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Little JS, Coughlin C, Hsieh C, Lanza M, Huang WY, Kumar A, Dandawate T, Tucker R, Gable P, Vazquez Deida AA, Moulton-Meissner H, Stevens V, McAllister G, Ewing T, Diaz M, Glowicz J, Winkler ML, Pecora N, Kubiak DW, Pearson JC, Luskin MR, Sherman AC, Woolley AE, Brandeburg C, Bolstorff B, McHale E, Fortes E, Doucette M, Smole S, Bunnell C, Gross A, Platt D, Desai S, Fiumara K, Issa NC, Baden LR, Rhee C, Klompas M, Baker MA. Neuroinvasive Bacillus cereus Infection in Immunocompromised Hosts: Epidemiologic Investigation of 5 Patients With Acute Myeloid Leukemia. Open Forum Infect Dis 2024; 11:ofae048. [PMID: 38434615 PMCID: PMC10906701 DOI: 10.1093/ofid/ofae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/24/2024] [Indexed: 03/05/2024] Open
Abstract
Background Bacillus cereus is a ubiquitous gram-positive rod-shaped bacterium that can cause sepsis and neuroinvasive disease in patients with acute leukemia or neutropenia. Methods A single-center retrospective review was conducted to evaluate patients with acute leukemia, positive blood or cerebrospinal fluid test results for B cereus, and abnormal neuroradiographic findings between January 2018 and October 2022. Infection control practices were observed, environmental samples obtained, a dietary case-control study completed, and whole genome sequencing performed on environmental and clinical Bacillus isolates. Results Five patients with B cereus neuroinvasive disease were identified. All patients had acute myeloid leukemia (AML), were receiving induction chemotherapy, and were neutropenic. Neurologic involvement included subarachnoid or intraparenchymal hemorrhage or brain abscess. All patients were treated with ciprofloxacin and survived with limited or no neurologic sequelae. B cereus was identified in 7 of 61 environmental samples and 1 of 19 dietary protein samples-these were unrelated to clinical isolates via sequencing. No point source was identified. Ciprofloxacin was added to the empiric antimicrobial regimen for patients with AML and prolonged or recurrent neutropenic fevers; no new cases were identified in the ensuing year. Conclusions B cereus is ubiquitous in the hospital environment, at times leading to clusters with unrelated isolates. Fastidious infection control practices addressing a range of possible exposures are warranted, but their efficacy is unknown and they may not be sufficient to prevent all infections. Thus, including B cereus coverage in empiric regimens for patients with AML and persistent neutropenic fever may limit the morbidity of this pathogen.
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Affiliation(s)
- Jessica S Little
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Cassie Coughlin
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Infection Control, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Candace Hsieh
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Infection Control, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Meaghan Lanza
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Infection Control, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Wan Yi Huang
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Infection Control, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Aishwarya Kumar
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Infection Control, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Tanvi Dandawate
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Infection Control, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Robert Tucker
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Infection Control, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Paige Gable
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Axel A Vazquez Deida
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heather Moulton-Meissner
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Valerie Stevens
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gillian McAllister
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thomas Ewing
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria Diaz
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Janet Glowicz
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Marisa L Winkler
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Microbiology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Nicole Pecora
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Microbiology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - David W Kubiak
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Pharmacy, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jeffrey C Pearson
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Pharmacy, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Marlise R Luskin
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Amy C Sherman
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ann E Woolley
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - Barbara Bolstorff
- Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Eileen McHale
- Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Esther Fortes
- Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Matthew Doucette
- Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Sandra Smole
- Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Craig Bunnell
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anne Gross
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Dana Platt
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sonali Desai
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Quality and Safety, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Karen Fiumara
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Infection Control, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Nicolas C Issa
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Lindsey R Baden
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Chanu Rhee
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Infection Control, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Healthcare Institute, Boston, Massachusetts, USA
| | - Michael Klompas
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Infection Control, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Healthcare Institute, Boston, Massachusetts, USA
| | - Meghan A Baker
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Infection Control, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Healthcare Institute, Boston, Massachusetts, USA
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Ohno Y, Sekizuka T, Kuroda M, Ikeda T. Outbreaks of Campylobacteriosis Caused by Drinking Raw Milk in Japan: Evidence of Relationship Between Milk and Patients by Using Whole Genome Sequencing. Foodborne Pathog Dis 2023; 20:375-380. [PMID: 37471207 DOI: 10.1089/fpd.2023.0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Abstract
Raw milk may contain some infectious bacteria and usually requires pasteurization before drinking. In this study, we report rare outbreaks of campylobacteriosis associated with raw milk in Japan, and the application of whole genome sequencing (WGS) to studies on foodborne diseases. In August 2018, there were three outbreaks of campylobacteriosis, presumably caused by the consumption of unpasteurized raw milk, derived from the same farm; thus, these three outbreaks seemed to be associated with a single contaminant at the farm. Therefore, we analyzed Campylobacter jejuni isolates obtained at the three locations using several genetic methods. The sequence type of each isolate, revealed by multilocus sequence typing, was ST-61, and the profile determined using pulsed-field gel electrophoresis was the same; however, neither method could distinguish these from previously obtained strains. Subsequently, we performed WGS and single nucleotide variant (SNV) analysis that provided evidence of clonality, indicating that C. jejuni contamination was attributed to the farm. As in this study, evidence suggests that SNV analysis provides molecular biological support in cases with sufficient epidemiological information. Hence, similar analytical methods may be used in other sporadic cases to elucidate the relevance of the cases.
