33 results on '"Edgar I. Campos-Madueno"'
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2. A new OCH β-lactamase from a Brucella pseudintermedia (Ochrobactrum pseudintermedium) strain isolated from Zophobas morio larvae
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Cindy Kundlacz, Claudia Aldeia, Yasmine Eddoubaji, Edgar I. Campos-Madueno, and Andrea Endimiani
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Brucella pseudintermedia ,Ochrobactrum ,Zophobas morio ,blaOCH ,AmpC ,Microbiology ,QR1-502 - Abstract
ABSTRACT: Objectives: OCH class C β-lactamases have been reported in several species belonging to the Brucella genus that were formerly known as Ochrobactrum. Moreover, only one complete genome of Brucella pseudintermedia has been published. In this work, we describe the genome of a B. pseudintermedia strain possessing a new blaOCH gene that was isolated from Zophobas morio larvae. Methods: Hybrid whole-genome sequencing analysis (Illumina and Nanopore) was used to identify and characterise the strain (Ops-OCH-23). Phylogenetic analyses based on the 16S rRNA gene sequence and a core-genome alignment were performed to study the relationships among Ops-OCH-23 and deposited genomes. Moreover, all deposited blaOCH genes were compared to the one found in Ops-OCH-23. Results: Ops-OCH-23 showed a susceptibility profile consistent with the production of AmpC β-lactamase(s). Its genome consisted of two chromosomes, of which one carried the blaOCH gene. Such gene encoded a new class C OCH β-lactamase among the fifteen so far reported. Two plasmids (120-Kb and 59-Kb) without any associated antimicrobial resistance genes were also found. Analysis of 16S rRNA revealed that Ops-OCH-23 shared 100% homology with four deposited B. pseudintermedia strains. Moreover, the core-genome analysis indicated that the closest match (279 ΔSNVs) to Ops-OCH-23 was strain CTOTU49018 isolated from an urban environment in Germany in 2013. Conclusion: We described the second complete genome of a B. pseudintermedia that also encoded a new OCH β-lactamase variant. Overall, this report expands our knowledge regarding this rarely isolated Brucella species that have been reported so far only a few times in human sources.
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- 2024
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3. A new in vivo model of intestinal colonization using Zophobas morio larvae: testing hyperepidemic ESBL- and carbapenemase-producing Escherichia coli clones
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Yasmine Eddoubaji, Claudia Aldeia, Edgar I. Campos-Madueno, Aline I. Moser, Cindy Kundlacz, Vincent Perreten, Markus Hilty, and Andrea Endimiani
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ESBL ,carbapenemase ,bacteriophages ,in vivo ,colonization ,ST131 ,Microbiology ,QR1-502 - Abstract
Finding strategies for decolonizing gut carriers of multidrug-resistant Escherichia coli (MDR-Ec) is a public-health priority. In this context, novel approaches should be validated in preclinical in vivo gut colonization models before being translated to humans. However, the use of mice presents limitations. Here, we used for the first time Zophobas morio larvae to design a new model of intestinal colonization (28-days duration, T28). Three hyperepidemic MDR-Ec producing extended-spectrum β-lactamases (ESBLs) or carbapenemases were administered via contaminated food to larvae for the first 7 days (T7): Ec-4901.28 (ST131, CTX-M-15), Ec-042 (ST410, OXA-181) and Ec-050 (ST167, NDM-5). Growth curve analyses showed that larvae became rapidly colonized with all strains (T7, ~106–7 CFU/mL), but bacterial load remained high after the removal of contaminated food only in Ec-4901.28 and Ec-042 (T28, ~103–4 CFU/mL). Moreover, larvae receiving a force-feeding treatment with INTESTI bacteriophage cocktail (on T7 and T10 via gauge needle) were decolonized by Ec-4901.28 (INTESTI-susceptible); however, Ec-042 and Ec-050 (INTESTI-resistant) did not. Initial microbiota (before administering contaminated food) was very rich of bacterial genera (e.g., Lactococcus, Enterococcus, Spiroplasma), but patterns were heterogeneous (Shannon diversity index: range 1.1–2.7) and diverse to each other (Bray–Curtis dissimilarity index ≥30%). However, when larvae were challenged with the MDR-Ec with or without administering bacteriophages the microbiota showed a non-significant reduction of the diversity during the 28-day experiments. In conclusion, the Z. morio larvae model promises to be a feasible and high-throughput approach to study novel gut decolonization strategies for MDR-Ec reducing the number of subsequent confirmatory mammalian experiments.
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- 2024
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4. Detection of blaCTX-M and blaDHA genes in stool samples of healthy people: comparison of culture- and shotgun metagenomic-based approaches
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Edgar I. Campos-Madueno, Claudia Aldeia, Vincent Perreten, Parham Sendi, Aline I. Moser, and Andrea Endimiani
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ESBL ,AmpC ,stool ,metagenomics ,Illumina ,enrichment ,Microbiology ,QR1-502 - Abstract
We implemented culture- and shotgun metagenomic sequencing (SMS)-based methods to assess the gut colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESC-R-Ent) in 42 volunteers. Both methods were performed using native and pre-enriched (broth supplemented with cefuroxime) stools. Native culture screening on CHROMID® ESBL plates resulted in 17 positive samples, whereas the pre-enriched culture (gold-standard) identified 23 carriers. Overall, 26 ESC-R-Ent strains (24 Escherichia coli) were identified: 25 CTX-M and 3 DHA-1 producers (2 co-producing CTX-Ms). Using the SMS on native stool (“native SMS”) with thresholds ≥60% for both identity and coverage, only 7 of the 23 pre-enriched culture-positive samples resulted positive for blaCTX-M/blaDHA genes (native SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 59.0%; specificity 100%). Moreover, an average of 31.5 and 24.6 antimicrobial resistance genes (ARGs) were detected in the 23 pre-enriched culture-positive and the 19 negative samples, respectively. When the pre-enriched SMS was implemented, more blaCTX-M/blaDHA genes were detected than in the native assay, including in stools that were pre-enriched culture-negative (pre-enriched SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 78.3%; specificity 75.0%). In addition, the pre-enriched SMS identified on average 38.6 ARGs/sample, whereas for the corresponding native SMS it was 29.4 ARGs/sample. Notably, stools resulting false-negative by using the native SMS had lower concentrations of ESC-R-Ent (average: ~105 vs. ~107 CFU/g) and E. coli classified reads (average: 193,959 vs. 1.45 million) than those of native SMS positive samples. Finally, the detection of blaCTX-M/blaDHA genes was compared with two well-established bioinformatic tools. In conclusion, only the pre-enriched SMS assured detection of most carriers of ESC-R-Ent. However, its performance was not comparable to the pre-enriched culture-based approach.
