Retrospective study of the incidence, risk factors, treatment outcomes of bacterial infections at uncommon sites in cirrhotic patients.

BACKGROUND: Bacterial infections (BI) negatively affect the natural course of cirrhosis. The most frequent BI are urinary tract infections (UTI), pneumonia, and spontaneous-bacterial peritonitis (SBP). AIM: To assess the relevance of bacterial infections beyond the commonly recognized types in patients with cirrhosis and to investigate their relationship with other clinical variables. METHODS: We retrospectively analyzed patients with cirrhosis and BI treated between 2015 and 2018 at our tertiary care center. BIs were classified as typical and atypical, and clinical as well as laboratory parameters were compared between the two groups. RESULTS: In a cohort of 488 patients with cirrhosis, we identified 225 typical BI (95 UTI, 73 SBP, 72 pulmonary infections) and 74 atypical BIs, predominantly cholangitis and soft tissue infections (21 each), followed by intra-abdominal BIs (n = 9), cholecystitis (n = 6), head/throat BIs (n = 6), osteoarticular BIs (n = 5), and endocarditis (n = 3). We did not observe differences concerning age, sex, or etiology of cirrhosis in patients with typical vs atypical BI. Atypical BIs were more common in patients with more advanced cirrhosis, as evidenced by Model of End Stage Liver Disease (15.1 ± 7.4 vs 12.9 ± 5.1; P = 0.005) and Child-Pugh scores (8.6 ± 2.5 vs 8.0 ± 2; P = 0.05). CONCLUSION: Atypical BIs in cirrhosis patients exhibit a distinct spectrum and are associated with more advanced stages of the disease. Hence, the work-up of cirrhosis patients with suspected BI requires detailed work-up to elucidate whether typical BI can be identified.

SARS-CoV-2-specific cellular and humoral immunity after bivalent BA.4/5 COVID-19-vaccination in previously infected and non-infected individuals.

Knowledge is limited as to how prior SARS-CoV-2 infection influences cellular and humoral immunity after booster-vaccination with bivalent BA.4/5-adapted mRNA-vaccines, and whether vaccine-induced immunity may indicate subsequent infection. In this observational study, individuals with prior infection (n = 64) showed higher vaccine-induced anti-spike IgG-antibodies and neutralizing titers, but the relative increase was significantly higher in non-infected individuals (n = 63). In general, both groups showed higher neutralizing activity towards the parental strain than towards Omicron-subvariants BA.1, BA.2 and BA.5. In contrast, CD4 or CD8 T cell levels towards spike from the parental strain and the Omicron-subvariants, and cytokine expression profiles were similar irrespective of prior infection. Breakthrough infections occurred more frequently among previously non-infected individuals, who had significantly lower vaccine-induced spike-specific neutralizing activity and CD4 T cell levels. In summary, we show that immunogenicity after BA.4/5-bivalent vaccination differs between individuals with and without prior infection. Moreover, our results may help to improve prediction of breakthrough infections.

Time series of chicken stool metagenomics and egg metabolomics in changing production systems: preliminary insights from a proof-of-concept.

BACKGROUND: Different production systems of livestock animals influence various factors, including the gut microbiota. METHODS: We investigated whether changing the conditions from barns to free-range chicken farming impacts the microbiome over the course of three weeks. We compared the stool microbiota of chicken from industrial barns after introducing them either in community or separately to a free-range environment. RESULTS: Over the six time points, 12 taxa-mostly lactobacilli-changed significantly. As expected, the former barn chicken cohort carries more resistances to common antibiotics. These, however, remained positive over the observed period. At the end of the study, we collected eggs and compared metabolomic profiles of the egg white and yolk to profiles of eggs from commercial suppliers. Here, we observed significant differences between commercial and fresh collected eggs as well as differences between the former barn chicken and free-range chicken. CONCLUSION: Our data indicate that the gut microbiota can undergo alterations over time in response to changes in production systems. These changes subsequently exert an influence on the metabolites found in the eggs. The preliminary results of our proof-of-concept study motivate larger scale observations with more individual chicken and longer observation periods.

Characterization of a unique attachment organelle: Single-cell force spectroscopy of Giardia duodenalis trophozoites.

