Using Wastewater Surveillance to Monitor Gastrointestinal Pathogen Infections in the State of Oklahoma

During the COVID-19 pandemic, wastewater surveillance was widely used to monitor temporal and geographical infection trends. Using this as a foundation, a statewide program for routine wastewater monitoring of gastrointestinal pathogens was established in Oklahoma. The results from 18 months of surveillance showed that wastewater concentrations of Salmonella, Campylobacter, and norovirus exhibit similar seasonal patterns to those observed in reported human cases (F = 4-29, p < 0.05) and that wastewater can serve as an early warning tool for increases in cases, offering between one- and two-weeks lead time. Approximately one third of outbreak alerts in wastewater correlated in time with confirmed outbreaks of Salmonella or Campylobacter and our results further indicated that several outbreaks are likely to go undetected through the traditional surveillance approach currently in place. Better understanding of the true distribution and burden of gastrointestinal infections ultimately facilitates better disease prevention and control and reduces the overall socioeconomic and healthcare related impact of these pathogens. In this respect, wastewater represents a unique opportunity for monitoring infections in real-time, without the need for individual human testing. With increasing demands for sustainable and low-cost disease surveillance, the usefulness of wastewater as a long-term method for tracking infectious disease transmission is likely to become even more pronounced.

Association of human leukocyte antigen DQ-rs3920AG genotype with Helicobacter pylori recurrence in Kafrelsheikh, Egypt

AIMS

The aim was to evaluate the role of HLA-DP/DQ single-nucleotide polymorphisms (SNPs) in Helicobacter pylori infection in Kafrelsheikh governorate, Egypt.

METHODS AND RESULTS

The study enrolled 120 persons; 48 naïve H. pylori-infected patients, 42 relapsers and 30 H. pylori-free controls. Gastroscopy, H. pylori stool antigen, anti-CagA and anti-VacA antibodies were determined. Genotyping of HLA-DPA1rs3077 (A/G) SNP and HLA-DQ-rs3920(A/G) SNP was done using real-time PCR. The antibody profile against H. pylori showed that 85.7% of patients with recurrent infection have IgG against CagA (p = 0.001*). There was a significant association between the occurrence of H. pylori infection and both HLA-DPA1rs3077AA and HLA-DQ-rs3920AG genotypes. Concerning H. pylori relapse, the HLA-DQ-rs3920AG genotype was detected in 78.6% of patients with recurrent infection (p = 0.002*). Patients carrying this genotype tend to be relapsers 9.8 times more than patients carrying other genotypes.

CONCLUSIONS

HLA-DPA1rs3077AA and/or HLA-DQ-rs3920AG genotypes could be risk factors for the occurrence of H. pylori infection. HLA-DQ-rs3920AG genotype is markedly linked to recurrent H. pylori infection.

SIGNIFICANCE AND IMPACT OF THE STUDY

Host factors as HLA gene polymorphism could be a predisposing factor for susceptibility, recurrence or chronicity of H. pylori and should be studied in different ethnic groups.

Systematic Review on the Correlation of Quantitative PCR Cycle Threshold Values of Gastrointestinal Pathogens With Patient Clinical Presentation and Outcomes

Background: Quantitative (q) polymerase chain reaction (PCR) cycle threshold (Ct) values represent the number of amplification cycles required for a positive PCR result and are a proxy of pathogen quantity in the tested sample. The clinical utility of Ct values remains unclear for gastrointestinal infections. Objectives: This systematic review assesses the global medical literature for associations between Ct values of gastrointestinal pathogens and patient presentation and clinical outcomes. Data Sources: MEDLINE, EMBASE, Cochrane library databases: searched January 14-17, 2020. Study Eligibility Criteria: Studies reporting on the presence or absence of an association between Ct values and clinical outcomes in adult and pediatric populations were included. Animal studies, reviews, meta-analyses, and non-English language studies were excluded. Participants: Humans infected with gastrointestinal pathogens, detected with qPCR. Interventions: Diagnostics assessing Ct values. Extracted data were reported narratively. Results: Thirty-three eligible studies were identified; the most commonly studied pathogens were Clostridioides difficile (n = 15), norovirus (n = 10), and rotavirus (n = 9). Statistically significant associations between low C. difficile Ct values and increased symptom severity or poor outcome were reported in 4/8 (50%) studies, and increased risk of death in 1/2 (50%) studies; no significant associations were found between Ct value and duration of symptoms or length of hospital stay. Among studies of norovirus, 5/7 (71%), mainly genogroup II, reported symptomatic cases with significantly lower median Ct values than controls. Significantly lower rotavirus Ct values were also observed in symptomatic cases vs. controls in 3/7 (43%) studies, and associated with more severe symptoms in 2/2 studies. Contradictory associations were identified for non-C. difficile bacterial and parasitic pathogens. Conclusions: In conclusion, some studies reported clinically useful associations between Ct values and patient or healthcare outcomes; additional, well-designed, large-scale trials are warranted based on these findings. Systematic Review Registration: [PROSPERO], identifier [CRD42020167239].

