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Article ; Online: Quantifying antibiotic impact on within-patient dynamics of extended-spectrum beta-lactamase resistance.

Niehus, Rene / van Kleef, Esther / Mo, Yin / Turlej-Rogacka, Agata / Lammens, Christine / Carmeli, Yehuda / Goossens, Herman / Tacconelli, Evelina / Carevic, Biljana / Preotescu, Liliana / Malhotra-Kumar, Surbhi / Cooper, Ben S

eLife

2020 Volume 9

Abstract: Antibiotic-induced perturbation of the human gut flora is expected to play an important role in mediating the relationship between antibiotic use and the population prevalence of antibiotic resistance in bacteria, but little is known about how ... ...

Abstract	Antibiotic-induced perturbation of the human gut flora is expected to play an important role in mediating the relationship between antibiotic use and the population prevalence of antibiotic resistance in bacteria, but little is known about how antibiotics affect within-host resistance dynamics. Here we develop a data-driven model of the within-host dynamics of extended-spectrum beta-lactamase (ESBL) producing
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Anal Canal/microbiology ; Anti-Bacterial Agents/adverse effects ; Anti-Bacterial Agents/therapeutic use ; Bacterial Load ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Enterobacteriaceae/drug effects ; Enterobacteriaceae/enzymology ; Enterobacteriaceae/genetics ; Europe ; Female ; Gastrointestinal Microbiome/drug effects ; Humans ; Male ; Middle Aged ; Models, Theoretical ; Prospective Studies ; Ribotyping ; Time Factors ; Young Adult ; beta-Lactam Resistance/genetics ; beta-Lactamases/genetics ; beta-Lactamases/metabolism
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2020-05-07
Publishing country	England
Document type	Comparative Study ; Journal Article ; Multicenter Study ; Observational Study ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.49206
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Article ; Online: Calcitriol and Its Analogs Establish the Immunosuppressive Microenvironment That Drives Metastasis in 4T1 Mouse Mammary Gland Cancer.

Pawlik, Agata / Anisiewicz, Artur / Filip-Psurska, Beata / Nowak, Marcin / Turlej, Eliza / Trynda, Justyna / Banach, Joanna / Gretkierewicz, Paweł / Wietrzyk, Joanna

International journal of molecular sciences

2018 Volume 19, Issue 7

Abstract: In our previous study, calcitriol and its analogs PRI-2191 and PRI-2205 stimulated 4T1 mouse mammary gland cancer metastasis. Therefore, we aimed to analyze the inflammatory response in 4T1-bearing mice treated with these compounds. Gene expression ... ...

Abstract	In our previous study, calcitriol and its analogs PRI-2191 and PRI-2205 stimulated 4T1 mouse mammary gland cancer metastasis. Therefore, we aimed to analyze the inflammatory response in 4T1-bearing mice treated with these compounds. Gene expression analysis of the splenocytes and regional lymph nodes demonstrated prevalence of the T helper lymphocytes (Th2) response with an increased activity of regulatory T (Treg) lymphocytes in mice treated with these compounds. We also observed an increased number of mature granulocytes and B lymphocytes and a decreased number of TCD4⁺, TCD4⁺CD25⁺, and TCD8⁺, as well as natural killer (NK) CD335⁺, cells in the blood of mice treated with calcitriol and its analogs. Among the splenocytes, we observed a significant decrease in NK CD335⁺ cells and an increase in TCD8⁺ cells. Calcitriol and its analogs decreased the levels of interleukin (IL)-1β and IL-10 and increased the level of interferon gamma (IFN-γ) in the plasma. In the tumor tissue, they caused an increase in the level of IL-10. Gene expression analysis of lung tissue demonstrated an increased level of osteopontin (
MeSH term(s)	Animals ; B-Lymphocytes/drug effects ; B-Lymphocytes/metabolism ; CD4-Positive T-Lymphocytes/drug effects ; CD4-Positive T-Lymphocytes/metabolism ; CD8-Positive T-Lymphocytes/drug effects ; CD8-Positive T-Lymphocytes/metabolism ; Calcitriol/analogs & derivatives ; Calcitriol/pharmacology ; Cells, Cultured ; Dihydroxycholecalciferols/pharmacology ; Enzyme-Linked Immunosorbent Assay ; Female ; Flow Cytometry ; Granulocytes/drug effects ; Granulocytes/metabolism ; Immunosuppressive Agents/pharmacology ; Mammary Neoplasms, Experimental/metabolism ; Mammary Neoplasms, Experimental/pathology ; Mice ; Mice, Inbred BALB C ; Osteopontin/genetics ; Real-Time Polymerase Chain Reaction ; Transforming Growth Factor beta/genetics
Chemical Substances	Dihydroxycholecalciferols ; Immunosuppressive Agents ; Transforming Growth Factor beta ; Osteopontin (106441-73-0) ; calcipotriene (143NQ3779B) ; 1 alpha,24-dihydroxyvitamin D3 (60965-80-2) ; Calcitriol (FXC9231JVH)
Language	English
Publishing date	2018-07-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms19072116
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Article ; Online: Evaluation of colistin stability in agar and comparison of four methods for MIC testing of colistin.

