Etiologic and clinical characterization of community acquired gastroenteritis in adult patients in a Chilean emergency room by the FilmArray GI panel

Campylobacter spp. Prevalence in Santiago, Chile: A Study Based on Molecular Detection in Clinical Stool Samples from 2014 to 2019

Campylobacter spp. is an emerging cause of infectious diarrhea worldwide. In South American countries such as Chile, its prevalence is underestimated due to inadequate detection methods. Gastrointestinal multiplex PCR panels (GMP) permit rapid and sensitive detection of bacterial pathogens and provide important epidemiological information. This study aimed to analyze Campylobacter epidemiology using the results of molecular methods and to compare molecular detection results to those of culture methods. We performed a retrospective, descriptive analysis of Campylobacter spp. detected in clinical stool samples between 2014-2019 by GMP and culture. Within 16,582 specimens examined by GMP, Campylobacter was the most prevalent enteropathogenic bacteria (8.5%), followed by Salmonella spp. (3.9%), Shigella spp./enteroinvasive Escherichia coli (EIEC) (1.9%), and Yersinia enterocolitica (0.8%). The highest Campylobacter prevalence occurred in 2014/2015. Campylobacteriosis affected more males (57.2%) and adults from 19-65 years (47.9%) and showed a bimodal seasonality with summer and winter peaks. In 11,251 routine stool cultures, Campylobacter spp. was detected in 4.6%, mostly C. jejuni (89.6%). Among 4533 samples tested by GMP and culture in parallel, GMP showed a superior sensitivity (99.1% versus 50%, respectively). The study suggests that Campylobacter spp. is the most frequent bacterial enteropathogen in Chile.

Outbreak of Arcobacter butzleri? An emerging enteropathogen

BACKGROUND

Arcobacter butzleri is a gram-negative rod, with microaerobic growth at an optimal temperature of 37°C. It was reported to be the fourth most common Campylobacter-like organism isolated from patients with diarrhoea.

OBJECTIVE

Characterise a potential outbreak of A. butzleri detected in a short period of time in the University Hospital Marqués de Valdecilla.

METHODS

Eight strains of A. butzleri were detected in our hospital in only two months. Isolates were identified by MALDI-TOF MS system and 16S rDNA sequencing. Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) and Pulsed Field Gel Electrophoresis (PFGE) were carried out to assess clonal relationship. Gradient strips (Etest) were used to determine susceptibility by agar diffusion.

RESULTS

ERIC-PCR and PFGE confirmed the lack of clonal relationship between strains. Erythromycin or ciprofloxacin might be appropriate for antibiotic treatment of infections.

CONCLUSIONS

A. butzleri is an emerging pathogen with increasing incidence, and may be underestimated.

Epidemiology of Aeromonas spp. isolated from stool in a tertiary hospital in Cantabria, Northern Spain, in the last five years

INTRODUCTION

The role of Aeromonas species in gastrointestinal disease is controversial. The aim of this study was to know the epidemiological distribution of Aeromonas spp. isolated from stool in our health area, determine the existence of diarrhea as a significant symptom, identification of existing species in our environment and association as co-pathogen.

METHODS

It was a retrospective descriptive study of isolates of Aeromonas spp. in feces (2016-2020). The protocol for these isolates included coproculture, identification by MALDI-TOF (Vitek-MS®, BioMerieux) and confirmation by multiplex PCR.

RESULTS

A total of 366 Aeromonas spp. isolates were analyzed being Aeromonas caviae the most prevalent species (289, 78.7%). A total of 58 (15.8%) co-infections were identified, being more frequent in pediatric age (49;84.5%) (p=0.01) and mostly associated with Campylobacter spp.

DISCUSSION

Aeromonas spp. prove to be a gastrointestinal pathogen more frequently associated with co-infections in pediatric age, evidencing its appearance especially with Campylobacter spp.

