Restriction enzyme analysis of plasmid DNA and bacteriophage typing of paired Staphylococcus aureus blood culture isolates

An Update on Molecular Diagnostics for COVID-19

A novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been recently identified as an infectious disease affecting the respiratory system of humans. This disease is caused by SARS-CoV-2 that was identified in Chinese patients having severe pneumonia and flu-like symptoms. COVID-19 is a contagious disease that spreads rapidly via droplet particles arising through sneezing and coughing action of an infected person. The reports of asymptomatic carriers changed the scenario of symptom based-diagnosis in COVID-19 and intensified the need for proper diagnosis of the majority of the population to combat the rapid transmission of virus. The diagnosis of positive cases is necessary to ensure prompt care to affected people and also to curb further spread of infection in the population. Collecting samples at the right time and from the exact anatomical site is crucial for proper molecular diagnosis. After the complete genome sequence was available, China formulated RT-PCR as a primary diagnostic procedure for detecting SARS-CoV-2. Many in-house and commercial diagnostic kits have been developed or are under development that have a potential to lower the burden of diagnosis on the primary diagnostic techniques like RT-PCR. Serological based diagnosis is another broad category of testing that can detect different serum antibodies like IgG, IgM, and IgA in an infected patient. PCR-based diagnostic procedures that are commonly used for pathogen detection need sophisticated machines and assistance of a technical expert. Despite their reliable accuracy, they are not cost-effective tests, which a common man can afford, so it becomes imperative to look for other diagnostic approaches, which could be cost effective, rapid, and sensitive with consistent accuracy. To make such diagnostics available to the common man, many techniques can be exploited among, which are Point of Care (POC), also known as bed side testing, which is developing as a portable and promising tool in pathogen diagnosis. Other lateral flow assay (LFA)-based techniques like SHERLOCK, CRISPR-Cas12a (AIOD-CRISPR), and FNCAS9 editor-limited uniform detection assay (FELUDA), etc. have shown promising results in rapid detection of pathogens. Diagnosis holds a critical importance in the pandemic situation when there is no potential drug for the pathogen available in the market. This review sums up the different diagnostic approaches designed or proposed to combat the crisis of widespread diagnosis due to the sudden outbreak of a novel pathogen, SARS-CoV-2 in 2019.

Coagulase gene polymorphisms of Staphylococcus aureus isolates from patients at Kosti Teaching Hospital, Sudan

Background

Staphylococcus aureus is a common cause of nosocomial infections. Epidemiological typing of S. aureus enables control of its spread. The objective of this study was to investigate coagulase gene polymorphisms of S. aureus isolated from patients at Kosti Hospital in Sudan.

Methods

In total, 110 S. aureus isolates were recovered from 110 patients who were enrolled in the study. S. aureus strains were isolated on blood agar and MacConkey agar and then identified by conventional tests. Resistance to methicillin was determined by detection of the mecA gene. Polymorphism in the coagulase gene (coa) was investigated using PCR followed by AluI RFLP analysis.

Results

Methicillin-resistant S. aureus accounted for 62/110 (56 %) of the isolates. PCR of the coa gene showed two different amplicons, one of 680 bp detected in 83/110 (75.5 %) of the isolates and one of 790 bp detected in 27/110 (24.5 %). When digested with the AluI enzyme, the 790 bp amplicon resulted in three restriction fragments of 500, 210 and 80 bp (coa1). Restriction of the 680 bp amplicon gave two patterns; the first (coa2) was found in 22/110 (20 %) of the isolates and showed four fragments of 210, 210, 180 and 80 bp, and the second (coa3) was found in 61/110 (55.5 %) and revealed three fragments of 390, 210 and 80 bp. Most of the coa3 isolates (75.4%) were methicillin-resistant.

Conclusion

Three polymorphic genotypes of S. aureus were identified in patients at Kosti Hospital. The coa3 genotype was the predominant one and was mostly detected in methicillin-resistant isolates.

Methicillin-Resistant Staphylococcus aureus in Extended-Care Facilities: Experiences in a Veterans Affairs Nursing Home and a Review of the Literature

Objectives:

To delineate the spread of methicillin-resistant Staphylococcus aureus (MRSA) in a nursing home care unit (NHCU), determine its consequences, and discuss this experience in the context of reports fi-om other nursing homes.

Design:

Observational and descriptive; routine and special surveillance for MRSA, including a facility-wide prevalence survey; characterization of MRSA isolates by disk diffusion and agar diluation susceptibility studies and restriction enzyme analysis of plasmid (REAP) DNA.

Setting and Patients:

A 120-bed skilled nursing facility that is an integral part of the Veterans' Affairs Medical Center (VAMC), Portland, Oregon. The patients are predominantly elderly men with severe underlying diseases and functional impairments.

Results:

An asymptomatic carrier brought MRSA into the NHCU in December 1987. During the next 15 months, 24 additional MRSA cases were detected. A prevalence survey conducted in March 1989 indicated that 39 (34%) of the 114 patients and 8 (7%) of the 117 employees were colonized or infected with MRSA. All strains were resistant to ciprofloxacin. REAP DNA indicated that 37 of 41 strains recovered in the March survey had identical patterns. Although 16 episodes of MRSA infection occurred in NHCU residents during 1988 through 1989, the outbreak had little effect on overall patterns of infectious morbidity and mortality in the facility. The outbreak, however, did result in an increased MRSA caseload at the medical center's acute-care division.

