Direct DNA Sequencing-Based Analysis of Microbiota Associated with Hematological Malignancies in the Eastern Province of Saudi Arabia

Abstract

Introduction. Bloodstream infections (BSI) among patients with hematological malignancies (HM) could predispose them to higher morbidity and mortality for various underlying conditions. Several microorganisms, either pathogenic or opportunistic normal human flora, could cause severe bacteremia and septicemia. While conventional methods have their own limitations, molecular methods such as next-generation sequencing (NGS) can detect these blood infections with more reliability, specificity, and sensitivity, in addition to information on microbial population landscape. Methodology. Blood samples from HM patients ( n = 50 ) and volunteer blood donor control individuals with no HM ( n = 50 ) were subjected to 16S rRNA gene amplification using standard PCR protocols. A metagenomic library was prepared, and NGS was run on a MiSeq (Illumina) sequencer. Sequence reads were analyzed using MiSeq Reporter, and microbial taxa were aligned using the Green Genes library. Results. 82% of the patients showed BSI with Gram-negative bacteria as the most predominant group. E. coli comprised a major chunk of the bacterial population (19.51%), followed by K. pneumoniae (17.07%). The CoNS and Viridans Streptococci groups are 17.07% and 14.63%, respectively. Other major species were S. aureus (9.75%), P. aeruginosa (7.31%), A. baumannii (4.87%), E. cloacae (4.87%), and P. mirabilis (4.87%). 34.14% of the cases among patients showed a Gram-positive infection, while 14.63% showed polymicrobial infections. Conclusion. Most of the BSI in patients were characterized by polymicrobial infections, unlike the control samples. Molecular methods like NGS showed robust, fast, and specific identification of infectious agents in BSI in HM, indicating the possibility of its application in routine follow-up of such patients for infections.

Clinical Application of Metagenomic Next-Generation Sequencing in Patients with Hematologic Malignancies Suffering from Sepsis

“…10 to no. 19), mNGS was able to identify additional pathogens from the blood samples compared with conventional methods. Aside from bacteria, the extra information provided by mNGS was mainly virus, including CMV, human mastadenovirus C, and herpes simplex virus type 1, which was discovered from seven pa- Our study showed that mNGS and conventional diagnostic methods reached comparable positive results in nine cases (case no.…”

“…10 to no. 19), eight (53.3%) patients had blood sampled prior to effective antimicrobial agents given and four (26.7%) patients had blood sampled on the same day when fever flared-up. For three patients, more information was required by conventional diagnostic methods (case no.…”

“…Our study successfully demonstrated the advantage of mNGS in diagnosing pathogens via serum samples among patients with hematologic malignancies who developed sepsis. Previous studies have shown the superiority of NGS methods targeting the 16S ribosomal RNA gene in the diagnosis of bacterial infection among immunocompromised patients [18][19][20]. Metagenomic NGS further provides effective diagnostic approaches in diagnosing atypical pathogens such as virus, fungi, and mycobacterium [7,14], which are more commonly seen among patients with hematologic malignancies than the general population.…”

Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions

“…Abdulhaq et al studied the tongue microbiota of children with autism spectrum disorder (ASD) in Jazan city and noted that there was no significant difference in the microbiota compared to that of healthy children [ 83 ]. Analysis of bacterial metagenome from blood samples of Saudi Arabian blood cancer patients with bloodstream infections showed the predominance of Gram-negative bacteria (82%) in which E. coli and K. pneumonia were higher [ 84 ]. Based on amplicon and metagenome sequencing, various bacteria associated with pneumonia, namely Acinetobacter baumannii , Pseudomonas aeruginosa and Streptococcus pneumonia , and several ARGs were reported to be present in the oropharyngeal swabs, tracheal aspirates, and throat swabs samples of Saudi patients infected with Middle East respiratory syndrome CoV (MERS-CoV) [ 85 ].…”

Cerebral vasculitis caused by Talaromyces marneffei and Aspergillus niger in a HIV-positive patient: a case report and literature review

“…However, conventional microbiological tests (CMTs) have competitive weaknesses, such as long turnaround time, complex process, low positive rate, and throughput. Metagenomic next-generation sequencing (mNGS), by contrast, directly detects the nucleic acid sequence of microorganisms in clinical specimens, skipping microbial culture (Gu et al 2019;Alzahrani et al 2021;Zhang et al 2020), and covers a variety of pathogenic microorganisms including viruses, bacteria, fungi, and parasites quickly and objectively (Gu et al 2019;Petersen et al 2020). Here, we exemplified an old man who had clinically suspected viral encephalitis and was ultimately diagnosed as fungal cerebral vasculitis using mNGS.…”