Comparison of Length of Hospital Stay for Community-Acquired Infections Due to Enteric Pathogens, Influenza Viruses and Multidrug-Resistant Bacteria: A Cross-Sectional Study in Hungary

Community-acquired infections (CAI) can affect the duration of care and mortality of patients. Therefore, we aimed to investigate these as well as factors influencing the length of hospital stay in patients with CAI due to enteric pathogens, influenza viruses and multidrug-resistant (MDR) bacteria. We obtained data on 531 patients with CAI from the medical databases of a Hungarian university hospital and analyzed their characteristics using a regression model. Patients with MDR bacterial infection had the highest mortality (26.24%) and they stayed significantly longer in the hospital than cases with other CAIs. Our results showed that infection by Clostridioides difficile (odds ratio (OR): 6.98, 95% confidence interval (CI): 1.03-47.48; p = 0.047), MDR Escherichia coli (OR: 7.64, 95% CI: 1.24-47.17; p = 0.029), MDR Klebsiella spp. (OR: 7.35, 95% CI: 1.15-47.07; p = 0.035) and hospitalization in the department of pulmonology (OR: 5.48, 95% CI: 1.38-21.76; p = 0.016) and surgery (OR: 4.19, 95% CI: 1.18-14.81; p = 0.026) significantly increased, whereas female sex (OR: 0.62, 95% CI: 0.40-0.97; p = 0.037) and hospitalization in the department of pediatrics (OR: 0.17, 95% CI: 0.04-0.64; p = 0.009) decreased the odds of staying in the hospital for more than 6 days. Our findings provide new information on the epidemiology of CAI and can contribute to the development of public health programs that decrease the burden of infections acquired in the community.

Genomic Analysis and Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli in Peru

Campylobacter is the leading cause of human bacterial gastroenteritis worldwide and has a major impact on global public health. Whole Genome Sequencing (WGS) is a powerful tool applied in the study of foodborne pathogens. The objective of the present study was to apply WGS to determine the genetic diversity, virulence factors and determinants of antimicrobial resistance of the populations of C. jejuni and C. coli in Peru. A total of 129 Campylobacter strains (108 C. jejuni and 21 C. coli) were sequenced using Illumina Miseq platform. In silico MLST analysis identified a high genetic diversity among those strains with 30 sequence types (STs), several of them within 11 clonal complexes (CC) for C. jejuni, while the strains of C. coli belonged to a single CC with 8 different STs. Phylogeny analysis showed that Peruvian C. jejuni strains were divided into 2 clades with 5 populations, while C. coli formed a single clade with 4 populations. Furthermore, in silico analyses showed the presence of several genes associated with adherence, colonization and invasion among both species: cadF (83.7%), jlpA (81.4%), racR (100%), dnaJ (83.7%), pebA (83.7%), pldA (82.1%), porA (84.5%), ceuE (82.9%), ciaB (78.3%), iamB (86.8%), and flaC (100%). The majority (82.9%) of the Campylobacter strains carried the cdtABC operon which code for cytolethal distending toxin (CDT). Half of them (50.4%) carried genes associated with the presence of T6SS, while the frequency of genes associated with T4SS were relatively low (11.6%). Genetic markers associated with resistance to quinolones, tetracycline (tetO, tetW/N/W), beta-lactamases (bla_oxa–61), macrolides (A2075G in 23S rRNA) were found in 94.5, 21.7, 66.7, 6.2, 69.8, and 18.6% of strains, respectively. The cmeABC multidrug efflux operon was present in 78.3% of strains. This study highlights the importance of using WGS in the surveillance of emerging pathogens associated with foodborne diseases, providing genomic information on genetic diversity, virulence mechanisms and determinants of antimicrobial resistance. The description of several Campylobacter genotypes having many virulence factors and resistance to quinolones and tetracyclines circulating in Peru provides important information which helps in the monitoring, control and prevention strategies of this emerging pathogen in our country.

Mapping of aetiologies of gastroenteritis: a systematic review and meta-analysis of pathogens identified using a multiplex screening array

OBJECTIVE

Emergence of molecular methods to screen stools could provide a more complete picture of pathogens causing gastroenteritis, allowing to adequately treat patients whenever required but, so far, no aggregate data have been released. Our objective was to report pathogens identified in patients suffering from gastroenteritis using a multiplex molecular array.

DESIGN

Medline and Embase were searched for original publications reporting pathogens identified with FilmArray GI panel in patients suffering from gastroenteritis. Proportions of pathogens were extracted and pooled using a model with random effects.

