Publications by authors named "Vincent Perreten"

137 Publications

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 Feb 22. Epub 2021 Feb 22.

Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland.

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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http://dx.doi.org/10.1093/jac/dkab028DOI Listing
February 2021

Novel SCCmec element containing the methicillin resistance gene mecD in Macrococcus bohemicus.

J Glob Antimicrob Resist 2021 Feb 8;24:360-362. Epub 2021 Feb 8.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.jgar.2021.02.001DOI Listing
February 2021

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 Feb 1. Epub 2021 Feb 1.

Department of Clinical Veterinary Medicine, University of Bern, Bern, Switzerland.

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 (bla and bla ) 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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http://dx.doi.org/10.1111/jvim.16038DOI Listing
February 2021

Genetic Features of Extended-Spectrum β-Lactamase-Producing from Poultry in Mayabeque Province, Cuba.

Antibiotics (Basel) 2021 Jan 22;10(2). Epub 2021 Jan 22.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland.

A total of 434 poultry cloacal samples were collected from seven different farms in different years (2013-2015) in the Cuban province of Mayabeque and analyzed for the presence of third-generation cephalosporin-resistant (3GC-R-). Sixty-two 3GC-R- isolates were recovered in total from the farms, with detection rates of 2.9% in 2013, 10.3% in 2014, and 28.7% in 2015. Characterization of 32 3GC-R- isolates revealed the presence of the extended-spectrum β-lactamase (ESBL) genes ( = 27), ( = 4), and together with ( = 1). The isolates also contained different proportions of genes conferring decreased susceptibility to sulfonamides (, , ), trimethoprim (, 7, 12, 14, 17), tetracyclines ((A), (B)), aminoglycosides (, , ), chloramphenicol (, ), macrolides ((A), (D)), and quinolones (, , ) as well as mutations in the fluoroquinolone-resistance determining regions of GyrA (S83L, D87N, D87Y) and ParC (S80I, E84G). The isolates belonged to 23 different sequence types and to phylogroups A ( = 25), B1 ( = 5), and D ( = 2), and they contained plasmid-associated incompatibility groups FII, X1, HI1, HI2, N, FIA, and FIB. These findings reveal a genetically diverse population of multiresistant ESBL-producing in poultry farms in Cuba, which suggests multiple sources of contamination and the acquisition of antibiotic resistance genes.
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http://dx.doi.org/10.3390/antibiotics10020107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7910960PMC
January 2021

Characterization of Third-Generation Cephalosporin-Resistant Isolated from Pigs in Cuba Using Next-Generation Sequencing.

Microb Drug Resist 2021 Jan 19. Epub 2021 Jan 19.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.

Resistance to third-generation cephalosporins (3GC) in has been reported worldwide from humans and animals, but the situation in Cuba is still poorly understood. This study aimed to gain new insights into the phenotypic and genotypic characteristics of third-generation cephalosporin-resistant (3GC-R) isolated from pigs in Cuba. Rectal swabs from 215 healthy pigs were taken from different municipalities in the western region of Cuba and spread on MacConkey agar supplemented with cefotaxime and ceftazidime. Ninety-six isolates were identified as 3GC-R and 87.5% of them were resistant to at least three antibiotic classes as determined by the measurement of the minimum inhibitory concentration (MIC) of 14 antibiotics. Twenty-seven different isolates were selected for Illumina next-generation sequencing, and subsequent analysis was performed for the detection of antibiotic resistance and virulence genes, plasmid incompatibility (Inc) groups, multilocus sequence typing (MLST), and core genome MLST (cgMLST). The sequenced isolates contained extended-spectrum β-lactamase genes ( = 17), ( = 5), and ( = 4) as well as with pAmpC gene ( = 2). They also harbored genes for resistance to other clinically important classes of antibiotics, as well as several diverse virulence factors. The 3GC-R were genetically highly diverse, belonging to 16 different sequence types. IncX1 was the most frequent Inc group. The presence of 3GC-R in pigs from Cuba containing several different antibiotic resistance mechanisms emphasizes the need for surveillance programs and the establishment of strategies for the prudent use of antibiotics in food-producing animals.
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http://dx.doi.org/10.1089/mdr.2020.0174DOI Listing
January 2021

The novel macrolide resistance genes mef(F) and msr(G) are located on a plasmid in Macrococcus canis and a transposon in Macrococcus caseolyticus.

J Antimicrob Chemother 2021 Jan;76(1):48-54

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.

