Резюме. Изучали распространенность штаммов, устойчивых к цефалоспоринам расширенного спектра и ка... more Резюме. Изучали распространенность штаммов, устойчивых к цефалоспоринам расширенного спектра и карбапенемам, среди K. pneumoniae и E. coli, выделенных из клинического материала пациентов семи стационаров Санкт-Петербурга в период с января по май 2012 г. Доля штаммов, устойчивых к цефалоспоринам, колебалась в различных стационарах: E. coli-от 7,8 до 50%, K. pneumoniae-от 25,4 до 88,4%. Устойчивость была обусловлена продукцией бета-лактамаз расширенного спектра семейства СТХ-М, которые относились главным образом к группе СТХ-М-1, а также СТХ-М-2 и СТХ-М-9. В трех стационарах выявили 22 полирезистентных штамма K. pneumoniae, устойчивых к карбапенемам. Метод MАLDI-TOF MS показал, что резистентность к карбапенемам у всех штаммов была обусловлена продукцией карбапенемаз, которые согласно результатам тестов ROSCO Diagnostica относились к классу металлоβ-лактамаз. У всех изученных штаммов выявлен ген металло-β-лактамазы New Delhi metallo-β-lactamase (blaNDM-1). Результаты проведенных исследований показали, что в странах Балтийского региона (включая Россию, Санкт-Петербург) ведущим механизмом резистентности к цефалоспоринам штаммов E. coli и K. pneumoniae, выделенных в стационарах, является продукция СТХ-М-1. Впервые в России выделены штаммы K. pneumoniae, продуцирующие металло-β-лактамазу NDM-1, причем одновременно в нескольких стационарах Санкт-Петербурга.
Eesmärk. Uuringu eesmärk oli kirjeldada muutusi antibiootikumide ambulatoorses kasutamises Eestis... more Eesmärk. Uuringu eesmärk oli kirjeldada muutusi antibiootikumide ambulatoorses kasutamises Eestis aastatel 2008–2018 ning võrrelda antibiootikumide kasutust Põhjamaadega. Metoodika. Ravimikasutuse andmed põhinevad hulgimüüjate kvartaliaruannetel ja on esitatud defineeritud päevadooside (DPD, inglise keeles defined daily dose, DDD) arvuna 1000 inimese kohta ööpäevas. Antibiootikumide kasutamise kvaliteeti hinnati Euroopa mikroobivastaste ainete tarbimise järelevalve võrgustiku (European Surveillance of Antimicrobial Consumption Network, ESAC-Net ehk ESAC-võrgustik) kvaliteedinäitajate kaudu. Tulemused. Antibiootikumide ambulatoorne kasutus oli Eestis 2018. aastal 10,2 DPDd 1000 inimese kohta ööpäevas, olles sarnane Soome, Rootsi, Taani ja Norra näitajatega (vastavalt 13,2; 10,8; 13,7 ja 14,0). Kogukasutuses ei ole Eestis aastatel 2008–2018 suuri muutusi aset leidnud, kuid muutunud on kasutatavate preparaatide spekter – ilma beetalaktamaasi inhibiitorita penitsilliinide kasutus vähene...
L’etude presentee ici a pour but d’evaluer les besoins en termes de surveillance des pathogenes i... more L’etude presentee ici a pour but d’evaluer les besoins en termes de surveillance des pathogenes invasifs a Gram negatif en Estonie. Les donnees de sensibilite aux antibiotiques des isolats invasifs de Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella spp, Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae et des enterocoques ont ete collectees conformement aux protocoles d’EARSS (European Antimicrobial Resistance Surveillance System). Si le taux de pathogenes a Gram positif est superieur a celui des Gram negatif, en revanche le taux de resistance aux antibiotiques chez les premieres est moindre. Le plus fort taux de resistance etait associe, en particulier, a A. baumannii et P. aeruginosa. La proportion de souches productrices de beta-lactamases a spectre elargi (BLSE) etait de 23% pour Klebsiella spp. et de 3,6% pour E. coli. Inclure les pathogenes invasifs a Gram negatif dans la surveillance de la resistance antimicrobienne permet de disposer d’information...
