Detection of major diarrheagenic bacterial pathogens by multiplex PCR panels

Investigation of antibacterial and anticancer activities of copper, aluminum and nickel doped zinc sulfide nanoparticles

First time compared the different metals doped ZnS nanoparticles for antibacterial and liver cancer cell line. In this study, copper, aluminum and nickel doped ZnS NPs were synthesized via co-precipitation method. The XRD analysis was confirmed the presence of cubic crystal structure and crystallite size decreased from 6 to 3 nm with doping elements. While as SEM micro-grains were revealed slightly irregular and agglomerated morphology with the presence of dopant elements. The presence of different dopant elements such as Cu, Al and Ni in ZnS NPs was identified via EDX analysis. The FTIR results demonstrate various vibrational stretching and bending modes attached to the surface of ZnS nanomaterials. After that the well diffusion method was used to conduct in-vitro bioassays for evaluation of antibacterial and anticancer activities against E.coli and B.cereus, as well as HepG2 liver cancer cell line. Our findings unveil exceptional results with maximum inhibition zone of approximately 9 to 23 mm observed against E.coli and 12 to 27 mm against B.cereus, respectively. In addition, the significant reduction in cell viability was achieved against the HepG2 liver cancer cell line. These favorable results highlight the potential of Ni doped ZnS NPs for various biomedical applications. In future, the doped ZnS nanomaterials will be suitable for hyperthermia therapy and wound healing process.

Clinical performance evaluation of TAQPATH Enteric Bacterial Select Panel for the detection of common enteric bacterial pathogens in comparison to routine stool culture and other qPCR-based diagnostic tests

IMPORTANCE

Enteric bacterial infections caused by Salmonella, Shigella, pathogenic Escherichia coli, and Campylobacter represent one of the most common causes of infectious enteritis worldwide. The timely and accurate diagnosis of pathogens causing gastroenteritis is crucial for patient care, public health, and disease surveillance. While stool culture has long been the standard and highly specific method for detecting enteric pathogens, it is labor-intensive and time-consuming with limited sensitivity. To improve patient outcomes, there is a need to implement new cost-effective approaches for the detection of bacterial enteric pathogens with higher sensitivity and faster time to result. This study shows that multiplex real-time polymerase chain reaction-based tests, such as the TAQPATH Enteric Bacterial Select Panel, are accurate and cost-effective diagnostic alternatives for the detection and differentiation of the most common enteric bacterial pathogens, offering quicker time to result and higher sensitivity compared to routine stool culture.

Nano-Biotechnology for Bacteria Identification and Potent Anti-bacterial Properties: A Review of Current State of the Art

Sepsis is a critical disease caused by the abrupt increase of bacteria in human blood, which subsequently causes a cytokine storm. Early identification of bacteria is critical to treating a patient with proper antibiotics to avoid sepsis. However, conventional culture-based identification takes a long time. Polymerase chain reaction (PCR) is not so successful because of the complexity and similarity in the genome sequence of some bacterial species, making it difficult to design primers and thus less suitable for rapid bacterial identification. To address these issues, several new technologies have been developed. Recent advances in nanotechnology have shown great potential for fast and accurate bacterial identification. The most promising strategy in nanotechnology involves the use of nanoparticles, which has led to the advancement of highly specific and sensitive biosensors capable of detecting and identifying bacteria even at low concentrations in very little time. The primary drawback of conventional antibiotics is the potential for antimicrobial resistance, which can lead to the development of superbacteria, making them difficult to treat. The incorporation of diverse nanomaterials and designs of nanomaterials has been utilized to kill bacteria efficiently. Nanomaterials with distinct physicochemical properties, such as optical and magnetic properties, including plasmonic and magnetic nanoparticles, have been extensively studied for their potential to efficiently kill bacteria. In this review, we are emphasizing the recent advances in nano-biotechnologies for bacterial identification and anti-bacterial properties. The basic principles of new technologies, as well as their future challenges, have been discussed.

