Comparison of the identification of coagulase-negative staphylococci by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and tuf sequencing

The increasing incidence of coagulase-negative staphylococci (CoNS) in hospital-acquired infections underlines the need for an accurate and simple identification of Staphylococcus isolates at the species level. Sequencing of the tuf gene has been shown to be the most accurate for the species identification of CoNS. We determined the species of 62 consecutive clinical and 31 reference CoNS isolates by tuf gene sequencing and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Species assignment by MALDI-TOF-MS and tuf sequencing was congruent in all cases. We conclude that MALDI-TOF-MS is accurate for identifying CoNS in routine clinical practice. The study also identified an unexpectedly high number of cases of Staphylococcus capitis infections among 62 consecutive CoNS isolates in 2009 at the University Medical Center Utrecht, the Netherlands

IS element IS16 as a molecular screening tool to identify hospital-associated strains of Enterococcus faecium

<p>Abstract</p> <p>Background</p> <p>Hospital strains of <it>Enterococcus faecium </it>could be characterized and typed by various molecular methods (MLST, AFLP, MLVA) and allocated to a distinct clonal complex known as MLST CC17. However, these techniques are laborious, time-consuming and cost-intensive. Our aim was to identify hospital <it>E. faecium </it>strains and differentiate them from colonizing and animal variants by a simple, inexpensive and reliable PCR-based screening assay. We describe here performance and predictive value of a single PCR detecting the insertion element, IS<it>16</it>, to identify hospital <it>E. faecium </it>isolates within a collection of 260 strains of hospital, animal and human commensal origins.</p> <p>Methods</p> <p>Specific primers were selected amplifying a 547-bp fragment of IS<it>16</it>. Presence of IS<it>16 </it>was determined by PCR screenings among the 260 <it>E. faecium </it>isolates. Distribution of IS<it>16 </it>was compared with a prevalence of commonly used markers for hospital strains, <it>esp </it>and <it>hyl</it>_<it>Efm</it>. All isolates were typed by MLST and partly by PFGE. Location of IS<it>16 </it>was analysed by Southern hybridization of plasmid and chromosomal DNA.</p> <p>Results</p> <p>IS<it>16 </it>was exclusively distributed only among 155 invasive strains belonging to the clonal complex of hospital-associated strains ("CC17"; 28 MLST types) and various vancomycin resistance genotypes (<it>van</it>A/B/negative). The five invasive IS<it>16</it>-negative strains did not belong to the clonal complex of hospital-associated strains (CC17). IS<it>16 </it>was absent in all but three isolates from 100 livestock, food-associated and human commensal strains ("non-CC17"; 64 MLST types). The three IS<it>16</it>-positive human commensal isolates revealed MLST types belonging to the clonal complex of hospital-associated strains (CC17). The values predicting a hospital-associated strain ("CC17") deduced from presence and absence of IS<it>16 </it>was 100% and thus superior to screening for the presence of <it>esp </it>(66%) and/or <it>hyl</it>_{<it>Efm </it>}(46%). Southern hybridizations revealed chromosomal as well as plasmid localization of IS<it>16</it>.</p> <p>Conclusions</p> <p>This simple screening assay for insertion element IS<it>16 </it>is capable of differentiating hospital-associated from human commensal, livestock- and food-associated <it>E. faecium </it>strains and thus allows predicting the epidemic strengths or supposed pathogenic potential of a given <it>E. faecium </it>isolate identified within the nosocomial setting.</p

Molecular characterization of MRSA collected during national surveillance between 2008 and 2019 in the Netherlands

