Abstract
SARS coronavirus 2 (SARS-CoV-2) continues to evolve and new variants emerge. Using nationwide Danish data, we estimate the transmission dynamics of SARS-CoV-2 Omicron subvariants BA.1 and ...BA.2 within households. Among 22,678 primary cases, we identified 17,319 secondary infections among 50,588 household contacts during a 1–7 day follow-up. The secondary attack rate (SAR) was 29% and 39% in households infected with Omicron BA.1 and BA.2, respectively. BA.2 was associated with increased susceptibility of infection for unvaccinated household contacts (Odds Ratio (OR) 1.99; 95%–CI 1.72-2.31), fully vaccinated contacts (OR 2.26; 95%–CI 1.95–2.62) and booster-vaccinated contacts (OR 2.65; 95%–CI 2.29–3.08), compared to BA.1. We also found increased infectiousness from unvaccinated primary cases infected with BA.2 compared to BA.1 (OR 2.47; 95%–CI 2.15–2.84), but not for fully vaccinated (OR 0.66; 95%–CI 0.57–0.78) or booster-vaccinated primary cases (OR 0.69; 95%–CI 0.59–0.82). Omicron BA.2 is inherently more transmissible than BA.1. Its immune-evasive properties also reduce the protective effect of vaccination against infection, but do not increase infectiousness of breakthrough infections from vaccinated individuals.
ABSTRACTTyping of methicillin-resistant Staphylococcus aureus (MRSA) is important in infection control and surveillance. The current nomenclature of MRSA includes the genetic background of the S. ...aureus strain determined by multilocus sequence typing (MLST) or equivalent methods like spa typing and typing of the mobile genetic element staphylococcal cassette chromosome mec (SCCmec), which carries the mecA or mecC gene. Whereas MLST and spa typing are relatively simple, typing of SCCmec is less trivial because of its heterogeneity. Whole-genome sequencing (WGS) provides the essential data for typing of the genetic background and SCCmec, but so far, no bioinformatic tools for SCCmec typing have been available. Here, we report the development and evaluation of SCCmecFinder for characterization of the SCCmec element from S. aureus WGS data. SCCmecFinder is able to identify all SCCmec element types, designated I to XIII, with subtyping of SCCmec types IV (2B) and V (5C2). SCCmec elements are characterized by two different gene prediction approaches to achieve correct annotation, a Basic Local Alignment Search Tool (BLAST)-based approach and a k-mer-based approach. Evaluation of SCCmecFinder by using a diverse collection of clinical isolates (n = 93) showed a high typeability level of 96.7%, which increased to 98.9% upon modification of the default settings. In conclusion, SCCmecFinder can be an alternative to more laborious SCCmec typing methods and is freely available at https://cge.cbs.dtu.dk/services/SCCmecFinder.IMPORTANCE SCCmec in MRSA is acknowledged to be of importance not only because it contains the mecA or mecC gene but also for staphylococcal adaptation to different environments, e.g., in hospitals, the community, and livestock. Typing of SCCmec by PCR techniques has, because of its heterogeneity, been challenging, and whole-genome sequencing has only partially solved this since no good bioinformatic tools have been available. In this article, we describe the development of a new bioinformatic tool, SCCmecFinder, that includes most of the needs for infection control professionals and researchers regarding the interpretation of SCCmec elements. The software detects all of the SCCmec elements accepted by the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements, and users will be prompted if diverging and potential new elements are uploaded. Furthermore, SCCmecFinder will be curated and updated as new elements are found and it is easy to use and freely accessible.
Ha
emophilus influenzae
is a gram-negative coccobacillus known to cause respiratory and invasive infections. It can possess a polysaccharide capsule that can be categorized into six different ...serotypes (i.e., Hia, Hib, Hic, Hid, Hie, and Hif) and non-encapsulated strains that are defined as non-typeable. Furthermore,
H. influenzae
can be characterized into eight biotypes (I–VIII). Traditionally, isolates have been serotyped and biotyped using phenotypic methods; however, these methods are not always reliable. In this study, we evaluate the use of whole-genome sequencing (WGS) for national surveillance and characterization of clinical Danish
H. influenzae
isolates. In Denmark, all clinical invasive isolates between 2014 and 2021 have been serotyped using a traditional phenotypic latex agglutination test as well as
in silico
serotyped using the
in silico
programs “hinfluenzae_capsule_characterization” and “hicap” to compare the subsequent serotypes. Moreover, isolates were also biotyped using a phenotypic enzyme test and the genomic data for the detection of the genes encoding ornithine, tryptophan, and urease. The results showed a 99–100% concordance between the two genotypic approaches and the phenotypic serotyping, respectively. The biotyping showed a 95% concordance between genotyping and phenotyping. In conclusion, our results show that in a clinical surveillance setting,
in silico
serotyping and WGS-based biotyping are a robust and reliable approach for typing clinical
H. influenzae
isolates.