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- 2023
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5. Escherichia ruysiae May Serve as a Reservoir of Antibiotic Resistance Genes across Multiple Settings and Regions
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Edgar I. Campos-Madueno, Claudia Aldeia, Parham Sendi, and Andrea Endimiani
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animal ,CTX-M-15 ,ESBL ,ST5792 ,environment ,Microbiology ,QR1-502 - Abstract
ABSTRACT Gut colonization with multidrug-resistant Enterobacterales (MDR-Ent) has reached worrisome levels worldwide. In this context, Escherichia ruysiae is a recently described species mostly found in animals. However, its spread and impact on humans is poorly understood. A stool sample from a healthy individual living in India was screened for the presence of MDR-Ent using culture-based methods. Colonies were routinely identified using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and phenotypically characterized by broth microdilution. Illumina and Nanopore whole-genome sequencing (WGS) platforms were implemented to generate a complete assembly. E. ruysiae genomes deposited in international databases were used for a core genome phylogenetic analysis. An extended-spectrum β-lactamase (ESBL)-producing E. coli strain (S1-IND-07-A) was isolated from the stool. WGS confirmed that S1-IND-07-A was indeed E. ruysiae, belonged to sequence type 5792 (ST5792), core genome (cg) ST89059, serotype O13/O129−:H56-like, clade IV phylogroup, and possessed five virulence factors. A copy of blaCTX-M-15 and five other antimicrobial resistance genes (ARGs) were detected in a conjugative IncB/O/K/Z plasmid. A database search identified 70 further E. ruysiae strains from 16 countries (44, 15, and 11 strains isolated from animals, the environment, and humans, respectively). The core genome phylogeny revealed five major STs: ST6467, ST8084, ST2371, ST9287, and ST5792. Three out of the seventy strains possessed important ARGs: OTP1704 (blaCTX-M-14; ST6467), SN1013-18 (blaCTX-M-15; ST5792), and CE1758 (blaCMY-2; ST7531). These strains were of human, environmental, and wild animal origin, respectively. E. ruysiae may acquire clinically important ARGs and transmit them to other species. Due to its zoonotic potential, further efforts are needed to improve routine detection and surveillance across One Health settings. IMPORTANCE Escherichia ruysiae is a recently described species of the cryptic clades III and IV of the genus Escherichia and is commonly found in animals and the environment. This work highlights the zoonotic potential of E. ruysiae, as it has been shown to colonize the human intestinal tract. Importantly, E. ruysiae may be associated with conjugative plasmids carrying clinically relevant antibiotic resistance genes. Therefore, it is important to closely monitor this species. Overall, this study highlights the need for improved identification of Escherichia species and continued surveillance of zoonotic pathogens in One Health settings.
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- 2023
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6. Genome stability during serial subculturing in hyperepidemic multidrug-resistant Klebsiella pneumoniae and Escherichia coli
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Aline I. Moser, Edgar I. Campos-Madueno, Vincent Perreten, and Andrea Endimiani
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SNVs ,Genome ,Plasmid ,Stability ,Klebsiella pneumoniae ,Escherichia coli ,Microbiology ,QR1-502 - Abstract
ABSTRACT: Objectives: Core-genome single nucleotide variant (cgSNV) analysis represents a powerful tool for epidemiological investigations of multidrug-resistant (MDR) bacteria. However, cgSNV thresholds to confirm whether isolates are the same clone are not formally defined. Methods: We implemented hybrid whole-genome sequencing to study the genomic changes of four MDR isolates belonging to hyperepidemic sequence types (STs) during 20 propagation steps (T20) on MacConkey and CHROMID(R) ESBL plates. The following strains were analyzed: Klebsiella pneumoniae AE-2247421 (OXA-48/NDM-1-producing, ST101), K. pneumoniae MCL-2017-2 (CTX-M-15-producing, ST307), Escherichia coli Ec-042 (OXA-181-producing, ST410), and E. coli Ec-050 (NDM-5-producing, ST167). The genome assembly at T5 and T20 was compared to that at time point zero (T0) and to two reference genomes. Results: At T20, AE-2247421 lost the IncL blaOXA-48-carrying plasmid when grown on CHROMID(R) ESBL plates, while a large fragment encompassing blaNDM-1 was lost from its IncC plasmid when grown on both plates. In contrast, no structural changes were noted for the other three strains. Regarding the cgSNVs, the following results were obtained at T5 and T20 (ranges considering the different agar plates and reference genomes): AE-2247421 (1–8 and 2–12 cgSNVs), MCL-2017-2 (both 1–2 cgSNVs), Ec-042 (both 0 cgSNVs), and Ec-050 (0–6 and 0–9 cgSNVs). Conclusion: We showed that structural changes and accumulation of cgSNVs can occur in few propagation steps under laboratory conditions. These changes might also arise in the clinical context in a short time, especially under antibiotics treatment. This phenomenon should be carefully considered because it might affect the final interpretation of epidemiological genomic analyses.
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- 2022
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7. Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: human and non-human settings may share high-risk clones
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Edgar I. Campos-Madueno, Aline I. Moser, Géraldine Jost, Carola Maffioli, Thomas Bodmer, Vincent Perreten, and Andrea Endimiani
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OXA-48 ,ST11 ,ST307 ,Plasmids ,Animals ,Environment ,Microbiology ,QR1-502 - Abstract
ABSTRACT: Background: The spread of carbapenemase-producing Klebsiella pneumoniae (CP-Kp) strains belonging to high-risk sequence types (STs) is a concern. For Switzerland, national data about the molecular features (especially the STs) of CP-Kp of human origin is not available. In veterinary clinics, ST11 and ST307 blaOXA-48-possessing K. pneumoniae strains have been recently reported. Methods: We analysed a collection of 285 K. pneumoniae genomes (170 were CP-Kp) isolated in Switzerland from human and non-human sources during 2006–2020. Whole-genome sequencing, core genome phylogenies and public databases were used to present a detailed overview regarding carbapenemases, STs and plasmids. Results: The top five STs were (main carbapenemase gene) ST512 (blaKPC-3), ST258 (blaKPC-2) and ST101 (blaOXA-48), consisting of strains of human origin only, and ST11 (blaOXA-48) and ST307 (blaOXA-48) strains isolated from human, animal and environmental sources. However, during 2016–2020, the main STs for CP-Kp were ST11 (17.6%), ST307 and ST101 (both 14.7%), whereas ST258 (5.9%) and ST512 (4.4%) significantly declined. Most carbapenemase genes were carried on plasmids already described. Core genome analysis revealed that ST11 K. pneumoniae of animal and human origin were closely related, whereas those of ST307 were distant. Conclusions: We described, for the first time, the features of the CP-Kp circulating in Switzerland in human and non-human settings. Our genomic analysis revealed that the emerging high-risk ST11 and ST307 lineages were often isolated from non-human settings. This study provided a baseline for further whole-genome sequencing-based One-Health surveillance of CP-Kp and emphasized the need for metadata to track dissemination routes between the different settings.
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- 2022
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8. Repatriation of a patient with COVID-19 contributed to the importation of an emerging carbapenemase producer
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Aline I. Moser, Edgar I. Campos-Madueno, Parham Sendi, Vincent Perreten, Peter M. Keller, Alban Ramette, and Andrea Endimiani
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Carbapenemase ,OXA-48 ,OXA-484 ,Plasmid ,SARS-CoV-2 ,IncX3 ,Microbiology ,QR1-502 - Abstract
ABSTRACT: Objectives: Patients hospitalised abroad can become colonised with multidrug-resistant bacteria and import them to their home countries. In this study, we characterised an OXA-484 carbapenemase-producing Escherichia coli strain from a Swiss patient infected by SARS-CoV-2 and repatriated from India. Methods: At admission to Switzerland (April 2021), the patient undertook a nasopharyngeal swab to search for SARS-CoV-2 and a rectal swab to detect multidrug-resistant bacteria. Both SARS-CoV-2 and E. coli isolates were whole-genome sequenced and analysed for phylogenetic relatedness. Results: The patient was infected with the SARS-CoV-2 B.1.617.2 lineage (VOC Delta), a lineage that began to be reported across Switzerland at that time. He was also colonised with a sequence type 410 (ST410) E. coli strain (L3452210II) producing OXA-484, a single amino acid variant of OXA-181. The blaOXA-484 gene was carried by a 51.5 kb IncX3 plasmid identical to those described in blaOXA-181-harbouring ST410 E. coli strains. Core genome analysis showed that L3452210II was identical (ΔSNV ≤23) to two ST410 OXA-484 producers recently reported in Qatar and Germany, but differed from other ST410 OXA-181 producers reported worldwide. Conclusion: The patient was infected by an emerging SARS-CoV-2 variant and also imported an E. coli producing OXA-484, an OXA-48-like carbapenemase not yet reported in Switzerland. The genetic background of L3452210II indicated that blaOXA-484 shared the same plasmid as blaOXA-181, but its bacterial host differed from most of the pandemic OXA-181-producing ST410 strains reported previously. This case description underlines that the COVID-19 crisis can contribute to the worldwide spread of emerging carbapenemase producers.
