RESUMEN
BACKGROUND: Before the COVID-19 pandemic there has been a constant increase in antimicrobial resistance (AMR) of Escherichia coli, the most common cause of urinary tract infections and bloodstream infections. The aim of this study was to investigate the impact of the COVID-19 pandemic on extended-spectrum ß-lactamase (ESBL) production in urine and blood E. coli isolates in Finland to improve our understanding on the source attribution of this major multidrug-resistant pathogen. METHODS: Susceptibility test results of 564,233 urine (88.3% from females) and 23,860 blood E. coli isolates (58.8% from females) were obtained from the nationwide surveillance database of Finnish clinical microbiology laboratories. Susceptibility testing was performed according to EUCAST guidelines. We compared ESBL-producing E. coli proportions and incidence before (2018-2019), during (2020-2021), and after (2022) the pandemic and stratified these by age groups and sex. RESULTS: The annual number of urine E. coli isolates tested for antimicrobial susceptibility decreased 23.3% during 2018-2022 whereas the number of blood E. coli isolates increased 1.1%. The annual proportion of ESBL-producing E. coli in urine E. coli isolates decreased 28.7% among males, from 6.9% (average during 2018-2019) to 4.9% in 2022, and 28.7% among females, from 3.0 to 2.1%. In blood E. coli isolates, the proportion decreased 32.9% among males, from 9.3 to 6.2%, and 26.6% among females, from 6.2 to 4.6%. A significant decreasing trend was also observed in most age groups, but risk remained highest among persons aged ≥ 60 years. CONCLUSIONS: The reduction in the proportions of ESBL-producing E. coli was comprehensive, covering both specimen types, both sexes, and all age groups, showing that the continuously increasing trends could be reversed. Decrease in international travel and antimicrobial use were likely behind this reduction, suggesting that informing travellers about the risk of multidrug-resistant bacteria, hygiene measures, and appropriate antimicrobial use is crucial in prevention. Evaluation of infection control measures in healthcare settings could be beneficial, especially in long-term care.
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COVID-19 , Infecciones por Escherichia coli , Escherichia coli , Infecciones Urinarias , beta-Lactamasas , Humanos , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Escherichia coli/enzimología , Finlandia/epidemiología , COVID-19/epidemiología , Femenino , Infecciones por Escherichia coli/epidemiología , Infecciones por Escherichia coli/microbiología , Masculino , Infecciones Urinarias/microbiología , Infecciones Urinarias/epidemiología , Persona de Mediana Edad , beta-Lactamasas/metabolismo , beta-Lactamasas/biosíntesis , Anciano , Adulto , Adolescente , Adulto Joven , Niño , Lactante , Preescolar , Anciano de 80 o más Años , Pruebas de Sensibilidad Microbiana , SARS-CoV-2 , Recién Nacido , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Bacteriemia/epidemiología , Bacteriemia/microbiología , Farmacorresistencia Bacteriana Múltiple , PandemiasRESUMEN
Reproducibility and quality of MALDI-TOF MS spectra are critical in the identification process, however, information on the factors affecting the identification scores are scarce. Here, we studied the influence of various factors during the identification process of human oral Capnocytophaga species. The influence of two incubation times, plate-spotting reproducibility of two examiners, extraction technique, storage period of plates, and different laser repetition rates on the quality of MALDI-TOF MS identification of 34 human Capnocytophaga strains (including C. gingivalis, C. granulosa, C. haemolytica, C. leadbetteri, C. ochracea, C. sputigena, and Capnocytophaga genospecies AHN8471) was examined. The identification rate did not show a significant difference (P = 0.05) between the two incubation times, except that C. haemolytica needed a longer incubation time to be recognized at the genus level. The reproducibility of spotting between two examiners was ensured by following the manufacturer's instructions. At the species level, formic acid extraction improved the identification of species with limited representation in the database, such as C. haemolytica and C. granulosa. The storage of plates for one week decreased the identification scores. No significant difference (P = 0.39) was observed between the 60 Hz and 120 Hz laser repetition rates for identifying Capnocytophaga species to the genus or species level. In conclusion, the MALDI TOF MS offers a reliable Capnocytophaga identification after following the universal protocol, while the formic acid extraction is restricted to species with a limited number of strains in the database.
