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1.
Antibiotics (Basel) ; 13(1)2024 Jan 19.
Article in English | MEDLINE | ID: mdl-38275330

ABSTRACT

The National Reference Centre for Enterococci receives an increasing number of linezolid-resistant Enterococcus isolates. Linezolid (LIN) resistance is mediated by G2576T 23S rDNA gene mutations and/or acquisition of resistance genes (cfr, optrA, poxtA). There are anecdotal reports that those resistance traits may be present in phenotypically linezolid-susceptible isolates. We aimed to determine the prevalence of LIN resistance genes and mutations in enterococci with a LIN MIC of 4 mg/L in broth microdilution (EUCAST = susceptible) isolated from German hospital patients 2019-2021. LIN MICs were additionally determined by ETEST® and VITEK2. Selected strains were subjected to LIN selective pressure and growth was monitored with increasing antibiotic concentrations. We received 195 isolates (LIN MIC = 4 mg/L). In total, 78/195 (40%) isolates contained either a putative resistance gene, the G2576T mutation, or a combination thereof. Very major error was high for broth microdilution. The ability to predict phenotypic resistance from genotypic profile was highest for G2576T-mediated resistance. Selection experiments revealed that, in particular, E. faecium isolates with resistance gene mutations or poxtA rapidly adapt to MICs above the clinical breakpoint. In conclusion, LIN resistance genes and mutations can be observed in phenotypically linezolid-susceptible enterococci. Those isolates may rapidly develop resistance under LIN selective pressure potentially leading to treatment failure.

2.
J Antimicrob Chemother ; 78(9): 2185-2191, 2023 09 05.
Article in English | MEDLINE | ID: mdl-37473450

ABSTRACT

BACKGROUND: In recent years, an increasing number of linezolid-resistant enterococci (LRE) was recognized at the German National Reference Centre (NRC) for Enterococci. National guidelines on infection prevention recommend screening for LRE in epidemiologically linked hospital settings without referring to a reliable and rapid diagnostic method. Since 2020, CHROMAgar™ provide a chromogenic linezolid screening agar, LIN-R, suitable to simultaneously screen for linezolid-resistant staphylococci and enterococci. OBJECTIVES: To assess the applicability of CHROMAgar™ LIN-R in clinical settings for detecting LRE directly from patient material and to infer prevalence rates of LRE amongst German hospital patients. METHODS: During the 3-month trial period, clinical samples were plated on CHROMAgar™ LIN-R. Antimicrobial susceptibility testing was performed using VITEK2 or disc diffusion. At the NRC, linezolid resistance was determined by broth microdilution, multiplex-PCR for cfr/optrA/poxtA and by a restriction-based assay for 23S rDNA mutations. RESULTS: The 12 participating study sites used 13 963 CHROMAgar™ LIN-R plates during the study period. Of 442 presumptive LRE, 192 were confirmed by phenotypic methods. Of these, 161 were received by the NRC and 121 (75%) were verified as LRE. Most of LR-E. faecium 53/81 (65%) exhibited a 23S rRNA gene mutation as the sole resistance-mediating mechanism, whereas optrA constituted the dominant resistance trait in LR-E. faecalis [39/40 (98%)]. Prevalence of LRE across sites was estimated as 1% (ranging 0.18%-3.7% between sites). CONCLUSIONS: CHROMAgar™ LIN-R represents a simple and efficient LRE screening tool in hospital settings. A high proportion of false-positive results demands validation of linezolid resistance by a reference method.


Subject(s)
Enterococcus faecium , Gram-Positive Bacterial Infections , Humans , Linezolid/pharmacology , Anti-Bacterial Agents/pharmacology , Prevalence , Drug Resistance, Bacterial/genetics , Enterococcus/genetics , Hospitals , Gram-Positive Bacterial Infections/epidemiology , Enterococcus faecium/genetics , Microbial Sensitivity Tests , Enterococcus faecalis
3.
Microorganisms ; 10(8)2022 Aug 09.
Article in English | MEDLINE | ID: mdl-36014021