Comparison of two commercial and one in-house real-time PCR assays for the diagnosis of bacterial gastroenteritis

Introduction

The aim of the study was a comparative evaluation of in-house real-time PCR and commercial real-time PCR (Fast Track Diagnostics (FTD), ampliCube/Mikrogen) targeting enteropathogenic bacteria from stool in preparation of Regulation (EU) 2017/746 on in vitro diagnostic medical devices.

Methods

Both 241 stool samples from patients and 100 samples from German laboratory control schemes (“Ringversuche”) were used to comparatively assess in-house real-time PCR, the FTD bacterial gastroenteritis kit, and the ampliCube gastrointestinal bacterial panels 1&2 either with the in-house PCRs as gold standard and as a test comparison without gold standard applying latent class analysis. Sensitivity, specificity, intra- and inter-assay variation and Cohen’s kappa were assessed.

Results

In comparison with the gold standard, sensitivity was 75–100% for strongly positive samples, 20–100% for weakly positive samples, and specificity ranged from 96 to 100%. Latent class analysis suggested that sensitivity ranges from 81.2 to 100% and specificity from 58.5 to 100%. Cohen’s kappa varied between moderate and nearly perfect agreement, intra- and inter-assay variation was 1–3 to 1–4 Ct values.

Conclusion

Acceptable agreement and performance characteristics suggested replaceability of the in-house PCR assays by the commercial approaches.

Performance of a new molecular assay for the detection of gastrointestinal pathogens

Introduction

Conventional diagnostic laboratory algorithms for determining the cause of infectious gastroenteritis include culture, biochemical identification and immunoassays. In addition, multiplex PCR-based testing has advanced into the gastroenterology diagnostic arena in recent years.

Aim

The purpose of this study was to evaluate the performance of a new molecular test (Diagnostics Solutions Laboratory GI-MAP) for the detection of bacterial and parasitic pathogens in stool samples spiked with known organisms.

Methodology

Faeces from a healthy human subject were pooled into a standard matrix and screened for the absence of bacteria, parasites and Helicobacter pylori antigen. Once confirmed negative single faecal aliquots from the matrix were spiked with solely one pathogen-type from a panel of 14 bacterial pathogens or one of 2 parasitic pathogens at a density of 5×10⁶ organisms ml⁻¹. Sixteen spiked samples in appropriate transport media were sent to two testing labs, specifically a reference site using the PCR-based BioFire FilmArray Gastrointestinal Panel, and a second lab using the GI-MAP assay. Seven negative control samples comprised solely of stool matrix were also submitted.

Results

Significant variability was found when the GI-MAP assay was used to test normal stool matrix with and without known bacteria and parasites at densities well within the expected limits of detection. The GI-MAP assay displayed a sensitivity of 80 % and a specificity of only 26 % due to many false positive results. This assay also reported quantitative numbers for pathogens. The BioFire FilmArray Gastrointestinal Panel achieved a sensitivity and specificity of 100 %.

Conclusion

The highly variable results for the GI-MAP assay were unexpected due to the precise pre-spike analysis and the overall maturation of nucleic acid amplification methods within the industry. Problematic to this assay is the poor level of specificity displayed by this assay reporting the presence of several pathogens, which could cause clinicians to treat with antibacterial and/or antiparasitic agents in the absence of any true pathogens.

Selective Killing of Shiga Toxin-Producing Escherichia coli with Antibody-Conjugated Chitosan Nanoparticles in the Gastrointestinal Tract

