Fecal carriage of extended-spectrum beta-lactamase-producing Enterobacterales in healthy Spanish schoolchildren

Background

Extended-spectrum ß-lactamase-producing Enterobacterales (ESBL-E) are a serious threat among emerging antibiotic resistant bacteria. Particularly, the number of cases of ESBL-E infections reported in children has been increasing in recent years, and approved antibiotic treatments for this age group are limited. However, information regarding the prevalence of colonization in European children, risk factors associated with colonization, and the characteristics of the colonizing strains is scarce. The aims of this study were to determine the prevalence of ESBL-E colonization in fecal samples of apparently healthy schoolchildren, to identify lifestyle routines associated with colonization, and to characterize clonal relationships and mechanisms of resistance in ESBL-E isolates.

Methods

A cohort of 887 healthy children (3-13  years old) from seven primary and secondary schools in the Madrid metropolitan area was recruited between April-June 2018, and sociodemographic information and daily habits were collected. Fecal samples were screened for ESBL-E carriage in selective medium. ESBL-E isolates were further characterized by assessing molecular epidemiology (PFGE and MLST), ESBL gene carriage, and antibiotic resistance profile. This information was analyzed in conjunction with the metadata of the participants in order to identify external factors associated with ESBL-E carriage.

Results

Twenty four ESBL-E, all but one Escherichia coli, were detected in 23 children (prevalence: 2.6%; 95% CI: 1.6-3.6%). Of these, seven contained the bla_CTX-M-14 allele, five the bla_CTX-M-15, five the bla_SHV-12, three the bla_CTX-M-27, three the bla_CTX-M-32, and one the bla_CTX-M-9. Significant clonal diversity was observed among the isolates that grouped into 22 distinct clusters (at <85% similarity of PFGE profile). ESBL-producing E. coli isolates belonged to 12 different STs, with ST10 (25%) and ST131 (17%) being the most frequent. Apart from ß-lactams, resistance to trimethoprim/sulfamethoxazole (46%), ciprofloxacin (33%), levofloxacin (33%), tobramycin (21%), and gentamicin (8%) were the most frequently detected.

Conclusion

The prevalence of ESBL-E in the studied cohort of children was lower than the average colonization rate previously detected in Europe for both children and adults. E. coli was the main ESBL-producing species detected and CTX-M were the most frequently identified ESBLs. High ST diversity suggests polyclonal dissemination. Compared to other STs, ST131 isolates were associated with resistance to various antimicrobials.

Establishing a molecular laboratory in COVID-19 pandemic: The experience of a regional laboratory in Spain

The high demand for COVID-19 diagnosis overwhelmed reference hospitals. Regional laboratories had to incorporate molecular technology to respond to the emergency. This work described the implementation of molecular diagnostic tools and the detection of SARS-CoV-2, in a regional hospital with no previous experience, from October 2020 to March 2022. The laboratory structure was significantly modified. The staff grew from 3 to 4 clinical microbiologists, and from 7 to 17 laboratory technicians to provide 24/7 coverage. A total of 144,442 samples were processed during the period of study. The highest peaks were reached in July 2021 with 25,285 samples processed, and between December 2021 and January 2022, with 32,245. COVID-19 pandemic has represented not only the challenge, but the opportunity to introduce Nucleic Acid Amplification Techniques (NAAT) in inexperienced laboratories. These secondary settings have shown an extraordinary ability to adapt and cannot be left behind in the progress of diagnostic techniques.

