Typing of Pseudomonas aeruginosa strains from patients with cystic fibrosis: phenotyping versus genotyping

Core Genome Multilocus Sequence Typing and Antibiotic Susceptibility Prediction from Whole-Genome Sequence Data of Multidrug-Resistant Pseudomonas aeruginosa Isolates

Over the past decade, whole-genome sequencing (WGS) has overtaken traditional bacterial typing methods for studies of genetic relatedness. Further, WGS data generated during epidemiologic studies can be used in other clinically relevant bioinformatic applications, such as antibiotic resistance prediction. Using commercially available software tools, the relatedness of 38 clinical isolates of multidrug-resistant Pseudomonas aeruginosa was defined by two core genome multilocus sequence typing (cgMLST) methods, and the WGS data of each isolate was analyzed to predict antibiotic susceptibility to nine antibacterial agents. The WGS typing and resistance prediction data were compared with pulsed-field gel electrophoresis (PFGE) and phenotypic antibiotic susceptibility results, respectively. Simpson's Diversity Index and adjusted Wallace pairwise assessments of the three typing methods showed nearly identical discriminatory power. Antibiotic resistance prediction using a trained analytical pipeline examined 342 bacterial-drug combinations with an overall categorical agreement of 92.4% and very major, major, and minor error rates of 3.6, 4.1, and 4.1%, respectively. IMPORTANCE Multidrug-resistant Pseudomonas aeruginosa isolates are a serious public health concern due to their resistance to nearly all or all of the available antibiotics, including carbapenems. Utilizing molecular approaches in conjunction with antibiotic susceptibility prediction software warrants investigation for use in the clinical laboratory workflow. These molecular tools coupled with antibiotic resistance prediction tools offer the opportunity to overcome the extended turnaround time and technical challenges of phenotypic susceptibility testing.

Pseudomonas aeruginosa: a clinical and genomics update

Antimicrobial resistance (AMR) has become a global medical priority that needs urgent resolution. Pseudomonas aeruginosa is a versatile, adaptable bacterial species with widespread environmental occurrence, strong medical relevance, a diverse set of virulence genes and a multitude of intrinsic and possibly acquired antibiotic resistance traits. P. aeruginosa causes a wide variety of infections and has an epidemic-clonal population structure. Several of its dominant global clones have collected a wide variety of resistance genes rendering them multi-drug resistant (MDR) and particularly threatening groups of vulnerable individuals including surgical patients, immunocompromised patients, Caucasians suffering from cystic fibrosis (CF) and more. AMR and MDR especially are particularly problematic in P. aeruginosa significantly complicating successful antibiotic treatment. In addition, antimicrobial susceptibility testing (AST) of P. aeruginosa can be cumbersome due to its slow growth or the massive production of exopolysaccharides and other extracellular compounds. For that reason, phenotypic AST is progressively challenged by genotypic methods using whole genome sequences (WGS) and large-scale phenotype databases as a framework of reference. We here summarize the state of affairs and the quality level of WGS-based AST for P. aeruginosa mostly from clinical origin.

Isolation of Infectious Cystic Fibrosis Patients: Results of a Systematic Review

Objective:

Respiratory tract infections significantly contribute to morbidity and mortality among cystic fibrosis (CF) patients. Therefore, pathogen transmission needs to be prevented. There are several guidelines for the care of CF patients, but no transparent systematic literature review has been published.

Methods:

We conducted a systematic literature review (January 1966 to September 2004) dealing with segregation of CF patients colonized withBurkholderia cepaciaspecies,Pandoraeaspecies,Pseudomonas aeruginosa, Stenotrophomonas maltophilia,orAlcaligenesspecies. Quality of studies was evaluated by taking patient population size, existence of control-patients, patient randomization, diagnostic approach, and bacteria typing methods into account.

Results:

One hundred ninety-nine studies were found. Evidence and quality of 102 publications were evaluated. In 99 publications, recommendations concerning segregation measures for infectious CF patients were determined including a total of 11,576 patients. No randomized, controlled trials had been conducted. Fifty of 56 authors strongly recommended isolation of CF patients infected withB. cepaciaorPandoraeaspecies. In 31 of 39 studies, interpatient spread ofPseudomonas aeruginosawas documented or had been brought to an end by isolation of patients. Only five studies had addressed S.maltophiliaorAlcaligenesspecies.

