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.

SME-4-producing Serratia marcescens from Argentina belonging to clade 2 of the S. marcescens phylogeny.

BACKGROUND: SME carbapenemases are increasingly reported, especially from North and South America. Here, we describe an SME-4-producing Serratia marcescens (SME-Sm) clinical isolate from Argentina and compare its genome with other SME-Sm and Sm isolates recovered from public databases. METHODS: Sm isolates were characterized by WGS using Illumina technology, susceptibility testing and MIC determination. Carbapenemase activity was revealed by biochemical tests based on imipenem hydrolysis. A whole-genome phylogeny was estimated for all the Sm isolates retrieved from public databases with kSNP3 and a whole-genome phylogenetic analysis based on non-recombinant core SNPs was inferred for Sm complete genomes and for those encoding any blaSME variants. RESULTS: Sm163 was resistant to amoxicillin, temocillin, aztreonam and carbapenems, remaining susceptible to extended-spectrum cephalosporins. WGS analysis of Sm163 revealed a genome of 5139329 bp and a chromosomally encoded blaSME-4 carbapenemase gene located on a genomic island closely related to SmarGI1-1 of Sm N11-02820. Comparison of the Sm genomes revealed that the 14 SME-Sm isolates possess this genomic island inserted at the same loci, that 13/14 belong to clade 1 and that 11/14 form a well-defined subcluster of cluster I of Sm clade 1, while Sm163 belongs to clade 2, suggesting that an SME-encoding genomic island may have been transferred between isolates from different clades. CONCLUSIONS: To the best of our knowledge this is the first report of an SME-4-encoding Sm from Argentina. The blaSME-4 gene is located on a SmarGI1-1-like genomic island. The genome of Sm163 belongs to clade 2, unlike all the other SME-Sm isolates, which belong to clade 1.

Current scenario of plasmid-mediated colistin resistance in Latin America.

Colistin resistance can occur by chromosomal mutations and by acquisition of plasmid-carrying determinants, mainly mcr-1. In the recent years, we have observed the outburst of this resistance gene in our region. Due to the risk of the rapid dissemination of mcr-1, this finding has worried and alerted different actors from the health field and has become one of the most prolific topics. Our review compiles available reports of well-documented mcr-1-positive strains of Enterobacteriaceae, obtained from different samples in Argentina and other countries of Latin America. Furthermore, it addresses the association of mcr-1 with ESBL resistance markers and outlines the platforms involved in their dissemination.

[Molecular epidemiology of carbapenem-resistant isolates of Acinetobacter baumannii in Argentina]. / Epidemiología molecular de aislados de Acinetobacter baumannii resistentes a carbapenems en Argentina.

One hundred sequential, epidemiologically unrelated carbapenem-resistant- Acinetobacter baumannii isolates from 11 hospitals in 10 Argentine provinces were collected between January and August 2016. Genes coding for Ambler class D and B carbapenemases were investigated by PCR using specific primers. All isolates were typed using the 3-locus sequence typing and blaOXA-51-like sequence-based typing techniques. The blaOXA-23 gene was recovered in all isolates studied. The population of carbapenem-resistant- A. baumannii in Argentina was principally associated with ST1 (45%), ST25 (34%) and ST79 (15%). ST25 was recovered in all the regions studied and CC2 was not detected.

Carbapenemases in Acinetobacter baumannii. Review of their dissemination in Latin America.

Carbapenem resistance in gram-negative bacteria by production of carbapenemases is one of the most challenging issues regarding healthcare worldwide. We review the epidemiology and prevalence of carbapenemases in carbapenem-resistant Acinetobacter baumannii isolates from Latin American countries. High resistance rates to antimicrobial agents, particularly to carbapenems, are observed in this region. OXA-23 is the most widely disseminated class D-carbapenemase; it is present in all the countries of the region and is frequently associated to endemic clones CC113/CC79, CC104/CC15, CC110/ST25 and CC109/CC1. The emergence of OXA-72 and NDM-1 represents a novel finding which is observed simultaneously and without clonal relatedness in different countries, some of which are distant from one another, whereas OXA-143 is only present in Brazil. Further collaborative intraregional studies would provide a better understanding of these issues in most of the countries and thus, policies to control the spread of these isolates could be implemented.