PCR diagnostics are insufficient for the detection of Diarrhoeagenic Escherichia coli in Ibadan, Nigeria

Understanding the contribution of different diarrhoeagenic Escherichia coli pathotypes to disease burden is critical to mapping risk and informing vaccine development. Targeting select virulence genes by PCR is the diagnostic approach of choice in high-burden, least-resourced African settings. We compared the performance of a commonly-used multiplex protocol to whole genome sequencing (WGS). PCR was applied to 3,815 E. coli isolates from 120 children with diarrhoea and 357 healthy controls. Three or more isolates per specimen were also Illumina-sequenced. Following quality assurance, ARIBA and Virulencefinder database were used to identify virulence targets. Root cause analysis of deviant PCR results was performed by examining target sensitivity using BLAST, Sanger sequencing false-positive amplicons, and identifying lineages prone to false-positivity using in-silico multilocus sequence typing and a Single Nucleotide Polymorphism phylogeny constructed using IQTree. The sensitivity and positive predictive value of PCR compared to WGS ranged from 0-77.8% while specificity ranged from 74.5-94.7% for different pathotypes. WGS identified more enteroaggregative E. coli (EAEC), fewer enterotoxigenic E. coli (ETEC) and none of the Shiga toxin-producing E. coli detected by PCR, painting a considerably different epidemiological picture. Use of the CVD432 target resulted in EAEC under-detection, and enteropathogenic E. coli eae primers mismatched more recently described intimin alleles common in our setting. False positive ETEC were over-represented among West Africa-predominant ST8746 complex strains. PCR precision varies with pathogen genome so primers optimized for use in one part of the world may have noticeably lower sensitivity and specificity in settings where different pathogen lineages predominate.

Phylogenetic Groups, Pathotypes and Antimicrobial Resistance of Escherichia coli Isolated from Western Lowland Gorilla Faeces (Gorilla gorilla gorilla) of Moukalaba-Doudou National Park (MDNP)

(1) Background: Terrestrial mammals in protected areas have been identified as a potential source of antimicrobial-resistant bacteria. Studies on antimicrobial resistance in gorillas have already been conducted. Thus, this study aimed to describe the phylogroups, pathotypes and prevalence of antimicrobial resistance of Escherichia coli isolated from western lowland gorilla's faeces living in MDNP. (2) Materials and Methods: Ninety-six faecal samples were collected from western lowland gorillas (Gorilla gorilla gorilla) during daily monitoring in the MDNP. Sixty-four E. coli isolates were obtained and screened for phylogenetic and pathotype group genes by polymerase chain reaction (PCR) after DNA extraction. In addition, antimicrobial susceptibility was determined by the disk diffusion method on Mueller Hinton agar. (3) Results: Sixty-four (64%) isolates of E. coli were obtained from samples. A high level of resistance to the beta-lactam family, a moderate rate for fluoroquinolone and a low rate for aminoglycoside was obtained. All E. coli isolates were positive in phylogroup PCR with a predominance of A (69% ± 11.36%), followed by B2 (20% ± 19.89%) and B1 (10% ± 8.90%) and low prevalence for D (1% ± 3.04%). In addition, twenty E. coli isolates (31%) were positive for pathotype PCR, such as EPEC (85% ± 10.82%) and EPEC/EHEC (15% ± 5.18%) that were obtained in this study. The majority of these MDR E. coli (DECs) belonged to phylogenetic group A, followed by MDR E. coli (DECs) belonging to group B2. (4) Conclusion: This study is the first description of MDR E. coli (DECs) assigned to phylogroup A in western lowland gorillas from the MDNP in Gabon. Thus, wild gorillas in MDNP could be considered as asymptomatic carriers of potential pathogenic MDR E. coli (DECs) that may present a potential risk to human health.

A one-step multiplex PCR-based assay for simultaneous detection and classification of virulence factors to identify five diarrheagenic E. coli pathotypes

Human diarrhea-causing strains of Escherichia coli are referred to as diarrheagenic E. coli (DEC). DEC can be divided into five main categories based on distinct epidemiological and clinical features, specific virulence determinants, and association with certain serotypes. In the present study, a simple and rapid one-step single reaction multiplex PCR (mPCR) assay was developed for the simultaneous identification and differentiation of five currently established DEC pathotypes causing gastrointestinal diseases. The mPCR incorporated 10 primer pairs to amplify 10 virulence genes specific to the different pathotypes (i.e., stx1 and stx2 for EHEC, elt and sth for ETEC, eaeA and bfpA for EPEC, aggR and astA for EAEC, and ipaH and invE for EIEC) and to generate DNA fragments of sufficiently different sizes to be unequivocally resolved. All strains were detected at concentrations ranging from 10⁴ to 10⁷ CFU/mL. To demonstrate the utility of the mPCR assay, 236 clinically isolated strains of DEC from two hospitals were successfully categorized. One-step mPCR technique reduced the cost and effort involved in the identification of various virulence factors in DEC. Thus, we demonstrated that the newly developed mPCR assay has the potential to be introduced as a diagnostic tool that can be utilized for the detection of DEC as an additional check in clinical laboratories and for confirmation in health and environment institutes, health centers, and reference laboratories.

