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The rapid detection and species-level differentiation of bacterial pathogens facilitates antibiotic stewardship and improves disease management. Here, we develop a rapid bacteriophage-based diagnostic assay to detect the most prevalent pathogens causing urinary tract infections:Escherichia coli, Klebsiellaspp., andEnterococcusspp. For each uropathogen, two virulent phages were genetically engineered to express a nanoluciferase reporter gene upon host infection. Using 206 patient urine samples, reporter phage-induced bioluminescence was quantified to identify bacteriuria and the assay was benchmarked against conventional urinalysis. Overall,E. coli, Klebsiellaspp., andEnterococcusspp. were each detected with high sensitivity (68%, 78%, 85%), specificity (99%, 99%, 99%), and accuracy (90%, 94%, 96%) at a resolution of ⩾103CFU/ml within 5 h. We further demonstrate how bioluminescence in urine can be used to predict phage antibacterial activity, demonstrating the future potential of reporter phages as companion diagnostics that guide patient-phage matching prior to therapeutic phage application.

PURPOSE Photoactivated chromophore for keratitis cross-linking (PACK-CXL) is used as an adjunct therapy to antibiotic medication in infectious keratitis. This experimental study aimed at quantifying the PACK-CXL efficacy as a function of UV fluence using several bacterial strains and irradiated volumes. METHODS Six distinct bacterial strains, including standardized strains and clinically isolated strains from patients with keratitis, were analyzed. Bacterial concentrations between 10 and 10 cells/mL were used (simulating small corneal ulcers). Volumes of either 11 μL (≈285 μm stromal thickness) or 40 μL (≈1000 μm stromal thickness) were irradiated within a microtiter plate at different fluences (5.4-27 J/cm) and irradiances (3, 9 and 18 mW/cm). The ratio of bacterial killing (B†) was determined to evaluate the antimicrobial efficacy of PACK-CXL. RESULTS B† was similar (51 ± 11%) in bacterial concentrations between 10 and 10 per ml. In 11 μL volume, Staphylococcus aureus (SA) 8325-4 ATCC 29213, Bacillus subtilis (BS) 212901, and Pseudomonas aeruginosa (PA) 2016-866624 were most sensitive to PACK-CXL at 5.4 J/cm (on average B† = 49 ± 8%), whereas Klebsiella oxytoca (KO) 2016-86624 (B† = 25%) was least sensitive. When irradiating a larger volume, B† was on average lower in 40 μL (19 ± 18%), compared with 11 μL (45 ± 17%, P < 0.001). By contrast, applying a higher UV fluence increased B† of SA ATCC 29213, from 50% at 5.4 J/cm to 92% at 10.8 J/cm, to 100% at 16.2 J/cm and above. CONCLUSIONS Applying higher UV fluences substantially increases the bacterial killing rates. Safety limits for clinical application require further investigation.

Periprosthetic joint infections (PJIs) remain a challenging complication after shoulder arthroplasty. The antimicrobial peptide α-defensin has been proposed as a new synovial fluid biomarker in diagnosing PJIs. To date, only little data are available on the diagnostic accuracy of α-defensin in shoulder PJIs; thus, we aimed to evaluate its diagnostic value in a cohort of patients with a suspected shoulder PJI. Between June 2016 and June 2018, we prospectively enrolled patients with a diagnostic shoulder aspiration due to painful shoulder arthroplasty or planned revision surgery. PJI diagnostics were performed according to the Musculoskeletal Infection Society (MSIS) criteria. All patients with an antibiotic therapy within two weeks before enrollment, insufficient amount of synovial aspirate, or bloody aspiration were excluded. α-Defensin was measured in the synovial fluid using the α-defensin lateral flow (ADLF) test (Synovasure®). Out of 60 patients, we could include 29 (59% female) patients with a mean age of 70 (range, 50–92) years. A shoulder PJI was detected in five cases (Staphylococcus aureus, n = 2; Staphylococcus epidermidis, n = 2; Cutibacterium acnes, n = 1). The ADLF test was positive in seven out of 29 cases. According to the MSIS criteria, the ADLF test was false-negative in two patients and false-positive in four patients, resulting in sensitivity, specificity, and positive and negative predictive value of 60%, 83%, 43%, and 91%, respectively. The overall accuracy was 79%. The ALDF test does not appear to be useful in predicting shoulder PJIs but may be used as an additional diagnostic factor in rejecting these infections.

Among 400 Aspergillus species from respiratory samples in Switzerland, Aspergillus fumigatus was the most frequent species. Non-fumigatus Aspergillus spp were more prevalent among solid organ transplant recipients and after azole exposure. Azole resistance was detected in 4 A fumigatus isolates, 3 of them with the “environmental” mutation TR34/L98H in the cyp51A gene.

Background The increasing incidence of candidemia and emergence of drug-resistant Candida species are major concerns worldwide. Long-term surveillance studies are needed. Methods The Fungal Infection Network of Switzerland (FUNGINOS) conducted a 15-year (2004–2018), nationwide, epidemiological study of candidemia. Hospital-based incidence of candidemia, Candida species distribution, antifungal susceptibility, and consumption were stratified in 3 periods (2004–2008, 2009–2013, 2014–2018). Population-based incidence over the period 2009–2018 derived from the Swiss Antibiotic Resistance Surveillance System (ANRESIS). Results A total of 2273 Candida blood isolates were studied. Population and hospital-based annual incidence of candidemia increased from 2.96 to 4.20/100 000 inhabitants (P = .022) and 0.86 to 0.99/10 000 patient-days (P = .124), respectively. The proportion of Candida albicans decreased significantly from 60% to 53% (P = .0023), whereas Candida glabrata increased from 18% to 27% (P < .0001). Other non-albicans Candida species remained stable. Candida glabrata bloodstream infections occurred predominantly in the age group 18–40 and above 65 years. A higher proportional increase of C glabrata was recorded in wards (18% to 29%, P < .0001) versus intensive care units (19% to 24%, P = .22). According to Clinical and Laboratory Standards Institute, nonsusceptibility to fluconazole in C albicans was observed in 1% of isolates, and anidulafungin and micafungin nonsusceptibility was observed in 2% of C albicans and C glabrata. Fluconazole consumption, the most frequently used antifungal, remained stable, whereas use of mold-active triazoles and echinocandins increased significantly in the last decade (P < .0001). Conclusions Over the 15-year period, the incidence of candidemia increased. A species shift toward C glabrata was recently observed, concurring with increased consumption of mold-active triazoles., The incidence of candidemia increased in Switzerland from 2004 to 2018. A species shift toward C glabrata was observed after 2013, now accounting for one fourth of all candidemia, concurring with increased consumption of mold-active triazoles.

