Description of a novel mutation in the atpC gene in optochin-resistant Streptococcus pneumoniae strains isolates from Tunisia.

Identification of Streptococcus pneumoniae among other α-haemolytic streptococci is based on phenotypic or genotypic characteristics such as colony morphology, bile solubility and optochin susceptibility. This study reports three optochin-resistant S. pneumoniae strains isolated from immunocompromised patients in Tunisia. The three isolates were positive for the bile solubility test. Biochemical identification with API® 20 Strep was not discriminatory for two strains. The three strains had different serotypes (6C, 19F and 23F) and three different sequence types (ST386, ST320 and ST326). Sequencing of the atpA and atpC genes for each strain showed only modification in atpC. The mutations Met13→Val or Val48→Ile were observed in two strains. However, in the third strain a novel type of mutation (Val15→Ile) was identified.

Molecular characterisation and epidemiology of extended-spectrum ß-lactamase-producing Klebsiella pneumoniae isolates from immunocompromised patients in Tunisia.

OBJECTIVES: This study investigated the prevalence of extended-spectrum ß-lactamase-producing Klebsiella pneumoniae (ESBL-KP) strains in the National Bone Marrow Transplant Center of Tunis between 2002 and 2011 as well as their associated antimicrobial resistance patterns and molecular features. METHODS: Antimicrobial susceptibility was determined by the disk diffusion method according to CA-SFM guidelines. All of the strains were screened for ß-lactamase genes, plasmid-encoded AmpC genes and integrons. Carbapenemase genes were analysed by PCR and sequencing for strains showing reduced susceptibility to ertapenem. Genetic relatedness was determined by pulsed-field gel electrophoresis (PFGE) and multilocus sequencing typing (MLST). RESULTS: A total of 128 non-repetitive ESBL-KP strains (23.4%) responsible for infection or colonisation were recovered among 548 K. pneumoniae strains. The isolates were also multidrug-resistant. Molecular analysis revealed the prevalence of blaSHV-type (92.2%), followed by blaOXA-1 (81.3%) and blaCTX-M-1 group (73.4%). Four ertapenem-resistant ESBL-KP strains (3.1%) carried the blaOXA-48 gene associated with the blaCTX-M-15 gene. Class 1 integrons were the most prevalent among the isolates (85.2%). High diversity was demonstrated by PFGE with limited clonal dissemination of 1 major (n=13 strains) and 11 minor clusters (each comprising 2-3 strains). MLST of representative strains also showed high diversity with two main epidemic clones: ST15, associated with the major cluster; and ST101, associated with five minor clusters (n=11 strains). CONCLUSIONS: This study provides relevant information on the epidemiology of ESBL-KP strains in oncohaematology patients, of which 18.8% belonged to the specific CTX-M-15 K. pneumoniae clones ST15 and ST101.

Genotyping of commensal Neisseria spp strains by pulsed-field gel electrophoresis and 16S rRNA gene sequencing.

BACKGROUND: We investigated the diversity of the primary sequences of the 16S rRNA genes among 46 commensal Neisseria strains and evaluated the use of this approach as a molecular typing tool in comparison with PFGE analysis. METHODS: Identification to the genus was done using conventional methods and API NH (bio-Mérieux® ). Identification to species level was based on 16S rRNA gene sequencing. PFGE analysis was done using SpeI. RESULTS: Fourteen, two, three and fourteen 16S rRNA sequence types were found among twenty Neisseria flavescens, two Neisseria sicca, five Neisseria macacae and nineteen Neisseria mucosa clinical isolates. Forty-three different PFGE patterns were found among the tested strains. CONCLUSION: We demonstrated a high diversity among 16S rRNA genes which was reflected by PFGE analysis.

First Description of KPC-2-Producing Escherichia coli and ST15 OXA-48-Positive Klebsiella pneumoniae in Tunisia.

