Microbial Characterization of Drinking Water Systems Receiving Groundwater and Surface Water as the Primary Sources of Water

Earlier descriptions of water distribution systems (WDS) microbial communities have relied on culturing techniques. These techniques are known to be highly selective in nature, but more importantly, they tend to grossly underestimate the microbial diversity of most environments. The goal of this ongoing study is to compare the microbial composition of a WDS receiving different sources of water. To circumvent some of the problems associated with culture-based techniques, sequence analysis of total community 16S rDNA clone libraries was performed. A total of 260 16S rDNA clones were analyzed in this study. Sequence comparisons with existing databases revealed that α-Proteobacteria and Mycobacterium sp. represented nearly 43% and 48% of the total clones examined, respectively. Other bacterial groups identified included members of the genera Legionella, Pseudomonas, and Agrobacterium. Seventy percent of the clones analyzed in this study showed at least 97% sequence identity with sequences available in current databases. While α-Proteobacteria is a numerically dominant group in chlorinated drinking water systems, the abundance of mycobacterial sequences in this study indicates that there are significant differences in microbial community structure between the WDS analyzed. These differences could be attributed to differences in water treatment or receiving water sources between the distribution systems. While some of the genera identified in this study have been associated with some public health risks, it should be noted that analysis of 16S rDNA clones does not confirm the presence of pathogenic strains of any organisms identified in this study, as current methods for detection and identification require several steps including selective enrichment, isolation, and final confirmation via in vitro studies. Future studies will focus on expanding sequencing databases to more accurately characterize these potential differences. This paper was presented at the 8th Annual Water Distribution Systems Analysis Symposium which was held with the generous support of Awwa Research Foundation (AwwaRF)

Spatial Description of Drinking Water Bacterial Community Structures in Bulk Water Samples Collected in a Metropolitan Distribution System

The description of microorganisms inhabiting drinking water distribution systems has commonly been performed using techniques that are biased towards easy to culture bacterial populations. As most environmental microorganisms cannot be grown on artificial media, our understanding of the microbial community structure of drinking water is very limited. To circumvent some of the problems associated with culture-based techniques, sequence analysis of 16S rRNA gene clone libraries was used in this study. Genomic DNA was extracted from bulk phase water from sampling sites within the distribution systems (WDS), and used to develop 16S rRNA gene clones libraries. Water samples were collected from areas within the distribution system fed by two distinct raw water sources. Over 2300 16S rDNA clones were analyzed in this study from a total of 31 different sites. Phylogenetic analyses showed that ?-Proteobacteria and Actinobacteria represented more than 90% of the total clones examined. In general, similar bacterial groups were observed in sites receiving groundwater and surface water sources suggesting that chlorination is an important selective force in shaping up the overall microbial community structure. While the communities were similar at the general bacterial group, there were some differences at finer phylogenetic levels. This is important as it suggests that differences in the sources and treatment technologies could select for different populations. Since more than half of the clones were associated with yet to be cultured bacteria, and in many cases with novel bacterial groups, the results further substantiate the need for the development of culture-independent methods to better identify drinking water and to study their in-situ spatial-temporal dynamics

Complete Genome Sequence of Streptacidiphilus sp. Strain 15-057A, Obtained from Bronchial Lavage Fluid

2 páginas.Streptacidiphilus sp. strain 15-057A was isolated from a bronchial lavage sample and represents the only member of the genus not isolated from acidic soils. A single circular chromosome of 7.01 Mb was obtained by combining Illumina and PacBio sequencing data. Bioinformatic analysis detected 63 putative secondary biosynthetic gene clusters and recognized 43 transposons.I.N. is grateful to Newcastle University for a postdoctoral fellowship.Peer reviewe

Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents.

Corynebacterium bovis is an opportunistic bacterial pathogen shown to cause eye and prosthetic joint infections as well as abscesses in humans, mastitis in dairy cattle, and skin disease in laboratory mice and rats. Little is known about the genetic characteristics and genomic diversity of C. bovis because only a single draft genome is available for the species. The overall aim of this study was to sequence and compare the genome of C. bovis isolates obtained from different species, locations, and time points. Whole-genome sequencing was conducted on 20 C. bovis isolates (six human, four bovine, nine mouse and one rat) using the Illumina MiSeq platform and submitted to various comparative analysis tools. Sequencing generated high-quality contigs (over 2.53 Mbp) that were comparable to the only reported assembly using C. bovis DSM 20582T (97.8 ± 0.36% completeness). The number of protein-coding DNA sequences (2,174 ± 12.4) was similar among all isolates. A Corynebacterium genus neighbor-joining tree was created, which revealed Corynebacterium falsenii as the nearest neighbor to C. bovis (95.87% similarity), although the reciprocal comparison shows Corynebacterium jeikeium as closest neighbor to C. falsenii. Interestingly, the average nucleotide identity demonstrated that the C. bovis isolates clustered by host, with human and bovine isolates clustering together, and the mouse and rat isolates forming a separate group. The average number of genomic islands and putative virulence factors were significantly higher (p<0.001) in the mouse and rat isolates as compared to human/bovine isolates. Corynebacterium bovis' pan-genome contained a total of 3,067 genes of which 1,354 represented core genes. The known core genes of all isolates were primarily related to ''metabolism" and ''information storage/processing." However, most genes were classified as ''function unknown" or "unclassified". Surprisingly, no intact prophages were found in any isolate; however, almost all isolates had at least one complete CRISPR-Cas system

The draft genomes of <i>Elizabethkingia anophelis</i> of equine origin are genetically similar to three isolates from human clinical specimens

<div><p>We report the isolation and characterization of two <i>Elizabethkingia anophelis</i> strains (OSUVM-1 and OSUVM-2) isolated from sources associated with horses in Oklahoma. Both strains appeared susceptible to fluoroquinolones and demonstrated high MICs to all cell wall active antimicrobials including vancomycin, along with aminoglycosides, fusidic acid, chloramphenicol, and tetracycline. Typical of the <i>Elizabethkingia</i>, both draft genomes contained multiple copies of β-lactamase genes as well as genes predicted to function in antimicrobial efflux. Phylogenetic analysis of the draft genomes revealed that OSUVM-1 and OSUVM-2 differ by only 6 SNPs and are in a clade with 3 strains of <i>Elizabethkingia anophelis</i> that were responsible for human infections. These findings therefore raise the possibility that <i>Elizabethkingia</i> might have the potential to move between humans and animals in a manner similar to known zoonotic pathogens.</p></div

Core genome single nucleotide polymorphism tree showing the position of OSUVM-1 and OSUVM-2 compared to the <i>Elizabethkingia anophelis</i> strains reported by Nicholson <i>et al</i>.

<p>Type strains are denoted by a superscript T, and the location of the isolates from this study is denoted by a bracket.</p