Conclusions:

During the last three years, MRSA colonization and infection have become common in the NHCU at the Portland VAMC; this experience parallels that reported by several nursing homes in other parts of the country.

Typing of human and bovine Staphylococcus aureus by RAPD-PCR and ribotyping-PCR

AIMS

To investigate genetic diversity among Staphylococcus aureus and to delineate the geographical distribution of the strains found.

METHODS AND RESULTS

RAPD-PCR and ribotyping-PCR were employed for the characterization of Staph. aureus isolates from bovine and nosocomial origin. Among the strains, five to nine groups were distinguished by RAPD-PCR, depending on which primer was used, while ribotyping-PCR distinguished seven ribotypes.

CONCLUSIONS, AND SIGNIFICANCE AND IMPACT OF THE STUDY

These results demonstrate the genetic heterogeneity of the strains studied, and the large dissemination of some clones throughout different regions and hosts, findings that may allow the monitoring of Staph. aureus infections.

Comparison of protein A gene sequencing with pulsed-field gel electrophoresis and epidemiologic data for molecular typing of methicillin-resistant Staphylococcus aureus

The epidemiologic relatedness of methicillin-resistant Staphylococcus aureus (MRSA) isolates is currently determined by analysis of chromosomal DNA restriction patterns by pulsed-field gel electrophoresis (PFGE). We have evaluated an alternative typing system (MicroSeq StaphTrack Kit; Perkin-Elmer Biosystems) based on the sequence analysis of the chromosomally encoded polymorphic repeat X region of the S. aureus protein A (spa) gene. A total of 69 clinical MRSA isolates were divided into 18 groups according to the number and nucleotide sequences of the spa repeats. Molecular typing results obtained both by spa sequencing and from the PFGE patterns were concordant except for one group, which contained 20 isolates recovered over a 2-year period from hospitalized patients at the Mayo Clinic. Although the spa typing patterns were indistinguishable for those isolates, PFGE analysis yielded seven related but distinguishable patterns. Further coagulase gene sequence analysis subtyped those 20 strains into four groups which followed distinct temporal and geographic distributions. During a 2-year epidemic period there were up to 7 fragment changes in PFGE patterns among epidemiologically related isolates, suggesting that PFGE may be unsuitable for long-term typing of strains involved in epidemics. Although more limited than PFGE in discriminatory power, spa sequencing analysis could be used as a screening method for typing of MRSA strains because of the shorter turnaround time, ease of use, and the inherent advantages of sequence analysis, storage, and sharing of information.

Molecular typing of Staphylococcus aureus based on PCR restriction fragment length polymorphism and DNA sequence analysis of the coagulase gene

A typing procedure for Staphylococcus aureus was developed based on improved PCR amplification of the coagulase gene and restriction fragment length polymorphism (RFLP) analysis of the product. All coagulase-positive staphylococci produced a single PCR amplification product of either 875, 660, 603, or 547 bp. Those strains of epidemic methicillin-resistant S. aureus 16 (EMRSA-16) studied all gave a product of 547 bp. PCR products were digested with AluI and CfoI, and the fragments were separated by gel electrophoresis. Ten distinct RFLP patterns were found among 85 isolates of methicillin-resistant S. aureus (MRSA) and 10 propagating strains (PS) of methicillin-sensitive S. aureus (MSSA) examined. RFLP patterns 1, 2, and 3 were specific to strains of EMRSA-3, -15, and -16, respectively. By contrast, RFLP patterns 4 and 5 were seen with a heterogeneous collection of strains, together with drug-resistant forms of S. aureus isolated in Europe and four propagating strains used for the international phage set. RFLP pattern 6 was given by the Airedale isolate and PS 95. RFLP pattern 7 encompassed EMRSA-2 (isolate 331), PS 94, and PS 96. An isolate from Germany gave RFLP pattern 8. Eight strains of MSSA gave patterns similar to those of methicillin-resistant strains (RFLP patterns 3, 4, 5, 6, and 7), but two, PS 42E and PS 71, gave unique RFLP patterns 9 and 10, respectively. The coagulase gene PCR products for 24 isolates of MRSA and two isolates of MSSA were sequenced for both strands. The sequences were aligned, and evolutionary lineages were inferred based on pairwise distances between isolates.

Phenotypic and genotypic characterization of nosocomial Staphylococcus aureus isolates from trauma patients

Staphylococcus aureus is a major cause of nosocomial infections. During the period from March 1992 to March 1994, the patients admitted to the intensive care unit of the University of Maryland Shock Trauma Center were monitored for the development of S. aureus infections. Among the 776 patients eligible for the study, 60 (7.7%) patients developed 65 incidents of nosocomial S. aureus infections. Of the clinical isolates, 43.1% possessed a polysaccharide type 5 capsule, 44.6% possessed a type 8 capsule, and the remaining 12.3% had capsules that were not typed by the type 5 or type 8 antibodies. Six antibiogram types were noted among the infection-related isolates, with the majority of the types being resistant only to penicillin and ampicillin. It was noted that the majority of cases of pneumonia were caused by relatively susceptible strains, while resistant strains were isolated from patients with bacteremia and other infections. Only 16 (6.3%) of the isolates were found to be methicillin-resistant S. aureus (MRSA). DNA fingerprinting by pulsed-field gel electrophoresis showed 36 different patterns, with characteristic patterns being found for MRSA strains and the strains with different capsular types. Clonal relationships were established, and the origins of the infection-related isolates in each patient were determined. We conclude that (i) nosocomial infection-related isolates from the shock trauma patients did not belong to a single clone, although the predominance of a methicillin-resistant genotype was noted, (ii) most infection-related S. aureus isolates were relatively susceptible to antibiotics, but a MRSA strain was endemic, and (iii) for practical purposes, the combination of the results of capsular and antibiogram typing can be used as a useful epidemiological marker.

