Laboratory Contamination Research Articles

Paenibacillus sp. TAB_01, an isolate recovered from cotton tissue culture plates and a potential novel species within the genus Paenibacillus was sequenced using Oxford Nanopore technology. The genome was 7.46 Mb with a G + C content of 52.14%, comprising 7353 total genes, including 6553 coding DNA sequences (CDS) and 159 RNA sequences, including 109 tRNA genes, 46 rRNA genes, and two CRISPR regions. In addition, the genome contains 6553 protein sequences. The results of the digital DNA-DNA hybridization analysis showed that the genome of Paenibacillus sp. TAB_01 shared 22.2% similarity with its closest genomic neighbor, Paenibacillus rigui. OrthoANIu analysis using USEARCH revealed 78% similarity, while ANI analysis using BLAST indicated 76.8% similarity between the two genomes. The MLSA-based phylogenetic tree showed that Paenibacillus sp. TAB_01 clustered within the Paenibacillus genus but formed a separate lineage. Furthermore, Paenibacillus sp. TAB_01 exhibited strong plant growth-promoting potential by producing 112.4 µg/mL of ammonium, 65.6 µg/mL of soluble inorganic phosphate, and 19.5 ng/mL of indole-3-acetic acid (IAA). These metabolites were quantified using colorimetric assays with high linearity (R² > 0.95). Genomic and metabolic properties indicate that Paenibacillus sp. TAB_01 represents a potentially novel species within the genus Paenibacillus, clearly distinct from its closest relatives.

Here we report the whole-genome sequence of Arthrobacter koreensis strain RMB17, an actinobacterium isolated as a recurring laboratory contaminant during marine bacteria cultivation in high-salt medium. The 3.4 Mbp genome was sequenced in its entirety using Oxford Nanopore technology, revealing a GC content of 65.88% with 165× sequence coverage.

The laboratory contaminant strain Noodlococcus was named for its coccoid cells and unusual colony morphology, which resembled a pile of noodles. Along with laboratory characterisation and electron microscopy, we generated a complete Noodlococcus genome sequence using Illumina and Oxford Nanopore data. The genome consisted of a single, circular, 2,732,108 bp chromosome that shared 97.5% average nucleotide identity (ANI) with the Kocuria rhizophila type strain TA68. We identified genomic features involved in replication (oriC), carotenoid synthesis (crt) and genome defence (CRISPR-Cas) and discovered four novel mobile elements (ISKrh4-7). Despite its environmental ubiquity and relevance to food production, bioremediation and human medicine, there have been few genomic studies of the Kocuria genus. We conducted a comparative, phylogenetic and pangenomic examination of all 257 publicly available Kocuria genomes, with a particular focus on the 56 that were identified as K. rhizophila. We found that there are two phylogenetically distinct clades of K. rhizophila, with within-clade ANI values of 96.7–100.0% and between-clade values of 89.5–90.4%. The second clade, which we refer to as Kocuria pseudorhizophila, exhibited ANI values of <95% relative to TA68 and should constitute a separate species. Delineation of the two clades would be consistent with the rest of the genus, where all other species satisfy the 95% ANI threshold criteria. Differences in the K. rhizophila and K. pseudorhizophila pangenomes likely reflect phenotypic as well as evolutionary divergence. This distinction is relevant to clinical and industrial settings, as strains and genomes from both clades are currently used interchangeably, which may lead to reproducibility issues and phenotype–genotype discordance. Investigating an innocuous laboratory contaminant has therefore provided useful insights into the understudied species K. rhizophila, prompting an unexpected reassessment of its taxonomy.

Diatom testing for closed organs should be carefully performed and interpreted: the effect of post-mortem change and resuscitation.

Investigating the effect of microtube capping/decapping methods on Escherichia coli collection contamination: Introducing a novel automatic microtube capper/decapper.

ABSTRACTObjectivesThis in vitro experimental study aimed to evaluate the effects of laboratory contamination of implant abutment screws and connection surfaces on reverse torque values (RTVs), as an indicator of screw preload loss.Material and MethodsForty‐five Dentis One Q implants and 45 CCM UCLA abutments were randomly assigned into three groups (n = 15 per group). Group 1 (control) involved uncontaminated abutments and screws with no restorations. Group 2 (screw contamination) used new abutments attached with screws contaminated by laboratory materials (porcelain powder, metal debris, and polishing paste). Group 3 (connection contamination) included screw‐retained restorations fabricated under contaminated conditions and attached using new screws. All samples were subjected to standardized torque (250 N·cm), thermocycling (1500 cycles between 5°C and 55°C), and subsequent RTV measurement. One‐way ANOVA and Tukey's post hoc tests were used for statistical analysis (α = 0.05).ResultsMean RTVs (SD) were 218 (0.15) N·cm (control), 181 (0.14) N·cm (screw contamination), and 207 (0.11) N·cm (connection contamination). RTVs in the screw contamination group were significantly lower than both the control (p < 0.001) and connection contamination groups (p < 0.001). The difference between the control and connection contamination groups was not statistically significant (p = 0.08).ConclusionsLaboratory contamination of implant components can significantly reduce reverse torque values, particularly in cases of screw contamination, indicating an increased risk of screw loosening. Contamination control during prosthetic procedures is essential to maintaining implant stability.

