An emerging Panton-Valentine leukocidin-positive CC5-meticillin-resistant Staphylococcus aureus-IVc clone recovered from hospital and community settings over a 17-year period from 12 countries investigated by whole-genome sequencing.

BACKGROUND: A novel Panton-Valentine leukocidin (PVL)-positive meticillin-resistant Staphylococcus aureus (MRSA) clonal complex (CC)5-MRSA-IVc ('Sri Lankan' clone) was recently described from Sri Lanka. Similar isolates caused a recent Irish hospital outbreak. AIM: To investigate the international dissemination and diversity of PVL-positive CC5-MRSA-IVc isolates from hospital and community settings using whole-genome sequencing (WGS). METHODS: Core-genome single nucleotide polymorphism (cgSNP) analysis, core-genome multi-locus sequence typing (cgMLST) and microarray-based detection of antimicrobial-resistance and virulence genes were used to investigate PVL-positive CC5-MRSA-IVc (N = 214 including 46 'Sri Lankan' clone) from hospital and community settings in 12 countries over 17 years. Comparators included 29 PVL-positive and 23 PVL-negative CC5/ST5-MRSA-I/II/IVa/IVc/IVg/V. RESULTS: Maximum-likelihood cgSNP analysis grouped 209/214 (97.7%) CC5-MRSA-IVc into Clade I; average of 110 cgSNPs between isolates. Clade III contained the five remaining CC5-MRSA-IVc; average of 92 cgSNPs between isolates. Clade II contained seven PVL-positive CC5-MRSA-IVa comparators, whereas the remaining 45 comparators formed an outlier group. Minimum-spanning cgMLST analysis revealed a comparably low average of 57 allelic differences between all CC5/ST5-MRSA-IVc. All 214 CC5/ST5-MRSA-IVc were identified as 'Sri Lankan' clone, predominantly spa type t002 (186/214) with low population diversity and harboured a similar range of virulence genes and variable antimicrobial-resistance genes. All 214 Sri Lankan clone isolates and Clade II comparators harboured a 9616-bp chromosomal PVL-encoding phage remnant, suggesting both arose from a PVL-positive meticillin-susceptible ancestor. Over half of Sri Lankan clone isolates were from infections (142/214), and where detailed metadata were available (168/214), most were community associated (85/168). CONCLUSIONS: Stable chromosomal retention of pvl may facilitate Sri-Lankan clone dissemination.

Transmission of endemic ST22-MRSA-IV on four acute hospital wards investigated using a combination of spa, dru and pulsed-field gel electrophoresis typing.

The transmission of meticillin-resistant Staphylococcus aureus (MRSA) between individual patients is difficult to track in institutions where MRSA is endemic. We investigated the transmission of MRSA where ST22-MRSA-IV is endemic on four wards using demographic data, patient and environmental screening, and molecular typing of isolates. A total of 939 patients were screened, 636 within 72 h of admission (on admission) and 303 >72 h after admission, and 1,252 environmental samples were obtained. Isolates were typed by spa, dru and pulsed-field gel electrophoresis (PFGE) typing. A composite dendrogram generated from the three sets of typing data was used to divide isolates into 'dendrogram groups' (DGs). Ten percent of patients (92/939) were MRSA-positive; 7 % (44/636) on admission and 16 % (48/303) >72 h after admission (p = 0.0007). MRSA was recovered from 5 % of environmental specimens (65/1,252). Most isolates from patients (97 %, 85/88) and the environment (97 %, 63/65) exhibited the ST22-MRSA-IV genotype. Four DGs (DG1, DG4, DG16 and DG17) accounted for 58 % of ST22-MRSA-IV isolates from patients. Epidemiological evidence suggested cross-transmission among 44/92 patients (48 %) but molecular typing confirmed probable cross-transmission in only 11 instances (13 %, 11/88), with the majority of cross-transmission (64 %; 7/11) occurring on one ward. In the setting of highly clonal endemic MRSA, the combination of local epidemiology, PFGE, spa and dru typing provided valuable insights into MRSA transmission.

