Phytobacter spp: the emergence of a new genus of healthcare-associated Enterobacterales encoding carbapenemases in Argentina: a case series.

Members of the genus Phytobacter (order Enterobacterales) are isolated from the natural environment and clinical settings. Identification of Phytobacter strains based on biochemical characteristics is complicated due to taxonomic confusion, and they are often misidentified by automated identification systems in laboratories. In this study we describe the first three clinical cases associated with Phytobacter spp. reported in Argentina. We describe the identification, the molecular analysis using whole genome sequencing and the potential clinical relevance.

Description of Corynebacterium hiratae sp. nov. isolated from a human tissue bone a novel member of Corynebacterium Genus.

BACKGROUND: Corynebacterium spp. are widely disseminated in the environment, and they are part of the skin and mucosal microbiota of animals and humans. Reports of human infections by Corynebacterium spp. have increased considerably in recent years and the appearance of multidrug resistant isolates around the world has drawn attention. OBJECTIVES: To describe a new species of Corynebacterium from human tissue bone is described after being misidentified using available methods. METHODS: For taxonomic analyses, phylogenetic analysis of 16S rRNA and rpoB genes, in silico DNA-DNA hybridization, average nucleotide and amino acid identity, multilocus sequence analysis, and phylogenetic analysis based on the complete genome were used. FINDINGS: Genomic taxonomic analyzes revealed values of in silico DNA-DNA hybridization, average nucleotide and amino acids identity below the values necessary for species characterization between the analyzed isolates and the closest phylogenetic relative Corynebacterium aurimucosum DSM 44532T. MAIN CONCLUSIONS: Genomic taxonomic analyzes indicate that the isolates analyzed comprise a new species of the Corynebacterium genus, which we propose to name Corynebacterium hiratae sp. nov. with isolate 332T (= CBAS 826T = CCBH 35,014T) as the type strain.

Caracterización de aislamientos de Klebsiella pneumoniae doble productores de carbapenemasas en un hospital universitario / Phenotypic and genotypic characterization of double carbapenemase producing Klebsiella pneumoniaeisolates in a University Hospital

La emergencia de aislamientos de Klebsiella pneumoniaedoble productores de carbapenemasas (KPC y NDM) es una de las consecuencias de la pandemia causada por SARS-CoV-2 que ha causado un impacto significativo en las tasas de resistencia a los antimicrobianos en las infecciones intrahospitalarias por esta enterobacteria. Estos aislamientos representan un desafío para los servicios de salud, por su detección y caracterización y posterior tratamiento. En este trabajo se describen los aislamientos portadores de KPC y NDM recuperados durante 2022 aislados de distintas muestras clínicas de pacientes internados en un hospital universitario de la Ciudad de Buenos Aires, se los caracteriza fenotípicamente y genotípicamente como portadores de ambas carbapenemasas y se destaca la excelente actividad in vitro de la combinación ceftazidima-avibactam y aztreonam en el tratamiento de estas infecciones en donde las alternativas terapéuticas estarían limitadas a antibióticos no ß-lactámicos con porcentajes de resistencia que superan el 70%

The emergence of double-carbapenemase (KPC and NDM) producing Klebsiella pneumoniae isolates is one of the consequences derived from the SARS CoV-2 pandemic, which has caused significant impact on the antimicrobial resistance rates in hospital acquired infections. These isolates represent a real challenge for Health Services due to their difficult detection and characterization and subsequent treatment. In the present work we describe the double carbapenemase producing isolates recovered during the year 2022 from clinical samples belonging to hospitalized patients at a University Hospital in Buenos Aires city, we report their phenotypic and genotypic characterization and the excellent "in vitro" activity of the ceftazidime-avibactam-aztreonam combination in the treatment of infections in which the therapeutical options are restricted to non ß- lactamic antimicrobials which hold resistance rates higher than 70%

Actinomyces europaeus (Gleimia europaea) asociado con absceso cerebral: comunicación de tres casos / Actinomyces europaeus (Gleimia europaea) associated with brain abscess: A reportof three cases

