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Difficult-to-treat infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are of concern in people living with HIV infection as they are more vulnerable to infection. We aimed to identify molecular characteristics of MRSA colonizing newly diagnosed HIV-infected adults in Tanzania. Individuals newly diagnosed with HIV infection were recruited in Dar es Salaam, Tanzania, from April 2017 to May 2018, as part of the randomized clinical trial CoTrimResist (ClinicalTrials.gov identifier: NCT03087890). Nasal/nasopharyngeal isolates of Staphylococcus aureus were susceptibility tested by disk diffusion method, and cefoxitin-resistant isolates were characterized by short-reads whole genome sequencing. Four percent (22/537) of patients carried MRSA in the nose/nasopharynx. MRSA isolates were frequently resistant towards gentamicin (95%), ciprofloxacin (91%), and erythromycin (82%) but less often towards trimethoprim-sulfamethoxazole (9%). Seventy-three percent had inducible clindamycin resistance. Erythromycin-resistant isolates harbored ermC (15/18) and LmrS (3/18) resistance genes. Ciprofloxacin resistance was mediated by mutations of the quinolone resistance-determining region (QRDR) sequence in the gyrA (S84L) and parC (S80Y) genes. All isolates belonged to the CC8 and ST8-SCCmecIV MRSA clone. Ninety-five percent of the MRSA isolates were spa-type t1476, and one exhibited spa-type t064. All isolates were negative for Panton-Valentine leucocidin (PVL) and arginine catabolic mobile element (ACME) type 1. All ST8-SCCmecIV-spa-t1476 MRSA clones from Tanzania were unrelated to the globally successful USA300 clone. Carriage of ST8 MRSA (non-USA300) was common among newly diagnosed HIV-infected adults in Tanzania. Frequent co-resistance to non-beta lactam antibiotics limits therapeutic options when infection occurs.

Raman optical spectroscopy promises label-free bacterial detection, identification, and antibiotic susceptibility testing in a single step. However, achieving clinically relevant speeds and accuracies remains challenging due to weak Raman signal from bacterial cells and numerous bacterial species and phenotypes. Here we generate an extensive dataset of bacterial Raman spectra and apply deep learning approaches to accurately identify 30 common bacterial pathogens. Even on low signal-to-noise spectra, we achieve average isolate-level accuracies exceeding 82% and antibiotic treatment identification accuracies of 97.0±0.3%. We also show that this approach distinguishes between methicillin-resistant and -susceptible isolates of Staphylococcus aureus (MRSA and MSSA) with 89±0.1% accuracy. We validate our results on clinical isolates from 50 patients. Using just 10 bacterial spectra from each patient isolate, we achieve treatment identification accuracies of 99.7%. Our approach has potential for culture-free pathogen identification and antibiotic susceptibility testing, and could be readily extended for diagnostics on blood, urine, and sputum. The use of Raman spectroscopy for pathogen identification is hampered by the weak Raman signal and phenotypic diversity of bacterial cells. Here the authors generate an extensive dataset of bacterial Raman spectra and apply deep learning to identify common bacterial pathogens and predict antibiotic treatment from noisy Raman spectra.

Antimicrobial resistance is a global health concern, and methicillin-resistant Staphylococcus aureus (MRSA) is one of the highest-priority organisms exhibiting this phenotype. Here, we performed a national surveillance integrating patient clinical data of S. aureus isolated from bloodstream infections. We performed genome sequencing, standardized antimicrobial susceptibility testing, and collected clinical metadata of 580 S. aureus isolates collected during 2019–2020. We focused on three predominant clonal complexes (CC1, CC5, and CC8) and assesses their microbiological and clinical significance, as well as their distribution across eastern and western Japan. Furthermore, we conducted a genomic comparison of the isolates of 2019–2000 with those of 1994–2000 and investigated the evolutionary trajectory of emerging clones from the three dominant clonal complexes. We revealed that the emerging MRSA ST764-SCC mec II showed the highest mortality rate within 30 days of hospitalization. This high-risk clone diverged from the New York/Japan clone (ST5-SCC mec II), which was inferred to have undergone repeated infections with phages carrying superantigen toxin genes and acquired antimicrobial resistance genes via mobile genetic elements, leading to its emergence around 1994. Overall, we provide a blueprint for a national genomic surveillance study that integrates clinical data and enables the identification and evolutionary characterization of a high-risk clone. Authors present results from a national surveillance in Japan that found MRSA strains causing bloodstream infections are predominantly from three clonal lineages. They also identified the emergence of highest 30-day-mortality MRSA clone ST764-SCC mec II and traced its evolutionary path.

