Accurate detection of copy number aberrations in FFPE samples using the mFAST-SeqS approach.

BACKGROUND: Shallow whole genome sequencing (Shallow-seq) is used to determine the copy number aberrations (CNA) in tissue samples and circulating tumor DNA. However, costs of NGS and challenges of small biopsies ask for an alternative to the untargeted NGS approaches. The mFAST-SeqS approach, relying on LINE-1 repeat amplification, showed a good correlation with Shallow-seq to detect CNA in blood samples. In the present study, we evaluated whether mFAST-SeqS is suitable to assess CNA in small formalin-fixed paraffin-embedded (FFPE) tissue specimens, using vulva and anal HPV-related lesions. METHODS: Seventy-two FFPE samples, including 36 control samples (19 vulva;17 anal) for threshold setting and 36 samples (24 vulva; 12 anal) for clinical evaluation, were analyzed by mFAST-SeqS. CNA in vulva and anal lesions were determined by calculating genome-wide and chromosome arm-specific z-scores in comparison with the respective control samples. Sixteen samples were also analyzed with the conventional Shallow-seq approach. RESULTS: Genome-wide z-scores increased with the severity of disease, with highest values being found in cancers. In vulva samples median and inter quartile ranges [IQR] were 1[0-2] in normal tissues (n = 4), 3[1-7] in premalignant lesions (n = 9) and 21[13-48] in cancers (n = 10). In anal samples, median [IQR] were 0[0-1] in normal tissues (n = 4), 14[6-38] in premalignant lesions (n = 4) and 18[9-31] in cancers (n = 4). At threshold 4, all controls were CNA negative, while 8/13 premalignant lesions and 12/14 cancers were CNA positive. CNA captured by mFAST-SeqS were mostly also found by Shallow-seq. CONCLUSION: mFAST-SeqS is easy to perform, requires less DNA and less sequencing reads reducing costs, thereby providing a good alternative for Shallow-seq to determine CNA in small FFPE samples.

Enterotoxigenic Staphylococcus aureus in Brazilian artisanal cheeses: Occurrence, counts, phenotypic and genotypic profiles.

The present study aimed to assess the occurrence and counts of Staphylococcus aureus in Brazilian artisanal cheeses (BAC) produced in five regions of Brazil: Coalho and Manteiga (Northeast region); Colonial and Serrano (South); Caipira (Central-West); Marajó (North); and Minas Artisanal cheeses, from Araxá, Campos das Vertentes, Cerrado, Serro and Canastra microregions (Southeast). The resistance to chlorine-based sanitizers, ability to attach to stainless steel surfaces, and antibiogram profile of a large set of S. aureus strains (n = 585) were assessed. Further, a total of 42 isolates were evaluated for the presence of enterotoxigenic genes (sea, seb, sec, sed, see, seg, sei, sej, and ser) and submitted to typing using pulsed-field gel electrophoresis (PFGE). BAC presented high counts of S. aureus (3.4-6.4 log CFU/g), varying from 25 to 62.5%. From the S. aureus strains (n = 585) assessed, 16% could resist 200 ppm of sodium hypochlorite, whereas 87.6% produced strong ability to attach to stainless steel surfaces, corroborating with S. aureus ability to persist and spread in the environment. Furthermore, the relatively high frequency (80.5%) of multidrug-resistant S. aureus and the presence of enterotoxin genes in 92.6% of the strains is of utmost attention. It reveals the lurking threat of SFP that can survive when conditions are favorable. The presence of enterotoxigenic and antimicrobial-resistant strains of S. aureus in cheese constitutes a potential risk to public health. This result calls for better control of cheese contamination sources, and taking hygienic measures is necessary for food safety. More attention should be paid to animal welfare and hygiene practices in some dairy farms during manufacturing to enhance the microbiological quality of traditional cheese products.

Estimation of country-specific tuberculosis resistance antibiograms using pathogen genomics and machine learning.

