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Eddoubaji Y, Aldeia C, Campos-Madueno EI, Moser AI, Kundlacz C, Perreten V, Hilty M, Endimiani A. A new in vivo model of intestinal colonization using Zophobas morio larvae: testing hyperepidemic ESBL- and carbapenemase-producing Escherichia coli clones. Front Microbiol 2024; 15:1381051. [PMID: 38659985 PMCID: PMC11039899 DOI: 10.3389/fmicb.2024.1381051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
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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Affiliation(s)
- Yasmine Eddoubaji
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Edgar I. Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Aline I. Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Cindy Kundlacz
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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Kundlacz C, Aldeia C, Eddoubaji Y, Campos-Madueno EI, Endimiani A. A new OCH β-lactamase from a Brucella pseudintermedia (Ochrobactrum pseudintermedium) strain isolated from Zophobas morio larvae. J Glob Antimicrob Resist 2024; 36:65-69. [PMID: 38128729 DOI: 10.1016/j.jgar.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
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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Affiliation(s)
- Cindy Kundlacz
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Yasmine Eddoubaji
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland.
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Donà V, Nordmann P, Kittl S, Schuller S, Bouvier M, Poirel L, Endimiani A, Perreten V. Emergence of OXA-48-producing Enterobacter hormaechei in a Swiss companion animal clinic and their genetic relationship to clinical human isolates. J Antimicrob Chemother 2023; 78:2950-2960. [PMID: 37923369 DOI: 10.1093/jac/dkad337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Enterobacter hormaechei producing the carbapenemase OXA-48 was identified repeatedly in infections in companion animals hospitalized at a Swiss veterinary clinic where OXA-48-producing Klebsiella pneumoniae was previously reported. OBJECTIVES To determine the genetic relatedness of animal and human E. hormaechei strains collected in Switzerland during 2017-22 and their mobile genetic elements. METHODS Hybrid assemblies for phylogenetic and comparative analysis of animal (n = 9) and human (n = 25) isolates were obtained by sequencing with Illumina, PacBio and Oxford Nanopore Technologies. Antimicrobial susceptibility was tested by broth microdilution. RESULTS The animal strains were identified as E. hormaechei subsp. xiangfangensis ST114 (n = 6) and ST418 (n = 2), and E. hormaechei subsp. hoffmannii ST78 (n = 1). Human E. hormaechei belonged to subspecies steigerwaltii (n = 10), xiangfangensis (n = 13), hoffmannii (n = 1) and hormaechei (n = 1), with a heterogeneous ST distribution differing from the animal strains, except for two ST114. Core-gene SNP analysis confirmed the clonality of the animal ST114 and ST418 isolates (0 to 10 SNPs), and close relatedness of animal and human ST114 strains (80-120 SNPs). The strains harboured the blaOXA-48 gene on ca. 63 kb IncL-type plasmids (n = 27); on ca. 72 kb IncL plasmids co-harbouring blaCTX-M-14 (n = 2); and on ca. 150-180 kb IncFIB (n = 4) or hybrid IncFIB/IncL (n = 1) plasmids. The blaOXA-48-harbouring plasmids and the blaDHA-1-carrying ISCR1 element in one animal ST114 and both ST418 clones were likely acquired from previously spreading K. pneumoniae strains. CONCLUSIONS Common ecological niches favour the spread of plasmid-borne carbapenemases among Enterobacterales and the emergence of MDR E. hormaechei clones.
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Affiliation(s)
- Valentina Donà
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Längassstrasse 122, CH-3012 Bern, Switzerland
| | - Patrice Nordmann
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
- Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Sonja Kittl
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Längassstrasse 122, CH-3012 Bern, Switzerland
| | - Simone Schuller
- Department of Clinical Veterinary Medicine, University of Bern, Bern, Switzerland
| | - Maxime Bouvier
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
- Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Laurent Poirel
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
- Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Längassstrasse 122, CH-3012 Bern, Switzerland
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Campos-Madueno EI, Aldeia C, Perreten V, Sendi P, Moser AI, Endimiani A. Detection of blaCTX-M and blaDHA genes in stool samples of healthy people: comparison of culture- and shotgun metagenomic-based approaches. Front Microbiol 2023; 14:1236208. [PMID: 37720151 PMCID: PMC10501143 DOI: 10.3389/fmicb.2023.1236208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023] Open
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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Affiliation(s)
- Edgar I. Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Aline I. Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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Campos-Madueno EI, Aldeia C, Sendi P, Endimiani A. Escherichia ruysiae May Serve as a Reservoir of Antibiotic Resistance Genes across Multiple Settings and Regions. Microbiol Spectr 2023; 11:e0175323. [PMID: 37318364 PMCID: PMC10434276 DOI: 10.1128/spectrum.01753-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
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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Affiliation(s)
- Edgar I. Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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Sendi P, Widmer N, Branca M, Thierstein M, Büchi AE, Güntensperger D, Blum MR, Baldan R, Tinguely C, Heg D, Theel ES, Berbari E, Tande AJ, Endimiani A, Gowland P, Niederhauser C. Do quantitative levels of antispike-IgG antibodies aid in predicting protection from SARS-CoV-2 infection? Results from a longitudinal study in a police cohort. J Med Virol 2023; 95:e28904. [PMID: 37386901 DOI: 10.1002/jmv.28904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/04/2023] [Accepted: 06/11/2023] [Indexed: 07/01/2023]
Abstract
In a COVID-19 sero-surveillance cohort study with predominantly healthy and vaccinated individuals, the objectives were (i) to investigate longitudinally the factors associated with the quantitative dynamics of antispike (anti-S1) IgG antibody levels, (ii) to evaluate whether the levels were associated with protection from SARS-CoV-2 infection, and (iii) to assess whether the association was different in the pre-Omicron compared with the Omicron period. The QuantiVac Euroimmun ELISA test was used to quantify anti-S1 IgG levels. The entire study period (16 months), the 11-month pre-Omicron period and the cross-sectional analysis before the Omicron surge included 3219, 2310, and 895 reactive serum samples from 949, 919, and 895 individuals, respectively. Mixed-effect linear, mixed-effect time-to-event, and logistic regression models were used to achieve the objectives. Age and time since infection or vaccination were the only factors associated with a decline of anti-S1 IgG levels. Higher antibody levels were significantly associated with protection from SARS-CoV-2 infection (0.89, 95% confidence interval [CI] 0.82-0.97), and the association was higher during the time period when Omicron was predominantly circulating compared with the ones when Alpha and Delta variants were predominant (adjusted hazard ratio for interaction 0.66, 95% CI 0.53-0.84). In a prediction model, it was estimated that >8000 BAU/mL anti-S1 IgG was required to reduce the risk of infection with Omicron variants by approximately 20%-30% for 90 days. Though, such high levels were only found in 1.9% of the samples before the Omicron surge, and they were not durable for 3 months. Anti-S1 IgG antibody levels are statistically associated with protection from SARS-CoV-2 infection. However, the prediction impact of the antibody level findings on infection protection is limited.
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Affiliation(s)
- Parham Sendi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Nadja Widmer
- Interregional Blood Transfusion Swiss Red Cross, Bern, Switzerland
| | | | - Marc Thierstein
- Division Operations, Cantonal Police Bern, Bern, Switzerland
| | - Annina Elisabeth Büchi
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Manuel Raphael Blum
- Department of General Internal Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland
| | - Rossella Baldan
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Dik Heg
- CTU Bern, University of Bern, Bern, Switzerland
| | - Elitza S Theel
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Elie Berbari
- Division of Public Health, Infectious Diseases, and Occupational Medicine Mayo Clinic, Rochester, Minnesota, USA
| | - Aaron J Tande
- Division of Public Health, Infectious Diseases, and Occupational Medicine Mayo Clinic, Rochester, Minnesota, USA
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Peter Gowland
- Interregional Blood Transfusion Swiss Red Cross, Bern, Switzerland
| | - Christoph Niederhauser
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Interregional Blood Transfusion Swiss Red Cross, Bern, Switzerland
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Raemy S, Casanova C, Baldan R, Barreto E, Tande AJ, Endimiani A, Leib SL, Fischer U, Sendi P. Penicillin-Susceptible Streptococcus pneumoniae Meningitis in Adults: Does the Ceftriaxone Dosing Matter? Antibiotics (Basel) 2023; 12:antibiotics12050878. [PMID: 37237781 DOI: 10.3390/antibiotics12050878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The recommended empiric ceftriaxone dosing regimen for acute bacterial meningitis in adults is 2 g every 12 h. After penicillin-susceptible Streptococcus pneumoniae is isolated as a causative microorganism, the ceftriaxone dose may be continued or reduced to a single dose of 2 g every 24 h, per institutional preference. There is no clear guidance that indicates the superiority of one regimen over the other. The objective of this study was to evaluate the susceptibility of S. pneumoniae in the cerebral spinal fluid (CSF) of patients with meningitis and the relationship between ceftriaxone dose and clinical outcomes. We identified 52 patients with S. pneumoniae meningitis with positive CSF cultures who were treated at the University Hospital, Bern, Switzerland, over a 19-year period. We collected clinical and microbiological data for evaluation. Broth microdilution and Etest methods were performed to test penicillin and ceftriaxone susceptibility. All isolates were susceptible to ceftriaxone. Ceftriaxone was empirically used in 50 patients, with a starting dosing regimen of 2 g every 24 h in 15 patients and 2 g every 12 h in 35 patients. In 32 patients started on a twice-daily regimen (91%), doses were reduced to once daily after a median of 1.5 (95% CI 1-2) days. The overall in-hospital mortality was 15.4% (n = 8), and 45.7% of patients reported at least one sequela of meningitis at the last follow-up (median 375, 95% CI 189-1585 days). We found no statistical difference in outcome between the 2 g every 24 h and the 2 g every 12 h ceftriaxone dosing regimens. A ceftriaxone total daily dose of 2 g may be associated with similar outcomes to a 4 g total daily dose, provided that the causative organism is highly susceptible to ceftriaxone. The persistence of neurological and infection sequelae at the last follow-up underscores the need for optimal treatment of these complex infections.
