Carbapenemase producing Enterobacteriaceae in intensive care units in Ecuador: Results from a multicenter study

Molecular epidemiology of carbapenem-resistant gram-negative bacilli in Ecuador

INTRODUCTION

Carbapenem-resistant gram-negative bacilli are a worldwide concern because of high morbidity and mortality rates. Additionally, the increasing prevalence of these bacteria is dangerous. To investigate the extent of antimicrobial resistance and prioritize the utility of novel drugs, we evaluated the molecular characteristics and antimicrobial susceptibility profiles of carbapenem-resistant Enterobacterales, Pseudomonas aeruginosa and Acinetobacter baumannii in Ecuador in 2022.

METHODS

Ninety-five clinical isolates of carbapenem non-susceptible gram-negative bacilli were collected from six hospitals in Ecuador. Carbapenem resistance was confirmed with meropenem disk diffusion assays following Clinical Laboratory Standard Institute guidelines. Carbapenemase production was tested using a modified carbapenemase inactivation method. Antimicrobial susceptibility was tested with a disk diffusion assay, the Vitek 2 System, and gradient diffusion strips. Broth microdilution assays were used to assess colistin susceptibility. All the isolates were screened for the blaKPC, blaNDM, blaOXA-48, blaVIM and blaIMP genes. In addition, A. baumannii isolates were screened for the blaOXA-23, blaOXA-58 and blaOXA-24/40 genes.

RESULTS

Carbapenemase production was observed in 96.84% of the isolates. The blaKPC, blaNDM and blaOXA-48 genes were detected in Enterobacterales, with blaKPC being predominant. The blaVIM gene was detected in P. aeruginosa, and blaOXA-24/40 predominated in A. baumannii. Most of the isolates showed co-resistance to aminoglycosides, fluoroquinolones, and trimethoprim/sulfamethoxazole. Both ceftazidime/avibactam and meropenem/vaborbactam were active against carbapenem-resistant gram-negative bacilli that produce serin-carbapenemases.

CONCLUSION

The epidemiology of carbapenem resistance in Ecuador is dominated by carbapenemase-producing K. pneumoniae harbouring blaKPC. Extensively drug resistant (XDR) P. aeruginosa and A. baumannii were identified, and their identification revealed the urgent need to implement strategies to reduce the dissemination of these strains.

Risk factors associated with colistin resistance in carbapenemase-producing Enterobacterales: a multicenter study from a low-income country

PURPOSE

The aim of this study was to assess the risk factors for colistin-resistant carbapenemase-producing Enterobacterales (CR-CPE), and describe the mortality associated with this organism, in a low-income country.

METHODS

A descriptive, observational, and prospective multicenter study was carried out in Guayaquil, Ecuador. All patients with carbapenem-resistant Enterobacterales admitted between December 2021 and May 2022 were enrolled. Infection definitions were established according to the Centers for Disease Control and Prevention (CDC) protocols. The presence of carbapenemase-producing Enterobacterales was confirmed with a multiplex PCR for blaKPC, blaNDM, blaOXA-48, blaVIM, and blaIMP genes. MCR-1 production was studied molecularly, and MLST assays were carried out.

RESULTS

Out of 114 patients enrolled in the study, 32 (28.07%) had at least one positive sample for CR-CPE. Klebsiella pneumoniae ST512-KPC-3 was the most frequent microorganism isolated. Parenteral feeding, β-lactamase inhibitor use, recent hemodialysis, and renal failure were all considered independent risk factors for carrying CR-CPE. A mortality of 41.22% was detected, but we could not find any difference between colistin-resistant and colistin-susceptible CPE. MCR-1 production was not detected in any of the isolates studied.

CONCLUSION

A significant burden for CR-CPE was found in a South American country that was mainly caused by the high-risk clone K. pneumoniae ST512-KPC-3 and not mediated by mcr-1 production. Its acquisition involved parenteral feeding, β-lactamase inhibitor use, recent hemodialysis, and renal failure as independent risk factors, demonstrating the critical need for infection prevention and stewardship programs to avoid dissemination to other countries in the region.