BACKGROUND: Global tuberculosis (TB) drug resistance (DR) surveillance focuses on rifampicin. We examined the potential of public and surveillance Mycobacterium tuberculosis (Mtb) whole-genome sequencing (WGS) data, to generate expanded country-level resistance prevalence estimates (antibiograms) using in silico resistance prediction. METHODS: We curated and quality-controlled Mtb WGS data. We used a validated random forest model to predict phenotypic resistance to 12 drugs and bias-corrected for model performance, outbreak sampling and rifampicin resistance oversampling. Validation leveraged a national DR survey conducted in South Africa. RESULTS: Mtb isolates from 29 countries (n=19 149) met sequence quality criteria. Global marginal genotypic resistance among mono-resistant TB estimates overlapped with the South African DR survey, except for isoniazid, ethionamide and second-line injectables, which were underestimated (n=3134). Among multidrug resistant (MDR) TB (n=268), estimates overlapped for the fluoroquinolones but overestimated other drugs. Globally pooled mono-resistance to isoniazid was 10.9% (95% CI: 10.2-11.7%, n=14 012). Mono-levofloxacin resistance rates were highest in South Asia (Pakistan 3.4% (0.1-11%), n=111 and India 2.8% (0.08-9.4%), n=114). Given the recent interest in drugs enhancing ethionamide activity and their expected activity against isolates with resistance discordance between isoniazid and ethionamide, we measured this rate and found it to be high at 74.4% (IQR: 64.5-79.7%) of isoniazid-resistant isolates predicted to be ethionamide susceptible. The global susceptibility rate to pyrazinamide and levofloxacin among MDR was 15.1% (95% CI: 10.2-19.9%, n=3964). CONCLUSIONS: This is the first attempt at global Mtb antibiogram estimation. DR prevalence in Mtb can be reliably estimated using public WGS and phenotypic resistance prediction for key antibiotics, but public WGS data demonstrates oversampling of isolates with higher resistance levels than MDR. Nevertheless, our results raise concerns about the empiric use of short-course fluoroquinolone regimens for drug-susceptible TB in South Asia and indicate underutilisation of ethionamide in MDR treatment.

Total joint arthroplasty versus trapeziectomy in the treatment of trapeziometacarpal joint arthritis: a randomized controlled trial.

The aim of this double anonymized, randomized controlled trial was to determine whether total joint arthroplasty has superior outcomes than trapeziectomy 1 year after surgery for trapeziometacarpal osteoarthritis. A total of 62 women aged 40 years and older, scheduled for surgery for stage II or III osteoarthritis of the trapeziometacarpal joint, were included and randomized to trapeziectomy or total joint arthroplasty. The primary outcome was the total score of the Michigan Hand Outcomes Questionnaire. Secondary outcomes were the Michigan Hand Outcomes Questionnaire subscale scores, Disability of the Arm, Shoulder and Hand Questionnaire, active range of motion, strength, return to work, patient satisfaction and complications. Data were collected at baseline and at 3 and 12 months. At 1 year, we found no superiority of total joint arthroplasty over trapeziectomy regarding the total score of the Michigan Hand Outcomes Questionnaire. The total joint arthroplasty did show a significant advantage in strength and range of motion.Level of evidence: I.

Effect of the introduction of screening for cancer precursor lesions on anal cancer incidence over time in people living with HIV: a nationwide cohort study.

