CUTIS-SEQ, a flexible bilocus sequence typing scheme that provides high resolution of Cutibacterium acnes strains across all subspecies

OBJECTIVES

A 'high resolution' Single Locus Sequence Typing (SLST) scheme has been described for the anaerobic skin bacterium Cutibacterium acnes that seemingly discriminates sequence types (STs) to a level commensurate with previously described Multilocus Sequence Typing (MLST) methods (MLST₄; MLST₈; MLST₉). However, no quantifiable evaluation of SLST versus MLST for differentiation of C. acnes strains, especially in relation to the subspecies of the bacterium, known as C. acnes subsp. acnes (type I), C. acnes subsp. defendens (type II) and C. acnes subsp. elongatum (type III), has been performed which is vital given its increasing use. To address this, we examined the discriminatory power of SLST versus MLST with a large group of isolates representative of all subspecies.

METHODS

Simpson's index of diversity (D) was used for quantitative comparison of the resolving power of the SLST and MLST schemes for 186 isolates of C. acnes covering all three subspecies.

RESULTS

When strains were considered collectively, SLST and all three MLST approaches had similar D values > 90%. However, at the subspecies level there were significant differences between the methods, most strikingly a reduced discrimination of type II and type III strains (D <80%) by SLST versus MLST₈, and to a lesser extent MLST₄. The MLST₉ method also performed poorly for type II strains (D <70%), but did display the best results for type I (D = 90%). By combining the SLST locus with the camp2 gene sequence to create a novel and flexible high-resolution Bilocus Sequence Typing (BLST) scheme, known as CUTIS-SEQ typing (CUTIbacterium acneS BilocuS sEQuence Typing), we achieved improved resolution at both species and, critically, subspp. levels.

CONCLUSIONS

CUTIS-SEQ provides an opportunity to improve differentiation of C. acnes isolates by SLST without significantly impacting laboratory workload, or compromising application to complex biological communities. A CUTIS-SEQ isolate database is now available as part of the C. acnes PubMLST database at https://pubmlst.org.

Genetic determinants of antimicrobial resistance in three multi-drug resistant strains of Cutibacterium acnes isolated from patients with acne: a predictive in silico study

Objectives. Using available whole genome data, the objective of this in silico study was to identify genetic mechanisms that could explain the antimicrobial resistance profile of three multi-drug resistant (MDR) strains (CA17, CA51, CA39) of the skin bacterium Cutibacterium acnes previously recovered from patients with acne. In particular, we were interested in detecting novel genetic determinants associated with resistance to fluoroquinolone and macrolide antibiotics that could then be confirmed experimentally.

Methods. A range of open source bioinformatics tools were used to ‘mine’ genetic determinants of antimicrobial resistance and plasmid borne contigs, and to characterise the phylogenetic diversity of the MDR strains.

Results. As probable mechanisms of resistance to fluoroquinolones, we identified a previously described resistance associated allelic variant of the gyrA gene with a ‘deleterious' S101L mutation in type IA1 strains CA51 (ST1) and CA39 (ST1), as well as a novel E761R ‘deleterious’ mutation in the type II strain CA17 (ST153). A distinct genomic sequence of the efflux protein YfmO which is potentially associated with resistance to MLSB antibiotics was also present in CA17; homologues in CA51, CA39, and other strains of Cutibacterium acnes , were also found but differed in amino acid content. Strikingly, in CA17 we also identified a circular 2.7 kb non-conjugative plasmid (designated pCA17) that closely resembled a 4.8 kb plasmid (pYU39) from the MDR Salmonella enterica strain YU39.

Conclusions. This study has provided a detailed explanation of potential genetic determinants for MDR in the Cutibacterium acnes strains CA17, CA39 and CA51. Further laboratory investigations will be required to validate these in silico results, especially in relation to pCA17.

"If I've got latent TB, I would like to get rid of it": Derivation of the CARD (Constraints, Actions, Risks, and Desires) Framework informed by South African healthcare worker perspectives on latent tuberculosis treatment

BACKGROUND

Healthcare workers (HWs) have at least twice the risk of tuberculosis (TB) compared to the general population. There is growing emphasis on latent TB infection (LTBI) in high-risk populations. Yet we know little about HWs' perspectives of LTBI testing and treatment to inform implementation in high-incidence settings. We developed a qualitative networked approach to analyze HWs' perspectives on LTBI testing and treatment.

METHODS

We conducted 22 in-depth interviews with nurse and physician stakeholders, who had been recruited as part of a larger study evaluating TB transmission risk in HWs at Tygerberg Hospital, Cape Town, South Africa. We performed open coding to identify emergent themes and selective coding to identify relevant text citations. We used thematic analysis to inductively derive the CARD (Constraints, Actions, Risks, Desires) framework.

RESULTS

All HWs desired to avoid developing TB but few felt this was actionable. Despite LTBI knowledge gaps, safety and cost concerns, most HWs reported hypothetical willingness to take LTBI treatment. The CARD framework showed that desire and action related to LTBI testing and treatment was clearly framed by the interactions between constraints, administrative action, and risk. The surprise HWs described on receiving a negative LTBI (Quantiferon-Plus) result suggests LTBI testing may recalibrate HWs' perceptions regarding the futility of actions to reduce their TB risk.

CONCLUSIONS

LTBI testing and treatment are acceptable to HWs and could counteract the perceived inevitability of occupational TB infection that currently may limit risk reduction action. This should be coupled with administrative leadership and infrastructural support. The CARD analytic framework is a helpful tool for implementation scientists to understand current practices within complex health systems. Application of CARD could facilitate the development of contextually-relevant interventions to address important public health problems such as occupational TB.

Pathways to diagnosis of pediatric TB patients: A mixed methods study from India

BACKGROUND

A significant proportion of pediatric tuberculosis (TB) patients go unnotified due to the challenges in diagnosis of TB among children. The experiences of this vulnerable group while going through the TB care cascade remain largely undocumented. The aim of this study was to explore the experiences of pediatric TB patients and families along the pathway to TB diagnosis and appropriate treatment in four cities of India.

