Journal of medical microbiology最新文献

{"title":"Vancomycin-sensitive <i>Enterococcus faecium</i> bacteraemia - hospital transmission and mortality in a Danish University Hospital.","authors":"Sanne Groenvall Kjaer Hansen,&nbsp;Louise Roer,&nbsp;Kasper Thystrup Karstensen,&nbsp;Silje Vermedal Hoegh,&nbsp;Frank Hansen,&nbsp;Kasper Klein,&nbsp;Flemming S Rosenvinge,&nbsp;Anette Holm,&nbsp;Marianne N Skov,&nbsp;Anette M Hammerum,&nbsp;Henrik Hasman","doi":"10.1099/jmm.0.001731","DOIUrl":"https://doi.org/10.1099/jmm.0.001731","url":null,"abstract":"<p><p><b>Introduction.</b> The emergence of vancomycin-resistant <i>Enterococcus faecium</i> (VREfm) has left the vancomycin-sensitive <i>E. faecium</i> (VSEfm) strains almost unnoticed.<b>Hypothesis.</b> Molecular characteristics, hospital transmission patterns and clinical impact of VSEfm have changed, and VSEfm is a predictor of VREfm introduction.<b>Aim.</b> We wanted to do a molecular characterization of VSEfm to identify hospital transmissions and links between VSEfm and VREfm, and to investigate the demographics, treatment and impact on mortality of VSEfm bacteraemia.<b>Methodology.</b> VSEfm and VREfm blood culture isolates from Odense University Hospital, Denmark, from 2015 to 2019 were characterized using whole-genome sequencing and core-genome multilocus sequence typing (cgMLST). Clonal shifts and diversity of the VREfm isolates were compared to the VSEfm isolates. Hospital records were used for clinical data and transmission investigation of VSEfm cases.<b>Results.</b> Six-hundred and thirty VSEfm isolates from 599 patients belonged to 42 sequence types (STs) and 131 complex types (CTs) in several clusters. Multiple types were involved in putative transmission, occurring over the entire period. Twenty-seven VREfm bacteraemia cases were included. No correlation between the VSEfm and VREfm clones was identified. The 30 day mortality was 40 %, but only in 6.3 % of the cases, VSEfm bacteraemia was the likely cause of death.<b>Conclusion.</b> The molecular types of VSEfm bacteraemia isolates are changing and diverse. No direct correlation between VSEfm and the introduction of VREfm was found, but widespread hospital transmission indicates a presence of risk factors that could facilitate transmission of other micro-organisms as well. VSEfm bacteraemia is rarely the cause of death, indicating that 30 day mortality does not reflect the cause of death.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":"72 7","pages":""},"PeriodicalIF":3.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9870443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple mechanisms of linezolid resistance in <i>Staphylococcus haemolyticus</i> detected by whole-genome sequencing.","authors":"Meerabai Manoharan,&nbsp;Ajit Ramesh Sawant,&nbsp;K Prashanth,&nbsp;Sujatha Sistla","doi":"10.1099/jmm.0.001737","DOIUrl":"https://doi.org/10.1099/jmm.0.001737","url":null,"abstract":"<p><p><b>Introduction.</b> Linezolid is an effective therapeutic option for treating severe infections caused by multidrug-resistant Gram-positive organisms. Several mechanisms have been reported to be responsible for resistance to this antibiotic.<b>Hypothesis or Gap Statement.</b> Although several mechanisms of linezolid resistance have been reported in <i>Staphylococcus haemolyticus</i>, the prevalence and potential for horizontal transfer of resistance genes have not been fully characterized, particularly among <i>S. haemolyticus</i> isolates from India.<b>Aim.</b> To perform whole-genome sequencing (WGS) of linezolid-resistant <i>S. haemolyticus</i> isolates to characterize the resistance mechanisms.<b>Methodology.</b> WGS was performed for 16 linezolid-resistant <i>S. haemolyticus</i> isolates to check for the presence of <i>cfr</i>, <i>optrA</i> and <i>poxtA</i> genes and mutations in 23S rRNA and ribosomal proteins (L3, L4 and L22) that are possible mechanisms implicated in linezolid resistance. Sequence types were identified using MLST finder. The minimum inhibitory concentration (MIC) of linezolid was determined using the E-test method. Polymerase chain reaction (PCR) was carried out for the detection of the <i>cfr</i> gene.<b>Results.