Resumen El absceso cerebral es una infección focal caracterizada por acumulación de pus enel parénquima cerebral; su diagnóstico es de urgencia debido a la alta mortalidad que acarrea.Presentamos tres casos de pacientes con abscesos cerebrales con foco otogénico de origen poli-microbiano, que presentaron en común el aislamiento de Actinomyces europaeus, agente nodescrito hasta el momento en esta localización. A. europaeus fue identificado por la metodo-logía convencional, por espectrometría de masas por desorción/ionización asistida por matriz(MALDI-TOF MS) y por secuenciación del gen ARNr 16S. La sensibilidad antibiótica se evaluó porel método epsilométrico. Todos los aislados presentaron sensibilidad a penicilina, vancomicinay linezolid, mientras que la sensibilidad a clindamicina y eritromicina fue variable. La iden-tificación por MALDI-TOF MS permitió arribar a nivel de especie de forma rápida y confiabley dar una respuesta oportuna y efectiva, evitando el retraso en el tratamiento, lo que sueleincrementar la morbimortalidad del cuadro clínico.

First nosocomial outbreak of SME-4-producing Serratia marcescens in South America / Primer brote nosocomial por Serratia marcescens productora de SME-4en Sudamérica

Abstract Carbapenemase-producing-Serratia marcescens isolates, although infrequent, are considered important nosocomial pathogens due to their intrinsic resistance to polymyxins, which limits therapeutic options. We describe a nosocomial outbreak of SME-4-producing S. marcescens in Buenos Aires city which, in our knowledge, represents the first one in South America.

Resumen Los aislamientos de origen nosocomial de Serratia marcescens productores de car-bapenemasa, si bien son infrecuentes, son considerados importantes patógenos debido a su resistencia intrínseca a las polimixinas, lo cual limita aún más las opciones terapéuticas. En este trabajo se describe un brote nosocomial causado por S. marcescens portadora de car-bapenemasa de tipo SME-4 en la Ciudad de Buenos Aires, el cual representaría el primero en Sudamérica.

Interspecies interactions in mixed-species biofilms formed by Enterococcus faecalis and gram-negative bacteria isolated from polymicrobial diabetic foot ulcers.

Diabetic foot ulcers (DFU) are exacerbated by bacterial colonisation. Here, a high prevalence of Enterococcus faecalis was observed in DFU patients from an Argentinean hospital. E. faecalis was frequently co-isolated with Escherichia coli, Morganella morganii, and Pseudomonas aeruginosa. The effect of interspecies interactions on bacterial growth was investigated in mixed-species macrocolony biofilms developed in Lubbock-Glc-agar. Similar cell counts were found for E. faecalis and M. morganii growing in mixed and single-species biofilms. An E. faecalis strain showed 1 Log higher cell counts in mixed biofilms with E. coli. Remarkably, E. faecalis strains showed 2 to 4 Log higher cell counts in mixed biofilms with P. aeruginosa. This effect was not observed in planktonic growth or biofilms developed in tryptic soy agar. The present findings reveal bacterial interactions that benefit E. faecalis in mixed-species biofilms, mainly with P. aeruginosa, in a medium that partially mimics the nutrients found in DFU.

MALDI-TOF MS-Based KPC Direct Detection from Patients' Positive Blood Culture Bottles, Short-Term Cultures, and Colonies at the Hospital.

Carbapenemase resistance in Enterobacterales is a global public health problem and rapid and effective methods for detecting these resistance mechanisms are needed urgently. Our aim was to evaluate the performance of a MALDI-TOF MS-based "Klebsiella pneumoniae carbapenemase" (KPC) detection protocol from patients' positive blood cultures, short-term cultures, and colonies in healthcare settings. Bacterial identification and KPC detection were achieved after protein extraction with organic solvents and target spot loading with suitable organic matrices. The confirmation of KPC production was performed using susceptibility tests and blaKPC amplification using PCR and sequencing. The KPC direct detection (KPC peak at approximately 28.681 Da) from patients' positive blood cultures, short-term cultures, and colonies, once bacterial identification was achieved, showed an overall sensibility and specificity of 100% (CI95: [95%, 100%] and CI95: [99%, 100%], respectively). The concordance between hospital routine bacterial identification protocol and identification using this new methodology from the same extract used for KPC detection was ≥92%. This study represents the pioneering effort to directly detect KPC using MALDI-TOF MS technology, conducted on patient-derived samples obtained from hospitals for validation purposes, in a multi-resistance global context that requires concrete actions to preserve the available therapeutic options and reduce the spread of antibiotic resistance markers.

