Drug Resistance Spread in 6 Metropolitan Regions, Germany, 2001–2018

We analyzed 1,397 HIV-1 pol sequences of antiretroviral therapy–naive patients in a total of 7 university hospitals in Bonn, Cologne, Frankfurt, Hamburg, Hannover, and Munich, Germany. Phylogenetic and network analysis elucidated numerous cases of shared drug resistance mutations among genetically linked patients; K103N was the most frequently shared mutation.

whom the exact start date of ART or history of prior ART was not accurately documented.
We performed statistical analyses by using Stata version 14 (StataCorp LP, https://www.stata.com). We applied Fisher exact or χ 2 test and univariable and multivariable logistic regression models, as appropriate, to determine characteristics that are associated with shared DRM and clustering. A shared DRM was defined as any DRM present in >2 genetically linked persons. Transmission network analyses revealed that 20.7% (289/1,397) of participants had a putative linkage forming 102 transmission clusters. The largest cluster included 12 participants, mostly MSM from Bonn, Cologne, Munich, and Frankfurt ( Figure 1, panels A, B). Participants <25 years and 25-45 years of age were significantly more likely to cluster compared with participants >45 years (<25 years, adjusted OR [aOR] 4.38, 95% CI 2.55-7.52, p<0.001; 25-45 years, aOR 1.91, 95% CI 1.36-2.678; p<0.001). Participants infected with HIV-1 subtype B were more likely to cluster than those with non-B subtype (aOR 4.05, 95% CI 2.37-6.90; p<0.001). Geospatial distribution differed; participants from Bonn were linked significantly more often than those from Cologne (aOR 1.63; 95% CI 1.06-2.49; p = 0.025), even though the cities are geographically close (Appendix Table).
The most frequently observed putatively shared DRM was K103N, detected in 9/19 (47.4%) participants forming 4 distinct clusters, predominantly originating from Cologne (7/9, 77.8%). The second  †E138A was not included in the drug resistance mutation/transmitted drug resistance mutation rate of our study population.

Conclusions
The increasing prevalence of DRMs in PLWH has become a serious matter of concern for clinicians and public health entities (4). In our study, we observed a 17.8% prevalence of DRMs, higher than in previous studies (6,7). The proportion of NNRTI resistance mutations was 8.9%, which is potentially associated with the common use of NNRTI in first-line ART regimens. K103N represented one quarter of NNRTI resistance mutations, reducing susceptibility to the first-generation drugs nevirapine and efavirenz (13). Transmission network analyses revealed that K103N was the most frequently shared DRM.
K65R, K70RT, and M184IV were the most common of the NRTI resistance mutations we observed, particularly among the risk group of MSM living in Cologne and Hannover, indicating potential resistance to preexposure prophylaxis (PrEP) with tenofovir/emtricitabine. Such resistance might be an upcoming challenge as PrEP use increases. Monitoring for HIV infections with these mutations is of utmost importance for preventing an epidemic among highrisk PrEP users; one mitigation is to consider alternative PrEP regimens in regions with high resistance.
Our study had several limitations. First, our sample population could have been biased because participants were not randomly selected; our dataset was limited to ART-naive patients who received an HIV diagnosis at 7 university hospitals during 2001-2018. Although  we know no reason why a university hospital setting would not be representative of the region, it is possible that populations treated outside these centers may have different transmission networks and risks; results are not generalizable to the entire regions or nationwide. Second, mixing of heterosexual patients and MSM in clusters may be due to missing single or multiple risk factors. Thus, their role could not be represented in the transmission networks. Third, we have not tested clinical correlates and drug resistance; the clinical relevance was inferred from the Stanford database.
In summary, we found that the overall rate of DRM was high in Germany. Network analysis elucidated cases of shared DRMs among genetically linked persons, mainly in MSM-dominated clusters. Our findings highlight regional differences and illustrate the need to test MSM, especially younger men, for HIV regularly and to evaluate local HIV programs and adapt screening and treatment strategies to local epidemics. The datasets used and analyzed during the current study are available from the corresponding author on reasonable request.