First clonal spread of KPC-producing Pseudomonas aeruginosa in Buenos Aires, Argentina

Genomic Differences Associated with Resistance and Virulence in Pseudomonas aeruginosa Isolates from Clinical and Environmental Sites

Pseudomonas aeruginosa is a pathogen that causes healthcare-associated infections (HAIs) worldwide. It is unclear whether P. aeruginosa isolated from the natural environment has the same pathogenicity and antimicrobial resistance potential as clinical strains. In this study, virulence- and resistance-associated genes were compared in 14 genomic sequences of clinical and environmental isolates of P. aeruginosa using the VFDB, PATRIC, and CARD databases. All isolates were found to share 62% of virulence genes related to adhesion, motility, secretion systems, and quorum sensing and 72.9% of resistance genes related to efflux pumps and membrane permeability. Our results indicate that both types of isolates possess conserved genetic information associated with virulence and resistance mechanisms regardless of the source. However, none of the environmental isolates were associated with high-risk clones (HRCs). These clones (ST235 and ST111) were found only in clinical isolates, which have an impact on human medical epidemiology due to their ability to spread and persist, indicating a correlation between the clinical environment and increased virulence. The genomic variation and antibiotic susceptibility of environmental isolates of P. aeruginosa suggest potential biotechnological applications if obtained from sources that are under surveillance and investigation to limit the emergence and spread of antibiotic resistant strains.

Genomics and Antimicrobial Susceptibility of Clinical Pseudomonas aeruginosa Isolates from Hospitals in Brazil

Pseudomonas aeruginosa, an opportunistic pathogen causing infections in immunocompromised patients, usually shows pronounced antimicrobial resistance. In recent years, the frequency of carbapenemases in P. aeruginosa has decreased, which allows use of new beta-lactams/combinations in antimicrobial therapy. Therefore, the in vitro evaluation of these drugs in contemporary isolates is warranted. We evaluated the antimicrobial susceptibility and genomic aspects of 119 clinical P. aeruginosa isolates from 24 different hospitals in Brazil in 2021-2022. Identification was performed via MALDI-TOF-MS, and antimicrobial susceptibility was identified through broth microdilution, gradient tests, or disk diffusion. Whole-genome sequencing was carried out using NextSeq equipment. The most active drug was cefiderocol (100%), followed by ceftazidime-avibactam (94.1%), ceftolozane-tazobactam (92.4%), and imipenem-relebactam (81.5%). Imipenem susceptibility was detected in 59 isolates (49.6%), and the most active aminoglycoside was tobramycin, to which 99 (83.2%) isolates were susceptible. Seventy-one different sequence types (STs) were detected, including twelve new STs described herein. The acquired resistance genes bla_CTX-M-2 and bla_KPC-2 were identified in ten (8.4%) and two (1.7%) isolates, respectively. Several virulence genes (exoSTUY, toxA, aprA, lasA/B, plcH) were also identified. We found that new antimicrobials are effective against the diverse P. aeruginosa population that has been circulating in Brazilian hospitals in recent years.

Characterization of blaKPC-2 harboring plasmids recovered from Pseudomonas aeruginosa ST654 and ST235 high-risk clones

OBJECTIVE

to describe two bla_KPC-2 plasmids recovered from P. aeruginosa isolates belonging to the ST654 and ST235 high-risk clones, and to compare with complete sequences of bla_KPC-2 harboring plasmids available in public databases.

METHODS

Antimicrobial susceptibility was determined according to CLSI guidelines. Genomes were sequenced using an Illumina MiSeq platform and bla_KPC-2 plasmid sequences were achieved using MinION platform. Sequences were analyzed using Unicycler and RAST. In silico predictions of the isolates sequence type (ST), antimicrobial resistance genes, plasmid replicon typing and MOB relaxases were fulfilled using bioinformatics tools.

RESULTS

PA_2047 and PA_HdC isolates corresponded to the high-risk clones ST654 and ST235, respectively. The carbapenem resistance was mediated by KPC-2. Both bla_KPC-2 harboring plasmids, pPA_2047 and pPA_HdC, were different among them, non-conjugative and untypable by PlasmidFinder. pPA_2047 presented high identity with a Pae-13 plasmid and these both located bla_KPC-2 in Tn4401b isoform. pPA_HdC displayed a novel architecture, and the genetic context of bla_KPC-2 was original. Besides the bla_KPC-2 gene, resistance genes to aminoglycosides and quinolones were detected, including the novel phosphotransferase CrpP in PA_HdC.