ABSTRACT

Hospital outbreaks with vancomycin-resistant enterococci (VRE) pose a serious health threat and a challenge to infection prevention and control (IPC). We herein report on a VRE outbreak of unprecedented extent in Southern Germany (October 2015-November 2019). We used descriptive epidemiology and whole-genome sequencing (WGS) for a detailed outbreak investigation. Of the 2905 cases, 2776 (95.3%) were colonized, whereas from 127 (3.7%), VRE could be isolated from otherwise sterile body fluids or sites unlikely for enterococci colonization. Cases had a median age of 78 years (IQR 68-84) and 1339/2905 (46%) were female. The majority of isolates sequenced belonged to the clonal lineage ST80/CT1013 (212/397, 53%). Nosocomial transmission was observed as well as the constant import of VRE into the hospital. Extensive IPC measures were implemented and terminated the outbreak in late 2019, eventually. Our study shows that the combination of epidemiological and genomic analyses is indispensable for comprehensive outbreak investigations. The adaptation of IPC measures to these findings, their timely implementation, and strict execution also allow containment of large VRE outbreaks in hospital settings.

4.
Open Forum Infect Dis ; 9(5): ofac114, 2022 May.
Article in English | MEDLINE | ID: mdl-35434175

ABSTRACT

Background: In September 2018, Burkholderia cepacia complex (BCC) infections in 3 patients associated with exposure to a mouthwash solution (MWS) were reported to the Robert Koch Institute (RKI). As the product was still on the market and the scale of the outbreak was unclear, a nation-wide investigation was initiated. Methods: We aimed to investigate BCC infections/colonizations associated with MWS. Hospitals, laboratories, and public health services were informed that BCC isolates should be sent to the RKI. These isolates were typed by pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) including development of an ad hoc core genome MLST (cgMLST) scheme. Results: In total, 36 patients from 6 hospitals met the case definition, the last patient in November 2018. Twenty-nine isolates from 26 of these patients were available for typing. WGS analysis revealed 2 distinct cgMLST clusters. Cluster 1 (Burkholderia arboris) contained isolates from patients and MWS obtained from 4 hospitals and isolates provided by the manufacturer. Patient and MWS isolates from another hospital were assigned to cluster 2 (B. cepacia). Conclusions: The combined clinical, epidemiological, and microbiological investigation, including whole-genome analysis, allowed for uncovering a supraregional BCC outbreak in health care settings. Strains of B. arboris and B. cepacia were identified as contaminating species of MWS bottles and subsequent colonization and putative infection of patients in several hospitals. Despite a recall of the product by the manufacturer in August 2018, the outbreak lasted until December 2018. Reporting of contaminated medical products and recalls should be optimized to protect patients.

6.
Epidemiol Infect ; 149: e161, 2021 07 02.
Article in English | MEDLINE | ID: mdl-34210375

ABSTRACT

Two general practitioners (GPs) with SARS-CoV-2 infection provided in-person patient care to patients of their joint medical practice before and after symptom onset, up until SARS-CoV-2 laboratory confirmation. Through active contact tracing, the local public health authorities recruited the cohort of patients that had contact with either GP in their putative infectious period. In this cohort of patient contacts, we assess the frequency and determinants of SARS-CoV-2-transmission from GPs to patients. We calculated incidence rate ratios (IRR) to explore the type of contact as an explanatory variable for COVID-19 cases. Among the cohort of 83 patient contacts, we identified 22 (27%) COVID-19 cases including 17 (21%) possible, three (4%) probable and two (2%) confirmed cases. All 22 cases had contact with a GP when the GP did not wear a mask, and/or when contact was ≥10 min. Importantly, patients who had contact <10 min with a GP wearing a facemask were at reduced risk (IRR 0.21; 95% CI 0.01-0.99) of COVID-19. This outbreak investigation adds to the body of evidence in supporting current guidelines on measures at preventing the transmission of SARS-CoV-2 in an outpatient setting.