Simple enzymatic method for rapid identification of a Staphylococcus aureus subspecies aureus biovar

In order to correctly identify a new biovar of Staphylococcus aureus subsp, aureus, (NBSA) a simple, rapid, and reliable enzymatic assay was developed. The assay was based on the detection of the production of three enzymes: alpha-glucosidase, beta-glucosidase and beta-N-acetyl-glucosaminidase. Of a total of 46 isolates of Staphylococcus aureus subsp. aureus from clinical specimens, the new assay correctly identified 19 as NBSA and 27 as typical Staphylococcus aureus subsp. aureus. Among the 19 NBSA isolates, 15 (79%) showed a clear biochemical profile while only four isolates (21%) showed a less well-defined enzymatic combination, due to a phenotypic alteration caused by subculturing. Since this assay is both simple to perform and inexpensive, it is potentially applicable in the laboratory.

In vivo stability and discriminatory power of methicillin-resistant Staphylococcus aureus typing by restriction endonuclease analysis of plasmid DNA compared with those of other molecular methods

We evaluated test discriminatory power and DNA type alterations among methicillin-resistant Staphylococcus aureus strains by testing 199 sequential isolates from 39 patients collected over 30 to 228 days. Isolates were typed by one or three different methods (restriction endonuclease analysis of plasmid DNA [REAP] with or without pulsed-field gel electrophoresis of genomic DNA [PFGE] and immunoblotting [IB]). REAP was highly discriminatory compared with PFGE and IB. However, the initial isolates from 4 of the 39 patients lacked detectable plasmid DNA and could not be typed by REAP. Typing of individual patient isolates showed that a different REAP type was identified only once every 138 days. Among 25 comparisons, seven sequential isolate pairs demonstrating REAP differences were also different by PFGE and IB. This likely represented the presence of more than one strain. Eighteen other pairs with REAP differences were identical or related to one another by PFGE and IB typing, and 17 of these differences were likely caused by a single genetic alteration within the same strain or clone. The rate of PFGE differences explicable by single genetic alterations among sequential isolates identical by REAP was similar to the overall rate for REAP differences in the whole collection. We conclude that REAP and PFGE typing differences explicable by single genetic alterations are relatively infrequent but not rare. These isolates should be examined by alternative typing systems to further support or refute clonality.

Evaluation of phenotypic and genotypic methods for epidemiological typing of Staphylococcus aureus isolates from bovine mastitis in Denmark

The value of five different typing methods (antibiogram typing, biotyping, phage typing, plasmid profiling and restriction fragment length polymorphism of the gene encoding 16S and 23S ribosomal RNA (ribotyping)), in discriminating 105 Staphylococcus aureus strains from bovine milk samples obtained from 105 different Danish dairy herds was investigated. A total of 85 strains (81%) proved susceptible to all of the 11 antibiotics tested, and the remaining 20 strains could be divided into 5 different antibiogram patterns. The predominant resistance pattern, penicillin resistance, was observed in 15 (75%) of the 20 antibiotic resistant strains. Biotyping assigned the strains to 14 different types, with the most common type accounting for 25.7% of the strains. Ninety eight (93.3%) strains could be typed by phages, assigning them to 19 different phage types. The predominant phage type accounted for 31.4% of the strains. Eight different plasmid profiles was observed among 24 (23%) strains harbouring plasmids. Ribotyping yielded 30 different types, with the most common accounting for 29.5% of the strains. The single most discriminatory typing method was ribotyping (0.863) followed by biotyping (0.842) and phage typing (0.795). Plasmid profiling (0.395) and antibiogram typing (0.327) had low discriminatory indices. Correspondence among ribotypes and the presence or absence of plasmids were observed, as was some degree of correspondence between ribotype, phage type and biotype. In general the correspondence between phage type and ribotype were stronger than between biotype and ribotype and between biotype and phage type. All combinations of two or more methods led to an improved index of discrimination compared to the individual methods indicating, that some subdivision of types had taken place. The combination of phage, bio- or ribotyping or all three methods in combination are considered to be an efficient combination of typing methods for epidemiological investigation of S. aureus mastitis.

Typing of Staphylococcus aureus strains by PCR-amplification of variable-length 16S-23S rDNA spacer regions: characterization of spacer sequences

To develop a rapid and accurate method of typing large numbers of clinical isolates of Staphylococcus aureus, the spacer region C of the rRNA operon [1391-507 (16S-23S)] was enzymically amplified from 322 strains. When the products were separated by denaturing PAGE, 15 variable-length rrn alleles were demonstrated, ranging in size from 906 to 1223 bp. The variable-length HpaII-digested region C [(region E; 1446-196 (16S-23S)] amplification products were cloned into M13mp18RF to sequence separate variable-length alleles. A total of 17 region E inserts were sequenced, aligned and divided into nine alleles by length (938-1174) and sequence properties. The 16S-23S spacer rDNA varied in length (303-551 bp) and in properties; three alleles contained a tRNAIle gene alone, two alleles contained a tRNAIle and a tRNAAla gene, and four alleles lacked tRNA genes. The sequences of two alleles showed less than 1% variation when isolated from two or three S. aureus strains. The 48 penicillin- and methicillin-sensitive strains were divided into 26 ribotypes; in contrast, the 274 methicillin-resistant S. aureus (MRSA) strains were divided into nine ribotypes (A-I) with 97% typing as either ribotype A or B (rrnL was missing in B). The sequence conservation of the rrn operons argues for the use of the 16S-23S spacer region as a stable and direct indicator of the evolutionary divergence of S. aureus strains.