METHODS

The study used a mixed methods, single phased, embedded design. The primary qualitative and secondary quantitative data were collected simultaneously by interviewing families of 100 randomly selected Xpert MTB/RIF positive pediatric TB patients, under the pediatric TB project, in 4 Indian cities using a semi-structured questionnaire. The qualitative component was analyzed to deduce patterns and themes on the patient and family experiences. Descriptive statistics were used to quantify various events along the TB care pathway including various delays (patient, diagnosis and total) and number of providers visited by patients during the diagnostic process.

RESULTS

The median patient, diagnostic and total delays were 3 (IQR: 2,5), 39 (IQR: 23, 91) and 43 days (IQR: 28.5, 98.5), respectively. Patients visited a median of 3 (IQR: 2,4) providers before accessing Xpert MTB/RIF testing. On an average, 68.4% of physicians ordered any test most of them being irrelevant for TB diagnosis. Qualitative data showed considerable suffering for children and their families before and after TB diagnosis including serious concerns of stigma, disruption in education and social life and recurrence of the disease.

CONCLUSION

Our study highlights the significant physical and social distress that the children with TB and their families undergo along the TB care pathway. It also shows diagnostic delay in excess of a month during which multiple providers were met and the patients underwent several diagnostic tests, most of them being inappropriate. Efforts to make Xpert MTB/RIF testing more accessible and part of physicians' toolkit will be of considerable value to ease the complexity of TB diagnosis in children. In addition, communication strategy needs to be developed and implemented to generate awareness among general population around pediatric TB and its management.

Immunohistochemical Detection of Potential Microbial Antigens in Granulomas in the Diagnosis of Sarcoidosis

Sarcoidosis may have more than a single causative agent, including infectious and non-infectious agents. Among the potential infectious causes of sarcoidosis, Mycobacterium tuberculosis and Propionibacterium acnes are the most likely microorganisms. Potential latent infection by both microorganisms complicates the findings of molecular and immunologic studies. Immune responses to potential infectious agents of sarcoidosis should be considered together with the microorganisms detected in sarcoid granulomas, because immunologic reactivities to infectious agents reflect current and past infection, including latent infection unrelated to the cause of the granuloma formation. Histopathologic data more readily support P. acnes as a cause of sarcoidosis compared with M. tuberculosis, suggesting that normally symbiotic P. acnes leads to granuloma formation in some predisposed individuals with Th1 hypersensitivity against intracellular proliferation of latent P. acnes, which may be triggered by certain host or drug-induced conditions. Detection of bacterial nucleic acids in granulomas does not necessarily indicate co-localization of the bacterial proteins in the granulomas. In the histopathologic diagnosis of sarcoidosis, M. tuberculosis-associated and P. acnes-associated sarcoidosis will possibly be differentiated in some patients by immunohistochemistry with appropriate antibodies that specifically react with mycobacterial and propionibacterial antigens, respectively, for each etiology-based diagnosis and potential antimicrobial intervention against sarcoidosis.

Pro-Inflammatory and Neurotrophic Factor Responses of Cells Derived from Degenerative Human Intervertebral Discs to the Opportunistic Pathogen Cutibacterium acnes

Previously, we proposed the hypothesis that similarities in the inflammatory response observed in acne vulgaris and degenerative disc disease (DDD), especially the central role of interleukin (IL)-1β, may be further evidence of the role of the anaerobic bacterium Cutibacterium (previously Propionibacterium) acnes in the underlying aetiology of disc degeneration. To investigate this, we examined the upregulation of IL-1β, and other known IL-1β-induced inflammatory markers and neurotrophic factors, from nucleus-pulposus-derived disc cells infected in vitro with C. acnes for up to 48 h. Upon infection, significant upregulation of IL-1β, alongside IL-6, IL-8, chemokine (C-C motif) ligand 3 (CCL3), chemokine (C-C motif) ligand 4 (CCL4), nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF), was observed with cells isolated from the degenerative discs of eight patients versus non-infected controls. Expression levels did, however, depend on gene target, multiplicity and period of infection and, notably, donor response. Pre-treatment of cells with clindamycin prior to infection significantly reduced the production of pro-inflammatory mediators. This study confirms that C. acnes can stimulate the expression of IL-1β and other host molecules previously associated with pathological changes in disc tissue, including neo-innervation. While still controversial, the role of C. acnes in DDD remains biologically credible, and its ability to cause disease likely reflects a combination of factors, particularly individualised response to infection.

Is the "Common Cold" Our Greatest Ally in the Battle Against SARS-CoV-2?

The discovery of T-cell responses to SARS-CoV-2 in non-infected individuals indicates cross-reactive immune memory from prior exposure to human coronaviruses (HCoV) that cause the common cold. This raises the possibility that “immunity” could exist within populations at rates that may be higher than serology studies estimate. Besides specialized research labs, however, there is limited ability to measure HCoV CD4+ and CD8+ T-cell responses to SARS-CoV-2 infection, which currently impedes interpretation of any potential correlation between COVID-19 disease pathogenesis and the calibration of pandemic control measures. Given this limited testing ability, an alternative approach would be to exploit the large cohort of currently available data from which statistically significant associations may be generated. This would necessitate the merging of several public databases including patient and contact tracing, which could be created by relevant public health organizations. Including data from both symptomatic and asymptomatic patients in SARS-CoV-2 databases and surveillance systems could provide the necessary information to allow for more informed decisions.

Cutibacterium acnes Infection Induces Type I Interferon Synthesis Through the cGAS-STING Pathway

Cutibacterium (previously Propionibacterium) acnes is an anaerobic, Gram-positive commensal of the human body. The bacterium has been associated with a variety of diseases, including acne vulgaris, prosthetic joint infections, prostate cancer, and sarcoidosis. The accumulation of C. acnes in diseases such as acne and prostate cancer has been shown to correlate with enhanced inflammation. While the C. acnes-induced proinflammatory axis, via NF-κB and MAPK signaling and inflammasome activation, has been investigated over the last few decades, the potential role of C. acnes in triggering the type I interferon (IFN-I) pathway has not been addressed. Our results show that C. acnes induces the IFN-I signaling axis in human macrophages by triggering the cGAS-STING pathway. In addition, IFN-I signaling induced by C. acnes strongly depends on the adapter protein TRIF in a non-canonical manner; these signaling events occurred in the absence of any detectable intracellular replication of the bacterium. Collectively, our results provide important insight into C. acnes-induced intracellular signaling cascades in human macrophages and suggest IFN-I as a factor in the etiology of C. acnes-induced diseases. This knowledge may be valuable for developing novel therapies targeting C. acnes in diseases where the accumulation of the bacterium leads to an inflammatory pathology.