Asunto(s)
Capnocytophaga , Formiatos , Humanos , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción/métodos , Reproducibilidad de los ResultadosRESUMEN
PURPOSE: Streptococcus pyogenes (mostly termed group A Streptococcus - GAS) is the most important bacterial causative of pharyngitis. However, epidemiology of GAS pharyngitis is not widely established. This study describes GAS pharyngitis cases and emm-type distribution in a prospective study covering over 2 years in two Hospital Districts in Finland. METHODS: A prospective, systematic collection of GAS pharyngitis isolates was conducted between March 2018 and December 2020 in two large Hospital Districts in Finland. Patient characteristics (age, gender) were included if available. All GAS isolates collected were emm typed. RESULTS: Altogether 1320 GAS pharyngitis strains were collected, 904 in the Hospital District 1 (HD1) and 416 in Hospital District 2 (HD2). In HD1, age and gender data were available. Females were overrepresented (58% of all cases). In addition, the age and gender distributions were noted to be significantly different (p < 0.0001) with females having a more uniform distribution until age of 40. emm28 was common among the age group of 20-29-year-olds and emm89 in children under 10 years of age, respectively. In HD1, most of the isolates were collected during winter and autumn months. Significant differences by season in the frequency of emm12, emm89, emm75 and group of "others" were observed. CONCLUSION: Age distribution among GAS pharyngitis cases was significantly different between genders (p < 0.0001). In addition, age group specific and seasonal variations in emm GAS types causing the disease were observed. These findings warrant further investigation, especially for understanding population-based spread of GAS even in more detail.
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Faringitis , Infecciones Estreptocócicas , Niño , Humanos , Femenino , Masculino , Adulto Joven , Adulto , Streptococcus pyogenes , Estudios Prospectivos , Finlandia/epidemiología , Antígenos Bacterianos/genética , Proteínas de la Membrana Bacteriana Externa/genética , Infecciones Estreptocócicas/epidemiología , Infecciones Estreptocócicas/microbiología , Proteínas Portadoras/genética , Faringitis/epidemiología , Faringitis/microbiología , GenotipoRESUMEN
PURPOSE: Streptococcus pyogenes (Group A Streptococcus, GAS) is an important human pathogen that can cause severe invasive (iGAS) infections. Throat carriage has been assumed to possibly lead to hematogenous seeding. Retrospective studies may estimate the incidence of throat carriage in iGAS patients inaccurately. In this study we aimed to gather data on the presence of GAS in the throat among iGAS patients in a prospective setting. METHODS: We conducted a prospective clinical study covering iGAS infections in adult patients in two university hospitals in Finland from June 2018 to July 2020. Recruited patients' throats were swabbed for culture and isothermal amplification tests (IAT) to search for GAS. The study was registered at ClinicalTrials.gov as ID NCT03507101. RESULTS: We enrolled 45 patients. Throat swabs were obtained from 39/45 (87%) patients. Ten patients (22%) had a positive IAT for GAS. They were statistically significantly more likely to be male (9/10 [90%] vs 13/29 [45%], p = .024). Several different emm types caused the iGAS infections. CONCLUSIONS: GAS was frequently observed in throat swabs of patients with iGAS infection. This may suggest that hematogenous seeding from the nasopharynx is a possible portal of entry.
Asunto(s)
Infecciones Estreptocócicas , Streptococcus pyogenes , Adulto , Femenino , Humanos , Masculino , Finlandia/epidemiología , Faringe , Estudios Prospectivos , Estudios Retrospectivos , Infecciones Estreptocócicas/epidemiologíaRESUMEN
Methicillin-resistant Staphylococcus aureus (MRSA) rates have remained relatively low in Finland. In Southwest Finland, however, annual MRSA incidence increased from 12 to 25/100,000 between 2007 and 2016 with spa t172 strain causing one fourth (237/983) of all cases. This provoked us to study the molecular epidemiology of t172-MRSA, aiming to better understand the transmission of this strain type. We combined epidemiological data and whole genome sequencing (WGS) of a set of 64 (27%, 64/237) t172-MRSA isolates covering 10 years. Isolates represented sporadic and index cases of all identified healthcare-associated outbreaks (HAOs) and family clusters (FCs). Among the included 62 isolates, core-genome MLST analysis revealed eight genomic clusters comprising 24 (38.7%) isolates and 38 (61.3%) non-clustered isolates. Cluster 1 comprised ten and the remaining seven clusters two isolates each, respectively. Two epidemiologically distinct HAOs were linked in cluster 1. FCs were involved in all clusters. All strains were associated with epidemic clonal complex CC59. We were able to confirm the spread of several successful t172-MRSA subclones in regional healthcare and the community. WGS complemented routine surveillance by revealing undetected links between t172-MRSA cases. Targeted, WGS-based typing could enhance MRSA surveillance without the need for routine WGS diagnostics.