[In vitro activity of ampicillin-ceftriaxone against Enterococcus faecalis isolates recovered from invasive infections]. / Actividad in vitro de ampicilina-ceftriaxona frente a aislamientos de Enterococcus faecalis recuperados de infecciones invasivas.

In vitro activity of the combination of ampicillin- ceftriaxone against 30 Enterococcus faecalis isolates recovered from invasive infections in patients admitted to Hospital de Clínicas José de San Martin in the city of Buenos Aires was assessed. Ampicillin- ceftriaxone synergies were determined by microdilution in Müeller-Hinton (MH) broth with and without subinhibitory concentrations of ceftriaxone. Synergy was detected in 22/30 isolates. A decrease in both minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) was observed in 14/30 isolates, whereas in 6/30 isolates the decrease was observed in the MIC value and only in the MBC value in the 2 remaining isolates. The bactericidal activity of the combination showed to be higher at low concentrations of ampicillin (< 1 µg/ml). We detected in vitro synergy using the ampicillin-ceftriaxone combination and thus, its efficacy was confirmed in the treatment of severe infections by E. faecalis.

[Frequency and antimicrobial resistance of Acinetobacter species in a university hospital of Buenos Aires City]. / Frecuencia de aislamiento y resistencia a los antimicrobianos de Acinetobacter spp. recuperadas de pacientes atendidos en un hospital universitario de la Ciudad Autónoma de Buenos Aires, Argentina.

Two-hundred Acinetobacter isolates belonging to 200 patients admitted to Hospital de Clínicas José de San Martín during the period March 2013-June 2014 were analyzed. The identification was performed by mass spectrometry and was confirmed by molecular methods. Susceptibility to antimicrobials was studied by the Vitek-2 system. A 94% correlation of both identification methods was found. Multidrug resistant Acinetobacter baumannii was the predominant genomic species (92.6%) in hospital-acquired infections, whereas Acinetobacter pitti and Acinetobacter nosocomialis accounted for 3.5% and 0.5% of the isolates recovered, respectively. In community-acquired infections a major predominance of the different genomic species was observed. Acinetobacter johnsonii and A. baumannii are the most frequent species, accounting for 45.9% of the isolates recovered. Resistance to carbapenems and minocycline was only observed in A. baumannii. Mass spectrophotometry was an effective tool for the identification of the different genomic species.

[Emergence of colistin-resistant Klebsiella pneumoniae. Microbiological and epidemiological characterization of the isolates producing and non-producing KPC-type carbapenemase]. / Emergencia de la resistencia a colistina en Klebsiella pneumoniae. Caracterización microbiológica y epidemiológica de aislamientos productores y no productores de carbapenemasa de tipo KPC.

Sixty-four colistin-resistant Klebsiella pneumoniae isolates recovered from clinical specimens from 57 patients admitted to Hospital de Clinicas Jose de San Martin during the period 2010-2012 were studied to describe the microbiological and epidemiological characteristics and factors associated with the emergence of colistin-resistance. Fifty-four colistin-susceptible K. pneumoniae isolates from the same period were also included in the study. The genetic relatedness among the isolates was studied by a PCR assay. Fifty percent of the resistant isolates were KPC-2 producers, 45.3% were ESBL producers and 4.7% only showed resistance to aminopenicilins. All KPC-producers (resistant and susceptible to colistin) were genotipically indistinguishable except for one, whereas the presence of 7 clonal types, which were different from the ones identified in the colistin-susceptible isolates, were detected among ESBL producers. The previous use of colistin was the main factor associated with the acquisition of resistance, and in the case of non-KPC producers the stay in ICU was another significant factor observed. Colistin resistance emerged in our hospital in the year 2010, reaching 3% in nosocomial isolates and maintaining this rate in successive years, due to the selection of resistant subpopulations in the epidemic clonal type in KPC-producers and due to the dispersion of colistin-resistant clonal types in non-KPC producing-isolates.

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.

[Resistance to extended-spectrum cephalosporins in non-inducible AmpC enterobacteria: evaluation of the new MIC breakpoints]. / Resistencia a cefalosporinas de espectro extendido en enterobacterias sin AmpC inducible: Evaluación de los nuevos puntos de corte.