The unicellular parasite Giardia duodenalis is the causative agent of giardiasis, a gastrointestinal disease with global spread. In its trophozoite form, G. duodenalis can adhere to the human intestinal epithelium and a variety of other, artificial surfaces. Its attachment is facilitated by a unique microtubule-based attachment organelle, the so-called ventral disc. The mechanical function of the ventral disc, however, is still debated. Earlier studies postulated that a dynamic negative pressure under the ventral disc, generated by persistently beating flagella, mediates the attachment. Later studies suggested a suction model based on structural changes of the ventral discs, substrate clutching or grasping, or unspecific contact forces. In this study, we aim to contribute to the understanding of G. duodenalis attachment by investigating detachment characteristics and determining adhesion forces of single trophozoites on a smooth glass surface (RMS = 1.1 ± 0.2 nm) by fluidic force microscopy (FluidFM)-based single-cell force spectroscopy (SCFS). Briefly, viable adherent trophozoites were approached with a FluidFM micropipette, immobilized to the micropipette aperture by negative pressure, and detached from the surface by micropipette retraction while retract force curves were recorded. These force curves displayed novel and so far undescribed characteristics for a microorganism, namely, gradual force increase on the pulled trophozoite, with localization of adhesion force shortly before cell detachment length. Respective adhesion forces reached 7.7 ± 4.2 nN at 1 µm s-1 pulling speed. Importantly, this unique force pattern was different from that of other eukaryotic cells such as Candida albicans or oral keratinocytes, considered for comparison in this study. The latter both displayed a force pattern with force peaks of different values or force plateaus (for keratinocytes) indicative of breakage of molecular bonds of cell-anchored classes of adhesion molecules or membrane components. Furthermore, the attachment mode of G. duodenalis trophozoites was mechanically resilient to tensile forces, when the pulling speeds were raised up to 10 µm s-1 and adhesion forces increased to 28.7 ± 10.5 nN. Taken together, comparative SCSF revealed novel and unique retract force curve characteristics for attached G. duodenalis, suggesting a ligand-independent suction mechanism, that differ from those of other well described eukaryotes.

Consensus definitions in imported human schistosomiasis: a GeoSentinel and TropNet Delphi study.

Terminology in schistosomiasis is not harmonised, generating misunderstanding in data interpretation and clinical descriptions. This study aimed to achieve consensus on definitions of clinical aspects of schistosomiasis in migrants and returning travellers. We applied the Delphi method. Experts from institutions affiliated with GeoSentinel and TropNet, identified through clinical and scientific criteria, were invited to participate. Five external reviewers revised and pilot-tested the statements. Statements focusing on the definitions of acute or chronic; possible, probable, or confirmed; active; and complicated schistosomiasis were managed through REDCap and replies managed in a blinded manner. Round 1 mapped the definitions used by experts; subsequent rounds were done to reach consensus, or quantify disagreement, on the proposed statements. Data were analysed with percentages, medians, and IQRs of a 5-point Likert scale. The study was terminated on the basis of consensus or stability-related and time-related criteria. 28 clinicians and scientists met the criteria for experts. 25 (89%) of 28 experts replied to Round 1, 18 (64%) of 28 to Round 2, 19 (68%) of 28 to Round 3, and 21 (75%) of 28 to at least two rounds. High-level consensus (79-100% agreement and IQRs ≤1) was reached for all definitions. Consensus definitions will foster harmonised scientific and clinical communication and support future research and development of management guidelines for schistosomiasis.

Antiparasitic stewardship: a call to action.

Tweetable abstract There is an urgent need to consider antiparasitic drugs in global efforts to achieve and implement equitable and sustainable antimicrobial stewardship initiatives worldwide.

Strongyloidiasis.