Background Aeromonas hydrophila is a gram-negative facultative anaerobic coccobacillus, which is an environmental opportunistic pathogen. A. hydrophila are involved in several infectious diseases such as gastroenteritis, septicemia and wound infections. However, gastroenteritis caused by Aeromonas spp. are rare and the clinical relevance of Aeromonas species in stool specimens is still under debate. Case presentation Our case concerns a 32-year-old woman who presented at hospital with a worsening watery diarrhea and fever requiring intensive care. A cholera-like illness was diagnosed. The patient had a past history of an anti-Hu syndrome with a myenteric ganglionitis. A molecular multiplex RT-PCR (QIAstat-Dx Gastrointestinal Panel, QIAGEN) covering a broad spectrum of diverse gastrointestinal pathogens performed directly from the stool was negative but the stool culture revealed growth of A. hydrophila. Further investigations of the A. hydrophila strain in cell cultures revealed the presence of a cytotoxic enterotoxin. Conclusions Although A. hydrophila rarely causes gastroenteritis, Aeromonas spp. should be considered as a causative agent of severe gastroenteritis with a cholera-like presentation. This case highlights the need to perform culture methods from stool samples when PCR-based methods are negative and gastrointestinal infection is suspected.

Antibiotic tolerant Staphylococcus aureus pose a great challenge to clinicians as well as to microbiological laboratories and are one reason for treatment failure. Antibiotic tolerant strains survive transient antibiotic exposure despite being fully susceptible in vitro. Thus, fast and reliable methods to detect tolerance in the routine microbiology laboratory are urgently required.We therefore evaluated the feasibility of the replica plating tolerance isolation system (REPTIS) to detect antibiotic tolerance in S. aureus isolates derived directly from patients suffering from different types of infections and investigated possible connections to clinical presentations and patient characteristics.One hundred twenty-five S. aureus isolates were included. Replica plating of the original resistance testing plate was used to assess regrowth in the zones of inhibition, indicating antibiotic tolerance. Bacterial regrowth was assessed after 24 and 48 hours of incubation and an overall regrowth score (ORS) was assigned. Regrowth scores were compared to the clinical presentation.Bacterial regrowth was high for most antibiotics targeting protein synthesis and relatively low for antibiotics targeting other cellular functions such as DNA-replication, transcription and cell wall synthesis, with the exception of rifampicin. Isolates with a blaZ penicillinase had lower regrowth in penicillin and ampicillin. Low ORSs were more prevalent among isolates recovered from patients with immunosuppression or methicillin-resistant S. aureus (MRSA) isolates.In conclusion, REPTIS is useful to detect antibiotic tolerance in clinical microbiological routine diagnostics. Rapid detection of antibiotic tolerance offers a new diagnostic readout that might allow more tailored treatments in the future.

Introduction In contrast to countries where carbapenemase-producing Enterobacterales (CPE) are endemic, only sporadic cases were reported in Switzerland until 2013. An aggravation of the epidemiological situation in neighbouring European countries indicated the need for a surveillance study in Switzerland. Aim We aimed to describe CPE distributions in Switzerland and identify epidemiological factors associated with changes in incidence. Methods Data on all human CPE isolates from 2013 to 2018 were collected by the Swiss Centre for Antibiotic Resistance (ANRESIS) and analysed for temporal and regional trends by Generalised Poisson regression. Isolates associated with infection or colonisation were included in a primary analysis; a secondary analysis included invasive isolates only. Statistical detection of regional clusters was performed with WHONET/SaTScan. Results We analysed 731 CPE isolates, of which 325 (44.5%) were associated with screenings and 173 (23.7%) with infections. Yearly detection of CPE isolates increased considerably during the study period from 65 to 212. The most frequently isolated species were Klebsiella pneumoniae (54%) and Escherichia coli (28%). The most frequent genotypes were OXA-48 (43%), KPC (21%) and NDM (14%). In contrast to the French-speaking parts of Switzerland (West, Geneva) where OXA-48 were the predominant genotypes (around 60%), KPC was the most frequently detected genotype in the Italian-speaking region (63%). WHONET/SaTScan outbreak detection analysis identified seven clusters in five regions of Switzerland. Conclusions In a first continuous surveillance of CPE in Switzerland, we found that the epidemiological situation aggravated nationwide and that regional patterns of CPE genotypes mirrored the situation in neighbouring European countries.