Estimation, Evaluation and Characterization of Carbapenem Resistance Burden from a Tertiary Care Hospital, Pakistan

Carbapenem resistance has become major concern in healthcare settings globally; therefore, its monitoring is crucial for intervention efforts to halt resistance spread. During May 2019–April 2022, 2170 clinical strains were characterized for antimicrobial susceptibility, resistance genes, replicon and sequence types. Overall, 42.1% isolates were carbapenem-resistant, and significantly associated with Klebsiella pneumoniae (K. pneumoniae) (p = 0.008) and Proteus species (p = 0.043). Carbapenemases were detected in 82.2% of isolates, with blaNDM-1 (41.1%) associated with the ICU (p < 0.001), cardiology (p = 0.042), pediatric medicine (p = 0.013) and wound samples (p = 0.041); blaOXA-48 (32.6%) was associated with the ICU (p < 0.001), cardiology (p = 0.008), pediatric medicine (p < 0.001), general surgery (p = 0.001), general medicine (p = 0.005) and nephrology (p = 0.020); blaKPC-2 (5.5%) was associated with general surgery (p = 0.029); blaNDM-1/blaOXA-48 (11.4%) was associated with general surgery (p < 0.001), and wound (p = 0.002), urine (p = 0.003) and blood (p = 0.012) samples; blaOXA-48/blaVIM (3.1%) was associated with nephrology (p < 0.001) and urine samples (p < 0.001). Other detected carbapenemases were blaVIM (3.0%), blaIMP (2.7%), blaOXA-48/blaIMP (0.1%) and blaVIM/blaIMP (0.3%). Sequence type (ST)147 (39.7%) represented the most common sequence type identified among K. pneumoniae, along with ST11 (23.0%), ST14 (15.4%), ST258 (10.9%) and ST340 (9.6%) while ST405 comprised 34.5% of Escherichia coli (E. coli) isolates followed by ST131 (21.2%), ST101 (19.7%), ST10 (16.0%) and ST69 (7.4%). Plasmid replicon types IncFII, IncA/C, IncN, IncL/M, IncFIIA and IncFIIK were observed. This is first report describing the carbapenem-resistance burden and emergence of blaKPC-2-ST147, blaNDM-1-ST340 and blaNDM-1-ST14 in K. pneumoniae isolates and blaNDM-1-ST69 and blaNDM-1/blaOXA-48-ST69 in E. coli isolates coharboring extended-spectrum beta-lactamases (ESBLs) from Pakistan.

Risk Factors of Clonally Related, Multi, and Extensively Drug-Resistant Acinetobacter baumannii in Severely Ill COVID-19 Patients

Background

The secondary infection of multi and extensively drug-resistant "Acinetobacter baumannii" in severely ill COVID-19 individuals is usually associated with extended hospitalisation and a high mortality rate. The current study aimed to assess the exact incidence rate of A. baumannii coinfection in severely ill COVID-19 patients admitted to intensive care unit (ICUs), to identify the possible mechanism of A. baumannii transfer to COVID-19 patients and to find out their resistance rate against different antibiotics.

Methods

Fifty severely ill "COVID-19" individuals on respiratory support were selected with samples being collected from the pharynx. In addition, another 60 samples were collected from the surrounding environment. Bacterial isolates were diagnosed by microbiological cultures and confirmed by "Vitek 2 system" and real-time PCR. The "Vitek 2 Compact system" was used to evaluate these isolates for antimicrobial susceptibility. The recovered isolates' DNA fingerprints and genetic similarities were performed using ERIC-PCR.

Results

Twenty-six samples were tested positive for A. baumannii (20 out of 50 samples taken from patients, 40%; 6 out of 60 swabs from a nosocomial setting, 10%). All A. baumannii strains isolated from the nosocomial sites were clonally related (have the same genetic lineage) to some strains isolated from patients. However, the majority of the patients' strains were categorised as belonging to the same genetic lineage. Furthermore, "the multi and extensively drug" resistance patterns were seen in all isolates. In addition, total isolates showed resistance to the most commonly tested antibiotics, while none of them was found to be resistant to tigecycline.

Conclusion

Secondary "A. baumannii" infection in severely ill "COVID-19" patients is a serious matter, especially when it has one spot of transmission in the ICU as well as when it is extensively drug-resistant, necessitating an immediate and tactical response to secure the issue.

Multicenter Study of Carbapenemase-Producing Enterobacterales in Havana, Cuba, 2016–2021