BACKGROUND: Incidence of anal cancer is high in people living with HIV, particularly in men who have sex with men (MSM). Screening for and treatment of precursor lesions might prevent progression to anal cancer in people living with HIV. We examined trends in incidence of and mortality after anal cancer diagnosis in people living with HIV, including the effect of screening from 2007 onwards, in the Netherlands. METHODS: In this observational cohort study, we analysed data from the ongoing open nationwide Dutch AIDS Therapy Evaluation in the Netherlands (ATHENA) cohort. We included all consenting adults living with HIV and identified all primary anal squamous cell carcinoma. We reported temporal trends in incident anal cancer cases from Jan 1, 1996, to Dec 31, 2020, and all-cause and anal cancer-related mortality in individuals diagnosed with anal cancer. Multivariable Poisson regression was used to explore risk factors for incident anal cancer and multivariable Cox regression was used to explore risk factors for anal cancer-related mortality. FINDINGS: Among 28 175 individuals in HIV care (59·7% MSM), 227 primary anal cancer cases were diagnosed. Despite the increasing average age of the cohort, crude incidence rates of anal cancer in MSM declined slowly over time, from 107·0 (95% CI 75·7-147·0) per 100 000 person-years in 1996-2005 to 93·7 (75·3-115·0) per 100 000 person-years in 2013-20 (p=0·49). Crude incidence rates in men who do not have sex with men (non-MSM) and women were generally lower than in MSM, but increased slightly over time, from 51·08 (95% CI 20·54-105·25) to 67·82 (40·83-105·91; p=0·52) per 100 000 person-years in non-MSM and from 8·09 (0·20-45·06) to 24·95 (10·03-51·40; p=0·29) per 100 000 person-years in women. The age-adjusted incidence rate in MSM in 2013-20 was significantly lower (rate ratio 0·62 [95% CI 0·41-0·92]) compared with in 1996-2005. Changes in risk factors (less smoking, cumulative exposure to CD4 count of <200 cells per µL, and plasma HIV-1 RNA of >1000 copies per mL) mostly explained the decrease in anal cancer risk over time in MSM. 3866 (23·0%) of 16 819 MSM participated in anal cancer screening at least once. TNM tumour staging was more favourable (Cochrane-Armitage test for trend p=0·033) in individuals diagnosed during screening. Crude anal cancer-associated 5-year mortality in people living with HIV decreased from 30·4% (1996-2005) to 18·3% (2013-20; odds ratio 0·48; p=0·070). Anal cancer-related mortality was 3·7% (95% CI 0·5-23·5) in all men who had been screened and 24·0% (95% CI 18·1-31·3) in men who had not been screened (p=0·023). In men, screening participation (hazard ratio [HR] 0·31, p=0·051) and cumulative exposure to CD4 counts of less than 200 cells per µL (HR 1·11 per year; p=0·0022) were independently associated with anal cancer-related mortality. INTERPRETATION: As anal cancer incidence is slowly declining in MSM but not in non-MSM and women, health-care professionals should not focus only on MSM for anal cancer prevention. Men diagnosed with anal cancer during screening had improved survival, probably because they were diagnosed at an earlier disease stage. Next to preventing anal cancer, these data are an important justification to screen those most at risk of anal cancer. FUNDING: None.

Can Intubation Be Improved with Endotracheal Tubes Marked with a Color Scale? Randomized Controlled Study.

OBJECTIVE: This study aimed to assess if a color scale in the endotracheal tube (ETT) can help operators to correctly select the size and depth of placement of the ETT and decrease the time required to complete the procedure and compared with the usual numeric ETT scale in a mannequin model. STUDY DESIGN: The study was conducted in eight centers. Each size of the ETT was identified with a different color. The experimental ETTs had two different colored areas, one for the mouthpiece and another to identify where the ETT should be taped above the lip (an area of 1 cm. The operators were trained as part of the protocol using an instructional video. Four clinical scenarios requiring endotracheal intubation were designed and randomly assigned. Each operator had to select the size and depth of ETT based on the birth weight (BW), and then had to perform four intubations. RESULTS: A total of 108 operators performed 432 intubations. No differences were found in the correct placement and selection of the ETT. Median time (in seconds) required for intubation using numeric versus experimental tube was: for ETT Ø NRP (Neonatal Resuscitation Program) 2.5, 11.5 versus 8 (p < 0.001), ETT Ø 3, 12 versus 10 (p < 0.001), ETT Ø 3.5, 15.5 versus12 (p = 0.003), ETT Ø 4, 12 versus11 (p = 0.019). CONCLUSION: No significant difference was observed in the selection and correct placement of the ETT. However, the intubation time was significantly shorter using the experimental ETT. This device could improve the effectiveness of intubation by reducing the time needed to properly place the ETT at mid trachea. KEY POINTS: · It is an innovative intervention to try to solve a great inconvenience of daily practice.. · The study also raises the difficulty in maintaining the ability of endotracheal intubation.. · It proposes a scale that ensures the correct location with a safe fixation zone..

DNA Methylation Analysis to predict Regression of high-grade anal Intraepithelial Neoplasia in HIV+ men (MARINE): a cohort study protocol.