Meticillin-susceptible Staphylococcus aureus transmission among healthcare workers, patients and the environment in a large acute hospital under non-outbreak conditions investigated using whole-genome sequencing.

BACKGROUND: The role of meticillin-susceptible Staphylococcus aureus (MSSA) colonization of healthcare workers (HCWs), patients and the hospital environment in MSSA transmission events (TEs) is poorly understood. AIMS: The role of meticillin-resistant Staphylococcus aureus (MRSA) was investigated recently under non-outbreak conditions in a large hospital with a history of endemic MRSA over 2 years using whole-genome sequencing (WGS). Numerous potential MRSA TEs were identified. The present study investigated MSSA TEs from the same sources during the same 2-year hospital study. METHODS: HCW (N=326) and patient (N=388) volunteers on nine wards were tested for nasal and oral MSSA colonization over 2 years. Near-patient environment (N=1164), high-frequency touch sites (N=810) and air (N=445) samples were screened for MSSA. Representative MSSA and clinical isolates were sequenced and analysed by core genome multi-locus sequence typing. Closely related isolates (≤24 allelic differences) were segregated into related isolate groups (RIGs). Potential TEs involving MSSA in RIGs from HCWs, patients and patient infections were identified in combination with epidemiological data. FINDINGS: In total, 635 MSSA were recovered: clinical isolates (N=82), HCWs (N=170), patients (N=120), and environmental isolates (N=263). Twenty-four clonal complexes (CCs) were identified among 406/635 MSSA sequenced, of which 183/406 segregated into 59 RIGs. Numerous potential HCW-to-patient, HCW-to-HCW and patient-to-patient TEs were identified, predominantly among CC5-MSSA, CC30-MSSA and CC45-MSSA. HCW, patient, clinical and environmental isolates were identified in 33, 24, six and 32 RIGs, respectively, with 19/32 of these containing MSSA related to HCW and/or patient isolates. CONCLUSIONS: WGS detected numerous potential hospital MSSA TEs involving HCWs, patients and environmental contamination under non-outbreak conditions.

Meticillin-resistant Staphylococcus aureus transmission among healthcare workers, patients and the environment in a large acute hospital under non-outbreak conditions investigated using whole-genome sequencing.

BACKGROUND: The role of meticillin-resistant Staphylococcus aureus (MRSA) colonization of healthcare workers (HCWs), patients and the hospital environment in MRSA transmission in non-outbreak settings is poorly understood. AIMS: To investigate transmission events (TEs) involving HCWs, patients and the environment under non-outbreak conditions in a hospital with a history of endemic MRSA using whole-genome sequencing (WGS). METHODS: HCW (N = 326) and patient (N = 388) volunteers on nine wards were tested for nasal and oral MRSA colonization over two years. Near-patient environment (N = 1164), high-frequency touch sites (N = 810) and air (N = 445) samples were screened for MRSA. Representative MRSA and clinical isolates were analysed by WGS and core-genome multi-locus sequence typing (cgMLST). Closely related isolates (≤24 allelic differences) were segregated into related isolated groups (RIGs). FINDINGS: In total, 155 MRSA were recovered: clinical isolates (N = 41), HCWs (N = 22), patients (N = 37), environmental isolates (N = 55). Nine clonal complexes (CCs) were identified among 110/155 MRSA sequenced with 77/110 assigned to CC22. Seventy-nine MRSA segregated into 17 RIGs. Numerous potential TEs were associated with CC22-MRSA (RIGs 1-15), CC45-MRSA (RIG-16) and CC8-MRSA (RIG-17). RIG-1, (the largest RIG) contained 24 ST22-MRSA-IVh from six HCWs, six patients, four clinical and eight environmental samples recovered over 17 months involving 7/9 wards. TEs involving HCW-to-patient, HCW-to-HCW, patient-to-patient and environmental contamination by HCW/patient isolates were evident. HCW, patient, clinical and environmental isolates were identified in four, nine, seven and 13 RIGs, respectively, with 12/13 of these containing isolates closely related to HCW and/or patient isolates. CONCLUSIONS: WGS detected numerous potential hospital MRSA TEs involving HCWs, patients and the environment under non-outbreak conditions.