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Pol S, Kallonen T, Mäklin T, Sar P, Hopkins J, Soeng S, Miliya T, Ling CL, Bentley SD, Corander J, Turner P. Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing. mBio 2024:e0078424. [PMID: 38682956 DOI: 10.1128/mbio.00784-24] [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: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
The nasopharynx is an important reservoir of disease-associated and antimicrobial-resistant bacterial species. This proof-of-concept study assessed the utility of a combined culture, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and targeted metagenomic sequencing workflow for the study of the pediatric nasopharyngeal bacterial microbiota. Nasopharyngeal swabs and clinical metadata were collected from Cambodian children during a hospital outpatient visit and then biweekly for 12 weeks. Swabs were cultured on chocolate and blood-gentamicin agar, and all colony morphotypes were identified by MALDI-TOF MS. Metagenomic sequencing was done on a scrape of all colonies from a chocolate agar culture and processed using the mSWEEP pipeline. One hundred one children were enrolled, yielding 620 swabs. MALDI-TOF MS identified 106 bacterial species/40 genera: 20 species accounted for 88.5% (2,190/2,474) of isolates. Colonization by Moraxella catarrhalis (92.1% of children on ≥1 swab), Haemophilus influenzae (87.1%), and Streptococcus pneumoniae (83.2%) was particularly common. In S. pneumoniae-colonized children, a median of two serotypes [inter-quartile range (IQR) 1-2, range 1-4] was detected. For the 21 bacterial species included in the mSWEEP database and identifiable by MALDI-TOF, detection by culture + MALDI-TOF MS and culture + mSWEEP was highly concordant with a median species-level agreement of 96.9% (IQR 86.8%-98.8%). mSWEEP revealed highly dynamic lineage-level colonization patterns for S. pneumoniae which were quite different to those for S. aureus. A combined culture, MALDI-TOF MS, targeted metagenomic sequencing approach for the exploration of the young child nasopharyngeal microbiome was technically feasible, and each component yielded complementary data. IMPORTANCE The human upper respiratory tract is an important source of disease-causing and antibiotic-resistant bacteria. However, understanding the interactions and stability of these bacterial populations is technically challenging. We used a combination of approaches to determine colonization patterns over a 3-month period in 101 Cambodian children. The combined approach was feasible to implement, and each component gave complementary data to enable a better understanding of the complex patterns of bacterial colonization.
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Affiliation(s)
- Sreymom Pol
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Tommi Mäklin
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Poda Sar
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Jill Hopkins
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Sona Soeng
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Clare L Ling
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | | | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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Arponen H, Vakkilainen S, Tomnikov N, Kallonen T, Silling S, Mäkitie O, Rautava J. Altered oral microbiome, but normal human papilloma virus prevalence in cartilage-hair hypoplasia patients. Orphanet J Rare Dis 2024; 19:169. [PMID: 38637854 PMCID: PMC11027548 DOI: 10.1186/s13023-024-03164-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/30/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Cartilage-hair hypoplasia (CHH) is a rare syndromic immunodeficiency with metaphyseal chondrodysplasia and increased risk of malignancy. In this cross-sectional observational study, we examined HPV status and oral microbiome in individuals with CHH. Oral brush samples were collected from 20 individuals with CHH (aged 5-59 years) and 41 controls (1-69 years). Alpha HPVs (43 types) were tested by nested PCR followed by bead-based probe hybridization. Separately, beta-, gamma-, mu- and nu- HPV types were investigated, and a genome-based bacterial microbiome sequencing was performed. RESULTS We found a similar alpha HPV prevalence in individuals with CHH (45%) and controls (36%). The HPV types of individuals with CHH were HPV-16 (25%), 27, 28, and 78, and of controls HPV-3, 16 (21%), 27, and 61. Beta HPV positivity and combined beta/gamma/mu/nu prevalence was detected in 11% and 11% of individuals with CHH and in 5% and 3% of the controls, respectively. Individuals with CHH differed from the controls in bacterial microbiota diversity, richness, and in microbial composition. Individuals with CHH had lower abundance of species Mitsuokella sp000469545, Parascardovia denticolens, Propionibacterium acidifaciens, UMGS1907 sp004151455, Salinicola halophilus, Haemophilus_A paraphrohaemolyticus, Fusobacterium massiliense, and Veillonella parvula, and higher abundance of Slackia exigua. CONCLUSIONS Individuals with CHH exhibit similar prevalence of HPV DNA but different bacterial microbiota on their oral mucosa compared to healthy controls. This may partly explain the previously observed high prevalence of oral diseases in CHH, and regular oral examination is warranted.
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Affiliation(s)
- Heidi Arponen
- Department of Oral and Maxillofacial Diseases, Helsinki University Hospital Head and Neck Center, University of Helsinki, Haartmaninkatu 1, Helsinki, Finland.
- Pediatric Research Center, Children's Hospital, University of Helsinki, Helsinki University Hospital, Helsinki, Finland.
- Western Uusimaa Wellbeing Services County, Espoo, Finland.
| | - Svetlana Vakkilainen
- Pediatric Research Center, Children's Hospital, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Natalie Tomnikov
- Institute of Biomedicine, University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Teemu Kallonen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Steffi Silling
- National Reference Centre for Papilloma- and Polyomaviruses, Institute of Virology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Outi Mäkitie
- Pediatric Research Center, Children's Hospital, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jaana Rautava
- Department of Oral and Maxillofacial Diseases, Helsinki University Hospital Head and Neck Center, University of Helsinki, Haartmaninkatu 1, Helsinki, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Pathology, HUSLAB Diagnostics, Helsinki, Finland
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Kalinen S, Kallonen T, Gunell M, Ettala O, Jambor I, Knaapila J, Syvänen KT, Taimen P, Poutanen M, Aronen HJ, Ollila H, Pietilä S, Elo LL, Lamminen T, Hakanen AJ, Munukka E, Boström PJ. Differences in Gut Microbiota Profiles and Microbiota Steroid Hormone Biosynthesis in Men with and Without Prostate Cancer. EUR UROL SUPPL 2024; 62:140-150. [PMID: 38500636 PMCID: PMC10946286 DOI: 10.1016/j.euros.2024.02.004] [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] [Accepted: 02/14/2024] [Indexed: 03/20/2024] Open
Abstract
Background Although prostate cancer (PCa) is the most common cancer in men in Western countries, there is significant variability in geographical incidence. This might result from genetic factors, discrepancies in screening policies, or differences in lifestyle. Gut microbiota has recently been associated with cancer progression, but its role in PCa is unclear. Objective Characterization of the gut microbiota and its functions associated with PCa. Design setting and participants In a prospective multicenter clinical trial (NCT02241122), the gut microbiota profiles of 181 men with a clinical suspicion of PCa were assessed utilizing 16S rRNA sequencing. Outcome measurements and statistical analysis Sequences were assigned to operational taxonomic units, differential abundance analysis, and α- and β-diversities, and predictive functional analyses were performed. Plasma steroid hormone levels corresponding to the predicted microbiota steroid hormone biosynthesis profiles were investigated. Results and limitations Of 364 patients, 181 were analyzed, 60% of whom were diagnosed with PCa. Microbiota composition and diversity were significantly different in PCa, partially affected by Prevotella 9, the most abundant genus of the cohort, and significantly higher in PCa patients. Predictive functional analyses revealed higher 5-α-reductase, copper absorption, and retinol metabolism in the PCa-associated microbiome. Plasma testosterone was associated negatively with the predicted microbial 5-α-reductase level. Conclusions Gut microbiota of the PCa patients differed significantly compared with benign individuals. Microbial 5-α-reductase, copper absorption, and retinol metabolism are potential mechanisms of action. These findings support the observed association of lifestyle, geography, and PCa incidence. Patient summary In this report, we found that several microbes and potential functions of the gut microbiota are altered in prostate cancer compared with benign cases. These findings suggest that gut microbiota could be the link between environmental factors and prostate cancer.
