Mixed models: getting the best use of parasitological data

Paterson, Steve; Lello, Joanne

doi:10.1016/s1471-4922(03)00149-1

Cited by 127 publications

(108 citation statements)

References 28 publications

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“…The influence of sample characteristics on identification results was assessed in a mixed-model approach accounting for cluster effects due to the inclusion of multiple aerobic and anaerobic culture bottles per patient (leading to pseudoreplicate observations on isogenic bacteria) (33). Using the MIXED procedure from the SPSS statistics software (version 16; SPSS Inc., Chicago), identification scores from direct mass spectrometry fingerprinting were modeled as a function of sample characteristics (culture condition, culture age, date of measurement, Gram reactivity, and type of organism) as fixed effects and replication as a random effect.…”

Section: Methodsmentioning

confidence: 99%

Rapid Identification of Bacteria from Positive Blood Culture Bottles by Use of Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Fingerprinting

Martin¹,

Rohde²,

Wolters³

et al. 2010

J Clin Microbiol

266

200

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Early and adequate antimicrobial therapy has been shown to improve the clinical outcome in bloodstream infections (BSI). To provide rapid pathogen identification for targeted treatment, we applied matrix-assisted laser desorption-ionization time of flight (MALDI-TOF) mass spectrometry fingerprinting to bacteria directly recovered from blood culture bottles. A total of 304 aerobic and anaerobic blood cultures, reported positive by a Bactec 9240 system, were subjected in parallel to differential centrifugation with subsequent mass spectrometry fingerprinting and reference identification using established microbiological methods. A representative spectrum of bloodstream pathogens was recovered from 277 samples that grew a single bacterial isolate. Species identification by direct mass spectrometry fingerprinting matched reference identification in 95% of these samples and worked equally well for aerobic and anaerobic culture bottles. Application of commonly used score cutoffs to classify the fingerprinting results led to an identification rate of 87%. Mismatching mostly resulted from insufficient bacterial numbers and preferentially occurred with Gram-positive samples. The respective spectra showed low concordance to database references and were effectively rejected by score thresholds. Spiking experiments and examination of the respective study samples even suggested applicability of the method to mixed cultures. With turnaround times around 100 min, the approach allowed for reliable pathogen identification at the day of blood culture positivity, providing treatment-relevant information within the critical phase of septic illness.

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Section: Methodsmentioning

confidence: 99%

Rapid Identification of Bacteria from Positive Blood Culture Bottles by Use of Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Fingerprinting

Martin¹,

Rohde²,

Wolters³

et al. 2010

J Clin Microbiol

266

200

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“…GLMM was used because it allowed us to pool all native bird species, by using individual infection status (infected or not) as the dependent variable, while controlling for sample size difference. Thus, information is not lost due to sample size restriction, since more weight will be given to data with larger sample size (Paterson andLello 2003, Jovani andTella 2006). In addition, GLMM is a powerful method to analyse parasitological data because it allows for the use of data that are not normally distributed, such as presence and absence data (infected or not), while controlling for correlations between measures that occur as a result of grouped observations (Paterson and Lello 2003).…”

Section: Statistical Analysesmentioning

confidence: 99%

“…Thus, information is not lost due to sample size restriction, since more weight will be given to data with larger sample size (Paterson andLello 2003, Jovani andTella 2006). In addition, GLMM is a powerful method to analyse parasitological data because it allows for the use of data that are not normally distributed, such as presence and absence data (infected or not), while controlling for correlations between measures that occur as a result of grouped observations (Paterson and Lello 2003). Furthermore, according to Sodhi et al (2008), GLMM are more appropriate than independent contrast analysis when categorical variables are included in the analysis, hence species can be used as a random effect to encompass variation among species and therefore control for phylogenetic effects (Bolker et al 2009).…”

Section: Statistical Analysesmentioning

confidence: 99%

Low prevalence of haemosporidian parasites in the introduced house sparrow (Passer domesticus) in Brazil