Background: The incidence of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) infections is increasing in the United States, and it is possible that municipal wastewater could be a reservoir of this microorganism. To date, no U.S. studies have evaluated the occurrence of MRSA in wastewater. Objective: We examined the occurrence of MRSA and methicillin-susceptible S. aureus (MSSA) at U.S. wastewater treatment plants. Methods: We collected wastewater samples from two Mid-Atlantic and two Midwest wastewater treatment plants between October 2009 and October 2010. Samples were analyzed for MRSA and MSSA using membrane filtration. Isolates were confirmed using biochemical tests and PCR (polymerase chain reaction). Antimicrobial susceptibility testing was performed by Sensititre® microbroth dilution. Staphylococcal cassette chromosome mec (SCCmec) typing, Panton-Valentine leucocidin (PVL) screening, and pulsed field gel electrophoresis (PFGE) were performed to further characterize the strains. Data were analyzed by two-sample proportion tests and analysis of variance. Results: We detected MRSA (n = 240) and MSSA (n = 119) in 22 of 44 (50%) and 24 of 44 (55%) wastewater samples, respectively. The odds of samples being MRSA-positive decreased as treatment progressed: 10 of 12 (83%) influent samples were MRSA-positive, while only one of 12 (8%) effluent samples was MRSA-positive. Ninety-three percent and 29% of unique MRSA and MSSA isolates, respectively, were multidrug resistant. SCCmec types II and IV, the pvl gene, and USA types 100, 300, and 700 (PFGE strain types commonly found in the United States) were identified among the MRSA isolates. Conclusions: Our findings raise potential public health concerns for wastewater treatment plant workers and individuals exposed to reclaimed wastewater. Because of increasing use of reclaimed wastewater, further study is needed to evaluate the risk of exposure to antibiotic-resistant bacteria in treated wastewater.

Current methods for differentiating isolates of predominant lineages of pathogenic bacteria often do not provide sufficient resolution to define precise relationships. Here, we describe a high-throughput genomics approach that provides a high-resolution view of the epidemiology and microevolution of a dominant strain of methicillin-resistant Staphylococcus aureus (MRSA). This approach reveals the global geographic structure within the lineage, its intercontinental transmission through four decades, and the potential to trace person-to-person transmission within a hospital environment. The ability to interrogate and resolve bacterial populations is applicable to a range of infectious diseases, as well as microbial ecology.

An international collection of Staphylococcus aureus of clonal complex (CC) 398 from diverse hosts spanning all continents and a 30 year-period is studied based on whole-genome sequencing (WGS) data. The collection consists of publicly available genomic data from 2994 strains and 134 recently sequenced Swiss methicillin-resistant S. aureus (MRSA) CC398 strains. A time-calibrated phylogeny reveals the presence of distinct phylogroups present in Asia, North and South America and Europe. European MRSA diverged from methicillin-susceptible S. aureus (MSSA) at the beginning of the 1950s. Two major European phylogroups (EP4 and EP5), which diverged approximately 1974, are the main drivers of MRSA CC398 spread in Europe. Within EP5, an emergent MRSA lineage spreading among the European horse population (EP5-Leq) diverged approximately 1996 from the pig lineage (EP5-Lpg), and also contains human-related strains. EP5-Leq is characterized by staphylococcal cassette chromosome mec (SCC mec ) IVa and spa type t011 (CC398-IVa-t011), and EP5-Lpg by CC398-SCC mec Vc-t011. The lineage-specific antibiotic resistance and virulence gene patterns are mostly mediated by the acquisition of mobile genetic elements like SCC mec , S. aureus Genomic Islands (SaGIs), prophages and transposons. Different combinations of virulence factors are present on S. aureus pathogenicity islands (SaPIs), and novel antimicrobial resistance gene containing elements are associated with certain lineages expanding in Europe. This WGS-based analysis reveals the actual evolutionary trajectory and epidemiological trend of the international MRSA CC398 population considering host, temporal, geographical and molecular factors. It provides a baseline for global WGS-based One-Health studies of adaptive evolution of MRSA CC398 as well as for local outbreak investigations. Authors perform a whole genome sequencing-based analysis of an international MRSA CC398 population, revealing the evolutionary trajectory and epidemiological trend considering host, temporal, geographical and molecular factors as well as lineage-associated mobile genetic elements.

