Trend in respiratory viruses' activity in the COVID-19 area.

OBJECTIVES: SARS-CoV-2 has impacted the detection of seasonal respiratory viruses. We retrospectively assessed the trend in the detection of 10 viruses in the COVID-19 area in 2 hospitals located in the Paris area. METHODS: All patients positive for a respiratory virus in two hospitals from September 2016 to August 2021 were retrospectively included. The rate of RT-PCR positive for each virus was calculated for the 2020-2021 season and the 2019-2020 season in comparison to a baseline of 3 seasons, i.e. 2016-2017, 2017-2018, and 2018-2019. RESULTS: Overall, 7,835 patients were tested positive from September 2016 to August 2021. The detection of respiratory virus dramatically falls on week-11 of 2020, as the number of RT-PCR performed. Then, 3 trends were identified: a) almost a disappearance for influenza; b) a 10-weeks delay in the seasonal outbreak for RSV; c) a persistence of circulation with variable activity for other viruses. In comparison to a baseline of three seasons (2016-2019), the rate of positive patients was lower during the 2020-2021 season for coronavirus (4.51% vs. 1.26%, P < 0.0001), adenovirus (1.93% vs. 1.34%, P = 0.14), bocavirus (0.58% vs. 0.11%, P = 0.08), and enterovirus (0.28% vs. 0.0%, P = 0.12). In contrast, the rate of hMPV-positive (1.92% vs. 2.83%, P = 0.03) and hPIV-positive (2.17% vs. 2.99%, P = 0.06) patients increased. CONCLUSIONS: The fall in the number of respiratory viruses detected might be related to the lower number of tests performed and the implementation of non pharmaceutical intervention (NPI). Then, all viruses except influenza are detected, probably as a consequence of high adherence to influenza vaccines. Despite, a lower number of tests being performed, the rate of hMPV-positive and hPIV-positive patients increased suggesting an active circulation of these viruses. Altogether, these findings suggest a persistent circulation of common respiratory viruses all over the COVID-19 era.

Evolution of antibiotic treatments for healthcare-associated infections caused by extended-spectrum beta-lactamase-producing Enterobacteriaceae in France.

BACKGROUND: Infections caused by extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBLE) remain a public health challenge. AIM: We traced the evolution of antibiotics prescribed for patients with ESBLE-healthcare associated infections (ESBLE-HAI) between 2012 and 2017, with a specific focus on treatments for lower urinary tract infections (LUTI). METHODS: We used the 2012 and 2017 French point prevalence survey data. Patients with ESBLE-HAI were defined as those diagnosed with at least one Enterobacteriaceae with ESBL production. Patients with LUTI caused by ESBLE (ESBLE-LUTI) were defined as those with LUTI as the reported infection site and diagnosed with ESBLE. We only analysed treatments intended for HAI. RESULTS: In 2017, more than half of treatments for ESBLE-HAIs were ß-lactams. While from 2012 to 2017 the proportion of carbapenem treatments decreased from 30% to 25%, penicillin treatments doubled. Among patients treated for ESBLE-LUTI, a larger proportion received a single antibiotic in 2017. The most frequently prescribed antibiotics for these infections were amoxicillin/clavulanic acid, nitrofurantoin and ofloxacin. More than one out of six treatments lasted for more than 7 days. Carbapenem use was halved between 2012 and 2017, and decreases were likewise observed for aminoglycosides. CONCLUSION: In accordance with French recommendations, comparison of the two most recent French point prevalence surveys showed an evolution in ESBLE-HAI treatment, especially for ESBLE-LUTI. However, treatment durations remained longer than recommended. Data from the 2022 survey should provide insights on the future evolution of prescription trends.

SARS-CoV-2 screening of asymptomatic health care workers: experience of a General hospital.