Strongyloidiasis is a neglected tropical disease caused primarily by the roundworm Strongyloides stercoralis. Strongyloidiasis is most prevalent in Southeast Asia and the Western Pacific. Although cases have been documented worldwide, global prevalence is largely unknown due to limited surveillance. Infection of the definitive human host occurs via direct skin penetration of the infective filariform larvae. Parasitic females reside in the small intestine and reproduce via parthenogenesis, where eggs hatch inside the host before rhabditiform larvae are excreted in faeces to begin the single generation free-living life cycle. Rhabditiform larvae can also develop directly into infectious filariform larvae in the gut and cause autoinfection. Although many are asymptomatic, infected individuals may report a range of non-specific gastrointestinal, respiratory or skin symptoms. Autoinfection may cause hyperinfection and disseminated strongyloidiasis in immunocompromised individuals, which is often fatal. Diagnosis requires direct examination of larvae in clinical specimens, positive serology or nucleic acid detection. However, there is a lack of standardization of techniques for all diagnostic types. Ivermectin is the treatment of choice. Control and elimination of strongyloidiasis will require a multifaceted, integrated approach, including highly sensitive and standardized diagnostics, active surveillance, health information, education and communication strategies, improved water, sanitation and hygiene, access to efficacious treatment, vaccine development and better integration and acknowledgement in current helminth control programmes.

A multi-pronged approach to improve blood culture diagnostics in different clinical departments: a single-centre experience.

PURPOSE: Blood culture (BC) diagnostics are influenced by many factors. We performed a targeted interdisciplinary analysis to analyse effects of various measures on BC diagnostics performance. METHODS: A diagnostic stewardship initiative was conducted at two intervention and two control wards in a German tertiary level hospital. The initiative comprised staff training on the correct indications and sampling for BC, implementation of information cards, labels to identify the collection site, regular BC bottle feedback including the number of bottles, filling volumes and identified pathogens; and the use of a specific sampling device (BD Vacutainer®). Before and after the interventions, two three-month measurement periods were performed, as well as a one-month follow-up period to assess the sustainability of the conducted measures. RESULTS: In total, 9362 BC bottles from 787 patients were included in the analysis. The number of BCs obtained from peripheral venous puncture could be increased at both intervention wards (44.0 vs. 22.2%, 58.3 vs. 34.4%), while arterial sampling could be reduced (30.6 vs. 4.9%). A total of 134 staff members were fully trained. The intervention led to a considerable increase in BC knowledge (from 62.4 to 79.8% correct answers) with differences between the individual professional groups. Relevant reduced contamination rates could be detected at both intervention wards. CONCLUSIONS: As knowledge on the correct BC sampling and strategies to reduce contamination varies considerably between clinical departments and healthcare professionals, a targeted training should be adapted to the specific needs of the individual professional groups. An additional filling device is not necessary.

Auritidibacter ignavus, an Emerging Pathogen Associated with Chronic Ear Infections.

We describe detection of the previously rarely reported gram-positive bacterium Auritidibacter ignavus in 3 cases of chronic ear infections in Germany. In all 3 cases, the patients had refractory otorrhea. Although their additional symptoms varied, all patients had an ear canal stenosis and A. ignavus detected in microbiologic swab specimens. A correct identification of A. ignavus in the clinical microbiology laboratory is hampered by the inability to identify it by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Also, the bacterium might easily be overlooked because of its morphologic similarity to bacterial species of the resident skin flora. We conclude that a high index of suspicion is warranted to identify A. ignavus and that it should be particularly considered in patients with chronic external otitis who do not respond clinically to quinolone ear drop therapy.

Combinatorial host-response biomarker signature (BV score) and its subanalytes TRAIL, IP-10, and CRP in children with Mycoplasma pneumoniae community-acquired pneumonia.

BACKGROUND: Host-response biomarkers to differentiate bacterial from viral etiology in children with respiratory infections have shown high accuracies, but are understudied in Mycoplasma pneumoniae (Mp) infections. METHODS: We compared BV scores (0-34 indicating viral, and 66-100 indicating bacterial etiology), TRAIL (pg/mL), IP-10 (pg/mL), and CRP (mg/L) serum levels between Mp positive (Mp+) and negative (Mp-) community-acquired pneumonia (CAP). We performed receiver operating characteristic (ROC) curve analyses for clinical features and biomarkers. RESULTS: Of 80 CAP patients (median age 6.3 years, 57.5% male), 26 were Mp + CAP. By comparing Mp + CAP with Mp-CAP patients, BV scores were lower (median 14.0, IQR 3.0-27.8 vs. 54.0, IQR 12.0-84.8; P = 0.0008), TRAIL levels were higher (86.5, IQR 67.4-123.0 vs. 65.5, IQR 42.5-103.9; P = 0.025), CRP levels were lower (12.9, IQR 4.0-22.3 vs. 36.7, IQR 13.0-132.8; P = 0.0019), and IP-10 levels were comparable (366.0, IQR 150.2-603.8 vs. 331.0, IQR 154.3-878.8; P = 0.73). ROC analyses yielded a comparable discriminatory accuracy for the combination of age, fever duration, respiratory symptoms duration, with either procalcitonin or BV (AUC 0.87 vs. 0.86, P = 0.94). CONCLUSIONS: Children with Mp + CAP have atypically low, viral levels of the BV score, underscoring the complementary role of microbiological testing.