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Affiliation(s)
- Samuel Raemy
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Rossella Baldan
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Erin Barreto
- Department of Pharmacy, Mayo Clinic, Rochester, MN 55902, USA
| | - Aaron J Tande
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55902, USA
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Stephen L Leib
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Urs Fischer
- Department of Neurology, University Hospital Bern, University of Bern, 3010 Bern, Switzerland
- Department of Neurology, University Hospital Basel, University of Basel, 4001 Basel, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
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Aldeia C, Campos-Madueno EI, Sendi P, Endimiani A. Complete Genome Sequence of the First Colistin-Resistant Raoultella electrica Strain. Microbiol Resour Announc 2023; 12:e0004723. [PMID: 37014211 DOI: 10.1128/mra.00047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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.
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Affiliation(s)
- Claudia Aldeia
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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Fernandez JE, Seth-Smith HMB, Nordmann P, Egli A, Endimiani A, Perreten V. Intra- and Interspecies Spread of a Novel Conjugative Multidrug Resistance IncC Plasmid Coharboring blaOXA-181 and armA in a Cystic Fibrosis Patient. Microbiol Spectr 2022; 10:e0312122. [PMID: 36154665 PMCID: PMC9603557 DOI: 10.1128/spectrum.03121-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/09/2022] [Indexed: 01/04/2023] Open
Abstract
A novel multidrug resistance conjugative 177,859-bp IncC plasmid pJEF1-OXA-181 coharboring the carbapenemase-coding blaOXA181 and the aminoglycoside resistance 16S rRNA methyltransferase-coding armA genes was detected in two unrelated Escherichia coli gut isolates of ST196 and ST648, as well as two ST35 Klebsiella pneumoniae gut and sputum isolates of a cystic fibrosis patient. The armA gene was located within the antimicrobial resistance island ARI-A and the blaOXA181 gene, which was preceded by IS903 and ISEcp1Δ was inserted within the transfer genes region without affecting conjugation ability. Comparative plasmid analysis with other related IncC plasmids showed the presence of blaOXA181, as well as its integration site, are thus far unique for these types of plasmids. This study illustrates the potential of a promiscuous multidrug resistance plasmid to acquire antibiotic resistance genes and to disseminate in the gut of the same host. IMPORTANCE Colocalization of carbapenemases and aminoglycoside resistance 16S rRNA methylases on a multidrug resistance conjugative plasmid poses a serious threat to public health. Here, we describe the novel IncC plasmid pJEF1-OXA-181 cocarrying blaOXA-181 and armA as well as several other antimicrobial resistance genes (ARGs) in different Enterobacterales isolates of the sputum and gut microbiota of a cystic fibrosis patient. IncC plasmids are conjugative, promiscuous elements which can incorporate accessory antimicrobial resistance islands making them key players in ARGs spread. This plasmid was thus far unique among IncC plasmids to contain a blaOXA-181 which was integrated in the transfer gene region without affecting its conjugation ability. This study highlights that new plasmids may be introduced into a hospital through different species hosted in one single patient. It further emphasizes the need of continuous surveillance of multidrug-resistant bacteria in patients at risk to avoid spread of such plasmids in the health care system.
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Affiliation(s)
- Javier E. Fernandez
- Division of Molecular bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Helena M. B. Seth-Smith
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Patrice Nordmann
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Division of Molecular bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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10
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Sendi P, Thierstein M, Widmer N, Babongo Bosombo F, Büchi AE, Güntensperger D, Blum MR, Baldan R, Tinguely C, Gahl B, Heg D, Theel ES, Berbari E, Endimiani A, Gowland P, Niederhauser C. Serosurveillance after a COVID-19 vaccine campaign in a Swiss police cohort. Immun Inflamm Dis 2022; 10:e640. [PMID: 35759237 PMCID: PMC9168549 DOI: 10.1002/iid3.640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION To assess the risk for COVID-19 of police officers, we are studying the seroprevalence in a cohort. The baseline cross-sectional investigation was performed before a vaccination campaign in January/February 2021, and demonstrated a seroprevalence of 12.9%. Here, we demonstrate serosurveillance results after a vaccination campaign. METHODS The cohort consists of 1022 study participants. The 3- and 6-month follow-up visits were performed in April/May and September 2021. Data on infection and vaccination rates were obtained via measuring antibodies to the nucleocapsid protein and spike protein and online questionnaires. RESULTS The mean age of the population was 41 (SD 8.8) years, 72% were male and 76% had no comorbidity. Seroconversion was identified in 1.05% of the study population at the 3-month visit and in 0.73% at the 6-month visit, resulting in an infection rate of 1.8% over a time period of 6 months. In comparison, the infection rate in the general population over the same time period was higher (3.18%, p = .018). At the 6-month visit, 77.8% of participants reported being vaccinated once and 70.5% twice; 81% had an anti-S antibody titer of >250 U/ml and 87.1% of ≥2 U/ml. No significant association between infection and job role within the department, working region, or years of experience in the job was found. Anti-spike antibody titers of vaccinated study participants showed a calculated decreasing trend 150-200 days after the second vaccine dose. CONCLUSION These data confirm the value of the vaccination campaign in an exposed group other than healthcare professionals.
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Affiliation(s)
- Parham Sendi
- Institute for Infectious Diseases, University of BernBernSwitzerland
| | | | - Nadja Widmer
- Interregional Blood Transfusion Swiss Red CrossBernSwitzerland
| | | | - Annina Elisabeth Büchi
- Department of Emergency MedicineInselspital, Bern University Hospital, University of BernBernSwitzerland
| | | | - Manuel Raphael Blum
- Department of General Internal MedicineInselspital, Bern University Hospital, University of BernBernSwitzerland
- Institute of Primary Health Care (BIHAM), University of BernBernSwitzerland
| | - Rossella Baldan
- Institute for Infectious Diseases, University of BernBernSwitzerland
| | | | | | - Dik Heg
- CTU Bern, University of BernBernSwitzerland
| | - Elitza S. Theel
- Division of Clinical MicrobiologyMayo ClinicRochesterMinnesotaUSA
| | - Elie Berbari
- Division of Infectious DiseasesMayo ClinicRochesterMinnesotaUSA
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of BernBernSwitzerland
| | - Peter Gowland
- Interregional Blood Transfusion Swiss Red CrossBernSwitzerland
| | - Christoph Niederhauser
- Institute for Infectious Diseases, University of BernBernSwitzerland
- Interregional Blood Transfusion Swiss Red CrossBernSwitzerland
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11
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Campos-Madueno EI, Mauri C, Meroni E, Paseiro PP, Consonni A, Luzzaro F, Endimiani A. Simultaneous gut colonization by Klebsiella grimontii and Escherichia coli co-possessing the bla KPC-3-carrying pQil plasmid. Eur J Clin Microbiol Infect Dis 2022; 41:1087-1091. [PMID: 35643963 PMCID: PMC9250482 DOI: 10.1007/s10096-022-04462-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022]
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.
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Affiliation(s)
- Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Carola Mauri
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Elisa Meroni
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Pablo Porragas Paseiro
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | | | - Francesco Luzzaro
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland.
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12
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Moser AI, Keller PM, Campos-Madueno EI, Poirel L, Nordmann P, Endimiani A. A Patient With Multiple Carbapenemase Producers Including an Unusual Citrobacter sedlakii Hosting an IncC bla NDM-1- and armA-carrying Plasmid. Pathog Immun 2022; 6:119-134. [PMID: 34988342 PMCID: PMC8714174 DOI: 10.20411/pai.v6i2.482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/11/2021] [Indexed: 12/21/2022] Open
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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Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Peter M Keller
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland.,French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland.,National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland.,French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland.,National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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13
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Campos-Madueno EI, Moser AI, Jost G, Maffioli C, Bodmer T, Perreten V, Endimiani A. Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: Human and non-human settings may share high-risk clones. J Glob Antimicrob Resist 2022; 28:206-215. [DOI: 10.1016/j.jgar.2022.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/30/2022] Open
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14
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Moser AI, Campos-Madueno EI, Sendi P, Perreten V, Keller PM, Ramette A, Endimiani A. Repatriation of a patient with COVID-19 contributed to the importation of an emerging carbapenemase producer. J Glob Antimicrob Resist 2021; 27:267-272. [PMID: 34718203 PMCID: PMC8552635 DOI: 10.1016/j.jgar.2021.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/07/2021] [Indexed: 11/28/2022] Open
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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Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Peter M Keller
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001, Bern, Switzerland.