Turlej-Rogacka, Agata / Xavier, Basil Britto / Janssens, Lore / Lammens, Christine / Zarkotou, Olympia / Pournaras, Spyros / Goossens, Herman / Malhotra-Kumar, Surbhi

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

2018 Volume 37, Issue 2, Page(s) 345–353

Abstract: Susceptibility testing for colistin remains challenging primarily due to its inherent properties. We evaluated colistin stability in agar and reproducibility of colistin MICs obtained by agar dilution, broth macro- and micro-dilution and MIC gradient ... ...

Abstract	Susceptibility testing for colistin remains challenging primarily due to its inherent properties. We evaluated colistin stability in agar and reproducibility of colistin MICs obtained by agar dilution, broth macro- and micro-dilution and MIC gradient strips on 3-7 iterations of each method using clinical Klebsiella pneumoniae (susceptible-CS, and resistant-CR, n = 2 each), mcr-harboring Escherichia coli (n = 2), and reference strains E. coli ATCC25922 and Pseudomonas aeruginosa ATCC27853. MICs for reference strains were not in the given range using Etest and broth microdilution (ATCC25922, 0.125 and 4 μg/ml, respectively). MICs of CR-1 and CR-2, and of the mcr-harboring E. coli showed high concordance between agar and broth dilution varying up to one 2-fold dilution. However, remarkable variations were observed on broth dilution with CS-1 and CS-2 (MIC range 0.25-32 and 0.5-64 μg/ml, respectively); whereas for agar dilution the MIC for both CS strains was 0.5 μg/ml in all the runs. MICs obtained by MIC gradient strips were lower than those obtained by dilution methods (1-2 dilutions for CS and mcr strains, and up to five dilutions for CR strains). To confirm uniform distribution of colistin in agar, a single strain was spotted in five different regions of the same plate. All spots showed concordant growth with maximum one dilution difference. No effect on MIC was found due to storage of colistin-containing agar plates for 7 days at 4 °C. In our hands, agar dilution was superior in terms of reproducibility and robustness, compared to broth dilution methods, for colistin MIC determination.
MeSH term(s)	Agar/chemistry ; Anti-Bacterial Agents/metabolism ; Anti-Bacterial Agents/pharmacology ; Colistin/metabolism ; Colistin/pharmacology ; Disk Diffusion Antimicrobial Tests/methods ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/drug effects ; Humans ; Klebsiella pneumoniae/drug effects ; Pseudomonas aeruginosa/drug effects
Chemical Substances	Anti-Bacterial Agents ; Agar (9002-18-0) ; Colistin (Z67X93HJG1)
Language	English
Publishing date	2018-02
Publishing country	Germany
Document type	Evaluation Studies ; 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/s10096-017-3140-3
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Article: Staphylococcal cassette chromosome mec (Sccmec) classification and typing methods: an overview.

Turlej, Agata / Hryniewicz, Waleria / Empel, Joanna

Polish journal of microbiology

2011 Volume 60, Issue 2, Page(s) 95–103

Abstract: Meticillin-resistant Staphylococcus aureus (MRSA) is one of the main causes of hospital-acquired infections, but since late 1990s also the community-acquired. For better understanding of the S.aureus epidemiology there is an urgent need for creation of ... ...