•

We developed a one-step single reaction mPCR to detect DEC strains.

•

10 prominently expressed genes characteristic to the five pathotypes were assayed.

•

All the strains were detected at concentrations ranging from 10⁴ to 10⁷ CFU/mL.

•

We show cost- and time-effective detection of DEC in clinical cultured samples.

High prevalence of small intestine bacteria overgrowth and asymptomatic carriage of enteric pathogens in stunted children in Antananarivo, Madagascar

Environmental Enteric Dysfunction (EED) refers to an incompletely defined syndrome of inflammation, reduced absorptive capacity, and reduced barrier function in the small intestine. It is widespread among children and adults in low- and middle-income countries and is also associated with poor sanitation and certain gut infections possibly resulting in an abnormal gut microbiota, small intestinal bacterial overgrowth (SIBO) and stunting.

We investigated bacterial pathogen exposure in stunted and non-stunted children in Antananarivo, Madagascar by collecting fecal samples from 464 children (96 severely stunted, 104 moderately stunted and 264 non-stunted) and the prevalence of SIBO in 109 duodenal aspirates from stunted children (61 from severely stunted and 48 from moderately stunted children). SIBO assessed by both aerobic and anaerobic plating techniques was very high: 85.3% when selecting a threshold of ≥10⁵ CFU/ml of bacteria in the upper intestinal aspirates. Moreover, 58.7% of the children showed more than 10⁶ bacteria/ml in these aspirates. The most prevalent cultivated genera recovered were Streptococcus, Neisseria, Staphylococcus, Rothia, Haemophilus, Pantoea and Branhamella. Feces screening by qPCR showed a high prevalence of bacterial enteropathogens, especially those categorized as being enteroinvasive or causing mucosal disruption, such as Shigella spp., enterotoxigenic Escherichia coli, enteropathogenic E. coli and enteroaggregative E. coli. These pathogens were detected at a similar rate in stunted children and controls, all showing no sign of severe diarrhea the day of inclusion but both living in a highly contaminated environment (slum-dwelling). Interestingly Shigella spp. was the most prevalent enteropathogen found in this study (83.3%) without overrepresentation in stunted children.

About 2 million children under the age of 5 suffer from stunted growth in Madagascar. Although deficient diet is the major cause of undernutrition, impaired absorption or assimilation caused by Environmental Enteric dysfunction (EED) has been proposed to play an important role in stunting. EED is widespread among children and adults in low- and middle-income countries (LMIC) and is also associated with undernutrition, poor sanitation, certain gut infections resulting in an abnormal gut microbiota and small intestinal bacterial overgrowth (SIBO) although the role of SIBO in EED remains unclear. The current study highlights the presence at high concentrations of bacterial taxa usually found in the oro-pharyngeal sphere in a high number of duodenal fluids of stunted children. This uncommon presence suggests a decompartmentalization of the gastrointestinal tract and a possible pro-inflammatory effect due to the ectopic presence of some of these bacteria in the duodenum.

The study also points to a high prevalence of enteropathogens (especially Shigella spp.) in the feces of both stunted and control children, hence preventing from proposing a direct association with stunting. This suggests that, beside combatting poverty and improving diet, environmental sanitation, quality of water sources, hygiene promotion and health education are key points to mitigate stunting and restore nutritional benefits.