Is Cutibacterium (previously Propionibacterium) acnes a potential pathogenic factor in the aetiology of the skin disease progressive macular hypomelanosis?

Progressive macular hypomelanosis (PMH) is a skin condition that normally causes symmetrically distributed hypopigmented macules on the front and back of the trunk, but rarely the face. To date, the pathophysiology of the condition is not well understood, but a role for the anaerobic skin bacterium Cutibacterium (previously Propionibacterium) acnes in the development of the disease has been proposed due to its sole presence within lesional, but not normal peri-lesional, skin. The success of antimicrobials in the treatment of PMH also provides circumstantial evidence that this association may be causal, although this is still to be proven. More recent culture and metagenomic typing studies indicate that strains of C. acnes subsp. elongatum (type III) may be important in the aetiology of the condition, which would help to explain why PMH does not normally affect the face since such strains are rarely present there, and why no association between this condition and acne vulgaris is found; acne appears to primarily involve type IA₁ strains from C. acnes subsp. acnes (type I). In this review, we summarize current knowledge on the relationship between C. acnes and PMH, and re-examine previous challenges to the view that the bacterium plays a role in the condition against the backdrop of newly emerged data.

Dr. Ram’s triage

Triage is a process of categorizing potential health and guiding care. It is based on the idea that all bodies are equal while potential vitality is not. I examine the triage processes used by Indian physicians as they collaborated with global health researchers to identify patients for a free, cutting-edge tuberculosis test. As I argue, triage forms and reforms social difference within global health despite its aspirations of standardization and experimentality. Problematizing triage as part of global health’s ordinary affect of affordability reveals local biologies, class biopolitics, and clinical speculation in the field. I conclude by considering new avenues of ethnographic inquiry that are opened by attending to the practiced and depoliticized biopolitics that occurs within clinics as everyday, nonreflexive decisions about how to organize resources and speculate on vitalities.

Propionibacterium avidum: A Virulent Pathogen Causing Hip Periprosthetic Joint Infection

Background

Propionibacteria are important members of the human skin microbiota, but are also opportunistic pathogens associated with periprosthetic joint infection (PJI). While the role of Propionibacterium acnes in PJI has been widely described, insight into the capacity of Propionibacterium avidum to cause PJI is limited.

Methods

An unusual cluster of 4 hip PJIs caused by P. avidum in one orthopedic center in 2015 prompted us to retrospectively identify and analyze clinical data related to previous P. avidum PJI cases (1997-2015). We also characterized the hemolytic and biofilm-producing capacity of our 4 clinical P. avidum strains isolated in 2015, and investigated their phylogenetic relationships by whole-genome sequencing.

Results

We retrospectively identified 13 P. avidum PJIs, with the majority being hip-related infections (n = 11). Preoperative synovial fluid cultures were P. avidum positive in 63.6% of cases. Six of 12 patients (50%) with available case histories were treated with an exchange of the prosthesis. In all but 1 of the 6 patients treated with debridement-retention of the prosthesis, treatment failed, thus requiring a 2-stage revision. The isolated P. avidum strains showed a more pronounced hemolytic activity, but a similar biofilm-forming ability when compared to P. acnes. Whole-genome sequencing identified 2 phylogenetic clusters highly related to P. avidum PJI strains isolated in Sweden.

Conclusions

We describe the largest series of P. avidum PJI predominantly located in the hip. Phylogenetic similarity of our P. avidum strains to PJI strains isolated elsewhere suggests that these invasive lineages may be common.

In the eye of the multiple beholders: Qualitative research perspectives on studying and encouraging quality of TB care in India

This paper outlines insights qualitative research brings to the study of quality of care. It advocates understanding care as sequential, interpersonal action aimed at improving health and documenting the networks in which care occurs. It assesses the strengths and weakness of contemporary quantitative and qualitative approaches to examining quality of care for tuberculosis (TB) before outlining three qualitative research programs aimed at understanding quality of TB in India. Three case studies focus on the diagnosis level in the cascade of TB care and use qualitative research to examine the clinical use of pharmaceuticals as diagnostics, the development of diagnostic tests, and the role of care providers in the utilization of diagnostic services. They show that 1) care must be understood as part of relationships over time, 2) the presence or absence of technologies does not always imply their expected use in care, 3) physicians' provision of care is often inflected by their perceptions of patient desires, and 4) effective care is not always perfectly aligned with global health priorities. Qualitative methods with a networked perspective on care provide novel findings that can and have been used when developing quality of care improvement interventions for TB.

Correction to: Intervertebral disc penetration by antibiotics used prophylactically in spinal surgery: implications for the current standards and treatment of disc infections

Unfortunately, the complete conflict of interest statement was missed out in the original publication. The same is given below.

Proposal of new combination, Cutibacterium acnes subsp. elongatum comb. nov., and emended descriptions of the genus Cutibacterium, Cutibacterium acnes subsp. acnes and Cutibacterium acnes subsp. defendens

In 2016, division of the genus Propionibacterium into four distinct genera was proposed. As a consequence, the species Propionibacterium acnes was transferred to Cutibacterium gen. nov. as Cutibacterium acnes comb. nov. The three recently proposed subspecies of P. acnes were not, however, accommodated in this proposal. Following a very recent validation of a new combination for C. acnes subsp. defendens and an automatically created C. acnes subsp. acnes , we now propose the new combination, C. acnes subsp. elongatum comb. nov. The type strain of Cutibacterium acnes subsp. elongatum is JCM 18919T (=NCTC 13655T). On the basis of further genomic and phenotypic (haemolysis and MALDI-TOF mass spectrometry) analyses of these subspecies, we also provide emended descriptions of the genus Cutibacterium Scholz and Kilian 2016, C. acnes subsp. acnes (Gilchrist 1900) Nouioui et al. 2018, and C. acnes subsp. defendens (McDowell et al. 2016) Nouioui et al. 2018.