</b> The study documented three different mechanisms of linezolid resistance in <i>S. haemolyticus</i>. Thirteen of the 16 isolates were phenotypically resistant to linezolid, of which 12 were positive for the <i>cfr</i> gene. The G2603T mutation in 23S rRNA was found in the majority of the isolates (<i>n</i>=13). Ten isolates had the R138V mutation in L3 ribosomal protein. Twelve isolates with the <i>cfr</i> gene in combination with either G2603T or R138V mutations displayed extremely high MIC values. Surprisingly, three phenotypically sensitive isolates were found to be positive for the <i>cfr</i> gene but negative for other resistance mechanisms. Importantly, in almost half of the isolates the <i>cfr</i> gene was present on a plasmid. ST3 and ST1 were found to be the predominant sequence types.<b>Conclusion.</b> All phenotypically resistant isolates exhibited two or three linezolid resistance mechanisms. The <i>cfr</i> gene was found on plasmids in many isolates, demonstrating its potential for horizontal transfer to more pathogenic organisms.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":"72 7","pages":""},"PeriodicalIF":3.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9911621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Malaria vaccines to moderate the impact of antibiotic resistance in endemic countries.","authors":"Maria Khan,&nbsp;Saba Khan","doi":"10.1099/jmm.0.001734","DOIUrl":"https://doi.org/10.1099/jmm.0.001734","url":null,"abstract":"<p><p>Swift and widespread deployment of an efficient malaria vaccine in Pakistan, together with basic control and preventive measures, could significantly decrease the economic and healthcare burden caused by drug-resistant malaria. Moreover, the RTS,S/AS01 vaccine has provided a much needed breakthrough after decades of growth, as an innovative vaccine for malaria in phase 3 clinical trials and currently undergoing implementation studies. Vaccination is a potentially critical component of efforts to arrest the development and dissemination of antimicrobial resistance, although little is known about the impact vaccination may have within low- and-middle-income countries.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":"72 7","pages":""},"PeriodicalIF":3.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9866988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying patient- and hospital-level antimicrobial resistance dynamics in <i>Staphylococcus aureus</i> from routinely collected data.","authors":"Quentin Leclerc,&nbsp;Alastair Clements,&nbsp;Helen Dunn,&nbsp;James Hatcher,&nbsp;Jodi A Lindsay,&nbsp;Louis Grandjean,&nbsp;Gwenan M Knight","doi":"10.1099/jmm.0.001724","DOIUrl":"https://doi.org/10.1099/jmm.0.001724","url":null,"abstract":"<p><p><b>Introduction.</b> Antimicrobial resistance (AMR) to all antibiotic classes has been found in the pathogen <i>Staphylococcus aureus</i>. The reported prevalence of these resistances varies, driven by within-host AMR evolution at the patient level, and between-host transmission at the hospital level. Without dense longitudinal sampling, pragmatic analysis of AMR dynamics at multiple levels using routine surveillance data is essential to inform control measures.<b>Gap Statement.</b> The value and limitations of routinely collected hospital data to gain insight into AMR dynamics at the hospital and individual levels simultaneously are unclear.<b>Methodology.</b> We explored <i>S. aureus</i> AMR diversity in 70 000 isolates from a UK paediatric hospital between 2000-2021, using electronic datasets containing multiple routinely collected isolates per patient with phenotypic antibiograms and information on hospitalization and antibiotic consumption.<b>Results.</b> At the hospital level, the proportion of isolates that were meticillin-resistant (MRSA) increased between 2014-2020 from 25-50 %, before sharply decreasing to 30%, likely due to a change in inpatient demographics. Temporal trends in the proportion of isolates resistant to different antibiotics were often correlated in MRSA, but independent in meticillin-susceptible <i>S. aureus</i>. Ciprofloxacin resistance in MRSA decreased from 70-40 % of tested isolates between 2007-2020, likely linked to a national policy to reduce fluoroquinolone usage in 2007. At the patient level, we identified frequent AMR diversity, with 4 % of patients ever positive for <i>S. aureus</i> simultaneously carrying, at some point, multiple isolates with different resistances. We detected changes over time in AMR diversity in 3 % of patients ever positive for <i>S. aureus</i>. These changes equally represented gain and loss of resistance.