Food-grade carrageenans and their implications in health and disease

Food additives, often used to guarantee the texture, shelf-life, taste, and appearance of processed foods, have gained widespread attention due to their increased link to the growing incidence of chronic diseases. As one of the most common additives, carrageenans have been used in human diets for hundreds of years. While classified as generally recognized as safe (GRAS) for human consumption, numerous studies since the 1980s have suggested that carrageenans, particularly those with random coil conformations, may have adverse effects on gastrointestinal health, including aggravating intestinal inflammation. While these studies have provided some evidence of adverse effects, the topic is still controversial. Some have suggested that the negative consequence of the consumption of carrageenans may be structure dependent. Furthermore, pre-existing conditions may predispose individuals to varied outcomes of carrageenan intake. In this review, structure-function relationships of various carrageenans in the context of food safety are discussed. We reviewed the molecular mechanisms by which carrageenans exert their biological effects. We summarized the findings associated with carrageenan intake in animal models and clinical trials. Moreover, we examined the interactions between carrageenans and the gut microbiome in the pathogenesis of gastrointestinal disorders. This review argues for personalized guidance on carrageenan intake based on individuals' health status. Future research efforts that aim to close the knowledge gap on the effect of low-dose and chronic carrageenan intake as well as interactions among food additives should be conducive to the improved safety profile of carrageenans in processed food products.

Efficacy of stool multiplex polymerase chain reaction assay in adult patients with acute infectious diarrhea

BACKGROUND

Recently, stool multiplex polymerase chain reaction (PCR) tests have been developed for identifying diarrhea-causing bacterial pathogens. Furthermore, fecal calprotectin is a well-known effective marker for intestinal mucosal inflammation.

AIM

To evaluate the efficacy of stool multiplex PCR and fecal calprotectin in acute infectious diarrhea.

METHODS

Overall, 400 patients with acute infectious diarrhea were enrolled from Kangdong Sacred Heart Hospital (January 2016 to December 2018). Multiplex PCR detected 7 enteropathogenic bacteria including Salmonella, Campylobacter, Shigella, Escherichia coli O157:H7, Aeromonas, Vibrio, and Clostridium difficile. We reviewed clinical and laboratory findings using stool multiplex PCR.

RESULTS

Stool multiplex PCR test detected considerably more bacterial pathogens than stool culture (49.2% vs 5.2%), with Campylobacter as the most common pathogen (54%). Patients with positive stool PCR showed elevated fecal calprotectin expression compared to patients with negative stool PCR (1124.5 ± 816.9 mg/kg vs 609 ± 713.2 mg/kg, P = 0.001). C-reactive protein (OR = 1.01, 95%CI: 1.001-1.027, P = 0.034) and sigmoidoscopy-detected colitis (OR = 4.76, 95%CI: 1.101-20.551, P = 0.037) were independent factors in stool PCR-based detection of bacterial pathogens. Sensitivity and specificity of calprotectin were evaluated to be 70.5% and 60.9%, respectively (adjusted cut-off value = 388 mg/kg).

CONCLUSION

Stool multiplex PCR test has increased sensitivity in detecting pathogens than conventional culture, and it is correlated with calprotectin expression. Stool multiplex PCR and calprotectin may be effective in predicting clinical severity of infectious diarrhea.

Etiologic features of diarrheagenic microbes in stool specimens from patients with acute diarrhea in Thailand

Many microbial species have been recognized as enteropathogens for humans. Here, we predicted the causative agents of acute diarrhea using data from multiplex quantitative PCR (qPCR) assays targeting 19 enteropathogens. For this, a case-control study was conducted at eight hospitals in Thailand. Stool samples and clinical data were collected from 370 hospitalized patients with acute diarrhea and 370 non-diarrheal controls. Multiple enteropathogens were detected in 75.7% and 13.0% of diarrheal stool samples using multiplex qPCR and bacterial culture methods, respectively. Asymptomatic carriers of enteropathogens were found among 87.8% and 45.7% of individuals by qPCR and culture methods, respectively. These results suggested the complexity of identifying causative agents of diarrhea. An analysis using the quantification cut-off values for clinical relevance drastically reduced pathogen-positive stool samples in control subjects from 87.8% to 0.5%, whereas 48.9% of the diarrheal stool samples were positive for any of the 11 pathogens. Among others, rotavirus, norovirus GII, Shigella/EIEC, and Campylobacter were strongly associated with acute diarrhea (P-value < 0.001). Characteristic clinical symptoms, epidemic periods, and age-related susceptibility to infection were observed for some enteropathogens. Investigations based on qPCR approaches covering a broad array of enteropathogens might thus improve our understanding of diarrheal disease etiology and epidemiological trends.