INTRODUCTION: Anal cancer precursors, or high-grade anal intraepithelial neoplasia (HGAIN), are highly prevalent in HIV-seropositive (HIV+) men who have sex with men (MSM). Around 30% of lesions regress within 1 year, but current histopathological assessment is unable to distinguish between HGAIN likely to regress and HGAIN likely to persist or progress to cancer. We aim to assess if host cell DNA methylation markers can predict regression of HGAIN, thus determining the need for immediate treatment or active surveillance. This could reduce overtreatment and the associated anal and psycho-sexual morbidity. METHODS AND ANALYSIS: This is an active surveillance cohort study in three centres located in Amsterdam, the Netherlands, in 200 HIV+ MSM diagnosed with HGAIN. Participants will not be treated, but closely monitored during 24 months of follow-up with 6 monthly visits including cytology, and high-resolution anoscopy with biopsies. The primary study endpoint is histopathological regression of each baseline HGAIN lesion at the end of the study. Regression is defined as ≤low grade anal intraepithelial neoplasia in the exit biopsy at 24 months. Regression proportions in lesions with low versus high methylation levels (ASCL1, ZNF582), other biomarkers (HPV genotype, HPV-E4, p16INK4A, Ki-67) and immunological markers at baseline will be compared. Main secondary endpoints are the histological and clinical outcome (ie, the number of octants affected by HGAIN) of each baseline HGAIN lesion and overall HGAIN disease (i.e., all lesions combined) after each visit. The health-related quality of life of the study group will be compared with that of a control group of 50 HIV+ MSM receiving regular HGAIN treatment. ETHICS AND DISSEMINATION: Ethics approval was obtained from the Institutional Review Board of the Academic Medical Center (Amsterdam, The Netherlands; reference no. 2021_099). Participants are required to provide written informed consent. Findings will be disseminated through publication in peer-reviewed scientific journals and presentations at international scientific conferences; dissemination to policy makers and the target patient group will be achieved through our (inter-)national network, professional associations and collaboration with a patient representative organisation. TRIAL REGISTRATION NUMBER: NL9664.

Shoulder muscle changes in patients with type 2 diabetes mellitus who have a painful shoulder: a quantitative muscle ultrasound study.

BACKGROUND: It is assumed that in patients with diabetic neuropathy, muscle denervation can result in shoulder disorders. Muscle denervation will lead to changes in muscle architecture, which can be assessed by quantitative muscle ultrasound (QMUS). The aim was to investigate whether increased muscle echogenicity, as a sign of neuropathy, is more often present in patients with shoulder pain who have type 2 diabetes mellitus (T2DM) than in those without. METHODS: Sixty-six patients with T2DM and 23 patients without diabetes mellitus (DM) having shoulder pain were included. Quantitative muscle ultrasound images were obtained bilaterally from the biceps brachii, deltoid, and supra- and infraspinatus muscles. The mean echogenicity (muscle ultrasound grey value) was transformed into z-scores and compared to reference values obtained from 50 healthy participants. Associations between muscle echogenicity and clinical variables were explored. RESULTS: In painful shoulders of both patients with T2DM and patients without DM, mean echogenicity z-scores of all muscles were significantly increased compared to healthy controls. No significant differences in echogenicity between patients with T2DM and those without DM were found. In patients with T2DM, a distal symmetric polyneuropathy was significantly associated with increased echogenicity of all muscles except the infraspinatus muscle. CONCLUSIONS: These findings indicate that patients with painful shoulders, irrespective of having T2DM, seem to have abnormal shoulder muscles. Future studies are needed to elucidate whether neuropathy or other conditions lead to these muscle changes.

Prognosis of shoulder pain in those with and without a psychological disorder: A prospective cohort study with a six-month follow-up.

BACKGROUND: Because shoulder pain can have an unfavorable prognosis, it is important to have a better understanding of factors that may influence recovery. OBJECTIVE: To determine the association between recovery from shoulder pain and the presence of depression, anxiety, and pain catastrophizing. METHODS: In a prospective cohort study with a six months follow-up, we included patients visiting an orthopaedic department with shoulder pain. Primary outcome was recovery from shoulder pain measured with the Shoulder Pain and Disability Index at three and six months. Information about depression and anxiety (Hospital Anxiety and Depression Scale), pain catastrophizing (Pain Catastrophizing Scale), and demographic and clinical factors were collected at baseline. A linear mixed model was used to estimate the effects of depression, anxiety, pain catastrophizing, and underlying shoulder disorders on recovery. RESULTS: We included 190 patients. There were no statistically significant associations between the presence of depression, anxiety, and pain catastrophizing, and three- and six-month recovery. Also between the underlying shoulder disorders and recovery at three and six months, there were no statistically significant associations. CONCLUSIONS: We could not prove that depression, anxiety, and pain catastrophizing, as well as underlying shoulder disorders, were associated with recovery of shoulder pain at six months.

