SARS-CoV-2 in the environment: Contamination routes, detection methods, persistence and removal in wastewater treatment plants

The present study reviewed the occurrence of SARS-CoV-2 RNA and the evaluation of virus infectivity in feces and environmental matrices. The detection of SARS-CoV-2 RNA in feces and wastewater samples, reported in several studies, has generated interest and concern regarding the possible fecal-oral route of SARS-CoV-2 transmission. To date, the presence of viable SARS-CoV-2 in feces of COVID-19 infected people is not clearly confirmed although its isolation from feces of six different patients. Further, there is no documented evidence on the infectivity of SARS-CoV-2 in wastewater, sludge and environmental water samples, although the viral genome has been detected in these matrices. Decay data revealed that SARS-CoV-2 RNA persisted longer than infectious particle in all aquatic environment, indicating that genome quantification of SARS-CoV-2 does not imply the presence of infective viral particles. In addition, this review also outlined the fate of SARS-CoV-2 RNA during the different steps in the wastewater treatment plant and focusing on the virus elimination along the sludge treatment line. Studies showed complete removal of SARS-CoV-2 during the tertiary treatment. Moreover, thermophilic sludge treatments present high efficiency in SARS-CoV-2 inactivation. Further studies are required to provide more evidence with respect to the inactivation behavior of infectious SARS-CoV-2 in different environmental matrices and to examine factors affecting SARS-CoV-2 persistence.

Upper and lower urinary tract infection caused by Klebsiella pneumoniae serotype K2 and CTX-M-15 beta-lactamase-producing serotype K1: a case report and characterization of serum killing resistance

CTX-M-15 beta-lactamase-producing Klebsiella pneumoniae serotype K1 was isolated from a patient with fatal upper urinary tract infection (UTI) complicated by sepsis caused by K. pneumoniae serotype K2. Transfer of a CTX-M-15 beta-lactamase plasmid from the K1 to the K2 strain was observed. However, plasmid acquisition by the K2 strain did not occur in vivo, suggesting that the K1 strain might not have contributed directly to the upper UTI. In addition, effects of K serotypes and plasmid acquisition on K. pneumoniae serum resistance were examined.

Species distribution and ribotype diversity of Burkholderia cepacia complex isolates from French patients with cystic fibrosis

A total of 153 Burkholderia cepacia strains obtained from 153 French patients with cystic fibrosis were identified as Burkholderia multivorans (51.6%) or Burkholderia cenocepacia (45.1%). Eighty-two genotypes were identified using PvuII and EcoRI ribotyping. B. multivorans genotype A (found in 32 French patients) and two other genotypes were also identified among isolates from Austrian, German, Italian, and Canadian patients.

Nosocomial transmission of CTX-M-2 beta-lactamase-producing Acinetobacter baumannii in a neurosurgery ward

Three strains of cefotaxime (CTX)-resistant Acinetobacter baumannii, FM0209680, FM0300106, and FM0301433, were isolated from transtracheal aspirate cultures of three patients with probable nosocomial infections in a neurosurgery ward in Japan. The CTX MICs for these isolates were greater than 128 microg/ml but were drastically reduced in the presence of 4 microg of clavulanic acid per ml. These strains were also resistant to ceftriaxone, cefpodoxime, and aztreonam but were susceptible to ceftazidime and imipenem. The profile of resistance to various broad-spectrum beta-lactams was transferred by conjugation. Strain FM0209680 was not eradicated from case patient 1 by administration of imipenem, ceftazidime, and levofloxacin, even after a 6-month hospitalization period. Strains FM0300106 and FM0301433 were isolated from case patients 2 and 3 during the sixth week following admission, respectively, and then each patient was colonized for 3 weeks. Eradication of FM0300106 was successfully obtained from case patient 2 by imipenem treatment, while administration of imipenem was continued to prevent pneumonia. Prophylactic antimicrobial therapy was discontinued in case patient 3 because of the lack of pneumonic symptoms, and FM0301433 disappeared after the discontinuation of antimicrobial chemotherapy. All three strains carried the bla(CTX-M-2) gene, and the appearance of colonies in the growth-inhibitory zones around disks of CTX and aztreonam in double-disk synergy tests suggested inducible beta-lactamase production in these A. baumannii strains. The ribotyping investigation suggested that all these strains belong to the same clonal lineage. The plasmids harbored by A. baumannii had the same restriction profile as those harbored by Proteus mirabilis strains previously isolated in a urology ward of the Funabashi Medical Center.

Presumed endocarditis caused by BRO beta-lactamase-producing Moraxella lacunata in an infant with Fallot's tetrad

A case of presumed endocarditis caused by Moraxella lacunata in a 15-month-old male infant with Fallot's tetrad is described. This infection may have occurred as the result of transmission of this organism between the father and his son. This is the first report of BRO beta-lactamase-producing M. lacunata causing presumed endocarditis.

Successful outcome of disseminated Fusarium infection with skin localization treated with voriconazole and amphotericin B-lipid complex in a patient with acute leukemia

A disseminated Fusarium oxysporum infection with skin localization was diagnosed in a woman with a relapse of B-acute leukemia during induction chemotherapy. The infection was refractory to amphotericin B-lipid complex alone but responded successfully when voriconazole was added.