Too eesmargiks oli analuusida metitsilliiniresistentse Staphylococcus aureus’e (MRSA) osakaalu, e... more Too eesmargiks oli analuusida metitsilliiniresistentse Staphylococcus aureus’e (MRSA) osakaalu, esinemissagedust ja antibiootikumitundlikkust Eesti haiglates. Tagasiulatuvad laboriandmed koguti 5 suuremast haiglast ajavahemikul 2006 kuni 2008. Uuringuperioodil diagnoositi 418 MRSA-juhtu: 4,6% S. aurus’e infektsioonidest. 10 000 voodipaeva kohta oli MRSA esinemissagedus 1,84. MRSA esinemissagedus olid aastati stabiilne, kuid eri haiglate andmed varieerusid oluliselt. MRSA tuvede resistentsus (resistentsete ja moodukalt tundlike tuvede protsent) oli jargmine: gentamutsiin 78%, klindamutsiin 62,5%, doksutsukliin 23%, erutromutsiin 72%, tsiprofloksatsiin 89%, trimetoprimsulfametoksasool 25,5% ja fusidiinhape 40,5%. Koik tuved olid vankomutsiinitundlikud. Verest ja liikvorist isoleeritud invasiivsete MRSA tuvede protsent kajastas hasti MRSA uldist sagedust. MRSA tuvede ravimiresistentsus aastate kaupa oli suur ja suhteliselt stabiilne, kuid varieerus haiglati. Eesti Arst 2010; 89(10):630...
Very few studies have analyzed how the composition of mother’s microbiota affects the development... more Very few studies have analyzed how the composition of mother’s microbiota affects the development of infant’s gut and oral microbiota during the first months of life. Here, microbiota present in the mothers’ gut, vagina, breast milk, oral cavity, and mammary areola were compared with the gut and oral microbiota of their infants over the first six months following birth. Samples were collected from the aforementioned body sites from seven mothers and nine infants at three different time points over a 6-month period. Each sample was analyzed with 16S rRNA gene sequencing. The gut microbiota of the infants harbored distinct microbial communities that had low similarity with the various maternal microbiota communities. In contrast, the oral microbiota of the infants exhibited high similarity with the microbiota of the mothers’ breast milk, mammary areola and mouth. These results demonstrate that constant contact between microbial communities increases their similarity. A majority of the...
Microbiological and Functional Aspects, Third Edition, 2004
... Lactic Acid Microflora and Its Role in the Welfare of the Host MARIKA MIKELSAAR, REET MANDAR, ... more ... Lactic Acid Microflora and Its Role in the Welfare of the Host MARIKA MIKELSAAR, REET MANDAR, EPP SEPP, and ... Lactobacilli are gram-positive, rod-shaped, facultatively anaerobic, nonsporulating, acid-tolerant, and catalase-negativebacteria witha DNA base composition ...
Objective: an increasing number of studies that are using high-throughput molecular methods are r... more Objective: an increasing number of studies that are using high-throughput molecular methods are rapidly extending our knowledge of gut microbial colonization in preterm infants whose immaturity and requirement for extensive treatment may result in altered colonization process. We aimed to describe the profile of gut microbiota in 50 extremely low birth weight (<1200 g) critically ill infants at three different time points during the first two months of life by using 16S rrNa gene specific sequencing. Patients and Methods: Stool samples were collected at the age of one week, one month and two months. Bacterial community profiling was done using universal amplification of 16S rrNa gene and 454 pyrosequencing. results: The diversity of gut microbiota in preterm neonates in the first week of life was low but increased significantly over two months. The gut microbiota was dominated by facultative anaerobic bacteria (Staphylococcus spp. and Enterobacteriaceae) and lacked colonization with bacteria known to provide resistance against pathogens (Bacteroides, Bifidobacterium, and Lactobacillus) throughout the study. Colonization of Escherichia coli and uncultured Veillionella was positively correlated with maturity. Infants born to mothers with chorioamnionitis had significantly higher bacterial diversity than those without. Conclusions: High prevalence and abundance of potentially pathogenic Enterobacteriaceae and Staphylococcaceae with low prevalence and abundance of colonization resistance providing taxa bifidobacteria, Bacteroides and lactobacilli may lead to high infection risk via microbial translocation from the gut. additionally, our data suggest that maternal chorioamnionitis may have an effect on the diversity of infants' gut microbiota; however, the mechanisms involved remain to be elucidated.
