High frequency of acquired virulence factors in carbapenemase-producing Klebsiella pneumoniae isolates from a large German university hospital, 2013-2021.

Carbapenemase-producing Klebsiella pneumoniae (CP-Kp) isolates are a public health concern as they can cause severe hospital-acquired infections that are difficult to treat. It has recently been shown that CP-Kp can take up virulence factors from hypervirulent K. pneumoniae lineages. In this study, 109 clinical CP-Kp isolates from the University Hospital Cologne were examined for the presence of acquired virulence factors using whole-genome sequencing and phenotypic tests, and results were linked to clinical data. The virulence factor iuc was present in 18/109 of the CP-Kp isolates. Other acquired virulence factors, such as ybt, cbt, iro, rmpA/rmpA2, peg-344, and hypervirulence-associated capsule types were detected in various combinations among these isolates. The iuc-positive isolates produced OXA-232 (n = 7), OXA-48 (n = 6), OXA-48+NDM (n = 3), NDM, and KPC (each n = 1), and 7/18 isolates were resistant to ceftazidime-avibactam, colistin, and/or cefiderocol. Four isolates carried hybrid plasmids that harbored acquired virulence factors alongside the carbapenemase genes blaNDM-1/5 or blaOXA-48. In 15/18 patients, iuc-positive CP-Kp were isolated from a clinically manifest infection site. Among these, four patients had osteomyelitis, and four patients died from pneumonia with OXA-232-producing ST231 isolates, three of them as part of an outbreak. In conclusion, acquired virulence factors are frequently detected in various combinations in carbapenemase-producing K. pneumoniae isolates in Germany, warranting continuous monitoring of infections caused by these strains.

Occurrence of antibiotic-resistant bacteria in the sea surface microlayer of coastal waters in the southern North Sea.

The emergence of antibiotic-resistant bacteria in coastal waters is a global health problem posing potential risks to the health of humans who depend on coastal resources. Monitoring and increased efforts are needed to maintain the health of marine ecosystems. The sea surface microlayer (SML) is poorly studied for antibiotic resistance of the inhabiting bacteria. Therefore, we examined the antibiotic resistance patterns of 41 bacterial strains isolated from the SML in a harbor in the southern North Sea. The strains are affiliated with 17 genera typically found in the marine environment. Using the disc diffusion assay, we found extensive resistance, particularly to gentamycin, kanamycin, nalidixic acid, penicillin, sulfadimidine, and streptomycin. A broth microdilution assay showed high minimum inhibitory concentrations (MICs) for most isolates for amikacin, aztreonam, ceftazidime, cefepime, minocycline, and tobramycin. Genome analysis of three strains affiliated with the genera Pseudoseohaeicola, Nereida, and Vibrio, all showing a highly resistant phenotype, revealed the presence of 57, 42, and 90 genes, respectively, associated with antibiotic resistance. Over 50 % of these genes are multidrug efflux pumps. Our study shows that the SML in anthropogenic-influenced coastal regions harbors a wide diversity of antibiotic-resistant bacteria equipped with a broad range of multidrug efflux pumps.

Emergence of OXA-48-like producing Citrobacter species, Germany, 2011 to 2022.

