The Rapid Identification of Anoplophora chinensis (Coleoptera: Cerambycidae) From Adult, Larval, and Frass Samples Using TaqMan Probe Assay

A molecular diagnostic method using TaqMan probe qPCR is presented for the identification of Anoplophora chinensis (Förster) (Coleoptera: Cerambycidae) from whole body insects (adults and larvae) and frass samples stored under different conditions. The results showed a perfect amplification of DNA from all samples; the repeatability and reproducibility of the protocol were very good, with standard deviations of inter-run and intra-run variability less than or equal to 0.5. The assay allowed to discern all A. chinensis samples from those of the other non-target wood-borer species, with 100% correspondence to the homologous sequences. No amplification or cross reactions were observed with A. glabripennis (Motschulsky) (Coleoptera: Cerambycidae), which is the most related species among those tested. The protocol was validated by an internal blind panel test which showed a good correspondence between the results obtained by different operators in the same lab. The analytical sensitivity for the lab frass with the Probe qPCR, namely the lowest amount of A. chinensis DNA that can be detected (LoD), was 0.64 pg/µl with a Cq of 34.87. The use of indirect evidence for the identification of a pest is an important feature of the method, which could be crucial to detect the presence of wood-boring insects. This diagnostic tool can help prevent the introduction of A. chinensis into new environments or delimit existing outbreak areas thanks to indirect frass diagnosis.

Development of Three Molecular Diagnostic Tools for the Identification of the False Codling Moth (Lepidoptera: Tortricidae)

Three molecular protocols using qPCR TaqMan probe, SYBR Green, and loop-mediated isothermal amplification (LAMP) methods were set up for the identification of larvae and adults of an African invasive moth, Thaumatotibia leucotreta (Meyrick, 1913) (Lepidoptera: Tortricidae). The DNA extracts from larval and adult samples of T. leucotreta were perfectly amplified with an average Ct value of 19.47 ± 2.63. All assays were demonstrated to be inclusive for T. leucotreta and exclusive for the nontarget species tested; the absence of false positives for nontarget species showed a 100% of diagnostic specificity and diagnostic sensitivity for all assays. With the SYBR Green protocol, the Cq values were only considered for values less than 22 (cutoff value) to prevent false-positive results caused by the late amplification of nonspecific amplicons. The limit of detection (LoD) for the qPCR probe protocol was equal to 0.02 pg/µl while a value equal to 0.128 pg/µl for the qPCR SYBR Green assay and LAMP method were established, respectively. The intrarun variabilities of reproducibility and repeatability in all the assays evaluated as CV%, ranged between 0.21 and 6.14, and between 0.33 and 9.52, respectively; the LAMP values were slightly higher than other assays, indicating a very low interrun variability. In order for an operator to choose the most desirable method, several parameters were considered and discussed. For future development of these assays, it is possible to hypothesize the setup of a diagnostic kit including all the three methods combined, to empower the test reliability and robustness.

Rapid Detection of Pityophthorus juglandis (Blackman) (Coleoptera, Curculionidae) with the Loop-Mediated Isothermal Amplification (LAMP) Method

The walnut twig beetle Pityophthorus juglandis is a phloem-boring bark beetle responsible, in association with the ascomycete Geosmithia morbida, for the Thousand Cankers Disease (TCD) of walnut trees. The recent finding of TCD in Europe prompted the development of effective diagnostic protocols for the early detection of members of this insect/fungus complex. Here we report the development of a highly efficient, low-cost, and rapid method for detecting the beetle, or even just its biological traces, from environmental samples: the loop-mediated isothermal amplification (LAMP) assay. The method, designed on the 28S ribosomal RNA gene, showed high specificity and sensitivity, with no cross reactivity to other bark beetles and wood-boring insects. The test was successful even with very small amounts of the target insect’s nucleic acid, with limit values of 0.64 pg/µL and 3.2 pg/µL for WTB adults and frass, respectively. A comparison of the method (both in real time and visual) with conventional PCR did not display significant differences in terms of LoD. This LAMP protocol will enable quick, low-cost, and early detection of P. juglandis in areas with new infestations and for phytosanitary inspections at vulnerable sites (e.g., seaports, airports, loading stations, storage facilities, and wood processing companies).