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Affiliation(s)
- Yuta Ohno
- Department of Infectious Diseases, Hokkaido Institute of Public Health, Hokkaido, Japan
| | - Tsuyoshi Sekizuka
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuya Ikeda
- Department of Infectious Diseases, Hokkaido Institute of Public Health, Hokkaido, Japan
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Blankenship HM, Dietrich SE, Burgess E, Wholehan J, Soehnlen M, Manning SD. Whole-Genome Sequencing of Shiga Toxin-Producing Escherichia coli for Characterization and Outbreak Investigation. Microorganisms 2023; 11:1298. [PMID: 37317272 DOI: 10.3390/microorganisms11051298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) causes high frequencies of foodborne infections worldwide and has been linked to numerous outbreaks each year. Pulsed-field gel electrophoresis (PFGE) has been the gold standard for surveillance until the recent transition to whole-genome sequencing (WGS). To further understand the genetic diversity and relatedness of outbreak isolates, a retrospective analysis of 510 clinical STEC isolates was conducted. Among the 34 STEC serogroups represented, most (59.6%) belonged to the predominant six non-O157 serogroups. Core genome single nucleotide polymorphism (SNP) analysis differentiated clusters of isolates with similar PFGE patterns and multilocus sequence types (STs). One serogroup O26 outbreak strain and another non-typeable (NT) strain, for instance, were identical by PFGE and clustered together by MLST; however, both were distantly related in the SNP analysis. In contrast, six outbreak-associated serogroup O5 strains clustered with five ST-175 serogroup O5 isolates, which were not part of the same outbreak as determined by PFGE. The use of high-quality SNP analyses enhanced the discrimination of these O5 outbreak strains into a single cluster. In all, this study demonstrates how public health laboratories can more rapidly use WGS and phylogenetics to identify related strains during outbreak investigations while simultaneously uncovering important genetic attributes that can inform treatment practices.
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Affiliation(s)
- Heather M Blankenship
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Stephen E Dietrich
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USA
| | - Elizabeth Burgess
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USA
| | - Jason Wholehan
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USA
| | - Marty Soehnlen
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI 48824, USA
| | - Shannon D Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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4
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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] [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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Joseph LA, Griswold T, Vidyaprakash E, Im SB, Williams GM, Pouseele HA, Hise KB, Carleton HA. Evaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA. Microb Genom 2023; 9. [PMID: 37133905 DOI: 10.1099/mgen.0.001012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Campylobacter is a leading causing of bacterial foodborne and zoonotic illnesses in the USA. Pulsed-field gene electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST) have been historically used to differentiate sporadic from outbreak Campylobacter isolates. Whole genome sequencing (WGS) has been shown to provide superior resolution and concordance with epidemiological data when compared with PFGE and 7-gene MLST during outbreak investigations. In this study, we evaluated epidemiological concordance for high-quality SNP (hqSNP), core genome (cg)MLST and whole genome (wg)MLST to cluster or differentiate outbreak-associated and sporadic Campylobacter jejuni and Campylobacter coli isolates. Phylogenetic hqSNP, cgMLST and wgMLST analyses were also compared using Baker's gamma index (BGI) and cophenetic correlation coefficients. Pairwise distances comparing all three analysis methods were compared using linear regression models. Our results showed that 68/73 sporadic C. jejuni and C. coli isolates were differentiated from outbreak-associated isolates using all three methods. There was a high correlation between cgMLST and wgMLST analyses of the isolates; the BGI, cophenetic correlation coefficient, linear regression model R 2 and Pearson correlation coefficients were >0.90. The correlation was sometimes lower comparing hqSNP analysis to the MLST-based methods; the linear regression model R 2 and Pearson correlation coefficients were between 0.60 and 0.86, and the BGI and cophenetic correlation coefficient were between 0.63 and 0.86 for some outbreak isolates. We demonstrated that C. jejuni and C. coli isolates clustered in concordance with epidemiological data using WGS-based analysis methods. Discrepancies between allele and SNP-based approaches may reflect the differences between how genomic variation (SNPs and indels) are captured between the two methods. Since cgMLST examines allele differences in genes that are common in most isolates being compared, it is well suited to surveillance: searching large genomic databases for similar isolates is easily and efficiently done using allelic profiles. On the other hand, use of an hqSNP approach is much more computer intensive and not scalable to large sets of genomes. If further resolution between potential outbreak isolates is needed, wgMLST or hqSNP analysis can be used.
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Affiliation(s)
- Lavin A Joseph
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Taylor Griswold
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eshaw Vidyaprakash
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sung B Im
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Grant M Williams
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Kelley B Hise
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Heather A Carleton
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Li C, Chen X, Wen R, Ma P, Gu K, Li C, Zhou C, Lei C, Tang Y, Wang H. Immunocapture Magnetic Beads Enhanced the LAMP-CRISPR/Cas12a Method for the Sensitive, Specific, and Visual Detection of Campylobacter jejuni. BIOSENSORS 2022; 12:bios12030154. [PMID: 35323424 PMCID: PMC8946501 DOI: 10.3390/bios12030154] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 05/03/2023]
Abstract
Campylobacter jejuni is one of the most important causes of food-borne infectious disease, and poses challenges to food safety and public health. Establishing a rapid, accurate, sensitive, and simple detection method for C. jejuni enables early diagnosis, early intervention, and prevention of pathogen transmission. In this study, an immunocapture magnetic bead (ICB)-enhanced loop-mediated isothermal amplification (LAMP) CRISPR/Cas12a method (ICB-LAMP-CRISPR/Cas12a) was developed for the rapid and visual detection of C. jejuni. Using the ICB-LAMP-CRISPR/Cas12a method, C. jejuni was first captured by ICB, and the bacterial genomic DNA was then released by heating and used in the LAMP reaction. After the LAMP reaction, LAMP products were mixed and detected by the CRISPR/Cas12a cleavage mixture. This ICB-LAMP-CRISPR/Cas12a method could detect a minimum of 8 CFU/mL of C. jejuni within 70 min. Additionally, the method was performed in a closed tube in addition to ICB capture, which eliminates the need to separate preamplification and transfer of amplified products to avoid aerosol pollution. The ICB-LAMP-CRISPR/Cas12a method was further validated by testing 31 C. jejuni-positive fecal samples from different layer farms. This method is an all-in-one, simple, rapid, ultrasensitive, ultraspecific, visual detection method for instrument-free diagnosis of C. jejuni, and has wide application potential in future work.
