Skip to main content
NCBI home page
Scientific Reports logoLink to Scientific Reports
. 2025 Jul 1;15:22323. doi: 10.1038/s41598-025-07253-6

Genomic analysis of contaminant Stenotrophomonas maltophilia, from placental swab culture, carrying antibiotic resistance: a potential hospital laboratory contaminant

Pisut Pongchaikul 1,2,3,✉, Piroon Jenjaroenpun 4, Paninee Mongkolsuk 1, Pornpun Vivithanaporn 1, Thidathip Wongsurawat 4, Perapon Nitayanon 5, Iyarit Thaipisuttikul 5, Jakkrit Khamphakul 6, Puntabut Warintaksa 7, Warawut Laolerd 6, Pitak Santanirand 6, Piya Chaemsaithong 7,✉
PMCID: PMC12216970  PMID: 40594762

Abstract

Acute chorioamnionitis has been considered as reflective of amniotic fluid infection. Standard microbiological work ups for causative microorganism of intra-amniotic infection is based on microbial identification. However, frequency of positive placental culture is varied depending on placental sampling techniques, contaminations, methods of microbiologic work ups or comprehensive microbiologic work ups. In this report, we performed a hybrid whole genome sequencing of a proven bacterial contaminant obtained from placental culture in a patient with preterm labor and acute chorioamnionitis. This is to unveil genetic characterization of contaminant Stenotrophomonas maltophilia habouring antibiotic resistance genes. Stenotrophomonas maltiphilia was proven to be bacterial contaminant since Ureaplasma urealyticum was subsequently demonstrated in amniotic fluid by 16 S rRNA gene Sanger sequencing. Cultivation results from other sources were no growth. We identified Stenotrophomonas maltiphilia strain RAOG732 which carried several antibiotic resistance genes, including aminoglycoside, fluoroquiolone and beta-lactam. Biofilm production genes were also identified in this genome. We firstly utilized a hybrid sequencing approach to investigate the genome of S. maltiphilia in the patient with preterm and acute chorioamnionitis, a proven bacterial laboratory contaminant. The analysis provided several antibiotic resistance-associated and genes biofilm-associated genes. The detection of S. maltiphilia raised the awareness of the colonization of biofilm-producing bacteria in hospitals, where surveillance for decontamination is necessary.

Keywords: Acute chorioamnionitis, Acute inflammatory lesion of the placenta, Acute funisitis, Amniotic fluid, Chorioamnionitis, Chorioamniotic membranes, Stenotrophomonas, Biofilm, Hybrid genome assembly, Infection, Intraamniotic infection, Nanopore, Placenta, Preterm labor

Subject terms: Clinical microbiology, Environmental microbiology, Microbial genetics

Introduction

Acute chorioamnionitis is the most frequent diagnosis in the placental pathology reports, and is generally considered to represent the presence of “intra-amniotic infection” or “amniotic infection syndrome”1–11. This condition is characterized by diffuse infiltration of neutrophils into chorioamniotic membranes7. The frequency of acute histologic chorioamnionitis changes as a function of gestation age with being highest in the early gestation indicating the importance of the inflammatory pathway in early preterm gestation3,12–15. The most common pathway for intraamniotic infection is the ascending microbial invasion from the lower genital tract16–18.

Microorganisms firstly colonise in the uterine decidua and subsequently propagate into chorioamniotic membranes and invade amniotic cavity19. Chorioamniotic passage of microorganisms can lead to the establishment of microbial invasion of the amniotic cavity, which induces a robust local inflammatory response accompanied by a dramatic increase in the concentrations of pro-inflammatory cytokines11,20–26. Chemotactic stimuli in the amniotic cavity then induce neutrophils migration into chorioamniotic membranes27–29, so acute chorioamnionitis is an indicative placental lesion of intra-amniotic infection. Therefore, histologic examination and microbiologic workups of the placenta can provide crucial information for clinical management of both mothers and fetuses i.e., for the determination of antibiotic treatment in both mothers and neonates. Similar pattern of pathogenesis could be observed in other infections, including Helicobacter pylori – associated gastritis30.

Previous studies demonstrated that frequencies of bacteria recovered from the chorioamniotic membranes cultures in women with acute histologic chorioamnionitis range from 20 to 70% with a higher frequency in early gestation4,5,27,31,32. The variation in frequencies of bacteria might be related to placental sampling techniques, contaminations, microbiologic work up methods or comprehensive microbiologic work ups. Specifically, proper placental microbiological culture requires diligence with the sampling technique. To illustrate, if the external placental surface is sampled instead of the subamniotic tissue, vaginal microorganisms may contaminate the sample. Comprehensive microbiological culture (including aerobe and anaerobe) from several sites is required to adequately identify microorganism causing in utero infection32.

Currently, next-generation sequencing has become a commonly used tool in pathogen identification and surveillance33–35. Yet, bacterial contamination in laboratory reagents, sequencing kits36,37, and common cross-contamination across samples38 can be found and have critical impacts on downstream analysis such as false alignments and erroneous downstream variant calls causing mis-mappings and distortion of the estimation of microbial abundance of different genera38–40.

In this report, we illustrated the use of whole genome hybrid assembly to characterize genomic characteristic of proven bacterial contaminant derived from placental culture in a woman with acute histologic chorioamnionitis in which we initially thought that this is a causative microorganism of intra-amniotic infection and preterm labor. The uniqueness of this report is that we performed a complete microbiologic work up from several sources to identify causative pathogens of acute chorioamnionitis. Our findings can facilitate researchers to eliminate putative contaminant species in low biomass clinical samples, including placental tissue or amniotic fluid.

