Phenotypic and Genotypic Assays to Evaluate Coagulase-Negative Staphylococci Biofilm Production in Bloodstream Infections

Coagulase-negative staphylococci (CoNS) are commensal on human body surfaces and, for years, they were not considered a cause of bloodstream infection and were often regarded as contamination. However, the involvement of CoNS in nosocomial infection is increasingly being recognized. The insertion of cannulas and intravascular catheters represents the primary source of CoNS entry into the bloodstream, causing bacteremia and sepsis. They owe their pathogenic role to their ability to produce biofilms on surfaces, such as medical devices. In this study, we evaluate the adhesive capacity of CoNS isolated from blood cultures by comparing a spectrophotometric phenotypic assay with genotypic analysis based on the evidence of the ica operon. We retrospectively reviewed the database of CoNS isolated from blood cultures from January to December 2021 that were considered responsible for 361 bloodstream infections. Eighty-nine CoNS were selected among these. Our data show that Staphylococcus epidermidis was the predominant species isolated, expressing greater adhesive capacities, especially those with the complete operon. Knowledge of the adhesive capabilities of a microorganism responsible for sepsis can be useful in implementing appropriate corrective and preventive measures, since conventional antibiotic therapy cannot effectively eradicate biofilms.

Migrations do not modify Mycobacterium tuberculosis resistance rates: a 20-year retrospective study

Tuberculosis (TB) caused by resistant strains is becoming a public health concern also in high-income countries. In Pavia province, Northern Italy, the prevalence of foreign-born has increased in recent years. Nevertheless, it is unclear if this has modified epidemiology and resistance patterns of Mycobacterium tuberculosis. We retrospectively collected data on all the Mycobacterium tuberculosis strains isolated by culture in the microbiology reference laboratory of the province of Pavia from 01/01/1998 to 31/12/2017. Overall, 919 patients were identified, 320 were foreign-born (34.8%). The proportion of cases due to foreign-born patients increased during the study period as did resistance to isoniazid (INH) (p = 0.01), while resistance to rifampicin (RIF) did not (p = 0.8). INH and RIF resistance were comparable among Italian and foreign-born patients (7.9% vs 9.7% for INH and 4% vs 5% for RIF, respectively). Twenty-height (3.05%) patients harboured MDR strains. Prevalence of MDR strains was not different between Italians and foreign-born patients (2.8% vs 3.4%, p = 0.6). During the study period the proportion of TB cases due to foreign-born patients and INH resistance increased. This increase was equal among Italian and foreign-born patients. Migrants in our area are not a driver of resistance to anti-mycobacterial drugs.

Disseminated Mycobacterium Avium Infection in a Child with Complete Interferon-γ Receptor 1 Deficiency due to Compound Heterozygosis of IFNGR1 for a Subpolymorphic Copy Number Variation and a Novel Splice-Site Variant

Complete interferon-γ receptor 1 deficiency is a monogenic primary immunodeficiency caused by IFNGR1 germline defects, with autosomal dominant or recessive inheritance, which results in invasive mycobacterial diseases with varying degrees of severity. Most of the autosomal recessive IFNGR1 mutations are homozygous loss-of-function single-nucleotide variants, whereas large genomic deletions and compound heterozygosity have been very rarely reported. Herein we describe the clinical presentation, diagnosis, and successful treatment with hematopoietic stem cell transplantation of a child with disseminated Mycobacterium avium infection due to compound heterozygosity for a subpolymorphic copy number variation and a novel splice-site variant.

Detection of mcr-4 positive Salmonella enterica serovar Typhimurium in clinical isolates of human origin, Italy, October to November 2016

In this study we report the detection of the recently described mcr-4 gene in two human isolates of Salmonella enterica serovar Typhimurium. The strains were isolated from faecal samples of two Italian patients with gastroenteritis, collected in 2016. The identified mcr-4 genes (variant mcr-4.2) differed from the mcr-4 gene originally described in a Salmonella strain of swine origin from Italy. Salmonella species could represent a hidden reservoir for mcr genes.