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- 2021
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9. Erratum to ‘Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: human and non-human settings may share high-risk clones’ [Journal of Global Antimicrobial Resistance 28 (2022) 206-215]
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Edgar I. Campos-Madueno, Aline I. Moser, Géraldine Jost, Carola Maffioli, Thomas Bodmer, Vincent Perreten, and Andrea Endimiani
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Microbiology ,QR1-502 - Published
- 2022
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10. First report of a blaVIM-1 metallo-β-lactamase-possessing Klebsiella michiganensis
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Edgar I. Campos-Madueno, Thomas Sigrist, Ursula M. Flückiger, Lorenz Risch, Thomas Bodmer, and Andrea Endimiani
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Klebsiella ,Carbapenemase ,VIM ,MBL ,Plasmid ,Integron ,Microbiology ,QR1-502 - Abstract
Objectives: Klebsiella michiganensis is an emerging pathogen. Like Klebsiella pneumoniae, this species is able to acquire antibiotic resistance genes (ARGs) via mobile genetic elements. In this context, K. michiganensis isolates producing carbapenemases of KPC, NDM, IMP and OXA-48-like types have already been reported. Here we characterised a strain (BD-50-Km) isolated from a rectal swab of a Turkish patient hospitalised in Switzerland. Methods: Species identification was initially performed using MALDI-TOF/MS. Antimicrobial susceptibility testing was done by the microdilution method. Whole-genome sequencing (WGS) was performed with both Illumina and Nanopore platforms and was used to confirm species identification, to characterise plasmids and to perform core-genome analyses. Results: BD-50-Km was initially identified as Klebsiella oxytoca and showed reduced susceptibility to imipenem. However, WGS indicated that the isolate was actually K. michiganensis. BD-50-Km carried the blaVIM-1 gene associated with a rare class 1 integron (In87) located on a pST1 196 kb IncC plasmid. This plasmid shares its backbone with many other IncC plasmids found in different species (including five K. michiganensis), but not the same In87 and the remaining region harbouring various ARGs. BD-50-Km belongs to the novel ST342. Moreover, core-genome analysis (single nucleotide variant analysis) showed that BD-50-Km was not closely related to any K. michiganensis strains deposited in NCBI (n = 212), including the 38 so far reported as possessing carbapenemase genes. Conclusion: This is the first report of a blaVIM-possessing K. michiganensis clinical isolate. The spread of plasmid-mediated VIM carbapenemases in this emerging pathogen represents an additional threat to our therapeutic armamentarium.
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- 2021
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11. Investigating the use of bacteriophages as a new decolonization strategy for intestinal carriage of CTX-M-15-producing ST131 Escherichia coli: An in vitro continuous culture system model
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Odette J. Bernasconi, Edgar I. Campos-Madueno, Valentina Donà, Vincent Perreten, Alessandra Carattoli, and Andrea Endimiani
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Bacteriophages ,Gut ,Multidrug-resistant ,Escherichia coli ,ST131 ,CTX-M-15 ,Microbiology ,QR1-502 - Abstract
Objectives: We investigated the use of bacteriophages as a strategy to decolonize intestinal carriers of multidrug-resistant Escherichia coli. Methods: A fermentor was used as a continuous culture system for 48 h. Two different pools of faeces (studies I and II) obtained from volunteers were spiked with a CTX-M-15-producing ST131 E. coli (strain 4901.28) susceptible to bacteriophages and challenged with three doses of INTESTI Bacteriophage cocktail administered at 2, 6 and 10 h after the inoculum. Bacterial typing was performed by implementing microdilution panels, spot test, rep-PCR and whole-genome sequencing (including cgMLST and single-nucleotide variant analysis) obtained using Nanopore and Illumina platforms. Results: In study I, bacteriophages decreased the numbers of 4901.28 dramatically (≤101 CFU/mL after 6 h). In contrast, during study II, a phage-resistant mutant of 4901.28 persisted in the continuous culture (104 CFU/mL at 48 h). Whole-genome sequencing revealed the presence of two additional plasmids in the mutant as well as 11 single-nucleotide variants, including one chromosomal in a glycosyltransferase family 2 protein that is responsible for the transfer of sugars to polysaccharides and lipids. In both studies, the commensal E. coli population remained unchanged by the phage treatment maintaining itself at 108 CFU/mL. Conclusions: Our data indicates that bacteriophage cocktails may be implemented to decolonize some intestinal carriers. However, the individual microbiota composition may have an impact on the development of phage resistance. Mechanisms underlying this phenomenon are likely to be various and complex. Further in vivo studies and protein expression experiments are needed to confirm our observations and hypotheses.
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- 2020
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12. Poor infection prevention and control standards are associated with environmental contamination with carbapenemase-producing Enterobacterales and other multidrug-resistant bacteria in Swiss companion animal clinics
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Janne S. Schmidt, Stefan P. Kuster, Aurélien Nigg, Valentina Dazio, Michael Brilhante, Helene Rohrbach, Odette J. Bernasconi, Thomas Büdel, Edgar I. Campos-Madueno, Stefanie Gobeli Brawand, Simone Schuller, Andrea Endimiani, Vincent Perreten, and Barbara Willi
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Infection prevention and control ,Small animal clinic ,Enterobacteriaceae ,Antimicrobial resistant pathogens ,Multidrug-resistant pathogens ,Colonization ,Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Intensive medical care in companion animal clinics could pose a risk for the selection and dissemination of multidrug-resistant organisms (MDROs). Infection prevention and control (IPC) concepts are key measures to reduce the spread of MDROs, but data on IPC standards in companion animal clinics is sparse. The study assessed IPC standards in seven companion animal clinics and practices in Switzerland by structured IPC audits and combined results with environmental MDRO contamination and MDRO carriage of the personnel. Methods IPC audits were held between August 2018 and January 2019. The observations in 34 IPC areas were scored based on predefined criteria (not fulfilled/partially fulfilled/fulfilled = score 0/1/2). Environmental swabs and nasal and stool samples from veterinary personnel were tested for methicillin-resistant (MR) staphylococci and macrococci and for colistin-resistant, extended-spectrum β-lactamase- and carbapenemase-producing (CP) Enterobacterales (CPE). Species was identified by MALDI-TOF MS, antimicrobial resistance determined by microdilution and β-lactam resistance gene detection, and genetic relatedness assessed by REP−/ERIC-PCR and multilocus sequence typing. Results Of a maximum total IPC score of 68, the institutions reached a median (range) score of 33 (19–55). MDROs were detected in median (range) 8.2% (0–33.3%) of the sampling sites. Clinics with low IPC standards showed extensive environmental contamination, i.e. of intensive care units, consultation rooms and utensils. CPE were detected in two clinics; one of them showed extensive contamination with CP Klebsiella pneumoniae (ST11, bla OXA-48) and MR Staphylococcus pseudintermedius (ST551, mecA). Despite low IPC scores, environmental contamination with MDROs was low in primary opinion practices. Three employees were colonized with Escherichia coli ST131 (bla CTX-M-15, bla CTX-M-27, bla CTX-M-14). Two employees carried CP E. coli closely related to environmental (ST410, bla OXA-181) and patient-derived isolates (ST167, bla NDM-5). MR Staphylococcus aureus (ST225, mecA) and MR S. pseudintermedius (ST551, mecA) of the same sequence types and with similar resistance profiles were found in employees and the environment in two clinics. Conclusions The study indicates that IPC standards in companion animal clinics are variable and that insufficient IPC standards could contribute to the evolution of MDROs which can be transferred between the environment and working personnel. The implementation of IPC concepts in companion animal clinics should urgently be promoted.