The aims of this study were to evaluate the in vitro activity of extended-spectrum cephalosporins (ESC) in non-inducible AmpC enterobacteria throµgh phenotypic and genotypic characterization of the mechanisms of resistance (ESBL, plasmid-mediated AmpC and KPC) and to evaluate the interpretation criteria proposed by the existing recommendations and the new breakpoints established by the CLSI and the EUCAST. Susceptibility tests and PCR multiplex for b/aSHV and b/aCTX-M and amplification using specific primers was performed. One hundred sixty nine resistant isolates: K/ebsie//a pneumoniae (95), Escherichia co/i (55), and Proteus mirabi/is (19) were recovered. ESC resistance was 56.2 %, 32.6%, and 11.2 %, respectively. ESBL was detected in 152 (90 %) isolates, plasmid-mediated AmpC in 12 (7 %) and KPC in 5 (3 %). The CLSI 2009 recommendations and the breakpoints sµggested by the CLSI 2010 and the EUCAST for ceftriaxone were efficacious to detect ESBL, whereas the different breakpoints for ceftazidime presented discrepancies. The CLSI 2010 breakpoints only detected 55 % of the ESBL-producing isolates due to the endemic presence of CTX-M ESBLs in our country. Regarding the plasmid-mediated AmpC producers, the recommendations of the CLSI 2010 and the EUCAST 2010 proved to be more efficient than the old ones.

Molecular and Phenotypic Characterization of a Multidrug-Resistant Escherichia coli Coproducing OXA-232 and MCR-1.1 in Argentina.

The spread of carbapenem-resistant Enterobacterales has raised concern in clinical settings due to the limited therapeutic options available. OXA-48-like enzymes are still sporadic in South America. The aim of this study was to characterize a multidrug-resistant Escherichia coli isolate from a hospitalized patient in Buenos Aires city. The isolate was characterized phenotypically by determination of its susceptibility pattern, synergistic and colorimetric tests, and molecularly, by PCR, whole genome sequencing, and plasmid analysis. It belonged to ST-744, phylogroup A, and serotype O162/O89: H9. It remained susceptible to ceftazidime, meropenem, aminoglycosides, trimethoprim/sulfamethoxazole, and tigecycline. The presence of blaOXA-232 harbored by a nonconjugative plasmid ColKp3, and blaCTX-M-14, mcr-1.1, and fosL1 in 2 conjugative plasmids, together with their genetic environment, was revealed. To the best of our knowledge, this is the first report of the coproduction of the enzyme OXA-232 and the mcr-1.1 gene in an E. coli clinical isolate in South America in a patient who had not received colistin therapy.

In Vitro Activity of Minocycline Against Multidrug-Resistant Acinetobacter baumannii Isolates-Evaluation of Clinical Breakpoints and Review of Literature.

Therapeutic options for the treatment of infections by multidrug-resistant Acinetobacter baumannii strains are often limited. Minocycline (MIN) is an old antibiotic, with excellent activity against A. baumannii isolates, which can be administered orally. Currently, there is no single criterion regarding the breakpoints for MIN and A. baumannii. The activity of MIN was examined against a collection of A. baumannii isolates recovered from 15 hospitals of 6 countries of South America. A review of the literature was also performed. In our series and most of the studies, the percentages of MIN susceptible isolates exceeded 50%, regardless of the breakpoints utilized (4-2 or 1 µg/mL). However, a greater number of isolates not harboring Tet B were considered resistant with the breakpoints of 1 or 2 µg/mL, whereas isolates with tet(B) genes were still detected with minimum inhibitory concentration below all breakpoints considered. Tetracycline susceptibility may be used as a screening to discriminate the populations with and without acquired resistance mechanisms to MIN. In this study, MIN-resistant subpopulations were found in isolates harboring Tet B, with MIC ≤1 µg/mL, and their frequency increased after incubation with MIN. These subpopulations were not detected in isolates not harboring Tet B. The clinical correlation of these subpopulations should be evaluated in future studies.

In-house rapid colorimetric method for detection of ceftazidime/avibactam resistance in carbapenem resistant Enterobacterales.

