Integron detection for prediction of trimethoprim/sulfamethoxazole susceptibility in children with Enterobacterales urinary tract infections.

OBJECTIVES: In some countries, third-generation cephalosporins (3GCs) serve as first-line therapy in children with urinary tract infections (UTIs). However, their use may contribute to the emergence of antibiotic resistance, notably among Gram-negative bacteria (GNB). Integrons are bacterial genetic elements involved in antibiotic resistance in GNB. Their absence is associated with >97% susceptibility to trimethoprim/sulfamethoxazole in adults infected with GNB. The objective of this study was to examine the value of integron detection directly from urine samples as a predictive marker of resistance to trimethoprim/sulfamethoxazole in children with GNB-related UTIs. METHODS: Children admitted to the Limoges University Hospital's paediatric emergency department between February 2018 and March 2019 with a suspicion of UTI were eligible for the study. Only confirmed cases presenting a positive urine culture with unique GNB were retained for further study analyses. Integrons were detected directly from urines using real-time PCR. RESULTS: The data of 72 patients were analysed and integrons were detected in 15 urine samples. The negative predictive value of integron detection for resistance to trimethoprim/sulfamethoxazole was 100% as all of the GNB (all were Enterobacterales) isolated from patients with no integrons detected in their urine samples were susceptible to trimethoprim/sulfamethoxazole. CONCLUSIONS: The detection of integrons in cases of paediatric patients with suspected UTI could help limit 3GC empirical use and empower an empirical first-line strategy better tailored to the needs of each patient.

Integrons, a predictive biomarker for antibiotic resistance in acute sepsis: the IRIS study.

BACKGROUND: Considering the increase in MDR Gram-negative bacteria (GNB), the choice of empirical antibiotic therapy is challenging. In parallel, use of broad-spectrum antibiotics should be avoided to decrease antibiotic selection pressure. Accordingly, clinicians need rapid diagnostic tools to narrow antibiotic therapy. Class 1-3 integrons, identified by intI1-3 genes, are genetic elements that play a major role in antibiotic resistance in GNB. OBJECTIVES: The objective of the IRIS study was to evaluate the negative and positive predictive values (NPVs and PPVs, respectively) of intI1-3 as markers of antibiotic resistance. METHODS: The IRIS study was an observational cross-sectional multicentre study that enrolled adult subjects with suspected urinary tract or intra-abdominal infections. intI1-3 were detected directly from routinely collected biological samples (blood, urine or intra-abdominal fluid) using real-time PCR. A patient was considered 'MDR positive' if at least one GNB, expressing acquired resistance to at least two antibiotic families among ß-lactams, aminoglycosides, fluoroquinolones and/or co-trimoxazole, was isolated from at least one biological sample. RESULTS: Over a 2 year period, 513 subjects were enrolled and 409 had GNB documentation, mostly Enterobacterales. intI1 and/or intI2 were detected in 31.8% of patients and 24.4% of patients were considered 'MDR positive'. The NPV of intI1 and/or intI2 as a marker of acquired antibiotic resistances was estimated at 92.8% (89.1%-95.5%). The NPVs for first-line antibiotics were all above 92%, notably >96% for resistance to third-generation cephalosporins. CONCLUSIONS: The IRIS study strongly suggests that the absence of intI1 and intI2 in biological samples from patients with GNB-related infections is predictive of the absence of acquired resistances.

Proteae: a reservoir of class 2 integrons?