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15
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Dazio V, Nigg A, Schmidt JS, Brilhante M, Campos-Madueno EI, Mauri N, Kuster SP, Brawand SG, Willi B, Endimiani A, Perreten V, Schuller S. Duration of carriage of multidrug-resistant bacteria in dogs and cats in veterinary care and co-carriage with their owners. One Health 2021; 13:100322. [PMID: 34522760 PMCID: PMC8424212 DOI: 10.1016/j.onehlt.2021.100322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 11/19/2022] Open
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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Key Words
- 3GC-R, Third Generation Cephalosporin-resistant
- 3GC-R-Ent., Third Generation Cephalosporin-resistant Enterobacterales
- AMR, Antimicrobial resistance
- CI, Confidence interval
- CLSI, Clinical and Laboratory Standards Institute
- COL-R, Colistin-resistant
- CP, Carbapenemase-producing
- CR, Carbapenem-resistant
- CRE, Carbapenem-resistant Enterobacterales
- Carbapenemase-producing Enterobacterales
- Co-carriage
- Companion animal
- ERIC-PCR, Enterobacterial repetitive intergenic consensus polymerase chain reaction
- ESBL, Extended spectrum β-lactamase
- ESBL-E. coli, ESBL-producing Escherichia coli
- ESBL-KP, ESBL-producing Klebsiella pneumoniae
- EUCAST, European Committee on Antimicrobial Susceptibility Testing
- Extended-spectrum β-lactamase
- IQR, Interquartile range
- KP, Klebsiella pneumoniae
- MALDI-TOF MS, Matrix-assisted laser desorption/ionization time of flight mass spectrometry
- MDR, Multidrug-resistant
- MDROs, Multidrug-resistant organisms
- MICs, Minimal inhibitory concentrations
- MLST, Multilocus sequence typing
- MR, Methicillin-resistant
- MRCoNS, Methicillin-resistant coagulase-negative staphylococci
- MRSA, Methicillin-resistant Staphylococcus aureus
- MRSP, Methicillin-resistant Staphylococcus pseudintermedius
- REP-PCR, Repetitive element palindromic polymerase chain reaction
- ST, Sequence type
- TMP-S, Trimethoprim/sulfamethoxazole
- Transmission
- WGS, Whole-genome sequencing
- pAmpC, Plasmid-encoded AmpC
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Affiliation(s)
- Valentina Dazio
- Department of Clinical Veterinary Medicine, University of Bern, Switzerland
| | - Aurélien Nigg
- Institute of Veterinary Bacteriology, University of Bern, Switzerland
| | - Janne S. Schmidt
- Clinic for Small Animal Internal Medicine, University of Zurich, Switzerland
| | - Michael Brilhante
- Institute of Veterinary Bacteriology, University of Bern, Switzerland
| | | | - Nico Mauri
- Tierklinik Aarau West AG, Oberentfelden, Switzerland
| | - Stefan P. Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University and University Hospital of Zurich, Faculty of Medicine, Zurich, Switzerland
| | | | - Barbara Willi
- Clinic for Small Animal Internal Medicine, University of Zurich, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Switzerland
| | - Simone Schuller
- Department of Clinical Veterinary Medicine, University of Bern, Switzerland
- Corresponding author at: Vetsuisse Faculty Bern, Länggassstrasse 128, CH-3012 Bern, Switzerland.
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16
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Moser AI, Kuenzli E, Campos-Madueno EI, Büdel T, Rattanavong S, Vongsouvath M, Hatz C, Endimiani A. Antimicrobial-Resistant Escherichia coli Strains and Their Plasmids in People, Poultry, and Chicken Meat in Laos. Front Microbiol 2021; 12:708182. [PMID: 34381435 PMCID: PMC8350485 DOI: 10.3389/fmicb.2021.708182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/05/2021] [Indexed: 01/05/2023] Open
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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Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Esther Kuenzli
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Thomas Büdel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | | | - Christoph Hatz
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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17
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Brilhante M, Gobeli Brawand S, Endimiani A, Rohrbach H, Kittl S, Willi B, Schuller S, Perreten V. Two high-risk clones of carbapenemase-producing Klebsiella pneumoniae that cause infections in pets and are present in the environment of a veterinary referral hospital. J Antimicrob Chemother 2021; 76:1140-1149. [PMID: 33615354 DOI: 10.1093/jac/dkab028] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/20/2021] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Infections with carbapenem-resistant Enterobacterales (CRE) are an emerging problem in pets and a major threat to public health. We determined the genetic relationships among carbapenemase-producing Klebsiella pneumoniae (CPKp) strains causing infections in hospitalized pets in a veterinary clinic and those found in the environment. METHODS WGS was performed with both the Illumina and Nanopore platforms. Searches of genetic features were performed using several databases and bioinformatics tools, and phylogeny was assessed by whole-genome MLST (wgMLST) using SeqSphere and SNP calling with Snippy. RESULTS WGS analysis of the CPKp strains identified all environmental and almost all animal strains as the high-risk clone ST11, with the exception of two strains that belonged to ST307. All CPKp belonged to novel complex types (CTs) and carried a conjugative 63 kb IncL plasmid encoding the carbapenemase gene blaOXA-48, yersiniabactin and other virulence factors. Although all CPKp ST11 strains carried additional similar IncR plasmids harbouring multiple antimicrobial resistance genes (ARGs), such as the plasmid-mediated blaDHA-1 AmpC gene, some structural variations were observed. The two ST307 strains carried identical 156 kb MDR IncFIB(K) plasmids with several ARGs, including the blaCTX-M-15 ESBL gene. Both wgMLST and cgSNP analysis confirmed that CPKp strains of the same ST were genetically highly related independent of the source of isolation. CONCLUSIONS This study demonstrated that the clinical CPKp strains were highly related to those contaminating the clinical environment. These findings confirmed nosocomial spread and highlight veterinary hospitals as a source of CPKp, which may further spread to animals, the environment and humans.
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Affiliation(s)
- Michael Brilhante
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Helene Rohrbach
- Department of Clinical Veterinary Medicine, University of Bern, Bern, Switzerland
| | - Sonja Kittl
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Barbara Willi
- Clinic for Small Animal Internal Medicine, University of Zurich, Zurich, Switzerland
| | - Simone Schuller
- Department of Clinical Veterinary Medicine, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
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18
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Moser AI, Kuenzli E, Büdel T, Campos-Madueno EI, Bernasconi OJ, DeCrom-Beer S, Jakopp B, Mohammed AH, Hassan NK, Fehr J, Zinsstag J, Hatz C, Endimiani A. Travellers returning from the island of Zanzibar colonized with MDR Escherichia coli strains: assessing the impact of local people and other sources. J Antimicrob Chemother 2021; 76:330-337. [PMID: 33257991 DOI: 10.1093/jac/dkaa457] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/05/2020] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVES Many travellers to low-income countries return home colonized at the intestinal level with extended-spectrum cephalosporin-resistant (ESC-R) and/or colistin-resistant (CST-R) Escherichia coli (Ec) strains. However, nothing is known about the local sources responsible for the transmission of these pathogens to the travellers. METHODS We compared the ESC-R- and CST-R-Ec strains found in the pre- (n = 23) and post-trip (n = 37) rectal swabs of 37 travellers from Switzerland to Zanzibar with those (i) contemporarily isolated from local people, poultry, retailed chicken meat (n = 31), and (ii) from other sources studied in the recent past (n = 47). WGS and core-genome analyses were implemented. RESULTS Twenty-four travellers returned colonized with ESC-R- (n = 29) and/or CST-R- (n = 8) Ec strains. Almost all ESC-R-Ec were CTX-M-15 producers and belonged to heterogeneous STs/core-genome STs (cgSTs), while mcr-positive strains were not found. Based on the strains' STs/cgSTs, only 20 subjects were colonized with ESC-R- and/or CST-R-Ec that were not present in their gut before the journey. Single nucleotide variant (SNV) analysis showed that three of these 20 travellers carried ESC-R-Ec (ST3489, ST3580, ST361) identical (0-20 SNVs) to those found in local people, chicken meat, or poultry. Three further subjects carried ESC-R-Ec (ST394, ST648, ST5173) identical or highly related (15-55 SNVs) to those previously reported in local people, fish, or water. CONCLUSIONS This is the first known study comparing the ESC-R- and/or CST-R-Ec strains obtained from travellers and local sources using solid molecular methods. We showed that for at least one-third of the returning travellers the acquired antibiotic-resistant Ec had a corresponding strain among resident people, food, animal and/or environmental sources.
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Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases, University of Bern, Bern
| | - Esther Kuenzli
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich.,Swiss Tropical and Public Health Institute, Basel.,University of Basel, Basel
| | - Thomas Büdel
- Institute for Infectious Diseases, University of Bern, Bern
| | | | | | - Susan DeCrom-Beer
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich
| | - Barbara Jakopp
- Department of Infectious Diseases and Hospital Hygiene, Aarau Cantonal Hospital, Aarau, Switzerland
| | | | | | - Jan Fehr
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Basel.,University of Basel, Basel
| | - Christoph Hatz
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich.,Swiss Tropical and Public Health Institute, Basel.,University of Basel, Basel
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Endimiani A, Brilhante M, Bernasconi OJ, Perreten V, Schmidt JS, Dazio V, Nigg A, Gobeli Brawand S, Kuster SP, Schuller S, Willi B. Employees of Swiss veterinary clinics colonized with epidemic clones of carbapenemase-producing Escherichia coli. J Antimicrob Chemother 2021; 75:766-768. [PMID: 31819979 DOI: 10.1093/jac/dkz470] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Michael Brilhante
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Janne S Schmidt
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Valentina Dazio
- Division of Small Animal Internal Medicine, Department of Clinical Veterinary Medicine, University of Bern, Bern, Switzerland
| | - Aurélien Nigg
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | - Stefan P Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University and University Hospital of Zurich, Zurich, Switzerland
| | - Simone Schuller
- Division of Small Animal Internal Medicine, Department of Clinical Veterinary Medicine, University of Bern, Bern, Switzerland
| | - Barbara Willi
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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20
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Büdel T, Kuenzli E, Campos-Madueno EI, Mohammed AH, Hassan NK, Zinsstag J, Hatz C, Endimiani A. On the island of Zanzibar people in the community are frequently colonized with the same MDR Enterobacterales found in poultry and retailed chicken meat. J Antimicrob Chemother 2021; 75:2432-2441. [PMID: 32562537 DOI: 10.1093/jac/dkaa198] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
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.
