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The human skin microbiota is quantitatively dominated by Gram-positive bacteria, detected by both culture and metagenomics. However, metagenomics revealed a huge variety of Gram-negative taxa generally considered from environmental origin. For species affiliation of bacteria in skin microbiota, clones of 16S rRNA gene and colonies growing on diverse culture media were analyzed. Species-level identification was achieved for 81% of both clones and colonies. Fifty species distributed in 26 genera were identified by culture, mostly belonging to Actinobacteria and Firmicutes, while 45 species-level operational taxonomic units distributed in 30 genera were detected by sequencing, with a high diversity of Proteobacteria. This mixed approach allowed the detection of 100% of the genera forming the known core skin Gram-negative microbiota and 43% of the known diversity of Gram-negative genera in human skin. The orphan genera represented 50% of the current skin pan-microbiota. Improved culture conditions allowed the isolation of Roseomonas mucosa, Aurantimonas altamirensis and Agrobacterium tumefaciens strains from healthy skin. For proteobacterial species previously described in the environment, we proposed the existence of skin-specific ecotypes, which might play a role in the fine-tuning of skin homeostasis and opportunistic infections but also act as a shuttle between environmental and human microbial communities. Therefore, skin-associated proteobacteria deserve to be considered in the One-Health concept connecting human health to the health of animals and the environment.

Objective: To assess the residual risk of waterborne contamination by Pseudomonas aeruginosa from a water network colonized by a single genotype [sequence type (ST) 299] despite the presence of antimicrobial filters in a medical intensive care unit (ICU)., Methods: During the first 19-month period since the ICU opened, contamination of the water network was assessed monthly by collecting water upstream of the filters. Downstream water was also sampled to assess the efficiency of the filters. P. aeruginosa isolates from patients were collected and compared with the waterborne ST299 P. aeruginosa by multiplex-rep polymerase chain reaction (PCR), pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. Cross-transmission events by other genotypes of P. aeruginosa were also assessed., Results: Overall, 1.3% of 449 samples of filtered water were positive for P. aeruginosa in inoculum, varying between 1 and 10 4  colony-forming units/100 mL according to the tap. All P. aeruginosa hydric isolates belonged to ST299 and displayed fewer than two single nucleotide polymorphisms (SNPs). Among 278 clinical isolates from 122 patients, 10 isolates in five patients showed identical profiles to the hydric ST299 clone on both multiplex-rep PCR and PFGE, and differed by an average of fewer than five SNPs, confirming the water network reservoir as the source of contamination by P. aeruginosa for 4.09% of patients. Cross-transmission events by other genotypes of P. aeruginosa were responsible for the contamination of 1.75% of patients., Discussion/conclusion: Antimicrobial filters are not sufficient to protect patients from waterborne pathogens when the water network is highly contaminated. A microbiological survey of filtered water may be needed in units hosting patients at risk of P. aeruginosa infections, even when all water points-of-use are fitted with filters., (Copyright © 2024 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

Importance: Microbial populations swiftly adapt to changing environments through horizontal gene transfer. While the mechanisms of gene transfer are well known, the impact of environmental conditions on the selection of transferred gene functions remains less clear. We investigated ICEs, specifically the ICE clc -type, in Pseudomonas aeruginosa clinical isolates. Our findings revealed co-evolution between ICEs and their hosts, with ICE transfers occurring within strains. Gene functions carried by ICEs are positively selected, including potential virulence factors and heavy metal resistance. Comparison to publicly available P. aeruginosa genomes unveiled widespread antibiotic-resistance determinants within ICE clc clades. Thus, the ubiquitous ICE clc family significantly contributes to P. aeruginosa 's adaptation and fitness in diverse environments., Competing Interests: The authors declare no conflict of interest.

