Streptococcus agalactiae carriage was evaluated by sampling four body sites in a group of 249 healthy individuals including both sexes and a wide range of ages; the aims were to study the population structure of colonizing strains by multilocus sequence typing (MLST) and to evaluate their diversity by serotyping, SmaI macrorestriction analysis, and PCR screening for genetic markers of highly virulent clones for neonates. The prevalences of carriage were 27% in women and 32% in men. The major positive body site was the genital tract (23% in women and 21% in men); skin, throats, and anal margins were also positive in 2%, 4%, and 14%, respectively. These human-colonizing strains belonged mostly to serotypes III (24%), Ia (21%), V (18%), and Ib (17%). Twenty-three sequence types (STs) were identified. The MLST characteristics of the strains isolated from a single anatomic site—genital (vagina [women] or from a sample of the first urination after arising from a night's sleep [men]), throat, skin, or anal margin—suggest a body site colonization specificity for particular STs: strains of STs 2, 10, 19, and 196 were isolated only from genital sites; strains of STs 1, 8, and 23 were isolated more frequently from throat florae; and strains recovered only from anal margin samples were more closely related to strains isolated from throats than to those from genital sites. Most strains of STs 1, 8, and 23—STs that are increasingly described as being responsible for adult infections—did not carry any markers of strains virulent for neonates, suggesting that the virulence of these strains is probably associated with other genetic determinants. In addition, the genetic diversities of the strains varied between STs: STs 2, 8, 10, 23, and 196 were the most diverse; STs 1 and 19 were more homogeneous; and ST 17 strains formed three distant groups.

Following a change in surgical practice, we noted that the rate at which Staphylococcus lugdunensis was isolated from samples from the plastic surgery unit of our hospital increased considerably. We investigated the sources of these S. lugdunensis strains, and we found that in the case of drain colonization or surgical site infection, the strain was more likely to have come from the patient's skin bacteria when the pubic site had been shaved preoperatively. To test the hypothesis of pubic site colonization, we evaluated the prevalence of S. lugdunensis carriage among the cutaneous flora of the inguinal area. We found that 22% of 140 incoming patients carried S. lugdunensis in this area and that carriage at both inguinal folds was frequent (68% of carriers). A study of the genetic structure of the total population, including the clinical ( n = 18) and the commensal ( n = 53) strains, revealed that the diversity of the species was low and that the population was composed of two major groups that diverged at a distance of 35%. No particular characteristics made it possible to distinguish between clinical and commensal strains. Only isolates producing β-lactamase were homogeneous; six of the eight β-lactamase-positive strains displayed the same pulsed-field gel electrophoresis pattern.

In the course of an annual 3-month bloodstream infections (BSI) survey conducted during a four-year period in 31 healthcare institutions located in three noncontiguous French regions, we report 18 ST398 Staphylococcus aureus BSI. ST398 BSI incidence showed a seven-fold increase during the study period (0.002 per 1,000 patient days in 2007 vs. 0.014 in 2010). ST398 BSI isolates differed from the pig-borne multiresistant clone: 17/18 BSI isolates were methicillin susceptible and none was of t011, t034 or t108 pig-borne spa-types. ST398 BSI isolates had homogenous resistance patterns (15/18 with only Ery^r) and prophagic content (all harboured the hlb-converting Sau3int phage). The clustering of BSI and pig-borne isolates by spa-typing and MLVA, the occurrence of Sau3int phage in BSI isolates and the lack of this phage in pig-borne isolates suggest that the emergence of BSI isolates could have arisen from horizontal transfer, at least of the Sau3int phage, in genetically diverse MSSA ST398 isolates. The acquisition of the phage likely plays a role in the increasing ability of the lysogenic ST398 isolates to colonize human. The mode of acquisition of the non pig-borne ST398 isolates by our 18 patients remains unclear. ST398 BSI were diagnosed in patients lacking livestock exposure and were significantly associated with digestive portals of entry (3/18 [16.7%] for ST398 vs. 19/767 [2.5%] for non ST398 BSI; p = .012). This raises the question of possible foodborne human infections. We suggest the need for active surveillance to study and control the spread of this human-adapted subclone increasingly isolated in the hospital setting.

It has been suggested that prophages in the ST398 S. aureus clone are responsible for expanding ST398's spectrum of action and increasing its ability to cause human infections. We carried out the first characterization of the various prophages carried by 76 ST398 bloodstream infection (BSI) isolates obtained over 9 years of observation. Whole-genome sequencing of 22 representative isolates showed (1) the presence of the φ3-prophage and diverse genetic features typical of animal-associated isolates (i.e., SCCmec XI element, Tn916 transposon and non φ3-prophages) in a majority of BSI isolates, (2) one BSI isolate devoid of the φ3-prophage but otherwise similar to an animal-infecting isolate, (3) 35 prophages carrying numerous genes previously associated with virulence or immune evasion in animal models of staphylococcal infections. The analysis of prophage content in all 76 BSI isolates showed an increasing prevalence of polylysogeny over time. Overall, over the course of the last 10 years, the BSI isolates appear to have acquired increasing numbers of genetic features previously shown to contribute to bacterial adaptation and virulence in animal models of staphylococcal infections. We hypothesize that lysogeny has played a significant role in increasing the ability of the ST398 clone to cause infections in humans. Our findings highlight the risk that the ST398 lineage will increase its threat to public health by continuing to acquire virulence and/or multiple antibiotic-resistance genes from hospital-associated clones of Staphylococcus aureus.

Legionella anisa is one of the most frequent species of Legionella other than Legionella pneumophila in the environment and may be hospital acquired in rare cases. We found that L. anisa may mask water contamination by L. pneumophila , suggesting that there is a risk of L. pneumophila infection in immunocompromised patients if water is found to be contaminated with Legionella species other than L. pneumophila .