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Affiliation(s)
- Thomas Büdel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Esther Kuenzli
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | | | | | | | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Christoph Hatz
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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21
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Moser AI, Viaggi V, Mauri C, Carattoli A, Luzzaro F, Endimiani A. An XDR Proteus vulgaris isolate hosting a novel blaNDM-1- and armA-carrying plasmid. J Antimicrob Chemother 2021; 76:1938-1941. [PMID: 33891008 DOI: 10.1093/jac/dkab111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Valentina Viaggi
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Carola Mauri
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | | | - Francesco Luzzaro
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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22
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Campos-Madueno EI, Sigrist T, Flückiger UM, Risch L, Bodmer T, Endimiani A. First report of a bla VIM-1 metallo-β-lactamase-possessing Klebsiella michiganensis. J Glob Antimicrob Resist 2021; 25:310-314. [PMID: 33957287 DOI: 10.1016/j.jgar.2021.03.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/24/2021] [Accepted: 03/31/2021] [Indexed: 12/29/2022] Open
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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Affiliation(s)
- Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | | | | | - Lorenz Risch
- Centre of Laboratory Medicine Dr Risch, Bern-Liebefeld, Switzerland
| | - Thomas Bodmer
- Centre of Laboratory Medicine Dr Risch, Bern-Liebefeld, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland.
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23
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Campos-Madueno EI, Gmuer C, Risch M, Bodmer T, Endimiani A. Characterisation of a new bla VIM-1-carrying IncN2 plasmid from an Enterobacter hormaechei subsp. steigerwaltii. J Glob Antimicrob Resist 2021; 24:325-327. [PMID: 33571706 DOI: 10.1016/j.jgar.2021.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/19/2021] [Accepted: 01/28/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | | | - Martin Risch
- Labormedizinisches Zentrum Dr Risch, Bern-Liebefeld and Buchs SG, Switzerland
| | - Thomas Bodmer
- Labormedizinisches Zentrum Dr Risch, Bern-Liebefeld and Buchs SG, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland.
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24
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Dazio V, Nigg A, Schmidt JS, Brilhante M, Mauri N, Kuster SP, Brawand SG, Schüpbach-Regula G, Willi B, Endimiani A, Perreten V, Schuller S. Acquisition and carriage of multidrug-resistant organisms in dogs and cats presented to small animal practices and clinics in Switzerland. J Vet Intern Med 2021; 35:970-979. [PMID: 33527554 PMCID: PMC7995377 DOI: 10.1111/jvim.16038] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/28/2020] [Accepted: 01/15/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The emergence and spread of multidrug-resistant organisms (MDRO) present a threat to human and animal health. OBJECTIVES To assess acquisition, prevalence of and risk factors for MDRO carriage in dogs and cats presented to veterinary clinics or practices in Switzerland. ANIMALS Privately owned dogs (n = 183) and cats (n = 88) presented to 4 veterinary hospitals and 1 practice. METHODS Prospective, longitudinal, observational study. Oronasal and rectal swabs were collected at presentation and 69% of animals were sampled again at discharge. Methicillin-resistant (MR) staphylococci and macrococci, cephalosporinase-, and carbapenemase-producing (CP) Enterobacterales were isolated. Genetic relatedness of isolates was assessed by repetitive sequence-based polymerase chain reaction and multilocus sequence typing. Risk factors for MDRO acquisition and carriage were analyzed based on questionnaire-derived and hospitalization data. RESULTS Admission prevalence of MDRO carriage in pets was 15.5% (95% confidence interval [CI], 11.4-20.4). The discharge prevalence and acquisition rates were 32.1% (95% CI, 25.5-39.3) and 28.3% (95% CI, 22-35.4), respectively. Predominant hospital-acquired isolates were extended spectrum β-lactamase-producing Escherichia coli (ESBL-E coli; 17.3%) and β-lactamase-producing Klebsiella pneumoniae (13.7%). At 1 institution, a cluster of 24 highly genetically related CP (blaoxa181 and blaoxa48 ) was identified. Multivariate analysis identified hospitalization at clinic 1 (odds ratio [OR], 5.1; 95% CI, 1.6-16.8) and days of hospitalization (OR 3-5 days, 4.4; 95% CI, 1.8-10.9; OR > 5 days, 6.2; 95% CI, 1.3-28.8) as risk factors for MDRO acquisition in dogs. CONCLUSIONS Veterinary hospitals play an important role in the selection and transmission of MDRO among veterinary patients.
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Affiliation(s)
- Valentina Dazio
- Department of Clinical Veterinary Medicine, University of Bern, Bern, Switzerland
| | - Aurélien Nigg
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Janne S Schmidt
- Clinic for Small Animal Internal Medicine, University of Zurich, Zürich, Switzerland
| | - Michael Brilhante
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Nico Mauri
- Tierklinik Aarau West AG, Oberentfelden, Switzerland
| | - Stephan P Kuster
- Better Together Healthcare Consulting, Steinackerstrasse 44, Wiesendangen, Zurich, Switzerland
| | | | | | - Barbara Willi
- Clinic for Small Animal Internal Medicine, University of Zurich, Zürich, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Faculty of Medicine, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Simone Schuller
- Department of Clinical Veterinary Medicine, University of Bern, Bern, Switzerland
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25
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Bleichenbacher S, Stevens MJA, Zurfluh K, Perreten V, Endimiani A, Stephan R, Nüesch-Inderbinen M. Environmental dissemination of carbapenemase-producing Enterobacteriaceae in rivers in Switzerland. Environ Pollut 2020; 265:115081. [PMID: 32806462 DOI: 10.1016/j.envpol.2020.115081] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/12/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
The aquatic environment takes on a key role in the dissemination of antimicrobial-resistant Enterobacteriaceae. This study assesses the occurrence of carbapenemase-producing Enterobacteriaceae (CPE) in freshwater samples from rivers, inland canals, and streams throughout Switzerland, and characterizes the isolated strains using phenotypic and NGS-based genotypic methods. CPE producing KPC-2 (n = 2), KPC-3 (n = 1), NDM-5 (n = 3), OXA-48 (n = 3), OXA-181 (n = 6), and VIM-1 (n = 2) were detected in 17/164 of the water samples. Seven Escherichia coli had sequence types (STs) that belonged to extra-intestinal pathogenic clonal lineages ST38, ST73, ST167, ST410, and ST648. The majority (16/17) of the carbapenemase genes were located on plasmids, including the widespread IncC (n = 1), IncFIIA (n = 1), and IncFIIB plasmids (n = 4), the epidemic IncL (n = 1) and IncX3 (n = 5) plasmids, a rare Col156 plasmid (n = 1), and the mosaic IncFIB, IncR, and IncQ plasmids (n = 3). Plasmids were composed of elements that were identical to those of resistance plasmids retrieved from clinical and veterinary isolates locally and worldwide. Our data show environmental dissemination of high-risk CPE clones in Switzerland. Epidemic and mosaic-like plasmids carrying clinically relevant carbapenemase genes are replicating and evolving pollutants of river ecosystems, representing a threat to public health and environmental integrity.
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Affiliation(s)
- Stephanie Bleichenbacher
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, 8057, Zurich, Switzerland
| | - Marc J A Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, 8057, Zurich, Switzerland
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, 8057, Zurich, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001, Bern, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, 8057, Zurich, Switzerland
| | - Magdalena Nüesch-Inderbinen
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, 8057, Zurich, Switzerland.
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26
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Nigg A, Brilhante M, Dazio V, Clément M, Collaud A, Gobeli Brawand S, Willi B, Endimiani A, Schuller S, Perreten V. Shedding of OXA-181 carbapenemase-producing Escherichia coli from companion animals after hospitalisation in Switzerland: an outbreak in 2018. ACTA ACUST UNITED AC 2020; 24. [PMID: 31576806 PMCID: PMC6774230 DOI: 10.2807/1560-7917.es.2019.24.39.1900071] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background Carbapenem-resistant Enterobacteriaceae pose a serious threat to public health worldwide, and the role of companion animals as a reservoir is still unclear. Aims This 4-month prospective observational study evaluated carriage of carbapenem-resistant Enterobacteriaceae at admission and after hospitalisation in a large referral hospital for companion animals in Switzerland. Methods Rectal swabs of dogs and cats expected to be hospitalised for at least 48 h were taken from May to August 2018 and analysed for the presence of carbapenem-resistant Enterobacteriaceae using selective agar plates. Resistant isolates were further characterised analysing whole genome sequences for resistance gene and plasmid identification, and ad hoc core genome multilocus sequence typing. Results This study revealed nosocomial acquisition of Escherichia coli harbouring the carbapenemase gene blaOXA-181, the pAmpC cephalosporinase gene blaCMY-42 as well as quinolone resistance associated with qnrS1 and mutations in the topoisomerases II (GyrA) and IV (ParC). The blaOXA-181 and qnrS1 genes were identified on a 51 kb IncX3 plasmid and blaCMY-42 on a 47 kb IncI1 plasmid. All isolates belonged to sequence type ST410 and were genetically highly related. This E. coli clone was detected in 17 of 100 dogs and four of 34 cats after hospitalisation (21.6%), only one of the tested animals having tested positive at admission (0.75%). Two positive animals were still carriers 4 months after hospital discharge, but were negative after 6 months. Conclusions Companion animals may acquire carbapenemase-producing E. coli during hospitalisation, posing the risk of further dissemination to the animal and human population and to the environment.