Background The skin commensal Cutibacterium avidum has been recognized as an emerging pathogen for periprosthetic joint infections (PJI). One currently assumes that the early occurring PJIs are a consequence of skin commensals contaminating the peri-implant tissue during surgery. We addressed whether standard skin antisepsis with povidone-iodine/alcohol before total hip arthroplasty (THA) is effective to eliminate colonizing bacteria with focus on C. avidum. Methods In a single-center, prospective study, we screened all patients for skin colonizing C. avidum in the groin before THA. Only in the patients positive for C. avidum, we preoperatively repeated skin swabs after the first and third skin antisepsis and antibiotic prophylaxis. We also obtained dermis biopsies for microbiology and fluorescence in situ hybridization (FISH). Results Fifty-one out of 60 patients (85%) were colonized on the skin with various bacteria, in particular with C. avidum in 12 out of 60. Skin antisepsis eliminated C. avidum in eight of ten (20%) colonized patients undergoing THA. Deeper skin (dermis) biopsies were all culture negative, but FISH detected single positive ribosome-rich C. avidum in one case near sweat glands. Conclusion Standard skin antisepsis was not effective to completely eliminate colonizing C. avidum on the skin in the groin of patients undergoing THA. Colonizing with C. avidum might pose an increased risk for PJI when considering a THA. Novel more effective antisepsis strategies are needed. Trial registration No clinical trial

AIMS OF THE STUDY Invasive streptococcal infections affect more than half a million patients worldwide every year and have a high lethality. Little is known about the epidemiology and microbiological characteristics of streptococcal infections in Switzerland. This case series study aims to describe the demographics, known risk factors for streptococcal skin and soft tissue infections, clinical presentations, treatment and outcomes of patients admitted to the University Hospital Zurich between 2000 and 2014 with invasive streptococcal infections caused by Streptococcus pyogenes (group A Streptococcus), Streptococcus dysgalactiae ssp. equisimilis or the Streptococcus anginosus group, as well as the microbiological characteristics of the clinical isolates. METHODS Data collected retrospectively from patients hospitalised between 2000 and 2014 with invasive streptococcal infections were analysed. M protein gene (emm) typing of the bacterial clinical isolates was carried out according to the Centers for Disease Control and Prevention guidelines. RESULTS A total of 86 patients with invasive beta-haemolytic streptococcal infections were included in this study, of which 49% presented with necrotising fasciitis. The median age was 44 years and half were female. The most common risk factor was acute skin lesions. C-reactive protein levels were significantly higher in patients with necrotising fasciitis, as were acute renal failure and distributive shock. Beta-lactam antibiotics were given to most patients, and intravenous immunoglobulins were given to 18% of patients within the first 24 hours. All patients suffering from necrotising fasciitis underwent surgery. The overall case fatality rate was 8.1% at 30 days post admission. All Group A Streptococcus strains were susceptible to penicillin and clindamycin, and we found resistance to tetracycline in 11.9% of strains. The most common emm-type isolated was emm1 (44.4%). CONCLUSIONS Invasive beta-haemolytic streptococcal infections, the most severe presentation of which is necrotising fasciitis, remain a serious clinical issue and require rapid diagnosis and treatment. This is the first representative analysis monitoring clinical and microbiological characteristics of patients with a severe invasive beta-haemolytic streptococcal infection and treated in Zurich, Switzerland. In addition to the detailed reporting of various clinical and microbiological characteristics, we show that C-reactive protein levels, acute renal failure and distributive shock were higher in the patients with necrotising fasciitis. We also found a low case fatality rate compared to other reports. The detailed clinical data and microbiological characteristics depicted in this study will lead to a better understanding of regional differences in severe invasive streptococcal infections.

Background Current standard skin antisepsis to prevent surgical site infections are ineffective to eradicate all skin-colonizing bacteria. Photodynamic therapy (PDT) has shown bactericidal effects in vitro, but no clinical study with improvements in skin antisepsis has been documented. Methods We investigated the effect of methyl aminolevulinate (MAL)-PDT versus no PDT for skin antisepsis treatment (povidone-iodine/alcohol) in the groin of 10 healthy participants. Skin swabs were taken at baseline, immediately after PDT, and after skin antisepsis treatment to cultivate bacteria. At day 7 and 21, bacterial cultures were repeated before and after antisepsis treatment without PDT. Skin biopsies were performed to examine the grade of inflammation. Results Skin-colonizing bacteria were found in all 20 participants at baseline sampling. Immediately after MAL-PDT, skin was sterile in 7 (70%) participants before and in all 10 (100%) participants after skin antisepsis treatment. In contrast, we found skin-colonizing bacteria in 5 (50%) participants of the control group receiving only skin antisepsis. After 7 and 21 days, skin sterility was similar to the baseline. We observed slight perivascular inflammation with lymphocytes and eosinophils without changes in the histomorphology of eccrine or sebaceous glands in skin biopsies. PDT was generally well tolerated except for localized redness. Conclusion MAL-PDT with skin antisepsis treatment sterilized skin immediately after its use but did not maintain sterility 7–21 days post-treatment. Due to local side effects, further clinical studies with less intensive PDT conditions or other photosensitizers are needed before PDT is integrated into clinical practice.

Background Disc diffusion is a reliable, accurate and cost-efficient procedure for antimicrobial susceptibility testing (AST) but requires long (18–24 h) incubation times. Reading of disc diffusion after short incubation times (6–8 h) by automated systems is feasible but should be categorized with time-adapted breakpoints to reduce errors. Objectives This study systematically compared early readings (6 and 8 h) of disc diffusion using an automated system with that of the standard 18 h EUCAST method. Time-adapted tentative breakpoints were proposed to discriminate susceptible from resistant isolates and areas of technical uncertainty were defined to minimize the risk of errors. Methods A total of 1106 Enterobacterales isolates with a wide variety of resistance mechanisms and resistance profiles were included. All isolates were analysed for susceptibility to amoxicillin/clavulanic acid, ceftriaxone, cefepime, meropenem, ciprofloxacin and gentamicin using the automated WASPLabTM system. Part of the collection (515 isolates) was also analysed for susceptibility to an additional 10 antibiotics. Results Separation between WT and non-WT populations was poorer at early incubation times than following standard incubation. Editing of rapid automated AST results after 6 and 8 h incubation with time-adapted breakpoints resulted in 84.0% and 88.5% interpretable results with assignment to the resistant or susceptible category. Major error and very major error rates for the 6 h readings were only 0.4% and 0.3%, virtually identical to those of 18 h AST reading. Conclusions Time-adapted clinical breakpoints in disc diffusion testing for Enterobacterales allow for accurate automated AST interpretation after shortened incubation times for a large number of antibiotics, with the additional possibility of subsequent confirmation after 18 h incubation.

