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Bogaerts B, Van den Bossche A, Verhaegen B, Delbrassinne L, Mattheus W, Nouws S, Godfroid M, Hoffman S, Roosens NHC, De Keersmaecker SCJ, Vanneste K. Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens. J Clin Microbiol 2024; 62:e0157623. [PMID: 38441926 PMCID: PMC11077942 DOI: 10.1128/jcm.01576-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024] Open
Abstract
Whole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which promises much lower error rates than the R9 chemistry. However, limited information is available on its performance for bacterial single-nucleotide polymorphism (SNP)-based outbreak investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) (https://github.com/BioinformaticsPlatformWIV-ISP/PACU), for constructing SNP phylogenies using Illumina and/or ONT R9/R10 sequencing data. The workflow was evaluated using outbreak data sets of Shiga toxin-producing Escherichia coli and Listeria monocytogenes by comparing ONT R9 and R10 with Illumina data. The performance of each sequencing technology was evaluated not only separately but also by integrating samples sequenced by different technologies/chemistries into the same phylogenomic analysis. Additionally, the minimum sequencing time required to obtain accurate phylogenetic results using nanopore sequencing was evaluated. PACU allowed accurate identification of outbreak clusters for both species using all technologies/chemistries, but ONT R9 results deviated slightly more from the Illumina results. ONT R10 results showed trends very similar to Illumina, and we found that integrating data sets sequenced by either Illumina or ONT R10 for different isolates into the same analysis produced stable and highly accurate phylogenomic results. The resulting phylogenies for these two outbreaks stabilized after ~20 hours of sequencing for ONT R9 and ~8 hours for ONT R10. This study provides a proof of concept for using ONT R10, either in isolation or in combination with Illumina, for rapid and accurate bacterial SNP-based outbreak investigation.
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Affiliation(s)
- Bert Bogaerts
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | | | - Stéphanie Nouws
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Maxime Godfroid
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Stefan Hoffman
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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Yuan Q, Gu B, Liu W, Wen X, Wang J, Tang J, Usman M, Liu S, Tang Y, Wang L. Rapid discrimination of four Salmonella enterica serovars: A performance comparison between benchtop and handheld Raman spectrometers. J Cell Mol Med 2024; 28:e18292. [PMID: 38652116 PMCID: PMC11037414 DOI: 10.1111/jcmm.18292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Foodborne illnesses, particularly those caused by Salmonella enterica with its extensive array of over 2600 serovars, present a significant public health challenge. Therefore, prompt and precise identification of S. enterica serovars is essential for clinical relevance, which facilitates the understanding of S. enterica transmission routes and the determination of outbreak sources. Classical serotyping methods via molecular subtyping and genomic markers currently suffer from various limitations, such as labour intensiveness, time consumption, etc. Therefore, there is a pressing need to develop new diagnostic techniques. Surface-enhanced Raman spectroscopy (SERS) is a non-invasive diagnostic technique that can generate Raman spectra, based on which rapid and accurate discrimination of bacterial pathogens could be achieved. To generate SERS spectra, a Raman spectrometer is needed to detect and collect signals, which are divided into two types: the expensive benchtop spectrometer and the inexpensive handheld spectrometer. In this study, we compared the performance of two Raman spectrometers to discriminate four closely associated S. enterica serovars, that is, S. enterica subsp. enterica serovar dublin, enteritidis, typhi and typhimurium. Six machine learning algorithms were applied to analyse these SERS spectra. The support vector machine (SVM) model showed the highest accuracy for both handheld (99.97%) and benchtop (99.38%) Raman spectrometers. This study demonstrated that handheld Raman spectrometers achieved similar prediction accuracy as benchtop spectrometers when combined with machine learning models, providing an effective solution for rapid, accurate and cost-effective identification of closely associated S. enterica serovars.
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Affiliation(s)
- Quan Yuan
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
| | - Bin Gu
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
| | - Wei Liu
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
| | - Xin‐Ru Wen
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
| | - Ji‐Liang Wang
- Department of Laboratory MedicineShengli Oilfield Central HospitalDongyingChina
| | - Jia‐Wei Tang
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Muhammad Usman
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
| | - Su‐Ling Liu
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Yu‐Rong Tang
- Department of Laboratory MedicineShengli Oilfield Central HospitalDongyingChina
| | - Liang Wang
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
- Division of Microbiology and Immunology, School of Biomedical SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
- School of Agriculture and Food SustainabilityUniversity of QueenslandBrisbaneQueenslandAustralia
- Centre for Precision Health, School of Medical and Health SciencesEdith Cowan UniversityPerthWestern AustraliaAustralia
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Zhou L, Ye Q, Zhou Q, Wang J, Li G, Xiang J, Huang J, Zhao Y, Zheng T, Zuo H, Li S. Antimicrobial resistance and genomic investigation of Salmonella isolated from retail foods in Guizhou, China. Front Microbiol 2024; 15:1345045. [PMID: 38510999 PMCID: PMC10951074 DOI: 10.3389/fmicb.2024.1345045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Salmonella is a major foodborne pathogen worldwide that causes severe morbidity and mortality. It is mainly caused by consuming contaminated food, with retail food considered the primary source. Methods In Guizhou, China, 102 Salmonella strains isolated from 2016 to 2021 underwent phenotypic antimicrobial resistance testing and whole-genome sequencing (WGS) to understand Salmonella diversity, including serotypes, sequencing types (STs), antimicrobial genes, virulence genes, plasmid types, multi-locus sequence types (MLST), and core genome MLST (cgMLST). Results and discussion S.Typhimurium was the dominant serotype, and O:4(B) was the leading serogroup. The most prevalent genotype was ST40. Phenotypic antimicrobial resistance identified 66.7% of the sampled isolates as multi-drug resistant (MDR). S.Enteritidis (n = 7), S.Typhimurium (n = 1), S.Indiana (n = 1), S.Kentucky (n = 1), S.Uganda (n = 1), all of which were MDR, were resistant to Colistin. Resistance rates varied significantly across different strains and food types, particularly meat products exhibiting higher resistance. Notably, significant increases in resistance were observed from 2016 to 2021 for the following: ≥ 1 resistant (P = 0.001), MDR (P = 0.001), ampicillin (P = 0.001), tetracycline (P < 0.001), chloramphenicol (P = 0.030), and trimethoprim/sulfamethoxazole (P = 0.003). The marked escalation in drug resistance over the recent years, coupled with the varying resistance rates among food sources, underscores the growing public health concern. Our findings highlight the need for a coordinated approach to effectively monitor and respond to Salmonella infections in Guizhou, China.
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Affiliation(s)
- Li Zhou
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
| | - Qian Ye
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Qian Zhou
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
| | - Jian Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province, Chengdu, China
| | - Guanqiao Li
- Institute of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Jingshu Xiang
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
| | - Jingyu Huang
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
| | - Yuanyuan Zhao
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Tianli Zheng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Haojiang Zuo
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province, Chengdu, China
| | - Shijun Li
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
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Prentice MB, Gilbertson MLJ, Storm DJ, Turner WC, Walsh DP, Pinkerton ME, Kamath PL. Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer ( Odocoileus virginianus). Microb Genom 2024; 10:001214. [PMID: 38536208 PMCID: PMC10995629 DOI: 10.1099/mgen.0.001214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/27/2024] [Indexed: 04/07/2024] Open
Abstract
With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating the characterization of whole microbial communities associated with emerging and endemic disease outbreaks. Here, we use metagenomic sequencing in a case-control study to identify microbes in lung tissue associated with newly observed pneumonia-related fatalities in 34 white-tailed deer (Odocoileus virginianus) in Wisconsin, USA. We identified 20 bacterial species that occurred in more than a single individual. Of these, only Clostridium novyi was found to substantially differ (in number of detections) between case and control sample groups; however, this difference was not statistically significant. We also detected several bacterial species associated with pneumonia and/or other diseases in ruminants (Mycoplasma ovipneumoniae, Trueperella pyogenes, Pasteurella multocida, Anaplasma phagocytophilum, Fusobacterium necrophorum); however, these species did not substantially differ between case and control sample groups. On average, we detected a larger number of bacterial species in case samples than controls, supporting the potential role of polymicrobial infections in this system. Importantly, we did not detect DNA of viruses or fungi, suggesting that they are not significantly associated with pneumonia in this system. Together, these results highlight the utility of metagenomic sequencing for identifying disease-associated microbes. This preliminary list of microbes will help inform future research on pneumonia-associated fatalities of white-tailed deer.
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Affiliation(s)
| | - Marie L. J. Gilbertson
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Wisconsin, USA
| | | | - Wendy C. Turner
- U.S. Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Wisconsin, USA
| | - Daniel P. Walsh
- U.S. Geological Survey, Montana Cooperative Wildlife Research Unit, University of Montana, Montana, USA
| | - Marie E. Pinkerton
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Wisconsin, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Maine, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, Maine, USA
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5
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Song M, Li Q, Liu C, Wang P, Qin F, Zhang L, Fan Y, Shao H, Chen G, Yang M. A comprehensive technology strategy for microbial identification and contamination investigation in the sterile drug manufacturing facility-a case study. Front Microbiol 2024; 15:1327175. [PMID: 38410390 PMCID: PMC10895062 DOI: 10.3389/fmicb.2024.1327175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/30/2024] [Indexed: 02/28/2024] Open
Abstract
Objective A comprehensive strategy for microbial identification and contamination investigation during sterile drug manufacturing was innovatively established in this study, mainly based on MALDI-TOF MS for the identification and complemented by sequencing technology on strain typing. Methods It was implemented to monitor the bacterial contamination of a sterile drug manufacturing facility, including its bacterial distribution features and patterns. In three months, two hundred ninety-two samples were collected covering multiple critical components of raw materials, personnel, environment, and production water. Results Based on our strategy, the bacterial profile across the production process was determined: 241/292 bacterial identities were obtained, and Staphylococcus spp. (40.25%), Micrococcus spp.(11.20%), Bacillus spp. (8.30%), Actinobacteria (5.81%), and Paenibacillus spp. (4.56%) are shown to be the most dominant microbial contaminants. With 75.8% species-level and 95.4% genus-level identification capability, MALDI-TOF MS was promising to be a first-line tool for environmental monitoring routine. Furthermore, to determine the source of the most frequently occurring Staphylococcus cohnii, which evidenced a widespread presence in the entire process, a more discriminating S. cohnii whole-genome SNP typing method was developed to track the transmission routes. Phylogenetic analysis based on SNP results indicated critical environment contamination is highly relevant to personnel flow in this case. The strain typing results provide robust and accurate information for the following risk assessment step and support effective preventive and corrective measures. Conclusion In general, the strategy presented in this research will facilitate the development of improved production and environmental control processes for the pharmaceutical industry, and give insights about how to provide more sound and reliable evidence for the optimization of its control program.
