Evaluation of surrogate tests for the presence of mecA-mediated methicillin resistance in Staphylococcus capitis, Staphylococcus haemolyticus, Staphylococcus hominis, and Staphylococcus warneri

Testing of staphylococci other tha

Structural and Evolutionary Analyses Show Unique Stabilization Strategies in the Type IV Pili of Clostridium difficile

Type IV pili are produced by many pathogenic Gram-negative bacteria and are important for processes as diverse as twitching motility, biofilm formation, cellular adhesion and horizontal gene transfer. However, many Gram-positive species, including C. difficile, also produce Type IV pili. Here, we identify the major subunit of the Type IV pili of C. difficile, PilA1, and describe multiple three-dimensional structures of PilA1, demonstrating the diversity found in three strains of C. difficile. We also model the incorporation of both PilA1 and a minor pilin, PilJ, into the pilus fiber. Although PilA1 contains no cysteine residues, and therefore cannot form the disulfide bonds found in all Gram-negative Type IV pilins, it adopts unique strategies to achieve a typical pilin fold. The structures of PilA1 and PilJ exhibit similarities with the Type IVb pilins from Gram-negative bacteria that suggest that the Type IV pili of C. difficile are involved in microcolony formation

A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC

The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way

Retrospective report of antimicrobial susceptibility observed in bacterial pathogens isolated from ocular samples at Mount Sinai Hospital, 2010 to 2015

Abstract Background Antimicrobial resistance has emerged as a major threat to global public health. Thus, the surveillance of changes in antimicrobial resistance in local and global settings is a paramount necessity. While many studies have tracked antimicrobial resistance, only a small percentage surveyed ocular isolates. The purpose of this study was to report the in vitro susceptibility of bacterial pathogens isolated from ocular samples in New York, NY from 2010 to 2015. Methods A retrospective review of ocular isolates was conducted. All organisms were collected by 25 separate inpatient wards and outpatient clinics, and were analyzed by the clinical microbiology laboratory at Mount Sinai Hospital. Clinical Laboratory and Standards Institute (CLSI) guidelines were followed for susceptibility testing and breakpoint interpretations. Results A total of 549 bacterial organisms were isolated from 1664 cultures (33%) during the 6-year study period. Of these, 358 isolates (65.2%) underwent susceptibility testing. 182 (50.8%) isolates were Gram-positive. The most common Gram-positive bacterium was Staphylococcus aureus (62.1%). Methicillin-resistance decreased in S. aureus isolates (31.3% in 2010, 14.1% in 2015) but was without significant change (p = 0.25). When analyzing all S. aureus isolates recovered during the study period, there were significantly more methicillin-resistant S. aureus (MRSA) isolates resistant to fluoroquinolones (p <0.0001), erythromycin (p <0.0001), and trimethoprim/sulfamethoxazole (TMP/SMZ; p <0.05). Overall, Streptococcus pneumoniae isolates showed reduced susceptibility to erythromycin, but were otherwise susceptible to the other antimicrobials tested. Haemophilus influenzae (26.1%) and Pseudomonas aeruginosa (23.9%) were the most common Gram-negative bacteria isolated. Resistance to ampicillin and TMP/SMZ was observed in several of the H. influenzae isolates. P. aeruginosa isolates did not show high resistance overall, however, it was noted that isolates resistant to meropenem were also resistant to other antimicrobials (p < 0.01). Conclusion Overall, antimicrobial resistance was infrequent for the Gram-negative and Gram-positive bacteria analyzed. While the MRSA isolates demonstrated increased resistance to multiple antimicrobial classes, this is expected for this pathogen. Due to the continued use of broad-spectrum oral and systemic antimicrobials to treat ocular infections, findings of this study and other surveillance studies specific to ocular isolates should be used as resources in effective decision making in the treatment of ocular disease

Association between gut colonization of vancomycin-resistant enterococci and liver transplant outcomes