Abstract	Meticillin-resistant Staphylococcus aureus (MRSA) is one of the main causes of hospital-acquired infections, but since late 1990s also the community-acquired. For better understanding of the S.aureus epidemiology there is an urgent need for creation of new typing method for SCCmec element. The molecular typing of MRSA for epidemiological purposes is investigated by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), spa typing and the SCCmec type assignment. In last few years not only new type of SCCmec (VI to XI) have been identified, but also additional subtypes (i.e. IVg-j) and different variants of already existed one (i.e. 5C2&5 and 2B2&5) were discovered. The aim of this review is to briefly summarize current knowledge about SCCmec classification and to discuss advantages and disadvantages of selected SCCmec typing methods.
MeSH term(s)	Chromosomes, Bacterial/genetics ; Community-Acquired Infections/microbiology ; Cross Infection/microbiology ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field/methods ; Genotype ; Humans ; Methicillin-Resistant Staphylococcus aureus/classification ; Methicillin-Resistant Staphylococcus aureus/genetics ; Methicillin-Resistant Staphylococcus aureus/isolation & purification ; Molecular Epidemiology/methods ; Molecular Typing/methods ; Multilocus Sequence Typing/methods ; Polymerase Chain Reaction/methods ; Staphylococcal Infections/microbiology
Chemical Substances	DNA, Bacterial
Language	English
Publishing date	2011
Publishing country	Poland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2234080-4
ISSN	1733-1331 ; 0137-1320
ISSN	1733-1331 ; 0137-1320
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Article ; Online: Calcitriol and Its Analogs Establish the Immunosuppressive Microenvironment That Drives Metastasis in 4T1 Mouse Mammary Gland Cancer

Agata Pawlik / Artur Anisiewicz / Beata Filip-Psurska / Marcin Nowak / Eliza Turlej / Justyna Trynda / Joanna Banach / Paweł Gretkierewicz / Joanna Wietrzyk

International Journal of Molecular Sciences, Vol 19, Iss 7, p

2018 Volume 2116

Abstract	In our previous study, calcitriol and its analogs PRI-2191 and PRI-2205 stimulated 4T1 mouse mammary gland cancer metastasis. Therefore, we aimed to analyze the inflammatory response in 4T1-bearing mice treated with these compounds. Gene expression analysis of the splenocytes and regional lymph nodes demonstrated prevalence of the T helper lymphocytes (Th2) response with an increased activity of regulatory T (Treg) lymphocytes in mice treated with these compounds. We also observed an increased number of mature granulocytes and B lymphocytes and a decreased number of TCD4+, TCD4+CD25+, and TCD8+, as well as natural killer (NK) CD335+, cells in the blood of mice treated with calcitriol and its analogs. Among the splenocytes, we observed a significant decrease in NK CD335+ cells and an increase in TCD8+ cells. Calcitriol and its analogs decreased the levels of interleukin (IL)-1β and IL-10 and increased the level of interferon gamma (IFN-γ) in the plasma. In the tumor tissue, they caused an increase in the level of IL-10. Gene expression analysis of lung tissue demonstrated an increased level of osteopontin (Spp1) and transforming growth factor β (TGF-β) mRNA. The expression of Spp1 was also elevated in lymph nodes. Calcitriol and its analogs caused prevalence of tumor-conducive changes in the immune system of 4T1 tumor-bearing mice, despite the induction of some tumor-disadvantageous effects.
Keywords	calcitriol ; vitamin D analogs ; breast cancer ; metastasis ; immunosuppression ; osteopontin ; TGF-β ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	616
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Quantifying antibiotic impact on within-patient dynamics of extended-spectrum beta-lactamase resistance

Rene Niehus / Esther van Kleef / Yin Mo / Agata Turlej-Rogacka / Christine Lammens / Yehuda Carmeli / Herman Goossens / Evelina Tacconelli / Biljana Carevic / Liliana Preotescu / Surbhi Malhotra-Kumar / Ben S Cooper

eLife, Vol

2020 Volume 9

Abstract	Antibiotic-induced perturbation of the human gut flora is expected to play an important role in mediating the relationship between antibiotic use and the population prevalence of antibiotic resistance in bacteria, but little is known about how antibiotics affect within-host resistance dynamics. Here we develop a data-driven model of the within-host dynamics of extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae. We use blaCTX-M (the most widespread ESBL gene family) and 16S rRNA (a proxy for bacterial load) abundance data from 833 rectal swabs from 133 ESBL-positive patients followed up in a prospective cohort study in three European hospitals. We find that cefuroxime and ceftriaxone are associated with increased blaCTX-M abundance during treatment (21% and 10% daily increase, respectively), while treatment with meropenem, piperacillin-tazobactam, and oral ciprofloxacin is associated with decreased blaCTX-M (8% daily decrease for all). The model predicts that typical antibiotic exposures can have substantial long-term effects on blaCTX-M carriage duration.
Keywords	antibiotic resistance ; within-host dynamics ; resistance carriage ; extended-spectrum beta-lactamase ; state-space model ; gut microbiota ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evaluation of GeneXpert PA assay compared to genomic and (semi-)quantitative culture methods for direct detection of Pseudomonas aeruginosa in endotracheal aspirates.