Intervertebral disc penetration by antibiotics used prophylactically in spinal surgery: implications for the current standards and treatment of disc infections

PURPOSE

The presence of Propionibacterium acnes in a substantial component of resected disc specimens obtained from patients undergoing discectomy or microdiscectomy has led to the suggestion that this prominent human skin and oral commensal may exacerbate the pathology of degenerative disc disease. This hypothesis, therefore, raises the exciting possibility that antibiotics could play an important role in treating this debilitating condition. To date, however, little information about antibiotic penetration into the intervertebral disc is available.

METHODS

Intervertebral disc tissue obtained from 54 microdiscectomy patients given prophylactic cefazolin (n = 25), clindamycin (n = 17) or vancomycin (n = 12) was assayed by high-performance liquid chromatography, with cefaclor as an internal standard, to determine the concentration of antibiotic penetrating into the disc tissue.

RESULTS

Intervertebral disc tissues from patients receiving the positively charged antibiotic clindamycin contained a significantly greater percentage of the antibacterial dose than the tissue from patients receiving negatively charged cefazolin (P < 0.0001) and vancomycin, which has a slight positive charge (P < 0.0001).

CONCLUSION

Positively charged antibiotics appear more appropriate for future studies investigating potential options for the treatment of low-virulence disc infections. These slides can be retrieved under Electronic Supplementary Material.

Clinical Utility of CINtec PLUS Triage in Equivocal Cervical Cytology and Human Papillomavirus Primary Screening

OBJECTIVES

While cervical cytology is accepted triage for human papillomavirus (HPV)-positive women, the efficiency of cervical screening could be improved by exploiting disease markers with higher specificity.

METHODS

CINtec PLUS triage alone and combined with HPV 16/18 genotyping was performed on ThinPrep samples from HPV-positive women. Clinical performance and the potential to reduce or expedite colposcopy referrals were evaluated.

RESULTS

The 2-year sensitivity and specificity for cervical intraepithelial neoplasia grade 3 or worse (CIN3+) were 90% and 42%, respectively. Specificity was improved over HPV testing in equivocal cytology and could cut the referral rate by about 40%. When combined with HPV 16/18 genotyping, CINtec PLUS triage of the 12 other high-risk HPV genotypes generally demonstrated better sensitivity for CIN3+ than separate triage of non-type-specific HPV-positive women. This strategy could reduce colposcopy referrals by 31%.

CONCLUSIONS

These findings highlight the potential of CINtec PLUS to improve management pathways in HPV-positive women. CINtec PLUS cytology represents a sensitive and efficient triage in HPV-positive women. The clinical performance of the dual-stain was most notable in women younger than 25 years and could potentially improve management pathways.

Variations in the quality of tuberculosis care in urban India: A cross-sectional, standardized patient study in two cities

BACKGROUND

India has the highest burden of tuberculosis (TB). Although most patients with TB in India seek care from the private sector, there is limited evidence on quality of TB care or its correlates. Following our validation study on the standardized patient (SP) method for TB, we utilized SPs to examine quality of adult TB care among health providers with different qualifications in 2 Indian cities.

METHODS AND FINDINGS

During 2014-2017, pilot programs engaged the private health sector to improve TB management in Mumbai and Patna. Nested within these projects, to obtain representative, baseline measures of quality of TB care at the city level, we recruited 24 adults to be SPs. They were trained to portray 4 TB "case scenarios" representing various stages of disease and diagnostic progression. Between November 2014 and August 2015, the SPs visited representatively sampled private providers stratified by qualification: (1) allopathic providers with Bachelor of Medicine, Bachelor of Surgery (MBBS) degrees or higher and (2) non-MBBS providers with alternative medicine, minimal, or no qualifications. Our main outcome was case-specific correct management benchmarked against the Standards for TB Care in India (STCI). Using ANOVA, we assessed variation in correct management and quality outcomes across (a) cities, (b) qualifications, and (c) case scenarios. Additionally, 2 micro-experiments identified sources of variation: first, quality in the presence of diagnostic test results certainty and second, provider consistency for different patients presenting the same case. A total of 2,652 SP-provider interactions across 1,203 health facilities were analyzed. Based on our sampling strategy and after removing 50 micro-experiment interactions, 2,602 interactions were weighted for city-representative interpretation. After weighting, the 473 Patna providers receiving SPs represent 3,179 eligible providers in Patna; in Mumbai, the 730 providers represent 7,115 eligible providers. Correct management was observed in 959 out of 2,602 interactions (37%; 35% weighted; 95% CI 32%-37%), primarily from referrals and ordering chest X-rays (CXRs). Unnecessary medicines were given to nearly all SPs, and antibiotic use was common. Anti-TB drugs were prescribed in 118 interactions (4.5%; 5% weighted), of which 45 were given in the case in which such treatment is considered correct management. MBBS and more qualified providers had higher odds of correctly managing cases than non-MBBS providers (odds ratio [OR] 2.80; 95% CI 2.05-3.82; p < 0.0001). Mumbai non-MBBS providers had higher odds of correct management than non-MBBS in Patna (OR 1.79; 95% CI 1.06-3.03), and MBBS providers' quality of care did not vary between cities (OR 1.15; 95% CI 0.79-1.68; p = 0.4642). In the micro-experiments, improving diagnostic certainty had a positive effect on correct management but not across all quality dimensions. Also, providers delivered idiosyncratically consistent care, repeating all observed actions, including mistakes, approximately 75% of the time. The SP method has limitations: it cannot account for patient mix or care-management practices reflecting more than one patient-provider interaction.

CONCLUSIONS

Quality of TB care is suboptimal and variable in urban India's private health sector. Addressing this is critical for India's plans to end TB by 2025. For the first time, we have rich measures on representative levels of care quality from 2 cities, which can inform private-sector TB interventions and quality-improvement efforts.

Is IL-1β Further Evidence for the Role of Propionibacterium acnes in Degenerative Disc Disease? Lessons From the Study of the Inflammatory Skin Condition Acne Vulgaris

The pathogenesis of degenerative disc disease is a complex and multifactorial process in which genetics, mechanical trauma, altered loading and nutrition present significant etiological factors. Infection of the intervertebral disc with the anaerobic bacterium Propionibacterium acnes is now also emerging as a potentially new etiological factor. This human commensal bacterium is well known for its long association with the inflammatory skin condition acne vulgaris. A key component of inflammatory responses to P. acnes in acne appears to be interleukin (IL)-1β. Similarly, in degenerative disc disease (DDD) there is compelling evidence for the fundamental roles of IL-1β in its pathology. We therefore propose that P. acnes involvement in DDD is biologically very plausible, and that IL-1β is the key inflammatory mechanism driving the host response to P. acnes infection. Since there is a solid theoretical basis for this phenomenon, we further propose that the relationship between P. acnes infection and DDD is causal.