Molecular characterization of drug-resistant Mycobacterium tuberculosis among Filipino patients derived from the national tuberculosis prevalence survey Philippines 2016.

Tuberculosis, caused by Mycobacterium tuberculosis, remains a high burden disease and leading cause of mortality in the Philippines. Understanding the genetic diversity of M. tuberculosis strains in the population, including those that are multi-drug resistant (MDR), will aid in formulating strategies for effective TB control and prevention. By whole genome sequencing of M. tuberculosis isolates (n = 100) from patients of the Philippine 2016 National Tuberculosis Prevalence Survey, we sought to provide a baseline assessment of the genotypic and phylogenetic characteristics of the isolates. The majority (96/100) of the isolates were EAI2-Manila strain-type (lineage 1), with one Lineage 2 (Beijing), one Lineage 3 (CAS1), and two Lineage 4 (LAM9) strains. The EAI2-Manila clade was not significantly associated with patient's phenotypic and in silico drug resistance profile. Five (5/6) MDR-TB isolates predicted by in silico profiling were concordant with phenotypic drug resistance profile. Twenty-one mutations were identified in nine drug resistance-related genes, all of which have been reported in previous studies. Overall, the results from this study contribute to the growing data on the molecular characteristics of Philippine M. tuberculosis isolates, which can help in developing tools for rapid diagnosis of TB in the country, and thereby reducing the high burden of disease.

Prevalent Morphometrically Assessed Vertebral Fractures in Individuals With Type 2 Diabetes, Prediabetes and Normal Glucose Metabolism: The Maastricht Study.

BACKGROUND: Type 2 diabetes (T2D) is frequently reported to be associated with an increased fracture risk. Epidemiological data on prevalent morphometric vertebral fractures (VFs) in T2D are sparse and even less is known in the prediabetic state. PURPOSE: To determine the association between prevalence and severity of morphometric VFs and glucose metabolism state: normal glucose metabolism (NGM), impaired glucose metabolism (prediabetes) or T2D. METHODS: This study included cross-sectional data from 3625 participants of the Maastricht Study who had a vertebral fracture assessment on lateral Dual Energy X-Ray Absorptiometry images. VFs were classified based on morphometric assessment into mild, moderate and severe VFs (respectively 20-24%, 25-39% or ≥40% reduction in expected vertebral body height). Logistic regression models were used to investigate the association between glucose metabolism status and the prevalence and severity of VFs. Analyses were adjusted for subject characteristics and life-style factors. RESULTS: T2D individuals were older (62.8 ± 7.5 years old) and less often female (30.5%) compared to the NGM group (57.7 ± 8.5 years old, and 58.8% female, respectively). At least one mild, moderate or severe prevalent VF was found in 8.6% of the men and 2.2% of the women in the T2D group, in 9.4% and 8.4% in the prediabetes group and in 9.1% and 4.8% in the NGM group, respectively. After adjustment T2D in women was associated with a lower probability of having a prevalent VF compared to NGM [adjusted OR 0.25 (95% CI 0.09-0.65)], while this was not the case for prediabetes. Furthermore, women with T2D had a significantly lower probability of a prevalent moderate or severe VF [adjusted OR 0.32 (95% CI 0.11-0.96)]. In men there was no significant association between T2D or prediabetes and prevalent VFs. CONCLUSION: Women with T2D had a lower probability of prevalent VFs compared to women with a normal glucose metabolism, while this was not the case for men with T2D and participants with prediabetes.

Large scale survey of yeasts in frozen concentrated orange juice (FCOJ): Occurrence, diversity, and resistance to peracetic acid.

