Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units.

BACKGROUND: Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity. METHODS: CMg using nanopore sequencing was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave. RESULTS: An 8-h CMg workflow was 92% sensitive (95% CI, 75-99%) and 82% specific (95% CI, 57-96%) for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of ß-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from 4 positive and 39 negative samples. Molecular typing using 24-h sequencing data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak involving 14 patients across three ICUs. CONCLUSION: CMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg.

Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma.

ADAPTeR is a prospective, phase II study of nivolumab (anti-PD-1) in 15 treatment-naive patients (115 multiregion tumor samples) with metastatic clear cell renal cell carcinoma (ccRCC) aiming to understand the mechanism underpinning therapeutic response. Genomic analyses show no correlation between tumor molecular features and response, whereas ccRCC-specific human endogenous retrovirus expression indirectly correlates with clinical response. T cell receptor (TCR) analysis reveals a significantly higher number of expanded TCR clones pre-treatment in responders suggesting pre-existing immunity. Maintenance of highly similar clusters of TCRs post-treatment predict response, suggesting ongoing antigen engagement and survival of families of T cells likely recognizing the same antigens. In responders, nivolumab-bound CD8+ T cells are expanded and express GZMK/B. Our data suggest nivolumab drives both maintenance and replacement of previously expanded T cell clones, but only maintenance correlates with response. We hypothesize that maintenance and boosting of a pre-existing response is a key element of anti-PD-1 mode of action.

Leprosy-an unusual cause of a suspicious nodule on mammography.

A routine mammogram identified changes thought to be due to a lymph node, which was confirmed on biopsy. The lymph node was infiltrated with macrophages and showed fragmented acid-fast bacilli. The patient had been treated for leprosy some years before and was still taking thalidomide for erythema nodosum leprosum. Leprosy-associated lymphadenopathy may be identified on routine breast screening.

COVID-19 autopsies: conclusions from international studies.

The rapid pace at which COVID-19 studies are being published is surpassed only by the spread of the virus and the destruction wreaked by the pandemic globally. Therefore, it is likely that, even in the few months prior to this article reaching print, the COVID-19 literature would have moved on. The authors of this article work at a centre for COVID autopsies in London, and the aim of the article is, using their first-hand experience of COVID-19 autopsies, to distil what in their judgement are the most valid and important findings of internationally published COVID-19 autopsy studies. The intention is to provide an illustrated summary of the pathology of the organ systems most often affected by COVID-19, which will be particularly useful to trainee histopathologists and to busy consultant surgical histopathologists who may not have encountered COVID-19 first hand. For the reader who wishes to probe further the question of pathogenesis, a few pertinent references are provided.

Endoscopic tumour morphology impacts survival in adenocarcinoma of the oesophagus.

BACKGROUND: Prognostication in oesophageal cancer on the basis of preoperative variables is challenging. Many of the accepted predictors of survival are only derived after surgical treatment and may be influenced by neoadjuvant therapy. This study aims to explore the relationship between pre-treatment endoscopic tumour morphology and postoperative survival. METHODS: Patients with endoscopic descriptions of tumours were identified from the prospectively managed databases including the OCCAMS database. Tumours were classified as exophytic, ulcerating or stenosing. Kaplan Meier survival analysis and multivariable Cox regression analyses were performed to determine hazard ratios (HR) with 95% confidence intervals. RESULTS: 262 patients with oesophageal adenocarcinoma undergoing potentially curative resection were pooled from St Thomas' Hospital (161) and the OCCAMS database (101). There were 70 ulcerating, 114 exophytic and 78 stenosing oesophageal adenocarcinomas. Initial tumour staging was similar across all groups (T3/4 tumours 71.4%, 70.2%, 74.4%). Median survival was 55 months, 51 months and 36 months respectively (p < 0.001). Rates of lymphovascular invasion (P = 0.0176), pathological nodal status (P = 0.0195) and pathological T stage (P = 0.0007) increased from ulcerating to exophytic to stenosing lesions. Resection margin positivity was 21.4% in ulcerating tumours compared to 54% in stenosing tumours (p < 0.001). When compared to stenosing lesions, exophytic and ulcerating lesions demonstrated a significant survival advantage on multivariable analysis (HR 0.56 95% CI 0.31-0.93, HR 0.42 95% CI 0.21-0.82). CONCLUSION: This study demonstrates that endoscopic morphology may be an important pre-treatment prognostic factor in oesophageal cancer. Ulcerating, exophytic and stenosing tumours may represent different pathological processes and tumour biology.