Objectives: To analyse macrolide resistance in a Macrococcus canis strain isolated from a dog with an ear infection, and determine whether the resistance mechanism is also present in other bacteria, and associated with mobile genetic elements.

Methods: The whole genome of M. canis Epi0082 was sequenced using PacBio and Illumina technologies. Novel macrolide resistance determinants were identified through bioinformatic analysis, and functionality was demonstrated by expression in Staphylococcus aureus. Mobile genetic elements containing the novel genes were analysed in silico for strain Epi0082 as well as in other bacterial strains deposited in GenBank.

Results: M. canis Epi0082 contained a 3212 bp operon with the novel macrolide resistance genes mef(F) and msr(G) encoding a efflux protein and an ABC-F ribosomal protection protein, respectively. Cloning in S. aureus confirmed that both genes individually confer resistance to the 14- and 15-membered ring macrolides erythromycin and azithromycin, but not the 16-membered ring macrolide tylosin. A reduced susceptibility to the streptogramin B pristinamycin IA was additionally observed when msr(G) was expressed in S. aureus under erythromycin induction. Epi0082 carried the mef(F)-msr(G) operon together with the chloramphenicol resistance gene fexB in a novel 39 302 bp plasmid pMiCAN82a. The mef(F)-msr(G) operon was also found in macrolide-resistant Macrococcus caseolyticus strains in the GenBank database, but was situated in the chromosome as part of a novel 13 820 bp or 13 894 bp transposon Tn6776.

Conclusions: The identification of mef(F) and msr(G) on different mobile genetic elements in Macrococcus species indicates that these genes hold potential for further dissemination of resistance to the clinically important macrolides in the bacterial population.
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http://dx.doi.org/10.1093/jac/dkaa405DOI Listing
January 2021

Environmental dissemination of carbapenemase-producing Enterobacteriaceae in rivers in Switzerland.

Environ Pollut 2020 Oct 22;265(Pt B):115081. Epub 2020 Jun 22.

Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, 8057, Zurich, Switzerland. Electronic address:

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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http://dx.doi.org/10.1016/j.envpol.2020.115081DOI Listing
October 2020

sp. nov., a new member of the ' group' isolated from healthy black bears.

Int J Syst Evol Microbiol 2020 Aug;70(8):4637-4645

Department of Biomedical and Diagnostic Sciences, University of Tennessee College of Veterinary Medicine, Knoxville, Tennessee, USA.

Six strains were isolated from healthy black bears () in the Great Smoky Mountains National Park, Tennessee, USA. Phylogenetic analysis based on complete genome, 16S rRNA, , , and genes, and MALDI-TOF-MS main spectral profiles revealed that the strains belonged to one species and showed the closest relatedness to members of the ' group' (SIG), which include , and . The strains were positive in SIG-specific and negative in individual species-specific PCR assays for the gene. The strains can be differentiated from the other SIG species by the absence of sucrose fermentation, from DSM 20373, CCUG 49543 and DSM 105366 by the absence of methyl β-d-glucopyranoside fermentation and from DSM 20771 by fermentation of trehalose. DNA relatedness of the type strain MI 10-1553 with the type strains of , , and was ≤48.2 % by digital DNA-DNA hybridization and ≤92.3 % by average nucleotide identity calculations. Iso-, anteiso-C and anteiso-C were the most common fatty acids. Polar lipids consisted of phosphadidylglycerols, phospholipids, glycolipid, diphosphatidylglycerol and aminophospholipid. Cell-wall peptidoglycan was of type A3α l-Lys-Gly (Ser; similar to A11.2 and A11.3). The respiratory quinone belonged to menaquinone 7 (MK-7). The G+C content of MI 10-1553 was 39.3 mol%. The isolated strains represent a novel species of the genus , for which we propose the name sp. nov. The type strain is MI 10-1553 (=ATCC TSD-55=CCOS 1900).
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http://dx.doi.org/10.1099/ijsem.0.004324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7660245PMC
August 2020

Investigating the use of bacteriophages as a new decolonization strategy for intestinal carriage of CTX-M-15-producing ST131 Escherichia coli: An in vitro continuous culture system model.

J Glob Antimicrob Resist 2020 09 23;22:664-671. Epub 2020 Jun 23.

Institute for Infectious Diseases, University of Bern, Bern, Switzerland. Electronic address:

Objectives: We investigated the use of bacteriophages as a strategy to decolonize intestinal carriers of multidrug-resistant Escherichia coli.