Molecular epidemiology for local outbreaks of methicillin resistant Staphylococcus aureus (MRSA). The need for several methods

Subtyping isolates may be useful for epidemiological studies of methicillin-resistant-Staphylococcus aureus (MRSA) outbreaks. Among subtyping methods, DNA-based techniques have been applied very effectively for this purpose. An outbreak of MRSA infections took place in one hospital in Barcelona early during 1991. From the beginning of the outbreak to December 92, 70 MRSA isolates from different patients and sources were collected. All strains were evaluated by restriction endonuclease analysis of plasmid DNA (REAP) and macrorestriction endonuclease analysis of genomic DNA using Sma I and pulsed-field-gel-electrophoresis (PFGE). Plasmid screening and REAP using Hind III demonstrated two plasmid subtypes: subtype A showing a large plasmid, and subtype B showing the same large plasmid plus a smaller one. Subtypes A and B corresponded to the more recent and older isolates, respectively, suggesting the loss of the small plasmid during the epidemic. PFGE using Sma I displayed two closely related profiles (PFGE subtype A and A'; CS = 0.90). These subtypes were different from those subtypes exhibited from 4 methicillin-susceptible-Staphylococcus aureus (MSSA) isolates from the same hospital and from 2 epidemiologically unrelated MRSA isolates. Almost all isolates showing PFGE subtype A preceded those isolates showing PFGE subtype A'. This fact and the similarity between both subtypes suggested minor chromosomal DNA rearrangement during the outbreak from a unique strain. While PFGE using Sma I is a useful tool in evaluation of clonal dissemination, our data suggest epidemic or local outbreaks may need several methods to best delineate the source and spread of MRSA strains. The reproducibility and discriminatory power of REAP makes it a useful adjunct in this context.

Outbreak of methicillin-resistant Staphylococcus aureus in a teaching hospital--epidemiological and microbiological surveillance

An outbreak of methicillin-resistant S. aureus (MRSA) in a large university teaching hospital occurred between December 1991 and May 1992, involving 7 different wards and more than 30 patients. Epidemiological typing was performed to control the epidemic and to identify the MRSA carriers. By a combination of various classical methods (antimicrobial susceptibility, phage typing) and molecular typing procedures (SDS-PAGE of extracellular proteins, plasmid DNA profile, restriction enzyme fragment pattern of chromosomal DNA), three different clones of MRSA could be discriminated. The epidemic clone A was recovered from 30 patients and from 3 staff members. By strict microbiological monitoring together with hygienic measures, the epidemic could be successfully controlled. It is concluded that a combination of phenotypic markers and DNA-based epidemiological markers is extremely useful in the microbiological surveillance of MRSA outbreaks.

Comparison of traditional and molecular methods of typing isolates of Staphylococcus aureus

Fifty-nine Staphylococcus aureus isolates and 1 isolate of Staphylococcus intermedius were typed by investigators at eight institutions by using either antibiograms, bacteriophage typing, biotyping, immunoblotting, insertion sequence typing with IS257/431, multilocus enzyme electrophoresis, restriction analysis of plasmid DNA, pulsed-field or field inversion gel electrophoresis, restriction analysis of PCR-amplified coagulase gene sequences, restriction fragment length polymorphism typing by using four staphylococcal genes as probes, or ribotyping. Isolates from four well-characterized outbreaks (n = 29) and a collection of organisms from two nursing homes were mixed with epidemiologically unrelated stock strains from the Centers for Disease Control and Prevention. Several isolates were included multiple times either within or between the sets of isolates to analyze the reproducibilities of the typing systems. Overall, the DNA-based techniques and immunoblotting were most effective in grouping outbreak-related strains, recognizing 27 to 29 of the 29 outbreak-related strains; however, they also tended to include 3 to 8 epidemiologically unrelated isolates in the same strain type. Restriction fragment length polymorphism methods with mec gene-associated loci were less useful than other techniques for typing oxacillin-susceptible isolates. Phage typing, plasmid DNA restriction analysis, and antibiogram analysis, the techniques most readily available to clinical laboratories, identified 23 to 26 of 29 outbreak-related isolates and assigned 0 to 6 unrelated isolates to outbreak strain types. No single technique was clearly superior to the others; however, biotyping, because it produced so many subtypes, did not effectively group outbreak-related strains of S. aureus.