Utility of an infectious and tropical disease histopathology diagnostic review service.

AIM: To assess the utility of a London-based infectious and tropical disease histopathology diagnostic review service. METHODS: The original and specialist review histopathology reports of 457 samples from over 3 years of referrals were compared retrospectively. RESULTS: Overall 329 (72.0%) showed no significant difference; 34 (7.4%) showed a non-clinically significant difference; and 94 (20.6%) showed a clinically significant difference. Of the 94 clinically significant discrepancies, 46 (48.9%) were incorrectly suspected infections; 19 (20.2%) were missed infections; 8 (8.5%) were different infections; and in 20 (21.3%), the specialist review yielded more specific identification of an organism or a more correct assessment of its viability. CONCLUSIONS: A review of histopathology cases by an infectious disease (ID) histopathology referral centre has yielded a 20.6% clinically significant error rate. Measures to improve training in ID histopathology in the UK are discussed.

Fatal cardiovascular instability secondary to hypercalcaemia and intracellular calcium deposition complicating T-cell leukaemia-lymphoma.

Adult T-cell leukaemia-lymphoma is a rare haematological malignancy, which can cause severe hypercalcaemia and metastatic calcification resulting in life-threatening arrhythmias.

The impact of brush cytology from endoscopic retrograde cholangiopancreatography (ERCP) on patient management at a UK teaching hospital.

INTRODUCTION: Patients with suspected pancreaticobiliary cancers frequently undergo endoscopic retrograde cholangiopancreatography (ERCP) to obtain brush cytology for confirmatory diagnosis. The outcome of this often leads to the management of the patient and can avoid more invasive investigations. There is a wide range of sensitivities and specificities reported in the literature. AIMS: To determine the accuracy of the brush cytology obtained at ERCP by performing a retrospective audit of all patients admitted to Guy's and St. Thomas' Hospital for ERCP during 2008-2013. Also, to evaluate the impact of cytology results on patient care following ERCP. METHOD: Data were collected from 4 January 2008 to 27 December 2013. This involved analysing EndoSoft (the in-house software for endoscopic data entry), Pathnet (the pathology database) and Electronic Patient Records. RESULTS: 162 patients underwent brush cytology during ERCP. 58 patients had positive cytology. With intention-to-treat analysis, sensitivity was 54.7%, specificity was 100.0% and negative predictive value was 53.9% with a positive predictive value of 100%. Patients with a positive brush cytology result required fewer investigations compared with patients with a negative cytology result. CONCLUSIONS: Our results compare favourably with previous studies in the field. Brush cytology has been ignored in recent times due to perceived poor results and efficacy. Our audit shows that it can reduce the number of investigations required to reach a diagnosis of malignancy and so is a valuable tool in the diagnosis of pancreaticobiliary malignancies. However, better guidance on preparation of samples for cytology is needed to reduce the number of insufficient samples.

Identifying HIV infection in diagnostic histopathology tissue samples--the role of HIV-1 p24 immunohistochemistry in identifying clinically unsuspected HIV infection: a 3-year analysis.

AIMS: Because of the clinical difficulty in identifying the early stages of human immunodeficiency virus (HIV) infection, the histopathologist often has to consider the diagnosis of HIV in tissue samples from patients with no previous suspicion of HIV infection. The aim was to investigate the practicality and utility of routine HIV-1 p24 immunohistochemistry on tissue samples received at a London histopathology laboratory. METHODS AND RESULTS: Over a 3-year period, HIV-1 p24 was evaluated immunohistochemically on 123 cases. Of these, 37 (30%) showed positive expression of p24 in lesional follicular dendritic cells (FDCs). Of these 37 cases, 11 were not clinically suspected to be HIV+ and had no prior serological evidence of HIV infection. These cases represented lymph node biopsies, tonsillar and nasopharyngeal biopsies and a parotid excision. In addition to expression on FDCs, in 22 cases (60%), p24 also highlighted mononuclear cells and macrophages. p24 was also useful in confirming the presence of HIV in lymphoid tissue in non-lymphoid organs such as the lung, anus, salivary gland and brain. Immunonegativity occurred in occasional known HIV+ cases, probably related to treatment or tissue processing. CONCLUSIONS: This study confirms the usefulness of this technique in detecting unsuspected HIV infection in lymphoid and non-lymphoid organs on histopathological material and should be part of routine evaluation of lymph nodes and lymphoid tissue in other organs if morphological or clinical features suggest HIV infection.