In the context of the recent re-emergence of mpox worldwide, the French Society for Hospital Hygiene (SF2H) performed a literature review of the transmission paths and proposed specific recommendations for healthcare workers (HCWs) caring for patients with suspected or confirmed MPXV. In developed countries, the risk of contamination among HCWs in healthcare facilities seemed to be very low, limited to contamination through needle stick injuries. Two additional contamination cases were reported and not fully explained. Beyond healthcare settings, the analysis of the literature highlighted (i) a main contamination route during sexual intercourse, mainly among men who have sex with men, and (ii) a very low secondary attack rate in other contexts, such as schools or jails. Numerous studies have reported molecular or virus identification on surfaces or in the air surrounding patients, without any association with the low secondary case incidence; moreover, the minimum infectious dose through air or mucosal exposure is still unknown. Owing to the lack of evidence of MPXV respiratory transmission in the healthcare setting, the SF2H recommends the implementation of standard and contact precautions combined with medical/surgical mask use. Owing to the lack of evidence of transcutaneous contamination, the SF2H recommends the use of gloves only if contact with cutaneous lesions or mucous membranes occurs. Regarding the risk of contamination from the environment in healthcare facilities, additional studies must be conducted to investigate this., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The hospital environment constitutes a reservoir of opportunistic pathogens responsible for healthcare-associated infections (HCAI) such as Pseudomonas aeruginosa ( Pa ). Pa persistence within technological niches, the increasing emergence of epidemic high-risk clones in HCAI, the epidemiological link between plumbing strains and clinical strains, make it a major nosocomial pathogen. Therefore, understanding the mechanisms of Pa adaptation to hospital water systems would be useful in preventing HCAI. This review deciphers how copper resistance contributes to Pa adaptation and persistence in a hospital environment, especially within copper water systems, and ultimately to its success as a causative agent of HCAI. Numerous factors are involved in copper homeostasis in Pa , among which active efflux conferring copper tolerance, and copper-binding proteins regulating the copper compartmentalization between periplasm and cytoplasm. The functional harmony of copper homeostasis is regulated by several transcriptional regulators. The genomic island GI-7 appeared as especially responsible for the copper resistance in Pa . Mechanisms of copper and antibiotic cross-resistance and co-resistance are also identified, with potential co-regulation processes between them. Finally, copper resistance of Pa confers selective advantages in colonizing and persisting in hospital environments but also appears as an asset at the host/pathogen interface that helps in HCAI occurrence.

Non-tuberculous mycobacteria (NTM) are opportunistic pathogens commonly colonizing hospital water systems, and may be responsible for healthcare-associated infections (HAI). Investigation of HAI and outbreaks caused by NTM necessitates water analyses. However, NTM are slow-growing bacteria within the mesophilic community present in water, and are difficult to detect. Prior to culture on specific media, their recovery usually requires decontamination and concentration steps. We assessed the effectiveness of filtration as regards the recovery of 7 NTM species in hospital water samples. We also compared the use of cetylpyridinium chloride (CPC) at different concentrations and Sodium Hydroxide (NaOH) 4% in decontamination of water samples with mesophilic bacteria. Our laboratory protocol showed that membrane filtration was suitable for concentration and recovery of NTM from water. Sample decontamination with CPC was more NTM-preservative than NaOH. A combination of CPC at 0.005% and filtration allowed detection of NTM at low concentrations, ranging from 3 to 98 CFU/100mL according to the NTM species., (Copyright © 2021 Elsevier Masson SAS. All rights reserved.)

SARS-CoV-2 mainly infects the respiratory tract, and presents significantly higher active replication in the upper airways. To remain viable and infectious, the SARS-CoV-2 virion must be complete and integral, which is not easily demonstrated in the environment by positive reverse transcriptase PCR results. Real-life conditions in healthcare settings may be conducive to SARS-CoV-2 RNA dissemination in the environment but without evidence of its viability and infectiveness in air. Theoretically, SARS-CoV-2 shedding and dissemination nonetheless appears to be air-mediated, and a distinction between "air" and "droplet" transmission is too schematic to reflect the reality of the respiratory particles emitted by patients, between which a continuum exists. Airborne transmission is influenced by numerous environmental conditions that are not transposable between different viral agents and situations in healthcare settings or in the community. Even though international guidelines on "droplet" versus "air" precautions and personal protective equipment (surgical versus respirator masks) are under discussion, the existing literature underscores the effectiveness of "droplet" precautions as a means of protecting healthcare workers. Differentiation in guidelines between healthcare venues, community settings and, more generally, confined environments is of paramount importance, especially insofar as it underlines the abiding pandemic-related need for systematic mask wearing by the general population., (Copyright © 2021 Elsevier Masson SAS. All rights reserved.)