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Affiliation(s)
- Sofia Kalinen
- Research Center for Infections and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Clinical Microbiome Bank, Microbe Center, Turku University Hospital and University of Turku, Turku, Finland
| | - Marianne Gunell
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Clinical Microbiome Bank, Microbe Center, Turku University Hospital and University of Turku, Turku, Finland
| | - Otto Ettala
- Department of Urology, Turku University Hospital and University of Turku, Turku, Finland
| | - Ivan Jambor
- Department of Diagnostic Radiology, Turku University Hospital and University of Turku, Turku, Finland
- Enterprise Service Group - Radiology, Mass General Brigham, Boston, MA
| | - Juha Knaapila
- Department of Urology, Turku University Hospital and University of Turku, Turku, Finland
| | - Kari T. Syvänen
- Department of Urology, Turku University Hospital and University of Turku, Turku, Finland
| | - Pekka Taimen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Pathology, Turku University Hospital, Turku, Finland
| | - Matti Poutanen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hannu J. Aronen
- Department of Diagnostic Radiology, Turku University Hospital and University of Turku, Turku, Finland
| | - Helena Ollila
- Turku Clinical Research Centre, Turku University Hospital, Turku, Finland
| | - Sami Pietilä
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L. Elo
- Institute of Biomedicine, University of Turku, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Tarja Lamminen
- Department of Urology, Turku University Hospital and University of Turku, Turku, Finland
| | - Antti J. Hakanen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Clinical Microbiome Bank, Microbe Center, Turku University Hospital and University of Turku, Turku, Finland
| | - Eveliina Munukka
- Clinical Microbiome Bank, Microbe Center, Turku University Hospital and University of Turku, Turku, Finland
- Biocodex: Biocodex Nordics, Espoo, Finland
| | - Peter J. Boström
- Department of Urology, Turku University Hospital and University of Turku, Turku, Finland
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Pöntinen AK, Gladstone RA, Pesonen H, Pesonen M, Cléon F, Parcell BJ, Kallonen T, Simonsen GS, Croucher NJ, McNally A, Parkhill J, Johnsen PJ, Samuelsen Ø, Corander J. Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study. Lancet Microbe 2024; 5:e142-e150. [PMID: 38219757 DOI: 10.1016/s2666-5247(23)00292-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND The effect of antibiotic usage on the success of multidrug-resistant (MDR) clones in a population remains unclear. With this genomics-based molecular epidemiology study, we aimed to investigate the contribution of antibiotic use to Escherichia coli clone success, relative to intra-strain competition for colonisation and infection. METHODS We sequenced all the available E coli bloodstream infection isolates provided by the British Society for Antimicrobial Chemotherapy (BSAC) from 2012 to 2017 (n=718) and combined these with published data from the UK (2001-11; n=1090) and Norway (2002-17; n=3254). Defined daily dose (DDD) data from the European Centre for Disease Prevention and Control (retrieved on Sept 21, 2021) for major antibiotic classes (β-lactam, tetracycline, macrolide, sulfonamide, quinolone, and non-penicillin β-lactam) were used together with sequence typing, resistance profiling, regression analysis, and non-neutral Wright-Fisher simulation-based modelling to enable systematic comparison of resistance levels, clone success, and antibiotic usage between the UK and Norway. FINDINGS Sequence type (ST)73, ST131, ST95, and ST69 accounted for 892 (49·3%) of 1808 isolates in the BSAC collection. In the UK, the proportion of ST69 increased between 2001-10 and 2011-17 (p=0·0004), whereas the proportions of ST73 and ST95 did not vary between periods. ST131 expanded quickly after its emergence in 2003 and its prevalence remained consistent throughout the study period (apart from a brief decrease in 2009-10). The extended-spectrum β-lactamase (ESBL)-carrying, globally disseminated MDR clone ST131-C2 showed overall greater success in the UK (154 [56·8%] of 271 isolates in 2003-17) compared with Norway (51 [18·3%] of 278 isolates in 2002-17; p<0·0001). DDD data indicated higher total use of antimicrobials in the UK, driven mainly by the class of non-penicillin β-lactams, which were used between 2·7-times and 5·1-times more in the UK per annum (ratio mean 3·7 [SD 0·8]). This difference was associated with the higher success of the MDR clone ST131-C2 (pseudo-R2 69·1%). A non-neutral Wright-Fisher model replicated the observed expansion of non-MDR and MDR sequence types under higher DDD regimes. INTERPRETATION Our study indicates that resistance profiles of contemporaneously successful clones can vary substantially, warranting caution in the interpretation of correlations between aggregate measures of resistance and antibiotic usage. Our study further suggests that in countries with low-to-moderate use of antibiotics, such as the UK and Norway, the extent of non-penicillin β-lactam use modulates rather than determines the success of widely disseminated MDR ESBL-carrying E coli clones. Detailed understanding of underlying causal drivers of success is important for improved control of resistant pathogens. FUNDING Trond Mohn Foundation, Marie Skłodowska-Curie Actions, European Research Council, Royal Society, and Wellcome Trust.
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Affiliation(s)
- Anna K Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.
| | - Rebecca A Gladstone
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Henri Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maiju Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital Research Support Services, Oslo, Norway
| | - François Cléon
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Gunnar Skov Simonsen
- Research Group for Host-Microbe Interaction, 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
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Alan McNally
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK; Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
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Kero K, Hieta N, Kallonen T, Ahtikoski A, Laine HK, Rautava J, Munukka E. Optimal sampling and analysis methods for clinical diagnostics of vaginal microbiome. Eur J Clin Microbiol Infect Dis 2023; 42:201-208. [PMID: 36624297 PMCID: PMC9837015 DOI: 10.1007/s10096-022-04545-x] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023]
Abstract
Next-generation sequencing-based microbiological analysis is a complex way to profile vaginal microbiome samples since each step affects the results gained. Methodologies for sample collection lack golden standards. We compared Puritan DNA/RNA swab (PS) and Copan FLOQ swab (CS) and provided consistent and reliable microbiome profiles analyzed by 16S rRNA gene sequencing. We collected two consecutive vaginal samples utilizing PS with room temperature storing and CS with instant freezing from 26 women. Variable region 4 of bacterial 16S rRNA gene was amplified with single PCR by custom-designed dual-indexed primers and sequenced with Illumina MiSeq system. Read quality control, operational taxonomic unit tables, and alpha and beta diversities analysis were performed, and community richness, diversity, and evenness were evaluated and compared between the two samplings and tests. Nineteen sample pairs produced detectable, intact DNA during the extraction protocol and/or further microbial profiles. Alpha bacterial diversity indices were independent on the collection protocol. No significant statistical differences were found in the measured beta diversity metrics between the collection methods. Of the women, 43% had Lactobacillus-dominated vaginal microbiome profile despite of collection method. Previously reported important vaginal microbiome phyla Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria were present in the sample set although their relative abundances varied among individuals. PS and CS enable constant vaginal microbiota sampling. The PS method with no need for instant freezing is suitable for on-site collections at clinics. Furthermore, it seems to be possible to take two samples instead of one with constant microbiological results.
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Affiliation(s)
- Katja Kero
- Department of Obstetrics and Gynecology, Turku University Hospital, University of Turku, Turku, Finland
| | - Niina Hieta
- Department of Dermatology, Turku University Hospital, University of Turku, Turku, Finland
| | - Teemu Kallonen
- Research Center for Cancer, Infections and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, Microbiome Biobank, University of Turku, Turku, Finland
| | - Anne Ahtikoski
- Department of Pathology, Turku University Hospital, University of Turku, Turku, Finland
| | - Hanna K Laine
- Department of Oral Pathology and Oral Radiology, Institute of Dentistry, Faculty of Medicine, University of Turku, Turku, Finland.
- Department of Oral and Maxillofacial Diseases, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 1, 00290, ClinicumHelsinki, Finland.
| | - Jaana Rautava
- Department of Oral Pathology and Oral Radiology, Institute of Dentistry, Faculty of Medicine, University of Turku, Turku, Finland
- Department of Oral and Maxillofacial Diseases, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 1, 00290, ClinicumHelsinki, Finland
- Department of Pathology, Medicum, Faculty of Medicine, University of Helsinki and HUS Diagnostic Center, HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Eveliina Munukka
- Institute of Biomedicine, Microbiome Biobank, University of Turku, Turku, Finland
- Biocodex Nordics, Metsänneidonkuja 8, Espoo, Finland
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Vanhatalo S, Munukka E, Kallonen T, Sippola S, Grönroos J, Haijanen J, Hakanen AJ, Salminen P. Appendiceal microbiome in uncomplicated and complicated acute appendicitis: A prospective cohort study. PLoS One 2022; 17:e0276007. [PMID: 36240181 PMCID: PMC9565418 DOI: 10.1371/journal.pone.0276007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022] Open
Abstract
Background Uncomplicated and complicated acute appendicitis seem to be two different forms of this common abdominal emergency. The contribution of appendiceal microbiota to appendicitis pathogenesis has been suggested, but differences between uncomplicated and complicated appendicitis are largely unknown. We compared the appendiceal microbiota in uncomplicated and complicated acute appendicitis. Methods This prospective single-center clinical cohort study was conducted as part of larger multicenter MAPPAC trial enrolling adult patients with computed tomography or clinically confirmed uncomplicated or complicated acute appendicitis. The microbial composition of the appendiceal lumen was determined using 16S rRNA gene amplicon sequencing. Results Between April 11, 2017, and March 29, 2019, 118 samples (41 uncomplicated and 77 complicated appendicitis) were available. After adjusting for age, sex, and BMI, alpha diversity in complicated appendicitis was higher (Shannon p = 0.011, Chao1 p = 0.006) compared to uncomplicated appendicitis. Microbial compositions were different between uncomplicated and complicated appendicitis (Bray-Curtis distance, P = 0.002). Species poor appendiceal microbiota composition with specific predominant bacteria was present in some patients regardless of appendicitis severity. Conclusion Uncomplicated and complicated acute appendicitis have different appendiceal microbiome profiles further supporting the disconnection between these two different forms of acute appendicitis. Study registration ClinicalTrials.gov NCT03257423.
