Molecular investigation of carbapenem resistance among multidrug-resistant Pseudomonas aeruginosa isolated clinically in Thailand

Molecular characterization of carbapenem-resistant Pseudomonas aeruginosa isolated from four medical centres in Iran

BACKGROUND

Understanding the mechanisms of antibiotic resistance is important for designing new therapeutic options and controlling resistant strains. The goal of this study was to look at the molecular epidemiology and mechanisms of resistance in carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates from Tabriz, Iran.

METHODS

One hundred and forty P. aeruginosa were isolated and antibiotic susceptibility patterns were determined. Overproduction of AmpC and efflux pumps were discovered using phenotypic techniques. Polymerase chain reaction (PCR) was used to determine the presence of carbapenemase-encoding genes. In addition, the expressions of OprD and efflux pumps were evaluated by the Real-Time PCR. Random amplified polymorphic DNA typing (RAPD) was performed for genotyping.

RESULTS

Among 140 P. aeruginosa isolates, 74 (52.8%) were screened as CRPA. Overexpression of efflux systems was observed in 81% of isolates, followed by decreased expression of OprD (62.2%), presence of carbapenemase genes (14.8%), and overproduction of AmpC (13.5%). In most isolates, carbapenem resistance was multifactorial (60.8%). According to our results, the prevalence of CRPA is at alarming levels. Overexpression of efflux systems was the most common mechanism of carbapenem resistance.

CONCLUSION

Most isolates may originate in patients themselves, but cross-infection is possible. Therefore, we suggest a pattern shift in the strategy of CRPA in our setting.

Phage Revolution Against Multidrug-Resistant Clinical Pathogens in Southeast Asia

Southeast Asia (SEA) can be considered a hotspot of antimicrobial resistance (AMR) worldwide. As recent surveillance efforts in the region reported the emergence of multidrug-resistant (MDR) pathogens, the pursuit of therapeutic alternatives against AMR becomes a matter of utmost importance. Phage therapy, or the use of bacterial viruses called bacteriophages to kill bacterial pathogens, is among the standout therapeutic prospects. This narrative review highlights the current understanding of phages and strategies for a phage revolution in SEA. We define phage revolution as the radical use of phage therapy in infectious disease treatment against MDR infections, considering the scientific and regulatory standpoints of the region. We present a three-phase strategy to encourage a phage revolution in the SEA clinical setting, which involves: (1) enhancing phage discovery and characterization efforts, (2) creating and implementing laboratory protocols and clinical guidelines for the evaluation of phage activity, and (3) adapting regulatory standards for therapeutic phage formulations. We hope that this review will open avenues for scientific and policy-based discussions on phage therapy in SEA and eventually lead the way to its fullest potential in countering the threat of MDR pathogens in the region and worldwide.

Molecular epidemiology and carbapenem resistance of Pseudomonas aeruginosa isolated from patients with burns

OBJECTIVE

The aim of this study was to investigate the molecular epidemiology and carbapenem resistance mechanisms of Pseudomonas aeruginosa isolated from patients with burns in Azerbaijan, Iran.

METHOD

Pseudomonas aeruginosa was isolated from 38 patients with burns. Disk diffusion and agar dilution methods were used to determine antibiotic susceptibility patterns. The overproduction of AmpC β-lactamase and efflux pumps were detected by phenotypic methods. The presence of carbapenemase-encoding genes was detected by multiplex polymerase chain reaction (PCR). Expression of the OprD gene and MexAB efflux pumps were also evaluated with real-time PCR. Random amplified polymorphic DNA typing (RAPD-PCR) was used for genotyping of carbapenem-resistant Pseudomonas aeruginosa (CRPA).