Asaia lannensis bacteremia in a 'needle freak' patient

The genus Asaia has gained much interest lately owing to constant new species discoveries and its role as a potential opportunistic pathogen to humans. Here we describe a transient bacteremia due to Asaia lannensis in a patient with a psychiatric disorder (compulsive self-injection of different substances). Common phenotypic methods of identification failed to identify this organism, and only restriction fragment lenght polymorphism of PCR-amplified 16S rRNA gene allowed for proper identification. The isolate was highly resistant to most antibiotics. The paper also discusses the currently available medical literature, acknowledges the potential problems linked to the isolation of these strains and proposes an approach to species identification that can be applied in a clinical microbiology laboratory.

Late-onset neonatal group B streptococcal disease associated with breast milk transmission: molecular typing using RAPD-PCR

Group B Streptococcus (GBS) is considered to be the major cause of neonatal sepsis and meningitis of bacterial origin. Late-onset GBS infection is infrequent and occurs between 1 week and 3 months of age. The transmission of GBS through the ingestion of breast milk is reported in the literature, but only a few of these cases have been confirmed by molecular techniques. In this article we report five cases of late-onset GBS disease: transmission through maternal milk was confirmed in four cases, using the random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) typing assay. In addition, the RAPD-PCR assay showed that each of the isolated clones belonged to a different RAPD genotype, thus revealing that the late-onset GBS infections were not epidemiologically related.

Widespread carbapenem resistant Acinetobacter baumannii clones in Italian hospitals revealed by a multicenter study

Population diversity, susceptibility to antibiotics including carbapenems of 277 Acinetobacter baumannii strains collected in 17 Italian hospitals over a 6-months' period was assessed. Semi-automated rep-PCR was used for screening strains for genotypic relatedness. AFLP analysis and MLST were used as definitive methods for strain, species and/or clone identification. Among the 277 strains, 49 rep-PCR types were distinguished with four types (1-4) predominant, indicating both intra- and interhospital spread. AFLP analysis allowed to distinguish 51 types and largely confirmed rep-typing results. Isolates with predominant rep-types 1 and 2 (in 3 and 9 hospitals) were allocated to EU clones I and II, respectively. Rep-type 3 (8 hospitals) belonged to a new clone ("Italian clone"). Rep-type 4 was found in 2 neighbouring hospitals. Two isolates from 2 locations belonged to EU clone III. Twenty-five isolates were identified by AFLP-analysis to A. pittii, emphasizing misidentification by phenotypic methods. MLST confirmed clone identification by AFLP; demonstrating also that the "Italian clone" was ST78, recently detected in different Mediterranean countries. Multidrug resistance, defined as resistance to 9 out of the 11 drugs tested, was common in 10 out of 17 hospitals. The high prevalence of carbapenem resistance was associated with OXA-58 found in 9 out of the 10 hospitals. A high percentage of noted very major errors in susceptibility testing, especially for amikacin and meropenem, was probably due to heteroresistant strains. The occurrence of carbapenem and multidrug resistance in A. baumannii was mainly confined to a limited number of clonal lineages of A. baumannii.

Clonal multidrug-resistant Corynebacterium striatum strains, Italy

We assessed the clinical relevance and performed molecular characterization of 36 multidrug-resistant strains of Corynebacterium striatum. Pulsed-field gel electrophoresis confirmed a single clone, possessing erm(X), tetA/B, cmxA/B, and aphA1 genes, but few related subclones. This strain is emerging as a pathogen in Italy.

Use of the DiversiLab semiautomated repetitive-sequence-based polymerase chain reaction for epidemiologic analysis on Acinetobacter baumannii isolates in different Italian hospitals

Acinetobacter baumannii is typically a nosocomial pathogen. Epidemiologic tools that can rapidly trace the spread of hospital-associated infections due to this microorganism are essential. Currently, amplified fragment length polymorphism and pulsed-field gel electrophoresis using ApaI, a macrorestriction enzyme, are the molecular techniques most widely used to type this microorganism. Unfortunately, they are technically demanding, requiring also well-trained personnel, and are time consuming. The aims of this study are 1) to evaluate the usefulness of the semiautomated repetitive-sequence-based polymerase chain reaction (rep-PCR) for typing A. baumannii, comparing this method with another semiautomated technique, such as ribotyping, and 2) to acquire information about the incidence, the clinical significance, and the susceptibility patterns of this microorganism in 13 different Italian hospitals in a 4-week period (total study population, >14000 beds). Twenty-eight A. baumannii were isolated in 7 different hospitals; 21 strains were analyzed with molecular methods. Automated ribotyping distinguished 6 different clusters of isolates, whereas rep-PCR appeared to be more discriminating, allowing us to distinguish 8 different clusters. Our study confirms the good discriminatory power of the semiautomated rep-PCR. Although expensive, this method is simple, fast, and reproducible, and in our opinion, it could be used in a hierarchic approach as a 1st-line typing tool if results of analysis are required in a short period or if a large number of isolates have to be analyzed.

