Next-generation sequencing of 16S rRNA for identification of invasive bacterial pathogens in a formalin-fixed paraffin-embedded placental specimen: a case report of perinatal fulminant Streptococcus pyogenes infection

Abstract

Intrauterine infection is one of the most important causes of maternal death. In perinatal emergency, we often miss an opportunity to obtain culture specimens. In this study, we tried to examine whether we investigated whether bacteria causing infection can be detected from a formalin-fixed paraffin-embedded (FFPE) placental specimen. We examined the placenta from a maternal invasive infection that resulted in infectious abortion at 18 weeks of gestation. The case was diagnosed by acute fever and abdominal pain, and the patient was cured after 3 weeks of intensive antimicrobial treatment. Four Streptococcus pyogenes strains were isolated from vaginal fluid and blood cultures of the patient. All of the strain types were emm1/ST28. We amplified the V1-V2 region of 16S rRNA from an FFPE placental specimen and sequencing was performed using a next-generation sequencer (NGS). Taxonomic analysis was then performed for sequenced data. We succeeded in detecting causative pathogens from the FFPE placenta: 69.1% of the predominantly identified bacteria were S. pyogenes and other small populations of bacteria were detected. Our results revealed the utility of NGS for 16S rRNA analysis of an FFPE placenta. This method may reveal previous perinatal invasive infections of unknown origin retrospectively. KeywordsStreptococcal toxic shock syndrome (STSS) • Intrauterine infection • Placenta • 16S rRNA sequencing • Formalin-fixed paraffin-embedded specimen * Tasuku Mariya

Metagenomics by next-generation sequencing (mNGS) in the etiological characterization of neonatal and pediatric sepsis: A systematic review

“…Regarding the design of the studies, in three, an initial prospective design was proposed for the inclusion of the patients and the collection of the sample which were all from the pediatric population ( 33 – 35 ); however, in all the studies, the mNGS analysis of the collected samples was conducted retrospectively on the samples which were stored and frozen. Two studies were case reports which were from the neonate population ( 36 , 37 ). The characteristics of the admitted studies are shown in Tables 1 , 2 .…”

“…Most of the studies include a small number of patients, except for the study by Anh et al (34), which analyses samples from 388 children. On the other hand, the analysed samples in the studies were blood (33)(34)(35)(36)(37) and cerebrospinal fluid (34,36). The Anh study had the particularity of analysing, in addition to the blood samples and CFS, samples of the pharyngeal swab, tracheal aspirate and Stool (34).…”

“…For example, in case 1, the microorganisms with 90% relative abundance were treptococcus, and in case two, the microorganisms identified with the highest relative abundance were Corynebacterium, among others. On the other hand, the study by Mariya et al (37) analyzed placental samples from three cases of chorioamnionitis and preterm birth and one from a full-term birth without pathology as a negative control for infection. Taxonomic analysis showed that S. pyogenes was the most prevalent bacterium (69.1%) in the placenta of case 1, and the second most common species was Burkholderia spp (18.2%).…”

Microbiome analysis in women with endometriosis: Does a microbiome exist in peritoneal fluid and ovarian cystic fluid?

“…Operational taxonomic units (OTUs) were constructed after quality filtering of the paired‐end reads. The OTUs were assigned to taxa using the database reported in a previous study 11 . Bacteria that were frequently observed in the negative control were grouped as background bacterial contamination (Supplemental Data 1), and after screening of the samples, the background‐contaminated bacteria were excluded from the microbiome profile.…”

Endometrial and vaginal microbiomes influence assisted reproductive technology outcomes

“…DNA was extracted from the endometrial and vaginal secretions of pregnant and nonpregnant patients using a previously reported protocol (Kyono et al, 2018b;Mariya et al, 2021). UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific Inc., Waltham, MA, USA) was used as a negative control.…”