RESUMEN

BACKGROUND: The microbial community composition of urban environments is primarily determined by human activity. The use of metagenomics to explore how microbial communities are shaped in a city provides a novel input that can improve decisions on public health measures, architectural design, and urban resilience. Of note, the sewage system in a city acts as a complex reservoir of bacteria, pharmaceuticals, and antimicrobial resistant (AMR) genes that can be an important source of epidemiological information. Hospital effluents are rich in patient-derived bacteria and can thus readily become a birthplace and hotspot reservoir for antibiotic resistant pathogens which are eventually incorporated into the environment. Yet, the scope to which nosocomial outbreaks impact the urban environment is still poorly understood. RESULTS: In this work, we extensively show that different urban waters from creeks, beaches, sewage spillways and collector pipes enclose discrete microbial communities that are characterized by a differential degree of contamination and admixture with human-derived bacteria. The abundance of human bacteria correlates with the abundance of AMR genes in the environment, with beta-lactamases being the top-contributing class to distinguish low vs. highly-impacted urban environments. Indeed, the abundance of beta-lactamase resistance and carbapenem resistance determinants in the urban environment significantly increased in a 1-year period. This was in line with a pronounced increase of nosocomial carbapenem-resistant infections reported during the same period that was mainly driven by an outbreak-causing, carbapenemase-producing Klebsiella pneumoniae (KPC) ST-11 strain. Genome-resolved metagenomics of urban waters before and after this outbreak, coupled with high-resolution whole-genome sequencing, confirmed the dissemination of the ST-11 strain and a novel KPC megaplasmid from the hospital to the urban environment. City-wide analysis showed that geospatial dissemination of the KPC megaplasmid in the urban environment inversely depended on the sewage system infrastructure. CONCLUSIONS: We show how urban metagenomics and outbreak genomic surveillance can be coupled to generate relevant information for infection control, antibiotic stewardship, and pathogen epidemiology. Our results highlight the need to better characterize and understand how human-derived bacteria and antimicrobial resistance disseminate in the urban environment to incorporate this information in the development of effluent treatment infrastructure and public health policies. Video Abstract.

Asunto(s)

RESUMEN

Resumen Los objetivos de este estudio fueron determinar el desempeño del panel BCID de FilmArray® y establecer el impacto de estos resultados en el tratamiento antimicrobiano de pacientes con bacteriemia en 11 hospitales de Latinoamérica. Se incluyeron 397 episodios de bacteriemia y se documentaron 551 microorganismos aislados de hemocultivos. La identificación microbiana fue correcta en el 91,4% (504/551) de los aislados y en el 98,6% (504/511) si se consideran solo los microorganismos incluidos en el panel BCID. La sensibilidad en la detección de los genes mecA, vanA/B y blaKPC fue del 100% y la especificidad fue del 97%, 100% y 99,6% respectivamente. La notificación temprana del resultado permitió cambios terapéuticos en 242 episodios (60,9%). El panel BCID es un método confiable y rápido para la detección de mecanismos críticos de resistencia y de los microorganismos más frecuentemente aislados de bacteriemias y permite la optimización temprana del tratamiento antimicrobiano.

Abstract The objectives of this study were to determine the performance of the BCID panel and to establish the impact of these results on the antimicrobial treatment of patients with bacteremia in 11 hospitals in Latin America. Three hundred and ninety-seven episodes of bacteremia were included and 551 microorganisms isolated from blood cultures were documented. Microbial identification was correct in 91.4% (504/551) of the isolates and in 98.6% (504/511) if only the microorganisms included in the BCID panel are considered. The sensitivity in the detection of the genes mecA, vanA/B and blaKPC was 100% and the specificity was 97%, 100% and 99.6% respectively. Early notification of the outcome allowed therapeutic changes in 242 episodes (60.9%). The BCID panel is a reliable and rapid method for the detection of critical resistance mechanisms and of the microorganisms most frequently isolated from bacteremia and it enables early optimisation of antimicrobial treatment.