Subject(s)
COVID-19 , Infectious Disease Transmission, Professional-to-Patient , Adult , Aged, 80 and over , COVID-19/prevention & control , COVID-19/transmission , Cohort Studies , Contact Tracing , Female , General Practitioners , Germany , Humans , Male , Middle Aged , SARS-CoV-2 , Young Adult
8.
Front Microbiol ; 12: 639660, 2021.
Article in English | MEDLINE | ID: mdl-33658988

ABSTRACT

BACKGROUND: As next generation sequencing (NGS) technologies have experienced a rapid development over the last decade, the investigation of the bacterial genetic architecture reveals a high potential to dissect causal loci of antibiotic resistance phenotypes. Although genome-wide association studies (GWAS) have been successfully applied for investigating the basis of resistance traits, complex resistance phenotypes have been omitted so far. For S. aureus this especially refers to antibiotics of last resort like daptomycin and ceftaroline. Therefore, we aimed to perform GWAS for the identification of genetic variants associated with DAP and CPT resistance in clinical S. aureus isolates. MATERIALS/METHODS: To conduct microbial GWAS, we selected cases and controls according to their clonal background, date of isolation, and geographical origin. Association testing was performed with PLINK and SEER analysis. By using in silico analysis, we also searched for rare genetic variants in candidate loci that have previously been described to be involved in the development of corresponding resistance phenotypes. RESULTS: GWAS revealed MprF P314L and L826F to be significantly associated with DAP resistance. These mutations were found to be homogenously distributed among clonal lineages suggesting convergent evolution. Additionally, rare and yet undescribed single nucleotide polymorphisms could be identified within mprF and putative candidate genes. Finally, we could show that each DAP resistant isolate exhibited at least one amino acid substitution within the open reading frame of mprF. Due to the presence of strong population stratification, no genetic variants could be associated with CPT resistance. However, the investigation of the staphylococcal cassette chromosome mec (SCCmec) revealed various mecA SNPs to be putatively linked with CPT resistance. Additionally, some CPT resistant isolates revealed no mecA mutations, supporting the hypothesis that further and still unknown resistance determinants are crucial for the development of CPT resistance in S. aureus. CONCLUSION: We hereby confirmed the potential of GWAS to identify genetic variants that are associated with antibiotic resistance traits in S. aureus. However, precautions need to be taken to prevent the detection of spurious associations. In addition, the implementation of different approaches is still essential to detect multiple forms of variations and mutations that occur with a low frequency.

9.
Antonie Van Leeuwenhoek ; 114(3): 235-251, 2021 Mar.
Article in English | MEDLINE | ID: mdl-33591460

ABSTRACT

The Gram-stain-negative, oxidase negative, catalase positive strain KPC-SM-21T, isolated from a digestate of a storage tank of a mesophilic German biogas plant, was investigated by a polyphasic taxonomic approach. Phylogenetic identification based on the nearly full-length 16S rRNA gene revealed highest gene sequence similarity to Acinetobacter baumannii ATCC 19606T (97.0%). Phylogenetic trees calculated based on partial rpoB and gyrB gene sequences showed a distinct clustering of strain KPC-SM-21T with Acinetobacter gerneri DSM 14967T = CIP 107464T and not with A. baumannii, which was also supported in the five housekeeping genes multilocus sequence analysis based phylogeny. Average nucleotide identity values between whole genome sequences of strain KPC-SM-21T and next related type strains supported the novel species status. The DNA G + C content of strain KPC-SM-21T was 37.7 mol%. Whole-cell MALDI-TOF MS analysis supported the distinctness of the strain to type strains of next related Acinetobacter species. Predominant fatty acids were C18:1 ω9c (44.2%), C16:0 (21.7%) and a summed feature comprising C16:1 ω7c and/or iso-C15:0 2-OH (15.3%). Based on the obtained genotypic, phenotypic and chemotaxonomic data we concluded that strain KPC-SM-21T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter stercoris sp. nov. is proposed. The type strain is KPC-SM-21T (= DSM 102168T = LMG 29413T).