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Affiliation(s)
- Minghui Song
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Qiongqiong Li
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Chengzhi Liu
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou, China
| | - Peien Wang
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Feng Qin
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Lichun Zhang
- Shanghai SPH New Asia Pharmaceutical Co., Ltd., Shanghai, China
| | - Yiling Fan
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
- China State Institute of Pharmaceutical Industry Co., Ltd., Shanghai, China
| | - Hong Shao
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- Shanghai Quality Inspection and Testing Center for Innovative Biological Products, Shanghai, China
| | - Guiliang Chen
- China State Institute of Pharmaceutical Industry Co., Ltd., Shanghai, China
- Shanghai Center for Drug Evaluation and Inspection, Shanghai, China
| | - Meicheng Yang
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
- China State Institute of Pharmaceutical Industry Co., Ltd., Shanghai, China
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Anbazhagan S, Himani KM, Karthikeyan R, Prakasan L, Dinesh M, Nair SS, Lalsiamthara J, Abhishek, Ramachandra SG, Chaturvedi VK, Chaudhuri P, Thomas P. Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains. Int Microbiol 2024; 27:101-111. [PMID: 37202587 DOI: 10.1007/s10123-023-00374-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Brucella abortus and Brucella melitensis are the primary etiological agents of brucellosis in large and small ruminants, respectively. There are limited comparative genomic studies involving Brucella strains that explore the relatedness among both species. In this study, we involved strains (n=44) representing standard, vaccine and Indian field origin for pangenome, single nucleotide polymorphism (SNP) and phylogenetic analysis. Both species shared a common gene pool representing 2884 genes out of a total 3244 genes. SNP-based phylogenetic analysis indicated higher SNP diversity among B. melitensis (3824) strains in comparison to B. abortus (540) strains, and a clear demarcation was identified between standard/vaccine and field strains. The analysis for virulence genes revealed that virB3, virB7, ricA, virB5, ipx5, wbkC, wbkB, and acpXL genes were highly conserved in most of the Brucella strains. Interestingly, virB10 gene was found to have high variability among the B. abortus strains. The cgMLST analysis revealed distinct sequence types for the standard/vaccine and field strains. B. abortus strains from north-eastern India fall within similar sequence type differing from other strains. In conclusion, the analysis revealed a highly shared core genome among two Brucella species. SNP analysis revealed B. melitensis strains exhibit high diversity as compared to B. abortus strains. Strains with absence or high polymorphism of virulence genes can be exploited for the development of novel vaccine candidates effective against both B. abortus and B. melitensis.
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Affiliation(s)
- S Anbazhagan
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, India
| | - K M Himani
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - R Karthikeyan
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Lakshmi Prakasan
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - M Dinesh
- Division of Pathology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Sonu S Nair
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Jonathan Lalsiamthara
- Department of Molecular Microbiology & Immunology, SOM, OHSU, Portland, OR, US, 97239, USA
| | - Abhishek
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - S G Ramachandra
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, India
| | - V K Chaturvedi
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Pallab Chaudhuri
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India.
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India.
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Mesa V, Delannoy J, Ferraris L, Diancourt L, Mazuet C, Barbut F, Aires J. Core-genome multilocus sequence typing and core-SNP analysis of Clostridium neonatale strains isolated in different spatio-temporal settings. Microbiol Spectr 2023; 11:e0276623. [PMID: 37909758 PMCID: PMC10714970 DOI: 10.1128/spectrum.02766-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Clostridium neonatale has been isolated from the fecal samples of asymptomatic neonates and cases of necrotizing enterocolitis (NEC). Taking advantage of a large collection of independent strains isolated from different spatio-temporal settings, we developed and established a cgMLST scheme for the molecular typing of C. neonatale. Both the cgMLST and cgSNP methods demonstrate comparable discrimination power. Results indicate geographic- and temporal- independent clustering of C. neonatale NEC-associated strains. No specific cgMLST clade of C. neonatale was genetically associated with NEC.
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Affiliation(s)
- Victoria Mesa
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Johanne Delannoy
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Laurent Ferraris
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Laure Diancourt
- Institut Pasteur, Université de Paris Cité, Centre National de Référence des Bactéries anaérobies et Botulisme, Paris, France
| | - Christelle Mazuet
- Institut Pasteur, Université de Paris Cité, Centre National de Référence des Bactéries anaérobies et Botulisme, Paris, France
| | - Frédéric Barbut
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
| | - Julio Aires
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculté de Pharmacie de Paris, Paris, France
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Rose R, Feehan A, Lain BN, Ashcraft D, Nolan DJ, Velez-Climent L, Huston C, LaFleur T, Rosenthal S, Fogel GB, Miele L, Pankey G, Garcia-Diaz J, Lamers SL. Whole-genome sequencing of carbapenem-resistant Enterobacterales isolates in southeast Louisiana reveals persistent genetic clusters spanning multiple locations. J Infect Public Health 2023; 16:1911-1917. [PMID: 37866269 DOI: 10.1016/j.jiph.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 10/02/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND We investigated 51 g-negative carbapenem-resistant Enterobacterales (CRE) isolates collected from 22 patients over a five-year period from six health care institutions in the Ochsner Health network in southeast Louisiana. METHODS Short genomic reads were generated using Illumina sequencing and assembled for each isolate. Isolates were classified as Enterobacter spp. (n = 20), Klebsiella spp. (n = 30), and Escherichia coli (n = 1) and grouped into 19 different multi-locus sequence types (MLST). Species and patient-specific core genomes were constructed representing ∼50% of the chromosomal genome. RESULTS We identified two sets of patients with genetically related infections; in both cases, the related isolates were collected > 6 months apart, and in one case, the isolates were collected in different locations. On the other hand, we identified four sets of patients with isolates of the same species collected within 21 days from the same location; however, none had genetically related infections. Genes associated with resistance to carbapenem drugs (blaKPC and/or blaCTX-M-15) were found in 76% of the isolates. We found three blaKPC variants (blaKPC-2, blaKPC-3, and blaKPC-4) associated with four different Enterobacter MLST variants, and two blaKPC variants (blaKPC-2, blaKPC-3) associated with seven different Klebsiella MLST variants. CONCLUSIONS Molecular surveillance is increasingly becoming a powerful tool to understand bacterial spread in both community and clinical settings. This study provides evidence that genetically related infections in clinical settings do not necessarily reflect temporal associations, and vice versa. Our results also highlight the regional genomic and resistance diversity within related bacterial lineages.
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Affiliation(s)
- Rebecca Rose
- BioInfoExperts, LLC, Thibodaux, LA, USA; FoxSeq, LLC, Thibodaux, LA, USA.
| | - Amy Feehan
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | - Deborah Ashcraft
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | | | | | | | | | | | - Lucio Miele
- Translational Science and Genetics at LSU Health Science Center, New Orleans, LA, USA
| | - George Pankey
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Julia Garcia-Diaz
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Susanna L Lamers
- BioInfoExperts, LLC, Thibodaux, LA, USA; FoxSeq, LLC, Thibodaux, LA, USA
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9
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Toorop MMA, Kraakman MEM, Hoogendijk IV, van Prehn J, Claas ECJ, Wessels E, Boers SA. A core-genome multilocus sequence typing scheme for the detection of genetically related Streptococcus pyogenes clusters. J Clin Microbiol 2023; 61:e0055823. [PMID: 37815371 PMCID: PMC10662357 DOI: 10.1128/jcm.00558-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/07/2023] [Indexed: 10/11/2023] Open
Abstract
The recently observed increase in invasive Streptococcus pyogenes infections causes concern in Europe. However, conventional molecular typing methods lack discriminatory power to aid investigations of outbreaks caused by S. pyogenes. Therefore, there is an urgent need for high-resolution molecular typing methods to assess genetic relatedness between S. pyogenes isolates. In the current study, we aimed to develop a novel high-resolution core-genome multilocus sequence typing (cgMLST) scheme for S. pyogenes and compared its discriminatory power to conventional molecular typing methods. The cgMLST scheme was designed with the commercial Ridom SeqSphere+ software package. To define a cluster threshold, the scheme was evaluated using publicly available data from nine defined S. pyogenes outbreaks in the United Kingdom. The cgMLST scheme was then applied to 23 isolates from a suspected S. pyogenes outbreak and 117 S. pyogenes surveillance isolates both from the Netherlands. MLST and emm-typing results were used for comparison to cgMLST results. The allelic differences between isolates from defined outbreaks ranged between 6 and 31 for isolates with the same emm-type, resulting in a proposed cluster threshold of <5 allelic differences out of 1,095 target loci. Seven out of twenty-three (30%) isolates from the suspected outbreak had an allelic difference of <2, thereby identifying a potential cluster that could not be linked to other isolates. The proposed cgMLST scheme shows a higher discriminatory ability when compared to conventional typing methods. The rapid and simple analysis workflow allows for extended detection of clusters of potential outbreak isolates and surveillance and may facilitate the sharing of sequencing results between (inter)national laboratories.
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Affiliation(s)
- Myrthe M. A. Toorop
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Margriet E. M. Kraakman
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Irene V. Hoogendijk
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric C. J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Els Wessels
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Stefan A. Boers
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
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10
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Bhandari M, Poelstra JW, Kauffman M, Varghese B, Helmy YA, Scaria J, Rajashekara G. Genomic Diversity, Antimicrobial Resistance, Plasmidome, and Virulence Profiles of Salmonella Isolated from Small Specialty Crop Farms Revealed by Whole-Genome Sequencing. Antibiotics (Basel) 2023; 12:1637. [PMID: 37998839 PMCID: PMC10668983 DOI: 10.3390/antibiotics12111637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023] Open
Abstract
Salmonella is the leading cause of death associated with foodborne illnesses in the USA. Difficulty in treating human salmonellosis is attributed to the development of antimicrobial resistance and the pathogenicity of Salmonella strains. Therefore, it is important to study the genetic landscape of Salmonella, such as the diversity, plasmids, and presence antimicrobial resistance genes (AMRs) and virulence genes. To this end, we isolated Salmonella from environmental samples from small specialty crop farms (SSCFs) in Northeast Ohio from 2016 to 2021; 80 Salmonella isolates from 29 Salmonella-positive samples were subjected to whole-genome sequencing (WGS). In silico serotyping revealed the presence of 15 serotypes. AMR genes were detected in 15% of the samples, with 75% exhibiting phenotypic and genotypic multidrug resistance (MDR). Plasmid analysis demonstrated the presence of nine different types of plasmids, and 75% of AMR genes were located on plasmids. Interestingly, five Salmonella Newport isolates and one Salmonella Dublin isolate carried the ACSSuT gene cassette on a plasmid, which confers resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline. Overall, our results show that SSCFs are a potential reservoir of Salmonella with MDR genes. Thus, regular monitoring is needed to prevent the transmission of MDR Salmonella from SSCFs to humans.
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Affiliation(s)
- Menuka Bhandari
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (M.B.); (M.K.)
| | - Jelmer W. Poelstra
- Molecular and Cellular Imaging Center, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA;
| | - Michael Kauffman
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (M.B.); (M.K.)
| | - Binta Varghese
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74074, USA; (B.V.); (J.S.)
| | - Yosra A. Helmy
- Department of Veterinary Science, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA;
| | - Joy Scaria
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74074, USA; (B.V.); (J.S.)
| | - Gireesh Rajashekara
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH 44691, USA; (M.B.); (M.K.)
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11
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Bianconi I, Aschbacher R, Pagani E. Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology. Antibiotics (Basel) 2023; 12:1580. [PMID: 37998782 PMCID: PMC10668849 DOI: 10.3390/antibiotics12111580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
Recent advancements in sequencing technology and data analytics have led to a transformative era in pathogen detection and typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming the standard for pathogen analysis and control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into pathogen epidemiology and the emergence of antimicrobial-resistant strains. Antimicrobial resistance (AMR) is a pressing global public health issue. While clinical laboratories have traditionally relied on culture-based antimicrobial susceptibility testing, the integration of genomic data into AMR analysis holds immense promise. Genomic-based AMR data can furnish swift, consistent, and highly accurate predictions of resistance phenotypes for specific strains or populations, all while contributing invaluable insights for surveillance. Moreover, genome sequencing assumes a pivotal role in the investigation of hospital outbreaks. It aids in the identification of infection sources, unveils genetic connections among isolates, and informs strategies for infection control. The One Health initiative, with its focus on the intricate interconnectedness of humans, animals, and the environment, seeks to develop comprehensive approaches for disease surveillance, control, and prevention. When integrated with epidemiological data from surveillance systems, genomic data can forecast the expansion of bacterial populations and species transmissions. Consequently, this provides profound insights into the evolution and genetic relationships of AMR in pathogens, hosts, and the environment.