Methods: A fermentor was used as a continuous culture system for 48h. Two different pools of faeces (studies I and II) obtained from volunteers were spiked with a CTX-M-15-producing ST131 E. coli (strain 4901.28) susceptible to bacteriophages and challenged with three doses of INTESTI Bacteriophage cocktail administered at 2, 6 and 10h after the inoculum. Bacterial typing was performed by implementing microdilution panels, spot test, rep-PCR and whole-genome sequencing (including cgMLST and single-nucleotide variant analysis) obtained using Nanopore and Illumina platforms.

Results: In study I, bacteriophages decreased the numbers of 4901.28 dramatically (≤10CFU/mL after 6h). In contrast, during study II, a phage-resistant mutant of 4901.28 persisted in the continuous culture (10CFU/mL at 48h). Whole-genome sequencing revealed the presence of two additional plasmids in the mutant as well as 11 single-nucleotide variants, including one chromosomal in a glycosyltransferase family 2 protein that is responsible for the transfer of sugars to polysaccharides and lipids. In both studies, the commensal E. coli population remained unchanged by the phage treatment maintaining itself at 10CFU/mL.

Conclusions: Our data indicates that bacteriophage cocktails may be implemented to decolonize some intestinal carriers. However, the individual microbiota composition may have an impact on the development of phage resistance. Mechanisms underlying this phenomenon are likely to be various and complex. Further in vivo studies and protein expression experiments are needed to confirm our observations and hypotheses.
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http://dx.doi.org/10.1016/j.jgar.2020.05.018DOI Listing
September 2020

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 06 23;9(1):93. Epub 2020 Jun 23.

Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.

Background: Intensive medical care in companion animal clinics could pose a risk for the selection and dissemination of multidrug-resistant organisms (MDROs). Infection prevention and control (IPC) concepts are key measures to reduce the spread of MDROs, but data on IPC standards in companion animal clinics is sparse. The study assessed IPC standards in seven companion animal clinics and practices in Switzerland by structured IPC audits and combined results with environmental MDRO contamination and MDRO carriage of the personnel.

Methods: IPC audits were held between August 2018 and January 2019. The observations in 34 IPC areas were scored based on predefined criteria (not fulfilled/partially fulfilled/fulfilled = score 0/1/2). Environmental swabs and nasal and stool samples from veterinary personnel were tested for methicillin-resistant (MR) staphylococci and macrococci and for colistin-resistant, extended-spectrum β-lactamase- and carbapenemase-producing (CP) Enterobacterales (CPE). Species was identified by MALDI-TOF MS, antimicrobial resistance determined by microdilution and β-lactam resistance gene detection, and genetic relatedness assessed by REP-/ERIC-PCR and multilocus sequence typing.

Results: Of a maximum total IPC score of 68, the institutions reached a median (range) score of 33 (19-55). MDROs were detected in median (range) 8.2% (0-33.3%) of the sampling sites. Clinics with low IPC standards showed extensive environmental contamination, i.e. of intensive care units, consultation rooms and utensils. CPE were detected in two clinics; one of them showed extensive contamination with CP Klebsiella pneumoniae (ST11, bla) and MR Staphylococcus pseudintermedius (ST551, mecA). Despite low IPC scores, environmental contamination with MDROs was low in primary opinion practices. Three employees were colonized with Escherichia coli ST131 (bla, bla, bla). Two employees carried CP E. coli closely related to environmental (ST410, bla) and patient-derived isolates (ST167, bla). 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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http://dx.doi.org/10.1186/s13756-020-00742-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310346PMC
June 2020

The Novel Macrolide Resistance Genes (D), (F), and (H) Are Present on Resistance Islands in Macrococcus canis, Macrococcus caseolyticus, and Staphylococcus aureus.

Antimicrob Agents Chemother 2020 04 21;64(5). Epub 2020 Apr 21.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland

Chromosomal resistance islands containing the methicillin resistance gene (McRI ) have been reported in Here, we identified novel macrolide resistance genes in on similar elements, called McRI These elements were also integrated into the 3' end of the 30S ribosomal protein S9 gene (), delimited by characteristic attachment () sites, and carried a related site-specific integrase gene () at the 5' end. They carried novel macrolide resistance genes belonging to the family of ABC subfamily F (ABC-F)-type ribosomal protection protein [(F) and (H)] and the macrolide efflux family [(D)]. Highly related (D)-(F) fragments were found on diverse McRI elements in , and Another McRI -like element identified in an strain lacked the classical site at the 3' end and carried the (H) gene but no neighboring gene. The expression of the novel resistance genes in resulted in a low-to-moderate increase in the MIC of erythromycin but not streptogramin B. In the (D)-(F) operon, the (F) gene was shown to be the crucial determinant for macrolide resistance. The detection of circular forms of McRI and the (D)-(F) fragment suggested mobility of both the island and the resistance gene subunit. The discovery of McRI in different species and indicates that these islands have a potential for dissemination of antibiotic resistance within the family.
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http://dx.doi.org/10.1128/AAC.00160-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7179620PMC
April 2020

OXA-181-Producing Extraintestinal Pathogenic Escherichia coli Sequence Type 410 Isolated from a Dog in Portugal.