Conclusions:

Patients colonized withB. cepaciaorPandoraeaspecies are to be separated from noncolonized patients in single rooms. Patients harboring multidrug-resistantPseudomonas aeruginosa, S. maltophilia,orAlcaligenesspecies may not share a room with immunocompromised patients, in intensive care units, or with other CF patients anywhere in the hospital.

Genotypic diversity of Pseudomonas aeruginosa in cystic fibrosis siblings in Qatar using AFLP fingerprinting

Pseudomonas aeruginosa is one of the primary pathogens in patients with cystic fibrosis (CF) and a major cause of morbidity and mortality. Reports of the spread of epidemic or transmissible strains of P. aeruginosa within and across CF centers raised the possibility of clonal spread among siblings with CF. This work reports the genotypic relatedness of P. aeruginosa in CF patients with the CFTR I1234V mutation, and to determine whether the genotypes are identical among CF siblings and among different families with the same CFTR mutation. Sixty-six P. aeruginosa isolates were obtained from sputa/deep-pharyngeal swabs from 27 CF patients belonging to 17 families. Genotypic relatedness was assessed using amplified fragment-length polymorphism (AFLP) fingerprinting. Twenty-three distinct genotypes of P. aeruginosa were identified. Eleven families each had one distinct genotype. In the other 6 families more than one genotype was observed; 3 families each showed two genotypes, 2 families each had three genotypes and 1 family had four genotypes of P. aeruginosa. In several cases, siblings with CF from the same family harbored the same strain of P. aeruginosa, which were different from the genotypes in other families. On the other hand, there was an overlap in P. aeruginosa between closely related families. Some patients show persistent colonization with the same genotype of P. aeruginosa over the longitudinal period. The presence of the same genotypes in siblings of the same family and closely related families suggests cross-transmission of P. aeruginosa or acquisition from common environmental exposure.

Molecular survey of beta-lactamases conferring resistance to newer beta-lactams in Enterobacteriaceae isolates from Polish hospitals

The first national survey of resistance to newer beta-lactams in nosocomial populations of Enterobacteriaceae in Poland was performed. The study covered all nonrepetitive enterobacterial isolates cultured from specimens from inpatients in 13 regional secondary-care hospitals from November 2003 to January 2004. Among 2,388 isolates, the predominant species was Escherichia coli (59.6%), followed by Proteus mirabilis (14.5%) and Klebsiella spp. (8.5%). The frequency of extended-spectrum beta-lactamases (ESBLs) was very high, with ESBLs present in 11.1% of all isolates and 40.4% of Klebsiella pneumoniae isolates, the latter value greatly exceeding that for E. coli (2.5%). The contribution of outbreak isolates was significant, resulting, for example, in a particularly high rate of ESBL producers among Serratia marcescens isolates (70.8%). The pool of ESBL types was overwhelmingly dominated (81.7%) by CTX-M-like beta-lactamases CTX-M-3 (80.6%) and CTX-M-15, with SHV types (17.5%; SHV-2, SHV-5, and SHV-12) and sporadic TEM-like enzymes (0.7%; TEM-19 and TEM-48) being the next most frequent. Acquired AmpC-type cephalosporinases were observed exclusively in P. mirabilis, in 20.5% of the isolates of this species (compared with the frequency of ESBL producers of 11.5% of P. mirabilis isolates). All these cephalosporinases (CMY-12, CMY-15, and a novel variant, CMY-38) originated from Citrobacter freundii. Four isolates of E. coli (two isolates), K. pneumoniae (one isolate), and P. mirabilis (one isolate) produced class A inhibitor-resistant beta-lactamases (TEM-30, TEM-32, TEM-37, and SHV-49), being the first of such producers identified in Poland. The survey documented both specific and more global characteristics of the epidemiology of the beta-lactamase-mediated resistance in enterobacteria from Polish hospitals and demonstrated that the ESBL frequency has reached an alarming level.

[Various typing methods of Pseudomonas aeruginosa strains isolated from cystic fibrosis patients]

Typing methods are essential to understand the epidemiology of bacterial infections. Strain typing is important for the detection of sources or routes of infections, identification between endemic and epidemic strains and prevention of transmission between patients. Some Pseudomonas aeruginosa cystic-fibrosis strains could not be typed with conventional typing methods. Due to the diverse phenotypic nature of P. aeruginosa, phenotyping methods are not discriminatory enough to identify strains belonging to the same genotype. Thus, molecular typing methods are required. These methods should be applied when data from phenotypic typing analysis becomes ambiguous, such as in cystic fibrosis. Molecular typing methods, developed over the past decade, are highly discriminatory in capacity and reproducibility. However, they are more likely applied in specialized laboratories since they are expensive and increase the workload. A reliable and low-cost typing system is required for better defining the epidemiology of this pathogen and designing more rational policies of infection control. Comparison between typing methods will pinpoint the limits and effectiveness of each method and will improve in turn the choice of a nonspecialized laboratory in terms of simplicity, time and cost.