BackgroundCarbapenemase-producing Enterobacterales are a public health threat worldwide and OXA-48 is the most prevalent carbapenemase in Germany and western Europe. However, the molecular epidemiology of OXA-48 in species other than Escherichia coli and Klebsiella pneumoniae remains poorly understood.AimTo analyse the molecular epidemiology of OXA-48 and OXA-48-like carbapenemases in Citrobacter species (spp.) in Germany between 2011 and 2022.MethodsData of 26,822 Enterobacterales isolates sent to the National Reference Centre (NRC) for Gram-negative bacteria were evaluated. Ninety-one Citrobacter isolates from 40 German hospitals harbouring bla OXA-48/OXA-48­like were analysed by whole genome sequencing and conjugation experiments.ResultsThe frequency of OXA-48 in Citrobacter freundii (CF) has increased steadily since 2011 and is now the most prevalent carbapenemase in this species in Germany. Among 91 in-depth analysed Citrobacter spp. isolates, CF (n = 73) and C. koseri (n = 8) were the most common species and OXA-48 was the most common variant (n = 77), followed by OXA-162 (n = 11) and OXA­181 (n = 3). Forty percent of the isolates belonged to only two sequence types (ST19 and ST22), while most other STs were singletons. The plasmids harbouring bla OXA­48 and bla OXA-162 belonged to the plasmid types IncL (n = 85) or IncF (n = 3), and plasmids harbouring bla OXA­181 to IncX3 (n = 3). Three IncL plasmid clusters (57/85 IncL plasmids) were identified, which were highly transferable in contrast to sporadic plasmids.ConclusionIn CF in Germany, OXA-48 is the predominant carbapenemase. Dissemination is likely due to distinct highly transmissible plasmids harbouring bla OXA­48 or bla OXA-48-like and the spread of the high-risk clonal lineages ST19 and ST22.

CHROMAgar™ LIN-R as an efficient screening tool to assess the prevalence of linezolid-resistant enterococci in German hospital patients-a multicentre study approach, 2021-2022.

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.

A side-by-side comparison of the new VITEK MS PRIME and the MALDI Biotyper sirius in the clinical microbiology laboratory.

PURPOSE: This study aims to evaluate the performance of two latest generation matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems in routine laboratory settings, focusing on turnaround time (TAT), time to results (TTR), hands-on time, and identification rate. METHODS: We conducted a time and motion study on three workflow scenarios to simulate different laboratory settings. Overall, 618 bacterial isolates from a tertiary hospital's laboratory were processed using the VITEK MS PRIME (bioMérieux) and the MALDI Biotyper sirius (Bruker Daltonics) and their corresponding databases VITEK IVD Database 3.2 and MBT reference library 12. RESULTS: The target preparation process showed no significant difference in TAT, but the Biotyper workflow had a shorter hands-on time by 3 to 6 min. In the measurement process, TTR was three to five times shorter for the Biotyper sirius while hands-on time was significantly shorter for VITEK MS PRIME (approximately 1.5 min per target). The identification rate without retesting was 97.9% for VITEK MS PRIME and 98.9% for Biotyper sirius. Both systems achieved 100% agreement at genus and 96.2% at species level. CONCLUSION: Both systems exhibited excellent identification rates for routine bacterial isolates. Due to its high speed, the Biotyper sirius is suited for laboratories with high sample throughput and a workflow designed for processing larger batches. The VITEK MS PRIME, with its "load and go" system accommodating up to 16 targets, reduces hands-on time, making it a reasonable choice for laboratories with fewer identifications overall but a higher number of targets and a workflow designed for parallel processing on different workstations.

Usefulness of screening for Candida auris colonisation in international patients admitted to a large university hospital.

INTRODUCTION: Candida auris is an emerging pathogen in health care-associated infections. In contrast to many other countries with rising numbers of C. auris, only seven cases have been reported in Germany from 2015 to 2017, mostly from patients who received prior medical treatment abroad. We therefore established a mandatory screening for C. auris colonisation at our tertiary care centre for all patients who were admitted as international patients or previously hospitalised in a foreign country within the past 6 months. METHODS: Colonisation of patients was assessed using a previously established screening protocol for multidrug resistant bacteria. Since 2017, all screening samples were additionally analysed for C. auris using CHROMagar Candida (CHROMagar, Paris, France). Yeast isolates were identified using matrix-assisted laser ionisation time-of-flight (MALDI TOF), except for C. albicans (identified by the typical green colour on chromogenic agar). Data were analysed retrospectively. RESULTS: Our study cohort included 655 patients and an overall number of 1399 samples. Fifty-three patients were colonised with Candida species (C. albicans, n = 37; C. glabrata, n = 14; others n = 9). No case of C. auris was detected. Candida spp. were mainly detected from respiratory samples (5.4% positive) and gastrointestinal specimen (5.2%). Laboratory costs were 14,689 € and analyses resulted in 98.7 h of additional technician's work. CONCLUSION: No colonisation with C. auris was detected among patients with previous hospitalisation abroad. Universal C. auris screening of patients with any contact to foreign health care does not seem to be cost-effective in our setting and more targeted screening strategies have to be developed.