RESULTS

Minimum inhibitory concentration (MIC) assays demonstrated high levels of resistance to all classes of antibiotics except colistin and polymyxin B. The initial screening by carbapenem disks indicated 24 isolates (63.15%) as CRPA. Different mechanisms of carbapenem resistance were observed, including carbapenemase production (8.4%), overexpression of AmpC (25%) and decreased expression of OprD (75%). The overexpression of MexAB efflux pumps was detected in 19 (79.1%) isolates by phenotypic assay or real-time PCR. The resistance to carbapenem was multifactorial in most cases (58.3%). The RAPD genotyping revealed different patterns with nine clusters.

CONCLUSION

According to our results, the prevalence of CRPA is at an alarming level. Our results did not demonstrate an epidemic clone. The most common mechanism of carbapenem resistance was decreased expression of OprD. Therefore, we suggest a reconsideration in the management of CRPA infections of patients in our burn care hospital in Azerbaijan, Iran.

Antimicrobial and antibiofilm activities of meropenem loaded-mesoporous silica nanoparticles against carbapenem-resistant Pseudomonas aeruginosa

The aims of the present study were the determination of antimicrobial and antibiofilm effects of meropenem-loaded mesoporous silica nanoparticles (MSNs) on carbapenem resistant Pseudomonas aeruginosa (P. aeruginosa) and cytotoxicity properties in vitro. The meropenem-loaded MSNs had shown antibacterial and biofilm inhibitory activities on all isolates at different levels lower than MICs and BICs of meropenem. The viability of HC-04 cells treated with serial concentrations as MICs and BICs of meropenem-loaded MSNs was 92-100%. According to the obtained results, meropenem-loaded MSNs display the significant antibacterial and antibiofilm effects against carbapenem resistant and biofilm forming P. aeruginosa and low cell toxicity in vitro. Then, the prepared system can be an appropriate option for the delivery of carbapenem for further evaluation in vivo assays.

It's Not Easy Being Green: A Narrative Review on the Microbiology, Virulence and Therapeutic Prospects of Multidrug-Resistant Pseudomonas aeruginosa

Pseudomonas aeruginosa is the most frequent cause of infection among non-fermenting Gram-negative bacteria, predominantly affecting immunocompromised patients, but its pathogenic role should not be disregarded in immunocompetent patients. These pathogens present a concerning therapeutic challenge to clinicians, both in community and in hospital settings, due to their increasing prevalence of resistance, and this may lead to prolonged therapy, sequelae, and excess mortality in the affected patient population. The resistance mechanisms of P. aeruginosa may be classified into intrinsic and acquired resistance mechanisms. These mechanisms lead to occurrence of resistant strains against important antibiotics-relevant in the treatment of P. aeruginosa infections-such as β-lactams, quinolones, aminoglycosides, and colistin. The occurrence of a specific resistotype of P. aeruginosa, namely the emergence of carbapenem-resistant but cephalosporin-susceptible (Car-R/Ceph-S) strains, has received substantial attention from clinical microbiologists and infection control specialists; nevertheless, the available literature on this topic is still scarce. The aim of this present review paper is to provide a concise summary on the adaptability, virulence, and antibiotic resistance of P. aeruginosa to a readership of basic scientists and clinicians.

AcGI1, a novel genomic island carrying antibiotic resistance integron In687 in multidrug resistant Achromobacter xylosoxidans in a teaching hospital in Thailand

This study investigated the genetic basis of multidrug resistance in two strains of Achromobacter xylosoxidans isolated from patients attending a hospital in Thailand in 2012. These isolates were highly resistant to cephalosporins, aminoglycosides, fluoroquinolones, co-trimoxazole and carbapenems. Whole genome sequencing revealed that the two isolates were not clonally related and identified a carbapenem resistance gene-habouring integron (In687), residing in a novel genomic island, AcGI1. This In687 shares 100% identical nucleotide sequence with ones found in Acinetobacter baumannii Aci 16, isolated from the same hospital in 2007. We report the first analysis of multidrug-resistant A. xylosoxidans isolated in Thailand, and the first example of this island in A. xylosoxidans. Our data support the idea that resistance has spread in Thailand via horizontal gene transfer between species and suggest the possibility of A. xylosoxidans may serve as a reservoir of antibiotic resistance, especially in hospital setting.