ABSTRACTEnzymatic and microbial depolymerization of plastic is emerging as a promising method for recycling plastics. This paper looks into the effects of household and laboratory contamination on waste plastic and the implications these have on the enzymatic degradation of PET. Specifically, we find that exogenous protein, whether initially contaminating the surface of the plastic substrate or present in the enzymatic hydrolysis reaction buffer, can substantially inhibit the degradation of PET. The degree of inhibition varied based on the type of protein as well as the type of PET hydrolyzing enzyme used. Several wash solutions were applied after surface fouling and shown to improve degradation and in some cases, restoring levels to that of unfouled plastics. Collectively, these findings can enable a better understanding of factors that influence enzymatic depolymerization including industrial pre‐processing as well as have implications for in situ degradation.

BackgroundAcinetobacter baumannii (A. baumannii) is a significant pathogen associated with nosocomial infections, predominantly affecting immunocompromised patients, and is linked to high mortality rates. To control infection rates, there is an urgent need for a diagnostic method that is cost-effective, rapid, and user-friendly, meeting the current demand for timely diagnosis.MethodsWe have developed a one-tube detection method for UV light unlocking based on RPA-CRISPR/Cas12a technology. This method utilizes the photodegradable chemical group NPOM-dt to chemically modify the crRNA base, preventing it from complementary pairing with the base of the target molecule, thereby temporarily silencing the CRISPR system. After RPA preamplification, the caged modification group on the crRNA was removed with brief irradiation with ultraviolet light to restore the activity of the CRISPR/Cas12a. system.ResultsOur results demonstrated that the detection system achieved a limit of detection as low as 10 copies/μL for target fragments, with no cross-reactivity observed with genomic DNA from six clinically common pathogenic bacteria, showcasing excellent sensitivity and specificity. Additionally, clinical validation was performed using 38 sputum samples. The system successfully identified A. baumannii in sputum specimens, with results consistent with those obtained via conventional PCR.ConclusionWe have successfully developed a light-controlled one-tube RPA-CRISPR/Cas12a detection system. It simplifies the operation and at the same time greatly reduces the risk of laboratory contamination caused by repeated tube opening, providing a new idea for the development of point-of-care testing (POCT).

Nucleic acid amplification testing (NAT) is a highly sensitive and specific testing technology for bloodborne infectious diseases. Since 2010, blood collection and supply institutions in China have widely adopted NAT technology for blood screening, greatly enhancing blood safety. Basing it on comparison with established quality systems in serological testing processes, we aimed to establish and continuously improve a quality monitoring system that meets the requirements of NAT procedure. Statistical analysis was conducted using the daily performance data of the Grifols Procleix Panther nucleic acid testing system in the laboratory from 2021 to 2022, including test frequency reactive rate, invalid test rate, system failures frequency, and laboratory contamination monitoring indicators. In 2021 and 2022, the annual discriminated rate on NAT yield donation were 39.11% and 39.29%, respectively. The average annual invalid test rates for the 4 units of Grifols Panther systems were 1.80%, 1.47%, 1.60%, and 1.51%, resulting in an overall invalid test rate of 1.60% (7881/493, 137). A total of 377 invalid runs occurred, with the most frequent invalid test reasons being 64 instances of insufficient internal control detection (“low internal control”), 55 instances of issues with verifying the volume of target capture reagent + samples (“VVFS”), and 49 instances of the presence of clots detected during aspiration (“CLT”). The most significant contributor to invalid test counts was pipette malfunction (“PMFR”), which accounted for 2136 invalid tests. In the laboratory contamination monitoring, a total of 792 monitoring tests were conducted over a 2-year period, during which hepatitis B virus DNA was detected once in a specimen centrifuge cup. Establishing systematic quality monitoring indicators can effectively and promptly identify potential quality risk factors, thereby ensuring the quality of blood testing.

