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Sundqvist, Martin
Publications (10 of 14) Show all publications
Säll, O., Thulin Hedberg, S., Neander, M., Tiwari, S., Dornon, L., Bom, R., . . . Mölling, P. (2019). Etiology of Central Nervous System Infections in a Rural Area of Nepal Using Molecular Approaches. American Journal of Tropical Medicine and Hygiene, 101(1), 253-259
Open this publication in new window or tab >>Etiology of Central Nervous System Infections in a Rural Area of Nepal Using Molecular Approaches
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2019 (English)In: American Journal of Tropical Medicine and Hygiene, ISSN 0002-9637, E-ISSN 1476-1645, Vol. 101, no 1, p. 253-259Article in journal (Refereed) Published
Abstract [en]

The etiology of infections of the central nervous system (CNS) in Nepal often remains unrecognized because of underdeveloped laboratory facilities. The aim of this study was to investigate the etiology of CNS infections in a rural area of Nepal using molecular methods. From November 2014 to February 2016, cerebrospinal fluid (CSF) was collected from 176 consecutive patients presenting at United Mission Hospital in Tansen, Nepal, with symptoms of possible CNS infection. After the CSF samples were stored and transported frozen, polymerase chain reaction (PCR) was performed in Sweden, targeting a total of 26 pathogens using the FilmArray® ME panel (BioFire, bioMerieux, Salt Lake City, UT), the MeningoFinder® 2SMART (PathoFinder, Maastricht, The Netherlands), and an in-house PCR test for dengue virus (DENV), Japanese encephalitis virus (JEV), and Nipah virus (NiV). The etiology could be determined in 23%. The bacteria detected were Haemophilus influenzae (n = 5), Streptococcus pneumoniae (n = 4), and Neisseria meningitidis (n = 1). The most common virus was enterovirus detected in eight samples, all during the monsoon season. Other viruses detected were cytomegalovirus (n = 6), varicella zoster virus (n = 5), Epstein-Barr virus (n = 3), herpes simplex virus (HSV) type 1 (HSV-1) (n = 3), HSV-2 (n = 3), human herpes virus (HHV) type 6 (HHV-6) (n = 3), and HHV-7 (n = 2). Cryptococcus neoformans/gatti was found in four samples. None of the samples were positive for DENV, JEV, or NiV. Of the patients, 67% had been exposed to antibiotics before lumbar puncture. In conclusion, the etiology could not be found in 77% of the samples, indicating that the commercial PCR panels used are not suitable in this setting. Future studies on the etiology of CNS infections in Nepal could include metagenomic techniques.

Place, publisher, year, edition, pages
HighWire Press, 2019
National Category
Infectious Medicine
Identifiers
urn:nbn:se:oru:diva-74617 (URN)10.4269/ajtmh.18-0434 (DOI)000476680300040 ()31162021 (PubMedID)2-s2.0-85068911912 (Scopus ID)
Funder
Swedish Society of Medicine
Note

Funding Agencies:

Region Örebro County's Research Committe

Örebro University

Folke Nordbring Foundation

Available from: 2019-06-05 Created: 2019-06-05 Last updated: 2019-08-12Bibliographically approved
Unemo, M., Hansen, M., Hadad, R., Lindroth, Y., Fredlund, H., Puolakkainen, M. & Sundqvist, M. (2019). Finnish new variant of Chlamydia trachomatis escaping detection in the Aptima Combo 2 assay also present in Orebro County, Sweden, May 2019. Eurosurveillance, 24(26), 10-14, Article ID 1900370.
Open this publication in new window or tab >>Finnish new variant of Chlamydia trachomatis escaping detection in the Aptima Combo 2 assay also present in Orebro County, Sweden, May 2019
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2019 (English)In: Eurosurveillance, ISSN 1025-496X, E-ISSN 1560-7917, Vol. 24, no 26, p. 10-14, article id 1900370Article in journal (Refereed) Published
Abstract [en]

We identified the first two cases of the Finnish new variant of Chlamydia trachomatis (F-nvCT) beyond Finland in two clinical urogenital specimens in Orebro County, Sweden. These Aptima Combo 2 assay-negative specimens were Aptima Chlamydia trachomatis (CT) assay positive and had the characteristic C1515T mutation in the 23S rRNA gene. From 22 March to 31 May 2019, 1.3% (2/158) of the CT-positive cases in Orebro County were missed because of the F-nvCT. International awareness, investigations and actions are essential.