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Staphylococcus aureus Resistente a Meticilina , Infecciones Estafilocócicas , Humanos , Staphylococcus aureus Resistente a Meticilina/genética , Infecciones Estafilocócicas/epidemiología , Tipificación de Secuencias Multilocus , Epidemiología Molecular , Secuenciación Completa del GenomaRESUMEN
Our aim was to study the detection of group A streptococcus (GAS) with different diagnostic methods in paediatric pharyngitis patients with and without a confirmed viral infection. In this prospective observational study, throat swabs and blood samples were collected from children (age 1-16 years) presenting to the emergency department with febrile pharyngitis. A confirmed viral infection was defined as a positive virus diagnostic test (nucleic acid amplification test [NAAT] and/or serology) together with an antiviral immune response of the host demonstrated by elevated (≥ 175 µg/L) myxovirus resistance protein A (MxA) blood concentration. Testing for GAS was performed by a throat culture, by 2 rapid antigen detection tests (StrepTop and mariPOC) and by 2 NAATs (Simplexa and Illumigene). Altogether, 83 children were recruited of whom 48 had samples available for GAS testing. Confirmed viral infection was diagnosed in 30/48 (63%) children with febrile pharyngitis. Enteroviruses 11/30 (37%), adenoviruses 9/30 (30%) and rhinoviruses 9/30 (30%) were the most common viruses detected. GAS was detected by throat culture in 5/30 (17%) with and in 6/18 (33%) patients without a confirmed viral infection. Respectively, GAS was detected in 4/30 (13%) and 6/18 (33%) by StrepTop, 13/30 (43%) and 10/18 (56%) by mariPOC, 6/30 (20%) and 9/18 (50%) by Simplexa, and 5/30 (17%) and 6/18 (30%) patients by Illumigene. CONCLUSION: GAS was frequently detected also in paediatric pharyngitis patients with a confirmed viral infection. The presence of antiviral host response and increased GAS detection by sensitive methods suggest incidental throat carriage of GAS in viral pharyngitis. WHAT IS KNOWN: â¢The frequency and significance of GAS-virus co-detection are poorly characterised in children with pharyngitis. â¢Detection of a virus and the antiviral host response likely indicates symptomatic infection. WHAT IS NEW: â¢Group A streptococcus (GAS) was detected in 17-43% of the children with confirmed viral pharyngitis depending on the GAS diagnostic method. â¢Our results emphasize the risk of detecting and treating incidental pharyngeal carriage of GAS in children with viral pharyngitis.
Asunto(s)
Faringitis , Infecciones Estreptocócicas , Virosis , Humanos , Niño , Lactante , Preescolar , Adolescente , Antivirales/uso terapéutico , Infecciones Estreptocócicas/diagnóstico , Infecciones Estreptocócicas/tratamiento farmacológico , Streptococcus pyogenes , Faringitis/diagnóstico , Fiebre , Inmunidad , Sensibilidad y EspecificidadRESUMEN
Our objective was to assess the incidence of bacteraemic Aerococcus urinae cases at Helsinki metropolitan area, Finland, from a 6-year study period (2013 to 2018) and to further characterize available cases. The study evaluates the outcome of commonly used cefuroxime treatment and determinate a set of A. urinae in vitro antimicrobial susceptibilities for benzylpenicillin, cefuroxime, and ceftriaxone. Clinical records of A. urinae bacteraemic patients were reviewed retrospectively. Antimicrobial susceptibility testing was performed by disk diffusion, gradient test, and broth microdilution for 139-141 clinical A. urinae isolates. Clinical data of 72/77 patients were combined with the in vitro susceptibilities. We found an increasing number of bacteraemic A. urinae cases within 6-year study period (p = 0.01). The patients were mainly elderly males, and all suffered from underlying conditions. A total of 27.3% of cases (21/77) showed polymicrobial blood cultures. Thirty-day mortality was 22.1%. Cefuroxime was the initial empiric antimicrobial agent given for 66/76 of the patients and treatment outcome was favorable for 20/22 patients who received cefuroxime at least up to day 5. All isolates were susceptible to benzylpenicillin and cefuroxime interpreted by EUCAST breakpoints for Aerococci and PK-PD breakpoints, respectively. MIC determinations gave variable results for ceftriaxone, 2.1-2.9% of the isolates were resistant. To conclude, it seems that the number of bacteraemic Aerococcus urinae cases is increasing at Helsinki metropolitan area, Finland, reflecting the growing blood culture sampling. Clinical A. urinae isolates were susceptible to cefuroxime in vitro. Treatment data indicate that empirical cefuroxime started for possibly urinary tract -derived community-acquired bacteraemia covers A. urinae.
