pellet was left to air-dry for 30 min. The dry DNA pellet was resuspended in Buffer EB (Qiagen), and submitted for sequencing. Processing and analysis of next-generation sequencing data. Genomes submitted for sequencing corresponded to the wild-type or mutant samples from generations 0 (wild type), 10, 20, and 30 of the initial T3 mutagenesis series, and generations 0 (wild type), 5, 10, and 15 of the T3/T7 parallel evolution series (12 samples total). The purified genomes were sequenced by QuickBiology Inc. (HiSeq X, 5M reads total per sample, 2.5M pairs, 2 × 150 PE), and raw data for reads aligned to the wild type reference genome were provided in the form of fastq.gz files. The fastq data for the mutant genome pools were processed using the following pipeline:

We present here the draft genome sequence of the first New Delhi metallo-β-lactamase (NDM-1)-producing Escherichia coli strain, belonging to sequence type 155 (ST155), isolated in Peru. Assembly of this draft genome resulted in 5,061,184 bp, revealing a clinically significant resistome for β-lactams, aminoglycosides, tetracyclines, phenicols, sulfonamides, trimethoprim, and fluoroquinolones.

Urinary tract infections (UTIs) are a common human infection. Antibiotic resistance in extended-spectrum β-lactamase (ESBL)-producing uropathogenic E. coli (UPEC) is a major therapeutic challenge due to limited treatment alternatives. The aim was to characterize the antimicrobial resistance (AMR) and dynamics of ESBL-producing UPEC isolates from UTI cases seen at a local hospital in Cusco, Peru. Ninety-nine isolates from respective patients were characterized against 18 different antibiotics. Latent class analysis (LCA) was used to evaluate the dynamics across the study time according to resistance patterns. The median age of patients was 51 years old, and nearly half were women. ESBL-producing UPEC isolates were slightly more frequent in outpatient services than emergency rooms, and there were higher resistance rates in males compared to females. Half of the ESBL producers were resistant to aminoglycosides and nitrofurantoin. Cefoxitin and fosfomycin resistance was 29.3% and 14.1%, respectively. Resistance to carbapenems was not observed. All isolates were multidrug-resistant bacteria, and 16.2% (16/99) were also classified as extensively drug-resistant bacteria. The resistance patterns varied across the study time and differed regarding sex and healthcare service. The study revealed high levels of AMR to commonly used antimicrobials and a dynamic circulation of ESBL-producing UPEC isolates with varying resistance patterns.

Salmonella enterica is a Gram-negative bacterium, recognized as one of the most important foodborne pathogens in the world. Bacteriophages represent a promising alternative to the biocontrol of Salmonella. Here, we report the isolation of five Salmonella bacteriophages, the sequencing of their full genomes, and initial genomic characterization.

The production of high‐quality recombinant proteins is critical to maintaining a continuous supply of biopharmaceuticals, such as therapeutic antibodies. Engineering mammalian cell factories presents a number of limitations typically associated with the proteotoxic stress induced upon aberrant accumulation of off‐pathway protein folding intermediates, which eventually culminate in the induction of apoptosis. In this review, we will discuss advances in cell engineering and their applications at different hierarchical levels of control of the expression of recombinant proteins, from transcription and translational to posttranslational modifications and subcellular trafficking. We also highlight challenges and unique opportunities to apply modern synthetic biology tools to the design of programmable cell factories for improved biomanufacturing of therapeutic proteins.