The aim of this study was to investigate the molecular features among Klebsiella pneumoniae and Escherichia coli strains showing a resistant/intermediate-resistant phenotype to ertapenem (R/IR-ERT), implicated in colonization/infection in patients of the Hematology and Graft Units of the National Bone Marrow Transplant Center of Tunisia (3-year period, 2011-2014). The major carbapenemase, extended-spectrum beta-lactamase, and plasmidic AmpC beta-lactamase genes were analyzed and characterized by PCR and sequencing. Genetic relatedness was determined by pulsed-field gel electrophoresis (PFGE) using XbaI and multilocus sequencing typing. The blaOXA-48 and blaKPC carbapenemase genes were detected among R/IR-ERT isolates. All R/IR-ERT K. pneumoniae strains (n = 19) had blaOXA-48 gene, and 14/19 strains also harbored the blaCTX-M-15 gene. Eight different PFGE patterns were detected among these K. pneumoniae isolates, and they showed eight different sequences types, ST11 and ST15 being the most prevalent ones. Two out of three R/IR-ERT E. coli isolates carried blaOXA-48 and one coproduced the blaCTX-M-15 gene. One E. coli strain, ascribed to the new sequence type ST5700, harbored the blaKPC-2 gene. E. coli isolates were not clonally related and belonged to different sequence types (ST5700, ST227, and ST58). To our knowledge, this is the first report in Tunisia of either KPC-2 carbapenemase in E. coli or OXA-48 carbapenemase in K. pneumoniae of lineage ST15.

Distribution of virulence associated traits among urine Escherichia coli isolates from patients in onco-hematology.

Escherchia coli is the most common etiological agent of urinary tract infections. In this study we had two goals: First of all, to find out if urine stains isolated from our patients--having the particularity of being immunocompromised--would have a virulence genes distribution different from the one observed in strains isolated from ordinary patients. Second, we wanted to identify a common virulence profile associated to these particular strains. The prevalence of virulence factors (VF)-encoding genes was analyzed by PCR. Of the tested VF-encoding genes, malX (80%), ompT (79%), fyuA (74%), usp (67%), chuA (66%), iroN (59%), iutA (56%), papC (36%), pap AH (30%), papEF (28%), hlyA (28%), papG allele II (25%), cnf1 (21%), focG (20%),cvaC (20%) and papG allele III (7%) were significantly associated to urinary strains. Virulence genes distribution of urinary strains isolated from onco-hematology patients and the one observed in strains isolated from ordinary patients are almost the same. The virulence profiles containing adhesins type 1, S and F1C fimbriae, siderophore genes and three individual genes ompT, usp and malX were present in half of the urinary strains and were significantly associated to them. Two virulence signatures occurred significantly in UTI-causing strains (12%). These findings provide first insight into the virulence of UTI-causing E. coli strains isolated in onco-hematology patients.

Serotype Distribution, Antibiotic Resistance and Clonality of Streptococcus pneumoniae Isolated from Immunocompromised Patients in Tunisia.

BACKGROUND: Pneumococcal disease, a major cause of morbidity and mortality globally, has higher incidence among young children, the elderly and the immunocompromised of all ages. In Tunisia, pneumococcal conjugate vaccines (PCVs) are not included in the national immunization program. Also, few studies have described the epidemiology of S. pneumoniae in this country and, in particular, no molecular typing studies have been performed. The aim of this study was to evaluate serotype distribution, antimicrobial resistance and clonality of Streptococcus pneumoniae isolated from neutropenic patients in Tunisia. METHODS: Fifty-nine S. pneumoniae were isolated from infection (n = 31) and colonization (n = 28) sites of patients (children and adults) attending the National Centre of Bone Marrow Transplantation in Tunis between 2005-2011. All isolates were characterized by serotype, antimicrobial resistance pattern and multilocus sequence typing (MLST). RESULTS: The majority (66.1%) of the isolates belonged to five serotypes all included in PCVs: 6B, 9V, 14, 19F and 23F. The potential coverage of the 10-valent and 13-valent PCV was of 71.2% and 76.3% respectively. Resistance rates were very high and 69.5% of the isolates were multidrug resistant: non-susceptibility rates to penicillin, amoxicillin and cefotaxime were 66.1%, 40.7% and 27.1%, respectively; resistance rates to erythromycin, clindamycin, tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole, were 69.5%, 61.0%, 37.3%, 22.0% and 67.8%, respectively. The most frequent serotypes had STs characteristic of multidrug resistant international clones known to be highly successful and important causes of pneumococcal infection: Spain 23F-ST81, France 9V/14-ST156, Spain 6B-ST90, 19F-ST320, and Portugal 19F-ST177. CONCLUSIONS: The majority of S. pneumoniae strains recovered from immunocompromised patients in Tunisia are representatives of multidrug resistant pandemic clones that express serotypes targeted by PCVs. To contain the burden of pneumococcal disease and improve treatment choices among Tunisian immunocompromised patients PCVs should be offered to all of them.