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Affiliation(s)
- Sanja Vanhatalo
- Research Center for Infections and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
- Laboratory Division, Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Eveliina Munukka
- Faculty of Medicine, Microbiome Biobank, University of Turku and Turku University Hospital, Turku, Finland
- Biocodex Nordics, Espoo, Finland
| | - Teemu Kallonen
- Research Center for Infections and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
- Laboratory Division, Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Faculty of Medicine, Microbiome Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Suvi Sippola
- Division of Digestive Surgery and Urology, Turku University Hospital, Turku, Finland
- Department of Surgery, University of Turku, Turku, Finland
| | - Juha Grönroos
- Division of Digestive Surgery and Urology, Turku University Hospital, Turku, Finland
- Department of Surgery, University of Turku, Turku, Finland
| | - Jussi Haijanen
- Division of Digestive Surgery and Urology, Turku University Hospital, Turku, Finland
- Department of Surgery, University of Turku, Turku, Finland
| | - Antti J. Hakanen
- Research Center for Infections and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
- Laboratory Division, Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Faculty of Medicine, Microbiome Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Paulina Salminen
- Division of Digestive Surgery and Urology, Turku University Hospital, Turku, Finland
- Department of Surgery, University of Turku, Turku, Finland
- * E-mail:
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Boström P, Kalinen S, Kallonen T, Gunell M, Jambor I, Taimen P, Poutanen M, Hakanen A, Munukka E. Gut microbiota signatures associate with prostate cancer risk. EUR UROL SUPPL 2022. [DOI: 10.1016/s2666-1683(22)00791-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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Hintikka JE, Munukka E, Valtonen M, Luoto R, Ihalainen JK, Kallonen T, Waris M, Heinonen OJ, Ruuskanen O, Pekkala S. Gut Microbiota and Serum Metabolome in Elite Cross-Country Skiers: A Controlled Study. Metabolites 2022; 12:metabo12040335. [PMID: 35448522 PMCID: PMC9028832 DOI: 10.3390/metabo12040335] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 12/11/2022] Open
Abstract
Exercise has been shown to affect gut the microbiome and metabolic health, with athletes typically displaying a higher microbial diversity. However, research on the gut microbiota and systemic metabolism in elite athletes remains scarce. In this study, we compared the gut microbiota profiles and serum metabolome of national team cross-country skiers at the end of an exhausting training and competitive season to those of normally physically-active controls. The gut microbiota were analyzed using 16S rRNA amplicon sequencing. Serum metabolites were analyzed using nuclear magnetic resonance. Phylogenetic diversity and the abundance of several mucin-degrading gut microbial taxa, including Akkermansia, were lower in the athletes. The athletes had a healthier serum lipid profile than the controls, which was only partly explained by body mass index. Butyricicoccus associated positively with HDL cholesterol, HDL2 cholesterol and HDL particle size. The Ruminococcus torques group was less abundant in the athlete group and positively associated with total cholesterol and VLDL and LDL particles. We found the healthier lipid profile of elite athletes to co-occur with known health-beneficial gut microbes. Further studies should elucidate these links and whether athletes are prone to mucin depletion related microbial changes during the competitive season.
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Affiliation(s)
- Jukka E. Hintikka
- Faculty of Sport and Health Sciences, University of Jyvaskyla, 40014 Jyväskylä, Finland; (J.K.I.); (S.P.)
- Correspondence:
| | - Eveliina Munukka
- Turku Microbiome Biobank, Institute of Biomedicine, University of Turku, 20500 Turku, Finland;
| | - Maarit Valtonen
- Research Institute for Olympic Sports, 40700 Jyväskylä, Finland;
| | - Raakel Luoto
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital, 20521 Turku, Finland; (R.L.); (O.R.)
| | - Johanna K. Ihalainen
- Faculty of Sport and Health Sciences, University of Jyvaskyla, 40014 Jyväskylä, Finland; (J.K.I.); (S.P.)
| | - Teemu Kallonen
- Clinical Microbiology, Turku University Hospital, 20521 Turku, Finland;
| | - Matti Waris
- Institute of Biomedicine, University of Turku, 20500 Turku, Finland;
| | - Olli J. Heinonen
- Paavo Nurmi Centre, Department of Health and Physical Activity, University of Turku, 20540 Turku, Finland;
| | - Olli Ruuskanen
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital, 20521 Turku, Finland; (R.L.); (O.R.)
| | - Satu Pekkala
- Faculty of Sport and Health Sciences, University of Jyvaskyla, 40014 Jyväskylä, Finland; (J.K.I.); (S.P.)
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9
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Wegner F, Roloff T, Huber M, Cordey S, Ramette A, Gerth Y, Bertelli C, Stange M, Seth-Smith HMB, Mari A, Leuzinger K, Cerutti L, Harshman K, Xenarios I, Le Mercier P, Bittel P, Neuenschwander S, Opota O, Fuchs J, Panning M, Michel C, Hallin M, Demuyser T, De Mendonca R, Savelkoul P, Dingemans J, van der Veer B, Boers SA, Claas ECJ, Coolen JPM, Melchers WJG, Gunell M, Kallonen T, Vuorinen T, Hakanen AJ, Bernhoff E, Hetland MAK, Golan Berman H, Adar S, Moran-Gilad J, Wolf DG, Leib SL, Nolte O, Kaiser L, Schmutz S, Kufner V, Zaheri M, Trkola A, Aamot HV, Hirsch HH, Greub G, Egli A. External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories. J Clin Microbiol 2022; 60:e0169821. [PMID: 34757834 PMCID: PMC8769736 DOI: 10.1128/jcm.01698-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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] [Received: 08/03/2021] [Accepted: 11/05/2021] [Indexed: 12/01/2022] Open
Abstract
This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.
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Affiliation(s)
- Fanny Wegner
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, University Hospital Geneva, Geneva, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Yannick Gerth
- Center for Laboratory Medicine, Saint Gall, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Madlen Stange
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Helena M. B. Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Alfredo Mari
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Karoline Leuzinger
- Clinical Virology, University Hospital Basel, Basel, Switzerland
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | | | | | | | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jonas Fuchs
- Institute of Virology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Marie Hallin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Paul Savelkoul
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jozef Dingemans
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
| | - Brian van der Veer
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
| | - Stefan A. Boers
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eric C. J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Marianne Gunell
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Tytti Vuorinen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Antti J. Hakanen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | | | - Hadar Golan Berman
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Jacob Moran-Gilad
- School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Dana G. Wolf
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
- Lautenberg Center for General and Tumor Immunology, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Oliver Nolte
- Center for Laboratory Medicine, Saint Gall, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, University Hospital Geneva, Geneva, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hege Vangstein Aamot
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology (EPIGEN), Akershus University Hospital and University of Oslo, Lørenskog, Norway
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Hans H. Hirsch
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University of Basel, Basel, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
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10
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Thorpe HA, Booton R, Kallonen T, Gibbon MJ, Couto N, Passet V, López-Fernández S, Rodrigues C, Matthews L, Mitchell S, Reeve R, David S, Merla C, Corbella M, Ferrari C, Comandatore F, Marone P, Brisse S, Sassera D, Corander J, Feil EJ. A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nat Microbiol 2022; 7:2054-2067. [PMID: 36411354 PMCID: PMC9712112 DOI: 10.1038/s41564-022-01263-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 07/19/2021] [Accepted: 10/10/2022] [Indexed: 11/22/2022]
Abstract
The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically and ecologically diverse. Many species are opportunistic pathogens and can harbour diverse classes of antimicrobial resistance genes. Healthcare-associated Klebsiella pneumoniae clones that are non-susceptible to carbapenems can spread rapidly, representing a high public health burden. Here we report an analysis of 3,482 genome sequences representing 15 Klebsiella species sampled over a 17-month period from a wide range of clinical, community, animal and environmental settings in and around the Italian city of Pavia. Northern Italy is a hotspot for hospital-acquired carbapenem non-susceptible Klebsiella and thus a pertinent setting to examine the overlap between isolates in clinical and non-clinical settings. We found no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside the clinical environment. Although we noted occasional transmission between clinical and non-clinical settings, our data point to a limited role of animal and environmental reservoirs in the human acquisition of Klebsiella spp. We also provide a detailed genus-wide view of genomic diversity and population structure, including the identification of new groups.
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Affiliation(s)
- Harry A. Thorpe
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Ross Booton
- grid.5337.20000 0004 1936 7603Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Teemu Kallonen
- grid.410552.70000 0004 0628 215XDepartment of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Marjorie J. Gibbon
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Natacha Couto
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Virginie Passet
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sebastián López-Fernández
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Carla Rodrigues
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Louise Matthews
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sonia Mitchell
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Richard Reeve
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sophia David
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Cristina Merla
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Marta Corbella
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Carolina Ferrari
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Francesco Comandatore
- grid.4708.b0000 0004 1757 2822Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences Luigi Sacco, Università di Milano, Milan, Italy
| | - Piero Marone
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Sylvain Brisse
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Davide Sassera
- grid.8982.b0000 0004 1762 5736Department of Biology and Biotechnology, Università di Pavia, Pavia, Italy
| | - Jukka Corander
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway ,grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.7737.40000 0004 0410 2071Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
| | - Edward J. Feil
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
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11
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Mäklin T, Kallonen T, Alanko J, Samuelsen Ø, Hegstad K, Mäkinen V, Corander J, Heinz E, Honkela A. Bacterial genomic epidemiology with mixed samples. Microb Genom 2021; 7:000691. [PMID: 34779765 PMCID: PMC8743562 DOI: 10.1099/mgen.0.000691] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 06/10/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstrate the effectiveness of our approach using closely related samples in a nosocomial setting, obtaining results that are comparable to those based on single-colony picks. Our results lend firm support to more widespread consideration of genomic epidemiology with mixed infection samples.