SARS-CoV-2 is mainly transmitted by respiratory droplets and contact with contaminated surfaces. It can be retrieved in faeces but there is no evidence of faecal-oral transmission, which is the main route of contamination in recreational waters. Standard cleaning and disinfecting procedures, microbiological control and health rules aim to prevent infectious risk regardless of the micro-organisms. In the context of progressive lockdown exit and hospital activities recovery, we assessed the risk of SARS-CoV-2 transmission in rehabilitation pools and therapeutic water environments in order to provide specific recommendations to control the spread of SARS-CoV-2 while ensuring essential rehabilitation care for patients., (Copyright © 2020 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

In the context of the COVID-19 pandemic, wearing a face mask has become usual and ubiquitous, in both hospitals and community. However, the general public is consuming surgical or filtering face piece (FFP) masks irrespective of their specificity, leading to global supply shortage for the most exposed persons, which are healthcare workers. This underlines the urgent need to clarify the indications of the different categories of mask, in order to rationalize their use. The study herein specifies the French position for the rational use of respiratory protective equipment for healthcare workers., (Copyright © 2020. Published by Elsevier Ltd.)

The investigation of an outbreak of Pseudomonas aeruginosa urinary tract infections after ambulatory cystoscopies identified a damaged cystoscope contaminated by P aeruginosa and acting as a relay object. This outbreak urges us not to trivialize urinary tract infections occurring after an elective cystoscopy. Patients should be advised to signal the occurrence of urologic symptoms after urologic exploration., (Copyright © 2019. Published by Elsevier Inc.)

In the context of a 3-month extended-spectrum beta-lactamase-producing Klebsiella pneumonia (ESBL-KP) outbreak in a neonatal care center (NCC), hygiene practices and hospital environment were investigated. ESBL-KP strains isolated from patients and environment were compared by molecular typing. The density of incidence of multi-drug-resistant bacteria (MDRB) was calculated from January 2014 to September 2016. The 3-month ESBL-KP outbreak involved 19 patients. Clinical strains from the 19 patients displayed the same molecular profile between them, and with a strain isolated from an incubator after cleaning. Furthermore, 52.4% of incubator mattresses were positive for diverse pathogens. Hygiene practices were acceptable except for external practitioners and parents. In addition to classical infection control (IC) measures, the replacement of mattresses and the improvement of incubators disinfection stopped the outbreak. The protocol of disinfection was revised and microbiological control was implemented. A significant decrease of MDRB incidence was concomitant (p value = 0.03219) but 3 months later, MDRB incidence increased again.Conclusion: This investigation highlighted incubators and mattresses as critical materials associated to infectious risk in NCC. NCC and IC teams should implement efficient protocol for incubators disinfection and monitoring. What is Known: • Environment in neonatal intensive care units is often suspected as reservoir for Enterobacteriaceae outbreaks but is scarcely investigated. • Incubators and mattresses offer wet and warm conditions suitable for pathogens multiplication, but microbiological survey is not performed routinely for assessing bacterial contamination. What is New: • Incubators and mattresses serve as reservoir for pathogens and relay in outbreak. • An infection control protocol associating efficient disinfection and microbiology analysis is proposed.