Discrimination of the chemotherapy resistance status of human leukemia and glioblastoma cell lines by MALDI-TOF-MS profiling.

Chemotherapy mistreatment is partially due to a lack of rapid and reliable tools to discriminate between sensitive and resistant phenotypes. In many cases, the resistance mechanism is not fully understood, contributing to the diagnostic tools' absence. This work aims to determine the capacity of MALDI-TOF-MS profiling to discriminate between chemotherapy-resistant and sensitive phenotypes in leukemia and glioblastoma cells. A multivariate analysis of two therapy-resistant leukemia cell lines (Ki562 and Kv562) and two TMZ-resistant glioblastoma cell lines (U251-R and LN229-R) and their sensitive counterparts was performed. In this work, we first show MALDI-TOF-MS patterns analysis ability to differentiate these cancer cell lines by their chemotherapy-resistant status. We present a rapid and inexpensive tool that would guide and complement the therapeutic decision.

First nosocomial outbreak of SME-4-producing Serratia marcescens in South America.

Carbapenemase-producing-Serratia marcescens isolates, although infrequent, are considered important nosocomial pathogens due to their intrinsic resistance to polymyxins, which limits therapeutic options. We describe a nosocomial outbreak of SME-4-producing S. marcescens in Buenos Aires city which, in our knowledge, represents the first one in South America.

Corynebacterium guaraldiae sp. nov.: a new species of Corynebacterium from human infections.

Non-diphtheria Corynebacterium species (NDC) belonging to the human skin and mucosa microbiota are frequently neglected as contaminants. However, reports of human infections by Corynebacterium spp. have increased considerably in recent years. In this study, a group of six NDC isolates of urine (n = 5) and sebaceous cyst (n = 1) from two South American countries were identified at genus level or misidentified based on API® Coryne and genetic/molecular analyses. The 16S rRNA (99.09-99.56%) and rpoB (96.18-97.14%) gene sequence similarities of the isolates were higher when compared with Corynebacterium aurimucosum DSM 44532 T. Multilocus sequence analysis (MLSA) indicated that these six NDC isolates compose a distinctive phylogenetic clade. Genome-based taxonomic analysis with the whole-genome sequences was able to separate these six isolates from other known Corynebacterium type strains. Average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between closely related type strains and the six isolates were considerably lower than the currently recommended threshold values for species circumscription. Phylogenetic and genomic taxonomy analyses indicated these microorganisms as a novel Corynebacterium species, for which we formally propose the name Corynebacterium guaraldiae sp. nov. with isolate 13T (= CBAS 827T = CCBH 35012T) as type strain.

[Actinomyces europaeus (Gleimia europaea) associated with brain abscess: A report of three cases]. / Actinomyces europaeus (Gleimia europaea) asociado con absceso cerebral: comunicación de tres casos.

A brain abscess is a focal infection characterized by a collection of pus in the brain parenchyma. It is a life-threatening condition that should be diagnosed and treated as soon as possible. We report here three cases of patients with otogenic brain abscesses of polymicrobial origin that had in common the isolation of Actinomyces europaeus, which has not been previously described in this location. A. europaeus was identified by the conventional methodology, matrix-associated laser deionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing. Antibiotic susceptibility was evaluated by the epsilometric method, and all isolates showed sensitivity to penicillin, vancomycin and linezolid, whereas susceptibility to clindamycin and erythromycin was variable. MALDI-TOF MS identification allowed a quick and reliable species level identification in order to provide a rapid and effective response to avoid treatment delay that could lead to increased morbidity and even mortality.