Endogenous viral elements (EVEs) serve as molecular fossils that record the ancient co-evolutionary arms race between viruses and their hosts. In this study, by analyzing 105 host crustacean genomes, we identified 252 infectious hypodermal and haematopoietic necrosis virus-derived EVEs (IHHNV-EVEs), which include 183 ancient and 6 recently inserted EVEs. These IHHNV-EVEs are widely distributed among Decapoda, Thoracica, and Isopoda, with some of them exhibiting a syntenic distribution relative toneighboringhost sequences, suggesting that the IHHNV or its ancestor are potential pathogens of these species with a long-time dynamic interaction during the evolutionary history. An expansion of IHHNV-EVEs was observed indecapodagenomes, reflecting a reinforced arm race betweendecapodaand IHHNV. Notably, we found that nearly all recent IHHNV-EVEs were laboratory contaminants, except for a single authentic integration in Penaeus monodon that persists intact across 16 samples from the 2 populations. These temporal dynamics-ancient genomic stabilization versus modern colonization activity-highlight that EVEs serve as dual archives: historical records of past conflicts and active participants in current evolutionary battles. Our findings redefine viral genomic colonization as a continuum, where ancient EVE fixation coexists with persistent integration processes, providing new insights into host-virus co-evolutionary trajectories.

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.

Stormwater runoff is a significant source of microplastics to surface water. This study addresses challenges in the sampling, treatment, and characterization of microplastics in existing stormwater control measures across various regions in the United States. Stormwater sediment samples were collected via traditional stormwater sampling approaches for particulate and inorganic contamination with portable automatic samplers, analyzed using visible and fluorescence microscopy with Nile red as a selective stain, and subsequently confirmed through Raman spectroscopy. The inclusion of laboratory and field blanks enabled the identification of contamination at key steps during sample handling. The results reveal that the filtration process is a significant source of laboratory contamination, while the sampling process itself could be a primary contributor to overall sample contamination. Additionally, it was found that using green fluorescence as the sole emission wavelength may underestimate MP quantities, as some particles emit fluorescence exclusively in the red spectrum. Raman analysis revealed interferences caused by pigments and additives in plastics, along with challenges evaluating particles in the low micron range (≤10 microns), which complicates a comprehensive analysis. The findings of this study emphasize the importance of implementing strong quality assurance and control measures when assessing the levels of microplastics in the environment, including sample collection, processing, and analysis.

ObjectivesCervical cancer is one of the most frequently diagnosed cancers and a leading cause of cancer-related deaths in women in low- and middle-income countries (LMICs), accounting for nearly 85% of the global cervical cancer burden. High-risk human papillomavirus (hrHPV) infection is the main cause of cervical cancer. Easy-to-use, rapid, scalable, high-throughput, and cost-effective HPV tests are urgently needed for low-resource settings. Atila Biosystems’ clinically validated ScreenFire HPV Risk Stratification (RS) assay identifies 13 hrHPV in 4 groups based on their oncogenic risk (i.e., HPV16, HPV18/45, HPV31/33/35/52/58, and HPV51/59/39/56/68). While the current standard format is subject to laboratory contamination Atila has developed an innovative, contamination-preventive Zebra BioDome format. Recently we published the analytical performance of ScreenFire RS Zebra BioDome on the BioRad CFX-96 real-time PCR instrument. This current study evaluated its analytical performance on three additional qPCR platforms: Atila Portable iAMP-PS96, Atila Powergene9600 Plus, and Thermo Fisher Quantstudio-7.MethodsWe tested 173 DNA samples from Nigerian women with cervical cancer. These samples were tested simultaneously using the ScreenFire HPV Zebra BioDome assay (M5FHPV-96) on four different real-time PCR machines (Atila portable iAMP-PS96, Atila Powergene9600 Plus, Thermo Fisher QuantStudio-7, and BioRad CFX-96). We used overall agreement rate and unweighted kappa values to compare different platforms.ResultsThe overall agreement for detection of hrHPV using Atila portable iAMP-PS96 was 96.5% with kappa value 0.95 (95% confidence interval: 0.91–0.99) compared to Thermo Fisher QuantStudio-7, and 97.1% with kappa value 0.96 (95% confidence interval: 0.92–0.99) compared to BioRad CFX-96. For genotype HPV16 and risk stratification (RS) genotype groups (HPV18/45, HPV31/33/35/52/58, and HPV51/59/39/56/68) agreement rates were all > 98.3%. For Atila Powergene9600 Plus the overall agreement was 98.8% with a kappa value of 0.98 (95% confidence interval: 0.96–1.0) compared to Thermo Fisher QuantStudio-7, and 96.5% with a kappa value of 0.96 (95% confidence interval: 0.94–0.99) compared to BioRad CFX-96. The agreements for the HPV16 and RS genotype groups (HPV18/45, HPV31/33/35/52/58, and HPV39/51/56/59/68) were at least 98.3%.ConclusionThe novel ScreenFire HPV Zebra BioDome format produced highly concordant hrHPV positivity and RS genotype results on all four qPCR platforms. The data suggests that this innovative technology has the potential to improve HPV testing uptake in low-resource settings without further investment in purchasing new equipment.