Parasitemia Levels in Trypanosoma cruzi Infection in Spain, an Area Where the Disease Is Not Endemic: Trends by Different Molecular Approaches

Trypanosoma cruzi infection has expanded globally through human migration. In Spain, the mother-to-child route is the mode of transmission contributing to autochthonous Chagas disease (CD); however, most people acquired the infection in their country of origin and were diagnosed in the chronic phase (imported chronic CD). In this context, we assessed the quantitative potential of the Loopamp Trypanosoma cruzi detection kit (Sat-TcLAMP) based on satellite DNA (Sat-DNA) to determine parasitemia levels compared to those detected by real-time quantitative PCRs (qPCRs) targeting Sat-DNA (Sat-qPCR) and kinetoplast DNA minicircles (kDNA-qPCR). This study included 173 specimens from 39 autochthonous congenital and 116 imported chronic CD cases diagnosed in Spain. kDNA-qPCR showed higher sensitivity than Sat-qPCR and Sat-TcLAMP. According to all quantitative approaches, parasitemia levels were significantly higher in congenital infection than in chronic CD (1 × 10-1 to 5 × 105 versus >1 × 10-1 to 6 × 103 parasite equivalents/mL, respectively [P < 0.001]). Sat-TcLAMP, Sat-qPCR, and kDNA-qPCR results were equivalent at high levels of parasitemia (P = 0.381). Discrepancies were significant for low levels of parasitemia and older individuals. Differences between Sat-TcLAMP and Sat-qPCR were not qualitatively significant, but estimations of parasitemia using Sat-TcLAMP were closer to those by kDNA-qPCR. Parasitemia changes were assessed in 6 individual cases in follow-up, in which trends showed similar patterns by all quantitative approaches. At high levels of parasitemia, Sat-TcLAMP, Sat-qPCR, and kDNA-qPCR worked similarly, but significant differences were found for the low levels characteristic of late chronic CD. A suitable harmonization strategy needs to be developed for low-level parasitemia detection using Sat-DNA- and kDNA-based tests. IMPORTANCE Currently, molecular equipment has been introduced into many health care centers, even in low-income countries. PCR, qPCR, and loop-mediated isothermal amplification (LAMP) are becoming more accessible for the diagnosis of neglected infectious diseases. Chagas disease (CD) is spreading worldwide, and in countries where the disease is not endemic, such as Spain, the parasite Trypanosoma cruzi is transmitted from mother to child (congenital CD). Here, we explore why LAMP, aimed at detecting T. cruzi parasite DNA, is a reliable option for the diagnosis of congenital CD and the early detection of reactivation in chronic infection. When the parasite load is high, LAMP is equivalent to any qPCR. In addition, the estimations of T. cruzi parasitemia in patients living in Spain, a country where the disease is not endemic, resemble natural evolution in areas of endemicity. If molecular tests are introduced into the diagnostic algorithm for congenital infection, early diagnosis and timely treatment would be accomplished, so the interruption of vertical transmission can be an achievable goal.

CARB-ES-19 Multicenter Study of Carbapenemase-Producing Klebsiella pneumoniae and Escherichia coli From All Spanish Provinces Reveals Interregional Spread of High-Risk Clones Such as ST307/OXA-48 and ST512/KPC-3

Objectives

CARB-ES-19 is a comprehensive, multicenter, nationwide study integrating whole-genome sequencing (WGS) in the surveillance of carbapenemase-producing K. pneumoniae (CP-Kpn) and E. coli (CP-Eco) to determine their incidence, geographical distribution, phylogeny, and resistance mechanisms in Spain.

Methods

In total, 71 hospitals, representing all 50 Spanish provinces, collected the first 10 isolates per hospital (February to May 2019); CPE isolates were first identified according to EUCAST (meropenem MIC > 0.12 mg/L with immunochromatography, colorimetric tests, carbapenem inactivation, or carbapenem hydrolysis with MALDI-TOF). Prevalence and incidence were calculated according to population denominators. Antibiotic susceptibility testing was performed using the microdilution method (EUCAST). All 403 isolates collected were sequenced for high-resolution single-nucleotide polymorphism (SNP) typing, core genome multilocus sequence typing (cgMLST), and resistome analysis.

