Comparison of a semiautomated commercial repetitive-sequence-based PCR method with spoligotyping, 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing, and restriction fragment length polymorphism-based analysis of IS6110 for Mycobacterium tuberculosis typing.

Fifty-two multidrug-resistant isolates of Mycobacterium tuberculosis representative of the currently predominant lineages in France were analyzed using repetitive-sequence-based PCR (rep-PCR) DiversiLab (DL), spoligotyping, 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing (MIRU-VNTR), and restriction fragment length polymorphism of IS6110 (IS6110-RFLP). DL, as opposed to MIRU-VNTR and IS6110-RFLP analysis, did not allow discrimination among half of the isolates, an indication of comparatively lower resolving power.

Ruling out false-positive urinary Legionella pneumophila serogroup 1 and Streptococcus pneumoniae antigen test results by heating urine.

We report here false-positive urinary Legionella pneumophila serogroup 1 and Streptococcus pneumoniae antigen test results due to rabbit antilymphocyte serum treatment and provide a simple and fast solution to rule them out by heating urine.

A surge of MDR and XDR tuberculosis in France among patients born in the Former Soviet Union.

A marked increase in the number of multidrug-resistant (MDR) tuberculosis (TB) cases entirely related to patients born in the Former Soviet Union was observed in France in the last two years. Very few cases were clustered, suggesting it is a consequence of recent immigration of patients already infected in their country of origin. This major increase challenges the existing structures for management of MDR and extensively drug-resistant TB (XDR-TB).

Long-term control of vancomycin-resistant Enterococcus faecium at the scale of a large multihospital institution: a seven-year experience.

Repeated outbreaks of vancomycin-resistant Enterococcus faecium (VRE) occurred between 2004 and 2010 in Assistance Publique--Hôpitaux de Paris (AP-HP), a 23,000-bed multi-hospital institution. From August 2004 to December 2005, the French guidelines for preventing cross-transmission of multiresistant bacteria were applied. Because the number of VRE cases continued to increase, an institutional control programme was implemented from January 2006 onwards: it foresees stopping transfer of VRE and contact patients, separating VRE and contact patients in distinct cohorts, intervention of a central infection control team to support local teams, and quick application of measures as soon as first VRE cases are identified. Between August 2004 and December 2010, 45 VRE outbreaks occurred in 21 of the 38 AP-HP hospitals, comprising 533 cases. Time series analysis showed that the mean number of cases increased by 0.8 cases per month (95% confidence interval (CI): 0.3 to 1.3, p=0.001) before, and decreased by 0.7 cases per month after implementation of the programme (95% CI: -0.9 to -0.5, p<0.001), resulting in a significant trend change of -1.5 cases per month (95% CI: -2.1 to -0.9, p<0.001). The number of cases per outbreak was significantly lower after implementation of the programme. A sustained and coordinated strategy can control emerging bacteria at the level of a large regional multihospital institution.

Molecular investigation of resistance to the antituberculous drug ethionamide in multidrug-resistant clinical isolates of Mycobacterium tuberculosis.

Ethionamide (ETH) needs to be activated by the mono-oxygenase EthA, which is regulated by EthR, in order to be active against Mycobacterium tuberculosis. The activated drug targets the enzyme InhA, which is involved in cell wall biosynthesis. Resistance to ETH has been reported to result from various mechanisms, including mutations altering EthA/EthR, InhA and its promoter, the NADH dehydrogenase encoded by ndh, and the MshA enzyme, involved in mycothiol biosynthesis. We searched for such mutations in 87 clinical isolates: 47 ETH-resistant (ETH(r)) isolates, 24 ETH-susceptible (ETH(s)) isolates, and 16 isolates susceptible to ETH but displaying an intermediate proportion of resistant cells (ETH(Sip); defined as ≥1% but <10% resistant cells). In 81% (38/47) of the ETH(r) isolates, we found mutations in ethA, ethR, or inhA or its promoter, which mostly corresponded to new alterations in ethA and ethR. The 9 ETH(r) isolates without a mutation in these three genes (9/47, 19%) had no mutation in ndh, and a single isolate had a mutation in mshA. Of the 16 ETH(Sip) isolates, 7 had a mutation in ethA, 8 had no detectable mutation, and 1 had a mutation in mshA. Finally, of the 24 ETH(s) isolates, 23 had no mutation in the studied genes and 1 displayed a yet unknown mutation in the inhA promoter. Globally, the mechanism of resistance to ETH remained unknown for 19% of the ETH(r) isolates, highlighting the complexity of the mechanisms of ETH resistance in M. tuberculosis.