van der Schalk, Thomas Ewout / Coppens, Jasmine / Timbermont, Leen / Turlej-Rogacka, Agata / Van Heirstraeten, Liesbet / Berkell, Matilda / Yu, Li / Lammens, Christine / Xavier, Basil Britto / Matheeussen, Veerle / Ieven, Margareta / McCarthy, Michael / Jorens, Philippe G / Ruzin, Alexey / Esser, Mark T / Kumar-Singh, Samir / Goossens, Herman / Malhotra-Kumar, Surbhi

Antimicrobial resistance and infection control

2021 Volume 10, Issue 1, Page(s) 110

Abstract: Introduction: Pseudomonas aeruginosa is a common cause of ventilator-associated pneumonia (VAP). Rapid and accurate detection of lower respiratory tract colonization and/or infection with P. aeruginosa may advise targeted preventive (antibody-based) ... ...

Abstract	Introduction: Pseudomonas aeruginosa is a common cause of ventilator-associated pneumonia (VAP). Rapid and accurate detection of lower respiratory tract colonization and/or infection with P. aeruginosa may advise targeted preventive (antibody-based) strategies and antibiotic therapy. To investigate this, we compared semi-quantitative culture results from 80 endotracheal aspirates (ETA) collected from mechanically-ventilated patients, to two culture and two non-culture-based methods for detection of P. aeruginosa. Methods: P. aeruginosa-positive (n = 40) and -negative (n = 40) ETAs from mechanically ventilated patients analyzed initally by (i) routine semi-quantitative culture, were further analyzed with (ii) quantitative culture on chromogenic ChromID P. aeruginosa and blood agar; (iii) enrichment in brain heart infusion broth followed by plating on blood agar and ChromID P. aeruginosa; (iv) O-antigen acetylase gene-based TaqMan qPCR; and (v) GeneXpert PA PCR assay. Results: Of the 80 ETA samples included, one sample that was negative for P. aeruginosa by semi-quantitative culture was found to be positive by the other four methods, and was included in an "extended" gold standard panel. Based on this extended gold standard, both semi-quantitative culture and the GeneXpert PA assay showed 97.6% sensitivity and 100% specificity. The quantitative culture, enrichment culture and O-antigen acetylase gene-based TaqMan qPCR had a sensitivity of 97.6%, 89.5%, 92.7%, and a specificity of 97.4%, 100%, and 71.1%, respectively. Conclusion: This first evaluation of the GeneXpert PA assay with ETA samples found it to be as sensitive and specific as the routine, hospital-based semi-quantitative culture method. Additionally, the GeneXpert PA assay is easy to perform (hands-on time ≈ 5 min) and rapid (≈ 55 min assay time). The combination of the high sensitivity and high specificity together with the rapid acquisition of results makes the GeneXpert PA assay a highly recommended screening technique. Where this equipment is not available, semi-quantitative culture remains the most sensitive of the culture methods evaluated here for P. aeruginosa detection in ETA samples.
MeSH term(s)	Bacteriological Techniques/methods ; Belgium ; Genomics ; Humans ; Polymerase Chain Reaction ; Pseudomonas aeruginosa/isolation & purification ; Respiration, Artificial ; Sensitivity and Specificity ; Trachea/microbiology
Language	English
Publishing date	2021-07-23
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2666706-X
ISSN	2047-2994 ; 2047-2994
ISSN (online)	2047-2994
ISSN	2047-2994
DOI	10.1186/s13756-021-00978-9
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Article ; Online: Unfavorable effect of calcitriol and its low-calcemic analogs on metastasis of 4T1 mouse mammary gland cancer.

Anisiewicz, Artur / Pawlik, Agata / Filip-Psurska, Beata / Turlej, Eliza / Dzimira, Stanisław / Milczarek, Magdalena / Gdesz, Katarzyna / Papiernik, Diana / Jarosz, Joanna / Kłopotowska, Dagmara / Kutner, Andrzej / Mazur, Andrzej / Wietrzyk, Joanna

International journal of oncology

2018 Volume 52, Issue 1, Page(s) 103–126

Abstract: Low vitamin D status is considered as a risk factor for breast cancer and has prognostic significance. Furthermore, vitamin D deficiency increases after adjuvant cancer therapy, which alters bone metabolism increasing the risk of osteoporosis. It is now ... ...