Aims It is the holiday season, but your toothbrush does not look very festive. It is damp and has been used and contaminated by someone else. To rectify this heinous crime, this study investigates the effectiveness of three household objects to disinfect toothbrushes. Design In-vitro study performed under conditions simulating everyday life. Materials and methods Twenty toothbrushes were contaminated using a mixture of saliva and trypticase soy broth containing Escherichia coli and Enterococcus faecalis. These contaminated toothbrushes were submerged in whisky, cooked in a microwave oven, or exposed to the hot air stream of a hairdryer, separately. Each treatment was performed on five toothbrushes for one minute. Untreated specimens (n = 5) served as controls. Toothbrushes were subsequently sonicated in sterile physiological saline, which was plated on selective agars. Bacterial counts were graded as low, medium, or high. Results Residual contamination was influenced by the disinfectant applied, both in E. coli (p

Tularemia is a bacterial zoonosis which is commonly transmitted through tick or insect bites or contact with meat of infected animals. We report the case of a 36-year-old man who developed fever, chills, headaches, and a painful, unilateral, inguinal lymphadenopathy with a red-livid skin discoloration after an insect bite on his abdomen. Ulceroglandular tularemia was diagnosed through polymerase chain reaction (PCR) and serology. Treatment with doxycycline for 21 days resulted in an excellent outcome.

Background A multitude of definitions determining multidrug resistance (MDR) of Gram-negative organisms exist worldwide. The definitions differ depending on their purpose and on the issueing country or organization. The MDR definitions of the European Centre for Disease Prevention and Control (ECDC) were primarily chosen to harmonize epidemiological surveillance. The German Commission of Hospital Hygiene and Infection Prevention (KRINKO) issued a national guideline which is mainly used to guide infection prevention and control (IPC) measures. The Swiss University Hospital Zurich (UHZ) – in absentia of national guidelines – developed its own definition for IPC purposes. In this study we aimed to determine the effects of different definitions of multidrug-resistance on rates of Gram-negative multidrug-resistant organisms (GN-MDRO). Methods MDR definitions of the ECDC, the German KRINKO and the Swiss University Hospital Zurich were applied on a dataset comprising isolates of Escherichia coli, Klebsiella pneumoniae, Enterobacter sp., Pseudomonas aeruginosa, and Acinetobacter baumannii complex. Rates of GN-MDRO were compared and the percentage of patients with a GN-MDRO was calculated. Results In total 11′407 isolates from a 35 month period were included. For Enterobacterales and P. aeruginosa, highest MDR-rates resulted from applying the ‘ECDC-MDR’ definition. ‘ECDC-MDR’ rates were up to four times higher compared to ‘KRINKO-3/4MRGN’ rates, and up to six times higher compared to UHZ rates. Lowest rates were observed when applying the ‘KRINKO-4MRGN’ definitions. Comparing the ‘KRINKO-3/4MRGN’ with the UHZ definitions did not show uniform trends, but yielded higher rates for E. coli and lower rates for P. aeruginosa. On the patient level, the percentages of GN-MDRO carriers were 2.1, 5.5, 6.6, and 18.2% when applying the ‘KRINKO-4MRGN’, ‘UHZ-MDR’, ‘KRINKO-3/4MRGN’, and the ‘ECDC-MDR’ definition, respectively. Conclusions Different MDR-definitions lead to considerable variation in rates of GN-MDRO. Differences arise from the number of antibiotic categories required to be resistant, the categories and drugs considered relevant, and the antibiotic panel tested. MDR definitions should be chosen carefully depending on their purpose and local resistance rates, as definitions guiding isolation precautions have direct effects on costs and patient care.

Background Aspergillus spp. of section Usti (A. ustus) represent a rare cause of invasive aspergillosis (IA). This multicenter study describes the epidemiology and outcome of A. ustus infections. Methods Patients with A. ustus isolated from any clinical specimen were retrospectively identified in 22 hospitals from 8 countries. When available, isolates were sent for species identification (BenA/CaM sequencing) and antifungal susceptibility testing. Additional cases were identified by review of the literature. Cases were classified as proven/probable IA or no infection, according to standard international criteria. Results Clinical report forms were obtained for 90 patients, of whom 27 had proven/probable IA. An additional 45 cases were identified from literature review for a total of 72 cases of proven/probable IA. Hematopoietic cell and solid-organ transplant recipients accounted for 47% and 33% cases, respectively. Only 8% patients were neutropenic at time of diagnosis. Ongoing antimold prophylaxis was present in 47% of cases. Pulmonary IA represented 67% of cases. Primary or secondary extrapulmonary sites of infection were observed in 46% of cases, with skin being affected in 28% of cases. Multiple antifungal drugs were used (consecutively or in combination) in 67% of cases. The 24-week mortality rate was 58%. A. calidoustus was the most frequent causal agent. Minimal inhibitory concentrations encompassing 90% isolates (MIC90) were 1, 8, >16, and 4 µg/mL for amphotericin B, voriconazole, posaconazole, and isavuconazole, respectively. Conclusions Aspergillus ustus IA mainly occurred in nonneutropenic transplant patients and was frequently associated with extrapulmonary sites of infection. Mortality rate was high and optimal antifungal therapy remains to be defined.

