Diarrheal-associated gut dysbiosis in cancer and inflammatory bowel disease patients is exacerbated by Clostridioides difficile infection.

Introduction: Low diversity gut dysbiosis can take different forms depending on the disease context. In this study, we used shotgun metagenomic sequencing and gas chromatography-mass spectrometry (GC-MS) to compared the metagenomic and metabolomic profiles of Clostridioides (Clostridium) difficile diarrheal cancer and inflammatory bowel disease (IBD) patients and defined the additive effect of C. difficile infection (CDI) on intestinal dysbiosis. Results: The study cohort consisted of 138 case-mix cancer patients, 43 IBD patients, and 45 healthy control individuals. Thirty-three patients were also infected with C. difficile. In the control group, three well-known enterotypes were identified, while the other groups presented with an additional Escherichia-driven enterotype. Bacterial diversity was significantly lower in all groups than in healthy controls, while the highest level of bacterial species richness was observed in cancer patients. Fifty-six bacterial species had abundance levels that differentiated diarrheal patient groups from the control group. Of these species, 52 and 4 (Bacteroides fragilis, Escherichia coli, Klebsiella pneumoniae, and Ruminococcus gnavus) were under-represented and over-represented, respectively, in all diarrheal patient groups. The relative abundances of propionate and butyrate were significantly lower in fecal samples from IBD and CDI patients than in control samples. Isobutyrate, propanate, and butyrate concentrations were lower in cancer, IBD, and CDI samples, respectively. Glycine and valine amino acids were over- represented in diarrheal patients. Conclusion: Our data indicate that different external and internal factors drive comparable profiles of low diversity dysbiosis. While diarrheal-related low diversity dysbiosis may be a consequence of systemic cancer therapy, a similar phenotype is observed in cases of moderate to severe IBD, and in both cases, dysbiosis is exacerbated by incidence of CDI.

Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection.

BACKGROUND: Clostridium difficile (C. difficile) is a major source of healthcare-associated infection with a high risk of recurrence, attributable to many factors such as usage of antibiotics, older age and immunocompromised status of the patients. C. difficile has also a highly diverse genome, which may contribute to its high virulence. Herein we examined whether the genome conservation, measured as non-synonymous to synonymous mutations ratio (dN/dS) in core genes, presence of single genes, plasmids and prophages increased the risk of reinfection in a subset of 134 C. difficile isolates from our previous study in a singly hemato-oncology ward. METHODS: C. difficile isolates were subjected to whole-genome sequencing (WGS) on Ion Torrent PGM sequencer. Genomes were assembled with MIRA5 and annotated with prokka and VRprofile. Logistic regression was used to asses the relationship between single gene presence and the odds of infection recurrence. DN/dS ratios were computed with codeml. Functional annotation was conducted with eggNOG-Mapper. RESULTS: We have found that the presence of certain genes, associated with carbon metabolism and oxidative phosphorylation, increased the odds of infection recurrence. More core genes were under positive selective pressure in recurrent disease isolates - they were mostly associated with the metabolism of aminoacids. Finally, prophage elements were more prevalent in single infection isolates and plasmids did not influence the odds of recurrence. CONCLUSIONS: Our findings suggest higher genetic plasticity in isolates causing recurrent infection, associated mainly with metabolism. On the other hand, the presence of prophages seems to reduce the isolates' virulence.

High Prevalence of Genetically Related Clostridium Difficile Strains at a Single Hemato-Oncology Ward Over 10 Years.

Aims: Clostridium difficile (C. difficile) infection (CDI) is the main cause of healthcare-associated infectious diarrhea. We used whole-genome sequencing (WGS) to measure the prevalence and genetic variability of C. difficile at a single hemato-oncology ward over a 10 year period. Methods: Between 2008 and 2018, 2077 stool samples were obtained from diarrheal patients hospitalized at the Department of Lymphoma; of these, 618 were positive for toxin A/B. 140 isolates were then subjected to WGS on Ion Torrent PGM sequencer. Results: 36 and 104 isolates were recovered from 36 to 46 patients with single and multiple CDIs, respectively. Of these, 131 strains were toxigenic. Toxin gene profiles tcdA(+);tcdB(+);cdtA/cdtB(+) and tcdA(+);tcdB(+);cdtA/cdtB(-) were identified in 122 and nine strains, respectively. No isolates showed reduced susceptibility to metronidazole and vancomycin. All tested strains were resistant to ciprofloxacin, and 72.9, 42.9, and 72.9% of strains were resistant to erythromycin, clindamycin, or moxifloxacin, respectively. Multi-locus sequence typing (MLST) identified 23 distinct sequence types (STs) and two unidentified strains. Strains ST1 and ST42 represented 31 and 30.1% of all strains tested, respectively. However, while ST1 was detected across nearly all years studied, ST42 was detected only from 2009 to 2011. Conclusion: The high proportion of infected patients in 2008-2011 may be explained by the predominance of more transmissible and virulent C. difficile strains. Although this retrospective study was not designed to define outbreaks of C. difficile, the finding that most isolates exhibited high levels of genetic relatedness suggests nosocomial acquisition.

