A microbiological and genomic perspective of globally collected Escherichia coli from adults hospitalized with invasive E. coli disease.

OBJECTIVES: Escherichia coli can cause infections in the urinary tract and in normally sterile body sites leading to invasive E. coli disease (IED), including bacteraemia and sepsis, with older populations at increased risk. We aimed to estimate the theoretical coverage rate by the ExPEC4V and 9V vaccine candidates. In addition, we aimed at better understanding the diversity of E. coli isolates, including their genetic and phenotypic antimicrobial resistance (AMR), sequence types (STs), O-serotypes and the bacterial population structure. METHODS: Blood and urine culture E. coli isolates (n = 304) were collected from hospitalized patients ≥60 years (n = 238) with IED during a multicentric, observational study across three continents. All isolates were tested for antimicrobial susceptibility, O-serotyped, whole-genome sequenced and bioinformatically analysed. RESULTS: A large diversity of STs and of O-serotypes were identified across all centres, with O25b-ST131, O6-ST73 and O1-ST95 being the most prevalent types. A total of 45.4% and 64.7% of all isolates were found to have an O-serotype covered by the ExPEC4V and ExPEC9V vaccine candidates, respectively. The overall frequency of MDR was 37.4% and ST131 was predominant among MDR isolates. Low in-patient genetic variability was observed in cases where multiple isolates were collected from the same patient. CONCLUSIONS: Our results highlight the predominance of MDR O25b-ST131 E. coli isolates across diverse geographic areas. These findings provide further baseline data on the theoretical coverage of novel vaccines targeting E. coli associated with IED in older adults and their associated AMR levels.

Feasibility of tracking invasive Escherichia coli disease among older adults in a community setting: A prospective observational study.

PURPOSE: Invasive Escherichia coli disease (IED) encompasses a diverse range of sterile site infections. This study evaluated the feasibility of capturing IED among community-dwelling older adults to inform the implementation of a phase 3 efficacy trial of a novel vaccine against IED (NCT04899336). METHODS: EXPECT-1 (NCT04087681) was a prospective, multinational, observational study conducted in medically stable participants aged ≥ 60 years. At least 50% of participants were selected based on a history of urinary tract infection (UTI) in the previous 10 years. The main outcomes were the incidence of IED and the number of hospitalisations reported by the site vs participant. The length of follow-up was 12 months. In a US-based substudy, a smartphone-based geofencing was evaluated to track hospital entries. RESULTS: In total, 4470 participants were enrolled (median age, 70.0 years); 59.5% (2657/4469) of participants had a history of UTI in the previous 10 years. Four IED events were captured through deployment of different tracking methods: a self-report, a general practitioner (GP) report, and a follow-up call. The incidence rate of IED was 98.6 events per 100,000 person-years. The number of reported hospitalisations was 2529/4470 (56.6%) by the site and 2177/4470 (48.7%) by participants; 13.8% of hospitalisations would have been missed if utilising only site reports. Geofencing detected 72 hospital entries. CONCLUSION: Deployment of multiple tracking methods can optimise detection of IED among community-dwelling older adults. Older adults with a history of UTI could be feasibly targeted for a phase 3 vaccine efficacy trial through a network of GPs.

Clinical presentation and antimicrobial resistance of invasive Escherichia coli disease in hospitalized older adults: a prospective multinational observational study.

