Publications by authors named "Andrea Endimiani"

145 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.
View Article and Find Full Text PDF

Download full-text PDF

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

Characterisation of a new bla-carrying IncN2 plasmid from an Enterobacter hormaechei subsp. steigerwaltii.

J Glob Antimicrob Resist 2021 Feb 8;24:325-327. Epub 2021 Feb 8.

Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jgar.2021.01.017DOI 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/jvim.16038DOI Listing
February 2021

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 Jan;76(2):330-337

Institute for Infectious Diseases, University of Bern, Bern.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/jac/dkaa457DOI Listing
January 2021

The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update.

Infect Dis Clin North Am 2020 12 30;34(4):659-676. Epub 2020 Sep 30.

Department of Pathology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, USA.

The evolution of resistance to antimicrobial agents in gram-negatives has challenged the role of the clinical microbiology laboratory to implement new methods for their timely detection. Recent development has enabled the use of novel methods for more rapid pathogen identification, antimicrobial susceptibility testing, and detection of resistance markers. Commonly used methods improve the rapidity of resistance detection from both cultured bacteria and specimens. This review focuses on the commercially available systems available together with their technical performance and possible clinical impact.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.idc.2020.08.001DOI Listing
December 2020

Emergence of Haemophilus parainfluenzae resistant to third-generation cephalosporins in Italy: potential role of PBP3 and PBP5 substitutions in high-level resistance.

Int J Antimicrob Agents 2020 Nov 9;56(5):106159. Epub 2020 Sep 9.

Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco (Italy).

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijantimicag.2020.106159DOI Listing
November 2020

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.
View Article and Find Full Text PDF

Download full-text PDF

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

Rapid Increase of CTX-M-Producing Shigella sonnei Isolates in Switzerland Due to Spread of Common Plasmids and International Clones.

Antimicrob Agents Chemother 2020 09 21;64(10). Epub 2020 Sep 21.

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

The Swiss Centre for Antibiotic Resistance (ANRESIS) has recently noted an increase of extended-spectrum cephalosporin-resistant (ESC-R) isolates nationwide (3.8% in 2016 versus 37.5% in 2019). To understand this phenomenon, we analyzed 25 representative isolates (of which 14 were ESC-R) collected in Switzerland during 2016 to 2019. Whole-genome sequencing was achieved using both the Illumina and the Nanopore platforms. Both ESC-R and extended-spectrum cephalosporin-susceptible isolates belonged to sequence type 152 (ST152). The ESC-R isolates carried in IncI1-pST57 ( = 5), in IncFII (F2:A-:B-) ( = 5), in IncI1-pST16, and , , or in other IncFII plasmids ( = 1 each). Plasmids having the same and Inc group exhibited high degrees of genetic identity to each other but also to plasmids previously reported in other Core-genome analysis showed that there were 4 main clusters, each of which included strains that differed by <58 single nucleotide variants (SNVs) and that consisted of both -positive and -negative isolates. Moreover, most isolates belonging to the same cluster shared an identical core-genome sequence type (cgST). For instance, cluster 1 included 4 isolates of cgST113036, of which only 3 harbored the IncI1-pST57 -positive plasmid. The 25 isolates were also subjected to phylogenetic comparison with deposited international strains. As a result, matching isolates (isolates that had the same cgST and that differed by <8 SNVs) have been reported in the United Kingdom, the United States, France, and the Netherlands. Overall, our results suggest that some common clusters can spread between continents and can be imported into other nations after international trips. Such clusters include, in part, isolates that do not possess -harboring plasmids, indicating their tendency to acquire them from other .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AAC.01057-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508577PMC
September 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13756-020-00742-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310346PMC
June 2020

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 2020 09;75(9):2432-2441

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

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/jac/dkaa198DOI Listing
September 2020

Whole-Genome Characterization of a Shewanella algae Strain Coharboring and Genes on a Novel IncC Plasmid.

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

Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AAC.00267-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7179626PMC
April 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.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/jac/dkz470DOI Listing
March 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
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

Intestinal colonisation with multidrug-resistant Enterobacteriaceae: Screening of Swiss military deployed to Kosovo.

J Glob Antimicrob Resist 2019 12 10;19:93-95. Epub 2019 Sep 10.

Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, Bern, 3001, Switzerland. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jgar.2019.08.027DOI Listing
December 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.

View Article and Find Full Text PDF

Download full-text PDF

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

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 10;74(10):2880-2890

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

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/jac/dkz296DOI Listing
October 2019

First Clinical Case of Acquisition of DHA-1 Plasmid-Mediated AmpC in a Salmonella enterica subsp. Isolate.

Antimicrob Agents Chemother 2019 10 23;63(10). Epub 2019 Sep 23.

