Complete mitochondrial genome of Gnathostoma binucleatum.

This report describes the mitochondrial genome of the parasite Gnathostoma binucleatum (G. binucleatum), which was obtained from naturally infected freshwater fish in Sinaloa, Mexico (22°46'00.1″N 105°40'21.8″W). G. binucleatum is responsible for human gnathostomiasis and is endemic to Mexico. It belongs to the Spirurida order of the Secernentea class of Nematoda.

Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen.

Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes' presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen.

Draft genome sequence of Escherichia coli M51-3: a multidrug-resistant strain assigned as ST131-H30 recovered from infant diarrheal infection in Mexico.

OBJECTIVES: In this study, we report the draft genome sequence of a multidrug-resistant (MDR)Escherichia coli strain recovered from stool sample of an outpatient infant girl with acute diarrheal infection in Mexico. METHODS: Antimicrobial susceptibility testing and PCR-based detection of diarrheagenic E. coli (DEC) were performed. In addition, genomic DNA from E. coli strain M51-3 was sequenced using Ion Torrent PGM platform with 200-bp chemistry and generated reads were de novo assembled using SPAdes v3.11. The draft genome was annotated and analyzed regarding multilocus sequence typing (MLST), serotyping, fimH typing, plasmid replicons, acquired antimicrobial resistance and virulence genes using web tools available at the Center for Genomic Epidemiology. RESULTS: A draft genome comprising 5 088 545 bp in length and 5308 protein-coding sequences was generated. In silico typification revealed that E. coli strain M51-3 belongs to ST131-O25:H4-H30 pandemic subclone. Several genes associated with resistance to ß-lactams [blaTEM-1B], aminoglycosides [aph(3'')-Ib, aadA5, aph(6)-Id and aac(3)-IId], sulfonamides [sul1 and sul2], trimethoprim [dfrA17], and tetracycline [tet(A)] were identified. Besides, point mutations in gyrA, parC, and parE genes were detected. Interestingly, the enterotoxin-coding virulence gene senB was evidenced. CONCLUSIONS: To our knowledge, this is the first draft genome of an E. coli ST131-O25:H4-H30 strain recovered from infant diarrheal stool sample in Mexico. The genome sequence of E. coli M51-3 presented here will be helpful to understand the genomic diversity of this highly virulent and MDR successfully pandemic bacterial pathogen.

Whole-genome sequencing of Staphylococcus aureus L401, a mecA-negative community-associated methicillin-resistant strain isolated from a healthy carrier.

OBJECTIVES: Methicillin-resistant Staphylococcus aureus (MRSA) is a human pathogen of great concern owing to its antimicrobial resistance and virulence properties. Here we report the first draft genome sequence of a mecA-negative community-associated MRSA strain isolated from a healthy young Mexican paediatric carrier in order to reveal the genomic structure underlying the multidrug-resistant phenotype and to discover the virulence properties of this strain. METHODS: The draft genome sequence of S. aureus L401 was obtained using an Ion Torrent™ PGM platform. De novo assembled contigs were annotated, and antimicrobial resistance genes and virulence factors were identified using ResFinder and VirulenceFinder, respectively. In addition, a mutational survey of native pbp, gdpP and yjbH genes was performed. In silico multilocus sequence typing (MLST) and spa typing were also performed. RESULTS: S. aureus L401 has a genome size of 2 831 587 bp with 2799 protein-coding sequences. Various antimicrobial resistance genes conferring resistance to aminoglycosides, ß-lactams, fluoroquinolones and macrolide-lincosamide-streptogramin B antimicrobials were found. Although both mecA and staphylococcal cassette chromosome mec (SCCmec) elements were absent, a missense mutation in PBP3 was identified. Moreover, genes encoding exfoliative toxin A, γ- and ß-haemolysin, and several enterotoxins were also identified. S. aureus L401 belongs to ST109 and spa type t209. CONCLUSION: The availability of this genome will allow an insight into S. aureus resistance and virulence determinants as well as its epidemiology, lineage, evolution and genomic features involved in the paediatric commensal carriage.