To the Editor—Rapid and reliable identification, characterization, and comparison of microorganisms from clinical samples are essential means for guiding clinical treatment as well as for detecting and controlling disease outbreaks. Developments in benchtop whole-genome sequencing (WGS) hold great promise for enhancing microbial diagnostics and thus for improving public health.Reference Koser, Fraser and Ioannou ^{1 –} Reference Leekitcharoenphon, Nielsen, Kaas, Lund and Aarestrup ⁶ The great value of WGS in studying bacterial evolution, disease outbreaks, and transmission has been demonstrated in recent studies,Reference Joensen, Scheutz and Lund ^{5 ,} Reference Leekitcharoenphon, Nielsen, Kaas, Lund and Aarestrup ⁶ and the technology is increasingly being implemented in routine clinical diagnostics in developed countries. There is huge potential for WGS to improve clinical diagnostics and infection control in developing countries where clinical laboratories do not have access to different routine typing methods and where the burden of infectious diseases is highest.

To test the feasibility of integrating WGS into the routine diagnostics workflow, in February 2015, a total of 18 bacterial genomes were sequenced on a benchtop sequencer (MiSeq; Illumina) at the Kilimanjaro Christian Medical Centre, the second largest referral hospital in northeastern Tanzania. Sequence data were immediately analyzed using open access web-based tools (http://cge.cbs.dtu.dk/services).

Two Enterococcus faecalis from different patients were identified, both having sequence type 415. A similar E. faecalis with sequence type 415 had been found in poultry and humans in Vietnam.Reference Poulsen, Bisgaard, Son, Trung and An ⁷ Single-nucleotide polymorphism analysisReference Leekitcharoenphon, Nielsen, Kaas, Lund and Aarestrup ^{6 ,} Reference Kaas, Leekitcharoenphon, Aarestrup and Lund ⁸ revealed complete similarity between these isolates and both had resistance gene lsa(A) encoding lincosamide and streptogramin A resistance.Reference Zankari, Hasman and Cosentino ⁹

Patient records revealed that the 2 patients were hospitalized in the same room and both were receiving ceftriaxone medication. Patient 1 had been hospitalized for 1 month when a swab sample was collected from a diabetic wound. Patient 2 had undergone emergency surgery for an abdominal gunshot wound, a week after which a swab sample was collected from the surgical wound. The exact match in sequence type strongly suggests nosocomial transmission. Owing to limited resources, the current routine microbiology workflow at our setting—as is the case in most laboratories in developing countries—does not include bacterial typing to identify nosocomial infections. The hospital infection prevention strategies are generic and focus on hygienic procedures rather than identification of microorganisms.

Availability of robust and rapid WGS allowing simultaneous genotyping of different microorganisms within a relatively short time holds the potential of controlling nosocomial infections and improving care. The decreasing initial and recurrent costs of WGS give optimism that in the near future this technology will be applied more widely in resource-limited settings, which are struggling with a disproportionately high burden of infectious diseases with suboptimal infection control strategies.