Background: Vancomycin-resistant enterococci (VRE) colonization is common in liver transplant recipients and has been associated with worse post-transplant outcomes. Methods: We conducted a retrospective cohort study at the University of Alberta Hospital including patients who underwent a liver transplant between September 2014 and December 2017. Results: Of 343 patients, 68 (19.8%) had pre-transplant VRE colonization and 27 (27/275, 9.8%) acquired VRE post-transplant, 67% were males and the median age was 56.5 years. VRE colonized patients at baseline had higher MELD scores and required longer post-transplant hospitalization. VRE colonization was associated with increased risk of early acute kidney injury (AKI) (64% vs 52%, p = 0. 044), clinically significant bacterial/fungal infection (29% vs 17%, p = 0. 012) and invasive VRE infection (5% vs 1%, p = 0. 017). Mortality at 2-years was 13% in VRE-colonized versus 7% in non-colonized (p = 0.085). On multivariate analysis, VRE colonization increased the risk of post-transplant AKI (HR 1.504, 95% CI: 1.077-2.100, p = 0.017) and clinically significant bacterial or fungal infection at 6 months (HR 2.038, 95%CI: 1.222-3.399, p = 0.006), and was associated with non-significant trend towards increased risk of mortality at 2-years post-transplant (HR 1.974 95% CI 0.890-4.378; p = 0.094). Conclusions: VRE colonization in liver transplant patients is associated with increased risk of early AKI, clinically significant infections, and a trend towards increased mortality at 2-years

Antimicrobial resistance (AMR) in COVID-19 patients: a systematic review and meta-analysis (November 2019–June 2021)

Abstract Background Pneumonia from SARS-CoV-2 is difficult to distinguish from other viral and bacterial etiologies. Broad-spectrum antimicrobials are frequently prescribed to patients hospitalized with COVID-19 which potentially acts as a catalyst for the development of antimicrobial resistance (AMR). Objectives We conducted a systematic review and meta-analysis during the first 18 months of the pandemic to quantify the prevalence and types of resistant co-infecting organisms in patients with COVID-19 and explore differences across hospital and geographic settings. Methods We searched MEDLINE, Embase, Web of Science (BioSIS), and Scopus from November 1, 2019 to May 28, 2021 to identify relevant articles pertaining to resistant co-infections in patients with laboratory confirmed SARS-CoV-2. Patient- and study-level analyses were conducted. We calculated pooled prevalence estimates of co-infection with resistant bacterial or fungal organisms using random effects models. Stratified meta-analysis by hospital and geographic setting was also performed to elucidate any differences. Results Of 1331 articles identified, 38 met inclusion criteria. A total of 1959 unique isolates were identified with 29% (569) resistant organisms identified. Co-infection with resistant bacterial or fungal organisms ranged from 0.2 to 100% among included studies. Pooled prevalence of co-infection with resistant bacterial and fungal organisms was 24% (95% CI 8–40%; n = 25 studies: I2 = 99%) and 0.3% (95% CI 0.1–0.6%; n = 8 studies: I2 = 78%), respectively. Among multi-drug resistant organisms, methicillin-resistant Staphylococcus aureus, carbapenem-resistant Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and multi-drug resistant Candida auris were most commonly reported. Stratified analyses found higher proportions of AMR outside of Europe and in ICU settings, though these results were not statistically significant. Patient-level analysis demonstrated > 50% (n = 58) mortality, whereby all but 6 patients were infected with a resistant organism. Conclusions During the first 18 months of the pandemic, AMR prevalence was high in COVID-19 patients and varied by hospital and geography although there was substantial heterogeneity. Given the variation in patient populations within these studies, clinical settings, practice patterns, and definitions of AMR, further research is warranted to quantify AMR in COVID-19 patients to improve surveillance programs, infection prevention and control practices and antimicrobial stewardship programs globally