Abstract	Low vitamin D status is considered as a risk factor for breast cancer and has prognostic significance. Furthermore, vitamin D deficiency increases after adjuvant cancer therapy, which alters bone metabolism increasing the risk of osteoporosis. It is now postulated that vitamin D supplementation in breast cancer treatment delays the recurrence of cancer thereby extending survival. We evaluated the impact of calcitriol and its low-calcemic analogs, PRI‑2191 and PRI‑2205, on the tumor growth, angiogenesis, and metastasis of 4T1 mouse mammary gland cancer. Gene expression analysis related to cancer invasion/metastasis, real‑time PCR, ELISA, western blotting, and histochemical studies were performed. In vitro studies were conducted to compare the effects of calcitriol and its analogs on 4T1 and 67NR cell proliferation and expression of selected proteins. Calcitriol and its analogs increased lung metastasis without influencing the growth of primary tumor. The levels of plasma 17β-estradiol and transforming growth factor β (TGFβ) were found to be elevated after treatment. Moreover, the results showed that tumor blood perfusion improved and osteopontin (OPN) levels increased, whereas vascular endothelial growth factor (VEGF) and TGFβ levels decreased in tumors from treated mice. All the studied treatments resulted in increased collagen content in the tumor tissue in the early step of tumor progression, and calcitriol caused an increase in collagen content in lung tissue. In addition, in vitro proliferation of 4T1 tumor cells was not found to be affected by calcitriol or its analogs in contrast to non-metastatic 67NR cells. Calcitriol and its analogs enhanced the metastatic potential of 4T1 mouse mammary gland cancer by inducing the secretion of OPN probably via host cells. In addition, OPN tumor overexpression prevailed over the decreasing tumor TGFβ level and blood vessel normalization via tumor VEGF deprivation induced by calcitriol and its analogs. Moreover, the increased plasma TGFβ and 17β-estradiol levels contributed to the facilitation of metastatic process.
Language	English
Publishing date	2018-01
Publishing country	Greece
Document type	Journal Article
ZDB-ID	1154403-x
ISSN	1791-2423 ; 1019-6439
ISSN (online)	1791-2423
ISSN	1019-6439
DOI	10.3892/ijo.2017.4185
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Article ; Online: Fecal carriage of ESBL-producing E. coli and K. pneumoniae in children in Guinea-Bissau: a hospital-based cross-sectional study.

Isendahl, Joakim / Turlej-Rogacka, Agata / Manjuba, Cristovão / Rodrigues, Amabelia / Giske, Christian G / Nauclér, Pontus

PloS one

2012 Volume 7, Issue 12, Page(s) e51981

Abstract: Background: In recent years, the world has seen a surge in extended-spectrum β-lactamase (ESBL)-producing bacteria. However, data on the dissemination of ESBL-producing Enterobacteriaceae in the community from systematically enrolled study subjects in ... ...