Methods

Clinical information

A 28-year-old para 0 at 24+ 1 weeks of gestation, presented to the Labor and Delivery Unit at our hospital due to advanced spontaneous preterm labor. She delivered by Cesarean delivery due to breech presentation. Placental histopathology demonstrated acute histologic chorioamnionitis. The enrollment and the use of clinical specimens of this patient were approved by the Institutional Research Board of the Faculty of Medicine, Ramathibodi Hospital, Mahidol University (COA.MURA 2022/675).

Clinical specimen collection and Microbiological investigation

Vaginal swab, amniotic fluid obtained during Cesarean delivery, umbilical cord blood, and placental swab at the space between chorioamniotic membranes were subjected to standard clinical laboratory examination for patients with spontaneous preterm labor, including cultivation-based identification and 16s rRNA gene sequencing (using primer 27F and 1492R). Histopathologic examination of the placenta was performed.

Placental swab cultivation

Cultivation of placental swab was performed by swabbing the placenta on chorioamniotic space using aseptic technique. The swab stick was kept in a sterile, capped container within the sterile operating field. The swab was inoculated on blood agar, MacConkey agar, and chocolate agar under an aerobic condition and on thioglycolate broth under an anaerobic condition.

Isolation and sequencing

Bacterial isolate was recovered from the placental swab under routine microbiological culture using aseptic technique. Species identification was performed based on biochemical characteristics (oxidase enzyme, Lysine decarboxylase test, and sugar fermentation) and matrix-assisted laser desorption/ionization Time-of-flight (MALDI-TOF) (Bruker Serius, Germany)41. Genomic DNA was extracted from bacterial colonies obtained from the culture. Whole genome sequencing was conducted with single molecular sequencing (Oxford Nanopore Technologies [ONT], UK) and Illumina short-read sequencing as described in the previous study42. Briefly, DNA library preparation was performed by using the Rapid Barcoding Sequencing Kit (SQK-RBK004; ONT). A total of 200 ng of genomic DNA was cleaved with transposase enzymes to produce chemically modified ends and a barcode was added to each DNA sample, finally ligated with an adapter. The library was loaded into the R9.4.1 flow cell (FLO-MIN106 version; ONT) and sequenced with the GridION device (ONT) with 72-hour sequencing. For Illumina short-read sequencing, 150-bp paired-end libraries were prepared with a TruSeq DNA PCR-free Kit and sequenced with the Illumina™ Novaseq sequencer (Illumina Inc., San Diego, CA, USA). To obtain high-quality reads, adapter sequences were trimmed by using Skewer v0.2.2. The sequence data from both platforms were combined for hybrid genome assembly. This protocol was approved by the Institutional Biosafety Committee of the Faculty of Medicine at Ramathibodi Hospital, Mahidol University (RAMA-IBC 2022-009).

Assembly and annotation

A hybrid genome assembly approach was selected to produce a de novo assembly of the S. maltophilia genome. Hybrid assembly was performed as described in Pongchaikul et al.42. The hybrid genome assembly procedures were depicted as a series of flowing steps. For short reads QC, we used the Fastp v0.20.1 tool to trim sequencing adapters and low-quality reads, followed by quality assessment with FastQC v0.11.843. For long reads, raw signals were processed, demultiplexed, and adapter trimmed, using Guppy v6.2.1 with the super accurate model (--c dna_r9.4.1_450bps_sup.cfg -r --trim_barcodes --barcode_kits SQK-RBK004) and Porechop v0.2.444. The quality of the ONT raw reads was assessed by using NanoPlot v1.28.1. The reads were filtered by NanoFilt v2.5.045, based on a mean quality score of 9, and only reads with a length of 1,000 bases were retained for the de novo assembly. Finally, we constructed the genomes with Unicycler v0.4.846, which incorporates hybrid assembly, correction, circularization, and rotation to produce high-quality genome assemblies. Gene annotation was performed in Dfast47. Multi-locus sequence typing assignment (MLST) was performed by using FastMLST software48.

Analysis of mobile genetic element, phage, potential antimicrobial resistance genes, and virulence-associated genes was executed by using the Mobile Element Finder, PHASTER, ResFinder version 4.1 and MLST service, respectively49–51. CRISPRCasFinder was used to determine potential CRISPR-Cas region on the chromosome52. Virulence-associated genes were obtained by using VFanalyzer53 and Virulence Finder54. Genome visualization was constructed using PROKSEE55.

Results

Culture from umbilical cord blood and amniotic fluid showed no growth of microorganisms. Amniotic fluid was subsequently investigated using molecular microbiological method for research purpose and the result demonstrated Ureaplasma urealyticum. Therefore, it is most likely a causative pathogen. Ureaplasma species and Mycoplasma species could not be identified from cultivation in our clinical microbiology unit since the culture of these species has not been performed in our hospital. Vaginal swab showed the growth of multiple organisms, which could be normal flora of vaginal mucosa. Placental histopathology showed “acute histologic chorioamnionitis and acute funisitis”.

For the placental swab, growing colonies were detected on the 3rd day after the aerobic culture of placental swab started. The identification of S. maltophila was confirmed by biochemical characteristic-based techniques (oxidase-negative, lysine decarboxylase-positive non-lactose fermentation, and strong maltose fermentation) and MALDI-ToF. Antibiotic susceptibility phenotype revealed the strain was resistant to Co-trimoxazole (MIC > 4 ug/ml) and Levofloxacin (MIC = 8 ug/ml) and less susceptible to Ceftazidime (MIC = 16 ug/ml). The colony was listed as the S. maltophilia RAOG732 strain and was then collected for whole genome sequencing.