BACKGROUND: Clinical data characterizing invasive Escherichia coli disease (IED) are limited. We assessed the clinical presentation of IED and antimicrobial resistance (AMR) patterns of causative E. coli isolates in older adults. METHODS: EXPECT-2 (NCT04117113) was a prospective, observational, multinational, hospital-based study conducted in patients with IED aged ≥ 60 years. IED was determined by the microbiological confirmation of E. coli from blood; or by the microbiological confirmation of E. coli from urine or an otherwise sterile body site in the presence of requisite criteria of systemic inflammatory response syndrome (SIRS), Sequential Organ Failure Assessment (SOFA), or quick SOFA (qSOFA). The primary outcomes were the clinical presentation of IED and AMR rates of E. coli isolates to clinically relevant antibiotics. Complications and in-hospital mortality were assessed through 28 days following IED diagnosis. RESULTS: Of 240 enrolled patients, 80.4% had bacteremic and 19.6% had non-bacteremic IED. One-half of infections (50.4%) were community-acquired. The most common source of infection was the urinary tract (62.9%). Of 240 patients, 65.8% fulfilled ≥ 2 SIRS criteria, and 60.4% had a total SOFA score of ≥ 2. Investigator-diagnosed sepsis and septic shock were reported in 72.1% and 10.0% of patients, respectively. The most common complication was kidney dysfunction (12.9%). The overall in-hospital mortality was 4.6%. Of 299 E. coli isolates tested, the resistance rates were: 30.4% for trimethoprim-sulfamethoxazole, 24.1% for ciprofloxacin, 22.1% for levofloxacin, 16.4% for ceftriaxone, 5.7% for cefepime, and 4.3% for ceftazidime. CONCLUSIONS: The clinical profile of identified IED cases was characterized by high rates of sepsis. IED was associated with high rates of AMR to clinically relevant antibiotics. The identification of IED can be optimized by using a combination of clinical criteria (SIRS, SOFA, or qSOFA) and culture results.

Performance characteristics of code-based algorithms to identify urinary tract infections in large United States administrative claims databases.

BACKGROUND: In real-world evidence research, reliability of coding in healthcare databases dictates the accuracy of code-based algorithms in identifying conditions such as urinary tract infection (UTI). This study evaluates the performance characteristics of code-based algorithms to identify UTI. METHODS: Retrospective observational study of adults contained within three large U.S. administrative claims databases on or after January 1, 2010. A targeted literature review was performed to inform the development of 10 code-based algorithms to identify UTIs consisting of combinations of diagnosis codes, antibiotic exposure for the treatment of UTIs, and/or ordering of a urinalysis or urine culture. For each database, a probabilistic gold standard was developed using PheValuator. The performance characteristics of each code-based algorithm were assessed compared with the probabilistic gold standard. RESULTS: A total of 2 950 641, 1 831 405, and 2 294 929 patients meeting study criteria were identified in each database. Overall, the code-based algorithm requiring a primary UTI diagnosis code achieved the highest positive predictive values (PPV; >93.8%) but the lowest sensitivities (<12.9%). Algorithms requiring three UTI diagnosis codes achieved similar PPV (>0.899%) and improved sensitivity (<41.6%). Algorithms requiring a single UTI diagnosis code in any position achieved the highest sensitivities (>72.1%) alongside a slight reduction in PPVs (<78.3%). All-time prevalence estimates of UTI ranged from 21.6% to 48.6%. CONCLUSIONS: Based on these findings, we recommend use of algorithms requiring a single UTI diagnosis code, which achieved high sensitivity and PPV. In studies where PPV is critical, we recommend code-based algorithms requiring three UTI diagnosis codes rather than a single primary UTI diagnosis code.

Development and performance characteristics of novel code-based algorithms to identify invasive Escherichia coli disease.