This study aimed to examine the spectrum and time course of gut and nasopharyngeal colonization w... more This study aimed to examine the spectrum and time course of gut and nasopharyngeal colonization with Gram-negative microorganisms , and to define the value of surveillance cultures in predicting late-onset sepsis in neonates admitted to neonatal intensive care units. Nasopharyngeal and rectal swabs were collected on admission and twice weekly thereafter in 278 neonates admitted within the first 72 h of life with risk factors of early-onset sepsis. Sterile body fluid cultures were obtained on admission and subsequently as clinically indicated. Approximately half of the rectal (693/1250, 55%) and nasopharyngeal (558/1153, 48%) samples but only 6% (32/555) of the sterile fluid samples in 26 patients were culture positive for Gramnegative organisms. In total, 2108 invasive and mucosal culture pairs were analysed. The overall sensitivity, specificity, and positive and negative predictive values of a mucosal sample to predict late-onset sepsis were 27%, 66%, 4% and 94%, respectively. Patients with pre-existing colonization with Klebsiella pneumoniae (P ¼ 0.011), Klebsiella oxytoca (P ¼ 0.002), Escherichia coli (P ¼ 0.003), Stenotrophomonas spp. (P ¼ 0.003) and Pseudomonas spp. (P 0.001) were more likely to develop late-onset sepsis. No such association was found for Acinetobacter baumannii, Serratia spp. or Enterobacter cloacae. In conclusion, routine mucosal cultures are inefficient for the prediction of Gram-negative late-onset sepsis in neonatal intensive care units. However, targeted screening for specific organisms in an outbreak (e.g. Klebsiella spp., E. coli, Stenotrophomonas spp. and Pseudomonas spp.) may offer an opportunity to improve infection control measures and enable timely initiation of appropriate antibiotic therapy.
European Journal of Clinical Microbiology & Infectious Diseases, 2010
The purpose of this study was to compare the impact of ampicillin and penicillin used for empiric... more The purpose of this study was to compare the impact of ampicillin and penicillin used for empiric treatment of early onset sepsis (EOS) on initial gut colonization by aerobic and facultative anaerobic microorganisms. A cluster-randomized, two-center, switch-over study was conducted in two paediatric intensive care units in Estonia and included 276 neonates. Rectal swabs were collected twice a week until discharge or day 60. Colonizing microbes were identified on species level and tested for ampicillin resistance (AR). The number of patients colonized with Gram negative microorganisms and Candida spp was similar in both treatment arms but ampicillin resulted in longer colonization duration (CD) of K. pneumonia (p=0.012), AR Serratia spp (p=0.012) and Candida spp (p=0.02) and penicillin in that of AR Acinetobacter spp (p=0.001). As for Gram positive microorganisms penicillin treatment was associated with a greater number of colonized patients and higher CD of Enterococcus spp and S. aureus but lower ones of S. haemolyticus and S. hominis. Influence of ampicillin and penicillin on initial gut colonization is somewhat different but these differences are of low clinical relevance and should not be a limiting step when choosing between these two antibiotics for the empiric treatment of EOS.
Aim: To characterize dynamics of mucosal colonization of neonates by common aerobic Gram negative... more Aim: To characterize dynamics of mucosal colonization of neonates by common aerobic Gram negative species and Candida spp. and to identify independent perinatal, neonatal, and environmental factors influencing the colonization process. Study design: The nasopharyngeal (n = 1145) and rectal (n = 1242) swabs were collected on admission and thereafter twice a week in neonates with risk factors of early onset sepsis (n = 276) admitted within the first 72 h of life. The association between colonization by different microbes and a total of 22 predefined risk factors was assessed using univariate and multiple logistic regression analyses. Results: Throughout the study about half of the patients had rectal (55.8%) or nasopharyngeal colonization (42.8%) with common Gram-negative microorganisms. Colonization dynamics and risk factors were in general similar for a given bacterial species in both mucosal sites; nonfermentative microbes more often found in nasopharyngeal swabs and Enterobacteriaceae in rectal swabs. All organisms except Escherichia coli were influenced by the duration of intensive care unit stay but other risk factors were species specific, perhaps reflecting their mode of acquisition. While colonization by E. coli and Candida albicans was associated with perinatal factors like term birth, vaginal delivery, and breast milk feeding; colonization by Klebsiella pneumoniae, Enteribacter cloacae, Acinetobacter spp. and non-albicans Candida spp. were mostly determined by hospital environment (treatment unit and period, artificial interventions and their duration) and gestation age ≤ 28 weeks. Conclusions: The knowledge of risk factor profiles may permit the development of strategies to prevent heavy colonization and subsequent invasive disease in high risk infants.