RESULTS

Fourteen studies (17,815 patients) were included in the analysis. Among the 7,071 patients (39.7%) with positive FilmArray, identified pathogens were EPEC (27.5%), Clostridium difficile (19.3%), Norovirus (15.1%), EAEC (15%), Campylobacter spp (11.8%), Salmonella spp (8.1%), ETEC (7.3%), Rotavirus (7.3%), Sapovirus (7.1%), STEC (5.2%), Shigella/EIEC (4.9%), Giardia lamblia (4%), Adenovirus (3.8%), Cryptosporidium spp (3.8%), Astrovirus (2.8%), Yersinia enterocolitica (1.7%), Escherichia coli O157 (1.1%), Plesiomonas shigelloides (1.1%), Cyclospora cayetanensis (0.7%), Vibrio spp (0.5%), Vibrio cholerae (0.3%) and Entamoeba histolytica (0.3%). When considering only studies with control group (microbiological examination of the stools performed by other methods), FilmArray identified at least one pathogen in 48.2% of patients versus 16.7% when using comparative diagnostic methods.

CONCLUSIONS

FilmArray GI panel was positive in 39.7% of patients suffering from gastroenteritis. This proportion has to be mitigated by the carriage rates of identified organisms. Ultimately, restricted ordering of molecular panels to those patients who might benefit from specific treatment could provide medical value by swift identification of the pathogen and more targeted therapy.

FilmArray GI-panel performance for the rapid and multiple detection of gastrointestinal microorganisms in foodborne illness outbreaks in Shenzhen during 2018-2019

Foodborne illness outbreaks can be caused by a great many of gastrointestinal microorganisms including bacteria, viruses and parasites. Acute gastroenteritis is most commonly found in such patients infected with at least one pathogen through food intake. The stool culture has been conventionally used to guide a single diagnosis and therapy. However, traditional methods for identification of a pathogen are time-consuming and have limited sensitivity, leading to false negatives and co-infection omission. The aim of this study was to characterize the multiple etiology of each foodborne illness outbreak in Shenzhen during 2018-2019 by the FilmArray GI panel, and to reveal the seasonality of each causative organism incurring outbreaks. All patients included had a FilmArray GI panel performance and the seasonal characteristics were recorded. A total of 173 patients suffered from foodborne illnesses in 32 outbreaks in Nanshan District of Shenzhen. In total, 365 microorganisms were detected of which 83.8% (306/365) corresponded to bacteria and 16.2% (59/365) to viruses. Co-infections with more than one microorganism were detected in 81.3% (26/32) of the outbreaks. In 153 (88.4%) of 173 patients at least two pathogens were identified. The most common diarrheal pathogen related to outbreaks was EPEC (56%), followed by ETEC (38%), Norovirus (34%), EAEC (28%), Vibrio (25%), Salmonella (22%), P. shigelloides (22%), C. difficile (16%), STEC (3%) and Sapovirus (3%). Bacterial outbreaks occurred with a seasonal distribution with the exception of C. difficile whereas Norovirus outbreaks predominated during the autumn-winter months. The use of the FilmArray GI panel has given us worthy information regarding the epidemiology of pathogens detected in patients with acute diarrhea. It also highlights the importance of multi-pathogen infections and the frequency of diarrheogenic E. coli in foodborne disease outbreaks. More significantly, the rapid and multiple findings may help quickly taking an appropriate precaution, control and treatment.

Evaluation of viral co-infections among patients with community-associated Clostridioides difficile infection

We assessed viral co-infections in 155 patients with community-associated Clostridioides difficile infection in five U.S. sites during December 2012–February 2013. Eighteen patients (12%) tested positive for norovirus (n = 10), adenovirus (n = 4), rotavirus (n = 3), or sapovirus (n = 1). Co-infected patients were more likely than non-co-infected patients to have nausea or vomiting (56% vs 31%; p = 0.04), suggesting that viral co-pathogens contributed to symptoms in some patients. There were no significant differences in prior healthcare or medication exposures or in CDI complications.