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Aerococcus , Bacteriemia , Infecciones por Bacterias Grampositivas , Anciano , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Bacteriemia/microbiología , Ceftriaxona/uso terapéutico , Cefuroxima/farmacología , Cefuroxima/uso terapéutico , Susceptibilidad a Enfermedades , Finlandia/epidemiología , Infecciones por Bacterias Grampositivas/tratamiento farmacológico , Infecciones por Bacterias Grampositivas/epidemiología , Infecciones por Bacterias Grampositivas/microbiología , Humanos , Masculino , Pruebas de Sensibilidad Microbiana , Estudios RetrospectivosRESUMEN
BACKGROUND: Four new variants of Chlamydia trachomatis (nvCTs), detected in several countries, cause false-negative or equivocal results using the Aptima Combo 2 assay (AC2; Hologic). We evaluated the clinical sensitivity and specificity, as well as the analytical inclusivity and exclusivity of the updated AC2 for the detection of CT and Neisseria gonorrhoeae (NG) on the automated Panther system (Hologic). METHODS: We examined 1004 clinical AC2 samples and 225 analytical samples spiked with phenotypically and/or genetically diverse NG and CT strains, and other potentially cross-reacting microbial species. The clinical AC2 samples included CT wild type (WT)-positive (n = 488), all four described AC2 diagnostic-escape nvCTs (n = 170), NG-positive (n = 214), and CT/NG-negative (n = 202) specimens. RESULTS: All nvCT-positive samples (100%) and 486 (99.6%) of the CT WT-positive samples were positive in the updated AC2. All NG-positive, CT/NG-negative, Trichomonas vaginalis (TV)-positive, bacterial vaginosis-positive, and Candida-positive AC2 specimens gave correct results. The clinical sensitivity and specificity of the updated AC2 for CT detection was 99.7 and 100%, respectively, and for NG detection was 100% for both. Examining spiked samples, the analytical inclusivity and exclusivity were 100%, i.e., in clinically relevant concentrations of spiked microbe. CONCLUSIONS: The updated AC2, including two CT targets and one NG target, showed a high sensitivity, specificity, inclusivity and exclusivity for the detection of CT WT, nvCTs, and NG. The updated AC2 on the fully automated Panther system offers a simple, rapid, high-throughput, sensitive, and specific diagnosis of CT and NG, which can easily be combined with detection of Mycoplasma genitalium and TV.
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Infecciones por Chlamydia/diagnóstico , Chlamydia trachomatis/genética , Técnicas de Amplificación de Ácido Nucleico/métodos , Análisis de Secuencia de ARN/métodos , Candida/genética , Candidiasis/diagnóstico , Candidiasis/microbiología , Infecciones por Chlamydia/microbiología , Reacciones Cruzadas , Femenino , Gonorrea/diagnóstico , Gonorrea/microbiología , Humanos , Neisseria gonorrhoeae/genética , ARN Bacteriano/genética , ARN Ribosómico 23S/genética , Sensibilidad y Especificidad , Tricomoniasis/diagnóstico , Tricomoniasis/parasitología , Trichomonas vaginalis/genéticaRESUMEN
OBJECTIVES: Accurte diagnostic methods are crucial for the detection of extended-spectrum ß-lactamase-producing Enterobacterales (ESBL-E). Besides culture-based gold-standard methods, new molecular gene detection tests are reaching the market. The aim of this study was to investigate the performance of the direct quantitative PCR (qPCR)-based methods Check-Direct ESBL and CPE Screen for BD MAXTM in relation to traditional culture-based methods for detection of ESBL-E faecal carriage. METHODS: Faecal samples were collected from healthy adult volunteers. Samples were cultured on chromogenic ESBL agar plates and were screened for ESBL-producing Escherichia coli and Klebsiella pneumoniae. Confirmed ESBL- and AmpC-producing isolates were further analysed using whole-genome sequencing. In addition, faecal samples were analysed using Check-Direct ESBL and CPE Screen for BD MAXTM and the results were compared with the gold-standard culture-based method. RESULTS: Of 176 faecal samples examined, 11 (6.3%) grew ESBL-producing E. coli or K. pneumoniae isolates. Among 173 analysed samples, Check-Direct ESBL Screen for BD MAXTM detected 22 (12.7%) ESBL-positive samples. No carbapenemase-producing isolates were detected. Two culture-positive samples remained negative with Check-Direct ESBL Screen for BD MAXTM. Culture-negative but qPCR-positive discrepancy was observed in 12 samples (6.9%). Altogether, concordant results were obtained for 158 samples (91.3%; 9 positive and 149 negative). CONCLUSION: Check-Direct ESBL Screen for BD MAXTM is a fast screening method for ESBL carriage. However, several discrepant results were observed, which hinders interpretation. More clinical samples should be tested in combination with culture to evaluate the true benefits of this method.