Shiga toxin-producing Escherichia coli (STEC) are critical foodborne pathogens, which cause serious human health issues, including hemolytic uremic syndrome. Illnesses caused by STEC lack effective treatments that target the elimination of these bacteria from the gastrointestinal tract without causing an adverse effect. Reducing this pathogen from a reservoir of STEC is an effective strategy, but the challenges remain due to the lack of efficient, selective antimicrobial agents. We developed specific antibody-conjugated chitosan nanoparticles (CNs) to selectively target and treat STEC in the gastrointestinal tract. Given the great broad-spectrum antimicrobial activity of CN, we conjugated antibodies to CN. Antibodies were raised and purified from egg yolks after immunization of hens with seven different O-side-chain antigens isolated from STEC (O26, O45, O103, O111, O121, O145, and O157). We prepared CN-immunoglobulin Y (IgY) conjugates by forming amide bonds at different ratios of CN:IgY (10:1, 10:2, and 10:4). The CN-IgY conjugated at a 10:2 ratio demonstrated significantly enhanced antimicrobial activity against E. coli O157:H7. Conjugates of CN and anti-STEC IgY antibodies killed corresponding STEC serotypes specifically and selectively, while showing no significant impact on nontargeted bacteria, including Salmonella enterica and Lactobacillus plantarum. The enhanced antimicrobial activity of CN-IgY against STEC was also confirmed in synthetic intestinal fluid, as well as an in vivo animal model of Caenorhabditis elegans. These results suggest that the CN-IgY conjugates have strong and specific antimicrobial activity and that they are also great candidates to eliminate pathogens selectively in the gastrointestinal tract without inhibiting beneficial bacteria.

Prospective Investigation of an Automated PCR/Nucleic Acid Microarray-Based Platform for Enteric Pathogen Testing

BACKGROUND

The Verigene Enteric Pathogens Test (Luminex Corporation) is a polymerase chain reaction (PCR)/nucleic acid microarray-based assay targeting 8 bacterial and viral pathogens that cause diarrhea.

OBJECTIVE

To compare traditional enteric culture methods with stool testing by Verigene EP (PCR/microarray).

METHODS

Tests were performed using PCR/microarray between February and August 2016. All specimens also underwent culture for Salmonella and Shigella; specimens that tested positive for bacterial pathogen(s) had confirmatory cultures.

RESULTS

Valid results were obtained for 99.3% of the 3795 stool specimens. Among these, 497 (13.2%) specimens tested positive for at least 1 pathogen by PCR/microarray; 45.5% of these tested positive for 1 or more bacterial pathogens. Agreement between positive bacterial PCR/microarray results and culture-based testing was 85.3%. Compared with cultures, PCR/microarray demonstrated 95.2% and 87.5% sensitivity and 99.8% and 99.8% specificity for Salmonella and Shigella, respectively.

CONCLUSIONS

The Verigene EP generated evaluable results for most stool specimens tested and demonstrated good agreement with bacterial cultures.

Characterization of Bacteria in Nigerian Yogurt as Promising Alternative to Antibiotics in Gastrointestinal Infections

Gastrointestinal infections are endemic in Nigeria and several factors contribute to their continual survival, including bacterial resistance to commonly used antibiotics. Nigerian yogurts do not include probiotics, and limited information is available about the antimicrobial properties of the fermenters in the yogurt against gastrointestinal pathogens. Therefore, the antimicrobial potentials of bacteria in Nigeria-produced yogurts against intestinal pathogens were investigated in this study. Viable counts of lactic acid bacteria (LAB) in 15 brands of yogurt were enumerated and the bacteria identified by partial sequencing of 16S rRNA gene. Susceptibility of the gastrointestinal pathogens (Salmonella, Shigella and E. coli ) to antibiotics by disc diffusion method, to viable LAB by the agar overlay method, and to the cell-free culture supernatant (CFCS) of the LAB were investigated. Co-culture analysis of LAB and pathogens were also done. Viable counts of 1.5 × 10¹¹ cfu/ml were observed in some yogurt samples. Two genera were identified: Lactobacillus (70.7%) and Acetobacter (29.3%). The Lactobacillus species reduced multidrug-resistant gastrointestinal pathogens by 4 to 5 log while the zones of inhibition ranged between 11 and 23. The Lactobacillus and Acetobacter strains examined displayed good activities against the multidrug-resistant tested pathogens. This is the first report of antimicrobial activities of acetic acid bacteria isolated from yogurt in Nigeria.