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Affiliation(s)
- Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China; (C.L.); (X.C.); (R.W.); (P.M.); (K.G.); (C.L.); (C.Z.); (C.L.)
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Xuan Chen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China; (C.L.); (X.C.); (R.W.); (P.M.); (K.G.); (C.L.); (C.Z.); (C.L.)
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Renqiao Wen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China; (C.L.); (X.C.); (R.W.); (P.M.); (K.G.); (C.L.); (C.Z.); (C.L.)
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Peng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China; (C.L.); (X.C.); (R.W.); (P.M.); (K.G.); (C.L.); (C.Z.); (C.L.)
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Kui Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China; (C.L.); (X.C.); (R.W.); (P.M.); (K.G.); (C.L.); (C.Z.); (C.L.)
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Cui Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China; (C.L.); (X.C.); (R.W.); (P.M.); (K.G.); (C.L.); (C.Z.); (C.L.)
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Changyu Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China; (C.L.); (X.C.); (R.W.); (P.M.); (K.G.); (C.L.); (C.Z.); (C.L.)
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China; (C.L.); (X.C.); (R.W.); (P.M.); (K.G.); (C.L.); (C.Z.); (C.L.)
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yizhi Tang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China; (C.L.); (X.C.); (R.W.); (P.M.); (K.G.); (C.L.); (C.Z.); (C.L.)
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
- Correspondence: (Y.T.); (H.W.); Tel./Fax: +86-028-8547-1599 (Y.T. & H.W.)
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China; (C.L.); (X.C.); (R.W.); (P.M.); (K.G.); (C.L.); (C.Z.); (C.L.)
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
- Correspondence: (Y.T.); (H.W.); Tel./Fax: +86-028-8547-1599 (Y.T. & H.W.)
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Virulence Comparison of Salmonella enterica Subsp. enterica Isolates from Chicken and Whole Genome Analysis of the High Virulent Strain S. Enteritidis 211. Microorganisms 2021; 9:microorganisms9112239. [PMID: 34835366 PMCID: PMC8619400 DOI: 10.3390/microorganisms9112239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 01/28/2023] Open
Abstract
Background: Salmonellaenterica is one of the common pathogens in both humans and animals that causes salmonellosis and threatens public health all over the world. Methods and Results: Here we determined the virulence phenotypes of nine Salmonellaenterica subsp. enterica (S. enterica) isolates in vitro and in vivo, including pathogenicity to chicken, cell infection, biofilm formation and virulence gene expressions. S. Enteritidis 211 (SE211) was highly pathogenic with notable virulence features among the nine isolates. The combination of multiple virulence genes contributed to the conferring of the high virulence in SE211. Importantly, many mobile genetic elements (MGEs) were found in the genome sequence of SE211, including a virulence plasmid, genomic islands, and prophage regions. The MGEs and CRISPR-Cas system might function synergistically for gene transfer and immune defense. In addition, the neighbor joining tree and the minimum spanning tree were constructed in this study. Conclusions: This study provided both the virulence phenotypes and genomic features, which might contribute to the understanding of bacterial virulence mechanisms in Salmonella enterica subsp. enterica. The first completed genomic sequence for the high virulent S. Enteritidis isolate SE211 and the comparative genomics and phylogenetic analyses provided a preliminary understanding of S. enterica genetics and laid the foundation for further study.
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Porterfield HS, Maakestad LJ, LaMarche MM, Thurman AL, Kienenberger ZE, Pitcher NJ, Hansen AR, Zirbes CF, Boyken L, Muyskens BL, Pezzulo AA, Singh SB, Twait E, Ford B, Diekema DJ, Reeb V, Fischer AJ. MRSA strains with distinct accessory genes predominate at different ages in cystic fibrosis. Pediatr Pulmonol 2021; 56:2868-2878. [PMID: 34219414 PMCID: PMC8395597 DOI: 10.1002/ppul.25559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 01/30/2023]
Abstract
RATIONALE Methicillin resistant Staphylococcus aureus (MRSA) is prevalent and consequential in cystic fibrosis (CF). Whole genome sequencing (WGS) could reveal genomic differences in MRSA associated with poorer outcomes or detect MRSA transmission. OBJECTIVES To identify MRSA genes associated with low lung function and potential MRSA transmission in CF. METHODS We collected 97 MRSA isolates from 74 individuals with CF from 2017 and performed short-read WGS. We determined sequence type (ST) and the phylogenetic relationship between isolates. We aligned accessory genes from 25 reference genomes to genome assemblies, classified isolates by accessory gene content, and correlated the accessory genome to clinical outcomes. RESULTS The most prevalent ST were ST5 (N = 55), ST8 (N = 15), and ST105 (N = 14). Closely related MRSA strains were shared by family members with CF, but rarely between unrelated individuals. Three clusters of MRSA were identified by accessory genome content. Cluster A, including ST5 and ST105, was highly prevalent at all ages. Cluster B, including ST8, was more limited to younger patients. Cluster C included 6 distantly related strains. Patients 20 years old and younger infected with Cluster A had lower forced expiratory volume in the first second (FEV1 ) and higher sputum biomass compared to similar-aged patients with Cluster B. CONCLUSIONS In this CF cohort, we identified MRSA subtypes that predominate at different ages and differ by accessory gene content. The most prevalent cluster of MRSA, including ST5 and ST105, was associated with lower FEV1 . ST8 MRSA was more common in younger patients and thus has the potential to rise in prevalence as these patients age.