"Before Xpert I only had my expertise": A qualitative study on the utilization and effects of Xpert technology among pediatricians in 4 Indian cities

Background

Diagnosing tuberculosis (TB) in children presents considerable challenges. Upfront testing on Xpert® MTB/RIF (‘Xpert’)—a rapid molecular assay with high sensitivity and specificity—for pediatric presumptive TB patients, as recommended by India’s Revised National Tuberculosis Control Program (RNTCP), can pave the way for early TB diagnosis. As part of an ongoing project implemented by Foundation for Innovative New Diagnostics (FIND) dedicated to providing upfront free-of-cost (FOC) Xpert testing to children seeking care in the public and private sectors, a qualitative assessment was designed to understand how national guidelines on TB diagnosis and Xpert technology have been integrated into the pediatric TB care practices of different health providers.

Methods

We conducted semi-structured interviews with a sample of health providers from public and private sectors engaged in the ongoing pediatric project in 4 major cities of India. Providers were sampled from intervention data based on sector of practice, number of Xpert referrals, and TB detection rates amongst referrals. A total of 55 providers were interviewed with different levels of FOC Xpert testing uptake. Data were transcribed and analyzed inductively by a medical anthropologist using thematic content analysis and narrative analysis.

Results

It was observed that despite guidance from RNTCP on the use of Xpert and significant efforts by FIND and state authorities to disseminate these guidelines, there was notable diversity in their implementation by different health care providers. Xpert, apart from being utilized as intended, i.e. as a first diagnostic test for children, was utilized variably–as an initial screening test (to rule out TB), confirmatory test (once TB diagnosis is established based on antibiotic trial or clinically) and/or only for drug susceptibility testing after TB diagnosis was confirmed. Most providers who used Xpert frequently reported that Xpert was an important tool for managing pediatric TB cases, by reducing the proportion of cases diagnosed only on clinical suspicion and by providing upfront information on drug resistance, which is seldom suspected in children. Despite non-standard use, these results showed that Xpert access helped raise awareness, aided in antibiotic stewardship, and reduced dependence on clinical diagnosis among those who diagnose and treat TB in children.

Conclusion

Access to free and rapid Xpert testing for all presumptive pediatric TB patients has had multiple positive effects on pediatricians’ diagnosis and treatment of TB. It has important effects on speed of diagnosis, empirical treatment, and awareness of drug resistance among TB treatment naive children. In addition, our study shows that access to public sector Xpert machines may be an important way to encourage Public-Private integration and facilitate the movement of patients from the private to public sector for anti-TB treatment. Despite availability of rapid and free Xpert testing, our study showed an alarming diversity of Xpert utilization strategies across different providers who may be moving toward suggested practice over time. The degree of diversity in TB diagnostic approaches in children reported here highlights the urgent need for concerted efforts to place Xpert early in diagnostic algorithms to positively impact the pediatric TB care pathway. A positive change in diagnostic algorithms may be possible with continued advocacy, time, and increased access.

Quantifying multiple sclerosis pathology in post mortem spinal cord using MRI

Multiple sclerosis (MS) is a common inflammatory, demyelinating and degenerative disease of the central nervous system. The majority of people with MS present with symptoms due to spinal cord damage, and in more advanced MS a clinical syndrome resembling that of progressive myelopathy is not uncommon. Significant efforts have been undertaken to predict MS-related disability based on short-term observations, for example, the spinal cord cross-sectional area measured using MRI. The histo-pathological correlates of spinal cord MRI changes in MS are incompletely understood, however a surge of interest in tissue microstructure has recently led to new approaches to improve the precision with which MRI indices relate to underlying tissue features, such as myelin content, neurite density and orientation, among others. Quantitative MRI techniques including T₁ and T₂, magnetisation transfer (MT) and a number of diffusion-derived indices have all been successfully applied to post mortem MS spinal cord. Combining advanced quantification of histological features with quantitative - particularly diffusion-based - MRI techniques provide a new platform for high-quality MR/pathology data generation. To more accurately quantify grey matter pathology in the MS spinal cord, a key driver of physical disability in advanced MS, remains an important challenge of microstructural imaging.

Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt?

The Gram-positive, anaerobic bacterium Propionibacterium acnes forms part of the normal microbiota on human skin and mucosal surfaces. While normally associated with skin health, P. acnes is also an opportunistic pathogen linked with a range of human infections and clinical conditions. Over the last decade, our knowledge of the intraspecies phylogenetics and taxonomy of this bacterium has increased tremendously due to the introduction of DNA typing schemes based on single and multiple gene loci, as well as whole genomes. Furthermore, this work has led to the identification of specific lineages associated with skin health and human disease. In this review we will look back at the introduction of DNA sequence typing of P. acnes based on recA and tly loci, and then describe how these methods provided a basic understanding of the population genetic structure of the bacterium, and even helped characterize the grapevine-associated lineage of P. acnes, known as P. acnes type Zappe, which appears to have undergone a host switch from humans-to-plants. Particular limitations of recA and tly sequence typing will also be presented, as well as a detailed discussion of more recent, higher resolution, DNA-based methods to type P. acnes and investigate its evolutionary history in greater detail.

Antisepsis of the skin before spinal surgery with povidone iodine-alcohol followed by chlorhexidine gluconate-alcohol versus povidone iodine-alcohol applied twice for the prevention of contamination of the wound by bacteria: a randomised controlled trial

AIMS

The aim of this study was to determine whether the sequential application of povidone iodine-alcohol (PVI) followed by chlorhexidine gluconate-alcohol (CHG) would reduce surgical wound contamination to a greater extent than PVI applied twice in patients undergoing spinal surgery.