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- 2020
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13. Duration of carriage of multidrug-resistant bacteria in dogs and cats in veterinary care and co-carriage with their owners
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Valentina Dazio, Aurélien Nigg, Janne S. Schmidt, Michael Brilhante, Edgar I. Campos-Madueno, Nico Mauri, Stefan P. Kuster, Stefanie Gobeli Brawand, Barbara Willi, Andrea Endimiani, Vincent Perreten, and Simone Schuller
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Carbapenemase-producing Enterobacterales ,Extended-spectrum β-lactamase ,Transmission ,Co-carriage ,Companion animal ,Medicine (General) ,R5-920 - Abstract
Background: The emergence and spread of multidrug-resistant organisms (MDROs) represent a threat to human and animal health. Objectives: To assess duration of carriage of MDROs in dogs and cats presented to veterinary clinics/hospitals in Switzerland. To estimate prevalence, duration of and risk factors for MDRO carriage in their owners and the occurrence of co-carriage in owner-pet pairs. Methods: Prospective, longitudinal, observational study. Nasal swabs and fecal samples were collected from 50 owners of dogs and cats presented to 3 large veterinary hospitals, 1 medium-sized clinic and 1 practice. If pet or owner tested positive for a MDRO, follow-up samples were collected for up to 8 months. Methicillin-resistant (MR) Staphylococcus aureus, MR S. pseudintermedius, MR coagulase-negative staphylococci (MRCoNS), MR Macrococcus spp., cephalosporinase- and carbapenemase-producing (CP) Enterobacterales were isolated and further characterized by MALDI-TOF MS, microdilution, β-lactam resistance gene detection, REP/ERIC-PCR, multilocus sequence typing or whole-genome sequencing. Risk factors for MDRO carriage in owners were explored based on questionnaire-derived data. Results: Five out of 50 owners carried 3rd generation cephalosporin-resistant Enterobacterales (3GC-R-Ent.), and 5/50 MRCoNS. In 3 dogs and 4 cats carriage of 3GC-R-Ent. persisted for up to 136 days after discharge (median 99 days, IQR 83 days, range 36–136 days), in two cats isolates were carbapenem-resistant. Owner-pet co-carriage was not observed. No specific risk factors for MDRO carriage in owners were identified. Conclusions: After discharge from veterinary care, dogs and cats may carry 3GC-R-Ent. for prolonged time periods. Carriage of MDROs was common in owners, but pet-owner co-carriage of the same MDRO was not observed.
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- 2021
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14. A Patient With Multiple Carbapenemase Producers Including an Unusual Citrobacter sedlakii Hosting an IncC blaNDM-1- and armA-carrying Plasmid
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Aline Moser, Peter Keller, Edgar I. Campos-Madueno, Laurent Poirel, Patrice Nordmann, and Andrea Endimiani
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carbapenemases ,NDM-1 ,Enterobacterales ,ArmA ,plasmid ,CPE ,Pathology ,RB1-214 ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Background. Patients colonized with multiple species of carbapenemase-producing Enterobacterales (CPE) are increasingly observed. This phenomenon can be due to the high local prevalence of these pathogens, the presence of important host risk factors, and the great genetic promiscuity of some carbapenemase genes. Methods. We analyzed 4 CPE (Escherichia coli, Klebsiella pneumoniae, Providencia stuartii, Citrobacter sedlakii), 1 extended-spectrum cephalosporin-resistant K. pneumoniae (ESC-R-Kp), and 1 carbapenemase-producing Acinetobacter baumannii simultaneously isolated from a patient transferred from Macedonia. Susceptibility tests were performed using a microdilution MIC system. The complete genome sequences were obtained by using both short-read and long-read whole-genome sequencing technologies. Results. All CPE presented high-level resistance to all aminoglycosides due to the expression of the armA 16S rRNA methylase. In C. sedlakii and E. coli (ST69), both the carbapenemase blaNDM-1 and armA genes were located on an identical IncC plasmid of type 1a. The K. pneumoniae (ST268) and P. stuartii carried chromosomal blaNDM-1 and blaOXA-48, respectively, while the ESC-R-Kp (ST395) harbored a plasmid-located blaCTX-M-15. In the latter 3 isolates, armA-harboring IncC plasmids similar to plasmids found in C. sedlakii and E. coli were also detected. The A. baumannii strain possessed the blaOXA-40 carbapenemase gene. Conclusions. The characterization of the genetic organization of IncC-type plasmids harbored by 3 different species from the same patient offered insights into the evolution of these broad- host-range plasmids. Moreover, we characterized here the first complete genome sequence of a carbapenemase-producing C. sedlakii strain, providing a reference for future studies on this rarely reported species.
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- 2021
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15. Characterisation of a new blaVIM-1-carrying IncN2 plasmid from an Enterobacter hormaechei subsp. steigerwaltii
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Edgar I. Campos-Madueno, Christian Gmuer, Martin Risch, Thomas Bodmer, and Andrea Endimiani
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Microbiology ,QR1-502 - Published
- 2021
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16. Antimicrobial-Resistant Escherichia coli Strains and Their Plasmids in People, Poultry, and Chicken Meat in Laos
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Aline I. Moser, Esther Kuenzli, Edgar I. Campos-Madueno, Thomas Büdel, Sayaphet Rattanavong, Manivanh Vongsouvath, Christoph Hatz, and Andrea Endimiani
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mcr-1 ,mcr-3 ,CTX-M ,E. coli ,Laos ,gut colonization ,Microbiology ,QR1-502 - Abstract
Antimicrobial resistant (AMR) Enterobacterales are widely distributed among the healthy population of the Indochinese peninsula, including Laos. However, the local reservoir of these pathogens are currently not known and possible sources such as agricultural settings and food have rarely been analyzed. In this work, we investigated the extended-spectrum cephalosporin- (ESC-) and colistin-resistant Escherichia coli strains (CST-R-Ec) isolated from the gut of local people, feces of poultry, and from chicken meat (60 samples each group) in Laos. Whole-genome sequencing (WGS) analysis based on both short- and long-read sequencing approaches were implemented. The following prevalence of ESC-R-Ec and CST-R-Ec were recorded, respectively: local people (70 and 15%), poultry (20 and 23.3%), and chicken meat (21.7 and 13.3%). Core-genome analysis, coupled with sequence type (ST)/core-genome ST (cgST) definitions, indicated that no common AMR-Ec clones were spreading among the different settings. ESC-R-Ec mostly possessed blaCTX–M–15 and blaCTX–M–55 associated to ISEcp1 or IS26. The majority of CST-R-Ec carried mcr-1 on IncX4, IncI2, IncP1, and IncHI1 plasmids similar or identical to those described worldwide; strains with chromosomal mcr-1 or possessing plasmid-mediated mcr-3 were also found. These results indicate a high prevalence of AMR-Ec in the local population, poultry, and chicken meat. While we did not observe the same clones among the three settings, most of the blaCTX–Ms and mcr-1/-3 were associated with mobile-genetic elements, indicating that horizontal gene transfer may play an important role in the dissemination of AMR-Ec in Laos. More studies should be planned to better understand the extent and dynamics of this phenomenon.