Genomic characteristics

Hybrid genome assembly provided a total number of 4,931,363 bp, consisting of 11 contigs. The largest contig was 2,650,926 bp with N50 of 2,650,926 bp and GC content of 66.0%. Genome annotation was processed in silico using Dfast software showing 4,570 CDs, 13 rRNAs and 75 tRNAs. Species identification, using a whole genome sequence, agreed with S. maltophilia with ANI of 97.98%, calculated by fastANI. Analyses of the whole genome sequence of S. maltophilia RAOG732 revealed that the strain belonged to ST820. MLST ST820 (a recently identified ST, biofilm formation, nosocomial infection)56.

To evaluate the comprehensive genome of S. maltophilia RAOG732, the prediction for antibiotic resistance genes, virulence-associated genes, CRISPR region, and potential bacteriophage region were performed (Fig. 1). Resfinder and Resistance gene identifier (RGI) identified a total number of six potential antibiotic resistance genes (Table 1). These genes covered the resistance against Aminoglycoside (3 genes), Fluoroquinolone (1 gene), Folate synthesis inhibitor (1 gene) and beta-lactam (1 gene). The occurrence of these resistance genes in SMA RAOG732 was concordant with resistance phenotype.

Fig. 1.

Fig. 1

Open in a new tab

The circular plot of Stenotrophomonas maltophilia RAOG732 genome. The innermost ring shows the distribution of Guanine-Cytosine (GC) content throughout the genome. The ring with purple and green density plots represents the GC skewness of the genome.

Table 1.

The presence of genetic basis of antimicrobial resistance-associated genes in the S.maltophilia RAOG732 genome.

Antibiotic group Protein name Gene name Function
Aminoglycoside Aminoglycoside-6’- acetyltransferase Iz aac(6’)-Iz Drug modification
Aminoglycoside-6’- acetyltransferase Ib7 aac(6’)-Ib7
Aminoglycoside-3’- phosphotransferase IIc aph(3’)-IIc
Fluoroquinolone Multidrug efflux RND transporter permease subunit oqxB Efflux pump
Folate synthesis inhibitor Sulfonamide resistant dihydropteroate synthase sul1 Receptor modification
Beta-lactam L1-family class A Beta-lactamase blaL1 Drug modification
Open in a new tab

For CRISPR-Cas and mobile genetic elements, a total number of four regions was identified as putative CRISPR-Cas regions; however, the evidence of predicted regions was categorized into “level 1”, which is less confident for being true CRISPR-Cas region. None of the potential phage regions was identified by PHASTER, PhaBOX, and PhaGAA.

For virulence of the strain, genes associated with adhesion (pilT and pilU) and catalase (katA) were identified with identity > 75%. The similarity of the nucleotide sequences of these genes were similar to gene sequences previously identified in Pseudomonas aeruginosa PA01 (pilT and pilU) and Neisseria meningitidis (katA). Since biofilm formation is considered a virulent phenotype of SMA, we identified three genes associated with biofilm production: rmlA gene, spgM gene, and rpfF gene. The smf-1 gene was not identified in this genome.

Discussion

This work has demonstrated the use of hybrid genome assembly to identify genomic characteristics, including antibiotic resistance genes, virulence factors and mobile genetic elements, in proven bacterial contaminants from the placental swab obtained from the patient with preterm labor and acute histologic chorioamnionitis. Genomic identification currently becomes a robust tool to elucidate genomic insight of the bacteria, especially causative pathogens. However, bacterial contamination could be observed during microbiological work up processes including specimen collection, transportation, and laboratory process for microorganism identification. This could raise the awareness of the presence of drug-resistance bacterial contamination in hospitals. More importantly, Stenotrophomonas maltophilia could be included in putative contaminants, to be removed, from low biomass clinical specimens.

Bacterial contamination during culture process and its consequences

Microbiological culture of clinical specimens has been used to identify the species of causative pathogen in patients with/or suspicious with infection. According to standard clinical microbiology recommendation, clinical specimens are collected using aseptic techniques and under sterile conditions from a clinical setting and transferred to the clinical microbiology unit within 2 h57. After transferring the clinical specimens from the container to standard culture media under sterile conditions with aseptic techniques in a biosafety cabinet, the culture plate is incubated at 37 °C. Unfortunately, even though these processes are performed under sterile conditions, contamination may still occur and lead to misidentification and the results could interfere with clinical decision making and patient management, which in some cases leads to the death of the patient58,59.

Contamination in hospital laboratory units is an important problem leading to consequences in the consideration for clinical management58. Notably, contamination could be a significant issue if such a problem occurs in a clinical microbiology unit, where it should deliver precise and accurate identification of pathogens. Identification of contaminants could affect patient care in terms of diagnosis, patient management and choice of given antibiotic. Misidentification of causative pathogens in pregnant women may lead to inappropriate use of antibiotics that can have an impact on gut dysbiosis in the neonate, possibly causing consequent health conditions, such as allergy or the susceptibility to neonatal infections and long-term pathologies60.