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Affiliation(s)
- Aurélien Nigg
- Institute of Veterinary Bacteriology, Bern, University of Bern
| | - Michael Brilhante
- Graduate School of Cellular and Biomedical Sciences, Bern, University of Bern.,Institute of Veterinary Bacteriology, Bern, University of Bern
| | - Valentina Dazio
- Department of Clinical Veterinary Medicine, Bern, University of Bern
| | - Mathieu Clément
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, Bern, University of Bern
| | | | | | - Barbara Willi
- Clinic for Small Animal Internal Medicine, University of Zurich, Zurich, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Simone Schuller
- Department of Clinical Veterinary Medicine, Bern, University of Bern
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27
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Schmidt JS, Kuster SP, Nigg A, Dazio V, Brilhante M, Rohrbach H, Bernasconi OJ, Büdel T, Campos-Madueno EI, Gobeli Brawand S, Schuller S, Endimiani A, Perreten V, Willi B. 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. Antimicrob Resist Infect Control 2020; 9:93. [PMID: 32576281 PMCID: PMC7310346 DOI: 10.1186/s13756-020-00742-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/29/2020] [Indexed: 12/16/2022] Open
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.
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Affiliation(s)
- Janne S Schmidt
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Stefan P Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University and University Hospital of Zurich, Zurich, Switzerland
| | - Aurélien Nigg
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Valentina Dazio
- Division of Small Animal Internal Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Michael Brilhante
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Helene Rohrbach
- Small Animal Clinic, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Odette J Bernasconi
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Thomas Büdel
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Stefanie Gobeli Brawand
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Simone Schuller
- Division of Small Animal Internal Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Barbara Willi
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
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28
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Clément M, Keller PM, Bernasconi OJ, Stirnimann G, Frey PM, Bloemberg GV, Sendi P, Endimiani A. First Clinical Case of In Vivo Acquisition of DHA-1 Plasmid-Mediated AmpC in a Salmonella enterica subsp. enterica Isolate. Antimicrob Agents Chemother 2019; 63:e00992-19. [PMID: 31358582 PMCID: PMC6761535 DOI: 10.1128/aac.00992-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/24/2019] [Indexed: 12/30/2022] Open
Abstract
A pan-susceptible Salmonella enterica serovar Worthington isolate was detected in the stool of a man returning from Sri Lanka. Under ceftriaxone treatment, a third-generation cephalosporin (3GC)-resistant Salmonella Worthington was isolated after 8 days. Molecular analyses indicated that the two isolates were identical. However, the latter strain acquired a blaDHA-1-carrying IncFII plasmid probably from a Citrobacter amalonaticus isolate colonizing the gut. This is the first report of in vivo acquisition of plasmid-mediated resistance to 3GCs in S. enterica.
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Affiliation(s)
- Mathieu Clément
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Peter M Keller
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Guido Stirnimann
- Department of Visceral Surgery and Medicine, Inselspital, University Hospital, University of Bern, Bern, Switzerland
| | - Pascal M Frey
- Department of General Internal Medicine, Inselspital, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Guido V Bloemberg
- Swiss National Centre for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, National Centre for Enteropathogenic Bacteria and Listeria (NENT), Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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29
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Egli A, Koch D, Danuser J, Hendriksen RS, Driesen S, Schmid DC, Neher R, Mäusezahl M, Seth-Smith HMB, Bloemberg G, Tschudin-Sutter S, Endimiani A, Perreten V, Greub G, Schrenzel J, Stephan R. Symposium report: One Health meets sequencing. Microbes Infect 2019; 22:1-7. [PMID: 31401354 DOI: 10.1016/j.micinf.2019.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 07/20/2019] [Accepted: 07/21/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, University of Basel, Basel, Switzerland.
| | - Daniel Koch
- Federal Office of Public Health, Liebefeld, Switzerland
| | - Jürg Danuser
- Federal Food Safety and Veterinary Office, Bern, Switzerland
| | | | | | | | - Richard Neher
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland; Biozentrum, University of Basel, Basel, Switzerland
| | | | - Helena M B Seth-Smith
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - Guido Bloemberg
- National Center for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Sarah Tschudin-Sutter
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Lausanne, Lausanne, Switzerland
| | - Jacques Schrenzel
- Bacteriology and Genomics Research Laboratories, University Hospital Geneva, Geneva, Switzerland
| | - Roger Stephan
- Institute for Food Safety and -hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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30
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Büdel T, Kuenzli E, Clément M, Bernasconi OJ, Fehr J, Mohammed AH, Hassan NK, Zinsstag J, Hatz C, Endimiani A. Polyclonal gut colonization with extended-spectrum cephalosporin- and/or colistin-resistant Enterobacteriaceae: a normal status for hotel employees on the island of Zanzibar, Tanzania. J Antimicrob Chemother 2019; 74:2880-2890. [DOI: 10.1093/jac/dkz296] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 01/27/2023] Open
Abstract
Abstract
Objectives
For low-income countries, data regarding the intestinal colonization with extended-spectrum cephalosporin-resistant (ESC-R) and colistin-resistant (CST-R) Enterobacteriaceae in the community are still scarce. Here, we investigated this phenomenon by analysing hotel employees in Zanzibar.
Methods
During June to July 2018, rectal swabs from 59 volunteers were screened implementing selective enrichments and agar plates. Species identification was achieved using MALDI-TOF MS. Strains were characterized using microdilution panels (MICs), microarray, PCRs for mcr-1/-8, repetitive extragenic palindromic-PCR (rep-PCR) and WGS.
Results
Colonization prevalence with ESC-R-, CST-R- and mcr-1-positive Enterobacteriaceae were 91.5%, 66.1% and 18.6%, respectively (average: 2.2 strains per volunteer). Overall, 55 ESC-R Escherichia coli (3 also CST-R), 33 ESC-R Klebsiella pneumoniae (1 also CST-R), 17 CST-R E. coli and 21 CST-R K. pneumoniae were collected. The following main resistance genes were found: ESC-R E. coli (blaCTX-M-15-like, 51.0%), ESC-R K. pneumoniae (blaCTX-M-9-like, 42.9%), CST-R E. coli (mcr-1, 55%) and CST-R K. pneumoniae (D150G substitution in PhoQ). ESBL-producing E. coli mainly belonged to ST361, ST636 and ST131, whereas all those that were mcr-1 positive belonged to ST46 that carried mcr-1 in a 33 kb IncX4 plasmid. ESBL-producing K. pneumoniae mainly belonged to ST17, ST1741 and ST101, whereas CST-R strains belonged to ST11.
Conclusions
We recorded remarkably high colonization prevalence with ESC-R and/or CST-R Enterobacteriaceae in hotel staff. Further research in the local environment, livestock and food chain is warranted to understand this phenomenon. Moreover, as Zanzibar is a frequent holiday destination, attention should be paid to the risk of international travellers becoming colonized and thereby importing life-threatening pathogens into their low-prevalence countries.
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Affiliation(s)
- Thomas Büdel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Esther Kuenzli
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Mathieu Clément
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Jan Fehr
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | | | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Christoph Hatz
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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Bernasconi OJ, Principe L, Viaggi V, Luzzaro F, Endimiani A. Novel vanA-carrying plasmid in a clinical isolate of Enterococcus avium. Int J Antimicrob Agents 2019; 53:876-877. [PMID: 30981925 DOI: 10.1016/j.ijantimicag.2019.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/01/2019] [Accepted: 04/06/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Odette J Bernasconi
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | - Luigi Principe
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Valentina Viaggi
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Francesco Luzzaro
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland.
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32
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Luzzaro F, Clément M, Principe L, Viaggi V, Bernasconi OJ, Endimiani A. Characterisation of the first extended-spectrum β-lactamase (ESBL)-producing Shigella sonnei clinical isolate in Italy. J Glob Antimicrob Resist 2019; 17:58-59. [PMID: 30877056 DOI: 10.1016/j.jgar.2019.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/01/2019] [Indexed: 11/29/2022] Open
Affiliation(s)
- Francesco Luzzaro
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Mathieu Clément
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Luigi Principe
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Valentina Viaggi
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Odette J Bernasconi
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland.
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33
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Allemann A, Kraemer JG, Korten I, Ramsey K, Casaulta C, Wüthrich D, Ramette A, Endimiani A, Latzin P, Hilty M. Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life. Front Microbiol 2019; 10:212. [PMID: 30863369 PMCID: PMC6399209 DOI: 10.3389/fmicb.2019.00212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022] Open
Abstract
Polymicrobial infections of the respiratory tract due to antibiotic resistant bacteria are a great concern in patients with cystic fibrosis (CF). We therefore aimed at establishing a functional metagenomic method to analyze the nasal resistome in infants with CF within the first year of life. We included samples from patients before antibiotic treatment, which allowed obtaining information regarding natural status of the resistome. In total, we analyzed 130 nasal swabs from 26 infants with CF and screened for β-lactams (ampicillin, amoxicillin-clavulanic acid, and cefuroxime) and other classes of antibiotic resistances (tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole). For 69 swabs (53% of total), we found at least one non-susceptible phenotype. Analyses of the inserts recovered from non-susceptible clones by nanopore MinION sequencing revealed a large reservoir of resistance genes including mobile elements within the antibiotic naïve samples. Comparing the data of the resistome with the microbiota composition showed that the bacterial phyla and operational taxonomic units (OTUs) of the microbiota rather than the antibiotic treatment were associated with the majority of non-susceptible phenotypes in the resistome. Future studies will reveal if characterization of the resistome can help in clinical decision-making in patients with CF.
