Biology subjects

Williams, C. T.

Publications and source records attributed to Williams, C. T..

3 recordsLinked to original sources

bioRxiv2021

MagnaExtract, a novel magnetic bead-based extraction method for the molecular detection of antimicrobial resistance genes in fresh water.

BackgroundThe environmental is increasingly recognised as an important reservoir of antimicrobial resistance (AMR) genes. Polymerase chain reaction (PCR) and whole genome sequencing (WGS) have great potential in the surveillance of AMR genes. However, molecular methods are dependent upon the isolation of high-quality DNA yields. Currently, there is no consensus for the optimum DNA extraction strategies from complex environmental matrices for downstream molecular applications. MethodsWe present a novel magnetic bead-based method for the isolation of antimicrobial resistance genes (ARGs) from river water in Malawi, named MagnaExtract. We present this with analytic limit of detection (LOD) as well as a case study in Southern Malawi. Here we compare the DNA yield and subsequent PCR output from MagnaExtract with commercially available QIAGEN kits and the crude boil and spin method, utilising a high-resolution melt analysis (HRM) PCR panel designed for the detection of third generation cephalosporin and carbapenem resistant genes. ResultsOf the 98 water samples evaluated we found the MagnaExtract method to be comparable, and in some instances superior to commercially available kits for the isolation of ARGs from river water samples. In addition, we found overnight incubation to promote the recovery of extended spectrum beta-lactamase (ESBL) genes and simultaneous reduction in the detection of carbapenemase genes. ConclusionThe MagnaExtract approach offers a simple, affordable, high yielding extraction method that could be used for the detection of ARGs isolated from river water samples in environmental surveillance campaigns in East Africa.

molecular biology↗

bioRxiv2020

Neotype designation and re-description of Forsskal's reticulate whipray Himantura uarnak

A serious impediment to the taxonomy of the reticulate whipray Himantura spp. species complex has been the absence of a type specimen for P. Forssk[a]ls H. uarnak. Here, reticulate whipray specimens were sampled from the Jeddah region, the assumed type locality of H. uarnak, and characterized genetically at the cytochrome-oxidase subunit 1 (CO1) locus. One of these specimens now in the fish collection of the California Academy of Sciences in San Francisco was designated as neotype. A maximum-likelihood phylogeny of all available CO1 gene sequences from the genus Himantura had the following topology: ((H. leoparda, H. uarnak), (H. undulata, (Himantura sp. 2, (H. australis + Himantura sp. 1))), H. tutul), where H. uarnak haplotypes formed a distinct sub-clade sister to H. leoparda. Based on these CO1 gene sequences, the geographic distribution of H. uarnak includes the eastern Mediterranean, the Red Sea, the East African coast, and the Arabian Sea. Two lineages in the reticulate whipray species complex remain to be named. NoticeThe present article in portable document (.pdf) format is a published work in the sense of the International Code of Zoological Nomenclature [International Commission on Zoological Nomenclature (ICZN)1999]. It has been registered in ZooBank (http://zoobank.org/), the online registration system for the ICZN. The ZooBank life science identifier for this publication is urn:lsid:zoobank.org:pub:B2113697-5EBF-4364-B50C-63019A1A076A. The online version of this work is archived and available from the bioRxiv (https://biorxiv.org/) repository.

zoology↗

bioRxiv2020

Piperacillin/tazobactam resistant, cephalosporin susceptible Escherichia coli bloodstream infections driven by multiple resistance mechanisms across diverse sequence types

Resistance to piperacillin/tazobactam (TZP) in Escherichia coli has predominantly been associated with mechanisms that confer resistance to third generation cephalosporins. Recent reports have identified E. coli strains with phenotypic resistance to piperacillin/tazobactam but susceptibility to third generation cephalosporins (TZP-R/3GC-S). In this study we sought to determine the genetic diversity of this phenotype in E. coli (n = 58) isolated between 2014-2017 at a single tertiary hospital in Liverpool, UK, as well as the associated resistance mechanisms. We compare our findings to a UK-wide collection of invasive E. coli isolates (n = 1509) with publicly available phenotypic and genotypic data. These data sets included the TZP-R/3GC-S phenotype (n = 68), a piperacillin/tazobactam and third generation cephalosporin-susceptible (TZP-S/3GC-S, n = 1271) phenotypes. The TZP-R/3GC-S phenotype was displayed in a broad range of sequence types which was mirrored in the same phenotype from the UK-wide collection, and the overall diversity of invasive E. coli isolates. The TZP-R/3GC-S isolates contained a diverse range of plasmids, indicating multiple acquisition events of TZP resistance mechanisms rather than clonal expansion of a particular plasmid or sequence type. The putative resistance mechanisms were equally diverse, including hyperproduction of TEM-1, either via strong promoters or gene amplification, carriage of inhibitor resistant {beta}-lactamases, and an S133G b/aCTX-M-15 mutation detected for the first time in clinical isolates. Several of these mechanisms were present at a lower abundance in the TZP-S/3GC-S isolates from the UK-wide collection, but without the associated phenotypic resistance to TZP. Our findings highlight the complexity of this cryptic phenotype and the need for continued phenotypic monitoring, as well as further investigation to improve detection and prediction of the TZP-R/3GC-S phenotype from genomic data.

microbiology↗