OBJECTIVES: Our aim was to confirm with a large panel of clinical isolates that class 2 integrons are highly prevalent in Proteae and to analyse their genetic characteristics. METHODS: Proteae (Proteus spp., Morganella spp. and Providencia spp.) isolates were collected from clinical samples during 2013 at Limoges University Hospital, France. The presence of class 1, 2 and 3 integrons was investigated by quantitative PCR. The presence of a stop codon in the intI2 gene was determined by Sanger sequencing. The gene cassette arrays of class 2 integrons were determined by PCR-RFLP and Sanger sequencing or next-generation sequencing when needed. RESULTS: Of the 327 Proteae collected, 103 (31.5%) harboured a class 2 integron and 45 (13.8%) a class 1 integron. No class 3 integrons were detected. One functional IntI2 integrase was detected in a Morganella morganii isolate. Six different gene cassette arrays were detected. Four had already been described in the literature: dfrA1-sat2-aadA1 (72 isolates), dfrA1-catB2-sat2-aadA1 (17), sat2-aadA1 (6) and lnu(F), dfrA1, aadA1 (1). We identified two new gene cassette arrays: (i) a new variant of the dfrA1 gene cassette (one isolate; the one with the functional IntI2); and (ii) the array dfrA1-gcu115-sat2 harbouring the new gcu115 gene cassette with two ORFs encoding proteins of unknown functions (five isolates). CONCLUSIONS: We showed a high frequency of class 2 integrons, as well as a diversity of gene cassette arrays, among Proteae. This work highlights that the Proteae tribe plays an important role as a reservoir of class 2 integrons.

Cytomegalovirus detected by qPCR in iris and ciliary body of immunocompetent corneal donors.

BACKGROUND: Cytomegalovirus (CMV) can cause a wide panel of ocular infections. The involvement of CMV as a cause of anterior uveitis in the immunocompetent patient is recent and remains poorly understood. OBJECTIVE: To investigate the presence of CMV in anterior uveal tissues of immunocompetent corneal donors. STUDY DESIGN: We collected aqueous humor, iris, and ciliary body from both eyes of 25 donors died at the Limoges University Hospital between January 2020 and July 2021. CMV serology was determined for all patients from post-mortem blood sample. Ocular tissues were split in 2 fragments for qPCR and 2 for histological analysis. CMV genomes copies were quantified by Multiplex qPCR after DNA extraction. RESULTS: 16 of 25 patients (64%) displayed positive CMV serology, with a median age of 67 years. Viremia was positive in 3 of 16 (19%) CMV-positive patients. No CMV DNA copies were found from the aqueous humor samples. CMV DNA was detected in iris and ciliary body of 28 of 32 eyes of seropositive donors, and 5 of 18 eyes of seronegative donors. The median viral copy number [IQR] was 2.41 × 102 [8.91 × 101 - 1.01 × 103] copies/1 × 106 cells in the CMV-positive group and 0.00 [0.00 - 3.54 × 102] copies/1 × 106 cells in the CMV-negative group (p<0.001). Histology and immunohistochemistry did not reveal any CMV lesions from any sample. CONCLUSION: CMV DNA was found in iris and ciliary body of immunocompetent seropositive patients, but also, although less frequently, from seronegative donors. These results highlight mechanisms of infection, latency and reactivation of CMV in ocular tissues.

Enterobacterales carrying chromosomal AmpC ß-lactamases in Europe (EuESCPM): Epidemiology and antimicrobial resistance burden from a cohort of 27 hospitals, 2020-2022.

INTRODUCTION: The ESCPM group (Enterobacter species including Klebsiella aerogenes - formerly Enterobacter aerogenes, Serratia species, Citrobacter freundii complex, Providencia species and Morganella morganii) has not yet been incorporated into systematic surveillance programs. METHODS: We conducted a multicentre retrospective observational study analysing all ESCPM strains isolated from blood cultures in 27 European hospitals over a 3-year period (2020-2022). Diagnostic approach, epidemiology, and antimicrobial susceptibility were investigated. RESULTS: Our study comprised 6,774 ESCPM isolates. MALDI-TOF coupled to mass spectrometry was the predominant technique for bacterial identification. Susceptibility to new ß-lactam/ß-lactamase inhibitor combinations and confirmation of AmpC overproduction were routinely tested in 33.3% and 29.6% of the centres, respectively. The most prevalent species were E. cloacae complex (44.8%) and S. marcescens (22.7%). Overall, third-generation cephalosporins (3GC), combined third- and fourth-generation cephalosporins (3GC + 4GC) and carbapenems resistance phenotypes were observed in 15.7%, 4.6%, and 9.5% of the isolates, respectively. AmpC overproduction was the most prevalent resistance mechanism detected (15.8%). Among carbapenemase-producers, carbapenemase type was provided in 44.4% of the isolates, VIM- (22.9%) and OXA-48-enzyme (16%) being the most frequently detected. E. cloacae complex, K. aerogenes and Providencia species exhibited the most notable cumulative antimicrobial resistance profiles, with the former displaying 3GC, combined 3GC + 4GC and carbapenems resistance phenotypes in 15.2%, 7.4%, and 12.8% of the isolates, respectively. K. aerogenes showed the highest rate of both 3GC resistant phenotype (29.8%) and AmpC overproduction (32.1%), while Providencia species those of both carbapenems resistance phenotype (42.7%) and carbapenemase production (29.4%). ESCPM isolates exhibiting both 3GC and combined 3GC + 4GC resistance phenotypes displayed high susceptibility to ceftazidime/avibactam (98.2% and 95.7%, respectively) and colistin (90.3% and 90.7%, respectively). Colistin emerged as the most active drug against ESCPM species (except those intrinsically resistant) displaying both carbapenems resistance phenotype (85.8%) and carbapenemase production (97.8%). CONCLUSIONS: This study presented a current analysis of ESCPM species epidemiology in Europe, providing insights to inform current antibiotic treatments and guide strategies for antimicrobial stewardship and diagnostics.

