Rapid and sensitive detection of Plesiomonas shigelloides by loop-mediated isothermal amplification of the hugA gene

Antimicrobial resistance in freshwater Plesiomonas shigelloides isolates: Implications for environmental pollution and risk assessment

Antibiotic resistance is known to impact treatment efficiency of Plesiomonas infections negatively with fatal outcomes. This study investigated antibiogram fingerprint of P. shigelloides (n = 182) isolated from three South Africa rivers using the disc diffusion technique. Environmental pollution and analogous health risk (given infections) that could associate with the freshwaters and empirical treatment of Plesiomonas were assessed using Antibiotic Resistance Index (ARI) and Multiple Antibiotic Resistance Indices (MARI), respectively. Thirteen EUCAST recommended (ERAs) and eleven non-recommended antibiotics (NAs) used as first line agents in the treatment of gastroenteritis and extraintestinal infections were tested. Resistance against ERAs decreased from cefoxitin (37.91%), cefuroxime (35.17%), cefepime (31.87%), ceftriaxone (29.67%), ciprofloxacin (18.13%), trimethoprim-sulfamethoxazole (10.44%), piperacillin/tazobactam (8.79%), ertapenem (4.95%), norfloxacin (4.40%), levofloxacin (2.75%), meropenem (1.10%) to imipenem (0.55%). The isolates had higher resistance (≥36.07%) against NAs but were susceptible to amikacin (67.58%), gentamycin (73.08%), and tetracycline (80.77%). MARI of the isolates were significantly different between ERAs and NAs (P-value < 0.05) and had an average of 0.17 ± 0.18 and 0.45 ± 0.13, respectively. About 33.87% and 95.63% of the isolates had MARI value from 0.23 to 0.62 and 0.27-0.82 to ERAs and NAs, respectively. Also, ERAs-based and NAs-based ARI across sampling units showed significantly different (P-value < 0.05) means of 0.18 ± 0.09 and 0.46 ± 0.05, respectively. MARI attributed low risk of empirical treatment to recommended antibiotics but higher risk to non-recommended antibiotics. Model estimated successful and unsuccessful empirical treatment of infections risks due to resistance in the isolates using recommended antibiotics as 65.93% and 34.07%, respectively; 1.65% and 98.35% in the case of non-recommended antibiotics, respectively. ARI based on recommended antibiotics identified potential environmental pollutions in a number of sites. Resistance in freshwater P. shigelloides especially against cephalosporin, quinolones and fluoroquinolones is distressing and might suggests high pollution of the freshwaters in the Eastern Cape Province.

Visual and rapid detection of Plesiomonas shigelloides using loop-mediated isothermal amplification method

Plesiomonas shigelloides is a common pathogen of aquatic animals and can pose a certain hazard to aquaculture. Here, we aimed to develop a loop-mediated isothermal amplification (LAMP) method for the visual detection of P. shigelloides to aid the diagnosis of infections caused by this pathogen in aquatic animals. We used LAMP to amplify P. shigelloides DNA and combined it with calcein or nucleic acid dipstick assay (NADA) to visualize the amplified products. The optimal LAMP amplification temperature was 64°C, and the reaction lasted for 50 min. The limit of detection of recombinant plasmids containing the target gene using the LAMP method was 2·0 × 10² copies per μl, which is ten times higher than that using conventional polymerase chain reaction (PCR). LAMP products could be visualized without agarose gel electrophoresis. We tested 85 fish specimens using the established LAMP method and conventional PCR. The detection rate was 42·4% using the LAMP method and 34·1% using conventional PCR. Based on our results, the LAMP method combined with calcein or NADA is a rapid, specific, sensitive and accurate method for visual detection of fish-derived P. shigelloides and can be used for the laboratory diagnosis of infections caused by it. SIGNIFICANCE AND IMPACT OF THE STUDY: The combination of loop-mediated isothermal amplification (LAMP) and calcein and nucleic acid dipstick assay (NADA) provided a rapid, specific and sensitive method for detecting Plesiomonas shigelloides, which is an important pathogen that causes diseases in aquatic animals worldwide. In the present study, the LAMP method showed a higher detection rate than conventional PCR for P. shigelloides using templates from 85 fish specimens. Thus, the LAMP method could be a reliable and convenient tool for diagnosing diseases in aquatic animals in the laboratory.