Annals of Clinical Microbiology and Antimicrobials, 2009
Background The aim of our study was to compare the presence of the intI1 gene and its association... more Background The aim of our study was to compare the presence of the intI1 gene and its associations with the antibiotic resistance of commensal Escherichia coli strains in children with/without previous antibiotic treatments and elderly hospitalized/healthy individuals. Methods One-hundred-and-fifteen intestinal E. coli strains were analyzed: 30 strains from 10 antibiotic-naive infants; 27 from 9 antibiotic-treated outpatient infants; 30 from 9 healthy elderly volunteers; and 28 from 9 hospitalized elderly patients. The MIC values of ampicillin, cefuroxime, cefotaxime, gentamicin, ciprofloxacin, and sulfamethoxazole were measured by E-test and IntI1 was detected by PCR. Results Out of the 115 strains, 56 (49%) carried class 1 integron genes. Comparing persons without medical interventions, we found in antibiotic-naive children a significantly higher frequency of integron-bearing strains and MIC values than in healthy elderly persons (53% versus 17%; p < 0.01). Evaluating medical i...
The Escherichia coli phylogenetic group B2 with integrons prevails in childhood recurrent urinary... more The Escherichia coli phylogenetic group B2 with integrons prevails in childhood recurrent urinary tract infections. APMIS 2013. The aim of our study was to characterize the phylogenetic groups of Escherichia coli, antibiotic resistance, and containment of class 1 integrons in the first attack of pyelonephritis and in subsequent recurrences in young children. Altogether, 89 urine E. coli isolates from 41 children with urinary tract infection (UTI) were studied for prevalence and persistence of phylogenetic groups by pulsed-field gel electrophoresis (PFGE), antibacterial resistance by minimal inhibitory concentrations (MIC) and class 1 integrons by PCR. Phylogenetic group B2 was most common (57%), followed by D (20%), A (18%) and B1 (5%). Overall resistance to betalactams was 61%, trimethoprimsulfamethoxazole 28%, and was not associated with phylogenetic groups. According to PFGE, the same clonal strain persisted in 77% of patients. The persistence was detected most often in phylogenetic group B2 (70%). Phylogenetic group B2 more often contained class 1 integrons than group A. Integron positive strains had higher MIC values of cefuroxime, cefotaxime, and gentamicin. In conclusion, phylogenetic group B2 was the most common cause of the first episode of pyelonephritis, as well as in case of the persistence of the same strain and contained frequently class 1 integrons in childhood recurrent UTI. An overall frequent betalactam resistance was equally distributed among phylogenetic groups.
Coagulase-negative staphylococci (CoNS) are the leading cause of late-onset sepsis (LOS) in neona... more Coagulase-negative staphylococci (CoNS) are the leading cause of late-onset sepsis (LOS) in neonates. Increasing resistance of CoNS to beta-lactams and aminoglycosides has led to widespread use of vancomycin, which in turn may lead to resistance to vancomycin. Thus, combination therapy of LOS has been advocated. We aimed to determine the interaction of oxacillin and gentamicin against CoNS. In 2005, 34 isolates of oxacillin-and gentamicin-resistant CoNS were obtained from blood samples of neonates with LOS. Combination effect was tested using the checkerboard method, E-test with the other antibiotic incorporated in the medium (E-test-1) and two E-test strips placed in a cross-formation (E-test-2). Of 34 isolates 61.8%, 53% and 73.5% revealed synergy or an additive effect when tested by the checkerboard method, E-test-1 and E-test-2, respectively. Results of all three tests were concordant for six (17.6%) isolates, four showing synergy, and two indifference. Our in vitro results support that combination therapy with penicillinase-resistant penicillin and aminoglycoside can be an alternative to vancomycin.
The high number of mutations in the Omicron variant of SARS-CoV-2 cause its immune escape when co... more The high number of mutations in the Omicron variant of SARS-CoV-2 cause its immune escape when compared to the earlier variants of concern (VOC). At least three vaccine doses are required for the induction of Omicron neutralizing antibodies and further reducing the risk for hospitalization. However, most of the studies have focused on the immediate response after the booster vaccination while the duration of immune response is less known. We here studied longitudinal serum samples from the vaccinated individuals up to three months after their third dose of the BNT162b2 vaccine for their capacity to produce protective antibodies and T cell responses to Wuhan and Omicron variants. After the second dose, the antibody levels to the unmutated spike protein were significantly decreased at three months, and only 4% of the individuals were able to inhibit Omicron spike interaction compared to 47%, 38%, and 14% of individuals inhibiting wild-type, delta, and beta variants’ spike protein. Nin...