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- 2021
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17. Complete Genome Sequence of the First Colistin-Resistant Raoultella electrica Strain
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Claudia Aldeia, Edgar I. Campos-Madueno, Parham Sendi, and Andrea Endimiani
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Immunology and Microbiology (miscellaneous) ,Genetics ,570 Life sciences ,biology ,610 Medicine & health ,Molecular Biology - Abstract
We present the full genome sequence of a colistin-resistant Raoultella electrica strain (MIC, >4 μg/mL) that was isolated from the stool of a healthy person living in India. The sequence consists of a chromosome and three plasmids (5,455,992-bp and 98,913-bp, 4,232-bp, and 3,961-bp, respectively). No previously described colistin resistance mechanisms were detected.
- Published
- 2023
18. Simultaneous gut colonization by Klebsiella grimontii and Escherichia coli co-possessing the blaKPC-3-carrying pQil plasmid
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Edgar I. Campos-Madueno, Carola Mauri, Elisa Meroni, Pablo Porragas Paseiro, Alessandra Consonni, Francesco Luzzaro, and Andrea Endimiani
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Microbiology (medical) ,Infectious Diseases ,570 Life sciences ,biology ,610 Medicine & health ,General Medicine ,biochemical phenomena, metabolism, and nutrition ,bacterial infections and mycoses - Abstract
Only two plasmid-mediated carbapenemases (KPC-2 and VIM-1) are reported in Klebsiella grimontii. Here, we report two blaKPC-3-positive isolates that were identified as K. oxytoca and E. coli by MALDI-TOF MS in the same rectal swab. Whole-genome sequencing indicated that K. oxytoca was actually K. grimontii of ST391, whereas E. coli was of ST10. In both, blaKPC-3 was carried by a pQil conjugative plasmid. The core-genome analysis identified additional blaKPC-positive K. grimontii strains from public databases, most of which were misidentified as K. oxytoca. Since K. grimontii represents an emerging reservoir of resistance traits, routine tools should improve their ability to detect this species.
- Published
- 2022
19. Intestinal colonization with multidrug-resistant Enterobacterales: screening, epidemiology, clinical impact, and strategies to decolonize carriers
- Author
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Edgar I. Campos-Madueno, Melika Moradi, Yasmine Eddoubaji, Fatemeh Shahi, Sina Moradi, Odette J. Bernasconi, Aline I. Moser, and Andrea Endimiani
- Subjects
Microbiology (medical) ,Infectious Diseases ,570 Life sciences ,biology ,610 Medicine & health ,General Medicine - Abstract
The clinical impact of infections due to extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing Enterobacterales (Ent) has reached dramatic levels worldwide. Infections due to these multidrug-resistant (MDR) pathogens—especially Escherichia coli and Klebsiella pneumoniae—may originate from a prior asymptomatic intestinal colonization that could also favor transmission to other subjects. It is therefore desirable that gut carriers are rapidly identified to try preventing both the occurrence of serious endogenous infections and potential transmission. Together with the infection prevention and control countermeasures, any strategy capable of effectively eradicating the MDR-Ent from the intestinal tract would be desirable. In this narrative review, we present a summary of the different aspects linked to the intestinal colonization due to MDR-Ent. In particular, culture- and molecular-based screening techniques to identify carriers, data on prevalence and risk factors in different populations, clinical impact, length of colonization, and contribution to transmission in various settings will be overviewed. We will also discuss the standard strategies (selective digestive decontamination, fecal microbiota transplant) and those still in development (bacteriophages, probiotics, microcins, and CRISPR-Cas-based) that might be used to decolonize MDR-Ent carriers.
- Published
- 2023
- Full Text
- View/download PDF
20. Complete Genome Sequence of
- Author
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Aline I, Moser, Yasmine, Eddoubaji, Edgar I, Campos-Madueno, and Andrea, Endimiani
- Abstract
Here, we present the complete genome sequence of
- Published
- 2022
21. Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: human and non-human settings may share high-risk clones
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Edgar I, Campos-Madueno, Aline I, Moser, Géraldine, Jost, Carola, Maffioli, Thomas, Bodmer, Vincent, Perreten, and Andrea, Endimiani
- Subjects
Klebsiella pneumoniae ,Carbapenem-Resistant Enterobacteriaceae ,Bacterial Proteins ,Animals ,Humans ,Switzerland ,beta-Lactamases ,Clone Cells ,Klebsiella Infections - Abstract
The spread of carbapenemase-producing Klebsiella pneumoniae (CP-Kp) strains belonging to high-risk sequence types (STs) is a concern. For Switzerland, national data about the molecular features (especially the STs) of CP-Kp of human origin is not available. In veterinary clinics, ST11 and ST307 blaWe analysed a collection of 285 K. pneumoniae genomes (170 were CP-Kp) isolated in Switzerland from human and non-human sources during 2006-2020. Whole-genome sequencing, core genome phylogenies and public databases were used to present a detailed overview regarding carbapenemases, STs and plasmids.The top five STs were (main carbapenemase gene) ST512 (blaWe described, for the first time, the features of the CP-Kp circulating in Switzerland in human and non-human settings. Our genomic analysis revealed that the emerging high-risk ST11 and ST307 lineages were often isolated from non-human settings. This study provided a baseline for further whole-genome sequencing-based One-Health surveillance of CP-Kp and emphasized the need for metadata to track dissemination routes between the different settings.
- Published
- 2021
22. Duration of carriage of multidrug-resistant bacteria in dogs and cats in veterinary care and co-carriage with their owners
- Author
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Stefan P. Kuster, Janne S. Schmidt, Vincent Perreten, Andrea Endimiani, Valentina Dazio, Michael Brilhante, Simone Schuller, Barbara Willi, Edgar I. Campos-Madueno, Stefanie Gobeli Brawand, Aurélien Nigg, and Nico Mauri
- Subjects
Veterinary medicine ,Medicine (General) ,3GC-R, Third Generation Cephalosporin-resistant ,MDROs, Multidrug-resistant organisms ,TMP-S, Trimethoprim/sulfamethoxazole ,Carbapenemase-producing Enterobacterales ,WGS, Whole-genome sequencing ,EUCAST, European Committee on Antimicrobial Susceptibility Testing ,MICs, Minimal inhibitory concentrations ,Medicine ,CP, Carbapenemase-producing ,health care economics and organizations ,REP-PCR, Repetitive element palindromic polymerase chain reaction ,CATS ,Animal health ,630 Agriculture ,Transmission (medicine) ,ERIC-PCR, Enterobacterial repetitive intergenic consensus polymerase chain reaction ,MALDI-TOF MS, Matrix-assisted laser desorption/ionization time of flight mass spectrometry ,Infectious Diseases ,Multidrug resistant bacteria ,COL-R, Colistin-resistant ,MDR, Multidrug-resistant ,Research Paper ,MRCoNS, Methicillin-resistant coagulase-negative staphylococci ,Co-carriage ,ESBL-KP, ESBL-producing Klebsiella pneumoniae ,AMR, Antimicrobial resistance ,MR, Methicillin-resistant ,R5-920 ,Extended-spectrum β-lactamase ,Enterobacterales ,MRSP, Methicillin-resistant Staphylococcus pseudintermedius ,pAmpC, Plasmid-encoded AmpC ,Transmission ,Feces ,CI, Confidence interval ,MLST, Multilocus sequence typing ,business.industry ,Public Health, Environmental and Occupational Health ,CLSI, Clinical and Laboratory Standards Institute ,IQR, Interquartile range ,ESBL, Extended spectrum β-lactamase ,ESBL-E. coli, ESBL-producing Escherichia coli ,Companion animal ,Carriage ,MRSA, Methicillin-resistant Staphylococcus aureus ,3GC-R-Ent., Third Generation Cephalosporin-resistant Enterobacterales ,Multilocus sequence typing ,KP, Klebsiella pneumoniae ,ST, Sequence type ,CR, Carbapenem-resistant ,business ,CRE, Carbapenem-resistant Enterobacterales - Abstract
Background The emergence and spread of multidrug-resistant organisms (MDROs) represent a threat to human and animal health. Objectives To assess duration of carriage of MDROs in dogs and cats presented to veterinary clinics/hospitals in Switzerland. To estimate prevalence, duration of and risk factors for MDRO carriage in their owners and the occurrence of co-carriage in owner-pet pairs. Methods Prospective, longitudinal, observational study. Nasal swabs and fecal samples were collected from 50 owners of dogs and cats presented to 3 large veterinary hospitals, 1 medium-sized clinic and 1 practice. If pet or owner tested positive for a MDRO, follow-up samples were collected for up to 8��months. Methicillin-resistant (MR) Staphylococcus aureus, MR S. pseudintermedius, MR coagulase-negative staphylococci (MRCoNS), MR Macrococcus spp., cephalosporinase- and carbapenemase-producing (CP) Enterobacterales were isolated and further characterized by MALDI-TOF MS, microdilution, ��-lactam resistance gene detection, REP/ERIC-PCR, multilocus sequence typing or whole-genome sequencing. Risk factors for MDRO carriage in owners were explored based on questionnaire-derived data. Results Five out of 50 owners carried 3rd generation cephalosporin-resistant Enterobacterales (3GC-R-Ent.), and 5/50 MRCoNS. In 3 dogs and 4 cats carriage of 3GC-R-Ent. persisted for up to 136��days after discharge (median 99��days, IQR 83��days, range 36-136��days), in two cats isolates were carbapenem-resistant. Owner-pet co-carriage was not observed. No specific risk factors for MDRO carriage in owners were identified. Conclusions After discharge from veterinary care, dogs and cats may carry 3GC-R-Ent. for prolonged time periods. Carriage of MDROs was common in owners, but pet-owner co-carriage of the same MDRO was not observed.