Lima¹,

Simpson

Fecchio

et al. 2010

Acta Parasitologica

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Species that are introduced to novel environments can lose their native pathogens and parasites during the process of introduction. The escape from the negative effects associated with these natural enemies is commonly employed as an explanation for the success and expansion of invasive species, which is termed the enemy release hypothesis (ERH). In this study, nested PCR techniques and microscopy were used to determine the prevalence and intensity (respectively) of Plasmodium spp. and Haemoproteus spp. in introduced house sparrows and native urban birds of central Brazil. Generalized linear mixed models were fitted by Laplace approximation considering a binomial error distribution and logit link function. Location and species were considered as random effects and species categorization (native or non-indigenous) as fixed effects. We found that native birds from Brazil presented significantly higher parasite prevalence in accordance with the ERH. We also compared our data with the literature, and found that house sparrows native to Europe exhibited significantly higher parasite prevalence than introduced house sparrows from Brazil, which also supports the ERH. Therefore, it is possible that house sparrows from Brazil might have experienced a parasitic release during the process of introduction, which might also be related to a demographic release (e.g. release from the negative effects of parasites on host population dynamics).

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“…Effects of treatment on the amount of DM, ADF, N, and TP were analysed using a mixed model analysis of variance with site as a random factor and treatment and month as fixed factors (Bennington and Thayne 1994;Paterson and Lello 2003). Interactions were allowed up to the second degree, as higher degree interactions are difficult to interpret.…”

Section: Data Treatment and Statistical Analysesmentioning

confidence: 99%

Simulated winter browsing may lead to induced susceptibility of willows to beavers in spring

et al. 2006

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Browsing may lead to an induced resistance or susceptibility of the plant to the herbivore. We tested the effect of winter browsing by Eurasian beavers (Castor fiber L., 1758) on food quality of holme willows (Salix dasyclados Wimm.) in and after the following growth season. Shrubs were pruned in February, and new shoots from these (cut) shrubs were compared with those of untreated (uncut) ones in May and November. The shoots were analysed for dry matter, nitrogen, acid detergent fibre, and total phenolics. In May, the leaves from the cut treatment had a better food quality (more water, more nitrogen, and less phenolics) than those from the uncut one. There was in part also a systemic response, with lower total phenolics in both the cut and untreated parts of pruned shrubs (uncut-cut) than in the uncut shrubs. In November, we did not find significant differences in biochemistry of bark among cut, uncut, or uncut-cut treatments. These results are in accordance with a cafeteria experiment in the field: in May the beavers preferred shoots from the cut treatment, but in November they showed no preference. The results suggest that willows invest in compensatory growth rather than a defence response early in the regrowing phase.Résumé : Le broutement peut provoquer chez la plante soit une résistance soit une vulnérabilité à l'herbivore. Nous avons vérifié l'effet du broutement en hiver par les castors d'Europe (Castor fiber L., 1758) sur la qualité de la nourriture fournie par le saule à rameaux velus (Salix dasyclados Wimm.) durant la saison suivante de croissance et par la suite. Nous avons émondé les buissons en février et comparé en mai et en novembre les nouvelles pousses de ces buissons « taillés » à celles de buissons « non taillés ». Nous avons soumis les pousses à des analyses de matière sèche, d'azote, de fibres au détergent acide et de substances phénoliques totales. En mai, les feuilles des buissons taillés représentent une nourriture de meilleure qualité (plus d'eau, plus d'azote, moins de substances phénoliques) que celles des buissons non taillés. Il y a aussi une ré-action systématique partielle, puisque les concentrations de substances phénoliques totales, tant dans les parties émondées que non émondées (« non taillés -taillés ») des buissons ébranchés, sont moins importantes que dans les buissons non traités. En novembre, il n'existe pas de différence biochimique significative entre les écorces des buissons taillés, non taillés et non taillés -taillés. Ces données s'accordent avec les résultats d'une expérience de type cafétéria faite en nature: en mai, les castors préfèrent les pousses provenant de buissons taillés, mais en novembre ils ne montrent aucune préfér-ence. Ces observations indiquent que les saules investissent en une croissance compensatoire plutôt qu'en une réaction de défense durant les premières phases de la régénération.[Traduit par la Rédaction]

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Mixed models: getting the best use of parasitological data

Cited by 127 publications

References 28 publications

Rapid Identification of Bacteria from Positive Blood Culture Bottles by Use of Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Fingerprinting

Rapid Identification of Bacteria from Positive Blood Culture Bottles by Use of Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Fingerprinting

Low prevalence of haemosporidian parasites in the introduced house sparrow (Passer domesticus) in Brazil

Simulated winter browsing may lead to induced susceptibility of willows to beavers in spring

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