Emergence of Tn1999.7, a New Transposon in blaOXA-48-Harboring Plasmids Associated with Increased Plasmid Stability.

OXA-48 is the most common carbapenemase in Enterobacterales in Germany and many other European countries. Depending on the genomic location of blaOXA-48, OXA-48-producing isolates vary in phenotype and intra- and interspecies transferability of blaOXA-48. In most bacterial isolates, blaOXA-48 is located on one of seven variants of Tn1999 (Tn1999.1 to Tn1999.6 and invTn1999.2). Here, a novel Tn1999 variant, Tn1999.7, is described, which was identified in 11 clinical isolates from 2016 to 2020. Tn1999.7 differs from Tn1999.1 by the insertion of the 8,349-bp Tn3 family transposon Tn7442 between the lysR gene and blaOXA-48 open reading frame. Tn7442 carries genes coding for a restriction endonuclease and a DNA methyltransferase as cargo, forming a type III restriction modification system. Tn1999.7 was carried on an ~71-kb IncL plasmid in 9/11 isolates. In one isolate, Tn1999.7 was situated on an ~76-kb plasmid, harboring an additional insertion sequence in the plasmid backbone. In one isolate, the plasmid size is only ~63 kb due to a deletion adjacent to Tn7442 that extends into the plasmid backbone. Mean conjugation rates of the Tn1999.7-harboring plasmids in J53 ranged from 4.47 × 10-5 to 2.03 × 10-2, similar to conjugation rates of other pOXA-48-type IncL plasmids. The stability of plasmids with Tn1999.7 was significantly higher than that of a Tn1999.2-harboring plasmid in vitro. This increase in stability could be related to the insertion of a restriction-modification system, which can promote postsegregational killing. The increased plasmid stability associated with Tn1999.7 could contribute to the further spread of OXA-48.

In Vitro Activity of Nitroxoline in Antifungal-Resistant Candida Species Isolated from the Urinary Tract.

Infections by drug-resistant fungi are increasingly reported worldwide; however, only few novel antifungals are being developed. The old antimicrobial nitroxoline is currently repurposed for oral treatment of bacterial urinary tract infections (UTI). Previously, antifungal activity has been demonstrated and in contrast to many antifungals nitroxoline reaches high urinary concentrations. In this study, the activity of nitroxoline was assessed in vitro in a collection of yeasts from the German National Reference Centre for Invasive Fungal Infections. Susceptibility was determined by broth microdilution (BMD) and disk diffusion (DD). The collection comprised 45 Candida isolates originating from the urinary tract. MICs of amphotericin, anidulafungin and azoles were analyzed using EUCAST BMD. Among the collection isolates, resistance to antifungals was common, e.g., for fluconazole the MIC50/90 was 16/>64 mg/L; in contrast MIC50/90 of nitroxoline was 2/2 mg/L (MIC range 0.25-4 mg/L), which is at least two dilutions below the EUCAST breakpoint for uncomplicated UTI defined for E. coli (susceptible ≤ 16mg/L). Activity of nitroxoline was high irrespective of resistance to other agents. As BMD is labor-intensive, DD was investigated as an alternative method using three different agars. Nitroxoline disks produced large inhibition zones on all agars (≥19mm), but the correlation of MICs and zone diameters was low, with the highest correlation recorded for the CLSI recommended agar for antifungal DD (Pearson's r = -0,52). In conclusion, isolates of different Candida species are highly susceptible to nitroxoline, which could be a promising antimicrobial to treat candiduria caused by multidrug resistant yeasts.