Rapid and Sensitive Detection of Tomato Brown Rugose Fruit Virus in Tomato and Pepper Seeds by Reverse Transcription Loop-Mediated Isothermal Amplification Assays (Real Time and Visual) and Comparison With RT-PCR End-Point and RT-qPCR Methods

Tomato brown rugose fruit virus (ToBRFV) represents an emerging viral threat to the productivity of tomato and pepper protected cultivation worldwide. This virus has got the status of quarantine organism in the European Union (EU) countries. In particular, tomato and pepper seeds will need to be free of ToBRFV before entering the EU and before coming on the market. Thus, lab tests are needed. Here, we develop and validate a one-step reverse transcription LAMP platform for the detection of ToBRFV in tomato and pepper leaves, by real-time assay [reverse transcription loop-mediated isothermal amplification (RT-LAMP)] and visual screening (visual RT-LAMP). Moreover, these methods can also be applied successfully for ToBRFV detection in tomato and pepper seeds. The diagnostic specificity and sensitivity of both RT-LAMP and visual RT-LAMP are both 100%, with a detection limit of nearly 2.25 fg/μl, showing the same sensitivity as RT-qPCR Sybr Green, but 100 times more sensitive than end-point RT-PCR diagnostic methods. In artificially contaminated seeds, the proposed LAMP assays detected ToBRFV in 100% of contaminated seed lots, for up to 0.025–0.033% contamination rates in tomato and pepper, respectively. Our results demonstrate that the proposed LAMP assays are simple, inexpensive, and sensitive enough for the detection of ToBRFV, especially in seed health testing. Hence, these methods have great potential application in the routine detection of ToBRFV, both in seeds and plants, reducing the risk of epidemics.

Development of a loop-mediated isothermal amplification (LAMP) assay for the identification of the invasive wood borer Aromia bungii (Coleoptera: Cerambycidae) from frass

The red-necked longhorn beetle Aromia bungii (Faldermann, 1835) (Coleoptera: Cerambycidae) is native to east Asia, where it is a major pest of cultivated and ornamental species of the genus Prunus. Morphological or molecular discrimination of adults or larval specimens is required to identify this invasive wood borer. However, recovering larval stages of the pest from trunks and branches causes extensive damage to plants and is timewasting. An alternative approach consists in applying non-invasive molecular diagnostic tools to biological traces (i.e., fecal pellets, frass). In this way, infestations in host plants can be detected without destructive methods. This paper presents a protocol based on both real-time and visual loop-mediated isothermal amplification (LAMP), using DNA of A. bungii extracted from fecal particles in larval frass. Laboratory validations demonstrated the robustness of the protocols adopted and their reliability was confirmed performing an inter-lab blind panel. The LAMP assay and the qPCR SYBR Green method using the F3/B3 LAMP external primers were equally sensitive, and both were more sensitive than the conventional PCR (sensitivity > 10³ to the same starting matrix). The visual LAMP protocol, due to the relatively easy performance of the method, could be a useful tool to apply in rapid monitoring of A. bungii and in the management of its outbreaks.

Molecular Identification of Anoplophora glabripennis (Coleoptera: Cerambycidae) From Frass by Loop-Mediated Isothermal Amplification

Anoplophora glabripennis (Motschulsky, 1853), native to eastern Asia, is a destructive woodborer of many ornamental species, leading to the decline and the death of the attacked trees. In outbreak areas as Europe or North America, this pest is usually identified using morphological or molecular analyses of adult or larval specimens. However, the procedures for collecting A. glabripennis specimens from infested plants are too expensive and time consuming for routine screening. A noninvasive diagnostic tool based on frass discrimination is therefore crucial for the rapid identification of A. glabripennis at different development stages in the host. This article describes a rapid diagnostic protocol based on loop-mediated isothermal amplification (LAMP). DNA extracted from A. glabripennis frass was amplified with both visual and real-time LAMP and compared with those of nontarget species. The results show that the method is reliable and accurate and therefore could be a promising diagnostic tool in phytosanitary surveys.

