J Med Cases

Journal of Medical Cases, ISSN 1923-4155 print, 1923-4163 online, Open Access

Article copyright, the authors; Journal compilation copyright, J Med Cases and Elmer Press Inc

Journal website https://jmc.elmerpub.com

Case Report

Volume 17, Number 5, May 2026, pages 213-220

Emergence of a Citrobacter amalonaticus Strain Co-Producing Three Carbapenemases: Molecular Insights and Resistance Profiles

↓ **Table 1.** Predictive Features of Plasmid Replicons, Predicted Mobility (Based on the Presence of Relaxase Genes), Corresponding Accession Numbers, and the Closest Taxonomic Matches
Sample ID	Number of contigs	Size	Rep type(s)	Rep type accession(s)	Relaxase type(s)	Predicted mobility	Mash neighbor identification
Plasmid replicon types were identified using ABRicate v1.0.1 screening against the PlasmidFinder database, plasmid reconstruction and contig binning were performed using MOB-suite (v3.10) via the Bactopia workflow. Underscores in identifiers reflect database-generated annotation names and were retained as reported.
99_S182:AA046	8	85,729	IncFIB,IncFII,rep_cluster_2272	000101__NZ_CP012345_00042,AJ851089,CP042519_00001	MOBF	Conjugative	Leclercia adecarboxylata
99_S182:AA002 (blaOXA-48)	9	76,687	IncL/M	JN626286	MOBP	Conjugative	Klebsiella pneumoniae
99_S182:AA624	7	48,854	-	-	-	Non-mobilizable	Citrobacter freundii
99_S182:AA810	1	12,614	-	-	-	Non-mobilizable	Escherichia coli
99_S182:AD090	1	11,161	-	-	-	Non-mobilizable	Escherichia coli
99_S182:novel_58d38249caaadef4bd119e14ee13c197	1	8,521	IncR	000204__CP008701_00115	-	Non-mobilizable	Escherichia coli
99_S182:AC292	1	8,497	IncP	000173__NC_007100_00053	MOBQ	Mobilizable	Citrobacter sp. CF971
99_S182:AC508 (blaKPC-2)	1	7,993	IncQ2	KX946994_00006	MOBP	Mobilizable	Klebsiella oxytoca

↓ Table 1. Predictive Features of Plasmid Replicons, Predicted Mobility (Based on the Presence of Relaxase Genes), Corresponding Accession Numbers, and the Closest Taxonomic Matches

Sample ID

Number of contigs

Size

Rep type(s)

Rep type accession(s)

Relaxase type(s)

Predicted mobility

Mash neighbor identification

Plasmid replicon types were identified using ABRicate v1.0.1 screening against the PlasmidFinder database, plasmid reconstruction and contig binning were performed using MOB-suite (v3.10) via the Bactopia workflow. Underscores in identifiers reflect database-generated annotation names and were retained as reported.

99_S182:AA046

85,729

IncFIB,IncFII,rep_cluster_2272

000101__NZ_CP012345_00042,AJ851089,CP042519_00001

MOBF

Conjugative

Leclercia adecarboxylata

99_S182:AA002 (blaOXA-48)

76,687

IncL/M

JN626286

MOBP

Conjugative

Klebsiella pneumoniae

99_S182:AA624

48,854

Non-mobilizable

Citrobacter freundii

99_S182:AA810

12,614

Non-mobilizable

Escherichia coli

99_S182:AD090

11,161

Non-mobilizable

Escherichia coli

99_S182:novel_58d38249caaadef4bd119e14ee13c197

8,521

IncR

000204__CP008701_00115

Non-mobilizable

Escherichia coli

99_S182:AC292

8,497

IncP

000173__NC_007100_00053

MOBQ

Mobilizable

Citrobacter sp. CF971

99_S182:AC508 (blaKPC-2)