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Affiliation(s)
- Tommi Mäklin
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Jarno Alanko
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Pharmacy, UT The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UT The Arctic University of Norway, Tromsø, Norway
| | - Veli Mäkinen
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Eva Heinz
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Antti Honkela
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
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12
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Mäklin T, Kallonen T, David S, Boinett CJ, Pascoe B, Méric G, Aanensen DM, Feil EJ, Baker S, Parkhill J, Sheppard SK, Corander J, Honkela A. High-resolution sweep metagenomics using fast probabilistic inference. Wellcome Open Res 2021; 5:14. [PMID: 34746439 PMCID: PMC8543175 DOI: 10.12688/wellcomeopenres.15639.2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2021] [Indexed: 01/13/2023] Open
Abstract
Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.
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Affiliation(s)
- Tommi Mäklin
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Christine J. Boinett
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - David M. Aanensen
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Edward J. Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Jukka Corander
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Antti Honkela
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
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13
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Kantele A, Kuenzli E, Dunn SJ, Dance DAB, Newton PN, Davong V, Mero S, Pakkanen SH, Neumayr A, Hatz C, Snaith A, Kallonen T, Corander J, McNally A. Dynamics of intestinal multidrug-resistant bacteria colonisation contracted by visitors to a high-endemic setting: a prospective, daily, real-time sampling study. Lancet Microbe 2021; 2:e151-e158. [PMID: 33821248 PMCID: PMC8009952 DOI: 10.1016/s2666-5247(20)30224-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Antimicrobial resistance is highly prevalent in low-income and middle-income countries. International travel contributes substantially to the global spread of intestinal multidrug-resistant Gram-negative bacteria. Hundreds of millions of annual visitors to low-income and middle-income countries are all exposed to intestinal multidrug-resistant Gram-negative bacteria resulting in 30-70% of them being colonised at their return. The colonisation process in high-exposure environments is poorly documented because data have only been derived from before travel and after travel sampling. We characterised colonisation dynamics by exploring daily stool samples while visiting a low-income and middle-income countries. METHODS In this prospective, daily, real-time sampling study 20 European visitors to Laos volunteered to provide daily stool samples and completed daily questionnaires for 22 days. Samples were initially assessed at Mahosot Hospital, Vientiane, Laos, for acquisition of extended-spectrum β-lactamase-producing (ESBL) Gram-negative bacteria followed by whole-genome sequencing of isolates at MicrobesNG, University of Birmingham, Birmingham, UK. The primary outcome of the study was to obtain data on the dynamics of intestinal multidrug-resistant bacteria acquisition. FINDINGS Between Sept 18 and Sept 20, 2015, 23 volunteers were recruited, of whom 20 (87%) European volunteers were included in the final study population. Although colonisation rates were 70% at the end of the study, daily sampling revealed that all participants had acquired ESBL-producing Gram-negative bacteria at some point during the study period; the colonisation status varied day by day. Whole-genome sequencing analysis ascribed the transient pattern of colonisation to sequential acquisition of new strains, resulting in a loss of detectable colonisation by the initial multidrug-resistant Gram-negative strains. 19 (95%) participants acquired two to seven strains. Of the 83 unique strains identified (53 Escherichia coli, 10 Klebsiella spp, and 20 other ESBL-producing Gram-negative bacteria), some were shared by as many as four (20%) participants. INTERPRETATION To our knowledge, this is the first study to characterise in real-time the dynamics of acquiring multidrug-resistant Gram-negative bacterial colonisation during travel. Our data show multiple transient colonisation events indicative of constant microbial competition and suggest that travellers are exposed to a greater burden of multidrug-resistant bacteria than previously thought. The data emphasise the need for preventing travellers' diarrhoea and limiting antibiotic use, addressing the two major factors predisposing colonisation. FUNDING The Finnish Governmental Subsidy for Health Science Research, The Scandinavian Society for Antimicrobial Chemotherapy, the Sigrid Jusélius Foundation, Biotechnology and Biological Sciences Research Council; Wellcome Trust, Medical Research Council; The Royal Society; Joint Programming Initiative on Antimicrobial Resistance, and European Research Council.
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Affiliation(s)
- Anu Kantele
- Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Esther Kuenzli
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Department of Public and Global Health, Epidemiology, Biostatistic and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Steven J Dunn
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - David A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Rue Mahosot, Vientiane, Lao
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London UK
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Rue Mahosot, Vientiane, Lao
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London UK
| | - Viengmon Davong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Rue Mahosot, Vientiane, Lao
| | - Sointu Mero
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Sari H Pakkanen
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Andreas Neumayr
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Christoph Hatz
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Department of Infectious Diseases and Hospital Hygiene, Cantonal Hospital, St Gallen, Switzerland
- Department of Infectious Diseases and Hospital Hygiene, Cantonal Hospital, St Gallen, Switzerland
| | - Ann Snaith
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Teemu Kallonen
- Department of Biostatistics, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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14
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Batisti Biffignandi G, Gibbon MJ, Corbella M, Thorpe HA, Merla C, Castelli M, Kallonen T, Pegrum K, Brisse S, Corander J, Marone P, Feil EJ, Sassera D. Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae. G3 (Bethesda) 2021; 11:6130821. [PMID: 33615377 PMCID: PMC8022944 DOI: 10.1093/g3journal/jkab019] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 11/14/2022]
Abstract
During a citywide microbiological screening project in Pavia (Italy) a bacterial strain isolated from the surface of an Automated Teller Machine was classified as a Klebsiella sp. by MALDI-TOF spectrometry, and shown to be susceptible to the most antimicrobial classes by phenotypic testing. After Illumina genome sequencing and subsequent assembly, a high-quality draft genome was obtained (size = 5,051,593 bp, N50 = 615,571 bp, largest contig = 1,328,029 bp, N_contig = 17, GC content = 51.58%, coverage = 141.42), absence of antimicrobial resistance genes was confirmed, but the strain resulted to be highly divergent from all Klebsiella, and more related to other Enterobacteriaceae. The higher values of 16S rRNA identity were with members of the genera Citrobacter, Salmonella, and “Superficieibacter.” An ortholog-based phylogenomic analysis indicated a sister group relationship with “Superficieibacter electus,” in a distinct clade from other members of the Enterobacteriaceae family. In order to evaluate whether the novel genome represents a new species of “Superficiebacter,” average nucleotide identity (ANI) and Hadamard analysis were performed on a dataset of 78 Enterobacteriaceae. The novel genome showed an ANI of 87.51% with S. electus, which compared on identity values between other members of the family, clearly indicates that the genome represents a new species within the genus “Superficieibacter.” We propose for the new species the name “Superficieibacter maynardsmithii.”
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Affiliation(s)
| | - Marjorie J Gibbon
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA 27AY, UK
| | - Marta Corbella
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Harry A Thorpe
- Department of Biostatistics, University of Oslo, Oslo N-0317, Norway
| | - Cristina Merla
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy
| | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku 20521, Finland
| | - Katie Pegrum
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA 27AY, UK
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris 75015, France
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo N-0317, Norway.,Parasites & Microbes, Wellcome Sanger Institute, Hinxton CB10 1SA, UK.,Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Piero Marone
- UOC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA 27AY, UK
| | - Davide Sassera
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia 27100, Italy
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15
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Madar Johansson M, Bélurier E, Papageorgiou AC, Sundin AP, Rahkila J, Kallonen T, Nilsson UJ, Maatsola S, Nyholm TKM, Käpylä J, Corander J, Leino R, Finne J, Teneberg S, Haataja S. The binding mechanism of the virulence factor Streptococcus suis adhesin P subtype to globotetraosylceramide is associated with systemic disease. J Biol Chem 2020; 295:14305-14324. [PMID: 32796033 DOI: 10.1074/jbc.ra120.014818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 06/16/2020] [Revised: 08/11/2020] [Indexed: 11/06/2022] Open
Abstract
Streptococcus suis is part of the pig commensal microbiome but strains can also be pathogenic, causing pneumonia and meningitis in pigs as well as zoonotic meningitis. According to genomic analysis, S. suis is divided into asymptomatic carriage, respiratory and systemic strains with distinct genomic signatures. Because the strategies to target pathogenic S. suis are limited, new therapeutic approaches are needed. The virulence factor S. suis adhesin P (SadP) recognizes the galabiose Galα1-4Gal-oligosaccharide. Based on its oligosaccharide fine specificity, SadP can be divided into subtypes PN and PO We show here that subtype PN is distributed in the systemic strains causing meningitis, whereas type PO is found in asymptomatic carriage and respiratory strains. Both types of SadP are shown to predominantly bind to pig lung globotriaosylceramide (Gb3). However, SadP adhesin from systemic subtype PN strains also binds to globotetraosylceramide (Gb4). Mutagenesis studies of the galabiose-binding domain of type PN SadP adhesin showed that the amino acid asparagine 285, which is replaced by an aspartate residue in type PO SadP, was required for binding to Gb4 and, strikingly, was also required for interaction with the glycomimetic inhibitor phenylurea-galabiose. Molecular dynamics simulations provided insight into the role of Asn-285 for Gb4 and phenylurea-galabiose binding, suggesting additional hydrogen bonding to terminal GalNAc of Gb4 and the urea group. Thus, the Asn-285-mediated molecular mechanism of type PN SadP binding to Gb4 could be used to selectively target S. suis in systemic disease without interfering with commensal strains, opening up new avenues for interventional strategies against this pathogen.