Heterogeneity of biofilms formed by nonmucoid Pseudomonas aeruginosa isolates from patients with cystic fibrosis

Biofilms are thought to play a key role in the occurrence of lung infections by Pseudomonas aeruginosa in patients with cystic fibrosis (CF). In this study, 20 nonmucoid P. aeruginosa isolates collected during different periods of chronic infection from eight CF patients were assessed with respect to phenotypic changes and in vitro biofilm formation. The physiological alterations were associated with a loss of motility (35% were nonmotile) and with decreased production of virulence factors (pyocyanin, proteases) and quorum-sensing molecules (45% of the isolates were unable to produce 3-O-C(12)-homoserine lactone quorum-sensing molecules). Compared with wild-type strain PAO 1, most P. aeruginosa isolates demonstrated different degrees of reduction of adherence on polystyrene surfaces. The in vitro biofilm formation of isolates was investigated in a hydrodynamic flow system. Confocal laser scanning microscope analysis showed that the biofilm structures of the P. aeruginosa isolates were highly variable in biomass and morphology. Biofilm development of six genotypically identical sequential isolates recovered from a particular patient at different time points of chronic infection (20 years) and after lung transplantation demonstrated significant changes in biofilm architectures. P. aeruginosa biofilm formation followed a trend of decreased adherence with progression of the chronic lung infection. The results suggest that the adherent characteristic of in vitro biofilm development was not essential for the longitudinal survival of nonmucoid P. aeruginosa during chronic lung colonization.

Evolution of TEM-type extended-spectrum beta-lactamases in clinical Enterobacteriaceae strains in Poland

Seventeen extended-spectrum beta-lactamase (ESBL)-producing isolates of the family Enterobacteriaceae recovered from 1998 to 2000 in hospitals of five different cities in Poland were analyzed. They expressed several TEM-type ESBLs, TEM-4, TEM-29, TEM-85, TEM-86, TEM-93, and TEM-94. TEM-85 (L21F, R164S, E240K, T265M), TEM-86 (L21F, R164S, A237T, E240K, T265M), TEM-93 (M182T, G238S, E240K), and TEM-94 (L21F, E104K, M182T, G238S, T265M) were identified for the first time. Including the enzymes described earlier, TEM-47, TEM-48, TEM-49, and TEM-68, the group of known ESBLs of the TEM family produced by enterobacteria in Polish hospitals has increased to 10 variants. Comparative sequence analysis of the genes coding for all these beta-lactamases revealed a view of their possible evolution, which, apart from the gradual acquisition of various mutations, could also have involved recombination events. Two different bla(TEM-1) gene alleles were precursors of the ESBL genes: bla(TEM-1A), which was the ancestor of bla(TEM-93), and bla(TEM-1F), from which all the remaining genes originated. The evolution of the bla(TEM-1F)-related genes most probably consisted of three major separate lineages, one of which, including bla(TEM-4), bla(TEM-47), bla(TEM-48), bla(TEM-49), bla(TEM-68), and bla(TEM-94), was highly structured itself and could have been initiated by the bla(TEM-25) gene, identified exclusively in France so far. Plasmid fingerprinting analysis revealed a high degree of diversity of plasmids carrying related bla(TEM) genes, which suggested either the intense diversification or transposition of bla(TEM) genes between different plasmids or some contribution of convergent evolution. The results of this study clearly demonstrate that the environment of Polish hospitals has been highly favorable for the rapid evolution of ESBLs.

Typing of Pseudomonas aeruginosa from hospitalized patients: a comparison of susceptibility and biochemical profiles with genotype