Subject(s)
Acinetobacter , Biofuels , Acinetobacter/genetics , Anaerobiosis , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/analysis , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
10.
Emerg Infect Dis ; 27(4)2021 04.
Article in English | MEDLINE | ID: mdl-33600301

ABSTRACT

We determined secondary attack rates (SAR) among close contacts of 59 asymptomatic and symptomatic coronavirus disease case-patients by presymptomatic and symptomatic exposure. We observed no transmission from asymptomatic case-patients and highest SAR through presymptomatic exposure. Rapid quarantine of close contacts with or without symptoms is needed to prevent presymptomatic transmission.


Subject(s)
COVID-19 , Contact Tracing , Disease Transmission, Infectious , Quarantine , SARS-CoV-2/isolation & purification , Adult , Asymptomatic Diseases/epidemiology , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/transmission , Contact Tracing/methods , Contact Tracing/statistics & numerical data , Disease Transmission, Infectious/prevention & control , Disease Transmission, Infectious/statistics & numerical data , Female , Germany/epidemiology , Humans , Incidence , Male , Quarantine/methods , Quarantine/organization & administration , Risk Adjustment , Symptom Assessment/methods , Symptom Assessment/statistics & numerical data
11.
Drug Resist Updat ; 53: 100732, 2020 12.
Article in English | MEDLINE | ID: mdl-33189998

ABSTRACT

Enterococci are commensals of the intestinal tract of many animals and humans. Of the various known and still unnamed new enterococcal species, only isolates of Enterococcus faecium and Enterococcus faecalis have received increased medical and public health attention. According to textbook knowledge, the majority of infections are caused by E. faecalis. In recent decades, the number of enterococcal infections has increased, with the increase being exclusively associated with a rising number of nosocomial E. faecium infections. This increase has been accompanied by the dissemination of certain hospital-acquired strain variants and an alarming progress in the development of antibiotic resistance namely vancomycin resistance. With this review we focus on a description of the specific situation of vancomycin resistance among clinical E. faecium isolates in Germany over the past 30 years. The present review describes three VRE episodes in Germany, each of which is framed by the beginning and end of the respective decade. The first episode is specified by the first appearance of VRE in 1990 and a country-wide spread of specific vanA-type VRE strains (ST117/CT24) until the late 1990s. The second decade was initially marked by regional clusters and VRE outbreaks in hospitals in South-Western Germany in 2004 and 2005, mainly caused by vanA-type VRE of ST203. Against the background of a certain "basic level" of VRE prevalence throughout Germany, an early shift from the vanA genotype to the vanB genotype in clinical isolates already occurred at the end of the 2000s without much notice. With the beginning of the third decade in 2010, VRE rates in Germany have permanently increased, first in some federal states and soon after country-wide. Besides an increase in VRE prevalence, this decade was marked by a sharp increase in vanB-type resistance and a dominance of a few, novel strain variants like ST192 and later on ST117 (CT71, CT469) and ST80 (CT1065). The largest VRE outbreak, which involved about 2,900 patients and lasted over three years, was caused by a novel and until that time, unknown strain type of ST80/CT1013 (vanB). Across all periods, VRE outbreaks were mainly oligoclonal and strain types varied over space (hospital wards) and time. The spread of VRE strains obviously respects political borders; for instance, both vancomycin-variable enterococci which were highly prevalent in Denmark and ST796 VRE which successfully disseminated in Australia and Switzerland, were still completely absent among German hospital patients, until to date.


Subject(s)
Anti-Bacterial Agents/pharmacology , Cross Infection/drug therapy , Enterococcus faecium/isolation & purification , Gram-Positive Bacterial Infections/drug therapy , Vancomycin-Resistant Enterococci/isolation & purification , Anti-Bacterial Agents/therapeutic use , Bacterial Proteins/genetics , Carbon-Oxygen Ligases/genetics , Cross Infection/diagnosis , Cross Infection/epidemiology , Cross Infection/microbiology , Enterococcus faecium/drug effects , Enterococcus faecium/genetics , Germany/epidemiology , Gram-Positive Bacterial Infections/diagnosis , Gram-Positive Bacterial Infections/epidemiology , Gram-Positive Bacterial Infections/microbiology , Humans , Prevalence , Vancomycin Resistance/genetics , Vancomycin-Resistant Enterococci/drug effects , Vancomycin-Resistant Enterococci/genetics
12.
J Antimicrob Chemother ; 75(12): 3491-3500, 2020 12 01.
Article in English | MEDLINE | ID: mdl-32780112

ABSTRACT

OBJECTIVES: WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. METHODS: The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. RESULTS: Genotype-phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype-phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. CONCLUSIONS: WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.