Abstract
Background
Female reproductive tract microbiota may affect human reproduction. The current study considered whether a more detailed characterization of the vaginal microbiota could improve ...prediction of risk of poor reproductive outcome in patients undergoing in vitro fertilization (IVF).
Methods
Vaginal samples from 120 patients undergoing IVF were sequenced using the V4 region of the 16S ribosomal RNA gene with clustering of Gardnerella vaginalis genomic clades. Abnormal vaginal microbiota was defined by microscopy and quantitative polymerase chain reaction (qPCR) for G. vaginalis and/or Atopobium vaginae above a threshold.
Results
Three major community state types with abundance of Lactobacillus crispatus, Lactobacillus iners, and a diverse community type were identified, including 2 subtypes, characterized by a high abundance of L. crispatus and L. iners, respectively, but in combination with common diversity type operational taxonomic units. No significant association between community state type and the reproductive outcome could be demonstrated; however, abnormal vaginal microbiota by qPCR and a grouping based on high Shannon diversity index predicted the reproductive outcome equally well.
Conclusions
The predictive value of 16S ribosomal RNA gene sequencing was not superior to the simpler and less expensive qPCR diagnostic approach in predicting the risk of a poor reproductive outcome in patients undergoing IVF.
Clinical Trials Registration
NCT02042352
Analysis of diagnostic methods for defining abnormal vaginal microbiota in patients undergoing in vitro fertilization treatment shows that quantitative polymerase chain reaction targeting Gardnerella vaginalis and Atopobium vaginae provides clinicians with a valid, robust, and accessible method of diagnosis.
The human vagina harbor a rich microbiota. The optimal state is dominated by lactobacilli that help to maintain health and prevent various diseases. However, the microbiota may rapidly change to a ...polymicrobial state that has been linked to a number of diseases. In the present study, the temporal changes of the vaginal microbiota in patients treated for sexually transmitted diseases or bacterial vaginosis (BV) and in untreated controls were studied for 26 days. The patients included 52 women treated with azithromycin, tetracyclines or moxifloxacin for present or suspected infection with Chlamydia trachomatis or Mycoplasma genitalium. Women with concurrent BV were also treated with metronidazole. The controls were 10 healthy women of matching age. The microbiota was analyzed by 16S rRNA gene deep sequencing, specific qPCRs and microscopy. There was generally good correlation between Nugent score and community state type (CST) and qPCR confirmed the sequencing results. By sequencing, more than 600 different taxa were found, but only 33 constituted more than 1 % of the sequences. In both patients and controls the microbiota could be divided into three different community state types, CST-I, CST-III and CST-IV. Without metronidazole, the microbiota remained relatively stable regarding CST although changes were seen during menstrual periods. Administration of metronidazole changed the microbiota from CST-IV to CST-III in approximately 50% of the treated patients. In contrast, the CST was generally unaffected by azithromycin or tetracyclines. In 30% of the BV patients, Gardnerella vaginalis was not eradicated by metronidazole. The majority of women colonized with Ureaplasma parvum remained positive after azithromycin while U. urealyticum was eradicated.
Escherichia coli sequence type (ST) 131 is of concern because it can acquire antimicrobial resistance and cause extraintestinal infections. E. coli ST131-H22 sublineage appears capable of being ...transmitted to humans through poultry. We report on multidrug-resistant ST131-H22 poultry isolates in Brazil closely related to international human and poultry isolates.
This study aimed to investigate the epidemiology, serotype distribution, phenotypical antibiogram, and molecular resistance gene characteristics of invasive
infections in Denmark from 2014 to 2022. ...Additionally, the potential impact of outdoor temperature and COVID-19 restrictions on the epidemiology of
was assessed.
Invasive
isolates were received from patients with positive culture results from cerebrospinal fluid, blood, or other sterile sites. Sample data were obtained from the Danish laboratory surveillance system/MiBa database, and whole-genome sequencing (WGS) was performed on the isolates. The incidence rates and distribution of
cases were analyzed, and antibiotic susceptibility were assessed.