Application of genomic DNA subtyping by pulsed field gel electrophoresis and restriction enzyme analysis of plasmid DNA to characterize methicillin-resistant Staphylococcus aureus from two nosocomial outbreaks

Pulsed-field gel electrophoresis (PFGE) and restriction enzyme analysis of plasmid DNA (REAP) were applied to study the epidemiologic relationship among methicillin-resistant Staphylococcus aureus (MRSA) isolates from outbreaks in two hospitals in São Paulo, Brazil: 82 MRSA isolates, 73 from a university hospital and nine from a general adult intensive care unit of a private hospital, were collected from 62 patients: 95% of the MRSAs were also resistant to gentamicin and ciprofloxacin. REAP subtyping of both collections identified six different subtypes: 55 (72.6%) MRSAs from the university hospital and nine isolates from the private hospital shared the same epidemic REAP subtype. Discrimination by restriction of genomic DNA with Sma I followed by PFGE enabled the identification of 14 DNA subtypes. Based on the combined REAP-genomic DNA subtype, the predominant subtype in the university hospital was A/A (44 isolates) whereas the epidemic subtype in the private hospital was A/M (seven isolates). The application of two typing methods showed better discrimination among MRSAs than did either method alone.

Random amplified polymorphic DNA assay is less discriminant than pulsed-field gel electrophoresis for typing strains of methicillin-resistant Staphylococcus aureus

Twenty-six strains of methicillin-resistant Staphylococcus aureus with different pulsed-field gel electrophoresis fingerprints were tested by random amplified polymorphic DNA assay with three primers, resulting in 15 to 20 different random amplified polymorphic DNA fingerprints. By summing the results for the three primers, the number of different fingerprints increased to 25, but two strains could not be differentiated. We conclude that pulsed-field gel electrophoresis remains the best method of typing methicillin-resistant S. aureus strains.

Exogenous or endogenous reservoirs of nosocomial Pseudomonas aeruginosa and Staphylococcus aureus infections in a surgical intensive care unit

OBJECTIVE

A 4 month prospective study was performed to assess the incidence and routes of endogenous or exogenous colonization and nosocomial infection caused by Staphylococcus aureus and Pseudomonas aeruginosa in surgical critically ill patients.

DESIGN

A total of 4634 specimens were obtained. Patient's nasal, scalp, and rectal swabs as well as tracheal secretion (TS) were cultured every second day beginning on the day of admission. Nasal swabs and hand cultures of the personnel as well as cultures from gowns were also taken. All isolates of S. aureus were phage typed and 116 of these isolates were also plasmid typed. P. aeruginosa isolates were sero- and pyocin typed. Resistance patterns were determined in all isolates.

SETTING

The study was carried out in the surgical intensive care unit (SICU) of an teaching hospital.

PATIENTS

During the study period each patient (a total of 153 patients) admitted to the SICU entered the study.

RESULTS

P. aeruginosa and S. aureus colonisation rate on admission were 5% and 36.5% respectively. Only 10 patients (6.5%) were colonized with P. aeruginosa during hospitalization, and only 7 patients (4.5%) acquired S. aureus in the surgical intensive care unit (SICU). The most common primary colonisation site of P. aeruginosa was the rectum, whereas S. aureus was predominantly found in nasal cultures. Horizontal transmission of S. aureus occurred in only 2 patients.

CONCLUSION

The study suggests that colonisation with P. aeruginosa and S. aureus occurs from endogenous rather than from exogenous sources and that the endogenous acquisition of both bacteria play a more important role in development of nosocomial infections than the exogenous route of transmission.

rRNA gene restriction patterns as an epidemiological marker in nosocomial outbreaks of Staphylococcus aureus infections

rRNA gene restriction patterns (ribotyping) were compared with phage typing, serotyping, enterotoxins and exfoliatin production in the analysis of 26 Staphylococcus aureus strains isolated from two different nosocomial outbreaks. Total DNA was cleaved by EcoRI restriction endonuclease. After agarose gel electrophoresis and Southern transfer, the hybridization of the membranes was done with radiolabelled 16S rRNA gene from Bacillus subtilis inserted into a plasmid vector. Six to 13 fragments were visualized. A core of common fragments was discerned for all strains tested. A full correlation between ribotyping and conventional markers was observed in only one of the outbreaks studied. In both outbreaks, ribotyping proved helpful in characterizing otherwise untypable strains.

Plasmid DNA analysis, biotyping, and antimicrobic susceptibility as subtyping tests for Klebsiella pneumoniae and Klebsiella oxytoca

We compared plasmid DNA analysis, biotyping by Vitek, and disk diffusion antimicrobic susceptibility as subtyping tests of Klebsiella pneumoniae and Klebsiella oxytoca. The 92 tested isolates were from alternate, culture-positive patients over 6 months. No outbreak or cluster of infections was recognized during this interval. Plasmid DNA was detected in 85% of the isolates. Each isolate except one had a reproducible absence of plasmid DNA or a reproducible plasmid DNA profile on repetitive testing. Restriction endonuclease enzyme analysis of plasmid DNA was necessary to distinguish differences among some isolates that had only large plasmids. Isolates with only large plasmids represented 18% of the collection. Of the 78 isolates with plasmid DNA, all but two were considered different from one another by plasmid DNA analysis. Biotyping and antimicrobic susceptibility testing were not highly reproducible. In addition, biotyping did not demonstrate a sufficient variety of patterns among the isolates for subtyping purposes. We conclude that plasmid DNA analysis is very useful as a subtyping test for isolates of K. pneumoniae and K. oxytoca. Neither biotyping nor antimicrobial susceptibility as performed in our laboratory had sufficient discriminatory power and reproducibility for subtyping these organisms.