Results

In total, 377 (93.5%) CP-Kpn and 26 (6.5%) CP-Eco isolates were collected from 62 (87.3%) hospitals in 46 (92%) provinces. CP-Kpn was more prevalent in the blood (5.8%, 50/853) than in the urine (1.4%, 201/14,464). The cumulative incidence for both CP-Kpn and CP-Eco was 0.05 per 100 admitted patients. The main carbapenemase genes identified in CP-Kpn were bla_OXA–48 (263/377), bla_KPC–3 (62/377), bla_VIM–1 (28/377), and bla_NDM–1 (12/377). All isolates were susceptible to at least two antibiotics. Interregional dissemination of eight high-risk CP-Kpn clones was detected, mainly ST307/OXA-48 (16.4%), ST11/OXA-48 (16.4%), and ST512-ST258/KPC (13.8%). ST512/KPC and ST15/OXA-48 were the most frequent bacteremia-causative clones. The average number of acquired resistance genes was higher in CP-Kpn (7.9) than in CP-Eco (5.5).

Conclusion

This study serves as a first step toward WGS integration in the surveillance of carbapenemase-producing Enterobacterales in Spain. We detected important epidemiological changes, including increased CP-Kpn and CP-Eco prevalence and incidence compared to previous studies, wide interregional dissemination, and increased dissemination of high-risk clones, such as ST307/OXA-48 and ST512/KPC-3.

Comparison of DNA extraction methods and real-time PCR assays for the molecular diagnostics of chronic Chagas disease

Aim: This work aimed to compare the sensitivity of four protocols for the detection of Trypanosoma cruzi DNA in 98 blood samples from chronic Chagas disease patients. Materials & methods: Two DNA extraction (automated and manual) methods and two T. cruzi satellite DNA qPCRs (with a recent design and the usually used set of primers) were analyzed. Results: Both DNA extraction methods and qPCR assays tested in this work gave comparable qualitative results, although the lowest Ct values were obtained when samples were analyzed using the new set of primers for T. cruzi satellite DNA. Conclusion: Our results encourage the implementation of automated DNA extraction systems and the new T. cruzi qPCR for the molecular diagnostics and treatment response monitoring of chronic Chagas disease patients.

Leishmania infantum asymptomatic infection in inflammatory bowel disease patients under anti-TNF therapy

BACKGROUND

In recent years anti-TNF therapy has been associated with leishmaniasis in immunocompromised patients from endemic areas. Nevertheless, data on asymptomatic Leishmania infection in such patients is scarce. The aim of this study was to determine the prevalence of asymptomatic infection in inflammatory bowel disease (IBD) patients treated with TNF inhibitors living in an endemic area (Catalonia) and to follow up them to study how the infection evolved.

METHODS

192 IBD patients (143 Crohn's disease; 49 ulcerative colitis) from Catalonia (Spain), an area endemic for L. infantum, were recruited. Peripheral blood samples were collected and tested for anti-Leishmania antibodies by Western blotting (WB). Leishmania kinetoplast DNA was detected in peripheral blood mononuclear cells (PBMC) by a quantitative PCR.

RESULTS

Serology was positive in 3.1% and Leishmania DNA was found in 8.8%, with a low parasitic load and humoral response. The prevalence was 10.9%, patients being considered infected if they tested positive by at least one of the techniques. Eight out of the 21 patients with asymptomatic leishmaniasis were monitored for 3-8 months after the first test. None of them showed an increased parasitemia or humoral response, or developed leishmaniasis during the follow-up period.

CONCLUSION

The prevalence of Leishmania asymptomatic infection detected in our IBD cohort is similar to that found in healthy population in close endemic areas. Due to the short monitoring period, it is not possible to reach a conclusion about the risk of Leishmania reactivation from this study.

Interregional spread in Spain of linezolid-resistant Enterococcus spp. isolates carrying the optrA and poxtA genes