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Affiliation(s)
- Harry S Porterfield
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA.,Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Lucas J Maakestad
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Mason M LaMarche
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Andrew L Thurman
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Zoe E Kienenberger
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Nicholas J Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Alexis R Hansen
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Christian F Zirbes
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Linda Boyken
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Bethany L Muyskens
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Alejandro A Pezzulo
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Sachinkumar B Singh
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Erik Twait
- State Hygienic Laboratory at the University of Iowa, Iowa City, Iowa, USA
| | - Bradley Ford
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Daniel J Diekema
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Valérie Reeb
- State Hygienic Laboratory at the University of Iowa, Iowa City, Iowa, USA
| | - Anthony J Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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Genomic Characterization of Fluoroquinolone-Resistant Thermophilic Campylobacter Strains Isolated from Layer Chicken Feces in Gangneung, South Korea by Whole-Genome Sequencing. Genes (Basel) 2021; 12:genes12081131. [PMID: 34440305 PMCID: PMC8391547 DOI: 10.3390/genes12081131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022] Open
Abstract
Thermophilic Campylobacter species of poultry origin have been associated with up to 80% of human campylobacteriosis cases. Layer chickens have received less attention as possible reservoirs of Campylobacter species. Initially, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of two archived Campylobacter isolates (Campylobacter jejuni strain 200605 and Campylobacter coli strain 200606) from layer chickens to five antimicrobials (ciprofloxacin, nalidixic acid, erythromycin, tetracycline, and gentamicin) were determined using broth microdilution while the presence of selected antimicrobial resistance genes was performed by polymerase chain reaction (PCR) using specific primers. Whole-genome sequencing (WGS) was performed by the Illumina HiSeq X platform. The analysis involved antimicrobial resistance genes, virulome, multilocus sequence typing (MLST), and phylogeny. Both isolates were phenotypically resistant to ciprofloxacin (MIC: 32 vs. 32 µg/mL), nalidixic acid (MIC: 128 vs. 64 µg/mL), and tetracycline (MIC: 64 vs. 64 µg/mL), but sensitive to erythromycin (MIC: 1 vs. 2 µg/mL) and gentamicin (MIC: 0.25 vs. 1 µg/mL) for C. jejuni strain 200605 and C. coli strain 200606, respectively. WGS confirmed C257T mutation in the gyrA gene and the presence of cmeABC complex conferring resistance to FQs in both strains. Both strains also exhibited tet(O) genes associated with tetracycline resistance. Various virulence genes associated with motility, chemotaxis, and capsule formation were found in both isolates. However, the analysis of virulence genes showed that C. jejuni strain 200605 is more virulent than C. coli strain 200606. The MLST showed that C. jejuni strain 200605 belongs to sequence type ST-5229 while C. coli strain 200606 belongs to ST-5935, and both STs are less common. The phylogenetic analysis clustered C. jejuni strain 200605 along with other strains reported in Korea (CP028933 from chicken and CP014344 from human) while C. coli strain 200606 formed a separate cluster with C. coli (CP007181) from turkey. The WGS confirmed FQ-resistance in both strains and showed potential virulence of both strains. Further studies are recommended to understand the reasons behind the regional distribution (Korea, China, and Vietnam) of such rare STs.
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Smith AR, Vowles M, Horth RZ, Smith L, Rider L, Wagner JM, Sangster A, Young EL, Schuckel H, Stewart J, Gruninger RJ, Rossi A, Oakeson KF, Nakashima AK. Infection control response to an outbreak of OXA-23 carbapenemase-producing carbapenem-resistant Acinetobacter baumannii in a skilled nursing facility in Utah. Am J Infect Control 2021; 49:792-799. [PMID: 33217512 DOI: 10.1016/j.ajic.2020.11.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/10/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Antibiotic-resistant Acinetobacter species are a growing public health threat, yet are not nationally notifiable, and most states do not mandate reporting. Additionally, there are no standardized methods to detect Acinetobacter species colonization. METHODS An outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB) was identified at a Utah ventilator unit in a skilled nursing facility. An investigation was conducted to identify transmission modes in order to control spread of CRAB. Culture-based methods were used to identify patient colonization and environmental contamination in the facility. RESULTS Of the 47 patients screened, OXA-23-producing CRAB were detected in 10 patients (21%), with 7 patients (15%) having been transferred from out-of-state facilities. Of patients who screened positive, 60% did not exhibit any signs or symptoms of active infection by chart review. A total of 38 environmental samples were collected and CRAB was recovered from 37% of those samples. Whole genome sequencing analyses of patient and environmental isolates suggested repeated CRAB introduction into the facility and highlighted the role of shared equipment in transmission. CONCLUSIONS The investigation demonstrated this ventilated skilled nursing facility was an important reservoir for CRAB in the community and highlights the need for improved surveillance, strengthened infection control and inter-facility communication within and across states.
