Biology subjects

McElheny, C. L.

Publications and source records attributed to McElheny, C. L..

4 recordsLinked to original sources

bioRxiv2023

Evolution of extended-spectrum β-lactamase-producing ST131 Escherichia coli at a single hospital over 15 years

Escherichia coli belonging to sequence type ST131 constitute a globally distributed pandemic lineage that causes multidrug-resistant extra-intestinal infections. ST131 E. coli frequently produce extended-spectrum {beta}-lactamases (ESBLs), which confer resistance to many {beta}-lactam antibiotics and make infections difficult to treat. We sequenced the genomes of 154 ESBL-producing E. coli clinical isolates belonging to the ST131 lineage from patients at the University of Pittsburgh Medical Center (UPMC) between 2004 and 2018. Isolates belonged to the well described ST131 clades A (8%), B (3%), C1 (33%), and C2 (54%). An additional four isolates belonged to another distinct subclade within clade C and encoded genomic characteristics that have not been previously described. Time-dated phylogenetic analysis estimated that the most recent common ancestor (MRCA) for all clade C isolates from UPMC emerged around 1989, consistent with previous studies. We identified multiple genes potentially under selection in clade C, including the cell wall assembly gene ftsI, the LPS biosynthesis gene arnC, and the yersiniabactin uptake receptor fyuA. Diverse ESBL genes belonging to the blaCTX- M, blaSHV, and blaTEM families were identified; these genes were found at varying numbers of loci and in variable numbers of copies across isolates. Analysis of ESBL flanking regions revealed diverse mobile elements that varied by ESBL type. Overall, our findings show that ST131 subclades C1 and C2 dominated and were stably maintained among patients in the same hospital and uncover possible signals of ongoing adaptation within the clade C ST131 lineage.

microbiology↗

bioRxiv2023

High-level ceftazidime-avibactam resistance in Escherichia coli conferred by the novel plasmid-mediated beta-lactamase CMY-185 variant

ObjectivesTo characterize a blaCMY variant associated with ceftazidime-avibactam (CZA) resistance from a serially collected Escherichia coli isolate. MethodsA patient with an intra-abdominal infection due to recurrent E. coli was treated with CZA. On day 48 of CZA therapy, E. coli with a CZA MIC of >256 mg/L was identified from abdominal drainage. Illumina WGS was performed on all isolates to identify potential resistance mechanisms. Site-directed mutants of CMY {beta}-lactamase were constructed to identify amino acid residues responsible for CZA resistance. ResultsWGS revealed that all three isolates were E. coli ST410. The CZA-resistant strain uniquely acquired a novel CMY {beta}-lactamase gene, herein called blaCMY-185, harbored on an IncI{gamma}-type conjugative plasmid. The CMY-185 enzyme possessed four amino acid substitutions relative to CMY-2 including A114E, Q120K, V211S, and N346Y and conferred high-level CZA resistance with an MIC of 32 mg/L. Single CMY-2 mutants did not confer reduced CZA susceptibility. However, double and triple mutants containing N346Y previously associated with CZA resistance in other AmpC enzymes, conferred CZA MICs ranging between 4 and 32 mg/L as well as reduced susceptibility to the newly developed cephalosporin, cefiderocol. Molecular modelling suggested that the N346Y substitution confers the reduction of avibactam inhibition due to the steric hindrance between the side chain of Y346 and the sulfate group of avibactam. ConclusionWe identified CZA resistance in E. coli associated with a novel CMY variant. Unlike other AmpC enzymes, CMY-185 appears to require an additional substitution on top of N346Y to confer CZA resistance.

microbiology↗

bioRxiv2022

Genomic epidemiology revealed the emergence and worldwide dissemination of ST383 carbapenem-resistant hypervirulent Klebsiella pneumoniae and hospital acquired infections of ST196 Klebsiella quasipneumoniae in Qatar

The emergence of carbapenem-resistant (CR) hypervirulent Klebsiella pneumoniae (hvKp) is a new threat to healthcare. In this study, we studied the molecular epidemiology of CR Klebsiella isolates in Qatar using whole genome sequence data. We also characterised the prevalence and genetic basis of hypervirulent phenotypes, and established the virulence potential using a Galleria mellonella model. One hundred CR Klebsiella isolates were recovered, and NDM and OXA-48 were the most common carbapenemases. Phylogenetic analysis indicated the presence of diverse sequence types and clonal lineages; one of them belonged to K. quaisipneumoniae ST196 that may be disseminated among several health care centres. Ten K. pneumoniae isolates carrying rmpA and/or rmpA2, and 2 isolates belonged to KL2, indicating the prevalence of classical hypervirulent (hv) isolates was not high. Isolates carrying CR and hv genes were confined mainly to ST231 and ST383 isolates. One ST383 isolate was further investigated by MinION sequencing, and the assembled genome indicated the blaNDM was located on an IncHI1B type plasmid (pFQ61_ST383_NDM-5), which also harbored several virulence factors, including the regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD and iutA), likely resulting from inversion and recombination events. In contrast, blaOXA-48 was located in an IncL-type plasmid. Comparative genomes indicated the recent evolution and emergence of CR-hv Kp ST383 via the acquisition of hybrid plasmids with both carbapenemase and virulence genes. CR-hv K. pneumoniae ST383 pose an emerging threat to global health due to their simultaneous hypervirulence and multidrug resistance.

microbiology↗

bioRxiv2020

Clinical and genomic epidemiology of carbapenem-non-susceptible Citrobacter spp. at a tertiary healthcare center over two decades

Carbapenem-non-susceptible Citrobacter spp. (CNSC) are increasingly recognized as healthcare-associated pathogens. Information regarding their clinical epidemiology, genetic diversity, and mechanisms of carbapenem resistance is lacking. We examined microbiology records of adult patients at the University of Pittsburgh Medical Center (UMPC) Presbyterian Hospital (PUH) from 2000-2018 for CNSC, as defined by ertapenem non-susceptibility. Over this timeframe, the proportion of CNSC increased from 4% to 10% (P=0.03), as did carbapenem daily defined doses/1000 patient days (6.52 to 34.5, R2=0.831, P<0.001), which correlated with the observed increase in CNSC (lag=0 years, R2=0.660). Twenty CNSC isolates from 19 patients at PUH and other UPMC hospitals were available for further analysis, including whole-genome short-read sequencing and additional antimicrobial susceptibility testing. Of the 19 patients, nearly all acquired CNSC in the healthcare setting and over half had polymicrobial cultures containing at least one other organism. Among the 20 CNSC isolates, C. freundii was the predominant species identified (60%). CNSC genomes were compared with genomes of carbapenem-susceptible Citrobacter spp. from UPMC, and with other publicly available CNSC genomes. Isolates encoding carbapenemases (blaKPC-2, blaKPC-3, and blaNDM-1) were also long-read sequenced, and their carbapenemase-encoding plasmid sequences were compared with one another and with publicly available sequences. Phylogenetic analysis of 102 UPMC Citrobacter spp. genomes showed that CNSC from our setting did not cluster together. Similarly, a global phylogeny of 64 CNSC genomes showed a diverse population structure. Our findings suggest that both local and global CNSC populations are genetically diverse, and that CNSC harbor carbapenemase-encoding plasmids found in other Enterobacterales.

microbiology↗