<b>Conclusion.</b> Within this routinely collected dataset, we found that 65 % of changes in resistance within a patient's <i>S. aureus</i> population could not be explained by antibiotic exposure or between-patient transmission of bacteria, suggesting that within-host evolution via frequent gain and loss of AMR genes may be responsible for these changing AMR profiles. Our study highlights the value of exploring existing routine surveillance data to determine underlying mechanisms of AMR. These insights may substantially improve our understanding of the importance of antibiotic exposure variation, and the success of single <i>S. aureus</i> clones.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":"72 7","pages":""},"PeriodicalIF":3.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9890605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hidden bugs in a newly opened hospital: the distribution of skin microbiota among healthcare workers in a newly opened teaching hospital.","authors":"Manggaiyakarasi Kamala Nathan,&nbsp;Azmiza Syawani Jasni,&nbsp;Siti Zulaikha Zakariah,&nbsp;Tengku Zetty Maztura Tengku Jamaluddin,&nbsp;Muhammad Mohd Isa,&nbsp;Rosni Ibrahim","doi":"10.1099/jmm.0.001732","DOIUrl":"https://doi.org/10.1099/jmm.0.001732","url":null,"abstract":"<p><p><b>Background.</b> Skin is a reservoir for millions of micro-organisms, all of which make up the skin microbiota. Hospitals have been identified as a favourable environment for transmitting micro-organisms and thus, it is important to know the distribution of skin microbiota among healthcare workers (HCWs), as such findings may provide baseline information for the distribution of skin microbiota in hospitals.<b>Hypothesis</b>. There is no significant association between the factors (age, gender, type of skin microenvironment, hand hygiene practices, usage of skin care products, current healthcare practices and previous workplace) and the distribution of the skin microbiota among HCWs.<b>Aim</b>. The study aims to identify type of skin microbiota and associated factors (age, gender, type of skin microenvironment, hand hygiene practices, use of skincare products, current healthcare practice, and previous workplace) that influence the growth of skin microbiota.<b>Method</b>. About 102 bacterial isolates were obtained from the skin of 63 healthcare workers in a newly opened teaching hospital, namely Hospital Pengajar Universiti Putra Malaysia (HPUPM). All isolated bacteria were subjected to phenotypic identification according to standard microbiological procedures.<b>Results.</b> The most common isolated skin microbiota were Gram-positive bacteria (84.3%), followed by Gram-negative bacteria (15.7%). A Chi-square test of independence was used to analyse the above factors and there was a significant association between the type of skin microenvironment and the distribution of skin microbiota (<i>P</i>=0.03) (type of skin microenvironment influences the distribution of skin microbiota).<b>Conclusion.</b> Coagulase-negative <i>Staphylococcus</i> spp. was the most common bacteria isolated from the skin of the healthcare workers. Even though coagulase-negative staphylococci (CoNS) are low pathogenic bacteria, but it may cause serious infection in high risk group of patients. Therefore, it is important to emphasize on the good hand hygiene practices and implement strict infection control measures to minimize the risk of HAI in newly opened hospitals.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":"72 7","pages":""},"PeriodicalIF":3.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9803485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"JMM Profile: West Nile virus.","authors":"Sanam Sewgobind,&nbsp;Fiona McCracken,&nbsp;Mirjam Schilling","doi":"10.1099/jmm.0.001730","DOIUrl":"https://doi.org/10.1099/jmm.0.001730","url":null,"abstract":"<p><p>West Nile virus (WNV) is a positive-sense single-stranded RNA virus belonging to the <i>Flaviviridae</i> family and is maintained in an enzootic cycle between avian hosts and mosquito vectors. Humans, horses and other mammals are susceptible to infection but are dead-end hosts due to a low viraemia. The disease can manifest itself in a variety of clinical signs and symptoms in people and horses from mild fever to severe encephalitis and morbidity. There are no vaccines licensed for human protection, but parts of Europe, North America, Africa and Australia have vaccines commercially available for horses.