Antimicrob Agents Chemother 2020 03 24;64(4). Epub 2020 Mar 24.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland

Two multidrug-resistant and carbapenemase-producing clones of sequence type 410 were isolated from fecal samples of a dog with skin infection on admission to an animal hospital in Portugal and 1 month after discharge. Whole-genome sequencing revealed a 126,409-bp Col156/IncFIA/IncFII multidrug resistance plasmid and a 51,479-bp IncX3 -containing plasmid. The chromosome and plasmids carried virulence genes characteristic for uropathogenic , indicating that dogs may carry multidrug-resistant isolates related to those causing urinary tract infections in humans.
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http://dx.doi.org/10.1128/AAC.02298-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7179305PMC
March 2020

Employees of Swiss veterinary clinics colonized with epidemic clones of carbapenemase-producing Escherichia coli.

J Antimicrob Chemother 2020 03;75(3):766-768

Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.

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http://dx.doi.org/10.1093/jac/dkz470DOI Listing
March 2020

Complete Circular Genome Sequence of a Multidrug-Resistant Escherichia coli Strain from Cuba Obtained with Nanopore and Illumina Hybrid Assembly.

Microbiol Resour Announc 2019 Nov 27;8(48). Epub 2019 Nov 27.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland

The complete genome sequence of a multidrug-resistant strain isolated from a healthy pig in Cuba was determined using short and long reads. This strain carried four plasmids, including a 42,683-kb IncX1 plasmid, which contains the third-generation cephalosporin resistance gene together with other disinfectant and antibiotic resistance genes.
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http://dx.doi.org/10.1128/MRA.01269-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883113PMC
November 2019

PFM-Like Enzymes Are a Novel Family of Subclass B2 Metallo-β-Lactamases from Pseudomonas synxantha Belonging to the Pseudomonas fluorescens Complex.

Antimicrob Agents Chemother 2020 01 27;64(2). Epub 2020 Jan 27.

Microbiology Unit, Department of Medicine, Faculty of Science, University of Fribourg, Fribourg, Switzerland.

A carbapenem-resistant isolate recovered from chicken meat produced the novel carbapenemase PFM-1. That subclass B2 metallo-β-lactamase shared 71% amino acid identity with β-lactamase Sfh-1 from The gene was chromosomally located and likely acquired. Variants of PFM-1 sharing 90% to 92% amino acid identity were identified in bacterial species belonging to the complex, including (PFM-2) and (PFM-3), highlighting that these species constitute reservoirs of PFM-like encoding genes.
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http://dx.doi.org/10.1128/AAC.01700-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6985737PMC
January 2020

Shedding of OXA-181 carbapenemase-producing from companion animals after hospitalisation in Switzerland: an outbreak in 2018.

Euro Surveill 2019 Sep;24(39)

Institute of Veterinary Bacteriology, Bern, University of Bern.

BackgroundCarbapenem-resistant Enterobacteriaceae pose a serious threat to public health worldwide, and the role of companion animals as a reservoir is still unclear.AimsThis 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.MethodsRectal 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.ResultsThis study revealed nosocomial acquisition of harbouring the carbapenemase gene , the pAmpC cephalosporinase gene as well as quinolone resistance associated with and mutations in the topoisomerases II (GyrA) and IV (ParC). The and genes were identified on a 51 kb IncX3 plasmid and on a 47 kb IncI1 plasmid. All isolates belonged to sequence type ST410 and were genetically highly related. This 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.ConclusionsCompanion animals may acquire carbapenemase-producing during hospitalisation, posing the risk of further dissemination to the animal and human population and to the environment.
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http://dx.doi.org/10.2807/1560-7917.ES.2019.24.39.1900071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6774230PMC
September 2019

Symposium report: One Health meets sequencing.

Microbes Infect 2020 Jan - Feb;22(1):1-7. Epub 2019 Aug 8.

Institute for Food Safety and -hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.