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Affiliation(s)
- Miralda Madar Johansson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Eva Bélurier
- Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, Turku, Finland
| | | | - Anders P Sundin
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Lund, Sweden
| | - Jani Rahkila
- Instrument Centre, Åbo Akademi University, Turku, Finland
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Blindern, Norway.,Department of Clinical Microbiology, Turku University Hospital, Turku, Finland.,Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Lund, Sweden
| | - Santeri Maatsola
- Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, Turku, Finland
| | - Thomas K M Nyholm
- Biochemistry Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Jarmo Käpylä
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Blindern, Norway.,Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom.,Helsinki Institute for Information Technology (HIIT), Department of Mathematics and Statistics, University of Helsinki, Finland
| | - Reko Leino
- Laboratory of Molecular Science and Technology, Åbo Akademi University, Turku, Finland
| | - Jukka Finne
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Susann Teneberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Sauli Haataja
- Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, Turku, Finland
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16
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Mäklin T, Kallonen T, David S, Boinett CJ, Pascoe B, Méric G, Aanensen DM, Feil EJ, Baker S, Parkhill J, Sheppard SK, Corander J, Honkela A. High-resolution sweep metagenomics using fast probabilistic inference. Wellcome Open Res 2020; 5:14. [PMID: 34746439 PMCID: PMC8543175 DOI: 10.12688/wellcomeopenres.15639.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2020] [Indexed: 12/29/2022] Open
Abstract
Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.
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Affiliation(s)
- Tommi Mäklin
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Christine J. Boinett
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - David M. Aanensen
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Edward J. Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Jukka Corander
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Antti Honkela
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
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17
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Musicha P, Msefula CL, Mather AE, Chaguza C, Cain AK, Peno C, Kallonen T, Khonga M, Denis B, Gray KJ, Heyderman RS, Thomson NR, Everett DB, Feasey NA. Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. J Antimicrob Chemother 2019; 74:1223-1232. [PMID: 30778540 PMCID: PMC6477993 DOI: 10.1093/jac/dkz032] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/27/2018] [Accepted: 01/08/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES ESBL-producing Klebsiella pneumoniae (KPN) pose a major threat to human health globally. We carried out a WGS study to understand the genetic background of ESBL-producing KPN in Malawi and place them in the context of other global isolates. METHODS We sequenced genomes of 72 invasive and carriage KPN isolates collected from patients admitted to Queen Elizabeth Central Hospital, Blantyre, Malawi. We performed phylogenetic and population structure analyses on these and previously published genomes from Kenya (n = 66) and from outside sub-Saharan Africa (n = 67). We screened for presence of antimicrobial resistance (AMR) genetic determinants and carried out association analyses by genomic sequence cluster, AMR phenotype and time. RESULTS Malawian isolates fit within the global population structure of KPN, clustering into the major lineages of KpI, KpII and KpIII. KpI isolates from Malawi were more related to those from Kenya, with both collections exhibiting more clonality than isolates from the rest of the world. We identified multiple ESBL genes, including blaCTX-M-15, several blaSHV, blaTEM-63 and blaOXA-10, and other AMR genes, across diverse lineages of the KPN isolates from Malawi. No carbapenem resistance genes were detected; however, we detected IncFII and IncFIB plasmids that were similar to the carbapenem resistance-associated plasmid pNDM-mar. CONCLUSIONS There are multiple ESBL genes across diverse KPN lineages in Malawi and plasmids in circulation that are capable of carrying carbapenem resistance. Unless appropriate interventions are rapidly put in place, these may lead to a high burden of locally untreatable infection in vulnerable populations.
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Affiliation(s)
- Patrick Musicha
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Chrispin Chaguza
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Amy K Cain
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | | | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Katherine J Gray
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Robert S Heyderman
- Division of Infection and Immunity, University College London, London, UK
| | - Nicholas R Thomson
- Quadram Institute Bioscience, Norwich, UK
- London School of Tropical Medicine, London, UK
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- University of Edinburgh, Edinburgh, UK
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
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18
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Räisänen K, Koivula I, Ilmavirta H, Puranen S, Kallonen T, Lyytikäinen O, Jalava J. Emergence of ceftazidime-avibactam-resistant Klebsiella pneumoniae during treatment, Finland, December 2018. Euro Surveill 2019; 24:1900256. [PMID: 31088601 PMCID: PMC6518965 DOI: 10.2807/1560-7917.es.2019.24.19.1900256] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 05/07/2019] [Indexed: 11/20/2022] Open
Abstract
In December 2018, a ceftazidime-avibactam (CAZ-AVI)-resistant KPC-2-producing Klebsiella pneumoniae strain was isolated in Finland. CAZ-AVI resistance was observed 34 days after CAZ-AVI treatment in a trauma patient transferred from a hospital in Greece who had been colonised with blaKPC-2-producing K. pneumoniae ST39, and later developed a bloodstream infection. The CAZ-AVI-resistant strain contained a novel 15 amino acid insertion in the KPC-2 protein causing structural changes proximal to the KPC-2 active site.
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Affiliation(s)
- Kati Räisänen
- Department of Health Security, National Institute for Health and Welfare, Helsinki, Finland
| | - Irma Koivula
- Kuopio University Hospital, Unit of Infections and Hospital hygiene, Kuopio University Hospital, Kuopio, Finland
| | | | - Santeri Puranen
- Aalto University, Department of Computer Science, Espoo, Finland
| | - Teemu Kallonen
- Department of Health Security, National Institute for Health and Welfare, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Outi Lyytikäinen
- Department of Health Security, National Institute for Health and Welfare, Helsinki, Finland
| | - Jari Jalava
- Department of Health Security, National Institute for Health and Welfare, Helsinki, Finland
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19
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McNally A, Kallonen T, Connor C, Abudahab K, Aanensen DM, Horner C, Peacock SJ, Parkhill J, Croucher NJ, Corander J. Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection. mBio 2019; 10:e00644-19. [PMID: 31015329 PMCID: PMC6479005 DOI: 10.1128/mbio.00644-19] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 12/18/2022] Open
Abstract
Escherichia coli is a major cause of bloodstream and urinary tract infections globally. The wide dissemination of multidrug-resistant (MDR) strains of extraintestinal pathogenic E. coli (ExPEC) poses a rapidly increasing public health burden due to narrowed treatment options and increased risk of failure to clear an infection. Here, we present a detailed population genomic analysis of the ExPEC ST131 clone, in which we seek explanations for its success as an emerging pathogenic strain beyond the acquisition of antimicrobial resistance (AMR) genes. We show evidence for evolution toward separate ecological niches for the main clades of ST131 and differential evolution of anaerobic metabolism, key colonization, and virulence factors. We further demonstrate that negative frequency-dependent selection acting across accessory loci is a major mechanism that has shaped the population evolution of this pathogen.IMPORTANCE Infections with multidrug-resistant (MDR) strains of Escherichia coli are a significant global public health concern. To combat these pathogens, we need a deeper understanding of how they evolved from their background populations. By understanding the processes that underpin their emergence, we can design new strategies to limit evolution of new clones and combat existing clones. By combining population genomics with modelling approaches, we show that dominant MDR clones of E. coli are under the influence of negative frequency-dependent selection, preventing them from rising to fixation in a population. Furthermore, we show that this selection acts on genes involved in anaerobic metabolism, suggesting that this key trait, and the ability to colonize human intestinal tracts, is a key step in the evolution of MDR clones of E. coli.
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Affiliation(s)
- Alan McNally
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Teemu Kallonen
- Infection Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Christopher Connor
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Khalil Abudahab
- Infection Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - David M Aanensen
- Infection Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Carolyne Horner
- British Society of Antimicrobial Chemotherapy, Birmingham, United Kingdom
| | - Sharon J Peacock
- Infection Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Julian Parkhill
- Infection Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Nicholas J Croucher
- Faculty of Medicine, School of Public Health, Imperial College, London, United Kingdom
| | - Jukka Corander
- Infection Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
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20
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Heinz E, Mather A, Petty N, Kallonen T, Semmler T, Wieler L, Elias W, Regua-Mangia A, Corander J, Gomez T, Jenkins C, Frankel G, Thomson N. The genomic (re)definition of EPEC. Access Microbiol 2019. [DOI: 10.1099/acmi.ac2019.po0310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Eva Heinz
- 1Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- 2Wellcome Trust Sanger Centre, Hinxton, United Kingdom
| | - Alison Mather
- 2Wellcome Trust Sanger Centre, Hinxton, United Kingdom
- 3Quadrate Institute Bioscience, Norwich, United Kingdom
| | - Nicola Petty
- 5Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- 4University of Technology Sydney, Sydney, Australia
| | - Teemu Kallonen
- 5Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- 6University of Oslo, Oslo, Norway
| | | | | | | | - Adriana Regua-Mangia
- 9Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jukka Corander
- 5Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- 6University of Oslo, Oslo, Norway
| | - Tânia Gomez
- 10Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Gad Frankel
- 12Imperial College London, London, United Kingdom
| | - Nicholas Thomson
- 13London School of Hygiene and Tropical Medicine, London, United Kingdom
- 5Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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21
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Gröndahl-Yli-Hannuksela K, Lönnqvist E, Kallonen T, Lindholm L, Jalava J, Rantakokko-Jalava K, Vuopio J. The first human report of mobile colistin resistance gene, mcr-1, in Finland. APMIS 2018; 126:413-417. [PMID: 29696722 DOI: 10.1111/apm.12834] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 11/28/2017] [Accepted: 02/08/2018] [Indexed: 11/28/2022]
Abstract
Colistin resistance mediated by mobile mcr-1 gene has raised concern during the last years. After steep increase in mcr-1 reports, other mcr-gene variants (mcr-2 to mcr-5) have been revealed as well. In 2016, a clinical study was conducted on asymptomatic stool carriage of extended spectrum beta-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae among Finnish adults. All suspected ESBL producing bacterial isolates were first tested by phenotypic ESBL-confirmation methods, and then further analyzed with whole genome sequencing to identify the resistance genes. We found one study subject carrying a colistin resistant E. coli with a transferrable mcr-1 gene. This multi-drug resistant isolate, although initially suspected to be an ESBL producer, did not carry any ESBL genes, but was proven to carry several other resistance genes by using whole genome sequencing. Sequence type was ST93. The mcr-1 gene was connected to IncX4 plasmid which suggests that the colistin resistance gene locates in the respective plasmid. Here, we report the finding of a mcr-1 harboring human E. coli isolate from Finland. Clinical antimicrobial resistance (AMR) rates are low in Finland, and mobile colistin resistance has not been reported previously. This highlights the importance of AMR surveillance also in populations with low levels of resistance.
