Effects of Vaccination with 10-Valent Pneumococcal Non-Typeable Haemophilus influenza Protein D Conjugate Vaccine (PHiD-CV) on the Nasopharyngeal Microbiome of Kenyan Toddlers.

OBJECTIVE: Pneumococcal conjugate vaccines reduce the prevalence of vaccine serotypes carried in the nasopharynx. Because this could alter carriage of other potential pathogens, we assessed the nasopharyngeal microbiome of children who had been vaccinated with 10-valent pneumococcal non-typeable Haemophilus influenzae protein-D conjugate vaccine (PHiD-CV). METHODS: Profiles of the nasopharyngeal microbiota of 60 children aged 12-59 months, who had been randomized to receive 2 doses of PHiD-CV (n=30) or Hepatitis A vaccine (n=30) 60 days apart, were constructed by 16S rRNA gene pyrosequencing of swab specimens collected before vaccination and 180 days after dose 1. RESULTS: Prior to vaccination, Moraxella catarrhalis (median of 12.3% of sequences/subject), Streptococcus pneumoniae (4.4%) and Corynebacterium spp. (5.6%) were the most abundant nasopharyngeal bacterial species. Vaccination with PHiD-CV did not significantly alter the species composition, abundance, or prevalence of known pathogens. Distinct microbiomes were identified based on the abundances of Streptococcus, Moraxella, and Haemophilus species. These microbiomes shifted in composition over the study period and were independent of age, sex, school attendance, antibiotic exposure, and vaccination. CONCLUSIONS: Vaccination of children with two doses of PHiD-CV did not significantly alter the nasopharyngeal microbiome. This suggests limited replacement carriage with pathogens other than non-vaccine strains of S. pneumoniae. TRIAL REGISTRATION: clinicaltrials.gov NCT01028326

The Human Nasal Microbiota and Staphylococcus aureus Carriage

BACKGROUND: Colonization of humans with Staphylococcus aureus is a critical prerequisite of subsequent clinical infection of the skin, blood, lung, heart and other deep tissues. S. aureus persistently or intermittently colonizes the nares of approximately 50% of healthy adults, whereas approximately 50% of the general population is rarely or never colonized by this pathogen. Because microbial consortia within the nasal cavity may be an important determinant of S. aureus colonization we determined the composition and dynamics of the nasal microbiota and correlated specific microorganisms with S. aureus colonization. METHODOLOGY/PRINCIPAL FINDINGS: Nasal specimens were collected longitudinally from five healthy adults and a cross-section of hospitalized patients (26 S. aureus carriers and 16 non-carriers). Culture-independent analysis of 16S rRNA sequences revealed that the nasal microbiota of healthy subjects consists primarily of members of the phylum Actinobacteria (e.g., Propionibacterium spp. and Corynebacterium spp.), with proportionally less representation of other phyla, including Firmicutes (e.g., Staphylococcus spp.) and Proteobacteria (e.g. Enterobacter spp). In contrast, inpatient nasal microbiotas were enriched in S. aureus or Staphylococcus epidermidis and diminished in several actinobacterial groups, most notably Propionibacterium acnes. Moreover, within the inpatient population S. aureus colonization was negatively correlated with the abundances of several microbial groups, including S. epidermidis (p = 0.004). CONCLUSIONS/SIGNIFICANCE: The nares environment is colonized by a temporally stable microbiota that is distinct from other regions of the integument. Negative association between S. aureus, S. epidermidis, and other groups suggests microbial competition during colonization of the nares, a finding that could be exploited to limit S. aureus colonization

Microbiological water quality monitoring in a resource-limited urban area: a study in Cameroon, Africa