Performance of MTBDR plus for detecting high/low levels of Mycobacterium tuberculosis resistance to isoniazid.

SETTING: We recently evaluated the Genotype MTBDR test for assessing Mycobacterium tuberculosis resistance to rifampicin (RMP) and isoniazid (INH) by detecting mutations in rpoB (codons 511-533) and katG (codon 315). A new version of the test, MTBDR plus, has been designed to also detect mutations in the regulatory region of inhA. OBJECTIVE: To evaluate the performance of MTBDR plus over MTBDR. RESULTS: In 113 isolates, MTBDR plus detected all 76 RMP-resistant (RMP-R) strains and all 64 INH-resistant (INH-R) strains with KatG-315 mutations, 59 of which displayed a high level of INH resistance. It also identified 18 strains undetectable by MTBDR, without mutation in KatG-315 but with a -15 C-->T mutation in the regulatory region of inhA, of which 15 displayed a low level of INH resistance. Thirteen INH-R strains, which mainly harboured mutations in KatG at positions other than 315, were undetected by MTBDR plus. CONCLUSION: MTBDR plus retains the accuracy shown by MTBDR in detecting RMP resistance and is more sensitive in detecting INH resistance (86% vs. 67%), particularly at low levels (minimum inhibitory concentration<1 mg/l, 69% vs. 17%). The negative predictive value of the test (the probability of a strain with a wild-type test being susceptible to INH) is >98% when the rate of INH is <10%, as it is in France.

Increase in hospital-acquired bloodstream infections caused by extended spectrum beta-lactamase-producing Escherichia coli in a large French teaching hospital.

Our goal was to determine the characteristics and the mode of acquisition of healthcare-associated bacteraemia due to CTX-M-producing Escherichia coli in a 1,800-bed hospital. Sixteen extended-spectrum beta-lactamase (ESBL)-producing E. coli strains were collected between 2001 and 2006 from patients with bloodstream infections. The incidence density of these infections increased from 0.002 to 0.02 per 1,000 days of hospitalisation during the study period. Most of the strains (87%) produced a CTX-M-type enzyme associated with TEM-1 (86%), OXA-30 (50%), AAC(3)-II (57%), AAC(6') (50%) and QnrS1 (7%). When present (n = 8), the bla (CTX-M-15) gene was always located downstream of the insertion sequence ISEcp1. Co-resistance was generally observed: fluoroquinolones (81%), trimethoprim-sulfamethoxazole (62%) and/or aminoglycosides (69%). Although the strains were found to be genetically unrelated, most of the cases were hospital-acquired (69%) or healthcare-associated (25%), underlining the need for infection control measures to limit the spread of ESBL-producing E. coli in hospital settings.

Multidisciplinary advisory teams to manage multidrug-resistant tuberculosis: the example of the French Consilium.