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Affiliation(s)
- Aurélie Allemann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Julia G Kraemer
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Institute for Work and Health (IST), University of Lausanne and University of Geneva, Epalinges, Switzerland
| | - Insa Korten
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Kathryn Ramsey
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Carmen Casaulta
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | | | - Daniel Wüthrich
- Applied Microbiology Research Unit, Department of Biomedicine, University of Basel, Basel, Switzerland.,Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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34
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Brilhante M, Donà V, Overesch G, Endimiani A, Perreten V. Characterisation of a porcine Escherichia coli strain from Switzerland carrying mcr-1 on a conjugative multidrug resistance IncHI2 plasmid. J Glob Antimicrob Resist 2018; 16:123-124. [PMID: 30583011 DOI: 10.1016/j.jgar.2018.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/13/2018] [Accepted: 12/15/2018] [Indexed: 11/15/2022] Open
Affiliation(s)
- Michael Brilhante
- Institute of Veterinary Bacteriology, University of Bern, Längassstrasse 122, CH-3012 Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Valentina Donà
- Institute of Veterinary Bacteriology, University of Bern, Längassstrasse 122, CH-3012 Bern, Switzerland; Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | - Gudrun Overesch
- Institute of Veterinary Bacteriology, University of Bern, Längassstrasse 122, CH-3012 Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Längassstrasse 122, CH-3012 Bern, Switzerland.
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35
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Golparian D, Donà V, Sánchez-Busó L, Foerster S, Harris S, Endimiani A, Low N, Unemo M. Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer. Sci Rep 2018; 8:17596. [PMID: 30514867 PMCID: PMC6279828 DOI: 10.1038/s41598-018-35750-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/10/2018] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is common, compromising gonorrhoea treatment internationally. Rapid characterisation of AMR strains could ensure appropriate and personalised treatment, and support identification and investigation of gonorrhoea outbreaks in nearly real-time. Whole-genome sequencing is ideal for investigation of emergence and dissemination of AMR determinants, predicting AMR, in the gonococcal population and spread of AMR strains in the human population. The novel, rapid and revolutionary long-read sequencer MinION is a small hand-held device that generates bacterial genomes within one day. However, accuracy of MinION reads has been suboptimal for many objectives and the MinION has not been evaluated for gonococci. In this first MinION study for gonococci, we show that MinION-derived sequences analysed with existing open-access, web-based sequence analysis tools are not sufficiently accurate to identify key gonococcal AMR determinants. Nevertheless, using an in house-developed CLC Genomics Workbench including de novo assembly and optimised BLAST algorithms, we show that 2D ONT-derived sequences can be used for accurate prediction of decreased susceptibility or resistance to recommended antimicrobials in gonococcal isolates. We also show that the 2D ONT-derived sequences are useful for rapid phylogenomic-based molecular epidemiological investigations, and, in hybrid assemblies with Illumina sequences, for producing contiguous assemblies and finished reference genomes.
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Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Valentina Donà
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Leonor Sánchez-Busó
- Pathogen Genomics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Sunniva Foerster
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Simon Harris
- Pathogen Genomics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
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36
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Büdel T, Clément M, Bernasconi OJ, Principe L, Perreten V, Luzzaro F, Endimiani A. Evaluation of EDTA- and DPA-Based Microdilution Phenotypic Tests for the Detection of MCR-Mediated Colistin Resistance in Enterobacteriaceae. Microb Drug Resist 2018; 25:494-500. [PMID: 30431401 DOI: 10.1089/mdr.2018.0275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The emergence of the colistin-resistant (COL-R) Enterobacteriaceae represents a worrying health issue. However, only a portion of these strains may carry the plasmid-mediated mcr colistin resistance genes. We evaluated the ability of both ethylenediaminetetraacetic acid (EDTA)-based and dipicolinic acid (DPA)-based broth microdilution (BMD) tests to detect mcr-1 to mcr-5 producers. Of 92 Enterobacteriaceae (85 COL-R), 44 mcr-positive strains (39 Escherichia coli, 3 Klebsiella pneumoniae, and 2 Salmonella spp.) were tested. EDTA (100 μg/mL) was tested in Mueller-Hinton broth (MHB), whereas the DPA (900 μg/mL) was used in cation-adjusted MHB. Results were categorized as positive if in presence of chelator strains exhibited ≥3 two fold MIC decrease compared to the COL MIC alone. The EDTA-based BMD assay detected 41 mcr-positive strains, but 22 false-positive strains (including 12 E. coli and 4 K. pneumoniae) were recorded (sensitivity [SN], 93.2%; specificity [SP], 54.2%). The DPA-based BMD assay detected 37 mcr-positive strains, with 7 false-negative (2 E. coli, 3 K. pneumoniae, 2 Salmonella spp.) strains (SN, 84.1%; SP, 100%). Overall, the EDTA-based BMD assay is not accurate to detect mcr producers, whereas the DPA-based BMD test ("colistin-MAC test") demonstrated good accuracy, but only when implemented for E. coli strains (SN, 94.9%; SP, 100%). With the aim to prevent the dissemination of mcr-possessing E. coli strains, the COL-MAC test could be implemented by clinical laboratories that are unable to perform molecular tests. Moreover, this assay could be applied to screen large collections of isolates to reveal the expression of new mcr-like genes not yet targeted by the current molecular assays.
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Affiliation(s)
- Thomas Büdel
- 1 Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Mathieu Clément
- 1 Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,2 Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Odette J Bernasconi
- 1 Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,2 Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Luigi Principe
- 3 Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Vincent Perreten
- 4 Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Francesco Luzzaro
- 3 Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Andrea Endimiani
- 1 Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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37
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Pires J, Kraemer JG, Kuenzli E, Kasraian S, Tinguely R, Hatz C, Endimiani A, Hilty M. Gut microbiota dynamics in travelers returning from India colonized with extended-spectrum cephalosporin-resistant Enterobacteriaceae: A longitudinal study. Travel Med Infect Dis 2018; 27:72-80. [PMID: 30339827 DOI: 10.1016/j.tmaid.2018.10.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/10/2018] [Accepted: 10/14/2018] [Indexed: 12/29/2022]
Abstract
BACKGROUND Intestinal colonization by extended-spectrum cephalosporin-resistant Enterobacteriaceae (ESC-R-Ent) has been attributed to travel to high prevalence countries. However, the dynamics of the microbiota changes during ESC-R-Ent colonization and whether there is a particular bacterial composition which is associated with subsequent colonization is unknown. METHODS Forty healthy volunteers living in Switzerland underwent screening before and after a trip to India, and also 3, 6 and 12 months after traveling. Culture-based ESC-R-Ent screening and microbiota analysis based on 16S rRNA amplicon sequencing were performed at all time points. RESULTS Prevalence of ESC-R-Ent colonization before traveling was 10% (n = 4), whereas it increased to 76% (n = 31) after the trip. Based on bacterial diversity analyses of the gut microbiota, there were few but significant differences for colonized versus non-colonized individuals. However, an alternative, cluster based analysis revealed that individuals remained in the same cluster over time indicating that neither traveling nor ESC-R-Ent colonization significantly influences bacterial composition. Moreover, none of the found microbiota clusters were significantly associated with subsequent risk of ESC-R-Ent colonization. CONCLUSION Based on their microbiota patterns, every volunteer was at the same risk of ESC-R-Ent colonization while traveling to India. Therefore, other risk factors for ESC-R-Ent colonization are responsible for this phenomenon.
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Affiliation(s)
- João Pires
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Julia G Kraemer
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Institute for Work and Health (IST), University of Lausanne and University of Geneva, Epalinges, Switzerland
| | - Esther Kuenzli
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Sara Kasraian
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Regula Tinguely
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Christoph Hatz
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
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38
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Kummer M, Šestáková N, Theurillat R, Huynh-Do U, Endimiani A, Sendi P, Thormann W. Monitoring of cefepime in urine by micellar electrokinetic capillary chromatography with ultraviolet detection and liquid chromatography coupled to mass spectrometry. J Sep Sci 2018; 41:4067-4074. [PMID: 30198147 DOI: 10.1002/jssc.201800763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/01/2018] [Accepted: 09/03/2018] [Indexed: 11/06/2022]
Abstract
Cefepime monitoring in urine by micellar electrokinetic capillary chromatography with UV detection and liquid chromatography coupled to mass spectrometry via electrospray ionization is described. For micellar electrokinetic capillary chromatography, sample preparation comprised urine dilution and dodecyl-sulfate protein precipitation at pH 4.5, whereas diluted urines were analyzed in the other assay. Both approaches provided suitable conditions for cefepime analysis in urines of healthy volunteers that were spiked with cefepime. Cefepime monitoring by micellar electrokinetic capillary chromatography in samples from patients taking multiple drugs were prone to interferences, whereas liquid chromatography coupled to mass spectrometry provided clean chromatograms and thus selective detection of cefepime in all samples. The latter assay was used to measure urinary cefepime in a prospective pilot study and to assess cefepime stability in urines at 25, 4, -20 and -70°C. The data suggest that urinary cefepime is stable for at least 72 h at all tested temperatures.
