Snapshot of COVID-19 superinfections in Marseille hospitals: where are the common pathogens?

Episodes of bacterial superinfections have been well identified for several respiratory viruses, notably influenza. In this retrospective study, we compared the frequency of superinfections in COVID-19 patients to those found in influenza-positive patients, and to controls without viral infection. We included 42 468 patients who had been diagnosed with COVID-19 and 266 261 subjects who had tested COVID-19 negative between 26 February 2020 and 1 May 2021. In addition, 4059 patients were included who had tested positive for the influenza virus between 1 January 2017 and 31 December 2019. Bacterial infections in COVID-19 patients were more frequently healthcare-associated, and acquired in ICUs, were associated with longer ICU stays, and occurred in older and male patients when compared to controls and to influenza patients (P < 0.0001 for all). The most common pathogens proved to be less frequent in COVID-19 patients, including fewer cases of bacteraemia involving E. coli (P < 0.0001) and Klebsiella pneumoniae (P = 0.027) when compared to controls. In respiratory specimens Haemophilus influenzae (P < 0.0001) was more frequent in controls, while Streptococcus pneumoniae (P < 0.0001) was more frequent in influenza patients. Likewise, species associated with nosocomial transmission, such as Pseudomonas aeruginosa and Staphylococcus epidermidis, were more frequent among COVID-19 patients. Finally, we observed a high frequency of Enterococcus faecalis bacteraemia among COVID-19 patients, which were mainly ICU-acquired and associated with a longer timescale to acquisition.

Incidence and Outcome of Coinfections with SARS-CoV-2 and Rhinovirus.

BACKGROUND: We aimed to compare the clinical severity in patients who were coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and rhinovirus or monoinfected with a single one of these viruses. METHODS: The study period ranged from 1 March 2020 to 28 February 2021 (one year). SARS-CoV-2 and other respiratory viruses were identified by real-time reverse-transcription-PCR as part of the routine work at Marseille University hospitals. Bacterial and fungal infections were detected by standard methods. Clinical data were retrospectively collected from medical files. This study was approved by the ethical committee of our institute. RESULTS: A total of 6034/15,157 (40%) tested patients were positive for at least one respiratory virus. Ninety-three (4.3%) SARS-CoV-2-infected patients were coinfected with another respiratory virus, with rhinovirus being the most frequent (62/93, 67%). Patients coinfected with SARS-CoV-2 and rhinovirus were significantly more likely to report a cough than those with SARS-CoV-2 monoinfection (62% vs. 31%; p = 0.0008). In addition, they were also significantly more likely to report dyspnea than patients with rhinovirus monoinfection (45% vs. 36%; p = 0.02). They were also more likely to be transferred to an intensive care unit and to die than patients with rhinovirus monoinfection (16% vs. 5% and 7% vs. 2%, respectively) but these differences were not statistically significant. CONCLUSIONS: A close surveillance and investigation of the co-incidence and interactions of SARS-CoV-2 and other respiratory viruses is needed. The possible higher risk of increased clinical severity in SARS-CoV-2-positive patients coinfected with rhinovirus warrants further large scale studies.

Rapid Isothermal Amplification for the Buccal Detection SARS-CoV-2 in the Context of Out-Patient COVID-19 Screening.

A commercially available isothermal amplification of SARS-CoV-2 RNA was applied to self-collected saliva samples using dry dental cotton rolls, which were held in the mouth for two minutes. Of 212 tests, isothermal amplification yielded three (0.14%) invalid results, 120 (56.6%) positive results and 89 (42%) negative results. Compared to reference RT-PCR assays routinely performed simultaneously on nasopharyngeal swabs, excluding the three invalid isothermal amplification assays and one RT-PCR invalid assay, these figures indicated that 119/123 (96.7%) samples were positive in both methods and 85/85 samples were negative in both methods. Four positive buccal swabs which were missed by the isothermal amplification, exhibited Ct values of 26-34 in reference RT-PCR assays. Positive isothermal amplification detection was achieved in less than 10 min. Supervision of the self-sampling procedure was key to achieve these performances. These data support the proposal to use the protocol reported in this paper, including supervised buccal self-sampling, to screen people suspected of having COVID-19 at the point of care.