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- 2021
23. Exploring the global spread of Klebsiella grimontii isolates possessing blaVIM-1 and mcr-9
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Thomas Bodmer, Aline Moser, Andrea Endimiani, Martin Risch, and Edgar I. Campos-Madueno
- Subjects
Klebsiella ,Salmonella ,Enterobacter ,610 Medicine & health ,Microbial Sensitivity Tests ,medicine.disease_cause ,Integron ,beta-Lactamases ,03 medical and health sciences ,Plasmid ,Bacterial Proteins ,Mechanisms of Resistance ,medicine ,Animals ,Pharmacology (medical) ,Retrospective Studies ,030304 developmental biology ,Pharmacology ,Genetics ,0303 health sciences ,biology ,030306 microbiology ,Klebsiella oxytoca ,biochemical phenomena, metabolism, and nutrition ,Plasmid-mediated resistance ,bacterial infections and mycoses ,biology.organism_classification ,Anti-Bacterial Agents ,Infectious Diseases ,biology.protein ,570 Life sciences ,MCR-1 ,Plasmids - Abstract
The spread of plasmid-mediated carbapenemases within Klebsiella oxytoca is well-documented. In contrast, data concerning the closely related species Klebsiella grimontii are scarce. In fact, despite the recent report of the first bla(KPC-2)-producing K. grimontii, nothing is known about its clonality and antibiotic resistance patterns. In a retrospective search in our collection, we identified 2 bla(VIM)-positive K. oxytoca strains. Whole-genome sequencing with both Illumina and Nanopore indicated that our strains actually belonged to K. grimontii and were of sequence type 172 (ST172) and ST189. Moreover, the two strains were associated with 297-kb IncHI2/HI2A-pST1 and 90.6-kb IncFII(Yp) plasmids carrying bla(VIM-1) together with mcr-9 and bla(VIM-1), respectively. In the IncHI2/HI2A plasmid, bla(VIM-1) was located in a class 1 integron (In110), while mcr-9 was associated with the qseC-qseB-like regulatory elements. Overall, this plasmid was shown to be very similar to those carried by other Enterobacterales isolated from food and animal sources (e.g., Salmonella and Enterobacter spp. detected in Germany and Egypt). The IncFII(Yp) plasmid was unique, and its bla(VIM-1) region was associated with a rare integron (In1373). Mapping of In1373 indicated a possible origin in Austria from an Enterobacter hormaechei carrying a highly similar plasmid. Core-genome phylogenies indicated that the ST172 K. grimontii belonged to a clone of identical Swedish and Swiss strains (≤15 single nucleotide variants [SNVs] to each other), whereas the ST189 strain was sporadic. Surveillance of carbapenemase-producing K. oxytoca strains should be reinforced to detect and prevent the dissemination of new species belonging to the Klebsiella genus.
- Published
- 2021
24. A Patient With Multiple Carbapenemase Producers Including an Unusual Citrobacter sedlakii Hosting an IncC blaNDM-1- and armA-carrying Plasmid
- Author
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Laurent Poirel, Aline Moser, Peter M. Keller, Edgar I. Campos-Madueno, Andrea Endimiani, and Patrice Nordmann
- Subjects
Microbiology (medical) ,Whole genome sequencing ,Genetics ,biology ,Klebsiella pneumoniae ,Providencia stuartii ,Immunology ,610 Medicine & health ,medicine.disease_cause ,biology.organism_classification ,Genome ,Acinetobacter baumannii ,Infectious Diseases ,Plasmid ,medicine ,Immunology and Allergy ,Citrobacter sedlakii ,570 Life sciences ,Molecular Biology ,Escherichia coli - Abstract
Background. Patients colonized with multiple species of carbapenemase-producing Enterobacterales (CPE) are increasingly observed. This phenomenon can be due to the high local prevalence of these pathogens, the presence of important host risk factors, and the great genetic promiscuity of some carbapenemase genes. Methods. We analyzed 4 CPE (Escherichia coli, Klebsiella pneumoniae, Providencia stuartii, Citrobacter sedlakii), 1 extended-spectrum cephalosporin-resistant K. pneumoniae (ESC-R-Kp), and 1 carbapenemase-producing Acinetobacter baumannii simultaneously isolated from a patient transferred from Macedonia. Susceptibility tests were performed using a microdilution MIC system. The complete genome sequences were obtained by using both short-read and long-read whole-genome sequencing technologies. Results. All CPE presented high-level resistance to all aminoglycosides due to the expression of the armA 16S rRNA methylase. In C. sedlakii and E. coli (ST69), both the carbapenemase blaNDM-1 and armA genes were located on an identical IncC plasmid of type 1a. The K. pneumoniae (ST268) and P. stuartii carried chromosomal blaNDM-1 and blaOXA-48, respectively, while the ESC-R-Kp (ST395) harbored a plasmid-located blaCTX-M-15. In the latter 3 isolates, armA-harboring IncC plasmids similar to plasmids found in C. sedlakii and E. coli were also detected. The A. baumannii strain possessed the blaOXA-40 carbapenemase gene. Conclusions. The characterization of the genetic organization of IncC-type plasmids harbored by 3 different species from the same patient offered insights into the evolution of these broad- host-range plasmids. Moreover, we characterized here the first complete genome sequence of a carbapenemase-producing C. sedlakii strain, providing a reference for future studies on this rarely reported species.