Резюме. Изучали распространенность штаммов, устойчивых к цефалоспоринам расширенного спектра и ка... more Резюме. Изучали распространенность штаммов, устойчивых к цефалоспоринам расширенного спектра и карбапенемам, среди K. pneumoniae и E. coli, выделенных из клинического материала пациентов семи стационаров Санкт-Петербурга в период с января по май 2012 г. Доля штаммов, устойчивых к цефалоспоринам, колебалась в различных стационарах: E. coli-от 7,8 до 50%, K. pneumoniae-от 25,4 до 88,4%. Устойчивость была обусловлена продукцией бета-лактамаз расширенного спектра семейства СТХ-М, которые относились главным образом к группе СТХ-М-1, а также СТХ-М-2 и СТХ-М-9. В трех стационарах выявили 22 полирезистентных штамма K. pneumoniae, устойчивых к карбапенемам. Метод MАLDI-TOF MS показал, что резистентность к карбапенемам у всех штаммов была обусловлена продукцией карбапенемаз, которые согласно результатам тестов ROSCO Diagnostica относились к классу металлоβ-лактамаз. У всех изученных штаммов выявлен ген металло-β-лактамазы New Delhi metallo-β-lactamase (blaNDM-1). Результаты проведенных исследований показали, что в странах Балтийского региона (включая Россию, Санкт-Петербург) ведущим механизмом резистентности к цефалоспоринам штаммов E. coli и K. pneumoniae, выделенных в стационарах, является продукция СТХ-М-1. Впервые в России выделены штаммы K. pneumoniae, продуцирующие металло-β-лактамазу NDM-1, причем одновременно в нескольких стационарах Санкт-Петербурга.
Eesmärk. Uuringu eesmärk oli kirjeldada muutusi antibiootikumide ambulatoorses kasutamises Eestis... more Eesmärk. Uuringu eesmärk oli kirjeldada muutusi antibiootikumide ambulatoorses kasutamises Eestis aastatel 2008–2018 ning võrrelda antibiootikumide kasutust Põhjamaadega. Metoodika. Ravimikasutuse andmed põhinevad hulgimüüjate kvartaliaruannetel ja on esitatud defineeritud päevadooside (DPD, inglise keeles defined daily dose, DDD) arvuna 1000 inimese kohta ööpäevas. Antibiootikumide kasutamise kvaliteeti hinnati Euroopa mikroobivastaste ainete tarbimise järelevalve võrgustiku (European Surveillance of Antimicrobial Consumption Network, ESAC-Net ehk ESAC-võrgustik) kvaliteedinäitajate kaudu. Tulemused. Antibiootikumide ambulatoorne kasutus oli Eestis 2018. aastal 10,2 DPDd 1000 inimese kohta ööpäevas, olles sarnane Soome, Rootsi, Taani ja Norra näitajatega (vastavalt 13,2; 10,8; 13,7 ja 14,0). Kogukasutuses ei ole Eestis aastatel 2008–2018 suuri muutusi aset leidnud, kuid muutunud on kasutatavate preparaatide spekter – ilma beetalaktamaasi inhibiitorita penitsilliinide kasutus vähene...
L’etude presentee ici a pour but d’evaluer les besoins en termes de surveillance des pathogenes i... more L’etude presentee ici a pour but d’evaluer les besoins en termes de surveillance des pathogenes invasifs a Gram negatif en Estonie. Les donnees de sensibilite aux antibiotiques des isolats invasifs de Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella spp, Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae et des enterocoques ont ete collectees conformement aux protocoles d’EARSS (European Antimicrobial Resistance Surveillance System). Si le taux de pathogenes a Gram positif est superieur a celui des Gram negatif, en revanche le taux de resistance aux antibiotiques chez les premieres est moindre. Le plus fort taux de resistance etait associe, en particulier, a A. baumannii et P. aeruginosa. La proportion de souches productrices de beta-lactamases a spectre elargi (BLSE) etait de 23% pour Klebsiella spp. et de 3,6% pour E. coli. Inclure les pathogenes invasifs a Gram negatif dans la surveillance de la resistance antimicrobienne permet de disposer d’information...