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Affiliation(s)
- Irene Bianconi
- Laboratory of Microbiology and Virology, Provincial Hospital of Bolzano (SABES-ASDAA), Lehrkrankenhaus der Paracelsus Medizinischen Privatuniversitätvia Amba Alagi 5, 39100 Bolzano, Italy; (R.A.); (E.P.)
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12
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Modesto M, Ngom-Bru C, Scarafile D, Bruttin A, Pruvost S, Sarker SA, Ahmed T, Sakwinska O, Mattarelli P, Duboux S. Bifidobacterium longum subsp. iuvenis subsp. nov., a novel subspecies isolated from the faeces of weaning infants. Int J Syst Evol Microbiol 2023; 73. [PMID: 37851001 DOI: 10.1099/ijsem.0.006013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Abstract
The species
Bifidobacterium longum
currently comprises four subspecies:
B. longum
subsp.
longum
,
B. longum
subsp.
infantis
,
B. longum
subsp.
suis
and
B. longum
subsp.
suillum
. Recently, several studies on
B. longum
suggested the presence of a separate clade containing four strains isolated from infants and one from rhesus macaque. These strains shared a phylogenetic similarity to
B. longum
subsp.
suis
DSM 20210T and
B. longum
subsp.
suillum
JCM1995T [average nucleotide identity (ANI) of 98.1 %) while showed an ANI of 96.5 % with both
B. longum
subsp.
infantis
and
B. longum
subsp.
longum
. The current work describes five novel additional
B. longum
strains isolated from Bangladeshi weaning infants and demonstrates their common phylogenetic origin with those of the previously proposed separated clade. Based on polyphasic taxonomic approach comprising loci multilocus sequence analysis and whole genome multilocus sequence typing, all ten examined strains have been confirmed as a distinct lineage within the species
B. longum
with
B. longum
subsp.
suis
and
B. longum
subsp.
suillum
as closest subspecies. Interestingly, these strains are present in weaning infants and primates as opposed to their closest relatives which have been typically isolated from pig and calves. These strains, similarly to
B. longum
subsp.
infantis
, show a common capacity to metabolize the human milk oligosaccharide 3-fucosyllactose. Moreover, they harbour a riboflavin synthesis operon, which differentiate them from their closest subspecies,
B. longum
subsp.
suis
and
B. longum
subsp.
suillum
. Based on the consistent results from genotypical, ecological and phenotypical analyses, a novel subspecies with the name
Bifidobacterium longum
subsp. iuvenis, with type strain NCC 5000T (=LMG 32752T=CCOS 2034T), is proposed.
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Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Catherine Ngom-Bru
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Donatella Scarafile
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Anne Bruttin
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Solenn Pruvost
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Shafiqul Alam Sarker
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Olga Sakwinska
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Stéphane Duboux
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
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13
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Leeper MM, Tolar BM, Griswold T, Vidyaprakash E, Hise KB, Williams GM, Im SB, Chen JC, Pouseele H, Carleton HA. Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA. Front Microbiol 2023; 14:1254777. [PMID: 37808298 PMCID: PMC10558246 DOI: 10.3389/fmicb.2023.1254777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Salmonella enterica is a leading cause of bacterial foodborne and zoonotic illnesses in the United States. For this study, we applied four different whole genome sequencing (WGS)-based subtyping methods: high quality single-nucleotide polymorphism (hqSNP) analysis, whole genome multilocus sequence typing using either all loci [wgMLST (all loci)] and only chromosome-associated loci [wgMLST (chrom)], and core genome multilocus sequence typing (cgMLST) to a dataset of isolate sequences from 9 well-characterized Salmonella outbreaks. For each outbreak, we evaluated the genomic and epidemiologic concordance between hqSNP and allele-based methods. We first compared pairwise genomic differences using all four methods. We observed discrepancies in allele difference ranges when using wgMLST (all loci), likely caused by inflated genetic variation due to loci found on plasmids and/or other mobile genetic elements in the accessory genome. Therefore, we excluded wgMLST (all loci) results from any further comparisons in the study. Then, we created linear regression models and phylogenetic tanglegrams using the remaining three methods. K-means analysis using the silhouette method was applied to compare the ability of the three methods to partition outbreak and sporadic isolate sequences. Our results showed that pairwise hqSNP differences had high concordance with cgMLST and wgMLST (chrom) allele differences. The slopes of the regressions for hqSNP vs. allele pairwise differences were 0.58 (cgMLST) and 0.74 [wgMLST (chrom)], and the slope of the regression was 0.77 for cgMLST vs. wgMLST (chrom) pairwise differences. Tanglegrams showed high clustering concordance between methods using two statistical measures, the Baker's gamma index (BGI) and cophenetic correlation coefficient (CCC), where 9/9 (100%) of outbreaks yielded BGI values ≥ 0.60 and CCCs were ≥ 0.97 across all nine outbreaks and all three methods. K-means analysis showed separation of outbreak and sporadic isolate groups with average silhouette widths ≥ 0.87 for outbreak groups and ≥ 0.16 for sporadic groups. This study demonstrates that Salmonella isolates clustered in concordance with epidemiologic data using three WGS-based subtyping methods and supports using cgMLST as the primary method for national surveillance of Salmonella outbreak clusters.
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Affiliation(s)
- Molly M. Leeper
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Beth M. Tolar
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Taylor Griswold
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Eshaw Vidyaprakash
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Kelley B. Hise
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Grant M. Williams
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Sung B. Im
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jessica C. Chen
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | - Heather A. Carleton
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
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14
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Ocejo M, Oporto B, Lavín JL, Hurtado A. Monitoring within-farm transmission dynamics of antimicrobial-resistant Campylobacter in dairy cattle using broth microdilution and long-read whole genome sequencing. Sci Rep 2023; 13:12529. [PMID: 37532746 PMCID: PMC10397349 DOI: 10.1038/s41598-023-39588-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/27/2023] [Indexed: 08/04/2023] Open
Abstract
Campylobacter jejuni and Campylobacter coli are important foodborne zoonotic pathogens and cause for concern due to the increasing trend in antimicrobial resistance. A long-run surveillance study was conducted in animals from different age groups in five dairy cattle farms to investigate the within-farm diversity and transmission dynamics of resistant Campylobacter throughout time. The resistance phenotype of the circulating isolates (170 C. jejuni and 37 C. coli) was determined by broth microdilution and a selection of 56 isolates were whole genome sequenced using the Oxford-Nanopore long-fragment sequencing technology resulting in completely resolved and circularized genomes (both chromosomes and plasmids). C. jejuni was isolated from all farms while C. coli was isolated from only two farms, but resistance rates were higher in C. coli than in C. jejuni and in calves than in adult animals. Some genotypes (e.g. ST-48, gyrA_T86I/tet(O)/blaOXA-61 in farm F1; ST-12000, aadE-Cc/tet(O)/blaOXA-489 in F4) persisted throughout the study while others were only sporadically detected. Acquisition of extracellular genes from other isolates and intracellular mutational events were identified as the processes that led to the emergence of the resistant genotypes that spread within the herds. Monitoring with Oxford Nanopore Technologies sequencing helped to decipher the complex molecular epidemiology underlying the within-farm dissemination of resistant Campylobacter.
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Affiliation(s)
- Medelin Ocejo
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain
| | - Beatriz Oporto
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain
| | - José Luis Lavín
- Applied Mathematics Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain
| | - Ana Hurtado
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Bizkaia, Spain.
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15
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Marotta F, Janowicz A, Romantini R, Di Marcantonio L, Di Timoteo F, Romualdi T, Zilli K, Barco L, D’Incau M, Mangone I, Cito F, Di Domenico M, Pomilio F, Ricci L, Garofolo G. Genomic and Antimicrobial Surveillance of Campylobacter Population in Italian Poultry. Foods 2023; 12:2919. [PMID: 37569189 PMCID: PMC10418777 DOI: 10.3390/foods12152919] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Campylobacter is one of the most common foodborne diseases worldwide with increasing rates of antibiotic resistance. Most cases of campylobacteriosis can be traced back to the consumption of poultry meat. Despite many efforts to reduce contamination in farms and in slaughterhouses, the persistence of this pathogen in poultry products remains a problem. This study aimed to evaluate the genetic diversity and antibiotic resistance of 542 C. jejuni and C. coli in Italian poultry, in the framework of two National Monitoring Programs. Genomes were screened for antibiotic resistance, virulence determinants and contextualized within a global collection of C. jejuni. ST2116, ST2863 and ST 832 were the most prevalent and significantly associated with Italian poultry. A worrying increase in resistance to quinolones, fluoroquinolones and tetracycline was observed in C. jejuni, while an increased occurrence of multidrug resistant (MDR) strains and strains resistant to macrolides was detected in C. coli. Low resistance rates were found for aminoglycosides. Molecular resistance determinants were consistent with the phenotypic resistance for tetracycline and quinolones. In silico analysis revealed 119 genes associated with virulence factors, with a notably higher prevalence of some genes in ST2863 genomes. This study highlights the increased resistance to macrolides and the emergence of MDR strains for C. coli, the genetic basis of AMR and the predominance of two genotypes among Campylobacter strains isolated from the Italian poultry farms.
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Affiliation(s)
- Francesca Marotta
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Anna Janowicz
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Romina Romantini
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Lisa Di Marcantonio
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Federica Di Timoteo
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Teresa Romualdi
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Katiuscia Zilli
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Lisa Barco
- Italian National Reference Laboratory for Salmonellosis, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, 35020 Padua, Italy;
| | - Mario D’Incau
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna “Bruno Ubertini”, 25124 Brescia, Italy;
| | - Iolanda Mangone
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Francesca Cito
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Marco Di Domenico
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Francesco Pomilio
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Lucilla Ricci
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
| | - Giuliano Garofolo
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale Teramo, Via Campo Boario 1, 64100 Teramo, Italy; (F.M.); (A.J.); (L.D.M.); (F.D.T.); (T.R.); (K.Z.); (I.M.); (F.C.); (M.D.D.); (F.P.); (L.R.); (G.G.)
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16
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Abad-Fau A, Sevilla E, Martín-Burriel I, Moreno B, Bolea R. Update on Commonly Used Molecular Typing Methods for Clostridioides difficile. Microorganisms 2023; 11:1752. [PMID: 37512924 PMCID: PMC10384772 DOI: 10.3390/microorganisms11071752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
This review aims to provide a comprehensive overview of the significant Clostridioides difficile molecular typing techniques currently employed in research and medical communities. The main objectives of this review are to describe the key molecular typing methods utilized in C. difficile studies and to highlight the epidemiological characteristics of the most prevalent strains on a global scale. Geographically distinct regions exhibit distinct strain types of C. difficile, with notable concordance observed among various typing methodologies. The advantages that next-generation sequencing (NGS) offers has changed epidemiology research, enabling high-resolution genomic analyses of this pathogen. NGS platforms offer an unprecedented opportunity to explore the genetic intricacies and evolutionary trajectories of C. difficile strains. It is relevant to acknowledge that novel routes of transmission are continually being unveiled and warrant further investigation, particularly in the context of zoonotic implications and environmental contamination.