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Infecciones por Escherichia coli , Klebsiella pneumoniae , Adulto , Escherichia coli/genética , Heces , Humanos , Klebsiella pneumoniae/genética , beta-Lactamasas/genéticaRESUMEN
The incidence of invasive group A streptococcal (GAS) infections has shown a fluctuating but increasing trend in Finland. The impact of infectious diseases specialist consultation (IDSC) on the antimicrobial therapy of GAS bacteremia has not been studied earlier. A retrospective study on adult GAS bacteremia in The Hospital District of Southwest Finland (HDSWF) was conducted from 2007 to 2018. Data on incidence of bacteremic GAS cases were gathered from the National Infectious Disease Register. Clinical data were obtained by reviewing the electronic patient records. The overall incidence of GAS bacteremia in HDSWF was 3.52/100,000, but year-to-year variation was observed with the highest incidence of 7.93/100,000 in 2018. A total of 212 adult GAS bacteremia cases were included. A record of IDSC was found (+) in 117 (55.2%) cases, not found (-) in 71 (33.5%) cases and data were not available in 24 (11.3%) cases. Among IDSC+ cases, 57.3% were on penicillin G treatment whereas in the group IDSC- only 22.5%, respectively (OR = 4.61, 95% CI 2.37-8.97; p < 0.001). The use of clindamycin as adjunctive antibiotic was more common among IDSC+ (54.7%) than IDSC- (21.7%) (OR = 4.51, 95% CI 2.29-8.87; p < 0.001). There was an increasing trend in incidence of GAS bacteremia during the study period. Narrow-spectrum beta-lactam antibiotics were chosen, and adjunctive clindamycin was more commonly used, if IDSC took place. This highlights the importance of availability of IDSC but calls for improved practice among infectious diseases specialists by avoiding combination therapy with clindamycin in non-severe invasive GAS infections.
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Antibacterianos/uso terapéutico , Bacteriemia/epidemiología , Bacteriemia/microbiología , Derivación y Consulta/estadística & datos numéricos , Infecciones Estreptocócicas/tratamiento farmacológico , Infecciones Estreptocócicas/microbiología , Streptococcus pyogenes/aislamiento & purificación , Adulto , Anciano , Antibacterianos/farmacología , Bacteriemia/tratamiento farmacológico , Clindamicina/farmacología , Clindamicina/uso terapéutico , Farmacorresistencia Bacteriana , Quimioterapia Combinada , Femenino , Finlandia/epidemiología , Humanos , Incidencia , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Estudios Retrospectivos , Infecciones Estreptocócicas/epidemiología , Streptococcus/efectos de los fármacos , Streptococcus/aislamiento & purificación , Streptococcus pyogenes/efectos de los fármacos , beta-Lactamas/farmacología , beta-Lactamas/uso terapéuticoRESUMEN
The incidence of methicillin-resistant Staphylococcus aureus (MRSA) has increased sharply in Hospital District of Southwest Finland (HD). To understand reasons behind this, a retrospective, population-based study covering 10 years was conducted. All new 983 MRSA cases in HD from January 2007 to December 2016 were analysed. Several data sources were used to gather background information on the cases. MRSA cases were classified as healthcare-associated (HA-MRSA), community-associated (CA-MRSA), and livestock contact was determined (livestock-associated MRSA, LA-MRSA). Spa typing was performed to all available strains. The incidence of MRSA doubled from 12.4 to 24.9 cases/100000 persons/year. The proportion of clinical infections increased from 25 to 32% in the 5-year periods, respectively, (p < 0.05). The median age decreased from 61 years in 2007 to 30 years in 2016. HA-MRSA accounted for 68% of all cases, of which 32% associated with 26 healthcare outbreaks. The proportion of CA-MRSA cases increased from 13% in 2007 to 43% in 2016. Of CA-MRSA cases, 43% were among family clusters, 32% in immigrants and 4% were LA-MRSA. The Gini-Simpson diversity index for spa types increased from 0.86 to 0.95 from the first to the second 5-year period. The proportion of a predominant strain t172 decreased from 43% in 2009 to 7% in 2016. The rise in the proportion of CA-MRSA, the switch to younger age groups, the complexity of possible transmission routes and the growing spa-type diversity characterize our current MRSA landscape. This creates challenges for targeted infection control measures, demanding further studies.