Carbapenem-Resistant but Cephalosporin-Susceptible Pseudomonas aeruginosa in Urinary Tract Infections: Opportunity for Colistin Sparing

This paper briefly reports the occurrence and epidemiology of carbapenem-resistant but cephalosporin-susceptible (Car-R/Ceph-S) Pseudomonas aeruginosa isolates from urinary tract infections (UTIs) in a tertiary-care hospital in the Southern Region of Hungary, and the phenotypic characterization of the possible resistance mechanisms in these isolates. Isolates and data were collected regarding P. aeruginosa UTIs corresponding to the period between 2008 and 2017. Susceptibility testing was performed using the Kirby-Bauer disk diffusion method; minimum inhibitory concentrations (MICs) of the isolates were determined using E-tests. The phenotypic detection of ampicillin C-type (AmpC) β-lactamases, efflux pump overexpression and carbapenemase production was also performed. P. aeruginosa represented n = 575 (2.72% ± 0.64%) from outpatient, and n = 1045 (5.43% ± 0.81%) from inpatient urinary samples, respectively. Based on the disk diffusion test, n = 359 (22.16%) were carbapenem-resistant; in addition to carbapenems, n = (64.34%) were also resistant to ciprofloxacin; n = (60.17%) to gentamicin/tobramycin; n = (58.51%) to levofloxacin; and n = (27.57%) to amikacin. From among the carbapenem-resistant isolates, n = 56 (15.59%) isolates were multidrug-resistant, while n = 16 (4.46%) were extensively drug-resistant. From among the Car-R/Ceph-S isolates (n = 57), overexpression of AmpC was observed in n = 7 cases (12.28%); carbapenemase production in n = 4 (7.02%); while overexpression of efflux pumps was present in n = 31 (54.39%) isolates. To spare last-resort agents, e.g., colistin, the use of broad-spectrum cephalosporins or safe, alternative agents should be considered in these infections.

A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas

Multidrug resistance (MDR) represents a global threat to health. Here, we used whole genome sequencing to characterise Pseudomonas aeruginosa MDR clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicates that: 1) these large plasmids comprise an emerging family present in different members of the Pseudomonas genus, and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the accessory genome of the megaplasmid family is highly flexible and diverse. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.

Characterization of carbapenem-resistant but cephalosporin-susceptible Pseudomonas aeruginosa

In this study, mechanisms of carbapenem resistance in carbapenem-resistant but cephalosporin-susceptible (Car-R/Ceph-S) Pseudomonas aeruginosa were investigated. A total of 243 P. aeruginosa isolates were studied. The disk diffusion and agar dilution methods were used for determination of antibiotic susceptibility patterns. AmpC and efflux pump overproductions were detected by phenotypic methods. The presence of carbapenemase-encoding genes was detected by polymerase chain reaction (PCR). The expression of OprD, MexAB-OprM, and MexXY-OprM efflux pumps was assessed by real-time PCR. According to disk diffusion method, altogether 116 P. aeruginosa isolates (47.7%) were carbapenem-resistant and among them, 23 isolates (19.8%) were cephalosporin-susceptible. Carbapenemase producer was not detected. Overexpression of AmpC was detected in one (4.3%) isolate that was ceftazidime-susceptible but cefepime-resistant. Overexpression of MexAB-OprM and MexXY-OprM efflux pumps was detected in 12 (60.9%) and 16 (68.8%) of isolates, respectively. A total of 16 (68.8%) isolates showed decreased expression of OprD. The Car-R/Ceph-S P. aeruginosa did not develop by carbapenemase production. The resistance to carbapenem was mediated in our clinical isolates by decreased expression of OprD and overexpression of MexAB-OprM and MexXY-OprM efflux systems or the combination of these mechanisms.

