Identification of source and sink populations for the emergence and global spread of the East-Asia clone of Community-Associated MRSA

Background: Our understanding of the factors influencing the emergence, dissemination and global distribution of epidemic clones of bacteria is limited. ST59 is a major epidemic clone of community-associated MRSA in East Asia, responsible for extensive morbidity and mortality, but has a much lower prevalence in other parts of the world. The geographic origin of ST59 and its international routes of dissemination are unclear and disputed in the literature. Results: To investigate the origin and spread of the ST59 clone, we obtained whole genome sequences of isolates from four continents, sampled over more than a decade, and carried out a time-scaled phylogeographic analysis. We discover that two distinct ST59 clades emerged concurrently, in East Asia and the USA, but underwent clonal expansion at different times. The East Asia clade was strongly enriched for gene determinants associated with antibiotic resistance, consistent with regional differences in antibiotic usage. Both clones spread independently to Australia and Europe, and we found evidence of the persistence of multi-drug resistance following export from East Asia. Direct transfer of strains between Taiwan and the USA was not observed in either direction, consistent with geographic niche exclusion. Conclusions: Our results resolve a longstanding controversy regarding the origin of the ST59 clone, revealing the major global source and sink populations and routes for the spread of multi-drug resistant clones. Additionally, our findings indicate that diversification of the accessory genome of epidemic clones partly reflects region-specific patterns of antibiotic usage, which may influence bacterial fitness after transmission to different geographic locations

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis.

Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: In this systematic analysis, we used a candidate gene approach to identify mutations associated with resistance or consistent with susceptibility for 13 WHO-endorsed antituberculosis drugs. We collected existing worldwide MTBC whole-genome sequencing data and phenotypic data from academic groups and consortia, reference laboratories, public health organisations, and published literature. We categorised phenotypes as follows: methods and critical concentrations currently endorsed by WHO (category 1); critical concentrations previously endorsed by WHO for those methods (category 2); methods or critical concentrations not currently endorsed by WHO (category 3). For each mutation, we used a contingency table of binary phenotypes and presence or absence of the mutation to compute positive predictive value, and we used Fisher's exact tests to generate odds ratios and Benjamini-Hochberg corrected p values. Mutations were graded as associated with resistance if present in at least five isolates, if the odds ratio was more than 1 with a statistically significant corrected p value, and if the lower bound of the 95% CI on the positive predictive value for phenotypic resistance was greater than 25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: We analysed 41 137 MTBC isolates with phenotypic and whole-genome sequencing data from 45 countries. 38 215 MTBC isolates passed quality control steps and were included in the final analysis. 15 667 associations were computed for 13 211 unique mutations linked to one or more drugs. 1149 (7·3%) of 15 667 mutations were classified as associated with phenotypic resistance and 107 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was more than 80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were identified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: We present the first WHO-endorsed catalogue of molecular targets for MTBC drug susceptibility testing, which is intended to provide a global standard for resistance interpretation. The existence of this catalogue should encourage the implementation of molecular diagnostics by national tuberculosis programmes. Funding: Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation

Pertussis seasonality evident in PCR and serological testing data, Queensland, Australia

We investigated the seasonality of pertussis in Queensland, Australia, between 2008 and 2011 using notification and laboratory data. Polymerase chain reaction and serology testing data demonstrate that in the vaccine era, pertussis remains a seasonal illness, with annual peaks in summer months, and that the seasonality of notification data is masked by testing trends

Randomized, controlled trial of topical exit-site application of honey (Medihoney) versus Mupirocin for the prevention of catheter-associated infections in hemodialysis patients

The clinical usefulness of hemodialysis catheters is limited by increased infectious morbidity and mortality. Topical antiseptic agents, such as mupirocin, are effective at reducing this risk but have been reported to select for antibiotic-resistant strains. The aim of the present study was to determine the efficacy and the safety of exit-site application of a standardized antibacterial honey versus mupirocin in preventing catheter-associated infections. A randomized, controlled trial was performed comparing the effect of thrice-weekly exit-site application of Medihoney versus mupirocin on infection rates in patients who were receiving hemodialysis via tunneled, cuffed central venous catheters. A total of 101 patients were enrolled. The incidences of catheter-associated bacteremias in honey-treated (n = 51) and mupirocin-treated (n = 50) patients were comparable (0.97 versus 0.85 episodes per 1000 catheter-days, respectively; NS). On Cox proportional hazards model analysis, the use of honey was not significantly associated with bacteremia-free survival (unadjusted hazard ratio, 0.94; 95% confidence interval, 0.27 to 3.24; P = 0.92). No exit-site infections occurred. During the study period, 2% of staphylococcal isolates within the hospital were mupirocin resistant. Thrice-weekly application of standardized antibacterial honey to hemodialysis catheter exit sites was safe, cheap, and effective and resulted in a comparable rate of catheter-associated infection to that obtained with mupirocin (although the study was not adequately powered to assess therapeutic equivalence). The effectiveness of honey against antibiotic-resistant microorganisms and its low likelihood of selecting for further resistant strains suggest that this agent may represent a satisfactory alternative means of chemoprophylaxis in patients with central venous catheters