Place, publisher, year, edition, pages
European Centre for Disease Prevention and Control, 2019
National Category
Infectious Medicine
Identifiers
urn:nbn:se:oru:diva-75223 (URN)10.2807/1560-7917.ES.2019.24.26.1900370 (DOI)000473116300003 ()31266590 (PubMedID)
Available from: 2019-07-26 Created: 2019-07-26 Last updated: 2019-07-26Bibliographically approved
Ingberg, E., Mölling, P., Jacobsson, S., Alm, E., Hedin, K. & Sundqvist, M. (2018). 16S metagenomics for bacterial identification versus cultures in acute pharyngotonsillitis patients and controls. In: : . Paper presented at 28th European Congress of Clinical Microbiology and Infectious Diseases, Madrid, Spain, 21-24 April, 2018.
Open this publication in new window or tab >>16S metagenomics for bacterial identification versus cultures in acute pharyngotonsillitis patients and controls
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2018 (English)Conference paper, Poster (with or without abstract) (Refereed)
Abstract [en]

Background: Sore throat/pharyngotonsillitis is a very common condition. While most cases are viral, the primary bacterial pathogen is group A beta-hemolytic streptococcus (Streptococcus pyogenes). Further, Fusobacterium necrophorum has over the last decade attracted attention. rnrnSequence-based techniques continue to gain ground in medical microbiology. To describe the microbiota in a sample, either the whole genomes (metagenomics) or marker genes/genomic regions (metataxonomics), such as the 16S rRNA gene, can be sequenced. Some studies have investigated how findings from these methods correspond to conventional microbiological methods for infectious diseases, such as cultures. However, no previous study has approached the condition acute pharyngotonsillitis this way.

Methods: Throat samples from patients with acute sore throat (n=129) and controls (n=86), both groups aged 15-45, were collected. DNA was extracted and the V3-V4 regions of the 16S rRNA genes were amplified using PCR. After normalization based on fragment analysis, and size selection with Ampure beads and PCR against adapter sequences coupled to the V3-V4 fragments, clonal amplifiction was performed with isothermal PCR. Finally, sequencing was performed on the Ion Torrent S5 XL. The SILVA database was used for taxonomic classification and the results were compared to culture findings for S. pyogenes and F. necrophorum, using Mann Whitney U tests.

Results: Among the 215 samples, 46 patients and 1 of the controls were culture-positive for S. pyogenes. For F. necrophorum, 20 patients and 3 controls were culture-positive. Seven of the samples were culture-positive for both S. pyogenes and F. necrophorum. rnrnIn the metataxonomic analysis, S. pyogenes were significantly more abundant among patients than controls (p=0.0046), and in samples culture-positive for S. pyogenes, compared to culture-negative (p<0.0001).

The percent of reads representing F. necrophorum were significantly higher in patients compared to controls (p<0.001), as well as in culture-positive samples compared to culture-negative (p<0.0001). rnrnAlthough significant differences between culture-positive and culture-negative samples were seen, even among culture-positive samples the abundance of S. pyogenes or F. necrophorum were on average low (2,1% and 10,6%, respectively) and with large variation (0-49,8% and 0-76,1%, respectively).

Conclusions: Findings from a metataxonomic 16S rRNA gene analysis differed regarding species of interest between groups based on symptoms of a sore throat or culture findings. However, the results were heterogeneous and difficult to interpret for a single sample.

National Category
Infectious Medicine
Identifiers
urn:nbn:se:oru:diva-67260 (URN)
Conference
28th European Congress of Clinical Microbiology and Infectious Diseases, Madrid, Spain, 21-24 April, 2018
Available from: 2018-06-14 Created: 2018-06-14 Last updated: 2018-06-14Bibliographically approved
Unemo, M., Salado-Rasmussen, K., Hansen, M., Olsen, A. O., Falk, M., Golparian, D., . . . Jensen, J. S. (2018). Clinical and analytical evaluation of the new Aptima Mycoplasma genitalium assay, with data on M. genitalium prevalence and antimicrobial resistance in M. genitalium in Denmark, Norway and Sweden in 2016. Clinical Microbiology and Infection, 24(5), 533-539
Open this publication in new window or tab >>Clinical and analytical evaluation of the new Aptima Mycoplasma genitalium assay, with data on M. genitalium prevalence and antimicrobial resistance in M. genitalium in Denmark, Norway and Sweden in 2016
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2018 (English)In: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 24, no 5, p. 533-539Article in journal (Refereed) Published
Abstract [en]

Objectives: Mycoplasma genitalium (MG) causes urethritis and cervicitis, potentially causing reproductive complications. Resistance in MG to first-line (azithromycin) and second-line (moxifloxacin) treatment has increased. We examined the clinical and analytical performance of the new Conformite Europeene (CE)/in vitro diagnostics (IVD) Aptima Mycoplasma genitalium assay (CE/IVD AMG; Hologic); the prevalence of MG, Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG); and MG resistance to azithromycin and moxifloxacin in Denmark, Norway and Sweden in 2016.