Stenotrophomonas maltophilia

Stenotrophomonas maltophilia (SMA), an aerobic, non-fermenting Gram-negative rod-shaped bacterium, is an environmental bacterium found in plants, food, and water sources61. In clinical obstetrics, SMA has been reported as one of the pathogens associated with spontaneous preterm labor or neonatal sepsis62–66. Rajia et al. reported that the presence of SMA in the placenta, together with exposure to cigarette smoke, were risk factors for preterm labor67. In addition, a recent case report demonstrated that SMA could be a causative pathogen of early neonatal sepsis in a neonate whose mother had no history of infection since SMA was isolated from neonatal blood culture obtained immediately after the birth and there was no other possible source of transmission from mother or hospital environment68.

However, SMA is also reported as a potential contaminant. A study by Jung et al. described the presence of SMA-positive DNA in amniotic fluid obtained from the patient with preterm labor without intra-amniotic inflammation and chorioamnionitis, therefore, suggesting the possibility of contamination69. In addition, SMA was isolated in neonatal blood in neonates with hospital-acquired late onset neonatal sepsis without evidence/history of maternal infection, suggesting contamination68,70. The contamination with SMA could be derived from the water system71 or inadequate cleaning and decontamination of medical devices72.

In our study, we identified SMA from colonies taken from the microbiological culture of the placental swab taken from the patient with preterm labor with acute histological chorioamnionitis. Only SMA was initially isolated from placental swab culture. There was no report of the identification of SMA from internal surveillance in our hospital. We are curtained that SMA is a contamination as we identified Ureaplasma urealyticum from amniotic fluid, a normally sterile site, using 16s rRNA gene sequencing. Therefore, SMA is considered as a contaminant.

Antimicrobial resistance in contaminant

Antibiotic resistance has been increasingly identified from the environment, including natural source and household73. The occurrence of antibiotic resistance in the environment could be a result of two main reasons: (1) inappropriate use of antibiotics and; (2) intrinsic resistance in the bacteria74,75. This problem is important when it involves the health and safety of the community, especially food and hospitals. Recent studies reported the detection of antimicrobial resistance genes in food, especially raw food and fermented food76,77. More seriously, the occurrence of antimicrobial resistance contamination has been observed in hospitals, particularly on working surfaces78,79, water system80,81, and medical devices72,82.

In our study, six genes associated with antimicrobial resistance were identified from the assembly. These genes were concordant with susceptibility profile (oqxB for fluoroquinolone resistance, sul1 for co-trimoxazole resistance, and blaL1 for ceftazidime). The oqxB is a component of efflux pump system OqxAB, conferring resistance to several antibiotics, including fluoroquinolone, tigecycline and nitrofurantoin, in various gram-negative bacteria, such as E. coli and S. maltophilia83,84. The sul1 gene is translated into a resistance variance of dihydropteroate synthase, which is associated with sulfonamide resistance in gram-negative bacteria85. Lastly, amino acid sequence of this gene was 100% identical to the L1-2 variant of BlaL1, which is an extended spectrum beta-lactamase (ESBL) and belongs to Ambler class B3 beta-lactamase. Since, blaL1 gene is located on the chromosome, this gene has been recognized as an intrinsic resistance gene in various gram-negative bacteria, especially S. maltophilia84,86. Identification of these genes confirmed the susceptibility profile of S. maltophilia RAOG732. It is noteworthy that the presence of sul1 gene in this strain could lead to the inability to use co-trimoxazole, a first-line drug for S. maltophilia87.

S. maltophilia RAOG732 belongs to ST820, which can produce biofilm56. Biofilm formation helps several bacterial species colonize on surfaces such as workstation and medical devices88,89. Interestingly, biofilm formation ability of S. maltophilia affects clinical outcome of the patients and is induced by exposure to antibiotics90,91. Our findings revealed the presence of three genes (rmlA, spgM, and rpfF) that have been previously shown to play a role in biofilm formation in SMA92,93. Therefore, the isolation of S. maltophilia in this patient could be due to the contamination during various processes although the detection of S. maltophilia in hospital environments has not been confirmed. The stringent cleaning with appropriate disinfectant must be utilized throughout the hospital to prevent biofilm formation and the colonization of S. maltophilia. Nevertheless, the main limitation of this study is that the sample could not be re-inoculated because the clinical specimen was discarded within 7 days according to the specimen handling recommendation.

Conclusions

Laboratory contamination can lead to problems in clinical medicine in terms of misidentification of causative pathogens, causing nosocomial infection and, importantly, distributing antibiotic resistance genes. This study is the first to characterise genomic of biofilm-producing S. maltophilia as a proven bacterial contaminant in hospitals. The analysis provided antibiotic resistance genes, which agree with antibiotic susceptibility profile. This finding raises the awareness of adequate disinfection of hospital environments to eradicate the colonization of antibiotic resistance bacteria that may cause serious hospital-associated infection.

Acknowledgements

The authors are thankful to clinical microbiology staffs and labour room staffs.

Author contributions

PP performed conceptualization, data analysis, drafting and finalizing the manuscript. PJ performed data analysis. PM performed microbiological examination and DNA extraction. PV contributed to laboratory investigation. TW conducted whole genome sequencing. PN performed microbiological examination and DNA extraction. IT and PS conducted microbiological analysis. JK and WL contributed to microbiological examination. PW contributed to patient management, specimen collection, and finalizing the manuscript. PC performed conceptualization, patient management, specimen collection, drafting and finalizing the manuscript. All authors reviewed the manuscript.