Dynamics of the digestive acquisition of bacterial carriage and integron presence by French preterm newborns according to maternal colonization: The DAIR3N multicentric study.

Objectives: The study aimed to describe the dynamics and risk factors of Gram-negative bacteria (GNB) acquisition in preterm infants. Methods: This prospective multicenter French study included mothers hospitalized for preterm delivery and their newborns, followed until hospital discharge. Maternal feces and vaginal fluids at delivery, and neonatal feces from birth to discharge were tested for cultivable GNB, potential acquired resistance, and integrons. The primary outcome was the acquisition of GNB and integrons in neonatal feces, and their dynamics, evaluated by survival analysis using the actuarial method. Risk factors were analyzed using Cox models. Results: Two hundred thirty-eight evaluable preterm dyads were included by five different centers over 16 months. GNB were isolated in 32.6% of vaginal samples, with 15.4% of strains producing extended-spectrum beta-lactamase (ESBL) or hyperproducing cephalosporinase (HCase), and in 96.2% of maternal feces, with 7.8% ESBL-GNB or HCase-GNB. Integrons were detected in 40.2% of feces and 10.6% of GNB strains. The mean (SD) length of stay of newborns was 39.5 (15.9) days; 4 died in the hospital. At least one infection episode occurred in 36.1% of newborns. The acquisition of GNB and integrons was progressive from birth to discharge. At discharge, half of newborns had ESBL-GNB or HCase-GNB, independently favored by a premature rupture of membranes (Hazard Ratio (HR), 3.41, 95% confidence interval (CI), 1.71; 6.81), and 25.6% had integrons (protective factor: multiple gestation, HR, 0.367, 95% CI, 0.195; 0.693). Conclusion: In preterm newborns, the acquisitions of GNB, including resistant ones, and integrons are progressive from birth to discharge. A premature rupture of membranes favored the colonization by ESBL-GNB or Hcase-GNB.

Alcaligenes xylosoxidans endophthalmitis following phacoemulsification and intraocular lens implantation.

Five consecutive cases of endophthalmitis that developed after cataract extraction by a single surgeon using the same operating room during one morning session are described. Following preoperative topical administration of ciprofloxacin, surgery consisted of phacoemulsification with peristaltic pump and fluid venting, polymethylmethacrylate intraocular lens implantation, and corneal suture. No complications occurred during surgery. All five patients developed endophthalmitis caused by infection with Alcaligenes xylosoxidans in less than 24 hours. Pulsed-field gel electrophoresis was used to prove similarity between strains. Bacterial inquiry on contamination of the operating room environment revealed massive colonization of phacoemulsifier irrigation channels by Pseudomonas fluorescens bacteria from an unestablished source. Four of the five patients ultimately recovered visual acuity better than 20/60.

Antibiotic Resistance Acquisition in the First Week of Life.

