Detection of bacterial and mycoplasma contamination in cell cultures by polymerase chain reaction

In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages

Although chromosomal instability (CIN) is a common phenomenon in cleavage-stage embryogenesis following in vitro fertilization (IVF)^1-3, its rate in naturally conceived human embryos is unknown. CIN leads to mosaic embryos that contain a combination of genetically normal and abnormal cells, and is significantly higher in in vitro-produced preimplantation embryos as compared to in vivo-conceived preimplantation embryos⁴. Even though embryos with CIN-derived complex aneuploidies may arrest between the cleavage and blastocyst stages of embryogenesis^5,6, a high number of embryos containing abnormal cells can pass this strong selection barrier^7,8. However, neither the prevalence nor extent of CIN during prenatal development and at birth, following IVF treatment, is well understood. Here we profiled the genomic landscape of fetal and placental tissues postpartum from both IVF and naturally conceived children, to investigate the prevalence and persistence of large genetic aberrations that probably arose from IVF-related CIN. We demonstrate that CIN is not preserved at later stages of prenatal development, and that de novo numerical aberrations or large structural DNA imbalances occur at similar rates in IVF and naturally conceived live-born neonates. Our findings affirm that human IVF treatment has no detrimental effect on the chromosomal constitution of fetal and placental lineages.

Sequence homologies between Mycoplasma and Chlamydia spp. lead to false-positive results in chlamydial cell cultures tested for mycoplasma contamination with a commercial PCR assay

Mycoplasma contamination is a frequent problem in chlamydial cell culture. After obtaining contradictory contamination results, we compared three commercial PCR kits for mycoplasma detection. One kit signaled contamination in mycoplasma-free Chlamydia pneumoniae cultures. Sequencing of cloned PCR products revealed primer homology with the chlamydial genome as the basis of this false-positive result.

Rapid and sensitive detection of Mollicutes in cell culture by polymerase chain reaction

Infections with Mollicutes species (such as Mycoplasma, Acholeplasma, and Ureaplasma) can induce a variety of problems in living organisms and laboratory cell cultures. Therefore, it is necessary to establish a routine diagnostic protocol for Mycoplasma infection in order to ensure reliable research results, as well as the safety of commercial biological products. For that purpose a novel PCR-based procedure using specific designed primers complementary to 16S rRNA genome region of mollicute species was evaluated. PCR was optimized and sensitivity and specificity was evaluated by defined cell count concentrations (2-31250 CFU/ml) of different strains of Mycoplasma, Acholeplasma and Ureaplasma. Amplicon (272 bp) was cloned by PCR-cloning and sequenced by dideoxy chain termination. PCR, was found to be able to detect 10 copies of mollicute target DNA. No cross-reactivity with genomic DNA of non-mollicute bacteria or human cell lines was observed. Forty seven human and animal cell lines were evaluated for mollicute contamination. Twenty five cell lines (53%) were correctly identified as contaminated by this molecular approach. The results of this study demonstrated that this PCR-based method is not only fast and reproducible, but also highly sensitive and specific for detecting contaminant mycoplasmas in cell cultures.

Natural killer cell IFN-gamma-activity is associated with Plasmodium falciparum infection during pregnancy

The ability of natural killer (NK) cells to produce gamma interferon (IFN-gamma) after ex vivo stimulation with crude schizont lysate of Plasmodium falciparum was studied in uninfected and P. falciparum-infected pregnant Gabonese women segregated according to the gravidity at the time of delivery. This activity was measured in purified NK cells as well as in whole blood from the periphery and cord. Crude schizont lysate-stimulated NK cells from primiparous women produced significantly more IFN-gamma than those from multiparous women (P<0.001). Women with malaria infection produced more IFN-gamma than negative women in peripheral blood (P<0.001) indicating that immunological determinants regulating the susceptibility to malaria in pregnant women are parasite-specific. These findings reveal that NK cells are major source of IFN-gamma when exposed to P. falciparum antigens in vitro in absence of any other co-stimulant.