Bloodstream Infections Caused by Magnusiomyces capitatus and Magnusiomyces clavatus: Epidemiological, Clinical, and Microbiological Features of Two Emerging Yeast Species.

Magnusiomyces clavatus and Magnusiomyces capitatus are emerging yeasts with intrinsic resistance to many commonly used antifungal agents. Identification is difficult, and determination of susceptibility patterns with commercial and reference methods is equally challenging. For this reason, few data on invasive infections by Magnusiomyces spp. are available. Our objectives were to determine the epidemiology and susceptibility of Magnusiomyces isolates from bloodstream infections (BSI) isolated in Germany and Austria from 2001 to 2020. In seven institutions, a total of 34 Magnusiomyces BSI were identified. Identification was done by internal transcribed spacer (ITS) sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Antifungal susceptibility was determined by EUCAST broth microdilution and gradient tests. Of the 34 isolates, M. clavatus was more common (n = 24) than M. capitatus (n = 10). BSI by Magnusiomyces spp. were more common in men (62%) and mostly occurred in patients with hemato-oncological malignancies (79%). The highest in vitro antifungal activity against M. clavatus/M. capitatus was observed for voriconazole (MIC50, 0.03/0.125 mg/L), followed by posaconazole (MIC50, 0.125/0.25 mg/L). M. clavatus isolates showed overall lower MICs than M. capitatus. With the exception of amphotericin B, low essential agreement between gradient test and microdilution was recorded for all antifungals (0 to 70%). Both species showed distinct morphologic traits on ChromAgar Orientation medium and Columbia blood agar, which can be used for differentiation if no MALDI-TOF MS or molecular identification is available. In conclusion, most BSI were caused by M. clavatus. The lowest MICs were recorded for voriconazole. Gradient tests demonstrated unacceptably low agreement and should preferably not be used for susceptibility testing of Magnusiomyces spp.

ß-1,3-d-Glucan and Galactomannan as Biomarkers for the Detection of Invasive Geotrichum and Magnusiomyces Infections: a Retrospective Evaluation.

Magnusiomyces and Geotrichum species are ascomycetous yeasts that can cause potentially life-threatening invasive fungal infections commonly referred to as geotrichosis. In this study, we aimed to estimate the incidence and mortality of these infections in a German tertiary care center. Furthermore, we evaluated the suitability of the fungal biomarkers galactomannan (GM) and ß-1,3-d-glucan (BDG), which are both recommended as surrogate markers for Magnusiomyces capitatus infection by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) and the European Confederation of Medical Mycology (ECMM) joint clinical guidelines for the diagnosis and management of rare invasive yeast infections for detection of invasive geotrichosis. Cases meeting the inclusion criteria for invasive Magnusiomyces/Geotrichum infection were retrospectively identified. Serum samples and culture supernatants were analyzed with two commercially available fungal antigen tests (Platelia Aspergillus Ag EIA and Wako ß-glucan test). For a control cohort, outpatient samples sent for lues testing were included. Thirty-eight cases of Magnusiomyces/Geotrichum infection were identified over an 11-year observation period. In the majority of cases, the fungus was isolated from intra-abdominal specimens of patients with a history of abdominal surgery/procedures (n = 32). All cases of fungemia occurred exclusively in haemato-oncologic patients (n = 14). Thirty-day survival was 42% in the fungemia and 43% in the intra-abdominal geotrichosis group. Serum samples were available for 23 patients (14 bloodstream and nine intra-abdominal infections). While BDG sensitivity was 65%, none of the sera was GM positive. This finding was supported by in vitro experiments analyzing fungal culture supernatants: M. capitatus secretes significant amounts of BDG but not GM. Specificity was 96% for BDG and 100% for GM. Magnusiomyces and Geotrichum infections are not limited to haemato-oncologic patients. Contrasting the current ESCMID/ECMM recommendation, our results indicate that GM is no suitable biomarker for the diagnosis of Magnusiomyces infection. Contrarily, BDG sensitivity is comparable to that of candidemia.

