Table 1.
Characterization of eligible articles that sought fluoroquinolone resistant clones in humans and animals**.
| Country | Organism | No. resistant**/No total | ID method | Study period | Study population | Genotyping tools | Resistance testing | References | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| WGS | MLST | ERIC-PCR | PFGE | Rep PCR | Other* | PMQR | QRDR | Efflux pump up- regulation | aac(6′)-Ib-cr | |||||||
| Angola | E. coli | 9/19 | B, S | 2009 | Stray dogs | – | – | – | √ | – | – | √ | – | – | – | Albrechtova et al., 2014a |
| Cameroon | V. cholerae O1 Ogawa El-tor | 0/9 | B, S, M | 2009 | Outbreak | – | – | – | – | – | – | – | √ | – | – | Quilici et al., 2010 |
| Central African Republic | Enterobacteriaceae | 33/121 | B, S | 2011 | Human/wildlife | – | – | – | √ | – | √ | – | – | Janatova et al., 2014 | ||
| Enterobacteriaceae | 65/65 | B | 2011–2012 | Clinical isolates (surgical site infections) | – | √ | √ | – | √ | – | √ | – | – | √ | Rafai et al., 2015 | |
| E. coli | 10/121 | B, M | 2011 | Gorillas and other wildlife | – | √ | – | – | – | – | √ | – | – | √ | Janatova et al., 2014 | |
| E. coli | 10/10 | B, M | 2000–2004 | Hospital clinical isolates | – | – | – | √ | √ | – | – | – | – | √ | Lavollay et al., 2006 | |
| S. Typhi | 0/19 | B, S | 1916–2004 | Various | √ | – | – | – | – | – | – | – | – | – | Holt et al., 2008 | |
| Cote d'Ivoire | E. coli, Enterobactericeae | 44/101 | B, S | 2012 | Human, dog, wild life | – | – | – | √ | – | – | √ | – | – | √ | Albrechtova et al., 2014b |
| DRC | Salmonella (NTS) | 0/233 | B, S | 2007–2011 | Community and Clinical isolates | – | – | – | √ | – | – | √ | √ | – | – | Lunguya et al., 2013 |
| V. cholerae | 0/1093 | B, S | 1997–2012 | Clinical Isolates | √ | – | – | – | – | MLVA | – | – | – | – | Miwanda et al., 2015 | |
| Ghana | E. coli | 23/293 | B, M | 2006–2008 | Clinical isolates from tertiary care hospitals | – | √ | – | – | – | – | √ | √ | – | – | Namboodiri et al., 2011 |
| E. coli | 28/29 | B, M | 2008–2009 | Clinical isolates: Blood, urine, sputum and wound | – | √ | – | – | – | – | – | – | – | – | Feglo et al., 2013 | |
| Ethiopia | Salmonella | 19/98 | B, S | 2000–2005 | Animal/Animal products | – | – | – | √ | – | – | – | – | – | – | Molla et al., 2007 |
| Kenya | E. coli | 66/289 | B, M | 2009 | Dogs (mainly), cats and humans | – | – | – | √ | – | – | √ | – | – | √ | Albrechtova et al., 2012 |
| E. coli | 12/17 | B, M | 2004–2005 | Clinical isolates: Urine | – | – | – | √ | – | – | √ | – | – | √ | Kariuki et al., 2007 | |
| V. cholerae | 1/76 | B, S | 2007–2010 | Clinical Isolates | – | – | – | √ | – | Ribo-typing | – | – | – | – | Mercy et al., 2014 | |
| S. Kentucky | 3/3 | B, S | 2000–2005 | Clinical Isolates | – | – | – | √ | – | √ | √ | – | – | Weill et al., 2006 | ||
| S. Typhi | 0/94 | B, S | 1988–2008 | Clinical isolates | √ | – | – | – | – | – | – | – | – | – | Kariuki et al., 2010 | |
| S. Typhi | 0/102 | B, S | 2001–2002 | Clinical isolates | – | – | – | √ | – | – | – | √ | – | – | Kariuki et al., 2004 | |
| S. Typhi | NS/55 | NS | 2001–2009 | Clinical isolates | √ | – | – | – | – | – | – | – | – | – | Wong et al., 2015 | |
| Malawi | S. Typhi | 0/112 | B, BC | 1998–2013 | Clinical isolates (blood) | √ | √ | – | – | – | – | – | – | – | – | Feasey et al., 2015 |
| S. Typhi | NS/112 | NS | 2004–2013 | Clinical isolates | √ | – | – | – | – | – | – | – | – | – | Wong et al., 2015 | |
| Nigeria | E. coli | 6/162 | B, S | 2006 | Poultry/Pigs | – | – | √ | – | – | – | √ | – | – | √ | Fortini et al., 2011 |
| E. coli | 57/114 | B, M | 2010–2011 | Human clinical isolates, bovine isolates from farms | – | √ | – | – | √ | – | √ | – | – | √ | Inwezerua et al., 2014 | |
| E. coli | 26/32 | B, M | 2011 | Humans (pregnant women) | – | √ | √ | – | – | – | √ | – | – | √ | Fortini et al., 2015 | |
| E. coli | 9/109 | B, M | 2008–2009 | Clinical isolates from tertiary care hospitals | – | ST131 and ST10 | √ | – | – | – | √ | – | – | √ | Aibinu et al., 2012a | |
| E. coli | 21/121 | B, M | 2005 | Healthy volunteers | – | √ | – | – | – | fliC -RFLP | – | √ | √ | – | Lamikanra et al., 2011 | |
| Salmonella (NTS) | 11/149 | B, S | 2009–2011 | Human/poutry/cattle/fish/vegetable | – | – | – | – | – | – | √ | – | – | – | Raufu et al., 2013 | |