Subject(s)
Anti-Bacterial Agents , Drug Resistance, Bacterial , Animals , Anti-Bacterial Agents/pharmacology , Genotype , Humans , Microbial Sensitivity Tests , Phenotype
13.
PLoS One ; 15(6): e0235160, 2020.
Article in English | MEDLINE | ID: mdl-32579600

ABSTRACT

Vancomycin-resistant E. faecium (VRE) are an important cause of nosocomial infections, which are rapidly transmitted in hospitals. To identify possible transmission routes, we applied combined genomics and contact-network modeling to retrospectively evaluate routine VRE screening data generated by the infection control program of a hemato-oncology unit. Over 1 year, a total of 111 VRE isolates from 111 patients were collected by anal swabs in a tertiary care hospital in Southern Germany. All isolated VRE were whole-genome sequenced, followed by different in-depth bioinformatics analyses including genotyping and determination of phylogenetic relations, aiming to evaluate a standardized workflow. Patient movement data were used to overlay sequencing data to infer transmission events and strain dynamics over time. A predominant clone harboring vanB and exhibiting genotype ST117/CT469 (n = 67) was identified. Our comprehensive combined analyses suggested intra-hospital spread, especially of clone ST117/CT469, despite of extensive screening, single room placement, and contact isolation. A new interactive tool to visualize these complex data was designed. Furthermore, a patient-contact network-modeling approach was developed, which indicates both the periodic import of the clone into the hospital and its spread within the hospital due to patient movements. The analyzed spread of VRE was most likely due to placement of patients in the same room prior to positivity of screening. We successfully demonstrated the added value for this combined strategy to extract well-founded knowledge from interdisciplinary data sources. The combination of patient-contact modeling and high-resolution typing unraveled the transmission dynamics within the hospital department and, additionally, a constant VRE influx over time.


Subject(s)
Contact Tracing/methods , Cross Infection/transmission , Gram-Positive Bacterial Infections/transmission , High-Throughput Nucleotide Sequencing/methods , Population Surveillance/methods , Tertiary Care Centers/statistics & numerical data , Algorithms , Anti-Bacterial Agents/pharmacology , Cross Infection/microbiology , Cross Infection/prevention & control , Enterococcus faecium/classification , Enterococcus faecium/drug effects , Enterococcus faecium/genetics , Germany/epidemiology , Gram-Positive Bacterial Infections/epidemiology , Gram-Positive Bacterial Infections/microbiology , Humans , Infection Control/methods , Models, Theoretical , Phylogeny , Population Dynamics , Retrospective Studies , Vancomycin/pharmacology , Vancomycin-Resistant Enterococci/drug effects , Vancomycin-Resistant Enterococci/genetics , Vancomycin-Resistant Enterococci/physiology
14.
Microb Drug Resist ; 26(6): 576-582, 2020 Jun.
Article in English | MEDLINE | ID: mdl-31895641

ABSTRACT

Tigecycline-resistant enterococci are only rarely detected worldwide. In 2017, the National Reference Centre for Staphylococci and Enterococci noticed a nosocomial cluster of tigecycline- and vancomycin-resistant Enterococcus faecium (TVRE) in a hospital of tertiary care in Northern Germany. Nineteen E. faecium isolates were analyzed by means of antimicrobial susceptibility testing and pulsed-field gel electrophoresis. A subset of isolates was subjected to whole-genome sequencing. The genetic basis of tigecycline resistance was assessed by ResFinder and by comparative analyses to known tetracycline and tigecycline resistance genes. Phylogenetic investigations revealed the clustering of 11 TVRE that exhibited genotype ST117/CT1489. Two tigecycline-susceptible isolates were unrelated. Characterization of the genetic determinant putatively responsible for tigecycline resistance revealed two chromosomal changes in the TVRE population: (1) a deletion within the ribosomal protein gene rpsJ and (2) a serine insertion in and removal of transcriptional regulation of the ribosomal protection protein Tet(M). We here report the first nosocomial cluster of TVRE in a German hospital and disclosed the resistance mechanism that was most likely causative for tigecycline insusceptibility. Clonal spread of TVRE isolates can be assumed because all isolates were highly related and harbored identical chromosomal alterations associated with tigecycline resistance.


