Upper airway microbiota development in infants with cystic fibrosis diagnosed by newborn screen

BACKGROUND

Changes in upper airway microbiota may impact early disease manifestations in infants with cystic fibrosis (CF). To investigate early airway microbiota, the microbiota present in the oropharynx of CF infants over the first year of life was assessed along with the relationships between microbiota and growth, antibiotic use and other clinical variables.

METHODS

Oropharyngeal (OP) swabs were collected longitudinally between 1 and 12 months of age from infants diagnosed with CF by newborn screen and enrolled in the Baby Observational and Nutrition Study (BONUS). DNA extraction was performed after enzymatic digestion of OP swabs. Total bacterial load was determined by qPCR and community composition assessed using 16S rRNA gene analysis (V1/V2 region). Changes in diversity with age were evaluated using mixed models with cubic B-splines. Associations between clinical variables and bacterial taxa were determined using a canonical correlation analysis.

RESULTS

1,052 OP swabs collected from 205 infants with CF were analyzed. Most infants (77%) received at least one course of antibiotics during the study and 131 OP swabs were collected while the infant was prescribed an antibiotic. Alpha diversity increased with age and was only marginally impacted by antibiotic use. Community composition was most highly correlated with age and was only moderately correlated with antibiotic exposure, feeding method and weight z-scores. Relative abundance of Streptococcus decreased while Neisseria and other taxa increased over the first year.

CONCLUSIONS

Age was more influential on the oropharyngeal microbiota of infants with CF than clinical variables including antibiotics in the first year of life.

Blastocystis subtypes in raw vegetables from street markets in northern Thailand

Blastocystis is a stramenopile protist of controversial pathogenicity. The organism colonizes a broad range of vertebrate and invertebrate hosts. Blastocystis has also been found in the environment both in water and soil. Several routes of transmission have been proposed including human to human, animal to human, and via contaminated food and water. In recent years, the presence of Blastocystis in vegetables has started to be explored. However, most studies have focused on microscopic detection. Moreover, works of this type from Asia are barely available. Hence, the aim of this preliminary study was to examine the occurrence of Blastocystis in raw vegetables sold in markets in northern Thailand. Fresh produce (n = 20) commonly used in Thai cuisine (Lanna) was purchased from two street markets and screened for Blastocystis using qPCR. Blastocystis was detected in 45% of the samples with the dominant subtype being ST3. Produce growing underground, such as galangal, carrot, and beetroot, were positive for the organism suggesting soil or inadequately composted manure as the source of contamination. To our knowledge, our study is the first to perform subtyping of Blastocystis in vegetables. Our results hint toward fresh produce being a, as yet, not widely explored, transmission route of Blastocystis in the studied community. Looking forward, large-scale investigations on the prevalence of this and other organisms under the One Health umbrella should be undertaken.

[Prevalence and molecular characterization of Cryptosporidium in captive-bred Mustela putorius furo in Jiangsu Province]

OBJECTIVE

To investigate the prevalence and molecular features of Cryptosporidium in captive-bred Mustela putorius furo in Jiangsu Province.

METHODS

A total of 290 fresh stool samples were collected from a ferret farm in Jiangsu Province on May 2017, and the small subunit rRNA (SSU rRNA) gene of Cryptosporidium was amplified in stool samples using nested PCR assay. The actin, cowp and gp60 genes were amplified in positive samples and sequenced to characterize Cryptosporidium species/genotypes.

RESULTS

A total of 18 stool samples were tested positive for Cryptosporidium SSU rRNA gene, with a detection rate of 6.2%. Sequence and phylogenetic analyses of SSU rRNA, actin and cowp genes characterized Cryptosporidium isolated from captive-bred ferrets as Cryptosporidium sp. ferret genotype. In addition, gp60 gene was amplified in 10 out of 18 stool samples tested positive for Cryptosporidium.

CONCLUSIONS

Cryptosporidium is widely prevalent in captive-bred ferrets in Jiangsu Province, and Cryptosporidium sp. ferret genotype is the only Cryptosporidium genotype in ferrets.

Blastocystis in tap water of a community in northern Thailand

Blastocystis is the most common protist in the gut of humans and other animals having global distribution. Occasionally, this organism has also been reported in the environment. Transmission to humans occurs via the fecal-oral route, while water also comprises a transmission route. Blastocystis has been commonly found in rivers, lakes, and wells. Nonetheless, there is limited data about the prevalence and genetic diversity of Blastocystis in tap water. The main aim of this study was to examine the presence of Blastocystis subtypes in tap water (n=20) in a community in northern Thailand. Molecular characterization using the small subunit ribosomal RNA was used to screen for Blastocystis and identify the diversity of subtypes in samples. The overall prevalence was 30% with only subtype three (ST3) encountered in the tap water. These results indicate that tap water has a potential role in the transmission of this subtype in the studied community. Further investigations should focus on expanding sampling to include additional housing complexes and screening for Blastocystis in humans who are exposed to this water.

