Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.

Funder: Queensland GovernmentSyphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides

Peritoneal Dialysis–Related Peritonitis Due to

Background: Abiotrophia defectiva is a fastidious aerobic gram-positive bacterium which is part of the normal flora of the human oral cavity. It is an unusual cause of peritoneal dialysis–related peritonitis. Case Presentation: We present a case of a man in his fifties with end-stage renal failure secondary to polycystic kidney disease who presented with a cloudy peritoneal fluid effluent and a cell count of 35 620 × 10 6 cells/L with 90% polymorphonuclear cells. The fluid was cultured per unit protocol, and the organism was identified as Abiotrophia defectiva . Post–peritonitis dialysis technique review revealed frequent lapses in the use of facemask and hand washing during cycler connection and disconnection. The patient responded well to vancomycin; however, he subsequently developed ultrafiltration failure and symptoms of fluid overload and uremia and was transferred to home hemodialysis. Conclusions: Abiotrophia defectiva is an unusual cause of peritoneal dialysis–related peritonitis. The organism is a normal commensal of the oral cavity and may cause peritonitis in patients with nonadherence to dialysis technique. In our case, the infection was followed by peritoneal membrane failure and transfer to hemodialysis. It remains to be seen if peritonitis with Abiotrophia defectiva heralds a worse outcome

Autochthonous North American Leprosy: A Second Case in Canada

Autochthonous leprosy was reported in the Southern USA in 2011 and has comprised an average of 34% of new cases from 2015 to 2020 in that country. We report a similar case in a patient from Western Canada. A 50-year old male patient presented with a four-year history of a chronic rash. Pathology stains revealed acid-fast bacilli prompting specialist referral. Examination was suspicious for leprosy, which was confirmed on slit skin smears and molecular testing. The patient responded well to treatment. Genotypic testing mapped the organism to the 3I-2 SNP type, which is of European origin and is the type found in implicated armadillo species in North America

Surveillance for Antimicrobial Resistance in Gonorrhea: The Alberta Model, 2012–2016

Alberta established a surveillance system in 2001 to monitor resistance to antibiotics used for the treatment of gonorrhea. A retrospective review of gonorrhea cases during the last five years was conducted. All cases of gonorrhea were reportable to public health by testing laboratories and clinicians. Specimens were primarily submitted for nucleic acid amplification testing (NAAT); three sentinel sites obtained specimens for culture and NAAT. The Provincial Laboratory for Public Health conducted E-tests on isolates for multiple antibiotics. A proportion of isolates and NAAT specimens were submitted to the National Microbiology Laboratory for sequence typing (ST). Data were combined and analyzed using SAS version 9.4. Between 2012 and 2016, 13,132 gonorrhea cases were reported; 22.0% (n = 2891) had isolates available for susceptibility testing. All culture positive isolates were susceptible to ceftriaxone. Decreased susceptibility (0.5 ug/mL) to cefixime was reported in four cases in 2014. Resistance to azithromycin (≥2 ug/mL) ranged between 0.4% and 1.8%. Many (n = 509) unique STs were identified; the most prevalent sequence groups (SG) were SG-7638 (n = 367), SG-5985 (n = 145), and SG-11299 (n = 127). The Alberta model for maintaining surveillance for antimicrobial resistance in gonorrhea employs culture and NAAT specimens, providing information crucial to informing provincial treatment guidelines

An unusual case of Erysipelothrix rhusiopathiae prosthetic joint infection from the Canadian Arctic: whole genome sequencing unable to identify a zoonotic source

Abstract Background Erysipelothrix rhusiopathiae is a zoonotic pathogen that causes erysipeloid and is most frequently associated with exposure to domestic swine. Infection of native and prosthetic joints is a rarely reported manifestation. Case presentation We describe a case of E. rhusiopathiae prosthetic joint infection in a woman with a history of exposure to wild animals in the Canadian Arctic. Patient management involved a 1-stage surgical revision exchange with an antibiotic impregnated cement spacer and 6 weeks of intravenous penicillin G followed by 6 weeks of oral amoxicillin. Ten previously reported cases of E. rhusiopathiae joint infection are reviewed. Recent increases in mortality due to infection with this organism among host animal populations in the Canadian Arctic have generated concern regarding a potential increase in human infections. However, whole genome sequencing (WGS) of the organism was unable to identify a zoonotic origin for this case. Conclusions Consideration should be given to E. rhusiopathiae as a cause of joint infections if the appropriate epidemiologic and host risk factors exist. Expanded use of WGS in other potential animal hosts and environmental sources may provide important epidemiologic information in determining the source of human infections

Post-Arrival Screening for Malaria in Asymptomatic Refugees Using Real-Time PCR

Malaria is a significant health risk to refugee populations originating from endemic areas, but there is little consensus on screening and/or treatment approaches for malaria in this population. Furthermore, detection of malaria in semi-immune asymptomatic refugees is limited by the sensitivity of diagnostic tests used for screening. We determined the prevalence of malaria by microscopy and real-time polymerase chain reaction (PCR) in a consecutive population of 324 asymptomatic refugees examined in Edmonton, Canada, during 2009–2010. Although all thick and thin blood smear results were negative, 10 subjects (3.1%) tested PCR positive for Plasmodium DNA. Interestingly, 6 of 10 PCR positive subjects are at risk of malaria relapse by P. vivax or P. ovale infections. These results suggest that appropriate guidelines for malaria screening should consider the risk of relapsing infections, and they highlight the potential usefulness of real-time PCR in the diagnosis of asymptomatic malaria