Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpert® System and a Mutation Associated with Different Target Gene Failure.

SARS-CoV-2 nucleic acid detection tests enable rapid virus detection; however, it is challenging to identify genotypes to comprehend the local epidemiology and infection routes in real-time qRT-PCR. At the end of June 2022, our hospital experienced an in-hospital cluster of COVID-19. When examined using the GeneXpert® System, the cycle threshold (Ct) value of the N2 region of the nucleocapsid gene of SARS-CoV-2 was approximately 10 cycles higher than that of the envelope gene. Sanger sequencing revealed a G29179T mutation in the primer and probe binding sites. A review of past test results revealed differences in Ct values in 21 of 345 SARS-CoV-2-positive patients, of which 17 cases were cluster-related and 4 were not. Including these 21 cases, 36 cases in total were selected for whole-genome sequencing (WGS). The viral genomes in the cluster-related cases were identified as BA.2.10, and those in the non-cluster cases were closely related and classified as being downstream of BA.2.10 and other lineages. Although WGS can provide comprehensive information, its use is limited in various laboratory settings. A measurement platform reporting and comparing Ct values of different target genes can improve test accuracy, enhance our understanding of infection spread, and be applied to the quality control of reagents.

Differential Dynamics of Humoral and Cell-Mediated Immunity with Three Doses of BNT162b2 SARS-CoV-2 Vaccine in Healthcare Workers in Japan: A Prospective Cohort Study.

Vaccines against SARS-CoV-2 with good efficacy are now available worldwide. However, gained immunity diminishes over time. Here, we investigate the course of both humoral and cell-mediated immunity in response to three doses of the Pfizer mRNA BNT162b2 SARS-CoV-2 vaccine in healthcare workers in Japan. SARS-CoV-2 anti-receptor-binding domain (RBD) antibodies (total Ig, IgG), neutralizing antibodies (NAb), and ELISpot were measured in serum and whole blood samples collected after each vaccine dose. ELISpot numbers were higher than the cutoff values in most participants at all times. It was suggested that the difference in behavior between humoral immunity and cell-mediated immunity with age is complementary. Anti-RBD total Ig, IgG, and NAb indicated a high correlation at each time point after vaccine doses. Total Ig was retained long-term after the second dose and increased significantly faster by the booster dose than IgG. Nab levels of all subjects were ≤20% six months after the second dose, and the correlation coefficient was greatly reduced. These are due to the avidity of each antibody and differences among commercial kits, which may affect the evaluation of immunokinetics in previous COVID-19 studies. Therefore, it is necessary to harmonize reagents categorized by the same characteristics.

Lactococcus lactis cholangitis and bacteremia identified by MALDI-TOF mass spectrometry: A case report and review of the literature on Lactococcus lactis infection.

Lactococcus lactis is a rare causative organism in humans. Cases of L. lactis infection have only rarely been reported. However, because it is often difficult to identify by conventional commercially available methods, its incidence may be underestimated. We herein report the case of a 70-year-old man with cholangiocarcinoma who developed L. lactis cholangitis and review previously reported cases of L. lactis infection. Our case was confirmed by matrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This case shows L. lactis is a potential causative pathogen of cholangitis and that MALDI-TOF MS can be useful for the rapid and accurate identification of L. lactis infection. We searched the literature for published case reports on cholangitis and any other infections caused by L. lactis, and thereby identified 36 cases, including our case. At least 66.7% (n = 24) of the cases had significant underlying conditions; 15 of the cases involved patients with an immunocompromised status. At least 41.7% (n = 15) had a significant food consumption history, such as the consumption of unpasteurized dairy products. The clinical sources of L. lactis were diverse and endocarditis was the most common diagnosis (n = 8), followed by hepatobiliary infection (n = 6), central nervous system infection (n = 5), and peritonitis (n = 4). The prognosis was favorable in most cases.

Pyelonephritis with bacteremia caused by Listeria monocytogenes: A case report.

Listeria monocytogenes is a well-known cause of meningitis, colitis, and bacteremia; however, obstructive pyelonephritis caused by L. monocytogenes has never been reported. We herein report on a 90-year-old Japanese woman with obstructive pyelonephritis and bacteremia due to uterus carcinoma invading the ureter. She was admitted to our hospital complaining of fever and chills, and her physical examination revealed left costovertebral angle tenderness. Computed tomography showed hydronephrosis and complete ureteral obstruction due to tumor invasion. Blood and urine cultures upon nephrostomy revealed the growth of L. monocytogenes. We treated the patient with two weeks of intravenous ampicillin and an additional one-week treatment of oral sulfamethoxazole/trimethoprim. This case shows the importance to recognize L. monocytogenes as a potential causative agent of urinary tract infection.

Burkholderia contaminans: unusual cause of biliary sepsis.

We report a case of biliary tract infection caused by a strain of Burkholderia contaminans, a member of the Burkholderia cepacia complex. The patient developed sepsis after endoscopic retrograde cholangiopancreatography (ERCP). Gram-negative bacilli were isolated from blood and bile cultures. Automated bacterial identification systems identified the organism as Burkholderia cepacia, whereas DNA sequence analysis revealed that the recA gene isolate was identical to that of B. contaminans. The patient responded to therapy with the antibiotics trimethoprim/sulfamethoxazole and biliary tract decompression. This case suggests that B. contaminans can be a causative agent of healthcare-associated biliary tract infections such as ERCP-related cholangitis.