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Affiliation(s)
- Mirjam Kummer
- Clinical Pharmacology Laboratory, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Nela Šestáková
- Clinical Pharmacology Laboratory, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Regula Theurillat
- Clinical Pharmacology Laboratory, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Uyen Huynh-Do
- Department of Nephrology and Hypertension, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Wolfgang Thormann
- Clinical Pharmacology Laboratory, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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39
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Principe L, Viaggi V, Clément M, Meroni E, Pini B, Endimiani A, Luzzaro F. Emergence of CTX-M-1-producing Salmonella enterica serovar Napoli: A novel 'enzyme-pathogen association' in the Italian extended-spectrum β-lactamase (ESBL) endemic context. J Glob Antimicrob Resist 2018; 15:101-102. [PMID: 30172832 DOI: 10.1016/j.jgar.2018.08.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 12/01/2022] Open
Affiliation(s)
- Luigi Principe
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Via dell'Eremo 9/11, 23900 Lecco, Italy
| | - Valentina Viaggi
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Via dell'Eremo 9/11, 23900 Lecco, Italy
| | - Mathieu Clément
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Elisa Meroni
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Via dell'Eremo 9/11, 23900 Lecco, Italy
| | - Beatrice Pini
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Via dell'Eremo 9/11, 23900 Lecco, Italy
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Francesco Luzzaro
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Via dell'Eremo 9/11, 23900 Lecco, Italy.
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40
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Bernasconi OJ, Donà V, Tinguely R, Endimiani A. In Vitro Activity of 3 Commercial Bacteriophage Cocktails Against Salmonella and Shigella spp. Isolates of Human Origin. Pathog Immun 2018; 3:72-81. [PMID: 30993249 PMCID: PMC6423893 DOI: 10.20411/pai.v3i1.234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/15/2018] [Indexed: 01/23/2023] Open
Abstract
Background: Salmonella and Shigella spp. are 2 of the most frequent and deadly enteric bacterial pathogens recorded worldwide. In developing countries Salmonella infections are responsible for many deaths annually and these mortality rates are prone to increase due to the emergence of resistance to antibiotics. In this overall scenario new alternative therapeutic approaches are needed. Methods: For the first time, we investigated the activity of 3 commercial bacteriophage cocktails (INTESTI, Septaphage, PYO) against a collection of contemporary Salmonella spp. (n = 30) and Shigella spp. (n = 20) strains isolated in Switzerland. Phage susceptibility was determined by implementing the spot test. Results: The overall susceptibility of Salmonella spp. to INTESTI and Septaphage was 87% and 77%, respectively. With regard to Shigella spp., the overall susceptibility to INTESTI and Septaphage was 95% and 55%, respectively. PYO was observed to be active against only 10% of Salmonella spp. but against 95% of Shigella spp. Conclusions: Our results seem promising, especially for the INTESTI biopreparation against Salmonella enterica infections. Nevertheless, such speculation should be supported by further in vivo studies to confirm efficacy and safety of the cocktails. We also emphasize the importance of large in vitro screening analyses aimed to assess the activity of such biopreparations against contemporary multidrug-resistant strains that are emerging worldwide.
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Affiliation(s)
- Odette J Bernasconi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Valentina Donà
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Regula Tinguely
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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Collineau L, Carmo LP, Endimiani A, Magouras I, Müntener C, Schüpbach-Regula G, Stärk KDC. Risk Ranking of Antimicrobial-Resistant Hazards Found in Meat in Switzerland. Risk Anal 2018; 38:1070-1084. [PMID: 28973821 DOI: 10.1111/risa.12901] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 08/02/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
Human exposure to bacteria resistant to antimicrobials and transfer of related genes is a complex issue and occurs, among other pathways, via meat consumption. In a context of limited resources, the prioritization of risk management activities is essential. Since the antimicrobial resistance (AMR) situation differs substantially between countries, prioritization should be country specific. The objective of this study was to develop a systematic and transparent framework to rank combinations of bacteria species resistant to selected antimicrobial classes found in meat, based on the risk they represent for public health in Switzerland. A risk assessment model from slaughter to consumption was developed following the Codex Alimentarius guidelines for risk analysis of foodborne AMR. Using data from the Swiss AMR monitoring program, 208 combinations of animal species/bacteria/antimicrobial classes were identified as relevant hazards. Exposure assessment and hazard characterization scores were developed and combined using multicriteria decision analysis. The effect of changing weights of scores was explored with sensitivity analysis. Attributing equal weights to each score, poultry-associated combinations represented the highest risk. In particular, contamination with extended-spectrum β-lactamase/plasmidic AmpC-producing Escherichia coli in poultry meat ranked high for both exposure and hazard characterization. Tetracycline- or macrolide-resistant Enterococcus spp., as well as fluoroquinolone- or macrolide-resistant Campylobacter jejuni, ranked among combinations with the highest risk. This study provides a basis for prioritizing future activities to mitigate the risk associated with foodborne AMR in Switzerland. A user-friendly version of the model was provided to risk managers; it can easily be adjusted to the constantly evolving knowledge on AMR.
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Affiliation(s)
| | - Luís Pedro Carmo
- Veterinary Public Health Institute, Vetsuisse, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Ioannis Magouras
- Veterinary Public Health Institute, Vetsuisse, University of Bern, Bern, Switzerland
| | - Cedric Müntener
- Institut für Veterinärpharmakologie und -toxikologie, Vetsuisse, University of Zurich, Zurich, Switzerland
| | | | - Katharina D C Stärk
- SAFOSO AG, Bern Liebefeld, Switzerland
- Royal Veterinary College, Hawkshead Lane, North Mymms, UK
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Pires J, Kuenzli E, Hauser C, Tinguely R, Kasraian S, Atkinson A, Rauch A, Furrer H, Perreten V, Marschall J, Hatz C, Endimiani A. Intestinal colonisation with extended-spectrum cephalosporin-resistant Enterobacteriaceae in different populations in Switzerland: prevalence, risk factors and molecular features. J Glob Antimicrob Resist 2017; 12:17-19. [PMID: 29175015 DOI: 10.1016/j.jgar.2017.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/13/2017] [Accepted: 11/13/2017] [Indexed: 12/11/2022] Open
Affiliation(s)
- João Pires
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Esther Kuenzli
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Christoph Hauser
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Regula Tinguely
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Sara Kasraian
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Andrew Atkinson
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Christoph Hatz
- Swiss Tropical and Public Health Institute, Basel, Switzerland; Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland.
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Babouee Flury B, Donà V, Buetti N, Furrer H, Endimiani A. First two cases of severe multifocal infections caused by Klebsiella pneumoniae in Switzerland: characterization of an atypical non-K1/K2-serotype strain causing liver abscess and endocarditis. J Glob Antimicrob Resist 2017; 10:165-170. [PMID: 28729207 DOI: 10.1016/j.jgar.2017.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/24/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND We describe the first two multifocal invasive infections due to Klebsiella pneumoniae recently observed in Switzerland. METHODS Phenotypic (MIC assays and string test) and molecular analyses (PCR/Sequencing for bla, virulence factor genes and whole genome sequencing for one strain) were performed to characterize the causative K. pneumoniae isolates. RESULTS Both K. pneumoniae isolates (Kp1 and Kp2) were pan-susceptible to antibiotics and produced narrow-spectrum SHV β-lactamases. However, only Kp1 was string test positive. Kp1 was of ST380 and caused liver abscess as well as pneumonia and orbital phlegmon in an Eritrean patient. It belonged to the hypervirulent capsular serotype K2 and harboured the classic virulence-associated rmpA and aerobactin genes, fulfilling both the clinical and microbiological definitions for an invasive K. pneumoniae syndrome. Kp2 was of ST1043 and caused both liver abscess and endocarditis in a Swiss patient. Moreover, it did not possess the classic virulence-associated genes. Whole genome sequencing identified less well-known virulence factors in Kp2 that might have contributed to its virulence. Among these there were genes important for intestinal colonization and/or invasion, such as genes involved in adhesion (e.g., fimABCD and mrkABCD), regulation of capsule polysaccharide biosynthesis (e.g., evgS-evgA), as well as iron uptake (iroN), energy conversion, and metabolism. DISCUSSION This report confirms the continuous dissemination of hypervirulent K. pneumoniae strains among patients of non-Asian descent in Europe. Moreover, it highlights the genetic background of an atypical hypervirulent K. pneumoniae causing a severe invasive infection despite not possessing the classical virulence characteristics of hypermucoviscous strains.
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Affiliation(s)
- Baharak Babouee Flury
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Valentina Donà
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Niccolò Buetti
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
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Pires J, Bernasconi OJ, Hauser C, Tinguely R, Atkinson A, Perreten V, Dona V, Rauch A, Furrer H, Endimiani A. Erratum to 'Intestinal colonisation with extended-spectrum cephalosporin- and colistin-resistant Enterobacteriaceae in HIV-positive individuals in Switzerland: molecular features and risk factors' [International Journal of Antimicrobial Agents 49/4 (2017) 519-521]. Int J Antimicrob Agents 2017; 50:276. [PMID: 28595854 DOI: 10.1016/j.ijantimicag.2017.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Joao Pires
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, Bern CH-3001, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Odette J Bernasconi
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, Bern CH-3001, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Christoph Hauser
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, Bern CH-3001, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Regula Tinguely
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, Bern CH-3001, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrew Atkinson
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, Bern CH-3001, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, Bern CH-3001, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Valentina Dona
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, Bern CH-3001, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andri Rauch
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, Bern CH-3001, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Hansjakob Furrer
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, Bern CH-3001, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, Bern CH-3001, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.