Subject(s)
Anti-Bacterial Agents/pharmacology , Enterococcus faecium/drug effects , Enterococcus faecium/genetics , Tigecycline/pharmacology , Vancomycin/pharmacology , Cross Infection/microbiology , Drug Resistance, Multiple, Bacterial/drug effects , Drug Resistance, Multiple, Bacterial/genetics , Genes, Bacterial/genetics , Genotype , Humans , Microbial Sensitivity Tests , Vancomycin-Resistant Enterococci/drug effects , Vancomycin-Resistant Enterococci/genetics
15.
BMC Infect Dis ; 19(1): 1078, 2019 Dec 23.
Article in English | MEDLINE | ID: mdl-31870418

ABSTRACT

BACKGROUND: Linezolid is an alternative treatment option for infections with multidrug-resistant Gram-positive bacteria including vancomycin-resistant enterococci. Some countries report an increasing number of isolates with resistance to linezolid. The recent publication of the Commission for Hospital Hygiene in Germany on enterococci/VRE recommends screening for linezolid-resistant enterococci (LRE). However, a suitable selective medium or a genetic test is not available. Our aim was to establish a selective screening agar for LRE detection and validate its application with a comprehensive collection of clinical LRE and linezolid-susceptible enterococci. METHODS: We decided to combine the selective power of an enterococcal screening agar with a supplementation of linezolid. Several rounds of analyses with reference, control and test strains and under varying linezolid concentrations of a wider and a smaller range were investigated and assessed. The collection of linezolid-resistant enterococcal control strains included isolates with different resistance mechanisms (23S rDNA mutations, cfr(B), optrA, poxtA). Finally, we validated our LRE screening agar with 400 samples sent to our National Reference Centre in 2019. RESULTS: Several rounds of pre-tests and confirmatory analyses favored Enterococcosel® Agar supplemented with a concentration of 2 mg/L linezolid. A 48 h incubation period was essential for accurate identification of LRE strains. Performance of the LRE screening agar revealed a sensitivity of 96.6% and a specificity of 94.4%. CONCLUSIONS: Here we describe preparation of a suitable screening agar and a procedure to identify LRE isolates with high accuracy.


Subject(s)
Anti-Bacterial Agents/pharmacology , Drug Resistance, Multiple, Bacterial , Gram-Positive Bacterial Infections/drug therapy , Linezolid/pharmacology , Vancomycin-Resistant Enterococci/isolation & purification , Agar , Feasibility Studies , Germany , Gram-Positive Bacterial Infections/microbiology , Humans , Mass Screening , Microbial Sensitivity Tests , Vancomycin-Resistant Enterococci/drug effects , Vancomycin-Resistant Enterococci/genetics
16.
J Antimicrob Chemother ; 74(10): 2926-2929, 2019 10 01.
Article in English | MEDLINE | ID: mdl-31335935

ABSTRACT

OBJECTIVES: In 2018, EUCAST issued a warning regarding unreliable results of gradient strip tests for confirming vancomycin resistance in enterococci. We compared the performance of various diagnostic standard and confirmatory tests to identify and determine vanB-type vancomycin resistance. METHODS: We analysed a collection of vanB-positive Enterococcus faecium isolates (n = 68) with low vancomycin MICs and compared the performance of VITEK® 2 (bioMérieux), broth microdilution and three gradient strip tests from different providers (Oxoid, Liofilchem and bioMérieux). For the latter we compared the standard procedure with a protocol with increased inoculum, a rich agar medium and a longer incubation time ('macromethod'). RESULTS: The sensitivity of VITEK® 2 was 81% compared with 72% for broth microdilution and 61%-63% for the three gradient strip tests using standard conditions. The macromethod substantially improved the performance of all strip tests resulting in a sensitivity of 89%-96% after 48 h of incubation. CONCLUSIONS: We recommend that EUCAST changes the present warning against the general use of MIC strips. When MIC strips are used to either exclude or confirm suspected vancomycin resistance in E. faecium, and a PCR is not available, the macromethod should be employed. For clinically relevant enterococci, where a rapid therapeutic decision is needed, a molecular test (e.g. PCR) should be favoured in order to save time and to further increase sensitivity.