Objective Infected aortic aneurysms are highly lethal, and management is very demanding, requiring an early diagnosis. The aim of this study was to evaluate the diagnostic accuracy of positron emission tomography/computed tomography with 18F-fluorodeoxyglucose (PET/CT) and contrast enhanced CT (CE-CT) in patients with suspected infected aortic aneurysms. Methods PET/CT was performed in patients with clinically suspected infected aortic aneurysms, and additional CE-CT was performed if feasible. Diagnostic accuracy was assessed by two independent readers using a four point grading score for both imaging modalities. Maximum standardised uptake values (SUVmax) were calculated for quantitative measurements of metabolic activity in PET/CT. The reference standard was a combination of clinical presentation, laboratory findings, and imaging. Results Ten patients were included prospectively in the study, 24 retrospectively; 16 patients (47%) prior to the start of antimicrobial treatment and all 34 patients prior to any vascular intervention. Thirteen of the 34 patients had an infected aortic aneurysm (38%). Proven infected aortic aneurysms were all metabolically active on PET/CT with a median SUVmax of 6.6 (interquartile range 4.7–21.8). Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of PET/CT for the diagnosis of infected aortic aneurysm was 100%, 71%, 68%, 100%, and 82%, for reader 1 and 85%, 71%, 65%, 88%, and 77%, for reader 2. Respective values for CE-CT, performed in 20 patients (59%), were 63%, 75%, 63%, 75%, and 70%, for reader 1 and 88%, 50%, 54%, 86%, and 65%, for reader 2. Conclusion The diagnostic accuracy of PET/CT in the detection of infected aortic aneurysms (n = 13) is high, and higher than CE-CT. While PET/CT demonstrates an excellent sensitivity, its specificity is hampered because of false positive findings.

Helicobacter pylori is a major human pathogen that causes a wide range of gastrointestinal pathology. Progression of H. pylori induced gastritis to more severe disease has been found to highly correlate with the array of virulence factors expressed by the pathogen. The objective of this study was twofold: first, to characterize the genetic diversity of H. pylori strains isolated from 41 non-atrophic gastritis patients in Switzerland, an issue that has not been investigated to date. And second, to assess the prevalence and sequence variation of H. pylori virulence factors (cagA, vacA, iceA and dupA) and genes encoding outer membrane proteins (OMPs, babA, babB, sabA, sabB, hopZ, hopQ and oipA) by whole genome sequencing (WGS) using an Illumina MiSeq platform. WGS identified high genetic diversity in the analyzed H. pylori strains. Most H. pylori isolates were assigned to hpEurope (95.0%, 39/41), and the remaining ones (5.0%, 2/41) to hpEastAsia, subpopulation hspEAsia. Analysis of virulence factors revealed that 43.9% of the strains were cagA-positive, and the vacA s1 allele was detected in 56.0% of the isolates. The presence of cagA was found to be significantly associated (P &lt, 0.001) with the presence of vacA s1, babA2 and hopQ allele 1 as well as expression of oipA. Moreover, we found an association between the grade of gastritis and H. pylori abundance in the gastric mucosa, respectively and the presence of cagA, vacA s1 and hopQ allele 1. Among our 41 gastritis patients, we identified seven patients infected with H. pylori strains that carried a specific combination of virulence factors (i.e cagA, vacA s1 allele and babA2 allele), recently implicated in the development of more severe gastrointestinal pathology, like peptic ulcer disease and even gastric cancer. To this end, WGS can be employed for rapid and detailed characterization of virulence determinants in H. pylori, providing valuable insights into the pathogenic capacity of the bacterium. This could ultimately lead to a higher level of personalized treatment and management of patients suffering from H. pylori associated infections.

Helicobacter pylori is a major human pathogen. Diagnosis of H. pylori infection and determination of its antibiotic susceptibility still mainly rely on culture and phenotypic drug susceptibility testing (DST) that is time-consuming and laborious. Whole genome sequencing (WGS) has recently emerged in medical microbiology as a diagnostic tool for reliable drug resistance prediction in bacterial pathogens. The aim of this study was to compare phenotypic DST results with the predictions based on the presence of genetic determinants identified in the H. pylori genome using WGS. Phenotypic resistance to clarithromycin, metronidazole, tetracycline, levofloxacin, and rifampicin was determined in 140 clinical H. pylori isolates by E-Test&reg, and the occurrence of certain single nucleotide polymorphisms (SNPs) in target genes was determined by WGS. Overall, there was a high congruence of &gt, 99% between phenotypic DST results for clarithromycin, levofloxacin, and rifampicin and SNPs identified in the 23S rRNA, gyrA, and rpoB gene. However, it was not possible to infer a resistance phenotype for metronidazole based on the occurrence of distinct SNPs in frxA and rdxA. All 140 H. pylori isolates analysed in this study were susceptible to tetracycline, which was in accordance with the absence of double or triple nucleotide substitutions in the 16S rRNA gene.