New Robbins device to evaluate antimicrobial activity against bacterial biofilms on central venous catheters.

BACKGROUND: Layouts of biomedical devices were tightly related with the emergence of Staphylococcus epidermidis as a major cause of nosocomial infections because of its ability to form biofilm on the biomaterial surfaces. This fact led researchers to develop in-vitro models to simulate what is really happening during biofilm formation process in order to have a better understanding of this phenomena and then to control it and to resolve the associated problems. The aim of this paper was to develop a homemade dynamic device based on instruments used in clinical practice, easy to mount, with low coast and with no sophisticated features. METHODS: used to evaluate this dispositive were hydrodynamic calculation and enumeration of bacterial cells on petri dishes and with real time polymerase chain reaction during simulation of Staphylococcus epidermidis biofilm eradication with daptomycin. RESULTS: With hydrodynamic calculation, Reynolds number was estimated to be 26.62 corresponding to a perfect laminar flux giving suitable dynamic growth environment for such experiment. Data recovered from cell enumeration with the two methods showed that bacterial colonization of the tested catheter segment was significantly reduced after 24 and 48h of treatment with daptomycin (P<0.01) reflecting a considerable reliability of this device. CONCLUSION: the simple dispositive developed in this work has shown acceptable hydrodynamic proprieties and good reliability making research on biofilm easy to reach.

Prevalence and genotyping of commensal Neisseria with reduced susceptibility to penicillin.

We analyzed 85 Neisseria spp. strains collected by swabbing from neutropenic patients to determine the prevalence of reduced susceptibility to penicillin and to ascertain the clonal relationship between these strains. High genetic diversity and an elevated level of penicillin resistance were found among commensal Neisseria clinical isolates.

Comparison of 16S rRNA sequencing with biochemical testing for species-level identification of clinical isolates of Neisseria spp.

We aimed to compare accuracy of genus and species level identification of Neisseria spp. using biochemical testing and 16S rRNA sequence analysis. These methods were evaluated using 85 Neisseria spp. clinical isolates initially identified to the genus level by conventional biochemical tests and API NH system (Bio-Mérieux(®)). In 34 % (29/85), more than one possibility was given by 16S rRNA sequence analysis. In 6 % (5/85), one of the possibilities offered by 16S rRNA gene sequencing, agreed with the result given by biochemical testing. In 4 % (3/85), the same species was given by both methods. 16S rRNA gene sequencing results did not correlate well with biochemical tests.

Strong biofilm production but not adhesion virulence factors can discriminate between invasive and commensal Staphylococcus epidermidis strains.