SETTING: The World Health Organization (WHO) recommends that multidrug-resistant tuberculosis (MDR-TB) treatment should be managed in collaboration with multidisciplinary advisory committees (consilia). A formal national Consilium has been established in France since 2005 to provide a centralised advisory service for clinicians managing MDR-TB and extensively drug-resistant (XDR-TB) cases.OBJECTIVE: Review the activity of the French TB Consilium since its establishment.DESIGN: Retrospective description and analysis of the activity of the French TB Consilium.RESULTS: Between 2005 and 2016, 786 TB cases or contacts of TB cases were presented at the French TB Consilium, including respectively 42% and 79% of all the MDR-TB and XDR-TB cases notified in France during this period. Treatment regimens including bedaquiline and/or delamanid were recommended for 42% of the cases presented at the French TB Consilium since 2009. Patients were more likely to be presented at the French TB Consilium if they were born in the WHO Europe Region, had XDR-TB, were diagnosed in the Paris region, or had resistance to additional drugs than those defining XDR-TB.CONCLUSION: The French TB Consilium helped supervise appropriate management of MDR/XDR-TB cases and facilitated implementation of new drugs for MDR/XDR-TB treatment.

Phenotypic detection of extended-spectrum beta-lactamase production in Enterobacteriaceae: review and bench guide.

Strains of Enterobacteriaceae producing an extended spectrum beta-lactamase have become a concern in medical bacteriology as regards both antimicrobial treatment and infection control in hospitals. Extended-spectrum beta-lactamase (ESBL) detection tests should accurately discriminate between bacteria producing these enzymes and those with other mechanisms of resistance to beta-lactams, e.g., broad-spectrum beta-lactamases, inhibitor-resistant beta-lactamases and cephalosporinase overproduction. Several phenotypic detection tests, based on the synergy between a third-generation cephalosporin and clavulanate, have been designed: the double-disk synergy test (DDST), ESBL Etests, and the combination disk method. These tests often need to be refined in order for them to detect an ESBL in some bacterial strains, such as those that also overproduce a cephalosporinase. The sensitivity of the DDST can be improved by reducing the distance between the disks of cephalosporins and clavulanate. The use of cefepime, a fourth-generation cephalosporin that is less rapidly inactivated by cephalosporinase than by ESBL, improves the detection of synergy with clavulanate when there is simultaneous stable hyperproduction of a cephalosporinase; alternatively, the cephalosporinase can be inactivated by performing phenotypic tests on a cloxacillin-containing agar. Some beta-lactamases can hydrolyse both third-generation cephalosporins and carbapenems, such as the metallo-beta-lactamases, which are not inhibited by clavulanate, but rather by EDTA. The production of an ESBL masked by a metallo-beta-lactamase can be detected by means of double inhibition by EDTA and clavulanate. Since extended-spectrum Ambler class D oxacillinases are weakly inhibited by clavulanate and not inhibited by EDTA, their detection is difficult in the routine laboratory.

Risk factors for extensive drug resistance in multidrug-resistant tuberculosis cases: a case-case study.

SETTINGS: Identification of extensively drug-resistant tuberculosis (XDR-TB) may be delayed because of the lack of availability of molecular testing for second-line drugs (SLDs). Early suspicion of XDR-TB is therefore necessary to avoid developing further drug resistance. OBJECTIVE: To identify the characteristics associated with XDR-TB among multidrug-resistant TB (MDR-TB) cases before the availability of second-line drug susceptibility testing (DST) results. METHODS: All MDR-TB cases with available second-line DST results recorded in France from 1998 to 2013 were classified as simple MDR-TB (no resistance to fluoroquinolones [FQs] or second-line injectable drugs [SLIDs]), pre-XDR-TB (resistance to FQs or SLIDs) and XDR-TB cases (resistance to both). RESULTS: A total of 833 MDR-TB cases were analysed, including 168 (20%) pre-XDR and 62 (7%) XDR-TB cases. A previous history of treatment was acknowledged among 41% of the cases; 12% were human immunodeficiency virus-positive. Characteristics independently associated with XDR-TB were foreign birth (OR 9.5), previous anti-tuberculosis treatment (OR 2.6), smear positivity (OR 4.5) and ethambutol (EMB) resistance (OR 9.1). Characteristics independently associated with pre-XDR-TB compared to simple MDR-TB cases were male sex (OR 1.6), birth in Europe (OR 2.6) and EMB resistance (OR 1.9). CONCLUSION: The presence of clinical or bacteriological characteristics associated with XDR-TB should lead to rapid molecular testing for resistance to SLDs before starting tailored treatment.