Enterovirus detection in patients with acute gastroenteritis in Switzerland

Acute gastroenteritis (GE) has a major impact on morbidity and mortality worldwide, yet comprehensive data regarding infectious agents including enteroviruses are scarce. We hypothesized that enteroviruses constitute a significant cause of acute GE. We analyzed 677 stool samples from 504 patients, which had been submitted for suspected infectious GE. 0.2 mL of stool suspension was extracted using the Abbott m2000_sp robot and analysed by multiplex nucleic acid testing (NAT) using the Luminex xTAG gastrointestinal pathogen panel (GPP) as well as by specific NATs detecting enteroviruses and polioviruses. Median age of the patients was 6.6 years (IQR 1.1-50.6; pediatric <18 years). 292 of 677 (43%) samples were positive for at least one pathogen. Enterovirus was detected in 5.3% (36/677) as sole pathogen (67%), and more frequently in children (P = 0.0054). Only rotavirus (18.6%) and norovirus (12.1%) were more frequent. Clostridium difficile and Campylobacter jejuni were detected in 5.5% and 2.2% of stools, respectively. Adenovirus, E. coli O157, Salmonella, Shiga toxin-producing E. coli (STEC), Shigella, Giardia lamblia, Cryptosporidium, and Entamoeba histolytica were rare (<1% of samples). Vibrio cholerae, Yersinia enterocolitica, enterotoxigenic E. coli (ETEC) and poliovirus were not detected. Thus, non-polio enteroviruses are the third most frequent pathogen in acute GE suggesting that enteroviruses may play an important role in GE even in developed, industrial health care settings.

Galleria mellonella as an in vivo model for assessing the protective activity of probiotics against gastrointestinal bacterial pathogens

The antagonistic activity against gastrointestinal bacterial pathogens is an important property of probiotic bacteria and a desirable feature for pre-selection of novel strains with probiotic potential. Pre-screening of candidate probiotics for antibacterial activity should be based on in vitro and in vivo tests. This study investigated whether the protective activity of probiotic bacteria against gastrointestinal bacterial pathogens can be evaluated using Galleria mellonella larvae as an in vivo model. Larvae were pre-inoculated with either of two widely used probiotic bacteria, Lactobacillus rhamnosus GG or Clostridium butyricum Miyairi 588, and then challenged with Salmonella enterica Typhimurium, enteropathogenic Escherichia coli or Listeria monocytogenes. Survival rates increased in the probiotic pretreated larvae compared with control larvae inoculated with pathogens only. The hemocyte density increased as well in the probiotic pretreated larvae, indicating that both probiotics induce an immune response in the larvae. The antibacterial activity of probiotics against the pathogens was also assayed by an in vitro agar spot test: results were partially consistent with those obtained by the G. mellonella protection assay. The results obtained, as a whole, suggest that G. mellonella larvae are a potentially useful in vivo model that can complement in vitro assays for pre-screening of candidate probiotics.

Epidemiology of Campylobacter jejuni infections in Sweden, November 2011-October 2012: is the severity of infection associated with C. jejuni sequence type?

BACKGROUND

Campylobacter jejuni is among the most frequent causes of bacterial gastroenteritis in Europe. Over 8,000 C. jejuni multilocus sequence typing sequence types (STs) have been described; ST-21 and ST-45 have been identified as the most frequent types in all human studies so far. In contrast to other STs, ST-22 has been associated with the Guillain-Barré syndrome and ST-677 was recently linked to severe systemic infections in Finland. We investigated risk factors associated with hospitalisation in individuals with C. jejuni infections acquired in Sweden.

METHODS

A total of 1,075 individuals with domestically acquired C. jejuni infection diagnosed between November 2011 and October 2012 in Sweden were included in this retrospective cohort study. Typing data for the isolates as well as clinical data including hospitalisation dates and diagnosis codes for individuals with C. jejuni infection were obtained. Factors associated with hospitalisation and length of hospitalisation were investigated by multivariable analysis.

RESULTS

A total of 289 individuals were hospitalised due to C. jejuni infection (26.8%); those with co-morbidities were over 14 times more likely to become hospitalised than those without (odds ratio [OR]: 14.39, 95% confidence interval [CI]: 6.84-30.26). Those with underlying co-morbidities were also hospitalised longer than those without (4.22 days vs. 2.86 days), although this was not statistically significant. C. jejuni ST-257 (OR: 2.38; CI: 1.08-5.23), but not ST-22 or ST-677, was significantly associated with hospitalisation.

CONCLUSION

ST-677 was not associated with increased hospitalisation or a longer hospital stay in our study whilst ST-257 was. However, individuals with C. jejuni infections were generally more frequently hospitalised than previously demonstrated; this requires further consideration including possible targeted interventions.

The abundant free-living amoeba, Acanthamoeba polyphaga, increases the survival of Campylobacter jejuni in milk and orange juice

BACKGROUND

Campylobacter jejuni is a common cause of human bacterial diarrhea in most parts of the world. Most C. jejuni infections are acquired from contaminated poultry, milk, and water. Due to health care costs and human suffering, it is important to identify all possible sources of infection. Unpasteurized milk has been associated with several outbreaks of C. jejuni infection. Campylobacter has been identified on fresh fruit, and other gastrointestinal pathogens such as Salmonella, E. coli O157:H7 and Cryptosporidium have been involved in fruit juice outbreaks. C. jejuni is sensitive to the acidic environment of fruit juice, but co-cultures with the amoeba, Acanthamoeba polyphaga, have previously been shown to protect C. jejuni at low pH.