- Published
- 2021
- Full Text
- View/download PDF
25. Characterization of a new blaVIM-1-carrying IncN2 plasmid from an Enterobacter hormaechei subsp. steigerwaltii
- Author
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Andrea Endimiani, Martin Risch, Edgar I. Campos-Madueno, Thomas Bodmer, and Christian Gmuer
- Subjects
Microbiology (medical) ,Genetics ,Plasmid ,Immunology ,Immunology and Allergy ,570 Life sciences ,biology ,610 Medicine & health ,Biology ,Microbiology ,QR1-502 ,ENTEROBACTER HORMAECHEI - Published
- 2021
26. Characterisation of a new bla
- Author
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Edgar I, Campos-Madueno, Christian, Gmuer, Martin, Risch, Thomas, Bodmer, and Andrea, Endimiani
- Subjects
Enterobacter ,Plasmids - Published
- 2020
27. Emergence of Haemophilus parainfluenzae resistant to third-generation cephalosporins in Italy: potential role of PBP3 and PBP5 substitutions in high-level resistance
- Author
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Odette J Bernasconi, Valentina Viaggi, Francesco Luzzaro, Luigi Principe, Andrea Endimiani, and Edgar I. Campos-Madueno
- Subjects
Microbiology (medical) ,Third generation cephalosporins ,High level resistance ,Infectious Diseases ,Haemophilus parainfluenzae ,570 Life sciences ,biology ,Pharmacology (medical) ,610 Medicine & health ,General Medicine ,Biology ,biology.organism_classification ,Microbiology - Published
- 2020
28. Rapid Increase of CTX-M-Producing Shigella sonnei Isolates in Switzerland Due to Spread of Common Plasmids and International Clones
- Author
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Francesco Luzzaro, Odette J Bernasconi, Andreas Kronenberg, Andrea Endimiani, Aline Moser, Thomas Bodmer, Peter M. Keller, Edgar I. Campos-Madueno, and Carola Maffioli
- Subjects
Shigella sonnei ,610 Medicine & health ,Microbial Sensitivity Tests ,Biology ,medicine.disease_cause ,beta-Lactamases ,03 medical and health sciences ,Antibiotic resistance ,Plasmid ,Mechanisms of Resistance ,Enterobacterales ,medicine ,Pharmacology (medical) ,Shigella ,Phylogeny ,030304 developmental biology ,Netherlands ,Pharmacology ,Genetics ,0303 health sciences ,Phylogenetic tree ,030306 microbiology ,Plasmid-mediated resistance ,biochemical phenomena, metabolism, and nutrition ,bacterial infections and mycoses ,United Kingdom ,Anti-Bacterial Agents ,Clone Cells ,Infectious Diseases ,Multilocus sequence typing ,570 Life sciences ,biology ,France ,Switzerland ,Plasmids - Abstract
The Swiss Centre for Antibiotic Resistance (ANRESIS) has recently noted an increase of extended-spectrum cephalosporin-resistant (ESC-R) Shigella sonnei isolates nationwide (3.8% in 2016 versus 37.5% in 2019). To understand this phenomenon, we analyzed 25 representative isolates (of which 14 were ESC-R) collected in Switzerland during 2016 to 2019. Whole-genome sequencing was achieved using both the Illumina and the Nanopore platforms. Both ESC-R and extended-spectrum cephalosporin-susceptible isolates belonged to sequence type 152 (ST152). The ESC-R isolates carried bla(CTX-M-3) in IncI1-pST57 (n = 5), bla(CTX-M-15) in IncFII (F2:A-:B-) (n = 5), bla(CTX-M-15) in IncI1-pST16, and bla(CTX-M-27), bla(CTX-M-55), or bla(CTX-M-134) in other IncFII plasmids (n = 1 each). Plasmids having the same bla and Inc group exhibited high degrees of genetic identity to each other but also to plasmids previously reported in other Enterobacterales. Core-genome analysis showed that there were 4 main clusters, each of which included strains that differed by
- Published
- 2020
29. Poor infection prevention and control standards are associated with environmental contamination with carbapenemase-producing Enterobacterales and other multidrug-resistant bacteria in Swiss companion animal clinics
- Author
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Valentina Dazio, Odette J Bernasconi, Michael Brilhante, Simone Schuller, Stefanie Gobeli Brawand, Barbara Willi, Andrea Endimiani, Janne S. Schmidt, Edgar I. Campos-Madueno, Vincent Perreten, Thomas Büdel, Aurélien Nigg, Stefan P. Kuster, Helene Rohrbach, University of Zurich, and Willi, Barbara
- Subjects
Colonization ,0301 basic medicine ,10253 Department of Small Animals ,Staphylococcus pseudintermedius ,Commission on Professional and Hospital Activities ,Drug resistance ,2726 Microbiology (medical) ,0403 veterinary science ,Feces ,Zoonosis ,Medical microbiology ,Drug Resistance, Multiple, Bacterial ,2736 Pharmacology (medical) ,Infection control ,Pharmacology (medical) ,Prospective Studies ,610 Medicine & health ,630 Agriculture ,biology ,Antimicrobial resistant pathogens ,resistant pathogens ,Pets ,04 agricultural and veterinary sciences ,Multidrug ,Infectious Diseases ,Equipment and Supplies ,Switzerland ,Microbiology (medical) ,medicine.medical_specialty ,Infection prevention and control ,040301 veterinary sciences ,030106 microbiology ,Nose ,lcsh:Infectious and parasitic diseases ,Animal Technicians ,Veterinarians ,Hospitals, Animal ,03 medical and health sciences ,Antibiotic resistance ,Enterobacteriaceae ,Internal medicine ,Intensive care ,parasitic diseases ,medicine ,Animals ,Humans ,lcsh:RC109-216 ,Infection Control ,business.industry ,Research ,Public Health, Environmental and Occupational Health ,2739 Public Health, Environmental and Occupational Health ,2725 Infectious Diseases ,Small animal clinic ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,Multidrug-resistant pathogens ,Carbapenem-Resistant Enterobacteriaceae ,Carriage ,Equipment Contamination ,570 Life sciences ,Multilocus sequence typing ,business - Abstract
Background Intensive medical care in companion animal clinics could pose a risk for the selection and dissemination of multidrug-resistant organisms (MDROs). Infection prevention and control (IPC) concepts are key measures to reduce the spread of MDROs, but data on IPC standards in companion animal clinics is sparse. The study assessed IPC standards in seven companion animal clinics and practices in Switzerland by structured IPC audits and combined results with environmental MDRO contamination and MDRO carriage of the personnel. Methods IPC audits were held between August 2018 and January 2019. The observations in 34 IPC areas were scored based on predefined criteria (not fulfilled/partially fulfilled/fulfilled = score 0/1/2). Environmental swabs and nasal and stool samples from veterinary personnel were tested for methicillin-resistant (MR) staphylococci and macrococci and for colistin-resistant, extended-spectrum β-lactamase- and carbapenemase-producing (CP) Enterobacterales (CPE). Species was identified by MALDI-TOF MS, antimicrobial resistance determined by microdilution and β-lactam resistance gene detection, and genetic relatedness assessed by REP−/ERIC-PCR and multilocus sequence typing. Results Of a maximum total IPC score of 68, the institutions reached a median (range) score of 33 (19–55). MDROs were detected in median (range) 8.2% (0–33.3%) of the sampling sites. Clinics with low IPC standards showed extensive environmental contamination, i.e. of intensive care units, consultation rooms and utensils. CPE were detected in two clinics; one of them showed extensive contamination with CP Klebsiella pneumoniae (ST11, blaOXA-48) and MR Staphylococcus pseudintermedius (ST551, mecA). Despite low IPC scores, environmental contamination with MDROs was low in primary opinion practices. Three employees were colonized with Escherichia coli ST131 (blaCTX-M-15, blaCTX-M-27, blaCTX-M-14). Two employees carried CP E. coli closely related to environmental (ST410, blaOXA-181) and patient-derived isolates (ST167, blaNDM-5). MR Staphylococcus aureus (ST225, mecA) and MR S. pseudintermedius (ST551, mecA) of the same sequence types and with similar resistance profiles were found in employees and the environment in two clinics. Conclusions The study indicates that IPC standards in companion animal clinics are variable and that insufficient IPC standards could contribute to the evolution of MDROs which can be transferred between the environment and working personnel. The implementation of IPC concepts in companion animal clinics should urgently be promoted.