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http://dx.doi.org/10.1016/j.micinf.2019.07.004DOI Listing
October 2020

Typing of Islands in Genetically Diverse Methicillin-Resistant Strains from Cattle.

Appl Environ Microbiol 2019 10 17;85(19). Epub 2019 Sep 17.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland

belongs to the normal bacterial flora of dairy cows and does not usually cause disease. However, methicillin-resistant strains were isolated from bovine mastitis milk. These bacteria had acquired a chromosomal island (McRI -1 or McRI -2) carrying the methicillin resistance gene To gain insight into the distribution of McRI types in from cattle, 33 -containing strains from Switzerland were characterized using molecular techniques, including multilocus sequence typing, antibiotic resistance gene identification, and PCR-based McRI typing. In addition, the same genetic features were analyzed in 27 -containing strains isolated from bovine bulk milk in England/Wales using publicly available whole-genome sequences. The 60 strains belonged to 24 different sequence types (STs), with strains belonging to ST5, ST6, ST21, and ST26 observed in both Switzerland and England/Wales. McRI -1 was found in different STs from Switzerland ( = 19) and England/Wales ( = 4). McRI -2 was only found in 7 strains from Switzerland, all of which belonged to ST6. A novel island, McRI -3, which contains a complete operon ( [where the subscript indicates ]) combined with the left part of McRI -2 and the right part of McRI -1, was found in heterogeneous STs from both collections (Switzerland,  = 7; England/Wales,  = 21). Two strains from England/Wales carried a truncated McRI -3. Phylogenetic analyses revealed no clustering of strains according to geographical origin or carriage of McRI -1 and McRI -3. Circular excisions were also detected for McRI -1 and McRI -3 by PCR. The analyses indicate that these islands are mobile and may spread by horizontal gene transfer between genetically diverse strains. Since its first description in 2017, the methicillin resistance gene has been detected in strains from different cattle sources and countries. Our study provides new insights into the molecular diversity of -carrying strains by using two approaches to characterize elements: (i) multiplex PCR for molecular typing of McRI and (ii) read mapping against reference sequences to identify McRI types In combination with multilocus sequence typing, this approach can be used for molecular characterization and surveillance of carrying .
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http://dx.doi.org/10.1128/AEM.01496-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6752026PMC
October 2019

Molecular Characterization and Antimicrobial Resistance of Livestock-Associated Methicillin-Resistant Isolates from Pigs and Swine Workers in Central Thailand.

Microb Drug Resist 2019 Nov 30;25(9):1382-1389. Epub 2019 Jul 30.

Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.

This study presents molecular characteristics of livestock-associated methicillin-resistant (LA-MRSA) from pigs and swine workers in central Thailand. Sixty-three MRSA isolates were recovered from pigs ( = 60) and humans ( = 3). Two major LA-MRSA lineages, including sequence type (ST) 398 and clonal complex 9 (ST9 and ST4576, a novel single-locus variant of ST9), were identified. ST398 had type t034 ( = 55). ST9 and ST4576 had t337 ( = 8) and carried staphylococcal cassette chromosome (SCC) IX only. MRSA-ST398-t034 contained various SCC, including SCC V ( = 42), a novel SCC composite island ( = 12), and a nontypeable SCC ( = 1). All isolates were multidrug resistant and carried common resistance genes found in LA-MRSA. This is the first report of the presence of swine MRSA ST398 and multidrug resistance gene in MRSA ST9 in Thailand. With identical molecular characteristics, pigs could be a source of MRSA ST398 spread to humans. A minor variation of genetic features and resistance gene carriage in both lineages represented a heterogeneous population and evolution of the endemic clones. A monitoring program and farm management, with prudent antimicrobial uses, should be implemented to reduce spreading. Strict hygiene and personal protection are also necessary to prevent transfer of LA-MRSA to humans.
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http://dx.doi.org/10.1089/mdr.2019.0011DOI Listing
November 2019

The (A) Gene from Brachyspira hyodysenteriae Confers Decreased Susceptibility to Pleuromutilins and Streptogramin A in Escherichia coli.

Antimicrob Agents Chemother 2019 09 23;63(9). Epub 2019 Aug 23.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland

The (A) gene suspected to confer resistance to pleuromutilins in was tested for functionality in AG100A and RN4220. Expression of the cloned (A) gene conferred decreased susceptibility to pleuromutilin (P) and streptogramin A (S) antibiotics in and had a minor effect in The finding provides evidence of the direct association of (A) with the PS resistance phenotype.
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http://dx.doi.org/10.1128/AAC.00930-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6709466PMC
September 2019

Non-aureus Staphylococci Species in the Teat Canal and Milk in Four Commercial Swiss Dairy Herds.