METHODS

To study the influence of A. polyphaga on the survival of C. jejuni in milk and juice, the bacteria were incubated in the two products at room temperature and at 4°C with the following treatments: A) C. jejuni preincubated with A. polyphaga before the addition of product, B) C. jejuni mixed with A. polyphaga after the addition of product, and C) C. jejuni in product without A. polyphaga. Bacterial survival was assessed by colony counts on blood agar plates.

RESULTS

Co-culture with A. polyphaga prolonged the C. jejuni survival both in milk and juice. The effect of co-culture was most pronounced in juice stored at room temperature. On the other hand, A. polyphaga did not have any effect on C. jejuni survival during pasteurization of milk or orange juice, indicating that this is a good method for eliminating C. jejuni in these products.

CONCLUSION

Amoebae-associated C. jejuni in milk and juice might cause C. jejuni infections.

The Pyromaniac Inside You: Salmonella Metabolism in the Host Gut

A metabolically diverse microbial community occupies all available nutrient-niches in the lumen of the mammalian intestine, making it difficult for pathogens to establish themselves in this highly competitive environment. Salmonella serovars sidestep the competition by using their virulence factors to coerce the host into creating a novel nutrient-niche. Inflammation-derived nutrients available in this new niche support a bloom of Salmonella serovars, thereby ensuring transmission of the pathogen to the next susceptible host by the fecal-oral route. Here we review the anaerobic food chain that characterizes resident gut-associated microbial communities along with the winning metabolic strategy Salmonella serovars use to edge out competing microbes in the inflamed intestine.

Spectrum of enteropathogens detected by the FilmArray GI Panel in a multicentre study of community-acquired gastroenteritis

The European, multicentre, quarterly point-prevalence study of community-acquired diarrhoea (EUCODI) analysed stool samples received at ten participating clinical microbiology laboratories (Austria, Finland, France, Germany, Greece, Ireland, Italy, Portugal, Romania, and the UK) in 2014. On four specified days, each local laboratory submitted samples from ≤20 consecutive patients to the Austrian Study Centre for further testing with the FilmArray GI Panel (BioFire Diagnostics, Salt Lake City, UT, USA). Of the 709 samples from as many patients received, 325 (45.8%) tested negative, 268 (37.8%) yielded only one organism, and 116 (16.4%) yielded multiple organisms. Positivity rates ranged from 41% (30 of 73 samples) in France to 74% (59 of 80 samples) in Romania. With the exception of Entamoeba histolytica and Vibrio cholerae, all of the 22 targeted pathogens were detected at least once. Enteropathogenic Escherichia coli, Campylobacter species, toxigenic Clostridium difficile, enteroaggregative E. coli, norovirus and enterotoxigenic E. coli were the six most commonly detected pathogens. When tested according to local protocols, seven of 128 positive samples (5.5%) yielded multiple organisms. Overall, the FilmArray GI Panel detected at least one organism in 54.2% (384/709) of the samples, as compared with 18.1% (128/709) when testing was performed with conventional techniques locally. This underlines the considerable potential of multiplex PCR to improve routine stool diagnostics in community-acquired diarrhoea. Classic culture methods directed at the isolation of specific pathogens are increasingly becoming second-line tools, being deployed when rapid molecular tests give positive results. This optimizes the yield from stool examinations and dramatically improves the timeliness of diagnosis.

Not all types of host contacts are equal when it comes to E. coli transmission

The specific processes that facilitate pathogen transmission are poorly understood, particularly for wild animal populations. A major impediment for investigating transmission pathways is the need for simultaneous information on host contacts and pathogen transfer. In this study, we used commensal Escherichia coli strains as a model system for gastrointestinal pathogens. We combined strain-sharing information with detailed host contact data to investigate transmission routes in mountain brushtail possums. Despite E. coli being transmitted via the faecal-oral route, we revealed that, strain-sharing among possums was better explained by host contacts than spatial proximity. Furthermore, and unexpectedly, strain-sharing was more strongly associated with the duration of brief nocturnal associations than day-long den-sharing. Thus, the most cryptic and difficult associations to measure were the most relevant connections for the transmission of this symbiont. We predict that future studies that employ similar approaches will reveal the importance of previously overlooked associations as key transmission pathways.