Surveillance of carbapenem resistance is particularly important for Enterobacterales, mainly in countries with limited healthcare resources. We conducted a cross-sectional study to detect carbapenem-resistant Enterobacterales at 10 sentinel hospitals in Havana, Cuba for a six year-period (2016–2021) by the National Reference Laboratory for Health Care-Associated Infections in the Pedro Kourí Institute. A total of 152 isolates were collected with phenotypic production of metallo-β-lactamase. NDM-type carbapenemase was detected in all the 152 isolates, and KPC-type enzyme gene was simultaneously identified in four NDM-positive isolates. The most abundant carbapenemase-producing Enterobacterales (CPE) species was Klebsiella pneumoniae (69.7%), followed by Enterobacter cloacae complex (13.2%), and Escherichia coli (5.9%). Over the study period, among CPE, prevalence of K. pneumoniae was almost constant, while Enterobacter spp. showed slightly increasing tendency. The urinary tract (36.2%) was the most prevalent source of infection with CPE, followed by bloodstream (26.3%) and surgical wound (17.1%), being frequently derived from Intensive Care Units (35.5%) and urology wards (21.7%). This study revealed the present situation of CPE in hospitals in Havana, Cuba, showing the emergence and dissemination of Enterobacterales producing NDM-type carbapenemase, mainly K. pneumoniae.

Empiric Treatment in HAP/VAP: “Don’t You Want to Take a Leap of Faith?”

Ventilator-associated pneumonia is a frequent cause of ICU-acquired infections. These infections are associated with high morbidity and mortality. The increase in antibiotic resistance, particularly among Gram-negative bacilli, makes the choice of empiric antibiotic therapy complex for physicians. Multidrug-resistant organisms (MDROs) related infections are associated with a high risk of initial therapeutic inadequacy. It is, therefore, necessary to quickly identify the bacterial species involved and their susceptibility to antibiotics. New diagnostic tools have recently been commercialized to assist in the management of these infections. Moreover, the recent enrichment of the therapeutic arsenal effective on Gram-negative bacilli raises the question of their place in the therapeutic management of these infections. Most national and international guidelines recommend limiting their use to microbiologically documented infections. However, many clinical situations and, in particular, the knowledge of digestive or respiratory carriage by MDROs should lead to the discussion of the use of these new molecules, especially the new combinations with beta-lactamase inhibitors in empirical therapy. In this review, we present the current epidemiological data, particularly in terms of MDRO, as well as the clinical and microbiological elements that may be taken into account in the discussion of empirical antibiotic therapy for patients managed for ventilator-associated pneumonia.

Perfil bacteriano del shock séptico en una unidad de cuidados intensivos de la altitud del seguro social del Perú

Conocer el perfil bacteriano del shock séptico permitirá una adecuada elección de antibióticos empíricos. Objetivos: a) Describir el perfil bacteriano del shock séptico en una unidad de cuidados intensivos de la altitud. b) Conocer la localización de los cultivos positivos. c) Identificar la sensibilidad y el mecanismo de resistencia bacteriana. d) Encontrar diferencias de los perfiles bacterianos de la altitud. Estudio retrospectivo transversal. Realizado en una unidad de cuidados intensivos a 3,250 “msnm”. Se incluyeron los cultivos positivos y antibiogramas de residentes de la altitud con shock séptico extraídos antes del inicio de los antibióticos durante 7 años. 1,212 muestras. Escherichia coli (18.48%). Las bacterias gramnegativas presentaron sensibilidad para colistina (94-99%) el principal mecanismo de resistencia fue betalactamasa de espectro extendido (43-91%). Staphylococcus aureus (22.19%). Las bacterias grampositivas presentaron sensibilidad para tigecilina, linezolid (100%) y vancomicina (36-100%) el principal mecanismo de resistencia fue ampicilina/sulbactam resistente productor de betalactamasa (50-97%) y meticilino resistente (87-100%). En Conclusión. - a) Escherichia coli la gramnegativa más frecuente y Staphylococcus aureus el grampositivo. b) El cultivo más frecuente provenía del tracto respiratorio inferior. c) De las gramnegativas, Pseudomona aeruginosa mostro elevada sensibilidad para colistina, el resto también para tigecilina. El mecanismo de resistencia más frecuente fue betalactamasa de espectro extendido. Las Bacterias grampositivas tienen una elevada sensibilidad para tigecilina, linezolid y vancomicina. Su mecanismo de resistencia más frecuente fue ampicilina/sulbactam resistente. d) No encontramos diferencias de los perfiles bacterianos informados en la altitud. Recomendamos confirmar los resultados de sensibilidad “in vitro” de Tigeciclina.