[Vibrio vulnificus infection of the skin and soft parts. Communication of a case diagnosed in Argentina]. / Infección de piel y partes blandas por Vibrio vulnificus. Comunicación de un caso diagnosticado en Argentina.

Vibrio vulnificus is one of the most virulent Vibrio species known. It is a bacterium with universal distribution. The first case registered in Uruguay occurred in 2001 and, since then, several infections have occurred per year. Recently, in this country, V. vulnificus was responsible for a fatal soft tissue infection. Although no cases of human infection with this species have been reported in Argentina, researchers have recently identified V. vulnificus in samples associated with microplankton in the Rio Negro estuary. We present the case of a severe skin and soft tissue infection by V. vulnificus from an open wound in a patient in contact with a marine aquatic environment on the coast of the River Plate, in Uruguay. Isolation of vibrios from wound specimens can cause rapidly progressing tissue damage, particularly V. vulnificus which has a high mortality rate without early and appropriate intervention. In our case, the rapid identification of the microorganism allowed us to support the empirical treatment used, which a good clinical evolution.

Vibrio vulnificus es una de las especies de Vibrio más virulentas que se conocen. Es una bacteria de distribución universal. El primer caso registrado en Uruguay se produjo en 2001, y desde entonces ocurren varias infecciones por año. Recientemente, en ese país, V. vulnificus fue responsable de una infección de partes blandas de curso letal. Aunque no han sido comunicados casos de infección humana por esta especie en Argentina, se ha identificado recientemente Vibrio vulnificus en muestras asociadas con microplancton en el estuario del Río Negro. Presentamos el caso de una infección grave de piel y partes blandas por V. vulnificus a partir de una herida abierta en un paciente en contacto con medio acuático marino en la costa de Uruguay del Río de la Plata. El aislamiento de vibrios en muestras de heridas puede causar un daño en los tejidos con rápida progresión, en particular V. vulnificus, que tiene una alta mortalidad sin la precoz y apropiada intervención. En nuestro caso, la rápida identificación del microorganismo permitió avalar el tratamiento empírico utilizado, con una buena evolución clínica.

Infección de piel y partes blandas por Vibrio vulnificus. Comunicación de un caso diagnosticado en Argentina / Vibrio vulnificus infection of the skin and soft parts. Communication of a case diagnosed in Argentina

Resumen Vibrio vulnificus es una de las especies de Vibrio más virulentas que se conocen. Es una bacteria de distribución universal. El primer caso registrado en Uruguay se produjo en 2001, y desde entonces ocurren varias infecciones por año. Recientemente, en ese país, V. vulnificus fue responsable de una infección de partes blandas de curso letal. Aunque no han sido comunicados casos de infección humana por esta especie en Argentina, se ha identificado recientemente Vibrio vulnificus en muestras asociadas con microplancton en el estuario del Río Negro. Presentamos el caso de una infección grave de piel y partes blandas por V. vulnificus a partir de una herida abierta en un paciente en contacto con medio acuático marino en la costa de Uruguay del Río de la Plata. El aislamiento de vibrios en muestras de heridas puede causar un daño en los tejidos con rápida progresión, en particular V. vulnificus, que tiene una alta mortalidad sin la precoz y apropiada intervención. En nuestro caso, la rápida identificación del microorganismo permitió avalar el tratamiento empírico utilizado, con una buena evolución clínica.

Abstract Vibrio vulnificus is one of the most virulent Vibrio species known. It is a bacterium with universal distribution. The first case registered in Uruguay occurred in 2001 and, since then, several infections have occurred per year. Recently, in this country, V. vulnificus was responsible for a fatal soft tissue infection. Although no cases of human infection with this species have been reported in Argentina, researchers have recently identified V. vulnificus in samples associated with microplankton in the Rio Negro estuary. We present the case of a severe skin and soft tissue infection by V. vulnificus from an open wound in a patient in contact with a marine aquatic environment on the coast of the River Plate, in Uruguay. Isolation of vibrios from wound specimens can cause rapidly progressing tissue damage, particularly V. vulnificus which has a high mortality rate without early and appropriate intervention. In our case, the rapid identification of the microorganism allowed us to support the empirical treatment used, which a good clinical evolution.