Typing techniques are essential for understanding hospital epidemiology, permitting the elucidation of the source of infection and routes of bacterial transmission. Although DNA-based techniques are the "gold standard" for the epidemiological study of Pseudomonas aeruginosa, antibiotic profiles and biochemical results are used because they are easy to perform and to interpret and relatively inexpensive. Antibiotypes (susceptibility profiles) and biotypes (biochemical profiles) were compared to genotypes established by DNA restriction enzyme analysis in 81 clinical isolates of P. aeruginosa from three hospitals in Porto Alegre, Brazil. The epidemiological relationship among patients was also evaluated. Susceptibility and restriction profiles were discrepant in more than 50% of the cases, and many antibiotypes were observed among isolates from the same genotype. Furthermore, susceptibility profiles did not allow the distinction of isolates from unrelated genotypes. Since a large number of isolates (63%) yielded the same biochemical results, only 10 biotypes were detected, showing that this typing method has a low discriminatory power. On the other hand, DNA restriction enzyme typing allowed us to establish 71 distinct types. Epidemiological data about the relation among P. aeruginosa isolates were not conclusive. The results of the present study indicate that the only method that can establish a clonal relation is DNA restriction enzyme typing, whereas the other methods may cause misleading interpretations and are inadequate to guide proper infection control measures.

Countrywide spread of CTX-M-3 extended-spectrum beta-lactamase-producing microorganisms of the family Enterobacteriaceae in Poland

Eighty-four clinical isolates of the family Enterobacteriaceae, recovered from 1998 to 2000 in 15 hospitals in 10 Polish cities, were analyzed. All the isolates produced beta-lactamases with pIs of 8.4 and 5.4, and the pI 8.4 enzymes were demonstrated to hydrolyze cefotaxime but not ceftazidime in the in vitro bioassay. PCR analysis and DNA sequencing have revealed that in all cases the pI 8.4 beta-lactamase was probably the CTX-M-3 extended-spectrum beta-lactamase (ESBL) variant, which was originally identified in 1996 in Praski Hospital in Warsaw. In the majority of isolates, bla(CTX-M-3) genes resided within large conjugative plasmids with similar fingerprints, which, in the context of the high degree of diversity of the randomly amplified polymorphic DNA types of the isolates, suggested that horizontal transfer of plasmids was likely the main mechanism of CTX-M-3 spread. The dissemination of plasmids was probably preceded by the center-to-center transmission of several strains, as indicated by the identification by pulsed-field gel electrophoresis of closely related or possibly related Klebsiella pneumoniae, Escherichia coli, and Citrobacter freundii isolates in five different hospitals. CTX-M-3-producing organisms revealed a very high degree of diversity in beta-lactam resistance levels and patterns. This was attributed to several factors, such as the production of other beta-lactamases including additional ESBLs, possible quantitative variations in CTX-M-3 expression, segregation of AmpC derepressed mutants, and permeability alterations.

Heterogeneity among infecting strains of Pseudomonas aeruginosa in diverse departments of a large Tunisian hospital

Clinical isolates of Pseudomonas aeruginosa were obtained during a half-year screening period of five different wards of the La Rabta Hospital (Tunis). Distinct clinical isolates (N= 82) were obtained from patients, 40 (48%) of which originated from the Department of Otolaryngology. In order to define the local epidemiology of this opportunistic organism, all strains were serotyped, analysed for pyocin production and genetically characterized with the help of pulsed-field gel electrophoresis (PFGE). The data show that, despite the frequent occurrence of identical serotypes, most of the isolates represent unique pyocin types (N= 53) and genotypes (N= 64). A combination of the pyocin and PFGE data showed that nearly all strains were of unique types, except for two pairs of strains. A limited number of strain clusters was observed on the basis of DNA typing data alone. This involved eight genotypes, some of which were clustered with respect to clinical environment or time. Genotype 22 occurred most frequently (6/83, 7%) and independently of time and locale, indicating that it may represent either a clonal type constituting a major fraction of all P. aeruginosa isolates in the region or a more prevalent organism. Despite a relatively high incidence of P. aeruginosa infections, the polyclonality of these strains shows that, in La Rabta Hospital, pseudomonal infections are not primarily due to excessive spread of a single bacterial genotype.

A novel complex mutant beta-lactamase, TEM-68, identified in a Klebsiella pneumoniae isolate from an outbreak of extended-spectrum beta-lactamase-producing Klebsiellae