Too eesmargiks oli analuusida metitsilliiniresistentse Staphylococcus aureus’e (MRSA) osakaalu, e... more Too eesmargiks oli analuusida metitsilliiniresistentse Staphylococcus aureus’e (MRSA) osakaalu, esinemissagedust ja antibiootikumitundlikkust Eesti haiglates. Tagasiulatuvad laboriandmed koguti 5 suuremast haiglast ajavahemikul 2006 kuni 2008. Uuringuperioodil diagnoositi 418 MRSA-juhtu: 4,6% S. aurus’e infektsioonidest. 10 000 voodipaeva kohta oli MRSA esinemissagedus 1,84. MRSA esinemissagedus olid aastati stabiilne, kuid eri haiglate andmed varieerusid oluliselt. MRSA tuvede resistentsus (resistentsete ja moodukalt tundlike tuvede protsent) oli jargmine: gentamutsiin 78%, klindamutsiin 62,5%, doksutsukliin 23%, erutromutsiin 72%, tsiprofloksatsiin 89%, trimetoprimsulfametoksasool 25,5% ja fusidiinhape 40,5%. Koik tuved olid vankomutsiinitundlikud. Verest ja liikvorist isoleeritud invasiivsete MRSA tuvede protsent kajastas hasti MRSA uldist sagedust. MRSA tuvede ravimiresistentsus aastate kaupa oli suur ja suhteliselt stabiilne, kuid varieerus haiglati. Eesti Arst 2010; 89(10):630...
Very few studies have analyzed how the composition of mother’s microbiota affects the development... more Very few studies have analyzed how the composition of mother’s microbiota affects the development of infant’s gut and oral microbiota during the first months of life. Here, microbiota present in the mothers’ gut, vagina, breast milk, oral cavity, and mammary areola were compared with the gut and oral microbiota of their infants over the first six months following birth. Samples were collected from the aforementioned body sites from seven mothers and nine infants at three different time points over a 6-month period. Each sample was analyzed with 16S rRNA gene sequencing. The gut microbiota of the infants harbored distinct microbial communities that had low similarity with the various maternal microbiota communities. In contrast, the oral microbiota of the infants exhibited high similarity with the microbiota of the mothers’ breast milk, mammary areola and mouth. These results demonstrate that constant contact between microbial communities increases their similarity. A majority of the...
Microbiological and Functional Aspects, Third Edition, 2004
... Lactic Acid Microflora and Its Role in the Welfare of the Host MARIKA MIKELSAAR, REET MANDAR, ... more ... Lactic Acid Microflora and Its Role in the Welfare of the Host MARIKA MIKELSAAR, REET MANDAR, EPP SEPP, and ... Lactobacilli are gram-positive, rod-shaped, facultatively anaerobic, nonsporulating, acid-tolerant, and catalase-negativebacteria witha DNA base composition ...
Objective: an increasing number of studies that are using high-throughput molecular methods are r... more Objective: an increasing number of studies that are using high-throughput molecular methods are rapidly extending our knowledge of gut microbial colonization in preterm infants whose immaturity and requirement for extensive treatment may result in altered colonization process. We aimed to describe the profile of gut microbiota in 50 extremely low birth weight (<1200 g) critically ill infants at three different time points during the first two months of life by using 16S rrNa gene specific sequencing. Patients and Methods: Stool samples were collected at the age of one week, one month and two months. Bacterial community profiling was done using universal amplification of 16S rrNa gene and 454 pyrosequencing. results: The diversity of gut microbiota in preterm neonates in the first week of life was low but increased significantly over two months. The gut microbiota was dominated by facultative anaerobic bacteria (Staphylococcus spp. and Enterobacteriaceae) and lacked colonization with bacteria known to provide resistance against pathogens (Bacteroides, Bifidobacterium, and Lactobacillus) throughout the study. Colonization of Escherichia coli and uncultured Veillionella was positively correlated with maturity. Infants born to mothers with chorioamnionitis had significantly higher bacterial diversity than those without. Conclusions: High prevalence and abundance of potentially pathogenic Enterobacteriaceae and Staphylococcaceae with low prevalence and abundance of colonization resistance providing taxa bifidobacteria, Bacteroides and lactobacilli may lead to high infection risk via microbial translocation from the gut. additionally, our data suggest that maternal chorioamnionitis may have an effect on the diversity of infants' gut microbiota; however, the mechanisms involved remain to be elucidated.
