Biomedical subjects

Teresa M Coque

Publications and source records attributed to Teresa M Coque.

7 recordsLinked to original sources

PubMed2026

The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the "robust-yet-fragile" architecture of human gut microbiomes.

BACKGROUND: Metagenomics enables detailed profiling of genes encoding antimicrobial resistance. However, most studies focus exclusively on antibiotic resistance genes (ARGs), excluding those associated with non-antibiotic antimicrobials (metals, biocides), and often rely on methods with low-sensitivity and low-specificity. Furthermore, they rarely examine populations exposed to minimal anthropogenic pollution. We analyzed fecal resistomes of 95 Wayampi individuals, an Indigenous community in remote French Guiana, using a targeted metagenomic capture platform covering 8667 genes, including ARGs, metal resistance genes (MRGs) and biocide resistance genes (BRGs) (PMID: 29335005). Resistome profiles were compared with those of Europeans to assess population-level differences. RESULTS: ARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs + BRGs gene richness was significantly higher in Wayampi (11,930 vs. 7419). Most genes appeared in a minority of individuals (mean 5% for ARGs, 2% for MRGs + BRGs), but several ARGs for tetracyclines [tet(32), tet(40), tet(O), tet(Q), tet(W), tet(X), tetAB(P)], aminoglycosides (ant6'-I, aph3-III), macrolides (ermB, ermF, mefA), and sulfonamides (sul2) were present in all individuals. Tetracycline resistance genes predominated overall, while beta-lactam resistance genes were more common in Wayampi, and genes conferring resistance to aminoglycosides, amphenicols, and folate inhibitors were more frequent in Europeans. Among MRGs, copper and arsenic resistance genes prevailed in both groups, followed by those for zinc, iron, cobalt, and nickel. Up to 76% of Wayampiis carried acquired MRGs for copper (pcoABCDRS and tcrB), silver (silACFPRS), arsenic (ars), and mercury (mer) detoxification. Shannon diversity indices were similar for ARGs, MRGs, and BRGs, but composition and evenness differed significantly. UMAP and ADONIS analyses distinguished cohorts based on ARG profiles (p < 0.001), but not on MRGs or BRGs. Correlation analysis revealed conserved gene-sharing networks and introgression of acquired ARGs and MRGs within both gut microbiomes. CONCLUSIONS: The diverse and balanced Wayampi resistome reflects a less perturbed microbiome compared to industrialized populations, and reveals a background of "core" and "shell" acquired ARGs and MRGs, consistent with the "robust-yet-fragile" architecture of scale-free networks. The patchy yet resilient gene distribution suggests varying levels of conserved gene sharing highways among populations, likely shaped by long-term microbial-human evolution, and supports a broader view on acquired antimicrobial resistance. Video Abstract.

Humans↗

PubMed2003

Multi-resistant Gram-negative bacilli: from epidemics to endemics.

PURPOSE OF REVIEW: Infections due to multi-drug resistant Gram-negative bacilli represent a worrying situation for the management of hospitalized patients. In addition, these bacteria are increasingly involved in epidemics throughout the world. This review focuses on recent data that may help to understand the emergence and dissemination of multi-drug resistant bacilli and the current trend from epidemic to endemic situations. RECENT FINDINGS: Well-established clones enhance their resistance phenotype by the acquisition of new resistant genes, via gene capture genetic units (plasmids, transposons or integrons), thus facilitating the co-selective process under different antimicrobial selective pressures and therefore the long-term persistence of organisms in selective environments. Not only resistant bacterial clones are selected, but also their genetic structures carrying resistance genes. Therefore, current epidemiology of multi-drug resistant bacilli is not only focused on bacterial clones but also on any kind of resistance gene capture units. In this scenario a multiclonal population structure of bacterial organisms corresponds to a collection of different strains sharing resistance genes carried by horizontally transferred genetic structures. As different strains tend to prefer different environments, this concept helps understand why the epidemiology of multi-drug resistant Gram-negative bacilli is moving from epidemics to endemics. SUMMARY: The emergence and spread of multi-drug resistant bacilli in the nosocomial setting should be understood in terms of a complex interplay of bacterial clonality, resistance genes and genetic structures promoting rapid dissemination of antimicrobial resistance. Intervention strategies in the forthcoming scenario should identify existing epidemic and/or endemic situations involving clonal organisms or resistance genes carried by epidemic gene capture units.

Cross Infection↗

PubMed2002

Allodemics.

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Bacteria↗

PubMed2002

Risk factors associated with ampicillin resistance in patients with bacteraemia caused by Enterococcus faecium.

Epidemiological characteristics of ampicillin-resistant, vancomycin-susceptible Enterococcus faecium are not well known. Recently, these strains have been proposed as the substratum for the later appearance of vancomycin-resistant E. faecium. To analyse this problem, the medical charts of patients with bacteraemia caused by E. faecium diagnosed in our institution during a 6 year period (1994-1999) were reviewed. Demographic data, clinical characteristics, antibiotic exposure and outcome were compared among patients with ampicillin-resistant (MIC > 16 mg/L, NCCLS criteria) and ampicillin-susceptible strains. Clonality between different strains was analysed by pulsed-field gel electrophoresis (PFGE). We evaluated 49 cases of E. faecium bacteraemia; 29 patients with ampicillin-resistant strains and 20 patients with -susceptible strains were identified. By logistic regression analysis, only previous administration of beta-lactams (OR: 6.3; 95% CI: 1.12-20.0) and urinary catheterization (OR:4.2; 95% CI: 1.3-30.0) were identified as predictors of ampicillin resistance in enterococcal bacteraemic patients. An elevated APACHE II score was the only independent factor associated with mortality in enterococcal bacteraemia (OR:13.5; 95% CI: 1.04-175.4). PFGE analysis revealed a strong association between specific ampicillin-resistant clones and the location of patients during hospitalization, suggesting nosocomial transmission. Bacteraemia caused by ampicillin-resistant enterococci was not associated with increased mortality when compared with bacteraemias caused by ampicillin-susceptible strains.