Interpreting carbapenem susceptibility testing results for Pseudomonas aeruginosa.

OBJECTIVES: Carbapenems are among the most powerful antipseudomonal agents. Limited data is available on drug susceptibility testing by routine methods (disc diffusion and Etest) for meropenem and doripenem. We aimed to compare the in vitro activity of imipenem, meropenem, and doripenem against Pseudomonas aeruginosa. METHODS: A total of 311 P. aeruginosa strains isolated from respiratory specimens in 170 patients who developed ventilator-associated pneumonia in two intensive care units were collected over a period of 31 months. The susceptibility of these isolates to imipenem, meropenem, and doripenem were determined by Etest and disc diffusion method. RESULTS: Considering either all isolates or only the first isolates recovered per patient (311 and 170 respectively), the susceptibility rate for doripenem was higher than that for meropenem and imipenem. When MICs determined by Etest were converted into interpretative categories (S, I, R) using French (CA-SFM) guidelines, a poor correlation was observed for meropenem and doripenem. The percentages of correlation with the disc diffusion method were 90.6% and 89.7% for imipenem, 80.5% and 82.6% for meropenem, and 80.5% and 73.3% for doripenem, for the first isolates and all isolates, respectively. The rate of minor errors was as high as 17.7% and 16.1% for meropenem and 17.7% and 25.7% for doripenem for the first isolates and all isolates, respectively. CONCLUSION: The accuracy of disc diffusion using CA-SFM guidelines appears unsatisfactory for all three carbapenems justifying guideline update for P. aeruginosa and carbapenems.

Molecular detection methods of resistance to antituberculosis drugs in Mycobacterium tuberculosis.

OBJECTIVE: Molecular methods predict drug resistance several weeks before phenotypic methods and enable rapid implementation of appropriate therapeutic treatment. We aimed to detail the most representative molecular tools used in routine practice for the rapid detection of resistance to antituberculosis drugs among Mycobacterium tuberculosis strains. MATERIALS AND METHODS: The molecular diagnosis of resistance to antituberculosis drugs in clinical samples or from in vitro cultures is based on the detection of the most common mutations in the genes involved in the development of resistance in M. tuberculosis strains (encoding either protein targets of antibiotics, or antibiotic activating enzymes) by commercial molecular kits or by sequencing. RESULTS: Three hypotheses could explain the discrepancies between the genotypic results and the phenotypic drug susceptibility testing results: a low percentage of resistant mutants precluding the detection by genotypic methods on the primary culture; a low level of resistance not detected by phenotypic testing; and other resistance mechanisms not yet characterized. DISCUSSION/CONCLUSIONS: Molecular methods have varying sensitivity with regards to detecting antituberculosis drug resistance; that is why phenotypic susceptibility testing methods are mandatory for detecting antituberculosis drug-resistant isolates that have not been detected by molecular methods. The questionable ability of existing phenotypic and genotypic drug susceptibility testing to properly classify strains as susceptible or resistant, and at what level of resistance, was raised for several antituberculosis agents.

Toxins of Bacillus anthracis.

Bacillus anthracis, a gram positive bacterium, is the causative agent of anthrax. This organism is capsulogen and toxinogenic. It secretes two toxins which are composed of three proteins: the protective antigen (PA), the lethal factor (LF) and the edema factor (EF). The lethal toxin (PA+LF) provokes a subit death in animals, the edema toxin (PA+EF) induces edema. The edema and the lethal factors are internalised into the eukaryotic target cells via the protective antigen. EF and LF exert a calmoduline dependent adenylate cyclase and a metalloprotease activity respectively. Progress in the structure-function relationship of these three proteins, their regulation mechanisms and their roles in pathogenesis and immunoprotection will be exposed.