| Salmonella (NTS) | 2/229 | B, S | 2010–2011 | Pigs | – | – | – | – | – | – | √ | – | – | – | Fashae and Hendriksen, 2014 | |
| S. Hiduddify | 24/130 | B, S | 2001 | Chickens/poultry meat | – | – | – | √ | – | – | – | – | – | – | Raufu et al., 2009 | |
| S. Kentucky | 197/197 | B, S | 1959–2008 | Human/Poultry/sea food/river/environment | – | √ | – | √ | – | – | √ | √ | – | √ | Le et al., 2011 | |
| S. Kentucky | 55/55 | B, S | 2007–2011 | Poultry/poultry sources | – | – | – | √ | – | – | – | – | – | – | Raufu et al., 2014 | |
| S. Kentucky | 54/70 | B, S | 1937–2013 | Humans/animals/environment | – | √ | – | √ | – | – | √ | √ | – | √ | Le et al., 2013 | |
| V. cholerae O1 and non O1 | 0/20 | B, S, M | 1971 –2010 | Outbreak, historical, environmental | – | – | – | √ | – | MLSA | – | √ | – | – | Marin et al., 2013 | |
| V. cholerae O1 Ogawa El-tor | 0/10 | B, S, M | 2009 | Outbreak | – | – | – | – | – | – | – | √ | – | – | Quilici et al., 2010 | |
| E. coli | NS/12 | B, M | 2000–2010 | Clinical isolates | – | √ | – | √ | – | Lineage PCR | – | √ | – | √ | Peirano et al., 2014 | |
| E. coli | 0/22 | B, M | 2008–2009 | Clinical isolates (Urine and pus) | – | – | – | √ | – | – | √ | – | – | √ | Peirano et al., 2011 | |
| Senegal | C. coli | 14/36 | B, M | 2000–2002 | Chicken | – | √ | – | – | – | – | – | √ | – | – | Kinana et al., 2007 |
| Salmonella (NTS) S. Typhi | 4/1623 | B, S, M | 1999–2009 | Clinical isolates | – | – | – | – | – | – | √ | √ | – | – | Harrois et al., 2014 | |
| C. jejuni | 19/46 | B, M | 2000–2002 | Chicken | – | √ | – | – | – | – | – | √ | – | – | Kinana et al., 2006 | |
| C. jejuni, C. coli | 81/181 | B, M | 2000–2003 | Poultry, Human | – | – | – | √ | – | – | – | √ | – | – | Cardinale et al., 2006 | |
| Sierra Leone | V. cholerae O1 | 0/15 | B, M, S | 2012 | Clinical isolates | – | – | – | √ | – | – | – | – | – | – | Mahmud et al., 2014 |
| South Africa | E. coli | 14/21 | B, M | 2012–2013 | Clinical isolates | – | √ | – | √ | – | – | √ | – | – | √ | Gqunta and Govender, 2015 |
| S. Typhi | 1/1 | B, S | 2010 | Clinical isolate | – | – | – | √ | – | – | √ | √ | – | – | Keddy et al., 2010 | |
| S. Typhi | 0/510 | B, S | 2003–2007 | Clinical isolates | – | – | – | √ | – | MLVA | √ | √ | – | – | Smith et al., 2010 | |
| S. Typhi | NS/41 | NS | 2004–2012 | Clinical isolates | √ | – | – | – | – | – | – | – | – | – | Wong et al., 2015 | |
| S. Kentucky | 1/1 | B, S | 2000–2005 | Clinical Isolates | – | – | – | √ | – | – | √ | √ | – | – | Weill et al., 2006 | |
| V. cholerae O1 Ogawa El-tor | 0/31 | B, S, M | 2008 | Outbreak | – | – | – | √ | – | – | – | – | – | Ismail et al., 2011 | ||
| Tanzania | S. Typhi | NS/52 | NS | 2006–2010 | Clinical isolates | √ | – | – | – | – | – | – | – | – | – | Wong et al., 2015 |
| S. Kentucky | 3/3 | B, S | 2000–2005 | Clinical Isolates | – | – | – | √ | – | √ | √ | – | – | Weill et al., 2006 | ||
KEY: ID method: B, Biochemistry; S, Serotyping; M, detection of target genes; BC, Blood culture; √, test was conducted; –, test not conducted; NS, Not stated (data not included in manuscript).
Other, where specific genotypic methods are used to identify clones of that enteric pathogen.
In some cases where fluoroquinolone-resistant clones were sought but only quinolone resistant or non-susceptible isolates were identified. Details of these studies are provided in Table S2.
WGS, Whole genome sequencing; MLST, Multi-locus sequence typing; MLSA, Multi-locus sequencing analysis; MLVA, multi-locus variable-number tandem repeat analyses; PFGE, pulse field gel electrophoresis; ERIC-PCR, Enterobacterial Repetitive Intergenic Consensus – PCR; REP-PCR, repetitive element palindromic PCR; RFLP, restriction fragment length polymorphism; NTS, Nontyphoidal Salmonella, Clinical Isolates – from humans; PMQR, plasmid mediated quinolone resistance (including qnrA, qnrB, qnrS, qnrC, qepA, and qnrVC3); QRDR, quinolone resistance-determining region [including sequencing the QRDR of DNA gyrase (gyrA, gryB) and topoisomerase IV (parC, parE) genes]; efflux, efflux up regulation testing; aac(6′)-Ib-cr, aminoglycoside acetyltransferace associated with ciprofloxacin resistance; DRC, Democratic Republic of the Congo.