Resumo Os objetivos deste estudo foram determinar o desempenho do painel BCID do FilmArray® e estabelecer o impacto desses resultados no tratamento antimicrobiano de pacientes com bacteremia em 11 hospitais da América Latina. Trezentos e noventa e sete episódios de bacteremia foram incluídos e 551 microrganismos isolados de hemoculturas foram documentados. A identificação microbiana foi correta em 91,4% (504/551) dos isolados e em 98,6% (504/511) considerando apenas os microrganismos incluídos no painel BCID. A sensibilidade na detecção dos genes mecA, vanA/B e blaKPC foi de 100% e a especificidade foi de 97%, 100% e 99,6% respectivamente. A notificação precoce do desfecho permitiu mudanças terapêuticas em 242 episódios (60,9%). O painel BCID é um método confiável e rápido para a detecção de mecanismos críticos de resistência e dos microrganismos mais frequentemente isolados da bacteremia e permite a otimização precoce do tratamento antimicrobiano.

Asunto(s)

RESUMEN

OBJECTIVES: The emergence and spread of carbapenem resistant clones is of major concern for global health. This study aimed to characterize the first detected Klebsiella pneumoniae ST15 harboring the epidemic carbapenemase OXA-48 in South America. METHODS: During a routine colonization screening with carbapenem-resistant bacteria, one K. pneumoniae strain (CGHM01) was isolated from the urine of a hospitalized patient suffering from a neurodegenerative disease in Uruguay. We used long-read whole-genome sequencing and a phylogenomic approach to characterize the emergence of K. pneumoniae CGHM01. RESULTS: K. pneumoniae CGHM01 is a multi-drug resistant strain carrying an IncL/M plasmid that encodes the carbapenemase gene blaOXA-48 within the Tn1999.2 transposon. Also, it carries an IncR plasmid harboring a class I integron with an array of antibiotic resistance genes including the extended-spectrum beta-lactamase blaCTX-M-15. Two copies of blaCTX-M-15 were also inserted in different positions of the chromosome. CGHM01 belongs to a ST15 sublineage that likely originated in continental Spain around 2012. CONCLUSIONS: The asymptomatic carriage of this strain in the urinary tract warns of difficulties for detection and reporting of emerging carbapenem-resistant clones in new geographic areas where these are not endemic.

Asunto(s)

RESUMEN

Resumen: Introducción: el inicio temprano de la antibioticoterapia adecuada en infecciones graves se asocia con reducción de la mortalidad. La identificación precoz del microorganismo es fundamental para realizar un tratamiento dirigido y disminuir la terapéutica inicial inapropiada. Objetivo: valorar la utilidad de una técnica de biología molecular por amplificación de ácidos nucleicos mediante reacción en cadena de polimerasa en tiempo real para diagnóstico microbiológico temprano y adecuación de la antibioticoterapia en pacientes con neumonías graves. Metodología: estudio retrospectivo observacional llevado a cabo en la unidad de cuidados intensivos del Hospital Maciel. Se analizaron muestras respiratorias de pacientes con diagnóstico o sospecha de neumonía. Se compararon los resultados microbiológicos obtenidos por técnicas convencionales y por biología molecular multiplex (panel neumonía). Resultados: se incluyeron 53 muestras obtenidas de 51 pacientes. El multiplex detectó al menos un microorganismo en 38 (71,7%) muestras frente a 30 (56.6%) desarrollos en cultivos tradicionales. La mayoría de las muestras se obtuvieron bajo antibioticoterapia previa (86.8%). El panel neumonía mostró un porcentaje de concordancia positiva combinado de 100% y un porcentaje de concordancia negativa del 94% para la identificación bacteriana en comparación con los métodos microbiológicos tradicionales. En 27 (51%) casos el resultado del panel de neumonía determinó un cambio en la conducta terapéutica. Conclusiones: la técnica de PCR permite la identificación temprana de microorganismos causantes de neumonía optimizando la terapéutica empírica inicial y racionalizando el uso de antimicrobianos. Un panel negativo aleja el planteo de infección respiratoria a gérmenes habituales y permite considerar diagnósticos diferenciales en cuanto a foco y/o etiología.