First Whole-Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium bovis BCG.

The attenuated BCG strain of Mycobacterium bovis is widely used as a vaccine against tuberculosis. However, in rare cases, it can be pathogenic to humans. Here, we report the first draft of a whole-genome sequence of a multidrug-resistant clinical isolate of M. bovis BCG.

Broad-range PCR: past, present, or future of bacteriology?

PCR targeting the gene encoding 16S ribosomal RNA (commonly named broad-range PCR or 16S PCR) has been used for 20 years as a polyvalent tool to study prokaryotes. Broad-range PCR was first used as a taxonomic tool, then in clinical microbiology. We will describe the use of broad-range PCR in clinical microbiology. The first application was identification of bacterial strains obtained by culture but whose phenotypic or proteomic identification remained difficult or impossible. This changed bacterial taxonomy and allowed discovering many new species. The second application of broad-range PCR in clinical microbiology is the detection of bacterial DNA from clinical samples; we will review the clinical settings in which the technique proved useful (such as endocarditis) and those in which it did not (such as characterization of bacteria in ascites, in cirrhotic patients). This technique allowed identifying the etiological agents for several diseases, such as Whipple disease. This review is a synthesis of data concerning the applications, assets, and drawbacks of broad-range PCR in clinical microbiology.

Impact of a 14-year screening programme on tuberculosis transmission among the homeless in Paris.

OBJECTIVE: To evaluate the impact of an active case-finding programme on tuberculosis (TB) transmission in homeless shelters in Paris, France. DESIGN: Between 1994 and 1997, an active case-finding programme was implemented in homeless shelters using a mobile radiological screening unit, and continued from 1997 to 2007. During these periods, the strains isolated from TB cases diagnosed in the homeless were genotyped by restriction fragment length polymorphism analysis using the insertion sequence IS6110 as a probe. RESULTS: Between 1994 and 2007, 313 new TB cases were diagnosed among the homeless population: 179 through the programme among shelter users, and 134 among homeless people not using shelters. Half of the strains were clustered in 35 distinct patterns (2-48 cases/cluster). The clustering of TB cases steadily decreased in shelters during the 13 years of the survey, from 14.3 to 2.7 related cases per year (P < 0.01) and from 75% to 30% of related cases among all TB cases (P < 0.01). In contrast, there was only a slight trend towards a decrease in homeless people not using shelters. CONCLUSION: Active case finding in homeless shelters resulted in a decrease in case clustering, mainly in shelter users. Genotyping contributed to confirming the positive impact of the intervention.

[Non-tuberculous mycobacterial infections related to esthetic care in France, 2001-2010]. / Infections à mycobactéries atypiques liées à des soins esthétiques en France, 2001-2010.

Non-tuberculous mycobacteria (NTM) infections usually occur in immunocompromised patients but also in immunocompetent patients following invasive procedures, especially for esthetic purposes. Since 2001, 20 episodes (57 cases) of NTM infections, seven of which (43 cases) were related to esthetic care, have been reported to the regional infection control coordinating centers (RICCC), the local health authorities (LHA), and the national institute for public health surveillance. Four notifications (40 cases) were related to non-surgical procedures performed by general practitioners in private settings: mesotherapy, carboxytherapy, and sclerosis of microvaricosities. The three other notifications (three cases) concerned surgical procedures-lifting and mammary prosthesis. Practice evaluations performed by the RICCC and LHA for five notifications showed deficiency of standard hygiene precautions and tap water misuse for injection equipment cleaning, or skin disinfection. Microbiological investigations (national reference center for mycobacteria) demonstrated the similarity of patient and environmental strains: in one episode (16 cases after mesotherapy), M. chelonae isolated from tap water was similar to those isolated from 11 cases. Healthcare-associated NTM infections are rare but have a potentially severe outcome. These cases stress the need of healthcare-associated infection notifications in outpatient settings.