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11
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Tong S, Ma L, Ronholm J, Hsiao W, Lu X. Whole genome sequencing of Campylobacter in agri-food surveillance. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2020.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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How To Prepare for the Unexpected: a Public Health Laboratory Response. Clin Microbiol Rev 2021; 34:34/3/e00183-20. [PMID: 33980686 PMCID: PMC8142518 DOI: 10.1128/cmr.00183-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Public health laboratories (PHLs) continue to face internal and external challenges to their abilities to provide successful, timely responses to public health crises and emerging threats. These laboratories are mandated to maintain the health of their communities by identifying, diagnosing, and warning constituents of potential and real health emergencies. Public health laboratories (PHLs) continue to face internal and external challenges to their abilities to provide successful, timely responses to public health crises and emerging threats. These laboratories are mandated to maintain the health of their communities by identifying, diagnosing, and warning constituents of potential and real health emergencies. Due to the changing characteristics of public health threats and their cross-jurisdictional nature, laboratories are facing increased pressure to ensure that they respond in a consistent and coordinated manner. Here, the Association of Public Health Laboratories (APHL) Emerging Leader Program Cohort 11 members have compiled stories from subject matter experts (SMEs) at PHLs with direct involvement in crises to determine the characteristics of a successful response. Experts examined a diverse selection of emerging threats from across PHLs, including infectious diseases, opioids, natural disasters, and government shutdowns. While no public health crisis will be identical to another, overarching themes were consistent across subjects. Experiences from SMEs that could improve future responses to emerging threats are highlighted.
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13
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Freivogel C, Visschers VHM. Antimicrobial-resistant bacteria in food: which behaviour change strategies increase consumers' risk awareness and preventive food-handling behaviour? Health Psychol Behav Med 2021; 9:350-379. [PMID: 34104565 PMCID: PMC8158281 DOI: 10.1080/21642850.2021.1912609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 03/30/2021] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVES We aimed to identify the potential of behaviour change strategies to effectively increase consumers' risk awareness, behavioural intention, and preventive food-handling behaviour to reduce the transmission risk of antimicrobial-resistant bacteria through food. The applied strategies targeted knowledge and determinants of the health action process approach (HAPA). We tested techniques that are expected to increase knowledge, risk perception, and positive outcome expectancy (Study 1) as well as those that increase planning and coping self-efficacy (Study 2) in two randomised control trials. METHODS In Study 1 (N = 328), a 2 × 2 between-subject design was employed to investigate the effects of an educational video about the spread of antimicrobial-resistant bacteria and a personalised risk message on knowledge, risk perception, outcome expectancy and consequently on intention regarding safe food-handling behaviour. In Study 2 (N = 129), we used a 2 × 2 design to examine to what extent goal setting (implemented vs. not implemented) and time (pre- vs. post-test) affected planning, coping self-efficacy, and preventive food-handling behaviour. RESULTS In Study 1, we found that the video increased knowledge and the perceived susceptibility of risk compared to the control video. We found no increase on the dependent variables after receiving the personalised risk message. In Study 2, goal setting significantly improved safe food-handling behaviour compared to the control condition. Moreover, participants in the goal-setting condition showed more planning of safe food-handling measures and of dealing with emerging barriers than participants in the control condition. CONCLUSIONS These findings demonstrate that the delivery of an educational video on the spread of antimicrobial-resistant bacteria is a useful strategy to increase risk awareness, whereas goal setting presents a promising approach to improve food-handling behaviour. Following the HAPA, an additional effective behaviour change technique is required that decreases negative outcome expectancies and improves coping self-efficacy, thereby further improving intention and behaviour.
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Affiliation(s)
- Claudia Freivogel
- School of Applied Psychology, University of Applied Sciences and Arts Northwestern Switzerland, Olten, Switzerland
| | - Vivianne H. M. Visschers
- School of Applied Psychology, University of Applied Sciences and Arts Northwestern Switzerland, Olten, Switzerland
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14
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Juraschek K, Borowiak M, Tausch SH, Malorny B, Käsbohrer A, Otani S, Schwarz S, Meemken D, Deneke C, Hammerl JA. Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal Escherichia coli. Microorganisms 2021; 9:microorganisms9030598. [PMID: 33799479 PMCID: PMC8000739 DOI: 10.3390/microorganisms9030598] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 01/01/2023] Open
Abstract
Antimicrobial resistance (AMR) is a major threat to public health worldwide. Currently, AMR typing changes from phenotypic testing to whole-genome sequence (WGS)-based detection of resistance determinants for a better understanding of the isolate diversity and elements involved in gene transmission (e.g., plasmids, bacteriophages, transposons). However, the use of WGS data in monitoring purposes requires suitable techniques, standardized parameters and approved guidelines for reliable AMR gene detection and prediction of their association with mobile genetic elements (plasmids). In this study, different sequencing and assembly strategies were tested for their suitability in AMR monitoring in Escherichia coli in the routines of the German National Reference Laboratory for Antimicrobial Resistances. To assess the outcomes of the different approaches, results from in silico predictions were compared with conventional phenotypic- and genotypic-typing data. With the focus on (fluoro)quinolone-resistant E.coli, five qnrS-positive isolates with multiple extrachromosomal elements were subjected to WGS with NextSeq (Illumina), PacBio (Pacific BioSciences) and ONT (Oxford Nanopore) for in depth characterization of the qnrS1-carrying plasmids. Raw reads from short- and long-read sequencing were assembled individually by Unicycler or Flye or a combination of both (hybrid assembly). The generated contigs were subjected to bioinformatics analysis. Based on the generated data, assembly of long-read sequences are error prone and can yield in a loss of small plasmid genomes. In contrast, short-read sequencing was shown to be insufficient for the prediction of a linkage of AMR genes (e.g., qnrS1) to specific plasmid sequences. Furthermore, short-read sequencing failed to detect certain duplications and was unsuitable for genome finishing. Overall, the hybrid assembly led to the most comprehensive typing results, especially in predicting associations of AMR genes and mobile genetic elements. Thus, the use of different sequencing technologies and hybrid assemblies currently represents the best approach for reliable AMR typing and risk assessment.