The emergence of linezolid-resistant Enterococcus spp. (LRE) due to transferable resistance determinants is a matter of concern. To understand the contribution of the plasmid-encoded optrA and poxtA genes to the emergence of LRE, clinical isolates from different Spanish hospitals submitted to the Spanish Reference Laboratory from 2015-2018 were analysed. Linezolid resistance mechanisms were screened in all isolates by PCR and sequencing. Genetic relatedness of Enterococcus spp. carrying optrA and poxtA was studied by PFGE and MLST. Antimicrobial susceptibility was tested by broth microdilution using EUCAST standards. A total of 97 LRE isolates were studied, in 94 (96.9%) of which at least one resistance determinant was detected; 84/97 isolates (86.6%) presented a single resistance mechanism as follows: 45/84 (53.6%) carried the optrA gene, 38/84 (45.2%) carried the G2576T mutation and 1/84 (1.2%) carried the poxtA gene. In addition, 5/97 isolates (5.2%) carried both optrA and the G2576T mutation and 5/97 (5.2%) carried both optrA and poxtA. The optrA gene was more frequent in Enterococcus faecalis (83.6%) than Enterococcus faecium (11.1%) and was mainly associated with community-acquired urinary tract infections. Carriage of the poxtA gene was more frequent in E. faecium (13.9%) than E. faecalis (1.6%). Among the optrA-positive E. faecalis isolates, two main clusters were detected by PFGE. These two clusters belonged to ST585 and ST480 and were distributed throughout 11 and 6 Spanish provinces, respectively. This is the first description of LRE carrying the poxtA gene in Spain, including the co-existence of optrA and poxtA in five isolates.

Serum IL-10 Levels and Its Relationship with Parasitemia in Chronic Chagas Disease Patients

It is known that the immunoregulatory networks in human Chagas disease play a key role in parasitemia control during the acute phase. However, little is known regarding the control of parasitemia during the chronic phase. The aim of the study was to describe the serum cytokine profile of Trypanosoma cruzi chronically infected patients and to evaluate its relationship with the presence or absence of parasitemia in peripheral blood. This is a prospective observational study where adult Chagas disease patients were included. Patients previously treated for Chagas disease, pregnant women, and immunosuppressed patients were excluded. Demographic and clinical information was collected, and T. cruzi real-time polymerase chain reaction (RT-PCR) and serum cytokine profile were determined in peripheral blood. Forty-five patients were included. Trypanosoma cruzi RT-PCR in peripheral blood resulted positive in 19 (42.2%) patients. No differences in the serum cytokine profile were found depending on cardiac or digestive involvement. However, patients with positive T. cruzi RT-PCR had a higher median concentration of IL-10 and IL-1beta and a lower median concentration of IL-8 than those with negative T. cruzi PCR. These results reinforce the key role that this anti-inflammatory cytokine (IL-10) plays in parasitemia control.

Usefulness of real-time PCR during follow-up of patients treated with Benznidazole for chronic Chagas disease: Experience in two referral centers in Barcelona

BACKGROUND

Antitrypanosomal treatment with Benznidazole (BZ) or Nifurtimox may be recommended for patients with chronic Chagas disease (CD) to reduce the onset or progression of symptoms. However, such treatment has limited efficacy and high level of toxic effects. In addition, the current cure biomarker (serology conversion) precludes any treatment assessment unless a prolonged follow-up is arranged. PCR is thus the most useful, alternative surrogate marker for evaluating responses to treatment. The aim of this study is to describe the usefulness of real-time PCR in monitoring BZ treatment within a large cohort of chronic CD cases in Barcelona.

METHODOLOGY/PRINCIPAL FINDINGS

A total of 370 chronic CD patients were monitored with real-time PCR post-BZ treatment. The median follow-up was 4 years (IQR 2.2-5.3y), with a median of 3 clinical visits (IQR 2-4). Only 8 patients (2.2%) presented with at least one incident of positive real-time PCR after treatment and were therefore considered as treatment failure. Four of those failure patients had completed full course treatment, whereas the remaining cases had defaulted with a statistical difference between both groups (p = 0.02). Half of the failure patients had undergone less than 4 years of follow-up monitoring all presented with parasitemia before treatment.

CONCLUSIONS/SIGNIFICANCE

BZ treatment failure was highly infrequent in our cohort. BZ discontinuation was a risk factor for positive real-time PCR results during clinical follow-up. Regular testing with real-time PCR during follow-up allows for early detection of treatment failure in patients with chronic CD.