Marburg virus (MARV) is one of the deadliest human zoonotic pathogens, historically traced back to Uganda, in East African-cave-dwelling Egyptian fruit bats (Rousettus aegyptiacus), the probable cradle of MARV. Since its first identification in Germany and Serbia in 1967 due to laboratory contamination, MARV has caused 18 outbreaks in humans in Sub-Saharan Africa, with the latest in Tanzania in 2025 and 2023, Rwanda in 2024, and Equatorial Guinea in 2023. Efforts to control MARV through bat extermination in Sub-Saharan Africa have been ineffective, likely due to incomplete extermination and the recolonization of infected juvenile fruit bats. Over the past two decades, extensive molecular epidemiological research has generated over 70 complete MARV genomes, enabling detailed phylogenetic analysis, though bat-derived sequences are still rare. Phylogenetic analysis of Sub-Saharan African Marburgviruses from 1975 shows clustering with sequences from humans and bats, indicating that the virus reservoir species in these regions are not considerably distinct. This review aims to consolidate MARV comprehensive genomic data to provide a clearer picture of the current Marburg virus disease situation in Sub-Saharan Africa and, in turn, highlights the need for active genomic surveillance to identify hotspots and prevent future global outbreaks.

During isolation of endophytic fungi from medicinal plants, one isolate of Mucorales appeared as contaminant in culture plates. A few days later, another isolate of Mucorales was found as laboratory contaminant on PDA media. Both isolates were examined morphologically and analyzed phylogenetically using ITS and LSU rDNA. Based on phylogenetic analysis and phenotypic characteristics, both isolates were recognized as a single new species of Syncephalastrum and named as Syncephalastrum bagoolii sp. nov. The latter differs from other species in the genus by forming merosporangiophores variable in length, curved, septate, simple or monopodially or sympodially branched, as well as globose, sub-globose, ovoid, and rarely papillate vesicles. Merosporangia contain up to 4-9 merospores and the basal ones commonly show a denticle attached. In this work the taxonomy and phylogeny of the new species are discussed and a table with morphological characteristics of all Syncephalastrum species is provided.

Dental simulation head model laboratories are crucial for clinical simulation training for stomatological students, yet the maintenance of their dental unit waterlines (DUWLs) has been overlooked. This study investigated water contamination in DUWLs within these laboratories and proposed solutions. Water samples were collected from 12 dental chairs in three laboratories at three time points: the beginning, middle, and end of the semester. At the start of the semester, severe contamination was observed, with colony counts of 11,5861715 CFU/ml for high-speed handpieces and 5375874 CFU/ml for three ways syringes. As the semester progressed, colony counts gradually decreased but remained above clinical thresholds. Both 20 mg/L organochlorine disinfectant and 20 mg/L chlorine dioxide were effective in reducing bacterial contamination below standard ranges three days post-disinfection. Microbial diversity analysis revealed Proteobacteria and Bacteroidota as the dominant bacterial phyla, with Ascomycota as the dominant fungal phylum. Potentially pathogenic bacteria such as Pseudomonas, Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, Mycobacterium, Legionella, Paenibacillus, Streptomyces, Acinetobacter, and Prevotella, as well as fungi like Fusarium and Penicillium, were detected. Therefore, urgent attention is needed to address DUWL contamination in dental laboratories, and it is recommended to disinfect DUWLs using either 20 mg/L organochlorine disinfectant or 20 mg/L chlorine dioxide every three days.

In vitro fertilization (IVF) is one of the most used assisted reproductive technology (ART) techniques today. However, the success of IVF procedures heavily relies on maintaining a sterile environment in laboratories. This narrative review examines the effects of microbiological contamination in IVF laboratories, exploring its sources, impacts on IVF outcomes, and preventive measures. We conducted a complete literature search using databases such as PubMed and Google Scholar, focusing on studies published within the last fifteen years. Our findings highlight that microbiological contamination can significantly impair embryo quality, reduce implantation and pregnancy rates, and increase the risk of miscarriage and infection. The review also discusses current best practices for contamination prevention and identifies areas for future research. This work emphasizes the critical importance of stringent sterility protocols in IVF laboratories and calls for continued vigilance and innovation in maintaining optimal conditions for assisted reproduction.

