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Article: Whole-Genome Sequencing of Extended-Spectrum Beta-Lactamase-Producing

Kurittu, Paula / Khakipoor, Banafsheh / Jalava, Jari / Karhukorpi, Jari / Heikinheimo, Annamari

2022 Volume 12, Page(s) 789280

Abstract: Antimicrobial resistance (AMR) is a growing concern in public health, particularly for the clinically relevant extended-spectrum beta-lactamase (ESBL) and AmpC-producing Enterobacteriaceae. Studies describing ESBL- ... ...

Abstract	Antimicrobial resistance (AMR) is a growing concern in public health, particularly for the clinically relevant extended-spectrum beta-lactamase (ESBL) and AmpC-producing Enterobacteriaceae. Studies describing ESBL-producing
Language	English
Publishing date	2022-01-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2021.789280
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Article ; Online: Increasing proportions of extended-spectrum β-lactamase-producing isolates among

Ilmavirta, Heikki / Ollgren, Jukka / Räisänen, Kati / Kinnunen, Tuure / Hakanen, Antti J / Jalava, Jari / Lyytikäinen, Outi

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2023 Volume 28, Issue 43

Abstract: ... ...

Abstract	Background
MeSH term(s)	Female ; Male ; Humans ; Escherichia coli ; Finland/epidemiology ; Sepsis ; Escherichia coli Infections/epidemiology ; beta-Lactamases ; Anti-Infective Agents
Chemical Substances	beta-Lactamases (EC 3.5.2.6) ; Anti-Infective Agents
Language	English
Publishing date	2023-10-26
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2023.28.43.2200934
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Article ; Online: Rapid detection of bacterial infection using a novel single-tube, four-colour flow cytometric method: Comparison with PCT and CRP.

Nuutila, Jari / Hohenthal, Ulla / Oksi, Jarmo / Jalava-Karvinen, Päivi

EBioMedicine

2021 Volume 74, Page(s) 103724

Abstract: Background: A key factor behind the unnecessary use of antibiotics is the lack of rapid and accurate diagnostic tests. In this study, we developed a novel and fast flow cytometric single-tube method to detect bacterial infections within 30 minutes.: ... ...

Abstract	Background: A key factor behind the unnecessary use of antibiotics is the lack of rapid and accurate diagnostic tests. In this study, we developed a novel and fast flow cytometric single-tube method to detect bacterial infections within 30 minutes. Methods: Quantitative flow cytometric four-colour analysis of host biomarkers CD35, CD64, CD329, and MHC class I expression on neutrophils and lymphocytes was performed on samples taken from 841 febrile patients with suspected infection. Obtained data was incorporated into the four-colour bacterial infection (FCBI)-index, using the developed bacterial infection algorithm. Findings: In distinguishing between microbiologically confirmed bacterial (n = 193) and viral (n = 291) infections, the FCBI-index method was superior to serum C-reactive protein (CRP) and procalcitonin (PCT). In 269 confirmed viral respiratory tract infections, 43% (95% CI: 37-49%) of the patients had an increased FCBI-index, suggesting probable bacterial coinfection. Interpretation: The proposed FCBI-index test might be a potent additional tool when assessing appropriateness of empiric antibiotic treatment. Funding: This study has been financially supported by Turku University Hospital (Turku, Finland) and The Finnish Medical Foundation.
MeSH term(s)	Algorithms ; Bacterial Infections/blood ; Bacterial Infections/diagnosis ; Diagnosis, Differential ; Diagnostic Tests, Routine ; Early Diagnosis ; Female ; Finland ; Flow Cytometry/instrumentation ; Flow Cytometry/methods ; Humans ; Male ; Procalcitonin/blood ; Receptors, Immunologic/blood ; Respiratory Tract Infections/blood ; Respiratory Tract Infections/virology ; Sensitivity and Specificity ; Virus Diseases/blood ; Virus Diseases/diagnosis
Chemical Substances	CRP protein, human ; Procalcitonin ; Receptors, Immunologic
Language	English
Publishing date	2021-11-26
Publishing country	Netherlands
Document type	Comparative Study ; Journal Article
ZDB-ID	2851331-9
ISSN	2352-3964
ISSN (online)	2352-3964
DOI	10.1016/j.ebiom.2021.103724
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Article ; Online: Particulate matter from car exhaust alters function of human iPSC-derived microglia.