PURPOSE: Evaluation of novel code-based algorithms to identify invasive Escherichia coli disease (IED) among patients in healthcare databases. METHODS: Inpatient visits with microbiological evidence of invasive bacterial disease were extracted from the Optum© electronic health record database between January 1, 2016 and June 30, 2020. Six algorithms, derived from diagnosis and drug exposure codes associated to infectious diseases and Escherichia coli, were developed to identify IED. The performance characteristics of algorithms were assessed using a reference standard derived from microbiology data. RESULTS: Among 97 194 eligible records, 25 310 (26.0%) were classified as IED. Algorithm 1 (diagnosis code for infectious invasive disease due to E. coli) had the highest positive predictive value (PPV; 96.0%) and lowest sensitivity (60.4%). Algorithm 2, which additionally included patients with diagnosis codes for infectious invasive disease due to an unspecified organism, had the highest sensitivity (95.5%) and lowest PPV (27.8%). Algorithm 4, which required patients with a diagnosis code for infectious invasive disease due to unspecified organism to have no diagnosis code for non-E. coli infections, achieved the most balanced performance characteristics (PPV, 93.6%; sensitivity, 78.1%; F1 score, 85.1%). Finally, adding exposure to antibiotics in the treatment of E. coli had limited impact on performance algorithms 5 and 6. CONCLUSION: Algorithm 4, which achieved the most balanced performance characteristics, offers a useful tool to identify patients with IED and assess the burden of IED in healthcare databases.

Registering medicines for low-income countries: how suitable are the stringent review procedures of the World Health Organisation, the US Food and Drug Administration and the European Medicines Agency?

New medicines are registered after a resource-demanding process. Unfortunately, in low-income countries (LICs), demand outweighs resources. To facilitate registration in LICs, stringent review procedures of the European Medicines Agency (EMA Article-58), Food and Drug Administration (FDA PEPFAR-linked review) and WHO Prequalification programme have been established. Only the PEPFAR-linked review gives approval, while the others make recommendations for approval. This study assessed the performance and discussed the challenges of these three stringent review procedures. Data from WHO, FDA, EMA, Medline and Internet were analysed. Over 60% of medicines reviewed by stringent review procedures are manufactured in India. Until 2012, WHO prequalified 400 medicines (211 vaccines, 130 antiretrovirals, 29 tuberculostatics, 15 antimalarials and 15 others). PEPFAR-linked review approved 156 antiretrovirals, while EMA Article 58 recommended approval of 3 antiretrovirals, 1 vaccine and 1 antimalarial. WHO Prequalification and PEPFAR-linked review are free of charge and as a result have accelerated access to antiretrovirals. They both built capacity in sub-Saharan Africa, although WHO prequalification relies technically on stringent regulatory authorities and financially on donors. Article-58 offers the largest disease coverage and strongest technical capacities, is costly and involves fewer LICs. To meet the high demand for quality medicines in LICs, these stringent review procedures need to enlarge their disease coverage. To improve registration, EMA Article 58 should actively involve LICs. Furthermore, LIC regulatory activities must not be fully resigned to stringent review procedure.

Lot-to-lot consistency, immunogenicity, and safety of the Ad26.ZEBOV, MVA-BN-Filo Ebola virus vaccine regimen: A phase 3, randomized, double-blind, placebo-controlled trial.

This phase-3, double-blind, placebo-controlled study (NCT04228783) evaluated lot-to-lot consistency of the Ad26.ZEBOV, MVA-BN-Filo Ebola vaccine regimen. Participants were randomized (6:6:6:1) to receive the two-dose regimen from three consecutively manufactured lots of Ad26.ZEBOV on Day 1 paired with three consecutively manufactured lots of MVA-BN-Filo on Day 57 (Groups 1-3) or two doses of placebo (Group 4). An additional cohort also received an Ad26.ZEBOV booster or placebo 4 months post-dose 2. Equivalence of the immunogenicity at 21 days post-dose 2 between any two groups was demonstrated if the 95% confidence interval (CI) of the Ebola virus glycoprotein (EBOV GP)-binding antibody geometric mean concentration (GMC) ratio was entirely within the prespecified margin of 0.5-2.0. Lot-to-lot consistency (i.e., consecutive lots can be consistently manufactured) was accomplished if equivalence was shown for all three pairwise comparisons. Results showed that the primary objective in the per-protocol immunogenicity subset (n = 549) was established for each pairwise comparison (Group 1 vs 2: GMC ratio = 0.9 [95% CI: 0.8, 1.1], Group 1 vs 3: 0.9 [0.8, 1.1], Group 2 vs 3: 1.0 [0.9, 1.2]). Equivalence of the three groups for the Ad26.ZEBOV component only was also demonstrated at 56 days post-dose 1. EBOV GP-binding antibody responses (post-vaccination concentrations >2.5-fold from baseline) were observed in 419/421 (99.5%) vaccine recipients at 21 days post-dose 2 and 445/460 (96.7%) at 56 days post-dose 1. In the booster cohort (n = 39), GMCs increased 9.0- and 11.8-fold at 7 and 21 days post-booster, respectively, versus pre-booster. Ad26.ZEBOV, MVA-BN-Filo was well tolerated, and no safety issues were identified.