Additional file 2: of Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA

List of core genome sites included in our analysis. Site numbers are relative to the published ST59 genome used as a reference for mapping short reads (GenBank accession CP003166). (TXT 20378 kb

Additional file 3: of Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA

Output from in silico antibiotic resistance testing. Genes associated with antibiotic resistance were detected using SRST2. Gene presence is denoted by the name of the gene (asterisks indicates at least one mismatched SNP or indel and a question mark indicates some low-depth bases, as described on the SRST2 website: https://github.com/katholt/srst2 ). Gene absence is denoted by a hyphen. The amino acid residue (IUPAC single letter code) is given for gyrA, grlA and grlB sites associated with fluoroquinolone resistance. Presence or absence of PVL based on mapping of short reads to lukF-PV and lukS-PV reference sequences is also reported. (XLSX 16 kb

Additional file 1: of Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA

Supplementary figures and table of isolates. Figure S1. Global distribution of reported ST59 isolates and sequencing in our study. Figure S2. Spatiotemporal distribution of CC59 sequences in this study. Figure S3. Maximum likelihood phylogeny of global CC59 sequences from humans. Figure S4. BEAST maximum clade credibility tree of global human CC59 sequences from humans. Figure S5. Posterior probabilities for ancestral location of USA-associated clade in subsampled runs. Figure S6. Posterior probabilities for ancestral location of East Asia-associated clade in subsampled runs. Figure S7. Bayes factors indicating support for links between countries in a symmetric BSSVS phylogeography analysis. Figure S8. Skyride plots for subsampled runs. Figure S9. Heatmaps of median number of transitions between countries for subsampled runs. Figure S10. Presence or absence of accessory genes amongst global CC59 isolates. Figure S11. Root-to-tip distance plot for RAxML phylogeny of S. aureus CC59 sequences. Table S1. 120 ST59 isolates included in phylogenetic analysis. (DOCX 1792 kb

The etiology of community-acquired pneumonia in Australia: Why penicillin plus doxycycline or a macrolide is the most appropriate therapy

Background. Available data on the etiology of community-acquired pneumonia (CAP) in Australia are very limited. Local treatment guidelines promote the use of combination therapy with agents such as penicillin or amoxycillin combined with either doxycycline or a macrolide. Methods. The Australian CAP Study (ACAPS) was a prospective, multicenter study of 885 episodes of CAP in which all patients underwent detailed assessment for bacterial and viral pathogens (cultures, urinary antigen testing, serological methods, and polymerase chain reaction). Antibiotic agents and relevant clinical outcomes were recorded. Results. The etiology was identified in 404 (45.6%) of 885 episodes, with the most frequent causes being Streptococcus pneumoniae (14%), Mycoplasma pneumoniae (9%), and respiratory viruses (15%; influenza, picornavirus, respiratory syncytial virus, parainfluenza virus, and adenovirus). Antibiotic-resistant pathogens were rare: only 5.4% of patients had an infection for which therapy with penicillin plus doxycycline would potentially fail. Concordance with local antibiotic recommendations was high (82.4%), with the most commonly prescribed regimens being a penicillin plus either doxycycline or a macrolide (55.8%) or ceftriaxone plus either doxycycline or a macrolide (36.8%). The 30-day mortality rate was 5.6% (50 of 885 episodes), and mechanical ventilation or vasopressor support were required in 94 episodes (10.6%). Outcomes were not compromised by receipt of narrowerspectrum β-lactams, and they did not differ on the basis of whether a pathogen was identified. Conclusions. The vast majority of patients with CAP can be treated successfully with narrow-spectrum β-lactam treatment, such as penicillin combined with doxycycline or a macrolide. Greater use of such therapy could potentially reduce the emergence of antibiotic resistance among common bacterial pathogens. Members of the study group are listed at the end of the text