Broiler Farms and Carcasses Are an Important Reservoir of Multi-Drug Resistant Escherichia coli in Ecuador

Antimicrobial resistance (AMR) is a major health threat for public and animal health in the twenty-first century. In Ecuador, antibiotics have been used by the poultry industry for decades resulting in the presence of multi-drug resistant (MDR) bacteria in the poultry meat production chain, with the consequent risk for public health. This study evaluated the prevalence of ESBL/AmpC and mcr genes in third-generation cephalosporin-resistant Escherichia coli (3GC-R E. coli) isolated from broiler farms (animal component), broiler carcasses (food component), and human enteritis (human component) in Quito-Ecuador. Samples were collected weekly from November 2017 to November 2018. For the animal, food, and human components, 133, 335, and 302 samples were analyzed, respectively. Profiles of antimicrobial resistance were analyzed by an automated microdilution system. Resistance genes were studied by PCR and Sanger sequencing. From all samples, 122 (91.7%), 258 (77%), and 146 (48.3%) samples were positive for 3GC-R E. coli in the animal, food, and human components, respectively. Most of the isolates (472/526, 89.7%) presented MDR phenotypes. The ESBL bla_CTX-M-55, bla_CTX-M-3, bla_CTX-M-15, bla_CTX-M-65, bla_CTX-M-27, and bla_CTX-M-14 were the most prevalent ESBL genes while bla_CMY-2 was the only AmpC detected gene. The mcr-1 gene was found in 20 (16.4%), 26 (10.1%), and 3 (2.1%) of isolates from animal, food, and human components, respectively. The implication of poultry products in the prevalence of ESBL/AmpC and mcr genes in 3GC-R must be considered in the surveillance of antimicrobial resistance.

Clinical Relevance of Antibiotic Susceptibility Profiles for Screening Gram-negative Microorganisms Resistant to Beta-Lactam Antibiotics

The increasing resistance to antibiotics is compromising the empirical treatment of infections caused by resistant bacteria. Rapid, efficient, and clinically applicable phenotypic methods are needed for their detection. This study examines the phenotypic behavior of β-lactam-resistant Gram-negative bacteria grown on ChromID ESBL medium with ertapenem, cefoxitin, and cefepime disks, reports on the coloration of colonies, and establishes a halo diameter breakpoint for the detection of carbapenemase-producing bacteria. We studied 186 β-lactam-resistant Gram-negative microorganisms (77 with extended spectrum beta lactamase (ESBL), 97 with carbapenemases, and 12 with AmpC β-lactamases (AmpC)). Susceptibility profiles of Gram-negative bacteria that produced ESBL, AmpC, and carbapenemases were similar to the expected profiles, with some differences in the response to cefepime of ESBL-producing microorganisms. Coloration values did not differ from those described by the manufacturer of ChromID ESBL medium. In the screening of carbapenemase production, inhibition halo diameter breakpoints for antibiotic resistance were 18 mm for Enterobacterales and ertapenem, 18 mm for Pseudomonas and cefepime, and 16 mm for Acinetobacter baumannii and cefepime. This innovative phenotypic approach is highly relevant to clinical laboratories, combining susceptibility profiles with detection by coloration of high-priority resistant microorganisms such as carbapenemase-producing A. baumannii, carbapenemase-producing Pseudomonas spp., and ESBL and/or carbapenemase-producing Enterobacterales.

Characterization of carbapenemase-producing Serratia marcescens and whole-genome sequencing for plasmid typing in a hospital in Madrid, Spain (2016–18)

Objectives

Carbapenemase-producing Enterobacterales (CPE) are increasingly recognized in nosocomial infections, also affecting ICU patients. We aimed to characterize the carbapenemase-producing Serratia marcescens (CPSm) isolates recovered in our hospital in Madrid (Spain) between March 2016 and December 2018.

Methods

Overall, 50 isolates from clinical and epidemiological surveillance samples were recovered from 24 patients admitted to the medical ICU and 10 non-ICU-related patients based on their phenotypic resistance. Carbapenemase characterization, antibiotic susceptibility, PFGE clonal relatedness, plasmid characterization, WGS (Illumina-NovaSeq 6000) and phylogenetic analysis were performed.

Results

A single isolate was finally considered for each patient, except for Patient 8 that was colonized by two different isolates (n = 35). Isolates were characterized as VIM-1 (n = 29) or OXA-48 producers (n = 6). Up to seven genetic lineages were found by PFGE, with dominance of two clones. Plasmid characterization confirmed that almost all CPSm carried the same ∼60 kb IncL OXA-48- or VIM-1-encoding plasmid, which was related to the globally disseminated IncL-pOXA-48a. WGS allowed plasmid reconstruction with two variants: IncL-pVIM-1 (∼65 kb) and IncL-pOXA-48 (∼62 kb). blaOXA-48–Tn1999 (∼5 kb) was the unique antibiotic resistance gene in pOXA-48, whereas pVIM-1 plasmids (∼8 kb) harboured a class 1 integron containing 5′-blaVIM-1+aacA4+dfrB1+aadA1+catB2+qacEDelta1+sul1-3′.