Health care workers (HCWs) are at major risk to be infected by SARS-CoV-2 and transmit the virus to the patients. Furthermore, travels are a major factor in the diffusion of the virus. We report our experience regarding the screening of asymptomatic HCWs returning from holidays, following the issue of a national guideline on 08/20/2020. The organization of the occupational health department and the clinical laboratory was adapted in order to start the screening on August, 24, 2020. All HCWs tested for SARS-CoV-2 the week before and 4 weeks after the implementation of the screening were included. The mean number of tests was analyzed per working day and working week. Overall, 502 (31.4%) HCWs were tested for SARS-CoV-2 during the study period. The mean number of HCWs tested per working day was 27.1. HCWs accounted for 36.9% (n = 167) and 11.2% (n = 84) of the tests performed in the 1st and the 4th week following the implementation of the guidelines. The number of tests performed each week in HCWs increased by at least 20-fold after the implementation of the guidelines. No asymptomatic HCW was tested positive. Screening of asymptomatic HCWs was poorly effective in the context of low circulation of the virus. We suggest giving priority to infection prevention and control measures and screening of symptomatic subjects and asymptomatic contacts.

Rapid and accurate eXDR screening: use Xpert Carba-R® with FecalSwab®.

The FecalSwab® displays high performances for stool culture, but it was not assessed for carbapenemase-producing Enterobacterales (CPE) screening. We assess the performances of the Xpert Carba-R v2® with the FecalSwab®. Using a collection of 12 CPE strains, the limit of detection was assessed at 158 CFU/swab [interquartile range 93-589]. In 2019, 1540 swabs were included by 4 hospital laboratories, of which 39 (2.5%) yield an invalid result. Among the 1501 valid, 87 (5.8%) were positives by culture and PCR and 25 (1.7%) were discrepant: 7 PCR-negative culture-positive, and 18 PCR-positive culture-negative. Two PCR-positive culture-negative results involved non-Enterobacterales strains: a KPC-producing Acinetobacter baumannii and a KPC-producing Aeromonas spp. The overall percent agreement was 98.3% and the Kappa value was 0.88. FecalSwab® is an accurate sampling device for CPE screening. It allows performing all eXDR screening using a single swab, simplifying the sample collection, and improving the patient comfort. Regarding discrepant, we suggest combining a CPE screening by both culture and Xpert Carba-R v2® methods.

Emergence of Imipenem Resistance in a CpxA-H208P-Variant-Producing Proteus mirabilis Clinical Isolate.

The Proteus mirabilis PmirS clinical isolate, which was susceptible to imipenem (0.5 µg/mL) and amikacin (1 µg/mL), was recovered from a bronchial aspirate of a patient who recently underwent lung transplantation. The P. mirabilis PmirR clinical isolate, which exhibited resistance to imipenem (16 µg/mL) and amikacin (24 µg/mL), was isolated 3 weeks later from the same patient and the same specimen type. Using short-read sequencing technology, these isolates appeared to be genetically identical except the cpxA gene of the PmirR isolate that was mutated leading to the His-208-Pro substitution. The structural alteration was localized in the histidine kinase, adenylate cyclase, methyl accepting protein, phosphatase (HAMP) domain, which is involved in the signal transduction between the sensor kinase and the regulator response of the CpxA/CpxR two-component system (TCS). No significant defect in the growth rate was found between the PmirS and PmirR isolates. This study suggests that alteration in CpxA might confer imipenem and amikacin resistance in P. mirabilis. This study brings new evidence that the TCS alteration could provide an adaptive capacity in a clinical context by conferring antibiotic resistance without fitness cost.

Carbapenemase-producing Enterobacterales outbreak: Another dark side of COVID-19.

In the hospital department dedicated to COVID-19-patient, infection prevention and control measures were upgraded. Therefore, the cross-transmission of other micro-organisms was thought unlikely to occur. However, we report an outbreak of NDM-5-producing Escherichia. coli in a 12-beds ICU dedicated to COVID-19 patients. This outbreak involved 6 patients of which 5 were asymptomatic carriers and 1 was infected. Several findings might have contributed to cross-transmission including the multiple-bedroom configuration of the department, uncomplete compliance for standard and contact precautions, overwork due to the burden of the disease, lack of training of staff for the care of ICU-patients, and misuse of gloves. Furthermore, as infection prevention and control measures were thought to be applied, contact patients were not screened for eXDR carriage. Applying rigorously standard and contact precautions and performing screening in contact patients when indicated must be the rules in COVID-19 wards.