The challenge of discordant serology in Chagas disease: The role of two confirmatory techniques in inconclusive cases

Serodiscordance in Chagas disease (CD) remains a challenge since individuals with inconclusive results are clinically complicated to manage. This work, conducted outside the endemic area, aims to compare two different confirmatory techniques for the diagnosis of CD in individuals without a definitive diagnosis, to analyze the performance of the screening techniques in this group of patients, and to describe the serological follow-up of these subjects over time. Sera from 48 individuals with repeatedly discordant results by one recombinant enzyme immunoassay (r-ELISA) and one native ELISA (n-ELISA), were included in the study. Confirmatory procedures were performed through TESA-blot, using trypomastigote antigens of Trypanosoma cruzi, and in-house WB (IH-WB) using a lysate from T. cruzi epimastigotes. Of the 48 sera, TESA-blot confirmed 22 (45.8%) cases and IH-WB 17 (35.4%). Both techniques showed a substantial agreement (k = 0.604). Confirmation defined as the positivity of one of the ELISA and at least one of the confirmatory tests was reached in 24/48 (50%) cases. We found a great dispersion of r-ELISA index values, especially among individuals with confirmatory negative results, ranging from 0.03-6.2. Additionally, n-ELISA yielded a better performance than r-ELISA in this cohort of patients, showing a significantly greater agreement with the confirmatory methods. Our results indicate that either confirmatory test could be an efficient tool to solve inconclusive cases regardless of which form of the parasite's life cycle they use. Also, most individuals remain with discordant serology throughout the short-term follow-up period time of study. Finally, we consider that it is necessary to establish a reference test feasible and commercialized in all areas to solve the problem of inconclusive results.

[Screening of parasitic diseases in the asymptomatic immigrant population]

Parasitic diseases suppose an important health problem in people from high endemic areas, so these must be discarded properly. Usually, these infections develop asymptomatically but, in propitious situations, are likely to reactivate themselves and can cause clinical symptoms and/or complications in the receiving country. Moreover, in some cases it is possible local transmission. Early diagnosis of these parasitic diseases made by appropriate parasitological techniques and its specific treatment will benefit both, the individual and the community. These techniques must be selected according to geoepidemiological criteria, patient's origin, migration route or time spent outside the endemic area; but other factors must also be considered as its sensitivity and specificity, implementation experience and availability. Given the high prevalence of intestinal parasites on asymptomatic immigrants, it is recommended to conduct a study by coproparasitological techniques. Because of its potential severity, the screening of asymptomatic malaria with sensitive techniques such as PCR (polymerase chain reaction) is also advisable. Serological screening for Chagas disease should be performed on all Latin American immigrants, except for people from the Caribbean islands. Other important parasites, which should be excluded, are filariasis and urinary schistosomiasis, by using microscopic examination. The aim of this paper is to review the different techniques for the screening of parasitic diseases and its advices within the care protocols for asymptomatic immigrants.

Prevalence of Chagas Disease among Solid Organ-Transplanted Patients in a Nonendemic Country

Reactivation of Chagas disease in the chronic phase may occur after solid organ transplantation, which may result in high parasitemia and severe clinical manifestations such as myocarditis and meningoencephalitis. The aim of the present study is to describe the prevalence of Chagas disease among solid organ-transplanted patients in a tertiary hospital from a nonendemic country. A cross-sectional study was performed at Vall d'Hebron University Hospital (Barcelona, Spain) from April to September 2016. Chagas disease screening was performed through serological tests in adult patients coming from endemic areas that had received solid organ transplantation and were being controlled in our hospital during the study period. Overall, 42 patients were included, 20 (47.6%) were male and median age was 50.5 (23-73) years. Transplanted organs were as follows: 18 kidneys, 17 lungs, and 7 livers. Three patients had Chagas disease, corresponding to a prevalence among this group of solid organ-transplanted patients of 7.1%. All three patients were born in Bolivia, had been diagnosed with Chagas disease and received specific treatment before the organ transplantation. We highly recommend providing screening tests for Chagas disease in patients with or candidates for solid organ transplantation coming from endemic areas, early treatment with benznidazole, and close follow-up to prevent clinical reactivations.

