First detection and origin of multi-drug resistant Klebsiella pneumoniae ST15 harboring OXA-48 in South America.

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.

Human microbiota drives hospital-associated antimicrobial resistance dissemination in the urban environment and mirrors patient case rates.

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.

Community-onset bacteremia due to extended-spectrum beta-lactamase-producing Escherichia coli: risk factors and prognosis.

BACKGROUND: There is little clinical information about community-onset bloodstream infections (COBSIs) caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBLEC). We investigated the prevalence and risk factors for COBSI due to ESBLEC, and described their clinical features and the impact of COBSI caused by ESBLEC on 14-day mortality. METHODS: Risk factors were assessed using a multicenter case-control-control study. Influence of ESBL production on mortality was studied in all patients with COBSI due to E. coli. Isolates and ESBLs were microbiologically characterized. Statistical analysis was performed using multivariate logistic regression. Thirteen tertiary care Spanish hospitals participated in the study. RESULTS: We included 95 case patients with COBSI due to ESBLEC, which accounted for 7.3% of all COBSI due to E. coli. The ESBL in 83 of these (87%) belonged to the CTX-M family of ESBL, and most were clonally unrelated. Comparison with both control groups disclosed association with health care (odds ratio [OR], 2.1; 95% confidence interval [CI], 1.2-3.8), urinary catheter use (OR, 3.1; 95% CI, 1.5-6.5), and previous antimicrobial use (OR, 2.7; 95% CI, 1.5-4.9) as independent risk factors for COBSI due to ESBLEC. Mortality among patients with COBSI due to ESBLEC was lower among patients who received empirical therapy with beta-lactam/beta-lactam inhibitor combinations or carbapenems (8%-12%) than among those receiving cephalosporins or fluoroquinolones (24% and 29%, respectively). Mortality among patients with COBSI due to E. coli was associated with inappropriate empirical therapy irrespective of ESBL production. CONCLUSIONS: ESBLEC is an important cause of COBSI due to E. coli. Clinicians should consider adequate empirical therapy with coverage of these pathogens for patients with risk factors.

Risk factors and prognosis of nosocomial bloodstream infections caused by extended-spectrum-beta-lactamase-producing Escherichia coli.

Extended-spectrum-beta-lactamase (ESBL)-producing Escherichia coli (ESBLEC) is an increasing cause of community and nosocomial infections worldwide. However, there is scarce clinical information about nosocomial bloodstream infections (BSIs) caused by these pathogens. We performed a study to investigate the risk factors for and prognosis of nosocomial BSIs due to ESBLEC in 13 Spanish hospitals. Risk factors were assessed by using a case-control-control study; 96 cases (2 to 16% of all nosocomial BSIs due to E. coli in the participating centers) were included; the most frequent ESBL was CTX-M-14 (48% of the isolates). We found CTX-M-15 in 10% of the isolates, which means that this enzyme is emerging as a cause of invasive infections in Spain. By repetitive extragenic palindromic sequence-PCR, most isolates were found to be clonally unrelated. By multivariate analysis, the risk factors for nosocomial BSIs due to ESBLEC were found to be organ transplant (odds ratio [OR]=4.8; 95% confidence interval [CI]=1.4 to 15.7), the previous use of oxyimino-beta-lactams (OR=6.0; 95% CI=3.0 to 11.8), and unknown BSI source (protective; OR=0.4; 95% CI=0.2 to 0.9), and duration of hospital stay (OR=1.02; 95% CI=1.00 to 1.03). The variables independently associated with mortality were a Pitt score of >1 (OR=3.9; 95% CI=1.2 to 12.9), a high-risk source (OR=5.5; 95% CI=1.4 to 21.9), and resistance to more than three antibiotics, apart from penicillins and cephalosporins (OR=6.5; 95% CI=1.4 to 30.0). Inappropriate empirical therapy was not associated with mortality. We conclude that ESBLEC is an important cause of nosocomial BSIs. The previous use of oxyimino-beta-lactams was the only modifiable risk factor found. Resistance to drugs other than penicillins and cephalosporins was associated with increased mortality.

Escherichia coli producing SHV-type extended-spectrum beta-lactamase is a significant cause of community-acquired infection.