Objectives: The fetus is considered sterile but recent studies have suggested that gut colonization could start before birth. Scarce data are available for the acquisition of resistant Gram-negative bacteria (GNB) during the first days of life. Several studies have shown that integrons play a major role in antibiotic resistance acquisition. In this work, we studied the dynamics of human intestinal acquisition of GNB and integrons during the first days of life. Methods: Meconium was collected at birth and a stool sample before hospital discharge (days 2 or 3) on 185 term neonates. GNB were searched by culture on each sample and class 1, 2, and 3 integrons from each GNB or directly from samples. Eight risk factors for integron and GNB acquisition were studied. Results: We isolated 228 GNB, 46 from meconium and the remainder from stools. No link was found between GNB isolation and antibiotic exposure during delivery, but antibiotic exposure during labor significantly selected blaTEM-positive amoxicillin-resistant Enterobacteria. Two-thirds of GNB were antibiotic-susceptible and most of the resistant isolates were acquired after birth. Integrons were detected in 18 of the 228 GNB isolates from 3 meconium and 20 stools. Antibiotic administration during delivery and vaginal carriage of Streptococcus agalactiae appeared as risk factors for integron acquisition. Conclusion: Gram-negative bacteria and integrons are mostly acquired after birth during the first days of life even if for some term neonates, meconium was not sterile. Antibiotic administration during delivery is a major risk for integron acquisition and for selection of amoxicillin-resistant Enterobacteria.

Integron Digestive Carriage in Human and Cattle: A "One Health" Cultivation-Independent Approach.

Objectives: Dissemination of antimicrobial resistance (AMR) is a global issue that requires the adoption of a "One-Health" approach promoting integration of human and animal health. Besides culture-dependent techniques frequently used for AMR surveillance, cultivation-independent methods can give additional insights into the diversity and reservoir of AMR genetic determinants. Integrons are molecular markers that can provide overall and reliable estimation of AMR dissemination. In this study, considering the "One-Health" approach, we have analyzed the integron digestive carriage from stools of humans and cattle living in a same area and exposed to different antibiotic selection pressures. Methods: Three collections of human [general population (GP) and intensive care unit patients (ICUs)] and bovine (BOV) stool samples were analyzed. The three main classes of integrons were detected using a multiplex qPCR both from total DNA extracted from stools, and from Gram-negative bacteria obtained by culture after an enrichment step. Results: With the cultivation-independent approach, integron carriage was 43.8, 52.7, and 65.6% for GP, ICU, and BOV respectively, percentages being at least twofold higher to those obtained with the cultivation-dependent approach. Class 1 integrons were the most prevalent; class 2 integrons seemed more associated to cattle than to humans; no class 3 integron was detected. The integron carriage was not significantly different between GP and ICU populations according to the antibiotic consumption, whatever the approach. Conclusion: The cultivation-independent approach constitutes a complementary exploratory method to investigate the integron digestive carriage of humans and bovines, notably within subjects under antibiotic treatment. The high frequency of carriage of integrons in the gut is of clinical significance, integrons being able to easily acquire and exchange resistant genes under antibiotic selective pressure and so leading to the dissemination of resistant bacteria.

Comparative Analysis of Bacterial Community Composition and Structure in Clinically Symptomatic and Asymptomatic Central Venous Catheters.