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Affiliation(s)
- Katharina Juraschek
- Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany;
- Correspondence: (K.J.); (J.A.H.)
| | - Maria Borowiak
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Simon H. Tausch
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Burkhard Malorny
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Annemarie Käsbohrer
- Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany;
- Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Saria Otani
- DTU Food, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800 Kgs Lyngby, Denmark;
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Diana Meemken
- Institute of Food Safety and Food Hygiene, Working Group Meat Hygiene, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Carlus Deneke
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Jens Andre Hammerl
- Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany;
- Correspondence: (K.J.); (J.A.H.)
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15
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Kelley BR, Ellis JC, Large A, Schneider LG, Jacobson D, Johnson JG. Whole-Genome Sequencing and Bioinformatic Analysis of Environmental, Agricultural, and Human Campylobacter jejuni Isolates From East Tennessee. Front Microbiol 2020; 11:571064. [PMID: 33224113 PMCID: PMC7674308 DOI: 10.3389/fmicb.2020.571064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/08/2020] [Indexed: 12/28/2022] Open
Abstract
As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health in both the developed and developing worlds. Despite its prevalence as a human pathogen, the source of these infections remains poorly understood due to the mutation frequency of the organism and past limitations of whole genome analysis. Recent advances in both whole genome sequencing and computational methods have allowed for the high-resolution analysis of intraspecies diversity, leading multiple groups to postulate that these approaches may be used to identify the sources of Campylobacter jejuni infection. To address this hypothesis, our group conducted a regionally and temporally restricted sampling of agricultural and environmental Campylobacter sources and compared isolated C. jejuni genomes to those that caused human infections in the same region during the same time period. Through a network analysis comparing genomes from various sources, we found that human C. jejuni isolates clustered with those isolated from cattle and chickens, indicating these as potential sources of human infection in the region.
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Affiliation(s)
- Brittni R Kelley
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Annabel Large
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Liesel G Schneider
- Department of Animal Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Daniel Jacobson
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jeremiah G Johnson
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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16
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Joseph LA, Francois Watkins LK, Chen J, Tagg KA, Bennett C, Caidi H, Folster JP, Laughlin ME, Koski L, Silver R, Stevenson L, Robertson S, Pruckler J, Nichols M, Pouseele H, Carleton HA, Basler C, Friedman CR, Geissler A, Hise KB, Aubert RD. Comparison of Molecular Subtyping and Antimicrobial Resistance Detection Methods Used in a Large Multistate Outbreak of Extensively Drug-Resistant Campylobacter jejuni Infections Linked to Pet Store Puppies. J Clin Microbiol 2020; 58:e00771-20. [PMID: 32719029 PMCID: PMC7512158 DOI: 10.1128/jcm.00771-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/16/2020] [Indexed: 12/23/2022] Open
Abstract
Campylobacter jejuni is a leading cause of enteric bacterial illness in the United States. Traditional molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST), provided limited resolution to adequately identify C. jejuni outbreaks and separate out sporadic isolates during outbreak investigations. Whole-genome sequencing (WGS) has emerged as a powerful tool for C. jejuni outbreak detection. In this investigation, 45 human and 11 puppy isolates obtained during a 2016-2018 outbreak linked to pet store puppies were sequenced. Core genome multilocus sequence typing (cgMLST) and high-quality single nucleotide polymorphism (hqSNP) analysis of the sequence data separated the isolates into the same two clades containing minor within-clade differences; however, cgMLST analysis does not require selection of an appropriate reference genome, making the method preferable to hqSNP analysis for Campylobacter surveillance and cluster detection. The isolates were classified as sequence type 2109 (ST2109)-a rarely seen MLST sequence type. PFGE was performed on 38 human and 10 puppy isolates; PFGE patterns did not reliably predict clustering by cgMLST analysis. Genetic detection of antimicrobial resistance determinants predicted that all outbreak-associated isolates would be resistant to six drug classes. Traditional antimicrobial susceptibility testing (AST) confirmed a high correlation between genotypic and phenotypic antimicrobial resistance determinations. WGS analysis linked C. jejuni isolates in humans and pet store puppies even when canine exposure information was unknown, aiding the epidemiological investigation during the outbreak. WGS data were also used to quickly identify the highly drug-resistant profile of these outbreak-associated C. jejuni isolates.
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Affiliation(s)
- Lavin A Joseph
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Louise K Francois Watkins
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica Chen
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kaitlin A Tagg
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Weems Design Studio, Inc., Suwanee, Georgia, USA
| | - Christy Bennett
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- IHRC, Inc., Atlanta, Georgia, USA
| | - Hayat Caidi
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jason P Folster
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mark E Laughlin
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lia Koski
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Rachel Silver
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Lauren Stevenson
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- CAITTA, Inc., Herndon, Virginia, USA
| | - Scott Robertson
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Janet Pruckler
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Megin Nichols
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Heather A Carleton
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Colin Basler
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cindy R Friedman
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Aimee Geissler
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kelley B Hise
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rachael D Aubert
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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17
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Pierquet J, Arendt SW, Rahamat S, Hall N, Mandernach S, Reeb V, Speltz M. Listeria monocytogenes Occurrence and Adherence to Recommendations: Small and Large Retail Delicatessens in Iowa. FOOD PROTECTION TRENDS 2020; 40:320-331. [PMID: 33815004 PMCID: PMC8017485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The goal of this research was to determine the prevalence of Listeria monocytogenes in Iowa retail delicatessens and assess environmental aspects that mitigate L. monocytogenes. Fifty-seven small and large retail delicatessens in Iowa were selected randomly. More small operations (n = 43) were included as compared with larger stores, given the higher frequency of violations. An environmental assessment instrument was used to determine environmental factors and practices. At least five microbial samples were collected per site. We collected 286 (74.3%) of 385 microbial samples from small deli operations and 99 (25.7%) of 385 samples from large deli operations. Samples were taken from various zone 1 and 2 areas, such as the slicer, deli case, and meat scale; three (0.08%) samples were positive for L. monocytogenes. Regarding environmental aspects, not preparing, holding or storing ready-to-eat products near raw products (n = 30, 53%) was practiced by the fewest delis. The majority of establishments were observed covering, wrapping, or protecting ready-to-eat products when not in use to prevent contamination (n = 56, 98.2%). Comparisons were made to the U.S. Department of Agriculture Food Safety and Inspection Service Guidance on environmental practices, and 60% of the operations surveyed were in adherence with at least seven of the eight recommendations.