Challenges in identification of enteroinvasive Escherichia coli and Shigella spp. in Lebanon

This study aimed to evaluate the routine identification tools available in Lebanon for differentiation of Escherichia coli and Shigella spp. The identification of 43 isolates defined as Shigella spp. by Api 20E was accessed using MALDI-TOF, serological testing, duplex PCR targeting ipaH (present in Shigella spp. and enteroinvasive E. coli "EIEC") and lacY (found in E. coli including EIEC but not Shigella spp.) as well as gyrB gene sequencing. Antibiotic susceptibility was investigated as well as Shiga-toxin production. All isolates were identified as E. coli by MALDI-TOF while the PCR showed a disparate group of 26 EIEC, 11 Shigella spp., 5 E. coli and 1 inactive E. coli. However, the sequencing of gyrB gene, which was recently described as a suitable marker for distinguishing E. coli and Shigella spp., identified all isolates as E. coli. Antibiotic resistance was noticeable against ß-lactams, rifampicin, trimethoprim-sulfamethoxazole, gentamicin, and ciprofloxacin. The most common variants of beta-lactamase genes were blaTEM-1, blaCTX-M-15, and blaCTX-M-3. A great discordance between the used methods in identification was revealed herein. An accurate identification technique able to distinguish E. coli from Shigella spp. in routine laboratories is a pressing need in order to select the appropriate treatment and assess the epidemiology of these bacteria.

Appropriate Use and Future Directions of Molecular Diagnostic Testing

Purpose of Review

Major technologic advances in two main areas of molecular infectious disease diagnostics have resulted in accelerated adoption or ordering, outpacing implementation, and clinical utility studies. Physicians must understand the limitations to and appropriate utilization of these technologies in order to provide cost-effective and well-informed care for their patients.

Recent Findings

Rapid molecular testing and, to a lesser degree, clinical metagenomics are now being routinely used in clinical practice. While these tests allow for a breadth of interrogation not possible with conventional microbiology, they pose new challenges for diagnostic and antimicrobial stewardship programs. This review will summarize the most recent literature on these two categories of technologic advances and discuss the few studies that have looked at utilization and stewardship approaches. This review also highlights the future directions for both of these technologies.

Summary

The appropriate utilization of rapid molecular testing and clinical metagenomics has not been well established. More studies are needed to assess their prospective impacts on patient management and antimicrobial stewardship efforts as the future state of infectious disease diagnostics will see continued expansion of these technologic advances.

Prevalence, risk factors and seasonal variations of different Enteropathogens in Lebanese hospitalized children with acute gastroenteritis

BACKGROUND

Acute gastroenteritis (AGE) is a major cause of pediatric morbidity and mortality around the world. It remains a frequent reason for infection-related admissions to emergency units among all age groups. Following the Syrian refugee crisis and insufficient clean water in our region, we sought to assess the etiological and epidemiological factors pertaining to AGE in South Lebanon.

METHODS

In this multi-center cross sectional clinical study, we analyzed the demographic, clinical and laboratory data of 619 Lebanese children from the age of 1 month to 5 years old who were admitted with AGE to pediatrics departments of three tertiary care centers in South Lebanon.

RESULTS

Our results revealed that males had a higher incidence of AGE (57.3%) than females. Enteropathogens were identified in 332/619 (53.6%) patients. Single pathogens were found in 294/619 (47.5%) patients, distributed as follows: Entamoeba histolytica in 172/619 (27.8%) patients, rotavirus in 84/619 (13.6%), and adenovirus in 38/619 (6.1%). Mixed co-pathogens were identified in 38/619 (6.1%) patients. Analyzing the clinical manifestations indicated that E. histolytica caused the most severe AGE. In addition, children who received rotavirus vaccine were significantly less prone to rotavirus infection.

CONCLUSIONS

Our findings alluded to the high prevalence of E. histolytica and other unidentified enteropathogens as major potential causes of pediatric AGE in hospitalized Lebanese children. This should drive us to widen our diagnostic panel by adopting new diagnostic techniques other than the routinely used ones (particularly specific for the pathogenic amoeba E. histolytica and for the unidentified enteropathogens), and to improve health services in this unfortunate area of the world where insanitary water supplies and lack of personal hygiene represent a major problem.