Outbreak of vancomycin-resistant Enterococcus spp. in an Italian general intensive care unit

Following the identification of two clinical isolates of vancomycin-resistant enterococci (VRE) from intensive care unit (ICU) patients, a surveillance programme detected that six of eight ICU patients were colonised by VRE. Standard epidemic control measures were instituted in the ICU. During a 16-month period, 13 (2.5%) of 509 ICU patients had VRE-positive swabs upon admission, and 43 (8.7%) of 496 VRE-negative patients were colonised by VRE in the ICU. Patients who acquired VRE in the ICU had a longer ICU stay (p < 0.0001). No other statistically significant differences were demonstrated. Two patients had documented infection (infection/colonisation index, 3.6%; overall VRE infection frequency, 0.4%), but both recovered and were discharged. VRE colonisation did not increase the mortality rate. Automated ribotyping identified three clusters containing, respectively, the first 52 Enterococcus faecium isolates, two Enterococcus faecalis isolates, and two further isolates of E. faecium. Multilocus sequence typing demonstrated that two E. faecium isolates representative of the two ribotypes belonged to sequence types 78 and 18, and that these two isolates belonged to the epidemic lineage C1, which includes isolates with a wide circulation in northern Italy. The outbreak was controlled by continuous implementation of the infection control programme, and by the opening of a new unit with an improved structural design and hand-washing facilities.

Identification of coagulase-negative staphylococci other than Staphylococcus epidermidis by automated ribotyping

As routine identification of coagulase-negative staphylococci is problematic, the performance of automated ribotyping was evaluated for identification of coagulase-negative staphylococci other than Staphylococcus epidermidis. In total, 177 isolates were tested, comprising 149 isolates from blood samples, 15 isolates that were not identified by internal transcribed spacer (ITS)-PCR in a previous study, and 13 reference strains. The identification results were compared with those obtained by the API 20 Staph system, with standard phenotypic and molecular methods as reference. Most (n = 166; 93.8%) isolates were identified correctly by automated ribotyping. For 61 isolates, API 20 Staph and ribotyping were in agreement, but for 105 isolates, ribotyping provided correct identification and API 20 Staph did not. Four isolates not identified by automated ribotyping were recognised correctly by API 20 Staph. The remaining seven isolates could not be identified by either of the two methods. Automated ribotyping was able to distinguish Staphylococcus capitis reliably from Staphylococcus caprae. The results demonstrate the value of automated ribotyping for identification of coagulase-negative Staphylococcus (CoNS) isolates from human sources and may help to clarify the clinical relevance of CoNS species. In addition, automated ribotyping was able to detect polymorphisms that may be useful for epidemiological purposes within S. capitis, Staphylococcus hominis, Staphylococcus haemolyticus, Staphylococcus simulans, S. caprae, Staphylococcus warneri, Staphylococcus lugdunensis, Staphylococcus schleiferi, Staphylococcus sciuri, Staphylococcus pasteuri and Staphylococcus xylosus.

Extended-spectrum beta-lactamase-producing Enterobacteriaceae in an Italian intensive care unit: clinical and therapeutical remarks

In this study we evaluated the prevalence of Enterobacteriaceae and the epidemiology of ESBL+ microorganisms in an ICU of our Institution over a 5-year period and analyzed the clinical features and outcomes of the infections caused by these microorganisms. The most frequent ESBL+ isolate was Proteus mirabilis (69 isolates, 58%); a high rate of positive results in the double-disk synergy test (DDS) was also recognized for Klebsiella pneumoniae (52 isolates, 51%), whereas this phenomenon was observed less frequently in other species. In 312 cases the isolated microorganism was considered to be the cause of infection; we documented 103 wound infections, 89 UTIs, 62 LRTIs, 30 primary bacteremias, 27 infections of indwelling catheters and 1 CNS infection. The overall mortality rate due to ESBL+ strains was 1%, compared with 10.6% rate caused by ESBL-negative Enterobacteriaceae. This could be explained because ESBL+ strains caused mostly localized infections (wound infections and UTIs), whereas systemic or severe infections were sustained by ESBL-negative strains, and therapy with carbapenems was started promptly after ESBL+ isolation (always within 24h after strain isolation).