Rapid and Accurate Diagnosis of the Respiratory Disease Pertussis on a Point-of-Care Biochip

BACKGROUND

Pertussis is a highly contagious respiratory disease caused by the bacterium Bordetella pertussis (B. pertussis). The infection is difficult to diagnose especially in underserved or resource-limited areas. We developed a low-cost and instrument-free diagnostic method for rapid and accurate detection of B. pertussis on a point-of-care (POC) testing device.

METHODS

We developed a paper/polymer hybrid microfluidic biochip integrated with loop-mediated isothermal amplification (LAMP) method for the rapid and accurate detection of B. pertussis. This microfluidic approach was validated by testing 100 de-identified remnant clinical nasopharyngeal swabs and aspirates, which were confirmed to be either positive or negative for B. pertussis by a validated real-time PCR assay at the Children's Hospital Los Angeles.

FINDINGS

The instrument-free detection results could be successfully read by the naked eye within 45 min with a limit of detection (LOD) of 5 DNA copies per well. Our optimized bacterial lysis protocol allowed the direct testing of clinical samples without any complicated sample processing/preparation (i.e. DNA extraction) or the use of any equipment (e.g. centrifuges). The validation of the microfluidic approach was accomplished by testing 100 clinical samples. High sensitivity (100%) and specificity (96%) with respect to real-time PCR were achieved.

INTERPRETATION

This microfluidic biochip shows great potential for point-of-care disease diagnosis in various venues including schools and physician's offices, especially in low-resource settings in developing nations.

FUNDING

NIH/NIAID under award number R21AI107415, NIH RCMI Pilot Grant, the Philadelphia Foundation, the Medical Center of the Americas Foundation.

Complete Genome Sequence of Multidrug-Resistant Plesiomonas shigelloides Strain MS-17-188

Plesiomonas shigelloides is a Gram-negative bacterium isolated from diverse environments. Here, we describe the complete genome sequence of the multidrug-resistant P. shigelloides strain MS-17-188, isolated from a diseased catfish. Availability of this genome will be beneficial for characterizing the molecular mechanisms of antibiotic resistance in this strain.

Rapid and sensitive detection of Plesiomonas shigelloides by cross‑priming amplification of the hugA gene

Plesiomonas shigelloides (P. shigelloides) is implicated as an aetiological agent of human gastroenteritis in humans, for which reliable laboratory detection of P. shigelloides is clinically and epidemiologically desirable. A simple molecular method for rapid detection of P. shigelloides using cross-priming amplification (CPA) has been developed, with hugA as the target. The hugA gene is required for haem iron utilisation and is critical for the survival and growth of P. shigelloides. The assay output was visualised as a colour change with no need to open the reaction tubes, and no false-positive results were detected for the 33 non- P. shigelloides strains examined to assess assay specificity. The limit of detection was 200 fg P. shigelloides DNA per reaction and 3×10³ CFU per g in human stools, which was 100 and 10-fold more sensitive than polymerase chain reaction, respectively. The CPA method was used to detect the presence of P. shigelloides in stool specimens from 70 patients with diarrhoea and 30 environmental water samples, with no difference in accuracy between the CPA assay and the biological culture. The present study, therefore, suggests that the P. shigelloides hugA CPA assay may represent a valuable tool for rapid and sensitive detection of P. shigelloides in primary care facilities and clinical laboratories.