Safety, Reactogenicity, Immunogenicity, and Dose Selection of 10-Valent Extraintestinal Pathogenic Escherichia coli Bioconjugate Vaccine (VAC52416) in Adults Aged 60-85 Years in a Randomized, Multicenter, Interventional, First-in-Human, Phase 1/2a Study.

Background: ExPEC10V is a bioconjugate vaccine containing O-antigen polysaccharides of 10 extraintestinal pathogenic Escherichia coli (ExPEC) serotypes. This phase 1/2a study (NCT03819049) assessed the safety, reactogenicity, and immunogenicity of ExPEC10V (VAC52416) to prevent invasive E coli disease in elderly adults. Methods: The observer-blind, active-controlled design included a 28-day screening, vaccination, 181-day follow-up, and 1-year follow-up. Participants (60-85 years of age) were randomized to ExPEC10V low dose (antigen dose range, 4-8 µg), ExPEC10V medium dose (4-16 µg), or ExPEC10V high dose (8-16 µg); 4-valent ExPEC vaccine (ExPEC4V); or 13-valent pneumococcal conjugate vaccine (PCV13). The incidence of adverse events (AEs; solicited, day 15; unsolicited, day 30; serious AEs, day 181) and immunogenicity (electrochemiluminescent-based assay [ECL] and multiplex opsonophagocytic assay [MOPA]) were assessed. Optimal ExPEC10V dose was determined from safety data through day 30 and an immunogenicity dose selection algorithm based on day 15 ECL and MOPA results. Results: A total of 416 participants were included (median age, 64.0 years; 54.8% female). The incidences of solicited local and systemic AEs were, respectively, 44.2% and 39.4% for low-dose, 52.9% and 46.1% for medium-dose, 57.7% and 45.2% for high-dose ExPEC10V, and 74.1% and 48.1% for PCV13. Five serious AEs, not vaccine related, were reported. The ECL revealed a robust antibody response to ExPEC10V through year 1. Opsonophagocytic killing activity was detected against all but serotype O8; this lack of response against serotype O8 was linked to low assay sensitivity. Based on the totality of data, high-dose ExPEC10V was considered optimal. Conclusions: ExPEC10V was well tolerated and immunogenic in elderly adults against all but serotype O8.

Epidemiology, Clinical Features, and Antimicrobial Resistance of Invasive Escherichia Coli Disease in Patients Admitted in Tertiary Care Hospitals.

