Prevalence of Cyclomodulin-Positive E. coli and Klebsiella spp. Strains in Mexican Patients with Colon Diseases and Antimicrobial Resistance

Distribution and virulence of Escherichia coli harboring cyclomodulins and supplementary virulence genes isolates from clinical and environmental samples

This study aimed to determine the prevalence of cyclomodulins (cdt, cnf, pks and cif) in Escherichia coli (E. coli) isolated from clinical and environmental samples, the presence of supplementary virulence genes (SVG), antibiotic resistance, and in vitro cytotoxicity. 413 E. coli were isolated from clinical (stool from obese subjects, normal weight subjects, children with diarrhea, and children without diarrhea; and urine from pregnant and non-pregnant women with urinary tract infections) and environmental (water and different foods) samples. PCR was performed to identify E. coli pathotypes, the four cyclomodulins, and 18 SVG; virulence score, cytotoxic assay, and antibiotic resistance assay were performed. Fifteen percent of E. coli were positive for cyclomodulins and were found in all isolation sources; however, in children with diarrhea, they were more frequent. The most frequent cyclomodulin was cdt. More DEC strains harbor cyclomodulins than non-DEC, and cyclomodulins were most frequent among aEPEC pathotype. SVG ehaC was associated with cyclomodulin-positive strains. Cyclomodulin-positive E. coli had a higher virulence score but no significant cytotoxic activity. They were slightly more resistant to antibiotics. In conclusion, cyclomodulins-positive E. coli was widely distributed in humans, food, and the environment, and they were associated with SVG ehaC, suggesting that these genes may play a role in the pathogenesis of the cyclomodulins. However, more research is needed.

Clinical Characteristics of Uncomplicated Acute Pyelonephritis Caused by Escherichia coli and Klebsiella pneumoniae

INTRODUCTION

This study compared the clinical characteristics and antimicrobial susceptibility of uncomplicated acute pyelonephritis (APN) caused by Escherichia coli and Klebsiella pneumoniae.

METHODS

We retrospectively reviewed the medical records of patients with uncomplicated APNs caused by E. coli and K. pneumoniae admitted to Keimyung University Dongsan Hospital between February 2014 and December 2021.

RESULTS

We enrolled 497 patients (372 with E. coli infection, 125 with K. pneumoniae infection). Male, healthcare-associated infection, solid tumors, liver cirrhosis, chronic renal disease, solid organ transplantation, and antibiotic usage within the last 3 months were more strongly associated with K. pneumoniae uncomplicated APNs than with E. coli. Bacteremia and fever occurred more frequently in E. coli uncomplicated APNs. Antimicrobial resistance rates to piperacillin/tazobactam and carbapenem were higher in K. pneumoniae. Antimicrobial resistance rates to aztreonam and ciprofloxacin were lower in K. pneumoniae. Thirty-day mortality was more observed in K. pneumoniae group in univariate analysis, but this difference was not observed after adjustment. Male sex, ultimately fatal disease in McCabe, and prior antibiotic use within 3 months were more associated with K. pneumoniae.

CONCLUSIONS

Male, underlying diseases, and prior antibiotic use was more associated with K. pneumoniae. Further study will be needed that microbiome of each situation and the related with the distribution of the strains.

ISOLATION, CHARACTERIZATION, AND ANTIMICROBIAL SUSCEPTIBILITY OF BACTERIA ISOLATED FROM SEA LION (ZALOPHUS CALIFORNIANUS) PUPS IN NORTHWESTERN MEXICO

Bacterial infections have been documented in marine mammals for decades, and some are considered emerging pathogens with zoonotic potential. The aerobic oral (n=16) and rectal (n=17) bacterial microbiota and their antimicrobial resistance were characterized for 17 apparently healthy California sea lion pups (Zalophus californianus) captured with a hoop net in Farallon Island, Sinaloa, Mexico, in 2016. Bacteriologic cultures, Analytical Profile Index, and PCR were used to identify bacterial species. The Escherichia coli phylogenetic groups were identified by PCR, Salmonella serotypes were identified, and resistance to antibiotics was evaluated. Overall, 39 bacterial species were isolated, including E. coli and Salmonella spp. (35.9% each) and Pseudomonas aeruginosa (28.2%). For E. coli, UNKNOWN phylogroup was the most prevalent (57.7%), followed by the A phylogroup (37.1%). Most Salmonella serotypes were identified as Newport (92.8%); serotype Saintpaul was also identified (7.2%). Sea lions with bacterial co-colonization included 24.2%, from which two bacterial species were isolated, and 3% with three species. Overall, 59% of bacteria were resistant to at least one antibiotic tested, and 25.6% were extensively drug resistant. Bacteria were highly resistant to ampicillin and cefotaxime. This study demonstrates the importance of characterizing the microbiome of sea lions, and the potential effect of pathogens with antimicrobial resistance on wildlife conservation and public health.

Metagenomic Analyses of Multiple Gut Datasets Revealed the Association of Phage Signatures in Colorectal Cancer

The association of colorectal cancer (CRC) and the human gut microbiome dysbiosis has been the focus of several studies in the past. Many bacterial taxa have been shown to have differential abundance among CRC patients compared to healthy controls. However, the relationship between CRC and non-bacterial gut microbiome such as the gut virome is under-studied and not well understood. In this study we conducted a comprehensive analysis of the association of viral abundances with CRC using metagenomic shotgun sequencing data of 462 CRC subjects and 449 healthy controls from 7 studies performed in 8 different countries. Despite the high heterogeneity, our results showed that the virome alpha diversity was consistently higher in CRC patients than in healthy controls (p-value <0.001). This finding is in sharp contrast to previous reports of low alpha diversity of prokaryotes in CRC compared to healthy controls. In addition to the previously known association of Podoviridae, Siphoviridae and Myoviridae with CRC, we further demonstrate that Herelleviridae, a newly constructed viral family, is significantly depleted in CRC subjects. Our interkingdom association analysis reveals a less intertwined correlation between the gut virome and bacteriome in CRC compared to healthy controls. Furthermore, we show that the viral abundance profiles can be used to accurately predict CRC disease status (AUROC >0.8) in both within-study and cross-study settings. The combination of training sets resulted in rather generalized and accurate prediction models. Our study clearly shows that subjects with colorectal cancer harbor a distinct human gut virome profile which may have an important role in this disease.