Preferential carriage of class 2 integrons in Acinetobacter baumannii CC113 and novel singletons

M S RAMÍREZ; S MONTAÑA; M CASSINI; D CENTRÓN

doi:10.1017/S0950268815000060

. 2015 Feb 20;143(14):3118–3121. doi: 10.1017/S0950268815000060

Preferential carriage of class 2 integrons in Acinetobacter baumannii CC113 and novel singletons

M S RAMÍREZ ^1,^2,^*, S MONTAÑA ¹, M CASSINI ³, D CENTRÓN ¹

PMCID: PMC9151031 PMID: 25697643

SUMMARY

Our understanding of the distribution of integrons associated with multidrug resistance in Acinetobacter baumannii isolates around the world remains incomplete. The association between the class 1 and 2 integron A. baumannii-positive isolates (n = 60), recovered since 1982 from 11 Argentinean hospitals, and the circulating lineages, was investigated. While class 2 integrons were highly significantly associated with clonal lineage CC113^B/CC79^P (P = 0·009) and novel singletons (P = 0·001), class 1 integrons were found not to be associated with CC109^B/CC1^P or other lineages. The study reveals a differential distribution of class 2 integrons in lineages, and suggests that the prevalence of intI2 in Argentina is related to the emergence of novel singletons in recent years and to the abundance of CC113^B/CC79^P, which has been the local dominant lineage for several decades.

Key words: Acinetobacter, integron, lineages

Acinetobacter baumannii has emerged as a major relevant global nosocomial pathogen in the last two decades, causing a variety of serious infections such as pneumonia and bacteraemia, often associated with high mortality [1]. In a CDC report published last year, A. baumannii was considered as a microorganism of serious concern, since about the 63% of the isolates are multidrug resistant with about 500 deaths each year attributed to its infections in the USA [2].

The accumulation of antibiotic resistance mechanisms occurs frequently in this species, underlining its genomic plasticity to evolve to extensive multidrug resistance in the nosocomial environment. Class 1 and 2 integrons have been frequently found in a variety of resistance determinants [3, 4]. However, a clear differential distribution of both these integron classes in clinical isolates across continents has been reported by different groups with class 1 integrons being frequently identified from Europe, USA and Australia, while class 2 integrons are more common in several countries in South America [3–5].

This prompted us to investigate if there was a particular dissemination of integrons in different A. baumannii lineages. We therefore analysed the association between the circulating clones in South America and the presence of class 1 and 2 integrases in A. baumannii isolates recovered from 1982 to 2014 from 11 hospitals. Some isolates included in the present work, were from previously published studies (Table 1) [3, 6–8] but hitherto had not been investigated for association of strain lineages with the presence of class 1 and 2 integrons.

Table 1.

Origin, clonal lineage and integron content of 60 isolates of Acinetobacter baumannii from 11 hospitals