CONCLUSION

This study expands the limited knowledge about the molecular epidemiology of bla_KPC-2 in P. aeruginosa from Latin America. Two novel plasmids harboring bla_KPC-2 were described which were untypable by their incompatibility group. The plasmid recovered from P. aeruginosa PA_HdC (ST235) displayed a novel architecture and an original context for bla_KPC-2. On the other hand, the genetic platform carrying bla_KPC-2 in P. aeruginosa PA_2047 (ST654) seems to a be a classical one.

Genetic Diversity of Multidrug-Resistant Pseudomonas aeruginosa Isolates Carrying bla VIM-2 and bla KPC-2 Genes That Spread on Different Genetic Environment in Colombia

Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen with an increase in the frequency of infections caused by multidrug resistant (MDR) and extensively drug resistant (XDR) strains, limiting the available therapeutic options. The most troublesome resistance is the acquisition and production of carbapenemases such as Verona integron-encoded metallo-β-lactamases (VIM), the most frequent and widespread, and the Klebsiella pneumoniae carbapenemases (KPC), which has continuously spread in the last decade. Its dissemination is linked to their location on mobile genetic elements (MGEs). In Colombia, VIM and KPC have been increasing in its frequency showing major successful dissemination. In this article, we molecularly characterized and analyzed the genetic context of bla _VIM and bla _KPC in carbapenem-resistant P. aeruginosa (CRPA) isolates from infected and colonized patients in two tertiary-care hospitals, one in Medellín and the other in a municipality close to Medellín, both areas with high carbapenemase endemicity in Colombia (2013-2015). Using whole-genome sequencing (WGS), we identified a remarkable variety of genetic backgrounds in these MDR P. aeruginosa isolates carrying bla _{KPC- 2} and bla _{VIM- 2}. There were a diversity of class 1 integron and variations in the gene cassettes associated to bla _{VIM- 2}, as well as a possible event of spread of bla _{KPC- 2} mediated by a plasmid that contained part of Tn4401b in one infection case. The dissemination of bla _{VIM- 2} and bla _{KPC- 2} in P. aeruginosa in this area in Colombia has been strongly influenced by successful international clones, carrying these genes and additional determinants of resistance on MGEs, accompanied by gene rearrangement under an antimicrobial selection pressure. These findings emphasize the need to implement control strategies based on rational antibiotic use.

Multidrug-Resistance Genes in Pseudomonas aeruginosa from Wound Infections in a Tertiary Health Institution in Osogbo, Nigeria

BACKGROUND

Multidrug Resistant Pseudomonas aeruginosa (MDRPA) is a ubiquitous opportunistic organism that poses threat to the management of infections globally.

OBJECTIVES

The objectives of the current research were to assess the antibiotic resistance profiles as well as Multiple Antibiotic Resistance (MAR) Index of clinical isolates of P. aeruginosa associated with wound infections. Presence of Extended Spectrum Beta Lactamase genes (bla CTX-M, bla SHV and bla TEM) and Carbapenemase genes (bla KPC and blaNDM) were also determined among the isolates.

METHODS

Swab samples were collected from 255 patients with wound infections. Bacterial identification was done by standard diagnostic tests. The identity of isolates was confirmed by the detection of the exoA gene using the PCR technique. Antibiotic susceptibility testing and resistance profile were determined using the disc diffusion method. Resistance genes were amplified by the PCR method.

RESULTS

A total of 235 (92.2%) bacterial isolates were recovered from the wounds of the 255 patients, of these, 124 (52.8%) were Gram-negative bacilli while the remaining 111 (47.2%) were Gram-positive cocci. A total of 69 Pseudomonas aeruginosa strains were recovered from the wound specimens. Imipenem was the most effective antibiotic against these isolates (92.8% isolates were susceptible) while all isolates were resistant to Meropenem, Cefepime, Ticarcillin, Amoxicillin-clavulanic acid, Cefotaxime, Ampicillin and Cefpodoxime. All 69 Pseudomonas aeruginosa isolates were multidrug resistant (MDR). Of the isolates selected for PCR, all were positive for TEM, CTX-M and SHV genes while one-third were blaKPC and blaNDM producers.