Matrix-assisted laser desorption ionization−time of flight mass spectrometry (MALDI-TOF MS) has entered clinical laboratories, facilitating identification of bacteria. Here, we evaluated the MALDI Biotyper (Bruker Daltonics) for the identification of fastidious Gram-negative rods (GNR). Three sample preparation methods, direct colony transfer, direct transfer plus on-target formic acid preparation, and ethanol-formic acid extraction, were analyzed for 151 clinical isolates. Direct colony transfer applied with the manufacturer's interpretation criteria resulted in overall species and genus identification rates of 43.0% and 32.5%, respectively; 23.2% of the isolates were not identified, and two misidentifications (1.3%) were observed. The species identification rates increased to 46.4% and 53.7% for direct transfer plus formic acid preparation and ethanol-formic acid extraction, respectively. In addition, we evaluated score value cutoff alterations. The identification rates hardly increased by reducing the genus cutoff, while reducing the 2.0 species cutoff to 1.9 and to 1.8 increased the identification rates to up to 66.2% without increasing the rate of misidentifications. This study shows that fastidious GNR can reliably be identified using the MALDI Biotyper. However, the identification rates do not reach those of nonfastidious GNR such as theEnterobacteriaceae. In addition, two approaches optimizing the identification of fastidious GNR by the MALDI Biotyper were demonstrated: formic acid-based on-target sample treatment and reductions in cutoff scores to increase the species identification rates.

Background An increase in the incidence of hip periprosthetic joint infections (PJIs) caused by Cutibacterium avidum has recently been detected after implantation of hip arthroplasties with an anterior surgical approach. We raised the question of whether skin colonization with C. avidum differs between the anterior and the lateral thigh as areas of surgical incision fields. Methods Between February and June 2017, we analyzed skin scrapings from the groin and the anterior and lateral thigh in all patients undergoing a primary hip arthroplasty. We anaerobically cultured plated swabs for Cutibacterium spp. for at least 7 days. Univariate logistic regression analysis was used to explore associations between body mass index (BMI) and colonization rate at different sites. Results Twenty-one of 65 patients (32.3%) were colonized with C. avidum at any side, mainly at the groin (n=16, 24.6%), which was significantly higher than at the anterior (n=5, 7.7%, P= 0.009) or lateral (n=6, 9.2%) thigh (P=0.019). Patients colonized with C. avidum did not differ in age or sex compared to non-colonized patients, but BMI was significantly higher (30.1 kg/m2 and 25.6 kg/m2, respectively, P=0.019). Furthermore, increased BMI was associated with colonization at the groin (odds ratio per unit BMI increase: 1.15, 95% confidence interval: 1.03-1.29, P=0.014). Conclusions The groin, rather than the anterior thigh, showed colonization for C. avidum in obese patients. Further studies are needed to evaluate current skin disinfection and draping protocols for hip arthroplasty surgeries, in particular in obese patients.

Corynebacterium spp. are rarely considered pathogens, but data on Corynebacterium spp. as a cause of orthopedic infections are sparse. Therefore, we asked how often Corynebacterium spp. caused an infection in a defined cohort of orthopedic patients with a positive culture. In addition, we aimed to determine the species variety and the susceptibility of isolated strains to define potential treatment strategies. We retrospectively assessed all bone and joint samples that were collected between 2006 and 2015 from an orthopedic ward and that were positive for Corynebacterium spp. by culture. The isolates were considered relevant to an infection if the same Corynebacterium sp. was present in at least two samples. We found 97 orthopedic cases with isolation of Corynebacterium spp. (128 positive samples). These were mainly Corynebacterium tuberculostearicum (n = 26), Corynebacterium amycolatum (n = 17), Corynebacterium striatum (n = 13), and Corynebacterium afermentans (n = 11). Compared to the species found in a cohort of patients with positive blood cultures hospitalized in nonorthopedic wards, we found significantly more C. striatum- and C. tuberculostearicum-positive cases but no C. jeikeium-positive cases in our orthopedic cohort. Only 16 out of 66 cases (24.2%) with an available diagnostic set of at least two samples had an infection. Antibiotic susceptibility testing (AST) showed various susceptibility results for all antibiotics except vancomycin and linezolid, to which 100% of the isolates were susceptible. The rates of susceptibility of corynebacteria isolated from orthopedic samples and of isolates from blood cultures were comparable. In conclusion, our study results confirmed that a Corynebacterium sp. is most often isolated as a contaminant in a cohort of orthopedic patients. AST is necessary to define the optimal treatment in orthopedic infections.

Aggregatibacterspecies are commensal bacteria of human mucosal surfaces that are sometimes involved in serious invasive infections. During the investigation of strains cultured from various clinical specimens, we encountered a coherent group of 10 isolates that could not be allocated to any validly named species by phenotype, mass spectrometry, or partial 16S rRNA gene sequencing. Whole-genome sequencing revealed a phylogenetic cluster related to but separate fromAggregatibacter aphrophilus. The meanin silicoDNA hybridization value for strains of the new cluster versusA. aphrophiluswas 56% (range, 53.7 to 58.0%), whereas the average nucleotide identity was 94.4% (range, 93.9 to 94.8%). The new cluster exhibited aggregative properties typical of the genusAggregatibacter. Key phenotypic tests for discrimination of the new cluster from validly namedAggregatibacterspecies are alanine-phenylalanine-proline arylamidase,N-acetylglucosamine, and β-galactosidase. The nameAggregatibacter kilianiiis proposed, with PN_528 (CCUG 70536Tor DSM 105094T) as the type strain.