Empiema necessitatis por Campylobacter rectus. Identificación rápida por MALDI-TOF MS / Empyema necessitatis caused by Campylobacter rectus. Rapid identification by MALDI-TOF MS

Resumen El empiema necessitatis (EN) constituye una muy rara complicación de un empiema pleural en el cual la infección se extiende a los tejidos blandos adyacentes. La etiología por anaerobios es muy infrecuente y se da en el curso de infecciones crónicas. Se presenta el primer caso de empiema necessitatis por Campylobacter rectus. La identificación de este agente se efectuó por espectrometría de masas (MALDI-TOF MS) y su sensibilidad antimicrobiana se determinó por el método epsilométrico.

Abstract Empyema necessitatis (EN) is a very rare complication of a pleural empyema, in which the infection extends to adjacent soft tissues. Anaerobic bacteria are very rare etiologic agents of EN, which occurs in the course of chronic infections. We present the first case of empyema necessitatis caused by Campylobacter rectus. Bacterial identification was carried out by mass spectrometry (MALDI-TOF MS) and antimicrobial susceptibility was determined by the epsilometer method.

Descripción de un caso de sepsis abdominal por Desulfovibrio desulfuricans / Description of a case of abdominal sepsis due to Desulfovibrio desulfuricans

Resumen Desulfovibrio spp. son bacterias anaerobias estrictas, ubicuas en la naturaleza, quepueden formar parte del tracto gastrointestinal humano o animal, pero también son bacteriasambientales presentes en el suelo y en el agua. Pueden persistir de manera asintomática enel intestino o comportarse como patógenos oportunistas, asociados con bacteriemia primariae infecciones intraabdominales. El número de infecciones por Desulfovibrio spp. puede estarsubestimado debido a su lenta velocidad de crecimiento y a que muchos laboratorios no realizancultivos en anaerobiosis de manera rutinaria. Pruebas sencillas, como el examen de la movilidaden fresco y de la morfología celular en la coloración de Gram, sumadas a la presencia de SH2en agar SIM y a la observación de una fluorescencia roja a pH alcalino bajo luz UV, seríanindicativas de Desulfovibrio spp. Se describe el caso de una bacteriemia por Desulfovibriodesulfuricans en una mujer con cuadro clínico de sepsis abdominal por apendicitis gangrenosacon fallo multiorgánico.

Abstract Desulfovibrio spp. are strict anaerobes that are ubiquitous in nature. They can reside in the human or animal gastrointestinal tract and, as they are also environmental bacteria, may be present in soil and water. They can persist asymptomatically in the intestine or behave as opportunistic pathogens associated with primary bacteremia and intraabdominal infections. Several Desulfovibrio spp. infections may be underestimated due to their slow growth rate and because many laboratories do not routinely perform anaerobic cultures. Simple tests such as motility detection on a fresh subculture, Gram stain to confirm cell morphology, presence of H2S in SIM agar and production of a red fluorescence in alkaline pH under UV light would be indicative of Desulfovibrio spp.

Peptidome profiling for the immunological stratification in sepsis: a proof of concept study.

Sepsis has been called the graveyard of pharmaceutical companies due to the numerous failed clinical trials. The lack of tools to monitor the immunological status in sepsis constrains the development of therapies. Here, we evaluated a test based on whole plasma peptidome acquired by MALDI-TOF-mass spectrometer and machine-learning algorithms to discriminate two lipopolysaccharide-(LPS) induced murine models emulating the pro- and anti-inflammatory/immunosuppression environments that can be found during sepsis. The LPS group was inoculated with a single high dose of LPS and the IS group was subjected to increasing doses of LPS, to induce proinflammatory and anti-inflammatory/immunosuppression profiles respectively. The LPS group showed leukopenia and higher levels of cytokines and tissue damage markers, and the IS group showed neutrophilia, lymphopenia and decreased humoral response. Principal component analysis of the plasma peptidomes formed discrete clusters that mostly coincided with the experimental groups. In addition, machine-learning algorithms discriminated the different experimental groups with a sensitivity of 95.7% and specificity of 90.9%. Data reveal the potential of plasma fingerprints analysis by MALDI-TOF-mass spectrometry as a simple, speedy and readily transferrable method for sepsis patient stratification that would contribute to therapeutic decision-making based on their immunological status.