Molecular analysis and experimental virulence of French and North American Escherichia coli neonatal meningitis isolates: identification of a new virulent clone

Phylogenetic relationships, virulence factors, alone and in specific combinations, and virulence in a rat meningitis model were examined among 132 isolates of Escherichia coli neonatal meningitis from France and North America. Isolates belonging to phylogenetic groups A (n=11), D (n=20), and B2 (n=99) had similar high prevalence rates of the siderophores aerobactin and yersiniabactin and the K1 capsule (>/=70%) yet induced different level of experimental bacteremia. Ectochromosomal DNA-like domains involved in blood-brain barrier passage (PAI III(536) [sfa/foc and iroN; 34%]; GimA [ibeA and ptnC; 38%]; PAI II(J96) [hly, cnf1, and hra; 10%]) were restricted to B2 isolates. Among group B2 isolates, representatives of the O45:K1 clonal group (n=30), which lacked these domains, were as able as the archetypal O18:K1 strain C5 to cause meningitis. Molecular epidemiology combined with experimental virulence assays demonstrate that known virulence factors are insufficient to fully explain the pathophysiology of ECNM and to allow for rational search for new virulence factors.

Characterization of members of the Legionellaceae family by automated ribotyping

In order to implement a new and reliable method for characterizing different species of Legionella, a genetic fingerprinting study with an automated ribotyping system (RiboPrinter) was completed with members of this genus which were deposited at the American Type Culture Collection. The RiboPrinter examined the different patterns of EcoRI digestion fragments from the rRNA operons of 110 strains, representing 48 of the 49 described Legionella species as well as 70 serogroups of those species. Distinctive and consistent patterns were obtained for the type strains of the 48 species investigated. Legionella pneumophila subsp. fraseri and L. pneumophila subsp. pascullei each generated a specific pattern, whereas L. pneumophila subsp. pneumophila produced six different fingerprint patterns. No correlation seemed to exist between the ribotypes obtained and the 15 serotypes of L. pneumophila. For the other species, those with two known serogroups presented two distinctive patterns with the RiboPrinter with the exception of L. hackeliae and L. quinlivanii, which yielded only one pattern. We also encountered ribotypes for strains which were not identified to the species level. The ribotypes generated for these strains with the RiboPrinter did not match those generated for known type strains, suggesting the putative description of new serogroups or species. Although the automated system did not have sufficient discriminatory ability to serve as an epidemiological tool in a clinical setting, it appeared to be a powerful tool for general genomic analysis of the Legionella isolates (e.g., determination of new species) and assessment of the interrelationship among Legionella strains through the RiboPrinter database connection.

Automated ribotyping provides rapid phylogenetic subgroup affiliation of clinical extraintestinal pathogenic Escherichia coli strains

Using the automated Riboprinter system, we have initiated the construction of an electronic Riboprint database composed of 72 ECOR reference strains and 15 archetypal virulent strains in order to provide a new simple molecular characterization method. More than 90% of the ECOR strains clustered in their original phylogenetic group. All but one of the archetypal virulent strains had a profile identical to that of one of the ECOR strains and could be easily affiliated with a phylogenetic group. This method appears to be an accurate and practical tool especially for investigating the genetic relationship between clinical extraintestinal pathogenic strains and B2 subgroup ECOR strains or archetypal pathotype strains.

A Vibrio splendidus strain is associated with summer mortality of juvenile oysters Crassostrea gigas in the Bay of Morlaix (North Brittany, France)

Juvenile oysters Crassostrea gigas cultured in the Bay of Morlaix (France) have suffered unexplained summer mortalities for over a decade. In the present study, we tested the hypothesis that a bacterial pathogen could be responsible for this phenomenon. A first attempt failed to isolate a bacterial pathogen from moribund or weak oysters. Only non-pathogenic, probably opportunistic, bacteria were isolated. As an alternative approach, we focused on oysters presenting reduced stress-response capacities (determined by circulating noradrenaline measurements), a characteristic of juvenile oysters entering an early phase of the disease. Cultures of bacterial isolates on TCBS plates revealed that a Vibrio strain was present in diseased oysters and scarce or absent in healthy oysters. Experimental infections indicated that this Vibrio can cause mortalities of juvenile oysters when injected at concentrations ranging from 10(4) to 10(8) CFU oyster(-1). Similarly to the summer mortality disease, the Vibrio isolate caused higher mortalities at higher temperatures; apparently, it could not be transmitted horizontally, it did not affect adult oysters and it induced stress-response dysfunctions in juvenile oysters. Phenotypic and genotypic characterizations identified the pathogen as Vibrio splendidus. Taken together, the present results satisfy Koch's postulate and suggest that this bacterial strain is probably responsible for the juvenile oyster summer mortalities in the Bay of Morlaix.

Simplified procedure for detection of enteric pathogenic viruses in shellfish by RT-PCR

Epidemiological evidence linking the transmission of enteric viral disease to shellfish has been known for a long time. A variety of methods have been described for the detection of viral contaminants in shellfish using RT-PCR. However, these methods generally include numerous, often fastidious and time consuming steps for virus release from shellfish tissues and viral RNA isolation. A simplified procedure based on the enzymatic liquefaction of shellfish digestive tissues without any mechanical homogenisation step, followed by a simple clarification of the lysate using dichloromethane extraction, was developed. Viral RNA is isolated directly from the shellfish extract by a guanidium thiocyanate-silica extraction method, adapted for the use of a vacuum manifold system. Virus-specific RT-PCR assays were set up for detection of genomic sequences of the predominant viral pathogens, HAV, Astrovirus and Norwalk-like viruses (from genogoups I or II). The specificity of the amplicons is confirmed finally by hybridisation with DIG-labelled specific probes. The overall procedure applied to shellfish samples spiked with HAV particles allowed a detection of 20 pfu of HAV per g of hepatopancreas. In addition, up to 20 samples can be tested within 24 h.