Characterization of methicillin-susceptible and methicillin-resistant Staphylococcus aureus isolates by molecular typing methods

Two groups of clinical Staphylococcus aureus isolates were examined by molecular typing methods. Detailed protocols for the technical procedures are described. By means of plasmid DNA profiles, plasmid DNA restriction enzyme digestion, as well as whole-cell DNA endonuclease digestions subjected to conventional agarose gel electrophoresis and pulsed-field gel electrophoresis, eight methicillin-susceptible S. aureus strains from three patients segregated into three different groups. Consecutive isolates from the same patient revealed identical fingerprints. Generally, good agreement between different molecular typing methods also was achieved in the investigation of 28 methicillin-resistant isolates. However, compared to whole-cell DNA restriction endonuclease analysis, plasmid DNA profiling (all but one strain had detectable plasmid DNA) showed a somewhat greater discriminatory ability. The techniques evaluated were reproducible and relatively easy to perform and provided valuable tools for studying the epidemiology of S. aureus in hospitals.

The utility of restriction endonuclease analysis and phage typing in the epidemiologic investigation of a Staphylococcus aureus outbreak in a neonatal nursery

Outbreaks of Staphylococcus aureus infections in neonatal units require prompt investigation and implementation of control measures. From January to March 1990, a marked increase in the number of S. aureus infections was observed in a neonatal nursery. Twenty-seven S. aureus isolates from 23 patients were analyzed by phage typing and restriction endonuclease analysis (REA). Only nine strains were differentiated by phage type. However, REA with HindIII, CfoI, and ClaI differentiated 20 strains. The REA results indicated that the outbreak was due to several different S. aureus strains and did not represent transmission of a single epidemic strain. REA may enable more accurate determination of the presence or absence of an epidemic strain during an outbreak than would traditional methods such as phage typing.

DNA fingerprinting by pulsed-field gel electrophoresis is more effective than ribotyping in distinguishing among methicillin-resistant Staphylococcus aureus isolates

Pulsed-field gel electrophoresis (PFGE) after SmaI restriction of DNA from 239 methicillin-resistant Staphylococcus aureus isolates (from 142 patients) produced 26 different fingerprints. The deduced chromosome sizes ranged from 2,200 to 3,100 kb (+/- 100 kb). A total of 81 isolates taken from 65 patients were then typed by PFGE and ribotyping with ClaI, EcoRI, and HindIII. Ribotypes were less discriminating than PFGE. Ribotyping did not discriminate isolates from a given PFGE fingerprint into different subsets. PFGE may be a more effective epidemiological tool than ribotyping for the typing of methicillin-resistant S. aureus strains.

Application of restriction endonuclease analysis of chromosomal DNA in the study of Staphylococcus aureus colonization in continuous ambulatory peritoneal dialysis patients

The relationship between nasal and skin colonization with Staphylococcus aureus and subsequent infection in continuous ambulatory peritoneal dialysis (CAPD) patients in Brazil has been documented by restriction endonuclease analysis of plasmid DNA. However, S. aureus strains without detectable plasmids have been identified. Using restriction endonuclease analysis of chromosomal DNA hybridized with an rRNA gene probe, we document the diversity of S. aureus strains without detectable plasmids colonizing CAPD patients. Ten paired strains without detectable plasmids from five patients were studied by restriction endonuclease analysis of chromosomal DNA and by phage typing. Five different profiles were obtained by restriction endonuclease analysis of chromosomal DNA. Although four of the ten paired isolates were nontypeable by phage typing, all were discriminated by restriction endonuclease analysis of chromosomal DNA. These results demonstrate that restriction endonuclease analysis of chromosomal DNA is a useful epidemiologic tool and complements the restriction endonuclease analysis of plasmid DNA of S. aureus by providing a means of typing strains without detectable plasmids.

Recurrent Staphylococcus aureus bacteremia

Sequential blood isolates from eight patients with 10 episodes of recurrent Staphylococcus aureus bacteremia were typed by restriction endonuclease analysis of plasmid DNA (REAP DNA fingerprinting) and immunoblotting. There were six early recurrences (within 2 months of stopping antimicrobial therapy) and four late recurrences. All early recurrences isolates were identical to initial isolates. These recurrences were defined as possible relapses. Three of four late recurrence isolates were different from the preceding isolates recovered from four patients. This was considered indicative of new infections. There was complete concordance between REAP DNA fingerprinting and immunoblot typing results. However, four isolates lacked plasmid DNA and could be typed only by immunoblotting. All initial isolates from different patients were different types by immunoblotting and by REAP DNA fingerprinting (except for those lacking plasmid DNA). The bacterial traits detected by these methods appear to be stable in vivo for up to 3 months. Relapsing infections were associated with the presence of intravascular foreign bodies and vancomycin therapy of the preceding episodes.

Restriction endonuclease analysis of Staphylococcus aureus plasmid DNA from three continents

Staphylococcus aureus isolates (n = 1201) from 20 centers in Europe, the USA and Brazil were evaluated for the presence of epidemiologic markers. Plasmid typing and restriction endonuclease analysis of plasmid DNA confirmed the presence of an apparently identical plasmid in 13% of clinical isolates. The plasmid was recovered from all 20 hospitals studied, with an overall frequency of greater than 10% on each of the three continents. Since relatively few staphylococcal plasmids may be shared by epidemiologically unrelated strains, there are inherent limitations to this otherwise useful technique. Additionally, these data demonstrate the importance of including unrelated strains of Staphylococcus aureus from the local region as controls when molecular typing methods are performed.