While typing methods are increasingly refined, the sampling of bacteria to be typed in healthcare-associated infection context retains less attention. Through 2 emblematic cases of in-hospital transmission of extensively drug-resistant bacteria producing carbapenemases, we demonstrate the impact of colony sampling in typing results. Because of intra-population diversity, typing several colonies of same species and resistotype was needed to fully track the transmission among patients. Bacterial population studies could better decipher transmission routes of healthcare-associated bacteria, thereby improving outbreak control., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Purpose: Vancomycin-resistant Enterococcus (VRE) faecium (VREfm) are highly resistant bacteria emerging worldwide and rarely studied using molecular tools in Algeria since their first report in 2006. The aim of the study was to investigate healthcare-associated infections (HAIs) involving the first VRE in Batna University Hospital, Algeria, and characterize isolates using molecular tools., Patients and Methods: Medical charts were reviewed for patients with VREfm. van genes were detected by multiplex polymerase chain reaction (PCR), and strains were characterized by automated repetitive sequence-based PCR (rep-PCR), multiplex rep-PCR, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST)., Results: During a 6-month period, VREfm infections occurred in four patients hospitalized in three wards. The four isolates were E. faecium vanA belonging to the hospital-adapted clonal complex 17. PCR-based methods did not discriminate the isolates but MLST and PFGE delineated a subgroup of three VREfm of identical pulsotype and sequence type (ST) 80 (yet identified for five isolates in the international PubMLST database) while the fourth isolate was of ST789 (not previously identified for a VREfm) and displayed an unrelated pulsotype. The three genotypically related isolates were recovered in patients who underwent surgery in the same department, suggesting an outbreak for which the source and route of transmission remained unidentified., Conclusion: This first molecular epidemiology study of VRE in Algeria was useful in delimiting an outbreak involving three of the four HAI cases and revealed rarely encountered genotypes. Considering the threat and burden of VRE infections worldwide, particularly in the USA, and the late emergence in Algeria, our study supports the urgent need for improved and early adequate infection control measures to avoid VRE spread in North African hospitals., Competing Interests: Disclosure The authors report no conflicts of interest in this work.

Recently, surgical site infections due to non-tuberculous mycobacteria (NTM) have been linked to heater-cooler unit contamination. The European Centre for Disease Prevention and Control and manufacturers now recommend the use of hydrogen peroxide in filtered water to fill heater-cooler unit tanks. After implementation of these measures in our hospital, heater-cooler units became heavily contaminated by opportunistic waterborne pathogens such as Pseudomonas aeruginosa and Stenotrophomonas maltophilia. No NTM were detected but fast-growing resistant bacteria could impair their detection. The efficiency of hydrogen peroxide and chlorhexidine-alcohol was compared in situ. Chlorhexidine-alcohol treatment stopped waterborne pathogen contamination and NTM were not cultured whereas their detection efficiency was probably improved., (Copyright © 2018 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

Placement of a central venous catheter (CVC) in the brachiocephalic vein (BCV) via the ultrasound (US)-guided supraclavicular approach was recently described in children. We aimed to determine the CVC maintenance-related complications at this site compared to the others (i.e., the femoral, the subclavian, and the jugular). We performed a retrospective data collection of prospectively registered data on CVC in young children hospitalized in a pediatric intensive care unit (PICU) during a 4-year period (May 2011 to May 2015). The primary outcome was a composite of central line-associated bloodstream infection (CLABSI) and deep-vein thrombosis (CLAT) according to the CVC site. Two hundred and twenty-five children, with respective age and weight of 7.1 (1.3-40.1) months and 7.7 (3.6-16) kg, required 257 CVCs, including 147 (57.2%) inserted in the BCV. The risk of the primary outcome was lower in the BCV than in the other sites (5.4 vs 16.4%; OR: 0.29; 95% CI: 0.12-0.70; p = 0.006). CLABSI incidence density rate (2.8 vs 8.96 per 1000 catheter days, p < 0.001) and CLAT incidence rate (2.7 vs 10%, p = 0.016) were also lower at this site., Conclusion: BCV catheterization via the US-guided supraclavicular approach may decrease CVC maintenance-related complications in children hospitalized in a PICU. What is Known: • Placement of a central venous catheter (CVC) in children is associated with mechanical risks during insertion, and with infectious and thrombotic complications during its maintenance. • Ultrasound (US)-guided supraclavicular catheterization of the brachiocephalic vein (BCV) is feasible in infants and children. What is New: • This observational study suggested that BCV catheterization via the US-guided supraclavicular approach was associated with a lower risk of CVC insertion and maintenance-related complications, compared with the other catheterization sites.

