15-1.33). First Nations Australians were disproportionately affected by shigellosis, with the notification rate in this population peaking in 2018 at 92.1 cases per 100,000 population. Over the study period, we also observed a shift in the testing method used to diagnose shigellosis, with culture independent diagnostic testing (CIDT) increasing from 2014; this also coincided with an increase in notifications of untyped Shigella. This change in testing methodology may have contributed to the observed increase in shigellosis notifications since 2014, with CIDT being more sensitive than culture dependent testing methods. The findings of this study provide important insights into the epidemiological characteristics of shigellosis in Australia, including identification of high-risk groups. This can be used to inform public health prevention and control strategies, such as targeted communication programs in First Nations communities and places with high levels of interaction between young children, such as childcare centres. Our study findings also highlight the implications of culture independent testing on shigellosis surveillance, particularly a reduction in the availability of species level information. This emphasises the continued importance of culture dependant testing for national surveillance of shigellosis.
Collapse
|
10
|
Huq AFMA, Biswas SK, Sheam MM, Syed SB, Elahi MT, Tang SS, Rahman MM, Roy AK, Paul DK. Identification and antibiotic pattern analysis of bacillary dysentery causing bacteria isolated from stool samples of infected patients. Biologia (Bratisl) 2023; 78:873-885. [PMID: 36573069 PMCID: PMC9769483 DOI: 10.1007/s11756-022-01299-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Bacillary dysentery is a type of dysentery and a severe form of shigellosis. This dysentery is usually restricted to Shigella infection, but Salmonella enterica and enteroinvasive Escherichia coli strains are also known as this infection's causative agents. The emergence of drug-resistant, bacillary dysentery-causing pathogens is a global burden, especially for developing countries with poor hygienic environments. This study aimed to isolate, identify, and determine the drug-resistant pattern of bacillary dysentery-causing pathogens from the stool samples of the Kushtia region in Bangladesh. Hence, biochemical tests, serotyping, molecular identification, and antibiotic profiling were performed to characterize the pathogens. Among one hundred fifty (150) stool samples, 18 enteric bacterial pathogens were isolated and identified, where 12 were Shigella strains, 5 were S. enterica sub spp. enterica strains and one was the E.coli strain. Among 12 Shigella isolates, 8 were Shigella flexneri 2a serotypes, and 4 were Shigella sonnei Phage-II serotypes. Except for three Salmonella strains, all isolated strains were drug-resistant (83%), whereas 50% were multidrug-resistant (MDR), an alarming issue for public health. In antibiotic-wise analysis, the isolated pathogens showed the highest resistance against nalidixic acid (77.78%), followed by tetracycline (38.89%), kanamycin (38.89%), amoxicillin (27.78%), streptomycin (27.78%), cefepime (22.22%), ceftriaxone (22.22%), ampicillin (16.67%), ciprofloxacin (16.67%), and chloramphenicol (16.67%). The existence of MDR organisms that cause bacillary dysentery in the Kushtia area would warn the public to be more health conscious, and physicians would administer medications cautiously. The gradual growth of MDR pathogenic microorganisms needs immediate attention, and the discovery of effective medications must take precedence. Supplementary information The online version contains supplementary material available at 10.1007/s11756-022-01299-x.
Collapse
Affiliation(s)
- Abul Fazel Mohammad Aminul Huq
- Department of Applied Nutrition and Food Technology, Faculty of Biological Sciences, Islamic University, 7003 Kushtia, Bangladesh
| | - Sudhangshu Kumar Biswas
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, 7003 Kushtia, Bangladesh
| | - Mohammad Moinuddin Sheam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, 7003 Kushtia, Bangladesh
| | - Shifath Bin Syed
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, 7003 Kushtia, Bangladesh
- Department of Animal Sciences, College of Agricultural, Human and Natural Resource Sciences, Washington State University, Pullman, WA USA
| | - Mohammad Toufiq Elahi
- Department of Applied Nutrition and Food Technology, Faculty of Biological Sciences, Islamic University, 7003 Kushtia, Bangladesh
| | - Swee-Seong Tang
- Division of Microbiology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Mohammad Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, 7003 Kushtia, Bangladesh
| | - Apurba Kumar Roy
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, 6205 Rajshahi, Bangladesh
| | - Dipak Kumar Paul
- Department of Applied Nutrition and Food Technology, Faculty of Biological Sciences, Islamic University, 7003 Kushtia, Bangladesh
| |
Collapse
|
11
|
Jose S, Devi SS, P S, Al-Khafaji K. Phytochemical constituents of Inula britannica as potential inhibitors of dihydrofolate reductase: A strategic approach against shigellosis. J Biomol Struct Dyn 2022; 40:11932-11947. [PMID: 34424817 DOI: 10.1080/07391102.2021.1966508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Shigella dysenteriae type 1 is considered as an epidemic in different developing countries, which is responsible for the most severe form of bacterial dysentery. It habitually can develop to the most severe form of dysentery with deadly complications. Development of drugs against this disease is still ongoing. Therefore, we used in silico studies to screen the Inula britannica phytocompounds that are used in traditional Chinese and Kampo Medicines and have activities against different diseases. Spinacetin, eupatin, chrysoeriol and diosmetin were successfully passed through the docking-based screening and absorption, distribution, metabolism, excretion and toxicity (ADMET) filtration. The estimated docking affinities of eupatin, diosmetin, chrysoeriol and spinacetin with Dihydrofolate reductase type 1 (DHFR-1), were -6.5, -6.5, -6.3 and -6.1 kcal/mol, respectively. Which were selected for further investigations based on their favorable ADME/Tox characteristics. Then, the 100 ns molecular dynamics (MD) simulations of apo DHFR, spinacetin-DHFR, eupatin-DHFR, chrysoeriol-DHFR and diosmetin-DHFR complexes were carried out. The RMSD fluctuations of the spinacetin, eupatin, chrysoeriol and diosmetin inside the binding site were explored. Subsequently, the effect of binding Spinacetin, eupatin, chrysoeriol and diosmetin upon the dynamic stability of protein was assessed. Additionally, Principal Component Analysis (PCA) and Hydrogen bond analysis was performed for the apo protein and the protein ligand complexes. The results revealed that chrysoeriol and eupatin has good inhibitory effects against DHFR-1 as treatment for Shigella dysenteriae type when compared to other compounds under study. Hence this study implies that eupatin and chrysoeriol are a significantly potential drug like molecule for the treatment of Shigellosis and must undergo validation through in vivo and in vitro experiments.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sandra Jose
- Department of Biotechnology, Vels Institute of Science, Technology and Advanced Studies, Chennai, Tamil Nadu, India
| | - Sreevidya S Devi
- School of Biosciences, Mar Athanasios College for Advanced Studies, Thiruvalla, Kerala, India
| | - Shakthi P
- Department of Biotechnology, Sri Krishna Arts and Science College, Coimbatore, Tamil Nadu, India
| | - Khattab Al-Khafaji
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey
| |
Collapse
|
12
|
Liu Y, Thaker H, Wang C, Xu Z, Dong M. Diagnosis and Treatment for Shiga Toxin-Producing Escherichia coli Associated Hemolytic Uremic Syndrome. Toxins (Basel) 2022; 15:10. [PMID: 36668830 PMCID: PMC9862836 DOI: 10.3390/toxins15010010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC)-associated hemolytic uremic syndrome (STEC-HUS) is a clinical syndrome involving hemolytic anemia (with fragmented red blood cells), low levels of platelets in the blood (thrombocytopenia), and acute kidney injury (AKI). It is the major infectious cause of AKI in children. In severe cases, neurological complications and even death may occur. Treating STEC-HUS is challenging, as patients often already have organ injuries when they seek medical treatment. Early diagnosis is of great significance for improving prognosis and reducing mortality and sequelae. In this review, we first briefly summarize the diagnostics for STEC-HUS, including history taking, clinical manifestations, fecal and serological detection methods for STEC, and complement activation monitoring. We also summarize preventive and therapeutic strategies for STEC-HUS, such as vaccines, volume expansion, renal replacement therapy (RRT), antibiotics, plasma exchange, antibodies and inhibitors that interfere with receptor binding, and the intracellular trafficking of the Shiga toxin.
Collapse
Affiliation(s)
- Yang Liu
- Department of Nephrology, The First Hospital of Jilin University, Changchun 130021, China
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Hatim Thaker
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Chunyan Wang
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Zhonggao Xu
- Department of Nephrology, The First Hospital of Jilin University, Changchun 130021, China
| | - Min Dong
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
13
|
Giannotti D, Boscaro V, Husnik F, Vannini C, Keeling PJ. At the threshold of symbiosis: the genome of obligately endosymbiotic ' Candidatus Nebulobacter yamunensis' is almost indistinguishable from that of a cultivable strain. Microb Genom 2022; 8:mgen000909. [PMID: 36748607 PMCID: PMC9837558 DOI: 10.1099/mgen.0.000909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Comparing obligate endosymbionts with their free-living relatives is a powerful approach to investigate the evolution of symbioses, and it has led to the identification of several genomic traits consistently associated with the establishment of symbiosis. 'Candidatus Nebulobacter yamunensis' is an obligate bacterial endosymbiont of the ciliate Euplotes that seemingly depends on its host for survival. A subsequently characterized bacterial strain with an identical 16S rRNA gene sequence, named Fastidiosibacter lacustris, can instead be maintained in pure culture. We analysed the genomes of 'Candidatus Nebulobacter' and Fastidiosibacter seeking to identify key differences between their functional traits and genomic structure that might shed light on a recent transition to obligate endosymbiosis. Surprisingly, we found almost no such differences: the two genomes share a high level of sequence identity, the same overall structure, and largely overlapping sets of genes. The similarities between the genomes of the two strains are at odds with their different ecological niches, confirmed here with a parallel growth experiment. Although other pairs of closely related symbiotic/free-living bacteria have been compared in the past, 'Candidatus Nebulobacter' and Fastidiosibacter represent an extreme example proving that a small number of (unknown) factors might play a pivotal role in the earliest stages of obligate endosymbiosis establishment.
Collapse
Affiliation(s)
- Daniele Giannotti
- Department of Biology, University of Pisa, Pisa, Italy,Department of Botany, University of British Columbia, Vancouver, Canada
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada,*Correspondence: Vittorio Boscaro,
| | - Filip Husnik
- Department of Botany, University of British Columbia, Vancouver, Canada,Okinawa Institute of Science and Technology, Okinawa, Japan
| | | | | |
Collapse
|
14
|
Adsit FG, Randall TA, Locklear J, Kurtz DM. The emergence of the tetrathionate reductase operon in the Escherichia coli/Shigella pan-genome. Microbiologyopen 2022; 11:e1333. [PMID: 36479628 PMCID: PMC9638481 DOI: 10.1002/mbo3.1333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Escherichia coli pathogenic variants (pathovars) are generally characterized by defined virulence traits and are susceptible to the evolution of hybridized identities due to the considerable plasticity of the E. coli genome. We have isolated a strain from a purified diet intended for research animals that further demonstrates the ability of E. coli to acquire novel genetic elements leading potentially to emergent new pathovars. Utilizing next generation sequencing to obtain a whole genome profile, we report an atypical strain of E. coli, EcoFA807-17, possessing a tetrathionate reductase (ttr) operon, which enables the utilization of tetrathionate as an electron acceptor, thus facilitating respiration in anaerobic environments such as the mammalian gut. The ttr operon is a potent virulence factor for several enteric pathogens, most prominently Salmonella enterica. However, the presence of chromosomally integrated tetrathionate reductase genes does not appear to have been previously reported in wild-type E. coli or Shigella. Accordingly, it is possible that the appearance of this virulence factor may signal the evolution of new mechanisms of pathogenicity in E. coli and Shigella and may potentially alter the effectiveness of existing assays using tetrathionate reductase as a unique marker for the detection of Salmonella enterica.