Funding

This research paper is supported by Specific League Funds from Mahidol University (Fundamental Fund: fiscal year 2024 by National Science Research and Innovation Fund (NSRF) (FF-024/2567, FF-028/2567)) and Faculty of Medicine Ramathibodi Hospital Research Funding, Mahidol University (RF-65090, RF-65048) and the Royal Thai College of Obstetrics and Gynecology (RTCOG). This research project has been funded by Mahidol University [Fundamental Fund: fiscal year 2024 by National Science Research and Innovation Fund (NSRF)] FF-024/2567: Project: Rapid identification of intraamniotic infection using nanopore-based sequencing in preterm labor/PPROM: to Piya Chaemsaithong and FF-028/2567 to Pisut Pongchaikul as well as the Royal Thai College of Obstetrics and Gynecology to Piya Chaemsaithong.

Data availability

The genome used in this study was available in the Genbank repository (SAMN34413089).

Declarations

Ethics approval and consent to participate

The protocols of this study were approved by the Institutional Research Board of the Faculty of Medicine, Ramathibodi Hospital, Mahidol University (COA.MURA2024/299). The protocol was in accordance with the Declaration of Helsinki. Informed consent was obtained from all participants.

Competing interests

The authors declare no competing interests.

Footnotes

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Contributor Information

Pisut Pongchaikul, Email: pisut.pon@mahidol.ac.th.

Piya Chaemsaithong, Email: piya.cha@mahidol.ac.th.