Strain	Year	Hospital/city	CC/pan-PCR pattern^*	intI1	intI2	Reference
Ab102	1983	H1^H/Buenos Aires	CC119	−	+	[9]
Ab109	1987	H1/Buenos Aires	CC119	−	+	[7]
Ab103	1993	H1/Buenos Aires	CC119	−	+	[9]
AbU1	2008	H1/Montevideo	CC119	−	+	[7]
Ab311	2002	H3/Buenos Aires	CC113^B/CC79^P	−	+	[7]
72	2002	H3/Buenos Aires	CC113^B/CC79^P	−	+	[9]
Ab49	2002	H3/Buenos Aires	CC113^B/CC79^P	−	+	[7]
Ab42	2002	H3/Buenos Aires	CC113^B/CC79^P	+	+	[7]
Ab171	2005	H1/Buenos Aires	CC113^B/CC79^P	−	+	[7]
Ab172	2005	H1/Buenos Aires	CC113^B/CC79^P	−	+	[7]
Ab173	2005	H1/Buenos Aires	CC113^B/CC79^P	−	+	[7]
Ab177	2006	H1/Buenos Aires	CC113^B/CC79^P	−	+	[9]
Ab181	2006	H1/Buenos Aires	CC113^B/CC79^P	−	+	[9]
Ab182	2006	H1/Buenos Aires	CC113^B/CC79^P	−	+	[9]
Ab181b	2006	H1/Buenos Aires	CC113^B/CC79^P	−	+	[7]
Ab177	2006	H1/Buenos Aires	CC113^B/CC79^P	−	+	[9]
Ab394	2007	H1/Rosario	CC113^B/CC79^P	−	+	[6, 7]
66	2012	H10/Buenos Aires	CC113^B/CC79^P	−	+	[8]
179	2012	H10/Buenos Aires	CC113^B/CC79^P	+	−	[8]
41 384	2013	H11/Buenos Aires	CC113^B/CC79^P	−	+	This work
66 285	2012	H9/Buenos Aires	CC110	+	−	This work
AbC3	2014	H10/Buenos Aires	CC110	−	+	This work
Ab110	1986	H1/Buenos Aires	CC109^B/CC1^P	+	−	[7]
Ab144	1987	H1/Buenos Aires	CC109^B/CC1^P	+	−	[7]
Ab155	1994	H1/Buenos Aires	CC109^B/CC1^P	+	−	[7]
Ab144	1997	H1/Buenos Aires	CC109^B/CC1^P	+	−	[7]
Ab115	1998	H1/Buenos Aires	CC109^B/CC1^P	+	−	[7]
Ab185	2006	H1/Buenos Aires	CC109^B/CC1^P	+	−	[7]
Ab304	2006	H3/Rosario	CC109^B/CC1^P	+	+	[6, 7]
Ab325	2007	H1/Rosario	CC109^B/CC1^P	+	−	[6, 7]
Ab326	2007	H1/Rosario	CC109^B/CC1^P	+	+	[6, 7]
Ab376	2007	H5/Rosario	CC109^B/CC1^P	+	−	[6, 7]
Ab49011	2008	H6/Rosario	CC109^B/CC1^P	−	+	[6, 7]
Ab49631	2008	H6/Rosario	CC109^B/CC1^P	+	+	[6, 7]
Ab50309	2008	H6/Rosario	CC109^B/CC1^P	−	+	[6, 7]
Ab65513	2009	H6/Rosario	CC109^B/CC1^P	−	+	[6, 7]
Ab65986	2009	H6/Rosario	CC109^B/CC1^P	−	+	[6, 7]
Ab66284	2009	H6/Rosario	CC109^B/CC1^P	+	−	[6, 7]
Ab66485	2009	H6/Rosario	CC109^B/CC1^P	+	−	[6, 7]
42	2011	H8/Buenos Aires	CC109^B/CC1^P	+	−	This work
14^*2	2014	H8/Buenos Aires	CC109^B/CC1^P	+	−	This work
14^*5	2014	H8/Buenos Aires	CC109^B/CC1^P	+	−	This work
Ab152	1997	H1/Buenos Aires	CC92^B/CC2^P	−	+	[7]
Ab125	1995	H1/Buenos Aires	Singleton (A)	−	+	[7]
Ab156	1997	H1/Buenos Aires	Singleton (ST600)	−	+	[7]
Ab138	1997	H1/Buenos Aires	Singleton (ST608)	−	+	[7]
Ab139	1997	H1/Buenos Aires	Singleton (B)	−	+	[9]
Ab145	1997	H1/Buenos Aires	Singleton (ST605)	−	+	[7]
Ab136	2001	H1/Buenos Aires	Singleton (ST614)	+	−	[7]
Ab174	2005	H1/Buenos Aires	Singleton (C)	−	+	[7]
Ab175	2005	H1/Buenos Aires	Singleton (C)	−	+	[7]
Ab176	2005	H1/Buenos Aires	Singleton (C)	−	+	[7]
Ab178	2006	H1/Buenos Aires	Singleton (ST605)	+	+	[7]
Ab179	2006	H1/Buenos Aires	Singleton (ST605)	+	+	[7]
Ab287	2006	H1/Rosario	Singleton (ST217)	+	+	[6, 7]
11 498	2009	H7/Buenos Aires	Singleton (p133)	−	+	This work
11 635	2010	H7/Buenos Aires	Singleton (p133)	+	−	This work
423	2011	H8/Buenos Aires	Singleton (p133)	−	+	This work
376	2011	H8/Buenos Aires	Singleton (p133)	−	+	This work
204	2012	H2/Buenos Aires	Singleton (p133)	+	+	This work

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CC, Clonal complex; PCR, polymerase chain reaction.

^B Bartual scheme; ^P Institut Pasteur scheme.

A total of 168 A. baumannii isolates was investigated by polymerase chain reaction (PCR) amplification of intI1 and intI2 genes using specific primers [3, 9]. Sixty isolates were positive either for class 1 (n = 17) or class 2 integrases (n = 35) or both (n = 8). Confirmatory DNA sequencing was performed on 23 of the 43 intI2 amplicons, and one intI1 amplicon [3]. All intI2 amplicons possessed the typical internal stop codon [3, 10], and the intI1 amplicon harboured one of the most common alleles of intI1 [9]. Isolates with class 1, or class 2 integrons were identified respectively in 9 and 10 of the 11 hospitals studied. Coexistence of both classes of integrons in the same strain was found in five hospitals from two cities, Buenos Aires and Rosario. Overall these results evidence the widespread presence of these genetic elements in nosocomial settings in Argentina.

The lineages of these 60 intI-positive isolates were determined by a pan-PCR assay [11] and multilocus sequence typing [12] which revealed the presence of six defined clonal complexes (CC) and at least nine singletons (Table 1) Statistical analysis was undertaken by the sign test which is a non-parametric test to confirm a zero median difference between continuous distributions of two random pairs. This showed high significant associations between intI2 and the CC113 lineage (P = 0·003) as well as between intI2 and the novel singletons (P = 0·01). In fact, 15/16 isolates of CC113^B/CC79^P and 15/17 isolates belonging to novel singletons harboured intI2.

