Postmortem radiographic, histological and bacteriological studies of terminal respiratory infections and other pulmonary lesions in hospital and non-hospital necropsies

Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic has posed multiple challenges to global public health. Clinical features and sequela of SARS-CoV-2 infection include long-term and short-term complications often clinically indistinguishable from bacterial sepsis and acute lung infection. Post-hoc studies of previous SARS outbreaks postulate secondary bacterial infections with microbial dysbiosis. Oral microbial dysbiosis, particularly the altered proportion of Firmicutes and Proteobacteria, observed in other respiratory virus infection, like influenza, has shown to be associated with increased morbidity and mortality. Oropharynx and lung share similar kinds of bacterial species. We hypothesized that alteration in the Human Oropharyngeal Microbiome in SARS-CoV-2 patients can be a clinical indicator of bacterial infection related complications. We made a longitudinal comparison of oropharyngeal microbiome of 20 SARS-CoV-2 patients over a period of 30 days; at three time points, with a 15 days interval; contrasting them with a matched group of 10 healthy controls. Present observation indicates that posterior segment of the oropharyngeal microbiome is a key reservoir for bacteria causing pneumonia and chronic lung infection on SARS-CoV-2 infection. Oropharyngeal microbiome is indeed altered and its α-diversity decreases, indicating reduced stability, in all SARS-CoV-2 positive individuals right at Day-1; i.e. within ~24 h of post clinical diagnosis. The dysbiosis persists long-term (30 days) irrespective of viral clearance and/or administration of antibiotics. There is a severe depletion of commensal bacteria phyla like Firmicutes among the patients and that depletion is compensated by higher proportion of bacteria associated with sepsis and severe lung infection from phyla Proteobacteria. We also found elevated proportions of certain genus that have previously been shown to be causal for lung pneumonia in studies of model organisms and human autopsies’ including Stenotrophomonas, Acenetobactor, Enterobactor, Klebsiella and Chryseobacterium that were to be elevated among the cases. We also show that responses to the antibiotics (Azithromycin and Doxycycline) are not uniform for all individuals.

Postmortem bacteriology in forensic pathology: diagnostic value and interpretation

The proof of a pathogenetic germ can be of evidential value for the medico-legal expertise concerning etiopathogenetic conclusions towards a causal relationship between infection and fatal outcome. In specific cases the forensic pathologist may be confronted with the decision whether cultures for postmortem bacteriological investigations should be obtained at autopsy. The present review surveys the value and practicability of postmortem bacteriological cultures in the light of the literature. The most promising media for postmortem bacteriological cultures are spleen and heart blood. In contrast, postmortem lung culture results are often unreliable due to frequently false positive results. The collection of specimens from at least two different sampling sites should be the standard procedure in cases where an underlying (potentially fatal) infection is presumed. Multiple postmortem cultures from different sampling sites raise the probability to identify the etiologic agent of antemortem infection. A careful correlation of culture results from different anatomical sampling sites with autopsy and histological findings is essential for the differentiation between vitally acquired infection and postmortem contamination. Various factors (e.g. the time interval between death and sampling of specimens, agonal spread of microorganisms or preceding antibiotic therapy prior to death) may limit the diagnostic utility of postmortem culture results. Contamination of specimens may, e.g. originate from inadequate sampling techniques, use of unsuitable transport media or postmortem growth of bacteria. The number of contaminated postmortem cultures increases when bowel manipulation or evisceration occurs prior to sampling and is depending on the anatomy of the sampling site. Polymicrobial growth can be considered contamination in the majority of cases. For the medico-legal expertise a thorough histological examination of inner organs and tissues is needed; the histological section has to represent the sampling site for culture. The presence of an underlying infection can be proven when postmortem bacteriological cultures yield a primary infectious pathogen and a cellular response in the affected tissue can be detected on the histopathological level. Postmortem bacteriology can be regarded as a reliable diagnostic tool for postmortem quality control of preceding diagnostic and therapeutic procedures and can serve as an additional indicator of nosocomial infections within a specific hospital environment. From the medico-legal point of view, a more widespread application of this valuable investigative procedure, that adds to diminish the number of otherwise unresolved deaths in forensic autopsy practice, is desirable.