Summary: Introduction: the early initiation of the adequate antibiotic therapy in severe infections is associated to a reduction in mortality. Early identification of the microorganism is essential to define directed therapy and decrease the initial inadequate treatment. Objective: to assess usefulness of a molecular biology technique by nucleic acid amplification through a polymerase chain reaction in real time for an early microbiological diagnosis and correction of the antibiotic therapy in patients with severe pneumonias. Method: retrospective, observational study conducted in the intensive care unit of Maciel Hospital. The respiratory samples of patients with a diagnosis of pneumonia or suspicious to have pneumonia were analyzed. The microbiological results obtained were compared using conventional techniques and multiplex molecular biology (pneumonia panel). Results: 53 samples obtained from 51 patients were included in the study. Multiplex detected at least one microorganism in 38 (71.7%) samples compared to 30 (56.6%) in traditional cultures. Most samples were obtained under the previous antibiotic therapy (86.8%). The pneumonia panel showed a combined positive agreement percentage of 100% and a negative agreement of 94% for the identification of bacteria when compared to the traditional microbiological methods. In 27 cases (51%) the pneumonia panel results determined changing the therapeutic behavior. Conclusions: the PCR technique allows for the early identification of microorganisms causing pneumonia, thus optimizing initial empirical therapy and rationalizing the use of antibiotics. A negative panel reduces the suspicion of a respiratory infection caused by the usual germs and enables considering differential diagnosis in terms of etiology or cause.

Resumo: Introdução: o início precoce da antibioticoterapia adequada em infecções graves está associado à redução da mortalidade. A identificação precoce do microrganismo é essencial para realizar o tratamento dirigido e reduzir o uso inicial inadequado de antimicrobianos. Objetivo: avaliar a utilidade de uma técnica de biologia molecular para amplificação de ácidos nucleicos por reação em cadeia da polimerase em tempo real para diagnóstico microbiológico precoce e adequação da antibioticoterapia em pacientes com pneumonia grave. Metodologia: estudo observacional retrospectivo realizado na unidade de terapia intensiva do Hospital Maciel. Amostras respiratórias de pacientes com diagnóstico ou suspeita de pneumonia foram analisadas. Os resultados microbiológicos obtidos por técnicas convencionais e por biologia molecular multiplex (painel de pneumonia) foram comparados. Resultados: foram incluídas 53 amostras obtidas de 51 pacientes. O multiplex detectou pelo menos um microrganismo em 38 (71,7%) amostras em comparação com 30 (56,6%) usando culturas tradicionais. A maioria das amostras foi obtida com antibioticoterapia prévia (86,8%). O painel de pneumonia mostrou uma concordância percentual positiva combinada de 100% e uma concordância percentual negativa de 94% para identificação bacteriana em comparação com métodos microbiológicos tradicionais. Em 27 (51%) casos, o resultado do painel de pneumonia determinou mudança no comportamento terapêutico. Conclusões: a técnica de PCR permite a identificação precoce de microrganismos causadores de pneumonia, otimizando a terapia empírica inicial e racionalizando o uso de antimicrobianos. Um painel negativo afasta a suspeita de infecção respiratória pelos germes usuais e permite considerar diagnósticos diferenciais em termos de foco e/ou etiologia.

Asunto(s)

