Community-acquired pneumonia caused by Yersinia enterocolitica in an immunocompetent patient

Profiling of Microbial Landscape in Lung of Chronic Obstructive Pulmonary Disease Patients Using RNA Sequencing

Purpose

The aim of the study was to use RNA sequencing (RNA-seq) data of lung from chronic obstructive pulmonary disease (COPD) patients to identify the bacteria that are most commonly detected. Additionally, the study sought to investigate the differences in these infections between normal lung tissues and those affected by COPD.

Patients and Methods

We re-analyzed RNA-seq data of lung from 99 COPD patients and 93 non-COPD smokers to determine the extent to which the metagenomes differed between the two groups and to assess the reliability of the metagenomes. We used unmapped reads in the RNA-seq data that were not aligned to the human reference genome to identify more common infections in COPD patients.

Results

We identified 18 bacteria that exhibited significant differences between the COPD and non-COPD smoker groups. Among these, Yersinia enterocolitica was found to be more than 30% more abundant in COPD. Additionally, we observed difference in detection rate based on smoking history. To ensure the accuracy of our findings and distinguish them from false positives, we double-check the metagenomic profile using Basic Local Alignment Search Tool (BLAST). We were able to identify and remove specific species that might have been misclassified as other species in Kraken2 but were actually Staphylococcus aureus, as identified by BLAST analysis.

Conclusion

This study highlighted the method of using unmapped reads, which were not typically used in sequencing data, to identify microorganisms present in patients with lung diseases such as COPD. This method expanded our understanding of the microbial landscape in COPD and provided insights into the potential role of microorganisms in disease development and progression.

Epizootic Yersinia enterocolitica in captive African green monkeys (Chlorocebus aethiops sabaeus)

Yersinia enterocolitica is a Gram-negative bacterium that typical results in enterocolitis in humans and poses significant worldwide risks to public health. An outbreak of yersiniosis in the Vervet/African green monkey colony at the WFSM during the winter of 2015-2016 accounted for widespread systemic infection with high morbidity and mortality. Most of the cases had extensive necrosis with suppuration and large colonies of bacilli in the large bowel and associated lymph nodes; however, the small intestine, stomach, and other organs were also regularly affected. Positive cultures of Yersinia enterocolitica were recovered from affected tissues in 20 of the 23 cases. Carrier animals in the colony were suspected as the source of the infection because many clinically normal animals were culture-positive during and after the outbreak. In this study, we describe the gross and histology findings and immune cell profiles in different organs of affected animals. We found increased numbers of myeloid-derived phagocytes and CD11C-positive antigen-presenting cells and fewer adaptive T and B lymphocytes, suggesting an immunocompromised state in these animals. The pathogen-mediated microenvironment may have contributed to the immunosuppression and rapid spread of the infection in the vervets. Further studies in vervets could provide a better understanding of Yersinia-mediated pathogenesis and immunosuppression, which could be fundamental to understanding chronic and systemic inflammatory diseases in humans.

COVID-19 presenting as severe, persistent abdominal pain and causing late respiratory compromise in a 33-year-old man

A 33-year-old man presented repeatedly with severe abdominal pain and diarrhoea. Renal colic was suspected, and he was admitted for pain management. Questioning elicited an additional history of sore throat and mild, dry cough. Inflammatory markers were mildly raised (C reactive protein (CRP) 40 mg/L). Initial nasopharyngeal swabs were negative for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) by PCR. CT of the kidneys, ureters and bladder (CT KUB) was normal; however, CT of the thorax showed multifocal bilateral peripheral areas of consolidation consistent with COVID-19 infection. He developed respiratory compromise and was transferred to the intensive care unit (ICU). Sputum was positive for SARS-CoV-2 by PCR, and culture grew Yersinia enterocolitica. He recovered following supportive management and treatment with piperacillin–tazobactam.