Background: : Staphylococcus lugdunensis endocarditis has been associated with an aggressive course. The aim of this study was to determine factors associated with the development of endocarditis in patients with S. lugdunensis bacteremia. Methods: : A retrospective analysis of all patients with S. lugdunensis bacteremia in three tertiary care centers in Switzerland was performed. Data regarding medical history, symptoms, and susceptibility of S. lugdunensis isolates were collected. Our results were reviewed in the context of the current literature. Results: : A total of 28 patients with S. lugdunensis bacteremia were identified. Of the 13 patients with endocarditis, all were community acquired. Cardiac surgery was performed in 85% of these patients; mortality was 23%, reflecting the aggressive course of this disease. In contrast, in the 15 patients without endocarditis, no complications associated with S. lugdunensis bacteremia were observed. In 73%, a probable source was identified in the form of a venous catheter or other foreign device. Only three of these episodes were community acquired. No difference was observed in susceptibility of the S. lugdunensis isolates to penicillin, which was 77% in endocarditis isolates, and 87% in isolates of bacteremia without endocarditis, respectively. Conclusion: : S. lugdunensis bacteremia is associated with endocarditis in up to 50% of patients. Every patient with community-acquired S. lugdunensis bacteremia should be carefully examined for signs of endocarditis. Once S. lugdunensis endocarditis is diagnosed, close monitoring is essential and surgical treatment should be considered early. In the nosocomial setting, endocarditis is far less frequent, and S. lugdunensis bacteremia is usually associated with a catheter or other foreign materials

Background: : There are considerable geographical differencesin the occurrence of extended-spectrum beta-lactamase(ESBL)-producing bacteria, both in the community and in thehospital setting. Our aim was to assess risk factors forbloodstream, urinary tract, and vascular catheter-associatedinfections with ESBL-producing Escherichia coli and Klebsiellapneumoniae at a tertiary care hospital in a low-prevalencecountry. Methods: : We performed a case-control study comparing 58patients with infections due to ESBL-producing E. coli orK. pneumoniae vs 116 controls with infections due to non-ESBL producing organisms at the University Hospital Zurich,Switzerland, between 1 July 2005 and 30 June 2007. Results: : Cases included 15 outpatients and 43 inpatients.Multivariable analyses found three risk factors for ESBL-producingisolates: begin of symptoms or recent antibioticpre-treatment in a foreign country (odds ratio [OR] 27.01,95% confidence interval [CI] 2.38-1,733.28], p = 0.042),antibiotic therapy within the year preceding the isolation ofthe ESBL-producing strain (OR 2.88, 95% CI 1.13-8.49,p = 0.025), and mechanical ventilation (OR 10.56, 95% CI1.06-579.10, p = 0.042). Conclusions: : The major risk factors for infections due toESBL-producing bacteria were travel in high-prevalencecountries, prior antibiotic use, and mechanical ventilationduring a stay in the intensive care unit. Community-acquiredinfections were documented in 17% of the patients.An early identification of risk factors is crucial to providingthe patients an optimal empiric antibiotic therapy and tokeep the use of carbapenems to a minimum

BACKGROUND There is a wide variation of perineural catheter (PNC) colonization rates in the literature. The impact of skin disinfection on PNC colonization and inflammation is not clear. The objective of this prospective, randomized clinical study was to investigate the influence of alcoholic skin disinfection before PNC removal on the detection of bacteria on PNC. METHODS Two hundred patients receiving a PNC for orthopaedic surgery were random- ized to receive (with-group) or not (without-group) a skin disinfection with a sprayed alcoholic solution before removal of the PNC. Bacterial colonization and contamination of the PNC and clinical signs of inflammation and infection of the PNC insertion site were evaluated. Skin disinfection with a sprayed alcoholic solution and sterile removal of the distal and subcutaneous part of the PNC was performed after 72h or earlier if signs of infection occurred with semiquantitative culture and enrichment culture of both parts. RESULTS Alcoholic skin disinfection before PNC removal significantly reduced bacterial colonization with a reduction from 28% to 14% and from 32% to 17% for the tip and the subcutaneous part of the PNC, respectively (p < 0.05). Clinical signs of inflammation at the PNC insertion site were similar (73%) in the two groups. The detection of colonization in 54 (27%) out of 200 PNC did not correlate with clinical signs of inflammation independently of the number of bacteria isolated. Redness was noted in 71 % and 68 % of patients in the WITHOUT- and WITH-alcoholic skin disinfection-group respectively. Local pain on pressure was present in 28% and 19% in the without- and with-group respectively. CONCLUSIONS Alcoholic skin disinfection before PNC removal reduced the detection of PNC colonisation by 50%. There was no correlation between clinical signs of inflammation and PNC colonization.

Irrigation water is a major source of fresh produce contamination with undesired microorganisms including antibiotic-resistant bacteria (ARB), and contaminated fresh produce can transfer ARB to the consumer especially when consumed raw. Nevertheless, no legal guidelines exist so far regulating quality of irrigation water with respect to ARB. We therefore examined irrigation water from major vegetable growing areas for occurrence of antibiotic-resistant indicator bacteria Escherichia coli and Enterococcus spp., including extended-spectrum β-lactamase (ESBL)-producing E. coli and vancomycin-resistant Enterococcus spp. Occurrence of ARB strains was compared to total numbers of the respective species. We categorized water samples according to total numbers and found that categories with higher total E. coli or Enterococcus spp. numbers generally had an increased proportion of respective ARB-positive samples. We further detected high prevalence of ESBL-producing E. coli with eight positive samples of thirty-six (22%), while two presumptive vancomycin-resistant Enterococcus spp. were vancomycin-susceptible in confirmatory tests. In disk diffusion assays all ESBL-producing E. coli were multidrug-resistant (n = 21) and whole-genome sequencing of selected strains revealed a multitude of transmissible resistance genes (ARG), with bla_CTX-M-1 (4 of 11) and bla_CTX-M-15 (3 of 11) as the most frequent ESBL genes. Overall, the increased occurrence of indicator ARB with increased total indicator bacteria suggests that the latter might be a suitable estimate for presence of respective ARB strains. Finally, the high prevalence of ESBL-producing E. coli with transmissible ARG emphasizes the need to establish legal critical values and monitoring guidelines for ARB in irrigation water. ISSN:1932-6203