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Affiliation(s)
- Ana Abad-Fau
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Eloísa Sevilla
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Inmaculada Martín-Burriel
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Bernardino Moreno
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Rosa Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
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17
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Tourasse NJ, Jolley KA, Kolstø AB, Økstad OA. Core genome multilocus sequence typing scheme for Bacillus cereus group bacteria. Res Microbiol 2023; 174:104050. [PMID: 36893969 DOI: 10.1016/j.resmic.2023.104050] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023]
Abstract
Core genome multilocus sequence typing (cgMLST) employs a strategy where the set of orthologous genes common to all members of a group of organisms are used for phylogenetic analysis of the group members. The Bacillus cereus group consists of species with pathogenicity towards insect species as well as warm-blooded animals including humans. While B. cereus is an opportunistic pathogen linked to a range of human disease conditions, including emesis and diarrhoea, Bacillus thuringiensis is an entomopathogenic species with toxicity toward insect larvae, and therefore used as a biological pesticide worldwide. Bacillus anthracis is a classical obligate pathogen causing anthrax, an acute lethal condition in herbivores as well as humans, and which is endemic in many parts of the world. The group also includes a range of additional species, and B. cereus group bacteria have been subject to analysis with a wide variety of phylogenetic typing systems. Here we present, based on analyses of 173 complete genomes from B. cereus group species available in public databases, the identification of a set of 1568 core genes which were used to create a core genome multilocus typing scheme for the group which is implemented in the PubMLST system as an open online database freely available to the community. The new cgMLST system provides unprecedented resolution over existing phylogenetic analysis schemes covering the B. cereus group.
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Affiliation(s)
- Nicolas J Tourasse
- Department of Pharmacology and Pharmaceutical Biosciences, University of Oslo, Norway; University of Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France.
| | | | - Anne-Brit Kolstø
- Department of Pharmacology and Pharmaceutical Biosciences, University of Oslo, Norway.
| | - Ole Andreas Økstad
- Department of Pharmacology and Pharmaceutical Biosciences, University of Oslo, Norway.
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Fernández-Caso B, Miqueleiz A, Alarcón T. Whole Genome Sequencing for Studying Helicobacter pylori Antimicrobial Resistance. Antibiotics (Basel) 2023; 12:1135. [PMID: 37508231 PMCID: PMC10376898 DOI: 10.3390/antibiotics12071135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Antibiotic resistance (AMR) is an alarming concern worldwide and Helicobacter pylori, one of the most prevalent bacteria, is not an exception. With antibiotics being its primary therapy, increasing resistance leads to a higher rate of treatment failure. Understanding the genomic mechanisms of resistance to clarithromycin, levofloxacin, metronidazole, amoxicillin, tetracycline, and rifampicin through next-generation sequencing-based molecular tools, such as whole genome sequencing (WGS), can be of great value, not only to direct a patient's treatment, but also to establish and optimize treatment guidelines according to the local epidemiology and to avoid the use of inappropriate antibiotics. WGS approaches allow us to gain insight into the genomic determinants involved in AMR. To this end, different pipelines and platforms are continuously being developed. In this study, we take a more detailed view of the use and progression of WGS for in-depth study of H. pylori's AMR.
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Affiliation(s)
| | - Ana Miqueleiz
- Department of Microbiology, Hospital Universitario de Navarra, 31008 Pamplona, Spain
| | - Teresa Alarcón
- Department of Microbiology, Hospital Universitario La Princesa, 28006 Madrid, Spain
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Jarocki P, Komoń-Janczara E, Młodzińska A, Sadurski J, Kołodzińska K, Łaczmański Ł, Panek J, Frąc M. Occurrence and genetic diversity of prophage sequences identified in the genomes of L. casei group bacteria. Sci Rep 2023; 13:8603. [PMID: 37237003 DOI: 10.1038/s41598-023-35823-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/24/2023] [Indexed: 05/28/2023] Open
Abstract
It is widely believed that microorganisms belonging to L. casei group can have positive effects on the human body. Therefore, these bacteria are used in many industrial processes, including the production of dietary supplements and probiotic preparations. When using live microorganisms in technological processes, it is important to use those without phage sequences within their genomes that can ultimately lead to lysis of the bacteria. It has been shown that many prophages have a benign nature, meaning that they don't directly lead to lysis or inhibit microbial growth. Moreover, the presence of phage sequences in the genomes of these bacteria increases their genetic diversity, which may contribute to easier colonization of new ecological niches. In the 439 analyzed genomes of the L. casei group, 1509 sequences of prophage origin were detected. The average length of intact prophage sequences analyzed was just under 36 kb. GC content of tested sequences was similar for all analyzed species (44.6 ± 0.9%). Analyzing the protein coding sequences collectively, it was found that there was an average of 44 putative ORFs per genome, while the ORF density of all phage genomes varied from 0.5 to 2.1. The average nucleotide identity calculated on sequence alignments for analyzed sequences was 32.7%. Of the 56 L. casei strains used in the next part of the study, 32 did not show culture growth above the OD600 value of 0.5, even at a mitomycin C concentration of 0.25 μg/ml. Primers used for this study allowed for the detection of prophage sequences for over 90% of tested bacterial strains. Finally, prophages of selected strains were induced using mitomycin C, phage particles were isolated and then genomes of viruses obtained were sequenced and analyzed.
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Affiliation(s)
- Piotr Jarocki
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland.
| | - Elwira Komoń-Janczara
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland
| | | | - Jan Sadurski
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland
| | - Kinga Kołodzińska
- Laboratory of Genomics and Bioinformatics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Łukasz Łaczmański
- Laboratory of Genomics and Bioinformatics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Jacek Panek
- Department of Soil and Plant System, Laboratory of Molecular and Environmental Microbiology, Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Magdalena Frąc
- Department of Soil and Plant System, Laboratory of Molecular and Environmental Microbiology, Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
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20
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Ramadan H, Al-Ashmawy M, Soliman AM, Elbediwi M, Sabeq I, Yousef M, Algammal AM, Hiott LM, Berrang ME, Frye JG, Jackson CR. Whole-genome sequencing of Listeria innocua recovered from retail milk and dairy products in Egypt. Front Microbiol 2023; 14:1160244. [PMID: 37234542 PMCID: PMC10206011 DOI: 10.3389/fmicb.2023.1160244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/14/2023] [Indexed: 05/28/2023] Open
Abstract
The similarity of the Listeria innocua genome with Listeria monocytogenes and their presence in the same niche may facilitate gene transfer between them. A better understanding of the mechanisms responsible for bacterial virulence requires an in-depth knowledge of the genetic characteristics of these bacteria. In this context, draft whole genome sequences were completed on five L. innocua isolated from milk and dairy products in Egypt. The assembled sequences were screened for antimicrobial resistance and virulence genes, plasmid replicons and multilocus sequence types (MLST); phylogenetic analysis of the sequenced isolates was also performed. The sequencing results revealed the presence of only one antimicrobial resistance gene, fosX, in the L. innocua isolates. However, the five isolates carried 13 virulence genes involved in adhesion, invasion, surface protein anchoring, peptidoglycan degradation, intracellular survival, and heat stress; all five lacked the Listeria Pathogenicity Island 1 (LIPI-1) genes. MLST assigned these five isolates into the same sequence type (ST), ST-1085; however, single nucleotide polymorphism (SNP)-based phylogenetic analysis revealed 422-1,091 SNP differences between our isolates and global lineages of L. innocua. The five isolates possessed an ATP-dependent protease (clpL) gene, which mediates heat resistance, on a rep25 type plasmids. Blast analysis of clpL-carrying plasmid contigs showed approximately 99% sequence similarity to the corresponding parts of plasmids of L. monocytogenes strains 2015TE24968 and N1-011A previously isolated from Italy and the United States, respectively. Although this plasmid has been linked to L. monocytogenes that was responsible for a serious outbreak, this is the first report of L. innocua containing clpL-carrying plasmids. Various genetic mechanisms of virulence transfer among Listeria species and other genera could raise the possibility of the evolution of virulent strains of L. innocua. Such strains could challenge processing and preservation protocols and pose health risks from dairy products. Ongoing genomic research is necessary to identify these alarming genetic changes and develop preventive and control measures.
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Affiliation(s)
- Hazem Ramadan
- Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
- Poultry Microbiological Safety and Processing Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | - Maha Al-Ashmawy
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Ahmed M. Soliman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Mohammed Elbediwi
- Evolutionary Biology, Institute for Biology, Freie Universität Berlin, Berlin, Germany
- Animal Health Research Institute, Agriculture Research Center, Cairo, Egypt
| | - Islam Sabeq
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Benha University, Tukh, Qalyubia, Egypt
| | - Mona Yousef
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Abdelazeem M. Algammal
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Lari M. Hiott
- Poultry Microbiological Safety and Processing Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | - Mark E. Berrang
- Poultry Microbiological Safety and Processing Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | - Jonathan G. Frye
- Poultry Microbiological Safety and Processing Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | - Charlene R. Jackson
- Poultry Microbiological Safety and Processing Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, United States
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21
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Blondeau LD, Deneer H, Rubin JE, Kanthan R, Sanche SE, Hamula CL, Blondeau JM. Zoonotic Staphylococcus pseudintermedius: an underestimated human pathogen? Future Microbiol 2023; 18:311-315. [PMID: 37158082 DOI: 10.2217/fmb-2023-0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Affiliation(s)
| | - Harry Deneer
- Department of Pathology & Laboratory Medicine, Saskatoon, SK, S7N 0W8, Canada
- University of Saskatchewan, Saskatoon, SK, S7N 5A2, Canada
| | - Joseph E Rubin
- Department of Veterinary Microbiology, Saskatoon, SK, S7N 5A2, Canada
- University of Saskatchewan, Saskatoon, SK, S7N 5A2, Canada
| | - Rani Kanthan
- Department of Pathology & Laboratory Medicine, Saskatoon, SK, S7N 0W8, Canada
- University of Saskatchewan, Saskatoon, SK, S7N 5A2, Canada
| | - Stephen E Sanche
- Division of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority, Saskatoon, SK, S7N 0W8, Canada
- Department of Medicine, Saskatoon, SK, S7N 0W8, Canada
- University of Saskatchewan, Saskatoon, SK, S7N 5A2, Canada
| | - Camille L Hamula
- Division of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority, Saskatoon, SK, S7N 0W8, Canada
- Department of Pathology & Laboratory Medicine, Saskatoon, SK, S7N 0W8, Canada
- University of Saskatchewan, Saskatoon, SK, S7N 5A2, Canada
| | - Joseph M Blondeau
- Division of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority, Saskatoon, SK, S7N 0W8, Canada
- Department of Biochemistry, Microbiology & Immunology, Saskatoon, SK, S7N 0W8, Canada
- Department of Pathology & Laboratory Medicine, Saskatoon, SK, S7N 0W8, Canada
- Department of Ophthalmology, Saskatoon, SK, S7N 0W8, Canada
- University of Saskatchewan, Saskatoon, SK, S7N 5A2, Canada
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22
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Dey S, Gaur M, Sykes EME, Prusty M, Elangovan S, Dixit S, Pati S, Kumar A, Subudhi E. Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis. Genes (Basel) 2023; 14:genes14051037. [PMID: 37239397 DOI: 10.3390/genes14051037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance. METHODS A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis. RESULTS The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621. CONCLUSIONS Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.