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":"72 7","pages":""},"PeriodicalIF":3.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10001998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serological status for TORCH in women of childbearing age: a decade-long surveillance (2012-2022) in Italy.","authors":"Emilia Palazzotto, Floriana Bonura, Cinzia Calà, Giuseppina Capra, Daniela Pistoia, Donatella Mangione, Chiara Mascarella, Giuseppe Minì, Marco Enea, Giovanni M Giammanco, Donatella Ferraro, Simona De Grazia","doi":"10.1099/jmm.0.001733","DOIUrl":"10.1099/jmm.0.001733","url":null,"abstract":"<p><p><b>Introduction.</b> Serological screening and seroprevalence data for TORCH infections represent a key instrument to estimate immunity and vaccination levels and exposure rates to prevent and treat TORCH congenital infections.<b>Hypothesis.</b> Serology allows us to identify women susceptible to primary infection.<b>Aim.</b> Assess the prevalence of women at risk of primary infections by TORCH pathogens in Palermo, Sicily, Italy, in the decade 2012-2022.<b>Methodology.</b> A retrospective study was performed to evaluate the serological status (IgG and/or IgM) of 2359 women of childbearing age (WCBA), ranging from 16 to 46 years, attending the AOUP 'P. Giaccone' University Hospital of Palermo.<b>Results.</b> The results showed an overall prevalence of anti-TORCH IgG of 90.5 % for herpesvirus (HSV), 81.2 % for rubella virus (RV), 72.1 % for cytomegalovirus (CMV), 20.9 % for <i>Toxoplasma gondii</i> (TOX) and 4.8 % for <i>Treponema pallidum</i> (TP). IgM positivity was 16.9 % for HSV2, 10.3 % for TOX, 4 % for CMV and, 2 % for RV. A recent/active infection by TP was confirmed in 28.3 % of the seropositive women. Our results indicate that only a small percentage of WCBA were subjected to a comprehensive TORCH serological screening, while most WCBA were only tested for a single pathogen. In addition, no significant differences were found in terms of the overall TORCH IgG seroprevalence among different age groups (<i>P</i>>0.05).<b>Conclusion.</b> Identifying WCBA at risk of exposure during pregnancy allows us to prevent and reduce possible congenital infections, providing detailed guidelines and instructions. The results of this study showed that in Italy the risk of acquiring a primary infection by a TORCH agent is still high, therefore effective prevention strategies, including serological screening, should be implemented.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":"72 7","pages":""},"PeriodicalIF":2.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9886241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MARGINAL NOTES, March 2023 - point of care?","authors":"T J J Inglis","doi":"10.1099/jmm.0.001740","DOIUrl":"https://doi.org/10.1099/jmm.0.001740","url":null,"abstract":"","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":"72 3","pages":""},"PeriodicalIF":3.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9893399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut bacteria and sex differences in colorectal cancer.","authors":"Xi Yang,&nbsp;Ping Li,&nbsp;Zhanbo Qu,&nbsp;Jing Zhuang,&nbsp;Yinhang Wu,&nbsp;Wei Wu,&nbsp;Qichun Wei","doi":"10.1099/jmm.0.001706","DOIUrl":"https://doi.org/10.1099/jmm.0.001706","url":null,"abstract":"<p><p><b>Introduction.</b> Differences in gut bacteria that are associated with the occurrence and development of colorectal cancer (CRC) exist between sexes, and males have a higher morbidity of CRC.<b>Gap Statement.</b> Clinical data for the relationship between gut bacteria and sexes in patients with CRC are not available and are needed to support individualized screening and treatment programmes.<b>Aim.</b> To analyse the relationship between gut bacteria and sexes in patients with CRC.<b>Methodology.</b> A total of 6 077 samples recruited by Fudan University's Academy of Brain Artificial Intelligence Science and Technology were included, and the gut bacteria composition mainly shows the top 30 genera. Linear discriminant analysis Effect Size (LEfSe) was used to analyse the differences in gut bacteria. Pearson correlation coefficients were calculated to demonstrate the relationship of discrepant bacteria. CRC risk prediction models were used to rank the importance of valid discrepant bacteria.<b>Results.