CONCLUSION

This study demonstrated high prevalence of carbapenem-resistant strains of P. aeruginosa, suggesting that there is an urgent need in Nigeria for the enactment and enforcement of policies and necessary laws restricting the availability and indiscriminate use of antibiotics.

Molecular epidemiology, resistance, and virulence properties of Pseudomonas aeruginosa cross-colonization clonal isolates in the non-outbreak setting

Pseudomonas aeruginosa is the predominant opportunistic pathogen leading to nosocomial infection and outbreak in hospitals. Hospitalized patients may be infected with this bacterium through close contact with contaminated environmental media. However, the molecular epidemiology, resistance, and virulence properties of Pseudomonas aeruginosa cross-colonization isolates has received limited attention in the non-outbreak setting. This study aims to investigate the epidemiological relationship of clinical and environmental P. aeruginosa isolates and to characterize the resistance and virulence properties of clonal clusters and sporadic strains in a non-outbreak setting. A total of 436 patients were screened for P. aeruginosa during hospitalization, and environmental samples were taken from their immediate ward media, including faucets, doorknobs, bedrails, pillows, quilts, and mattresses. As a result, 100 P. aeruginosa isolates were obtained, including 74 clinical strains and 26 environmental strains. By using Pulsed-Field Gel Electrophoresis, the fingerprint displayed 20 distinct clusters and 44 sporadic strains. According to identical genotypes, there were clear P. aeruginosa cross-colonization processes from the ward media to inpatients, indicating faucets, bedrails, and pillows as the main propagation media that had been contaminated by clonal isolates previously detected in other patients. In addition, there were P. aeruginosa transmission processes between inpatients that were unexplained for lack of epidemiological evidence. As compared to sporadic strains of P. aeruginosa, clonal clusters are more capable of producing high-level biofilm, developing multi-drug resistance and inducing high-degree cytotoxicity. Among P. aeruginosa clonal clusters, there was a strong positive correlation between antibiotic resistance and biofilm production. We conclude that constant cross-colonization of P. aeruginosa clonal isolates will pose a long-term serious threat in terms of nosocomial outbreaks. Thus, strict disinfection and sterilization procedures should be implemented for ward media, and P. aeruginosa in environments and patients should be closely monitored, especially those strains with strong resistance and virulence.

The epidemiology of carbapenemases in Latin America and the Caribbean

INTRODUCTION

Enterobacteriaceae, Pseudomonas spp., and Acinetobacter spp. infections are major causes of morbidity and mortality, especially due to the emergence and spread of β-lactamases. Carbapenemases, which are β-lactamases with the capacity to hydrolyze or inactivate carbapenems, have become a serious concern as they have the largest hydrolytic spectrum and therefore limit the utility of most β-lactam antibiotics. Areas covered: Here, we present an update of the current status of carbapenemases in Latin America and the Caribbean. Expert commentary: The increased frequency of reports on carbapenemases in Latin America and the Caribbean shows that they have successfully spread and have even become endemic in some countries. Countries such as Brazil, Colombia, Argentina, and Mexico account for the majority of these reports. Early suspicion and detection along with implementation of antimicrobial stewardship programs in all healthcare settings are crucial for the control and prevention of carbapenemase-producing bacteria.

Similar frequencies of Pseudomonas aeruginosa isolates producing KPC and VIM carbapenemases in diverse genetic clones at tertiary-care hospitals in Medellín, Colombia