Jäntti, Henna / Jonk, Steffi / Gómez Budia, Mireia / Ohtonen, Sohvi / Fagerlund, Ilkka / Fazaludeen, Mohammad Feroze / Aakko-Saksa, Päivi / Pebay, Alice / Lehtonen, Šárka / Koistinaho, Jari / Kanninen, Katja M / Jalava, Pasi I / Malm, Tarja / Korhonen, Paula

Particle and fibre toxicology

2024 Volume 21, Issue 1, Page(s) 6

Abstract: Background: Air pollution is recognized as an emerging environmental risk factor for neurological diseases. Large-scale epidemiological studies associate traffic-related particulate matter (PM) with impaired cognitive functions and increased incidence ... ...

Abstract	Background: Air pollution is recognized as an emerging environmental risk factor for neurological diseases. Large-scale epidemiological studies associate traffic-related particulate matter (PM) with impaired cognitive functions and increased incidence of neurodegenerative diseases such as Alzheimer's disease. Inhaled components of PM may directly invade the brain via the olfactory route, or act through peripheral system responses resulting in inflammation and oxidative stress in the brain. Microglia are the immune cells of the brain implicated in the progression of neurodegenerative diseases. However, it remains unknown how PM affects live human microglia. Results: Here we show that two different PMs derived from exhausts of cars running on EN590 diesel or compressed natural gas (CNG) alter the function of human microglia-like cells in vitro. We exposed human induced pluripotent stem cell (iPSC)-derived microglia-like cells (iMGLs) to traffic related PMs and explored their functional responses. Lower concentrations of PMs ranging between 10 and 100 µg ml Conclusions: Our study indicates that traffic-related air pollutants alter the function of human microglia and warrant further studies to determine whether these changes contribute to adverse effects in the brain and on cognition over time. This study demonstrates human iPSC-microglia as a valuable tool to study functional microglial responses to environmental agents.
MeSH term(s)	Humans ; Particulate Matter/toxicity ; Particulate Matter/analysis ; Microglia/chemistry ; Induced Pluripotent Stem Cells/chemistry ; Automobiles ; Reactive Oxygen Species ; Vehicle Emissions/toxicity ; Vehicle Emissions/analysis ; Neurodegenerative Diseases
Chemical Substances	Particulate Matter ; Reactive Oxygen Species ; Vehicle Emissions
Language	English
Publishing date	2024-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2170936-1
ISSN	1743-8977 ; 1743-8977
ISSN (online)	1743-8977
ISSN	1743-8977
DOI	10.1186/s12989-024-00564-y
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Article: Genomic epidemiology of nosocomial carbapenemase-producing

Heljanko, Viivi / Johansson, Venla / Räisänen, Kati / Anttila, Veli-Jukka / Lyytikäinen, Outi / Jalava, Jari / Weijo, Irma / Lehtinen, Jaana-Marija / Lehto, Kirsi-Maarit / Lipponen, Anssi / Oikarinen, Sami / Pitkänen, Tarja / Heikinheimo, Annamari

Frontiers in microbiology

2023 Volume 14, Page(s) 1165751

Abstract: Multi-drug resistance is emerging ... ...

Abstract	Multi-drug resistance is emerging in
Language	English
Publishing date	2023-05-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1165751
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Article ; Online: Rapid detection of bacterial infection using a novel single-tube, four-colour flow cytometric method

Jari Nuutila / Ulla Hohenthal / Jarmo Oksi / Päivi Jalava-Karvinen

EBioMedicine, Vol 74, Iss , Pp 103724- (2021)

Comparison with PCT and CRP

2021

Abstract: ABSTRACT: Background: A key factor behind the unnecessary use of antibiotics is the lack of rapid and accurate diagnostic tests. In this study, we developed a novel and fast flow cytometric single-tube method to detect bacterial infections within 30 ... ...