References

  • 1.Blanc, W. A. Amniotic infection syndrome; pathogenesis, morphology, and significance in circumnatal mortality. Clin. Obstet. Gynecol.2, 705–734 (1959). [PubMed] [Google Scholar]
  • 2.Blanc, W. A. Pathology of the placenta and cord in ascending and in haematogenous infection. Ciba Found. Symp.77, 17–38 (1979). [DOI] [PubMed] [Google Scholar]
  • 3.Russell, P. Inflammatory lesions of the human placenta. III. The histopathology of villitis of unknown aetiology. Placenta1 (3), 227–244 (1980). [DOI] [PubMed] [Google Scholar]
  • 4.Hillier, S. L. et al. A case-control study of chorioamnionic infection and histologic chorioamnionitis in prematurity. N Engl. J. Med.319 (15), 972–978 (1988). [DOI] [PubMed] [Google Scholar]
  • 5.Hillier, S. L., Krohn, M. A., Kiviat, N. B., Watts, D. H. & Eschenbach, D. A. Microbiologic causes and neonatal outcomes associated with chorioamnion infection. Am. J. Obstet. Gynecol.165 (4 Pt 1), 955–961 (1991). [DOI] [PubMed] [Google Scholar]
  • 6.Romero, R. et al. The relationship between acute inflammatory lesions of the preterm placenta and amniotic fluid microbiology. Am. J. Obstet. Gynecol.166 (5), 1382–1388 (1992). [DOI] [PubMed] [Google Scholar]
  • 7.Redline, R. W. et al. Society for pediatric pathology PSAFINC: amniotic infection syndrome: nosology and reproducibility of placental reaction patterns. Pediatr. Dev. Pathol.6 (5), 435–448 (2003). [DOI] [PubMed] [Google Scholar]
  • 8.Redline, R. W. Placental inflammation. Semin Neonatol. 9 (4), 265–274 (2004). [DOI] [PubMed] [Google Scholar]
  • 9.Fox, H. S. N. Infections and Inflammatory Lesions of the Placenta. In: Pathology of the Placenta. edn. Edited by Third. China: ELSEVIER; (2007).
  • 10.Benirschke, K. B. G. & Baergen, R. N. Infectious Diseases. In: Pathology of the Human Placenta. edn. Edited by Sixth. Berlin Heidelberg: Springer; (2012).
  • 11.Kim, C. J. et al. Acute chorioamnionitis and funisitis: definition, pathologic features, and clinical significance. Am. J. Obstet. Gynecol.213 (4 Suppl), S29–52 (2015). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.van Hoeven, K. H. et al. Clinical significance of increasing histologic severity of acute inflammation in the fetal membranes and umbilical cord. Pediatr. Pathol. Lab. Med.16 (5), 731–744 (1996). [PubMed] [Google Scholar]
  • 13.Srinivas, S. K., Ernst, L. M., Edlow, A. G. & Elovitz, M. A. Can placental pathology explain second-trimester pregnancy loss and subsequent pregnancy outcomes? Am. J. Obstet. Gynecol.199 (4), 402e401–402e405 (2008). [DOI] [PubMed] [Google Scholar]
  • 14.Lee, S. M. et al. Acute histologic chorioamnionitis is a risk factor for adverse neonatal outcome in late preterm birth after preterm premature rupture of membranes. PLoS One. 8 (12), e79941 (2013). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Kim, S. M. et al. The relationship between the intensity of intra-amniotic inflammation and the presence and severity of acute histologic chorioamnionitis in preterm gestation. J. Matern Fetal Neonatal Med.28 (13), 1500–1509 (2015). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Romero, R. & Mazor, M. Infection and preterm labor. Clin. Obstet. Gynecol.31 (3), 553–584 (1988). [DOI] [PubMed] [Google Scholar]
  • 17.Pongchaikul, P. et al. Molecular evidence that GBS early neonatal sepsis results from ascending infection: comparative hybrid genomics analyses show that microorganisms in the vaginal ecosystem, amniotic fluid, chorioamniotic membranes, and neonatal blood are the same. J. Perinat. Med.52 (9), 977–990 (2024). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.Warintaksa, P. et al. Successful eradication of group B Streptococcus intraamniotic infection with antibiotics in preterm prelabor rupture of the membranes. Am. J. Obstet. Gynecol.231 (4), e130–e134 (2024). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Kim, M. J. et al. Widespread microbial invasion of the chorioamniotic membranes is a consequence and not a cause of intra-amniotic infection. Lab. Invest.89 (8), 924–936 (2009). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Chaemsaithong, P. et al. The rapid diagnosis of intraamniotic infection with nanopore sequencing. Am J. Obstet. Gynecol (2025). [DOI] [PubMed]
  • 21.Romero, R., Avila, C., Santhanam, U. & Sehgal, P. B. Amniotic fluid Interleukin 6 in preterm labor. Association with infection. J. Clin. Invest.85 (5), 1392–1400 (1990). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Romero, R. et al. Neutrophil attractant/activating peptide-1/interleukin-8 in term and preterm parturition. Am. J. Obstet. Gynecol.165 (4 Pt 1), 813–820 (1991). [DOI] [PubMed] [Google Scholar]
  • 23.Romero, R. et al. Interleukin 6 determination in the detection of microbial invasion of the amniotic cavity. Ciba Found. Symp.167, 205–220 (1992). discussion 220 – 203. [DOI] [PubMed] [Google Scholar]
  • 24.Romero, R. et al. Amniotic fluid interleukin-6 determinations are of diagnostic and prognostic value in preterm labor. Am. J. Reprod. Immunol.30 (2–3), 167–183 (1993). [DOI] [PubMed] [Google Scholar]
  • 25.Goldenberg, R. L., Andrews, W. W. & Hauth, J. C. Choriodecidual infection and preterm birth. Nutr. Rev.60 (5 Pt 2), S19–25 (2002). [DOI] [PubMed] [Google Scholar]
  • 26.Steel, J. H. et al. Bacteria and inflammatory cells in fetal membranes do not always cause preterm labor. Pediatr. Res.57 (3), 404–411 (2005). [DOI] [PubMed] [Google Scholar]
  • 27.Williams, M. R., Azcutia, V., Newton, G., Alcaide, P. & Luscinskas, F. W. Emerging mechanisms of neutrophil recruitment across endothelium. Trends Immunol.32 (10), 461–469 (2011). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Kolaczkowska, E. & Kubes, P. Neutrophil recruitment and function in health and inflammation. Nat. Rev. Immunol.13 (3), 159–175 (2013). [DOI] [PubMed] [Google Scholar]
  • 29.Tecchio, C., Micheletti, A. & Cassatella, M. A. Neutrophil-derived cytokines: facts beyond expression. Front. Immunol.5, 508 (2014). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Rahimkhani, M., Mordadi, A., Kazemian, K. & Khalili, H. Comparison of Helicobacter pylori detection methods: it’s association with leukocytosis and monocytosis. Infect. Disord Drug Targets. 20 (6), 920–924 (2020). [DOI] [PubMed] [Google Scholar]
  • 31.Pankuch, G. A. et al. Placental microbiology and histology and the pathogenesis of chorioamnionitis. Obstet. Gynecol.64 (6), 802–806 (1984). [PubMed] [Google Scholar]
  • 32.Bhola, K. et al. Placental cultures in the era of peripartum antibiotic use. Aust N Z. J. Obstet. Gynaecol.48 (2), 179–184 (2008). [DOI] [PubMed] [Google Scholar]