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Affiliation(s)
- Jennifer Pierquet
- Iowa Dept. of Inspection and Appeals, 321 East 12th St., Des Moines, IA 50319, USA
| | - Susan W. Arendt
- Iowa State University, 2320 Osborn Drive, Ames, IA 50011, USA
| | | | - Nancy Hall
- State Hygienic Laboratory, University of Iowa, Coralville, IA 52241, USA
| | - Steven Mandernach
- Association of Food and Drug Officials, 155 West Market St., York, PA 17401, USA
| | - Valerie Reeb
- State Hygienic Laboratory, University of Iowa, Coralville, IA 52241, USA
| | - Mark Speltz
- Iowa Dept. of Inspection and Appeals, 321 East 12th St., Des Moines, IA 50319, USA
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18
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Xiang Y, Li F, Dong N, Tian S, Zhang H, Du X, Zhou X, Xu X, Yang H, Xie J, Yang C, Liu H, Qiu S, Song H, Sun Y. Investigation of a Salmonellosis Outbreak Caused by Multidrug Resistant Salmonella Typhimurium in China. Front Microbiol 2020; 11:801. [PMID: 32411120 PMCID: PMC7200987 DOI: 10.3389/fmicb.2020.00801] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/03/2020] [Indexed: 01/05/2023] Open
Abstract
The rapid emergence of multidrug resistant Salmonella is a global public-health concern as outbreaks in recent years have mostly been caused by multidrug resistant strains. Here, we evaluated an outbreak in China caused by multidrug resistant Salmonella enterica serovar Typhimurium (S. Typhimurium) by employing an epidemiological and laboratory investigation using conventional methods and whole genome sequencing (WGS). Eleven of the 12 people who participated in a banquet showed gastrointestinal symptoms, and 8S. Typhimurium strains were recovered. Isolated outbreak strains showed multidrug resistance (MDR), and decreased susceptibility to ciprofloxacin, a first-line drug recommended by WHO for clinical treatment of intestinal infections. Antimicrobial resistance (AMR) gene analysis indicated that the MDR phenotype of these outbreak strains may be due to the presence of a number of AMR genes, including the blaOXA-1 and blaTEM-1 β-lactamase genes, which are often plasmid-borne and easily transferred. Further virulence gene analysis indicated that these outbreak strains also carried a large number of virulence genes, including 2 types of Salmonella pathogenicity islands (SPI-1 and SPI-2) and many adhesion-related virulence genes. Cluster analysis based on pulse-field gel electrophoresis data and phylogenetic analysis based on WGS revealed that the outbreak clone was closely related to and thus probably derived from local strains. This outbreak caused by multidrug resistant S. Typhimurium highlights the need for government improved strategies for the prevention and control of Salmonella infections.
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Affiliation(s)
- Ying Xiang
- Academy of Military Medical Sciences, Beijing, China.,Chinese PLA Center for Disease Control and Prevention, Beijing, China.,Center for Disease Control and Prevention of Southern Theatre Command, Guangzhou, China
| | - Fuxiang Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Nian Dong
- Xingcheng Special Service Recuperation Center of PLA Strategic Support Force, Huludao, China
| | - Sai Tian
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Haoran Zhang
- Academy of Military Medical Sciences, Beijing, China
| | - Xinying Du
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xuan Zhou
- Second Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Hongxia Yang
- Shanxi Province Center for Disease Control and Prevention, Taiyuan, China
| | - Jing Xie
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chaojie Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbo Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Shaofu Qiu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yansong Sun
- Academy of Military Medical Sciences, Beijing, China
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Yu H, Elbediwi M, Zhou X, Shuai H, Lou X, Wang H, Li Y, Yue M. Epidemiological and Genomic Characterization of Campylobacter jejuni Isolates from a Foodborne Outbreak at Hangzhou, China. Int J Mol Sci 2020; 21:E3001. [PMID: 32344510 PMCID: PMC7215453 DOI: 10.3390/ijms21083001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/18/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Foodborne outbreaks caused by Campylobacter jejuni have become a significant public health problem worldwide. Applying genomic sequencing as a routine part of foodborne outbreak investigation remains in its infancy in China. We applied both traditional PFGE profiling and genomic investigation to understand the cause of a foodborne outbreak in Hangzhou in December 2018. METHOD A total of 43 fecal samples, including 27 sick patients and 16 canteen employees from a high school in Hangzhou city in Zhejiang province, were recruited. Routine real-time fluorescent PCR assays were used for scanning the potential infectious agents, including viral pathogens (norovirus, rotavirus, adenovirus, and astrovirus), and bacterial pathogens (Salmonella, Shigella, Campylobacter jejuni, Vibrio parahaemolyticus and Vibrio cholerae). Bacterial selection medium was used to isolate and identify the positive bacteria identified by molecular test. Pulsed field gel electrophoresis (PFGE), and next generation sequencing (NGS) were applied to fifteen recovered C. jejuni isolates to further understand the case linkage of this particular outbreak. Additionally, we retrieved reference genomes from the NCBI database and performed a comparative genomics analysis with the examined genomes produced in this study. RESULTS The analyzed samples were found to be negative for the queried viruses. Additionally, Salmonella, Shigella, Vibrio parahaemolyticus and Vibrio cholera were not detected. Fifteen C. jejuni strains were identified by the real-time PCR assay and bacterial selection medium. These C. jejuni strains were classified into two genetic profiles defined by the PFGE. Out of fifteen C. jejuni strains, fourteen have a unified consistent genotype belonging to ST2988, and the other strain belongs to ST8149, with a 66.7% similarity in comparison with the rest of the strains. Moreover, all fifteen strains harbored blaOXA-61 and tet(O), in addition to a chromosomal mutation in gyrA (T86I). The examined fourteen strains of ST2988 from CC354 clone group have very minimal genetic difference (3~66 SNPs), demonstrated by the phylogenomic investigation. CONCLUSION Both genomic investigation and PFGE profiling confirmed that C. jejuni ST2988, a new derivative from CC354, was responsible for the foodborne outbreak Illustrated in this study.