Detection of volatile organic compounds in headspace of Klebsiella pneumoniae and Klebsiella oxytoca colonies.

Introduction: Early diagnosis of infections and sepsis is essential as adequate therapy improves the outcome. Unfortunately, current diagnostics are invasive and time-consuming, making diagnosis difficult, especially in neonatology. Novel non-invasive analytical methods might be suitable to detect an infection at an early stage and might even allow identification of the pathogen. Our aim is to identify specific profiles of volatile organic compounds (VOCs) of bacterial species. Methods: Using multicapillary column-coupled ion mobility spectrometry (MCC/IMS), we performed headspace measurements of bacterial cultures from skin and anal swabs of premature infants obtained during weekly screening for bacterial colonization according to KRINKO. We analyzed 25 Klebsiella pneumoniae (KP) cultures on MacConkey (MC) agar plates, 25 Klebsiella oxytoca (KO) cultures on MC agar and 25 bare MC agar plates as a control group. Results: Using MCC/IMS, we identified a total of 159 VOC peaks. 85 peaks allowed discriminating KP and bare MC agar plates, and 51 peaks comparing KO and bare MC agar plates and 6 peaks between KP and KO (significance level of p < 0.05 after Bonferroni post hoc analysis), respectively. Peaks P51 (n-Decane) and P158 (Phenylethyl Alcohol), showed the best sensitivity/specificity/ positive predictive value/negative predictive value of 99.9% each (p < 0.001) for KP. P158 showed the best sensitivity/specificity/positive predictive value/negative predictive value of 99.9% each (p < 0.001) for KO. Comparing KP and KO, best differentiation was enabled using peaks P72, P97 and P16 with sensitivity/specificity/positive predictive value/negative predictive value of 76.0%, 84.0%, 82.6%, 77.8%, respectively (p < 0.05). Discussion: We developed a method for the analysis of VOC profiles of bacteria. Using MCC/IMS, we demonstrated that VOCs derived from bacteria are clearly distinguishable from a bare agar plate. Characteristic peaks obtained by MCC/IMS are particularly suitable for the species-specific identification and differentiation of KP and KO. Thus, MCC/IMS might be a useful tool for in vitro diagnostics. Future studies must clarify whether similar patterns of VOCs can be detected in vivo in patients that are colonized or infected with KP or KO to enable rapid and accurate diagnosis of bacterial colonization.

Attitudes of primary care physicians towards antimicrobial stewardship and the impact of a multi-part training course - a pilot study.

Background: A plethora of antimicrobial stewardship (AMS) programs has been initiated during the past years, focusing on hospital settings. Primary-care physicians have seldom been addressed, although the majority of antibiotic prescriptions are issued for outpatients. We sought to investigate attitudes of primary-care physicians and the impact of a customized training course. Methods: Primary-care physicians in southwest Germany were invited to a multi-part training course on AMS in the primary-care setting. Participants were asked to answer a questionnaire about their attitude and factors that hinder them from implementing AMS or enable them to perform AMS. In addition, a knowledge assessment exam at the beginning and end of the training was conducted on selected infectious diseases/syndromes. Results: In total, 36 primary-care physicians participated in the training course. The predominant age group was 51-60 years old (36%; 13/36). The majority, 23/35 (66%), indicated never having had AMS training, while 22/35 (63%) acknowledged partly implementing AMS activities in their daily routine. The primary barrier was lack of expertise, while the main motives were reducing antimicrobial resistance and optimizing patient care. The provision of guidelines was regarded as more important than feedback on their prescription behavior. Exam performance improved from the initial to the final exam on all topics. Conclusion: Customized AMS training courses are a feasible and potentially complimentary tool to address antibiotic misuse in the primary-care setting.