Totally implanted venous access ports (TIVAPs) are commonly used catheters for the management of acute or chronic pathologies. Although these devices improve health care, repeated use of this type of device for venous access over long periods of time is also associated with risk of colonization and infection by pathogenic bacteria, often originating from skin. However, although the skin microbiota is composed of both pathogenic and nonpathogenic bacteria, the extent and the consequences of TIVAP colonization by nonpathogenic bacteria have rarely been studied. Here, we used culture-dependent and 16S rRNA gene-based culture-independent approaches to identify differences in bacterial colonization of TIVAPs obtained from two French hospitals. To explore the relationships between nonpathogenic organisms colonizing TIVAPs and the potential risk of infection, we analyzed the bacterial community parameters between TIVAPs suspected (symptomatic) or not (asymptomatic) of infection. Although we did not find a particular species assemblage or community marker to distinguish infection risk on an individual sample level, we identified differences in bacterial community composition, diversity, and structure between clinically symptomatic and asymptomatic TIVAPs that could be explored further. This study therefore provides a new view of bacterial communities and colonization patterns in intravascular TIVAPs and suggests that microbial ecology approaches could improve our understanding of device-associated infections and could be a prognostic tool to monitor the evolution of bacterial communities in implants and their potential susceptibility to infections. IMPORTANCE Totally implanted venous access ports (TIVAPs) are commonly used implants for the management of acute or chronic pathologies. Although their use improves the patient's health care and quality of life, they are associated with a risk of infection and subsequent clinical complications, often leading to implant removal. While all TIVAPs appear to be colonized, only a fraction become infected, and the relationship between nonpathogenic organisms colonizing TIVAPs and the potential risk of infection is unknown. We explored bacteria present on TIVAPs implanted in patients with or without signs of TIVAP infection and identified differences in phylum composition and community structure. Our data suggest that the microbial ecology of intravascular devices could be predictive of TIVAP infection status and that ultimately a microbial ecological signature could be identified as a tool to predict TIVAP infection susceptibility and improve clinical management.

Urine Contamination in Nontoilet-trained and Uncircumcised Boys.

OBJECTIVE: To assess any differences between the initial and midstream urine samples from nontoilet-trained, uncircumcised boys. Contamination during urine collection makes the diagnosis of urinary tract infections (UTIs) difficult in nontoilet-trained children, especially in uncircumcised boys. Whether the contamination comes mainly from the initial stream or the contact between urine and perineal skin is not known in this population. MATERIALS AND METHODS: A prospective diagnostic study between early and midstream urine samples was conducted on asymptomatic patients with no suspicion of UTI. The clean void method was performed in nontoilet-trained boys under general anesthesia. The exclusion criteria were circumcision, older than 3 years of age, recent antibiotics treatment, and recent UTI. Urinalysis and urine culture were performed, allowing a comparison between early and midstream urine samples. RESULTS: Forty-four patients were enrolled in the study, and 31 satisfactory samples were obtained. A higher contamination rate was found in the early stream (n = 16; 51%) than in the midstream (n = 5; 16%) (P < .01). The positive culture from the early stream sample was statistically associated with a lower age (P = .02). The contamination rate of the first stream is 3-fold higher than for the midstream when collecting urine for urine culture. CONCLUSION: The clean void method in nontoilet-trained, uncircumcised boys provides low-quality urine samples for both early and midstream urine samples. The benefit of catching midstream urine samples for the diagnosis of UTI in this population is even more important when the children are young.

Integron-associated antibiotic resistance in enteroaggregative and enteroinvasive Escherichia coli.

Ten enteroinvasive (EIEC) and 25 enteroaggregative (EaggEC) E. coli strains isolated from Senegalese patients were analyzed for their integron content. All strains were resistant to at least two antibiotics. Four EIEC and 15 EaggEC were found to carry a class 1 integron. An identical integron carrying a single dfrA5 cassette, conferring resistance to trimethoprim, was identified in all four EIEC strains. Five EaggEC strains harbored an integron with a single cassette, dfrA7, while the remaining 10 strains carried two integrons, one with a single cassette, aadA1a conferring resistance to streptomycin and spectinomycin, and the second one bearing two cassettes, dfrA13 and oxa5, the later being a beta-lactam resistance cassette. The presence of these integrons is worrying, because trimethoprim is largely used for diarrheal disease therapy in Africa. Thus, the presence of integrons in diarrheagenic strains is of public health importance because a limited number of antibiotics are available in developing countries.

Value of integron detection for predicting antibiotic resistance in patients with Gram-negative septicaemia.