Strongyloides stercoralis infection increases the likelihood to detect Trypanosoma cruzi DNA in peripheral blood in Chagas disease patients

OBJECTIVES

In a previous study performed by our group, Strongyloides stercoralis infection in patients with Chagas disease was associated with higher proportion of Trypanosoma cruzi DNA detection in peripheral blood. The aim of the study was to confirm this association in a larger cohort of patients.

METHODS

Cross-sectional study of all patients with Chagas disease diagnosed from 2005 to 2015 during blood donation at the Catalan Blood Bank. Demographic data and T. cruzi RT-PCR were collected. S. stercoralis infection diagnosis was based on a serological test.

RESULTS

Two hundred and two blood donors were included. T. cruzi RT-PCR was positive in 72 (35.6%) patients, and S. stercoralis serology was positive in 22 (10.9%) patients. Patients with positive S. stercoralis serology had higher proportion of positive T. cruzi RT-PCR than those with negative serology (54.5% vs. 33.3%, P = 0.050), and the difference increased when taking a serological index cut-off of 2.5, which increases the specificity of the test to detect a confirmed strongyloidiasis (60% vs. 33%, P = 0.017).

CONCLUSIONS

Patients with Chagas disease with positive S. stercoralis serology had higher proportion of positive T. cruzi RT-PCR in peripheral blood than those with negative serology, which reflects the potential immunomodulatory effects of S. stercoralis in T. cruzi co-infected patients.

Dicrocoelium dendriticum: An Unusual Parasitological Diagnosis in a Reference International Health Unit

Finding Dicrocoelium dendriticum eggs in human feces is exceptional and there are few prevalence data available. True infection occurs after accidental ingestion of ants containing metacercariae and spurious infection through the consumption of infected animal liver. Differential diagnosis between true and pseudo-infections is performed through stool examination after a diet free of liver. In addition, microscopy can help to differentiate the type of infection. We report six cases, all from sub-Saharan Africa, detection of this fluke at the Tropical Medicine Unit Vall d'Hebron-Drassanes (Barcelona, Spain). Dicrocoelium dendriticum transit eggs were visualized in five cases and there were no subsequent visualizations after diet, which reinforces that all these cases were false parasitism. In one case, few embryonated eggs were observed and the patient was treated for a possible true parasitism. There is a need to investigate the prevalence of D. dendriticum in our country focusing on the distinction between true and spurious infections.

Serodiscordance in chronic Chagas disease diagnosis: a real problem in non-endemic countries

According to the WHO, chronic Chagas disease (CD) diagnosis is based on two serological techniques. To establish a definitive diagnosis, the results must be concordant. In cases of discordances, the WHO proposes repeating serology in a new sample, and if results remain inconclusive, a confirmatory test should be performed. This study, conducted at two Tropical Medicine Units in Europe over 4 years, aims to assess the diagnostic yield of TESA- (trypomastigote excreted-secreted antigens) blot as a confirmatory technique in patients with inconclusive and discordant results. Of 4939 individuals screened, 1124 (22.7%) obtained positive results and 165 (3.3%) discordant results. Serology was repeated in 88/165 sera and discrepancies were solved in 25/88 (28.4%) cases. Patients without a definitive diagnosis were classified in two different groups: Group 1, including patients with inconclusive results despite retesting (n = 63), and Group 2, including patients with discordant results not retested (n = 77). TESA-blot was performed for all of Group 1 and 39/77 of Group 2 and was positive for 33/63 (52.4%) and 21/39 (53.8%), respectively. Analysis of Group 1 results showed a moderate agreement between results of the ELISA based on native antigen and TESA-blot (κ 0.53). In contrast, a clear disagreement was observed between the ELISA based on recombinant antigens and TESA-blot (κ <0). A sizeable proportion of patients are suspected to have CD with inconclusive results or in whom re-testing is not feasible. TESA-blot was positive in half of these patients, highlighting the need for a confirmatory assay in European centres caring for exposed individuals.