Staphylococcus epidermidis is a leading cause of hospital-acquired infections, mostly associated with the use of medical devices in immunocompromised patients. It originates from the patient's own skin flora, which is subject to severe changes as a result of selective pressure exerted by the hospital environment. This notion led us to compare S. epidermidis isolates from catheter related infections (CRI), non-catheter related bacteremia (NCRB) and catheter hub cultures (commensal isolates). The collection comprised 47 CRI strains from the Bone Marrow Transplant Centre of Tunis, 25 NCRB strains and 25 commensal isolates from patients hospitalized in the same center. Antimicrobial resistance and virulence-associated genes (icaABC, aap, atlE, bhp, fbe, embp, and IS256), polysaccharide intercellular adhesin synthesis, and biofilm formation were investigated. The clonal relationship of strains was investigated by pulsed field gel electrophoresis. Whereas bhp, atlE, fbe, embp, and aap were almost ubiquitously amplified, resistance to oxacillin, kanamycin, tobramycin, gentamicin, cotrimoxazole, and fosfomycin, biofilm production, ica genes, and IS256 were significantly more frequent in invasive (CRI and NCRB strains) than in commensal strains. Moreover, strong biofilm production was significantly more frequent among CRI strains than in NCRB strains. In conclusion, when S. epidermidis is isolated from blood cultures, the detection of strong biofilm production may be significant with regard to judging whether the detected strain is an etiologic agent of CRI.

Phenotypic and genotypic characterization of Salmonella enterica recovered from poultry meat in Tunisia and identification of new genetic traits.

Thirty-seven Salmonella enterica isolates obtained from poultry meat in Tunisia were included in this study for characterization of antibiotic resistance mechanisms. High percentages of resistance were detected to ampicillin, sulfonamides, tetracycline, nalidixic acid, and streptomycin (32.4%-89.2%), and lower percentages to amoxicillin-clavulanic acid, kanamycin, amikacin, trimethoprim-sulfamethoxazol, and chloramphenicol (2.7%-18.9%). All strains showed susceptibility to ceftazidime, cefotaxime, gentamicin, and ciprofloxacin. Class 1 integrons were detected in 30% of Salmonella isolates, and four different gene cassette arrangements were detected, including genes implicated in resistance to aminoglycosides (aadA1 and aadA2) and trimethoprim (dfrA1). Four different Pc variants (PcW, PcH1, PcH1(TTN-10), PcW(TGN-10)) with inactive P2 have been found among these isolates. Integron-positive isolates were ascribed to eight different serotypes. A Salmonella Schwarzengrund isolate harbored a new class 1 integron containing the qacH-dfrA1b-aadA1b-catB2 gene cassette arrangement, with the very unusual PcH1(TTN-10) promoter, which has been registered in GenBank (accession no. HQ874651). Different plasmid replicon types were demonstrated among integron-positive isolates: IncI1 (8 isolates), IncN (8), IncP (2), IncFIB (2), and IncFII (2). Ten different pulsed-field gel electrophoresis profiles were detected among the 11 integron-positive isolates and 8 different sequence types were identified by multilocus sequence typing, one of them (registered as ST867) was new, detected in 3 Salmonella Zanzibar isolates. A high diversity of clones is observed among poultry Salmonella isolates and a high proportion of them show a multiresistant phenotype with very diverse mobile genetic structures that could be implicated in bacterial dissemination in different environments.

Molecular epidemiology of methicillin-resistant Staphylococcus hominis (MRSHo): low clonality and reservoirs of SCCmec structural elements.

BACKGROUND: Methicillin resistant Staphylococcus hominis (MRSHo) are important human pathogens in immunocompromised patients. However, little is known regarding its population structure and staphylococcal chromosomal cassette mec (SCCmec) content. METHODOLOGY/PRINCIPAL FINDINGS: To assess the population structure and the SCCmec content of S. hominis, 34 MRSHo and 11 methicillin-susceptible S. hominis (MSSHo) from neutropenic patients collected over a 3-year period were studied. The genetic backgrounds of S. hominis isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and SCCmec types were determined by PCR. Cassette chromosome recombinases (ccr) were characterized by PCR and ccrB sequencing. The 34 S. hominis isolates were classified into as many as 28 types and 32 subtypes (SID = 99.82%); clonal dissemination was occasionally observed. The main SCCmec structures identified were SCCmec type VI (4B) (20%), SCCmec VIII (4A) (15%), and a new SCCmec composed of mec complex A in association with ccrAB1 (38%); 27% of the isolates harbored non-typeable SCCmec. Overall, a high prevalence of mec complex A (73.5%), ccrAB1 (50%) and ccrAB4 (44%) were found. Importantly, ccrB1 and ccrB4 from both MRSHo and MSSHo showed a high nucleotide sequence homology with those found in S. aureus SCCmec I, VI and VIII respectively (>95%). CONCLUSIONS/SIGNIFICANCE: The S. hominis population showed a limited clonality and a low genetic diversity in the allotypes of ccr and classes of mec complex. Moreover, our data suggest that S. hominis might have been a privileged source of mec complex A, ccrB1 and ccrB4, for the assembly of primordial SCCmec types.