The importance of Good Manufacturing Practices (GMP) in the pharmaceutical industry to ensure the quality and safety of drug products. GMP aims to ensure that all pharmaceutical preparations, including sterile drugs such as infusions and injections, meet strict quality standards. Sterility testing is an important aspect even though it has limitations, such as long incubation times and low probability of detecting contamination. Therefore, any sterility test results that do not meet the requirements must be further investigated to find the cause, either from laboratory errors or contamination in the production process. In addition, the implementation of technical and managerial aspects in accordance with GMP, such as temperature and humidity control, is very important to maintain product quality. This article also highlights the use of modern technologies, such as Service Oriented Architecture (SOA), to improve efficiency and transparency in the drug production process, so that it can meet all the provisions set.

BackgroundGenomic analysis has revealed extensive contamination among laboratory-maintained microbes including malaria parasites, Mycobacterium tuberculosis, and Salmonella spp. Here, we provide direct evidence for recent contamination of a laboratory schistosome parasite population, and we investigate its genomic consequences. The Brazilian Schistosoma mansoni population SmBRE has several distinctive phenotypes, showing poor infectivity, reduced sporocyst number, low levels of cercarial shedding and low virulence in the intermediate snail host, and low worm burden and low fecundity in the vertebrate rodent host. In 2021 we observed a rapid change in SmBRE parasite phenotypes, with a 10-fold increase in cercarial production and fourfold increase in worm burden.MethodsTo determine the underlying genomic cause of these changes, we sequenced pools of SmBRE adults collected during parasite maintenance between 2015 and 2023. We also sequenced another parasite population (SmLE) maintained alongside SmBRE without phenotypic changes.ResultsWhile SmLE allele frequencies remained stable over the 8-year period, we observed sudden changes in allele frequency across the genome in SmBRE between July 2021 and February 2023, consistent with expectations of laboratory contamination. (i) SmLE-specific alleles increased in the SmBRE population from 0 to 41–46% across the genome between September and October 2021, reflecting the timing and magnitude of the contamination event. (ii) After contamination, strong selection (s ≅0.23) drove the replacement of low-fitness SmBRE with high-fitness SmLE alleles. (iii) Allele frequency changed rapidly across the whole genome, except for a region on chromosome 4, where SmBRE alleles remained at high frequency.ConclusionsWe were able to detect contamination in this case because SmBRE shows distinctive phenotypes. However, this would likely have been missed with phenotypically similar parasites. These results provide a cautionary tale about the importance of tracking the identity of parasite populations, but also showcase a simple approach to monitor changes within populations using molecular profiling of pooled population samples to characterize single-nucleotide polymorphisms. We also show that genetic drift results in continuous change even in the absence of contamination, causing parasites maintained in different labs (or sampled from the same lab at different times) to diverge.Graphical

BackgroundEasy-to-use, rapid, scalable, high-throughput, and cost-effective HPV tests are urgently needed for low-resource settings. Atila Biosystems’ high-throughput, cost-effective, and clinically validated ScreenFire HPV Risk Stratification (RS) assay identifies 13 high risk HPV (hrHPV) in 4 groups based on their oncogenic risk (i.e., HPV16, HPV18/45, HPV31/33/35/52/58, and HPV51/59/39/56/68). The current standard format is subject to laboratory contamination, which is common for any molecular PCR test. To overcome this drawback, Atila has recently upgraded it into an innovative, contamination-free Zebra BioDome format. The contamination-free feature makes this novel assay format more suitable for large-scale community- and population-based cervical screening. This study evaluated the analytical performance of the Zebra BioDome format.MethodsWe conducted a study to test the analytical performance of Zebra Biodome format in comparison to the results of using the ScreenFire HPV RS assay standard format on Biorad CFX-96 real-time PCR instrument. We used overall agreement rate and unweighted kappa value to compare the performance.ResultsThe overall agreement for detection of hrHPV was 96.0% with unweighted kappa value 0.94 (95% confidence interval: 0.90–0.98). The agreement rates between hrHPV genotype 16 and risk stratification genotype group (HPV18/45, HPV31/33/35/52/58, and HPV51/59/39/56/68) were all > 97.5%.ConclusionThe innovative ScreenFire HPV RS assay Zebra BioDome format produced highly concordant results with the standard format. The shared features by the two assay formats, such as easy-to-use, high throughput, cost-appropriate, and no requirements for DNA extraction. The unique contamination-prevention feature along with no requirement of preparation of reagents make the Zebra BioDome format more suitable for large-scale HPV screening to reduce global cervical cancer burden.