Background: Invasive Escherichia coli disease (IED), including bloodstream infection, sepsis, and septic shock, can lead to high hospitalization and mortality rates. This multinational study describes the clinical profile of patients with IED in tertiary care hospitals. Methods: We applied clinical criteria of systemic inflammatory response syndrome (SIRS), sepsis, or septic shock to patients hospitalized with culture-confirmed E coli from urine or a presumed sterile site. We assessed a proposed clinical case definition against physician diagnoses. Results: Most patients with IED (N = 902) were adults aged ≥60 years (76.5%); 51.9%, 25.1%, and 23.0% of cases were community-acquired (CA), hospital-acquired (HA), and healthcare-associated (HCA), respectively. The urinary tract was the most common source of infection (52.3%). Systemic inflammatory response syndrome, sepsis, and septic shock were identified in 77.4%, 65.3%, and 14.1% of patients, respectively. Patients >60 years were more likely to exhibit organ dysfunction than those ≤60 years; this trend was not observed for SIRS. The case-fatality rate (CFR) was 20.0% (60-75 years, 21.5%; ≥75 years, 22.2%), with an increase across IED acquisition settings (HA, 28.3%; HCA, 21.7%; CA, 15.2%). Noticeably, 77.8% of patients initiated antibiotic use on the day of culture sample collection. A total of 65.6% and 40.8% of E coli isolates were resistant to ≥1 agent in ≥1 or ≥2 drug class(es). A 96.1% agreement was seen between the proposed clinical case definition and physician's diagnoses of IED. Conclusions: This study contributes valuable, real-world data about IED severity. An accepted case definition could promote timely and accurate diagnosis of IED and inform the development of novel preventative strategies.

Efficacy and safety of intermittent preventive treatment in schoolchildren with sulfadoxine/pyrimethamine (SP) and SP plus piperaquine in Democratic Republic of the Congo: a randomised controlled trial.

In endemic areas, malaria and its adverse effects in schoolchildren may be prevented by intermittent preventive treatment (IPTsc). However, the most appropriate drug regimen for IPTsc remains to be identified. A randomised controlled trial was conducted in Kinshasa, DRC. Enrolled schoolchildren were assigned to a passive control arm (n = 212), sulfadoxine/pyrimethamine (SP) (n = 202) or SP plus piperaquine (SP/PQ) (n = 202). The primary endpoint was haemoglobin (Hb) change. Secondary endpoints were anaemia, parasitaemia prevalence and clinical malaria incidence. Data were analysed by modified intention-to-treat (mITT) and per-protocol. A linear mixed mode was used due to repeated measurements. Of 616 enrolled children, 410 (66.6%) were eligible for mITT analysis. The control arm was used as reference. After 12 months, the Hb level increased by 0.20 g/dL (95% CI -0.61 to 0.47; P = 0.168) and 0.39 g/dL (0.12-0.66; P <0.01) in the SP and SP/PQ arms, respectively. SP treatment reduced anaemia, malaria parasitaemia and clinical malaria by 10% (0-20%; P = 0.06), 19% (2-33%; P = 0.042) and 25% (-32 to 57%; P = 0.37), respectively. The corresponding values for SP/PQ were 28% (19-37%; P <0.001), 40% (26-52%; P <0.001) and 58% (17-79%; P <0.01). No deaths or severe adverse events (SAEs) were observed. SP/PQ offered substantial protection against anaemia, malaria parasitaemia and clinical malaria and showed no SAEs. SP/PQ, a combination of two long-acting non-artemisinin-based antimalarials, may be a valuable option for IPTsc in Africa.

Malaria, schistosomiasis and soil transmitted helminth burden and their correlation with anemia in children attending primary schools in Kinshasa, Democratic Republic of Congo.