Systematic Comparison of Three Commercially Available Combination Disc Tests and the Zinc-Supplemented Carbapenem Inactivation Method (zCIM) for Carbapenemase Detection in Enterobacterales Isolates.

Detection of carbapenemases in Enterobacterales is crucial for patient treatment and infection control. Among others, combination disc tests (CDTs) with different inhibitors (e.g., EDTA) and variations of the carbapenem inactivation method (CIM) are recommended by EUCAST or the CLSI and are used by many laboratories as they are relatively inexpensive. In this study, we compare three commercially available CDTs, faropenem disc testing (FAR), and the zinc-supplemented CIM (zCIM) test for the detection of carbapenemase-producing Enterobacterales (CPE). The Rosco KPC/MBL and OXA-48 Confirm kit (ROS-CDT), the Liofilchem KPC&MBL&OXA-48 disc kit (LIO-CDT), Mastdiscs Combi Carba plus (MAST-CDT), FAR, and zCIM were challenged with 106 molecularly characterized CPE and 47 non-CPE isolates. The sensitivities/specificities were 86% (confidence interval [CI], 78 to 92%)/98% (CI, 89 to 100%) for MAST-CDT and ROS-CDT, 96% (CI, 91 to 99%)/87% (CI, 74 to 95%) for LIO-CDT, and 99% (CI, 95 to 100%)/81% (CI, 67 to 91%) for FAR compared to 98% (CI, 93 to 100%)/100% (CI, 92 to 100%) for zCIM. The CDTs showed great performance differences depending on the carbapenemase class, with MAST-CDT and LIO-CDT best detecting class B, ROS-CDT best detecting class A, and LIO-CDT best detecting class D carbapenemases. The overall performance of commercially available CDTs was good but varied greatly for different carbapenemases and between manufacturers, compared with FAR and zCIM, which performed well for all carbapenemase types. For reliable carbapenemase detection, CDTs should preferably not be used as the sole test but can be part of a diagnostic strategy when combined with other assays (e.g., CIM-based, immunochromatographic, or molecular tests).

Failure of Vitek2 to reliably detect vanB-mediated vancomycin resistance in Enterococcus faecium.

OBJECTIVES: The increasing prevalence of VRE necessitates their reliable detection, especially for low-level resistance mediated by vanB in Enterococcus faecium. In this prospective study we analysed if vanB-mediated vancomycin resistance can be reliably detected by Vitek2. METHODS: One thousand, three hundred and forty-four enterococcal isolates from routine clinical specimens were tested by Vitek2 (bioMérieux, Nürtingen, Germany). Additionally, a bacterial suspension (with a turbidity equivalent to that of a 0.5 McFarland standard) was inoculated on chromID VRE screening agar (bioMérieux) and incubated for 48 h. If vancomycin tested susceptible by Vitek2 but growth was detected on the screening agar, PCR for vanA/vanB was performed (GeneXpert vanA/B test, Cepheid, Frankfurt, Germany). For isolates that tested susceptible to vancomycin by Vitek2 but were vanA/B positive, MICs were determined before and after cultivation in broth with increasing concentrations of vancomycin. RESULTS: One hundred and fifty-six out of 491 E. faecium were VRE and were predominantly vanB positive (81.0%). Of these, Vitek2 did not identify 14 as VRE (sensitivity 91.0%). By broth microdilution 9/14 isolates demonstrated high MICs (≥32 mg/L) and 5/14 showed low vancomycin MICs, which did not increase despite vancomycin exposure. Three of the 14 isolates demonstrated growth on chromID VRE; after vancomycin exposure seven additional isolates were able to grow on chromID VRE. CONCLUSIONS: Vitek2 fails to detect vanB-mediated vancomycin resistance consistently, especially, but not limited to, low-level resistance. As this may lead to treatment failure and further dissemination of vanB VRE, additional methods (e.g. culture on VRE screening agar or PCR) are necessary to reliably identify vanB-positive enterococci in clinical routine.

