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Background
• Congregate settings such as urban jails may facilitate spread of MRSA1,2
• Jails may be a location where individuals already colonized with MRSA (from preceding exposures) intermingle with other individuals, potentially augmenting spread of MRSA
Methods
• Study Setting: Cook County Jail in Chicago, IL which is one of the largest single-site jails in the US
• Males were enrolled within 72 hours of jail intake• Surveillance cultures of the anterior nares, throat, and
inguinal area were collected at entrance to the jail to determine the prevalence of MRSA colonization
• Surveillance cultures were repeated at Day 30 for those who remained incarcerated to determine the rate of MRSA acquisition during incarceration
• A survey was administered and chart review performed to identify predictors of MRSA acquisition
• Whole genome sequencing was performed with integration of epidemiologic data
Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus (MRSA) DURING Incarceration at a Large Inner-City Jail
Kyle J. Popovich, MD MS, FIDSA1,2, Evan S Snitkin, PhD3, Stefan J Green, PhD4, Alla Aroutcheva, MD PhD1,2, Michael Schoeny1, PhD, Darjai Payne, BS MPH1, Stephanie N Thiede, BS3, Chad Zawitz, MD5, Bala Hota MD MPH1, Mary K Hayden, MD1, Robert A Weinstein MD1,2
1Rush University Medical Center, Chicago, IL, 2Cook County Health and Hospitals System, Chicago, IL, 3University of Michigan Medical Center, Ann Arbor, MI, 4University of Illinois at Chicago, Chicago, IL, 5Cermak Health Services, Chicago, IL
Contact Information:Kyle Popovich, MD, MS, FIDSARush University Medical Center
600 S. Paulina St. Suite 143Chicago, IL 60612T: 312-942-4451
Conclusions
• There is a high burden of MRSA entering the jail (19% colonized at intake)
• Genomic analysis of acquisition, intake, and clinical isolates suggests spread of incoming strains and possible networks of spread of prevalent MRSA strains during incarceration
• Sharing of personal items during incarceration is associated with MRSA acquisition and could be a focus of an intervention
• Future study of epidemiologic and location data may inform targeting of infection control interventions within the jail
Results
• 800 males enrolled (19% colonized with MRSA at intake)• 12 MRSA acquisitions detected at Day 30 (Table)• USA300 clinical isolates (mostly skin infections) may
originate from transmission within the jail or perhaps be due to more virulent strains (Figure 1)
• Sequenced clinical USA300 isolates were more likely to be genetically similar to each other in comparison to intake USA300 MRSA strains (p<0.001) (Figure 2)
• 7/12 (58%) acquisition isolates were within 40 SNVs from another isolate that was sequenced (5 were similar to intake isolates and 2 were similar to clinical isolates)
• Acquisition strains from those sharing personal items (versus not) tended to have closer genetic relatedness (19 SNVs versus 56 SNVs, p=0.22)
References1. MRSA skin or soft tissue infections in a state prison--Mississippi, 2000. MMWR. 2001;50(42):919-22.2. Miller LG, Diep BA. Clinical practice: colonization, fomites, and virulence: rethinking the pathogenesis of
community-associated MRSA infection. Clin Infect Dis. 2008;46(5):752-60.