</b> <i>Bacteroides, Eubacterium</i> and <i>Faecalibacterium</i> were the top three bacteria in males with CRC, while <i>Bacteroides, Subdoligranulum</i> and <i>Eubacterium</i> were the top three bacteria in females with CRC. The abundance of gut bacteria (<i>Escherichia</i>, <i>Eubacteriales</i>, <i>Clostridia,</i> etc.) was higher in males with CRC compared with that in females with CRC. In addition, <i>Dorea</i> and <i>Bacteroides</i> were important CRC-related bacteria (<i>P</i><0.001). Finally, the importance of discrepant bacteria was ranked based on CRC risk prediction models. <i>Blautia, Barnesiella</i> and <i>Anaerostipes</i> were the top three important discrepant bacteria between males with CRC and females with CRC. The value of AUC was 1.0, the sensitivity was 92.0 %, the specificity was 68.4 %, and the accuracy was 83.3 % in the discovery set.<b>Conclusion.</b> Gut bacteria were correlated with sexes and CRC. It is necessary to consider gender when gut bacteria are used to treat and predict CRC.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":"72 6","pages":""},"PeriodicalIF":3.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9965554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterisation of key genotypic and phenotypic traits of clinical cystic fibrosis <i>Staphylococcus aureus</i> isolates.","authors":"Micaela Mossop,&nbsp;Luca Robinson,&nbsp;Jhih-Hang Jiang,&nbsp;Anton Y Peleg,&nbsp;Luke V Blakeway,&nbsp;Nenad Macesic,&nbsp;Audrey Perry,&nbsp;Stephen Bourke,&nbsp;Fatima R Ulhuq,&nbsp;Tracy Palmer","doi":"10.1099/jmm.0.001703","DOIUrl":"https://doi.org/10.1099/jmm.0.001703","url":null,"abstract":"<p><p><b>Introduction.</b> One third of people with CF in the UK are co-infected by both <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i>. Chronic bacterial infection in CF contributes to the gradual destruction of lung tissue, and eventually respiratory failure in this group.<b>Gap Statement.</b> The contribution of <i>S. aureus</i> to cystic fibrosis (CF) lung decline in the presence or absence of <i>P. aeruginosa</i> is unclear. Defining the molecular and phenotypic characteristics of a range of <i>S. aureus</i> clinical isolates will help further understand its pathogenic capabilities.<b>Aim.</b> Our objective was to use molecular and phenotypic tools to characterise twenty-five clinical <i>S. aureus</i> isolates collected from mono- and coinfection with <i>P. aeruginosa</i> from people with CF at the Royal Victoria Infirmary, Newcastle upon Tyne.<b>Methodology.</b> Genomic DNA was extracted and sequenced. Multilocus sequence typing was used to construct phylogeny from the seven housekeeping genes. A pangenome was calculated using Roary, and cluster of Orthologous groups were assigned using eggNOG-mapper which were used to determine differences within core, accessory, and unique genomes. Characterisation of sequence type, clonal complex, <i>agr</i> and <i>spa</i> types was carried out using PubMLST, eBURST, AgrVATE and spaTyper, respectively. Antibiotic resistance was determined using Kirby-Bauer disc diffusion tests. Phenotypic testing of haemolysis was carried out using ovine red blood cell agar plates and mucoid phenotypes visualised using Congo red agar.<b>Results.</b> Clinical strains clustered closely based on <i>agr</i> type, sequence type and clonal complex. COG analysis revealed statistically significant enrichment of COG families between core, accessory and unique pangenome groups. The unique genome was significantly enriched for replication, recombination and repair, and defence mechanisms. The presence of known virulence genes and toxins were high within this group, and unique genes were identified in 11 strains. Strains which were isolated from the same patient all surpassed average nucleotide identity thresholds, however, differed in phenotypic traits. Antimicrobial resistance to macrolides was significantly higher in the coinfection group.<b>Conclusion.</b> There is huge variation in genetic and phenotypic capabilities of <i>S. aureus</i> strains. Further studies on how these may differ in relation to other species in the CF lung may give insight into inter-species interactions.</p>","PeriodicalId":16343,"journal":{"name":"Journal of medical microbiology","volume":"72 6","pages":""},"PeriodicalIF":3.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9611933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}