[The colonization of the digestive tract multidrug-resistant strains hospitalized patients in Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology].

INTRODUCTION: The aim of the study was a retrospective analysis of intestinal flora for the presence of multidrug-resistant strains, isolated from patients hospitalized in clinics Oncology Center from 01.01.2010 to 30.09.2015 r. METHODS: The multi-resistant strains were isolated from stool and rectal swabs. In order to increase the potential of multiple-resistant strains, the material was plated on the appropriate substrate. Determination of resistance mechanisms performed by general recommendations. RESULTS: Results of this study showed among isolated multiple-resistance strains a high proportion of Enterobacteriaceae strains producing ß-lactamase mainly ESBL. Klebsiella pneumoniae consist of 31.9% of isolated strains, E. coli 28.74% and Enterococcus faecium VER -21.15%. CONCLUSIONS: It is important to determine the microbiological status of hospitalized patients because colonized gastrointestinal tract multi-resistant strains may be one of the sources of serious infections.

[Etiology of infection associated with neoplastic changes of organs in the head and neck in patients hospitalized in the Oncology Centre in Warsaw].

INTRODUCTIONS: According to clinical observations primary neoplastic lesions in the head and neck are often complicated by infection. The incidence of postoperative complications of cancer lesions of the head and neck, oral cavity, upper airways or larynx is from 19% up to 47% cases but in extensive and long-term operations can reach 80%. METHODS: We retrospectively evaluated results of microbiological investigations of 312 clinical specimens collected from patients from Clinical Head and Neck Cancers of On- cology Center in Warsaw in the years 2008 -2012. All samples of clinical materials were plated on the suitable culture media and incubated according to the recommendations. RESULTS: The study has shown that from all collected clinical specimens 491 strains have been isolated. Nearly half of the cultured bacteria were Gram-positive cocci (48.7%), mainly methicillin-sensitive Staphylococcus aureus. Most Gram-negative bacteria isolated from neoplastic lesions in the head and neck belong to Enterobacteriaceae (21%), 23,4% of cultured bacteria grown anaerobically and they were mainly Gram-negative rods. CONCLUSIONS: The presence of diverse bacterial flora colonizing the mucous membranes of the mouth and throat may be the reason of difficulties in interpretation of microbiological investigation. It must be remembered that knowledge of colonizing and pathogenic flora of the area of head and neck enables appropriate preoperative prevention and empiric therapy.

Comparative characterization of repABC-type replicons of Paracoccus pantotrophus composite plasmids.

The repABC replicons have an unusual structure, since they carry genes coding for partitioning (repA, repB) and replication (repC) proteins, which are organized in an operon. So far, the presence of these compact bi-functional modules has been reported only in the megaplasmids of the Rhizobiaceae and within the plasmid pTAV1 (107kb) of Paracoccus versutus. We studied the distribution of repABC-type replicons within bacteria belonging to the genus Paracoccus. We found that repABC replicons occur only in the group of pTAV1-like plasmids: pKLW1, pHG16-a, pWKS2, and pPAN1, harbored by different strains of Paracoccus pantotrophus. A partial sequencing approach followed by phylogenetic analysis revealed that these replicons constitute a distinct evolutionary branch of repABC replicons. Incompatibility studies showed that they represent two incompatibility groups designated IncABC1 (pTAV1, pKLW1, and pHG16-a) and IncABC2 (pPAN1). Sequence comparison using available databases allowed the identification, within plasmid pRS241d of Rhodobacter sphaeroides 2.4.1, of an additional sequence highly homologous to the paracoccal repABC replicons, which has been included in comparative analyses.