Utility of 16S <scp>rDNA</scp> Sequencing for Identification of Rare Pathogenic Bacteria

Loong, Shih Keng; Khor, Chee‐Sieng; Jafar, Faizatul Lela; AbuBakar, Sazaly

doi:10.1002/jcla.21980

Cited by 30 publications

(24 citation statements)

References 19 publications

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“…In contrast to 16S analyses, Whole Metagenome Sequencing (WMS) enables the analysis of the microbial phylogenetic composition and functional diversity 87 . WMS may detect microheterogeneity and genetic intraspecies variations, while bypassing the introduction of additional biases during the PCR amplification steps required in 16S rRNA gene analysis 87 , 88 . In addition, the high similarity of 16S rRNA amplicon sequences impairs the taxonomic resolution 89 .…”

Section: Discussionmentioning

confidence: 99%

A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America

San‐Juan‐Vergara

Zurek

Ajami

et al. 2018

Sci Rep

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HIV infection has a tremendous impact on the immune system's proper functioning. The mucosaassociated lymphoid tissue (MALT) is significantly disarrayed during HIV infection.Compositional changes in the gut microbiota might contribute to the mucosal barrier disruption, and consequently to microbial translocation. We performed an observational, cross-sectional study aimed at evaluating changes in the fecal microbiota of HIV-infected individuals from Colombia. We analyzed the fecal microbiota of 37 individuals via 16S rRNA gene sequencing; 25 HIV-infected patients and 12 control (non-infected) individuals, which were similar in body mass index, age, gender balance and socioeconomic status. To the best of our knowledge, no such studies have been conducted in Latin American countries. Given its compositional nature, microbiota data were normalized and transformed using Aitchison's Centered Log-Ratio. Overall, a change in the network structure in HIV-infected patients was revealed by using the SPIEC-EASI MB tool. Genera such as Blautia, Dorea, Yersinia, Escherichia-Shigella complex, Staphylococcus, and Bacteroides were highly relevant in HIV-infected individuals. Differential abundance analysis by both sparse Partial Least Square-Discriminant Analysis and Random Forest identified a greater abundance of Lachnospiraceae-OTU69, Blautia, Dorea, Roseburia, and Erysipelotrichaceae in HIV-infected individuals. We show here, for the first time, a predominantly Lachnospiraceae-based signature in HIV-infected individuals.The health complications arising from HIV infection associated to developing acquired immunodeficiency syndrome impose a heavy physical and psychological toll on people 1 . Approximately 78 million people have been diagnosed with HIV, of whom ~35 million people have died. In 2015 alone, there were 36.7 million people living with HIV 1,2 . Among the 4 HIV groups, M is the most widely distributed group and is comprised of nine subtypes. Subtype C is responsible for about one-half of all global infections, while subtype B, the prevalent virus in Colombia, is the most widespread 3,4 . A mucosal barrier integrated by the intestinal epithelium and the underlying immune system favors tolerance towards bacteria present in the intestine lumen [5][6][7][8][9] . Commensal bacteria of the intestinal microbiota also contribute to the mucosal barrier by competing for space and resources with potentially pathobiontic bacteria 10 . HIV

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Section: Discussionmentioning

confidence: 99%

A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America

San‐Juan‐Vergara

Zurek

Ajami

et al. 2018

Sci Rep

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“…Chromosomal DNA of all pure-cultured bacteria isolates was extracted using NucleoSpin Tissue kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions. Subsequently, 16S rDNA sequencing [ 18 ] was performed to identify the respective isolates’ species identity. Only members of the genus Bordetella were selected for this study and they were stocked in −80°C until further use.…”

Section: Methodsmentioning

confidence: 99%

Recovery of <i>Bordetella bronchiseptica</i> sequence type 82 and <i>B. pseudohinzii</i> from urban rats in Terengganu, Malaysia

Loong

Che-Mat-Seri

Osama

et al. 2018

The Journal of Veterinary Medical Science

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Rodents have historically been associated with zoonotic pandemics that claimed the lives of large human populations. Appropriate pathogen surveillance initiatives could contribute to early detection of zoonotic infections to prevent future outbreaks. Bordetella species are bacteria known to cause mild to severe respiratory disease in mammals and, some have been described to infect, colonize and spread in rodents. There is a lack of information on the population diversity of bordetellae among Malaysian wild rodents. Here, bordetellae recovered from lung tissues of wild rats were genotypically characterized using 16S rDNA sequencing, MLST and nrdA typing. A novel B. bronchiseptica ST82, closely related to other human-derived isolates, was discovered in three wild rats (n=3) from Terengganu (5.3333° N, 103.1500° E). B. pseudohinzii, a recently identified laboratory mice inhabitant, was also recovered from one rat (n=1). Both bordetellae displayed identical antimicrobial resistance profiles, indicating the close phylogenetic association between them. Genotyping using the 765-bp nrdA locus was shown to be compatible with the MLST-based phylogeny, with the added advantage of being able to genotype non-classical bordetellae. The recovery of B. pseudohinzii from wild rat implied that this bordetellae has a wider host range than previously thought. The findings from this study suggest that bordetellae surveillance among wild rats in Malaysia has to be continued and expanded to other states to ensure early identification of species capable of causing public health disorder.

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“…To date, little is known on the prevalence of culturable pathogenic bacteria harbored within ticks. Bacterial culture and isolation are essential as they have long been accepted as the gold standard for laboratory confirmation of bacterial infections (Loong et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Culturable pathogenic bacteria in ticks parasitizing farm animals and rodents in Malaysia

et al. 2020

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Utility of 16S rDNA Sequencing for Identification of Rare Pathogenic Bacteria

Cited by 30 publications

References 19 publications

A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America

A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America

Recovery of <i>Bordetella bronchiseptica</i> sequence type 82 and <i>B. pseudohinzii</i> from urban rats in Terengganu, Malaysia

Culturable pathogenic bacteria in ticks parasitizing farm animals and rodents in Malaysia

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