Plesiomonas shigelloides Revisited

After many years in the family Vibrionaceae, the genus Plesiomonas, represented by a single species, P. shigelloides, currently resides in the family Enterobacteriaceae, although its most appropriate phylogenetic position may yet to be determined. Common environmental reservoirs for plesiomonads include freshwater ecosystems and estuaries and inhabitants of these aquatic environs. Long suspected as being an etiologic agent of bacterial gastroenteritis, convincing evidence supporting this conclusion has accumulated over the past 2 decades in the form of a series of foodborne outbreaks solely or partially attributable to P. shigelloides. The prevalence of P. shigelloides enteritis varies considerably, with higher rates reported from Southeast Asia and Africa and lower numbers from North America and Europe. Reasons for these differences may include hygiene conditions, dietary habits, regional occupations, or other unknown factors. Other human illnesses caused by P. shigelloides include septicemia and central nervous system disease, eye infections, and a variety of miscellaneous ailments. For years, recognizable virulence factors potentially associated with P. shigelloides pathogenicity were lacking; however, several good candidates now have been reported, including a cytotoxic hemolysin, iron acquisition systems, and lipopolysaccharide. While P. shigelloides is easy to identify biochemically, it is often overlooked in stool samples due to its smaller colony size or relatively low prevalence in gastrointestinal samples. However, one FDA-approved PCR-based culture-independent diagnostic test system to detect multiple enteropathogens (FilmArray) includes P. shigelloides on its panel. Plesiomonads produce β-lactamases but are typically susceptible to many first-line antimicrobial agents, including quinolones and carbapenems.

Multiple Endonuclease Restriction Real-Time Loop-Mediated Isothermal Amplification: A Novel Analytically Rapid, Sensitive, Multiplex Loop-Mediated Isothermal Amplification Detection Technique

Loop-mediated isothermal amplification (LAMP) is restricted to detecting a single target, limiting the usefulness of this method. To achieve multiplex LAMP-based detection, we developed a novel approach we called the multiple endonuclease restriction real-time-LAMP assay. In this system, the LAMP forward or backward inner primers contain 5' end short sequences that are recognized by the restriction endonuclease Nb.BsrDI, and the new forward or backward inner primers were modified at the 5' end with a fluorophore and in the middle with a dark quencher. Nb.BsrDI digests the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which releases the quenching, resulting in a gain of signal. The assay permitted real-time detection of single or multiple target sequences in a single tube, and the positive results can be obtained in as short as 12 minutes. The novel methodology is highly efficient and specific, detecting down to 250 fg of DNA per reaction of Listeria DNA tested, and was successful in evaluating raw meat samples. The multiple endonuclease restriction real-time-LAMP technology, which is an extension of LAMP to accommodate robust, target-specific, and multiplex detection, provides a molecular diagnostic tool with less detection time and high sensitivity and specificity compared with those of LAMP and quantitative real-time PCR.

Development and Diagnostic Evaluation of Loop-Mediated Isothermal Amplification Using a New Gene Target for Rapid Detection of Helicobacter pylori

BACKGROUND

Helicobacter pylori cause chronic gastritis and subsequent diseases like gastric and duodenal ulcers and gastric adenocarcinoma. Current methods for detecting H. pylori have several disadvantages and it is of utmost importance to develop a simple, quick, accurate, and cost-effective diagnostic test.

OBJECTIVES

The aim of this study was to set up and evaluate a diagnostic value of loop- mediated isothermal amplification (LAMP) for detecting H. pylori.

PATIENTS AND METHODS

The analytical sensitivity values (limit of detection) of LAMP and polymerase chain reaction (PCR) were determined using serial dilutions of H. pylori DNA. Analytical specificity of the methods using new designed primers targeted ureC gene was also determined.

RESULTS

The detection limits of the LAMP and PCR assay were similar and were 10 fg of pure DNA of H. pylori, which is equal to 6 copy numbers of H. pylori genome. Analytical specificity of the tests was 100% because the tests were positive only with H. pylori DNA.