  • 33.Petzold, M., Prior, K., Moran-Gilad, J., Harmsen, D. & Luck, C. Epidemiological information is key when interpreting whole genome sequence data - lessons learned from a large Legionella pneumophila outbreak in warstein, germany, 2013. Euro Surveill22(45). 17-00137, 10.2807/1560-7917.ES.2017.22.45.17-00137 (2017). [DOI] [PMC free article] [PubMed]
  • 34.Pollett, S. et al. Genomic epidemiology as a public health tool to combat Mosquito-Borne virus outbreaks. J. Infect. Dis.221 (Suppl 3), S308–S318 (2020). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Chaemsaithong, P. et al. Rapid diagnosis of intra-amniotic infection using nanopore-based sequencing. J. Perinat. Med.51 (6), 769–774 (2023). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 36.Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based Microbiome analyses. BMC Biol.12, 87 (2014). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 37.de Goffau, M. C. et al. Recognizing the reagent Microbiome. Nat. Microbiol.3 (8), 851–853 (2018). [DOI] [PubMed] [Google Scholar]
  • 38.Merchant, S., Wood, D. E. & Salzberg, S. L. Unexpected cross-species contamination in genome sequencing projects. PeerJ2, e675 (2014). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Goig, G. A., Blanco, S., Garcia-Basteiro, A. L. & Comas, I. Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability. BMC Biol.18 (1), 24 (2020). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 40.Woods, H. J. et al. A functional linear modeling approach to sleep-wake cycles in dogs. Sci. Rep.10 (1), 22233 (2020). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 41.Carroll KC, Pfaller MA, American Society for Microbiology: Manual of clinical microbiology, 13th edition. edn. Hoboken, NJ Washington, DC ASM Press,: Wiley;; 2023.
  • 42.Pongchaikul, P. et al. Genomic analysis of Enterococcus faecium strain RAOG174 associated with acute chorioamnionitis carried antibiotic resistance gene: is it time for precise Microbiological identification for appropriate antibiotic use? BMC Genom.24 (1), 405 (2023). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 43.http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  • 44.https://github.com/rrwick/Porechop
  • 45.De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M. & Van Broeckhoven, C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics34 (15), 2666–2669 (2018). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 46.Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol.13 (6), e1005595 (2017). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 47.Tanizawa, Y., Fujisawa, T. & Nakamura, Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics34 (6), 1037–1039 (2018). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 48.Guerrero-Araya, E., Munoz, M., Rodriguez, C. & Paredes-Sabja, D. FastMLST: A Multi-core tool for multilocus sequence typing of draft genome assemblies. Bioinform Biol. Insights. 15, 11779322211059238 (2021). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 49.Joensen, K. G. et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J. Clin. Microbiol.52 (5), 1501–1510 (2014). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 50.Arndt, D. et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res.44 (W1), W16–21 (2016). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 51.Johansson, M. H. K. et al. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: mobileelementfinder. J. Antimicrob. Chemother.76 (1), 101–109 (2021). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 52.Couvin, D. et al. CRISPRCasFinder, an update of crisrfinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res.46 (W1), W246–W251 (2018). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 53.Liu, B., Zheng, D., Jin, Q., Chen, L. & Yang, J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res.47 (D1), D687–D692 (2019). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 54.Malberg Tetzschner, A. M., Johnson, J. R., Johnston, B. D., Lund, O. & Scheutz, F. In Silico genotyping of Escherichia coli isolates for extraintestinal virulence genes by use of Whole-Genome sequencing data. J Clin. Microbiol58(10), e01269-20, 10.1128/JCM.01269-20 (2020). [DOI] [PMC free article] [PubMed]
  • 55.Grant, J. R. et al. Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Res.51 (W1), W484–W492 (2023). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 56.Strateva, T. et al. Analysis of biofilm formation in nosocomial Stenotrophomonas maltophilia isolates collected in bulgaria: an 11-year study (2011–2022). Acta Microbiol. Immunol. Hung.70 (1), 11–21 (2023). [DOI] [PubMed] [Google Scholar]
  • 57.Ruoff, K. L. General Approaches to Identification of Aerobic Gram-Positive Cocci. In: Manual of Clinical Microbiology. edn.; : 304–307. (2011).
  • 58.Doern, G. V. et al. Practical guidance for clinical microbiology laboratories: A comprehensive update on the problem of blood culture contamination and a discussion of methods for addressing the problem. Clin Microbiol. Rev33(1). e00009-19, 10.1128/CMR.00009-19 (2019). [DOI] [PMC free article] [PubMed]
  • 59.Rahimkhani, M. & Rajabi, Z. MRSA and VRSA isolated from patients hospitalized in the ICU, NICU and surgical departments of hospitals. Proceedings of the National Academy of Sciences, India Section B: Biological Sciences 94:5. (2024).
  • 60.Martinez de Tejada, B. Antibiotic use and misuse during pregnancy and delivery: benefits and risks. Int. J. Environ. Res. Public. Health. 11 (8), 7993–8009 (2014). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 61.Brooke, J. S. Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clin. Microbiol. Rev.25 (1), 2–41 (2012). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 62.Viswanathan, R., Singh, A. K., Ghosh, C. & Basu, S. Stenotrophomonas maltophilia causing early onset neonatal sepsis. Indian Pediatr.48 (5), 397–399 (2011). [DOI] [PubMed] [Google Scholar]
  • 63.Issaoui, S. et al. [Neonatal infection with Stenotrophomonas maltophilia (2 case studies)]. Arch. Pediatr.19 (4), 404–407 (2012). [DOI] [PubMed] [Google Scholar]
  • 64.Shakiba, T., Sadeghnia, A. & Karbasizade, V. Detection of Bla (CTX-M15) and Bla (OXA-48) genes in Gram-negative isolates from neonatal sepsis in central of Iran. Iran. J. Microbiol.11 (4), 280–287 (2019). [PMC free article] [PubMed] [Google Scholar]
  • 65.Soren, C., Jagtap, S., Malathi, V. & Aparnadevi, L. Stenotrophomonas maltophilia: a rare cause of early onset neonatal sepsis. Int. J. Contemp. Pediatr.5, 2006–2007 (2018). [Google Scholar]