Collapse
Affiliation(s)
- Floyd G. Adsit
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - Thomas A. Randall
- Integrative BioinformaticsNational Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - Jacqueline Locklear
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - David M. Kurtz
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| |
Collapse
|
15
|
An allergist's approach to food poisoning. Ann Allergy Asthma Immunol 2022; 130:444-451. [PMID: 36334721 DOI: 10.1016/j.anai.2022.10.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Foodborne illnesses represent a significant global health concern. These preventable diseases lead to substantial mortality and morbidity worldwide. Substantial overlap with food allergy exists with similar clinical presentations and symptom onset. Knowledge of the typically implicated microorganisms and toxins can help properly identify these diseases. A thorough history is essential to differentiate between these 2 disorders. The types of food implicated may be similar including milk, egg, fish, and shellfish. The timing of symptom onset may overlap and lead to misdiagnosis of disorders such as food protein-induced enterocolitis syndrome. Classically, histamine-related food poisoning is also typically confused with true food allergy and may be seen as related to fish and cheese. Knowledge of epidemiology, patterns, and etiology of allergic conditions and foodborne illness may help the allergist differentiate among these common diseases.
Collapse
|
16
|
Multiple Mechanisms Confer Resistance to Azithromycin in Shigella in Bangladesh: a Comprehensive Whole Genome-Based Approach. Microbiol Spectr 2022; 10:e0074122. [PMID: 35876510 PMCID: PMC9430107 DOI: 10.1128/spectrum.00741-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shigella is the second leading cause of diarrheal deaths worldwide. Azithromycin (AZM) is a potential treatment option for Shigella infection; however, the recent emergence of AZM resistance in Shigella threatens the current treatment strategy. Therefore, we conducted a comprehensive whole genome-based approach to identify the mechanism(s) of AZM resistance in Shigella. We performed antimicrobial susceptibility tests, polymerase chain reaction (PCR), Sanger (amplicon) sequencing, and whole genome-based bioinformatics approaches to conduct the study. Fifty-seven (38%) of the Shigella isolates examined were AZM resistant; Shigella sonnei exhibited the highest rate of resistance against AZM (80%). PCR amplification for 15 macrolide resistance genes (MRGs) followed by whole-genome analysis of 13 representative Shigella isolates identified two AZM-modifying genes, mph(A) (in all Shigella isolates resistant to AZM) and mph(E) (in 2 AZM-resistant Shigella isolates), as well as one 23S rRNA-methylating gene, erm(B) (41% of AZM-resistant Shigella isolates) and one efflux pump mediator gene, msr(E) [in the same two Shigella isolates that harbored the mph(E) gene]. This is the first report of msr(E) and mph(E) genes in Shigella. Moreover, we found that an IncFII-type plasmid predominates and can possess all four MRGs. We also detected two plasmid-borne resistance gene clusters: IS26-mph(A)-mrx(A)-mph(R)(A)-IS6100, which is linked to global dissemination of MRGs, and mph(E)-msr(E)-IS482-IS6, which is reported for the first time in Shigella. In conclusion, this study demonstrates that MRGs in association with pathogenic IS6 family insertion sequences generate resistance gene clusters that propagate through horizontal gene transfer (HGT) in Shigella. IMPORTANCEShigella can frequently transform into a superbug due to uncontrolled and rogue administration of antibiotics and the emergence of HGT of antimicrobial resistance factors. The advent of AZM resistance in Shigella has become a serious concern in the treatment of shigellosis. However, there is an obvious scarcity of clinical data and research on genetic mechanisms that induce AZM resistance in Shigella, particularly in low- and middle-income countries. Therefore, this study is an approach to raise the alarm for the next lifeline. We show that two key MRGs [mph(A) and erm(B)] and the newly identified MRGs [mph(E) and msr(E)], with their origination in plasmid-borne pathogenic islands, are fundamental mechanisms of AZM resistance in Shigella in Bangladesh. Overall, this study predicts an abrupt decrease in the effectiveness of AZM against Shigella in the very near future and suggests prompt focus on seeking a more effective treatment alternative to AZM for shigellosis.
Collapse
|
17
|
Truong J, Cointe A, Le Roux E, Bidet P, Michel M, Boize J, Mariani-Kurkdjian P, Caseris M, Hobson CA, Desmarest M, Titomanlio L, Faye A, Bonacorsi S. Clinical impact of a gastrointestinal PCR panel in children with infectious diarrhoea. Arch Dis Child 2022; 107:601-605. [PMID: 34921002 DOI: 10.1136/archdischild-2021-322465] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 11/28/2021] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Multiplex gastrointestinal PCR (GI-PCR) allows fast and simultaneous detection of 22 enteric pathogens (including Campylobacter, Salmonella, Shigella/enteroinvasive Escherichia coli (EIEC), among other bacteria, parasites and viruses). However, its impact on the management of children with infectious diarrhoea remains unknown. PATIENTS/DESIGN All children eligible for stool culture from May to October 2018 were prospectively included in a monocentric study at Robert-Debré University-Hospital. INTERVENTION A GI-PCR (BioFire FilmArray) was performed on each stool sample. MAIN MEASURES Data on the children's healthcare management before and after GI-PCR results were collected. Stool culture results were also reported. RESULTS 172 children were included. The main criteria for performing stool analysis were mucous/bloody diarrhoea and/or traveller's diarrhoea (n=130). GI-PCR's were positive for 120 patients (70%). The main pathogens were enteroaggregative E. coli (n=39; 23%), enteropathogenic E. coli (n=34; 20%), Shigella/EIEC (n=27; 16%) and Campylobacter (n=21; 12%). Compared with stool cultures, GI-PCR enabled the detection of 21 vs 19 Campylobacter, 12 vs 10 Salmonella, 27 Shigella/EIEC vs 13 Shigella, 2 vs 2 Yersinia enterocolitica, 1 vs 1 Plesiomonas shigelloides, respectively. Considering the GI-PCR results and before stool culture results, the medical management was revised for 40 patients (23%): 28 initiations, 2 changes and 1 discontinuation of antibiotics, 1 hospitalisation, 2 specific room isolations related to Clostridioides difficile infections, 4 additional test prescriptions and 2 test cancellations. CONCLUSION The GI-PCR's results impacted the medical management of gastroenteritis for almostone-fourth of the children, and especially the prescription of appropriate antibiotic treatment before stool culture results.
Collapse
Affiliation(s)
- Jeanne Truong
- General Paediatrics, Robert Debré University Hospital, AP-HP, Paris, France .,Université de Paris, UFR de médecine Paris-Nord, Paris, Île-de-France, France
| | - Aurélie Cointe
- Microbiology Laboratory, Robert-Debré University Hospital, AP-HP, Paris, Île-de-France, France.,IAME UMR 1137, INSERM, Paris, Île-de-France, France
| | - Enora Le Roux
- Unité d'Epidémiologie Clinique, Robert Debré University Hospital, AP-HP, Paris, France.,ECEVE UMR-1123, INSERM, Paris, Île-de-France, France
| | - Philippe Bidet
- Microbiology Laboratory, Robert-Debré University Hospital, AP-HP, Paris, Île-de-France, France.,IAME UMR 1137, INSERM, Paris, Île-de-France, France
| | - Morgane Michel
- ECEVE UMR-1123, INSERM, Paris, Île-de-France, France.,URC Eco, Hôtel-Dieu, AP-HP, Paris, France
| | - Julien Boize
- Department of Paediatric Emergency Care, Robert Debré University Hospital, AP-HP, Paris, Île-de-France, France
| | | | - Marion Caseris
- General Paediatrics, Robert Debré University Hospital, AP-HP, Paris, France
| | - Claire Amaris Hobson
- Université de Paris, UFR de médecine Paris-Nord, Paris, Île-de-France, France.,IAME UMR 1137, INSERM, Paris, Île-de-France, France
| | - Marie Desmarest
- Department of Paediatric Emergency Care, Robert Debré University Hospital, AP-HP, Paris, Île-de-France, France
| | - Luigi Titomanlio
- Université de Paris, UFR de médecine Paris-Nord, Paris, Île-de-France, France.,Department of Paediatric Emergency Care, Robert Debré University Hospital, AP-HP, Paris, Île-de-France, France.,U1141, INSERM, Paris, France
| | - Albert Faye
- General Paediatrics, Robert Debré University Hospital, AP-HP, Paris, France.,Université de Paris, UFR de médecine Paris-Nord, Paris, Île-de-France, France.,ECEVE UMR-1123, INSERM, Paris, Île-de-France, France
| | - Stéphane Bonacorsi
- Microbiology Laboratory, Robert-Debré University Hospital, AP-HP, Paris, Île-de-France, France.,IAME UMR 1137, INSERM, Paris, Île-de-France, France
| |
Collapse
|
18
|
Monecke S, Schaumburg F, Shittu AO, Schwarz S, Mühldorfer K, Brandt C, Braun SD, Collatz M, Diezel C, Gawlik D, Hanke D, Hotzel H, Müller E, Reinicke M, Feßler AT, Ehricht R. Description of Staphylococcal Strains from Straw-Coloured Fruit Bat (Eidolon helvum) and Diamond Firetail (Stagonopleura guttata) and a Review of their Phylogenetic Relationships to Other Staphylococci. Front Cell Infect Microbiol 2022; 12:878137. [PMID: 35646742 PMCID: PMC9132046 DOI: 10.3389/fcimb.2022.878137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/16/2022] [Indexed: 12/30/2022] Open
Abstract
The phylogenetic tree of the Staphylococcus aureus complex consists of several distinct clades and the majority of human and veterinary S. aureus isolates form one large clade. In addition, two divergent clades have recently been described as separate species. One was named Staphylococcus argenteus, due to the lack of the “golden” pigment staphyloxanthin. The second one is S. schweitzeri, found in humans and animals from Central and West Africa. In late 2021, two additional species, S. roterodami and S. singaporensis, have been described from clinical samples from Southeast Asia. In the present study, isolates and their genome sequences from wild Straw-coloured fruit bats (Eidolon helvum) and a Diamond firetail (Stagonopleura guttata, an estrildid finch) kept in a German aviary are described. The isolates possessed staphyloxanthin genes and were closer related to S. argenteus and S. schweitzeri than to S. aureus. Phylogenetic analysis revealed that they were nearly identical to both, S. roterodami and S. singaporensis. We propose considering the study isolates, the recently described S. roterodami and S. singaporensis as well as some Chinese strains with MLST profiles stored in the PubMLST database as different clonal complexes within one new species. According to the principle of priority we propose it should be named S. roterodami. This species is more widespread than previously believed, being observed in West Africa, Southeast Asia and Southern China. It has a zoonotic connection to bats and has been shown to be capable of causing skin and soft tissue infections in humans. It is positive for staphyloxanthin, and it could be mis-identified as S. aureus (or S. argenteus) using routine procedures. However, it can be identified based on distinct MLST alleles, and “S. aureus” sequence types ST2470, ST3135, ST3952, ST3960, ST3961, ST3963, ST3965, ST3980, ST4014, ST4075, ST4076, ST4185, ST4326, ST4569, ST6105, ST6106, ST6107, ST6108, ST6109, ST6999 and ST7342 belong to this species.