Sustainable reduction of bioreactor contamination in an industrial fermentation pilot plant

Facility experience primarily in drug-oriented fermentation equipment (producing small molecules such as secondary metabolites, bioconversions, and enzymes) and, to a lesser extent, in biologics-oriented fermentation equipment (producing large molecules such as recombinant proteins and microbial vaccines) in an industrial fermentation pilot plant over the past 15 years is described. Potential approaches for equipment design and maintenance, operational procedures, validation/verification testing, medium selection, culture purity/sterility analysis, and contamination investigation are presented, and those approaches implemented are identified. Failure data collected for pilot plant operation for nearly 15 years are presented and best practices for documentation and tracking are outlined. This analysis does not exhaustively discuss available design, operational and procedural options; rather it selectively presents what has been determined to be beneficial in an industrial pilot plant setting. Literature references have been incorporated to provide background and context where appropriate.

Plasmodium falciparum: a major role for IgG3 in antibody-dependent monocyte-mediated cellular inhibition of parasite growth in vitro

In an attempt to identify parasite antigen-specific antibody isotype(s) mediating inhibition of growth in vitro, we tested unfractionated sera and their corresponding purified antibody isotype-containing fractions in in vitro assays with asexual-stage parasites of Plasmodium falciparum in the presence or absence of monocytes. Using affinity purification techniques we fractionated individual and pooled serum samples from semi-immune Gabonese adults, to obtain samples containing either IgG1, 2, 3, and 4, IgG1, 2, and 4, or IgG3 alone, and a non-IgG fraction. Antibodies were quantified spectrophotometrically and the presence of different isotypes in individual fractions was confirmed by protein gel electrophoresis. In the absence of monocytes, we observed inhibition of parasite growth with whole serum and varying levels of either growth enhancement or inhibition with purified Ig-containing fractions. When used in a standardized assay of antibody-dependent cellular inhibition (ADCI) with a monocyte:infected erythrocyte ratio of 1:1, seven of eight serum samples inhibited growth to a mean level of 42%, and the different Ig-containing fractions displayed varying mean levels of inhibition: IgG3, 44%; IgG1--4, 22%; IgG1, 2, and 4, 10%; and non-IgG, - 10%. The results suggest that, among the different isotypes present in the serum of semi-immune individuals, parasite antigen-specific IgG3 in particular may play an important role in controlling parasitemia via an ADCI mechanism involving monocyte- derived mediators.

Purification of Encephalitozoon cultures contaminated by mycoplasmas by murine intraperitoneal inoculation

Encephalitozoon species are strict intracellular microsporidia. Cocultures with eukaryotic cell lines can become accidently contaminated by mycoplasmas. We propose a decontamination protocol based on differential cell targeting after intraperitoneal inoculation in mice. Mycoplasma-free microsporidia were isolated from the brains and spleens of inoculated mice 24 h postinoculation by using the centrifugation shell vial system. Identification was confirmed by direct sequencing of PCR-amplified 16S rRNA.

The use of a 16s rDNA directed PCR for the detection of endodontopathogenic bacteria

The study evaluates a 16S rDNA directed polymerase chain reaction (PCR) to detect and differentiate bacteria in necrotic root canal samples. The examination focused on species that are fastidious concerning culture or are difficult to differentiate after culturing by biochemical methods. In the described PCR assay, a universal 16S rDNA directed forward primer in combination with a highly specific reversed one was used to amplify taxon specific gene fragments of 230 to 950 bp length. A similar PCR reaction using a universal 16S rDNA reversed primer was also established to demonstrate bacteria in root canal specimens in general. A first application of this method revealed the presence of Actinomycetales-species, Fusobacterium nucleatum, "Streptococcus milleri," and, presumably for the first time described in infected root canals, Bacteroides forsythus. The identity of amplificons was confirmed by generating sequence information and comparison to gene databanks.