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Infecciones Comunitarias Adquiridas/epidemiología , Infección Hospitalaria/epidemiología , Staphylococcus aureus Resistente a Meticilina/clasificación , Staphylococcus aureus Resistente a Meticilina/aislamiento & purificación , Infecciones Estafilocócicas/epidemiología , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Animales , Portador Sano/epidemiología , Portador Sano/microbiología , Niño , Preescolar , Infecciones Comunitarias Adquiridas/microbiología , Infección Hospitalaria/microbiología , Femenino , Finlandia/epidemiología , Humanos , Lactante , Recién Nacido , Ganado/microbiología , Masculino , Staphylococcus aureus Resistente a Meticilina/genética , Persona de Mediana Edad , Epidemiología Molecular , Tipificación Molecular , Estudios Retrospectivos , Infecciones Estafilocócicas/microbiología , Adulto JovenRESUMEN
In 2019, more than 200 cases of Chlamydia trachomatis negative/equivocal by the Aptima Combo 2 assay (AC2, target: 23S rRNA) with slightly elevated relative light units (RLUs), but positive by the Aptima Chlamydia trachomatis assay (ACT, target: 16S rRNA) have been detected in Finland To identify the cause of the AC2 CT false-negative specimens, we sequenced parts of the CT 23S rRNA gene in 40 specimens that were AC2 negative/equivocal but ACT positive. A single nucleotide polymorphism (SNP; C1515T in the C. trachomatis 23S rRNA gene) was revealed in 39 AC2/ACT discordant specimens. No decrease in the number of mandatorily notified C. trachomatis cases was observed nationally in Finland in 2010-2019. When RLUs obtained for AC2 negative specimens were retrospectively evaluated in 2011-2019, a continuous increase in the proportion of samples with RLUs 10-19 was observed since 2014, and a slight increase in the proportion of samples with RLUs 20-84 in 2017-2019, indicating that the Finnish new variant of C. trachomatis might have been spreading nationally for several years. This emphasizes that careful surveillance of epidemiology, positivity rate and test performance are mandatory to detect any changes affecting detection of infections.
RESUMEN
Since February 2019, over 160 Chlamydia trachomatis (CT) cases testing negative or equivocal by Aptima Combo 2 (AC2) but positive by Aptima CT test run with Panther instruments occurred in Finland. The AC2 test targets chlamydial 23S rRNA while the CT test targets 16S rRNA. Sequencing of 10 strains revealed a nucleotide substitution in 23S rRNA. The significance of this for the failure of the AC2 test to detect the variant is not yet known.
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Infecciones por Chlamydia/diagnóstico , Infecciones por Chlamydia/genética , Chlamydia trachomatis/genética , Adolescente , Adulto , Técnicas Bacteriológicas/métodos , Técnicas Bacteriológicas/normas , Infecciones por Chlamydia/epidemiología , Chlamydia trachomatis/aislamiento & purificación , Reacciones Falso Negativas , Femenino , Finlandia/epidemiología , Humanos , Masculino , Persona de Mediana Edad , Juego de Reactivos para Diagnóstico/normas , Adulto JovenRESUMEN
Urinary tract infections (UTIs) are a common problem worldwide. The most prevalent causative pathogen of UTI is Escherichia coli, focus of this study. The current golden standard for detecting UTI is bacterial culture, creating a major workload for hospital laboratories - cost-effective and rapid mass screening of patient samples is needed. Here we present an alternative approach to screen patient samples with a single-step assay utilising time-resolved luminescence and luminescence modulating biosensing phages. Filamentous phage M13 was biopanned for binding luminescence quenching metal (copper) and further E. coli. The screening assay luminescence modulation was further enhanced by selecting right chemical environment for the functioning phage clones. Semi-specific interaction between phage, target bacteria and metal was detected by modulation in the signal of a weakly chelating, easily quenchable lanthanide complex. In the presence of the target pathogen, the phages collected quenching metal from solution to the bacterial surface changing the quenching effect on the lanthanide label and thus modulating the signal. Our method was compared with the bacterial culture data obtained from 70 patient samples. The developed proof-of-principle screening assay showed sensitivity and a specificity at the 90% mark when compared to culture method although some samples had high turbidity and even blood. The detection limit of E. coli was in the range of 1000-10 000 colony forming units/mL. Untreated urine sample was screened and time-resolved luminescence signal result was achieved within 10â¯min in a single incubation step.