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Affiliation(s)
| | - Emilia Lönnqvist
- Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, Turku, Finland
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Laura Lindholm
- National Institute for Health and Welfare, Expert Microbiology Unit, Helsinki, Finland
| | - Jari Jalava
- National Institute for Health and Welfare, Infectious Disease Control and Vaccinations, Helsinki, Finland
| | | | - Jaana Vuopio
- Institute of Biomedicine, Research Center for Cancer, Infections and Immunity, University of Turku, Turku, Finland
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22
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Musicha P, Feasey NA, Cain AK, Kallonen T, Chaguza C, Peno C, Khonga M, Thompson S, Gray KJ, Mather AE, Heyderman RS, Everett DB, Thomson NR, Msefula CL. Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting. J Antimicrob Chemother 2017; 72:1602-1609. [PMID: 28333330 PMCID: PMC5437524 DOI: 10.1093/jac/dkx058] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 08/30/2016] [Accepted: 02/01/2017] [Indexed: 12/24/2022] Open
Abstract
Objectives Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi. Methods Ninety-four E. coli isolates from patients admitted to Queen's Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics. Results Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was bla CTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates]. Conclusions This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance.
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Affiliation(s)
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Amy K Cain
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Teemu Kallonen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Chrispin Chaguza
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Margaret Khonga
- Microbiology Unit, Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Sarah Thompson
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Katherine J Gray
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Alison E Mather
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Division of Infection and Immunity, University College London, London, UK
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.,Microbiology Unit, Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
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Runcharoen C, Raven KE, Reuter S, Kallonen T, Paksanont S, Thammachote J, Anun S, Blane B, Parkhill J, Peacock SJ, Chantratita N. Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand. Genome Med 2017; 9:81. [PMID: 28877757 PMCID: PMC5588602 DOI: 10.1186/s13073-017-0471-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [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: 04/13/2017] [Accepted: 08/22/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas. METHODS We conducted a survey of extended β-lactamase (ESBL)-producing E. coli isolated from patients, canals and livestock wastewater in eastern Thailand between 2014 and 2015, and analyzed isolates using whole genome sequencing. RESULTS The bacterial collection of 149 isolates consisted of 84 isolates from a single hospital and 65 from the hospital sewer, canals and farm wastewater within a 20 km radius. E. coli ST131 predominated the clinical collection (28.6%), but was uncommon in the environment. Genome-based comparison of E. coli from infected patients and their immediate environment indicated low genetic similarity overall between the two, although three clinical-environmental isolate pairs differed by ≤ 5 single nucleotide polymorphisms. Thai E. coli isolates were dispersed throughout a phylogenetic tree containing a global E. coli collection. All Thai ESBL-positive E. coli isolates were multidrug resistant, including high rates of resistance to tobramycin (77.2%), gentamicin (77.2%), ciprofloxacin (67.8%) and trimethoprim (68.5%). ESBL was encoded by six different CTX-M elements and SHV-12. Three isolates from clinical samples (n = 2) or a hospital sewer (n = 1) were resistant to the carbapenem drugs (encoded by NDM-1, NDM-5 or GES-5), and three isolates (clinical (n = 1) and canal water (n = 2)) were resistant to colistin (encoded by mcr-1); no isolates were resistant to both carbapenems and colistin. CONCLUSIONS Tackling ESBL-producing E. coli in this setting will be challenging based on widespread distribution, but the low prevalence of resistance to carbapenems and colistin suggests that efforts are now required to prevent these from becoming ubiquitous.
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Affiliation(s)
- Chakkaphan Runcharoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand
| | - Kathy E Raven
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Sandra Reuter
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Teemu Kallonen
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Suporn Paksanont
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand
| | - Jeeranan Thammachote
- Division of Clinical Microbiology, Medical Technology Department, Bhuddhasothon Hospital, Chachoengsao, 24000, Thailand
| | - Suthatip Anun
- Division of Clinical Microbiology, Medical Technology Department, Bhuddhasothon Hospital, Chachoengsao, 24000, Thailand
| | - Beth Blane
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sharon J Peacock
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand.,Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand.
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24
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Brodrick HJ, Raven KE, Kallonen T, Jamrozy D, Blane B, Brown NM, Martin V, Török ME, Parkhill J, Peacock SJ. Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom. Genome Med 2017; 9:70. [PMID: 28738847 PMCID: PMC5525225 DOI: 10.1186/s13073-017-0457-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Residents of long-term care facilities (LTCF) may have high carriage rates of multidrug-resistant pathogens, but are not currently included in surveillance programmes for antimicrobial resistance or healthcare-associated infections. Here, we describe the value derived from a longitudinal epidemiological and genomic surveillance study of drug-resistant Escherichia coli in a LTCF in the United Kingdom (UK). METHODS Forty-five of 90 (50%) residents were recruited and followed for six months in 2014. Participants were screened weekly for carriage of extended-spectrum beta-lactamase (ESBL) producing E. coli. Participants positive for ESBL E. coli were also screened for ESBL-negative E. coli. Phenotypic antibiotic susceptibility of E. coli was determined using the Vitek2 instrument and isolates were sequenced on an Illumina HiSeq2000 instrument. Information was collected on episodes of clinical infection and antibiotic consumption. RESULTS Seventeen of 45 participants (38%) carried ESBL E. coli. Twenty-three of the 45 participants (51%) had 63 documented episodes of clinical infection treated with antibiotics. Treatment with antibiotics was associated with higher risk of carrying ESBL E. coli. ESBL E. coli was mainly sequence type (ST)131 (16/17, 94%). Non-ESBL E. coli from these 17 cases was more genetically diverse, but ST131 was found in eight (47%) cases. Whole-genome analysis of 297 ST131 E. coli from the 17 cases demonstrated highly related strains from six participants, indicating acquisition from a common source or person-to-person transmission. Five participants carried highly related strains of both ESBL-positive and ESBL-negative ST131. Genome-based comparison of ST131 isolates from the LTCF study participants with ST131 associated with bloodstream infection at a nearby acute hospital and in hospitals across England revealed sharing of highly related lineages between the LTCF and a local hospital. CONCLUSIONS This study demonstrates the power of genomic surveillance to detect multidrug-resistant pathogens and confirm their connectivity within a healthcare network.
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Affiliation(s)
- Hayley J. Brodrick
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Kathy E. Raven
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Teemu Kallonen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Dorota Jamrozy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Nicholas M. Brown
- Cambridge Public Health England Microbiology and Public Health Laboratory, Box 236, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- British Society for Antimicrobial Chemotherapy, 53 Regent Place, Birmingham, B1 3NJ UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ UK
| | - Veronique Martin
- British Society for Antimicrobial Chemotherapy, 53 Regent Place, Birmingham, B1 3NJ UK
- Department of Medical Microbiology, Pathology Sciences Building 1, Southmead Hospital, Bristol, BS10 5NB UK
| | - M. Estée Török
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Cambridge Public Health England Microbiology and Public Health Laboratory, Box 236, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ UK
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
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25
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Kallonen T, Brodrick HJ, Harris SR, Corander J, Brown NM, Martin V, Peacock SJ, Parkhill J. Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131. Genome Res 2017; 27:gr.216606.116. [PMID: 28720578 PMCID: PMC5538559 DOI: 10.1101/gr.216606.116] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [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: 10/11/2016] [Accepted: 06/07/2017] [Indexed: 12/19/2022]
Abstract
Escherichia coli associated with urinary tract infections and bacteremia has been intensively investigated, including recent work focusing on the virulent, globally disseminated, multidrug-resistant lineage ST131. To contextualize ST131 within the broader E. coli population associated with disease, we used genomics to analyze a systematic 11-yr hospital-based survey of E. coli associated with bacteremia using isolates collected from across England by the British Society for Antimicrobial Chemotherapy and from the Cambridge University Hospitals NHS Foundation Trust. Population dynamics analysis of the most successful lineages identified the emergence of ST131 and ST69 and their establishment as two of the five most common lineages along with ST73, ST95, and ST12. The most frequently identified lineage was ST73. Compared to ST131, ST73 was susceptible to most antibiotics, indicating that multidrug resistance was not the dominant reason for prevalence of E. coli lineages in this population. Temporal phylogenetic analysis of the emergence of ST69 and ST131 identified differences in the dynamics of emergence and showed that expansion of ST131 in this population was not driven by sequential emergence of increasingly resistant subclades. We showed that over time, the E. coli population was only transiently disturbed by the introduction of new lineages before a new equilibrium was rapidly achieved. Together, these findings suggest that the frequency of E. coli lineages in invasive disease is driven by negative frequency-dependent selection occurring outside of the hospital, most probably in the commensal niche, and that drug resistance is not a primary determinant of success in this niche.