This study aimed to examine the spectrum and time course of gut and nasopharyngeal colonization w... more This study aimed to examine the spectrum and time course of gut and nasopharyngeal colonization with Gram-negative microorganisms , and to define the value of surveillance cultures in predicting late-onset sepsis in neonates admitted to neonatal intensive care units. Nasopharyngeal and rectal swabs were collected on admission and twice weekly thereafter in 278 neonates admitted within the first 72 h of life with risk factors of early-onset sepsis. Sterile body fluid cultures were obtained on admission and subsequently as clinically indicated. Approximately half of the rectal (693/1250, 55%) and nasopharyngeal (558/1153, 48%) samples but only 6% (32/555) of the sterile fluid samples in 26 patients were culture positive for Gramnegative organisms. In total, 2108 invasive and mucosal culture pairs were analysed. The overall sensitivity, specificity, and positive and negative predictive values of a mucosal sample to predict late-onset sepsis were 27%, 66%, 4% and 94%, respectively. Patients with pre-existing colonization with Klebsiella pneumoniae (P ¼ 0.011), Klebsiella oxytoca (P ¼ 0.002), Escherichia coli (P ¼ 0.003), Stenotrophomonas spp. (P ¼ 0.003) and Pseudomonas spp. (P 0.001) were more likely to develop late-onset sepsis. No such association was found for Acinetobacter baumannii, Serratia spp. or Enterobacter cloacae. In conclusion, routine mucosal cultures are inefficient for the prediction of Gram-negative late-onset sepsis in neonatal intensive care units. However, targeted screening for specific organisms in an outbreak (e.g. Klebsiella spp., E. coli, Stenotrophomonas spp. and Pseudomonas spp.) may offer an opportunity to improve infection control measures and enable timely initiation of appropriate antibiotic therapy.
European Journal of Clinical Microbiology & Infectious Diseases, 2010
The purpose of this study was to compare the impact of ampicillin and penicillin used for empiric... more The purpose of this study was to compare the impact of ampicillin and penicillin used for empiric treatment of early onset sepsis (EOS) on initial gut colonization by aerobic and facultative anaerobic microorganisms. A cluster-randomized, two-center, switch-over study was conducted in two paediatric intensive care units in Estonia and included 276 neonates. Rectal swabs were collected twice a week until discharge or day 60. Colonizing microbes were identified on species level and tested for ampicillin resistance (AR). The number of patients colonized with Gram negative microorganisms and Candida spp was similar in both treatment arms but ampicillin resulted in longer colonization duration (CD) of K. pneumonia (p=0.012), AR Serratia spp (p=0.012) and Candida spp (p=0.02) and penicillin in that of AR Acinetobacter spp (p=0.001). As for Gram positive microorganisms penicillin treatment was associated with a greater number of colonized patients and higher CD of Enterococcus spp and S. aureus but lower ones of S. haemolyticus and S. hominis. Influence of ampicillin and penicillin on initial gut colonization is somewhat different but these differences are of low clinical relevance and should not be a limiting step when choosing between these two antibiotics for the empiric treatment of EOS.
Aim: To characterize dynamics of mucosal colonization of neonates by common aerobic Gram negative... more Aim: To characterize dynamics of mucosal colonization of neonates by common aerobic Gram negative species and Candida spp. and to identify independent perinatal, neonatal, and environmental factors influencing the colonization process. Study design: The nasopharyngeal (n = 1145) and rectal (n = 1242) swabs were collected on admission and thereafter twice a week in neonates with risk factors of early onset sepsis (n = 276) admitted within the first 72 h of life. The association between colonization by different microbes and a total of 22 predefined risk factors was assessed using univariate and multiple logistic regression analyses. Results: Throughout the study about half of the patients had rectal (55.8%) or nasopharyngeal colonization (42.8%) with common Gram-negative microorganisms. Colonization dynamics and risk factors were in general similar for a given bacterial species in both mucosal sites; nonfermentative microbes more often found in nasopharyngeal swabs and Enterobacteriaceae in rectal swabs. All organisms except Escherichia coli were influenced by the duration of intensive care unit stay but other risk factors were species specific, perhaps reflecting their mode of acquisition. While colonization by E. coli and Candida albicans was associated with perinatal factors like term birth, vaginal delivery, and breast milk feeding; colonization by Klebsiella pneumoniae, Enteribacter cloacae, Acinetobacter spp. and non-albicans Candida spp. were mostly determined by hospital environment (treatment unit and period, artificial interventions and their duration) and gestation age ≤ 28 weeks. Conclusions: The knowledge of risk factor profiles may permit the development of strategies to prevent heavy colonization and subsequent invasive disease in high risk infants.