[Accreditation of the screening for the rectal carriage of vanA and/or vanB Vancomycin-resistant enterococci by an accredited laboratory under the standard NF EN ISO/IEC 17025:2005]. / Accréditation du dépistage du portage rectal des entérocoques résistants aux glycopeptides vanA et/ou vanB par un laboratoire déjà accrédité en portée B selon la norme NF EN ISO/CEI 17025:2005.

The quality of the screening of vanA and/or vanB Vancomycin-resistant enterococcal (VRE) carriage by patients transferred from foreign countries plays a role in the management of risks linked to extensively drug resistant organisms (XDRO). Accreditation of the screening according to the NF EN ISO 15189 and NF EN ISO/IEC 17025 standards contributes to satisfy the level of quality. Our laboratory was already accredited according to the NF EN ISO/IEC 17025 standard. We used its quality management system and the type B widened flexible scope to identify the required criteria based on microbiology and infection control standards and those of Afnor and Cofrac, and to validate the screening procedure. Accreditation was obtained for use of the Type B scope, for culture-based detection and identification (codes BA1 and BA5), for determination of the minimal inhibitory concentrations of glycopeptides (code BA6), and for the detection of resistance genes to glycopeptides by polymerase chain reaction (code BA8). The maturity of our quality management system contributed to validate the screening procedures following the required criteria of the NF EN ISO/IEC 17025 standard.

Molecular Characterization of Carbapenem-Nonsusceptible Enterobacterial Isolates Collected during a Prospective Interregional Survey in France and Susceptibility to the Novel Ceftazidime-Avibactam and Aztreonam-Avibactam Combinations.

An interregional surveillance program was conducted in the northwestern part of France to determine the prevalence of carbapenem-nonsusceptible Enterobacteriaceae (CNSE) isolates and their susceptibility to ceftazidime-avibactam and aztreonam-avibactam combinations. Nonduplicate CNSE clinical isolates were prospectively collected from six hospitals between June 2012 and November 2013. MICs of ceftazidime and aztreonam, alone or combined with a fixed concentration of avibactam (4 µg/ml), and those of carbapenems (comparator agents) were determined. MICs of ertapenem in combination with phenylalanine arginine-naphthylamide dihydrochloride (PAßN) were also determined to assess active efflux. Genes encoding carbapenemases, plasmid-mediated AmpC enzymes, extended-spectrum ß-lactamases (ESBLs), and major outer membrane proteins (OMPs) were amplified and sequenced. OMPs were also extracted for SDS-PAGE analysis. Among the 139 CNSE isolates, mainly Enterobacter spp. and Klebsiella pneumoniae, 123 (88.4%) were ertapenem nonsusceptible, 12 (8.6%) exhibited reduced susceptibility to all carbapenems, and 4 Proteeae isolates (2.9%) were resistant to imipenem. Carbapenemase production was detected in only two isolates (producing OXA-48 and IMI-3). In contrast, OMP deficiency, in association with AmpCs and/or ESBLs (mainly CTX-M-9, SHV-12, and CTX-M-15), was largely identified among CNSE isolates. The ceftazidime-avibactam and aztreonam-avibactam combinations exhibited potent activity against CNSE isolates (MIC50/MIC90, 1/1 µg/ml and 0.5/0.5 µg/ml, respectively) compared to that of ceftazidime and aztreonam alone (MIC50/MIC90, 512/512 µg/ml and 128/512 µg/ml, respectively). This study reveals the in vitro activity of ceftazidime-avibactam and aztreonam-avibactam combinations against a large collection of porin-deficient enterobacterial isolates that are representative of the CNSE recovered in the northern part of France.