This study aimed to evaluate the occurrence and diversity of yeasts in frozen concentrated orange juice (FCOJ) and assess the resistance of yeasts to peracetic acid. One thousand five hundred (n = 1500) samples of frozen concentrated orange juice (FCOJ) were analyzed, and 280 yeast strains were isolated and identified. Candida represented 37% of all isolates, and the main species identified were Candida pseudointermedia and C. orthopsilosis. Other yeasts identified were Starmerella, Wickerhamiella, Wickerhamiella, Clavispora, Kodamaea, Meyerozyma, Rhodotorula, Trichosporon, Wickerhamomyces, Kluyveromyces, Hanseniaspora, Saccharomyces, Torulaspora, and Zygosaccharomyces. The exogenous origin of the contamination in FCOJ samples analyzed was shown by the high diversity, corroborated by the Simpson (D) and Shannon (H') indices. From a total of 227 yeasts strains tested, more than 20% were able to withstand peracetic acid concentrations >200 ppm, with emphasis on W. anomalus (300 ppm), W. sergipensis (350 ppm), C. rugopelliculosa (350 ppm), K. marxianus (450 ppm), C. parapsilosis (500 ppm), C. pseudointermedia (500 ppm), W. sorbosivorans (500 ppm), C. boleticola (600 ppm), S. cerevisiae (700 ppm) and C. orthopsilosis (750 ppm). This study adds novel data regarding the occurrence and diversity of yeasts present in FCOJ and their resistance to a chemical compound commonly employed in the sanitization of processing and distribution premises and vehicles. These findings are essential to support the development of measures for proper mitigation of contamination of orange juice towards reducing the risks of spoilage by yeasts during FCOJ transportation/storage or when FCOJ is used as an ingredient.

The use and safety of corticosteroid injections for shoulder pain in general practice: a retrospective cohort study.

BACKGROUND: Guidelines for shoulder pain in general practice recommend treatment with corticosteroid injections (CSI) if initial pain management fails. However, little is known about the actual use and safety of CSIs in treatment by general practitioners (GP). OBJECTIVE: The objective of this study was to gain insight into the use and safety of CSIs for patients with a new episode of shoulder pain in general practice. METHODS: A retrospective cohort study was conducted using a healthcare database containing the electronic medical records of approximately 200,000 patients in general practice. A search algorithm was constructed to identify patients with a new episode of shoulder pain between January 2012 and December 2017. Data on the use of CSIs in 2 random samples (n = 1,000) were manually validated for a 12-month period after the diagnosis. RESULTS: In total, 26% of the patients with a new episode of shoulder pain received a CSI. The patient's age (OR 1.03, 95% CI 1.02-1.04) and a history of shoulder pain (OR 1.52, 95% CI 1.13-2.12) were significantly associated with the administration of a CSI. Half of the patients received the CSI in the first consultation. The patient's age was positively associated with the likelihood of receiving the CSI in the first consultation (OR 1.01, 95% CI 1.00-1.02). No serious adverse reactions were recorded by the GP. CONCLUSION: In contrast to the guidelines, CSIs were frequently administered in the first consultation. Older patients and patients with a history of shoulder pain were more likely to receive a CSI for shoulder pain.

[Shoulder complaints]. / Schouderklachten.

Shoulder complaints are a very prevalent condition and a significant cause of morbidity and disability. Most patients with shoulder complaints are primarily seen by general physicians. The guideline, as developed by the Dutch College of General Physicians (NHG) in 2019, formulates a basic algorithm to start early conservative management of shoulder complaints. This article describes several causes of shoulder complaints more extensively and offers possible tools to obtain a more precise diagnosis. With a better knowledge of the multiple causes of shoulder complaints, most shoulder complaints can be adequately managed by general physicians, thus preventing unnecessary referrals.

High throughput screening of technological and biopreservation traits of a large set of wild lactic acid bacteria from Brazilian artisanal cheeses.