Background: Water networks in hospitals are frequently contaminated by opportunistic premise plumbing pathogens (OPPPs) leading to installation of antimicrobial filters on water points-of-use (POU) in order to limit patients' exposure., Aim: To assess the spread of OPPPs through secondary water routes (outside the plumbing system) in an adult haematology unit in which 52 out of 73 water POU were high risk for patients and protected by antimicrobial filters., Methods: An observational audit identified six secondary water routes for which bacteria tracking and typing were performed in 315 surface samplings. Bacterial isolates were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and compared to the infra-species level by multiplex repetitive element sequence-based polymerase chain reaction and/or by restriction fragment length polymorphism in pulse-field gel electrophoresis., Findings: Pseudomonas aeruginosa and Stenotrophomonas maltophilia, as well as non-pathogenic OPPP indicators, were detected in water collected upstream of antimicrobial filters. P. aeruginosa was the sole OPPP retrieved from tested surfaces (5.1%). The same clone of P. aeruginosa spread from water source to dry surfaces in the same room and cross-contaminated two sinks in different rooms. Three clones of non-pathogenic OPPP indicators spread more widely in different rooms., Conclusion: A strategy based on filtration of most (but not all) water POU in a haematology unit could be sufficient to limit the spread of OPPPs to the environment, provided a functional mapping of 'high-risk' POU has been undertaken. The residual spread of OPPPs and OPPP indicators linked to non-filtered water POU argues for careful monitoring of non-filtered water use., (Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

The naturally acquired microbiota of Anopheles can influence vector's susceptibility to Plasmodium and its capacity to transmit them. Microbiota modification is a new challenge to limit disease transmission but it still needs advanced knowledges on bacterial community in Anopheles , especially in wild and infected specimens from diverse origin and species. Bacterial culture and 16S rRNA gene-PCR associated to Temporal Temperature Gradient Electrophoresis (TTGE) were applied to explore the bacterial diversity in the abdomen of 100 wild specimens (eight Anopheles species) collected in the Binh Phuoc Province, Vietnam. Culture and PCR-TTGE were complementary. The bacterial richness of the mosquito collection encompassed 105 genera belonging to seven phyla, mostly Proteobacteria , Firmicutes , and Actinobacteria . Staphylococcus , Clostridium , and Bacillus in Firmicutes were the most prevalent genera. However, Proteobacteria represented by 57 genera was the most diversified phylum in Anopheles microbiota. The high overall of Anopheles -associated bacteria is confirmed with, to our knowledge, 51 genera described for the first time in Anopheles microbiota. However, the diversity per specimen was low with average diversity index and the average Shannon-Wiener score (H) of 4.843 and 5.569, respectively. The most represented bacterial genera were present in <30% of the specimens. Consequently, the core microbiota share by Anopheles from Binh Phuoc was very narrow, suggesting that Anopheles microbiota was greatly influenced by local environments. The repertory of bacterial genera in two specimens of An. dirus and An. pampanai naturally infected by Plasmodium vivax was also described as preliminary results. Finally, this study completed the repertory of bacteria associated to wild Anopheles . Anopheles associated-bacteria appeared specimen-dependent rather than mosquitoe species- or group-dependent. Their origin and the existence of Anopheles -specific bacterial taxa are discussed.