Abstract	ABSTRACT: Background: A key factor behind the unnecessary use of antibiotics is the lack of rapid and accurate diagnostic tests. In this study, we developed a novel and fast flow cytometric single-tube method to detect bacterial infections within 30 minutes. Methods: Quantitative flow cytometric four-colour analysis of host biomarkers CD35, CD64, CD329, and MHC class I expression on neutrophils and lymphocytes was performed on samples taken from 841 febrile patients with suspected infection. Obtained data was incorporated into the four-colour bacterial infection (FCBI)-index, using the developed bacterial infection algorithm. Findings: In distinguishing between microbiologically confirmed bacterial (n = 193) and viral (n = 291) infections, the FCBI-index method was superior to serum C-reactive protein (CRP) and procalcitonin (PCT). In 269 confirmed viral respiratory tract infections, 43% (95% CI: 37–49%) of the patients had an increased FCBI-index, suggesting probable bacterial coinfection. Interpretation: The proposed FCBI-index test might be a potent additional tool when assessing appropriateness of empiric antibiotic treatment. Funding: This study has been financially supported by Turku University Hospital (Turku, Finland) and The Finnish Medical Foundation.
Keywords	Flow cytometry ; Host biomarker ; Differential diagnostic ; Bacterial infection ; Viral infection ; Medicine ; R ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Evaluation of two commercial carbapenemase gene assays, the Rapidec Carba NP test and the in-house Rapid Carba NP test, on bacterial cultures.

Österblad, Monica / Lindholm, Laura / Jalava, Jari

The Journal of antimicrobial chemotherapy

2016 Volume 71, Issue 7, Page(s) 2057–2059

Language	English
Publishing date	2016-07
Publishing country	England
Document type	Letter
ZDB-ID	191709-2
ISSN	1460-2091 ; 0305-7453
ISSN (online)	1460-2091
ISSN	0305-7453
DOI	10.1093/jac/dkw077
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Zs.MO 124: Show issues

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Article ; Online: A single-tube two-color flow cytometric method for distinguishing between febrile bacterial and viral infections.

Nuutila, Jari / Hohenthal, Ulla / Oksi, Jarmo / Jalava-Karvinen, Päivi

Journal of microbiological methods

2018 Volume 152, Page(s) 61–68

Abstract: The aim of this study was to develop a rapid single-tube two-color flow cytometric method to distinguish between febrile bacterial and viral infections. In this prospective comparative study, the quantitative flow cytometric analysis of CD35 and CD64 on ... ...

Abstract	The aim of this study was to develop a rapid single-tube two-color flow cytometric method to distinguish between febrile bacterial and viral infections. In this prospective comparative study, the quantitative flow cytometric analysis of CD35 and CD64 on isolated human leukocytes was obtained from 286 hospitalized febrile patients, of which 197 patients were found to have either a bacterial (n = 136) or viral (n = 61) infection. The data from infected patients was compared to 49 healthy controls and 23 patients in an inflammatory state. We developed a flow cytometric marker for bacterial infections, defined as the two-color bacterial infection index (TC-BI-index), by incorporating the quantitative analysis of CD35 and CD64 on isolated neutrophils, monocytes, and B-lymphocytes, which displayed 90% sensitivity and specificity in distinguishing between microbiologically confirmed bacterial (n = 77) and viral infections (n = 61) within 45 min. We propose that TC-BI-index test will be useful in assisting physicians to ascertain whether antibiotic treatment is required, thus limiting unnecessary antimicrobial usage.
MeSH term(s)	B-Lymphocytes/immunology ; Bacterial Infections/diagnosis ; Biomarkers ; Diagnostic Tests, Routine/methods ; Fever/microbiology ; Fever/virology ; Flow Cytometry/methods ; Humans ; Leukocytes/immunology ; Monocytes/immunology ; Neutrophils/immunology ; Prospective Studies ; Receptors, Cell Surface/analysis ; Receptors, Complement 3b ; Receptors, IgG ; Sensitivity and Specificity ; Virus Diseases/diagnosis
Chemical Substances	Biomarkers ; Receptors, Cell Surface ; Receptors, Complement 3b ; Receptors, IgG
Language	English
Publishing date	2018-07-29
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604916-3
ISSN	1872-8359 ; 0167-7012
ISSN (online)	1872-8359
ISSN	0167-7012
DOI	10.1016/j.mimet.2018.07.015
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Article ; Online: Emergence of ceftazidime-avibactam-resistant

Räisänen, Kati / Koivula, Irma / Ilmavirta, Heikki / Puranen, Santeri / Kallonen, Teemu / Lyytikäinen, Outi / Jalava, Jari

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2019 Volume 24, Issue 19

Abstract: In December 2018, a ceftazidime-avibactam (CAZ-AVI)-resistant KPC-2- ... ...