OBJECTIVES: Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBLEC) is an increasingly significant cause of community-acquired infection worldwide. The epidemiological features of CTX-M- and SHV-producing ESBLEC causing community-acquired infections are compared. METHODS: A multicentre cohort study including all community-acquired infections caused by ESBLEC in four geographical areas of Spain was carried out. ESBL characterization was by isoelectric focusing, PCR and sequencing. Demographics, previous healthcare contact, co-morbidity, use of antimicrobials, invasive procedures and type of infection were collected for all patients. Patients with CTX-M- and SHV-producing isolates were compared using logistic regression. RESULTS: One hundred and twenty-two cases (95% urinary tract infections) were included. ESBLs were characterized in 112 isolates; 77 isolates (69%) produced CTX-M, 36 (32%) produced SHV and 7 (6%) produced TEM enzymes (8 produced >1 ESBL). Patients with isolates producing CTX-M enzymes only (CTX-M group, n = 70) and SHV enzymes only (SHV group, n = 31) were compared. There were no differences in terms of underlying disease, previous healthcare contact, invasive procedures, antibiotic use or type of infection. Multivariate analysis including geographical area showed that a Charlson Index score of >2 (OR = 4.0; 95% CI = 1.2-12.6) was associated with SHV isolates, while age >60 (4.7; 1.7-12.5) was associated with CTX-M isolates. CONCLUSIONS: SHV-producing ESBLEC is a significant cause of community-acquired infection in Spain; the clinical epidemiology of such isolates seems very similar to that of CTX-M-producing E. coli.

High rate of intestinal colonization with extended-spectrum-beta-lactamase-producing organisms in household contacts of infected community patients.

Fecal carriage of extended-spectrum-beta-lactamase (ESBL)-producing organisms was detected in 70% of index cases of patients (n = 40) with community-acquired infections due to ESBL producers and reached 16.7% in household contacts (n = 54). A total of 66% of ESBL-producing organisms from index cases were indistinguishable from isolates from household contacts by pulsed-field gel electrophoresis. Patients with community infections and members of their households represent a reservoir for ESBL producers, increasing dispersal of resistance in healthy people.

Utilidad de las técnicas de biología molecular en neuroinfecciones / Usefulness of molecular biology techniques in neuroinfectious diseases / Utilidade das técnicas de biologia molecular em neuroinfecções

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.

Endotipsitis: an emerging prosthetic-related infection in patients with portal hypertension.

The transjugular intrahepatic portosystemic shunt (TIPS) is an option for the treatment of portal hypertension. However, TIPS infection (endotipsitis) is distinctly uncommon. We report 3 new patients and review 23 published cases of endotipsitis. We calculate an incidence of 1.33% in patients undergoing the procedure. Twenty-three cases (88%) occurred more than a month after the procedure. The most common presentation included fever and primary bacteremia or fungemia. Gram-positive (18 cases), gram-negative microorganisms (10 cases), and fungi (3 cases) were the etiologic agents. Diagnosis may be difficult to establish, and new diagnostic criteria have been proposed. Twenty patients responded well to antibiotic treatment, and the 6 remaining patients died because of the infection. Endotipsitis is a new infectious disease to be considered in patients with a TIPS and bloodstream infection that is not clearly attributable to another source. Prolonged courses of antimicrobial agents can be curative, but liver transplantation is also an option to consider.

Leishmaniasis visceral en Uruguay / Visceral leishmaniasis in Uruguay

La leishmaniasis comprende un grupo de enfermedades zoonóticas causadas por protozoarios del género Leishmania y transmitidas mediante flebótomos. Se describen tres formas clínicas básicas: formas cutáneas, cutáneo-mucosas y viscerales, siendo esta última, la presentación más grave por su alta letalidad cuando no se realiza tratamiento específico. Leishmaniasis visceral (LV) es causada por L. donovani complex que incluye L donovani en el subcontinente indio, Asia y África, L. infantum en la cuenca mediterránea y L. chagasi en América del Sur. La infección en el hombre se puede dar a partir de parásitos provenientes de un reservorio animal (ciclo zoonótico) Leishmaniasis tienen una distribución mundial muy amplia, estimándose unos 14 millones de personas infectadas, con una incidencia anual de 2 millones de nuevos casos, de los cuales 500.000 son de leishmaniasis visceral. En nuestro continente se registraron, entre 2001 y 2014, unos 48.700 casos de leishmaniasis visceral de los cuales el 33,4% de los casos se registraron en menores de 5 años y en el 6,7% en pacientes infectados con VIH. La mortalidad global es de del 6,6%. En nuestro país, en el litoral norte, específicamente Salto, desde el año 2010 se han diagnosticado en forma progresiva casos de leishmaniasis canina coincidiendo con la identificación del vector: Lutzomyia longipalpis. Aún no hay casos en personas identificados. Esto ha producido un cambio epidemiológico inédito en nuestro país.