Comparison of stool samples and rectal swabs with and without pre-enrichment for the detection of third-generation cephalosporin-resistant Enterobacterales (3GCREB).

To establish the optimal detection of third-generation cephalosporin-resistant Enterobacterales (3GCREB), the performance of four different screening methods has been investigated: stool samples without (A) and with (B) pre-enrichment and rectal swabs without (C) and with (D) pre-enrichment were contrasted. Pre-enrichment approaches (B and D) increased the detection of 3GCREB carriers by 29.4% (20/68 3GCREB carriers only found using pre-enrichment, p < 0.0001) compared to direct plating approaches (A and C). Moreover, the study demonstrates a minor advantage of stool samples in contrast to rectal swabs in both cases (with and without pre-enrichment). Registration number: DRKS00022520, 24 July 2020.

Prevalence of third-generation cephalosporin-resistant Enterobacterales colonization on hospital admission and ESBL genotype-specific risk factors: a cross-sectional study in six German university hospitals.

OBJECTIVES: To assess the admission prevalence of third-generation cephalosporin-resistant Enterobacterales (3GCREB) and to assess whether risk factors vary by ß-lactamase genotype. METHODS: Adult patients were recruited within 72 h of admission to general wards of six university hospitals in 2014 and 2015. Rectal swabs were screened for 3GCREB and isolates were analysed phenotypically and genotypically. Patients were questioned on potential risk factors. Multivariable analyses were performed to identify risk factors for 3GCREB colonization and for specific ß-lactamases. RESULTS: Of 8753 patients screened, 828 were 3GCREB positive (9.5%). Eight hundred and thirteen isolates were available for genotyping. CTX-M-15 was the most common ESBL (38.0%), followed by CTX-M-1 (22.5%), CTX-M-14 (8.7%), CTX-M-27 (7.5%) and SHV-ESBL (4.4%). AmpC was found in 11.9%. Interestingly, 18 Escherichia coli isolates were AmpC positive, 12 of which (67%) contained AmpC on a gene of plasmid origin [CMY (n = 10), DHA (n = 2)]. Risk factors for 3GCREB colonization varied by genotype. Recent antibiotic exposure and prior colonization by antibiotic-resistant bacteria were risk factors for all ß-lactamases except CTX-M-14 and CTX-M-27. Travel outside Europe was a risk factor for CTX-M-15 and CTX-M-27 [adjusted OR (aOR) 3.49, 95% CI 2.88-4.24 and aOR 2.73, 95% CI 1.68-4.43]. A previous stay in a long-term care facility was associated with CTX-M-14 (aOR 3.01, 95% CI 1.98-4.59). A preceding hospital stay in Germany increased the risk of CTX-M-15 (aOR 1.27, 95% CI 1.14-1.41), while a prior hospital stay in other European countries increased the risk of SHV-ESBL colonization (aOR 3.85, 95% CI 1.67-8.92). CONCLUSIONS: The detection of different ESBL types is associated with specific risk factor sets that might represent distinct sources of colonization and ESBL-specific dissemination routes.

Comparison of nine different selective agars for the detection of carbapenemase-producing Enterobacterales (CPE).