Multidrug-resistant Enterobacteriaceae are a major public health threat and complicate the choice of drugs for empirical antibiotic therapy, especially in sepsis patients who require rapid, appropriate treatment. The objective of this study was to examine the value of integrons as a global predictive marker of acquired antibiotic resistance in septicaemia-causing Enterobacteriaceae by direct detection in positive blood cultures. The integron genetic marker can be detected in a single test, whereas multiple PCRs are needed to detect the hundreds of known antibiotic resistance genes. A total of 166 positive blood cultures were included in the study, and integrons were detected with a quantitative PCR method both in positive blood cultures and isolated Enterobacteriaceae. The results of integron detection directly on positive blood cultures were consistent in 98.8% of cases with integron detection in isolated Enterobacteriaceae. Negative predictive values (NPVs) were >90% for resistance to third-generation cephalosporins, aminoglycosides, ciprofloxacin and trimethoprim/sulfamethoxazole. In the current context of antibiotic stewardship, these good NPVs indicate that this method might be useful for preserving broad-spectrum antibiotics. The results of this proof-of-concept study must be confirmed in order to demonstrate the clinical relevance of integron detection, not only in positive blood cultures but also, to gain time, in raw biological samples.

Early bacterial genome detection in body fluids from patients with severe sepsis: a pilot study.

PURPOSE: The purpose of this study is to evaluate the feasibility and interest of real-time polymerase chain reaction (RT-PCR) testing for bacterial genomes in body fluids other than blood in patients with acute severe sepsis. METHODS: Twenty-six consecutive patients admitted for severe sepsis or septic shock were prospectively studied. Body fluids were sampled as clinically indicated and tested using standard microbiological methods and modified RT-PCR methods (universal PCR and specific PCRs). Results of standard microbiological tests were compared with those of PCR tests. RESULTS: Direct RT-PCR testing was successfully performed on all nonblood body fluids. Of 29 body fluids collected, 23 were positive for at least 1 microorganism with conventional tests. Of 18 microbiological tests positive for a single microorganism, 15 fully agreed with RT-PCR assays, and the remaining 3 samples were infected with bacteria not screened by PCR testing. Among the 5 polymicrobial results obtained with conventional tests, RT-PCR agreed in 4 patients. The RT-PCR tests allowed additional clinically relevant bacterial identification in 3 of 6 samples with negative microbiological culture. CONCLUSIONS: Our results indicate that direct PCR testing may improve the detection of bacteria in body fluids other than blood in patients with acute severe sepsis.

A 1 year surveillance study of glycopeptide-intermediate Staphylococcus aureus strains in a French hospital.

OBJECTIVES: Glycopeptides are the drugs of choice to treat infections due to methicillin-resistant Staphylococcus aureus, but since 1995, glycopeptide-intermediate S. aureus (GISA) and heterogeneous GISA (hGISA) have been reported worldwide. Detection of reduced susceptibility to glycopeptides in S. aureus is very difficult in a routine clinical laboratory. The aim of this study was to investigate the prevalence of hGISA/GISA strains using a three-step approach during a 1 year period. METHODS: The following algorithm was adopted: (i) brain heart infusion agar with 4 mg/L teicoplanin was used to screen S. aureus strains for reduced susceptibility to glycopeptides; (ii) for each agar screen-positive strain, an Etest macromethod using modified cut-off values (vancomycin and teicoplanin > or =4 mg/L) was used to detect potential hGISA/GISA; and (iii) the population analysis profile (PAP) method was finally used to confirm the hGISA/GISA phenotype. RESULTS: In total, 2300 strains of S. aureus were screened and 255 (11%) were categorized as hGISA with the PAP method, whereas no GISA strains were detected. Standard MIC values and current MIC breakpoints could not discriminate the hGISA/GISA phenotype from glycopeptide-susceptible S. aureus. Thus laboratories using currently standardized MIC methods cannot be expected to detect S. aureus strains that may exhibit reduced susceptibility to glycopeptides. Molecular typing by PFGE revealed that 238 strains belonged to the same clone. CONCLUSIONS: A clonal hGISA strain has disseminated within our hospital. The method described in this study has to be further investigated to see if it is applicable to other S. aureus strains.

Integron-associated antibiotic resistance in Salmonella enterica serovar typhi from Asia.

Eighteen of 25 isolates of Salmonella enterica serovar Typhi were multidrug resistant and contained class 1 integrons with a single cassette, dfrVII or aadA1. The dfrVII-containing integron was likely borne on an IncHI1 plasmid. Salmonella serovar Typhi could become resistant to broad-spectrum cephalosporins by integrating cassettes, such as veb-1, a common cassette in Asia.