Abstract	Background: In recent years, the world has seen a surge in extended-spectrum β-lactamase (ESBL)-producing bacteria. However, data on the dissemination of ESBL-producing Enterobacteriaceae in the community from systematically enrolled study subjects in Africa remains limited. To determine the prevalence, phenotypic resistance patterns and genetic characteristics of ESBL-producing E. coli and K. pneumoniae in fecal carriage and to analyze associated risk factors in children attending a pediatric emergency department in Guinea-Bissau. Methodology/principal findings: From June to September 2010, children <5 years of age with fever or tachycardia attending a pediatric emergency ward during the day was screened for ESBL carriage in feces. Socio-demographic and health seeking behavior data was collected. Antibiotic susceptibility was tested with VITEK2 and EUCAST disk diffusion method, molecular characterization of ESBL-encoding genes was performed with multiplex PCR and clonal relatedness was established by automated rep-PCR. Of 408 enrolled children 133 (32.6%) were ESBL carriers. In total, 83 E. coli and 91 K. pneumoniae ESBL-producing isolates were obtained. Nearly all isolates were multidrug-resistant. Co-resistance to ciprofloxacin, trimethoprim-sulfamethoxazole and aminoglycosides was common. Of the isolates, 38.5% were co-resistant to these classes plus extended-spectrum cephalosporins, which infers resistance to all easily available antibiotic agents for treatment of gram-negative sepsis in Guinea-Bissau. The predominant resistance-encoding gene subgroup was bla(CTX-M-1) and epidemiologic typing showed that the bacterial ESBL population was highly diverse both for E. coli and K. pneumoniae. Bed sharing with another child <5 years of age was a risk factor for ESBL carriage, indicating crowding as a potential risk factor for transmission of ESBL-producing bacteria. Conclusions/significance: Prevalence of ESBL-producing bacteria in this population was high and clonally diverse. This is alarming considering the limited diagnostic and treatment possibilities in Guinea-Bissau and other resource-poor countries.
MeSH term(s)	Adolescent ; Anti-Bacterial Agents/pharmacology ; Child ; Child, Preschool ; Cross Infection ; Cross-Sectional Studies ; Enterobacteriaceae Infections/epidemiology ; Enterobacteriaceae Infections/microbiology ; Escherichia coli/drug effects ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Feces/microbiology ; Guinea-Bissau ; Humans ; Infant ; Infant, Newborn ; Klebsiella pneumoniae/drug effects ; Klebsiella pneumoniae/genetics ; Klebsiella pneumoniae/metabolism ; Microbial Sensitivity Tests ; Prevalence ; Risk Factors ; beta-Lactam Resistance/genetics ; beta-Lactamases/biosynthesis ; beta-Lactamases/genetics
Chemical Substances	Anti-Bacterial Agents ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2012-12-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0051981
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Article ; Online: Four genotyping schemes for phylogenetic analysis of Pseudomonas aeruginosa: comparison of their congruence with multi-locus sequence typing.

Maâtallah, Makaoui / Bakhrouf, Amina / Habeeb, Muhammed Asif / Turlej-Rogacka, Agata / Iversen, Aina / Pourcel, Christine / Sioud, Olfa / Giske, Christian G

PloS one

2013 Volume 8, Issue 12, Page(s) e82069

Abstract: Several molecular typing schemes have been proposed to differentiate among isolates and clonal groups, and hence establish epidemiological or phylogenetic links. It has been widely accepted that multi-locus sequence typing (MLST) is the gold standard for ...

Abstract	Several molecular typing schemes have been proposed to differentiate among isolates and clonal groups, and hence establish epidemiological or phylogenetic links. It has been widely accepted that multi-locus sequence typing (MLST) is the gold standard for phylogenetic typing/long-term epidemiological surveillance, but other recently described methods may be easier to carry out, especially in settings with limited access to DNA sequencing. Comparing the performance of such techniques to MLST is therefore of relevance. A study was therefore carried out with a collection of P. aeruginosa strains (n = 133) typed by four typing schemes: MLST, multiple-locus variable number tandem repeat analysis (MLVA), pulsed-field gel electrophoresis (PFGE) and the commercial DiversiLab microbial typing system (DL). The aim of this study was to compare the results of each typing method with MLST. The Simpson's indices of diversity were 0.989, 0.980, 0.961 and 0.906 respectively for PFGE, MLVA, DL and MLST. The congruence between techniques was measured by the adjusted Wallace index (W): this coefficient indicates the probability that a pair of isolates which is assigned to the same type by one typing method is also typed as identical by the other. In this context, the congruence between techniques was recorded as follow: MLVA-type to predict MLST-type (93%), PFGE to MLST (92%), DL to MLST (64.2%), PFGE to MLVA (63.5%) and PFGE to DL (61.7%). Conversely, for all above combinations, prediction was very poor. The congruence was increased at the clonal complex (CC) level. MLST is regarded the gold standard for phylogenetic classification of bacteria, but is rather laborious to carry out in many settings. Our data suggest that MLVA can predict the MLST-type with high accuracy, and even higher when studying the clonal complex level. Of the studied three techniques MLVA was therefore the best surrogate method to predict MLST.
MeSH term(s)	Electrophoresis, Gel, Pulsed-Field ; Genotype ; Genotyping Techniques/methods ; Minisatellite Repeats/genetics ; Multilocus Sequence Typing/methods ; Phylogeny ; Pseudomonas aeruginosa/classification ; Pseudomonas aeruginosa/genetics ; Pseudomonas aeruginosa/isolation & purification
Language	English
Publishing date	2013-12-11
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0082069
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