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Affiliation(s)
- Suchanda Dey
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
| | - Mahendra Gaur
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
| | - Ellen M E Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T2N2, Canada
| | - Monica Prusty
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, India
| | - Selvakumar Elangovan
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, India
| | - Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
| | | | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T2N2, Canada
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, India
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Campos-Madueno EI, Moradi M, Eddoubaji Y, Shahi F, Moradi S, Bernasconi OJ, Moser AI, Endimiani A. Intestinal colonization with multidrug-resistant Enterobacterales: screening, epidemiology, clinical impact, and strategies to decolonize carriers. Eur J Clin Microbiol Infect Dis 2023; 42:229-54. [PMID: 36680641 DOI: 10.1007/s10096-023-04548-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
The clinical impact of infections due to extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing Enterobacterales (Ent) has reached dramatic levels worldwide. Infections due to these multidrug-resistant (MDR) pathogens-especially Escherichia coli and Klebsiella pneumoniae-may originate from a prior asymptomatic intestinal colonization that could also favor transmission to other subjects. It is therefore desirable that gut carriers are rapidly identified to try preventing both the occurrence of serious endogenous infections and potential transmission. Together with the infection prevention and control countermeasures, any strategy capable of effectively eradicating the MDR-Ent from the intestinal tract would be desirable. In this narrative review, we present a summary of the different aspects linked to the intestinal colonization due to MDR-Ent. In particular, culture- and molecular-based screening techniques to identify carriers, data on prevalence and risk factors in different populations, clinical impact, length of colonization, and contribution to transmission in various settings will be overviewed. We will also discuss the standard strategies (selective digestive decontamination, fecal microbiota transplant) and those still in development (bacteriophages, probiotics, microcins, and CRISPR-Cas-based) that might be used to decolonize MDR-Ent carriers.
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24
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Rashid SJ, Nale JY, Millard AD, Clokie MRJ. Novel ribotype/sequence type associations and diverse CRISPR-Cas systems in environmental Clostridioides difficile strains from northern Iraq. FEMS Microbiol Lett 2023; 370:fnad091. [PMID: 37723612 PMCID: PMC10806358 DOI: 10.1093/femsle/fnad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 07/27/2023] [Accepted: 09/15/2023] [Indexed: 09/20/2023] Open
Abstract
The environment is a natural reservoir of Clostridioides difficile, and here, we aimed to isolate the pathogen from seven locations in northern Iraq. Four of the sites yielded thirty-one isolates (ten from soils, twenty-one from sediments), which together represent ribotypes (RTs) 001 (five), 010 (five), 011 (two), 035 (two), 091 (eight), and 604 (nine). Twenty-five of the isolates (∼81%) are non-toxigenic, while six (∼19%) encode the toxin A and B genes. The genomes of eleven selected isolates represent six sequence types (STs): ST-3 (two), ST-15 (one), ST-107 (five), ST-137 (one), ST-177 (one), and ST-181 (one). Five novel RT/ST associations: RT011/ST-137, RT035/ST-107, RT091/ST-107, RT604/ST-177, and RT604/ST-181 were identified, and the first three are linked to RTs previously uncharacterized by multilocus sequence typing (MLST). Nine of the genomes belong to Clade 1, and two are closely related to the cryptic C-I clade. Diverse multiple prophages and CRISPR-Cas systems (class 1 subtype I-B1 and class 2 type V CRISPR-Cas systems) with spacers identical to other C. difficile phages and plasmids were detected in the genomes. Our data show the broader diversity that exists within environmental C. difficile strains from a much less studied location and their potential role in the evolution and emergence of new strains.
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Affiliation(s)
- Srwa J Rashid
- Medical Laboratory Technology Department, Koya Technical Institute, Erbil Polytechnic University, Erbil, Kurdistan, Iraq
| | - Janet Y Nale
- Centre for Epidemiology and Planetary Health, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Andrew D Millard
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, University Road, Leicester LE1 7RH, UK
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Lienen T, Grobbel M, Tenhagen BA, Maurischat S. Plasmid-Coded Linezolid Resistance in Methicillin-Resistant Staphylococcus aureus from Food and Livestock in Germany. Antibiotics (Basel) 2022; 11:antibiotics11121802. [PMID: 36551459 PMCID: PMC9774410 DOI: 10.3390/antibiotics11121802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Resistance of methicillin-resistant Staphylococcus aureus (MRSA) from food and livestock to last resort antibiotics such as linezolid is highly concerning, since treatment options for infections in humans might be diminished. Known mechanisms of linezolid resistance include point mutations in the 23S rRNA gene and in the ribosomal proteins L3, L4 and L22 as well as an acquisition of the cfr, optrA or poxtA gene. The objective of our study was to characterize antimicrobial resistance (AMR) determinants and phylogenetic relationships among linezolid-resistant (LR-) MRSA from food and livestock. In total, from more than 4000 incoming isolates in the years 2012 to 2021, only two strains from 2015 originating from pig samples exhibited linezolid resistance in the antimicrobial susceptibility testing with MICs of ≥8 mg/L. These LR-MRSA were characterized in detail by whole-genome sequencing and phylogenetic analyses using cgMLST. The LR-MRSA strains showed resistances to ten and eight different antibiotics, respectively. Both strains harbored plasmid-coded cfr genes mediating the linezolid resistance. The cfr genes showed identical sequences in both strains. In addition to the cfr gene, genes for phenicol and clindamycin resistance were detected on the respective plasmids, opening the possibility for a co-selection. The LR-MRSA differed distantly in the phylogenetic analyses and also to other MRSA from pig samples in the year 2015. In conclusion, the occurrence of LR-MRSA in food and livestock seems to be very rare in Germany. However, carriage of plasmids with linezolid resistance determinants could lead to further linezolid-resistant strains by horizontal gene transfer.
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Brangsch H, Singha H, Laroucau K, Elschner M. Sequence-based detection and typing procedures for Burkholderia mallei: Assessment and prospects. Front Vet Sci 2022; 9:1056996. [PMID: 36452150 PMCID: PMC9703372 DOI: 10.3389/fvets.2022.1056996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/26/2022] [Indexed: 10/28/2023] Open
Abstract
Although glanders has been eradicated in most of the developed world, the disease still persists in various countries such as Brazil, India, Pakistan, Bangladesh, Nepal, Iran, Bahrain, UAE and Turkey. It is one of the notifiable diseases listed by the World Organization for Animal Health. Occurrence of glanders imposes restriction on equestrian events and restricts equine movement, thus causing economic losses to equine industry. The genetic diversity and global distribution of the causing agent, Burkholderia (B.) mallei, have not been assessed in detail and are complicated by the high clonality of this organism. Among the identification and typing methods, PCR-based methods for distinguishing B. mallei from its close relative B. pseudomallei as well as genotyping using tandem repeat regions (MLVA) are established. The advent and continuous advancement of the sequencing techniques and the reconstruction of closed genomes enable the development of genome guided epidemiological tools. For achieving a higher genomic resolution, genotyping methods based on whole genome sequencing data can be employed, like genome-wide single nucleotide polymorphisms. One of the limitations in obtaining complete genomic sequences for further molecular characterization of B. mallei is its high GC content. In this review, we aim to provide an overview of the widely used detection and typing methods for B. mallei and illustrate gaps that still require development. The genomic features of Burkholderia, their high homology and clonality will be first described from a comparative genomics perspective. Then, the commonly used molecular detection (PCR systems) and typing systems (e.g., multilocus sequence typing, variable number of tandem repeat analysis) will be presented and put in perspective with recently developed genomic methods. Also, the increasing availability of B. mallei genomic sequences and evolution of the sequencing methods offers exciting prospects for further refinement of B. mallei typing, that could overcome the difficulties presently encountered with this particular bacterium.
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Affiliation(s)
- Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health, Jena, Germany
| | | | - Karine Laroucau
- Bacterial Zoonosis Unit, Animal Health Laboratory, French Food Agency (Anses), Maisons-Alfort, France
| | - Mandy Elschner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health, Jena, Germany
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27
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Kaur S, Payne M, Luo L, Octavia S, Tanaka MM, Sintchenko V, Lan R. MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens. Database 2022; 2022:6823527. [PMID: 36367311 PMCID: PMC9650772 DOI: 10.1093/database/baac094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/30/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022]
Abstract
Multilevel genome typing (MGT) enables the genomic characterization of bacterial isolates and the relationships among them. The MGT system describes an isolate using multiple multilocus sequence typing (MLST) schemes, referred to as levels. Thus, for a new isolate, sequence types (STs) assigned at multiple precisely defined levels can be used to type isolates at multiple resolutions. The MGT designation for isolates is stable, and the assignment is faster than the existing approaches. MGT’s utility has been demonstrated in multiple species. This paper presents a publicly accessible web service called MGTdb, which enables the assignment of MGT STs to isolates, along with their storage, retrieval and analysis. The MGTdb web service enables upload of genome data as sequence reads or alleles, which are processed and assigned MGT identifiers. Additionally, any newly sequenced isolates deposited in the National Center for Biotechnology Information’s Sequence Read Archive are also regularly retrieved (currently daily), processed, assigned MGT identifiers and made publicly available in MGTdb. Interactive visualization tools are presented to assist analysis, along with capabilities to download publicly available isolates and assignments for use with external software. MGTdb is currently available for Salmonella enterica serovars Typhimurium and Enteritidis and Vibrio cholerae. We demonstrate the usability of MGTdb through three case studies — to study the long-term national surveillance of S. Typhimurium, the local epidemiology and outbreaks of S. Typhimurium, and the global epidemiology of V. cholerae. Thus, MGTdb enables epidemiological and microbiological investigations at multiple levels of resolution for all publicly available isolates of these pathogens. Database URL: https://mgtdb.unsw.edu.au
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Affiliation(s)
- Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , New South Wales 2052, Australia
- School of Computer Science and Engineering, University of New South Wales , New South Wales 2052, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , New South Wales 2052, Australia
| | - Lijuan Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , New South Wales 2052, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , New South Wales 2052, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , New South Wales 2052, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology—Public Health, Institute of Clinical Pathology and Medical Research—NSW Health Pathology, Westmead Hospital , New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney , New South Wales 2006, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , New South Wales 2052, Australia
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Khoder M, Osman M, Kassem II, Rafei R, Shahin A, Fournier PE, Rolain JM, Hamze M. Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity. Int J Mol Sci 2022; 23:13456. [PMID: 36362240 PMCID: PMC9657967 DOI: 10.3390/ijms232113456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 10/27/2023] Open
Abstract
Genome sequencing facilitates the study of bacterial taxonomy and allows the re-evaluation of the taxonomic relationships between species. Here, we aimed to analyze the draft genomes of four commensal Neisseria clinical isolates from the semen of infertile Lebanese men. To determine the phylogenetic relationships among these strains and other Neisseria spp. and to confirm their identity at the genomic level, we compared the genomes of these four isolates with the complete genome sequences of Neisseria gonorrhoeae and Neisseria meningitidis and the draft genomes of Neisseria flavescens, Neisseria perflava, Neisseria mucosa, and Neisseria macacae that are available in the NCBI Genbank database. Our findings revealed that the WGS analysis accurately identified and corroborated the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) species identities of the Neisseria isolates. The combination of three well-established genome-based taxonomic tools (in silico DNA-DNA Hybridization, Ortho Average Nucleotide identity, and pangenomic studies) proved to be relatively the best identification approach. Notably, we also discovered that some Neisseria strains that are deposited in databases contain many taxonomical errors. The latter is very important and must be addressed to prevent misdiagnosis and missing emerging etiologies. We also highlight the need for robust cut-offs to delineate the species using genomic tools.