BACKGROUND: Anaemia reduces cognitive potential in school children, retards their growth and predisposes them to other diseases. As there is a paucity of data on the current burden of P. falciparum, S. mansoni and soil transmitted helminths (STH) infections and their correlation with schoolchildren's anemia in the Democratic Republic of Congo (DRC), we collect these data. METHODS: This study reports baseline data collected from a randomized controlled trial investigating the impact of IPT with SP and SP-PQ on anemia and malaria morbidity in Congolese schoolchildren (Trial registration: NCT01722539; PACTR201211000449323). S. mansoni and STH infections were assessed using kato-katz technique. Malaria infection and hemoglobin concentration were assessed using Blood smear and Hemocontrol device, respectively. RESULTS: A total of 616 primary schoolchildren from 4 to 13 years old were enrolled in the study. The prevalence of Plasmodium spp. infection was 18.5% (95%CI:15.6-21.9). Amongst those infected, 24 (21%), 40 (35.1%), 40 (35.1%), 10 (8.8%), had light, moderate, heavy, very high malaria parasite density, respectively. Above 9 years of age (p = 0.02), male and history of fever (p = 0.04) were both associated with malaria infection. The overall prevalence of S. mansoni infection was 6.4% (95%CI:4.4-9.1). Girls were associated with S. mansoni infection (p = 0.04). T. trichiura was the most prevalent STH infection (26.3%), followed by A. lumbricoides (20.1%). Co-infection with malaria-S. mansoni and malaria-STH was, respectively, 1.5% (CI95%:0.7-3.3) and 6.4% (CI95% 4.4-9.1). The prevalence of anemia was found to be 41.6% (95%CI:37.7-45.6) and anemia was strongly related with Plasmodium ssp infection (aOR:4.1; CI95%:2.6-6.5;p<0.001) and S. mansoni infection (aOR:3.3;CI95%:1.4-7.8;p<0.01). CONCLUSION: Malaria and S. mansoni infection were strongly associated with high prevalence of anemia in schoolchildren. Therefore, specific school-based interventions, such as intermittent preventive treatment or prophylaxis, LLITN distribution, anthelminthic mass treatment and micronutrient supplementation are needed to improve school children's health.

Intermittent preventive treatment: efficacy and safety of sulfadoxine-pyrimethamine and sulfadoxine-pyrimethamine plus piperaquine regimens in schoolchildren of the Democratic Republic of Congo: a study protocol for a randomized controlled trial.

BACKGROUND: In malaria endemic areas, schoolchildren usually have asymptomatic malaria infections and consequently remain untreated. Therefore, intermittent preventive treatment with sulfadoxine-pyrimethamine in schoolchildren would be a plausible strategy in malaria stable transmission areas to prevent anaemia and malnutrition. However, in contrast to infancy and pregnancy, antimalaria intermittent preventive treatment in children has been barely investigated. As the implementation of intermittent preventive treatment may be challenged by sulfadoxine-pyrimethamine resistance, sulfadoxine-pyrimethamine combined with piperaquine may be a better alternative than sulfadoxine-pyrimethamine monotherapy. A clinical trial is being conducted to assess the efficacy and safety of intermittent preventive treatments versus controls in Democratic Republic of Congo (DRCongo) schoolchildren and their impact on sulfadoxine-pyrimethamine resistance. METHODS/DESIGN: A phase IIIb, randomised, controlled trial will enroll asymptomatic schoolchildren. For interventions, sulfadoxine-pyrimethamine is compared to sulfadoxine-pyrimethamine plus piperaquine and to a control group. The two treatments are given four-monthly from baseline for a year as a single dose for sulfadoxine-pyrimethamine and two doses at 24-hour intervals for piperaquine. All participants receive praziquantel and albendazole as mass-treatment for helminthiasis at enrolment. The primary endpoint is haemoglobin concentration change at 12 months follow-up. Secondary endpoints are malaria parasite load and malaria prevalence, at baseline and at month 12. Malaria and helminthiasis incidence will be monitored throughout the study. Statistical analysis will use multilevel modelling due to repeated measurements and clustering effect of participants. DISCUSSION: The very few studies on intermittent preventive treatment in schoolchildren in malaria stable transmission areas have contradictory results. This randomised controlled trial is unique in comparing efficacy and safety of a prophylactic combination therapy to monotherapy or a control group after 12 months follow-up. Resistance markers for sulfadoxine-pyrimethamine (including break through parasitaemias) will also be recorded. Its uniqueness lies also in the fact that we use piperaquine, a long acting antimalarial, in combination with sulfadoxine-pyrimethamine. Artemisinin derivatives have been excluded as it is part of the treatment policies in virtually all malaria endemic countries. Our findings may, therefore, contribute to the public health of youngsters who fail to thrive and grow due to multiple morbidities. TRIAL REGISTRATION: NCT01722539; PACTR201211000449323.