Background. Propionibacteria are important members of the human skin microbiota, but are also opportunistic pathogens associated with periprosthetic joint infections (PJI). While the role of Propionibacterium acnes in PJI has been widely described, insight into the capacity of Propionibacterium avidum to cause PJI is limited. Methods. An unusual cluster of four hip PJIs caused by P. avidum in one orthopedic center in 2015 prompted us to retrospectively identify and analyze clinical data related to previous P. avidum PJI cases (1997-2015). We also characterized the hemolytic and biofilm-producing capacity of our four clinical P. avidum strains isolated in 2015, and investigated their phylogenetic relationships by whole genome sequencing. Results. We retrospectively identified 13 P. avidum PJIs, with the majority being hip-related infections (n=11). Preoperative synovial fluid cultures were P. avidum positive in 63.6% of cases. Six out of 12 patients (50%) with available case histories were treated with an exchange of the prosthesis. In all but one of the six patients treated with debridement-retention of the prosthesis, treatment failed thus requiring a two-stage revision. The isolated P. avidum strains showed a more pronounced hemolytic activity, but a similar biofilm-forming ability when compared to P. acnes. Whole genome sequencing identified two phylogenetic clusters highly related to P. avidum PJI strains isolated in Sweden. Conclusions. We describe the largest series of P. avidum PJI predominantly located in the hip. Phylogenetic similarity of our P. avidum strains to PJI strains isolated elsewhere suggests these invasive lineages may be common.

Breakthrough candidemia (BTC) on fluconazole was associated with non-susceptible Candida spp. and increased mortality. This nationwide FUNGINOS study analyzed clinical and mycological BTC characteristics.A 3-year prospective study was conducted in 567 consecutive candidemias. Species identification and antifungal susceptibility testing (CLSI) were performed in the FUNGINOS reference laboratory. Data were analyzed according to STROBE criteria.43/576 (8%) BTC occurred: 37/43 (86%) on fluconazole (28 prophylaxis, median 200 mg/day). 21% BTC vs. 23% non-BTC presented severe sepsis/septic shock. Overall mortality was 34% vs. 32%. BTC was associated with gastrointestinal mucositis (multivariate OR 5.25, 95%CI 2.23-12.40, p 0.001) and graft-versus-host-disease (6.25, 1.00-38.87, p = 0.05), immunosuppression (2.42, 1.03-5.68, p = 0.043), and parenteral nutrition (2.87, 1.44-5.71, p = 0.003). Non-albicans Candida were isolated in 58% BTC vs. 35% non-BTC (p = 0.005). 63% of 16 BTC occurring after 10-day fluconazole were non-susceptible (Candida glabrata, Candida krusei, Candida norvegensis) vs. 19% of 21 BTC (C. glabrata) following shorter exposure (7.10, 1.60-31.30, p = 0.007). Median fluconazole MIC was 4 mg/l vs. 0.25 mg/l (p 0.001). Ten-day fluconazole exposure predicted non-susceptible BTC with 73% accuracy.Outcomes of BTC and non-BTC were similar. Fluconazole non-susceptible BTC occurred in three out of four cases after prolonged low-dose prophylaxis. This implies reassessment of prophylaxis duration and rapid de-escalation of empirical therapy in BTC after short fluconazole exposure.

Background The purpose of this study was to evaluate prospectively the presence and impact of the gastric carcinogen Helicobacter pylori (H. pylori) in the upper aerodigestive tract. Previous studies suggested it could represent a risk factor for head and neck squamous cell carcinoma (HNSCC). Methods Serology, rapid urease test, and quantitative polymerase chain reaction (qPCR) for H. pylori were performed in patients with head and neck cancer (N = 56) and cancer-free controls (N = 90). Comparison between groups was done using logistic regression analysis. Results Rates of positive serology and rapid urease test did not differ between the 2 groups in logistic regression analysis (p = .677 and p = .633, respectively). Birth in a developing country and age above 50 years old were predictors of positive serology (p

Ureaplasma urealyticum and Mycoplasma hominis are common inhabitants of the human genital tract. Increasingly, serious and sometimes fatal infections in immunocompromised hosts have been reported, highlighting their pathogenic potential. We reviewed the clinical impact of positive Ureaplasma spp. and Mycoplasma spp. urine cultures in 10 renal allograft recipients who presented with sterile leukocyturia. Five recipients remained asymptomatic. Five patients were symptomatic with dysuria or pain at the graft site. Three patients developed biopsy-proven acute graft pyelonephritis with graft dysfunction. One of these patients additionally showed a renal abscess as demonstrated by magnetic resonance imaging (MRI). All were successfully treated. A literature search revealed a substantial number of case reports with severe and sometimes fatal Ureaplasma spp. or Mycoplasma spp. infections in immunocompromised patients. Colonization rate is high in renal transplant patients. A subset of patients is at risk for invasive disease.

We analyzed surgically resected endocardial specimens from 49 patients by broad-range PCR. PCR results were compared with (1) results of previous blood cultures, (2) results of culture and Gram staining of resected specimens, and (3) clinical data (Duke criteria). Molecular analyses of resected specimens and previous blood cultures showed good overall agreement. However, in 18% of patients with sterile blood cultures, bacterial DNA was found in the resected materials. When data from patients with definite or rejected cases of infective endocarditis (IE) were included, the sensitivity, specificity, and positive and negative predictive values of broad-range PCR were 82.6%, 100%, 100%, and 76.5%, respectively, overall, and 94.1%, 100%, 100%, and 90%, for cases of native valve endocarditis. The sensitivity, specificity, and positive and negative predictive values of culture of resected specimens from patients with native valve endocarditis were 17.6%, 88.9%, 75%, and 36.4%. We recommend broad-range PCR of surgically resected endocardial material in cases of possible IE, in cases of suspected IE in which blood cultures are sterile, and in cases in which organisms grow in blood cultures but only Duke minor criteria are met. We propose to add molecular techniques to the pathologic criteria of the Duke classification scheme.