Collapse
Affiliation(s)
- Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- *Correspondence: Stefan Monecke,
| | - Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Adebayo O. Shittu
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Christian Brandt
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Maximilian Collatz
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | | | - Dennis Hanke
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Martin Reinicke
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Andrea T. Feßler
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller-University, Jena, Germany
| |
Collapse
|
19
|
Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Sci Rep 2022; 12:6868. [PMID: 35477739 PMCID: PMC9046306 DOI: 10.1038/s41598-022-10827-3] [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: 01/14/2022] [Accepted: 03/31/2022] [Indexed: 11/08/2022] Open
Abstract
Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.
Collapse
|
20
|
van den Beld MJC, Rossen JWA, Evers N, Kooistra-Smid MAMD, Reubsaet FAG. MALDI-TOF MS Using a Custom-Made Database, Biomarker Assignment, or Mathematical Classifiers Does Not Differentiate Shigella spp. and Escherichia coli. Microorganisms 2022; 10:microorganisms10020435. [PMID: 35208889 PMCID: PMC8878589 DOI: 10.3390/microorganisms10020435] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 12/22/2022] Open
Abstract
Shigella spp. and E. coli are closely related and cannot be distinguished using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) with commercially available databases. Here, three alternative approaches using MALDI-TOF MS to identify and distinguish Shigella spp., E. coli, and its pathotype EIEC were explored and evaluated using spectra of 456 Shigella spp., 42 E. coli, and 61 EIEC isolates. Identification with a custom-made database resulted in >94% Shigella identified at the genus level and >91% S. sonnei and S. flexneri at the species level, but the distinction of S. dysenteriae, S. boydii, and E. coli was poor. With biomarker assignment, 98% S. sonnei isolates were correctly identified, although specificity was low. Discriminating markers for S. dysenteriae, S. boydii, and E. coli were not assigned at all. Classification models using machine learning correctly identified Shigella in 96% of isolates, but most E. coli isolates were also assigned to Shigella. None of the proposed alternative approaches were suitable for clinical diagnostics for identifying Shigella spp., E. coli, and EIEC, reflecting their relatedness and taxonomical classification. We suggest the use of MALDI-TOF MS for the identification of the Shigella spp./E. coli complex, but other tests should be used for distinction.
Collapse
Affiliation(s)
- Maaike J. C. van den Beld
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; (N.E.); (F.A.G.R.)
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (M.A.M.D.K.-S.)
- Correspondence: ; Tel.: +31-88-689-3454
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (M.A.M.D.K.-S.)
- Department of Pathology, University of Utah School of Medicine, 30 N 1900 E, Salt Lake City, UT 84132, USA
- Laboratory of Clinical Microbiology and Infectious Diseases, Isala Hospital, Dr. Van Heesweg 2, 8025 AB Zwolle, The Netherlands
| | - Noah Evers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; (N.E.); (F.A.G.R.)
| | - Mirjam A. M. D. Kooistra-Smid
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.W.A.R.); (M.A.M.D.K.-S.)
- Department of Medical Microbiology, Certe, Van Swietenlaan 2, 9728 NZ Groningen, The Netherlands
| | - Frans A. G. Reubsaet
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; (N.E.); (F.A.G.R.)
| |
Collapse
|
21
|
Abdalla SE, Abia ALK, Amoako DG, Perrett K, Bester LA, Essack SY. Food animals as reservoirs and potential sources of multidrug-resistant diarrheagenic E. coli pathotypes: Focus on intensive pig farming in South Africa. Onderstepoort J Vet Res 2022; 89:e1-e13. [PMID: 35144444 PMCID: PMC8832000 DOI: 10.4102/ojvr.v89i1.1963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/25/2021] [Accepted: 11/10/2021] [Indexed: 12/01/2022] Open
Abstract
Background Diarrheagenic E. coli (DEC) strains are a major cause of diarrheal diseases in both developed and developing countries. Healthy asymptomatic animals may be reservoirs of zoonotic DEC, which may enter the food chain via the weak points in hygiene practices. Aim We investigated the prevalence of DEC along the pig production continuum from farm-to-fork. Methods A total of 417 samples were collected from specific points along the pig production system, that is, farm, transport, abattoir and food. E. coli was isolated and enumerated using Colilert. Ten isolates from each Quanti-tray were selected randomly and phenotypically identified using eosin methylene blue agar selective media. Real-time polymerase chain reaction (PCR) was used to confirm the species and to classify them into the various diarrheagenic pathotypes. Antimicrobial susceptibility was determined against a panel of 20 antibiotics using the Kirby-Bauer disk diffusion method and EUCAST guideline. Results The final sample size consisted of 1044 isolates, of which 45.40% (474/1044) were DEC and 73% (762/1044) were multidrug-resistant. Enteroinvasive E. coli (EIEC) was the most predominant DEC at all the sampling sites. Conclusion The presence of DEC in food animal production environments and food of animal origin could serve as reservoirs for transmitting these bacteria to humans, especially in occupationally exposed workers and via food. Adherence to good hygienic practices along the pig production continuum is essential for mitigating the risk of transmission and infection, and ensuring food safety.
Collapse
Affiliation(s)
- Shima E Abdalla
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban.
| | | | | | | | | | | |
Collapse
|
22
|
He P, Wang H, Yan Y, Zhu G, Chen Z. Development and Application of a Multiplex Fluorescent PCR for Shigella Detection and Species Identification. J Fluoresc 2022; 32:707-713. [PMID: 35044573 DOI: 10.1007/s10895-021-02876-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 12/17/2021] [Indexed: 11/25/2022]
Abstract
This study was to develop a multiplex fluorescent PCR for Shigella detection and species identification. Five primer pairs for Shigella detection and species identification were designed by Primer Premier 5.0. The multiplex fluorescent PCR was optimized by varying single parameter while other parameters were maintained. The multiplex fluorescent PCR assay could correctly detect Shigella and identify four Shigella species with a detection limits of 10 pg genomic DNA per reaction. Testing different strains and clinical samples confirmed the sensitivity and specificity of the multiplex fluorescent PCR. The newly developed multiplex fluorescent PCR assay is simple, sensitive and specific for Shigella detection and species identification. It has a potential to be used in routine Shigella detection and species identification in clinical laboratories.
Collapse
Affiliation(s)
- Peiyan He
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Zhejiang, Jiaxing, 314050, China
| | - Henghui Wang
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Zhejiang, Jiaxing, 314050, China
| | - Yong Yan
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Zhejiang, Jiaxing, 314050, China
| | - Guoying Zhu
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Zhejiang, Jiaxing, 314050, China
| | - Zhongwen Chen
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Zhejiang, Jiaxing, 314050, China.
| |
Collapse
|
23
|
Zhang X, Payne M, Nguyen T, Kaur S, Lan R. Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping. Microb Genom 2021; 7:000704. [PMID: 34889728 PMCID: PMC8767346 DOI: 10.1099/mgen.0.000704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/05/2021] [Indexed: 11/23/2022] Open
Abstract
Shigella and enteroinvasive Escherichia coli (EIEC) cause human bacillary dysentery with similar invasion mechanisms and share similar physiological, biochemical and genetic characteristics. Differentiation of Shigella from EIEC is important for clinical diagnostic and epidemiological investigations. However, phylogenetically, Shigella and EIEC strains are composed of multiple clusters and are different forms of E. coli, making it difficult to find genetic markers to discriminate between Shigella and EIEC. In this study, we identified 10 Shigella clusters, seven EIEC clusters and 53 sporadic types of EIEC by examining over 17000 publicly available Shigella and EIEC genomes. We compared Shigella and EIEC accessory genomes to identify cluster-specific gene markers for the 17 clusters and 53 sporadic types. The cluster-specific gene markers showed 99.64% accuracy and more than 97.02% specificity. In addition, we developed a freely available in silico serotyping pipeline named Shigella EIEC Cluster Enhanced Serotype Finder (ShigEiFinder) by incorporating the cluster-specific gene markers and established Shigella and EIEC serotype-specific O antigen genes and modification genes into typing. ShigEiFinder can process either paired-end Illumina sequencing reads or assembled genomes and almost perfectly differentiated Shigella from EIEC with 99.70 and 99.74% cluster assignment accuracy for the assembled genomes and read mapping respectively. ShigEiFinder was able to serotype over 59 Shigella serotypes and 22 EIEC serotypes and provided a high specificity of 99.40% for assembled genomes and 99.38% for read mapping for serotyping. The cluster-specific gene markers and our new serotyping tool, ShigEiFinder (installable package: https://github.com/LanLab/ShigEiFinder, online tool: https://mgtdb.unsw.edu.au/ShigEiFinder/), will be useful for epidemiological and diagnostic investigations.
Collapse
Affiliation(s)
- Xiaomei Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Thanh Nguyen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|
24
|
MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes. N Biotechnol 2021; 65:42-52. [PMID: 34411700 DOI: 10.1016/j.nbt.2021.08.002] [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] [Received: 02/08/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/12/2022]
Abstract
The substantial reduction in experimental cost of next-generation sequencing techniques makes it feasible to assemble a bacterial genome of unknown species de novo and acquire substantial genetic information from environmental samples. Many bioinformatics tools and algorithms have also been developed for prokaryotes, but complex parameter settings and command line-based user interfaces cause a significant entry barrier for novices. Efficient construction of pipelines that integrate all the available genomic data poses a major challenge to the understanding of unknown pathogens. MiDSystem is a comprehensive online system for analyzing genomic data from microbiomes. With a user-friendly interface, MiDSystem supports both de novo assembly and metagenomic analysis pipelines. It is designed to automatically analyze whole genome shotgun sequencing data of bacteria submitted by users. Multiple analytical steps can be performed directly on the system, and the results generated from the embedded tools are visualized in an online summary report to make it more interpretable. Constructing a genome de novo has gradually become the foundation of bacterial studies. Taking both single species and metagenomic samples into consideration, MiDSystem can greatly reduce the time and effort for analysis of bacterial genomic data. Use of MiDSystem will enable more focus to be placed on understanding the etiology of bacterial infections and microorganism ecologies.