Background Rising methicillin-resistant Staphylococcus aureus (MRSA) poses a global health threat, contributing to serious infections with high mortality rates. Integrons are recognized as significant genetic elements in disseminating multidrug-resistant (MDR) strains. This study focuses on assessing the prevalence of integron classes 1, 2, and 3 in S. aureus strains from four major cities in Iran. Methods This cross-sectional study analyzed 183 S. aureus isolates from Shiraz, Tehran, Isfahan, and Yazd in Iran. The isolates were identified using specific biochemical and molecullar tests. The Kirby-Bauer disc diffusion method and microbroth dilution method were employed to determine the susceptibility of the isolates to relevant antibiotics and vancomycin, respectively. The macrolide-lincosamide-streptogramin B (MLS B ) resistance phenotype was also evaluated using the D-test. All isolates were sought for presence of the intI 1, intI 2, and intI 3 genes. Results Among 183 S. aureus isolates, high resistance rates were noted: 86.3% for erythromycin, 66.1% for ciprofloxacin, and 61.7% for clindamycin, while all isolates were susceptible to linezolid and vancomycin. Of the 183 isolates, 59.6% were identified as MRSA and 78.1% as MDR. According to the D-test results, 112/183 (61.2%), 29/183 (15.8%), 25/183 (13.7%), and 17/183 (9.7%) of S. aureus isolates showed constitutive resistance-MLS B , inducible resistance-MLS B , sensitive, and resistance to macrolide-streptogramin B (MS) phenotypes, respectively. The intI 1 gene was found in 14 out of 183 S. aureus isolates (7.6%), while none were positive for the intI 2 or intI 3 genes. Notably, 11/14 (78.5%) and 13/14 (92.8%) intI 1-positive isolates were MRSA and MDR, respectively. Conclusions The distribution of MRSA and MDR S. aureus isolates in Iran seems concerning. Although the prevalence of intI 1 was not as high as in prior studies, almost all S. aureus harbored the intI 1 gene were MRSA and MDR.

Staphylococci are important opportunistic pathogens in human and veterinary medicine in addition to being part of the normal flora of the skin and mucous membranes of mammals and birds. The rise of antimicrobial resistance amongst staphylococci warrants closer investigation of the diversity of skin commensal organisms—including coagulase-negative staphylococci (CoNS)—due to their potential as a source of resistance genes. This study is aimed at characterising the commensal staphylococci—including methicillin-resistant Staphylococcus species (spp.)—from mucocutaneous sites of dogs and cats from remote New South Wales (NSW), Australia. Pet dogs and cats were recruited from participants in a community companion animal health programme in six communities in western NSW. Three swabs were collected from each animal (anterior nares, oropharynx, and perineum) and from skin lesions or wounds if present and cultured on selective media for Staphylococcus spp. In total, 383 pets (303 dogs, 80 cats) were enrolled. Staphylococcus spp. were isolated from 67.3% of dogs and 73.8% of cats (494 isolates). The diversity of CoNS was high (20 species) whilst only three coagulase-positive spp. were isolated (S. pseudintermedius, S. aureus, S. intermedius). The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) carriage in dogs was high (2.6%) relative to other studies but was only a small proportion of overall commensal staphylococci. No cats carried MRSA and no MRSP was isolated from either species. Dogs were significantly more likely to carry coagulase-positive staphylococci than cats (P < 0.001). Amongst dogs, males and those with skin lesions were more likely to carry S. pseudintermedius. This study highlights important differences in the diversity and patterns of carriage of commensal staphylococci between dogs and cats in remote NSW, Australia.