Regarding class 1 integrons, 16 of the 25 intI1-positive isolates were assigned to lineage CC109^B/CC1^P. Only two isolates of CC113 harboured a class 1 integron and the other six intI1-positive isolates corresponded to singletons, and one to CC110. No statistical association between CC109^B/CC1^Pand class 1 integrons (P = 0·052345) was found. However, CC109 was infrequently reported in Argentinean isolates recovered during the period 1982–2010 [12]. Interestingly, eight isolates possessed both integrons and belonged to different CCs or singletons; three were of lineage CC109^B/CC1^P, one of CC113^B/CC79^P, and five of different singletons (Table 1). These last results suggest that novel singletons may play a role in the double acquisition of integrons.

In conclusion, we describe a marked association between intI2 and CC113^B/CC79^P, which is the most frequently isolated lineage of A. baumannii in Argentinean isolates during the years 1992–2009 and this explains the hitherto high frequency of intI2 observed in isolates from Argentina [3, 6, 7, 12]. In addition, several novel singletons frequently containing intI2, some harbouring both classes of integrons, were evident.

ACKNOWLEDGEMENTS

M.S.R., and D.C. are members of the career investigator programme of CONICET, Argentina. This study was supported by grants PIP 11420100100152 (CONICET) and PICT 0120 (ANPCyT) awarded to M.S.R., and UBACyT 2014–2017 (UBA) and PICT 0014 (ANPCyT) awarded to D.C.

DECLARATION OF INTEREST

None.

REFERENCES

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[ref1] 1.Roca I, et al. The Acinetobacter baumannii oxymoron: commensal hospital dweller turned pan-drug-resistant menace. Frontiers in Microbiology 2012; 3: 148. [DOI] [PMC free article] [PubMed] [Google Scholar]

[ref2] 2.Centers for Disease Control. Antibiotic resistance threats in the United States. 2013. (http://www.cdc.gov/drugresistance/threat-report-2013/).

[ref3] 3.Ramirez MS, et al. Novel insights about class 2 integrons from experimental and genomic epidemiology. Antimicrobial Agents and Chemotherapy 2010; 54: 699–706. [DOI] [PMC free article] [PubMed] [Google Scholar]

[ref4] 4.Turton JF, et al. Detection and typing of integrons in epidemic strains of Acinetobacter baumannii found in the United Kingdom. Journal of Clinical Microbiology 2005; 43: 3074–3082. [DOI] [PMC free article] [PubMed] [Google Scholar]

[ref5] 5.Fonseca EL, et al. Class 2 integrons in multidrug-resistant Acinetobacter baumannii circulating in different Brazilian geographic regions. International Journal of Antimicrobial Agents 2011; 38: 95–96. [DOI] [PubMed] [Google Scholar]

[ref6] 6.Ramirez MS, et al. Increasing frequency of class 1 and 2 integrons in multidrug-resistant clones of Acinetobacter baumannii reveals the need for continuous molecular surveillance. International Journal of Antimicrobial Agents 2011; 37: 175–177. [DOI] [PubMed] [Google Scholar]

[ref7] 7.Ramirez MS, et al. Spreading of AbaR-type genomic islands in multidrug resistance Acinetobacter baumannii strains belonging to different clonal complexes. Current Microbiology 2013; 67: 9–14. [DOI] [PubMed] [Google Scholar]

[ref8] 8.Vilacoba E, et al. Outbreak of extensively drug-resistant Acinetobacter baumannii indigo-pigmented strains. Journal of Clinical Microbiology 2013; 51: 3726–3730. [DOI] [PMC free article] [PubMed] [Google Scholar]

[ref9] 9.Nardelli M, et al. Class 1 integrons in environments with different degrees of urbanization. PLoS ONE 2012; 7: e39223. [DOI] [PMC free article] [PubMed] [Google Scholar]

[ref10] 10.Hansson K, et al. IntI2 integron integrase in Tn7. Journal of Bacteriology 2002; 184: 1712–1721. [DOI] [PMC free article] [PubMed] [Google Scholar]

[ref11] 11.Yang JY, et al. Pan-PCR, a computational method for designing bacterium-typing assays based on whole-genome sequence data. Journal of Clinical Microbiology 2013; 51: 752–758. [DOI] [PMC free article] [PubMed] [Google Scholar]

[ref12] 12.Stietz MS, et al. Acinetobacter baumannii extensively drug resistant lineages in Buenos Aires hospitals differ from the international clones I-III. Infection, Genetics and Evolution 2013; 14: 294–301. [DOI] [PubMed] [Google Scholar]

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Preferential carriage of class 2 integrons in Acinetobacter baumannii CC113 and novel singletons

M S RAMÍREZ

S MONTAÑA

M CASSINI

D CENTRÓN

SUMMARY

Table 1.

ACKNOWLEDGEMENTS

DECLARATION OF INTEREST

REFERENCES

ACTIONS

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PERMALINK

Preferential carriage of class 2 integrons in Acinetobacter baumannii CC113 and novel singletons

M S RAMÍREZ

S MONTAÑA

M CASSINI

D CENTRÓN

SUMMARY

Table 1.

ACKNOWLEDGEMENTS

DECLARATION OF INTEREST

REFERENCES

ACTIONS

PERMALINK

RESOURCES

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