Collapse
|
25
|
Mollasalehi H, Vahedipour N, Taghvamanesh A, Minai-Tehrani D. Development of one-pot single specific primer-LAMP (SSP-LAMP) for identification of Shigella genus using 16S rDNA. Anal Biochem 2021; 636:114452. [PMID: 34762873 DOI: 10.1016/j.ab.2021.114452] [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: 08/10/2021] [Revised: 11/03/2021] [Accepted: 11/07/2021] [Indexed: 11/16/2022]
Abstract
Ribosomal RNA gene as a high-copy number nucleo-biomarker is extremely conserved among bacteria which limits its application to the discriminative detection approaches. We have developed a colorimetric isothermal amplification method called "single specific primer-LAMP (SSP-LAMP)" requiring only one specific primer for the amplification of the target and applied to the identification of the 16S rRNA gene in the Shigella genus. A region with high sequence homology in the genus and low homology with other bacteria was considered as the most appropriate. In that regard, a 23 bp sequence in the 16S rRNA gene of the genus was targeted based on the alignment of the gene with fifty-three closely related bacterial species, and a single specific primer along with five degenerate primers were designed. Using hydroxy-naphthol blue (HNB) as an indicator and gel electrophoresis, the proposed approach of SSP-LAMP was able to detect S. boydii, S. sonnei, S. flexneri and S. dysenteriae specifically while other species remained unidentified. The SSP-LAMP method could provide a rapid one-pot point-of-care method for molecular diagnostics of pathogens in many circumstances mainly samples with high genetic homogeneity.
Collapse
Affiliation(s)
- Hamidreza Mollasalehi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran.
| | - Narges Vahedipour
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran
| | - Ahang Taghvamanesh
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran
| | - Dariush Minai-Tehrani
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran
| |
Collapse
|
26
|
Halimeh FB, Rafei R, Osman M, Kassem II, Diene SM, Dabboussi F, Rolain JM, Hamze M. Historical, current, and emerging tools for identification and serotyping of Shigella. Braz J Microbiol 2021; 52:2043-2055. [PMID: 34524650 PMCID: PMC8441030 DOI: 10.1007/s42770-021-00573-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
The Shigella genus includes serious foodborne disease etiologic agents, with 4 species and 54 serotypes. Identification at species and serotype levels is a crucial task in microbiological laboratories. Nevertheless, the genetic similarity between Shigella spp. and Escherichia coli challenges the correct identification and serotyping of Shigella spp., with subsequent negative repercussions on surveillance, epidemiological investigations, and selection of appropriate treatments. For this purpose, multiple techniques have been developed historically ranging from phenotype-based methods and single or multilocus molecular techniques to whole-genome sequencing (WGS). To facilitate the selection of the most relevant method, we herein provide a global overview of historical and emerging identification and serotyping techniques with a particular focus on the WGS-based approaches. This review highlights the excellent discriminatory power of WGS to more accurately elucidate the epidemiology of Shigella spp., disclose novel promising genomic targets for surveillance methods, and validate previous well-established methods.
Collapse
Affiliation(s)
- Fatima Bachir Halimeh
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14850, USA
| | - Issmat I Kassem
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, 1109 Experiment Street, Griffin, GA, 30223-1797, USA
| | - Seydina M Diene
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Jean-Marc Rolain
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
| |
Collapse
|
27
|
Pakbin B, Brück WM, Rossen JWA. Virulence Factors of Enteric Pathogenic Escherichia coli: A Review. Int J Mol Sci 2021; 22:9922. [PMID: 34576083 PMCID: PMC8468683 DOI: 10.3390/ijms22189922] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 12/18/2022] Open
Abstract
Escherichia coli are remarkably versatile microorganisms and important members of the normal intestinal microbiota of humans and animals. This harmless commensal organism can acquire a mixture of comprehensive mobile genetic elements that contain genes encoding virulence factors, becoming an emerging human pathogen capable of causing a broad spectrum of intestinal and extraintestinal diseases. Nine definite enteric E. coli pathotypes have been well characterized, causing diseases ranging from various gastrointestinal disorders to urinary tract infections. These pathotypes employ many virulence factors and effectors subverting the functions of host cells to mediate their virulence and pathogenesis. This review summarizes new developments in our understanding of diverse virulence factors associated with encoding genes used by different pathotypes of enteric pathogenic E. coli to cause intestinal and extraintestinal diseases in humans.
Collapse
Affiliation(s)
- Babak Pakbin
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Switzerland;
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin 15315-3419, Iran
| | - Wolfram M. Brück
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Switzerland;
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| |
Collapse
|
28
|
Abstract
PURPOSE OF REVIEW Several types of Escherichia coli cause acute diarrhea in humans and are responsible for a large burden of disease globally. The purpose of this review is to summarize diarrheagenic Escherichia coli (DEC) pathotype definitions and discuss existing and emerging molecular, genomic, and gut microbiome methods to detect, define, and study DEC pathotypes. RECENT FINDINGS DEC pathotypes are currently diagnosed by molecular detection of unique virulence genes. However, some pathotypes have defied coherent molecular definitions because of imperfect gene targets, and pathotype categories are complicated by hybrid strains and isolation of pathotypes from asymptomatic individuals. Recent progress toward more efficient, sensitive, and multiplex DEC pathotype detection has been made using emerging PCR-based technologies. Genomics and gut microbiome detection methods continue to advance rapidly and are contributing to a better understanding of DEC pathotype diversity and functional potential. SUMMARY DEC pathotype categorizations and detection methods are useful but imperfect. The implementation of molecular and sequence-based methods and well designed epidemiological studies will continue to advance understanding of DEC pathotypes. Additional emphasis is needed on sequencing DEC genomes from regions of the world where they cause the most disease and from the pathotypes that cause the greatest burden of disease globally.
Collapse
|
29
|
Australia's notifiable disease status, 2016: Annual report of the National Notifiable Diseases Surveillance System. ACTA ACUST UNITED AC 2021; 45. [PMID: 34074234 DOI: 10.33321/cdi.2021.45.28] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Abstract In 2016, a total of 67 diseases and conditions were nationally notifiable in Australia. The states and territories reported 330,387 notifications of communicable diseases to the National Notifiable Diseases Surveillance System. Notifications have remained stable between 2015 and 2016. In 2016, the most frequently notified diseases were vaccine preventable diseases (139,687 notifications, 42% of total notifications); sexually transmissible infections (112,714 notifications, 34% of total notifications); and gastrointestinal diseases (49,885 notifications, 15% of total notifications). Additionally, there were 18,595 notifications of bloodborne diseases; 6,760 notifications of vectorborne diseases; 2,020 notifications of other bacterial infections; 725 notifications of zoonoses and one notification of a quarantinable disease.
Collapse
Affiliation(s)
-
- Australian Government Department of Health
| |
Collapse
|
30
|
Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev N, Gelfand MS, Bochkareva OO. High Rates of Genome Rearrangements and Pathogenicity of Shigella spp. Front Microbiol 2021; 12:628622. [PMID: 33912145 PMCID: PMC8072062 DOI: 10.3389/fmicb.2021.628622] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.
Collapse
Affiliation(s)
- Zaira Seferbekova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia
| | - Alexey Zabelkin
- Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia.,JetBrains Research, Saint Petersburg, Russia.,Bioinformatics Institute, Saint Petersburg, Russia
| | - Yulia Yakovleva
- Bioinformatics Institute, Saint Petersburg, Russia.,Department of Cytology and Histology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Robert Afasizhev
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia
| | - Natalia O Dranenko
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia
| | - Nikita Alexeev
- Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga O Bochkareva
- Institute for Information Transmission Problems (The Kharkevich Institute, RAS), Moscow, Russia.,Institute of Science and Technology (IST Austria), Klosterneuburg, Austria
| |
Collapse
|
31
|
Yu D, Banting G, Neumann NF. A review of the taxonomy, genetics, and biology of the genus Escherichia and the type species Escherichia coli. Can J Microbiol 2021; 67:553-571. [PMID: 33789061 DOI: 10.1139/cjm-2020-0508] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Historically, bacteriologists have relied heavily on biochemical and structural phenotypes for bacterial taxonomic classification. However, advances in comparative genomics have led to greater insights into the remarkable genetic diversity within the microbial world, and even within well-accepted species such as Escherichia coli. The extraordinary genetic diversity in E. coli recapitulates the evolutionary radiation of this species in exploiting a wide range of niches (i.e., ecotypes), including the gastrointestinal system of diverse vertebrate hosts as well as non-host natural environments (soil, natural waters, wastewater), which drives the adaptation, natural selection, and evolution of intragenotypic conspecific specialism as a strategy for survival. Over the last few years, there has been increasing evidence that many E. coli strains are very host (or niche)-specific. While biochemical and phylogenetic evidence support the classification of E. coli as a distinct species, the vast genomic (diverse pan-genome and intragenotypic variability), phenotypic (e.g., metabolic pathways), and ecotypic (host-/niche-specificity) diversity, comparable to the diversity observed in known species complexes, suggest that E. coli is better represented as a complex. Herein we review the taxonomic classification of the genus Escherichia and discuss how phenotype, genotype, and ecotype recapitulate our understanding of the biology of this remarkable bacterium.
Collapse
Affiliation(s)
- Daniel Yu
- School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada.,School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada
| | - Graham Banting
- School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada.,School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada
| | - Norman F Neumann
- School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada.,School of Public Health, University of Alberta, Edmonton, AB T6G IC9, Canada
| |
Collapse
|
32
|
Lagerqvist N, Löf E, Enkirch T, Nilsson P, Roth A, Jernberg C. Outbreak of gastroenteritis highlighting the diagnostic and epidemiological challenges of enteroinvasive Escherichia coli, County of Halland, Sweden, November 2017. ACTA ACUST UNITED AC 2020; 25. [PMID: 32156328 PMCID: PMC7068165 DOI: 10.2807/1560-7917.es.2020.25.9.1900466] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An outbreak of gastroenteritis with 83 cases occurred at a conference venue in November 2017 in Halland County, Sweden. Stool samples from two venue visitors and a symptomatic secondary case attributed to household transmission were PCR-positive for the ipaH gene, a target found in both Shigella spp. and enteroinvasive Escherichia coli (EIEC). EIEC was isolated from stool samples and whole genome sequencing analysis confirmed EIEC O96:H19 to be the aetiological agent. A cohort study was conducted among venue attendees and employees and the findings implicated contaminated leafy greens as the vehicle of infection, however, no microbiological evidence could support the study results. Here, we report the investigation into the first recorded EIEC outbreak in Sweden and illustrate the challenges associated with the differential laboratory diagnostics of Shigella/EIEC in an outbreak setting.