Role of outer membrane permeability, efflux mechanism, and carbapenemases in carbapenem-nonsusceptible Pseudomonas aeruginosa from Dubai hospitals: Results of the first cross-sectional survey

OBJECTIVES

Carbapenem resistance in Pseudomonas aeruginosa is growing and results from variable mechanisms. The objectives of the current study were to investigate mechanisms of carbapenem resistance and genetic relatedness of P. aeruginosa isolates recovered in Dubai hospitals.

METHODS

From June 2015 through June 2016, carbapenem-nonsusceptible P. aeruginosa were collected from 4 hospitals in Dubai, and subjected to antimicrobial susceptibility testing, molecular investigation of carbapenemases by PCR-sequencing, analysis of outer membrane porin OprD2 and multidrug efflux channel MexAB-OprM levels by qPCR, and fingerprinting by ERIC-PCR.

RESULTS

Out of 1969 P. aeruginosa isolated during the study period, 471 (23.9%) showed reduced carbapenem susceptibility. Of these, 37 were analyzed and 32% of them produced VIM-type metallo-β-lactamases, including VIM-2, VIM-30, VIM-31, and VIM-42, while GES-5 and GES-9 co-existed with VIM in 5.4% of isolates. Outer membrane impermeability was observed in 73% of isolates and 75.6% displayed overproduced MexAB-OprM. ERIC-PCR revealed one large clone including most carbapenemase-producing isolates indicating clonal dissemination.

CONCLUSION

This is the first study on carbapenem-nonsusceptible P. aeruginosa from Dubai, incriminating VIM production as well as outer membrane permeability and efflux systems as resistance mechanisms. Further studies on carbapenem-nonsusceptible P. aeruginosa in Dubai are warranted for containment of such health hazard.

Epidemiology and risk factors of extensively drug-resistant Pseudomonas aeruginosa infections

BACKGROUND

The incidence of nosocomial infections from extensively drug-resistant Pseudomonas aeruginosa (XDR-PA) has been increasing worldwide. We investigated the prevalence and factors associated with XDR-PA infections, including the factors that predict mortality.

METHODS

We retrospectively studied a cohort of adult, hospitalized patients with P. aeruginosa (PA) infections between April and December 2014.

RESULTS

Of the 255 patients with PA infections, 56 (22%) were due to XDR-PA, 32 (12.5%) to multidrug resistant Pseudomonas aeruginosa (MDR-PA), and 167 (65.5%) to non-MDR PA. Receiving total parenteral nutrition (adjusted OR [aOR] 6.21; 95% CI 1.05-36.70), prior carbapenem use (aOR 4.88; 95% CI 2.36-10.08), and prior fluoroquinolone use (aOR 3.38; 95% CI 1.44-7.97) were independently associated with the XDR-PA infections. All XDR-PA remained susceptible to colistin. Factors associated with mortality attributable to the infections were the presence of sepsis/septic shock (aOR 11.60; 95% CI 4.66-28.82), admission to a medical department (aOR 4.67; 95% CI 1.81-12.06), receiving a central venous catheter (aOR 3.78; 95% CI 1.50-9.57), and XDR-PA infection (aOR 2.73; 95% CI 1.05-7.08).

CONCLUSION

The prevalence of XDR-PA infections represented almost a quarter of Pseudomonas aeruginosa hospital-acquired infections and rendered a higher mortality. The prompt administration of an appropriate empirical antibiotic should be considered when an XDR-PA infection is suspected.