Catheter-related bacteremia due to Lactobacillus rhamnosus in a single-lung transplant recipient

There is still a major debate about the pathogenicity of Lactobacillus spp. and some reports emphasize that these microorganisms are never isolated from endovascular devices. In this report we present a case of catheter-related bacteremia due to L. rhamnosus in a patient who underwent a single-lung transplant.

Catheter-related bacteremia due to Kocuria kristinae in a patient with ovarian cancer

We report on the first case of a catheter-related recurrent bacteremia caused by Kocuria kristinae, a gram-positive microorganism belonging to the family Micrococcaceae, in a 51-year-old woman with ovarian cancer. This unusual pathogen may cause opportunistic infections in patients with severe underlying diseases.

[Methicillin-resistant Staphylococcus aureus (MRSA) in an intensive care unit: a one-year survey]

Methicillin-resistant Staphylococcus aureus (MRSA) is frequently isolated in nosocomial outbreaks. In our study, we analysed the occurrence of colonisation and infection in an Intensive Care Unit of our hospital during a 12-month period. We also evaluated the possibility of using automated ribotyping as a molecular method in order to type the isolates. Twice a week a nasal swab and a rectal swab were performed on all patients; from ventilator-assisted patients, a sputum culture was also taken. All the MRSA isolated were identified by using commonly phenotypic procedures and on all isolates susceptibility tests were performed. An automated ribotyping using EcoRI was also done. Out of 292 patients enrolled in the study, 205 were never colonised (group N); among the other 87 who were colonised by MRSA (29.8%), 40 patients (group A) were MRSA carriers at the time of admission, while 47 (group B) were colonised in the ICU. Twenty-seven patients (11 from group A, 15 from group B and 1 from group N) developed 31 infections due to MRSA. Patients from group A exhibited, as a rule, worse clinical conditions than those from the other two groups. For the former group, MRSA infection was frequently systemic (sepsis), while in group B pneumonia was the predominant infection. The prevalence of colonisations in our study was 30%, which is a value comparable to those presented by other authors in similar cases. MRSA colonisation is a necessary condition for subsequent infections in almost all cases, with an average lag of 7 days. Susceptibility tests were non-discriminating among the isolates: all the strains were susceptible to glycopeptides; nearly all of them were resistant to erythromycin, clindamycin, ciprofloxacin and gentamicin. Automated ribotyping allowed us to distinguish 12 different ribogroups, the most frequent of which was composed of 146 isolates. In our study, this molecular method was able to define a possible endemic clone that should be better investigated by using methods with a higher discriminatory power, such as RAPD or PFGE. The method that we employed is highly reliable, easy to perform and not time-consuming. In our opinion, it could be the method of choice in the first screening of high numbers of isolates.

Vancomycin-resistant Enterococcus faecium infection in three children given allogeneic hematopoietic stem cell transplantation: clinical and microbiologic features

BACKGROUND AND OBJECTIVES

The emergence of vancomycin-resistant enterococci (VRE) as nosocomial pathogens is a major problem in the US; in Europe, VRE nosocomial infections are uncommon and only rarely have been reported in Pediatric or Neonatal Units. The aim of this study is to report on the clinical and microbiological features of VRE infections in 3 children given hematopoietic stem cell transplantation (HSCT).

PATIENTS AND METHODS

Five episodes of vancomycin-resistant Enterococcus faecium (VREF) infection were diagnosed in 3 children given an allogeneic HSCT. Molecular methods, such as random amplification of polymorphic DNA (RAPD) fingerprinting and automated ribotyping, were used in order to define the circulation of strains.

RESULTS

All the isolates were resistant to all commercially available agents and showed the VanA genotypic profile. All children were successfully treated with the combination of quinupristin/dalfopristin (QD) plus teicoplanin (TEC), although treatment was not sufficient to eradicate the micro-organism promptly from the gastrointestinal tract. All our children are still alive. After the first isolation of VRE, a surveillance protocol was started and we documented that the rate of colonization in children and their mothers was less than 1.5%. The RAPD method demonstrated the possible nosocomial transmission of one strain.