Collapse
Affiliation(s)
- Nina Lagerqvist
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Public Health Agency of Sweden, Solna, Sweden
| | - Emma Löf
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Public Health Agency of Sweden, Solna, Sweden
| | - Theresa Enkirch
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Public Health Agency of Sweden, Solna, Sweden
| | - Peter Nilsson
- Clinical Microbiology, County Hospital, Halmstad, Sweden
| | - Adam Roth
- Public Health Agency of Sweden, Solna, Sweden
| | | |
Collapse
|
33
|
van den Beld MJC, Reubsaet FAG, Pijnacker R, Harpal A, Kuiling S, Heerkens EM, Hoeve-Bakker BJA(D, Noomen RCEA, Hendriks ACA, Borst D, van der Heide H, Kooistra-Smid AMD(M, Rossen JWA. A Multifactorial Approach for Surveillance of Shigella spp. and Entero-Invasive Escherichia coli Is Important for Detecting (Inter)national Clusters. Front Microbiol 2020; 11:564103. [PMID: 33193150 PMCID: PMC7604320 DOI: 10.3389/fmicb.2020.564103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/22/2020] [Indexed: 01/08/2023] Open
Abstract
Shigella spp. and entero-invasive Escherichia coli (EIEC) can cause mild diarrhea to dysentery. In Netherlands, although shigellosis is a notifiable disease, there is no laboratory surveillance for Shigella spp. and EIEC in place. Consequently, the population structure for circulating Shigella spp. and EIEC isolates is not known. This study describes the phenotypic and serological characteristics, the phenotypic and genetic antimicrobial resistance (AMR) profiles, the virulence gene profiles, the classic multi-locus sequence types (MLST) and core genome (cg)MLST types, and the epidemiology of 414 Shigella spp. and EIEC isolates collected during a cross-sectional study in Netherlands in 2016 and 2017. S. sonnei (56%), S. flexneri (25%), and EIEC (15%) were detected predominantly in Netherlands, of which the EIEC isolates were most diverse according to their phenotypical profile, O-types, MLST types, and cgMLST clades. Virulence gene profiling showed that none of the isolates harbored Shiga toxin genes. Most S. flexneri and EIEC isolates possessed nearly all virulence genes examined, while these genes were only detected in approximately half of the S. sonnei isolates, probably due to loss of the large invasion plasmid upon subculturing. Phenotypical resistance correlated well with the resistant genotype, except for the genes involved in resistance to aminoglycosides. A substantial part of the characterized isolates was resistant to antimicrobials advised for treatment, i.e., 73% was phenotypically resistant to co-trimoxazole and 19% to ciprofloxacin. AMR was particularly observed in isolates from male patients who had sex with men (MSM) or from patients that had traveled to Asia. Furthermore, isolates related to international clusters were also circulating in Netherlands. Travel-related isolates formed clusters with isolates from patients without travel history, indicating their emergence into the Dutch population. In conclusion, laboratory surveillance using whole genome sequencing as high-resolution typing technique and for genetic characterization of isolates complements the current epidemiological surveillance, as the latter is not sufficient to detect all (inter)national clusters, emphasizing the importance of multifactorial public health approaches.
Collapse
Affiliation(s)
- Maaike J. C. van den Beld
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Frans A. G. Reubsaet
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Roan Pijnacker
- Infectious Diseases, Epidemiology and Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Airien Harpal
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Sjoerd Kuiling
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Evy M. Heerkens
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - B. J. A. (Dieneke) Hoeve-Bakker
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Ramón C. E. A. Noomen
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Amber C. A. Hendriks
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Dyogo Borst
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Han van der Heide
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - A. M. D. (Mirjam) Kooistra-Smid
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Medical Microbiology, Certe, Groningen, Netherlands
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| |
Collapse
|
34
|
Pathogen flows from on-site sanitation systems in low-income urban neighborhoods, Dhaka: A quantitative environmental assessment. Int J Hyg Environ Health 2020; 230:113619. [PMID: 32942223 DOI: 10.1016/j.ijheh.2020.113619] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 08/16/2020] [Accepted: 08/27/2020] [Indexed: 01/17/2023]
Abstract
BACKGROUND Despite wide usage of on-site sanitation, there is limited field-based evidence on the removal or release of pathogens from septic tanks and other primary treatment systems, such as anaerobic baffled reactors (ABR). In two low-income areas in Dhaka, we conducted a cross-sectional study to explore pathogen loads discharged from commonly used on-site sanitation-systems and their transport in nearby drains and waterways. METHODS We collected samples of drain water, drain sediment, canal water, and floodwater from April-October 2019. Sludge, supernatant, and effluent samples were also collected from septic tanks and ABRs. We investigated the presence and concentration of selected enteric pathogens (Shigella, Vibrio cholerae (V. cholerae), Salmonella Typhi (S. Typhi), Norovirus Genogroup-II (NoV-GII), and Giardia) and presence of Cryptosporidium in these samples using quantitative polymerase chain reaction (qPCR).The equivalent genome copies (EGC) of individual pathogens were estimated in each sample by interpolation of the mean Ct value to the corresponding standard curve and the dilution factor for each sample type. Absolute quantification was expressed as log10 EGC per 100 mL for the water samples and log10 EGC per gram for the sediment samples. RESULTS Among all samples tested (N = 151), 89% were contaminated with Shigella, 68% with V. cholerae and NoV-GII, 32% with Giardia, 17% with S. Typhi and 6% with Cryptosporidium. A wide range of concentration of pathogens [range: mean log10 concentration of Giardia = 0.74 EGC/100 mL in drain ultrafiltration samples to mean log10 concentration of NoV-GII and Giardia = 7.11 EGC/100 mL in ABR sludge] was found in all environmental samples. The highest pathogen concentrations were detected in open drains [range: mean log10 concentration = 2.50-4.94 EGC/100 mL], septic tank effluent [range: mean log10 concentration = 3.32-4.65 EGC/100 mL], and ABR effluent [range: mean log10 concentration = 2.72-5.13 EGC/100 mL]. CONCLUSIONS High concentrations of pathogens (particularly NoV-GII, V.cholerae and Shigella) were frequently detected in environmental samples from two low-income urban neighbourhoods of Dhaka city. The numerous environmental exposure pathways for children and adults make these findings of public health concern. These results should prompt rethinking of how to achieve safe sanitation solutions that protect public health in dense low-income areas. In particular, improved management and maintenance regimes, further treatment of liquid effluent from primary treatment processes, and appropriate application of onsite, decentralised and offsite sanitation systems given the local context.
Collapse
|
35
|
Tufon KA, Fokam DPY, Kouanou YS, Meriki HD. Case report on a swift shift in uropathogens from Shigella flexneri to Escherichia coli: a thin line between bacterial persistence and reinfection. Ann Clin Microbiol Antimicrob 2020; 19:31. [PMID: 32727466 PMCID: PMC7392695 DOI: 10.1186/s12941-020-00374-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022] Open
Abstract
Background Urinary tract infections (UTI) are mostly caused by bacteria. Urine cultures are usually a definitive measure to select the appropriate antibiotics for the elimination of a uropathogen and subsequent recovery from the infection. However, the preferred antibiotics as determined by urine culture and sensitivity may still not eliminate the infection and would require further examination to ascertain the cause of treatment failure which could be unresolved bacteriuria, bacterial persistence, immediate reinfection with a different uropathogen or misdiagnosis. Case presentation A 2-years 7 months-old female was admitted in the Regional hospital of Buea following persistent fever. An auto medication with amoxicillin was reported. Urinalysis was done on the first day and the sediment of the cloudy urine revealed many bacteria and few pus cells. Ceftriaxone was prescribed as empirical treatment and a request for urine and blood culture was made. Three days after admission, the temperature and CRP were 39.0 °C and 96 mg/l, respectively. The urine culture results (> 105 CFU/ml of Shigella flexneri sensitive to ofloxacin) were presented to the doctor on the 4th day of admission. Patient was put on ofloxacin. Three days after, the temperature (38.5 °C) and CRP (24 mg/l) were still elevated. The blood culture result came out negative. A second urine culture was requested which came back positive (> 105 CFU/ml of Escherichia coli resistant to ofloxacin and sensitive to meropenem and amikacin). Ofloxacin was discontinued and the patient put on meropenem and amikacin. The third urine culture recorded no significant growth after 48 h of incubation. The patient was discharged looking healthy once more with a normal body temperature. Conclusion Antibiotics tailored towards the elimination of a particular bacterial species may as well provide a favorable environment for other bacterial species that are resistant to it in the course of treating a UTI episode. This apparent treatment failure may first of all require a second urine culture for confirmation rather than considering the possibilities of a misdiagnosis.
Collapse
Affiliation(s)
- Kukwah Anthony Tufon
- Buea Regional Hospital, Southwest Region, Buea, Cameroon. .,Department of Allied Health, Faculty of Health Science, Biaka University, Buea, Cameroon. .,Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon.
| | - Djike Puepi Yolande Fokam
- Buea Regional Hospital, Southwest Region, Buea, Cameroon.,Department of Internal Medicine and Paediatrics, Faculty of Health Science, University of Buea, Buea, Cameroon
| | | | - Henry Dilonga Meriki
- Buea Regional Hospital, Southwest Region, Buea, Cameroon.,Department of Allied Health, Faculty of Health Science, Biaka University, Buea, Cameroon.,Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
| |
Collapse
|
36
|
Michelacci V, Tozzoli R, Arancia S, D'Angelo A, Boni A, Knijn A, Prosseda G, Greig DR, Jenkins C, Camou T, Sirok A, Navarro A, Schelotto F, Varela G, Morabito S. Tracing Back the Evolutionary Route of Enteroinvasive Escherichia coli (EIEC) and Shigella Through the Example of the Highly Pathogenic O96:H19 EIEC Clone. Front Cell Infect Microbiol 2020; 10:260. [PMID: 32582565 PMCID: PMC7283534 DOI: 10.3389/fcimb.2020.00260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/04/2020] [Indexed: 11/13/2022] Open
Abstract
Enteroinvasive Escherichia coli (EIEC) cause intestinal illness through the same pathogenic mechanism used by Shigella spp. The latter species can be typed through genomic and phenotypic methods used for E. coli and have been proposed for reclassification within E. coli species. Recently the first appearance of a highly pathogenic EIEC O96:H19 was described in Europe as the causative agent of two large outbreaks that occurred in Italy and in the United Kingdom. In contrast to Shigella spp and to the majority of EIEC strains, EIEC O96:H19 fermented lactose, lacked pathoadaptive mutations, and showed good fitness in extracellular environment, similarly to non-pathogenic E. coli, suggesting they have emerged following acquisition of the invasion plasmid by a non-pathogenic E. coli. Here we describe the whole genome comparison of two EIEC O96:H19 strains isolated from severe cases of diarrhea in Uruguay in 2014 with the sequences of EIEC O96:H19 available in the public domain. The phylogenetic comparison grouped all the O96:H19 strains in a single cluster, while reference EIEC strains branched into different clades with Shigella strains occupying apical positions. The comparison of the virulence plasmids showed the presence of a complete conjugation region in at least one O96:H19 EIEC. Reverse Transcriptase Real Time PCR experiments confirmed in this strain the expression of the pilin-encoding gene and conjugation experiments suggested its ability to mobilize an accessory plasmid in a recipient strain. Noteworthy, the tra region was comprised between two reversely oriented IS600 elements, which were also found as remnants in another EIEC O96:H19 plasmid lacking the tra locus. We hypothesize that an IS-mediated recombination mechanism may have caused the loss of the conjugation region commonly observed in EIEC and Shigella virulence plasmids. The results of this study support the hypothesis of EIEC originating from non-pathogenic E. coli through the acquisition of the virulence plasmid via conjugation. Remarkably, this study showed the ability of a circulating EIEC strain to mobilize plasmids through conjugation, suggesting a mechanism for the emergence of novel EIEC clones.