- Published
- 2020
30. Whole-Genome Characterization of a Shewanella algae Strain Coharboring bla CTX-M-15 and armA Genes on a Novel IncC Plasmid
- Author
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Alessandra Carattoli, Thomas Büdel, Odette J Bernasconi, Edgar I. Campos-Madueno, Christoph Hatz, Esther Kuenzli, and Andrea Endimiani
- Subjects
Pharmacology ,biology ,Strain (chemistry) ,610 Medicine & health ,Shewanella algae ,Acinetobacter ,biology.organism_classification ,Shewanella ,Genome ,Microbiology ,Infectious Diseases ,Plasmid ,ArmA ,CTX-M-15 ,ESBL ,Extended-spectrum β-lactamase ,IncC ,Plasmids ,570 Life sciences ,Pharmacology (medical) ,Gene - Published
- 2020
31. Whole-Genome Characterization of a Shewanella algae Strain Coharboring
- Author
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Andrea, Endimiani, Odette J, Bernasconi, Thomas, Büdel, Edgar I, Campos-Madueno, Esther, Kuenzli, Christoph, Hatz, and Alessandra, Carattoli
- Subjects
Shewanella ,Whole Genome Sequencing ,Methyltransferases ,Microbial Sensitivity Tests ,beta-Lactams ,Tanzania ,beta-Lactamases ,Anti-Bacterial Agents ,Feces ,Drug Resistance, Multiple, Bacterial ,Animals ,Chickens ,Letter to the Editor ,Genome, Bacterial ,Plasmids - Published
- 2020
32. On the island of Zanzibar people in the community are frequently colonized with the same MDR Enterobacterales found in poultry and retailed chicken meat
- Author
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Jakob Zinsstag, Christoph Hatz, Edgar I. Campos-Madueno, Nadir Khatib Hassan, Thomas Büdel, Andrea Endimiani, Ali Haji Mohammed, and Esther Kuenzli
- Subjects
0301 basic medicine ,Microbiology (medical) ,Veterinary medicine ,Meat ,Escherichia coli Proteins ,Klebsiella pneumoniae ,030106 microbiology ,medicine.disease_cause ,Tanzania ,Poultry ,beta-Lactamases ,03 medical and health sciences ,Human gut ,Enterobacterales ,medicine ,Escherichia coli ,Animals ,Pharmacology (medical) ,Colonization ,Escherichia coli Infections ,Pharmacology ,Islands ,biology ,biology.organism_classification ,Anti-Bacterial Agents ,030104 developmental biology ,Infectious Diseases ,Colistin ,Intestinal colonization ,Chickens ,medicine.drug - Abstract
Objectives Intestinal colonization with extended-spectrum cephalosporin-resistant (ESC-R) and colistin-resistant (CST-R) Enterobacterales (Ent) can be driven by contact with colonized animals and/or contamination of the food chain. We studied the ESC-R-Ent and COL-R-Ent colonizing poultry as well as contaminating chicken meat in Zanzibar (Tanzania). Results were compared with recently published data obtained from rectal swabs of people in the community. Methods During June and July 2018, we collected poultry faecal material (n = 62) and retail chicken meat (n = 37) samples. ESC-R and CST-R strains were isolated implementing selective approaches and characterized with different molecular methods, including WGS coupled with core-genome analyses. Results The prevalence of ESC-R-Ent and CST-R-Ent, respectively, were: 88.7% and 48.4% in poultry; and 43.2% and 18.9% in chicken meat. Overall, the following strains and main resistance mechanisms were found in the two settings: 69 ESC-R Escherichia coli (CTX-M-15 subgroup, 75%), 34 ESC-R Klebsiella pneumoniae (CTX-M-9 group, 54.5%), 24 non-ESC-R but CST-R E. coli (mcr-1, 95.8%) and 17 non-ESC-R but CST-R K. pneumoniae (D150G substitution in PhoQ). Several clones (differing by only 0–13 single nucleotide variants) were concomitantly and frequently found in human and non-human settings: mcr-1-carrying E. coli ST46; CTX-M-15-producing E. coli ST361; CTX-M-14-producing K. pneumoniae ST17; and CTX-M-15-producing K. pneumoniae ST1741. Conclusions This is one of the few studies that have assessed the occurrence of identical MDR Enterobacterales in human and non-human settings. The frequent human gut colonization observed in the community might be favoured by the spread of ESC-R-Ent and CST-R-Ent in poultry and chicken meat. Further studies with a One Health approach should be carried out to better investigate this phenomenon.
- Published
- 2020
33. Investigating the use of bacteriophages as a new decolonization strategy for intestinal carriage of CTX-M-15-producing ST131 Escherichia coli: an in vitro continuous culture system model
- Author
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Odette J Bernasconi, Vincent Perreten, Edgar I. Campos-Madueno, Alessandra Carattoli, Andrea Endimiani, and Valentina Donà
- Subjects
0301 basic medicine ,Microbiology (medical) ,CTX-M-15 ,bacteriophages ,ST131 ,030106 microbiology ,Immunology ,Population ,Mutant ,multidrug-resistant ,610 Medicine & health ,medicine.disease_cause ,Microbiology ,beta-Lactamases ,Bacteriophage ,03 medical and health sciences ,0302 clinical medicine ,Plasmid ,In vivo ,medicine ,Humans ,Immunology and Allergy ,030212 general & internal medicine ,education ,Escherichia coli ,Escherichia coli Infections ,education.field_of_study ,630 Agriculture ,biology ,biology.organism_classification ,QR1-502 ,In vitro ,Multiple drug resistance ,570 Life sciences ,gut ,escherichia coli ,Plasmids - Abstract
Objectives We investigated the use of bacteriophages as a strategy to decolonize intestinal carriers of multidrug-resistant Escherichia coli. Methods A fermentor was used as a continuous culture system for 48 h. Two different pools of faeces (studies I and II) obtained from volunteers were spiked with a CTX-M-15-producing ST131 E. coli (strain 4901.28) susceptible to bacteriophages and challenged with three doses of INTESTI Bacteriophage cocktail administered at 2, 6 and 10 h after the inoculum. Bacterial typing was performed by implementing microdilution panels, spot test, rep-PCR and whole-genome sequencing (including cgMLST and single-nucleotide variant analysis) obtained using Nanopore and Illumina platforms. Results In study I, bacteriophages decreased the numbers of 4901.28 dramatically (≤101 CFU/mL after 6 h). In contrast, during study II, a phage-resistant mutant of 4901.28 persisted in the continuous culture (104 CFU/mL at 48 h). Whole-genome sequencing revealed the presence of two additional plasmids in the mutant as well as 11 single-nucleotide variants, including one chromosomal in a glycosyltransferase family 2 protein that is responsible for the transfer of sugars to polysaccharides and lipids. In both studies, the commensal E. coli population remained unchanged by the phage treatment maintaining itself at 108 CFU/mL. Conclusions Our data indicates that bacteriophage cocktails may be implemented to decolonize some intestinal carriers. However, the individual microbiota composition may have an impact on the development of phage resistance. Mechanisms underlying this phenomenon are likely to be various and complex. Further in vivo studies and protein expression experiments are needed to confirm our observations and hypotheses.
- Published
- 2020
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