Roseomonas spp. are increasingly involved in human infectious diseases. The environmental source for infection is generally admitted in published cases owing to the origin of most Roseomonas species and to their affiliation to the family Acetobacteraceae in Rhodospirillales, which mainly groups environmental bacteria. For a better delineation of Roseomonas habitat and infectious reservoir, we related phenotype, phylotype (16S rRNA gene), genomotype (pulsed-field gel electrophoresis) and origin of 33 strains isolated from humans, hospital environment and natural environment. Genetic and metagenomic databases were also surveyed. The population structure of the genus showed clades associated with humans, whereas others grouped environmental strains only. Roseomonas mucosa is the main human-associated species and the study supported the idea that opportunistic infections due to this species are related to the patient skin microbiota rather than to the environment. In contrast, some strains belonging to other species isolated from patients with cystic fibrosis were related to environmental clades, suggesting an exogenous source for patient colonization. Accurate knowledge about the reservoirs of opportunistic pathogens that have long been considered of environmental origin is still needed and would be helpful to improve infection control and epidemiological survey of emerging human pathogens., (Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)

The non-tuberculous mycobacteria (NTM) Mycobacterium wolinskyi caused bacteraemia and massive colonization of an aortic prosthesis in a patient 16 days after cardiac surgery, necessitating repeat surgery and targeted antimicrobial chemotherapy. The infection control team investigated the source and conditions of infection. Peri-operative management of the patient complied with recommendations. The environmental investigation showed that although M. wolinskyi was not recovered, diverse NTM species were present in water from point-of-use taps and heater-cooler units for extracorporeal circulation. This case and increasing evidence of emerging NTM infections in cardiac surgery led to the implementation of infection control procedures in cardiac surgery wards., (Copyright © 2016 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

The human skin microbiota is quantitatively dominated by Gram-positive bacteria, detected by both culture and metagenomics. However, metagenomics revealed a huge variety of Gram-negative taxa generally considered from environmental origin. For species affiliation of bacteria in skin microbiota, clones of 16S rRNA gene and colonies growing on diverse culture media were analyzed. Species-level identification was achieved for 81% of both clones and colonies. Fifty species distributed in 26 genera were identified by culture, mostly belonging to Actinobacteria and Firmicutes , while 45 species-level operational taxonomic units distributed in 30 genera were detected by sequencing, with a high diversity of Proteobacteria . This mixed approach allowed the detection of 100% of the genera forming the known core skin Gram-negative microbiota and 43% of the known diversity of Gram-negative genera in human skin. The orphan genera represented 50% of the current skin pan-microbiota. Improved culture conditions allowed the isolation of Roseomonas mucosa , Aurantimonas altamirensis and Agrobacterium tumefaciens strains from healthy skin. For proteobacterial species previously described in the environment, we proposed the existence of skin-specific ecotypes, which might play a role in the fine-tuning of skin homeostasis and opportunistic infections but also act as a shuttle between environmental and human microbial communities. Therefore, skin-associated proteobacteria deserve to be considered in the One-Health concept connecting human health to the health of animals and the environment.

Propionibacterium acnes belongs to the normal skin microbiota, but it is also responsible for acne vulgaris and causes serious infections such as endocarditis and surgical site infections (SSI). The P. acnes population is structured into phylogenetic groups, with phylotype I being associated with acne. Herein, we explore the link between phylotypes and clinical origins in a collection of P. acnes isolated from different body sites, involved in deep infections or healthcare-associated infections (HAI), with particular emphasis on strains from cardiac SSI. Cardiac SSI have been further studied in terms of P. acnes population dynamics during the care pathway. The recA and tly genes phylotypes were compared to hemolytic behavior, susceptibility to antimicrobial agents, and clinical origins. An original approach of recA polymerase chain reaction temporal temperature gel electrophoresis (PCR-TTGE) was developed and applied for the direct identification of P. acnes phylotypes in surgical samples, in order to assess their temporal dynamics during the surgical course. Our results underlined the preferential involvement of IA-2/IB and II phylogroups in HAI and SSI. Unlike IA and II, type IA-2/IB presented a gradual increase with the depth of sampling in the peroperative phase of cardiac surgery. Phylotypes IA and IA-2/IB were both predominant in scar tissues and on postoperative skin, suggesting a specific predisposition to recolonize skin. Particular association of the phylotype IA-2/IB with SSI and its propensity to colonize wounds in cardiac surgery was observed. We assumed that the follow-up of P. acnes phylotypes during pathological processes could give new clues for P. acnes pathogenicity.