7,993

IncQ2

KX946994_00006

MOBP

Mobilizable

Klebsiella oxytoca

↓ **Table 2.** Description of *Bla*OXA-48 and *Bla*KPC-2 Carbapenemase Gene and Its Associated Antibiotics Resistance Profile
Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
The table shows in silico prediction of the genomic location of the genes, sequence identity, and coverage (100%). Assembled contigs were screened against curated antimicrobial resistance databases (ResFinder/CARD) using sequence alignment tools (BLAST) with a defined threshold coverage (≥ 90%). BlaOXA-48 is a class D carbapenemase that is often associated with mild resistance to carbapenems and difficult to detect phenotypically, whereas blaKPC-2 is a class A carbapenemase that often demonstrates a high level of resistance to all β-lactam agents.
1526	2323	blaOXA-48_1	0/0	100	100	AY236073	blaOXA-48	Amoxicillin, amoxicillin + clavulanic acid, ampicillin, ampicillin + clavulanic acid, imipenem, meropenem, piperacillin, piperacillin + tazobactam
360	1241	blaKPC-2_1	0/0	100	100	AY034847	blaKPC-2	Amoxicillin, amoxicillin + clavulanic acid, ampicillin, ampicillin + clavulanic acid, aztreonam, cefepime, cefotaxime, cefoxitin, ceftazidime, ertapenem, imipenem, meropenem, piperacillin, piperacillin + tazobactam, ticarcillin, ticarcillin + clavulanic acid

↓ Table 2. Description of BlaOXA-48 and BlaKPC-2 Carbapenemase Gene and Its Associated Antibiotics Resistance Profile

Start

End

Gene

Gaps

Coverage

Identity

Accession

Product

Resistance

The table shows in silico prediction of the genomic location of the genes, sequence identity, and coverage (100%). Assembled contigs were screened against curated antimicrobial resistance databases (ResFinder/CARD) using sequence alignment tools (BLAST) with a defined threshold coverage (≥ 90%). BlaOXA-48 is a class D carbapenemase that is often associated with mild resistance to carbapenems and difficult to detect phenotypically, whereas blaKPC-2 is a class A carbapenemase that often demonstrates a high level of resistance to all β-lactam agents.

1526

2323

blaOXA-48_1

0/0

100

AY236073

blaOXA-48

Amoxicillin, amoxicillin + clavulanic acid, ampicillin, ampicillin + clavulanic acid, imipenem, meropenem, piperacillin, piperacillin + tazobactam

360

1241

blaKPC-2_1

0/0

100

AY034847

blaKPC-2

Amoxicillin, amoxicillin + clavulanic acid, ampicillin, ampicillin + clavulanic acid, aztreonam, cefepime, cefotaxime, cefoxitin, ceftazidime, ertapenem, imipenem, meropenem, piperacillin, piperacillin + tazobactam, ticarcillin, ticarcillin + clavulanic acid

↓ **Table 3.** Antimicrobial Resistance Markers Predicted to Be Chromosomally Encoded (Identified Using ResFinder, CARD, and ARG-ANNOT)
Contig	Start	End	Gene	Gaps	Coverage	Identity	Accession	Product	Resistance
99_S182_00081	320	1132	blaNDM-1_1	0/0	100	100	FN396876	blaNDM-1	Amoxicillin, amoxicillin + clavulanic acid, ampicillin, ampicillin + clavulanic acid, cefepime, cefixime, cefotaxime, cefoxitin, ceftazidime, ertapenem, imipenem, meropenem, piperacillin, piperacillin + tazobactam
99_S182_00063	2782	4041	cmlA1_1	0/0	100	100	M64556	cmlA1	Chloramphenicol
99_S182_00063	11531	12452	mph(A)_2	1/1	100	100	U36578	mph(A)	Erythromycin, azithromycin, spiramycin, telithromycin
99_S182_00063	4977	5633	qnrVC4_1	0/0	100	100	GQ891757	qnrVC4	Ciprofloxacin

↓ Table 3. Antimicrobial Resistance Markers Predicted to Be Chromosomally Encoded (Identified Using ResFinder, CARD, and ARG-ANNOT)

Contig

Start

End

Gene

Gaps

Coverage

Identity

Accession

Product

Resistance

99_S182_00081

320

1132

blaNDM-1_1

0/0

100

FN396876

blaNDM-1

Amoxicillin, amoxicillin + clavulanic acid, ampicillin, ampicillin + clavulanic acid, cefepime, cefixime, cefotaxime, cefoxitin, ceftazidime, ertapenem, imipenem, meropenem, piperacillin, piperacillin + tazobactam

99_S182_00063

2782

4041

cmlA1_1

0/0

100

M64556

cmlA1

Chloramphenicol

99_S182_00063

11531

12452

mph(A)_2

1/1

100

U36578

mph(A)

Erythromycin, azithromycin, spiramycin, telithromycin

99_S182_00063

4977

5633

qnrVC4_1

0/0

100

GQ891757

qnrVC4

Ciprofloxacin