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Affiliation(s)
- Teemu Kallonen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Hayley J Brodrick
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Simon R Harris
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jukka Corander
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
- Department of Biostatistics, University of Oslo, 0372 Oslo, Norway
| | - Nicholas M Brown
- Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom
| | - Veronique Martin
- British Society of Antimicrobial Chemotherapy, Birmingham B1 3NJ, United Kingdom
| | - Sharon J Peacock
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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26
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Budzyńska PM, Kyläniemi MK, Kallonen T, Soikkeli AI, Nera KP, Lassila O, Alinikula J. Bach2 regulates AID-mediated immunoglobulin gene conversion and somatic hypermutation in DT40 B cells. Eur J Immunol 2017; 47:993-1001. [DOI: 10.1002/eji.201646895] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/09/2017] [Accepted: 03/13/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Paulina M Budzyńska
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
- Turku Doctoral Programme of Biomedical Sciences and Turku Doctoral Programme of Molecular Medicine; University of Turku; Turku Finland
| | - Minna K Kyläniemi
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Teemu Kallonen
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Anni I Soikkeli
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Kalle-Pekka Nera
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Olli Lassila
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
- Departament of Medical Microbiology and Immunology; Turku University Hospital; Turku Finland
| | - Jukka Alinikula
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
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27
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Xu Y, Liu B, Gröndahl-Yli-Hannuksila K, Tan Y, Feng L, Kallonen T, Wang L, Peng D, He Q, Wang L, Zhang S. Whole-genome sequencing reveals the effect of vaccination on the evolution of Bordetella pertussis. Sci Rep 2015; 5:12888. [PMID: 26283022 PMCID: PMC4539551 DOI: 10.1038/srep12888] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [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: 04/02/2015] [Accepted: 07/10/2015] [Indexed: 12/11/2022] Open
Abstract
Herd immunity can potentially induce a change of circulating viruses. However, it remains largely unknown that how bacterial pathogens adapt to vaccination. In this study, Bordetella pertussis, the causative agent of whooping cough, was selected as an example to explore possible effect of vaccination on the bacterial pathogen. We sequenced and analysed the complete genomes of 40 B. pertussis strains from Finland and China, as well as 11 previously sequenced strains from the Netherlands, where different vaccination strategies have been used over the past 50 years. The results showed that the molecular clock moved at different rates in these countries and in distinct periods, which suggested that evolution of the B. pertussis population was closely associated with the country vaccination coverage. Comparative whole-genome analyses indicated that evolution in this human-restricted pathogen was mainly characterised by ongoing genetic shift and gene loss. Furthermore, 116 SNPs were specifically detected in currently circulating ptxP3-containing strains. The finding might explain the successful emergence of this lineage and its spread worldwide. Collectively, our results suggest that the immune pressure of vaccination is one major driving force for the evolution of B. pertussis, which facilitates further exploration of the pathogenicity of B. pertussis.
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Affiliation(s)
- Yinghua Xu
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
| | - Bin Liu
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China
| | | | - Yajun Tan
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
| | - Lu Feng
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China
| | - Teemu Kallonen
- Department of Medical Microbiology and Immunology, Turku University, Turku 20520, Finland
| | - Lichan Wang
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
| | - Ding Peng
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China
| | - Qiushui He
- 1] Department of Medical Microbiology and Immunology, Turku University, Turku 20520, Finland [2] Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku 20520, Finland [3] Department of Medical Microbiology, Capital Medical University, Beijing 100069, P. R. China
| | - Lei Wang
- 1] TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, P.R. China [2] Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, Tianjin 300457, P. R. China [3] State Key Laboratory of Medicinal Chemical Biology, Nankai University 300457, Tianjin, P. R. China
| | - Shumin Zhang
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes of Food and Drug Control, Beijing 100050, P. R. China
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29
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Tahvanainen J, Kyläniemi MK, Kanduri K, Gupta B, Lähteenmäki H, Kallonen T, Rajavuori A, Rasool O, Koskinen PJ, Rao KVS, Lähdesmäki H, Lahesmaa R. Proviral integration site for Moloney murine leukemia virus (PIM) kinases promote human T helper 1 cell differentiation. J Biol Chem 2012; 288:3048-58. [PMID: 23209281 PMCID: PMC3561529 DOI: 10.1074/jbc.m112.361709] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [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] [Indexed: 01/15/2023] Open
Abstract
The differentiation of human primary T helper 1 (Th1) cells from naïve precursor cells is regulated by a complex, interrelated signaling network. The identification of factors regulating the early steps of Th1 cell polarization can provide important insight in the development of therapeutics for many inflammatory and autoimmune diseases. The serine/threonine-specific proviral integration site for Moloney murine leukemia virus (PIM) kinases PIM1 and PIM2 have been implicated in the cytokine-dependent proliferation and survival of lymphocytes. We have established that the third member of this family, PIM3, is also expressed in human primary Th cells and identified a new function for the entire PIM kinase family in T lymphocytes. Although PIM kinases are expressed more in Th1 than Th2 cells, we demonstrate here that these kinases positively influence Th1 cell differentiation. Our RNA interference results from human primary Th cells also suggest that PIM kinases promote the production of IFNγ, the hallmark cytokine produced by Th1 cells. Consistent with this, they also seem to be important for the up-regulation of the critical Th1-driving factor, T box expressed in T cells (T-BET), and the IL-12/STAT4 signaling pathway during the early Th1 differentiation process. In summary, we have identified PIM kinases as new regulators of human primary Th1 cell differentiation, thus providing new insights into the mechanisms controlling the selective development of human Th cell subsets.
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Affiliation(s)
- Johanna Tahvanainen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi, 20520 Turku, Finland
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Barkoff AM, Gröndahl-Yli-Hannuksela K, Vuononvirta J, Mertsola J, Kallonen T, He Q. Differences in avidity of IgG antibodies to pertussis toxin after acellular pertussis booster vaccination and natural infection. Vaccine 2012; 30:6897-902. [DOI: 10.1016/j.vaccine.2012.09.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 08/14/2012] [Accepted: 09/02/2012] [Indexed: 11/26/2022]
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Kallonen T, Mertsola J, Mooi F, He Q. Rapid detection of the recently emerged Bordetella pertussis strains with the ptxP3 pertussis toxin promoter allele by real-time PCR. Clin Microbiol Infect 2012; 18:E377-9. [DOI: 10.1111/j.1469-0691.2012.04000.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Bokhari H, Said F, Syed MA, Mughal A, Kazi YF, Kallonen T, He Q, King AJ, Heuvelman K, Mooi FR. Molecular typing ofBordetella parapertussisisolates circulating in Pakistan. ACTA ACUST UNITED AC 2011; 63:373-80. [DOI: 10.1111/j.1574-695x.2011.00861.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 08/10/2011] [Accepted: 08/15/2011] [Indexed: 11/28/2022]
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33
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van Gent M, Bart MJ, van der Heide HGJ, Heuvelman KJ, Kallonen T, He Q, Mertsola J, Advani A, Hallander HO, Janssens K, Hermans PW, Mooi FR. SNP-based typing: a useful tool to study Bordetella pertussis populations. PLoS One 2011; 6:e20340. [PMID: 21647370 PMCID: PMC3103551 DOI: 10.1371/journal.pone.0020340] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 04/29/2011] [Indexed: 11/19/2022] Open
Abstract
To monitor changes in Bordetella pertussis populations, mainly two typing methods are used; Pulsed-Field Gel Electrophoresis (PFGE) and Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA). In this study, a single nucleotide polymorphism (SNP) typing method, based on 87 SNPs, was developed and compared with PFGE and MLVA. The discriminatory indices of SNP typing, PFGE and MLVA were found to be 0.85, 0.95 and 0.83, respectively. Phylogenetic analysis, using SNP typing as Gold Standard, revealed false homoplasies in the PFGE and MLVA trees. Further, in contrast to the SNP-based tree, the PFGE- and MLVA-based trees did not reveal a positive correlation between root-to-tip distance and the isolation year of strains. Thus PFGE and MLVA do not allow an estimation of the relative age of the selected strains. In conclusion, SNP typing was found to be phylogenetically more informative than PFGE and more discriminative than MLVA. Further, in contrast to PFGE, it is readily standardized allowing interlaboratory comparisons. We applied SNP typing to study strains with a novel allele for the pertussis toxin promoter, ptxP3, which have a worldwide distribution and which have replaced the resident ptxP1 strains in the last 20 years. Previously, we showed that ptxP3 strains showed increased pertussis toxin expression and that their emergence was associated with increased notification in the Netherlands. SNP typing showed that the ptxP3 strains isolated in the Americas, Asia, Australia and Europe formed a monophyletic branch which recently diverged from ptxP1 strains. Two predominant ptxP3 SNP types were identified which spread worldwide. The widespread use of SNP typing will enhance our understanding of the evolution and global epidemiology of B. pertussis.