Carbapenem-resistant Pseudomonas aeruginosa has become a serious health threat worldwide due to the limited options available for its treatment. Understanding its epidemiology contributes to the control of antibiotic resistance. The aim of this study was to describe the clinical and molecular characteristics of infections caused by carbapenem-resistant P. aeruginosa isolates in five tertiary-care hospitals in Medellín, Colombia. A cross-sectional study was conducted in five tertiary-care hospitals from June 2012 to March 2014. All hospitalized patients infected by carbapenem-resistant P. aeruginosa were included. Clinical information was obtained from medical records. Molecular analyses included PCR for detection of bla(VIM), bla(IMP), bla(NDM), bla(OXA-48), and bla(KPC) genes plus pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) for molecular typing. A total of 235 patients were enrolled: 91.1% of them were adults (n = 214), 88.1% (n = 207) had prior antibiotic use, and 14.9% (n = 35) had urinary tract infections. The bla(VIM-2) and bla(KPC-2) genes were detected in 13.6% (n = 32) and 11.5% (n = 27), respectively, of all isolates. Two isolates harbored both genes simultaneously. For KPC-producing isolates, PFGE revealed closely related strains within each hospital, and sequence types (STs) ST362 and ST235 and two new STs were found by MLST. With PFGE, VIM-producing isolates appeared highly diverse, and MLST revealed ST111 in four hospitals and five new STs. These results show that KPC-producing P. aeruginosa is currently disseminating rapidly and occurring at a frequency similar to that of VIM-producing P. aeruginosa isolates (approximately 1:1 ratio) in Medellín, Colombia. Diverse genetic backgrounds among resistant strains suggest an excessive antibiotic pressure resulting in the selection of resistant strains.

Characterization of carbapenem-resistant Pseudomonas aeruginosa clinical isolates, carrying multiple genes coding for this antibiotic resistance

Background

Carbapenemase genes are one of the most frequent mechanisms reported in carbapenem-resistant P. aeruginosa; however, description of P. aeruginosa co-harbouring two or more carbapenemases is unusual.

Methods

In this study we evaluated the presence of carbapenemase genes and the clonality of P. aeruginosa isolates obtained from a hospital over a 12-year period. A total of 127 isolates of carbapenem-resistant P. aeruginosa recovered from 109 patients feces (four samples), rectal swab (three samples), nasal swab (one sample) and anal abscess (one sample), were evaluated. Minimum inhibitory concentrations of the following antibiotics imipenem, meropenem and polymyxin E were determined by broth microdilution. The molecular profile of isolates was evaluated by pulsed field gel electrophoresis (PFGE). PCR for the following carbapenemase genes bla_IMP;bla_SPM;bla_VIM;bla_SIM;bla_NDM;bla_KPC;bla_GES and nucleotide sequencing to confirm the enzyme gene types were performed and compared with the database available on the Internet (BLAST-http://www.ncbi.nlm.nhi.gov/blast/).

Results

All isolates were carbapenem-resistant, their MIC₅₀ and MIC₉₀ were respectively 64 μg/mL and 256 μg/mL to imipenem and 32 μg/mL and 256 μg/mL to meropenem, all isolates except one (MIC = 8 mg/L) were susceptible to polymyxin E. The most frequent carbapenemase genes identified were bla_SPM identified in 41 isolates (32%), followed by 10 with bla_kpc and 5 with bla_VIM (3.9%). All belonged to the class SPM-1 and VIM-2. In 2011, one isolate harbouring three carbapenemase genes (SPM-1, VIM-2 and KPC-2) that belonged to a new clone was identified in a hematopoietic stem cell transplanted patient. Then, 19 carbapenem-resistant P. aeruginosa were identified in an outbreak that occurred in the bone marrow transplant unit, all positive for SPM-1 gene, and 9 (47.3%) harbored both SPM-1 and KPC.

Conclusion

Our findings showed that PCR for KPC gene should be performed to evaluate carbapenem resistance in P. aeruginosa and that this agent can harbor more than one carbapenemase gene. Attention should be focused on the possible rapid spread of KPC in P. aeruginosa isolates and for the fact that P. aeruginosa may become a reservoir of this transmissible resistance mechanism.

Current status of carbapenemases in Latin America

Enterobacteriaceae and non fermenting Gram-negative bacilli have become a threat to public health, in part due to their resistance to multiple antibiotic classes, which ultimately have led to an increase in morbidity and mortality. β-lactams are currently the mainstay for combating infections caused by these microorganisms, and β-lactamases are the major mechanism of resistance to this class of antibiotics. Within the β-lactamases, carbapenemases pose one of the gravest threats, as they compromise one of our most potent lines of defense, the carbapenems. Carbapenemases are being continuously identified worldwide; and in Latin America, numerous members of these enzymes have been reported. In this region, the high incidence of reports implies that carbapenemases have become a menace and that they are an issue that must be carefully studied and analyzed.