***See poster 1229 and oral presentation number 159 for additional abstracts from this project
Objective
• To examine the rate of MRSA acquisition during incarceration
• To characterize the genomic epidemiology of MRSA strains entering the jail, MRSA acquisition isolates, and archived clinical MRSA isolates from male detainees
1247
Table. Epidemiologic Predictors of MRSA Acquisition During IncarcerationEpidemiologicFactor MRSAAcquisition
(n=12)NoMRSAAcquisition(n=131) OR 95%CI Pvalue
ExposurespriortoincarcerationHistoryofBenzodiazepineuse 5(42%) 27(21%) 2.75 0.81,9.35 0.11Heroinuseinthepastyear 5(42%) 21(16%) 3.67 1.06,12.68 0.04Methamphetamineuse 3(25%) 23(18%) 1.57 0.39,6.23 0.53Injectiondruguseinpastyear 2(17%) 13(10%) 1.82 0.36,9.2 0.47Homelessorunstablehousing 7(58%) 62(47%) 1.67 0.51,5.48 0.4HIVinfection 9(75%) 91(69%) 1.32 0.34,5.13 0.69Takingantiretroviralsa 3(33%) 59(66%) 0.26 0.06,1.12 0.07
ExposuresduringincarcerationParticipatingindrugtreatmentclasses 4(33%) 22(17%) 2.48 0.69,8.95 0.17Sharingofpersonalitemsb 7(58%) 29(22%) 4.92 1.45,16.67 0.01Anyskininfectionsduringincarceration 1(8%) 4(3%) 2.89 0.3,28.11 0.36Visittoinfirmary 4(33%) 20(15%) 2.77 0.76,10.09 0.12Numberoftimesshoweredinthepastweek,mean(SD) 4.8(1.8) 6(2.7) 0.81 0.62,1.07 0.13
a143 reached the Day 30 study visit. There were 100 HIV-infected patients that reached Day 30 Study Visit; 9 HIV-infected patients acquired MRSA and 91 did notbPersonal items shared by individuals who acquired MRSA included towel, toothpaste, uniform, and deodorant
Closest Pair Clinical < Closest Pair Intake ? USA300 p_val= 7.67611578145617e−09
distance between closest pair
Freq
uenc
y
0 100 200 300 400 500
010
2030
40 ClinicalIntake
Genomic Distance Between Pairs
Freq
uenc
y
Kolmogorov-Smirnov TestComparing Distributions
p < 0.001
Funding: NIAID R01 (Popovich-PI)
Maximum likelihood tree generated by RAxML. Clusters with 90% bootstrap support are indicated by the grey circle. Highlighted labels indicate a 90% bootstrap-supported cluster with all intake or all clinical isolates (can also include acquisition isolates).
Figure 2. Genomic Distance Between Pairs of USA300 MRSA
Clinical Infection and Intake Colonization Isolates
Distribution of SNV distances between closest-pairs within intake and clinical isolates. One-sided Kolmogorov-Smirnov test on the distribution of clinical vs. intake closest-pair SNV distances indicate that clinical isolates tend to have closer pairs than intake isolates.
126KP
22KP
621N
8256KP463T
194N
76KP
8291KP
72KP
91KP
403N
50KP
79KP
113KP
165KP
133KP
181K
P
545N
54KP
633N
44KP21
G
32KP
8177
KP
412T
149K
P
150KP
171K
P
567G
151K
P
7797
KP
161K
P
62KP
263N
114KP
166KP
179KP
112KP
797G
9KP452N
31KP
7647
KP
318T
123KP
182KP
131N
13-30N
7751KP
20KP
170KP
615-30N
424N
213-30N
130K
P
168KP
326T
7696KP
8057KP
103G
19KP
37T
7453KP
731T
37KP
5KP
60KP
609-3
0G
36KP
670N
7643
KP
179T
222-
30T
69KP
87KP
17KP
7676
KP
513N
339N
61KP