A duplex real-time PCR with probe for simultaneous detection of Geosmithia morbida and its vector Pityophthorus juglandis

The cultivation of walnuts (Juglans sp.) in Europe retains high economic, social, and environmental value. The recent reporting of the Thousand Cankers Disease (TCD) fungus, Geosmithia morbida, and of its vector, Pityophthorus juglandis, in walnut trees in Italy is alarming the whole of Europe. Although Italy is at present the only foothold of the disease outside North America, given the difficulties inherent in traditional identification of both members of this beetle/fungus complex, a rapid and effective protocol for the early detection and identification of TCD organisms is an absolute priority for Europe. Here we report the development of an effective and sensitive molecular tool based on simplex/duplex qPCR assays for the rapid, accurate and highly specific detection of both the bionectriaceous fungal pathogen and its bark-beetle vector. Our assay performed excellently, detecting minute amounts of target DNA without any non-specific amplification. Detection limits from various and heterogeneous matrices were lower than other reported assays. Our molecular protocol could assist in TCD organism interception at entry points, territory monitoring for the early identification and eradication of outbreaks, delineation of quarantine areas, and tracing back TCD entry and dispersal pathways.

Heat-and-moisture exchangers used with biweekly circuit tubing changes: effect on costs and pneumonia rates

In 1991, heat-and-moisture exchangers were introduced with biweekly ventilator circuit tubing changes, resulting in elimination of multiple pieces of respiratory equipment and reduced labor costs. The annual savings were $157,000, totalling $1.5 million since the onset of the program. There have been no increases in rates of ventilator-associated pneumonia.

A clinical decision process model for evaluating vancomycin use with modified HICPAC guidelines. Hospital Infection Control Practice Advisory Committee

OBJECTIVE

The objective of this study was to evaluate a clinical decision process model for the appropriateness of vancomycin use, using modified Hospital Infection Control Practice Advisory Committee (HICPAC) guidelines.

DESIGN

All nondialysis vancomycin use was reviewed using the retrospective chart review method. The HICPAC guidelines were modified to distinguish between documented and suspected infections and appropriateness of vancomycin use initially and after 3 days of therapy. Data were collected on both vancomycin-use orders and vancomycin-use days.

SETTING

446-bed health maintenance organization teaching hospital.

RESULTS

758 uses of vancomycin from 1993 through 1995 were evaluated using the modified HICPAC guidelines. Initial use was appropriate in 71% of the cases, with 26% used for documented infections and 74% for suspected infections. Of the 536 orders of initial appropriate use, 176 courses of treatment with vancomycin were discontinued appropriately within 3 days. Ongoing use evaluation after 3 days revealed appropriate use in 45%, inappropriate ongoing use in 25%, and empirical ongoing use in 30% of the cases. There were adequate clinical or laboratory data available in 70% of cases after 3 days to discontinue vancomycin or to reclassify from suspected to documented infections or indications. Vancomycin-use evaluation solely after 3 days would not have disclosed 537 initial inappropriate vancomycin-use days, which were 44% of the total inappropriate use days.

CONCLUSIONS

Comprehensive evaluation of vancomycin use with HICPAC guidelines should include a modification to encompass initial and 3-day reevaluation, because most initial use is for suspected, and not documented, infections. HICPAC guidelines do not address the issues of differentiating suspected from documented infection indications or ongoing empirical use. The clinical decision process model is a framework for documentation and data collection for use evaluation and addresses issues not covered in HICPAC vancomycin guidelines. This model could be used by other medical centers for evaluation of vancomycin or other antibiotics.

American Society of Anesthesiology scoring discrepancies affecting the National Nosocomial Infection Surveillance System: surgical-site-infection risk index rates

The American Society of Anesthesiology (ASA) scoring was performed for the National Nosocomial Infection Surveillance (NNIS) System surgical-site-infection (SSI) risk indexing in 250 prosthetic-joint surgeries. There were ASA scoring discrepancies in 59% of 116 ASA-3 surgeries and 2 out of 10 ASA-3 SSI. The original ASA scoring led to an uncorrected SSI rate of 5.8 per 100 surgeries in the NNIS risk group 0; with corrected ASA scores, the rate was 4.5 per 100 surgeries.

Association between severity of illness and mortality from nosocomial infection

BACKGROUND

For the years 1987 through 1992, a study was undertaken to analyze nosocomial infection mortality data and to stratify risk according to severity of underlying illness to compare with published data from the Centers for Disease Control and Prevention.

METHODS

Nosocomial infections that contributed to or caused death were identified. In addition, during 1990 through 1992, severity of illness was determined as the subjective estimate of the risk of death or lack of risk of death during the current hospital admission before the onset of the nosocomial infection. These groups were named +SIC and -SIC, respectively.