[Description of a case of abdominal sepsis due to Desulfovibrio desulfuricans]. / Descripción de un caso de sepsis abdominal por Desulfovibrio desulfuricans.

Desulfovibrio spp. are strict anaerobes that are ubiquitous in nature. They can reside in the human or animal gastrointestinal tract and, as they are also environmental bacteria, may be present in soil and water. They can persist asymptomatically in the intestine or behave as opportunistic pathogens associated with primary bacteremia and intraabdominal infections. Several Desulfovibrio spp. infections may be underestimated due to their slow growth rate and because many laboratories do not routinely perform anaerobic cultures. Simple tests such as motility detection on a fresh subculture, Gram stain to confirm cell morphology, presence of H2S in SIM agar and production of a red fluorescence in alkaline pH under UV light would be indicative of Desulfovibrio spp. Here we report the case of Desulfovibrio desulfuricans bacteremia in a woman with clinical picture of abdominal sepsis due to gangrenous appendicitis with multiple organ failure.

Dolosigranulum pigrum en absceso corneal / Dolosigranulum pigrum in corneal abscess

Resumen Dolosigranulum pigrum es un coco gram positivo, anaerobio facultativo, que forma parte de la microbiota oral y del tracto respiratorio superior. Aunque los reportes de infecciones por este microorganismo son escasos, se lo ha asociado a un amplio espectro de enfermedades infecciosas. Se describe el caso de un hombre adulto con un absceso corneal del que se aisló D. pigrum. El microorganismo fue identificado por espectrometría de masas (MALDI-TOF MS) y secuenciación del gen 16S ARNr. A su vez, se logró la identificación presuntiva mediante pruebas fenotípicas claves, como la disposición en racimos en la coloración de Gram, la prueba negativa de la catalasa, la producción de pirrolidonil arilamidasa y leucina aminopeptidasa, el crecimiento en NaCl al 6,5% y la hidrólisis de esculina. Los datos de la literatura y el presente caso respaldan la asociación del microorganismo con infecciones oculares, a menudo de curso destructivo, principalmente en pacientes de edad avanzada.

Abstract Dolosigranulum pigrum is a gram-positive, facultatively anaerobic coccus, which is part of the oral and upper respiratory tract microbiota. Although reports of infections by this microorganism are scarce, it has been associated with a wide spectrum of infectious diseases. The case of an elderly man with a lower corneal abscess, in which Dolosigranulum pigrum was isolated, is described. The microorganism was identified by mass spectrometry (MALDI-TOF MS) and by the sequencingof the 16S rRNAgene. Furthermore, the presumptive identification of the causative agent was achieved by using key phenotypic tests such as the cluster arrangement in Gram stain, the negative catalase test, the production of pyrrolidonyl arylamidase and leucine aminopeptidase activity, the growth in 6.5% NaCl and esculin hydrolysis. The data from the literature (and the present case) support the association of the microorganism with ocular infections, which often take a destructive course, mainly in elderly patients.

[Empyema necessitatis caused by Campylobacterrectus. Rapid identification by MALDI-TOF MS]. / Empiema necessitatis por Campylobacter rectus. Identificación rápida por MALDI-TOF MS.

Empyema necessitatis (EN) is a very rare complication of a pleural empyema, in which the infection extends to adjacent soft tissues. Anaerobic bacteria are very rare etiologic agents of EN, which occurs in the course of chronic infections. We present the first case of empyema necessitatis caused by Campylobacter rectus. Bacterial identification was carried out by mass spectrometry (MALDI-TOF MS) and antimicrobial susceptibility was determined by the epsilometer method.