Conclusions

Our results confirm the dissemination of CPSm within our institution in both ICU and non-ICU environments, representing two prevalent CPSm clones, and the same IncL-pOXA-48 plasmid previously described in other Enterobacterales, but containing the blaVIM-1 gene. This also reinforces the relevance of species different from Klebsiella pneumoniae or Escherichia coli in the CPE landscape and circulating lineages and plasmids in local CPE epidemiology.

High clinical impact of rapid susceptibility testing on CHROMID ESBL® medium directly from swabs

Background

Antibiotic resistance is a serious public health challenge exacerbated by the widespread use of β-lactam and glycopeptide antibiotics. The identification of resistances is crucial, and CHROMID ESBL medium has been developed to detect enterobacteria with extended-spectrum β-lactamases (ESBL). The objective of this study was to evaluate the potential of this medium to detect other types of resistant bacteria.

Methods

Vancomycin, cefoxitin, imipenem, and cefepime disks were used to measure growth on CHROMID ESBL medium of β-lactam-resistant Gram-negative (83 with ESBL, 57 with carbapenemases, 35 with AmpC and 3 Stenotrophomonas maltophilia) and Gram-positive [37 vancomycin-susceptible (vancoS) microorganisms and 21 vancomycin-resistant (vancoR) Enterococcus faecium] clinical isolates (retrospective study) and colonization by the aforementioned bacteria (prospective study), using 649 rectal swabs, 314 pharyngeal swabs, and 44 swabs from other localizations.

Results

Retrospective study: species grown on the medium exhibited different colors. Growth on the medium was observed for: all ESBL enterobacteria, which were susceptible to imipenem and cefoxitin; 95% of isolates with carbapenemases, mostly resistant to imipenem; 80% of those with AmpC; 86% of vancoR E. faecium isolates; and 42% of vancoS E. faecalis isolates, with large growth inhibition halos around the vancomycin disk. Prospective study: vancoR E. faecium, ESBL Klebsiella, Pseudomonas with carbapenemases, A. baumannii (mostly from rectal swabs), S. maltophilia, Achromobacter xylosoxidans, and Burkholderia cenocepacia (mostly from pharyngeal swabs) were isolated from the 246 positive samples.

Conclusions

CHROMID ESBL medium permitted the differential growth of Gram-negative bacteria, many with ESBL and carbapenemases. ESBL enterobacteria were susceptible to imipenem, carbapenemase-producing microorganisms grew around the imipenem disk, and vancoR E. faecium was isolated on the medium. Results of the prospective study demonstrate the potential clinical relevance of this medium. S. maltophilia was more frequently detected with pharyngeal swabs and ESBL Klebsiella, A. baumannii, and Pseudomonas with rectal swabs.

Tracking KPC-3-producing ST-258 Klebsiella pneumoniae outbreak in a third-level hospital in Granada (Andalusia, Spain) by risk factors and molecular characteristics

The objective of this study was to determine clinical-epidemiological characteristics of the patients and the genetic characteristics of carbapenemase KPC-3-producing Klebsiella pneumoniae isolates belonging to sequence type ST258. The eligible study population was all patients with isolates detected between October 2015 and March 2017. Clinical-epidemiological and microbiological data were gathered on risk factors associated with infection by this clone. Antimicrobial susceptibility was determined using MicroScan system and diffusion in agar. Genes encoding carbapenemases were detected using PCR and Sanger sequencing. The sequence type was assigned by MLST, and the genetic relationship among clinical isolates was determined by pulsed field electrophoresis and by analysis of the genetic environment. The study included 23 individuals with isolates of KPC-3/ST258; the mean age was 77 year, and mean stay pre-isolation was 32 days; 81% received empirical antimicrobial treatment. Isolates were only susceptible to gentamicin (CIM ≤ 2 mg/L), tigecycline (CIM ≤ 1 mg/L), and colistin (CIM ≤ 2 mg/L). The isolates belonged to ST258, with five pulse types or subgroups. All isolates showed amplification of KPC, which was identified as KPC-3 variant. Gene _blaKPC-3 was flanked by insertion sequences Kpn6 and Kpn7 within Tn4401 transposon isoform a. We report, for the first time in Spain, an 18-month outbreak by KPC-3-producing ST258 K. pneumoniae. Its acquisition was associated with a history of antimicrobial therapy, with three treatment options, and with high mortality. The detection of different pulse types is attributable to different introductions of the clone in our setting, supporting the need for multi-resistant isolate surveillance studies.