This study aimed to evaluate technological (acidification, proteolysis, lipolysis, resistance to low pH, NaCl, and bile salts) and biopreservation (antimicrobial activity against foodborne pathogens) features of 1002 LAB by high throughput screening (HTS) methods. The LAB was isolated from 11 types of Brazilian artisanal cheeses (BAC) marketed in the main 5 producing regions. Remarkable intra-species variability in acidification rates have been found, which was most pronounced between isolates from Mina's artisanal cheeses, Caipira and Coalho cheeses. Lacticaseibacillus paracasei and Levilactobacillus brevis showed the fastest acidification rate; however, all isolates showed slower acidification rates than a lactococcal control strain (4.3 × lower). When testing inhibitory effects, > 75% of LAB isolates could inhibit the growth of Staphylococcus aureus ATCC 19095 and Listeria monocytogenes ATCC 7644. Two of these isolates, identified as Lactiplantibacillus plantarum and Lentilactobacillus buchneri, the sterile and neutral supernatants alone, were sufficient to inhibit L. monocytogenes growth. Principal component analysis (PCA) allowed the identification of functional groups based on proteolytic and lipolytic activity, osmotic stress resistance, and inhibition of L. monocytogenes. The type of cheese the isolates were recovered from influenced properties such as anti-listerial compounds and lipolytic enzyme production. The use of HTS and multivariate statistics allowed insights into a diverse set of LAB technological and biopreservation properties. These findings allow a profound knowledge of the heterogeneity of a large set of isolates, which can be further used to design starter cultures with varied and combined properties, such as biopreservation and technological features. Besides that, HTS makes it possible to analyze a vast panel of LAB strains, reducing costs and time within laboratory analysis, while avoiding the loss of information once all LAB are tested at the same time (differently from the traditional labor-intensive approach, in which a few numbers of strains is tested per time).

Characterisation of anal intraepithelial neoplasia and anal cancer in HIV-positive men by immunohistochemical markers p16, Ki-67, HPV-E4 and DNA methylation markers.

Human papillomavirus (HPV)-induced anal intraepithelial neoplasia (AIN, graded 1-3) is highly prevalent in HIV-positive (HIV+) men who have sex with men (MSM), but only a minority of lesions progresses to cancer. Our study aimed to characterise comprehensively anal tissue samples from a cross-sectional series (n = 104) of HIV+ MSM and longitudinal series (n = 40) of AIN2/3 progressing to cancer using different biomarkers. The cross-sectional series consisted of 8 normal, 26 AIN1, 45 AIN2, 15 AIN3 and 10 anal squamous cell carcinoma. Tissue sections were immunohistochemically (IHC) stained for p16 (viral transformation marker), Ki-67 (cellular proliferation marker) and HPV-E4 (viral production marker). We evaluated the expression of IHC markers and compared it with DNA methylation, a marker for malignant transformation. E4 positivity decreased, whereas p16 and Ki-67 scores and methylation marker positivity increased (P values < .001) with increasing severity of anal lesions. Within AIN2, a heterogeneous biomarker pattern was observed concerning E4, p16 and methylation status, reflecting the biological heterogeneity of these lesions. In the longitudinal series, all AIN2/3 and carcinomas showed high p16 and Ki-67 expression, strong methylation positivity and occasional E4 positivity. We earlier showed that high methylation levels are associated with progression to cancer. The observed E4 expression in some AIN2/3 during the course of progression to cancer and absence of E4 in a considerable number of AIN1 lesions make the potential clinical significance of E4 expression difficult to interpret. Our data show that IHC biomarkers can help to characterise AIN; however, their prognostic value for cancer risk stratification, next to objective methylation analysis, appears to be limited.

HPV vaccination to prevent recurrence of anal intraepithelial neoplasia in HIV+ MSM.

OBJECTIVE: Anal cancer precursor lesions high-grade anal intraepithelial neoplasia (HGAIN) are highly prevalent among HIV+ MSM. Treatment of HGAIN is frustrated by high recurrence rates. We investigated the efficacy of the quadrivalent human papillomavirus (qHPV) vaccine as posttreatment adjuvant in preventing HGAIN recurrence in HIV+ MSM. DESIGN: Randomized, double-blind, placebo-controlled, multicentre trial. SETTING: Three HIV outpatient clinics in Amsterdam, the Netherlands. SUBJECTS: HIV+ MSM with CD4+ cell count more than 350 cells/µl, biopsy-proven intra-anal HGAIN successfully treated in the past year, and lesions still in remission at enrolment, as assessed by high-resolution anoscopy (HRA). INTERVENTION: Participants were randomized to three doses of qHPV (Gardasil-4, MSD) or placebo with vaccinations at 0, 2, and 6 months. HRA was repeated at 6, 12, and 18 months. MAIN OUTCOME MEASURE: The primary outcome was cumulative, biopsy-proven HGAIN recurrence rate at 18 months, evaluated in an intention-to-treat (ITT) (received all vaccinations) and per-protocol analysis (all vaccinations and complete follow-up). RESULTS: We randomized 126 participants of which 64 (50.8%) received qHPV and 62 (49.2%) placebo. All participants received three vaccinations, and in both groups for two participants follow-up was incomplete. We found no difference (P = 0.38) in cumulative HGAIN recurrence rates between the qHPV (44/64, 68.8%) and placebo group (38/62, 61.3%) in the ITT analysis [absolute risk reduction -7.5 (95% confidence interval (CI) -24.1 to 9.2)]. This was similar in the per-protocol analysis. CONCLUSION: Despite adequate serological responses to qHPV vaccination, short-term recurrence of HGAIN was not prevented. These findings do not support qHPV vaccination as a treatment adjuvant to prevent HGAIN recurrence in HIV+ MSM.