  • 66.Behera, B. Stenotrophomonas maltophilia, an emerging pathogen in newborns: three case reports and a review of the literature. World J. Clin. Infect. Dis.11 (1), 11–18 (2021). [Google Scholar]
  • 67.Rajia, R., Massi, M. N., Ahmad, M., Arifuddin, S. & Miskad, U. A. Parity, exposure to cigarette smoke and the presence of bacteria Stenotrophomonas maltophilia are related to preterm labor incidence. Enfermería Clínica. 30, 524–527 (2020). [Google Scholar]
  • 68.Mutlu, M., Kader, Ş. & Aslan, Y. A dangerous causative microorganism of early onset neonatal sepsis: Stenotrophomonas maltophilia. Two case reports and a review of the literature. J. Matern Fetal Neonatal Med.35 (25), 6077–6079 (2022). [DOI] [PubMed] [Google Scholar]
  • 69.Jung, E. et al. Bacteria in the amniotic fluid without inflammation: early colonization vs. contamination. J. Perinat. Med.49 (9), 1103–1121 (2021). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 70.Lin, Y. et al. Metagenomic analysis identified Stenotrophomonas maltophilia pneumonia in an infant suffering from unexplained very severe pneumonia. Front. Pediatr.7, 380 (2019). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 71.Yashar, M. et al. Stenotrophomonas maltophilia outbreak originating from a Pull-out faucet in a pediatric intensive care unit in turkey: insights from clinical records and molecular typing. Am J. Infect. Control, 605–610 (2023). [DOI] [PubMed]
  • 72.Liu, B. & Tong, S. An investigation of Stenotrophomonas maltophilia-positive culture caused by fiberoptic bronchoscope contamination. BMC Infect. Dis.19 (1), 1072 (2019). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 73.Larsson, D. G. J. & Flach, C. F. Antibiotic resistance in the environment. Nat. Rev. Microbiol.20 (5), 257–269 (2022). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 74.Kraemer, S. A., Ramachandran, A. & Perron, G. G. Antibiotic pollution in the environment: from microbial ecology to public policy. Microorganisms7(6), 180, 10.3390/microorganisms7060180(2019). [DOI] [PMC free article] [PubMed]
  • 75.Singh, A. K., Kaur, R., Verma, S. & Singh, S. Antimicrobials and antibiotic resistance genes in water bodies: pollution, risk, and control. Frontiers Environ. Science 10, 1–13, (2022).
  • 76.Jans, C. et al. Consumer exposure to antimicrobial resistant Bacteria from food at Swiss retail level. Front. Microbiol.9, 362 (2018). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 77.Samad, M. A. et al. Microbial contamination and antibiotic resistance in marketed food in bangladesh: current situation and possible improvements. Antibiotics (Basel)12(3), 555, 10.3390/antibiotics12030555. (2023). [DOI] [PMC free article] [PubMed]
  • 78.Chaoui, L., Mhand, R., Mellouki, F. & Rhallabi, N. Contamination of the Surfaces of a Health Care Environment by Multidrug-Resistant (MDR) Bacteria. Int J Microbiol 2019:3236526. (2019). [DOI] [PMC free article] [PubMed]
  • 79.Odoyo, E. et al. Environmental contamination across multiple hospital departments with multidrug-resistant bacteria pose an elevated risk of healthcare-associated infections in Kenyan hospitals. Antimicrob. Resist. Infect. Control. 12 (1), 22 (2023). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 80.Cervia, J. S., Ortolano, G. A. & Canonica, F. P. Hospital tap water as a source of stenotrophomonas maltophilia infection. Clin. Infect. Dis.46 (9), 1485–1487 (2008). [DOI] [PubMed] [Google Scholar]
  • 81.Sukhum, K. V. et al. Antibiotic-resistant organisms Establish reservoirs in new hospital built environments and are related to patient blood infection isolates. Commun. Med. (Lond). 2, 62 (2022). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 82.Gideskog, M., Welander, J. & Melhus, A. Cluster of S. maltophilia among patients with respiratory tract infections at an intensive care unit. Infect. Prev. Pract.2 (4), 100097 (2020). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 83.Li, J. et al. The nature and epidemiology of oqxab, a multidrug efflux pump. Antimicrob. Resist. Infect. Control. 8, 44 (2019). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 84.Brooke, J. S. Advances in the microbiology of Stenotrophomonas maltophilia. Clin. Microbiol. Rev.34 (3), e0003019 (2021). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 85.Schildkraut, C. L., Marmur, J. & Doty, P. The formation of hybrid DNA molecules and their use in studies of DNA homologies. J. Mol. Biol.3, 595–617 (1961). [DOI] [PubMed] [Google Scholar]
  • 86.Okazaki, A. & Avison, M. B. Induction of L1 and L2 beta-lactamase production in Stenotrophomonas maltophilia is dependent on an AmpR-type regulator. Antimicrob. Agents Chemother.52 (4), 1525–1528 (2008). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 87.Rhoads, D. D. Stenotrophomonas maltophilia susceptibility testing challenges and strategies. J. Clin. Microbiol.59 (9), e0109421 (2021). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 88.Gupta, P., Sarkar, S., Das, B., Bhattacharjee, S. & Tribedi, P. Biofilm, pathogenesis and prevention–a journey to break the wall: a review. Arch. Microbiol.198 (1), 1–15 (2016). [DOI] [PubMed] [Google Scholar]
  • 89.Khatoon, Z., McTiernan, C. D., Suuronen, E. J., Mah, T. F. & Alarcon, E. I. Bacterial biofilm formation on implantable devices and approaches to its treatment and prevention. Heliyon4 (12), e01067 (2018). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 90.Pompilio, A. et al. Biofilm formation among Stenotrophomonas maltophilia isolates has clinical relevance: the ANSELM prospective multicenter study. Microorganisms9(1), 49, 10.3390/microorganisms9010049, (2020). [DOI] [PMC free article] [PubMed]
  • 91.Di Bonaventura, G., Spedicato, I., D’Antonio, D., Robuffo, I. & Piccolomini, R. Biofilm formation by Stenotrophomonas maltophilia: modulation by quinolones, trimethoprim-sulfamethoxazole, and Ceftazidime. Antimicrob. Agents Chemother.48 (1), 151–160 (2004). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 92.Zhuo, C., Zhao, Q. Y. & Xiao, S. N. The impact of spgm, rpff, RmlA gene distribution on biofilm formation in Stenotrophomonas maltophilia. PLoS One. 9 (10), e108409 (2014). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 93.Bostanghadiri, N. et al. Antibiotic resistance, biofilm formation, and biofilm-associated genes among Stenotrophomonas maltophilia clinical isolates. BMC Res. Notes. 14 (1), 151 (2021). [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The genome used in this study was available in the Genbank repository (SAMN34413089).

Articles from Scientific Reports are provided here courtesy of Nature Publishing Group

RESOURCES