PATIENTS AND METHODS

A single-centre, interventional, two arm, parallel group randomised controlled trial was undertaken, involving 407 patients who underwent elective spinal surgery. For 203 patients, the skin was disinfected before surgery using PVI (10% [w/w (1% w/w available iodine)] in 95% industrial denatured alcohol, povidone iodine; Videne Alcoholic Tincture) twice, and for 204 patients using PVI once followed by CHG (2% [w/v] chlorhexidine gluconate in 70% [v/v] isopropyl alcohol; Chloraprep with tint). The primary outcome measure was contamination of the wound determined by aerobic and anaerobic bacterial growth from samples taken after disinfection.

RESULTS

The detection of viable bacteria in any one of the samples taken after disinfection (culture-positive) was significantly lower in the group treated with both PVI and CHG than in the group treated with PVI alone (59 (29.1%) versus 85 (41.7%), p = 0.009; odds ratio 0.574; 95% confidence interval, 0.380 to 0.866).

CONCLUSIONS

Antisepsis of the skin with the sequential application of PVI and CHG more effectively reduces the contamination of a surgical wound than PVI alone. Cite this article: Bone Joint J 2017;99-B:1354-65.

Thin high-order shims for small dipole NMR magnets

An NMR shim coil design method that addresses the severe spatial constraints of miniaturized dipole magnets is introduced. The fundamental design element, a collection of straight wires, is shown to be sufficient for producing a complete set of shim fields of high mathematical order. In accord with these theoretical considerations, a shim set is constructed using four wires in each of four directions to create all first through fourth order fields, except one. This shim set, with its supporting structure, occupies only 2mm of the available 5mm gap in a small 1.6T magnet. However, the fields produced by the individual wires are found to differ significantly from theoretical expectations. To produce the desired harmonic shim fields, the magnetic field of each of the 32 wires is mapped in three dimensions, and linear combinations of these maps are formed. The resulting shim fields are found to be very pure. The shims are used in a prototype high-resolution NMR magnet in which the 1.0mm sample size is only possible due to the thinness of the shim set. The resulting spectra demonstrate shimming to high resolution (<25ppb FWHM) without undue heating effects.

Intra- and inter-observer reproducibility of CINtec® PLUS in ThinPrep® cytology preparations

BACKGROUND

This study evaluated the intra- and inter-observer reproducibility of the dual-stain biomarker, CINtec^® PLUS cytology in ThinPrep^® specimens, for improved specificity in the detection of cervical disease in women testing human papillomavirus (HPV) positive.

METHODS

A total of 972 cases of HPV-positive women from a triage and primary HPV screening population were selected from an ongoing study evaluating the clinical performance of CINtec^® PLUS cytology. For reproducibility analyses, three cytotechnologists rescreened sets of slides which they had previously reported themselves and which were previously reported by each of the other cytotechnologists. The original results of slides previously screened by each of the three cytotechnologists were also compared with the results of an expert reference evaluator.

RESULTS

Intra- and inter-observer agreement for paired evaluations between reviewers ranged from 82.8% to 94.9% (kappa 0.65-0.91) and 89.2% to 93% (kappa 0.83-0.88), respectively. Reproducibility analyses between the cytotechnologists and the reference evaluator revealed agreements ranging from 95.5% to 98% (kappa 0.89-0.96).

CONCLUSION

Evaluation of the dual-stain biomarker showed a high level of agreement across all evaluators suggesting that CINtec^® PLUS cytology will perform well in the hands of cytotechnologists and pathologist reviewers and could be introduced into cellular pathology laboratories that employ ThinPrep^® LBC with a minimum effort.

Alternative medicine: an ethnographic study of how practitioners of Indian medical systems manage TB in Mumbai

BACKGROUND

Mumbai is a hot spot for drug-resistant TB, and private practitioners trained in AYUSH systems (Ayurveda, yoga, Unani, Siddha and homeopathy) are major healthcare providers. It is important to understand how AYUSH practitioners manage patients with TB or presumptive TB.

METHODS

We conducted semi-structured interviews of 175 Mumbai slum-based practitioners holding degrees in Ayurveda, homeopathy and Unani. Most providers gave multiple interviews. We observed 10 providers in clinical interactions, documenting: clinical examinations, symptoms, history taking, prescriptions and diagnostic tests.

RESULTS

No practitioners exclusively used his or her system of training. The practice of biomedicine is frequent, with practitioners often using biomedical disease categories and diagnostics. The use of homeopathy was rare (only 4% of consultations with homeopaths resulted in homeopathic remedies) and Ayurveda rarer (3% of consultations). For TB, all mentioned chest x-ray while 31 (17.7%) mentioned sputum smear as a TB test. One hundred and sixty-four practitioners (93.7%) reported referring TB patients to a public hospital or chest physician. Eleven practitioners (6.3%) reported treating patients with TB. Nine (5.1%) reported treating patients with drug-susceptible TB with at least one second-line drug.

CONCLUSIONS

Important sources of health care in Mumbai's slums, AYUSH physicians frequently use biomedical therapies and most refer patients with TB to chest physicians or the public sector. They are integral to TB care and control.

Bacterial proteases and haemostasis dysregulation in the CF lung

BACKGROUND

Pathogenic bacteria which chronically colonise the cystic fibrosis (CF) lung produce a number of virulence determinants, including distinct proteolytic activities. The potential role bacterial proteases play on haemostatic dysregulation within the CF lung is, however, poorly defined, despite haemoptysis being a common complication in CF.

METHODS

The potential impact of known CF pathogens (Pseudomonas aeruginosa and Burkholderia cepacia complex spp.) on haemostasis was examined for their ability to degrade fibrinogen and dysregulate fibrin clot formation and platelet aggregation.

RESULTS

Results demonstrate that key CF pathogens growing as a biofilm on mucin exhibit considerable fibrinogenolytic activity, resulting in fibrinogen breakdown, impaired clot formation, and modulation of platelet aggregation. Human neutrophil elastase may also contribute to fibrinogen breakdown and dysregulated clot formation at high concentration.

CONCLUSION

Bacterial-derived proteases may play an important role in the dysregulation of airway haemostasis, and potentially contribute to episodes of haemoptysis within the CF lung.