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Affiliation(s)
- May Khoder
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
- Institut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, France
| | - Marwan Osman
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Issmat I Kassem
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA 30223-1797, USA
| | - Rayane Rafei
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Ahmad Shahin
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Pierre Edouard Fournier
- Institut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, France
| | - Jean-Marc Rolain
- Institut de Recherche pour le Développement (IRD), Microbes, Evolution, Phylogénie et Infection (MEPHI), Faculté de Médecine et de Pharmacie, Aix Marseille Université, 13005 Marseille, France
| | - Monzer Hamze
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
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Zheng K, Hong Y, Guo Z, Debnath SC, Yan C, Li K, Chen G, Xu J, Wu F, Zheng D, Wang P. Acinetobacter sedimenti sp. nov., isolated from beach sediment. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748468 DOI: 10.1099/ijsem.0.005609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, non-haemolytic, oxidase-negative, catalase-positive bacillus strain (A3.8T) was isolated from beach sediment from Zhairuo Island, PR China. The strain grew at pH 6.0-9.0 (optimum, 7.0), with 0-4.5 % NaCl (optimum, 2 %) and at 10-35 °C (optimum, 30 °C). Its whole-genome sequence was 2.5 Mb in size, with a DNA G+C content of 41.6 mol%. On the basis of the results of core genome phylogenetic analysis, A3.8T represents a separate branch within the clade formed by five species of the genus Acinetobacter with 'Acinetobacter marinus' as the most closely related species. The average nucleotide identity compared with the closely related species of the genus Acinetobacter was below 83.66 % and digital DNA-DNA hybridization values were less than 28.80 %. The predominant fatty acids included C18 : 1ω9c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). Q-9 was the major respiratory quinone. The polar lipids are mainly composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two phospholipids, an aminolipid and four unknown lipids. A3.8T cannot assimilate dl-lactate and weakly utilizes l-glutamate, l-leucine, l-phenylalanine and l-tartrate, which distinguishes it from other species of the genus Acinetobacter. On the basis of the genotype, phenotype and biochemical data, strain A3.8T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter sedimenti sp. nov. is proposed. The type strain is A3.8T (=MCCC 1K07161T=LMG 32568T).
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Affiliation(s)
- Kaiwen Zheng
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China
| | - Yi Hong
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Center, 311200 Hangzhou, PR China
| | - Zhen Guo
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Center, 311200 Hangzhou, PR China
| | - Sanjit Chandra Debnath
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China.,Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, Devon EX4 4HB, UK
| | - Cen Yan
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China
| | - Kejing Li
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China
| | - Gen Chen
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China
| | - Jinzhong Xu
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China
| | - Fabai Wu
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Center, 311200 Hangzhou, PR China
| | - Daoqiong Zheng
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China
| | - Pinmei Wang
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China
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Murr L, Huber I, Pavlovic M, Guertler P, Messelhaeusser U, Weiss M, Ehrmann M, Tuschak C, Bauer H, Wenning M, Busch U, Bretschneider N. Whole-Genome Sequence Comparisons of Listeria monocytogenes Isolated from Meat and Fish Reveal High Inter- and Intra-Sample Diversity. Microorganisms 2022; 10:2120. [DOI: 10.3390/microorganisms10112120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/15/2022] [Accepted: 10/21/2022] [Indexed: 11/16/2022] Open
Abstract
Interpretation of whole-genome sequencing (WGS) data for foodborne outbreak investigations is complex, as the genetic diversity within processing plants and transmission events need to be considered. In this study, we analyzed 92 food-associated Listeria monocytogenes isolates by WGS-based methods. We aimed to examine the genetic diversity within meat and fish production chains and to assess the applicability of suggested thresholds for clustering of potentially related isolates. Therefore, meat-associated isolates originating from the same samples or processing plants as well as fish-associated isolates were analyzed as distinct sets. In silico serogrouping, multilocus sequence typing (MLST), core genome MLST (cgMLST), and pangenome analysis were combined with screenings for prophages and genetic traits. Isolates of the same subtypes (cgMLST types (CTs) or MLST sequence types (STs)) were additionally compared by SNP calling. This revealed the occurrence of more than one CT within all three investigated plants and within two samples. Analysis of the fish set resulted in predominant assignment of isolates from pangasius catfish and salmon to ST2 and ST121, respectively, potentially indicating persistence within the respective production chains. The approach not only allowed the detection of distinct subtypes but also the determination of differences between closely related isolates, which need to be considered when interpreting WGS data for surveillance.
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Mafuna T, Matle I, Magwedere K, Pierneef RE, Reva ON. Comparative Genomics of Listeria Species Recovered from Meat and Food Processing Facilities. Microbiol Spectr 2022; 10:e0118922. [PMID: 36066257 PMCID: PMC9604131 DOI: 10.1128/spectrum.01189-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/12/2022] [Indexed: 12/30/2022] Open
Abstract
Listeria species (spp.) are contaminants that can survive in food, on equipment, and on food processing premises if appropriate hygiene measures are not used. Homologous stress tolerance genes, virulence gene clusters such as the prfA cluster, and clusters of internalin genes that contribute to the pathogenic potential of the strains can be carried by both pathogenic and nonpathogenic Listeria spp. To enhance understanding of the genome evolution of virulence and virulence-associated properties, a comparative genome approach was used to analyze 41 genome sequences belonging to L. innocua and L. welshimeri isolated from food and food processing facilities. Genetic determinants responsible for disinfectant and stress tolerance were identified, including the efflux cassette bcrABC and Tn6188_qac_1 disinfectant resistance determinant, and stress survival islets. These disinfectant-resistant genes were more frequently found in L. innocua (12%) than in L. welshimeri (2%). Several isolates representing the presumed nonpathogenic L. innocua still carried virulence-associated genes, including LGI2, LGI3, LIPI-3, and LIPI-4 which were absent in all L. welshimeri isolates. The mobile genetic elements identified were plasmids (pLGUG1 and J1776) and prophages (PHAGE_Lister_vB_LmoS_188, PHAGE_Lister_LP_030_3, PHAGE_Lister_A118, PHAGE_Lister_B054, and PHAGE_Lister_vB_LmoS_293). The results suggest that the presumed nonpathogenic isolates especially L. innocua can carry genes relevant to the strain's virulence and stress tolerance in the food and food processing facilities. IMPORTANCE This study provides genomic insights into the recently expanded genus in order to gain valuable information about the evolution of the virulence and stress tolerance properties of the genus Listeria and the distribution of these genetic elements pertinent to the pathogenic potential across Listeria spp. and clonal lineages in South Africa (SA).
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Affiliation(s)
- T. Mafuna
- Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - I. Matle
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - K. Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - R. E. Pierneef
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - O. N. Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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Patel MA, Pandey A, Patel AC, Patel SS, Chauhan HC, Shrimali MD, Patel PA, Mohapatra SK, Chandel BS. Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India. Front Microbiol 2022; 13:996214. [PMID: 36312963 PMCID: PMC9614321 DOI: 10.3389/fmicb.2022.996214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Worldwide dissemination of extended-spectrum -lactamase (ESBL)-producing Escherichia coli constitutes an emerging global health issue, with animal food products contributing as potential reservoirs. ESBL E. coli infection is associated with the high mortality and mobility rate in developing countries due to less susceptibility to antibiotics. The present study aimed to elucidate the molecular characteristics and sequence-based analysis of ESBL E. coli in the Gujarat state of India. This study included 108 E. coli strains were isolated from different poultry farms (broiler and layer) in the Banaskantha District. PCR was employed to identify genotypic ESBL-producing antimicrobial resistance genes. Overall, a high occurrence of ESBL genes was found in poultry farms due to the high usage of antimicrobials. The PCR analysis revealed that 79.62% of isolates were detected positive with one or more ESBL genes. Among them, blaTEM (63.88%) was found to be the predominant genotype, followed by blaSHV (30.55%) and blaOXA (28.70%). In the blaCTX-M group, a higher occurrence was observed in blaCTX-M-9 (23.14%), followed by blaCTX-M-2 (24.07%) and blaCTX-M-1 (22.22%). We used the whole-genome sequencing (WGS) method to evaluate the antimicrobial resistance genes, virulence factors, single nucleotide polymorphisms (SNPs), plasmid replicons, and plasmid-mediated AMR genes of one ESBL E. coli isolated. We examined the genetic relatedness of a human pathogenic E. coli strain by comparing its sequence with the broad geographical reference E. coli sequences. Escherichia coli ST 681 was determined using multi-locus sequence typing. We compared our findings to the reference sequence of Escherichia coli str. K- 12 substr. MG1655. We found 24,937 SNPs with 21,792 in the genic region, 3,145 in the intergenic region, and six InDels across the genome. The WGS analysis revealed 46 antimicrobial resistance genes and seven plasmid-mediated AMR genes viz., tetA, qnrS1, dfrA14, sul2, aph(3”)-lb, aph(6)-ld, and Aph(3’)-la. The ST 681 was found to have Cib, traT, and terC virulence factors and two plasmid replicons, IncFII(pHN7A8) and IncI1-I(Alpha). This study revealed a higher occurrence of ESBL E. coli detected in poultry.
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Affiliation(s)
- Mitul A. Patel
- Department of Biotechnology, Sankalchand Patel University, Visnagar, India
- *Correspondence: Mitul A. Patel,
| | - Aparna Pandey
- Department of Biochemistry, Dental College, Sankalchand Patel University, Visnagar, India
| | - A. C. Patel
- Department of Veterinary Microbiology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - S. S. Patel
- Department of Veterinary Microbiology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - H. C. Chauhan
- Department of Veterinary Microbiology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - M. D. Shrimali
- Department of Animal Biotechnology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - Pankaj A. Patel
- Department of Physiology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - S. K. Mohapatra
- Department of Animal Biotechnology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - B. S. Chandel
- Department of Animal Biotechnology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
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Rahman M, Lim S, Park Y. Genome-Wide Searching Single Nucleotide-Polymorphisms (SNPs) and SNPs-Targeting a Multiplex Primer for Identification of Common Salmonella Serotypes. Pathogens 2022; 11:1075. [PMID: 36297133 PMCID: PMC9611365 DOI: 10.3390/pathogens11101075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 12/04/2022] Open
Abstract
A rapid and high-quality single-nucleotide polymorphisms (SNPs)-based method was developed to improve detection and reduce salmonellosis burden. In this study, whole-genome sequence (WGS) was used to investigate SNPs, the most common genetic marker for identifying bacteria. SNP-sites encompassing 15 sets of primers (666–863 bp) were selected and used to amplify the target Salmonella serovar strains, and the amplified products were sequenced. The prevalent Salmonella enterica subspecies enterica serovars, including Typhimurium; Enteritidis, Agona, enterica, Typhi, and Abony, were amplified and sequenced. The amplified sequences of six Salmonella serovars with 15 sets of SNP-sites encompassing primers were aligned, explored SNPs, and SNPs-carrying primers (23 sets) were designed to develop a multiplex PCR marker (m-PCR). Each primer exists in at least two SNPs bases at the 3′ end of each primer, such as one was wild, and another was a mismatched base by transition or transversion mutation. Thus, twenty-three sets of SNP primers (242–670 bp), including 13 genes (SBG, dedA, yacG, mrcB, mesJ, metN, rihA/B, modA, hutG, yehX, ybiY, moeB, and sopA), were developed for PCR confirmation of target Salmonella serovar strains. Finally, the SNPs in four genes, including fliA gene (S. Enteritidis), modA (S. Agona and S. enterica), sopA (S. Abony), and mrcB (S. Typhimurium and S. Typhi), were used for detection markers of six target Salmonella serotypes. We developed an m-PCR primer set in which Salmonella serovars were detected in a single reaction. Nevertheless, m-PCR was validated with 21 Salmonella isolates (at least one isolate was taken from one positive animal fecal, and n = 6 reference Salmonella strains) and non-Salmonella bacteria isolates. The SNP-based m-PCR method would identify prevalent Salmonella serotypes, minimize the infection, and control outbreaks.