Detection of the turkey pathogens Mycoplasma meleagridis and M. iowae by amplification of genes coding for rRNA

PCR-based diagnostic tests using oligonucleotides specific to 16S rRNA were designed for the specific detection of the turkey pathogens Mycoplasma meleagridis and M. iowae. This method of detection was shown to be rapid, species specific, and unaffected by strain variation or the presence of other organisms. Detection of M. meleagridis in clinical samples by PCR was achieved and later confirmed by culture and growth inhibition. Definitive identification by culture and growth inhibition required up to 3 weeks, whereas positive results from PCR testing were obtained within a day and negative samples were confirmed within 4 days.

Mycoplasma contamination of chlamydiae isolated from clinical specimens

Ten Chlamydia pneumoniae strains were screened for Mycoplasma contamination using two differently designed Mycoplasma-specific polymerase chain reactions (PCR). The primers of the Mycoplasma-specific PCR designed by Spaepen et al. (9) cross-reacted with all of the C. pneumoniae strains giving false-positive results. When the 10 strains of C. pneumoniae were tested for mycoplasmas with the PCR designed by Harasawa et al. (5), only 3 were positive. Mycoplasmas were cultured from these three C. pneumoniae strains confirming the latter PCR results. The PCR of Harasawa et al. (5) was highly specific for mycoplasmas and did not cross-react with C. pneumoniae. These findings suggest that chlamydiae should be periodically screened for Mycoplasma contamination. Careful attention to primer design is important if PCR is chosen as the screening method.

Rapid, sensitive PCR-based detection of mycoplasmas in simulated samples of animal sera

A fast and simple method to detect mycoplasmal contamination in simulated samples of animal sera by using a PCR was developed. The following five mycoplasma species that are major cell culture contaminants belonging to the class Mollicutes were investigated: Mycoplasma arginini, Acholeplasma laidlawii, Mycoplasma hyorhinis, Mycoplasma orale, and Mycoplasma fermentans. After a concentration step involving seeded sera, genus-specific primers were used to amplify a 717-bp DNA fragment within the 16S rRNA gene of mycoplasmas. In a second step, the universal PCR was followed by amplification of variable regions of the 16S rRNA gene by using species-specific primers, which allowed identification of contaminant mycoplasmas. With this method, 10 fg of purified DNA and 1 to 10 color-changing units of mycoplasmas could be detected. Since the sensitivity of the assay was increased 10-fold when the amplification products were hybridized with an internal mycoplasma-specific 32P-labelled oligonucleotide probe, a detection limit of 1 to 10 genome copies per PCR sample was obtained. This highly sensitive, specific, and simple assay may be a useful alternative to methods currently used to detect mycoplasmas in animal sera.

Detection of mycoplasma contaminations by the polymerase chain reaction

The polymerase chain reaction (PCR) has been used for the general detection of Mollicutes. 25 Mycoplasma and Acholeplasma species were detected including important contaminants of cell cultures such as M. orale, M. arginini, M. hyorhinis, M. fermentans, A. laidlawii and additional human and animal mycoplasmas. PCR reactions were performed using a set of nested primers defined from conserved regions of the 16S rRNA gene. The detection limit was determined to be 1 fg mycoplasma DNA, which is equivalent to 1-2 genome copies of the 16S rRNA coding region. The identity of the amplification products was confirmed by agarose gel electrophoresis and restriction enzyme analysis. DNA from closely and distantly related micro-organisms did not give rise to specific amplification products. The method presented here offers a much more sensitive, specific and rapid assay for the detection of mycoplasmas than the existing ones.

Phylogenetic analysis of Mycoplasma penetrans, isolated from HIV-infected patients

A novel mycoplasmal species designated as Mycoplasma penetrans has recently been isolated from patients infected with human immunodeficiency virus. The 16S rRNA gene from this mycoplasma was cloned and its nucleotide sequence determined. This sequence was aligned with previously published homologous sequences from several mycoplasmas and with related Gram-positive bacteria and a phylogenetic tree was constructed. The results indicate that M. penetrans belongs to the evolutionary group Pneumoniae.