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Affiliation(s)
- Marjolein van Gent
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marieke J. Bart
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Han G. J. van der Heide
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Kees J. Heuvelman
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Teemu Kallonen
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku, Finland
- Turku Graduate School for Biomedical Sciences, University of Turku, Turku, Finland
| | - Qiushui He
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku, Finland
| | - Jussi Mertsola
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku, Finland
| | - Abdolreza Advani
- Department of Bacteriology, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Hans O. Hallander
- Department of Bacteriology, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | | | - Peter W. Hermans
- Laboratory of Pediatric Infectious Diseases, Radboud University Nijmegen Medical Center, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Frits R. Mooi
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- * E-mail:
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Zhang L, Xu Y, Zhao J, Kallonen T, Cui S, Xu Y, Hou Q, Li F, Wang J, He Q, Zhang S. Effect of vaccination on Bordetella pertussis strains, China. Emerg Infect Dis 2011; 16:1695-701. [PMID: 21029526 PMCID: PMC3294513 DOI: 10.3201/eid1611.100401] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [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] [Indexed: 12/01/2022] Open
Abstract
Strains in China may differ from those in countries that have long histories of high vaccination coverage. Whole-cell pertussis vaccine was introduced in China in the early 1960s. We used standard typing methods to compare 96 Bordetella pertussis isolates collected before and after introduction of vaccination, during 1953–2005. The following vaccine-type alleles of the pertussis toxin (ptx) gene were characteristic for all prevaccination strains: ptxA2, ptxA3, and ptxA4. The shift to ptxA1 occurred since 1963. All isolates collected since 1983 contained ptxA1. Pertactin (prn) allele 1, prn1, was predominant, although prn2 and prn3 have been detected since 2000. Serotypes fimbriae (Fim) 2 and Fim2,3 were found in all isolates collected before 1986. During 1997–2005, Fim3 became prevalent. Although changes in electrophoresis profiles over time were observed, the predominant profiles during 1997–2005 resembled those during the prevaccine era and those found in Europe before the 1990s. B. pertussis strains in China may differ from those in countries that have a long history of high vaccine coverage.
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Affiliation(s)
- Liu Zhang
- National Institute for the Control of Pharmaceutical and Biological Products, Beijing, People's Republic of China
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Dakic G, Kallonen T, Elomaa A, Pljesa T, Vignjevic-Krastavcevic M, He Q. Bordetella pertussis vaccine strains and circulating isolates in Serbia. Vaccine 2009; 28:1188-92. [PMID: 19945417 DOI: 10.1016/j.vaccine.2009.11.036] [Citation(s) in RCA: 7] [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: 09/01/2009] [Revised: 11/11/2009] [Accepted: 11/11/2009] [Indexed: 11/16/2022]
Abstract
In Serbia, whole cell pertussis vaccine was introduced in 1957. Current composition of the vaccine has been used since 1985 and contains four autochthonous strains of Bordetella pertussis isolated from 1957 to 1984. To monitor changes in bacterial population, 70 isolates collected from 1953 to 2000 were studied together with the vaccine strains. The methods included serotyping of fimbriae (Fim), genotyping of pertactin (prn) and pertussis toxin S1 subunit (ptxA), and pulsed-field gel electrophoresis analysis. Shift from ptxA2 to ptxA1 has been observed in isolates since the late of 1960s. All isolates from 1980 to 1984 harbored ptxA1. Re-appearance of the ptxA2 allele followed an addition of the two strains harboring ptxA1 in the vaccine in 1985. The allele prn1 was predominant among the Serbian isolates, though prn3 and prn11 have been detected since 1981 and 1984. The allele prn2 was found only in two strains isolated in 2000. Serotype Fim2.3 disappeared before 1980 and serotype Fim2 became predominant since then. The Serbian vaccine strains showed differences in ptxA and prn. The results of this present study indicate that the B. pertussis population in Serbia is different from other vaccinated populations and that this difference may be related to the vaccine used.
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Affiliation(s)
- Gordana Dakic
- Institute of Virology, Vaccine and Sera Torlak, Belgrade, Serbia
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Heikkinen E, Kallonen T, Saarinen L, Sara R, King AJ, Mooi FR, Soini JT, Mertsola J, He Q. Comparative genomics of Bordetella pertussis reveals progressive gene loss in Finnish strains. PLoS One 2007; 2:e904. [PMID: 17878939 PMCID: PMC1975675 DOI: 10.1371/journal.pone.0000904] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Accepted: 08/23/2007] [Indexed: 11/18/2022] Open
Abstract
Background Bordetella pertussis is a Gram-negative bacterium that infects the human respiratory tract and causes pertussis or whooping cough. The disease has resurged in many countries including Finland where the whole-cell pertussis vaccine has been used for more than 50 years. Antigenic divergence has been observed between vaccine strains and clinical isolates in Finland. To better understand genome evolution in B. pertussis circulating in the immunized population, we developed an oligonucleotide-based microarray for comparative genomic analysis of Finnish strains isolated during the period of 50 years. Methodology/Principal Findings The microarray consisted of 3,582 oligonucleotides (70-mer) and covered 94% of 3,816 ORFs of Tohama I, the strain of which the genome has been sequenced [1]. Twenty isolates from 1953 to 2004 were studied together with two Finnish vaccine strains and two international reference strains. The isolates were selected according to their characteristics, e.g. the year and place of isolation and pulsed-field gel electrophoresis profiles. Genomic DNA of the tested strains, along with reference DNA of Tohama I strain, was labelled and hybridized. The absence of genes as established with microarrays, was confirmed by PCR. Compared with the Tohama I strain, Finnish isolates lost 7 (8.6 kb) to 49 (55.3 kb) genes, clustered in one to four distinct loci. The number of lost genes increased with time, and one third of lost genes had functions related to inorganic ion transport and metabolism, or energy production and conversion. All four loci of lost genes were flanked by the insertion sequence element IS481. Conclusion/Significance Our results showed that the progressive gene loss occurred in Finnish B. pertussis strains isolated during a period of 50 years and confirmed that B. pertussis is dynamic and is continuously evolving, suggesting that the bacterium may use gene loss as one strategy to adapt to highly immunized populations.
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Affiliation(s)
- Eriikka Heikkinen
- Pertussis Reference Laboratory, National Public Health Institute, Turku, Finland
| | - Teemu Kallonen
- Pertussis Reference Laboratory, National Public Health Institute, Turku, Finland
- Turku Graduate School of Biomedical Sciences, University of Turku, Turku, Finland
| | - Lilli Saarinen
- Finnish DNA Microarray Centre, Turku Centre for Biotechnology, University of Turku, Åbo Akademi University, Turku, Finland
| | - Rolf Sara
- Finnish DNA Microarray Centre, Turku Centre for Biotechnology, University of Turku, Åbo Akademi University, Turku, Finland
| | - Audrey J. King
- Laboratory for Infectious Diseases and Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Frits R. Mooi
- Laboratory for Infectious Diseases and Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Juhani T. Soini
- Finnish DNA Microarray Centre, Turku Centre for Biotechnology, University of Turku, Åbo Akademi University, Turku, Finland
| | - Jussi Mertsola
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Qiushui He
- Pertussis Reference Laboratory, National Public Health Institute, Turku, Finland
- * To whom correspondence should be addressed. E-mail:
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Tahvanainen J, Pykäläinen M, Kallonen T, Lähteenmäki H, Rasool O, Lahesmaa R. Enrichment of nucleofected primary human CD4+ T cells: a novel and efficient method for studying gene function and role in human primary T helper cell differentiation. J Immunol Methods 2006; 310:30-9. [PMID: 16516225 DOI: 10.1016/j.jim.2005.11.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Revised: 11/29/2005] [Accepted: 11/30/2005] [Indexed: 02/04/2023]
Abstract
Identification of key factors mediating the differentiation of naïve CD4(+) T helper cells into Th1 and Th2 subsets is important for understanding the molecular mechanisms of the development of autoimmune diseases as well as asthma and allergy. Functional importance of a given gene in the initiation of human T helper cell differentiation has been hard to study due to the difficulty in transfecting primary resting human T lymphocytes. In this study we have successfully transfected human primary CD4(+) T helper cells using Amaxa's Nucleofection technology. To overcome the background caused by untransfected cells, we have developed a system for enriching nucleofected unstimulated human primary T helper cells that express the gene of interest. This is achieved by introducing a plasmid construct containing a bicistronic unit coding for a truncated mouse MHC class l H-2K(k) cell surface marker followed by selection of H-2K(k) positive cells using antibody coated beads. We demonstrate that the nucleofected and enriched H-2K(k) positive T helper cells differentiate into Th1 and Th2 cells as well as the non-transfected control cells. We also show that by using this novel method, introduction of an shRNA targeting Stat6, a key molecule driving the Th2 cell development, results in impaired Th2 cell differentiation, as expected. The method described here, enables fast and feasible preparation of highly pure transfected primary CD4(+) T cell cultures ideal for studying the influence of overexpression or knockdown of a given gene on T helper cell differentiation and other primary human T cell functions.
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Affiliation(s)
- Johanna Tahvanainen
- Turku Centre for Biotechnology, Turku University and Abo Akademi University, Finland.
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