Leishmaniasis comprises a group of zoonotic diseases caused by protozoa of the genus Leishmania and transmitted by sandflies. There are three basic clinical forms: cutaneous, cutaneous-mucous and visceral, the latter being the most serious presentation due to its high lethality rate if no specific therapy is initiated. Visceral leishmaniasis (VL) is caused by L. donovani complex, which includes L donovani in the Indian subcontinent, Asia and Africa, L. infantum in the Mediterranean basin and L. chagasi in South America. The infection occurs from parasites harboured in an animal reservoir (zoonotic cycle) Leishmaniasis has a very wide global distribution, with an estimated14 million people infectedand an annual incidence of 2 million new cases, of which 500,000 correspond to visceral leishmaniasis. In our continent between 2001 and 2014, approximately 48,700 cases of visceral leishmaniasis were registered.33.4% of these were in children under 5 years of age and 6.7% occured in patients infected with HIV. The overall mortality was 6.6%. In our country, in the north, specifically in Salto, since 2010, cases of canine leishmaniasis have been identified progressively, coinciding with the identification of the vector: Lutzomyia longipalpis. No cases in humans have yet been identified. This has caused an unprecedented epidemiological change in our country.

Intravenous colistin sulphomethate sodium for therapy of infections due to multidrug-resistant gram-negative bacteria.

OBJECTIVE: To assess the efficacy and toxicity of intravenous colistin in the treatment of infections due to multidrug-resistant gram-negative bacteria. METHODS: Retrospective cohort study. RESULTS: Sixty patients received colistin sulphomethate sodium (mean dose, 4.4mg/kg/day; median duration, 20days). The main infections were pneumonia or tracheobronchitis (63.3%), intra-abdominal (10%), urinary tract (8.3%), and surgical site infection (6.6%), primary bacteremia (5%), catheter infection (3.3%), meningitis (1.6%), and soft-tissue infection (1.6%). The responsible bacteria were Acinetobacter spp. (50%), P. aeruginosa (23.3%), K. pneumoniae (13.3%), Enterobacter spp. (10%), E. coli (1.6%), and S. maltophilia (1.6%). Eight patients (13%) received colistin monotherapy, and 52 (87%) received combination therapy with other antibiotics such as beta-lactams (15 cases), aminoglycosides (14), beta-lactams and aminoglycosides (15), or ciprofloxacin (8). A favourable response was observed in 43 cases (71.7%). Overall mortality was 26.7%. Despite the common use of combination therapy with aminoglycosides (48%), nephrotoxicity during colistin therapy was observed in only 10.9% of patients; most of them had previous renal failure. CONCLUSION: Colistin appears to be an effective and safe drug for therapy of severe infections due to multidrug-resistant gram-negative bacteria. Despite the concomitant use of aminoglycosides in a high proportion of patients, renal toxicity was an uncommon adverse event.

Community infections caused by extended-spectrum beta-lactamase-producing Escherichia coli.

BACKGROUND: Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is an increasingly important group of community pathogens worldwide. These organisms are frequently resistant to many of the antimicrobial agents usually recommended for the treatment of infections caused by E coli, such as penicillins, cephalosporins, fluoroquinolones, and trimethoprim-sulfamethoxazole. Data concerning risk factors, clinical features, and therapeutic options for such infections are scarce. METHODS: A case-control study was performed to investigate the risk factors for all types of community-acquired infections caused by ESBL-producing E coli in 11 Spanish hospitals from February 2002 to May 2003. Controls were randomly chosen from among outpatients with a clinical sample not yielding ESBL-producing E coli. The clinical features of these infections were investigated in the case patients. The efficacy of fosfomycin tromethamine and amoxicillin-clavulanate potassium was observationally studied in patients with cystitis. RESULTS: A total of 122 cases were included. Risk factors selected by multivariate analysis included the following: age older than 60 years; female sex; diabetes mellitus; recurrent urinary tract infections (UTIs); previous invasive procedures of the urinary tract; follow-up in outpatient clinic; and previous receipt of aminopenicillins, cephalosporins, and fluoroquinolones. Urinary tract infections accounted for 93% of the cases; 6% of the patients were bacteremic and 10% needed hospitalization. The cure rate of patients with cystitis was 93% with fosfomycin therapy (all isolates were susceptible); among patients treated with amoxicillin-clavulanate, cure rates were 93% for those with susceptible isolates (minimum inhibitory concentration < or =8 microg/mL) and 56% for those with intermediate or resistant isolates (minimum inhibitory concentration > or =16 microg/mL) (P = .02). CONCLUSIONS: In predisposed patients, ESBL-producing E coli is a notable cause of community-acquired infection, and particularly UTI. Fosfomycin and amoxicillin-clavulanate appear to be effective for cystitis caused by susceptible isolates.