Front Vet Sci 2019 12;6:186. Epub 2019 Jun 12.

Vetsuisse Faculty, Clinic for Ruminants, University of Bern, Bern, Switzerland.

Non-aureus staphylococci (NAS) are frequently found in milk samples as well as on the teat apex and in the teat canal and are known to be a cause of subclinical mastitis. The objective of this study was to investigate the relationship between NAS species colonizing the teat canal and those causing intramammary infection (IMI) in four commercial dairy herds. Teat canal swabs were obtained and thereafter milk samples were aseptically collected and evaluated for the presence of staphylococci using selective agar plates. Species identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The relationship between NAS species distribution and sample type (teat canal vs. milk samples) was quantified using hierarchical multivariable logistic regression models. The most prevalent NAS species in teat canal swabs were (35%), (10%), and (7%), whereas in milk samples (5%), (5%), and (4%) were most prevalent. There were significantly higher odds for (OR = 215), (OR = 20), (OR = 22), (OR = 13), and (OR = 10) to be present in teat canal swabs than in milk samples. Differences between herds in NAS species distribution were found and were most pronounced for and a -like species. This information aids in the understanding of NAS species as an etiology of IMI and should be taken into account when interpreting milk culture results.
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http://dx.doi.org/10.3389/fvets.2019.00186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582780PMC
June 2019

Macrococcus canis contains recombinogenic methicillin resistance elements and the mecB plasmid found in Staphylococcus aureus.

J Antimicrob Chemother 2019 09;74(9):2531-2536

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.

Objectives: To analyse the genetic context of mecB in two Macrococcus canis strains from dogs, compare the mecB-containing elements with those found in other Macrococcus and Staphylococcus species, and identify possible mobilizable mecB subunits.

Methods: Whole genomes of the M. canis strains Epi0076A and KM0218 were sequenced using next-generation sequencing technologies. Multiple PCRs and restriction analysis confirmed structures of mecB-containing elements, circularization and recombination of mecB subunits.

Results: Both M. canis strains contained novel composite pseudo (Ψ) staphylococcal cassette chromosome mec (SCCmec) elements. Integration site sequences for SCC flanked and subdivided composite ΨSCCmecEpi0076A (69569 bp) into ΨSCC1Epi0076A-ΨSCCmecEpi0076A-ΨSCC2Epi0076A and composite ΨSCCmecKM0218 (24554 bp) into ΨSCCKM0218-ΨSCCmecKM0218. Putative γ-haemolysin genes (hlgB and hlgC) were found at the 3' end of both composite elements. ΨSCCmecKM0218 contained a complete mecB gene complex (mecIm-mecR1m-mecB-blaZm) downstream of a new IS21-family member (ISMaca1). ΨSCCmecEpi0076A carried a blaZm-deleted mecB gene complex similar to that reported in 'Macrococcus goetzii' CCM4927T. A second mecB gene was found on the 81325 bp MDR plasmid pKM0218 in KM0218. This plasmid contained a complete Tn6045-associated mecB gene complex distinct from that of ΨSCCmecKM0218. pKM0218 was almost identical to the mecB-containing plasmid recently reported in Staphylococcus aureus (overall 99.96% nucleotide identity). Mobilization of mecB within an unconventional circularizable structure was observed in Epi0076A as well as chromosomal plasmid insertion via recombination of mecB operons in KM0218.

Conclusions: Our findings provide evidence of both the continuing evolution of mecB-containing elements in macrococci and M. canis as a potential source of the mecB-containing plasmid found in staphylococci.
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http://dx.doi.org/10.1093/jac/dkz260DOI Listing
September 2019

Correction for Wüthrich et al., "A Novel Trimethoprim Resistance Gene, , Characterized from Escherichia coli from Calves".

mSphere 2019 Jun 19;4(3). Epub 2019 Jun 19.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland

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http://dx.doi.org/10.1128/mSphere.00390-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584376PMC
June 2019

A Novel Trimethoprim Resistance Gene, , Characterized from Escherichia coli from Calves.

mSphere 2019 05 8;4(3). Epub 2019 May 8.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland

Whole-genome sequencing of trimethoprim-resistant strains MF2165 and PF9285 from healthy Swiss fattening calves revealed a so far uncharacterized dihydrofolate reductase gene, Functionality and association with trimethoprim resistance were demonstrated by cloning and expressing in The DfrA35 protein showed the closest amino acid identity (49.4%) to DfrA20 from and to the Dfr determinants DfrG (41.2%), DfrD (40.8%), and DfrK (40.0%) found in Gram-positive bacteria. The gene was integrated within a florfenicol/chloramphenicol-sulfonamide resistance IS element (-IS--) next to a Tn-like transposon that contained genes with resistance to sulfonamides (), streptomycin (), gentamicin/tobramycin/kanamycin (), and quaternary ammonium compounds (Δ). A search of GenBank databases revealed that was present in 26 other strains from different origins as well as in The presence of associated with IS in from animals, as well as its presence in other strains from different sources and countries and in , highlights the global spread of this gene and its potential for further dissemination. The genetic link of IS- with other antibiotic and disinfectant resistance genes showed that multidrug-resistant may be selected and maintained by the use of either one of several antimicrobials.
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http://dx.doi.org/10.1128/mSphere.00255-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506621PMC
May 2019

Outbreaks of a Methicillin-Resistant Clone ST398-t011 in a Hungarian Equine Clinic: Emergence of Rifampicin and Chloramphenicol Resistance After Treatment with These Antibiotics.

Microb Drug Resist 2019 Oct 8;25(8):1219-1226. Epub 2019 May 8.

Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland.

Between July 2011 and May 2016, a total of 40 strains originating from 36 horses were confirmed as methicillin resistant (methicillin-resistant [MRSA]) in a university equine clinic. An additional 10 MRSA strains from 36 samples of clinic workers were obtained in October 2017. The first equine isolate represented the sequence type ST398, -type t011, and SCC IV. This isolate was resistant to a wide spectrum of antimicrobial agents. MRSA strains with the same genotype and with very similar resistance profiles were isolated on 21 more occasions from September 2013 to September 2014. A second outbreak occurred from May 2015 until May 2016. The first isolate in this second outbreak shared the same genotype, but was additionally resistant to chloramphenicol. The second isolate from August 2015 also showed resistance to rifampicin. The clone was isolated 18 times. Most of the human isolates shared the same genotype as the isolates from horses and their resistance patterns showed only slight differences. We can conclude that the MRSA-related cases at the Department and Clinic of Equine Medicine were all nosocomial infections caused by the same clonal lineage belonging to the clonal complex 398. The clonal complex 398 of equine origin is reported for the first time in Hungary. In addition, our observation of the emergence of new resistance to antimicrobial agents within the clonal lineage after treatment with antibiotics is of concern. Strict hygiene regulations have been introduced to lower the incidence of MRSA isolation and the related clinical disease.
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http://dx.doi.org/10.1089/mdr.2018.0384DOI Listing
October 2019

Characterisation of a porcine Escherichia coli strain from Switzerland carrying mcr-1 on a conjugative multidrug resistance IncHI2 plasmid.

J Glob Antimicrob Resist 2019 03 21;16:123-124. Epub 2018 Dec 21.

Institute of Veterinary Bacteriology, University of Bern, Längassstrasse 122, CH-3012 Bern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.jgar.2018.12.007DOI Listing
March 2019

Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform.

Swiss Med Wkly 2018 12 15;148:w14693. Epub 2018 Dec 15.

SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Facing multidrug resistant (MDR) bacterial pathogens is one of the most important challenges for our society. The spread of highly virulent and resistant pathogens can be described using molecular typing technologies; in particular, whole genome sequencing (WGS) data can be used for molecular typing purposes with high resolution. WGS data analysis can explain the spatiotemporal patterns of pathogen transmission. However, the transmission between compartments (human, animal, food, environment) is very complex. Interoperable and curated metadata are a key requirement for fully understanding this complexity. In addition, high quality sequence data are a key element between centres using WGS data for diagnostic and epidemiological applications. We aim to describe steps to improve WGS data analysis and to implement a molecular surveillance platform allowing integration of high resolution WGS typing data and epidemiological data.
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http://dx.doi.org/10.4414/smw.2018.14693DOI Listing
December 2018

Evaluation of EDTA- and DPA-Based Microdilution Phenotypic Tests for the Detection of MCR-Mediated Colistin Resistance in Enterobacteriaceae.

Microb Drug Resist 2019 May 15;25(4):494-500. Epub 2018 Nov 15.