A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC

The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.Fil: de Hoog, Sybren. Radboud University Medical Center; Países Bajos. Foundation Atlas of Clinical Fungi; Países Bajos. Peking University First Hospital; China. Universidade Federal do Paraná; BrasilFil: Walsh, Thomas J.. International Society for Human and Animal Mycology; Estados Unidos. University of Maryland; Estados Unidos. Center for Innovative Therapeutics and Diagnostics; Estados Unidos. International Mycological Association; Estados Unidos. Mycoses Study Group, Education and Research Consortium; Estados UnidosFil: Ahmed, Sarah A.. Radboudumc-CWZ Centre of Expertise for Mycology; Países Bajos. International Society for Human and Animal Mycology; Estados Unidos. Foundation Atlas of Clinical Fungi; Países BajosFil: Alastruey Izquierdo, Ana. International Society for Human and Animal Mycology; Estados Unidos. Spanish National Centre for Microbiology; España. Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases; SuizaFil: Alexander, Barbara D.. Duke University; Estados Unidos. Fungal Diagnostics Laboratory Consortium; Estados UnidosFil: Cavling Arendrup, Maiken. Copenhagen University Hospital Rigshospitalet; Dinamarca. European Committee of Antimicrobial Susceptibility Testing; DinamarcaFil: Babady, Esther. Fungal Diagnostics Laboratory Consortium; Estados Unidos. Memorial Sloan Kettering Cancer Cente; Estados Unidos. Asia Pacific Society for Medical Mycology; ChinaFil: Bai, Feng Yan. Chinese Academy of Sciences; República de China. Mycology Committee of Chinese Society for Microbiology; Estados UnidosFil: Balada Llasat, Joan Miquel. Fungal Diagnostics Laboratory Consortium; Estados Unidos. Ohio State University; Estados UnidosFil: Borman, Andrew. Public Health England; Reino UnidoFil: Chowdhary, Anuradha. European Society of Clinical Microbiology and Infectious Diseases; Estados Unidos. University of Delhi; IndiaFil: Clark, Andrew. University of Texas; Estados Unidos. Fungal Diagnostics Laboratory Consortium; Estados UnidosFil: Colgrove, Robert C.. Infectious Diseases Society of America; Estados Unidos. Mount Auburn Hospital; Estados UnidosFil: Cornely, Oliver A.. European Confederation of Medical Mycology; Suiza. Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases ; Suiza. University of Cologne; AlemaniaFil: Dingle, Tanis C.. Institut National de Santé Publique du Québec; Canadá. Clinical and Laboratory Standards Institute; Canadá. Fungal Diagnostics Laboratory Consortium; CanadáFil: Dufresne, Philippe J.. Fungal Diagnostics Laboratory Consortium; Canadá. Institut National de Santé Publique du Québec; Canadá. Clinical and Laboratory Standards Institute; CanadáFil: Fuller, Jeff. Fungal Diagnostics Laboratory Consortium; Reino Unido. London Health Sciences Center; Reino UnidoFil: Gangneux, Jean Pierre. Universite de Rennes I; Francia. European Confederation of Medical Mycology; FranciaFil: Gibas, Connie. University of Texas; Estados UnidosFil: Heather Glasgow. Fungal Diagnostics Laboratory Consortium; Estados Unidos. St. Jude Children’s Research Hospital; Estados UnidosFil: Gräser, Yvonne. Humboldt University; AlemaniaFil: Guillot, Jacques. l'Alimentation Nantes-Atlantique; FranciaFil: Groll, Andreas H.. University Children’s Hospital; Alemania. Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases; SuizaFil: Haase, Gerhard. RWTH Aachen University Hospital; AlemaniaFil: Vitale, Roxana Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; ArgentinaFil: Westblade, Lars. Fungal Diagnostics Laboratory Consortium; Estados Unidos. Weill Cornell Medical College; Estados UnidosFil: Wiederhold, Nathan. Fungal Diagnostics Laboratory Consortium; Estados Unidos. Mycoses Study Group, Education and Research Consortium; Estados Unidos. University of Texas; Estados Unidos. Clinical and Laboratory Standards Institute; Estados Unidos. Medical Mycological Society of the Americas; Estados UnidosFil: White, Lewis. Public Health Wales Microbiology; Reino UnidoFil: Wojewoda, Christina M.. University of Vermont Medical Center; Estados UnidosFil: Zhang, Sean X.. University Johns Hopkins; Estados Unidos. International Society for Human and Animal Mycology; Estados Unidos. Fungal Diagnostics Laboratory Consortium; Estados Unido