Pulsed Field Gel Electrophoresis types of Candida albicans isolates from an intensive care unit in a Tunisian hospital.

Candida albicans is the most important cause of fungal infections in intensive care units. The aim of this work was to compare the profiles of C. albicans in order to specify their genetic polymorphism and to determine the origin of these infections. Thirty-five C. albicans strains were collected from different clinical samples of 12 patients and three health-workers in an intensive care unit (ICU) in Rabta hospital of Tunisia, between August 2007 and April 2008. After digestion with BssHII, the isolates were typed by pulsed field gel electrophoresis (PFGE). The PFGE profiles were analyzed using a visual method, which showed three PFGE types (A, B and C) and the dendrogram generated three clusters (clusters I to III). An average similarity coefficient of 0.83, suggests that isolates are related.

Escherichia coli of poultry food origin as reservoir of sulphonamide resistance genes and integrons.

The antimicrobial resistance phenotype and genotype, the flanking regions of sulphonamide resistance genes and the integrons were analyzed in 166 Escherichia coli isolates recovered from poultry meat in Tunisia. High percentages of resistance were detected to ampicillin, streptomycin, nalidixic acid, sulphonamide and tetracycline (66-95%), and lower percentages to gentamicin, amoxicillin-clavulanic acid and cefoxitin (1-4%). The bla(TEM), tet(A)/tet(B), aph(3')-Ia, aac(6')-Ib-cr, aac(3)-II and cmlA genes were identified in 92, 82, 29, 2, 2 and 7 isolates, respectively. Class 1 and/or class 2 integrons were detected in 52% of E. coli isolates and five different gene cassette arrangements were identified in the variable regions of class 1 integrons, which included antimicrobial resistance determinants. Sixty-eight isolates contained the sul1 gene and 37 of them presented this gene into a class 1 integron structure. The sul3 gene was detected associated with non-classic class 1 integrons in 4 out of 46 sul3-positive isolates. The sul2 gene was detected in 66 isolates, 51 of them were linked to strA/B genes in seven different genetic structures. Seventy-three-per-cent of integron-positive isolates presented resistance to at least five different antimicrobial families versus 38.7% of integron-negative isolates. Our study highlights the role of commensal E. coli isolates from poultry meat as an important reservoir for sulphonamide resistance genes and integrons carrying antimicrobial resistance genes.

Prevalence of Mycoplasma pneumoniae-associated respiratory tract infections in hospitalized children: results of a 4-year prospective study in Tunis.

Specific microbiologic, molecular, and serologic assays are hardly available in Tunis to confirm a suspected infection of Mycoplasma pneumoniae (MP). These diagnosis methods were used for the first time in a Tunisian prospective study to estimate the prevalence of MP infection in children and to evaluate their usefulness for diagnosis. A total of 540 children hospitalized in Tunis for lower respiratory tract infections (LRTIs) between 2005 and 2009 and 580 clinical specimens were investigated for the presence of MP by culture and by end-point polymerase chain reaction (PCR) targeting the P1 and the 16S rRNA genes. Real-time PCR was also used for MP detection on 158 respiratory samples. A total of 525 serum samples were tested for detection of MP-specific IgM and IgG. The P1 adhesin type and the antibiotic susceptibility testing were determined for the 9 clinical strains isolated during the study period. MP was detected in 33 (5.7%) clinical samples. Specific MP seropositivity was confirmed in 54 serum samples (10.3%), among which 19 (3.6%) were indicative of acute MP infection. MP infection was confirmed in 39 (7.2%) patients: 24 positive by PCR and/or culture, 10 serologically positive only, and 5 confirmed positive by both methods. MP infections occurred throughout the year with a slight decrease in autumn. The 9 MP isolates were susceptible to erythromycin, tetracycline, and ciprofloxacin, and all belonged to type I. The prevalence of MP infection in children with LRTI was 7.2% between 2005 and 2009, in Tunisia. Combination of direct detection and serology was required to enhance the clinical sensitivity of MP detection in clinical specimens.