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Villa L, Feudi C, Fortini D, Brisse S, Passet V, Bonura C, Endimiani A, Mammina C, Ocampo AM, Jimenez JN, Doumith M, Woodford N, Hopkins K, Carattoli A. Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone. Microb Genom 2017; 3:e000110. [PMID: 28785421 PMCID: PMC5506382 DOI: 10.1099/mgen.0.000110] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 03/22/2017] [Indexed: 02/05/2023] Open
Abstract
The global spread of Klebsiella pneumoniae producing Klebsiella pneumoniae carbapenemase (KPC) has been mainly associated with the dissemination of high-risk clones. In the last decade, hospital outbreaks involving KPC-producing K. pneumoniae have been predominantly attributed to isolates belonging to clonal group (CG) 258. However, results of recent epidemiological analysis indicate that KPC-producing sequence type (ST) 307, is emerging in different parts of the world and is a candidate to become a prevalent high-risk clone in the near future. Here we show that the ST307 genome encodes genetic features that may provide an advantage in adaptation to the hospital environment and the human host. Sequence analysis revealed novel plasmid-located virulence factors, including a cluster for glycogen synthesis. Glycogen production is considered to be one of the possible adaptive responses to long-term survival and growth in environments outside the host. Chromosomally-encoded virulence traits in the clone comprised fimbriae, an integrative conjugative element carrying the yersiniabactin siderophore, and two different capsular loci. Compared with the ST258 clone, capsulated ST307 isolates showed higher resistance to complement-mediated killing. The acquired genetic features identified in the genome of this new emerging clone may contribute to increased persistence of ST307 in the hospital environment and shed light on its potential epidemiological success.
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Affiliation(s)
| | | | | | | | | | | | - Andrea Endimiani
- 4Institute of Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Ana Maria Ocampo
- 5Grupo de Microbiología Básica y Aplicada, Escuela de Microbiología Universidad de Antioquia, Medellín, Colombia
| | - Judy Natalia Jimenez
- 5Grupo de Microbiología Básica y Aplicada, Escuela de Microbiología Universidad de Antioquia, Medellín, Colombia
| | - Michel Doumith
- 6Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Neil Woodford
- 6Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Katie Hopkins
- 6Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
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Donà V, Bernasconi OJ, Kasraian S, Tinguely R, Endimiani A. A SYBR ® Green-based real-time PCR method for improved detection of mcr-1-mediated colistin resistance in human stool samples. J Glob Antimicrob Resist 2017; 9:57-60. [PMID: 28400211 DOI: 10.1016/j.jgar.2017.01.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/13/2017] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES The aim of this study was to design a rapid and sensitive real-time PCR (rt-PCR) method for colistin resistance mcr-1 gene detection in human faecal samples. METHODS Stools (n=88) from 36 volunteers were analysed. To isolate mcr-1-producing Enterobacteriaceae, samples were enriched overnight in Luria-Bertani (LB) broth containing 2mg/L colistin and were then plated on selective agar plates with 4mg/L colistin. A SYBR® Green-based rt-PCR targeting mcr-1 was then designed. For method validation and to establish the limit of detection (LOD), total DNA was extracted from mcr-1-negative and mcr-1-positive Escherichia coli. rt-PCR was also performed with DNA extracted from 88 native stools and after enriching them in LB broth containing colistin. RESULTS Based on the culture approach, three unique volunteers resulted colonised with mcr-1-harboring E. coli strains. For culture isolates, rt-PCR exhibited a LOD of 10 genomic copies/reaction, with both sensitivity and specificity of 100%. Nevertheless, when testing native stools, only two of the three mcr-1-positive specimens were detected. However, after enrichment in LB broth containing colistin, the rt-PCR was strongly positive for all culture-positive samples. The average cycle threshold was 22, granting rapid and confident detection of positive specimens within 30 cycles. No false positives were observed for the remaining 85 culture-negative specimens. CONCLUSIONS A rapid rt-PCR for detection of mcr-1 from stool specimens was developed. The detection rate was increased by testing selective broth enrichments. This approach also has the advantage of concomitant isolation of mcr-1-harboring strains for further antimicrobial susceptibility and genetic testing.
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Affiliation(s)
- Valentina Donà
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | - Odette J Bernasconi
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Sara Kasraian
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | - Regula Tinguely
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland.
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Pires J, Bernasconi OJ, Hauser C, Tinguely R, Atkinson A, Perreten V, Donà V, Rauch A, Furrer H, Endimiani A. Intestinal colonisation with extended-spectrum cephalosporin- and colistin-resistant Enterobacteriaceae in HIV-positive individuals in Switzerland: molecular features and risk factors. Int J Antimicrob Agents 2017; 49:519-521. [DOI: 10.1016/j.ijantimicag.2017.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/13/2017] [Accepted: 02/19/2017] [Indexed: 12/20/2022]
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Seiffert SN, Carattoli A, Schwendener S, Collaud A, Endimiani A, Perreten V. Plasmids Carrying blaCMY -2/4 in Escherichia coli from Poultry, Poultry Meat, and Humans Belong to a Novel IncK Subgroup Designated IncK2. Front Microbiol 2017; 8:407. [PMID: 28360894 PMCID: PMC5350095 DOI: 10.3389/fmicb.2017.00407] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 02/27/2017] [Indexed: 01/27/2023] Open
Abstract
The blaCMY -2/4-carrying IncB/O/K-like plasmids of seven Escherichia coli strains from poultry, poultry meat and human urine samples were examined using comparative analysis of whole plasmid sequences. The incompatibility group was determined by analysis of the incRNAI region and conjugation assays with strains containing the IncK and IncB/O reference plasmids. Strains were additionally characterized using MLST and MIC determination. The complete DNA sequences of all plasmids showed an average nucleotide identity of 91.3%. Plasmids were detected in E. coli sequence type (ST) 131, ST38, ST420, ST1431, ST1564 and belonged to a new plasmid variant (IncK2) within the IncK and IncB/O groups. Notably, one E. coli from poultry meat and one from human contained the same plasmid. The presence of a common recently recognized IncK2 plasmid in diverse E. coli from human urine isolates and poultry meat production suggests that the IncK2 plasmids originated from a common progenitor and have the capability to spread to genetically diverse E. coli in different reservoirs. This discovery is alarming and stresses the need of rapidly introducing strict hygiene measures throughout the food chain, limiting the spread of such plasmids in the human settings.
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Affiliation(s)
- Salome N Seiffert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of BernBern, Switzerland; Institute for Infectious Diseases, University of BernBern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of BernBern, Switzerland
| | - Alessandra Carattoli
- Institute for Infectious Diseases, University of BernBern, Switzerland; Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di SanitàRome, Italy
| | - Sybille Schwendener
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern Bern, Switzerland
| | - Alexandra Collaud
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern Bern, Switzerland
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Bernasconi OJ, Donà V, Tinguely R, Endimiani A. In vitro activity of three commercial bacteriophage cocktails against multidrug-resistant Escherichia coli and Proteus spp. strains of human and non-human origin. J Glob Antimicrob Resist 2017; 8:179-185. [PMID: 28232228 DOI: 10.1016/j.jgar.2016.12.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 12/18/2016] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES Bacteriophages may represent a therapeutic alternative to treat infections caused by multidrug-resistant (MDR) pathogens. However, studies analysing their activity against MDR Enterobacteriaceae are limited. METHODS The in vitro lytic activity of three commercial bacteriophage cocktails (PYO, INTESTI and Septaphage) was evaluated against 70 Escherichia coli and 31 Proteus spp. of human and non-human origin. Isolates were characterised by phenotypic and genotypic methods and included 82 MDR strains [44 extended-spectrum-β-lactamase (ESBL)-producers (18 CTX-M-15-like, including ST131/ST648 E. coli); 27 plasmid-mediated AmpC β-lactamase (pAmpC)-producers (23 CMY-2-like, including ST131 E. coli); 3 ESBL+pAmpC-producers; and 8 carbapenemase-producers]. Phage susceptibility was determined by the spot test. RESULTS E. coli susceptibility to PYO, INTESTI and Septaphage was 61%, 67% and 9%, whereas that of Proteus spp. was 29%, 39% and 19%, respectively. For the subgroup of ESBL-producing E. coli/Proteus spp., the following susceptibility rates were recorded: PYO, 57%; INTESTI, 59%; and Septaphage, 11%. With regard to pAmpC-producers, 59%, 70% and 11% were susceptible to PYO, INTESTI and Septaphage, respectively. Five of eight carbapenemase-producers and three of four colistin-resistant E. coli were susceptible to PYO and INTESTI. CONCLUSIONS This is the first study analysing the activity of the above three cocktails against well-characterised MDR E. coli and Proteus spp. The overall narrow spectrum of activity observed could be related to the absence of specific bacteriophages targeting these contemporary MDR strains that are spreading in different settings. Therefore, bacteriophages targeting emerging MDR pathogens need to be isolated and integrated in such biopreparations.
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Affiliation(s)
- Odette J Bernasconi
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Freiestrasse 1, CH-3012 Bern, Switzerland
| | - Valentina Donà
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | - Regula Tinguely
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland.
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50
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Pires J, Bernasconi OJ, Kasraian S, Hilty M, Perreten V, Endimiani A. Intestinal colonisation with extended-spectrum cephalosporin-resistant Escherichia coli in Swiss pets: molecular features, risk factors and transmission with owners. Int J Antimicrob Agents 2016; 48:759-760. [PMID: 27692239 DOI: 10.1016/j.ijantimicag.2016.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/15/2016] [Accepted: 08/28/2016] [Indexed: 12/19/2022]
Affiliation(s)
- João Pires
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Odette J Bernasconi
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Sara Kasraian
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland; Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland.
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