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Matthewman C, Narin A, Huston H, Hopkins CE. Systems to model the personalized aspects of microbiome health and gut dysbiosis. Mol Aspects Med 2022; 91:101115. [PMID: 36104261 DOI: 10.1016/j.mam.2022.101115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/03/2022] [Indexed: 01/17/2023]
Abstract
The human gut microbiome is a complex and dynamic microbial entity that interacts with the environment and other parts of the body including the brain, heart, liver, and immune system. These multisystem interactions are highly conserved from invertebrates to humans, however the complexity and diversity of human microbiota compositions often yield a context that is unique to each individual. Yet commonalities remain across species, where a healthy gut microbiome will be rich in symbiotic commensal biota while an unhealthy gut microbiota will be experiencing abnormal blooms of pathobiont bacteria. In this review we discuss how omics technologies can be applied in a personalized approach to understand the microbial crosstalk and microbial-host interactions that affect the delicate balance between eubiosis and dysbiosis in an individual gut microbiome. We further highlight the strengths of model organisms in identifying and characterizing these conserved synergistic and/or pathogenic host-microbe interactions. And finally, we touch upon the growing area of personalized therapeutic interventions targeting gut microbiome.
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Diricks M, Merker M, Wetzstein N, Kohl TA, Niemann S, Maurer FP. Delineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing. Nat Commun 2022; 13:4936. [PMID: 35999208 DOI: 10.1038/s41467-022-32122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/19/2022] [Indexed: 11/08/2022] Open
Abstract
Mycobacterium abscessus is an emerging multidrug-resistant non-tuberculous mycobacterium that causes a wide spectrum of infections and has caused several local outbreaks worldwide. To facilitate standardized prospective molecular surveillance, we established a novel core genome multilocus sequence typing (cgMLST) scheme. Whole genome sequencing data of 1991 isolates were employed to validate the scheme, re-analyze global population structure and set genetic distance thresholds for cluster detection and taxonomic identification. We confirmed and amended the nomenclature of the main dominant circulating clones and found that these also correlate well with traditional 7-loci MLST. Dominant circulating clones could be linked to a corresponding reference genome with less than 250 alleles while 99% of pairwise comparisons between epidemiologically linked isolates were below 25 alleles and 90% below 10 alleles. These thresholds can be used to guide further epidemiological investigations. Overall, the scheme will help to unravel the apparent global spread of certain clonal complexes and as yet undiscovered transmission routes.
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Liu S, Zhao K, Huang M, Zeng M, Deng Y, Li S, Chen H, Li W, Chen Z. Research progress on detection techniques for point-of-care testing of foodborne pathogens. Front Bioeng Biotechnol 2022; 10:958134. [PMID: 36003541 PMCID: PMC9393618 DOI: 10.3389/fbioe.2022.958134] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/30/2022] [Indexed: 11/21/2022] Open
Abstract
The global burden of foodborne disease is enormous and foodborne pathogens are the leading cause of human illnesses. The detection of foodborne pathogenic bacteria has become a research hotspot in recent years. Rapid detection methods based on immunoassay, molecular biology, microfluidic chip, metabolism, biosensor, and mass spectrometry have developed rapidly and become the main methods for the detection of foodborne pathogens. This study reviewed a variety of rapid detection methods in recent years. The research advances are introduced based on the above technical methods for the rapid detection of foodborne pathogenic bacteria. The study also discusses the limitations of existing methods and their advantages and future development direction, to form an overall understanding of the detection methods, and for point-of-care testing (POCT) applications to accurately and rapidly diagnose and control diseases.
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Affiliation(s)
- Sha Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Kaixuan Zhao
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Meiyuan Huang
- Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Department of Pathology, Central South University, Zhuzhou, China
| | - Meimei Zeng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Wen Li
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
- *Correspondence: Zhu Chen,
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Kawaka F. Characterization of symbiotic and nitrogen fixing bacteria. AMB Express 2022; 12:99. [PMID: 35907164 PMCID: PMC9339069 DOI: 10.1186/s13568-022-01441-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
Symbiotic nitrogen fixing bacteria comprise of diverse species associated with the root nodules of leguminous plants. Using an appropriate taxonomic method to confirm the identity of superior and elite strains to fix nitrogen in legume crops can improve sustainable global food and nutrition security. The current review describes taxonomic methods preferred and commonly used to characterize symbiotic bacteria in the rhizosphere. Peer reviewed, published and unpublished articles on techniques used for detection, classification and identification of symbiotic bacteria were evaluated by exploring their advantages and limitations. The findings showed that phenotypic and cultural techniques are still affordable and remain the primary basis of species classification despite their challenges. Development of new, robust and informative taxonomic techniques has really improved characterization and identification of symbiotic bacteria and discovery of novel and new species that are effective in biological nitrogen fixation (BNF) in diverse conditions and environments.
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Affiliation(s)
- Fanuel Kawaka
- Department of Biological Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O. Box 210-40601, Bondo, Kenya.
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Kulik T, Molcan T, Fiedorowicz G, van Diepeningen A, Stakheev A, Treder K, Olszewski J, Bilska K, Beyer M, Pasquali M, Stenglein S. Whole-genome single nucleotide polymorphism analysis for typing the pandemic pathogen Fusarium graminearum sensu stricto. Front Microbiol 2022; 13:885978. [PMID: 35923405 PMCID: PMC9339996 DOI: 10.3389/fmicb.2022.885978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Recent improvements in microbiology and molecular epidemiology were largely stimulated by whole- genome sequencing (WGS), which provides an unprecedented resolution in discriminating highly related genetic backgrounds. WGS is becoming the method of choice in epidemiology of fungal diseases, but its application is still in a pioneer stage, mainly due to the limited number of available genomes. Fungal pathogens often belong to complexes composed of numerous cryptic species. Detecting cryptic diversity is fundamental to understand the dynamics and the evolutionary relationships underlying disease outbreaks. In this study, we explore the value of whole-genome SNP analyses in identification of the pandemic pathogen Fusarium graminearum sensu stricto (F.g.). This species is responsible for cereal diseases and negatively impacts grain production worldwide. The fungus belongs to the monophyletic fungal complex referred to as F. graminearum species complex including at least sixteen cryptic species, a few among them may be involved in cereal diseases in certain agricultural areas. We analyzed WGS data from a collection of 99 F.g. strains and 33 strains representing all known cryptic species belonging to the FGSC complex. As a first step, we performed a phylogenomic analysis to reveal species-specific clustering. A RAxML maximum likelihood tree grouped all analyzed strains of F.g. into a single clade, supporting the clustering-based identification approach. Although, phylogenetic reconstructions are essential in detecting cryptic species, a phylogenomic tree does not fulfill the criteria for rapid and cost-effective approach for identification of fungi, due to the time-consuming nature of the analysis. As an alternative, analysis of WGS information by mapping sequence data from individual strains against reference genomes may provide useful markers for the rapid identification of fungi. We provide a robust framework for typing F.g. through the web-based PhaME workflow available at EDGE bioinformatics. The method was validated through multiple comparisons of assembly genomes to F.g. reference strain PH-1. We showed that the difference between intra- and interspecies variability was at least two times higher than intraspecific variation facilitating successful typing of F.g. This is the first study which employs WGS data for typing plant pathogenic fusaria.
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Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
- *Correspondence: Tomasz Kulik,,
| | - Tomasz Molcan
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences (PAN), Warsaw, Poland
| | - Grzegorz Fiedorowicz
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anne van Diepeningen
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Alexander Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kinga Treder
- Department of Agriculture Systems, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | | | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Marco Beyer
- Agro-Environmental Systems, Environmental Monitoring and Sensing Unit, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Sebastian Stenglein
- National Scientific and Technical Research Council, Godoy Cruz, Argentina
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Argentina
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39
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Zhang Z, Dong Y, Xiang F, Wang Y, Hou Q, Ni H, Cai W, Liu W, Yang S, Guo Z. Analysis of bacterial diversity and genetic evolution of Lacticaseibacillus paracasei isolates in fermentation pit mud. J Appl Microbiol 2022; 133:1821-1831. [PMID: 35802775 DOI: 10.1111/jam.15672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 04/13/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
Abstract
AIMS Since little is known about the genetic diversity of lactic acid bacteria (LAB) isolates from the fermentation pit mud (FPM), we sought to evaluate the bacterial structure, identify the LAB isolates and investigate the genotype and genetic diversity of the LAB isolates. METHODS AND RESULTS Using high-throughput MiSeq sequencing, we identified seven dominant bacterial genera in FPM. Lactobacillus had the highest abundance. We isolated 55 LAB strains. These isolates were all identified as Lacticaseibacillus paracasei. Using an extant multilocus sequence typing (MLST) scheme, isolates were assigned to 18 sequence types (STs) and three clonal complexes. ST1, the largest group, mainly comprised FPM isolates. Niche-specific ST2 to ST18 only contained FPM isolates. Isolates could be divided into four lineages, with most assigned to Lineage 1. Only one FPM isolate was classified as L. paracasei subsp. paracasei. Other isolates could not be classified at the subspecies level using the seven MLST loci. CONCLUSIONS Lactobacilli account for a high proportion of bacteria in pit mud. Based on the traditional culture method, L. paracasei was the dominant species, and these isolates exhibit a high ethanol tolerance, high intraspecific diversity and specific genetic profiles. SIGNIFICANCE AND IMPACT OF THE STUDY The study described the characterization of FPM bacterial diversity, giving an insight into the genetic diversity of L. paracasei strains present in FPM.
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Affiliation(s)
- Zhendong Zhang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Yun Dong
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Fanshu Xiang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Qiangchuan Hou
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Hui Ni
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China.,School of Food Science, Shihezi University, Shihezi, Xinjiang Autonomous Region, People's Republic of China
| | - Wenchao Cai
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China.,School of Food Science, Shihezi University, Shihezi, Xinjiang Autonomous Region, People's Republic of China
| | - Wenhui Liu
- Hubei Guxiangyang Liquor Industry Co., Ltd., Xiangyang, People's Republic of China
| | - Shaoyong Yang
- Hubei Guxiangyang Liquor Industry Co., Ltd., Xiangyang, People's Republic of China
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
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Le CT, Price EP, Sarovich DS, Nguyen TTA, Powell D, Vu-Khac H, Kurtböke Dİ, Knibb W, Chen SC, Katouli M. Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam. Microb Genom 2022; 8. [PMID: 35786440 PMCID: PMC9455698 DOI: 10.1099/mgen.0.000845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South Central Coast region of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. PFGE identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and SNP genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0–5 SNPs). There was no association between geographical origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. The Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 220 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55 to 7.96 Mbp in size, have an average G+C content of 68.2 % and encode 7 602–7958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into the epidemiology and pathogenicity of N. seriolae and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.
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Affiliation(s)
- Cuong T. Le
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Institute for Aquaculture, Nha Trang University, Nha Trang, Vietnam
| | - Erin P. Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Derek S. Sarovich
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Thu T. A. Nguyen
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
| | - Daniel Powell
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Hung Vu-Khac
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - D. İpek Kurtböke
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Wayne Knibb
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan, ROC
| | - Mohammad Katouli
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- *Correspondence: Mohammad Katouli,
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Gulumbe BH, Bazata AY, Bagwai MA. Campylobacter Species, Microbiological Source Tracking and Risk Assessment of Bacterial pathogens. Borneo J Pharm 2022. [DOI: 10.33084/bjop.v5i2.3363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Campylobacter species continue to remain critical pathogens of public health interest. They are responsible for approximately 500 million cases of gastroenteritis per year worldwide. Infection occurs through the consumption of contaminated food and water. Microbial risk assessment and source tracking are crucial epidemiological strategies to monitor the outbreak of campylobacteriosis effectively. Various methods have been proposed for microbial source tracking and risk assessment, most of which rely on conventional microbiological techniques such as detecting fecal indicator organisms and other novel microbial source tracking methods, including library-dependent microbial source tracking and library-independent source tracking approaches. However, both the traditional and novel methods have their setbacks. For example, while the conventional techniques are associated with a poor correlation between indicator organism and pathogen presence, on the other hand, it is impractical to interpret qPCR-generated markers to establish the exact human health risks even though it can give information regarding the potential source and relative human risk. Therefore, this article provides up-to-date information on campylobacteriosis, various approaches for source attribution, and risk assessment of bacterial pathogens, including next-generation sequencing approaches such as shotgun metagenomics, which effectively answer the questions of potential pathogens are there and in what quantities.