Methods: From February 2016 to February 2017, urogenital and extragenital (only in Denmark) specimens from consecutive attendees at three sexually transmitted disease clinics were tested with the CE/ IVD AMG, the research-use-only MG Alt TMA-1 assay (Hologic), Aptima Combo 2 (CT/NG) assay and a laboratory-developed TaqMan real-time mgpB quantitative real-time PCR (qPCR). Resistance-associated mutations were determined by sequencing. Strains of MG and other mycoplasma species in different concentrations were also tested.

Results: In total 5269 patients were included. The prevalence of MG was 7.2% (382/5269; 4.9-9.8% in the countries). The sensitivity of the CE/IVD AMG, MG Alt TMA-1 and mgpB qPCR ranged 99.13-100%, 99.13 -100% and 73.24-81.60%, respectively, in the countries. The specificity ranged 99.57-99.96%, 100% and 99.69-100%, respectively. The prevalence of resistance-associated mutations for azithromycin and moxifloxacin was 41.4% (120/290; 17.7-56.6%) and 6.6% (18/274; 4.1-10.2%), respectively. Multidrug resistance was found in all countries (2.7%; 1.1-4.2%).

Conclusions: Both transcription-mediated amplification (TMA)-based MG assays had a highly superior sensitivity compared to the mgpB qPCR. The prevalence of MG and azithromycin resistance was high. Validated and quality-assured molecular tests for MG, routine resistance testing of MG-positive samples and antimicrobial resistance surveillance are crucial.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
16S rRNA, 23S rRNA, Antimicrobial resistance, Aptima, Azithromycin, Hologic, Moxifloxacin, Mycoplasma genitalium, parC
National Category
Infectious Medicine Microbiology in the medical area
Identifiers
urn:nbn:se:oru:diva-66889 (URN)10.1016/j.cmi.2017.09.006 (DOI)000430656300015 ()28923377 (PubMedID)2-s2.0-85032198941 (Scopus ID)
Note

Funding Agencies:

Örebro County Council Research Committee  

Foundation for Medical Research at Örebro University Hospital, Örebro, Sweden  

Available from: 2018-05-08 Created: 2018-05-08 Last updated: 2018-08-30Bibliographically approved
Rapp, E., Samuelsen, Ø. & Sundqvist, M. (2018). Detection of carbapenemases with a newly developed commercial assay using Matrix Assisted Laser Desorption Ionization-Time of Flight. Journal of Microbiological Methods, 146, 37-39
Open this publication in new window or tab >>Detection of carbapenemases with a newly developed commercial assay using Matrix Assisted Laser Desorption Ionization-Time of Flight
2018 (English)In: Journal of Microbiological Methods, ISSN 0167-7012, E-ISSN 1872-8359, Vol. 146, p. 37-39Article in journal (Refereed) Published
Abstract [en]

This study evaluated the performance of the MBT STAR-Carba kit (Bruker Daltonics), to detect carbapenemase producing Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter spp. in comparison with the RAPIDEC® CARBA NP test (BioMerieux). MBT STAR-Carba allowed the detection of carbapenemases in Enterobacteriaceae and P. aeruginosa.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Mass-spectrometry; Hydrolysis; Carbapenems; Enterobacteriaceae; Pseudmonoas aeruginosa; Acinetobacter spp.
National Category
Microbiology
Identifiers
urn:nbn:se:oru:diva-64502 (URN)10.1016/j.mimet.2018.01.008 (DOI)000428490300008 ()29360488 (PubMedID)2-s2.0-85041603783 (Scopus ID)
Note

Funding Agency:

Research committee at the University Hospital Örebro

Available from: 2018-01-25 Created: 2018-01-25 Last updated: 2018-08-20Bibliographically approved
Nestor, D., Malmvall, B.-E., Masonda, Y. P., Msafiri, J. & Sundqvist, M. (2018). Detection of extended-spectrum beta-lactamase production in Enterobacteriales from patients with suspected urinary tract infections, Tabora region, Rural Tanzania [Letter to the editor]. Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS), 126(8), 700-702
Open this publication in new window or tab >>Detection of extended-spectrum beta-lactamase production in Enterobacteriales from patients with suspected urinary tract infections, Tabora region, Rural Tanzania
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2018 (English)In: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS), ISSN 0903-4641, E-ISSN 1600-0463, Vol. 126, no 8, p. 700-702Article in journal, Letter (Refereed) Published
Place, publisher, year, edition, pages
Wiley-Blackwell Publishing Inc., 2018
National Category
Immunology in the medical area Microbiology in the medical area
Identifiers
urn:nbn:se:oru:diva-68469 (URN)10.1111/apm.12863 (DOI)000440136000007 ()2-s2.0-85050749564 (Scopus ID)
Available from: 2018-08-15 Created: 2018-08-15 Last updated: 2018-08-31Bibliographically approved
Thulin Hedberg, S., Eriksson, L., Demontis, M. A., Mölling, P., Sundqvist, M., Taylor, G., . . . Andersson, S. (2018). Droplet digital PCR for absolute quantification of proviral load of human T-cell lymphotropic virus (HTLV) types 1 and 2. Journal of Virological Methods, 260, 70-74
Open this publication in new window or tab >>Droplet digital PCR for absolute quantification of proviral load of human T-cell lymphotropic virus (HTLV) types 1 and 2
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2018 (English)In: Journal of Virological Methods, ISSN 0166-0934, E-ISSN 1879-0984, Vol. 260, p. 70-74Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Human T-lymphotrophic virus (HTLV) types 1 and 2 cause lifelong infection whereby most infected individuals are asymptomatic whilst a minority develop infection-related disease. These latter patients invariably have been found to have high proviral load (PVL). Therefore, infected patients are monitored by determining the proportion of lymphocytes that are infected with HTLV-1/2. An increase in PVL has been shown to represent an increasing risk of developing HTLV-associated diseases. Monitoring of PVL requires a reliable and sensitive method. In this study assays based on droplet digital PCR (ddPCR) were established and evaluated for detection and quantification of HTLV-1/2.

OBJECTIVES: To develop two parallel assays to detect the tax genes and determine the PVL of HTLV-1 and -2.

STUDY DESIGN: Sixty-seven clinical samples from patients infected with HTLV-1 or HTLV-2 were analysed. The samples had previously been analysed with a qPCR and a comparison between ddPCR and qPCR was performed. The specificity of the assays were determined by analyzing samples from 20 healthy blood donors.

RESULTS: The ddPCR was a stable and sensitive method for detection and quantification of HTLV-1 and -2. When comparing the qPCR and ddPCR the correlation was high (Pearsons correlation coefficient 0.96). The variability of the ddPCR was very low with intra-assay coefficient of variation (CV) of 0.97-3.3% (HTLV-1) and 1.7-8.2% (HTLV-2) and inter-assay CV of 1.8-6.1% (HTLV-1) and 1.2-12.9% (HTLV-2).

