Antimicrobial resistance in Neisseria gonorrhoeae and Mycoplasma genitalium isolates from the private healthcare sector in South Africa: A pilot study.

BACKGROUND: Reports have emerged globally of antimicrobial resistance (AMR) in Neisseria gonorrhoeae and Mycoplasma genitalium infections. In South Africa (SA), there are substantial differences between private and public healthcare with regard to antimicrobial drug prescribing practice, which could affect AMR patterns of private and public healthcare patients. OBJECTIVES: To perform a pilot study to determine the frequency of AMR of N. gonorrhoeae and M. genitalium in patients accessing SA's private healthcare sector. METHODS: In this cross-sectional study, N. gonorrhoeae-positive cultures and M. genitalium DNA samples were collected from a private healthcare reference laboratory from August 2018 to August 2019. In N. gonorrhoeae-positive cultures, antimicrobial susceptibility testing was performed, followed by N. gonorrhoeae multiantigen sequence typing (NG-MAST) to determine genetic relatedness of the isolates. To determine macrolide and fluoroquinolone resistance rates, M. genitalium-positive samples were analysed by sequencing the 23S rRNA, gyrA and parC genes. RESULTS: Twenty-one N. gonorrhoeae- and 27 M. genitalium-positive specimens were included in this analysis. High rates of resistance were detected among gonococcal isolates, with 90% resistance to tetracycline, 86% to penicillin and 62% to ciprofloxacin, but no resistance to azithromycin, cefixime and ceftriaxone. NG-MAST revealed genetically diverse isolates with 83% novel NG-MAST sequence types. Macrolide and fluoroquinolone resistance-associated mutations were detected in 18.5% (n=5/27) and 7.4% (n=2/27) of M. genitalium strains, respectively. CONCLUSIONS: We observed high frequencies of ciprofloxacin, penicillin and tetracycline resistance in N. gonorrhoeae and macrolide resistance-associated mutations in M. genitalium in private healthcare sector patients in SA. This finding highlights the need to use diagnostics for sexually transmitted infections and to include the private healthcare sector in antimicrobial surveillance and stewardship programmes.

Klebsiella pneumoniae ST307 with OXA-181: threat of a high-risk clone and promiscuous plasmid in a resource-constrained healthcare setting.

INTRODUCTION: Klebsiella pneumoniae with OXA-48-like enzymes were introduced into Tshwane Tertiary Hospital (TTH) (Pretoria, South Africa) during September 2015, causing nosocomial outbreaks. METHODS: PCR methodologies and WGS were used to characterize K. pneumoniae with carbapenemases (n = 124) from TTH (July 2015-December 2016). RESULTS: PCR was used to track K. pneumoniae ST307 with OXA-181 among 60% of carbapenemase-positive isolates in different wards/units over time and showed the transmission of IncX3 plasmids to other K. pneumoniae clones. WGS identified different ST307 clades: 307_OXA181 (consisting of two lineages, A and B) with OXA-181 on IncX3 plasmids (named p72_X3_OXA181) and clade 307_VIM with VIM-1 on IncFII plasmids. Clade 307_OXA181 lineage B was responsible for the rapid increase and transmission of OXA-181 K. pneumoniae in various wards/units throughout TTH, while the numbers of clade 307_OXA181 lineage A and clade 307_VIM remained low. Separate outbreaks were due to K. pneumoniae ST17 and ST29 with p72_X3_OXA181 plasmids. CONCLUSIONS: The high-risk clone K. pneumoniae ST307 with OXA-181 rapidly spread to different wards/units despite infection and prevention measures. ST307 clades and lineages seemingly acted differently in outbreak situations. This study also highlighted the threat of promiscuous plasmids such as p72_X3_OXA181.

Performance evaluation of three commercial molecular assays for the detection of Mycobacterium tuberculosis from clinical specimens in a high TB-HIV-burden setting.

BACKGROUND: A major challenge faced by countries with a high burden of tuberculosis (TB) is early detection especially in individuals with paucibacillary disease which is common in HIV endemic settings. Remarkable efforts have been made globally to accelerate the development and expansion of new diagnostic technologies that allow better and earlier diagnosis of active tuberculosis particularly directly from clinical specimens with a few commercial options available. These include GenoType MTBDRplus Version 2.0 (Hain Lifescience), Xpert® MTB/RIF (Cepheid) and Anyplex™ plus MTB/NTM/DR-TB Real-time detection (Seegene). We evaluated the diagnostic performance of these three commercial molecular assays for the detection of Mycobacterium tuberculosis complex from clinical specimens in a high TB-HIV-burden setting. METHODS: This was a retrospective laboratory-based study using stored remnant sediments from clinical specimens of presumptive pulmonary TB cases. A stratified sample of smear positive TB, smear negative TB and TB culture negatives was included. All the samples were tested on the three molecular assays following the manufacturers' instructions; except for Anyplex™plus, for which DNA extraction was performed using the NucliSENS® easyMAG® platform (bioMerieux). Samples were also processed for liquid TB culture and time-to-culture positivity was recorded. RESULTS: Of the 90 sediments processed, 81 were analyzable across all three systems. The overall sensitivity was highest for Xpert® MTB/RIF (89.1%) followed by GenoType MTBDRplus (70.9%) and Anyplex™ plus (65.5%). The specificity and sensitivity in smear positive cases was comparable across all systems. There was a significant difference in sensitivity between Xpert® MTB/RIF and the other two assays for smear-negative cases (P < 0.05). The performance in cases where the time-to-culture positivity was ≥ 20 days was also significantly poorer for both Anyplex™ plus and GenoType MTBDRplus compared to Xpert® MTB/RIF (P < 0.05). Xpert® MTB/RIF achieved 100% specificity, while Anyplex™ plus and GenoType MTBDRplus achieved 96.2 and 92.3% respectively. CONCLUSION: The Xpert® MTB/RIF was superior to the other two assays for the detection of TB in smear negative specimens notably when bacterial loads are very low in sputum. It is important that studies reporting on test performance stratify their results by time-to-culture positivity to accurately assess clinical performance especially in high HIV settings.