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42
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Thomson NM, Gilroy R, Getino M, Foster-Nyarko E, van Vliet AH, La Ragione RM, Pallen MJ. Remarkable genomic diversity among Escherichia isolates recovered from healthy chickens. PeerJ 2022; 10:e12935. [PMID: 35251780 PMCID: PMC8896058 DOI: 10.7717/peerj.12935] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/23/2022] [Indexed: 01/11/2023] Open
Abstract
The genus Escherichia has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of E. coli as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of Escherichia in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for E. coli, in silico phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of Escherichia, except for E. albertii, Shigella, and E. coli phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were E. coli phylogroups A and B1 and E. ruysiae (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every Escherichia phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic E. coli. Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies.
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Affiliation(s)
| | - Rachel Gilroy
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom,Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom,Department of Infection Biology, London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom
| | - Arnoud H.M. van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Roberto M. La Ragione
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom,Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich, Norfolk, United Kingdom,Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
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43
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Billington C, Kingsbury JM, Rivas L. Metagenomics Approaches for Improving Food Safety: A Review. J Food Prot 2022; 85:448-464. [PMID: 34706052 DOI: 10.4315/jfp-21-301] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/21/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole genome sequencing. This approach is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, next-generation sequencing is still anchored in the traditional laboratory practice of the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding and shotgun and long-read metagenomics, are part of the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed alongside current limitations and knowledge gaps and new opportunities arising from the use of this technology. HIGHLIGHTS
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Affiliation(s)
- Craig Billington
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Joanne M Kingsbury
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Lucia Rivas
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
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44
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Rahman M, Lim S, Park Y. Development of Single Nucleotide Polymorphism (SNP)-Based Triplex PCR Marker for Serotype-Specific Escherichia coli Detection. Pathogens 2022; 11:115. [PMID: 35215059 PMCID: PMC8874422 DOI: 10.3390/pathogens11020115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/29/2021] [Accepted: 01/14/2022] [Indexed: 01/27/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are one of the most common forms of genetic variation and as such are powerful tools for the identification of bacterial strains, their genetic diversity, phylogenetic analysis, and outbreak surveillance. In this study, we used 15 sets of SNP-containing primers to amplify and sequence the target Escherichia coli. Based on the combination of the 15-sequence primer sets, each SNP site encompassing forward and reverse primer sequences (620–919 bp) were aligned and an SNP-based marker was designed. Each SNP marker exists in at least two SNP sites at the 3′ end of each primer; one natural and the other artificially created by transition or transversion mutation. Thus, 12 sets of SNP primers (225–488 bp) were developed for validation by amplifying the target E. coli. Finally, a temperature gradient triplex PCR kit was designed to detect target E. coli strains. The selected primers were amplified in three genes (ileS, thrB, and polB), with fragment sizes of 401, 337, and 232 bp for E. coli O157:H7, E. coli, and E. coli O145:H28, respectively. This allele-specific SNP-based triplex primer assay provides serotype-specific detection of E. coli strains in one reaction tube. The developed marker would be used to diagnose, investigate, and control food-borne E. coli outbreaks.
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45
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Montso PK, Bezuidenhout CC, Mienie C, Somorin YM, Odeyemi OA, Mlambo V, Ateba CN. Genetic diversity and whole genome sequence analysis data of multidrug resistant atypical enteropathogenic Escherichia coli O177 strains: An assessment of food safety and public health implications. Int J Food Microbiol 2022; 365:109555. [DOI: 10.1016/j.ijfoodmicro.2022.109555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/12/2022] [Accepted: 01/21/2022] [Indexed: 11/28/2022]
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46
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Bagal UR, Phan J, Welsh RM, Misas E, Wagner D, Gade L, Litvintseva AP, Cuomo CA, Chow NA. MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris. Methods Mol Biol 2022; 2517:215-228. [PMID: 35674957 DOI: 10.1007/978-1-0716-2417-3_17] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Candida auris is an urgent public health threat characterized by high drug-resistant rates and rapid spread in healthcare settings worldwide. As part of the C. auris response, molecular surveillance has helped public health officials track the global spread and investigate local outbreaks. Here, we describe whole-genome sequencing analysis methods used for routine C. auris molecular surveillance in the United States; methods include reference selection, reference preparation, quality assessment and control of sequencing reads, read alignment, and single-nucleotide polymorphism calling and filtration. We also describe the newly developed pipeline MycoSNP, a portable workflow for performing whole-genome sequencing analysis of fungal organisms including C. auris.
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Affiliation(s)
- Ujwal R Bagal
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John Phan
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rory M Welsh
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Elizabeth Misas
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nancy A Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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47
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Bedoya-Correa CM, Rincón-Rodríguez RJ, Parada-Sanchez MT. Acidogenic and aciduric properties of Streptococcus mutans serotype c according to its genomic variability. Eur J Oral Sci 2021; 129:e12824. [PMID: 34865249 DOI: 10.1111/eos.12824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/27/2021] [Indexed: 11/24/2022]
Abstract
Streptococcus mutans (S. mutans) has a wide genetic diversity that contributes to its phenotypic heterogeneity, and may be related to attributes associated with acidogenicity and aciduricity. The aim of this study was to evaluate the acidogenic and aciduric properties of S. mutans serotype c isolates from saliva of schoolchildren according to the genomic variability. S. mutans isolates were identified by polymerase chain reaction. Fifty S. mutans serotype c isolates were genotyped by pulsed field gel electrophoresis and tested for their ability to produce and resist acid. Three specific genotypes were identified in the caries-active group and only one in the caries-free group. Although isolates were similarly acidogenic, an exclusive caries-active genotype had the greatest glycolytic activity. In contrast, isolates exhibited variable aciduricity, and three caries-active genotypes were the least aciduric. We concluded that there is genetic variability within serotype c. Acid production was similar regardless of the caries status but correlated with the number of genotypes. In addition, resistance to acid could be an important characteristic for the establishment and colonisation of specific genotypes in children with caries. However, it is important to evaluate children's intrinsic characteristics and other phenotypic properties to explain the physiopathological behaviour of the different genotypes.
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48
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Sanabria AM, Janice J, Hjerde E, Simonsen GS, Hanssen AM. Shotgun-metagenomics based prediction of antibiotic resistance and virulence determinants in Staphylococcus aureus from periprosthetic tissue on blood culture bottles. Sci Rep 2021; 11:20848. [PMID: 34675288 PMCID: PMC8531021 DOI: 10.1038/s41598-021-00383-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/08/2021] [Indexed: 11/20/2022] Open
Abstract
Shotgun-metagenomics may give valuable clinical information beyond the detection of potential pathogen(s). Identification of antimicrobial resistance (AMR), virulence genes and typing directly from clinical samples has been limited due to challenges arising from incomplete genome coverage. We assessed the performance of shotgun-metagenomics on positive blood culture bottles (n = 19) with periprosthetic tissue for typing and prediction of AMR and virulence profiles in Staphylococcus aureus. We used different approaches to determine if sequence data from reads provides more information than from assembled contigs. Only 0.18% of total reads was derived from human DNA. Shotgun-metagenomics results and conventional method results were consistent in detecting S. aureus in all samples. AMR and known periprosthetic joint infection virulence genes were predicted from S. aureus. Mean coverage depth, when predicting AMR genes was 209 ×. Resistance phenotypes could be explained by genes predicted in the sample in most of the cases. The choice of bioinformatic data analysis approach clearly influenced the results, i.e. read-based analysis was more accurate for pathogen identification, while contigs seemed better for AMR profiling. Our study demonstrates high genome coverage and potential for typing and prediction of AMR and virulence profiles in S. aureus from shotgun-metagenomics data.
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Affiliation(s)
- Adriana Maria Sanabria
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway.
| | - Jessin Janice
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Norwegian Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Erik Hjerde
- Centre for Bioinformatics, Department of Chemistry, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Gunnar Skov Simonsen
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Anne-Merethe Hanssen
- Research Group for Host-Microbe Interaction, Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway.
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49
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Feucherolles M, Nennig M, Becker SL, Martiny D, Losch S, Penny C, Cauchie HM, Ragimbeau C. Investigation of MALDI-TOF Mass Spectrometry for Assessing the Molecular Diversity of Campylobacter jejuni and Comparison with MLST and cgMLST: A Luxembourg One-Health Study. Diagnostics (Basel) 2021; 11:1949. [PMID: 34829296 DOI: 10.3390/diagnostics11111949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 11/17/2022] Open
Abstract
There is a need for active molecular surveillance of human and veterinary Campylobacter infections. However, sequencing of all isolates is associated with high costs and a considerable workload. Thus, there is a need for a straightforward complementary tool to prioritize isolates to sequence. In this study, we proposed to investigate the ability of MALDI-TOF MS to pre-screen C. jejuni genetic diversity in comparison to MLST and cgMLST. A panel of 126 isolates, with 10 clonal complexes (CC), 21 sequence types (ST) and 42 different complex types (CT) determined by the SeqSphere+ cgMLST, were analysed by a MALDI Biotyper, resulting into one average spectra per isolate. Concordance and discriminating ability were evaluated based on protein profiles and different cut-offs. A random forest algorithm was trained to predict STs. With a 94% similarity cut-off, an AWC of 1.000, 0.933 and 0.851 was obtained for MLSTCC, MLSTST and cgMLST profile, respectively. The random forest classifier showed a sensitivity and specificity up to 97.5% to predict four different STs. Protein profiles allowed to predict C. jejuni CCs, STs and CTs at 100%, 93% and 85%, respectively. Machine learning and MALDI-TOF MS could be a fast and inexpensive complementary tool to give an early signal of recurrent C. jejuni on a routine basis.
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50
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Wyrębek J, Molcan T, Myszczyński K, van Diepeningen AD, Stakheev AA, Żelechowski M, Bilska K, Kulik T. Uncovering Diagnostic Value of Mitogenome for Identification of Cryptic Species Fusarium graminearum Sensu Stricto. Front Microbiol 2021; 12:714651. [PMID: 34531839 PMCID: PMC8439580 DOI: 10.3389/fmicb.2021.714651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Fungal complexes are often composed of morphologically nearly indistinguishable species with high genetic similarity. However, despite their close relationship, they can exhibit distinct phenotypic differences in pathogenicity and production of mycotoxins. Many plant pathogenic and toxigenic fungi have been shown to consist of such cryptic species. Identification of cryptic species in economically important pathogens has added value in epidemiologic studies and provides opportunities for better control. Analysis of mitochondrial genomes or mitogenomics opens up dimensions for improved diagnostics of fungi, especially when efficient recovery of DNA is problematic. In comparison to nuclear DNA, mitochondrial DNA (mtDNA) can be amplified with improved efficacy due to its multi-copy nature. However, to date, only a few studies have demonstrated the usefulness of mtDNA for identification of cryptic species within fungal complexes. In this study, we explored the value of mtDNA for identification of one of the most important cereal pathogens Fusarium graminearum sensu stricto (F.g.). We found that homing endonucleases (HEGs), which are widely distributed in mitogenomes of fungi, display small indel polymorphism, proven to be potentially species specific. The resulting small differences in their lengths may facilitate further differentiation of F.g. from the other cryptic species belonging to F. graminearum species complex. We also explored the value of SNP analysis of the mitogenome for typing F.g. The success in identifying F.g. strains was estimated at 96%, making this tool an attractive complement to other techniques for identification of F.g.
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Affiliation(s)
- Joanna Wyrębek
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tomasz Molcan
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Alexander A Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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