Berberine inhibits the MexXY-OprM efflux pump to reverse imipenem resistance in a clinical carbapenem-resistant Pseudomonas aeruginosa isolate in a planktonic state

Pseudomonas (P.) aeruginosa is an ubiquitous and metabolically versatile opportunistic pathogen and may cause various life-threatening diseases. Due to increasing emergence of resistance to carbapenems, novel drugs with improved antibacterial activities compared with those of traditional antibiotics are required. In the present study, berberine (BEB), a natural isoquinoline alkaloid, was used in combination with imipenem (IMP), a commonly-used carbapenem, to investigate their antibacterial activities against a clinical P. aeruginosa isolate PA012 and the potential mechanism. Screening revealed that the minimum inhibitory concentrations (MICs) of BEB and IMP were 512 and 256 µg/ml, respectively. The combination of BEB (1/4 MIC) and IMP (1/8 MIC) exhibited a synergistic effect with a fractional inhibitory concentration index of 0.375. The synergism of BEB and IMP was also demonstrated in a time-kill test and by scanning electron microscopic observation. Treatment with BEB at ¼ MIC in combination with IMP at 1/16, 1/8, 1/4 and ½ MIC revealed a concentration-dependent promoting effect of IMP on the intracellular accumulation of BEB and inhibition of bacterial adhesion. Further analysis of gene expression revealed that BEB (1/4 MIC) combined with IMP (1/8 MIC) decreased MexZ, MexX, MexY and outer membrane protein (Opr)M by 38, 35, 46 and 49% in PA012. In conclusion, these results suggested that IMP had synergistic effects with BEB against the clinical isolate PA012 via inhibition of the MexXY-OprM efflux pump.

Molecular epidemiological survey of bacteremia by multidrug resistant Pseudomonas aeruginosa: the relevance of intrinsic resistance mechanisms

The bacterial factors associated with bacteremia by multidrug-resistant and extensively drug-resistant P. aeruginosa, including overexpression of efflux pumps, AmpC overproduction, and loss/alteration of the OprD porin in isolates that are non-Metallo-β-Lactamase producing were analyzed in a retrospective study. Molecular analyses included strain typing by Pulsed Field Gel Electrophoresis and identification of key genes via qualitative and quantitative PCR-based assays. Previous use of carbapenems and tracheostomy was independently associated with the development of bacteremia by extensively drug-resistant and multidrug-resistant strains of P. aeruginosa. A high consumption of antimicrobials was observed, and 75.0% of the isolates contained amplicons with the blaSPM-1 and blaVIM genes. Of the 47 non-Metallo-β-Lactamase isolates, none had another type of carbapenemase. However, the isolates exhibited high rates of hyperproduction of AmpC, loss of the OprD porin (71.4%) and the presence of MexABOprM (57.1%) and MexXY (64.3%). This study suggests that in non-Metallo-β-Lactamase isolates, the association of intrinsic resistance mechanisms could contributes to the expression of multidrug-resistant/extensively drug-resistant phenotypes.

First Report of blaIMP-14 on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131

The bla_IMP-14 carbapenem resistance gene has largely previously been observed in Pseudomonas aeruginosa and Acinetobacter spp. As part of global surveillance and sequencing of carbapenem-resistant Escherichia coli, we identified a sequence type 131 strain harboring bla_IMP-14 within a class 1 integron, itself nested within an ∼54-kb multidrug resistance region on an epidemic IncA/C₂ plasmid. The emergence of bla_IMP-14 in this context in the ST131 lineage is of potential clinical concern.

Epidemiology and molecular characterization of multidrug-resistant Gram-negative bacteria in Southeast Asia

BACKGROUND

Multidrug-resistant Gram-negative bacteria (MDRGN), including extended-spectrum β-lactamases (ESBLs) and multidrug-resistant glucose-nonfermenting Gram-negative bacilli (nonfermenters), have emerged and spread throughout Southeast Asia.

METHODS

We reviewed and summarized current critical knowledge on the epidemiology and molecular characterization of MDRGN in Southeast Asia by PubMed searches for publications prior to 10 March 2016 with the term related to "MDRGN definition" combined with specific Southeast Asian country names (Thailand, Singapore, Malaysia, Vietnam, Indonesia, Philippines, Laos, Cambodia, Myanmar, Brunei).