Assigning responsibility: using feedback to achieve sustained control of methicillin-resistant Staphylococcus aureus

Sustained control of endemic methicillin-resistant Staphylococcus aureus (MRSA) originating from multiple sources has not been reported. We describe a simple, inexpensive program based on feedback to physicians that resulted in significant reduction of nosocomial MRSA. When nosocomial cases were identified, the epidemiologist contacted the team resident to encourage increased emphasis on hand washing. Handouts, periodic hand cultures of house staff, and monthly presentations at morning report were also employed. In the first 15 months, nosocomial MRSA decreased from 1.025 to 0.508 cases per 1,000 patient days (p less than 0.01). Monthly rates were significantly decreased for 9 months of 1989 and the first 2 months of 1990. Feedback and assignment of responsibility resulted in a 50% reduction in nosocomial MRSA that has been sustained for 15 months.

Reproducibility of Staphylococcus epidermidis plasmid profiles

The plasmid profiles of six isolates of Staphylococcus epidermidis were repetitively evaluated over an 8-month period. Each isolate was subcultured and stored at three different temperatures (-70 degrees C, -20 degrees C, and room temperature) and plasmid DNA was prepared from each subculture at 0, 1, 4, and 8 months by two different methods of plasmid extraction [using mixed alkyltrimethylammonium bromide (ATAB) or Brij 58 and deoxycholate (modified Parisi)]. Plasmid DNA bands were lost from two isolates when subcultures were kept at room temperature. This plasmid loss was confirmed by repetitive extractions and electrophoresis, as well as by restriction endonuclease analysis of the ATAB preparations. Profiles were otherwise highly related to one another, with occasional exceptions being extra or missing plasmid DNA bands of high molecular size. The latter findings were not reproducible. Plasmid DNA extracted by the modified Parisi method was not reliably digested with restriction endonuclease enzymes. We conclude that the plasmid profiles of Staphylococcus epidermidis isolates are highly reproducible as long as isolates are stored at less than or equal to -20 degrees C. Minor discrepancies in the number of plasmid DNA bands of large molecular size may occur. These are resolvable by repetitive testing or restriction endonuclease analysis of ATAB-extracted plasmid DNA preparations.

The clinical microbiology laboratory as an aid in infection control. The application of molecular techniques in epidemiologic studies of methicillin-resistant Staphylococcus aureus

A microbiologic surveillance study was performed in order to estimate the point prevalence, source, and nosocomial acquisition of methicillin-resistant Staphylococcus aureus (MRSA) within the Iowa City Veterans Affairs Medical Center (IC VAMC). Immediately following the microbiologic surveillance study, a cluster of nosocomial MRSA infections was detected by routine infection control surveillance. An epidemiologic investigation was conducted and all isolates of MRSA detected during the microbiologic surveillance study and the subsequent cluster of nosocomial infections were characterized by restriction endonuclease analysis of plasmid DNA (REAP). REAP subtyping defined a total of ten distinct subtypes from 24 patients infected or colonized with MRSA. The documentation of a single subtype of MRSA (subtype A2) in nine patients from the surgical service, eight of which were hospitalized in the surgical intensive care unit, provided convincing evidence of a breakdown of infection control practices in that unit. REAP subtyping was a highly discriminating means of identifying different subtypes among the various isolates of MRSA and was useful in directing infection control efforts to specific problem areas within the hospital. Molecular typing methods, such as REAP, when used appropriately in conjunction with careful epidemiologic investigation provide an effective approach to the investigation and control of the spread of MRSA within the hospital.

Pulsed field gel electrophoresis as a new epidemiological tool for monitoring methicillin-resistant Staphylococcus aureus in an intensive care unit

Pulsed field gel electrophoresis (PFGE) of bacterial DNA was used in a 1-month epidemiological study of methicillin-resistant Staphylococcus aureus (MRSA) in a 15-bed Intensive Care Unit (ICU). Patient and hospital staff carriage as well as distribution of MRSA in the ICU environment were investigated, and a total of 3802 samples produced 175 isolates. The stability and the reproducibility of the PFGE method were satisfactory. Moreover, the plasmid content of the strains so far examined had no influence on the PFGE profiles of the MRSA strains. The polymorphic profiles observed also account for the use of this method as an epidemiological tool for investigating MRSA. Among 30 patients who stayed more than 4 days in the unit, PFGE analysis showed 11 episodes of colonization in nine patients, whereas lysotyping and plasmid DNA analysis demonstrated only eight and seven such episodes in the same patients, respectively. The combination of PFGE with lysotyping and plasmid analysis may provide a greater discriminatory capacity between MRSA isolates.

Methicillin-resistant Staphylococcus aureus in extended-care facilities: experiences in a Veterans' Affairs nursing home and a review of the literature

OBJECTIVES

To delineate the spread of methicillin-resistant Staphylococcus aureus (MRSA) in a nursing home care unit (NHCU), determine its consequences, and discuss this experience in the context of reports from other nursing homes.

DESIGN

Observational and descriptive; routine and special surveillance for MRSA, including a facility-wide prevalence survey; characterization of MRSA isolates by disk diffusion and agar dilution susceptibility studies and restriction enzyme analysis of plasmid (REAP) DNA.

SETTING AND PATIENTS

A 120-bed skilled nursing facility that is an integral part of the Veterans' Affairs Medical Center (VAMC), Portland, Oregon. The patients are predominantly elderly men with severe underlying diseases and functional impairments.