Histopathologic examination and reporting of esophageal carcinomas following preoperative neoadjuvant therapy: practical guidelines and current issues.

Neoadjuvant chemoradiotherapy is being increasingly offered to patients with invasive esophageal carcinoma in an effort to downstage the tumor and consequently increase the rate of curative resection. A substantial amount of data has suggested that pathologic tumor regression following neoadjuvant therapy is an important predictor of local recurrence and long-term survival in esophageal cancer. Therefore, it is important that these posttreatment resection specimens are handled in a standardized manner and a reproducible method of tumor regression grading is used. Pathologic examination of such specimens is not straightforward, and, in fact, it presents a particular challenge to pathologists, especially when a good response to neoadjuvant therapy has been achieved and little or no residual tumor remains. We provide some guidelines for handling and reporting such specimens and outline the commonly used tumor regression grading systems for posttreatment esophagectomy specimens.

Kawasaki syndrome during pregnancy: a case report and literature review.

Kawasaki disease (KD) is characterized by persistent fever, mucous membrane hyperaemia, cervical lymph node enlargement, exanthema and periungual desquamation. It is seen mainly in children, with <60 cases reported in adults. We present the case, the first to the best of our knowledge, of a 17-year-woman who developed KD during the second trimester of pregnancy and died 47 days postpartum from cardiac arrest due to acute myocardial infarction. The case, the medical history, the clinical outcome and the postmortem findings are discussed, and we review the literature on adult KD.

Cytologic diagnosis of pancreatic endocrine tumors by endoscopic ultrasound-guided fine-needle aspiration: a review.

Precise localization and diagnosis of pancreatic endocrine tumors (PETs) is important, because pancreatic PETs have different clinical and biological behavior and treatment modalities than do exocrine pancreatic tumors. In contrast to the much more common exocrine adenocarcinomas, cytologic studies of PET are relatively rare and many cytopathologists lack experience with the cytomorphologic features of these tumors.During the last 10 yr, endoscopic ultrasound (EUS)-guided fine-needle aspiration (FNA) has matured into an accurate, highly sensitive, and cost-effective modality for the preoperative localization of pancreatic PETs. This has resulted in an increased number of PETs first sampled as cytology specimens. This manuscript focuses on the cytomorphologic features most suggestive of pancreatic PETs, differential diagnosis, and diagnostic pitfalls of PETs. The technical development of EUS-guided FNA and the ancillary studies for pancreatic PETs are also reviewed. The data summarized in this review indicate that EUS-FNA is a valuable method in the recognition of pancreatic PETs and in most cases cytopathologists could reach a correct diagnosis of these tumors, including their hormone producing capability on aspirated cytologic material.

Pathological and clinical significance of increased intraepithelial lymphocytes (IELs) in small bowel mucosa.

Intestinal intraepithelial lymphocytes (IELs) belong to a unique T-cell population interspersed between epithelial cells of both the small and large intestine. It is becoming increasingly recognised that an increased number of IELs with a normal villous architecture is within the wide spectrum of histological abnormalities observed in coeliac disease. An increased number of IELs is the earliest pathological change following gluten challenge and a high IEL count may be the only sign of gluten sensitivity. Therefore, the finding of a raised IEL count with normal villous architecture is of sufficient clinical importance to be reported in routine small bowel biopsies. However, it is evident that not all small intestinal biopsy specimens showing increased IELs are explained by gluten sensitivity. Increased IELs in small bowel mucosa have also been associated with autoimmune disorders, tropical sprue, food protein intolerance, Helicobacter pylori-associated gastritis, peptic duodenitis, parasitic and viral infections, as well as the development of intestinal lymphoma. Histological examination of a biopsy specimen of the small bowel remains the diagnostic gold standard for coeliac disease. There will be an ever increasing demand for histological confirmation of gluten sensitivity in patients in whom the classic microscopic appearance of flattened villi may not have fully developed. The more widespread recognition by histopathologists of the pattern of injury manifested by increased numbers of IELs in intestinal biopsy specimens will certainly help in early diagnosis of coeliac disease, lessen diagnostic confusion and influence the modern practice of gastrointestinal tract medicine. This review discusses some of the recent developments in clinical pathology pertaining to increased IELs in small bowel mucosal biopsies.