Discrimination between hypervirulent and non-hypervirulent ribotypes of Clostridioides difficile by MALDI-TOF mass spectrometry and machine learning.

Hypervirulent ribotypes (HVRTs) of Clostridioides difficile such as ribotype (RT) 027 are epidemiologically important. This study evaluated whether MALDI-TOF can distinguish between strains of HVRTs and non-HVRTs commonly found in Europe. Obtained spectra of clinical C. difficile isolates (training set, 157 isolates) covering epidemiologically relevant HVRTs and non-HVRTs found in Europe were used as an input for different machine learning (ML) models. Another 83 isolates were used as a validation set. Direct comparison of MALDI-TOF spectra obtained from HVRTs and non-HVRTs did not allow to discriminate between these two groups, while using these spectra with certain ML models could differentiate HVRTs from non-HVRTs with an accuracy >95% and allowed for a sub-clustering of three HVRT subgroups (RT027/RT176, RT023, RT045/078/126/127). MALDI-TOF combined with ML represents a reliable tool for rapid identification of major European HVRTs.

Evaluation of the Qvella FAST System and the FAST-PBC cartridge for rapid species identification and antimicrobial resistance testing directly from positive blood cultures.

Blood culture diagnostics require rapid and accurate identification (ID) of pathogens and antimicrobial susceptibility testing (AST). Standard procedures, involving conventional cultivation on agar plates, may take up to 48 hours or more until AST completion. Recent approaches aim to shorten the processing time of positive blood cultures (PBC). The FAST System is a new technology, capable of purifying and concentrating bacterial/fungal pathogens from positive blood culture media and producing a bacterial suspension called "liquid colony" (LC), which can be further used in downstream analyses (e.g., ID and AST). Here, we evaluated the performance of the FAST System LC generated from PBC in comparison to our routine workflow including ID by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using Sepsityper, AST by automatized MicroScan WalkAway plus and directly inoculated disk diffusion (DD), and MICRONAUT-AM for yeast/fungi. A total of 261 samples were analyzed, of which 86.6% (226/261) were eligible for the comparative ID and AST analyses. In comparison to the reference technique (culture-grown colonies), ID concordance of the FAST System LC and Sepsityper was 150/154 (97.4%) and 123/154 (79.9%), respectively, for Gram positive; 67/70 (95.7%) and 64/70 (91.4%), respectively, for Gram negative. For AST, categorical agreement (CA) of the FAST System LC in comparison to the routine workflow for Gram-positive bacteria was 96.1% and 98.7% for MicroScan and DD, respectively. Similar results were obtained for Gram-negative bacteria with 96.6% and 97.5% of CA for MicroScan and DD, respectively. Taken together, the FAST System LC allowed the laboratory to significantly reduce the time to obtain correct ID and AST (automated MicroScan) results 1 day earlier and represents a promising tool to expedite the processing of PBC.

Differences in SARS-CoV-2 specific humoral and cellular immune responses after contralateral and ipsilateral COVID-19 vaccination.

BACKGROUND: Individual doses of dual-dose vaccine-regimens are sequentially administered into the deltoid muscle, but little attention has so far been paid to the immunological effects of choosing the ipsilateral or the contralateral side for the second dose. METHODS: In an observational study, 303 previously naive individuals were recruited, who received the second dose of the COVID-19 vaccine BNT162b2 on either the ipsilateral (n = 147) or the contralateral side (n = 156). Spike-specific IgG, IgG-avidity, and neutralizing antibodies were quantified using ELISA and a surrogate assay 2 weeks after dose 2. A subgroup of 143 individuals (64 ipsilateral, 79 contralateral) was analysed for spike-specific CD4 and CD8 T-cells using flow-cytometry. FINDINGS: Median spike-specific IgG-levels did not differ after ipsilateral (4590 (IQR 3438) BAU/ml) or contralateral vaccination (4002 (IQR 3524) BAU/ml, p = 0.106). IgG-avidity was also similar (p = 0.056). However, neutralizing activity was significantly lower after contralateral vaccination (p = 0.024). Likewise, median spike-specific CD8 T-cell levels were significantly lower (p = 0.004). Consequently, the percentage of individuals with detectable CD8 T-cells was significantly lower after contralateral than after ipsilateral vaccination (43.0% versus 67.2%, p = 0.004). Spike specific CD4 T-cell levels were similar in both groups, but showed significantly higher CTLA-4 expression after contralateral vaccination (p = 0.011). These effects were vaccine-specific, as polyclonally stimulated T-cell levels did not differ. INTERPRETATION: Both ipsilateral and contralateral vaccination induce a strong immune response, but secondary boosting is more pronounced when choosing vaccine administration-routes that allows for drainage by the same lymph nodes used for priming. Higher neutralizing antibody activity and higher levels of spike-specific CD8 T-cells may have implications for protection from infection and severe disease and support general preference for ipsilateral vaccination. FUNDING: Financial support was provided in part by the State chancellery of the Saarland to M.S.

