Multidrug resistance and class 1 integron presence in Escherichia coli isolates from a polluted drainage ditch's water.

The impact of contamination of water drainage ditches in the development of antibiotic-resistant bacteria has been scarcely studied in Mexico. In this regard, 101 isolates of E. coli were obtained from water samples from a ditch in Sinaloa, during one year. The antimicrobial resistant profiles, the presence of the class 1 integron and evolutionary relationship of intI1 sequences were determined. The 47.5% of strains were resistant and 5.9% multidrug resistant (MDR) with an average multiple antibiotic resistance index value of 0.45. The highest resistance was registered with ß-lactam (39.6%) and quinolone (9.9%). The intI1 gene was detected in 11.9% of the isolates, and no association with MDR was found. Sequence were associated with human and animal host isolates. MDR E. coli isolates with intI1 gene highlight the potential risk of the ditch's water to human health. An attenuation effect of MDR E. coli isolates in the outlet water was observed.

Draft genome sequence of uropathogenic Escherichia coli U13824, a multidrug-resistant (MDR) and extended-spectrum-ß-lactamase (ESBL)-producing UPEC strain isolated from an adult woman with urinary tract infection.

Urinary tract infections (UTIs) caused by multidrug-resistant and extended-spectrum ß-lactamase-producing uropathogenic Escherichia coli are a worldwide concern. We report the draft genome of E. coli U13824 isolated from a female outpatient with UTI. This genome's availability strengthens the genomic surveillance of antimicrobial resistance and the spreading of these strains.

Molecular Identification of the Etiological Agent of Human Gnathostomiasis in an Endemic Area of Mexico.

Human gnathostomiasis, which is endemic in Mexico, is a worldwide health concern. It is mainly caused by the consumption of raw or insufficiently cooked fish containing the advanced third-stage larvae (AL3A) of Gnathostoma species. The diagnosis of gnathostomiasis is based on epidemiological surveys and immunological diagnostic tests. When a larva is recovered, the species can be identified by molecular techniques. Polymerase chain reaction (PCR) amplification of the second internal transcription spacer (ITS-2) is useful to identify nematode species, including Gnathostoma species. This study aims to develop a duplex-PCR amplification method of the ITS-2 region to differentiate between the Gnathostoma binucleatum and G. turgidum parasites that coexist in the same endemic area, as well as to identify the Gnathostoma larvae recovered from the biopsies of two gnathostomiasis patients from Sinaloa, Mexico. The duplex PCR established based on the ITS-2 sequence showed that the length of the amplicons was 321 bp for G. binucleatum and 226 bp for G. turgidum. The amplicons from the AL3A of both patients were 321 bp. Furthermore, the length and composition of these amplicons were identical to those deposited in GenBank as G. binucleatum (accession No. JF919679), corroborating our previous morphological finding that G. binucleatum is the etiological agent for human gnathostomiasis in the endemic area of Sinaloa, Mexico.

Association of phylogenetic distribution and presence of integrons with multidrug resistance in Escherichia coli clinical isolates from children with diarrhoea.

BACKGROUND: Escherichia coli strains include both commensal and virulent clones distributed in different phylogenetic groups. Antimicrobial resistance is an increasingly serious public health threat at the global level and integrons are important mobile genetic elements involved in resistance dissemination. This paper aims to determine the phylogenetic groups and presence of class 1 (intl1) and 2 (intl2) integrons in E. coli clinical isolates from children with diarrhoea, and to associate these characteristics with their antimicrobial resistance. METHODS: Phylogeny and presence of integrons (intl1 and intl2) were analysed by PCR and amplicon sequencing in 70 E. coli isolates from children with and without diarrhoea (35 of each group) from Sinaloa, Mexico; these variables were analysed for correlation with the antimicrobial resistance profile of the isolates. RESULTS: The most frequent phylogroups were A (42.9%) and B2 (15.7%). The E. coli isolates from children with diarrhoea were distributed in all phylogroups; while strains from children without diarrhoea were absent from phylogroups C, E, and clade I. The 17.1% of the isolates carried integrons (15.7% intI1 and 1.4% intI2); 28.6% of the isolates from children with diarrhoea showed the class 1 integron. Strains of phylogroup A showed the highest frequency of integrons (33.3%). The association of multidrug resistance and the presence of integrons was identified in 58.3% of strains isolated from children with diarrhoea included in phylogroups A and B2. The sequence analysis of intl1 and intl2 showed silent point mutations and similarities with plasmids of some APEC and AIEC strains. CONCLUSION: Commensal E. coli strains are potential disseminators of antimicrobial resistance, and the improvement in the use of antimicrobials to treat childhood diarrhoea is essential for the control of such resistance.

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.

Draft Genome Sequence of Escherichia coli Strain M15-4, a Typical Enteropathogenic E. coli Strain Isolated in Mexico.

We present here the first draft genome sequence of a typical enteropathogenic Escherichia coli serotype O55:H51 strain, M15-4, isolated from a 2-month-old infant girl with acute diarrhea. The study of this Mexican isolate will provide insights to the virulence and drug resistance traits involved in its pathogenic potential.

Draft Genome Sequence of a Mexican Community-Associated Methicillin-Resistant Staphylococcus epidermidis Strain.

We report here the first draft genome sequence of a Mexican communitarian methicillin-resistant Staphylococcus epidermidis (MRSE) strain whose genome harbors a wide variety of resistance determinants. The availability of this genome will allow the study of antibiotic resistance in Mexican staphylococci from a genomic perspective.