The incidence and management of shoulder complaints in general practice: a retrospective cohort study.

BACKGROUND: Shoulder pain is the third most common musculoskeletal complaint in primary care. The international guidelines for general practitioners (GPs) recommend a stepwise treatment of shoulder pain. Little is known about the actual distribution of these treatments in current practice. OBJECTIVE: To gain insight in the incidence and current management of shoulder complaints in Dutch general practice. METHODS: A retrospective cohort study was conducted using a health care database containing the full electronic medical records of approximately 200 000 patients in Dutch general practice. A search algorithm was constructed to identify incident cases of shoulder complaints from January 2012 to December 2017. Data on the management of shoulder complaints were manually validated in a random sample of 1000 cases. RESULTS: The overall incidence of shoulder complaints was 30.3 (95% confidence interval 29.9-30.7) per 1000 person-years. More than half of the patients (58.6%) consulted their GP only once, 44.4% two times or more and 19.7% three times or more. For most patients (58.1%), the GP applied a wait-and-see policy or prescription of oral medication in the first consultation. However, no less than 42.9% of the patients were referred or received an injection already in the first consultation. CONCLUSIONS: There is a wide variety of treatments for shoulder complaints applied by the GP. Some patients are referred or received an injection already in the first consultation. The stepwise approach recommended by the guideline, might not always be applicable due to the diversity of patient- and shoulder characteristics presented in general practice.

Clinical and cost effectiveness of a corticosteroid injection versus exercise therapy for shoulder pain in general practice: protocol for a randomised controlled trial (SIX Study).

INTRODUCTION: Shoulder pain is common and the prognosis is often unfavourable. Dutch guidelines on the treatment of shoulder pain in primary care recommend a corticosteroid injection or a referral to exercise therapy, if initial pain management fails and pain persists. However, evidence of the effectiveness of a corticosteroid injection compared with exercise therapy, especially in the long term, is limited. This trial will assess the clinical effectiveness and cost effectiveness of a corticosteroid injection compared with physiotherapist-led exercise therapy over 12 months follow-up in patients with shoulder pain in primary care. METHODS AND ANALYSIS: The SIX Study is a multicentre, pragmatic randomised clinical trial in primary care. A total of 213 patients with shoulder pain, aged ≥18 years presenting in general practice will be included. Patients will be randomised (1:1) into two groups: a corticosteroid injection or 12 sessions of physiotherapist-led exercise therapy. The effect of the allocated treatment will be assessed through questionnaires at 6 weeks and after 3, 6, 9 and 12 months. The primary outcome is patient's reported shoulder pain-intensity and function, measured with the Shoulder Pain and Disability Index, over 12 months follow-up. Secondary outcomes include cost effectiveness, pain-intensity, function, health-related quality of life, sleep quality, patient's global perceived effect, work absence, healthcare utilisation and adverse events. Between group differences will be evaluated using a repeated measurements analysis with linear effects models. A cost-utility analysis will be performed to assess the cost effectiveness using quality-adjusted life years from a medical and societal perspective. ETHICS AND DISSEMINATION: This study was approved by the Medical Ethics Committee of Erasmus MC University Medical Center Rotterdam (MEC 2020-0300). All participants will give written informed consent prior to data collection. The results from this study will be disseminated in international journals and implemented in the primary care guidelines on shoulder pain. TRIAL REGISTRATION NUMBER: Dutch Trial Registry (NL8854).