Twenty-two Klebsiella pneumoniae and two K. oxytoca extended-spectrum beta-lactamase (ESBL)-producing isolates were collected in 1996 from patients in two pediatric wards of the University Hospital in Wrocław, Poland. Molecular typing has revealed that the K. pneumoniae isolates represented four different epidemic strains. Three kinds of enzymes with ESBL activity (pI values of 5.7, 6.0, and 8.2) were identified. The pI 6.0 beta-lactamases belonged to the TEM family, and sequencing of the bla(TEM) genes amplified from representative isolates revealed that these enzymes were TEM-47, previously identified in K. pneumoniae isolates from pediatric hospitals in Lódz and Warsaw. One of the TEM-47-producing strains from Wrocław was very closely related to the isolates from the other cities, and this indicated countrywide spread of the epidemic strain. The pI 5.7 beta-lactamase was produced by a single K. pneumoniae isolate for which, apart from oxyimino-beta-lactams, the MICs of beta-lactam-inhibitor combinations were also remarkably high. Sequencing revealed that this was a novel TEM beta-lactamase variant, TEM-68, specified by the following combination of mutations: Gly238Ser, Glu240Lys, Thr265Met, and Arg275Leu. The new enzyme has most probably evolved from TEM-47 by acquiring the single substitution of Arg275, which before was identified only twice in enzymes with inhibitor resistance (IR) activity. TEM-68 was shown to be a novel complex mutant TEM beta-lactamase (CMT-2) which combines strong ESBL activity with relatively weak IR activity and, when expressed in K. pneumoniae, is able to confer high-level resistance to a wide variety of beta-lactams, including inhibitor combinations. This data confirms the role of the Arg275Leu mutation in determining IR activity and documents the first isolation of K. pneumoniae producing the complex mutant enzyme.

Exchange of Pseudomonas aeruginosa strains among cystic fibrosis siblings

The molecular epidemiology of Pseudomonas aeruginosa infection in cystic fibrosis (CF) siblings was analysed by DNA fingerprinting using arbitrary primed polymerase chain reaction. A total of 306 strains collected from six pairs of siblings over a period of 20-126 months (median 64) was studied. Fifty-four different P. aeruginosa genotypes were recognized. Two out of six pairs of siblings were ultimately colonized by identical strains, and it was shown that a single P. aeruginosa clone can persist in an individual patient for over ten years. No overlap in P. aeruginosa genotypes was encountered between families, whereas in all families at least transient cross-colonization with the same genotype was observed. This finding demonstrates that P. aeruginosa cross-infection or acquisition of the same strain from an identical environmental source exists within the family situation, but does not always result in a long-term colonization by identical genotypes in all family members suffering from CF.

Arbitrary primed PCR fingerprinting and serotyping of clinical Pseudomonas aeruginosa strains

Arbitrary primed PCR (AP-PCR) analysis was compared with serotyping as a means of high-resolution typing of Pseudomonas aeruginosa. Seventy-four isolates from 3 different hospitals and 18 reference strains were studied. Serotyping provided good index of discrimination, although eleven isolates could not be serotyped. Genomic DNA was amplified with a single 10 nucleotide primer (sequence 5'-AGG GGT CTT G-3'). The strains were genetically diverse and 61 different AP-PCR profiles of 2-7 bands between 0.3 and 2.4 kb were obtained. AP-PCR profiles were not consistently associated with serotypes, but they clearly subtyped strains of the same serotype. Numerical analysis of AP-PCR patterns defined 7 groups at the 55% similarity level, and identified predominant strains in each hospital. The results show that AP-PCR analysis provides a simple and practical approach to typing P. aeruginosa that is more discriminatory than traditional serotyping scheme. We suggest that maximum discrimination can be achieved by a combination of both methods.

Comparative typing of Pseudomonas aeruginosa by random amplification of polymorphic DNA or pulsed-field gel electrophoresis of DNA macrorestriction fragments

Eighty-seven strains of Pseudomonas aeruginosa were typed by random amplification of polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) of macrorestriction fragments. Stains were clustered on the basis of interpretative criteria as presented previously for the PFGE analysis. Clusters of strains were also defined on the basis of epidemiological data and subsequently reanalyzed by RAPD. It was found that in an RAPD assay employing the enterobacterial repetitive intergenic consensus sequence ERIC2 as a primer, single band differences can be ignored; in this case, clonally related strains could be grouped as effectively and reliably as with PFGE. These data could be corroborated by the use of other primer species. However, some primers either showed reduced resolution or, in contrast, identified DNA polymorphisms beyond epidemiologically and PFGE-defined limits. Apparently, different primers define different windows of genetic variation. It is suggested that criteria for interpretation of the ERIC2 PCR fingerprints can be simple and straightforward: when single band differences are ignored, RAPD-determined grouping of P. aeruginosa is congruent with that obtained by PFGE. Consequently, this implies that RAPD can be used with trust as a first screen in epidemiological characterization of P. aeruginosa. The ability to measure the rate of molecular evolution of the P. aeruginosa genome clearly depends on the choice of restriction enzyme or primer when RAPD or PFGE, respectively, is applied for the detection of DNA polymorphisms.