Collapse
Affiliation(s)
- Valeria Michelacci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Rosangela Tozzoli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Silvia Arancia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Alfio D'Angelo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Arianna Boni
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Gianni Prosseda
- Department of Biology and Biotechnology "Charles Darwin", Università Sapienza di Roma, Rome, Italy
| | - David R Greig
- Gastrointestinal Bacteria Reference Unit (GBRU), Public Health England, E. coli, Shigella, Yersinia and Vibrio Reference Service, National Infection Service, London, United Kingdom
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit (GBRU), Public Health England, E. coli, Shigella, Yersinia and Vibrio Reference Service, National Infection Service, London, United Kingdom
| | - Teresa Camou
- Departamento de Laboratorios, Ministerio de Salud Pública, Montevideo, Uruguay
| | - Alfredo Sirok
- Departamento de Laboratorios, Ministerio de Salud Pública, Montevideo, Uruguay
| | - Armando Navarro
- Public Health Department, Medicine Faculty, Universidad Nacional Autónoma de Mexico (UNAM), Mexico City, Mexico
| | - Felipe Schelotto
- Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
| | - Gustavo Varela
- Departamento de Bacteriología y Virología, Facultad de Medicina, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| |
Collapse
|
37
|
Halimeh FB, Rafei R, Diene S, Mikhael M, Mallat H, Achkar M, Dabboussi F, Hamze M, Rolain JM. Challenges in identification of enteroinvasive Escherichia coli and Shigella spp. in Lebanon. Acta Microbiol Immunol Hung 2020; 67:100-106. [PMID: 32223306 DOI: 10.1556/030.2020.01102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 12/23/2019] [Indexed: 02/01/2023]
Abstract
This study aimed to evaluate the routine identification tools available in Lebanon for differentiation of Escherichia coli and Shigella spp. The identification of 43 isolates defined as Shigella spp. by Api 20E was accessed using MALDI-TOF, serological testing, duplex PCR targeting ipaH (present in Shigella spp. and enteroinvasive E. coli "EIEC") and lacY (found in E. coli including EIEC but not Shigella spp.) as well as gyrB gene sequencing. Antibiotic susceptibility was investigated as well as Shiga-toxin production. All isolates were identified as E. coli by MALDI-TOF while the PCR showed a disparate group of 26 EIEC, 11 Shigella spp., 5 E. coli and 1 inactive E. coli. However, the sequencing of gyrB gene, which was recently described as a suitable marker for distinguishing E. coli and Shigella spp., identified all isolates as E. coli. Antibiotic resistance was noticeable against ß-lactams, rifampicin, trimethoprim-sulfamethoxazole, gentamicin, and ciprofloxacin. The most common variants of beta-lactamase genes were blaTEM-1, blaCTX-M-15, and blaCTX-M-3. A great discordance between the used methods in identification was revealed herein. An accurate identification technique able to distinguish E. coli from Shigella spp. in routine laboratories is a pressing need in order to select the appropriate treatment and assess the epidemiology of these bacteria.
Collapse
Affiliation(s)
- Fatima Bachir Halimeh
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
- 2Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Rayane Rafei
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Seydina Diene
- 2Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Mary Mikhael
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Hassan Mallat
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marcel Achkar
- 3Laboratory of Clinical Biology, NINI Hospital, Tripoli, Lebanon
| | - Fouad Dabboussi
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Jean-Marc Rolain
- 2Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| |
Collapse
|
38
|
Shen Y, Nie J, Kuang L, Zhang J, Li H. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 2020; 14:323-362. [PMID: 32207561 PMCID: PMC7936329 DOI: 10.1111/1751-7915.13560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.
Collapse
Affiliation(s)
- Youming Shen
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jiyun Nie
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China.,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixue Kuang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jianyi Zhang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Haifei Li
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| |
Collapse
|
39
|
Superstructure formation by RodZ hexamers of Shigella sonnei maintains the rod shape of bacilli. PLoS One 2020; 15:e0228052. [PMID: 32053625 PMCID: PMC7018016 DOI: 10.1371/journal.pone.0228052] [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: 08/22/2019] [Accepted: 01/06/2020] [Indexed: 11/19/2022] Open
Abstract
The rod shape of bacilli is maintained by bacterial cytoskeletal protein MreB, an actin homolog that acts in concert with the inner membrane protein RodZ. We previously reported RodZ binds RNA to control the posttranscriptional regulation of invE (virB), which controls the type III secretion system essential for the virulence of Shigella. Here, we show that purified RodZ forms "superstructures" of high molecular mass that dissociate into a midsized "basal complex" in the presence of nonionic detergent, or to a monomer in the presence of dithiothreitol. We used mass spectrometry to show that the basal complex was a hexamer. Electrophoresis mobility shift assays combined with gel filtration detected the RNA-binding activity in fractions containing molecules larger than the basal hexamer. The superstructure was consistently detected with MreB in crude cell lysates of S. sonnei that were fractionated using gel filtration. Immunofluorescence microscopy using two different super-resolution settings showed that wild-type RodZ was distributed in cells as separate dots. Consistent with the superstructure comprising homohexamers, majority of the dots distributed among areas of discrete values. In addition, simultaneous immunodetection of MreB provided the first evidence of colocalization with RodZ as larger patch like signals. These findings indicate that native RodZ forms clusters of various sizes, which may correspond to a superstructure comprising multiple hexamers required for the RNA-binding activity.
Collapse
|
40
|
Hendriks ACA, Reubsaet FAG, Kooistra-Smid AMDM, Rossen JWA, Dutilh BE, Zomer AL, van den Beld MJC. Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity. BMC Genomics 2020; 21:138. [PMID: 32041522 PMCID: PMC7011524 DOI: 10.1186/s12864-020-6555-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/04/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND We investigated the association of symptoms and disease severity of shigellosis patients with genetic determinants of infecting Shigella and entero-invasive Escherichia coli (EIEC), because determinants that predict disease outcome per individual patient could be used to prioritize control measures. For this purpose, genome wide association studies (GWAS) were performed using presence or absence of single genes, combinations of genes, and k-mers. All genetic variants were derived from draft genome sequences of isolates from a multicenter cross-sectional study conducted in the Netherlands during 2016 and 2017. Clinical data of patients consisting of binary/dichotomous representation of symptoms and their calculated severity scores were also available from this study. To verify the suitability of the methods used, the genetic differences between the genera Shigella and Escherichia were used as control. RESULTS The isolates obtained were representative of the population structure encountered in other Western European countries. No association was found between single genes or combinations of genes and separate symptoms or disease severity scores. Our benchmark characteristic, genus, resulted in eight associated genes and > 3,000,000 k-mers, indicating adequate performance of the algorithms used. CONCLUSIONS To conclude, using several microbial GWAS methods, genetic variants in Shigella spp. and EIEC that can predict specific symptoms or a more severe course of disease were not identified, suggesting that disease severity of shigellosis is dependent on other factors than the genetic variation of the infecting bacteria. Specific genes or gene fragments of isolates from patients are unsuitable to predict outcomes and cannot be used for development, prioritization and optimization of guidelines for control measures of shigellosis or infections with EIEC.
Collapse
Affiliation(s)
- Amber C A Hendriks
- Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Frans A G Reubsaet
- Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - A M D Mirjam Kooistra-Smid
- Department of Medical Microbiology, Certe, Groningen, the Netherlands
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Maaike J C van den Beld
- Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| |
Collapse
|
41
|
van den Beld MJC, Warmelink E, Friedrich AW, Reubsaet FAG, Schipper M, de Boer RF, Notermans DW, Petrignani MWF, van Zanten E, Rossen JWA, Friesema IHM, Kooistra-Smid AMDM. Incidence, clinical implications and impact on public health of infections with Shigella spp. and entero-invasive Escherichia coli (EIEC): results of a multicenter cross-sectional study in the Netherlands during 2016-2017. BMC Infect Dis 2019; 19:1037. [PMID: 31818261 PMCID: PMC6902317 DOI: 10.1186/s12879-019-4659-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/25/2019] [Indexed: 11/10/2022] Open
Abstract
Background Shigella spp. and entero-invasive E. coli (EIEC) use the same invasive mechanism to cause diarrheal diseases. Public health regulations apply only to Shigella spp. infections, but are hampered by the lack of simple methods to distinguish them from EIEC. In the last decades, molecular methods for detecting Shigella spp. and EIEC were implemented in medical microbiological laboratories (MMLs). However, shigellosis cases identified with molecular techniques alone are not notifiable in most countries. Our study investigates the impact of EIEC versus Shigella spp. infections and molecular diagnosed shigellosis versus culture confirmed shigellosis for re-examination of the rationale for the current public health regulations. Methods In this multicenter cross-sectional study, fecal samples of patients suspected for gastro-enteritis, referred to 15 MMLs in the Netherlands, were screened by PCR for Shigella spp. or EIEC. Samples were cultured to discriminate between the two pathogens. We compared risk factors, symptoms, severity of disease, secondary infections and socio-economic consequences for (i) culture-confirmed Shigella spp. versus culture-confirmed EIEC cases (ii) culture positive versus PCR positive only shigellosis cases. Results In 2016–2017, 777 PCR positive fecal samples with patient data were included, 254 of these were culture-confirmed shigellosis cases and 32 were culture-confirmed EIEC cases. EIEC cases were more likely to report ingestion of contaminated food and were less likely to be men who have sex with men (MSM). Both pathogens were shown to cause serious disease although differences in specific symptoms were observed. Culture-negative but PCR positive cases were more likely report travel or ingestion of contaminated food and were less likely to be MSM than culture-positive cases. Culture-negative cases were more likely to suffer from multiple symptoms. No differences in degree of secondary infections were observed between Shigella spp. and EIEC, and culture-negative and culture-positive cases. Conclusions No convincing evidence was found to support the current guidelines that employs different measures based on species or detection method. Therefore, culture and molecular detection methods for Shigella spp. and EIEC should be considered equivalent for case definition and public health regulations regarding shigellosis. Differences were found regarding risks factors, indicating that different prevention strategies may be required.
Collapse
Affiliation(s)
- Maaike J C van den Beld
- Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands. .,Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | | | - Alexander W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Frans A G Reubsaet
- Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Maarten Schipper
- Department of Statistics, Informatics and Mathematical Modeling, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Richard F de Boer
- Certe, Department of Medical Microbiology, Groningen, the Netherlands
| | - Daan W Notermans
- Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Mariska W F Petrignani
- Public health service GGD Amsterdam, Amsterdam, the Netherlands.,National Coordination Centre for Communicable Disease Control, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Evert van Zanten
- Certe, Department of Medical Microbiology, Groningen, the Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ingrid H M Friesema
- Infectious Diseases, Epidemiology and Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - A M D Mirjam Kooistra-Smid
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Certe, Department of Medical Microbiology, Groningen, the Netherlands
| | | |
Collapse
|
42
|
Rautureau GJP, Palama TL, Canard I, Mirande C, Chatellier S, van Belkum A, Elena-Herrmann B. Discrimination of Escherichia coli and Shigella spp. by Nuclear Magnetic Resonance Based Metabolomic Characterization of Culture Media. ACS Infect Dis 2019; 5:1879-1886. [PMID: 31545890 DOI: 10.1021/acsinfecdis.9b00199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Dysentery is a major health threat that dramatically impacts childhood morbidity and mortality in developing countries. Various pathogenic agents cause dysentery, such as Shigella spp. and Escherichia coli, which are very closely related if not identical species. Sensitive and precise detection and identification of the infectious agent is important to target the best therapeutic strategy, but the differential diagnosis of these two groups remains a challenge using conventional methods. Here, we present a nuclear magnetic resonance (NMR) based multivariate classification model employing bacterial metabolic footprints in postculture growth media with remarkable segregation capability, including the discrimination of lactose negative E. coli and Shigella spp. Our results confirm the potential of metabolomic markers in the field of bacterial identification for the distinction of even very closely related species.