1 Institute for Infectious Diseases, University of Bern, Bern, Switzerland.

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 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 positive strains (39 , 3 , and 2 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 -positive strains, but 22 false-positive strains (including 12 and 4 ) were recorded (sensitivity [SN], 93.2%; specificity [SP], 54.2%). The DPA-based BMD assay detected 37 positive strains, with 7 false-negative (2 , 3 , 2 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 strains (SN, 94.9%; SP, 100%). With the aim to prevent the dissemination of -possessing 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 -like genes not yet targeted by the current molecular assays.
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http://dx.doi.org/10.1089/mdr.2018.0275DOI Listing
May 2019

Limited added value of fungal ITS amplicon sequencing in the study of bovine abortion.

Heliyon 2018 Nov 5;4(11):e00915. Epub 2018 Nov 5.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland.

Bovine mycotic abortion is sporadic and caused by different ubiquitous and opportunistic fungi. Recently, a broad spectrum of bacterial opportunists involved in bovine abortion was revealed by 16S rRNA gene amplicon sequencing. We hypothesized that fungal organisms potentially involved in bovine abortion also might remain undetected by conventional culture. In this retrospective study, we therefore applied fungal internal transcribed spacer 2 (ITS2) region amplicon sequencing to 74 cases of bovine abortion submitted to our diagnostic service. The investigation was complemented by fungal culture and, retrospectively, by data from bacteriological, virological and parasitological analyses and histopathological examination of placentas. Fungal DNA was found in both the placentas and abomasal contents, with 92 fungal genera identified. In 18 cases, >75% of the reads belonged to one specific fungal genus: (n = 7), (n = 4), (n = 3), unidentified (n = 3), (n = 1), (n = 1), (n = 1), (n = 1) and (n = 1) with one case harboring two different genera. By culture, in contrast, fungal agents were detected in only 6 cases. Inflammatory and/or necrotizing lesions were found in 27/40 histologically assessed placentas. However, no lesion-associated fungal structures were detected in HE- and PAS-stained specimens. Complementary data revealed the presence of one or more non-fungal possible abortifacient: , , spp., subsp. , , , , , subsp. , , , Schmallenbergvirus, . The mycobiota revealed by sequencing did not differ between cases with or without a possible infectious etiology. Our study suggests that amplicon sequencing of the ITS2 region from DNA isolated from bovine abortion does not provide additional information or new insight into mycotic abortion and without complementary analyses may easily lead to a false interpretation of the role of fungal organisms in bovine abortion.
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http://dx.doi.org/10.1016/j.heliyon.2018.e00915DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6222074PMC
November 2018

Characterization of Staphylococcal Cassette Chromosome Elements from Methicillin-Resistant Infections in Australian Animals.

mSphere 2018 11 7;3(6). Epub 2018 Nov 7.

Sydney School of Veterinary Science, University of Sydney, NSW, Australia

We examined the oxacillin resistance phenotype and genomic structure of staphylococcal cassette chromosome (SCC) elements from 77 veterinary methicillin-resistant (MRSP) isolates. Isolates were characterized by oxacillin broth microdilution, whole-genome sequencing, and bioformatics analysis. Five previously described SCC elements, and a sixth novel element, were identified: SCC III (also known as II-III), ΨSCC, and SCC (a SCC VII variant), all previously described in MRSP, and SCC IVg and SCC V, previously described in both methicillin-resistant (MRSA) and MRSP. The sixth element was novel and found among nine geographically clustered isolates. This novel pseudostaphylococcal cassette chromosome (ΨSCC) contained a class A gene complex but lacked genes. It also harbored heavy metal (cadmium) resistance determinants. The median oxacillin MIC values among ΨSCC, SCC III, and SCC V isolates were significantly higher than those determined for the SCC VII variant isolates and ΨSCC and SCC IVg isolates. ΨSCC was found exclusively in sequence type 497 (ST497), an MRSP clone that is locally successful in Victoria, Australia. Future studies are necessary to determine if this clone has disseminated further afield and if ΨSCC has moved into other MRSP lineages or staphylococcal species. is a significant veterinary pathogen and occasional cause of infections in humans. β-Lactams are an important group of antimicrobials used to treat staphylococcal infections in humans and animals. However, when staphylococci become methicillin resistant via the acquisition of a mobile genetic element called staphylococcal cassette chromosome (SCC), they become resistant to all β-lactams. This study detected a novel SCC element among a cluster of methicillin-resistant isolates from animals in Australia. It also detected SCC elements in that had high similarity to those identified in methicillin-resistant , demonstrating how human and animal pathogens can share the same resistance determinants.
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http://dx.doi.org/10.1128/mSphere.00491-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6222048PMC
November 2018