Annals of Clinical Microbiology and Antimicrobials, 2009
Background The aim of our study was to compare the presence of the intI1 gene and its association... more Background The aim of our study was to compare the presence of the intI1 gene and its associations with the antibiotic resistance of commensal Escherichia coli strains in children with/without previous antibiotic treatments and elderly hospitalized/healthy individuals. Methods One-hundred-and-fifteen intestinal E. coli strains were analyzed: 30 strains from 10 antibiotic-naive infants; 27 from 9 antibiotic-treated outpatient infants; 30 from 9 healthy elderly volunteers; and 28 from 9 hospitalized elderly patients. The MIC values of ampicillin, cefuroxime, cefotaxime, gentamicin, ciprofloxacin, and sulfamethoxazole were measured by E-test and IntI1 was detected by PCR. Results Out of the 115 strains, 56 (49%) carried class 1 integron genes. Comparing persons without medical interventions, we found in antibiotic-naive children a significantly higher frequency of integron-bearing strains and MIC values than in healthy elderly persons (53% versus 17%; p < 0.01). Evaluating medical i...
The Escherichia coli phylogenetic group B2 with integrons prevails in childhood recurrent urinary... more The Escherichia coli phylogenetic group B2 with integrons prevails in childhood recurrent urinary tract infections. APMIS 2013. The aim of our study was to characterize the phylogenetic groups of Escherichia coli, antibiotic resistance, and containment of class 1 integrons in the first attack of pyelonephritis and in subsequent recurrences in young children. Altogether, 89 urine E. coli isolates from 41 children with urinary tract infection (UTI) were studied for prevalence and persistence of phylogenetic groups by pulsed-field gel electrophoresis (PFGE), antibacterial resistance by minimal inhibitory concentrations (MIC) and class 1 integrons by PCR. Phylogenetic group B2 was most common (57%), followed by D (20%), A (18%) and B1 (5%). Overall resistance to betalactams was 61%, trimethoprimsulfamethoxazole 28%, and was not associated with phylogenetic groups. According to PFGE, the same clonal strain persisted in 77% of patients. The persistence was detected most often in phylogenetic group B2 (70%). Phylogenetic group B2 more often contained class 1 integrons than group A. Integron positive strains had higher MIC values of cefuroxime, cefotaxime, and gentamicin. In conclusion, phylogenetic group B2 was the most common cause of the first episode of pyelonephritis, as well as in case of the persistence of the same strain and contained frequently class 1 integrons in childhood recurrent UTI. An overall frequent betalactam resistance was equally distributed among phylogenetic groups.
Coagulase-negative staphylococci (CoNS) are the leading cause of late-onset sepsis (LOS) in neona... more Coagulase-negative staphylococci (CoNS) are the leading cause of late-onset sepsis (LOS) in neonates. Increasing resistance of CoNS to beta-lactams and aminoglycosides has led to widespread use of vancomycin, which in turn may lead to resistance to vancomycin. Thus, combination therapy of LOS has been advocated. We aimed to determine the interaction of oxacillin and gentamicin against CoNS. In 2005, 34 isolates of oxacillin-and gentamicin-resistant CoNS were obtained from blood samples of neonates with LOS. Combination effect was tested using the checkerboard method, E-test with the other antibiotic incorporated in the medium (E-test-1) and two E-test strips placed in a cross-formation (E-test-2). Of 34 isolates 61.8%, 53% and 73.5% revealed synergy or an additive effect when tested by the checkerboard method, E-test-1 and E-test-2, respectively. Results of all three tests were concordant for six (17.6%) isolates, four showing synergy, and two indifference. Our in vitro results support that combination therapy with penicillinase-resistant penicillin and aminoglycoside can be an alternative to vancomycin.
The high number of mutations in the Omicron variant of SARS-CoV-2 cause its immune escape when co... more The high number of mutations in the Omicron variant of SARS-CoV-2 cause its immune escape when compared to the earlier variants of concern (VOC). At least three vaccine doses are required for the induction of Omicron neutralizing antibodies and further reducing the risk for hospitalization. However, most of the studies have focused on the immediate response after the booster vaccination while the duration of immune response is less known. We here studied longitudinal serum samples from the vaccinated individuals up to three months after their third dose of the BNT162b2 vaccine for their capacity to produce protective antibodies and T cell responses to Wuhan and Omicron variants. After the second dose, the antibody levels to the unmutated spike protein were significantly decreased at three months, and only 4% of the individuals were able to inhibit Omicron spike interaction compared to 47%, 38%, and 14% of individuals inhibiting wild-type, delta, and beta variants’ spike protein. Nin...
Uploads
Papers by Epp Sepp