Understanding the role of Propionibacterium acnes in acne vulgaris: The critical importance of skin sampling methodologies

Acne vulgaris is a chronic inflammatory skin condition classified by the Global Burden of Disease Study as the eighth most prevalent disease worldwide. The pathophysiology of the condition has been extensively studied, with an increase in sebum production, abnormal keratinization of the pilosebaceous follicle, and an inflammatory immune response all implicated in its etiology. One of the most disputed points, however, is the role of the gram-positive anaerobic bacterium Propionibacterium acnes in the development of acne, particularly when this organism is also found in normal sebaceous follicles of healthy skin. Against this background, we now describe the different sampling strategies that have been adopted for qualitative and quantitative study of P acnes within intact hair follicles of the skin and discuss the strengths and weaknesses of such methodologies for investigating the role of P acnes in the development of acne.

Emendation of Propionibacterium acnes subsp. acnes (Deiko et al. 2015) and proposal of Propionibacterium acnes type II as Propionibacterium acnes subsp. defendens subsp. nov

Recently, it has been proposed that strains of Propionibacterium acnes from the type III genetic division should be classified as P. acnessubsp. elongatum subsp. nov., with strains from the type I and II divisions collectively classified as P. acnessubsp. acnes subsp. nov. Under such a taxonomic re-appraisal, we believe that types I and II should also have their own separate rank of subspecies. In support of this, we describe a polyphasic taxonomic study based on the analysis of publicly available multilocus and whole-genome sequence datasets, alongside a systematic review of previously published phylogenetic, genomic, phenotypic and clinical data. Strains of types I and II form highly distinct clades on the basis of multilocus sequence analysis (MLSA) and whole-genome phylogenetic reconstructions. In silico or digital DNA-DNA similarity values also fall within the 70-80 % boundary recommended for bacterial subspecies. Furthermore, we see important differences in genome content, including the presence of an active CRISPR/Cas system in type II strains, but not type I, and evidence for increasing linkage equilibrium within the separate divisions. Key biochemical differences include positive test results for β-haemolytic, neuraminidase and sorbitol fermentation activities with type I strains, but not type II. We now propose that type I strains should be classified as P. acnessubsp. acnes subsp. nov., and type II as P. acnessubsp. defendens subsp. nov. The type strain of P. acnessubsp. acnes subsp. nov. is NCTC 737T (=ATCC 6919T=JCM 6425T=DSM 1897T=CCUG 1794T), while the type strain of P. acnessubsp. defendens subsp. nov. is ATCC 11828 (=JCM 6473=CCUG 6369).

Use of standardised patients to assess antibiotic dispensing for tuberculosis by pharmacies in urban India: a cross-sectional study

BACKGROUND

India's total antibiotic use is the highest of any country. Patients often receive prescription-only drugs directly from pharmacies. Here we aimed to assess the medical advice and drug dispensing practices of pharmacies for standardised patients with presumed and confirmed tuberculosis in India.

METHODS

In this cross-sectional study in the three Indian cities Delhi, Mumbai, and Patna, we developed two standardised patient cases: first, a patient presenting with 2-3 weeks of pulmonary tuberculosis symptoms (Case 1); and second, a patient with microbiologically confirmed pulmonary tuberculosis (Case 2). Standardised patients were scheduled to present each case once to sampled pharmacies. We defined ideal management for both cases a priori as referral to a health-care provider without dispensing antibiotics or steroids or both.

FINDINGS

Between April 1, 2014, and Nov 29, 2015, we sampled 622 pharmacies in Delhi, Mumbai, and Patna. Standardised patients completed 1200 (96%) of 1244 interactions. We recorded ideal management (defined as referrals without the use of antibiotics or steroids) in 80 (13%) of 599 Case 1 interactions (95% CI 11-16) and 372 (62%) of 601 Case 2 interactions (95% CI 58-66). Antibiotic use was significantly lower in Case 2 interactions (98 [16%] of 601, 95% CI 13-19) than in Case 1 (221 [37%] of 599, 95% CI 33-41). First-line anti-tuberculosis drugs were not dispensed in any city. The differences in antibiotic or steroid use and number of medicines dispensed between Case 1 and Case 2 were almost entirely attributable to the difference in referral behaviour.

INTERPRETATION

Only some urban Indian pharmacies correctly managed patients with presumed tuberculosis, but most correctly managed a case of confirmed tuberculosis. No pharmacy dispensed anti-tuberculosis drugs for either case. Absence of a confirmed diagnosis is a key driver of antibiotic misuse and could inform antimicrobial stewardship interventions.

FUNDING

Grand Challenges Canada, Bill & Melinda Gates Foundation, Knowledge for Change Program, and World Bank Development Research Group.

Health changing conversations: clinicians' experience of health coaching in the East of England

The changing nature of healthcare and the challenge of long-term conditions require a paradigm shift in the mindset and behaviours of professionals. Central to this is the quality of clinician-patient communication, which determines how responsibility is shared. Health coaching training for clinicians provides them with new mindsets, communication skills and behaviour change techniques that transform the clinician--patient relationship and enables patients to become more active participants in their care. This training improves patient experience and health behaviours, provides self-management support and can reduce demand and costs. This article describes the East of England health coaching training programme and provides an overview of the evidence, required competencies and challenges clinicians experience when putting health coaching into practice. It illustrates that health coaching is a mechanism to deliver person-centred care. More must be done to provide clinicians with these much-needed skills especially in the management of long-term conditions.

HPV16 and HPV18 genotyping triage in young women with borderline cytology or mild dyskaryosis: effect of age on genotype-specific risk of high-grade CIN

OBJECTIVE

Human papillomavirus (HPV) triage of borderline cytology or mild dyskaryosis is limited by the higher prevalence of HPV in women with these findings relative to those with high-grade cervical intraepithelial neoplasia (≥CIN2). This is particularly relevant in young women in whom HPV prevalence is discernible. In a previous analysis of HPV triage and colposcopy outcomes in Northern Ireland, we revealed a substantial amount of prevalent high-grade disease in women below 30 years of age. We explored the role of genotyping for HPV16/HPV18 in this population by assessing the risk of high-grade lesions associated with these genotypes and the effect of age on type-specific risk.

METHODS

Of the 866 women eligible for HPV triage, those who tested positive for HPV were referred to colposcopy. The relative risk of ≥CIN2 for HPV16, HPV18 and non-HPV16/18 high-risk genotype positivity was determined for cobas(®) HPV Test-positive results.