In resource-limited developing nations, such as Cameroon, the expense of modern water-quality monitoring techniques is prohibitive to frequent water testing, as is done in the developed world. Inexpensive, shelf-stable 3M™ Petrifilm™ Escherichia coli/Coliform Count Plates potentially can provide significant opportunity for routine water-quality monitoring in the absence of infrastructure for state-of-the-art testing. We used shelf-stable E. coli/coliform culture plates to assess the water quality at twenty sampling sites in Kumbo, Cameroon. Culture results from treated and untreated sources were compared to modern bacterial DNA pyrosequencing methods using established bioinformatics and statistical tools. Petrifilms were reproducible between replicates and sampling dates. Additionally, cultivation on Petrifilms suggests that treatment by the Kumbo Water Authority (KWA) greatly improves water quality as compared with untreated river and rainwater. The majority of sequences detected were representative of common water and soil microbes, with a minority of sequences (<40%) identified as belonging to genera common in fecal matter and/or causes of human disease. Water sources had variable DNA sequence counts that correlated significantly with the culture count data and may therefore be a proxy for bacterial load. Although the KWA does not meet Western standards for water quality (less than one coliform per 100 mL), KWA piped water is safer than locally available alternative water sources such as river and rainwater. The culture-based technology described is easily transferrable to resource-limited areas and provides local water authorities with valuable microbiological safety information with potential to protect public health in developing nations

The microbiome of the middle meatus in healthy adults.

Rhinitis and rhinosinusitis are multifactorial disease processes in which bacteria may play a role either in infection or stimulation of the inflammatory process. Rhinosinusitis has been historically studied with culture-based techniques, which have implicated several common pathogens in disease states. More recently, the NIH Human Microbiome Project has examined the microbiome at a number of accessible body sites, and demonstrated differences among healthy and diseased patients. Recent DNA-based sinus studies have suggested that healthy sinuses are not sterile, as was previously believed, but the normal sinonasal microbiome has yet to be thoroughly examined. Middle meatus swab specimens were collected from 28 consecutive patients presenting with no signs or symptoms of rhinosinusitis. Bacterial colonization was assessed in these specimens using quantitative PCR and 16S rRNA pyrosequencing. All subjects were positive for bacterial colonization of the middle meatus. Staphylococcus aureus, Staphylococcus epidermidis and Propionibacterium acnes were the most prevalent and abundant microorganisms detected. Rich and diverse bacterial assemblages are present in the sinonasal cavity in the normal state, including opportunistic pathogens typically found in the nasopharynx. This work helps establish a baseline for understanding how the sinonasal microbiome may impact diseases of the upper airways

Eucaryotic Diversity in a Hypersaline Microbial Mat▿ †

To determine the eucaryotic diversity of the hypersaline Guerrero Negro microbial mat, we amplified 18S rRNA genes from DNA extracted from this mat and constructed and analyzed clone libraries. The extent of eucaryotic diversity detected was remarkably low, only 15 species among 890 clones analyzed. Six eucaryotic kingdoms were represented, as well as a novel cluster of sequences. Nematode sequences dominated the clone libraries

Phylum- and species-level diversity.

<p>(A) Phylum-level classification for each subject demonstrates community diversity, but also variability between subjects. Only phyla with median relative abundances greater than 0.5% are shown. (B) Species-level analysis with a minimum 0.5% abundance demonstrates diversity and variability between subjects.</p

Effects of smoking on the healthy microbiome.

<p>Differences in the species-level (panel A) percent relative abundances of 16S rRNA sequences between subjects categorized by history of smoking are shown. Only taxa with percent relative abundances greater than 0.5% are included; the abundant species are normalized to 100% in order to better depict between-group differences. Although multivariate analyses of microbiome datasets did not reveal a significant association between smoking and microbiome composition (p = 0.15), select taxa differed significantly in percent relative abundance between smoking categories (panel B).</p

Age-associated differences in the healthy microbiome.

<p>Differences in the phylum-level (panel A) and species-level (panel B) percent relative abundances of 16S rRNA sequences between subjects categorized by age (over or under 50 years of age) are shown. Only taxa with percent relative abundances greater than 0.5% are included; the abundant species are normalized to 100% in order to better depict between-group differences. Multivariate analyses of microbiome datasets revealed significant differences at both the phylum-level (*: p = 0.03) and species-level (**: p = 0.004).</p