Collapse
Affiliation(s)
- Gilles J. P. Rautureau
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Tony L. Palama
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Isabelle Canard
- bioMérieux, Innovation Unit—Microbiology Research, 38390 La Balme-les-Grottes, France
| | - Caroline Mirande
- bioMérieux, Innovation Unit—Microbiology Research, 38390 La Balme-les-Grottes, France
| | - Sonia Chatellier
- bioMérieux, Innovation Unit—Microbiology Research, 38390 La Balme-les-Grottes, France
| | - Alex van Belkum
- bioMérieux, Innovation Unit—Microbiology Research, 38390 La Balme-les-Grottes, France
| | - Bénédicte Elena-Herrmann
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
- Université Grenoble Alpes, CNRS, INSERM, IAB, Allée des Alpes, 38000 Grenoble, France
| |
Collapse
|
43
|
Zhang J, Xu Y, Ling X, Zhou Y, Lin Z, Huang Z, Guan H, Xiao Y, Xu W, Kan B. Identification of diarrheagenic Escherichia coli by a new multiplex PCR assay and capillary electrophoresis. Mol Cell Probes 2019; 49:101477. [PMID: 31682897 DOI: 10.1016/j.mcp.2019.101477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/12/2019] [Accepted: 10/30/2019] [Indexed: 01/18/2023]
Abstract
Diarrheagenic Escherichia coli (DEC) is a set of the most common pathogens causing diarrhea. DEC strains are classified into five pathotypes based on the possession of different virulence genes: enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC) or Shiga toxin-producing E. coli (STEC), enteroaggregative E. coli (EAEC), enterotoxigenic E. coli (ETEC), and enteroinvasive E. coli (EIEC). The development of an easy-to-use method to detect the specific virulence genes and distinguish the pathotypes is essential for the diagnosis and surveillance of DEC infections. In this study, a multiplex PCR assay (mPCR) specific to nine virulence genes and an internal control was designed for the identification of five DEC pathotypes. A temperature switch PCR (TSP) strategy was used in the PCR amplification. The PCR products were detected by capillary electrophoresis. The limit of detection (LOD) of the 10-plex reaction was 5 × 103 copies/reaction for stx2 and 5 × 102 copies/reaction for the other targets. The mPCR showed very high specificity, and inclusivity and exclusivity were both 100%. When the mPCR assay was used for the detection of 221 cryopreserved diarrhea specimens, DEC colonies were detected from 49 specimens, and the positive rate was 22.2%. The mPCR assay was sensitive and specific, and the amplified product could be analyzed easily. Thus, this method could be used effectively to identify the suspected colonies of DEC in the primary culture of the specimen.
Collapse
Affiliation(s)
- Jingyun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Yang Xu
- Shanghai Changning District Center for Disease Control and Prevention, 39 Yunwushan Road, Changning District, Shanghai, 200051, China
| | - Xia Ling
- Wuxi Center for Disease Control and Prevention, 499 Jincheng Road, Wuxi, Jiangsu, 214023, China
| | - Yongming Zhou
- Yunnan Center for Disease Control and Prevention, 158 Dongsi Street, Kunming City, Yunnan, 650022, China
| | - Zheng Lin
- Shanghai Changning District Center for Disease Control and Prevention, 39 Yunwushan Road, Changning District, Shanghai, 200051, China
| | - Zheng Huang
- Shanghai Changning District Center for Disease Control and Prevention, 39 Yunwushan Road, Changning District, Shanghai, 200051, China
| | - Hongxia Guan
- Wuxi Center for Disease Control and Prevention, 499 Jincheng Road, Wuxi, Jiangsu, 214023, China
| | - Yong Xiao
- Wuxi Center for Disease Control and Prevention, 499 Jincheng Road, Wuxi, Jiangsu, 214023, China
| | - Wen Xu
- Yunnan Center for Disease Control and Prevention, 158 Dongsi Street, Kunming City, Yunnan, 650022, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control. National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China.
| |
Collapse
|
44
|
Day MJ, Hopkins KL, Wareham DW, Toleman MA, Elviss N, Randall L, Teale C, Cleary P, Wiuff C, Doumith M, Ellington MJ, Woodford N, Livermore DM. Extended-spectrum β-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and Scotland: an epidemiological surveillance and typing study. THE LANCET. INFECTIOUS DISEASES 2019; 19:1325-1335. [PMID: 31653524 DOI: 10.1016/s1473-3099(19)30273-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 05/13/2019] [Accepted: 05/21/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND Extended-spectrum β-lactamase-producing Escherichia coli isolates (ESBL-E coli) cause more than 5000 cases of bacteraemias annually in the UK. The contribution of the food chain to these infections is debated. We aimed to identify the most important reservoirs of ESBL-E coli that colonise and infect humans to identify strategic intervention points. METHODS Sampling for ESBL-E coli was done between Aug 1, 2013, and Dec 15, 2014. We used selective media to seek ESBL-E coli in routinely submitted samples from human faeces, and prospectively collected samples from sewage, farm slurry, and retail foodstuffs in London, East Anglia, northwest England, Scotland, and Wales. We sequenced recovered isolates and compared these isolates with 293 bloodstream and 83 veterinary surveillance ESBL-E coli isolates from the same regions. FINDINGS 2157 (11%) of 20 243 human faeces samples contained ESBL-E coli, including 678 (17%) of 3995 in London. ESBL-E coli also were frequent in sewage and retail chicken (104 [65%] of 159 meat samples), but were rare in other meats and absent from plant-based foods (0 of 400 fruit and vegetable samples). Sequence type (ST) 131 dominated among ESBL-E coli from human blood (188 [64%] of 293 isolates), faeces (128 [36%] of 360), and sewage (14 [22%] of 65) with STs 38 and 648 also widespread; CTX-M-15 was the predominant ESBL in these lineages (319 [77%] of 416). By contrast, STs 602, 23, and 117-mostly with CTX-M-1 ESBL-dominated among food and veterinary isolates (68 [31%] of 218), with only two ST131 organisms recovered. ST10 occurred in both animals and humans, being frequent in surveillance bovines (11 [22%] of 51 cattle) and representing 15 (4%) of 360 human faecal isolates (but only three [1%] of 293 from bacteraemias); however, both human and animal ST10 isolates were diverse in serotype. INTERPRETATION Most human bacteraemias with ESBL-E coli in the UK involve internationally prevalent human-associated STs, particularly ST131; non-human reservoirs made little contribution to invasive human disease. Any interventions that seek to target food or livestock can affect the numbers of human infections caused by ESBL-E coli; prevention of the spread of resistant lineages among humans is more vital. FUNDING NIHR Policy Research.
Collapse
Affiliation(s)
- Michaela J Day
- National Infection Service, Public Health England, London, UK
| | - Katie L Hopkins
- National Infection Service, Public Health England, London, UK
| | - David W Wareham
- Barts and The London School of Medicine and Dentistry, London, UK
| | | | - Nicola Elviss
- National Infection Service, Public Health England, London, UK
| | | | | | | | | | - Michel Doumith
- National Infection Service, Public Health England, London, UK
| | | | - Neil Woodford
- National Infection Service, Public Health England, London, UK
| | - David M Livermore
- National Infection Service, Public Health England, London, UK; University of East Anglia, Norwich, Norfolk, UK.
| |
Collapse
|
45
|
Wang Y, Li A, Zhang L, Waqas M, Mehmood K, Iqbal M, Muyou C, Li Z, Lian Y, Sizhu S, Li J. Probiotic potential of Lactobacillus on the intestinal microflora against Escherichia coli induced mice model through high-throughput sequencing. Microb Pathog 2019; 137:103760. [PMID: 31562897 DOI: 10.1016/j.micpath.2019.103760] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/09/2019] [Accepted: 09/24/2019] [Indexed: 12/29/2022]
Abstract
The aim of this study was to evaluate the antibacterial potential of Lactobacillus screened from Tibetan yaks on clinical symptoms and intestinal microflora in enteroinvasive Escherichia coli (EIEC) induced mice model. In vitro study, Lactobacillus reuteri (LR1) exhibited stronger resistance to acid and bile and inhibited the growth of EIEC than Lactobacillus mucosae (LM1). The mice were randomly divided into four groups i.e. the LR1 group (LR1 1 × 109 CFU/day), LM1 group (LM1 1 × 109 CFU/day), blank control group and control group. Mice in control, LR1, and LM1 groups were challenged with EIEC on day 23. The body weight in the control and LM1 groups were significantly decreased after the infection with EIEC (P < 0.05), whereas the body weight of mice in the LR1 group did not change significantly (P > 0.05). The lowest diarrhea rate was recorded in the LR1 group after infection with EIEC. The results showed that the number of pathogens in the control group was higher than that in the experimental groups. The sequence analysis and OTU classification showed that the duodenum, ileum, and cecum of mice in the LR1 group had the highest number of OTUs compared with other groups. Whereas, the diversity analysis showed that in duodenum, ileum and cecum of mice in the LR1 group had the highest abundance and diversity. The composition of intestinal microbes indicated the presence of high proportions of Firmicutes, Proteobacteria and Bacteroidetes. Heat map analysis indicated high abundance of Bdello vibrio in the duodenum of mice in the LR1 group, while many pathogens were found in the different part of intestines in the control group, such as Streptococcus, Clostridium and Pseudomonas. In conclusion, pre-supplementation of LR1 alleviate the clinical symptoms caused by E. coli, and promote a healthy gut flora.