INTERPRETATION AND CONCLUSIONS

Our experience demonstrates that VRE infection is a life-threatening complication in children given HSCT. Prompt diagnosis of this infection and its treatment with the combination of QD and TEC can successfully manage this severe infection in profoundly immunocompromised patients.

Bacillus cereus fatal bacteremia and apparent association with nosocomial transmission in an intensive care unit

Bacillus cereus has sometimes been implicated in food poisoning and in opportunistic infections of seriously ill patients. This report describes an unusual case of persistent bacteremia and multiple organ failure associated with B. cereus in a patient admitted to our institution for lung cancer. The patient was undergoing treatment with an antimicrobial agent (imipenem) that was shown to be effective against the micro-organism in vitro. No portal of entry for the strain was detected. After treatment with vancomycin, also shown to be effective in vitro, no clinical improvement was noted and the patient died. Molecular studies showed that the same strain caused an episode of pseudobacteremia in another patient admitted to the same ICU room.

Typing of methicillin-resistant Staphylococcus aureus (MRSA) strains from an intensive care unit by random amplified polymorphic DNA (RAPD)

The identification and control of methicillin-resistant Staphylococcus aureus (MRSA) is of primary concern in intensive care units (ICUs) worldwide. The introduction and circulation of particular strains is best studied by genomic procedures and random amplified polymorphic DNA (RAPD) is well suited for this task. In this study 14 isolates of MRSA, obtained over an 8 month period from the blood cultures of 12 patients in an ICU at our hospital, were typed by RAPD method using seven primers. Three separate groups were distinguished and clustering of certain types in time and space was noted. These results suggest that although different strains of MRSA were involved in this outbreak, cross-infection with individual types occurred. RAPD fingerprinting is a relatively simple method that allows epidemiologic investigation of MRSA outbreaks in hospital infection.

Rapid identification of Mycobacterium tuberculosis and Mycobacterium avium by polymerase chain reaction and restriction enzyme analysis within sigma factor regions

A single Polymerase Chain Reaction (PCR) within the rpoV gene was developed to rapidly distinguish mycobacteria isolated from clinical specimens. The species identifications of Mycobacterium avium complex (MAC) and Mycobacterium tuberculosis were congruent with standard typing techniques. The analysis was targeted toward the identification of species-specific markers for the clinically relevant M. tuberculosis and M. avium. In addition, HaeIII digestion of the amplification products yielded isolates-specific bands.

Rapid drug susceptibility of Mycobacterium avium complex using a fluorescence quenching method

Mycobacteria Growth Indicator Tube (MGIT) is a recently introduced rapid growth detection method which uses an oxygen quenched fluorescent indicator. The present study evaluated the ability of this new method to determine the drug susceptibility of Mycobacterium avium complex (MAC). Thirty strains recovered from patients with AIDS were tested for susceptibility to clarithromycin, rifabutin, ciprofloxacin, azithromycin and amikacin using MGIT. Results were compared to susceptibilities determined by the agar dilution method. The results obtained showed a 100% correlation between MGIT and the agar dilution method for rifabutin and clarithromycin. There was a 100% correlation between the two methods for azithromycin against 27 strains. MGIT was well correlated with the agar dilution method for detecting resistance to clarithromycin, rifabutin and azithromycin in 4 days, but the correlation was poor when susceptibilities to ciprofloxacin and amikacin were determined. This rapid method is non-radiometric, noninvasive and does not require any special instruments.

Cloning and nucleotide sequence of an archaebacterial glutamine synthetase gene: phylogenetic implications

The glnA gene of the thermophilic sulphur-dependent archaebacterium Sulfolobus solfataricus was identified by hybridization with the corresponding gene of the cyanobacterium Spirulina platensis and cloned in Escherichia coli. The nucleotide sequence of the 1696 bp DNA fragment containing the structural gene for glutamine synthetase was determined, and the derived amino acid sequence (471 residues) was compared to the sequences of glutamine synthetases from eubacteria and eukaryotes. The homology between the archaebacterial and the eubacterial enzymes is higher (42%-49%) than that found with the eukaryotic counterpart (less than 20%). This was true also when the five most conserved regions, which it is possible to identify in both eubacterial and eukaryotic glutamine synthetases, were analysed.