Human skin associated microbiota are increasingly described by culture-independent methods that showed an unexpected diversity with variation correlated with several pathologies. A role of microbiota disequilibrium in infection occurrence is hypothesized, particularly in surgical site infections. We study the diversities of operative site microbiota and its dynamics during surgical pathway of patients undergoing coronary-artery by-pass graft (CABG). Pre-, per-, and post-operative samples were collected from 25 patients: skin before the surgery, superficially and deeply during the intervention, and healing tissues. Bacterial diversity was assessed by DNA fingerprint using 16S rRNA gene PCR and Temporal Temperature Gel Electrophoresis (TTGE). The diversity of Operational Taxonomic Units (OTUs) at the surgical site was analyzed according to the stage of surgery. From all patients and samples, we identified 147 different OTUs belonging to the 6 phyla Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria, and Fusobacteria. High variations were observed among patients but common themes can be observed. The Firmicutes dominated quantitatively but were largely encompassed by the Proteobacteria regarding the OTUs diversity. The genera Propionibacterium and Staphylococcus predominated on the preoperative skin, whereas very diverse Proteobacteria appeared selected in peri-operative samples. The resilience in scar skin was partial with depletion in Actinobacteria and Firmicutes and increase of Gram-negative bacteria. Finally, the thoracic operative site presents an unexpected bacterial diversity, which is partially common to skin microbiota but presents particular dynamics. We described a complex bacterial community that gathers pathobionts and bacteria deemed to be environmental, opportunistic pathogens and non-pathogenic bacteria. These data stress to consider surgical microbiota as a "pathobiome" rather than a reservoir of individual potential pathogens.

Background: In the context of a methicillin-susceptible Staphylococcus aureus (MSSA) outbreak, we aimed to improve our knowledge of S. aureus (SA) epidemiology in the neonatal care center (NCC) of a tertiary care teaching hospital., Methods: We performed a complete one-year review of SA carrier, colonized or infected patients. Monthly prevalence and incidence of SA intestinal carriage, colonization and infection were calculated and the types of infection analysed. During the MSSA outbreak, strains were studied for antimicrobial resistance, content of virulence genes and comparative fingerprint in Pulsed-Field Gel Electrophoresis. Hand hygiene and catheter-related practices were assessed by direct observational audits. Environmental investigation was performed in search of a SA reservoir., Results: Epidemiological analyses showed 2 or 3 prevalence peaks on a background of SA endemicity. In the NCC, during 2009, overall MSSA prevalence did not decrease below 5.5%, while mean MRSA prevalence was about 1.53%. Analysis of infection cases revealed that the outbreak corresponded to the emergence of catheter-related infections and was probably related to the relaxation in infection control practices in a context of high colonization pressure. Health care workers' white coats appeared as a potential environmental reservoir that could perpetuate SA circulation in the ward., Conclusion: This report emphasizes the importance of integrating MSSA along with methicillin-resistant SA in a program of epidemiological surveillance in the NCC.

Ochrobactrum intermedium is considered as an emerging human environmental opportunistic pathogen with mild virulence. The distribution of isolates and sequences described in literature and databases showed frequent association with human beings and polluted environments. As population structures are related to bacterial lifestyles, we investigated by multi-locus approach the genetic structure of a population of 65 isolates representative of the known natural distribution of O. intermedium. The population was further surveyed for genome dynamics using pulsed-field gel electrophoresis and genomics. The population displayed a clonal epidemic structure with events of recombination that occurred mainly in clonal complexes. Concerning biogeography, clones were shared by human and environments and were both cosmopolitan and local. The main cosmopolitan clone was genetically and genomically stable, and grouped isolates that all harbored an atypical insertion in the rrs. Ubiquitism and stability of this major clone suggested a clonal succes in a particular niche. Events of genomic reduction were detected in the population and the deleted genomic content was described for one isolate. O. intermedium displayed allopatric characters associated to a tendancy of genome reduction suggesting a specialization process. Considering its relatedness with Brucella, this specialization might be a commitment toward pathogenic life-style that could be driven by technological selective pressure related medical and industrial technologies.