RESUMEN

Carbapenemase production in Enterobacterales clinical isolates is a global threat. Multi-drug resistant Klebsiella pneumoniae harboring carbapenemases are a major concern among the hospital settings in Latin America. Aim: The aim of this study was to analyze the genetic relatedness between three isolates of K. pneumoniae recovered from one patient in the same bacteriological round on the same day, which exhibited different susceptibility profiles to carbapenems (CP) and to colistin (Col). Isolates' profiles were as follows (susceptible-S/resistant-R): CPS/ColR, CPR/ColR, and CPR/ColS. Pulse-field gel electrophoresis, multilocus sequence typing, and whole genome sequencing were performed. Conjugation assays were carried out and PCR determination in transconjugants (Tcs) was made for: blaCTX-M-groups, blaNDM, blaKPC, blaTEM, qnr alleles, aac(6')Ib-cr, ermB, and plasmid incompatibility groups (Inc). Results: All isolates belonged to the same clone, to ST258 and harbored blaCTX-M-14, blaCTX-M-15, qnrA1, qnrB1, aac(6')Ib-cr, and wzi154 (capsule-locus KL107). One isolate had additional wzi gene, wzi109 (capsule-locus KL36). In CPR isolates, the pattern was explained for blaNDM-1 or blaNDM-1/blaKPC-2 presence, and in ColR for IS5-like element insertion in mgrB at different positions. Co-mobilization of blaNDM-1/qnrA1 was associated to a different plasmid Inc (A/C-FII) in both blaNDM-1 donors. Mobilization of blaCTX-M-14 was related to IncI1 in one donor. Conclusion: These findings highlight the potential plasticity of ST258 K. pneumoniae clone. To the best of our knowledge, this is the first description of blaNDM-1/blaKPC-2-producing K. pneumoniae ST258 in Latin America.

Asunto(s)

RESUMEN

OBJECTIVE: This report described the first Escherichia coli (E. coli) isolates harbouring mcr-1 in Uruguay. METHODS: Three E. coli isolates were obtained from blood, urine and rectal swabs from different patients in two hospitals. Extended-spectrum ß-lactamases (ESBL), plasmid-encoded (pAmpC) ß-lactamases, plasmid-mediated quinolone resistance (PMQR) genes, class 1 integrons, and mcr-1, mcr-2 and mcr-3 were sought and characterised in three E. coli isolates. Transfer of resistance determinants was assessed by conjugation. Clonality was analysed by multilocus sequence typing. RESULTS: All isolates were categorised as being colistin-resistant and the mcr-1 gene was detected. Two isolates were also resistant to oxyimino cephalosporins: one on account of blaCMY-2 and the other due to blaCTX-M-15, the latter also harbouring transferable quinolone-resistance genes (aac(6')Ib-cr and qnrB). All mcr-1 genes were transferred by conjugation to recipient strains. The mcr-1-bearing isolates belonged to sequence types ST10, ST93 and ST5442. CONCLUSIONS: ST10 is considered as a high-risk clone worldwide. This type of mcr-1-harbouring clone is a major concern for human and animal health and must be under close surveillance. This study detected the presence of mcr-1 for the first time in Uruguay, albeit in an allodemic manner, associated with different antibiotic-resistance genes and from diverse clinical contexts. Considering that colistin is often the last therapeutic option available for multidrug-resistant Gram-negative bacilli infections, it is important to maximise precautions to avoid dissemination of isolates carrying mcr-1.

Asunto(s)

RESUMEN

In Montevideo (2013-2018), 8 Campylobacter fetus extraintestinal infections were reported. The polyclonal nature of strains revealed by whole-genome sequencing and the apparent lack of epidemiological links was incompatible with a single contamination source, supporting alternative routes of transmission.

Asunto(s)

RESUMEN

Resumen: Introducción: un porcentaje de las infecciones del sistema nervioso central permanece sin diagnóstico etiológico. Las técnicas de amplificación de ácidos nucleicos mediante reacción en cadena de la polimerasa en tiempo real pueden disminuir este porcentaje. Objetivo: describir la etiología de las neuroinfecciones y valorar la utilidad de las técnicas de biología molecular en el diagnóstico y su impacto en el tratamiento antimicrobiano. Metodología: estudio observacional, descriptivo, retrospectivo a partir de registros clínicos. Se incluyeron mayores de 18 años asistidos en un hospital público de Montevideo durante un período de 32 meses, a quienes que se les realizaron técnicas de biología molecular en líquido cefalorraquídeo por sospecha clínica de neuroinfección. Resultados: se incluyeron 109 pacientes. En pacientes sin infección por VIH ni antecedentes neuroquirúrgicos (67%), se identificó microorganismo responsable en 16 casos, 8 bacterias y 9 virus. Todos identificados por técnicas de biología molecular modificando el tratamiento antimicrobiano empírico en 25 casos (34,2%). En portadores de VIH (25,7%), se detectaron microorganismos en 14 pacientes (50%). Seis virus, 5 bacterias y 7 hongos (Cryptococcus neoformans). El estudio por técnicas de biología molecular determinó el diagnóstico de 17 microorganismos y modificó el plan antimicrobiano inicial en 12 casos (42,9%). En pacientes con antecedente de neurocirugía reciente (7,3%), se aislaron seis microorganismos, tres de ellos exclusivamente mediante cultivo. Se modificó el tratamiento en tres casos (37,5%). Conclusiones: las técnicas de biología molecular deben considerarse complementarias. El impacto que generan en el diagnóstico y tratamiento justifica el uso de estas técnicas a pesar de su mayor costo.