Subject(s)
Enterococcus faecium/isolation & purification , Microbial Sensitivity Tests/methods , Vancomycin-Resistant Enterococci/isolation & purification , Anti-Bacterial Agents/pharmacology , Bacterial Proteins/genetics , Drug Resistance, Bacterial , Enterococcus faecium/genetics , Gram-Positive Bacterial Infections/microbiology , Humans , Sensitivity and Specificity , Vancomycin/pharmacology , Vancomycin-Resistant Enterococci/genetics
17.
J Microbiol Methods ; 160: 101-103, 2019 05.
Article in English | MEDLINE | ID: mdl-30940534

ABSTRACT

Linezolid-resistant enterococcus spp. are increasingly recognized by diagnostic laboratories. Resistance can be mediated by the expression of cfr, optrA or poxtA. We developed a multiplex-PCR to simultaneously detect all three genes. The PCR is suitable for microbiological diagnostics in order to restrict further spread of resistances in enterococci.


Subject(s)
Drug Resistance, Bacterial/genetics , Enterococcus faecalis , Enterococcus faecium , Multiplex Polymerase Chain Reaction/methods , DNA, Bacterial/genetics , Enterococcus faecalis/genetics , Enterococcus faecalis/isolation & purification , Enterococcus faecium/genetics , Enterococcus faecium/isolation & purification , Genes, Bacterial/genetics , Linezolid/therapeutic use , Plasmids/genetics
18.
J Clin Microbiol ; 57(3)2019 03.
Article in English | MEDLINE | ID: mdl-30651394

ABSTRACT

Among enterococci, Enterococcus faecalis occurs ubiquitously, with the highest incidence of human and animal infections. The high genetic plasticity of E. faecalis complicates both molecular investigations and phylogenetic analyses. Whole-genome sequencing (WGS) enables unraveling of epidemiological linkages and putative transmission events between humans, animals, and food. Core genome multilocus sequence typing (cgMLST) aims to combine the discriminatory power of classical multilocus sequence typing (MLST) with the extensive genetic data obtained by WGS. By sequencing a representative collection of 146 E. faecalis strains isolated from hospital outbreaks, food, animals, and colonization of healthy human individuals, we established a novel cgMLST scheme with 1,972 gene targets within the Ridom SeqSphere+ software. To test the E. faecalis cgMLST scheme and assess the typing performance, different collections comprising environmental and bacteremia isolates, as well as all publicly available genome sequences from the NCBI and SRA databases, were analyzed. In more than 98.6% of the tested genomes, >95% good cgMLST target genes were detected (mean, 99.2% target genes). Our genotyping results not only corroborate the known epidemiological background of the isolates but exceed previous typing resolution. In conclusion, we have created a powerful typing scheme, hence providing an international standardized nomenclature that is suitable for surveillance approaches in various sectors, linking public health, veterinary public health, and food safety in a true One Health fashion.


Subject(s)
Bacterial Typing Techniques/methods , Enterococcus faecalis/genetics , Genome, Bacterial/genetics , Animals , Bacterial Proteins/genetics , Enterococcus faecalis/classification , Enterococcus faecalis/isolation & purification , Environmental Microbiology , Genotype , Gram-Positive Bacterial Infections/epidemiology , Gram-Positive Bacterial Infections/microbiology , Humans , Molecular Epidemiology , Multilocus Sequence Typing , One Health , Phylogeny , Polymorphism, Single Nucleotide
19.
Drug Resist Updat ; 40: 25-39, 2018 09.
Article in English | MEDLINE | ID: mdl-30447411