Ampicillin Resistance↗

PubMed2002

High occurrence of esp among ampicillin-resistant and vancomycin-susceptible Enterococcus faecium clones from hospitalized patients.

The ability to colonize patients successfully may be essential for the emergence and spread of resistant nosocomial strains. We determined the presence of Esp, a surface protein involved in colonization ability in Enterococcus faecalis, in 96 Enterococcus faecium isolates from hospitalized patients (77 PFGE clones), 33 faecal isolates from healthy volunteers (32 clones) and 20 environmental isolates (20 clones). Esp was found significantly more often in E. faecium isolated from hospitalized patients than in isolates from the community setting (26% versus 6%, P < 0.01) and was significantly more common among ampicillin-resistant than among ampicillin-susceptible strains (37% versus 4%, P < 0.001), regardless of the isolation site. The frequency of the esp gene in the hospital clearly correlates with antibiotic-resistant E. faecium clones. This observation indicates that antibiotic-resistant variants may frequently arise under antibiotic selective pressure among esp-positive clones reaching ecological abundance in the nosocomial habitat.

Ampicillin Resistance↗

PubMed2002

Genes encoding TEM-4, SHV-2, and CTX-M-10 extended-spectrum beta-lactamases are carried by multiple Klebsiella pneumoniae clones in a single hospital (Madrid, 1989 to 2000).

Over a 12-year period (1989 to 2000), 159 Klebsiella pneumoniae isolates harboring extended-spectrum beta-lactamases (ESBLs) (4.8% of the total number of K. pneumoniae isolates obtained) were recovered from 58 patients, who were mainly hospitalized in intensive care and surgery units. For 62 representative isolates from 58 patients, 31 clonal types harboring TEM-4 (n = 5), SHV-2 (n = 7), SHV2a (n = 4), SHV-5 (n = 1), CTX-M-10 (n = 13), or CTX-M-9 (n = 1) beta-lactamases were identified by pulsed-field gel electrophoresis. This is the first report to document the presence of the CTX-M-10 or the CTX-M-9 beta-lactamase in K. pneumoniae. These beta-lactamases were previously identified in Escherichia coli isolates from Spain. Only two of five K. pneumoniae TEM-4 clones caused more than a single case of infection, with one of them spreading for 9 months. A single plasmid was detected among these TEM-4 clones. Only two of seven K. pneumoniae clones containing SHV-2 and three of four strains harboring SHV-2a were detected in more than one case of infection. Plasmids encoding SHV-2 or SHV-2a were unrelated. Four of 13 K. pneumoniae CTX-M-10 clones were found in more than one patient, with two of them recovered 2 and 5 years apart. As in the case of the SHV-2 isolates, we were unable to document a common transmissible genetic element that could explain the polyclonal structure of our isolates. Nevertheless, the spread of a single gene may be suggested by the presence of a conserved set of noncoding polymorphisms in the sequences. Most ESBL-producing K. pneumoniae clones were ephemeral, being poorly selected and maintained in the hospital setting, but the genes encoding ESBL persisted successfully over the years that the strains were recovered, probably as a minority gene population in the hospital metagenome.

DNA, Bacterial↗

PubMed2002

Epidemiology of extended-spectrum beta-lactamase-producing Enterobacter isolates in a Spanish hospital during a 12-year period.

Fifteen Enterobacter clinical isolates (11 Enterobacter cloacae isolates, 3 Enterobacter aerogenes isolates, and 1 Enterobacter gergoviae isolate), representing 0.4% of all Enterobacter isolates recovered in our hospital from 1989 to 2000, were suspected of harboring an extended-spectrum beta-lactamase (ESBL). These isolates were recovered from 14 different patients. ESBLs were transferred by conjugation into an Escherichia coli recipient strain. Pulsed-field gel electrophoresis (PFGE) revealed a single clone of E. aerogenes and six different clones of E. cloacae. Four of these E. cloacae clonal types were represented by only one isolate each, but the other two were represented by three and four isolates, respectively. Isoelectric focusing, susceptibility phenotyping, PCR analysis, and sequencing demonstrated the presence of three different ESBLs. The most frequent was the recently characterized CTX-M-10 ESBL, which was found in the E. gergoviae isolate and in all but one of the E. cloacae isolates. The remaining E. cloacae isolate harbored a TEM-27 ESBL, and the three E. aerogenes isolates harbored a TEM-24 ESBL. PFGE revealed that our E. aerogenes strain was indistinguishable from the French TEM-24-producing E. aerogenes endemic clone. Although a low prevalence of ESBL-producing Enterobacter isolates was found in our institution over a 12-year period, a diversity of nonepidemic E. cloacae clones was detected, as was the persistence of the CTX-M-10 beta-lactamase. The presence of the TEM-24-producing E. aerogenes French clone in our institution also demonstrates the intercountry dissemination of ESBL-producing isolates.

Bacterial Proteins↗