RESULTS

An asymptomatic carrier brought MRSA into the NHCU in December 1987. During the next 15 months, 24 additional MRSA cases were detected. A prevalence survey conducted in March 1989 indicated that 39 (34%) of the 114 patients and 8 (7%) of the 117 employees were colonized or infected with MRSA. All strains were resistant to ciprofloxacin. REAP DNA indicated that 37 of 41 strains recovered in the March survey had identical patterns. Although 16 episodes of MRSA infection occurred in NHCU residents during 1988 through 1989, the outbreak had little effect on overall patterns of infectious morbidity and mortality in the facility. The outbreak, however, did result in an increased MRSA caseload at the medical center's acute-care division.

CONCLUSIONS

During the last three years, MRSA colonization and infection have become common in the NHCU at the Portland VAMC; this experience parallels that reported by several nursing homes in other parts of the country.

Comparison of genomic DNAs of different enterococcal isolates using restriction endonucleases with infrequent recognition sites

Epidemiologic evaluation of enterococci has been limited by the lack of a simple and effective method for comparing strains. In this study, we have compared chromosomal restriction endonuclease digestion patterns of 27 isolates of Enterococcus faecalis from three different locations by using pulsed-field electrophoresis of large chromosomal fragments (14 to 1,000 kilobases). All but two isolates generated a clear, evaluable pattern with a single lysis and digestion, and the remaining two were visualized when a larger quantity of bacteria was used. All isolates from different locations generated different restriction patterns, as did most isolates within a single location; there was also evidence of spread of strains between individuals in each location. The ease with which this analysis can be performed, together with the clarity and polymorphism seen in the patterns, suggests that this technique will be very useful for epidemiological evaluations of nosocomial enterococcal infections.

Staphylococcus aureus colonization and infection in patients on continuous ambulatory peritoneal dialysis

Staphylococcus aureus is the most common cause of peritonitis in patients undergoing peritoneal dialysis in Brazil. Using restriction endonuclease analysis of plasmid DNA, we investigated the importance of chronic carriage of S. aureus in the development of peritonitis in patients on continuous ambulatory peritoneal dialysis at the Division of Nephrology, Escola Paulista de Medicina, Sao Paulo, Brazil. A total of 117 isolates (30 patients) of S. aureus were available for typing, including 51 isolates (22 patients) from the nares, 58 isolates (27 patients) from pericatheter skin, and 8 isolates (6 patients) from peritoneal fluid, from patients with peritonitis. Restriction endonuclease subtyping showed that although most patients harbored more than one subtype of S. aureus, in the majority of patients nasal and/or pericatheter skin isolates with identical restriction endonuclease digest patterns were recovered on more than one occasion. Furthermore, 95% of patients with both nasal and pericatheter colonization were colonized with the same subtypes at both sites. All of the patients with peritonitis were infected with a subtype which colonized the nares, pericatheter skin, or both. These results demonstrate the importance of an endogenous source of S. aureus in the development of continuous ambulatory peritoneal dialysis-associated peritonitis.

Rapid field inversion gel electrophoresis in combination with an rRNA gene probe in the epidemiological evaluation of staphylococci

A rapid field inversion gel electrophoresis (FIGE) protocol was combined with an rRNA gene probe in the analysis of staphylococci that were difficult to study epidemiologically by conventional means. The following groups of clinical isolates were examined: (i) predominantly antibiotic-susceptible Staphylococcus aureus strains containing no detectable plasmids and unresponsive to bacteriophage typing and (ii) methicillin-resistant Staphylococcus epidermidis strains carrying a single plasmid ca. 30 kilobases in size. The results indicated that strain interrelationships could be established on the basis of SmaI-generated chromosomal restriction fragment length polymorphisms (RFLPs) analyzed by FIGE. RFLP analysis of strains known to be unrelated established the importance of minor differences in DNA banding patterns as indicators of strain dissimilarities. Hybridization studies with an rRNA gene probe confirmed this conclusion. These results suggest that FIGE analysis of chromosomal RFLPs (especially in combination with molecular probes) is an important addition to the armamentarium of molecular epidemiology.

Diversity and stability of restriction enzyme profiles of plasmid DNA from methicillin-resistant Staphylococcus aureus

Nosocomial infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a significant epidemiological problem. Detecting the sources of epidemic strains and preventing their access to patients, however, depend upon the availability of techniques to reliably distinguish among MRSA strains. We evaluated restriction enzyme analysis of plasmid DNA for use as an epidemiological marker of MRSA strains. The diversity of plasmid types was assessed by examining 120 clinical and environmental MRSA isolates from five southern California hospitals and from the American Type Culture Collection. Thirty-seven distinctive EcoRI digestion patterns were observed. We characterized each strain by the number of plasmids it contained and the sizes of the fragments that were generated by EcoRI. Very few of the isolates (4.2%) lacked plasmids, and some (6.7%) contained DNA that was not digested by EcoRI. Several isolates (12.5%) contained two or more plasmids. We were able to assess the stability of MRSA plasmid types by tracking epidemic strains over a 2-year period. We also examined successive isolates from 10 individual patients during their hospitalization. In all but one case, the patient's plasmid profiles remained unchanged. We conclude that the diversity and stability of MRSA plasmid types make them excellent epidemiological markers. In support of this conclusion, we found that our data provided significant epidemiological insights. Two epidemic strains, accounting for more than half of the infections, were identified in the five hospitals. The remaining cases were sporadic, caused by MRSA strains that appeared very infrequently and that may have originated from sources outside the hospitals.