Biology subjects

Mira, P.

Publications and source records attributed to Mira, P..

3 recordsLinked to original sources

bioRxiv2021

Estimating Microbial Population Data from Optical Density

The spectrophotometer has been used for decades to measure the density of bacterial populations as the turbidity expressed as optical density - OD. However, the OD alone is an unreliable metric and is only proportionately accurate to cell titers to about an OD of 0.1. The relationship between OD and cell titer depends on the configuration of the spectrophotometer, the length of the light path through the culture, the size of the bacterial cells, and the cell culture density. We demonstrate the importance of plate reader calibration to identify the exact relationship between OD and cells/ml. We use four bacterial genera and two sizes of micro-titer plates (96-well and 384-well) and show that the cell/ml per unit OD depends heavily on the bacterial cell size and plate size. We applied our calibration curve to real growth curve data and conclude the cells/ml - rather than OD - is a metric that can be used to directly compare results across experiments, labs, instruments, and species.

microbiology↗

bioRxiv2021

Genetic interplay between type II topoisomerase enzymes and chromosomal ccdAB toxin-antitoxin in E. coli

Fluoroquinolones are one of the most widely used class of antibiotics. They target two type II topoisomerase enzymes: gyrase and topoisomerase IV. Resistance to these drugs, which is largely caused by mutations in their target enzymes, is on the rise and becoming a serious public health risk. In this work, we analyze the sequences of 352 extraintestinal E. coli clinical isolates to gain insights into the selective pressures shaping the type II topoisomerase mutation landscape in E. coli. We identify both Quinolone Resistance-Determining Region (QRDR) and non-QRDR mutations, outline their mutation trajectories, and show that they are likely driven by different selective pressures. We confirm that ciprofloxacin resistance is specifically and strongly associated with QRDR mutations. By contrast, non-QRDR mutations are associated with the presence of the chromosomal version of ccdAB, a toxin-antitoxin operon, where the toxin CcdB is known to target gyrase. We also find that ccdAB and the evolution of QRDR mutation trajectories are partially incompatible. Finally, we identify partial deletions in CcdB and additional mutations that likely facilitate the compatibility between the presence of the ccdAB operon and QRDR mutations. These "permissive" mutations are all found in ParC (a topoisomerase IV subunit). This, and the fact that CcdB-selected mutations frequently map to topoisomerase IV, strongly suggests that this enzyme (in addition to gyrase) is likely a target for the toxin CcdB in E. coli, although an indirect effect on global supercoiling cannot be excluded. This work opens the door for the use of the presence of ccdB and of the proposed permissive mutations in the genome as genetic markers to assess the risk of quinolone resistance evolution and implies that certain strains may be genetically more refractory to evolving quinolone resistance through mutations in target enzymes.

microbiology↗

bioRxiv2018

Functionally redundant forms of extended-spectrum beta-lactamases and aminoglycoside modifying enzymes drive the evolution of two distinct multidrug resistance gene clusters in clinical populations of EXPEC

We evaluate the distribution of genetic markers for antibiotic resistance in 276 genomic sequences of Extraintestinal Pathogenic E. coli from two hospitals on the U.S. West coast. Plasmid-borne genes encoding drug-inactivating enzymes dominate the distribution of aminoglycoside and {beta}-lactam resistance markers. These genes can be assigned based on their distribution to two mutually exclusive complementarity groups (CGs: CG1 and CG2) with each displaying genetic linkage and minimal functional overlap. CG1 includes genes encoding OXA-1 and AAC(6)-Ib-cr, frequently also CTX-M-15, and sometimes AAC(3)-IIe.2, a variant of AAC(3)-IIe; CG2 includes AAC(3)-IId tightly linked to TEM-1, and occasionally also to genes encoding CTX-M-14-like {beta}-lactamases. This binary distribution of aminoglycoside and {beta}-lactamase resistance genes suggests a convergence between two different evolutionary solutions, and results in a ubiquitous functional redundancy in the clinical populations. CG1 and CG2 are largely carried in IncF plasmids, of which we distinguish seven classes based on Rpt-A1 sequence homology. Both CG1 and CG2 genes are found in two different IncF plasmid classes, demonstrating their pervasive mobility across plasmid backbones. Different CG genes and IncF plasmid classes are found in a wide range of MLSTs, highlighting the prevalence of horizontal gene transfer. We also identify at least five clonally expanding MLSTs, which represent high-risk clones: ST131, ST95, ST73, ST127, and ST69. The identification of clonally-expanding types, the discovery of CGs that are ubiquitously spread in diverse clinical strains, and the functional redundancy that these two groups represent have significant implications for monitoring and controlling the spread of resistance.

microbiology↗