CONCLUSIONS

The analytical sensitivity of LAMP and PCR methods, using the designed primers, was 8 times more than any other reported methods. The designed methods are specific and sensitive for detection of H. pylori in different clinical and environmental samples.

Development and Evaluation of a Loop-Mediated Isothermal Amplification Method for Rapid Detection of Aspergillus fumigatus

Aspergillus fumigatusis a conditional pathogen and the major cause of life-threatening invasive aspergillosis (IA) in immunocompromised patients. The early and rapid detection ofA. fumigatusinfection is still a major challenge. In this study, the new member of the fungal annexin family, annexin C4, was chosen as the target to design a loop-mediated isothermal amplification (LAMP) assay for the rapid, specific, and sensitive detection ofA. fumigatus The evaluation of the specificity of the LAMP assay that was developed showed that no false-positive results were observed for the 22 non-A. fumigatusstrains, including 5 species of theAspergillusgenus. Its detection limit was approximately 10 copies per reaction in reference plasmids, with higher sensitivity than that of real-time quantitative PCR (qPCR) at 10(2)copies for the same target. Clinical samples from a total of 69 patients with probable IA (n =14) and possible IA (n= 55) were subjected to the LAMP assay, and positive results were found for the 14 patients with probable IA (100%) and 34 patients with possible IA (61.82%). When detection using the LAMP assay was compared with that using qPCR in the 69 clinical samples, the LAMP assay demonstrated a sensitivity of 89.19% and the concordance rate for the two methods was 72.46%. Accordingly, we report that a valuable LAMP assay for the rapid, specific, and simple detection ofA. fumigatusin clinical testing has been developed.

Rapid and sensitive detection of Listeria monocytogenes by cross-priming amplification of lmo0733 gene

Listeria monocytogenes is a food-borne pathogen that causes severe opportunistic infection in humans and animals. This study reports the development of single cross-priming amplification (S-CPA) and double CPA (D-CPA) assays targeting species-specific gene lmo0733 for identifying L. monocytogenes strains. The CPA assays were performed at a constant temperature 64 °C using seven specific primers and evaluated for specificity and sensitivity. The color change of positive amplification was directly observed by Loopamp^® Fluorescent Detection Reagent (FD), and the DNA products were visualized as a ladder-like banding pattern on 2.5% gel electrophoresis. Moreover, the positive reactions were also detected by real-time measurement of turbidity. 50 L. monocytogenes and 46 non-L. monocytogenes strains were used for the method verification, and the specificity was 100%. The limit of detection (LoD) of the S-CPA and D-CPA assays was 2.5 pg DNA per reaction and 10-fold more sensitive than PCR. A total of 60 pork samples were tested for L. monocytogenes using the S-CPA assay developed in the study, and the accuracy of the S-CPA and the culture-biotechnical method was 100% identical. The results suggested that the S-CPA assay was a rapid, sensitive, and valuable tool for detection of L. monocytogenes in food products.

Loop-mediated isothermal amplification for Rickettsia typhi (the causal agent of murine typhus): problems with diagnosis at the limit of detection

Murine typhus is a flea-borne disease of worldwide distribution caused by Rickettsia typhi. Although treatment with tetracycline antibiotics is effective, treatment is often misguided or delayed due to diagnostic difficulties. As the gold standard immunofluorescence assay is imperfect, we aimed to develop and evaluate a loop-mediated isothermal amplification (LAMP) assay. LAMP assays have the potential to fulfill the WHO ASSURED criteria (affordable, sensitive, specific, user friendly, robust and rapid, equipment free, deliverable to those who need them) for diagnostic methodologies, as they can detect pathogen-derived nucleic acid with low technical expenditure. The LAMP assay was developed using samples of bacterial isolates (n = 41), buffy coat specimens from R. typhi PCR-positive Lao patients (n = 42), and diverse negative controls (n = 47). The method was then evaluated prospectively using consecutive patients with suspected scrub typhus or murine typhus (n = 266). The limit of detection was ∼40 DNA copies/LAMP reaction, with an analytical sensitivity of <10 DNA copies/reaction based on isolate dilutions. Despite these low cutoffs, the clinical sensitivity was disappointing, with 48% (95% confidence interval [95% CI], 32.5 to 62.7%) (specificity, 100% [95% CI, 100 to 100%]) in the developmental phase and 33% (95% CI, 9.2 to 56.8%) (specificity, 98.5% [95% CI, 97.0% to 100%]) in the prospective study. This low diagnostic accuracy was attributed to low patient R. typhi bacterial loads (median, 210 DNA copies/ml blood; interquartile range, 130 to 500). PCR-positive but LAMP-negative samples demonstrated significantly lower bacterial loads than LAMP-positive samples. Our findings highlight the diagnostic challenges for diseases with low pathogen burdens and emphasize the need to integrate pathogen biology with improved template production for assay development strategies.