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

A pan-susceptible serovar Worthington isolate was detected in the stool of a man returning from Sri Lanka. Under ceftriaxone treatment, a third-generation cephalosporin (3GC)-resistant Worthington was isolated after 8 days. Molecular analyses indicated that the two isolates were identical. However, the latter strain acquired a -carrying IncFII plasmid probably from a isolate colonizing the gut. This is the first report of acquisition of plasmid-mediated resistance to 3GCs in .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AAC.00992-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6761535PMC
October 2019

Activity of 3 Commercial Bacteriophage Cocktails Against and spp. Isolates of Human Origin.

Pathog Immun 2018 29;3(1):72-81. Epub 2018 May 29.

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

Background: and spp. are 2 of the most frequent and deadly enteric bacterial pathogens recorded worldwide. In developing countries 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 () against a collection of contemporary spp. (n = 30) and spp. (n = 20) strains isolated in Switzerland. Phage susceptibility was determined by implementing the spot test.

Results: The overall susceptibility of spp. to and was 87% and 77%, respectively. With regard to spp., the overall susceptibility to and was 95% and 55%, respectively. was observed to be active against only 10% of spp. but against 95% of spp.

Conclusions: Our results seem promising, especially for the biopreparation against infections. Nevertheless, such speculation should be supported by further studies to confirm efficacy and safety of the cocktails. We also emphasize the importance of large screening analyses aimed to assess the activity of such biopreparations against contemporary multidrug-resistant strains that are emerging worldwide.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.20411/pai.v3i1.234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423893PMC
May 2018

Novel vanA-carrying plasmid in a clinical isolate of Enterococcus avium.

Int J Antimicrob Agents 2019 06 11;53(6):876-877. Epub 2019 Apr 11.

Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijantimicag.2019.04.006DOI Listing
June 2019

Characterisation of the first extended-spectrum β-lactamase (ESBL)-producing Shigella sonnei clinical isolate in Italy.

J Glob Antimicrob Resist 2019 06 12;17:58-59. Epub 2019 Mar 12.

Institute for Infectious Diseases (IFIK), University of Bern, Friedbühlstrasse 51, CH-3001 Bern, Switzerland. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jgar.2019.03.004DOI Listing
June 2019

Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life.

Front Microbiol 2019 26;10:212. Epub 2019 Feb 26.

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

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2019.00212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6399209PMC
February 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:

View Article and Find Full Text PDF

Download full-text PDF

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

Whole-Genome Sequence of the First Extended-Spectrum β-Lactamase-Producing Strain of Salmonella enterica subsp. enterica Serovar Napoli.

Microbiol Resour Announc 2018 Sep 13;7(10). Epub 2018 Sep 13.

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

We report here the whole-genome sequence of the first extended-spectrum β-lactamase (ESBL)-producing strain of Salmonella enterica subsp. enterica serovar Napoli, LC0541/17, isolated from the stools of an ambulatory pediatric patient in northern Italy. The strain was of sequence type 474 (ST474) and possessed a 90-kb IncI1 ST49 plasmid carrying the ESBL gene.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/MRA.00973-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256604PMC
September 2018

Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer.

Sci Rep 2018 12 4;8(1):17596. Epub 2018 Dec 4.

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.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-35750-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6279828PMC
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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1089/mdr.2018.0275DOI Listing
May 2019

Gut microbiota dynamics in travelers returning from India colonized with extended-spectrum cephalosporin-resistant Enterobacteriaceae: A longitudinal study.

Travel Med Infect Dis 2019 Jan - Feb;27:72-80. Epub 2018 Oct 17.

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

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tmaid.2018.10.012DOI Listing
April 2019

Monitoring of cefepime in urine by micellar electrokinetic capillary chromatography with ultraviolet detection and liquid chromatography coupled to mass spectrometry.

J Sep Sci 2018 Nov 25;41(21):4067-4074. Epub 2018 Sep 25.

Clinical Pharmacology Laboratory, Institute for Infectious Diseases, University of Bern, Bern, Switzerland.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jssc.201800763DOI Listing
November 2018

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 12 30;15:101-102. Epub 2018 Aug 30.

Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Via dell'Eremo 9/11, 23900 Lecco, Italy. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jgar.2018.08.023DOI Listing
December 2018

The EDTA-based disk-combination tests are unreliable for the detection of MCR-mediated colistin-resistance in Enterobacteriaceae.

J Microbiol Methods 2018 10 20;153:31-34. Epub 2018 Aug 20.

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

We evaluated several EDTA-based combined-disk tests to detect 25 mcr producers among 48 Enterobacteriaceae. Colistin disks plus EDTA (292/584 μg) on MH and CAMH agar were used. Results were positive if with chelator there was an inhibition zone increase ≥3 mm compared to colistin alone. All tests resulted unreliable (sensitivity ≤68%).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2018.08.008DOI Listing
October 2018