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Affiliation(s)
- Hua Yu
- Hangzhou Center for Disease Control and Prevention, Hangzhou 310021, China; (H.Y.); (X.L.); (H.W.)
| | - Mohammed Elbediwi
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China; (M.E.); (Y.L.)
- Animal Health Research Institute, Agriculture Research Centre, Cairo 11865, Egypt
| | - Xiaohong Zhou
- Xiacheng Center for Disease Control and Prevention, Hangzhou 310003, China; (X.Z.); (H.S.)
| | - Huiqun Shuai
- Xiacheng Center for Disease Control and Prevention, Hangzhou 310003, China; (X.Z.); (H.S.)
| | - Xiuqin Lou
- Hangzhou Center for Disease Control and Prevention, Hangzhou 310021, China; (H.Y.); (X.L.); (H.W.)
| | - Haoqiu Wang
- Hangzhou Center for Disease Control and Prevention, Hangzhou 310021, China; (H.Y.); (X.L.); (H.W.)
| | - Yan Li
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China; (M.E.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
| | - Min Yue
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China; (M.E.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
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Alegbeleye OO, Sant’Ana AS. Pathogen subtyping tools for risk assessment and management of produce-borne outbreaks. Curr Opin Food Sci 2020. [DOI: 10.1016/j.cofs.2020.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Macori G, Bellio A, Bianchi DM, Chiesa F, Gallina S, Romano A, Zuccon F, Cabrera-Rubio R, Cauquil A, Merda D, Auvray F, Decastelli L. Genome-Wide Profiling of Enterotoxigenic Staphylococcus aureus Strains Used for the Production of Naturally Contaminated Cheeses. Genes (Basel) 2019; 11:E33. [PMID: 31892220 PMCID: PMC7016664 DOI: 10.3390/genes11010033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. More than 20 staphylococcal enterotoxins with emetic activity can be produced by specific strains responsible for staphylococcal food poisoning, one of the most common food-borne diseases. Whole genome sequencing provides a comprehensive view of the genome structure and gene content that have largely been applied in outbreak investigations and genomic comparisons. In this study, six enterotoxigenic S. aureus strains were characterised using a combination of molecular, phenotypical and computational methods. The genomes were analysed for the presence of virulence factors (VFs), where we identified 110 genes and classified them into five categories: adherence (n = 31), exoenzymes (n = 28), genes involved in host immune system evasion (n = 7); iron uptake regulatory system (n = 8); secretion machinery factors and toxins' genes (n = 36), and 39 genes coding for transcriptional regulators related to staphylococcal VFs. Each group of VFs revealed correlations among the six enterotoxigenic strains, and further analysis revealed their accessory genomic content, including mobile genetic elements. The plasmids pLUH02 and pSK67 were detected in the strain ProNaCC1 and ProNaCC7, respectively, carrying out the genes sed, ser, and selj. The genes carried out by prophages were detected in the strain ProNaCC2 (see), ProNaCC4, and ProNaCC7 (both positive for sea). The strain ProNaCC5 resulted positive for the genes seg, sei, sem, sen, seo grouped in an exotoxin gene cluster, and the strain ProNaCC6 resulted positive for seh, a transposon-associated gene. The six strains were used for the production of naturally contaminated cheeses which were tested with the European Screening Method for staphylococcal enterotoxins. The results obtained from the analysis of toxins produced in cheese, combined with the genomic features represent a portrait of the strains that can be used for the production of staphylococcal enterotoxin-positive cheese as reference material.
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Affiliation(s)
- Guerrino Macori
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Alberto Bellio
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Daniela Manila Bianchi
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Francesco Chiesa
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095 Grugliasco, Italy;
| | - Silvia Gallina
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Angelo Romano
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Fabio Zuccon
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996, Ireland-APC Microbiome Ireland, University College Cork, T12YT20 Cork, Ireland;
| | - Alexandra Cauquil
- European Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Laboratory for Food Safety, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France; (A.C.); (D.M.); (F.A.)
| | - Déborah Merda
- European Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Laboratory for Food Safety, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France; (A.C.); (D.M.); (F.A.)
| | - Fréderic Auvray
- European Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Laboratory for Food Safety, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France; (A.C.); (D.M.); (F.A.)
| | - Lucia Decastelli
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
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Status and potential of bacterial genomics for public health practice: a scoping review. Implement Sci 2019; 14:79. [PMID: 31409417 PMCID: PMC6692930 DOI: 10.1186/s13012-019-0930-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
Background Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist’s perspective. Methods In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. Results Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. Conclusions For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist’s perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance. Electronic supplementary material The online version of this article (10.1186/s13012-019-0930-2) contains supplementary material, which is available to authorized users.
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