ABSTRACT

Vancomycin-resistant enterococci (VRE) are important nosocomial pathogens. Invasive VRE infections are difficult to treat since common therapeutic options including ampicillin and glycopeptides often fail. In vitro, most VRE remain susceptible to last-resort antibiotics such as linezolid, tigecycline and daptomycin. However, neither tigecycline nor linezolid act in a bactericidal manner, and daptomycin has proven activity only at high dosages licensed for treating enterococcal endocarditis. Despite these pharmacological and therapeutic limitations, reports on resistance to these last-resort drugs in VRE, and enterococci in general, have increased in recent years. In this review, we briefly recapitulate the current knowledge on the mode of action as well as the known and novel mechanisms of resistance and describe surveillance data on resistance to linezolid, tigecycline and daptomycin in enterococci. In addition, we also suggest a common nomenclature for designating enterococci and VRE with resistances to these important last-resort antibiotics.


Subject(s)
Anti-Bacterial Agents/pharmacology , Daptomycin/pharmacology , Linezolid/pharmacology , Tigecycline/pharmacology , Vancomycin Resistance/drug effects , Vancomycin-Resistant Enterococci/drug effects , Anti-Bacterial Agents/therapeutic use , Bacterial Proteins/genetics , Carbon-Oxygen Ligases/genetics , Daptomycin/therapeutic use , Genotype , Gram-Positive Bacterial Infections/drug therapy , Humans , Linezolid/therapeutic use , Microbial Sensitivity Tests , Mutation , Tigecycline/therapeutic use , Vancomycin Resistance/genetics , Vancomycin-Resistant Enterococci/genetics
20.
Int J Antimicrob Agents ; 52(6): 819-827, 2018 Dec.
Article in English | MEDLINE | ID: mdl-30236952

ABSTRACT

The number of linezolid-resistant Enterococcus spp. isolates received by the National Reference Centre for Staphylococci and Enterococci in Germany has been increasing since 2011. Although the majority are E. faecium, clinical linezolid-resistant E. faecalis have also been isolated. With respect to the newly discovered linezolid resistance protein OptrA, the authors conducted a retrospective polymerase chain reaction screening of 698 linezolid-resistant enterococcus clinical isolates. That yielded 43 optrA-positive strains, of which a subset was analysed by whole-genome sequencing in order to infer linezolid resistance-associated mechanisms and phylogenetic relatedness, and to disclose optrA genetic environments. Multiple optrA variants were detected. The originally described variant from China (optrAWT) was the only variant shared between the two Enterococcus spp.; however, distinct optrAWT loci were detected for E. faecium and E. faecalis. Generally, optrA localized to a plethora of genetic backgrounds that differed even for identical optrA variants. This suggests transmission of a mobile genetic element harbouring the resistance locus. Additionally, identical optrA variants detected on presumably identical plasmids, that were present in unrelated strains, indicates dissemination of the entire optrA-containing plasmid. In accordance, in vitro conjugation experiments verified transfer of optrA plasmids between enterococci of the same and of different species. In conclusion, multiple optrA variants located on distinct plasmids and mobile genetic elements with the potential for conjugative transfer are supposedly causative for the emergence of optrA-positive enterococci. Hence, rapid dissemination of the resistance determinant under selective pressure imposed by extensive use of last-resort antibiotics in clinical settings could be expected.


Subject(s)
Anti-Infective Agents/pharmacology , Drug Resistance, Bacterial , Enterococcus faecalis/drug effects , Enterococcus faecium/drug effects , Genes, Bacterial , Gram-Positive Bacterial Infections/microbiology , Oxazolidinones/pharmacology , Chloramphenicol/pharmacology , Conjugation, Genetic , Enterococcus faecalis/classification , Enterococcus faecalis/genetics , Enterococcus faecalis/isolation & purification , Enterococcus faecium/classification , Enterococcus faecium/genetics , Enterococcus faecium/isolation & purification , Gene Order , Gene Transfer, Horizontal , Genetic Variation , Germany , Humans , Interspersed Repetitive Sequences , Polymerase Chain Reaction , Retrospective Studies , Whole Genome Sequencing
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