RESULTS

The relative risk of high-grade CIN was significantly greater in women infected with HPV16 and/or HPV18 compared with non-HPV16/18 infections, regardless of age (2.23 and 0.45, respectively). In women under 30 years of age, HPV16-associated risk of ≥CIN2 was significantly greater than that of HPV18 and the non-HPV16/18 genotypes (1.74 versus 1.03 and 0.58, respectively). In women aged ≥30 years, HPV18 infection presented the greatest risk of ≥CIN2 (3.03). The relative risk of ≥CIN2 associated with non-HPV16/18 genotypes was lower (range, 0.32-0.58) for both age groups.

CONCLUSION

This analysis demonstrates the value of genotyping for HPV16/HPV18 and age stratification to improve the specificity of HPV triage and to tailor management relative to the risk of high-grade CIN and cancer.

Addressing the challenges of sleep/wake class imbalance in bed based non-contact actigraphic recordings of sleep

Utilising strategically positioned bed-mounted accelerometers, the Passive Sleep Actigraphy platform aims to deliver a non-contact method for identifying periods of wakefulness during night-time sleep. One of the key problems in developing data driven approaches for automatic sleep monitoring is managing the inherent sleep/wake class imbalance. In the current study, actigraphy data from three participants over a period of 30 days was collected. Upon examination, it was found that only 10% contained wake data. Consequently, this resulted in classifier overfitting to the majority class (sleep), thereby impeding the ability of the Passive Sleep Actigraphy platform to correctly identify periods of wakefulness during sleep; a key measure in the identification of sleep problems. Utilising Spread Subsample and Synthetic Minority Oversampling Techniques, this paper demonstrates a potential solution to this issue, reporting improvements of up to 28% in wake detection when compared to baseline data while maintaining an overall classifier accuracy of 90%.

Current and future trends in biomarker discovery and development of companion diagnostics for arthritis

Musculoskeletal diseases such as rheumatoid arthritis are complex multifactorial disorders that are chronic in nature and debilitating for patients. A number of drug families are available to clinicians to manage these disorders but few tests exist to target these to the most responsive patients. As a consequence, drug failure and switching to drugs with alternate modes of action is common. In parallel, a limited number of laboratory tests are available which measure biological indicators or 'biomarkers' of disease activity, autoimmune status, or joint damage. There is a growing awareness that assimilating the fields of drug selection and diagnostic tests into 'companion diagnostics' could greatly advance disease management and improve outcomes for patients. This review aims to highlight: the current applications of biomarkers in rheumatology with particular focus on companion diagnostics; developments in the fields of proteomics, genomics, microbiomics, imaging and bioinformatics and how integration of these technologies into clinical practice could support therapeutic decisions.

The opportunistic pathogen Propionibacterium acnes: insights into typing, human disease, clonal diversification and CAMP factor evolution

We previously described a Multilocus Sequence Typing (MLST) scheme based on eight genes that facilitates population genetic and evolutionary analysis of P. acnes. While MLST is a portable method for unambiguous typing of bacteria, it is expensive and labour intensive. Against this background, we now describe a refined version of this scheme based on two housekeeping (aroE; guaA) and two putative virulence (tly; camp2) genes (MLST₄) that correctly predicted the phylogroup (IA₁, IA₂, IB, IC, II, III), clonal complex (CC) and sequence type (ST) (novel or described) status for 91% isolates (n = 372) via cross-referencing of the four gene allelic profiles to the full eight gene versions available in the MLST database (http://pubmlst.org/pacnes/). Even in the small number of cases where specific STs were not completely resolved, the MLST₄ method still correctly determined phylogroup and CC membership. Examination of nucleotide changes within all the MLST loci provides evidence that point mutations generate new alleles approximately 1.5 times as frequently as recombination; although the latter still plays an important role in the bacterium's evolution. The secreted/cell-associated ‘virulence’ factors tly and camp2 show no clear evidence of episodic or pervasive positive selection and have diversified at a rate similar to housekeeping loci. The co-evolution of these genes with the core genome might also indicate a role in commensal/normal existence constraining their diversity and preventing their loss from the P. acnes population. The possibility that members of the expanded CAMP factor protein family, including camp2, may have been lost from other propionibacteria, but not P. acnes, would further argue for a possible role in niche/host adaption leading to their retention within the genome. These evolutionary insights may prove important for discussions surrounding camp2 as an immunotherapy target for acne, and the effect such treatments may have on commensal lineages.

An expanded multilocus sequence typing scheme for propionibacterium acnes: investigation of 'pathogenic', 'commensal' and antibiotic resistant strains

The Gram-positive bacterium Propionibacterium acnes is a member of the normal human skin microbiota and is associated with various infections and clinical conditions. There is tentative evidence to suggest that certain lineages may be associated with disease and others with health. We recently described a multilocus sequence typing scheme (MLST) for P. acnes based on seven housekeeping genes (http://pubmlst.org/pacnes). We now describe an expanded eight gene version based on six housekeeping genes and two ‘putative virulence’ genes (eMLST) that provides improved high resolution typing (91eSTs from 285 isolates), and generates phylogenies congruent with those based on whole genome analysis. When compared with the nine gene MLST scheme developed at the University of Bath, UK, and utilised by researchers at Aarhus University, Denmark, the eMLST method offers greater resolution. Using the scheme, we examined 208 isolates from disparate clinical sources, and 77 isolates from healthy skin. Acne was predominately associated with type IA₁ clonal complexes CC1, CC3 and CC4; with eST1 and eST3 lineages being highly represented. In contrast, type IA₂ strains were recovered at a rate similar to type IB and II organisms. Ophthalmic infections were predominately associated with type IA₁ and IA₂ strains, while type IB and II were more frequently recovered from soft tissue and retrieved medical devices. Strains with rRNA mutations conferring resistance to antibiotics used in acne treatment were dominated by eST3, with some evidence for intercontinental spread. In contrast, despite its high association with acne, only a small number of resistant CC1 eSTs were identified. A number of eSTs were only recovered from healthy skin, particularly eSTs representing CC72 (type II) and CC77 (type III). Collectively our data lends support to the view that pathogenic versus truly commensal lineages of P. acnes may exist. This is likely to have important therapeutic and diagnostic implications.