Multilocus genotyping of Giardia duodenalis from pigs in Korea

Giardia duodenalis (syn. G. intestinalis, G. lamblia) is an important zoonotic parasite infecting livestock (including pigs) through ingesting cysts in contaminated food or water. This parasite has been classified into eight different genetic assemblages, A to H. Here, we examined the individual-level prevalence of G. duodenalis in domestic pig farms and confirmed host specificity by genotype comparisons. Samples were collected from southern and central Korea, between May 2017 and January 2019. DNA directly extracted from 745 pig fecal specimens were tested by PCR for G. duodenalis small subunit ribosomal RNA (ssu rRNA), glutamate dehydrogenase (gdh), and β-giardin gene sequences. Based on ssu rRNA PCR, 110 (14.8%) were positive for G. duodenalis. Infection risk was the highest in the fattener group (31/139, 22.3%) and during the autumn season (52/245, 21.2%: p < .001). No statistically significant differences in risk for infection were observed between fecal types (normal versus diarrheal). Fifty ssu rRNA samples, three gdh samples, and five β-giardin samples were successfully sequenced and genotyped. Ssu rRNA assemblage sequence analysis identified E (40.0%, 20/50), D (34.0%, 17/50), C (24.0%, 12/50), and A (2.0%, 1/50). The gdh locus identified three samples as assemblage E, and the β-giardin locus identified four samples as assemblage E and one as assemblage C. Assemblage A sequences obtained (ssu rRNA; MK430919) had 100% identity with Giardia sequences isolated from a Korean individual (AJ293301), indicating the potential of zoonotic transmission. Continuous management and monitoring for prevention of transmission and protection of animal and human health are essential.

Visual assessment of parasitic burden in infected macrophage by plasmonic detection of leishmania specific marker RNA

Visceral leishmaniasis is a neglected tropical disease and may prove fatal if not diagnosed and treated early. The amastigotes of Leishmania donovani nest in the macrophage of human host and thus, determination of parasitic burden in the infected macrophages has been the most crucial step in diagnosis, dose determination and medical management of relapse cases of this fatal disease. Microscopic count following Giemsa staining and other morphological analysis are the classical ways vastly used in the resource stringent endemic areas. The current method introduced a high throughput, rapid, cheap, non-gel, non-PCR and nonculture based visual detection platform employing salt triggered aggregation of gold nanoparticle in presence of extracted total RNA from infected macrophages and leishmania specific oligo-nucleotide probe to determine the parasite burden in macrophages. Amastigote's small subunit ribosomal RNA (SSU rRNA, PMID 1565128) was used as the leishmania specific marker and its abundance in the total RNA extracts of infected macrophages were determined by this visual colorimetric assay.

Natural infection of Plasmodium brasilianum in humans: Man and monkey share quartan malaria parasites in the Venezuelan Amazon

Background

The quartan malaria parasite Plasmodium malariae is the widest spread and best adapted human malaria parasite. The simian Plasmodium brasilianum causes quartan fever in New World monkeys and resembles P. malariae morphologically. Since the genetics of the two parasites are nearly identical, differing only in a range of mutations expected within a species, it has long been speculated that the two are the same. However, no naturally acquired infection with parasites termed as P. brasilianum has been found in humans until now.

Methods

We investigated malaria cases from remote Yanomami indigenous communities of the Venezuelan Amazon and analyzed the genes coding for the circumsporozoite protein (CSP) and the small subunit of ribosomes (18S) by species-specific PCR and capillary based-DNA sequencing.

Findings

Based on 18S rRNA gene sequencing, we identified 12 patients harboring malaria parasites which were 100% identical with P. brasilianum isolated from the monkey, Alouatta seniculus. Translated amino acid sequences of the CS protein gene showed identical immunodominant repeat units between quartan malaria parasites isolated from both humans and monkeys.

Interpretation

This study reports, for the first time, naturally acquired infections in humans with parasites termed as P. brasilianum. We conclude that quartan malaria parasites are easily exchanged between humans and monkeys in Latin America. We hypothesize a lack of host specificity in mammalian hosts and consider quartan malaria to be a true anthropozoonosis. Since the name P. brasilianum suggests a malaria species distinct from P. malariae, we propose that P. brasilianum should have a nomenclatorial revision in case further research confirms our findings. The expansive reservoir of mammalian hosts discriminates quartan malaria from other Plasmodium spp. and requires particular research efforts.

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We found human infections with ‘Plasmodium brasilianum’, a quartan malaria parasite of New World monkeys in South America

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We show that in areas of close contact humans and non-human primates are concurrently infected with quartan malaria parasites

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We conclude that quartan malaria parasites can transcend host species boundaries with impunity

We found naturally acquired infections in humans with Plasmodium brasilianum parasites, a quartan malaria parasite which usually infects more than 35 monkey species in South America. This confirms that malaria parasites, which cause the quartan type of fever (two days without fever between fever peaks), are easily exchanged between humans and monkeys in Latin America. The wide host reservoir of quartan malaria parasites requires particular malaria research efforts.