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Shuman, H. A.

Publications and source records attributed to Shuman, H. A..

2 recordsLinked to original sources
bioRxiv2020

Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing

We conducted two studies of water samples from buildings with normal occupancy and water usage compared to water from buildings that were unoccupied with little or no water usage due to the COVID-19 shutdown. Study 1 had 52 water samples obtained ad hoc from buildings in four metropolitan locations in different states in the US and a range of building types. Study 2 had 36 water samples obtained from two buildings in one metropolitan location with matched water sample types. One of the buildings had been continuously occupied, and the other substantially vacant for approximately 3 months. All water samples were analyzed using 16S rRNA amplicon sequencing with a MinION from Oxford Nanopore Technologies. More than 127 genera of bacteria were identified, including genera with members that are known to include more than 50 putative frank and opportunistic pathogens. While specific results varied among sample locations, 16S rRNA amplicon abundance and the diversity of bacteria were higher in water samples from unoccupied buildings than normally occupied buildings as was the abundance of sequenced amplicons of genera known to include pathogenic bacterial members. In both studies Legionella amplicon abundance was relatively small compared to the abundance of the other bacteria in the samples. Indeed, when present, the relative abundance of Legionella amplicons was lower in samples from unoccupied buildings. Legionella did not predominate in any of the water samples and were found, on average, in 9.6% of samples in Study 1 and 8.3% of samples in Study 2. SynopsisComparison of microbial community composition in the plumbing of occupied and unoccupied buildings during the COVID-19 pandemic shutdown. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/209346v3_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@e3b50borg.highwire.dtl.DTLVardef@182ebc9org.highwire.dtl.DTLVardef@45f69eorg.highwire.dtl.DTLVardef@142210f_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗
bioRxiv2020

Acinetobacter baumannii NCIMB8209: A rare environmental strain displaying extensive insertion sequence-mediated genome remodeling resulting in the loss of exposed cell structures and defensive mechanisms

Acinetobacter baumannii represents nowadays an important nosocomial pathogen of poorly defined reservoirs outside the clinical setting. Here we conducted whole-genome sequencing analysis of the Acinetobacter sp. NCIMB8209 collection strain, isolated in 1943 from the aerobic degradation (retting) of desert guayule shrubs. NCIMB8209 contained a 3.75 Mb chromosome and a plasmid of 134 kb. Phylogenetic analysis based on core genes indicated NCIMB8209 affiliation to A. baumannii, a result supported by the identification of a chromosomal blaOXA-51-like gene. Seven genomic islands lacking antimicrobial resistance determinants, 5 regions encompassing phage-related genes and, notably, 93 insertion sequences (IS) were found in this genome. NCIMB8209 harbors most genes linked to persistence and virulence described in contemporary A. baumannii clinical strains, but many of them encoding components of surface structures are interrupted by IS. Moreover, defense genetic islands against biological aggressors such as type 6 secretion systems or crispr/cas are absent from this genome. These findings correlate with a low capacity of NCIMB8209 to form biofilm and pellicle, low motility on semisolid medium, and low virulence towards Galleria mellonella and Caenorhabitis elegans. Searching for catabolic genes and concomitant metabolic assays revealed the ability of NCIMB8209 to grow on a wide range of substances produced by plants including aromatic acids and defense compounds against external aggressors. All the above features strongly suggest that NCIMB8209 has evolved specific adaptive features to a particular environmental niche. Moreover, they also revealed that the remarkable genetic plasticity identified in contemporary A. baumannii clinical strains represents an intrinsic characteristic of the species. IMPORTANCEAcinetobacter baumannii (Ab) is an ESKAPE opportunistic pathogen, with poorly defined natural habitats/reservoirs outside the clinical setting. Ab arose from the Acb complex as the result of a population bottleneck, followed by a recent population expansion from a few clinically-relevant clones endowed with an arsenal of resistance and virulence genes. Still, the identification of virulence traits and the evolutionary paths leading to a pathogenic lifestyle has remained elusive, and thus the study of non-clinical ("environmental") Ab isolates is necessary. We conducted here comparative genomic and virulence studies on Ab NCMBI8209 isolated in 1943 from the microbiota responsible of the decomposition of guayule, and therefore well differentiated both temporally and epidemiologically from the nowadays predominant multidrug-resistant strains. Our work provides insights on the adaptive strategies used by Ab to escape from host defenses, and may help the adoption of measures aimed to limit its further dissemination.

microbiology↗