Background.Although the Netherlands is a country with a low endemic level, methicillin-resistant Staphylococcus aureus (MRSA) poses a significant health care problem. Therefore, high coverage national MRSA surveillance has been in place since 1989. To monitor possible changes in the type-distribution and emergence of resistance and virulence, MRSA isolates are molecularly characterized.Methods.All 43,321 isolates from 36,520 persons, collected 2008–2019, were typed by multiple-locus variable number tandem repeats analysis (MLVA) with simultaneous PCR detection of the mecA, mecC and lukF-PV genes, indicative for PVL. Next-generation sequencing data of 4991 isolates from 4798 persons were used for whole genome multi-locus sequence typing (wgMLST) and identification of resistance and virulence genes.Results.We show temporal change in the molecular characteristics of the MRSA population with the proportion of PVL-positive isolates increasing from 15% in 2008–2010 to 25% in 2017–2019. In livestock-associated MRSA obtained from humans, PVL-positivity increases to 6% in 2017–2019 with isolates predominantly from regions with few pig farms. wgMLST reveals the presence of 35 genogroups with distinct resistance, virulence gene profiles and specimen origin. Typing shows prolonged persistent MRSA carriage with a mean carriage period of 407 days. There is a clear spatial and a weak temporal relationship between isolates that clustered in wgMLST, indicative for regional spread of MRSA strains.Conclusions.Using molecular characterization, this exceptionally large study shows genomic changes in the MRSA population at the national level. It reveals waxing and waning of types and genogroups and an increasing proportion of PVL-positive MRSA

Undernutrition among HIV-positive children in Dar es Salaam, Tanzania: antiretroviral therapy alone is not enough

BackgroundThe prevalence of HIV/AIDS has exacerbated the impact of childhood undernutrition in many developing countries, including Tanzania. Even with the provision of antiretroviral therapy, undernutrition among HIV-positive children remains a serious problem. Most studies to examine risk factors for undernutrition have been limited to the general population and ART-naive HIV-positive children, making it difficult to generalize findings to ART-treated HIV-positive children. The objectives of this study were thus to compare the proportions of undernutrition among ART-treated HIV-positive and HIV-negative children and to examine factors associated with undernutrition among ART-treated HIV-positive children in Dar es Salaam, Tanzania.MethodsFrom September to October 2010, we conducted a cross-sectional survey among 213 ART-treated HIV-positive and 202 HIV-negative children in Dar es Salaam, Tanzania. We measured the children\u27s anthropometrics, socio-demographic factors, food security, dietary habits, diarrhea episodes, economic status, and HIV clinical stage. Data were analyzed using both univariate and multivariate methods.ResultsART-treated HIV-positive children had higher rates of undernutrition than their HIV-negative counterparts. Among the ART-treated HIV-positive children, 78 (36.6%) were stunted, 47 (22.1%) were underweight, and 29 (13.6%) were wasted. Households of ART-treated HIV-positive children exhibited lower economic status, lower levels of education, and higher percentages of unmarried caregivers with higher unemployment rates. Food insecurity was prevalent in over half of ART-treated HIV-positive children\u27s households. Furthermore, ART-treated HIV-positive children were more likely to be orphaned, to be fed less frequently, and to have lower body weight at birth compared to HIV-negative children.In the multivariate analysis, child\u27s HIV-positive status was associated with being underweight (AOR = 4.61, 95% CI 1.38-15.36 P = 0.013) and wasting (AOR = 9.62, 95% CI 1.72-54.02, P = 0.010) but not with stunting (AOR = 0.68, 95% CI 0.26-1.77, P = 0.428). Important factors associated with underweight status among ART-treated HIV-positive children included hunger (AOR = 9.90, P = 0.022), feeding frequency (AOR = 0.02, p \u3c 0.001), and low birth weight (AOR = 5.13, P = 0.039). Factors associated with wasting among ART-treated HIV-positive children were diarrhea (AOR = 22.49, P = 0.001) and feeding frequency (AOR = 0.03, p \u3c 0.001).ConclusionHIV/AIDS is associated with an increased burden of child underweight status and wasting, even among ART-treated children, in Dar es Salaam, Tanzania. In addition to increasing coverage of ART among HIV-positive children, interventions to ameliorate poor nutrition status may be necessary in this and similar settings. Such interventions should aim at promoting adequate feeding patterns, as well as preventing and treating diarrhea