Prevalence and diversity of integrons and associated resistance genes in Escherichia coli isolates from poultry meat in Tunisia.

Fifty-five Escherichia coli isolates were acquired from chicken and turkey meat obtained from two slaughterhouses in Tunis. Eighty-nine percent, 80%, 78%, 67%, 45%, 27%, 7%, 4%, and 2% of these isolates showed resistance to tetracycline, trimethoprim/sulfamethoxazole, streptomycin, nalidixic acid, ampicillin, chloramphenicol, ciprofloxacin, colistine, and gentamicin, respectively. No resistance was detected to cefotaxime, ceftazidime, or amikacin. bla(TEM) gene was found in 22 of 25 ampicillin-resistant isolates, and 1 isolate harbored bla(OXA-1) gene. Tetracycline resistance was predominately mediated by the tetA gene. The sul1, sul2, and sul3 genes, alone or combined, were detected in 46 of 48 sulfonamide-resistant isolates, and sul1 and sul3 were included in class 1 integrons in some cases. Sixty percent of isolates harbored integrons (class 1, 30 isolates; class 2, 5 isolates). Class 2 integrons contained in all cases the dfrA1-sat1-aadA1-orfX gene cassette arrangement. Nine gene cassette arrangements have been detected among class 1 integrons, containing different alleles of dfrA (five alleles) and aadA (2 alleles) genes, which encode trimethoprim and streptomycin resistance, respectively. An uncommon gene cassette array (sat-psp-aadA2-cmlA1-aadA1-qacH-IS440-sul3) has been identified in three class 1 integron-positive isolates, and one additional isolate had this same structure with the insertion of IS26 inside the aadA1 gene (included in GenBank with accession no. FJ160769). The 55 studied isolates belong to the four phylogenic groups of E. coli, and phylogroups A and D were the most prevalent ones. At least one virulence-associated gene (fimA, papC, or aer) was detected in 44 of the 55 (80%) studied isolates. E. coli isolates of poultry origin could be a reservoir of antimicrobial-resistance genes and of integrons, and its evolution should be tracked in the future.

Typing of staphylococcal cassette chromosome mec encoding methicillin resistance in Staphylococcus aureus strains isolated at the bone marrow transplant centre of Tunisia.

Staphylococcal Cassette Chromosome mec (SCCmec) is a mobile genetic element that carries the gene mecA mediating the methicillin resistance in staphylococci. It is composed of mec and ccr gene complexes. Six SCCmec types have been defined so far. SCCmec typing of 13 methicillin-resistant Staphylococcus aureus (MRSA) out of 72 (18%) non redundant S. aureus strains recovered in 1998-2007 at the Bone Marrow Transplant Centre of Tunis was carried out. The isolates were identified by conventional methods. Antibiotic susceptibility was determined by oxacillin and cefoxitin disks and oxacillin MIC by E-test. Methicillin resistance was detected by mecA PCR. The SCCmec complex types were determined by PCR. The epidemiology of MRSA has been investigated by PFGE. Among 13 mecA positive strains, 12 were resistant to oxacillin (MIC = 3 to >256 microg/microl) and to cefoxitin and one strain was pre-resistant: susceptible to oxacillin (MIC = 0.19 microg/microl) and to cefoxitin. Hospital-acquired MRSA (HA-MRSA) strains had essentially SCCmec type IV (nine strains) or III (two strains) or I (one strain). One strain shown to carry ccrAB1 and ccrAB2 genes in combination with class B mec. Seven of 13 MRSA strains isolated from 2000 to 2006 were classified with major similarity group A harbored SCCmec type IV.