RESULTS

It was determined that the data from death certificates in cases of known nosocomial infection were not sufficient to determine whether nosocomial infection contributed to or caused death. There was a 24% increase in cases of nosocomial infection contributing to or causing death when a physician reviewed deaths in patients with nosocomial infections who did not have a diagnosis of nosocomial infection listed on the death certificate. The rates for nosocomial infections contributing to or causing death are as follows: nosocomial pneumonia, 20%; and bloodstream infections, 19%. In patients who died and had severity of illness determination, there was a statistically significant difference in the rates of nosocomial infections contributing to or causing death between -SIC and +SIC groups for both nosocomial pneumonia and bloodstream infections. The rates for bloodstream infections were as follows: -SIC, 5%; and +SIC, 21%. For nosocomial pneumonia, the rates were as follows: -SIC, 13%; and +SIC, 23%.

CONCLUSION

In published reports from the Centers for Disease Control and Prevention, a rate of 13% is given for nosocomial pneumonia and bloodstream infections contributing to or causing death; however, there is no stratification for severity of illness in these reports. The presence of life-threatening illness before the onset of nosocomial pneumonia or bloodstream infection accounts for most deaths among our patients. For valid comparisons, mortality outcome data for nosocomial infections should be stratified for risk according to severity of underlying illness.

An effective continuous quality improvement approach to the prevention of ventilator-associated pneumonia

In 1989, our medical center used continuous quality improvement concepts in the creation of a Nosocomial Pneumonia Prevention Team whose aim was to significantly reduce nosocomial ventilator-associated pneumonia. The team included representatives from nursing, respiratory therapy, pulmonary medicine, internal medicine, anesthesiology, education and training, and infection control. Because the majority of mechanically ventilated patients were located in the intensive care unit, this unit became the focus of the prevention efforts. Team meetings were held regularly, with all representatives brainstorming barriers, possible interventions, methods of outcome measurement, and frequency of evaluation. Policies and procedures were reviewed, surveillance was increased, handwashing practices were surveyed, periodic feedback to staff was begun, and an educational program was developed and presented. During 1990, we observed a 57% reduction in ventilator-associated pneumonia from the baseline years, 1987 and 1988. Statistical comparison of proportions by z test indicated a p value less than 0.05. Fifteen cases of nosocomial ventilator-associated pneumonia were prevented and a cost saving of $105,000 was realized. Performance of traditional surveillance for outliers, coupled with literature-based thresholds, can lead to tolerance of inordinately high endemic rates. Infection control programs can significantly reduce endemic rates of nosocomial ventilator-associated pneumonia through continuous quality improvement methods and multidisciplinary interventions, with standard infection control procedures used for improvement.

Severity of illness classification for infection control departments: a study in nosocomial pneumonia

BACKGROUND

A subjective severity of illness classification was evaluated in a study of nosocomial pneumonia. This is a 5-category system based on the determination of the control of underlying illness and the risk of death during current hospital admission.

METHODS

A case-control study was performed with 128 cases of nosocomial pneumonia and 252 control patients. An additional 60 case and 90 control patients were used to compare this classification with APACHE II scoring in intensive care unit patients.

RESULTS

In univariate analysis, the severity illness classification was significantly associated with nosocomial pneumonia risk (p < 0.01). APACHE II adequately predicted mortality rate but was not statistically significantly associated with nosocomial pneumonia risk among intensive care unit patients. In logistic regression analysis, the severity of illness classification, surgery, age, nasogastric tube placement, and histamine blockers each showed significant independent association with nosocomial pneumonia.

CONCLUSIONS

The role of the severity of illness classification for risk stratification in nosocomial pneumonia is valid. Its roles in the evaluation of surgical wound infection, nosocomial bacteremia, and quality of care remain to be determined in subsequent studies.

Treatment of coccidioidal meningitis with fluconazole

Fluconazole was administered at doses of 50-400 mg/d to 18 patients (15 men, three women) with coccidioidal meningitis. After a mean duration of treatment of 9.8 months, 10 (67%) of 15 assessable patients had responded, one (7%) of 15 had partially responded, and four (27%) of 15 had not responded to therapy. Five (63%) of eight assessable patients receiving fluconazole as sole therapy responded or partially responded. Two patients discontinued fluconazole after initially responding to therapy, and both experienced relapse. The toxicity of fluconazole remains minimal at doses to 400 mg/d. The penetration of fluconazole into cerebrospinal fluid is substantial at all doses studied. Thus fluconazole continues to show promise even as sole therapy against coccidioidal meningitis. Not all patients respond, however, and relapse may be a problem with the currently studied doses and durations of therapy.