Summary: Introduction: a certain percentage of infections of the central nervous system have no etiological diagnosis. Nucleic acids amplification techniques by means of a polymerase chain reaction in real time may reduce this percentage. Objective: to describe etiology of neuroinfectious diseases and assess the usefulness of molecular biology techniques in their diagnosis, as well as its impact on antimicrobial treatment. Method: observational, descriptive, retrospective study based on clinical records which included patients older than 18 years old, who had been assisted in a public hospital in Montevideo for over 32 months and had undergone molecular biology techniques with cerebrospinal fluid (CSF) given the clinical suspicion of neuroinfection. Results: 109 patients were included in the study. Among non-HIV infected patients who had not undergone neurosurgeries the responsible microorganism was identified in 16 cases (8 bacteria and 9 virus). They were all identified by molecular biology techniques by modifying the empiric antimicrobial therapy in 25 cases (34.2%). In carriers of HIV (25.7%), microorganisms were identified in 14 patients (50%). Six virus, 5 bacteria and 7 fungi (Cryptococcus neoformans). Molecular biology techniques defined the diagnosis of 17 microorganisms and modified the initial antimicrobial plan in 12 cases (42.9%). In patients with a history of recent neurosurgery (7.3%), 6 microorganisms were isolated, 3 of them exclusively through cultures. Treatment was modified in 3 cases (37.5%). Conclusions: molecular biology techniques need to be regarded as a complement. The impact that have in diagnosis and therapy justify their use despite its higher cost.

Resumo: Introdução: uma proporção das infecções do sistema nervoso central permanece sem diagnóstico etiológico. As técnicas de ampliação de ácidos nucléicos por reação em cadeia da polimerase em tempo real, podem diminuir esta proporção. Objetivo: descrever a etiologia das neuro infecções e avaliar a utilidade das técnicas de biologia molecular no diagnóstico e seu impacto no tratamento antimicrobiano. Metodologia: estudo observacional, descritivo, retrospectivo de prontuários de pacientes. Foram incluídos pacientes maiores de 18 anos, atendidos em um hospital público de Montevidéu, durante um período de 32 meses. Foram realizadas técnicas de biologia molecular ao líquido cefalorraquidiano por suspeita clínica de neuroinfecção. Resultados: foram incluídos 109 pacientes. Em pacientes sem infecção por VIH e sem antecedentes neurocirúrgicos (67%), o microrganismo responsável em 16 casos, sendo 8 bactérias e 9 vírus. Todos foram identificados por técnicas de biologia molecular modificando el tratamento antimicrobiano empírico em 25 casos (34,2%). Em portadores de VIH (25,7%), foram detectados microrganismos em 14 pacientes (50%). Seis vírus, 5 bactérias e 7 leveduras (Cryptococcus neoformans). O estudo por técnicas de biologia molecular permitiu o diagnóstico de 17 microrganismos e modificou o tratamento antimicrobiano inicial em 12 casos (42,9%). Em pacientes com antecedentes de neurocirurgia recente (7,3%), foram isolados 6 microrganismos, em 3 casos exclusivamente por cultura. O tratamento foi modificado em 3 casos (37,5%). Conclusões: as técnicas de biologia molecular devem ser consideradas como complementares. O impacto que causam sobre o diagnóstico e o tratamento justifica seu uso apesar de seu maior custo.

Asunto(s)

Asunto(s)