Comparison of conventional PCR, multiplex PCR, and loop-mediated isothermal amplification assays for rapid detection of Arcobacter species

This study aimed to develop a loop-mediated isothermal amplification (LAMP) method for the rapid detection of Arcobacter species. Specific primers targeting the 23S ribosomal RNA gene were used to detect Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii. The specificity of the LAMP primer set was assessed using DNA samples from a panel of Arcobacter and Campylobacter species, and the sensitivity was determined using serial dilutions of Arcobacter species cultures. LAMP showed a 10- to 1,000-fold-higher sensitivity than multiplex PCR, with a detection limit of 2 to 20 CFU per reaction in vitro. Whereas multiplex PCR showed cross-reactivity with Campylobacter species, the LAMP method developed in this study was more sensitive and reliable than conventional PCR or multiplex PCR for the detection of Arcobacter species.

Real-time fluorescence loop mediated isothermal amplification for the detection of Acinetobacter baumannii

BACKGROUND

Detection of Acinetobacter baumannii has been relying primarily on bacterial culture that often fails to return useful results in time. Although DNA-based assays are more sensitive than bacterial culture in detecting the pathogen, the molecular results are often inconsistent and challenged by doubts on false positives, such as those due to system- and environment-derived contaminations. In addition, these molecular tools require expensive laboratory instruments. Therefore, establishing molecular tools for field use require simpler molecular platforms. The loop-mediated isothermal amplification method is relatively simple and can be improved for better use in a routine clinical bacteriology laboratory. A simple and portable device capable of performing both the amplification and detection (by fluorescence) of LAMP in the same platform has been developed in recent years. This method is referred to as real-time loop-mediated isothermal amplification. In this study, we attempted to utilize this method for rapid detection of A. baumannii.

METHODOLOGY AND SIGNIFICANT FINDINGS

Species-specific primers were designed to test the utility of this method. Clinical samples of A. baumannii were used to determine the sensitivity and specificity of this system compared to bacterial culture and a polymerase chain reaction method. All positive samples isolated from sputum were confirmed to be the species of Acinetobacter by 16S rRNA gene sequencing. The RealAmp method was found to be simpler and allowed real-time detection of DNA amplification, and could distinguish A. baumannii from Acinetobacter calcoaceticus and Acinetobacter genomic species 3. DNA was extracted by simple boiling method. Compared to bacterial culture, the sensitivity and specificity of RealAmp in detecting A. baumannii was 98.9% and 75.0%, respectively.

CONCLUSION

The RealAmp assay only requires a single unit, and the assay positivity can be verified by visual inspection. Therefore, this assay has great potential of field use as a molecular tool for detection of A. baumannii.

Genome Sequence of Plesiomonas shigelloides Strain 302-73 (Serotype O1)

Plesiomonas shigelloides, the only species of the genus, is an emergent pathogenic bacterium associated with human diarrheal and extraintestinal disease. We present the whole-genome sequence analysis of the representative strain for the O1 serotype (strain 302-73), providing a tool for studying bacterial outbreaks, virulence factors, and accurate diagnostic methods.