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The diagnosis of Q fever is challenging due to nonspecific symptoms and negative standard blood culture results. Serological testing through immunofluorescence assay (IFA) is the most commonly used method for diagnosing this disease. Polymerase chain reaction (PCR) tests can also be used to detect bacterial DNA if taken at an appropriate time. Once the presence of bacteria is confirmed in a sample, an enrichment step is required before characterizing it through sequencing. Cultivating C. burnetii is challenging as it can only be isolated by inoculation into cell culture, embryonated eggs, or animals. In this article, we describe the isolation of C. burnetii from a valve specimen in Vero cells. We conducted genome sequencing and taxonomy profiling of this isolate and were able to determine its taxonomic affiliation. Furthermore, Multispacer sequence typing (MST) analysis suggests that the infection originated from a local strain of C. burnetii found around northern Israel and Lebanon. This novel strain belongs to a previously described genotype MST6, harboring the QpRS plasmid, never reported in Israel.

SARS-CoV-2 Omicron strain emergence raised concerns that its enhanced infectivity is partly due to altered spread/contamination modalities. We therefore sampled high-contact surfaces and air in close proximity to patients who were verified as infected with the Omicron strain, using identical protocols applied to sample patients positive to the original or Alpha strains. Cumulatively, for all 3 strains, viral RNA was detected in 90 of 168 surfaces and 6 of 49 air samples (mean cycle threshold [Ct]=35.2±2.5). No infective virus was identified. No significant differences in prevalence were found between strains.

The genetic identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is based on viral RNA extraction prior to RT-qPCR assay. However, recent studies have supported the elimination of the extraction step. This study was performed to assess the necessity for the RNA extraction, by comparing the efficacy of RT-qPCR in several direct approaches versus the gold standard RNA extraction, in the detection of SARS-CoV-2 in laboratory samples, as well as in clinical oro-nasopharyngeal SARS-CoV-2 swabs. The findings showed an advantage for the extraction procedure; however a direct no-buffer approach might be an alternative, since it identified more than 60% of positive clinical specimens.

In the event of a bioterror attack, a prompt, sensitive and definite identification of the agents involved is of major concern for confirmation of the event and for mitigation of countermeasures. Whether the information from intelligence forces is limited concerning the biothreat identity or one suspects the presence of a novel or engineered agent, the genetic identification of microorganisms in an unknown sample is challenging. High-throughput sequencing (HTS) technologies can sequence a heterogeneous mixture of genetic materials with high sensitivity and speed; nevertheless, despite the enormous advantages of HTS, all previous reports have analyzed unknown samples in a timeframe of a few days to a few weeks. This timeframe might not be relevant to an emergency scenario. Here, we present an HTS-based approach for deciphering the genetic composition of unknown samples within a working day. This outcome is accomplished by a rapid library preparation procedure, short-length sequencing and a prompt bioinformatics comparison against all available microbial genomic sequences. Using this approach, as a proof of concept, we were able to detect two spiked-in biothreat agents, B. anthracis and Y. pestis, in a variety of environmental samples at relevant concentrations and within a short timeframe of eight hours.