Abstract	In December 2018, a ceftazidime-avibactam (CAZ-AVI)-resistant KPC-2-producing
MeSH term(s)	Anti-Bacterial Agents/therapeutic use ; Azabicyclo Compounds/therapeutic use ; Bacterial Proteins/metabolism ; Ceftazidime/therapeutic use ; Drug Combinations ; Drug Resistance, Bacterial ; Humans ; Klebsiella Infections/diagnosis ; Klebsiella Infections/drug therapy ; Klebsiella pneumoniae/drug effects ; Klebsiella pneumoniae/genetics ; Klebsiella pneumoniae/isolation & purification ; Microbial Sensitivity Tests ; Treatment Outcome ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; beta-Lactamase Inhibitors/therapeutic use
Chemical Substances	Anti-Bacterial Agents ; Azabicyclo Compounds ; Bacterial Proteins ; Drug Combinations ; avibactam, ceftazidime drug combination ; beta-Lactamase Inhibitors ; Trimethoprim, Sulfamethoxazole Drug Combination (8064-90-2) ; Ceftazidime (9M416Z9QNR)
Language	English
Publishing date	2019-05-14
Publishing country	Sweden
Document type	Case Reports ; Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2019.24.19.1900256
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Article ; Online: Molecular epidemiology of carbapenemase-producing Enterobacterales in Finland, 2012-2018.

Räisänen, Kati / Lyytikäinen, Outi / Kauranen, Jari / Tarkka, Eveliina / Forsblom-Helander, Benita / Grönroos, Juha O / Vuento, Risto / Arifulla, Dinah / Sarvikivi, Emmi / Toura, Saija / Jalava, Jari

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

2020 Volume 39, Issue 9, Page(s) 1651–1656

Abstract: Carbapenemase-producing Enterobacterales (CPE) pose an increasing threat to patient safety and healthcare systems globally. We present molecular epidemiology of CPE in Finland during 2012-2018 with detailed characteristics of CPE strains causing clusters ...

Abstract	Carbapenemase-producing Enterobacterales (CPE) pose an increasing threat to patient safety and healthcare systems globally. We present molecular epidemiology of CPE in Finland during 2012-2018 with detailed characteristics of CPE strains causing clusters during the same time period. All Finnish clinical microbiology laboratories send Enterobacterales isolates with reduced susceptibility to carbapenems or isolates producing carbapenemase to the reference laboratory for further characterization by whole genome sequencing (WGS). In total, 231 CPE strains from 202 patients were identified during 2012-2018. Of the strains, 59% were found by screening and 32% from clinical specimens, the latter were most commonly urine. Travel and/or hospitalization history abroad was reported for 108/171 strains (63%). The most common species were Klebsiella pneumoniae (45%), Escherichia coli (40%), and Citrobacter freundii (6%), and the most common carbapenemase genes bla
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacterial Proteins/metabolism ; Child ; Child, Preschool ; Disease Outbreaks ; Enterobacteriaceae/genetics ; Enterobacteriaceae/isolation & purification ; Enterobacteriaceae/metabolism ; Enterobacteriaceae Infections/epidemiology ; Enterobacteriaceae Infections/microbiology ; Female ; Finland/epidemiology ; Humans ; Infant ; Male ; Middle Aged ; Molecular Epidemiology ; Whole Genome Sequencing ; Young Adult ; beta-Lactamases/metabolism
Chemical Substances	Bacterial Proteins ; beta-Lactamases (EC 3.5.2.6) ; carbapenemase (EC 3.5.2.6)
Language	English
Publishing date	2020-04-19
Publishing country	Germany
Document type	Journal Article
ZDB-ID	603155-9
ISSN	1435-4373 ; 0934-9723 ; 0722-2211
ISSN (online)	1435-4373
ISSN	0934-9723 ; 0722-2211
DOI	10.1007/s10096-020-03885-w
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