Carriage of linezolid-resistant enterococci (LRE) among humans and animals in Nigeria: coexistence of the cfr, optrA, and poxtA genes in Enterococcus faecium of animal origin.

OBJECTIVES: In contrast to increasing reports of the emergence of linezolid-resistant enterococci (LRE) emanating from many countries in Europe, Asia, and North America, data on its status and dissemination from the African continent remain scarce, with the information available limited to countries in North Africa. This study investigated the carriage of LRE and the genetic mechanism of resistance among Enterococcus faecium and Enterococcus faecalis strains recovered from humans and animals in Makurdi, Nigeria. METHODS: We conducted a cross-sectional study between June 2020 and July 2021 during which 630 non-duplicate human and animal faecal samples were collected and processed for the recovery of LRE. The genetic mechanisms for resistance were investigated using polymerase chain reaction (PCR) and Sanger sequencing. RESULTS: Linezolid-resistant enterococci were recovered from 5.87% (37/630; 95% CI: 4.17-8.00) of the samples, with the prevalence in animals and humans being 6.22% [(28/450); 95% CI: 4.17-8.87] and 5.00% [(9/180); 95% CI: 2.31-9.28], respectively. All isolates remained susceptible to vancomycin. No known point mutation mediating linezolid resistance was detected in the 23S rRNA and ribosomal protein genes; however, acquisition of one or more potentially transferable genes (cfr, optrA, and poxtA) was observed in 26 of the 37 LRE isolates. Co-existence of all three transferable genes in a single isolate was found in four E. faecium strains of animal origin. CONCLUSION: This study provides baseline evidence for the emergence and active circulation of LRE driven majorly by the acquisition of the optrA gene in Nigeria. To the best of our knowledge, our study is the first to report a co-carriage of all three transferable linezolid resistance determinants in E. faecium. Active LRE surveillance is urgently required to understand the extent of LRE spread across sub-Saharan Africa and to develop tailored mitigation strategies.

Recipient-Reported Reactogenicity of Different SARS-CoV-2 Vaccination Regimens among Healthcare Professionals and Police Staff in Germany.

The rapid availability of effective vaccines against SARS-CoV-2 was key during the COVID-19 pandemic. However, vaccine hesitancy and relatively low vaccine coverage rates among the general population and particularly vulnerable populations such as healthcare staff reduced the potential benefits of these vaccines. During the early phase of the pandemic, fear of vaccine-related adverse events was common among individuals who refused vaccination. Between March and May 2021, we comparatively assessed the self-reported reactogenicity of different SARS-CoV-2 prime-boost regimens using mRNA-based (BNT162b2 and mRNA-1273) and vector-based vaccines (ChAdOx1 nCoV-19) in (a) healthcare workers (HCW), and (b) police staff from southwest Germany. The majority of participants (71.8%; 1564/2176) received a homologous vaccination. Among HCW, 75.0% were female, whereas 70.0% of police staff were male. The most frequently reported reactions following the first vaccine administration were pain at the injection site (77.94%; 1696/2176), tiredness (51.75%; 1126/2176), and headache (40.44%; 880/2176), which were more commonly reported by HCW as compared to police staff. In homologous, mRNA-based and heterologous vaccination schedules, more reactions were reported after the second vaccine dose. We conclude that the frequency and intensity of self-perceived vaccine reactogenicity may differ between specific population groups and might be mitigated by tailored communication strategies.