Diarrheagenic Escherichia coli Associated with Acute Gastroenteritis in Children from Soriano, Uruguay

INTRODUCTION

Acute diarrheal disease still deserves worldwide attention due to its high morbidity and mortality, especially in developing countries. While etiologic determination is not mandatory for management of all individual cases, it is needed for generating useful epidemiologic knowledge. Diarrheagenic Escherichia coli (DEC) are relevant enteropathogens, and their investigation requires specific procedures to which resources and training should be dedicated in reference laboratories.

METHODOLOGY

Following the hypothesis that enteric pathogens affecting children in towns located in the interior of Uruguay may be different from those found in Montevideo, we conducted a diagnostic survey on acute diarrheal disease in 83 children under 5 years of age from populations in the south of the country.

RESULTS

DEC pathotypes were the only bacterial pathogens found in diarrheal feces (20.48%), followed by rotavirus (14.45%) and enteric adenovirus (4.81%). Atypical EPEC (aEPEC) was the most frequent DEC pathotype identified, and unexpectedly, it was associated with bloody diarrheal cases. These patients were of concern and provided with early consultation, as were children who presented with vomiting, which occurred most frequently in rotavirus infections. aEPEC serotypes were diverse and different from those previously reported in Montevideo children within the same age group and different from serotypes identified in regional and international studies. Enteroinvasive (EIEC) O96 : H19, associated with large outbreaks in Europe, was also isolated from two patients. Antibiotic susceptibility of pathogenic bacteria identified in this study was higher than that observed in previous national studies, which had been mainly carried out in children from Montevideo.

CONCLUSION

The reduced number of detected species, the marked prevalence of aEPEC, the scarce resistance traits, and the diverse range of serotypes in the virulent DEC identified in this study confirm that differences exist between enteropathogens affecting children from interior towns of Uruguay and those circulating among children in Montevideo.

Molecular surveillance of canine distemper virus in diarrhoetic puppies in northeast China from May 2014 to April 2015

To trace the prevalence of canine distemper virus (CDV) in diarrhoetic dogs, a total of 201 stool samples were collected in the Heilongjiang province of northeastern China from May 2014 to April 2015. The 201 fecal samples were subjected to the detection of CDV by using RT-PCR targeting the partial N gene, phylogenetic analysis based on the complete H gene, and co-infection analysis. Results indicated that 24.88% (50/201) of the samples were positive for CDV. The fifty CDV samples exhibited an overall co-infection rate of 94% (47/50) with four enteric viruses (82%, 41/50) and five bacteria (72%, 36/50). The positivity rate of CDV exhibited differences among regions, seasons, ages and immunization status. Phylogenetic analysis of the complete H genes (n=6) revealed that the CDV strains identified in our study belonged to the Asia-1 group, and showed genetic diversities. These data provide evidence that there are a number of genetically diverse CDV Asia-1 strains circulating in diarrhoetic dogs in northeastern China; the CDV-affected animals exhibit the high co-infection with other enteric viruses and bacteria.

Sensitive detection of Escherichia coli O157:H7 based on cascade signal amplification in ELISA

In this study, cascade signal amplification in ELISA involving double-antibody sandwich ELISA and indirectly competitive ELISA was established to sensitively detect Escherichia coli O157:H7. In the double-antibody sandwich ELISA, a complex was formed comprising anti-E. coli O157:H7 polyclonal antibody, E. coli O157:H7, biotinylated anti-E. coli O157:H7 monoclonal antibody, streptavidin, and biotinylated β-lactamase. Penicillin solution was then added into the ELISA well and hydrolyzed by β-lactamase. Afterward, the penicillin solution was transferred to indirectly competitive ELISA. The concentration of penicillin can be sensitively detected in indirectly competitive ELISA. In the cascade signal amplification system, increasing the amount of added E. coli O157:H7 resulted in more β-lactamase and less penicillin. The detection sensitivity of E. coli O157:H7, which was 20cfu/mL with the cascade signal amplification in ELISA, was 1,000-fold higher than that of traditional ELISA. Furthermore, the novel method can be used to detect E. coli O157:H7 in milk (2cfu/g). Therefore, this new signaling strategy will facilitate analyses of highly sensitive foodborne pathogens.