Abstract:
Human pathogens can survive and grow in hot springs. For water quality assessment,
Escherichia coli or Enterococci are the main thermotolerant enteric bacteria commonly used
to estimate the load of pathogenic bacteria in water. However, most of the environmental
bacteria are unculturable thus culture methods may cause bias in detection of most pathogens.
Illumina sequencing can provide a more comprehensive and accurate insight into
environmental bacterial pathogens, which can be used to develop better risk assessment
methods and promote public health awareness. In this study, high-throughput Illumina
sequencing was used to identify bacterial pathogens from five hot springs; Maiwooi, Akwar,
Garbanabra, Elegedi and Gelti, in Eritrea. Water samples were collected from the five hot
springs. Total community DNA was extracted from samples using the phenol-chloroform
method. The 16S rRNA gene variable region (V4—V7) of the extracted DNA was amplified
and library construction done according to Illumina sequencing protocol. The sequence
reads (length >200 bp) from Illumina sequencing libraries ranged from 22,091 sequences in
the wet sediment sample from Garbanabra to 155,789 sequences in the mat sample from
Elegedi. Taxonomy was assigned to each OTU using BLASTn against a curated database
derived from GreenGenes, RDPII, SILVA SSU Reference 119 and NCBI. The proportion of
potential pathogens from the water samples was highest in Maiwooi (17.8%), followed by
Gelti (16.7%), Akwar (13.6%) and Garbanabra (10.9%). Although the numbers of DNA
sequence reads from Illumina sequencing were very high for the Elegedi (104,328), corresponding
proportion of potential pathogens very low (3.6%). Most of the potential pathogenic
bacterial sequences identified were from Proteobacteria and Firmicutes. Legionella
and Clostridium were the most common detected genera with different species. Most of the
potential pathogens were detected from the water samples. However, sequences belonging
to Clostridium were observed more abundantly from the mat samples. This study employed
high-throughput sequencing technologies to determine the presence of pathogenic bacteria
in the five hot springs in Eritrea.