CONCLUSIONS: The ddPCR reliably quantified HTLV DNA in clinical samples and could be a useful tool for monitoring of PVLs in HTLV-infected individuals.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Absolute quantification, Clinical monitoring, Droplet digital PCR - ddPCR, Human T-cell lymphotropic virus – HTLV, Pro-viral load – PVL
National Category
Microbiology in the medical area Clinical Laboratory Medicine
Identifiers
urn:nbn:se:oru:diva-68507 (URN)10.1016/j.jviromet.2018.07.003 (DOI)000442057400012 ()30006102 (PubMedID)2-s2.0-85050084367 (Scopus ID)
Available from: 2018-08-16 Created: 2018-08-16 Last updated: 2018-08-31Bibliographically approved
Lamy, B. & Sundqvist, M. (2018). Towards an improved diagnosis of bloodstream infection: promises and hurdles. Clinical Microbiology and Infection, 24(9), 933-934
Open this publication in new window or tab >>Towards an improved diagnosis of bloodstream infection: promises and hurdles
2018 (English)In: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 24, no 9, p. 933-934Article in journal, Editorial material (Other academic) Published
Place, publisher, year, edition, pages
Elsevier, 2018
National Category
Infectious Medicine Microbiology in the medical area
Identifiers
urn:nbn:se:oru:diva-68965 (URN)10.1016/j.cmi.2018.02.025 (DOI)000441882800004 ()29501662 (PubMedID)
Available from: 2018-09-19 Created: 2018-09-19 Last updated: 2018-09-19Bibliographically approved
Säll, O., Thulin-Hedberg, S., Bom, R., Dornon, L., Tiwari, S., Neander, M., . . . Mölling, P. (2017). Etiology of CNS infections in Nepal using the FilmArray meningitis/encephalitis panel. Paper presented at 30th International Congress of Chemotherapy and Infection (ICC), Taipei, Taiwan, November 24-27, 2017. International Journal of Antimicrobial Agents, 50(Suppl. 2), S66-S66
Open this publication in new window or tab >>Etiology of CNS infections in Nepal using the FilmArray meningitis/encephalitis panel
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2017 (English)In: International Journal of Antimicrobial Agents, ISSN 0924-8579, E-ISSN 1872-7913, Vol. 50, no Suppl. 2, p. S66-S66Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
Elsevier, 2017
National Category
Infectious Medicine Pharmacology and Toxicology Microbiology in the medical area
Identifiers
urn:nbn:se:oru:diva-62996 (URN)10.1016/S0924-8579(17)30422-3 (DOI)000416028900142 ()
Conference
30th International Congress of Chemotherapy and Infection (ICC), Taipei, Taiwan, November 24-27, 2017
Available from: 2017-12-07 Created: 2017-12-07 Last updated: 2018-08-13Bibliographically approved
Månsson, E., Hellmark, B., Stegger, M., Andersen, P. S., Sundqvist, M. & Söderquist, B. (2017). Genomic relatedness of Staphylococcus pettenkoferi isolates of different origins. Journal of Medical Microbiology, 66(5), 601-608
Open this publication in new window or tab >>Genomic relatedness of Staphylococcus pettenkoferi isolates of different origins
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2017 (English)In: Journal of Medical Microbiology, ISSN 0022-2615, E-ISSN 1473-5644, Vol. 66, no 5, p. 601-608Article in journal (Refereed) Published
Abstract [en]

Purpose: The aim of the study was to characterize clinical and environmental Staphylococcus pettenkoferi isolates with regard to genomic diversity and antibiotic susceptibility pattern. Repetitive-sequence-based PCR and core genome phylogenetic analysis of whole-genome sequencing (WGS) data verified the presence of distinct clades comprising closely related S. pettenkoferi isolates from different geographical locations and origins.

Methodology: Phylogenetic relationships between 25 S. pettenkoferi isolates collected from blood cultures and intra-operative air sampling were determined by repetitive-sequence-based PCR typing and analysis of similar to 157 000 SNPs identified in the core genome after WGS. Antibiotic susceptibility testing and tests for biofilm production (microtitre plate assay) were performed.

Results: Repetitive-sequence-based PCR as well as WGS data demonstrated the close relatedness of clinically significant blood culture isolates to probable contaminants, as well as to environmental isolates. Antibiotic-susceptibility testing demonstrated a low level of antimicrobial resistance. The mecA gene was present in two cefoxitin-resistant isolates. No isolates were found to produce biofilm.

Conclusion: Close genomic relatedness of S. pettenkoferi isolates from different geographical locations and origins were found within clades, but with substantial genomic difference between the two major clades. The ecological niche of S. pettenkoferi remains unconfirmed, but the presence of S. pettenkoferi in the air of the operating field favours the suggestion of a role in skin flora. Identification of S. pettenkoferi in clinical samples should, in a majority of cases, most likely be regarded as a probable contamination, and its role as a possible pathogen in immunocompromised hosts remains to be clarified.

Place, publisher, year, edition, pages
Microbiology Society, 2017
Keywords
Staphylococcus pettenkoferi, genotypic relatedness, repetitive-sequence based PCR typing, whole-genome sequencing
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:oru:diva-58000 (URN)10.1099/jmm.0.000472 (DOI)000401984900007 ()28530888 (PubMedID)2-s2.0-85019900525 (Scopus ID)
Note

Funding Agencies:

Örebro County Council Research Committee, Örebro, Sweden

Centre for Clinical Research, Västerås  

County Council of Västmanland Research Fund 

Available from: 2017-06-13 Created: 2017-06-13 Last updated: 2018-07-31Bibliographically approved
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