523N
13KP
7406
KP
229N
669T
110KP
7693
KP
35KP
582G
302T
7679KP
163KP
30KP
281N
205T
10KP
16KP
141KP
576N
127KP
443N
67KP
169KP
78KP
143KP
105KP
53KP128KP
7580
KP
187KP
21KP
82KP
176K
P
7177KP
610N58K
P
7779KP
14K
P
221N
57KP
7792KP
121KP
733N
264N
6KP
662T
122KP
116K
P
678N
723N
74KP
276G15KP
542G
292N
664G
7420
KP 8157KP
139KP
106-30N
173KP
598N
25KP
106K
P
8271
KP
344N
56KP
38T
186KP787N
96KP
4T
8205KP
45KP
8117KP
80G
563N606N
189KP
118K
P
239N
561N
165N
325N
705N
199-30N
137KP
108G
7725KP
66N
663T
20N
154KP
398N
498T
140K
P
644-30G
99KP
377N
125K
P
528G
607T
94KP
188KP
28KP
119KP
131K
P
86KP
714-30N
55KP
7677KP
638N
77KP
7752KP
29KP
519N
178K
P
580N
266G
192KP
127N
156KP
204N
91N
219T
336T
175N 134N
242T
39N146KP
220N
117KP138K
P
185KP
3KP
34KP
7485KP
7489KP
307T
190T
27KP
153KP
70KP
177KP
160KP
85KP
81KP
115K
P
299T
48N
651N
790G
384N
7577KP
100KP
52KP
657N
277T
667G
594T779N
120KP
18N
104K
P
159KP
7184KP
59K
P
148KP
7644KP
109KP
134KP
135KP
18KP
172KP
97KP
526T
7418KP
178N
223T
8289KP
65N
33KP
49KP
66KP
320T
124K
P
361N
472N
98K
P
Legend
Acquisition
Clinical
Intake
Pure Clinical Cluster*
Pure Intake Cluster*
Bootstrap > 90%
Tree scale: 0.001
126KP
22KP
621N
8256KP463T
194N
76KP
8291KP
72KP
91KP
403N
50KP
79KP
113KP
165KP
133KP
181K
P
545N
54KP
633N
44KP21
G
32KP
8177
KP
412T
149K
P
150KP
171K
P
567G
151K
P
7797
KP
161K
P
62KP
263N
114KP
166KP
179KP
112KP
797G
9KP452N
31KP
7647
KP
318T
123KP
182KP
131N
13-30N
7751KP
20KP
170KP
615-30N
424N
213-30N
130K
P
168KP
326T
7696KP
8057KP
103G
19KP
37T
7453KP
731T
37KP
5KP
60KP
609-3
0G
36KP
670N
7643
KP
179T
222-
30T
69KP
87KP
17KP
7676
KP
513N
339N
61KP
523N
13KP
7406
KP
229N
669T
110KP
7693
KP
35KP
582G
302T
7679KP
163KP
30KP
281N
205T
10KP
16KP
141KP
576N
127KP
443N
67KP
169KP
78KP
143KP
105KP
53KP128KP
7580
KP
187KP
21KP
82KP
176K
P
7177KP
610N58K
P
7779KP
14K
P
221N
57KP
7792KP
121KP
733N
264N
6KP
662T
122KP
116K
P
678N
723N
74KP
276G
15KP
542G
292N
664G
7420
KP 8157KP
139KP
106-30N
173KP
598N
25KP
106K
P
8271
KP
344N
56KP
38T
186KP787N
96KP
4T
8205KP
45K
P
8117KP
80G
563N606N
189KP
118K
P
239N
561N
165N
325N
705N
199-30N
137KP
108G
7725KP
66N
663T
20N
154K
P
398N
498T
140K
P
644-30G
99KP
377N
125K
P
528G
607T
94KP
188KP
28KP
119KP
131K
P
86KP
714-30N
55KP
7677KP
638N
77KP
7752KP
29KP
519N
178K
P
580N
266G
192KP
127N
156KP
204N
91N
219T
336T
175N 134N
242T
39N146K
P
220N
117KP138K
P
185KP
3KP
34KP
7485KP
7489KP
307T
190T
27KP
153KP
70KP
177KP
160KP
85KP
81KP
115K
P
299T
48N
651N
790G
384N
7577KP
100KP
52KP
657N
277T
667G
594T779N
120KP
18N
104K
P
159KP
7184KP
59K
P
148KP
7644KP
109KP
134KP
135KP
18KP
172KP
97KP
526T
7418KP
178N
223T
8289KP
65N
33KP
49KP
66KP
320T
124K
P
361N
472N
98K
P
Legend
Acquisition
Clinical
Intake
Pure Clinical Cluster*
Pure Intake Cluster*
Bootstrap > 90%
Tree scale: 0.001
Figure 1. Genomic Epidemiology of USA300 MRSA Intake, Clinical, and Acquisition Isolates
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