A rapid colorimetric method, the Andrade screening antimicrobial test, was compared with the E-test method to detect ceftazidime/avibactam (CZA) resistance in carbapenem resistant Enterobacterales clinical isolates. A 106 non-duplicated isolates (86 susceptible and 20 resistant to CZA) were chosen for validation. The sensitivity and specificity were 100%. This method investigates CZA resistance regardless of the resistance mechanism involved. It represents an economical and easy technique that can be applied to routine microbiology laboratories. It allows the detection of CZA resistance at 3 hours of incubation and consequently, the early implementation of accurate therapeutic interventions.

In vitro synergistic activity of aztreonam (AZT) plus novel and old ß-lactamase inhibitor combinations against metallo-ß-lactamase-producing AZT-resistant Enterobacterales.

The emergence of metallo-ß-lactamase (MBL)-producing Enterobacterales, mainly New Delhi metallo-ß-lactamase (NDM), represents a clinical threat due to the limited therapeutic alternatives. Aztreonam (AZT) is stable to MBLs, but most MBL-producing Enterobacterales isolates usually co-harbour other ß-lactamases that confer resistance to AZT and, consequently, its use is restricted in these isolates. We compared the ability of sulbactam (SUL), tazobactam (TAZ), clavulanic acid (CLA) and avibactam (AVI) to restore the AZT activity in MBL-producing AZT-resistant Enterobacterales isolates. A collection of 64 NDM-producing AZT-resistant Enterobacterales from five hospitals in Buenos Aires city, Argentina, were studied during the period July-December 2020. MICs were determined using the agar dilution method with Mueller-Hinton agar according to Clinical and Laboratory Standards Institute (CLSI) recommendations. AVI, SUL and TAZ were used at a fixed concentration of 4 mg l-1, whereas CLA was used at a fixed concentration of 2 mg l-1. A screening method based on disc diffusion to evaluate this synergy was also conducted. Detection of bla KPC, bla OXA, bla NDM, bla VIM, bla CTXM-1, bla PER-2 and bla CIT was performed by PCR. The AZT-AVI combination restored the AZT activity in 98.4 % of AZT-resistant strains, whereas CLA, TAZ and SUL did so in 70.3, 15.6 and 12.5 %, respectively, in isolates co-harbouring extended-spectrum ß-lactamases, but were inactive in isolates harbouring AmpC-type enzymes and/or KPC. The synergy screening test showed an excellent negative predictive value to confirm the absence of synergy, but positive results should be confirmed by a quantitative method. The excellent in vitro performance of the AZT-CLA combination represents a much more economical alternative to AZT-AVI, which could be of use in the treatment of MBL-producing, AZT-resistant Enterobacterales.

In vitro synergistic activity of the sulbactam/avibactam combination against extensively drug-resistant Acinetobacter baumannii.

Introduction. The therapeutic options to treat Acinetobacter baumannii infections are very limited.Aim. Our aim was to evaluate the activity of sulbactam combined directly with avibactam or the ampicillin-sulbactam/ceftazidime-avibactam combination against extensively drug-resistant A. baumannii isolates.Methodology. Extensively drug-resistant A. baumannii isolates (n=127) collected at several South American hospitals were studied. Synergy with the sulbactam/avibactam combination was assessed in all isolates using the agar dilution method. Avibactam was used at a fixed concentration of 4 mg l-1. A disc diffusion synergy test was also performed. Synergy by a time-kill experiment was performed in a selected isolate.Results. Synergy with sulbactam/avibactam was demonstrated in 124 isolates and it showed MIC values ≤4 mg l-1. This synergy was not detected in the three New Delhi metallo-ß-lactamase-harbouring isolates. Similar results were observed with the disc diffusion synergy test of ampicillin-sulbactam/ceftazidime-avibactam. In the time-kill experiments, sulbactam/avibactam showed a rapid synergistic and bactericidal activity in ampicillin-sulbactam-resistant isolates.Conclusions. This study demonstrated that the sulbactam/avibactam combination displayed synergistic activity against A. baumannii isolates. This synergy was observed when both inhibitors were also used as part of the commercially available combinations: ampicillin-sulbactam and ceftazidime-avibactam.