A total of 1,007 invasive
cases were identified, with serotyping conducted for 752 (74.7%) isolates. The median incidence per year of
was 2.0 cases per 100,000, with the highest incidence in 2014 and the lowest in 2020. The majority of
isolates were non-typeable
(NTHi), while the most prominent serotypes were serotype f followed by serotype b. Bacteremia cases accounted for the majority (88.6%) of occurrences, although meningitis cases showed an increasing trend during the time period. The age group 85+ exhibited the highest incidence. The implementation of COVID-19 preventive interventions in 2020 resulted in a significant reduction in
incidence, which returned to pre-COVID levels in 2021. A negative correlation was observed between monthly
cases and outdoor temperature. An overall level of genetic beta-lactamase resistance of 26.3% was observed divided into 10.6% beta-lactamase-positive ampicillin-resistant (gBLPAR), 13.6% beta-lactamase-negative ampicillin-resistant (gBLNAR) and 2.1% beta-lactamase-positive amoxicillin clavulanate-resistant (gBLPACR). Other non-beta-lactam resistance traits were detected in 7.6% of isolates (primarily aminoglycoside-modifying enzymes).
The overall incidence of
in Denmark returned to stable levels after the COVID-19 epidemic, with NTHi strains dominating. The COVID-19 preventive interventions led to a major reduction in incidence. A significant negative correlation between the incidence of
and temperature was observed. The study revealed an overall genetic beta-lactam resistance rate of 26.3%, and the concordance between genotypic and phenotypic beta-lactam resistance was high (98.2%).
Since its emergence in the early 2000s, livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398 (LA-MRSA CC398) has led to an increasing number of human infections in ...Denmark and other European countries with industrial pig production. LA-MRSA CC398 is primarily associated with skin infections among pig farm workers but is also increasingly recognized as a cause of life-threatening disease among elderly and immunocompromised people. Pig farm workers may serve as vehicles for the spread of LA-MRSA CC398 and other farm-origin bacteria between farms and into the general population. Yet, little is known about the bacterial community dynamics in pig farm workers and other persons with long- and short-term exposure to the pig farm environment. To gain insight into this, we investigated the nasal microbiomes in pig farm workers during a workweek on four LA-MRSA CC398-positive pig farms, as well as in short-term visitors two hours before, immediately after, and 48 hours after a 1-hour visit to another LA-MRSA CC398-positive pig farm. S. aureus and LA-MRSA CC398 carriage was quantified by means of culture, and the composition of the bacterial communities was investigated through sequencing of the 16S rRNA gene. Pig farm workers often carried LA-MRSA CC398 and other bacteria from the pig farm environment, both at work and at home, although at lower levels at home. In contrast, short-term visitors were subject to a less dramatic and rapidly reversible change in the nasal bacterial community composition. These results suggest that pig farm workers may be an important source of LA-MRSA CC398 and perhaps other pathogens of human and veterinary relevance.
Atopic dermatitis (AD) patients have an altered skin bacterial community, with an abundance of Staphylococcus aureus associated with flares, highlighting that microbial organisms may be important for ...disease exacerbation. Despite strong evidence of association between bacterial skin colonisation and AD, very limited knowledge regarding the eukaryotic microbial community, including fungi and ectoparasites, in AD exists. In this study, we compared the skin and nasal eukaryotic microbial community between adult AD patients (n = 55) and non-AD healthy controls (n = 45) using targeted 18S rRNA amplicon sequencing. Analysis was based on the presence or absence of eukaryotic microorganisms.
The cutaneous composition of the eukaryotic microbial community and the alpha-diversity differed significantly between AD patients and non-AD individuals, with increased species richness on AD skin. Alpha-diversity and beta-diversity were similar on lesional and non-lesional skin of patients. The ectoparasite Demodex folliculorum and the yeast Geotrichum candidum were significantly more prevalent on the skin of AD patients. The prevalence of D. folliculorum on lesional skin was greater among patients recently treated with topical corticosteroid. Malassezia was one of the most frequently detected genera at all sites, with M. globosa and M. restricta being the most prevalent. M. restricta was under represented in the anterior nares of AD patients as compared to the non-AD control population.
Significant differences in the eukaryotic microbial communities were found between AD patients and non-AD individuals, with the most striking finding being the significantly overrepresentation of D. folliculorum on AD skin. Whether D. folliculorum can contribute to skin inflammation in AD needs further investigation.
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