Collapse
Affiliation(s)
- Yaping Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Aoyun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Lihong Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Muhammad Waqas
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Khalid Mehmood
- University College of Veterinary & Animal Sciences, Islamia University of Bahawalpur, 61100, Pakistan
| | - Mudassar Iqbal
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; University College of Veterinary & Animal Sciences, Islamia University of Bahawalpur, 61100, Pakistan
| | - Can Muyou
- Institute of Grass Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Tibet, 860000, PR China
| | - Zhixing Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Yi Lian
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Suolang Sizhu
- College of Animals Husbandry and Veterinary Medicine, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, 860000, PR China
| | - Jiakui Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; College of Animals Husbandry and Veterinary Medicine, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, 860000, PR China.
| |
Collapse
|
46
|
Rapid culture-based identification of Shiga toxin-producing Escherichia coli and Shigella spp./Enteroinvasive E. coli using the eazyplex® EHEC complete assay. Eur J Clin Microbiol Infect Dis 2019; 39:151-158. [PMID: 31529306 DOI: 10.1007/s10096-019-03704-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/04/2019] [Indexed: 12/14/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) and Shigella spp./enteroinvasive E. coli (EIEC) are common diarrheagenic bacteria that cause sporadic diseases and outbreaks. Clinical manifestations vary from mild symptoms to severe complications. For microbiological diagnosis, culture confirmation of a positive stool screening PCR test is challenging because of time-consuming methods for isolation of strains, wide variety of STEC pathotypes, and increased emergence of non-classical strains with unusual serotypes. Therefore, molecular assays for the rapid identification of suspect colonies growing on selective media are very useful. In this study, the performance of the newly introduced eazyplex® EHEC assay based on loop-mediated isothermal amplification (LAMP) was evaluated using 18 representative STEC and Shigella strains and 31 isolates or positive-enrichment broths that were collected from clinical stool samples following screening by BD MAX™ EBP PCR. Results were compared to real-time PCR as a reference standard. Overall, sensitivities and specificities of the eazyplex® EHEC were as follows: 94.7% and 100% for Shiga toxin 1 (stx1), 100% and 100% for stx2, 93.3% and 97.1% for intimin (eae), 100% and 100% for enterohemolysin A (ehlyA), and 100% and 100% for invasion-associated plasmid antigen H (ipaH) as Shigella spp./EIEC target, respectively. Sample preparation for LAMP took only some minutes, and the time to result of the assay ranged from 8.5 to 13 min. This study shows that eazyplex® EHEC is a very fast and easy to perform molecular assay that provides reliable results as a culture confirmation assay for the diagnosis of STEC and Shigella spp./EIEC infections.
Collapse
|
47
|
Fuhrmeister E, Ercumen A, Pickering AJ, Jeanis KM, Ahmed M, Brown S, Arnold BF, Hubbard AE, Alam M, Sen D, Islam S, Kabir MH, Kwong LH, Islam M, Unicomb L, Rahman M, Boehm AB, Luby SP, Colford JM, Nelson KL. Predictors of Enteric Pathogens in the Domestic Environment from Human and Animal Sources in Rural Bangladesh. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:10023-10033. [PMID: 31356066 PMCID: PMC6727619 DOI: 10.1021/acs.est.8b07192] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 05/19/2023]
Abstract
Fecal indicator organisms are measured to indicate the presence of fecal pollution, yet the association between indicators and pathogens varies by context. The goal of this study was to empirically evaluate the relationships between indicator Escherichia coli, microbial source tracking markers, select enteric pathogen genes, and potential sources of enteric pathogens in 600 rural Bangladeshi households. We measured indicators and pathogen genes in stored drinking water, soil, and on mother and child hands. Additionally, survey and observational data on sanitation and domestic hygiene practices were collected. Log10 concentrations of indicator E. coli were positively associated with the prevalence of pathogenic E. coli genes in all sample types. Given the current need to rely on indicators to assess fecal contamination in the field, it is significant that in this study context indicator E. coli concentrations, measured by IDEXX Colilert-18, provided quantitative information on the presence of pathogenic E. coli in different sample types. There were no significant associations between the human fecal marker (HumM2) and human-specific pathogens in any environmental sample type. There was an increase in the prevalence of Giardia lamblia genes, any E. coli virulence gene, and the specific E. coli virulence genes stx1/2 with every log10 increase in the concentration of the animal fecal marker (BacCow) on mothers' hands. Thus, domestic animals were important contributors to enteric pathogens in these households.
Collapse
Affiliation(s)
- Erica
R. Fuhrmeister
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Ayse Ercumen
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
- Department
of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Amy J. Pickering
- Civil
and Environmental Engineering, Tufts University, Medford, Massachusetts 02153, United States
| | - Kaitlyn M. Jeanis
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Mahaa Ahmed
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Sara Brown
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Benjamin F. Arnold
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
| | - Alan E. Hubbard
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
| | - Mahfuja Alam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Debashis Sen
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Sharmin Islam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Mir Himayet Kabir
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Laura H. Kwong
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Mahfuza Islam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Leanne Unicomb
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Mahbubur Rahman
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Alexandria B. Boehm
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Stephen P. Luby
- Woods
Institute for the Environment, Stanford
University, Stanford, California 94305, United States
| | - John M. Colford
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
| | - Kara L. Nelson
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| |
Collapse
|
48
|
Abstract
The consistent, sporadic transmission of shigellosis in Taiwan necessitates an exploration of risk factors for the occurrence of shigellosis. The purpose of this study was to study the epidemiologic characteristics and the relationship between climatic factors and the incidence of shigellosis in Taiwan. We collected data from cases of shigellosis reported to the Taiwan Centers for Disease Control (Taiwan CDC) from 2001 to 2016. Climatic data were obtained from the Taiwan Central Weather Bureau. The relationships between weather variability and the incidence of shigellosis in Taiwan were determined via Poisson regression analyses. During the 16-year study period, a total of 4171 clinical cases of shigellosis were reported to the Taiwan CDC. Among them, 1926 (46.2%) were classified as confirmed cases. The incidence of shigellosis showed significant seasonality, with the majority of cases occurring in summertime (for oscillation, P < .001). The number of shigellosis cases started to increase when temperatures reached 21°C (r = 0.88, P < .001). Similarly, the number of shigellosis cases began to increase at a relative humidity of 70-74% (r = 0.75, P < .005). The number of shigellosis cases was positively associated with the mean temperature and relative humidity in the period preceding the infection. In conclusion, the occurrence of shigellosis is significantly associated with increasing temperature and relative humidity in Taiwan. Therefore, these factors could be regarded as warning signals indicating the need to implement preventive measures.
Collapse
Affiliation(s)
- Chian-Ching Chen
- Department of Business Administration, National Taiwan University of Science and Technology
| | - Chuan-Yao Lin
- Research Center for Environmental Changes, Academia Sinica, Taipei
| | - Kow-Tong Chen
- Department of Occupational Medicine, Tainan Municipal Hospital (Managed by Show Chwan Medical Care Corporation)
- Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| |
Collapse
|
49
|
Wang Y, Li A, Liu J, Mehmood K, Wangdui B, Shi H, Luo X, Zhang H, Li J. L. pseudomesenteroides and L. johnsonii isolated from yaks in Tibet modulate gut microbiota in mice to ameliorate enteroinvasive Escherichia coli-induced diarrhea. Microb Pathog 2019; 132:1-9. [PMID: 30999021 DOI: 10.1016/j.micpath.2019.04.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/17/2019] [Accepted: 04/11/2019] [Indexed: 01/07/2023]
Abstract
Enteroinvasive Escherichia coli (EIEC) are well-known food-borne pathogens that cause animal intestinal diseases. Lactobacillus is believed to inhibit intestinal pathogens and maintain a healthy gut microbiota. This study aimed to investigate the effects of pre-supplementation of Lactobacillus from yaks (4500m) to prevent the clinical symptoms and the improvement of the disordered flora caused by E. coli infection. Forty healthy mice were randomized to four study groups (n = 10); Leuconostoc pseudomesenteroides (LP1), Lactobacillus johnsonii (LJ1), blank control, and control groups. Mice in the LP1, LJ1, and control groups were intraperitoneally challenged with EIEC O124 (1 × 109 CFU) on day 23. After two days, the mice in control group were recorded for high mortality. The diarrhea in LP1 and LJ1 groups was much lower than that in the control group, and no death was recorded. In histopathology, pre-supplementation of LJ1 and LP1 relieved the damage to the liver, spleen and duodenum caused by E. coli. In addition, the normal intestinal microecology was also affected by infection of EIEC, including an increase in relative abundance of Proteobacteria. At the same time, the beneficial bacteria were increased and harmful bacteria were decreased in different intestinal segments of the LJ1 and LP1 groups compared to the control group. In conclusion, pre-supplementation of LP1 and LJ1 can mitigate EIEC-induced intestinal flora dysbiosis and can also reduce EIEC-associated diarrhea.
Collapse
Affiliation(s)
- Yaping Wang
- College of Animals Husbandry and Veterinary Medicine, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, 860000, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Aoyun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Juanjuan Liu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Khalid Mehmood
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; (c)University College of Veterinary & Animal Sciences, Islamia University of Bahawalpur, 63100, Pakistan
| | - Basang Wangdui
- Institute of Animal Husbandry, Academy of Agriculture and Animal Husbandry, Tibet Autonomous Region, PR China
| | - Hongmei Shi
- Animal Husbandry and Veterinary Science Research Institute of Gannan Prefecture, PR China
| | - Xiaolin Luo
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, 624400, PR China
| | - Hui Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Jiakui Li
- College of Animals Husbandry and Veterinary Medicine, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, 860000, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.
| |
Collapse
|
50
|
In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification. Appl Environ Microbiol 2019; 85:AEM.00165-19. [PMID: 30709819 DOI: 10.1128/aem.00165-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/21/2022] Open
Abstract
Bacteria of the genus Shigella, consisting of 4 species and >50 serotypes, cause shigellosis, a foodborne disease of significant morbidity, mortality, and economic loss worldwide. Classical Shigella identification based on selective media and serology is tedious, time-consuming, expensive, and not always accurate. A molecular diagnostic assay does not distinguish Shigella at the species level or from enteroinvasive Escherichia coli (EIEC). We inspected genomic sequences from 221 Shigella isolates and observed low concordance rates between conventional designation and molecular serotyping: 86.4% and 80.5% at the species and serotype levels, respectively. Serotype determinants for 6 additional serotypes were identified. Examination of differentiation gene markers commonly perceived as characteristic hallmarks in Shigella showed high variability among different serotypes. Using this information, we developed ShigaTyper, an automated workflow that utilizes limited computational resources to accurately and rapidly determine 59 Shigella serotypes using Illumina paired-end whole-genome sequencing (WGS) reads. Shigella serotype determinants and species-specific diagnostic markers were first identified through read alignment to an in-house curated reference sequence database. Relying on sequence hits that passed a threshold level of coverage and accuracy, serotype could be unambiguously predicted within 1 min for an average-size WGS sample of ∼500 MB. Validation with WGS data from 380 isolates showed an accuracy rate of 98.2%. This pipeline is the first step toward building a comprehensive WGS-based analysis pipeline of Shigella spp. in a field laboratory setting, where speed is essential and resources need to be more cost-effectively dedicated.IMPORTANCE Shigella causes diarrheal disease with serious public health implications. However, conventional Shigella identification methods are laborious and time-consuming and can be erroneous due to the high similarity between Shigella and enteroinvasive Escherichia coli (EIEC) and cross-reactivity between serotyping antisera. Further, serotype interpretation is complicated for inexperienced users. To develop an easier method with higher accuracy based on whole-genome sequencing (WGS) for Shigella serotyping, we systematically examined genomic information of Shigella isolates from 53 serotypes to define rules for differentiation and serotyping. We created ShigaTyper, an automated pipeline that accurately and rapidly excludes non-Shigella isolates and identifies 59 Shigella serotypes using Illumina paired-end WGS reads. A serotype can be unambiguously predicted at a data processing speed of 538 MB/min with 98.2% accuracy from a regular laptop. Once it is installed, training in bioinformatics analysis and Shigella genetics is not required. This pipeline is particularly useful to general microbiologists in field laboratories.
Collapse
|