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Bacteriófago M13/química , Técnicas Biosensibles/métodos , Escherichia coli/aislamiento & purificación , Orina/microbiología , Bacteriófago M13/metabolismo , Cobre/química , Humanos , Elementos de la Serie de los Lantanoides/química , Mediciones Luminiscentes , Infecciones Urinarias/diagnóstico , Infecciones Urinarias/microbiologíaRESUMEN
Objectives: To examine performance of EUCAST disc diffusion and supplementary MIC methods for detection of Enterobacteriaceae with reduced susceptibility to meropenem using EUCAST screening recommendations. Methods: Sixty-one Nordic laboratories delivered data on EUCAST disc diffusion (n = 61), semi-automated meropenem MIC (n = 23; VITEK2, n = 20 and Phoenix, n = 3) and gradient meropenem MIC (n = 58) methods. The strains (n = 27) included the major carbapenemase classes (A, n = 4; B, n = 9; D, n = 6) involved in the global spread of carbapenemase-producing Enterobacteriaceae (CPE) and non-CPE strains (n = 8) covering a range of broth microdilution (BMD) meropenem MICs. Results: A triplicate Klebsiella variicola (meropenem MIC 0.5 mg/L) harbouring OXA-48 and Escherichia coli ATCC 25922 showed an overall good precision. Meropenem zone diameters below the EUCAST screening cut-off (<27 mm) were reported for strains with MIC ≥1 mg/L (n = 21), irrespective of resistance mechanism. For three strains (MIC = 0.5 mg/L) with OXA-48/-181, eight laboratories provided meropenem zone diameters above the screening cut-off. Very major errors (VMEs) were not observed. The overall distributions of major errors (MEs) and minor errors (mEs) were 9% and 36% (disc diffusion), 26% and 18% (VITEK2) and 7% and 20% (gradient MIC), respectively. Differences in ME and mE distributions between disc diffusion and MIC gradient tests compared with semi-automated methods were significant (P < 0.0001), using BMD MICs as a reference for categorization. Conclusions: The EUCAST disc diffusion method is a robust method to screen for CPE but isolates with meropenem MICs <1 mg/L pose challenges. The high ME rate in semi-automated methods might deter appropriate use of carbapenems in CPE infections with limited therapeutic options.
Asunto(s)
Antibacterianos/farmacología , Enterobacteriaceae Resistentes a los Carbapenémicos/efectos de los fármacos , Pruebas Antimicrobianas de Difusión por Disco/normas , Enterobacteriaceae/efectos de los fármacos , Meropenem/farmacología , Pruebas de Sensibilidad Microbiana/normas , Proteínas Bacterianas , Enterobacteriaceae Resistentes a los Carbapenémicos/aislamiento & purificación , Carbapenémicos/farmacología , Técnicas de Laboratorio Clínico/estadística & datos numéricos , Enterobacteriaceae/aislamiento & purificación , Escherichia coli/efectos de los fármacos , Humanos , Klebsiella/efectos de los fármacos , Pruebas de Sensibilidad Microbiana/métodos , beta-LactamasasRESUMEN
Colistin resistance mediated by mobile mcr-1 gene has raised concern during the last years. After steep increase in mcr-1 reports, other mcr-gene variants (mcr-2 to mcr-5) have been revealed as well. In 2016, a clinical study was conducted on asymptomatic stool carriage of extended spectrum beta-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae among Finnish adults. All suspected ESBL producing bacterial isolates were first tested by phenotypic ESBL-confirmation methods, and then further analyzed with whole genome sequencing to identify the resistance genes. We found one study subject carrying a colistin resistant E. coli with a transferrable mcr-1 gene. This multi-drug resistant isolate, although initially suspected to be an ESBL producer, did not carry any ESBL genes, but was proven to carry several other resistance genes by using whole genome sequencing. Sequence type was ST93. The mcr-1 gene was connected to IncX4 plasmid which suggests that the colistin resistance gene locates in the respective plasmid. Here, we report the finding of a mcr-1 harboring human E. coli isolate from Finland. Clinical antimicrobial resistance (AMR) rates are low in Finland, and mobile colistin resistance has not been reported previously. This highlights the importance of AMR surveillance also in populations with low levels of resistance.