RESULTS

There were a total of 175 publications from the following countries: Thailand (77), Singapore (35), Malaysia (32), Vietnam (23), Indonesia (6), Philippines (1), Laos (1), and Brunei (1). We did not find any publications on MDRGN from Myanmar and Cambodia. We did not include publications related to Shigella spp., Salmonella spp., and Vibrio spp. and non-human related studies in our review. English language articles and abstracts were included for analysis. After the abstracts were reviewed, data on MDRGN in Southeast Asia from 54 publications were further reviewed and included in this study.

CONCLUSIONS

MDRGNs are a major contributor of antimicrobial-resistant bacteria in Southeast Asia. The high prevalence of ESBLs has been a major problem since 2005 and is possibly related to the development of carbapenem resistant organisms in this region due to the overuse of carbapenem therapy. Carbapenem-resistant Acinetobacter baumannii is the most common pathogen associated with nosocomial infections in this region followed by carbapenem-resistant Pseudomonas aeruginosa. Although Southeast Asia is not an endemic area for carbapenem-resistant Enterobacteriaceae (CRE), recently, the rate of CRE detection has been increasing. Limited infection control measures, lack of antimicrobial control, such as the presence of active antimicrobial stewardship teams in the hospital, and outpatient antibiotic restrictions, and travel throughout this region have likely contributed to the increase in MDRGN prevalence.

Efflux-mediated fluoroquinolone resistance in the multidrug-resistant Pseudomonas aeruginosa clinical isolate PA7: identification of a novel MexS variant involved in upregulation of the mexEF-oprN multidrug efflux operon

The emergence of multidrug-resistant Pseudomonas aeruginosa has become a serious problem in medical settings. P. aeruginosa clinical isolate PA7 is resistant to fluoroquinolones, aminoglycosides, and most β-lactams but not imipenem. In this study, enhanced efflux-mediated fluoroquinolone resistance of PA7 was shown to reflect increased expression of two resistance nodulation cell division (RND) -type multidrug efflux operons, mexEF-oprN and mexXY-oprA. Such a clinical isolate has rarely been reported because MexEF-OprN-overproducing mutants often increase susceptibility to aminoglycosides apparently owing to impairment of the MexXY system. A mutant of PA7 lacking three RND-type multidrug efflux operons (mexAB-oprM, mexEF-oprN, and mexXY-oprA) was susceptible to all anti-pseudomonas agents we tested, supporting an idea that these RND-type multidrug efflux transporters are molecular targets to overcome multidrug resistance in P. aeruginosa. mexEF-oprN-upregulation in P. aeruginosa PA7 was shown due to a MexS variant harboring the Valine-155 amino acid residue. This is the first genetic evidence shown that a MexS variant causes mexEF-oprN-upregulation in P. aeruginosa clinical isolates.

Persistence of Pseudomonas aeruginosa in a pulmonary nodule with late relapse

Lung nodules are common diagnostic challenges in hematopoietic stem cell transplantation and solid organ transplantation. Pseudomonas aeruginosa is a known cause of lung abscess in these patients, but its ability to persist for months in a quiescent lung nodule and later cause recurrent infection is not well known or documented. A patient with a history of acute pre-B-cell lymphoblastic leukemia had enlargement and cavitation of a small right upper lobe pulmonary nodule 10 months after allogeneic hematopoietic stem cell transplantation. The nodule was the remnant of a presumed P. aeruginosa septic embolus that occurred 2.5 months after transplantation. With antibiotic treatment, the nodule had shrunk in size to <1 cm and remained stable. Transthoracic needle aspiration grew P. aeruginosa indistinguishable by molecular typing from isolates obtained 7.5 months earlier from blood and bronchoalveolar lavage fluid. Sub-centimeter pulmonary nodules attributable to previously treated P. aeruginosa may harbor viable organisms and lead to recrudescent infection.