The rapid identification of patients colonized with carbapenem-resistant Enterobacterales (CRE) is important for infection control purposes. Here, we compared and evaluated nine different agars for the detection of carbapenemase-producing Enterobacterales (CPE) from clinical samples. In the study, 69 CPE and 40 carbapenemase-negative isolates were included. Overall, seven commercially available screening agars were assessed: Brilliance CRE (Oxoid), Chromatic CRE (Liofilchem), chromID CARBA and chromID OXA-48 (both bioMérieux), three ESBL agars (Chromatic ESBL [Liofilchem], chromID ESBL [bioMérieux], Brilliance ESBL [Oxoid]), and two agars produced in-house (McCARB and McCARB-T). The sensitivity of CRE agars for CPE detection ranged from 34.8 to 98.6%. Brilliance CRE and McCARB/McCARB-T showed the overall highest sensitivity (98.6 and 97.1%, respectively). OXA-48 producers were the most difficult to detect; only 4/9 agars detected all isolates (McCARB/McCARB-T, Chromatic CRE, ChromID OXA-48). Additionally, all ESBL-negative OXA-48 isolates failed to grow on ESBL screening agars. Specificity ranged from 30 (Brilliance ESBL) to 100% (ChromID OXA-48). The limit of detection for different CPE in spiked stool samples ranged from 1.5 × 101 to 1.5 × 103 CFU/ml. Overall, Brilliance CRE and the McCARB in-house agars showed the best performance and were able to detect most CPE, including almost all OXA-48. ESBL agars were not suitable for detection of CPE alone, as OXA-48 isolates negative for ESBL were suppressed. The highest sensitivity was achieved by a combination of a CRE agar and an ESBL agar.

Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study.

BACKGROUND: The selection pressure exercised by antibiotic drugs is an important consideration for the wise stewardship of antimicrobial treatment programs. Treatment decisions are currently based on crude assumptions, and there is an urgent need to develop a more quantitative knowledge base that can enable predictions of the impact of individual antibiotics on the human gut microbiome and resistome. RESULTS: Using shotgun metagenomics, we quantified changes in the gut microbiome in two cohorts of hematological patients receiving prophylactic antibiotics; one cohort was treated with ciprofloxacin in a hospital in Tübingen and the other with cotrimoxazole in a hospital in Cologne. Analyzing this rich longitudinal dataset, we found that gut microbiome diversity was reduced in both treatment cohorts to a similar extent, while effects on the gut resistome differed. We observed a sharp increase in the relative abundance of sulfonamide antibiotic resistance genes (ARGs) by 148.1% per cumulative defined daily dose of cotrimoxazole in the Cologne cohort, but not in the Tübingen cohort treated with ciprofloxacin. Through multivariate modeling, we found that factors such as individual baseline microbiome, resistome, and plasmid diversity; liver/kidney function; and concurrent medication, especially virostatic agents, influence resistome alterations. Strikingly, we observed different effects on the plasmidome in the two treatment groups. There was a substantial increase in the abundance of ARG-carrying plasmids in the cohort treated with cotrimoxazole, but not in the cohort treated with ciprofloxacin, indicating that cotrimoxazole might contribute more efficiently to the spread of resistance. CONCLUSIONS: Our study represents a step forward in developing the capability to predict the effect of individual antimicrobials on the human microbiome and resistome. Our results indicate that to achieve this, integration of the individual baseline microbiome, resistome, and mobilome status as well as additional individual patient factors will be required. Such personalized predictions may in the future increase patient safety and reduce the spread of resistance. TRIAL REGISTRATION: ClinicalTrials.gov, NCT02058888 . Registered February 10 2014.

Candida auris in Germany and Previous Exposure to Foreign Healthcare.

The emerging yeast Candida auris has disseminated worldwide. We report on 7 cases identified in Germany during 2015-2017. In 6 of these cases, C. auris was isolated from patients previously hospitalized abroad. Whole-genome sequencing and epidemiologic analyses revealed that all patients in Germany were infected with different strains.

Results from a Prospective In Vitro Study on the Mecillinam (Amdinocillin) Susceptibility of Enterobacterales.

The activity of mecillinam (amdinocillin) was assessed in Enterobacterales (n = 420) isolated from urine samples between 2016 and 2017. Mecillinam susceptibilities were 97.4% in Escherichia coli isolates (294/302), 89.7% in Klebsiella spp. isolates (52/58), and 93.3% in Proteus mirabilis isolates (28/30). Among extended-spectrum ß-lactamase (ESBL) producers, 95.2% (99/104) were mecillinam susceptible, including two OXA-48-producing Klebsiella pneumoniae isolates. In Enterobacter spp. and Citrobacter spp., MICs were low (MIC50 = 0.5 mg/liter). In conclusion, the activity of mecillinam was high in Enterobacterales, even among multidrug-resistant isolates.