Asunto(s)
Colistina/farmacología , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Farmacorresistencia Bacteriana/genética , Finlandia , Humanos , Plásmidos , Estudios Prospectivos , beta-Lactamasas/genéticaRESUMEN
Reliable distinction of Streptococcus pneumoniae and viridans group streptococci is important because of the different pathogenic properties of these organisms. Differentiation between S. pneumoniae and closely related Sreptococcusmitis species group streptococci has always been challenging, even when using such modern methods as 16S rRNA gene sequencing or matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. In this study, a novel algorithm combined with an enhanced database was evaluated for differentiation between S. pneumoniae and S. mitis species group streptococci. One hundred one clinical S. mitis species group streptococcal strains and 188 clinical S. pneumoniae strains were identified by both the standard MALDI Biotyper database alone and that combined with a novel algorithm. The database update from 4,613 strains to 5,627 strains drastically improved the differentiation of S. pneumoniae and S. mitis species group streptococci: when the new database version containing 5,627 strains was used, only one of the 101 S. mitis species group isolates was misidentified as S. pneumoniae, whereas 66 of them were misidentified as S. pneumoniae when the earlier 4,613-strain MALDI Biotyper database version was used. The updated MALDI Biotyper database combined with the novel algorithm showed even better performance, producing no misidentifications of the S. mitis species group strains as S. pneumoniae All S. pneumoniae strains were correctly identified as S. pneumoniae with both the standard MALDI Biotyper database and the standard MALDI Biotyper database combined with the novel algorithm. This new algorithm thus enables reliable differentiation between pneumococci and other S. mitis species group streptococci with the MALDI Biotyper.
Asunto(s)
Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción/métodos , Streptococcus mitis/clasificación , Streptococcus pneumoniae/clasificación , Algoritmos , Bases de Datos de Compuestos Químicos , Humanos , Infecciones Estreptocócicas/microbiología , Streptococcus mitis/química , Streptococcus mitis/aislamiento & purificación , Streptococcus pneumoniae/química , Streptococcus pneumoniae/aislamiento & purificaciónRESUMEN
OBJECTIVES: Besides group A streptococcus (GAS), microbial causes of pharyngitis in children are not well known. We aimed to document the viral and bacterial aetiology of pharyngitis and to assess the pathogenic role of viruses by determining the myxovirus resistance protein A (MxA) in the blood as a marker of interferon response. METHODS: In this prospective observational study, throat swabs and blood samples were collected from children (age 1-16 years) presenting to the emergency department with febrile pharyngitis. Microbial cause was sought by bacterial culture, polymerase chain reaction, and serology. Blood MxA level was determined. RESULTS: A potential pathogen was detected in 88% of 83 patients: GAS alone in 10%, GAS and viruses in 13%, group C or G streptococci alone in 2% and together with viruses in 3%, and viruses alone in 59% of cases. Enteroviruses, rhinoviruses, and adenoviruses were the most frequently detected viruses. Blood MxA levels were higher in children with viral (880 [245-1250] µg/L; median [IQR]) or concomitant GAS-viral (340 [150-710] µg/L) than in those with sole GAS (105 [80-160] µg/L) infections. CONCLUSIONS: Detection of respiratory viruses simultaneously with elevated blood MxA levels supports the causative role of viruses in the majority of children with pharyngitis.
Asunto(s)
Biomarcadores/sangre , Proteínas de Resistencia a Mixovirus/sangre , Faringitis/diagnóstico , Faringitis/virología , Virosis/diagnóstico , Adolescente , Niño , Preescolar , Femenino , Fiebre , Humanos , Lactante , Interferones/inmunología , Masculino , Proteínas de Resistencia a Mixovirus/aislamiento & purificación , Faringitis/etiología , Faringitis/microbiología , Faringe/microbiología , Faringe/virología , Reacción en Cadena de la Polimerasa , Estudios Prospectivos , Pruebas Serológicas , Infecciones Estreptocócicas/diagnóstico , Infecciones Estreptocócicas/microbiología , Streptococcus pyogenes/aislamiento & purificación , Virosis/virología , Virus/aislamiento & purificaciónRESUMEN
This paper describes an integrated microsystem for rapid separation, enrichment, and detection of bacteria from blood, addressing the unmet clinical need for rapid sepsis diagnostics. The blood sample is first processed in an acoustophoresis chip, where red blood cells are focused to the center of the channel by an acoustic standing wave and sequentially removed. The bacteria-containing plasma proceeds to a glass capillary with a localized acoustic standing wave field where the bacteria are trapped onto suspended polystyrene particles. The trapped bacteria are subsequently washed while held in the acoustic trap and released into a polymer microchip containing dried polymerase chain reaction (PCR) reagents, followed by thermocycling for target sequence amplification. The entire process is completed in less than 2 h. Testing with Pseudomonas putida spiked into whole blood revealed a detection limit of 1000 bacteria/mL for this first-generation analysis system. In samples from septic patients, the system was able to detect Escherichia coli in half of the cases identified by blood culture. This indicates that the current system detects bacteria in patient samples in the upper part of the of clinically relevant bacteria concentration range and that a further developed acoustic sample preparation system may open the door for a new and faster automated method to diagnose sepsis.