LMB-1 producing Citrobacter freundii from Argentina, a novel player in the field of MBLs.

Carbapenemase-producing Enterobacterales expressing OXA-48, KPC, NDM, VIM or IMP enzymes are increasingly reported worldwide. We have characterized LMB-1, a novel metallo-ß-lactamase (MBL) of Ambler class B3 from Citrobacter freundii 164 (Cf164) clinical isolate from Buenos Aires, Argentina. Cf164 displayed reduced susceptibility to carbapenems but gave inconsistent results with carbapenemase confirmatory tests, indicating the presence of a weak carbapenemase. Analysis of whole-genome sequencing (WGS) of Cf164 using Resfinder revealed four ß-lactamase genes coding for CTX-M-8, PER-2, TEM-1 and CMY-150, a novel chromosomally-encoded CMY variant. Kinetic parameters of purified CMY-150 did not reveal any carbapenemase activity. However, CMY-150 conferred higher minimum inhibitory concentrations (MICs) to E. coli for ceftazidime and aztreonam compared with CMY-2. The in-house-developed ß-lactamase search software (ResMiner) in WGS data revealed a novel subclass B3 MBL named LMB-1. LMB-1 conferred resistance to penicillins and expanded-spectrum cephalosporins and reduced susceptibility to carbapenems in E. coli. The blaLMB-1 gene was located on a 176-kb IncA/C2 plasmid. LMB-1 shared 99% amino acid sequence identity with the MBL encoded in the chromosome of Rheinheimera pacifica, it's likely progenitor. Despite repeated attempts, LMB-1 could not be purified, thus only specific activities could indicate hydrolysis of carbapenems. Here we report on CMY-150, a novel CMY-2 variant that confers increased ceftazidime and aztreonam MICs to E. coli and the first description of LMB-1 in Argentina. This work underlines the need for several carbapenemase-producing Enterobacteriaceae (CPE) confirmatory tests, as this novel enzyme might have been missed using only one.

In-house rapid colorimetric method for detection of colistin resistance in Enterobacterales: A significant impact on resistance rates.

A rapid colorimetric method, the Andrade Screening Antimicrobial Test (ASAT) was evaluated to detect colistin resistance in Enterobacteriales clinical isolates. The sensitivity and specificity were 90.7% and 100%, respectively. In 10/26 E. coli isolates the automatized method failed to detect the resistance, whereas the ASAT detected it accurately. Most of these isolates showed COL MIC values in the range 4-8 µg mL-1 and carried mcr-1. As regards K. pneumoniae COL- resistant isolates, discrepancies between the Phoenix system and the ASAT were observed only in 3/44 isolates, most of them carried the blaKPC gene and showed COL MIC values >16 µg mL-1.

Discrepancies in susceptibility testing to colistin in Acinetobacter baumannii: The influence of slow growth and heteroresistance.

The increasing use of polymyxins as last-resort drugs for managing infections by Acinetobacter baumannii has led to the emergence of resistance. This study aimed to determine the resistance mechanisms in Acinetobacter baumannii isolates with colistin MIC ≥ 4 mg/L and to relate the mechanisms of resistance with the difficulties in detecting them. Absolute agreement among the different methodologies (Phoenix automatized system, broth and agar dilution, and a rapid colorimetric test) in the 140 colistin-susceptible isolates was observed; whereas in the 25 resistant isolates, the performance varied according to the colistin MIC value. Most of the discrepancies (irrespective of the methodology that was used) were observed in isolates with an MIC value close to the breakpoint. The number of errors in each method in the resistant isolates was as follows: rapid test, four of 25 (16%); agar dilution, eight of 25 (32%); Phoenix system, 13 of 25 (52%) and its manual reading at 24 h, eight of 25 (32%). Categorical errors were detected in 13 isolates: slow growth was the main reason in five isolates, whereas in the remaining eight isolates, slow growth was detected together with a low proportion of colistin-resistant subpopulations and the colistin MIC value was close to the breakpoint value. To understand the probable reason for the observed MIC values, sequencing of genes associated with colistin resistance was performed. Mutations at lpxA, lpxC, and pmrB genes were detected and it was observed that isolates carrying mutations in lpxC presented slow growth at killing curves.