Information about the prevalence of Staphylococcus aureus resistance to antimicrobial drugs has mainly been obtained from invasive strains, although the commensal microbiota is thought to be an important reservoir of resistance. We aimed to compare the prevalence of nasal S aureus carriage and antibiotic resistance, including meticillin-resistant S aureus (MRSA), in healthy patients across nine European countries. In this cross-sectional study, nasal swabs were obtained from 32 206 patients recruited by family doctors participating in existing nationwide family doctor networks in Austria, Belgium, Croatia, France, Hungary, Spain, Sweden, the Netherlands, and the UK. Eligible patients were aged 4 years or older (≥18 years in the UK) and presented with a non-infectious disorder. Swabs were sent to national microbiological laboratories for identification and isolation of S aureus. Antibiotic resistance testing was done at one central microbiological laboratory. We established the genotypic structure of the isolated MRSA strains with the spa typing method. S aureus was isolated from 6956 (21·6%) of 32 206 patients swabbed. The adjusted S aureus prevalence for patients older than 18 years ranged from 12·1% (Hungary) to 29·4% (Sweden). Except for penicillin, the highest recorded resistance rate was to azithromycin (from 1·6% in Sweden to 16·9% in France). In total, 91 MRSA strains were isolated, and the highest MRSA prevalence was reported in Belgium (2·1%). 53 different spa types were detected—the most prevalent were t002 (n=9) and t008 (n=8). The prevalence of S aureus nasal carriage differed across the nine European countries assessed, even after correction for age, sex, and family doctor. Generally, the prevalence of resistance, including that of MRSA, was low. The MRSA strains recorded showed genotypic heterogeneity, both within and between countries. European Commission, 7th Framework Programme(grant agreement 223083).

Background Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most prevalent bacterial pathogens leading to various kinds of infections, but the characteristics of this superbug with both strong biofilm-producing and intracellular invasive capabilities is rarely reported. This study aimed to investigate the genotypic and phenotypic features of this superbug with above two properties. Methods Phenotypic resistance profiling of MRSA clinical isolates was performed via the VITEK 2 AST-GP67 Test Kit. Biofilm production was assessed via crystal violet staining and the Congo red agar (CRA) method. The biofilm-degrading activity was tested using Proteinase K, Dispersin B, and DNase I. The intracellular invasive capability was evaluated via dilution plate count and immunofluorescence assay. Genotyping was performed using multilocus sequence typing and staphylococcal protein A typing methods, and virulence genes were detected via polymerase chain reaction. Flow cytometry was performed to assess the cytotoxicity of the dominant MRSA clones. Results A high prevalence (21.6%) of MRSA isolates exhibiting strong biofilm-forming capability was observed in this study, including 70 strains with the highest level of biofilm production (optical density > 0.4). DNase I exhibited the most effective biofilm-degrading activity, with the biofilm-degrading percentage of 78.6% of the strains exceeding 50%. Simultaneously, 71.4% of the isolates exhibited strong invasive capability into A549 cells. ST5-t2460 (48.6%), ST59-t437 (20%), and ST239-t030 (11.4%) were identified as the predominant clones. In particular, ST5-t2460 and ST239-t030 clones exhibited broader antibiotic resistance to gentamicin, ciprofloxacin, levofloxacin, moxifloxacin, and tetracycline compared with ST59-t437 clone. In addition, a higher percentage of the isolates belonging to ST5-t2460 (91.2%) and ST239-t030 (100%) clones demonstrated stronger intracellular invasive capability relative to those belonging to ST59-t437 clone (14.3%). Furthermore, ST5-t2460 and ST239-t030 clones displayed stronger cytotoxicity and carried higher proportions of adhesion-related genes ( fnbA , sdrD , sasC ) and other virulence genes ( sea , seb , sec , isdB , lukE-D , tsst-1 ). Conclusions This is the first report of the phenotypic–genotypic characteristics of MRSA with both strong biofilm-producing and virulence potential, with ST5-t2460, ST59-t437, and ST239-t030 clones accounting for the major genotypes. Further exploration of specific virulence genes correlating to the pathogenesis of this superbug is deemed essential for developing targeted infection control and treatment strategies in the future.