Systematic Comparison of Four Methods for Detection of Carbapenemase-Producing Enterobacterales Directly from Blood Cultures.

Early identification of infections caused by carbapenemase-producing Enterobacterales (CPE) can help to optimize patient treatment and improve outcome. In this study, protocols for rapid detection of carbapenemase production directly from positive blood cultures were developed applying a concentration and hemolysis step before a test for carbapenemase production was performed. Four different methods (three modified colorimetric assays [ß-Carba, bcCarba NP, and NeoRapid Carb] and a variation of the carbapenem inactivation method [CIM] test with blood cultures [bcCIM]) were assessed on blood cultures spiked with 185 different molecularly characterized Enterobacterales isolates. The challenge collection included 81 carbapenemase-negative isolates and 104 CPEs (OXA-48 [n = 25], NDM [n = 20], KPC [n = 18], VIM [n = 25], GIM [n = 5], OXA-48-like [n = 9], and OXA-48-like plus NDM [n = 2]). The sensitivity/specificity was 99.0%/95.1% for bcCarba NP, 99.0%/91.4% for NeoRapid Carb, 100%/95.1% for ß-Carba and 100%/100% for bcCIM. Weakly hydrolyzing carbapenemases (e.g., OXA-48-like) were also well detected by the assays. The time to result was 20 to 45 min for ß-Carba, 2 to 3 h for bcCarba NP, 2.5 to 2 h for NeoRapid Carb, and 18 to 24 h for bcCIM. In conclusion, all assays demonstrated good detection of CPE. The protocols can be easily implemented in any clinical microbiology laboratory and could help to optimize therapy early in bloodstream infections by CPE.

Rapid and Easy Detection of Carbapenemases in Enterobacterales in the Routine Laboratory Using the New GenePOC Carba/Revogene Carba C Assay.

The novel, real-time PCR-based GenePOC Carba assay on the microfluidic revogene platform (GenePOC, Québec, Canada; now Meridian Bioscience, Cincinnati, OH, USA) was recently designed for the detection of blaKPC, blaNDM, blaVIM, blaOXA-48-like, and blaIMP The goals of this study were to evaluate the performance of this assay, to assess its suitability for the routine microbiology laboratory, and to compare it to the Xpert Carba-R assay for the detection of carbapenemase-producing Enterobacterales (CPE) strains. The Xpert Carba-R assay (Cepheid) and the GenePOC Carba assay were challenged with a collection of 176 clinical Enterobacterales isolates. The collection included 133 CPE strains producing a total of 139 carbapenemases, including VIM (n = 48), OXA-48-like (n = 40), NDM (n = 29), KPC (n = 13), and IMP (n = 9). Six isolates produced two different carbapenemases, and 43 carbapenemase-negative isolates were included as negative controls. The overall sensitivity for carbapenemase detection was 96.4% (95% confidence interval [CI], 91.9% to 98.5%) for the Xpert Carba-R assay and 100% (95% CI, 97.3% to 100%) for the GenePOC assay. The four most common carbapenemases (NDM, KPC, OXA-48-like, and VIM) were detected with a sensitivity of 100% (95% CI, 97.1% to 100%) by the two tests, with all double carbapenemase producers being correctly detected by both assays. The sensitivity of the Xpert Carba-R assay for IMP was 44.4% (95% CI, 18.9% to 73.3%), while that of the GenePOC assay was 100% (95% CI, 70.1% to 100%). The specificity of both assays was 100% (95% CI, 91.8% to 100%). The GenePOC Carba assay showed excellent sensitivity and specificity for the five most common carbapenemases, including IMP variants. Its simplicity and short turnaround time make it suitable for use in the routine microbiology laboratory for CPE detection.